Raising the bar on statistical significance

I was searching the early edition of PNAS for the abstract of yet another sloppy “science by press release” that didn’t bother to give the the title of the paper or the DOI, and came across this paper, so it wasn’t a wasted effort.

Steve McIntyre recently mentioned:

Mann rose to prominence by supposedly being able to detect “faint” signals using “advanced” statistical methods. Lewandowsky has taken this to a new level: using lew-statistics, lew-scientists can deduce properties of population with no members.

Josh (N=0) humor aside, this new paper makes me wonder how many climate science findings would fail evidence thresholds under this new proposed standard?pvalue_curve

Revised standards for statistical evidence

Valen E. Johnson

Significance

The lack of reproducibility of scientific research undermines public confidence in science and leads to the misuse of resources when researchers attempt to replicate and extend fallacious research findings. Using recent developments in Bayesian hypothesis testing, a root cause of nonreproducibility is traced to the conduct of significance tests at inappropriately high levels of significance. Modifications of common standards of evidence are proposed to reduce the rate of nonreproducibility of scientific research by a factor of 5 or greater.

Abstract

Recent advances in Bayesian hypothesis testing have led to the development of uniformly most powerful Bayesian tests, which represent an objective, default class of Bayesian hypothesis tests that have the same rejection regions as classical significance tests. Based on the correspondence between these two classes of tests, it is possible to equate the size of classical hypothesis tests with evidence thresholds in Bayesian tests, and to equate P values with Bayes factors. An examination of these connections suggest that recent concerns over the lack of reproducibility of scientific studies can be attributed largely to the conduct of significance tests at unjustifiably high levels of significance. To correct this problem, evidence thresholds required for the declaration of a significant finding should be increased to 25–50:1, and to 100–200:1 for the declaration of a highly significant finding. In terms of classical hypothesis tests, these evidence standards mandate the conduct of tests at the 0.005 or 0.001 level of significance.

From the discussion:

The correspondence between P values and Bayes factors based on UMPBTs suggest that commonly used thresholds for statistical significance represent only moderate evidence against null hypotheses. Although it is difficult to assess the proportion of all tested null hypotheses that are actually true, if one assumes that this proportion is approximately one-half, then these results suggest that between 17% and 25% of marginally significant scientific findings are false. This range of false positives is consistent with nonreproducibility rates reported by others (e.g., ref.5). If the proportion of true null hypotheses is greater than one-half, then the proportion of false positives reported in the scientific literature, and thus the proportion of scientific studies that would fail to replicate, is even higher.

In addition, this estimate of the nonreproducibility rate of scientific findings is based on the use of UMPBTs to establish the rejection regions of Bayesian tests. In general, the use of other default Bayesian methods to model effect sizes results in even higher assignments of posterior probability to rejected null hypotheses, and thus to even higher estimates of false-positive rates.

This phenomenon is discussed further in SI Text, where Bayes factors obtained using several other default Bayesian procedures are compared with UMPBTs (seeFig. S1). These analyses suggest that the range 17–25% underestimates the actual proportion of marginally significant scientific findings that are false.

Finally, it is important to note that this high rate of nonreproducibility is not the result of scientific misconduct, publication bias, file drawer biases, or flawed statistical designs; it is simply the consequence of using evidence thresholds that do not represent sufficiently strong evidence in favor of hypothesized effects.

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The full paper is here: http://www.pnas.org/content/early/2013/10/28/1313476110.full.pdf

The SI is here: Download Supporting Information (PDF)

For our layman readers who might be a bit behind on statistics, here is a primer on statistical significance and P-values as it relates to weight loss/nutrition, which is something that you can easily get your mind around.

Gross failure of scientifical nutritional studies is another topic McIntyre recently discussed: A Scathing Indictment of Federally-Funded Nutrition Research

So, while some dicey science findings might simply be low threshold problems, there are real human conduct problems in science too.

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219 thoughts on “Raising the bar on statistical significance

  1. This is the reason so many nutritional findings are reversed. You know. Trans fats are good. Trans fats are bad. Soon to be followed by meat eating is banned. Too many natural trans fats.

    The Atkins diet? There are problems.
    A few small, short studies suggest Atkins raises HDL cholesterol and lowers blood pressure, reducing the risk of heart attack and stroke. But many of the studies were small and short, and some of the positive findings did not carry enough statistical weight to be trustworthy. And all that fat worries most experts.

    http://health.usnews.com/best-diet/atkins-diet

  2. Stats can’t be saved by tweaking.

    The only proper standard for science is NO STATS. If a result has to be reached by statistics, it’s not a scientific result. Only well-calibrated measurements plus a well-balanced experiment can give scientific results.

  3. Still my favorite Stats prof saying, “Numbers are like people, torture them enough and they’ll tell you whatever you want to hear.”

  4. The only proper standard for science is NO STATS. If a result has to be reached by statistics, it’s not a scientific result. Only well-calibrated measurements plus a well-balanced experiment can give scientific results.

    Nonsense. Many areas of science are inherently statistical. Chemical reactions for example, or quantum effects, or thermodynamics. The Second Law of Thermodynamics is entirely statistical in origin.

  5. Interesting that in climate scientology, you can be 95% sure on little evidence, where as in particlar physics, 6-sigma results are required to come close to verifying something.

  6. polistra says-

    “If a result has to be reached by statistics, it’s not a scientific result.”

    William Briggs, statistician to the stars, doesn’t go that far, but what he writes is still pretty damning-

    “If you need statistics to prove something, and you have no proof except statistical proof, then what you have proved probably isn’t true. Statistical evidence is the lowest form of evidence there is. What a depressing conclusion.”
    William Briggs, statistician, October 5, 2011

  7. In fiscal year 2012-13 ended September, the US Government spent $2.5 billion on climate research (among $20 billion more spent on climate change for clean energy, international assistance, tax credits etc.)

    http://www.powerlineblog.com/archives/2013/11/why-does-the-global-warming-hoax-persist.php

    If you assume this $2.5 billion supports X number of researchers at $125,000 each, there would be 20,000 climate researchers. It is just an industry which has no incentive to say “oops, we got it wrong.” If a single scientist said so, he would be side-lined in short order because there are 20,000 other researchers in the US that depend on the $2.5 billion of income to keep coming in.

    So, that is just the US. Globally, $359 billion was spent on climate change last year. If the same ratios applied to this number, there would be $40.4 billion spent on climate research supporting 320,000 researchers.

    http://climatepolicyinitiative.org/publication/global-landscape-of-climate-finance-2013/

    Those are the only statistics that count in this field.

  8. Thanks for the citations that I will read in light of my slim understanding of E. T. Jaynes that did science – physics – with Bayesian statistics.

    I appreciated the “torture” comment above; statistics, people or the internet can be tortured into providing any desired statement.

  9. Well, this is not new in biology and medical research (the one I do). Statistical significance in clinical trials sometimes leads to wired conclusions but only those that are based on biologically relevant responses are eventually brought to the bedside. The majority of clinical trial (those based on “unexpected” findings are simply forgotten over the years.
    Thus, going beyond the statistical significance and making clinical studies that are intrinsically mechanistic is the only way to produce good medical science.
    In a nutshell….. it is better to understand what you are talking about

  10. Well, it’s a good start….

    Finally, it is important to note that this high rate of nonreproducibility is not the result of scientific misconduct, publication bias, file drawer biases, or flawed statistical designs; it is simply the consequence of using evidence thresholds that do not represent sufficiently strong evidence in favor of hypothesized effects.

    This is a false statement, IF scientists intentionally refuse to archive of share their data for use by would be replicators, the motives of whom the original scientist seems to think he has a right to impugn. It’s also false IF the statistical result coincidentally match reality. A high degree of correlation STILL won’t prove causation. With smoothing of temperature graphs using multi-year averages, CO2 being released by the oceans during warmer periods would match a hypothesis that human emissions caused the higher CO2 levels. That’s the difficulty with correlations, you need to test EVERYTHING, EVEN THE THINGS YOU DON’T KNOW, to see whether or not other things might also be correlated. This is, for the most part, impossible when testing a system as complex as the Earth’s climate. Ergo, statistics will always leave us needing more. Conclusions based on statistics will always be suspect if they are used to deduce causality.

  11. This seems like real non-news to anyone with a little background in statistics. It has always puzzled me that some branches of science seem content with p-values as high as 0.05!

  12. John Brignell has indeed been talking about this sort of thing for years. His critique of the “evidence” against secondary smoking, for example, is particularly withering.

  13. I’m not sure I understand this proposal. The idea is to reduce occurrences of nonconfirmation by requiring a significance level of, say, 0.005 instead of 0.05. But under these new standards there will be results which just barely pass the test. When those results are subjected to a repeat study for reconfirmation wouldn’t they be equally likely to miss significance as marginal results under the older regime?

    Of course, adopting this stricter standard would result in far fewer studies achieving significance in the first place, and that would of itself reduce non-confirmation.

    I’m not a statistician, so I’m happy to admit that I may have missed something.

  14. Actually, whether or not a causal linkage exists between two factors is almost never of any importance, irregardless of whether your tests can detect same. What’s important is the strength of the linkage. Using the word “significant” in the term “statistical significance” has confused more folks than any other phrase in science, misleading them into believing that the detected linkage
    is “significant,” i.e. a strong linkage, which the test results actually say nothing about. Simply
    using a larger sample size makes for a more powerful statistical test and allows trivial linkages to be detected as “statistically significant.” Just assuring ourselves that real, actual linkages exist is rarely of any value. We need to know HOW strong the linkage is, not simply whether one exists or not (i.e. whether the null hypothesis can be rejected).

  15. M Simon says:
    November 12, 2013 at 4:23 am
    “This is the reason so many nutritional findings are reversed. You know. Trans fats are good. Trans fats are bad. Soon to be followed by meat eating is banned. Too many natural trans fats.

    The Atkins diet? There are problems.
    A few small, short studies suggest Atkins raises HDL cholesterol and lowers blood pressure, reducing the risk of heart attack and stroke. But many of the studies were small and short, and some of the positive findings did not carry enough statistical weight to be trustworthy. And all that fat worries most experts.”

    Well, maybe you should first point to a study that shows a correlation between fat consumption and heart attacks, without leaving out all data points that would destroy the correlation.

    And please, the site you linked to says “The theory:The body is an engine; carbs are the gas that makes it go.”

    Oh please. Ask any bicyclist on what fuel he runs most of the time. That site is a bad joke and misrepresents what they attack.
    Atkins BTW has not invented the low carb diet.

    http://www.lowcarb.ca/corpulence/corpulence_full.html

  16. You have 100 people in a company, of which 5 are actually using drugs. You employ a drug test that is 95% reliable. It will deliver 5 false positives. There is a 50-50 chance that someone identified as using drugs is actually using drugs.

    What scientists routinely fail to account for is that statistical significance needs to be considered in the context of how “rare” the thing you are looking for is. When you are looking for hay in a haystack, 95% reliability works perfectly well. You will vary rarely find a needle instead of hay.

    However, when you are looking for the needle in the haystack, then 95% reliability is worthless. Most of what you identify as “needles” will in fact be hay.

    The problem is that for most of climate research, what they are looking for is the needles in the haystack. They want to, for example, identify the very small human temperature signal from the much larger daily and annual temperature signal. So when they apply the 95% test they get hockey sticks when the reality is closer to hockey pucks.

  17. ss Since this is something of my game, I’ll summarize the idea. In Bayesian probability analysis, one rarely just states hypotheses. One states hypotheses based on various assumptions. Sometimes these assumptions are actually stated, sometimes they are not. Sometimes they are (in some rigorously defensible sense) true and sufficiently accurate beyond reasonable doubt — the assumption of Galilean or Newtonian gravity for near-Earth-surface physics problems — and sometimes they are basically little more than educated guesses with little or no solid evidence.

    The simplest learning example of the latter is a coin flip. Suppose you meet up with a total stranger, who wants to bet you $1 a flip on 100 successive flips, and you get heads. You say to yourself “Hmm, a two sided coin, zero sum game, random walk, I expect to win or lose no more than $10-15 (with equal probability) and it will help to pass the time, sure.” You have intuitively used Bayesian reasoning. You picked a prior probability for a two-sided coin of 0.5 heads or tails, from symmetry and maximum entropy principles.

    You didn’t have to. You could have said to yourself “Gee, a complete stranger wants to play a game of ‘chance’ with me with his coin, where he gets to pick heads for me. I’ll bet that he’s playing with a biased coin so that if I take this sucker bet, my expectation is to lose $100 or close to it.” This too is a Bayesian prior. You go ahead and take the bet anyway because you are bored and because you can count on proving that he cheated if the winning gets too lopsided.

    They are also the basis for the null hypothesis — The coin has p(heads) = 0.5 or the coin has p(heads) = 0.0 respectively.

    In traditional hypothesis testing, one assumes the null hypothesis, conducts an experiment, and determines the probability of obtaining the observed sequence given the null hypothesis. If you assumed p = 0.5 and the results of the first 8 flips were all tails, the probability of this outcome is 1/256 \approx 0.004. Based on additional prior knowledge you have (basically, the reasoning in the second case that it is unwise to gamble with strangers, especially with their cards, dice, coins) you might well have rejected the null hypothesis at the seventh flip or even the sixth. Since the bet is cheap, you might even go two more flips, but at the tenth flip you’ve already reached your expected win/loss threshold based on a random sequence of flips of an unbiased coin and the p-value is down to less than 0.001. Time to offer the stranger a counter-bet — using the same coin, for the rest of the bets you get tails and he gets heads OR nobody pays off and everybody walks away.

    In Bayesian probability theory, one doesn’t reason exactly this way. Instead, one can allow the results of the experiment to modify you assertion of prior probabilities so that they basically asymptotically agree with the data however you start them out. Before the first flip your prior estimate of p(heads) is 0.5, but after a single flip — whether or not it comes out heads or tails — this is not true. If you get tails at the end of one flip, the probability p(heads) is strictly less than 0.5, and it montonically descends with every sequential flip of tails.

    This approach (really, no approach) is going to be particularly reliable with only five or six flips because (in the words of George Marsaglia, a giant of hypothesis testing and random numbers) “p happens”. If you conduct many such experiments, not only will sequences of six tails in a row occur, but they’ll occur one in sixty-four randomly selected sequences of six coin flips, even if the coin is unbiased!

    This is precisely the kind of reasoning that is not being conducted in climate science. In part this is because it is a house of cards — if you knock a single card loose on the ground floor, you risk the whole thing tumbling down. The list of (Bayesian prior) assumptions is staggering, and in the case of many of them there is simply no possibility of directly measuring them and setting them on the basis of direct empirical evidence, or there is some evidentiary basis for a number, but there is a rather wide range of possible/probable error in that number.

    This multiplicity of Bayesian priors has the following effect. It becomes quite possible to obtain good agreement with a limited sequence of data with incorrect prior assumptions. This, in turn, means that limits on p have to be made more stringent. If one uses the coin metaphor, an additional (unstated) Bayesian prior assumption is that it is possible for you to detect it if your opponent switches coins! Of course, your opponent in addition to being a scoundrel could be an unemployed magician, and swapping coins “invisibly” could be child’s play to him. In that event, he might play you with a fair coin for the first ten or twenty throws, allowing you to conclude that the coin is a fair coin, and then swap in the unfair coin for a few throws out of every ten for the rest of the way. You end up losing with complete certainty, but at a rate just over the expected win/loss threshold. He makes (say) $20 or $25 instead of $100, but he kept you in the game until the end because you could have just been unlucky with a fair coin and you had direct evidence of apparently fair sequences.

    In more mathematical theories the same thing often happens if you have nonlinear functions with parametric partially cancelling parts contributing to some result, function forms with a lot of covariance. One can often get good agreement with a segment of data with a mutually varying range of certain parameters, so that any prior assumption in this range will apparently work. It’s only when one applies the theory outside of the range where the accidental cancellation “works” that the problem emerges. Once again naively applying a hypothesis test to the range of data used to justify a Bayesian assumption of parameters is completely incorrect, as is applying the assumption to a naively selected trial set, and the requirements for passing a hypothesis test at all have to be made much more stringent in the meantime to account for the lack of evidence for the Bayesian priors themselves. The evidence has to both agree with the null hypothesis and affirm the prior assumptions, and to the extent that it has to do the latter without outside support it takes a lot more evidence to affirm the priors in the sense of not rejecting the null hypothesis. You have many “and” operators in the Bayesian logic — if the primary theory is correct AND this parameter is correct AND this second parameter is correct AND this third parameter is correct, what are the chances of observing the data — and the computation of that chance has to be diluted by accounting for all of the OTHER values of the prior assumptions that might lead to the same agreement with the data but effectively constitute a different theory.

    And then there is data dredging, which is very nearly another version of the same thing.

    So when there are 30+ GCMs, each with dozens of parameters in a complex theory with many countervarying nonlinear contributions, that are in good agreement with an indifferently selected monotonic training set of data, that is not yet particularly good evidence that the theory is correct. The real test comes when one applies it to new data outside of the training set, ideally data that does not conform to the monotonic behavior of the training set. If the theory (EACH GCM, one at a time) can correctly predict the alteration of the monotonic behavior, then it becomes more plausible. To the extent that it fails to do so, it becomes less plausible. Finally, as theories become less plausible, a Bayesian would go in and modify the prior assumptions to try to reconstruct good agreement between the theory and observation, just as you might change your prior beliefs about the fairness of the coin above, if you start seeing highly improbable outcomes (given the assumptions).

    It is this latter step that is proceeding far too slowly in climate science.

    rgb

  18. In defence of the claim that statistics has been used successfully in science, jimmi-the-dalek says above that:

    “Nonsense. Many areas of science are inherently statistical. Chemical reactions for example, or quantum effects, or thermodynamics. The Second Law of Thermodynamics is entirely statistical in origin.”

    This is true in one sense but rather misleading. The sort of ‘statistics’ used in quantum physics and classical thermodynamics is radically different from that used in climate science. The first is deductive, the second inductive. In thermodynamics we make assumptions about the probabilities of elementary events and then use the calculus of probabilities to derive probabilities for complex events. This is a process as rigorous as anything in mathematics, and the results are compared with experiment – eg.time of flight observations for the Maxwell-Boltzmann distribution. Compared with what happens in climate science this can hardly be called ‘statistics’ at all – ‘stochastic’ might be a better word for it. In climate science they start with the experimental results – time-series and so on – and use genuinely statistical methods to try to find trends, correlations and causality.

    Of course, in the experimental testing of quantum results, say, statistics in this second sense is used – as we saw with the detection of the Higgs particle – but that is another matter. I think the reliance of any science on statistical analyses, to the extent we see in climate science, is a real cause for concern – especially when the level of competence shown has been criticised so heavily by those whose competence non-experts such as myself have no reason to doubt.

  19. published in German in 1854, is known as the Clausius statement:

    Heat can never pass from a colder to a warmer body without some other change, connected therewith, occurring at the same time.

    Statistical mechanics was initiated in 1870 with the work of Austrian physicist Ludwig Boltzmann…

    Both the above from Wiki.

    jimmi_the_dalek says:

    November 12, 2013 at 4:48 am
    The Second Law of Thermodynamics is entirely statistical in origin.

    Since, the Clausius statement preceded the initiation of statistical mechanics by some 16 years I find it hard to understand how you can say that the second law is entirely statistical in origin.

  20. rgbatduke says:
    November 12, 2013 at 6:45 am
    and sometimes they are basically little more than educated guesses with little or no solid evidence.
    =============
    the assumption that some trees make better thermometers than other trees, and that one tree in particular is a better thermometer than all other trees.

    if you look at 1000 trees, you will find that one tree better follows the thermometer records than all the others. and if you repeat this study, you will find than in another set of 1000 trees, there is one tree that better matches the thermometer records.

    climate science teaches the reason that one tree in 1000 better matches the thermometer records is that this tree is a better thermometer. thus this tree can be used reliably as a thermometer proxy outside the time in which we have thermometers.

    chance tells us that if you look at 1000 trees there will always be 1 tree that better matches the thermometer records, and the reason has nothing to do with being a better thermometer. climate science rejects chance as the cause. Of this they are 97% certain.

  21. I don’t understand. P=.05 should mean that the null hypothesis is correct only 5% of the time. How does this turn into error rates of approximately 20% — supposing that biases are accounted for?
    What is the basic idea that changes 5% to 20%?

  22. Perhaps the biggest assumption in modern science is the assumption that the purpose of science is to conduct research, to discover “The Truth”.

    What if the true purpose of science is to attract funding? What scientific body would welcome a study that said “nothing to worry about, you can cut our funding”?

  23. Jim Rose says:
    November 12, 2013 at 7:19 am
    What is the basic idea that changes 5% to 20%?
    =======
    You have 100 people in a company, of which 5 are actually using drugs. You employ a drug test that is 95% reliable. It will deliver 5 false positives. There is a 50-50 chance that someone identified as using drugs is actually using drugs.

    You believe your test will be 95% accurate, but in fact 50% of the time it incorrectly identified the drug user. Since you don’t know there are only 5 drug users, when the test tells you there are 10 drug users, you believe the test. 5 innocent employees get fired along with the 5 guilty.

    100 scientists conduct studies, of which 5 produce real positives. At the 95% significance, 5 produce false positives. Only the positives get published, as negative results do not attract attention. 5 true positive along with 5 false positives. 50% of the published papers are false.

  24. I don’t believe raising thresholds much helps and I don’t believe 0.005 or 0.001 levels are needed for avoiding bad science.
    In fact such a conclusion that raising thresholds to such levels will mean better science looks to me more insane than logical. It in my opinion defies probability theory, and it would in my opinion inevitably generate more false negatives than are now the false positives – at least quite definitely for normal distribution.
    Statistics should anyway be considered only supporting, indirect evidence. As people shouldn’t be sentenced on indirect evidence, also scientist should have also other, direct evidence for their hypotheses. There are also hypotheses which aren’t testable by statistics after all. And where they are, the statistics is powerful, but still not omnipotent – it can’t replace common sense. Science shouldn’t be an industry to produce knowledge, deemed true if just passing statistical tests.
    It is on the other hand substantial for the scientific method that it should be based on falsification – one comes with a hypothesis, tests it, comes to conclusion publishes it and then other comes, finds the flaws and falsifies it. And the falsification should be then taken most seriously. Not like in the climate science where the GST shows no change or even cooling and the global reports without change still talk about global warming, that it is due to CO2 and demand even more money and power anyway.
    Science is not here for itself, it is a social phenomena driven both by competence and competition. It should be the nature of the science, not just believe, that if one raises thresholds it will automatically mean less junk science, less nonreproducibility. It doesn’t work like that and there are no “shortcuts” from ignorance to knowledge through restriction of science, the way there goes only through honesty, dedication and freedom of conscience in my opinion.

  25. Jim Rose: I don’t understand. P=.05 should mean that the null hypothesis is correct only 5% of the time. How does this turn into error rates of approximately 20% — supposing that biases are accounted for?
    What is the basic idea that changes 5% to 20%?

    The p-value is an estimate of the conditional probability of a result at least as far from the observed prediction given that the null hypothesis is true. Only rarely would that result in 5% of the true null hypotheses being reported true, or the literature only having false rejections of the null hypothesis in 5% of published papers. What changes the 5% to 20% (speaking loosely) is the fact that the null hypotheses are actually true (or at least very accurate) more often than the researchers expect them to be.

    The proposal in the focus paper and the reasoning behind it are not that new. The debate about what significance level to use is probably at least a century old now. The penalty for insisting on low p-values is a higher than desirable rate of false non-rejection of false null hypotheses, aka “high rate of type ii errors”.

    What has to be recognized is that single reported studies, without replication, are not as reliable as you would like them to be. That is not a problem solved by adopting smaller p-values, but by a deeper appreciation of the prevalence and size of random variation (the agglomeration of all the variation than is not directly relateable to the focus of the study and measurable covariates.)

  26. 10 thousand Olympic athletes are tested for drug use with a test that is 99.99% accurate. what are the odds that an athlete identified as a drug user is a drug user?

  27. Nice explanation of applying Bayesian statistics to the flip of a coin. There is one huge difference between your example and the use of statistics in climate science. In your example, the statistician knows what the event space is. The event space consists of readily observable and readily definable physical phenomena, namely, flips of the coin. Climate science does not have the luxury of a readily observable or readily definable event space. Permit me to illustrate by reference to Michael Mann’s work on tree rings. What is (was) an event for Mann? It was the measurement of the width of a tree ring. For Mann, a series of events that together make up a proxy record consists of measurements of tree ring widths for the same kind of tree taken from trees scattered about the surface of the Earth. Does that count as a legitimate event space? Clearly not because tree ring growth is not determined by the tree but by the ever changing environment in which the tree grows. Did Mann investigate the several environments in order to establish readily observable and definable phenomena? Not in the least. All he did was a little hand waving to the effect that the sample trees were pretty much located at the the tree line (on mountains of course).

    The usual Alarmist response to my point is that all the differences among the samples can be accommodated through powerful statistical techniques. This response does not climb above childishness.

    I have “attacked” the soft underbelly of climate science by using Mann as my example. But the same is true throughout climate science. Climate scientists sometimes talk about heat content and sometimes talk about temperature measurement and they make the egregious assumption that the two are interdefinable. Climate scientists sometimes talk about temperatures taken in the atmosphere and sometimes about temperature taken on the surface or beneath the surface of the oceans. To summarize, climate scientists are the only so-called hard scientists now practicing who are quite willing to take any two series of measurements and assume that they are comparable. The worst offenders are the “paleoclimatologists” who are quite willing to take 50 existing “paleo” series and treat them as comparable while giving no thought to the actual events of measurement that occurred at some time in some readily observable and definable environment. Most climate scientists have no idea what their event space is.

  28. This post & discussion highlights one thing for sure – climate science is inherently statistical (which we all knew) but also it makes you want to have a statistician as co-author for any publication, given the complexities of the statistical analysis needed to come up with a credible conclusion.

  29. While Bayes’s theorem is correct, Bayesian parameter estimation generally suffers from the lack of uniqueness of the prior probability density function with consequent violation of Aristotle’s law of non-contradiction. In particular, the method by which climatologists extract numerical values for the equilibrium climate sensitivity (TECS) from global temperature data violates non-contradiction.

    There is an exception to the rule that Bayesian methods violate non-contradiction. It occurs in the circumstance that a sequence of events, for example a sequence of coin flips, underlies the model. In this case, the so-called “uninformative” prior probability density function is unique and non-contradiction is not violated.

    However, no events underlie the IPCC climate models. In setting up this state of affairs, climatologists have ensured that the conclusions of their arguments violate non-contradiction. Rather than being one value for TECS, for example, values are of infinite number.

  30. @ polistra says:
    November 12, 2013 at 4:28 am
    “Stats can’t be saved by tweaking. The only proper standard for science is NO STATS. If a result has to be reached by statistics, it’s not a scientific result. Only well-calibrated measurements plus a well-balanced experiment can give scientific results.”

    In fact, a number of scientific disciplines are observational and are unable to reach direct results by experiment. Major examples: astronomy, paleontology, evolutionary biology, Some of their findings are “consistent with” some experiments done in another context, but most of their findings are not reached through experimental methods. Of course, observational sciences still require careful measurements, and thus the other condition set by Polistra (well-calibrated measurements) generally applies, although one has to be careful about the basis for calibration (cf climate models calibrated to the rapidly warming 1970-2000 period).

  31. and what about a sentence like we have 95% confidence that a fact is true…

    so if fact is not true we are not wrong but unlucky….

    what about a sentence like …extreme events will be more extreme…we can say that …with low confidence….i can say with low confidence it will not rain tomorrow…

    they can never be wrong…

  32. From ‘Revised Standards for Statistical Evidence’ by Valen E. Johnson published in PNAS,

    “Finally, it is important to note that this high rate of nonreproducibility is not the result of scientific misconduct, publication bias, file drawer biases, or flawed statistical designs; it is simply the consequence of using evidence thresholds that do not represent sufficiently strong evidence in favor of hypothesized effects.”

    – – – – – – –

    That statement ignores the situation where the researcher(s) choose consciously and intentionally to use “evidence thresholds that do not represent sufficiently strong evidence in favor of hypothesized effects” and then obfuscating that they have done so.

    John

  33. Where is the damn like button, +, whatever on the comments. There is a nice list above of people who get it. I was watching a show about angels a long time ago. A person came on and said, “I fell through the ice, an angel appeared and said, ‘Go this way’, and I followed her advice and found the hole to get back out!”

    My wife said … “What about all the people who fell through the ice and saw the angel and followed their directions and didn’t get out!”

    This exactly corresponds to the “One tree in 1000 matches temperature better!”

    This why you look at the absolute value of data and do not get too enamored of Anomaly Data. If the anomaly data lets you make accurate predictions on the unknown, awesome. Keep that absolute chart posted next to you though to remind you of the underlying magnitudes.

    The inverse of Risk Ratio is Survivability Factor. Even with smoking, the survivability of smoking and lung cancer is 92% over 60 years. There is a 92% chance you won’t get lung cancer.

  34. This is one of the reasons I abandoned a PhD in Sociology, a discipline that regularly works at the p=0.05 or even p=0.1 level. Very little was reproducible, and hardly anyone even tried.

  35. “This approach (really, no approach) is going to be particularly reliable with only five or six flips because …” — rgbatduke @6:45

    rgb wrote a great bit on this, but it is distinctly different from what the paper is proposing. The papers stated problem, and its proposed solution, is to singly publish more papers that are reproucible.

    Without reproducing them.

    This is absurd in the first order, for if you make one mistake, one deceit, or one oversight, one bad choice with outliers and otherwise cleaning your dataset, with one paper: You have flipped the coin exactly once. To flip the coin five or six times you need to repeat the exact experiment of the paper, another four or five times.

    Bayesian notions are pretty clever and terribly interesting: And point out exactly why experiments that are not replicated are nonsense. But this paper is precisely about non-replication. Faith, Trust, whatever you like. But it’s a misplaced solution.

  36. Great issue. A probability estimate, a “p” level, is derived internally – based on the data of the study, only. It therefore cannot be any sort of statement about the world outside of that data set.

    A p value only helps contribute to the evaluation of how convincing the study outcome is.

    The problem is that some people value it for more than that.

    Bradford Hill, instrumental in fingering tobacco smoking as a cause of lung cancer, has his well-recognized 1965 paper on “Association or Causation?” He gives the well-recognized criteria for helping assess observational data. “Statistical likelihood” is not in that list of nine aspects, and is briefly mentioned and put well in its place toward the end of the article.

  37. Robert says:
    November 12, 2013 at 9:17 am
    “This is one of the reasons I abandoned a PhD in Sociology, a discipline that regularly works at the p=0.05 or even p=0.1 level. Very little was reproducible, and hardly anyone even tried.”

    Find on youtube Harald Eia and his series Hjernevask or Brainwash. He’s a Norwegian sociologist and comedian and has fun confronting his Norwegian sociologist colleagues with inconvenient facts.

  38. tumetuestumefaisdubien1 says: @ November 12, 2013 at 7:36 am

    I don’t believe raising thresholds much helps and I don’t believe 0.005 or 0.001 levels are needed for avoiding bad science.
    In fact such a conclusion that raising thresholds to such levels will mean better science looks to me more insane than logical….
    >>>>>>>>>>>>>>>>>>>>>
    You should be doing what we did in QC. (This depends of course on the cost of the item and the cost of the tests.)
    Taking ferd berple’s example of drug testing.
    The sample from each person gets split before testing. Part of the sample is used for testing the rest is retained. You know that out of the ten who tested positive approx. five maybe false positives. You then use the more expensive but more accurate test to retest the retains for all ten to confirm the positives. (Splitting the sample is what is done for drug testing truck drivers.)

    In science it is independent replication usually by at least two independent labs. If it can not be replicated it gets tossed into the dustbin of history.

    I see no reason to change this but the confirmation testing by an independent lab or two or three is an absolute must and this is what is missing in Climate Science.

  39. I think the climate science (and to be fair, quite often in other science areas!) – it would be fair to say that many researchers use the ‘P’ value simply because without it, the casual reader/interpreter would realise that the research doesn’t pass the ‘sniff’ test? In other words, it’s like an imaginary forcefield, protecting/deflecting the actual research from external attack..(hmm, is there a cartoon in there somewhere?)
    Anyway, for some as yet unknown reason, many folk are incapable of ‘reverse analysis’ from statistical ‘results’, especially when reading data from ‘surveys’.
    As for P values in climate science (which, in such a large, complex and chaotic system, cannot actually be adequately defined) – I think it can be adequately summed up in the simple phrase:
    ‘They are taking the P…’

  40. polistra says:
    November 12, 2013 at 4:28 am

    The only proper standard for science is NO STATS. If a result has to be reached by statistics, it’s not a scientific result. Only well-calibrated measurements plus a well-balanced experiment can give scientific results.

    Measurements, no matter how well calibrated and careful, are subject to observational errors and accuracy inherent in the equipment used for measurement. The mathematical method used to evaluate those errors is statistics. Until the results of the experiment are evaluated in light of the potential and real errors of measurement, the results are not scientific.

  41. A problem inherent with increasing the level of confidence required to accept the hypothesis, is that you increase the possibility of rejecting an hypothesis that is actually true. This has not been considered here, but I’ve not yet read the original paper, to if or how that is approached.

  42. ferd berple asked, “10 thousand Olympic athletes are tested for drug use with a test that is 99.99% accurate. what are the odds that an athlete identified as a drug user is a drug user?

    In the first place, there are normally two accuracy measures for a test: the percentage of true positives which are correctly reported as positives (i.e., not false negatives), and the percentage of true negatives which are correctly reported as negatives (i.e., not false positives). The two accuracy measures are not often the same, though in some cases it is possible to adjust cut-off thresholds to make them the same.

    For real-world tests, there may also be some results reported as “inconclusive.”

    But, for the sake of this conversation & simplicity, let’s assume that for this hypothetical drug test both accuracy measures are 99.99% (i.e., 1 in 10,000 erroneous results), and test results are never reported as inconclusive.

    Then the answer to your question depends on how many actual drug users there are in the population of 10,000.

    Example 1: 10,000 “clean” athletes, zero drug users.
    The most likely outcome is that one athlete will be identified as a drug user.
    The odds that an athlete identified as a drug user is a drug user are zero.

    Example 2: zero “clean” athletes, 10,000 drug users.
    The most likely outcome is that 9999 athletes will be identified as drug users.
    The odds that an athlete identified as a drug user is a drug user are 100%.

    Example 3: 5000 “clean” athletes, 5000 drug users.
    Approximately 5000 athletes will be identified as drug users.
    The odds that an athlete identified as a drug user is a drug user are 99.99%.

    Example 4: 9999 “clean” athletes, one drug user.
    The most likely outcome is that two athletes will be identified as drug users.
    The odds that an athlete identified as a drug user is a drug user are 50%.

    Example 5: 9995 “clean” athletes, five drug users.
    The most likely outcome is that six athletes will be identified as drug users.
    The odds that an athlete identified as a drug user is a drug user are about 83%.

    Note, though, that if you know the accuracy of the test with high confidence, you can infer the approximate percentage of the population which are drug users, even if your confidence in any particular result is inadequate. For instance, for your hypothetical test case, if your test identified six athletes as drug users, you could say with reasonable confidence that some of the 10,000 athletes (best est. 0.2%) are drug users, even though you would not have sufficient evidence to convict any of the six suspected drug users from competition.

  43. As pointed out by others, John Brignell’s posts at
    http://www.numberwatch.co.uk also argue this point.
    He argues persuasively that in the
    old days, statistical giants such as R.A. Fisher would
    regard the p=0.05 level as merely the first gate
    that some hypothesis would have to get through,
    not as some kind of “final proof”.

  44. Tighter stats requirements do not address the very real problem that correlation does not equal causality.

    This problem is especially important whenever system-response metrics are chosen to be mega-scopic functionals; functions of functions that map important details to a single number. By its very name, the global average surface temperature is not a valid system-response metic.

    Weather is local, climate is local, valid system response metrics should focus at this scale.

    Equally, so long as the energy content for the various sub-systems remains a focus, metics directly related to the physical scale of the data for each sub-system should be developed. The production, transport, and storage of the phases ( solid,liquid,vapor ) of water, a critically important sub-system, as calculated by GCMs should be compared with data for that sub-system. Conservation of mass is a good response metric.

    Internally to the GCMs, verification of the numerical solution methods is a mathematical problem that does not need stats. Verification, meaning that the coded equations are correctly solved, is a critically important metric that is completely ignored in Climate Science. While ignoring verification Climate Science insists that evaluation of the models is a valid processes. It is not. Verification must always, without exceptions, precede validation.

    For me, looking at tighter stats for mega-scopic metrics has got the problems upside down.

  45. Using recent developments in Bayesian hypothesis testing, a root cause of nonreproducibility is traced to the conduct of significance tests at inappropriately high levels of significance.

    Huh? “Inappropriately High?” as in Too High? or not high enought?

    Finally, it is important to note that this high rate of nonreproducibility is not the result of scientific misconduct, publication bias, file drawer biases, or flawed statistical designs;
    Well, not necessarily the result. These do happen. There just may be other reasons.

    it is simply the consequence of using evidence thresholds that do not represent sufficiently strong evidence in favor of hypothesized effects.
    Ah…. this would classify as flawed statistical design and a bias toward publication of insignificant results. I’m not willing to rule out scientific misconduct at this point. Insufficient skepticism of one’s own work is probably in the mix, too.

  46. John Brignell. A tribute to John Daily (still waiting for greenhouse)

    http://www.john-daly.com/

    “Most of his admirers around the world never met him, but nevertheless held him in great esteem, simply on the basis of his writings. Forget all the pornographers, mass mailers and virus producers; one Daly is sufficient justification for the existence of the World Wide Web.”

    Daly,McKitrick, McIntyre, Pielke, Watts, ……..

  47. M Simon says: “This is the reason so many nutritional findings are reversed. You know. Trans fats are good. Trans fats are bad. Soon to be followed by meat eating is banned. Too many natural trans fats. ”

    Often true. Another problem is the problem of the “healthy user” benefiting from the “healthy user effect.” People who TEND to do things that are believed to be healthy also TEND to do other supposedly healthy habits. They will, overall, reap benefits of what really contributes to a long, healthy life – probably regular exercise, a decent diet, and good stress management in the face of life’s slings and arrows via economic stability and or social relationships.

    So, a behavior can have a somewhat BAD influence, but in some longitudinal study, be mathematically seen as healthy. The healthy habits carry the day, and the bad habit is a fellow traveler.

    The extreme is the now-well-recognized reversal of hormone replacement therapy from being preventive of heart disease to being a predictor of heart disease: health-conscious women accepted and sustained their hormone prescriptions, until a randomized controlled trial tested this with much less ‘healthy user’ bias.

  48. DirkH November 12, 2013 at 6:06 am

    I have read anecdotes that go both ways. The metabolism of the body can change over time. Do post menopausal women metabolize differently? We do know that the metabolism changes with age.

    I have no dog in the fight. I personally prefer a meat diet.

    And what are the odds that the body is “trained” by early consumption? How big is that effect? Is it an effect?

    Are cyclists representative of the general population?

    More study is required.

  49. Regarding Mann: assuming he did everything properly, his model in the end is not quite scientific. And no forecast or estimate of the future ever can be. Likewise, it will be quite a day when “evolution” is scientifically confirmed.

    In the long run, science depends upon making an a priori prediction, specifying a disprovable test of that prediction, then gathering that actual evidence to observe whether the prediction is accurate or not. We do not know what will happen in the future. A predciton can be based on some good science, but a prediction of what the future will be like can never be observable – until it happens, at which time it is no longer the future. So, patently, a prediction cannot quite ever be “confirmed,” or “scientiftic” in the way other things can be scientific facts.

    Beyond micro-evolution, evolutionalry theory suffers the same weakness. We will never see the cow-like animal again adapt itself back to underwater life as the whale-like animal. Evolution of the various species makes sense, and has a lot of evidence to support it, but it is not observed. If our species pays attention and keeps record long enough, say, a million years, sure, we might observe a new species emerge from recognized species. But we have not yet.

  50. John Whitman – the paragraph about ‘this isn’t scientific misconduct’ really sounds to me like it was helicoptered in to mollify some editor or reviewer.

    Clearly, there’s several potential reasons for choosing a ‘relaxed’ confidence interval. Maybe it’s appropriate to the situation. Maybe it’s just “the way it’s always been done” in that field. Maybe it’s what a grad student found in some statistical cookbook. Or someone fiddled up a spreadsheet and plugged in numbers until he got the results they “needed”. At some point it DOES slide far enough down the continuum to move past laziness and ignorance into misconduct.

  51. Bill Marsh at 4:42 am: +5 “Numbers are like people…” Made my day!
    chris y 5:05 am, +1 briggs quote.
    Bill Illis 5:17 am, +2 The only statistics that count: $$$$. +2
    rgbatduke 6:45 am +1 Always worth a read (and reread).
    MCT 6:53 am +1 statistics (physics, causal) vs. stocastics (climate, corelatvie). I like the concept.
    Jquip 9:31 am, +1 But this paper is precisely about non-replication.
    Brad Tittle 9:16 am “Where is the damn Like button, + ?” Do it yourself. ;-)
    Gail Combs 9:53 am +1 Independent confirmation testing/splitting.

  52. Dan Hughes says:
    November 12, 2013 at 10:36 am

    Tighter stats requirements do not address the very real problem that correlation does not equal causality.

    Correlation is the first step in a sorting process. If there is causation there will be correlation. If there is no correlation look elsewhere for possible mechanisms of cause between variables. It’s more productive to look for causation first among the variables that are most highly correlated.

    Correlation is just a clue. The problem is when it is taken as proof, which is a problem with the scientist not the procedure.

  53. JEM — in case you didn’t see my post soon after yours on the heart attack thread on 11/10 (perhaps you did…) — HOW ARE YOU DOING? I hope all is going very well. I’ll keep praying, but, IT WOULD BE NICE TO KNOW!
    #(:))

    JM

  54. ferd berple says:
    November 12, 2013 at 7:25 am

    Perhaps the biggest assumption in modern science is the assumption that the purpose of science is to conduct research, to discover “The Truth”.

    What if the true purpose of science is to attract funding? What scientific body would welcome a study that said “nothing to worry about, you can cut our funding”?

    I posted the following on CA yesterday:

    Daniel S. Greenberg is a Washington-based journalist who has recently turned to fiction after a long career writing about science policy and politics. He is the author of three non-fiction books, “The Politics of Pure Science,” “Science, Money, and Politics,” and “Science for Sale,” all published by the University of Chicago Press. His novel, “Tech Transfer: Science, Money, Love, and the Ivory Tower,” published in 2010, was described by the New York Times as “a hilarious” and “mordant satire about scientists and universities and how they do business.” (NY Times, Science section, book review, May 25, 2010).

    Greenberg has served as a reporter for the Washington Post, as news editor of Science magazine, and as a columnist for the New England Journal of Medicine and The Lancet. For many years, he wrote an op-ed column that appeared in the Washington Post and other newspapers, and contributed to many publications, including the New York Times, the Economist, Harper’s, Smithsonian, Nature, and The Chronicle of Higher Education. He founded and for 25 years edited Science & Government Report, an international newsletter which was acquired by John Wiley & Sons in 1997.

    Some of his books are cheap in used versions, available here:

    http://www.amazon.com/Daniel-S.-Greenberg/e/B001HD15GW/ref=sr_ntt_srch_lnk_1?qid=1384202495&sr=1-1

  55. Evolution of the various species makes sense, and has a lot of evidence to support it, but it is not observed.

    It is observed for fast reproducing species. Bacteria come to mind. From this the rest is inferred. Some do not care for the inference. They may (or may not) have a point.

  56. Gail Combs says:
    November 12, 2013 at 9:53 am
    “Taking ferd berple’s example of drug testing.”
    Drug testing of employees is not science and anyway a drug test which has 95% confidence is a screening cheap crap which anyway needs retest in case of positive in any case.

    “In science it is independent replication usually by at least two independent labs. If it can not be replicated it gets tossed into the dustbin of history.
    I see no reason to change this but the confirmation testing by an independent lab or two or three is an absolute must and this is what is missing in Climate Science.”

    Confirmation is matter of church, not science.
    The point in science is not confirmation, replication, the point is falsification. If something is confirmed than good, but if not, then it actually belongs to the dustbin of history. The point of scientific method is falsifiability (a hypothesis which is not falsifiable, is not scientific hypothesis by definition). If a claim, for example “man is responsible for global warming, because we made model XYZ123, tuned it and it shows he is and we predict temperature rise with it this and this” is a dangerous claim in science – because immediately the reality shows that the temperature is significantly not following the model, the model is falsified and belongs to dustbin of history. You actually don’t need anything like “confirmation” for it.

  57. In climate ‘science’ the only effect that rising the statistical bar will have is for more run time on the computers to ‘ensure ‘ they get the results ‘required ‘
    Its simple really , start with what your ‘results ‘ then produce the ‘data’ that supports them.

  58. M Simon: ” Bacteria come to mind. From this the rest is inferred. Some do not care for the inference.”

    You missed the point in that we haven’t observed bacteria turn into bivalves. And we will not reunobserve bivalves going backwards through time into bacteria. As we go through time in the other direction. It is not testable, and in a condition of passive observation that requires time machines, impossible. eg. When it you can’t slap it up on a lab table, on demand, the best you get is passive observation. And in this, unless you have time machines, time goes one way and its pace; not ours.

    People get a rather religious burr about it when you mention the ‘E’ word from the great Chuck D. But it remains that anything that is inherently stateful and chaotic, and that cannot be built on demand in a lab, has no valid inferences but an absolute crapload of observations. Simply look at the condition of astronomy and the ages of time it took to get from rather impressive Neolithic devices for measuring the heavens on to about Galileo. And that’s for something as simple as a first-order approximation of an ellipse. This remains true in every similar case, even for treemometers and IPCC models.

  59. You mean you want us to run more simulations with the same model, or set of models, to bring those error bars in tight? I hear you man! That’s why we are writing a grant proposal for $1 bn more computing power – so that we can report the output of our models to even more decimal places. Hopefully more decimal places will make our simulations better because we do not know the difference between accuracy and precision. [/sarc]

  60. TheLastDemocrat says:
    November 12, 2013 at 11:23 am

    In the long run, science depends upon making an a priori prediction, specifying a disprovable test of that prediction, then gathering that actual evidence to observe whether the prediction is accurate or not. We do not know what will happen in the future. A predciton can be based on some good science, but a prediction of what the future will be like can never be observable – until it happens, at which time it is no longer the future. So, patently, a prediction cannot quite ever be “confirmed,” or “scientiftic” in the way other things can be scientific facts.

    Beyond micro-evolution, evolutionalry theory suffers the same weakness. We will never see the cow-like animal again adapt itself back to underwater life as the whale-like animal. Evolution of the various species makes sense, and has a lot of evidence to support it, but it is not observed. If our species pays attention and keeps record long enough, say, a million years, sure, we might observe a new species emerge from recognized species. But we have not yet.

    Jquip says:
    November 12, 2013 at 12:51 pm

    M Simon: ” Bacteria come to mind. From this the rest is inferred. Some do not care for the inference.”

    You missed the point in that we haven’t observed bacteria turn into bivalves. And we will not reunobserve bivalves going backwards through time into bacteria. As we go through time in the other direction. It is not testable, and in a condition of passive observation that requires time machines, impossible. eg. When it you can’t slap it up on a lab table, on demand, the best you get is passive observation. And in this, unless you have time machines, time goes one way and its pace; not ours.

    People get a rather religious burr about it when you mention the ‘E’ word from the great Chuck D. But it remains that anything that is inherently stateful and chaotic, and that cannot be built on demand in a lab, has no valid inferences but an absolute crapload of observations. Simply look at the condition of astronomy and the ages of time it took to get from rather impressive Neolithic devices for measuring the heavens on to about Galileo. And that’s for something as simple as a first-order approximation of an ellipse. This remains true in every similar case, even for treemometers and IPCC models.

    ————————–

    I don’t know how the myth persists that speciation has not been observed. It has repeatedly, both in the lab & in the field, as well of course as inferred from the fossil & genomic record, plus many other independent lines of evidence. The macro-evolution of new species, however defined, from other species is an observation, not just an inference, ie a scientific fact.

    The instances are too many to recount all here, or the correct predictions made on the basis of evolutionary theory, which is of course itself still developing, just as is the theory of gravitation, for instance.

    In the case of microbes, simple mutations can produce a new species. Good example are the two not at all closely related bacteria which have acquired the ability to metabolize nylon by-products. It’s harder to say what constitutes a species with bacteria than with eukaryotes, but a switch from getting energy from sugar or other natural substances to nylon byproducts in my book counts as speciation, just as insects evolving from eating sugar to blood does.

    New plant species arise essentially overnight due to hybridization & polyploidy, which is less common in animals, but has also been observed in the wild & recreated in the lab. “Darwinian” evolution, ie by natural selection, has also been observed in animals, & while gradual, can still be quite rapid (eg two decades), even in species with fairly long generation times. As luck would have it, Darwin’s Galapagos finches have recently been found to provide examples:

    http://en.wikipedia.org/wiki/Peter_and_Rosemary_Grant

    Gradual speciation taking place over longer periods can still be directly observed, as with the ongoing separation of polar bears from their brown bear kin.

    As for whales evolving from terrestrial artiodactyls (much smaller than cows), the fossil, anatomical & genomic evidence is overwhelming. While, despite an excellent & improving fossil record exists, some inference is called for, but such was also the case for the earth orbiting the sun until direct observation was possible. The same applies to other major transitions, not just speciation but changes from one higher Linnaean or common classification to another, eg from “fish” to “amphibian” to “reptile” to “bird”.

    Evolution is both an observed, scientific fact & a body of theory seeking to explain that fact.

  61. is this method similar to what the epa did with the meta study on second hand smoke? the studies found NO significant stat correlation so they altered what is significant to claim there was??

  62. I disagree with the blanket conclusion in the article because:

    1) The researcher sets the p-value. It determines the level of false positive error he is willing to allow into the study.
    2) Selecting an appropriate p-value for hypothesis testing depends on several factors including the objective and conditions of the study. For example, we can and should run screens at much lower stringency since you need to eliminate false negatives and are willing to accept more false-positives.
    3) A p-value of 0.0001 or 0.2 can be quite appropriate depending upon the objective of the study. In either case, it should be possible to reproduce the study under the right set of conditions.
    4) The power and the level of false negative error rate is the critical factor once we have selected an appropriate p-value.
    5) Understanding critical sources of error in the study, taking steps to control them, including appropriate sample size (reps etc), are as critical for reproducing results as the p value.

    Statistics is a tool. It can be a very good one if we use it appropriately and a very bad one if we do not. Kind of like a wrench or backhoe or just about any other tool.

  63. ‘Some do not care for the inference. They may (or may not) have a point.’
    It is not an inference; it is just that in cases of slowly reproducing species we can observe only smaller changes over the same amount of time. The extent of evolution directly observable is less.
    The question is not whether species evolve. By their very characteristics as living organisms, they must and they do. It is a mathematical certainty. The question is whether evolution explains all of the biological variation we see around us.

  64. tumetuestumefaisdubien1 says:
    November 12, 2013 at 11:40 am

    Gail Combs says:
    November 12, 2013 at 9:53 am
    “Taking ferd berple’s example of drug testing.”

    Drug testing of employees is not science and anyway a drug test which has 95% confidence is a screening cheap crap which anyway needs retest in case of positive in any case.
    [Agreed, I was just using it as an example.]

    “In science it is independent replication usually by at least two independent labs. If it can not be replicated it gets tossed into the dustbin of history.
    I see no reason to change this but the confirmation testing by an independent lab or two or three is an absolute must and this is what is missing in Climate Science.”

    Confirmation is matter of church, not science.
    >>>>>>>>>>>>>>>>
    I disagree, but then I worked in industrial chemistry. If a new reaction or method can not be duplicated by others it gets tossed. Think Fleischmann, Pons and Cold Fusion.

    I should not however have used ‘confirmation’ when I meant verification and validation.

  65. Here is a fascinating article about genuine scientists producing results which are initially reproducible, then later are not!

    The New Yorker – December 13, 2010
    The Truth Wears Off
    Is there something wrong with the scientific method?
    by Jonah Lehrer

    Unfortunately, I couldn’t find the effect,” he said. “But the worst part was that when I submitted these null results I had difficulty getting them published. The journals only wanted confirming data. It was too exciting an idea to disprove, at least back then.” For Simmons, the steep rise and slow fall of fluctuating asymmetry is a clear example of a scientific paradigm, one of those intellectual fads that both guide and constrain research: after a new paradigm is proposed, the peer-review process is tilted toward positive results. But then, after a few years, the academic incentives shift—the paradigm has become entrenched—so that the most notable results are now those that disprove the theory….”
    [Page 3]

    “…The problem of selective reporting is rooted in a fundamental cognitive flaw, which is that we like proving ourselves right and hate being wrong. “It feels good to validate a hypothesis,” Ioannidis said. “It feels even better when you’ve got a financial interest in the idea or your career depends upon it….”
    [Page 4]

    “…Even the law of gravity hasn’t always been perfect at predicting real-world phenomena. (In one test, physicists measuring gravity by means of deep boreholes in the Nevada desert found a two-and-a-half-per-cent discrepancy between the theoretical predictions and the actual data.)….Just because an idea is true doesn’t mean it can be proved. And just because an idea can be proved doesn’t mean it’s true.”
    [Page 5]

  66. tumetuestumefaisdubien1 says: @ November 12, 2013 at 11:40 am

    …The point of scientific method is falsifiability (a hypothesis which is not falsifiable, is not scientific hypothesis by definition). If a claim, for example “man is responsible for global warming, because we made model XYZ123, tuned it and it shows he is and we predict temperature rise with it this and this” is a dangerous claim in science – because immediately the reality shows that the temperature is significantly not following the model, the model is falsified and belongs to dustbin of history. You actually don’t need anything like “confirmation” for it.
    >>>>>>>>>>>>>>>>
    Actually after the examples we have seen in climate science I think you do need independent checking . Actually after what I have seen go on in industry I KNOW you do.

    However you are correct that falsification is the main point. I was just saying it badly.

  67. milodon: “I don’t know how the myth persists that speciation has not been observed.”

    Yeh, you know. I didn’t say ‘speciation’ and detailing all the sophist redefinition and name-changing about ‘evolution’ and ‘species’ is about as thoroughly voluminous as the same treatments for Anthropogenic Global Warming, I mean Climate Change, sorry, I mean Climate that isn’t changing. And is not changing due to Natural Causes er… Water vapor feedbacks, nuts. I mean it’s been proven that it’s humanity. So fast… I mean it’s obviously the Koch brothers. And not only is it as stupid and voluminous; it’s almost guaranteed to be religious (like Cllimastrology) but off topic. But hey, if you can’t make your error bars big enough, undefine your words.

    Point is, inferences that go backwards in time are in every case invalid. It’s pure pro causa non causa. And the only validity to an inference that goes forward in time is that we have validated it enough — observationally — that we can get it some inductive assurety in future uses.

  68. polistra says:
    November 12, 2013 at 4:28 am

    Stats can’t be saved by tweaking.

    The only proper standard for science is NO STATS. If a result has to be reached by statistics, it’s not a scientific result. Only well-calibrated measurements plus a well-balanced experiment can give scientific results.

    SO, was the Higgs Boson identified or not?

    There are no – as in “none” – scientific disciplines whose study is not entwined with statistics in some fashion. ANY time the word “quantifiable” emerges, statistics is lurking. Ideally, the issue is merely accuracy of multiple measurements, as in calculating the “real” value of G – the gravitational constant – an empirical constant, that is dependent upon repeated measures for a estimated value. Since the use of G is essential in critically important modern topics like orbital mechanics, statistics measuring accuracy or similarity of repeated measures is critical. In fact, “well calibrated” measurements are only determined to be “well calibrated” statistically. If a standard is used in the calibration, that standard was supplied with an “error.” Read up on the Michelson-Morley measurement of the speed of light. They used repeated measures, and then estimated the speed of light statistically, with an estimated error based upon the dispersion of measurements from multiple experiments. As described in Wikipedia, for the current value in use:

    By combining many such measurements, a best fit value for the light time per unit distance is obtained. As of 2009, the best estimate, as approved by the International Astronomical Union (IAU), is:[88][89]…

    light time for unit distance: 499.004783836(10) s
    c = 0.00200398880410(4) AU/s = 173.144632674(3) AU/day.

    The relative uncertainty in these measurements is 0.02 parts per billion (2×10−11),

    Note the use of “best estimate,” “best fit,” and “relative uncertainty” – which is quantified. Statistics again. That is purtedly “hard science.” In the real world, compared to the complexities of any field science including meteorology, measuring the speed of light is a comparatively simple effort.

  69. M Simon says:
    November 12, 2013 at 11:21 am
    “And what are the odds that the body is “trained” by early consumption? How big is that effect? Is it an effect?
    Are cyclists representative of the general population? ”

    I don’t think there’s a training effect by early consumption. Maybe some epigenetic inheritance, gene methylation patterns determined by the mother during pregnancy; I guess this also influences body size, just a guess.

    In Germany and the Netherlands cyclists are representative of the general population, even though the Dutch won’t believe me; they also believe that it is mandatory to wear a bicycle helmet in Germany, but it ain’t.

    Well, I thought you might have THE conclusive study that shows the link between fat and heart attacks but I guess I’ll have to wait then…

    What I recently found is this:

    David Diamond, Ph.D., of the University of South Florida College of Arts and Sciences shares his personal story about his battle with obesity. Diamond shows how he lost weight and reduced his triglycerides by eating red meat, eggs and butter.

  70. “Using recent developments in Bayesian hypothesis testing, a root cause of nonreproducibility is traced to the conduct of significance tests at inappropriately high levels of significance.”

    Oopsie daisy!

  71. Jquip says:
    November 12, 2013 at 2:00 pm

    What redefinition? Speciation means the origin of species, same as in the title of Darwin’s book, which dealt with the evolutionary process of natural selection, one means of speciation. Call it macro-evolution if you want. It’s not only based upon inferences from observations of the past, but, as I showed, upon direct observation in the present & in the lab. I’ve made new species myself. It’s fun & easy.

    Both the fact & theory of evolution make testable hypotheses, which have not been falsified. That new species, genera, families, orders, classes & phyla arise from existing taxa is an observable fact as well as an inference that explains observations best. Comparing evolution with CACA is what Warmunistas do. Descent with modification, ie evolution is valid science, describing objective reality. CACA is anti-scientific.

    I’d be interested in your better explanation for such observed phenomena as shared, derived pseudogenes in, let’s say, primate lineages such as humans, other great apes, lesser apes, Old World & New World monkeys & tarsiers. Or how about the fact that human chromosome 2 results from the fusion of two smaller chromosomes conserved in chimps & bonobos?

  72. JEM on November 12, 2013 at 11:25 am

    @John Whitman on November 12, 2013 at 9:15 am

    – – – – – – –

    JEM,

    Thanks for your comment.

    I think ‘helicoptered in’ has some plausibility given that the nature of peer review does not prevent it per se. If peer review process documentation were publicly available after the peer review process completes, then science could correct itself more efficiently than it currently does.

    John

  73. 10 thousand Olympic athletes are tested for drug use with a test that is 99.99% accurate. what are the odds that an athlete identified as a drug user is a drug user?

    50-50, even odds. One (very likely) true postive, one false positive. One reason that physicians should not give everybody that walks through the door a full spectrum of tests, especially for low prevalence conditions. If prevalence is one in 10,000, and you test everybody with a test that has a 1% false positive/negative rate, (99% accurate, as it were) you’ll get 1% of 10,000 or 100 false positives and one true positive 99% of the time (you’ll actually MISS that true positive 1% of the time, sigh).

    Nearly all of the 100 people identified will be false positives, and you’ll have to do infinitely more tests, spending infinitely more money, to weed out the false positives and find the one lonely true positive. Not enough insurance money in the world… not to mention spending weeks thinking you might have brain cancer when you don’t. That’s why physicians have to have OTHER reasons to suspect a low-prevalence condition before they give you a test for it. The other reasons “promote” you from a Bayesian prior of randomly selected from a low prevalence base population to a much more refined population of people that actually exhibit symptoms for the disease AND have the disease, which ordinarily will have a much higher prevalence. Maybe enough to get to even odds.

    And good examples, BTW, especially the data dredging example. I didn’t do this (prevalence) particular example and probably should have. I also like the “Let’s make a deal” example to illustrate why additional information changes the prior odds.

    On the Lets Make a Deal show, one would often select (say) door number three in hopes of winning the Carribean Vacation package. Before showing you what was behind door number three, Monte opens one of the remaining two doors (say, door number one) to show you that it contains the barbecue set worth a whopping $150. He then asks if you want to change doors to number two before he opens them.

    If Monte either always does this, or randomly decides to do this without being influenced by whether or not door three contains the big prize, the answer is “yes”. You improve your chances of winning if you switch to door number two, because you can take advantage of the additional knowledge associated with knowing that door one didn’t contain the prize in the second pick. Proving this is an entertaining exercise. But kind of irrelevant to hypothesis testing…

    rgb

  74. milodon: “I’d be interested in your better explanation for …”

    Stop there, Sparky. I am not required to give you any explanation at all; let alone one that is ‘worse’ or ‘better’ by your purely subjective judgement. Nor was the big E from Chuck D central to the point: It is, purely, a passive observational. And it is quite required to be, since if we monkied about with intelligent purpose that would be… the theory of its detractors.

    If you wish to attack the salient points then:
    a) Establish how one can make a valid inference about things we never observed and cannot.
    b) Establish how one can make a valid inference when nothing is claimed, or no time is claimed for its culmination. (cf: The 17 217 years of Santer. Global Warming entails heating cooling and more less severe weather events.)
    c) Establish how we can state what will occur, in a chaotic system with feedbacks. When those feedbacks are not known, not described, or not describable.

    And I guarantee you this: If you succeed, in any measure, establishing the validity of these as unimpeachable, then so to is Climate Change. And just about every religion that has ever existed. As well as the totality of psychic and other esp claims.

  75. Gail Combs says:
    November 12, 2013 at 1:51 pm
    “I disagree, but then I worked in industrial chemistry. If a new reaction or method can not be duplicated by others it gets tossed. Think Fleischmann, Pons and Cold Fusion.
    I should not however have used ‘confirmation’ when I meant verification and validation.”

    I’m quite not sure Cold fusion has anything with chemistry or rather even whether it has to do with anything. Verification in science purely means to inequivocally set criteria for a hypothesis or theory to be true or false and then test whether the hypothesis or theory passes the criteria or not. Validation means assesment whether a scientific method is suitable and adquate for a defined purpose or not or in the case of mathematical modeling, whether the output of the model fits the observation or not and quantification of difference for deciding whether the model is or isn’t falsifiedl. So I quite still don’t completely understand what you’re talking about.
    Independent replication of some scientific results is of course good if somebody does it, but somebody tries something like that only if the original claim is plausible, well supported and the independent researcher has a motivation to look into the issue. Otherwise nobody of course bothers. Definitely not in basic research.
    For example: some credible reputable solar scientists published a claim that according to recent data from certain satellite some bands of solar spectrum vary not in phase with solar cycle. And because it looked interesting and plausible when one briefly checked the data and could have interesting implications if true I decided to replicate their results. And after month or so of work I indeed found that in some important bands indeed the solar activity consistently doesn’t variate in phase with solar cycle, moreover I’ve found additional facts, which have likely broad implications and aren’t in any sense part of the original claim – which paradoxicly all relates to the fact, that in other band, where they also claimed the same peculiar variation I’ve found that the data contain clear outliers which spoil the slopes and when taken out the peculiar variation artifact disappears. So partially I replicated some of the original results and partially I also falsified other, but the combination of the sucesful replication of one claim and failure to replicate the other together imply something yet different which is worth of further examination, because it not only means the replication of one and falsification of other claim, but in complex could mean a potential falsification of whole theory of the solar variation and its relation to earth insolation. Science is often history of accidental finding of something when looking for something else, because simply what we don’t know we can’t anticipate to find. So often also the falsification of some previous claim means not only tossing it in the dustbin of history, but also finding something else, sometimes much more interesting that what was falsified and that’s why even it could look destructive for a layman the principle of falsification in science is the way to the truth not only byl elimination of untrue, but also finding the new implications of it not be true.

  76. I have been expressing my contempt for years at the use of .90 and .95 “certainties” in CS (or anywhere). The reasons for requiring high-sigma results to reject the Null are many, and demonstrate their relevance with great regularity. Confirmation bias seems to be the currently dominant one.

  77. rgbatduke: ” But kind of irrelevant to hypothesis testing….”

    Contrary, in fact. As you already know how many doors, how many goats, and how many sports cars there are. But in the false positive condition you’re asking for people to be properly analytical rather than improperly analytical. But this still doesn’t inform you of whether or not you had zero drug users in fact, when you found 2 or 3 by test. After all, if the suspecting people aren’t terribly good at it, then they’ll only test the drug-free in the first place.

    Quite strictly,there’s nothing wrong with hypo testing by statistics. But you cannot be demonstrating it on edge cases, outliers, or miracles. Or you’re simply lost in every case.

  78. Statistics is merely a tool that is used when you don’t know. It too often gives the perception that you do know. Most assumptions in statistics are false. They are convenient, but don’t match reality. Most distributions in the world are not Gaussian, heck, most often they are multi-modal. There is not such thing as “standard deviation”. It’s a false construct based on gross assumptions known to be false. Few things in this world are linear, or merely log functions, but statisticians presume this quite often. There are many uncontrolled variables, measurement errors, noise, non-linearity, multivariate effects and interactions, bias, feed-back loops, associated chaos, etc. When someone says something is statistically significant what they are really saying is “I don’t know, but I’ll pretend that I do, and try to convince you I’m right.”

  79. You missed the point in that we haven’t observed bacteria turn into bivalves.

    That wasn’t my point. We have seen bacteria change into a different kind of bacteria with different environmental requirements. From that we infer the rest.

  80. Jquip says:
    November 12, 2013 at 4:33 pm

    I didn’t require you to do anything. Nor do I find all your points salient. But I will nevertheless reply to the questions you put to me,

    “a) Establish how one can make a valid inference about things we never observed and cannot.”

    Evolution makes valid inferences about observations. Paleontologists & anatomists for example observe that Indohyus, an herbivorous, cat-sized, deer-like artiodactyl in the family Raoellidae from the early Eocene of Kashmir, shared derived traits with cetaceans. Among these is a bone growth pattern diagnostically characteristic of cetaceans, not found in any other group. In cladistic phylogeny, that makes the Raoellidae the closest sister group to Cetacea, descending from a common ancestral group. Indohyus also shows signs of aquatic adaptations, including a thick, heavy outer coating & dense limb bones that reduce buoyancy to facilitate staying underwater, adaptions found in the hippopotamus. This suggests a similar survival strategy to modern mammals which dive into water & hides submerged for some minutes when threatened by a bird of prey.

    To these observations have been added those of Pakicetus, another latter early Eocene genus from northern Pakistan, found by a river then near the shore of the Tethys Sea, & also fluvial deposits from northwest India. Thus Pakicetids probably lived in an arid environment with ephemeral streams & moderately developed floodplains. Analysis of their stable oxygen isotopes shows they still drank fresh water. Although hoofed, they appear to have been predators, eating land animals which came down to the water to drinking or riverine aquatic organisms.

    While certain anatomical features show them to be cetaceans, their elongated cervical vertebrae & four, fused sacral vertebrae are consistent with Artiodactyla, making the Pakicetidae one of the earliest fossils recovered following the Cetacean/Artiodactyla divergence event.

    Features of both their skulls & post-cranial anatomy lead Pakicetids to be classified as cetaceans. An important trait is the structure of their auditory bulla, which is formed from the ectotympanic bone only. The shape of the ear region in pakicetids is highly unusual & the skull is cetacean-like, although a blowhole is still absent at this stage. Their dorsal orbits (eye sockets) face up), as in crocodilesm which eye placement helps submerged predators observe potential prey above the water. Pakicetid teeth also resemble those of fossil whales, being less like a dog’s incisors, with a serrated triangular shape, & more similar to a shark’s tooth. However, pakicetids were able to listen underwater, by using enhanced bone conduction, rather than depending on tympanic membrane like general land mammals.

    Their bones are unusually thick (osteosclerotic), which is probably an adaptation to make the animal heavier to counteract the buoyancy of the water. Morphological analysis found that pakicetids display no aquatic skeletal adaptation; rather are adapted for running & jumping. Thus they were most likely an aquatic wader.

    It is normal in science to make inferences based upon observations, as did Copernicus to develop his heliocentric hypothesis. Paleontologists study the anatomy of extinct creatures, then, based upon their observations, make predictions which can be tested. I wonder why you think that observations of fossils don’t count while observations of light from stars millions of light years away do.

    The discoveries of paleontologists are reinforced by those of molecular biologists & geneticists studying the genomes of whales, hippos, artiodactyls (even-toed ungulates) & for comparison, other mammals. Paleontologists, based upon prior observations, predict where & in what rock strata to dig to find more early whale fossils of more recent date, & have been successful doing so.

    The same is true for every class, order, family & genus put to comparable tests. For instance, paleontologists predicted that proto-mammals would be found with both the “reptilian” & mammalian jaw joint, & sure enough, they were. (Mammals are unique among vertebrates in having only a single lower jaw bone, the dentary. The other former jaw bones have evolved into the mammalian middle ear.) It’s the scientific method in action, unlike anti-scientific CACA.

    Of course, as I pointed out previously, today we don’t need to rely on inferences to observe evolution in action. Macro-evolution is the same process as micro-evolution, just run for more time in the case of gradual evolution. There is no magic genetic barrier that keeps one species from evolving into a new one, given selective pressure to do so or simple reproductive isolation. The processes can be & have been observed all around us.

    “b) Establish how one can make a valid inference when nothing is claimed, or no time is claimed for its culmination. (cf: The 17 217 years of Santer. Global Warming entails heating cooling and more less severe weather events.)”

    Why would I want to establish such a thing? I think CACA advocates’ constant moving of goal posts is yet another indication that they don’t practice science. I don’t see what this has to do with evolution.

    “c) Establish how we can state what will occur, in a chaotic system with feedbacks. When those feedbacks are not known, not described, or not describable.”

    See above.

  81. M Simon: “We have seen bacteria change into a different kind of bacteria with different environmental requirements.”

    My eye color, hair color, and build are different than my parents. Obviously I’m a new species. And again: Not the point. But it does highlight that getting too loose or strict with a bounded range leads to absurdity.

  82. Those of us who studied the non-belief-based sciences have usually been taught how to recognise appropriate statistical techniques. But we were warned not to try it ourselves for real research. Rather to get a specialist Statistician on the job. Sciences like Climate and Nutrition have shown the stupidity of doing otherwise. Brett Keane, NZ

  83. milodon: “In cladistic phylogeny, that makes the Raoellidae the closest sister group to Cetacea…”

    For your response to a), let me just sum that up as “it looks the same, therefore it is the same, therefore the process we didn’t observe occur is the only one that could occur.” Now cast that to climatology. Specificaly to ‘lines that go up’ or ‘treemometers’ and add in a dose of ‘therefore man did it.’

    ” I don’t see what this has to do with evolution.

    None of it has anything to do with evolution. It has to do with what is required for a valid inference. What is it that constitutes ‘proof’? Or disproof, validation, verification, falsification, etc. But it’s all rooted in passive observationals: That is, we cannot slap it on a table an do it, but must hang out peering at the night sky and wait. (Astronomy, this time,)

    Validate the inferences based on the constraints of time and passive observationals. If that works, then the gig is up and Climate Science is indisputable.

  84. Jquip says:
    November 12, 2013 at 5:57 pm

    No, you’re not a new species. You inherited genes from your parents, along with some mutations all your own. Those genes are just reshuffled. It seems that you have never studied the science of biology whose most elementary tenets seem to mystify you. Why then do you feel compelled to comment on the subject?

    For sexually reproducing organisms, the usual definition of a species is that its members can normally produce fertile offspring with each other, unlike hybrids like mules. There are many instances of ring species, in which one subspecies can produce fertile offspring with the other subspecies nearest it, but not with those at the extremes of the species’ range. Zebras used to be a good example, but some of its subspecies have gone extinct.

  85. Jquip says:
    November 12, 2013 at 6:02 pm

    I’ll make one last attempt.

    In biology, geology, astronomy, physics, any science with an historical component, the testable assumption is made that processes which we observe occurring now also happened in the past, unless evidence emerges to suggest otherwise.

    In the case of evolution, science can now look at genomes & see precisely what the differences & similarities are on the molecular level between different species, genera, families, orders, classes, what have you, from bacteria, archaea & unicellular eukaryotes to sequoia trees, giant fungal rings & blue whales.

    The inferences made from the fossil record & other entirely independent lines of evidence are still helpful however, as we complete genomes for few organisms. Similarly the age of the sun can be derived independently in at least two ways, & they both agree closely.

    Do you have the same objection to geology as to biology? Geologists inferred from the evidence that the continents were once conjoined, but until the discovery of seafloor spreading in the 1950s lacked a good explanation for the observations that supported this inference. Same was true of evolution before Darwin & Wallace. Scientists inferred that it had happened from fossils & anatomy, but didn’t know how. The falsified consensus was shown wrong by new hypotheses with abundant supporting evidence.

    Now compare & contrast these valid sciences with “consensus climate science”, in which what should be subject to investigation is simply assumed, no falsifiable predictions are made, GIGO models based upon false assumptions are accepted as “evidence”, which can be “validated” by comparison with other GIGO models & when models are shown false, the goalposts are simply moved.

    Comparing the scientific fact of evolution with CACA does the greatest possible disservice to the skeptical case against CACA. (I prefer “case” to “cause”, since a cause is what the anti-scientific scientivists like Mann have.)

  86. PS: Re “therefore the process we didn’t observe occur is the only one that could occur”. No one says it’s the only one that could occur. It’s just that no one has come up with a better explanation than darwinian directional & 29th century stochastic processes leading to evolution. The alternatives on offer, ie inheritance of acquired characteristics or sequential special creation by a supernatural force or being, have real problems.

    This is why I asked if you could come up with a better explanation for observations in the whale lineage. Biology would embrace your hypothesis if it did a better job of explaining observations. Science has looked since 1859 without success. Rather more & more supporting evidence keeps piling up, adding to the theory but not falsifying it, as with Einstein’s improvement on Newton’s conception of gravity.

  87. When CACA advocates like Gore ask, “What else could be melting the ice but man-made CO2″, skeptics have good answers, more convincing than CACA. When people opposed to evolution say it could be something else, they can’t offer any convincing alternatives. Anti-scientific ID is demonstrably just a stalking horse for creationism.

  88. milodon: You seem to be struggling still with what I believe, rather than what the question is. So just assume I’m a true believer of evolution and already know these things. The question isn’t biology or geology: It is what makes the *form of inference* valid. Because it is absolutely certain that our wishes for the topic cannot. Lay down the rules for what makes the argument valid.

  89. Jquip says:
    November 12, 2013 at 6:55 pm

    I was trying to understand what your objections are to the scientific method. What makes a “form of inference” valid has long been known & used with huge success. First, the inference needs not to have been shown false. Second, it should enjoy support from other lines of evidence or new observations along the same line. Third, it should explain observations better than any competing hypotheses.

    Evolution passes these tests with flying colors. CACA fails epically in every case & particular.

  90. Since some of the comments have strayed into the medical lab (where I’ve worked for 25 years) I thought I would throw in a couple of semi-relevant comments. In the lab the terms “95% confidence level” and “accuracy” are both important, but very different. There seems to be a little mixing of the two. For quantitative tests our quality control samples (run at least 3 times per day) must yield results within 2SD of the mean, or corrective action must be taken and documented. For us this statistical 95% level means we can be 95% certain that any deviation from the “true” level of the analyte is caused by randomness in the testing process (equipment, operator, reagents) rather than error such as malfunction, operator error, or contaminated reagents. Accuracy is related but refers to the correctness of the result. In Qualitative tests (pos/neg) such as drug screens (they can also be quantitative, but usually not) I’m pretty sure the accuracy rate is much higher than 95%. I doubt if a test procedure with accuracy that low would ever be approved for use. Usually “false positives”, which are usually interfering substances such as medications, can be sorted out through patient history and confirmation/verification using other methods without certain interferences. I’m certainly no expert on drug testing, I would guess the incidence of people being said to have a drug in them that was not there is much less than 1%. ( I know these are just examples people are using, but it seems as if there is some idea that they are real) I do wholeheartedly agree with rgb@duke about overtesting. There is a huge amount of overtesting. Mostly I think due to defensive medicine and partly due to convenience. I guess this doesn’t have much to do with Bayesian theory (which my basic statistics class did not include), but I have always suspected that statistical significance was somehow being misused.

  91. milondonharlani,

    I find your comments on evolution very interesting. I wish I had time to discuss them at length but I do not. I want to draw your attention to an article that I find very interesting:

    http://www.theguardian.com/science/2013/oct/17/skull-homo-erectus-human-evolution

    The topic of interest is the relationship between natural variability and speciation as these concepts were discussed by Darwin. The context is pre-Mendel and pre-Crick and Watson. The evidence is limited to the fossil record.

    Briefly, would you agree that the evidence for several species has been called into question by the discovery in this article?

  92. Milodon sez: “There is no magic genetic barrier that keeps one species from evolving into a new one, given selective pressure to do so or simple reproductive isolation. The processes can be & have been observed all around us.”

    Well, there is. At least, as far as I was taught in high school. We learned about sexual reproduction. The chromosomes line up in their pairs, then pulled into two complementary sets, then the cell splits in two, with a set in each cell, if all goes well, and you have two gametes (sorry to get technical with the language); you get a cell that has only half of the otherwise paired set of chromosomes.

    A new member of the species results if a male gamete and a female gamete meet and combine, and their half-sets of DNA are able to match up. The resulting double-strand DNA then gets unzipped when and where necessary so that one of the strands can code for proteins. And so on.

    If the genes don’t match up one-to-one, all of this may fail. If the chromosomes don’t line up, one to one, then all of this may fail.

    So, a puzzle is: how does a gene get added to a strand of chromosome, and find a complementary gene in an opposite-sex gamete, allowing this process to carry on, with the newly added gene?

    In short, how do genes get added?

    I appreciate the frequent use of the term “assume,” and like terms, in milodon’s comments, making the case for me, that these building blocks of evolutionary theory/of speciation are based on logic and reason, and not on science.

    [ ] I will; have to look into these bacteria that have a nylon fetish – if they can reproduce with the original bacteria, I might not consider them a new species.
    [ ] conducting generations of reproduction and getting an organism that uses a new energy/food source may not necessarily be proof of a new species. The ability to eat nylon either was latent, and was made prominent by micro-evolution, or was a capability added by a genetic mutation or mutations that carried forward. A site mutation or mutations that has some advantage, but where the genes and the chromosomes can still be described, and replicate, the same way, may not be the same as the theory that explains where new species come from. If the genes are arranged the same way, and the chromosomes also, then it sounds like the same organism.

    Great interest is being paid to humans that ought to be suffering from HIV, but are not. They are humans. A wildly rare, latent trait may be being expressed. The organism is still Homo sapiens.

    [ ] It could be argued that producing a new species in the lab is proof of intelligent design, not natural selection: it takes quite a lot of purposeful intellectually-guided action to produce that new species. Sure, it helps make the case. The examples of this supposedly happening “in the wild” would be observable evidence of natural selection as the mechanism for the great variety of species we see, with their quite varying number, and pattern, of genes and chromosomes.

  93. Theo Goodwin says:
    November 13, 2013 at 7:28 am

    Yes. I’ve always been a lumper rather than a splitter in taxonomy. Some paleontologists like to assign new species names to their finds, ie they’re splitters, so that we have for instance H. ergaster in Africa & H. erectus in Asia, with H. antecessor later in Europe. The problem arises with extinct species even more than with extant ones, whose mating behavior & genomes can be observed. IMO all the H. habilis-grade specimens are one species, the H. erectus grade all one & H. sapiens all one, with notable subspecies like H. sapiens neanderthalensis.

    Thanks to Darwin & Wallace, identifying species is less important than it was when creationism held sway. Linnaeus wanted to lump humans & chimps together in genus Homo, but knew the consequences would be horrific if he did, so created the genus Pan for our closest living cousins. Biologists today realize that all categorization of living things is fraught with difficulty. Taxonomy now however has systematic means with which to do so, thanks to cladistics, & more tools, like genomics, at its disposal, rather than simply anatomical comparisons.

  94. “I was trying to understand what your objections are to the scientific method. What makes a “form of inference” valid has long been known & used with huge success. First, the inference needs not to have been shown false. Second, it should enjoy support from other lines of evidence or new observations along the same line. Third, it should explain observations better than any competing hypotheses.”

    Logic and reason are great tools to use to strive to test claims of knowledge. Inference is a matter of logic and or reason.

    Logic and or reason is not the same as the scientific method. Logic/reason, combined with empiricism, by using a priori predictions to be supported or disproven by empiric observations, is science.

    Proper inference is great, but is not, itself, “science.” Macro-evolution is, for the most part, very reasonable. Many great arguments can be made.

    Arguments can also be made that increasing anti-oxidants will keep me safer from cancer, and that massive doses of vitamin C will keep me safe from a rhinovirus. Until we set up an a priori, disprovable test, then go conduct the test, then if successful hope that others can replicate it, these are just compelling, reasonable arguments.

    I make a big point about this partly because our school kids have no ability to evaluate scientific claims – they are not being taught this properly. They are instead being taught another strategy for ascertaining knowledge: not logic/reason, not science, not empiricism, but the Edicts from The Authorities. Ninety Five Percent of all credible scientists are apparently telling my children that man-made global warming has put us on the brink of calamity. “Science” is that which is consensus of the popular scientists.

    In the old days, people studied rhetoric, debate, logic (deductive and inductive), science, and natural science.

    Nowadays, ask a college kid what rhetoric is. Ask how “science” is the same as or different from “natural science.” Ask them to define a debatable issue, and provide arguments for both sides, with rebuttals. Ask them to note the difference between deductive and inductive logic.

    They likely will not have answers to these questions. By “answers,” I mean accurate answers. People need to be able to recognize the difference between a pronouncement from an august panel, a logical argument, and a scientific test.

  95. TheLastDemocrat says:
    November 13, 2013 at 8:25 am

    Sexual reproduction is not a barrier to forming new species. Quite the opposite. It facilitates it, which you’d know had you read my comments about polyploidy & hybridization, two of the ways in which new species can be created overnight. It also helps make new mutations, since the process often goes awry, as shown by genetic birth defects.

    There is no barrier in the total genome that keeps one population of a species from accumulating differences in its genome from that of another population of the same species. Evolution works on the whole genome, which is reshuffled at each generation. The process of sexual reproduction is the mechanism by which that occurs, but the genes & non-coding material are passed down to succeeding generations. It shouldn’t be hard to understand this distinction, but apparently you missed out on population genetics in high school. And also about the genetic code.

    Bacteria don’t normally reproduce with other bacteria. Their standard method of reproduction is asexual, by splitting. Don’t know how you missed that part in high school. This fact makes it harder to define species in prokaryotes than eukaryotes, like us. Bacteria do however engage in a form of sex, by transferring genes directly between each other. Based upon how they do this, they can be said to have six “sexes”.

    Bacteria Typically have only one circular chromosome, with its DNA arranged in a circle. But not all; some bacteria have multiple circular chromosomes, & many have linear chromosomes & linear plasmids. However their chromosomes don’t line up with those of a mate, as in sexually reproducing organisms. They just replicate & split, one copy going with each daughter cell. Really, before you comment on biology, you should acquire an elementary understanding of its basics.

    Chromosomes lining up in the same way is not what makes a species. A wild horse suspecies for instance has one less chromosome than the domestic horses, but the two forms can still interbreed & produce fertile offspring.

    Chromosomes line up pretty much the same way in all mammals. When mistakes occur, the resulting animal may still be of the same species as its parent, as for instance with Downs Syndrome children. However when a previously diploid organism goes triploid, a new species might or might not emerge. Humans have polyploid tissue within our bodies, for instance, but new species of important grain crops have arisen both naturally & artificially through polyploid reproduction of the whole genome or through combination of the genomes of two parent species, even from different genera.

    The process of trait expression is usually well explained by Mendelian processes, to which recent understanding of other genomic factors has been added. It’s some magical process that just happens to pop up now & then. There are underlying genetic reasons for traits such as suddenly being able to eat nylon or showing resistance to a disease virus. Medical science looks for such genetic variation in order to make new drugs & vaccines.

    No, it could not be argued that producing a new species in the lab is proof of intelligent design, not natural selection. For one thing, selection is only one process of evolution. It’s not the one at work when I in the lab or a mutagenic agent in nature remove a base pair from a genome to create a deletion mutation, or replace one with a different base pair to create a substitution mutation.

    For another it takes no intelligence for a passing cosmic ray to knock a base pair out of an organism’s genome in one of its gametes. It just happens. It takes no purposeful intellectually-guided action at all to produce a new species. The examples of this happening “in the wild” are not supposed. Natural & sexual selection have indeed been observed repeatedly as the mechanism for the evolution of many species, but also non-directional, stochastic processes have been as well, such as the founder’s principle, reproductive isolation & genetic drift. Again, I don’t know how you missed all this in high school.

    There is zero evidence for the anti-scientific religious doctrine of intelligent design in the origin of species & all the evidence in the world against it & in favor of evolutionary processes, about which science learns more all the time.

    But please let me know when you decide whether you consider the nylon eating strains of genera Flavobacterium & Pseudomonas to be species. And also the many strains of deadly pathogens which have evolved resistance to antibiotic drugs, like the MRSA that killed one of my best friends at age 61. And the insects which have evolved to eat blood instead of flower nectar, juices & decaying matter. Ditto whether the mosquito Anopheles gambiae is currently undergoing speciation into the M(opti) & S(avanah) molecular forms, since some pesticides that work on the M form will not work anymore on the S form. Thanks.

  96. One of the interesting things about the concept of species is that there are so many of them. There is, in fact, to use Sterelny and Griffiths’ words, a flock of species concepts:

    * Phenetic species concepts define species by appealing to the intrinsic similarities between organisms. The idea is to purge species identification of theoretical commitments.

    * Biological species concepts define species by appealing to reproductive isolation. One version of the biological species concept is the recognition concept, which defines species as systems of mate recognition.

    * Cohesion species concepts generalise the biological species concept by recognising that gene flow is not the only factor that holds one population together and makes it recognisably different from others.

    * Ecological species concepts define species by appealing to the fact that members of species are in competition with one another, since they need the same resources.

    * Phylogenetic and evolutionary species concepts define species as segments of the tree of life. A species is a lineage of organisms, distinguished from other lineages by its distinctive evolutionary trajectory, and bounded in time by its origin in a speciation event and its disappearance by further speciation, or extinction.

    [From Sterelny and Griffiths Sex and Death p 193]

    It would be surprising indeed if all of these disparate ways that biologists view species produced agreement on which organisms were members of which species.

    Milo, you say you are a lumper, rather than a splitter, yet you refer to the Galapagos finches as an example of separate species. You also refer to ring species as an example of speciation in action. Since the reproductive isolation here is based on mate recognition, then I imagine we can then refer to Bob Brown and his partner as separate species ;-) Dandelions and culinary garlics are examples of species that are reproductively isolated because there is no possibility of sexual exchange of genetic material between each other. If this garlic plant cannot exchange genetic material with that garlic plant over there why aren’t they separate species? “They can’t produce fertile offspring” yet they are members of the same species. There are animals, such as certain salamanders that fall into the same category.

    I suspect that this line of discussion while very interesting, has little to do with the head topic.

  97. milodonharlani says:
    November 13, 2013 at 9:26 am
    “There is zero evidence for the anti-scientific religious doctrine of intelligent design ”

    Zero?

    http://en.wikipedia.org/wiki/Origin_of_life#Coenzyme_world

    Oh, and maybe you could avoid the word “anti scientific”; it puts you on a level with the average liberal propagandist like this Mooney person; use “unscientific” to describe things that can’t be explained with the scientific method.

    “Again, I don’t know how you missed all this in high school.”

    You have a very high opinion of public school systems. Do you have evidence for that? Just kidding. I sure knew more about genetics than my biology teacher. He just wasn’t that interested in the topic.

  98. Well, Milodon Harlani. So you are STILL trying the spread the word about Neo-Darwinism. You do realize, don’t you, that in your almost daily promoting of the theory of evolution and of Darwin’s Origin of Species ideas as if they are fact and not conjecture, you are acting like one who is promoting ones’ religion? I am hopeful that your constantly pushing Darwinism is because you have some doubt as to its truth (perhaps, only subconsciously) and will open your mind to the possibility that you are mistaken. Your level of anger when confronted with Intelligent Design is, you know, quite telling… .

    It is incredible to me that you could actually have watched the videos featuring Dr. Stephen Meyer and David Berlinski which I posted last summer in response to your assertions and still say that there is “no evidence” for Intelligent Design theory. It is obvious you have not yet honestly evaluated the evidence for Intelligent Design theory. In case you can bring yourself to do that now, here are some fine minds who disagree with your views:

    Signature in the Cell — Dr. Stephen Meyer

    Critique of Darwinian Evolution 1/3 — David Berlinski

    David Berlinski 2/3

    David Berlinski 3/3

    Best wishes to you, Mr. Harlani, whenever you do set out on a quest for the facts,

    Janice

  99. Would it be safe to remark – within the context of the conversation – that many beautiful things have undeniably and incontrovertibly come out of the planet’s poor dust, at a statistically significant rate, since the formation of the earth and the development of the seas?

    And for some this is cause to have a little faith and to sing :)

  100. The Pompous Git says:
    November 13, 2013 at 10:41 am

    Quite so. The fact that it’s often hard to define a species is a consequence of evolution. At any one time lots of subspecies are in the process of becoming new species. Species are clearly separate when the transitional forms no longer exist. In human evolution, for instance, there was a time when different forms of genus Homo might have existed, but the boundaries are fairly arbitrary as among H. erectus & H. ergaster, for instance.

    Reproductive isolation in ring species isn’t always based upon mate selection. There may be physical isolation as well. Zebra subspecies would mate with either their own or neighboring subspecies, but the most northerly subspecies can’t produce fertile offspring with the most southerly, despite gene flow in between.

    As for the new species of Galapagos finches, I might well lump them as subspecies, but the biologists who have studied them consider them separate. As I said, because there’s a continuum, it’s often hard to define species, sometimes impossible. Species are often clear cut but not always. Creationists believe in hard & fast “kinds”, each individually created. Biologists not only don’t, but would expect there to be such definitional problems.

  101. DirkH says:
    November 13, 2013 at 10:54 am

    Intelligent Design, like CACA, is not just unscientific, but anti-scientific, & for the same reason. ID advocates look at flagella in bacteria & are happy to throw up their hands & give up, saying, “These structures are irreducibly complex, so couldn’t have evolved, therefore a Designer made them.” That’s anti-scientific, just as when Prince Albert says, “What else but CO2 could be causing Arctic sea ice to melt?” The pro-scientific attitude is to look for other explanations, test them & see whether they explain observations better than competing hypotheses, rather than shrug & ask, “What else could it be?”

    In fact, there are better explanations for sea ice melt than CO2 & for bacterial flagella than a Designer poofing into existence these structures which, among other advantages, help pathogens infect people.

    It wasn’t I who rated US high schools highly. The Last Democrat felt that his high school class equipped him to comment knowledgeably on biology.

  102. Janice Moore says:
    November 13, 2013 at 11:33 am

    I am not trying to spread the word about “Neo-Darwinism”. I don’t comment on biology daily & to the best of my recollection have only done so in response to erroneous or dubious comments by others.

    I have heard all the rubbish in your videos over & over for years. I’ve already repeatedly replied to the only sciencey hypothesis yet presented by ID advocates, ie the cracked concept of “irreducible complexity”. I’ll respond further when you, Janice Moore, yourself make the arguments that you find so persuasive in favor of the anti-scientific religious doctrine of ID, which was promoted only to get around US court rulings against teaching creationism in public schools.

    If you believe there is a shred of evidence in favor of ID, please by all means, present it here yourself. You feel qualified to discuss climate science, so why not biology as well? What are you afraid of?

  103. DirkH says:
    November 13, 2013 at 10:54 am

    It’s a common mistake for non-biologists to confuse abiogenesis, the origin of life, with evolution. They’re two different processes, although evolution kicked in early on in the development of life on earth. As with evolution, the anti-scientific religious doctrine of intelligent design contributes nothing at all to research into the origin of life.

    If you’d like to discuss the recent wonderful breakthroughs in the study of abiogenesis, I’d be happy to oblige, moderators permitting.

  104. Zeke says:
    November 13, 2013 at 11:37 am

    I have nothing against faith, but science is based upon doubt. I suppose you could call the belief that the universe is comprehensible & that processes we see in action today occurred in the past to be forms of faith, but we have evidence that these assumptions are valid, since humans have had success based upon them.

    Truly, “many beautiful things have undeniably and incontrovertibly come out of the planet’s poor dust, at a statistically significant rate, since the formation of the earth and the development of the seas”. The question for science is how have these things come about.

    Many scientists share a sense of awe & wonder before the universe, & some even think the universe itself might have been designed, however crazy a crock ID is as opposed to the fact of evolution.

    Promoting as “science” the baseless, evidence-free, anti-scientific religious doctrine ID on the leading climate skeptic blog IMO just gives ammunition to CACA advocates looking to besmirch it & skepticism.

  105. I hinted above that this probably is not the thread, or the place to debate evolutionary biology, or the origin of life. Biologists disagree among themselves about such things. FWIW, I’m more than happy to provide the resources for such a debate. I recently reblogged some of my thoughts from 2005 here:

    http://thepompousgit.wordpress.com/2013/08/16/on-species/

    and to whet your appetite I commence by quoting Kevin Kelly, editor of Wired magazine:

    So prevailing is the logic of nonrandom variation that I was at first flabbergasted in my failure to find any biologists working today who still believe mutations to be truly random. Their nearly unanimous acknowledgment that mutations are “not truly random” means to them (as far as I can tell) that individual mutations may be less than random — ranging from near-random to plausible; but they still believe that statistically, over the long haul, a mass of mutations behaves randomly. “Oh, randomness is just an excuse for ignorance,” quips Lynn Margulis.

    This weak version of nonrandom mutation is hardly even an issue anymore, but a stronger version is more of a juicy heresy. It says that variations can be chosen in a deliberate way. Rather than have the gene bureaucracy merely edit random variations, have it produce variations by some agenda. Mutations would be created by the genome for specific purposes. Direct mutations could spur the blind process of natural selection out of its slump and propel it toward increasing complexity. In a sense, the organism would direct mutations of its own making in response to environmental factors. Ironically, there is more hard lab evidence at hand for the strong version of directed mutation than for the weak version.

    According to the laws of neodarwinism, the environment, and only the environment, can select mutations; and the environment can never induce or direct mutations. In 1988 Harvard geneticist John Cairns and colleagues published evidence of environmentally induced mutations in the bacterium E. coli. Their claim was audacious: that under certain conditions the bacteria spontaneously crafted needed mutations in direct response to stresses in their environment. Cairns also had the gall to end his paper by suggesting that whatever process was responsible for the directed mutations “could, in effect, provide a mechanism for the inheritance of acquired characteristics” — a bald allusion to Darwin’s rival-in-theory Jean-Baptiste Lamarck.

  106. The Pompous Git says:
    November 13, 2013 at 12:42 pm

    There is no such thing as the “laws of neodarwinism”, a cartoonish misunderstanding of biology in general & evolutionary theory in particular. The source of mutations doesn’t have to be from the environment. Just the process of replication introduces mutations in each generation. You & I each have several acquired in this way.

    The tendency of organisms to produce mutations has long been recognized. What might come as a surprise to the man in the street is old hat to biologists. Some have indeed tried to argue that this tendency is a form of Lamarackian inheritance of acquired traits, but the “traits” being inherited in this case are mutations, so this is a distinction without a difference from other evolutionary processes.

  107. @milodonharlani

    It is clear that this topic is interesting to many, but this is Anthony’s blog. Without a specific OK from him, or the Mods, I am unwilling to go further with this discussion. It is very OT.

  108. Arguably it is OT, although discussion of what is science & isn’t could IMO be considered relevant. Comparison of ID with the only slightly more scientific CACA could be instructive.

  109. Thank you for sharing that Zeke. That was beautiful.
    *************************************************

    Dear Mr. Harlani,

    When our host invites us to discuss Intelligent Design theory at length, I will do my best to answer any questions you have. Until then, know that you are being prayed for earnestly by someone (perhaps, by more than one of us) who cares about you. And, do bear in mind that you may be confusing the evidence for design with its implications.

    Sadly, but with hope,

    Janice

  110. @ milodonharlani

    More than happy to discuss what science is and isn’t, but again it’s not about the head post topic. I have been meaning to finish an essay on science and submitting it to Anthony but haven’t managed to get a round twit. I have, however, managed to affix automatic vent openers to the vents in my greenhouse. Now I don’t have to race in and out of the house on showery, partially clouded days. I am calling this the enhanced greenhouse effect. And that’s OT for this thread, too :-)

  111. The Pompous Git says:
    November 13, 2013 at 1:36 pm

    Not sure that an EGHGE would be off topic for any thread on WUWT, but you’re right, a new topic would be better. Good on ya, mayte!

  112. Janice Moore says:
    November 13, 2013 at 1:30 pm

    Prayers are always welcome. I pray daily myself.

    Since our host was allowing comments on ID, I don’t see why you keep refusing to state what evidence persuades of the scientific validity of ID but not of evolution. On a blog it’s customary to make your case in your own words, using supporting quotations or links in order to bolster it. The fact is there is no evidence whatsoever in favor of ID. Its humiliated proponents were laughed out of the US District Court for the Middle District of Pennsylvania. But I would have liked to read what you yourself personally, based upon your research & study, might consider such evidence.

    Thanks.

  113. OK, I can’t resist! The “non-existent” laws of neoDarwinism:

    Life is cellular
    All living organisms possess genes
    All life processes occur through biochemistry
    Mendel’s First Law: “The Law of Segregation states that every individual possesses a pair of alleles (assuming diploidy) for any particular trait and that each parent passes a randomly selected copy (allele) of only one of these to its offspring.”
    Mendel’s Second Law: “The Law of Independent Assortment, also known as “Inheritance Law”, states that separate genes for separate traits are passed independently of one another from parents to offspring.”

  114. Re Intelligent Design, I can do no better than quote physicist Paul Davies:

    “Scientists are slowly waking up to an inconvenient truth — the universe looks suspiciously like a fix. The issue concerns the very laws of nature themselves. For 40 years, physicists and cosmologists have been quietly collecting examples of all too convenient “coincidences” and special features in the underlying laws of the universe that seem to be necessary in order for life, and hence conscious beings, to exist. Change any one of them and the consequences would be lethal. Fred Hoyle, the distinguished cosmologist, once said it was as if “a super-intellect has monkeyed with physics”.

    To see the problem, imagine playing God with the cosmos. Before you is a designer machine that lets you tinker with the basics of physics. Twiddle this knob and you make all electrons a bit lighter, twiddle that one and you make gravity a bit stronger, and so on. It happens that you need to set thirty something knobs to fully describe the world about us. The crucial point is that some of those metaphorical knobs must be tuned very precisely, or the universe would be sterile.

    Example: neutrons are just a tad heavier than protons. If it were the other way around, atoms couldn’t exist, because all the protons in the universe would have decayed into neutrons shortly after the big bang. No protons, then no atomic nucleuses [sic] and no atoms. No atoms, no chemistry, no life. Like Baby Bear’s porridge in the story of Goldilocks, the universe seems to be just right for life.”

  115. milodonharlani says:
    November 13, 2013 at 12:12 pm
    “It’s a common mistake for non-biologists to confuse abiogenesis, the origin of life, with evolution.”

    Maybe for you “evolution” means ONLY Neo-Darwinian evolution. For me it means any process that combines mutation/variation with selection, as I’m a computer scientist. No need to argue; just a clarification.

    Without a pre-cellular evolution the complexity needed for the first cell absolutely kills you; and ID becomes a necessity. Simple combinatorics without a selection + mutation process (a.k.a. evolution, a.k.a. information processing) does not work on the timescale available.

    See Kurzweil’s Law Of Accelerating Returns.

  116. milodonharlani says:
    November 13, 2013 at 12:01 pm
    “Intelligent Design, like CACA, is not just unscientific, but anti-scientific, & for the same reason.”

    CACA as you call it has been created by the UN together with all the Green NGO’s; so I guess it’s not the same reason.

    “ID advocates look at flagella in bacteria & are happy to throw up their hands & give up, saying, “These structures are irreducibly complex, so couldn’t have evolved, therefore a Designer made them.””

    It doesn’t help your case to overgeneralize; in fact I have not the slightest problem with macro-evolution. I also have no problem with an interfering God, as that is not a contradiction at all.
    Well, it’s getting late here in EU territory; it was fun to talk to you. Good night and take care.

  117. milodonharlani says:
    November 13, 2013 at 2:11 pm (replying to)

    Janice Moore ( Gail Combs search reference here.)
    November 13, 2013 at 1:30 pm

    Since our host was allowing comments on ID, I don’t see why you keep refusing to state what evidence persuades of the scientific validity of ID but not of evolution. On a blog it’s customary to make your case in your own words, using supporting quotations or links in order to bolster it. The fact is there is no evidence whatsoever in favor of ID. Its humiliated proponents were laughed out of the US District Court for the Middle District of Pennsylvania. But I would have liked to read what you yourself personally, based upon your research & study, might consider such evidence.

    I would politely challenge you, then, to find any “error” or out-of-sequence event that differs between your version of the Big Bang and evolution and what is in our original documents and the oral stories that preceded those documents. That is, matter condensing from light from the initial energy that began expanding like a wind into “nothing”. Then, that newly cooled matter grouping into the stars and cosmos and – at the same time – being separated by gravity into what is now our planet with its atmosphere and (one single large) ocean and one single original continental mass.

    After that (single) ocean was formed on our planet, plants were the first life, but the atmosphere remained cloudy until these first plants released oxygen and locked up the CO2 and free iron into terrestrial beds. (The stars and moon could become visible only after life cleared the atmosphere.) But, once life began in the sea, it quickly spread spread to the land and changed into what we call dinosaurs (well certainly the predecessors of birds), then mammals (and the domesticated animals), then what we now call snakes, then (finally) man.

    Please notice that the word “created” only appears once in our original documents, and those tales were told by a culture that not only did NOT have convenient Indo-Arabic numerals, but also did NOT have a zero, a decimal place, or convenient powers-of-ten notation. (Please, write 14 billion in Roman numerals.) Still, it is remarkable that these itinerant shepherds wandering between the numerous seas and oceans of our own era got all of the geology, plate tectonics, evolution, biology, chemistry, astronomy, and nuclear physics of today’s science correct. But I will claim no “Divine Inspiration” was involved in Genesis. It is, after all, up to you to find an earlier reference to any of these “recent discoveries” in the literature. 8<)

    By the way, please, in any edition of any book or court case discussing your so-called ridicule of ID, replace "evolution" or Nature" or "natural selection" with "a designer" …. You will find that there is no difference.

  118. Actually I thought it would be interesting to see if the cosmological model accepted by mainstream science – that is, the Big Bang and the Planetary Nebula Hypothesis – might be a good match for the old Roman paraphrases of diverse pre-classical pagan creation stories written in (some say bad) meter by Ovid. That would make an interesting comparison!

    RACook, If there is a similarity between Genesis and the Big Bang and its subsequent epochs, this might be because the originator of this theory was a Catholic Priest. But you are welcome to it. :) :D
    I am not a Catholic myself, but as I understand, Big Bang and so on are officially recognized as truth by the Catholic Church.

    RACook, There is one problem with interpreting Genesis in that way. The plants were created on the third day, before the sun and moon were made. Was there some long period when plant life flourished and yet there was no sun? Another source of light is implied because the light is given on the first day, and separated from darkness. The sun, moon, and stars are given on the fourth day. Also, the Hebrew word for create (bara) (as opposed to made, asa) is used twice, not once. He made man “in His image, male and female He created them.” That is the primary teaching of the Scriptures that is totally irreconcilable with Darwinism. We are, according to the “itinerate wandering shepherds,” eternal beings, spiritually unique from the animal world, having rationality and liberty, and living forever, like the angels. I suppose this belief has been found most inconvenient by various Empires and Governments. Various totalitarian States, historically, have diagnosed Christians with a mental disorder.

  119. The area under the curve in the tail of the Gaussian distribution shown in the figure is not a p-value. William M. Briggs, Statistician to the Stars, does an excellent job of debunking p-values. I strongly suggest everyone here check out his web site: http://wmbriggs.com/blog/.

  120. Zeke says:
    November 13, 2013 at 4:20 pm

    RACook, There is one problem with interpreting Genesis in that way. The plants were created on the third day, before the sun and moon were made. Was there some long period when plant life flourished and yet there was no sun? Another source of light is implied because the light is given on the first day, and separated from darkness. The sun, moon, and stars are given on the fourth day.

    Thank you for the compliment, and the correction. Indeed, it may be critical, even vital (in its original Latin version of “life”!) that “creation” DID happen only twice – the second time being when the “soul” was created. After all, everything (we are taught) was already created a long time prior to a man’s (and woman’s) “soul” (mind, intellect, thought process, inventiveness, etc came into their being…

    There is one problem with interpreting Genesis in that way. The plants were created on the third day, before the sun and moon were made. Was there some long period when plant life flourished and yet there was no sun? Another source of light is implied because the light is given on the first day, and separated from darkness. The sun, moon, and stars are given on the fourth day.

    You are correct in a first level reading (or interpretation) of that text. But think a bit. We are told that the stars and sun and moon were already gathered together “above” when the earth was formed “below”; and “the waters above” certainly is a valid description of the dust, plasma, ions, fluids, and gases above the atmosphere. It’s just that “waters” one time refers to liquid fluids, and the other time refers to all fluids and gases everywhere in the cosmos.

    But, the original earth’s atmosphere was opaque – like Venus, Jupiter, Saturn, Neptune, and Uranus. Nothing could be seen above it. Little light could get through, certainly not enough for life as we know it. (And, Hansen is correct: Venus is lethally too hot for life. ) But, after the plants broke that CO2 and SO2 and xxx and yyy and zzz into today’s benign oxygen and nitrogen mix, light could get through. (Note though that the oxygen we require for life was deadly to everything else that required an oxygen-free atmosphere.

    Most importantly, light can get through the new atmosphere both ways: We can “see” the stars and plants and moon for the first time, and they were “set” in their places to aid in navigation and travel. And wonder. All science began really with astronomy. In every civilization. Everywhere. Without the stars to inspire wonderment, would anything past fire (and that also not possible without oxygen!) have ever been discovered?

    So, “No” the two are not incompatible: The stars and moon were already formed and present and yielding light as they do now. It’s jusut that they were not visible from the earth. Yet. Note too that the collision that formed the moon had to happen BEFORE life started: certainly nothing could have survived that heat shock and impact melting all else.

  121. The Pompous Git says:
    November 13, 2013 at 2:30 pm

    The refs sent me to the penalty box for several hours, so will keep my replies brief.

    How exactly do those “laws” constitute “Neo-Darwinism”? By “Neo-Darwinism” do you mean the Modern Synthesis, which isn’t so modern any more? What makes the observations that life is cellular & biochemical laws & part of Neo-Darwinism, rather than just biology in general, for instance? As I’m sure you’re aware, “law” in science is less clearly defined than “hypothesis” or even “theory”.

  122. The Pompous Git says:
    November 13, 2013 at 2:34 pm

    You are confusing the hypothesis of a designed universe, to which I’ve alluded as still a defensible metaphysical position, with the doctrine of “Intelligent Design”, which is specifically about biological structures & processes. It was invented to get around court rulings against teaching creationism in public schools & despite losing in federal court is still pushed by groups such as the Discovery Institute.

  123. DirkH says:
    November 13, 2013 at 2:39 pm

    As I’ve commented here before, the term “evolution” in biology means both the observed fact of evolution & the body of theory explaining how it works. Maybe I should repeat that in every comment on evolution.

    “Without a pre-cellular evolution the complexity needed for the first cell absolutely kills you; and ID becomes a necessity. Simple combinatorics without a selection + mutation process (a.k.a. evolution, a.k.a. information processing) does not work on the timescale available.”

    Your error in assuming that combinatorial math controls abiogenesis is a common one. Kurzweil’s Law Of Accelerating Returns doesn’t apply.

    Neither I nor abiogenesis researchers “need” intelligent design to explain the development of life from its precursor chemicals. Nothing could be farther from the truth. There is no reason whatsoever to posit such a supernatural, anti-scientific fantasy.

    Instead of making a baseless assertion, how about actually studying what is known & not known about the prebiotic processes that led to the first living things?

    What do you suppose the timescale available to be? If life arose from its precursors on earth, there were at the very least 700 million years before the first hint of life in the geological record. If life arose extraterrestrially, then on the order of ten billion years is available.

    Many of the ingredients of life as we know it self-assemble, like some peptides, PAHs & the lipids that form cell membranes. Precursor compounds existed on the early earth in great abundance. They didn’t even need to be made here, although they could have been from simpler compounds, but arrived on space rocks, just as they still do. The number of complex organic chemicals in meteorites is astonishing.

    http://en.wikipedia.org/wiki/Murchison_meteorite

    Naturally occurring chemicals helped catalyze the synthesis of the first biologicals, ie RNA strands capable of replication. For instance, polycyclic aromatic hydrocarbons (PAHs) are common in the interstellar medium, comets & meteorites.

    http://amesteam.arc.nasa.gov/Research/cosmic.html

    In a self-ordered PAH stack, the separation between adjacent rings is 0.34 nm. Remarkably, this is the same separation found between adjacent nucleotides of RNA & DNA. Smaller molecules attach themselves naturally to the PAH rings. However PAH rings, while forming, will swivel around on one another, which tends to dislodge attached compounds in collisions with those above & below. Hence, preferential attachment of flat molecules is encouraged, such as pyrimidine & purine nucleobases, the key constituents (& information carriers) of RNA & DNA. These bases are similarly amphiphilic, so also tend to line up in similar stacks.

    Ice has also been found to catalyze formation of RNA, which has been discovered to act both as an enzyme in protein formation & information source. Great strides have been made recently in understanding the pathways from complex organic compounds to life. Some key issue remain, but it’s just chemistry, not magic.

    http://www.nature.com/nature/journal/v502/n7472/full/502412d.html

    Ice is gaining support at the expense of fire, ie oceanic thermal vents as the cradle of life.

    You are right however that evolution probably started working very early in the history of life, selecting fitter proto-cells & eventually leading to the differentiation in functions between RNA & DNA. for instance.

  124. @ milodonharlani

    First, I quote Theodosius Dobzhansky: “Nothing in Biology Makes Sense Except in the Light of Evolution”. In the world I inhabit, NeoDarwinism = the Modern Synthesis = The Received View in Biology. Biology has scientific laws just as other disciplines. Most theories invoke those laws. Live with it.

    It is not I who confuse Intelligent Design with creationism. There is a world outside the USA that does not accept as Gospel Truth everything that comes out of the USA. Or anywhere else for that matter. I don’t give a fiddler’s fart that creationists attempt to own a term; they don’t.

    I’m currently rereading Ernst Mayr’s One Long Argument. The first sentence reads: “A modern evolutionist turns to Darwin’s work again and again.” Why does using the term “evolutionist” make me a creationist and not Mayr? I know you haven’t gone that far, but many have. And you have taken me to task for using it.

    The chapter I’m reading is titled, incidentally: A Hard Look at Soft Inheritance: Neo-Darwinism. See above.

  125. Zeke says:
    November 13, 2013 at 4:20 pm

    “I am not a Catholic myself, but as I understand, Big Bang and so on are officially recognized as truth by the Catholic Church.”

    The Roman, Greek & Russian Orthodox Catholic Churches also recognize the scientific validity of evolution. In 1973, the great evolutionary biologist & devout Russian Orthodox Christian Theodosius Dobzhansky published in American Biology Teacher his famous essay, “Nothing in Biology Makes Sense Except in the Light of Evolution”, criticizing creationism & espousing theistic evolution. That same year I told my fundamentalist students at an originally Baptist college that they were free to inject God into the history of life on earth at any point they chose, although evolution works fine without divine intervention.

    To your excellent exegesis on the creation myth in Genesis 1, I’d add that the vault or firmament of heaven in Hebrew is “raqiya` (רקיע)”, which means something pounded out (the word is onomatopoetic, like English “racket”), as in a sheet of metal, to which the firmament is compared elsewhere in the Old Testament. This solid dome of heaven separates the waters above the vault from the waters below it. This is a monotheistic reworking of the Mesopotamian creation myth, picked up by the Judean prisoners during the Babylonian Captivity.

    Note further that when God does get around to creating the sun & moon, He sets them in the newly minted vault, but later in the Bible we learn that the sun rises as a bridegroom or a strong man to run a race & travels over the flat earth that forms the floor of the dome, returning afterwards to the place of his origin. And we learn further that God Himself opens & shuts the storehouses of rain, snow & other precipitation above the dome. And we learn about the water that wells from under the immovable pillars of the earth.

    Then there’s the second creation story in Genesis, which begins in Chapter 2 after the snippet of the end of the first story in the chapter’s initial verses. The order of creation in the second story–man, plants, animals, & then woman from the man’s rib–differs markedly from the order in the first story–plants, sun & moon, animals, men & women together.

    I will grant however that it’s a lot easier to read modern biology into the biblical accounts than it is modern astronomy, geology, meteorology or hydrology. Genesis says that the waters brought forth creatures, & that’s sort of what happened. But the land bringing forth the plants doesn’t quite make it. Green plants spread onto land from the waters, & evolved after animals, not before them.

  126. The Pompous Git says:
    November 13, 2013 at 7:24 pm

    The ID that Janice Moore & I were discussing was specifically the ID movement in the US, which is about biological creationism not cosmological. It’s not about the kind of design posited by the physicist whom you quoted, but about the kind of propagandists of whom she posted video. The point isn’t that ID is American (& also popular in Muslim countries), but that it was specifically biological. So the cosmos was off an already off topic.

    I couldn’t agree with Dobzhansky more, whom I quoted above. But why do I have to live with your idea of what constitutes “Neo-Darwinist” laws? Those you cited aren’t unique to “Darwinism”. That there are phenomena in biology called “laws” by some doesn’t make them necessarily Neo-Darwinistic/ian. The Modern Synthesis of the interwar years, if that’s what you meant, is now being challenged as Newtonian physics (“Newtonism”?) was by Einstein, with advances in understanding of how genomes work. Please cite what Dobzhansky, Mayr or other leading evolutionary biologists consider the “laws” of Neo-Darwinism, then we can discuss them, if allowed.

  127. RACookPE1978 says:
    November 13, 2013 at 5:18 pm

    “There is one problem with interpreting Genesis in that way. The plants were created on the third day, before the sun and moon were made. Was there some long period when plant life flourished and yet there was no sun?”

    No, there was not such a period. There are chemosynthetic autotrophs which don’t need sunlight, but they’re not plants.

    “We are told that the stars and sun and moon were already gathered together “above” when the earth was formed “below”; and “the waters above” certainly is a valid description of the dust, plasma, ions, fluids, and gases above the atmosphere. It’s just that “waters” one time refers to liquid fluids, and the other time refers to all fluids and gases everywhere in the cosmos.”

    No, this is not a valid description of anything. Waters in Genesis means liquid H2O. It doesn’t mean plasma, ions, other fluids and gases above the atmosphere.

    Nor is your quotation from Genesis correct. The sun & moon in Genesis 1 were not “gathered”. That was the waters. God said “Let there be” the sun & moon, & there they were. He “set” them in the vault of heaven.

    “But, the original earth’s atmosphere was opaque – like Venus, Jupiter, Saturn, Neptune, and Uranus. Nothing could be seen above it. Little light could get through, certainly not enough for life as we know it. (And, Hansen is correct: Venus is lethally too hot for life. ) But, after the plants broke that CO2 and SO2 and xxx and yyy and zzz into today’s benign oxygen and nitrogen mix, light could get through. (Note though that the oxygen we require for life was deadly to everything else that required an oxygen-free atmosphere.”

    The composition of earth’s atmosphere in the Hadean Eon remains unclear, although under investigation by geologists. In science, unlike religion, evidence is required to support speculations. Some geologists believe that the earliest atmosphere included large amounts of nitrogen. Others believe that it was composed largely of carbon dioxide & water vapor, along with some other volcanic gases from steaming vents & volcanoes. Early in the Hadean, earth’s atmosphere was probably too hot to allow liquid water to condense, but inclusions in younger strata suggest sedimentary rocks formed later in the Eon, which implies existence of surface water.

    The second atmosphere of the earth in the Archean Eon is better understood. It consisted largely of nitrogen plus carbon dioxide & inert gases, produced by volcanic outgassing, supplemented by gases generated during the late heavy bombardment of earth by huge asteroids. A major part of carbon dioxide emissions was soon dissolved in water & built up carbonate sediments.

    Water-related sediments have been found dating from as early as 3.8 billion years ago. About 3.4 billion years ago, nitrogen was the major part of this then stable second atmosphere. Hints of early life forms have been found as early as 3.5 billion years ago, or possibly even 3.8 Ba.

    A third atmosphere developed during the Great Oxygenation Event. Free oxygen did not exist in the atmosphere until about 2.4 Ba. Its appearance is indicated by the end of the banded iron formations. You’re right that the photosynthetic organisms which made this oxygen created a catastrophic crisis for other living things. But these organisms would have needed light, so the second atmosphere under which they evolved wasn’t opaque.

    “So, “No” the two are not incompatible: The stars and moon were already formed and present and yielding light as they do now. It’s jusut that they were not visible from the earth. Yet. Note too that the collision that formed the moon had to happen BEFORE life started: certainly nothing could have survived that heat shock and impact melting all else.”

    If by “the two” you mean creation accounts in Genesis (& other parts of the Bible) & what science has been able to infer from actual physical evidence, then yes, they are incompatible. The Bible is not a science text. As Cesare Cardinal Baronio said to Galileo, “The Bible teaches us how to go to heaven, not how the heavens go”.

  128. The Pompous Git says:
    November 13, 2013 at 9:30 pm

    You’re right it’s silly to argue about this, but sillier still IMO was your listing “laws” which aren’t part of Neo-Darwinism. ie the Modern Synthesis, as the “laws of Neo-Darwinism”. The Modern Synthesis, along with the rest of biology since the early 19th century, of course assumes that life is cellular & biochemical, but those facts aren’t what distinguish it from “Paleo-Darwinism” or any other theory in biology. I would have thought that to a philosopher these distinction would be obvious.

  129. @ milodonharlani

    Of course we can expect Kevin Kelly to know all this stuff backwards… And it’s kinda handy, I suppose, to distract as much as possible from directed evolution which was the point of Kelly’s piece :-) Evolution’s all really, really, really random; like over 30 distinct species of plants acquiring the same gene complex (C4) virtually simultaneously. No need to explain that stuff.

    BTW how long have Mendel’s laws not been part of the Modern Synthesis? They were the last time I looked.

  130. The Pompous Git says:
    November 13, 2013 at 10:26 pm

    Mendel’s ” Law of Segregation” & “Law of Independent Assortment”, as amended by population genetics, were indeed part of the Modern Synthesis. That life is cellular & biochemical aren’t, since those facts are givens for all of biology. But much has changed since the 1930s, including what “gene” means. A “Post-Modern Synthesis” is emerging.

    Kevin Kelly is not a biologist, if you’re referring to whom I think you are. There is no such thing in biology as “directed evolution”, since there is no Director. There is however “directional” evolution, which is driven by good, old-fashioned selection, as opposed to stochastic processes.

    Why does the evolution of the C4 pathway from the C3 in different plant lineages strike you as somehow remarkable? For starters, it wasn’t “nearly simultaneous”. Different species developed the C4 pathways at different times, which was helpful in their environments. Then, when CO2 levels dropped in the Oligocene, these plants enjoyed selective advantages over other plants (some might have developed C4 even earlier). This selective pressure got really intense in the late Miocene, when an apparent explosion of C4 abundance occurred, but that doesn’t mean that the pathway suddenly evolved then. In the Pliocene & even more during the Pleistocene glaciations, this tendency was reinforced.

    http://www.cas.miamioh.edu/~meicenrd/anatomy/Ch10_Photosynthetic/IJPS_Keeley_Rundel2003.pdf

    No need to posit a Director. Just good, old-fashioned darwinian natural selection. Survival of the fittest, where “fitter” means better able to conserve water & get by with less CO2 in a drier, lower CO2 environment.

    To say nothing of the CAM pathway, which is ancient, but originated in the sea, perhaps oddly now that it’s prevalent in desert succulents.

  131. I should perhaps add that the origin of the C4 pathway in every plant with it hasn’t been dated by molecular phylogeny (at least that I know), & some might well not have arisen from mutations induced by the stress of lowered CO2 until the late Miocene. Organisms as I noted are capable of increasing their mutation rates not just from mutagenic agents but from replication errors & other internal means.

    I haven’t studied every C4 plant’s evolutionary history in enough detail to know if some of their lineages might indeed not have developed this capability until the late Miocene “explosion”. But the above linked study appears to cover them all & presents the molecular clock evidence for the calculated dates of their origins.

  132. milodonharlani says:
    November 13, 2013 at 8:38 am

    Thanks. It is interesting that you find that the “splitters” have created their own problems.

  133. Theo Goodwin says:
    November 14, 2013 at 7:08 am

    Other paleontologists have been reluctant to rein in their peers who gave new genus & species names to their fossil discoveries in the field, & taxonomists largely went along. One victory was changing the Leakeys’ original generic name Zinjanthropus to Paranthropus or Australopithecus, which already existed for related African hominids.

    Many animal species were evolving then in response to the same climatic & geological forces that caused the late Miocene-Pliocene “explosion” of C4 plants, ie drier conditions led to the expansion of grasslands & contraction of opening up of forests (trees are C3), as per my discussion above with TPG. This encouraged the evolution of less arboreal, more terrestrial primates, like our hominid ancestors, as well as the adaptive radiation of African antelope genera. Same happened earlier in the Miocene with horses, which started out as small woodland creatures, but adapted to life on the new American grasslands.

  134. Dear Mr. Harlani,

    If you were not convinced by the arguments and evidence cited by Dr. Stephen Meyer and Dr. David Berlinski (in the videos I posted for you above), then it would be pointless for me to try to persuade you.

    When you genuinely seek the facts, to the extent they are discoverable, you will find them.

    Janice

  135. Janice Moore says:
    November 14, 2013 at 9:07 am

    They present no evidence whatsoever. There is none. If you think there is, please state it. Otherwise, your belief in ID is an example of religious faith. ID is not science. It is anti-science. But if you think it is science supported by evidence, surely you can state the reasons why.

    Berlinski & Meyer are both philosophers, not biologists, who work for the Discovery Institute. It’s their job to attack science with ridiculous assertions designed to appeal to their co-religionsts. Their “arguments” are sheer anti-scientific garbage, but if they convince you, then please state why, as I’ve repeatedly asked & as is normal in [blog] discussions.

  136. @ milodonharlani

    Fearlessly plagiarised and adapted from a piece I wrote several years ago:

    The Git has a bit of a bee in his bonnet about random mutation being the cause of macroevolution that is the core of NeoDarwinism. Merely having a gene mutate gradually into some other gene won’t do. If the gene has an important function for the organism it inhabits, then the organism would suffer from the disappearance of that function. Ohno’s Hypothesis has it that the gene must first be duplicated and the duplicate gene then proceeds to mutate into the new gene with the new function. During the period of mutation, the gene is not expressed (and is therefore not subject to Natural Selection), but at some random point in time becomes expressed. For example, a plant that previously utilised the C3 photosynthetic process, overnight as it were, gains the C4 photosynthetic process and is a new and distinctly different species. So the story goes, some thirty odd plant species virtually simultaneously and randomly discovered the C4 process in the blink of an evolutionary eye.

    This argument bears more than passing resemblance to the stories The Git read when he was a tadpole. At the end of an episode in The Wizard, Fearless Dick would be helplessly bound by fierce African natives looking forward to a bit of white flesh for supper. At the beginning of the next episode, one would read: “With a bound, Dick sprang free!”

    This does not make the Ohno Hypothesis wrong, merely less probable. It would help, of course, if there were any evidence to support it. Despite the reputed abundance of gene duplication, The Git’s searches have turned up no evidence that macroevolution works in this way. Here’s some evidence about what does happen from Nature:

    Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

    Csaba Pál, Balázs Papp & Martin J. Lercher compared the genome of E. coli with those of its closest relatives. “Under realistic parameter settings, we estimated that 15-32 genes were transferred horizontally into the E. coli metabolic network since its divergence from the Salmonella lineage, vastly outnumbering the one (1) identified gene duplication over the same period.” The duplicated gene “functions in the same enzymatic reaction” as the original. They observe, “Most changes to the metabolic network of Escherichia coli in the past 100 million years are due to horizontal gene transfer, with little contribution from gene duplicates.”

    And from Trends in Genetics a piece about corals and sea anemones:

    “The resulting data set… implies that much of the genetic complexity commonly assumed to have arisen much later in animal evolution is actually ancestral. The most surprising implication of these analyses, however, is that anthozoans have retained a substantial number of genes not previously known in the animal kingdom. Two possibilities remain to explain the presence of these genes in the anthozoan genomes:

    (i) lateral gene transfer (LGT); or

    (ii) conservation of ancient genes that have been lost from those animals for which complete sequences are available.

    Although we cannot rule out LGT in all cases, we favor the latter explanation for most of these matches…

    In many respects, the complexity of the anthozoan gene set does not differ substantially from that of vertebrates and frequently exceeds that of the model invertebrates Drosophila and Caenorhabditis… One possible interpretation of the counterintuitive genetic complexity of cnidarians could be that they are actually highly derived deuterostomes. However, this interpretation is strongly contradicted by a large body of phylogenetic data, which indicates that cnidarians are a monophyletic group basal within the Eumetazoa and forming the sister group to the Bilateria….

    Four general conclusions emerge from this work. First, a link between morphological complexity and gene number is illusory. Second, the common ancestor of cnidarians and ‘higher’ animals (the Ureumetazoa) was surprisingly complex at the genetic level. Third, a small percentage of genes in the two anthozoans represents preserved ancient genes that were present in the common ancestor but have been lost in the ‘higher’ animals so far examined… Finally, gene loss has had a major role in animal evolution, and has been particularly extensive in the ecdysozoan model organisms… The remarkable genetic complexity of anthozoan cnidarians implies that most of the qualitative genetic differences between animals and other eukaryotes are ancestral…”

    Neither of these published research papers support the Doctrine of the NeoDarwinian Synthesis as presented by Richard Dawkins (for example): that speciation is caused by genes randomly evolving into new genes in situ. Note that this is not the same as the Creationist claim: “organisms do not evolve; speciation does not occur.” Funnily enough, both papers are compatible with Intelligent Design. But then they are also compatible with Panspermia. And doubtless many other theories that have yet to be invented.

  137. The Pompous Git says:
    November 14, 2013 at 10:49 am

    I think it’s OK to plagiarize yourself.

    You fundamentally misunderstand both the Modern Synthesis & present knowledge of genomes. You seem to be under the impression that the Modern Synthesis is some sort of ruling paradigm for evolution, & that pointing out its problems somehow vitiates evolutionary biology in the 21st century, thus making the anti-scientific religious doctrine of ID in some way plausible or supportable. Nothing could be farther from the truth, on all counts.

    Random mutation is not “the cause of macroevolution that is the core of NeoDarwinism”, ie the Modern Synthesis. I don’t know where you got this deeply mistaken, indeed cartoonish, idea.

    Darwin, who didn’t know how inheritance works, discussed the store of variation in each species or variety of reproducing organisms. He identified two types of variation, “sports” & small differences. After the rediscovery of Mendel & decades of research into how inheritance actually works & the development of population genetics statistics, in the 1930s the Modern Synthesis or “Neo-Darwinism” arose, which, as I noted, isn’t so modern anymore & hasn’t been for some time. Evolutionary theory, like gravitational & other well-established theories, improves with new observations & analytical techniques.

    But let’s assume for the sake of argument that a core concept in the Modern Synthesis was that evolution is driven by natural & sexual selection acting on variation produced by genetic mutation & by genetic recombination (chromosomal crossovers & other “errors” in replication). This is OK as far as it goes, but doesn’t explain all evolution, by a long shot. While the synthesis recognized what would now be called “stochastic” factors like genetic drift, reproductive isolation & the founder’s principle, it afforded them less preeminence. Today evolution under selective pressures is called “directional” to distinguish it from stochastic processes, & evolutionary biologists try to assess the relative importance of both forces.

    An important distinction to bear in mind is that while some sources of mutation (such as cosmic rays) certainly are in some sense “random”, selective pressures acting upon the genetic variation thus produced aren’t. (Neither really are stochastic processes, even though statistical in nature.) Even random sources of mutation can & do occur at predictable rates. To a certain extent selection can be a self-fulfilling process. A rapidly changing environment not only selects for variation that is beneficial in it but might have been less so or not at all under previous conditions, but can increase the rate of mutation. Stresses of various kinds can naturally produce more replication errors, for instance.

    You write, “Merely having a gene mutate gradually into some other gene won’t do. If the gene has an important function for the organism it inhabits, then the organism would suffer from the disappearance of that function. Ohno’s Hypothesis has it that the gene must first be duplicated and the duplicate gene then proceeds to mutate into the new gene with the new function. During the period of mutation, the gene is not expressed (and is therefore not subject to Natural Selection), but at some random point in time becomes expressed.”

    Ohno was wrong about that. He didn’t know then what we know now, & was already shown wrong even before we found out as much as we have about genomics. We also don’t think of genes in the same way he did. Evolution works on populations of organisms, not on individuals, except in terms of their reproductive success, ie “fitness”. Different versions of genes may be expressed “at random times”, according to the rules of population genetics (ie, allele recessivity or dominance, etc) but will increase in a population if the trait for which it codes confers selective advantage.

    Genes, whatever those might be, don’t necessarily mutate gradually into some other gene. That’s not how it usually works at all. Most mutations are deleterious. Some are deleterious in one environment but beneficial in another. For instance, consider the nylon-eating bacteria, whose point mutation must have occurred many times in the past, but only became adaptive once nylon by-products entered the environment. However selection doesn’t need new mutations upon which to act. Organisms have a store of varying alleles in their genes, from whatever natural sources, inherited from ancestors distant & close.

    Consider the woolly mammoth. Its ancestral population of steppe mammoths displayed variation in hairiness, ear size, trunk length & “finger” shape, tooth structure, body fat, you name it, just like any mammal population. This variation occurs naturally, as Darwin observed. When the climate got colder, pre-existing variation adaptive in this new environment was selected for, quite rapidly producing a new species. This also happens when an environmental niche opens up by the extinction of its prior occupier due to whatever natural change or calamity & conditions return to those close to previous. The remarkably rapid evolution of the mosasaurs from small terrestrial lizard relatives is a good example.

    A store of genetic variation exists in populations, lurking, hiding & waiting, as it were, for an opportune time to increase in relative proportion in the genome under the right circumstances.

    You continue, “For example, a plant that previously utilised the C3 photosynthetic process, overnight as it were, gains the C4 photosynthetic process and is a new and distinctly different species. So the story goes, some thirty odd plant species virtually simultaneously and randomly discovered the C4 process in the blink of an evolutionary eye.”

    As I’ve already tried to explain, apparently not very well, the development of the C4 pathway occurred many times in many plant lineages over tens of millions of years. But except for niche environments in the Oligocene world, it didn’t confer selective advantage on the populations in which it arose, until in the late Miocene & Pliocene so many regions got so much drier & CO2 levels fell so low that these adaptations become highly selected for. Also, environments for the types of plants with C4 pathways, such as grasslands, simply expanded greatly, increasing their dominance over C3 plants like trees. So the apparent C4 “explosion” at this time offers an excellent example of what I’m trying to explain about how evolution works.

    I fail to see how the fact that bacteria engage in horizontal transfer of genetic material in any way argues against evolution. Recombinant DNA wasn’t considered in the Modern Synthesis because it hadn’t been discovered yet. That was done as a young man by my esteemed professor Joshua Lederberg. It’s not every guy who gets a Nobel Prize aged 33 for his PhD thesis, typed by his wife.

    That corals & sea anemones have a store of genetic variation ancient in origin is not in the least surprising, since most if not all organisms do. There is a large supply of “deeply conserved” genetic material dealing with basic life functions, & also a lot of “junk DNA” left over from our ancestors that isn’t expressed in some present life forms. Again, you seem to find commonplace present knowledge in some way disruptive of present evolutionary biology.

    Dawkins wrote in 1976. Many of his colleagues questioned his work then & even more do today. I’m not sure he’d even try to support much of his prior work, in light of what is now known about genomics. Like any body of theoretical & experimental science, evolutionary biology develops as new information becomes available. But nothing whatsoever in what has been learned since the 1930s or 1970s lends any support whatsoever to the outrageous lies of ID promoters.

    It’s like saying that because Einstein improved upon Newton, the sun must go around the earth.

    What you imagine, based upon misunderstanding of evolutionary theory, to be compatible with ID, isn’t. Nothing in biology is compatible with ID. A difference between your attempt to comprehend biology & the blatant falsehoods spread by professional ID advocates is that they probably know they’re intentionally telling lies, whereas with further study of contemporary biology, you will be open to reality. I’d recommend you start with former Human Genome Project director & now NIH chief Francis Collins’ demolition of ID, “The Language of God”. It’s intended for his fellow Christians, but the parts on ID apply across the belief system board.

  138. Despite milodonharlani’s claims that a universe created by God is not an example of intelligent design, there is a most fascinating book that is rather famous among philosophers who believe it contains arguments central to any credible intelligent design thesis. Richard Swinburne’s The Existence of God contains a Bayesian argument that the existence of God is more likely than his non-existence. The book’s focus is on how we explain things in epistemology and science. The only major “flaw”, if it can be called that, is that a logical consequence of Swinburne’s argument is that in a universe devoid of humans (thinking beings), God could not exist. God can only exist in a universe occupied by thinking beings.

    J.L. Mackie, Swinburne’s major critic, fails to address explanation in his rejoinderThe Miracle of Theism. Consequently, Swinburne’s central them goes unchallenged. The Git did have a lecturer who claimed he had successfully challenged Swinburne in his Doctorate. But then that lecturer also claimed that Aristotle’s works were reintroduced into Western thought by Augustine of Hippo (it was Thomas Aquinas) and corrected the Git’s use of the word “apologetics” to “apologists” in his major essay.

  139. @ milodonharlani

    I do not for one instant believe that Richard Swinburne (theologian), Sir John Polkinghorne (physicist), James Hannan (physicist), Simon Conway Morris (paeleontolist), Albert Einstein (physicist), Martin Gardner (mathematician) and ever so many others who believe that the universe was created by God are “liars”, or “anti-science”. When I contrast their arguments with the likes of prominent atheists such as Richard Dawkins, George H Smith, and Richard Carrier it is the former who make the most sense. Indeed, in his book The God Delusion Dawkins claims that Einstein and Gardner were actually atheists, a claim that is belied by Einstein and Gardner’s own statements on the matter.

    That there exist people who do tell “Lies for God” as Ian Plimer put it is beyond doubt. That such exist is not evidence that all believers in God are liars.

    You say I misunderstand what I have read about the random nature of evolution. Yet Gould in Life’s Grandeur states quite baldly that a rerun of life on Earth would result in an entirely different resulting population of organisms. Another writer whose name currently escapes me claimed that the evolution of eyes in this iteration would most likely not occur in a rerun. It is not only myself who finds this difficult to believe; after all, eyes appear to have arisen independently at least five times! Conway Morris wrote a book about evidence for the opposite (Life’s Solution: Inevitable Humans in a Lonely Universe. Evolution appears to converge on a limited number of designs rather than diverging in some random way. That is, it seems to follow laws whose mechanism we have yet to discover.

    You write: “I fail to see how the fact that bacteria engage in horizontal transfer of genetic material in any way argues against evolution.” Not once have I written, or said, anything “against evolution”. I have written and said that evolution, particularly as popularised by its advocates, is frequently contradicted by discoveries made by researchers in the field. In an account far more recent than 1976 (River Out of Eden) Dawkins claims that when speciation occurs, that movement of genes between the new species is impossible (not rare, nor infrequent — impossible). One doesn’t need HGT to know that claim was patently absurd.

    It’s worth pointing out that my taking Dawkins to task for some of his more absurd arguments was what caused me to be labelled a Creationist. I am in fact an agnostic despite the fact that many believers in God marshal far better arguments in their favour than any I have found made by atheists.

    It remains the case that in my opinion an intelligent designer of the universe would have designed a universe that is identical to the universe we inhabit and observe. This is not an observation unique to me, but appears to be shared by ever so many scientists, not only “mere philosophers”.

  140. The Pompous Git says:
    November 14, 2013 at 1:49 pm

    You’re still conflating a putatively designed universe with the biological ID which Janice Moore propounds. The paid liars to whom I referred were heroes like the Discovery Institute’s Meyer & his gang of goons.

    There exists zero, zip, nada, no evidence whatsoever on this planet for intelligent design in evolution. Conway Morris may have danced around it regarding the Cambrian Explosion, but that event has been found to have smaller, softer precursor organisms in the late Pre-Cambrian, just as there were C4 plants long before they exploded in the late Miocene. I happen to think Morris’ view is plausible on the larger question, at least in the present state of our lack of knowledge. Humans may not be inevitable, but I feel there is good reason to conclude that life is in some chemical environments inevitable only in a universe like ours (when I said that, Willis told me that I wasn’t talking science on a science blog, despite his autobiography being posted here). There are important arguments against the views of a designed universe with inevitable life, so I too am agnostic on it.

    But biological ID is another matter entirely. It is simply creationism repackaged, badly as it turns out, which is one reason why its advocates became such hilarious laughingstocks at trial. I’ve called it anti-scientific for the reasons I gave previously. Your approach is similar. You say, aha!, there are phenomena which seem to me (you) not to accord well with my conception of Neo-Darwinism, therefore there must be an Intelligent Designer! The scientific approach would be to study more, see what has been found out in biology since 1936 & 1976 (even 2004, date of Morris’ “Life’s Solution”), & at least consider alternative scientific hypotheses.

    As it is, there is, as I said, no evidence whatsoever in support of the hypothesis of an Intelligent Designer intervening in or controlling evolution on earth. If he, she or it exists, it’s a very stupid designer, as well as cruel, deceptive & incompetent. There are often better ways to design from scratch most biological structures than those jerry-rigged features which evolution has produced, working with the materials previous generations of living things have provided.

    People of course are free, as I’ve also said, to inject God or the Designer into observed evolution at any point. You can be as teleological as you wanna be. And indeed there are still evolutionary biologists & chemists like Collins who believe in the Christian God, but being scientists reject emphatically the lies of the likes of the Discovery Institute’s paid shills.

    The only ID proponent at the Pennsylvania trial with any scientific standing was Behe, perpetrator of the anti-scientific concept “irreducible complexity”. As primary witness for the defense, he was asked to support the idea that ID was legitimate science. Under cross examination, he conceded that “there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred”. (Nor have any emerged since.) In response to a question about astrology, Behe explained: “Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless… would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and… many other theories as well”.

    Given your greenhouse & comments on plants, I take it that you have some familiarity with plant breeding. Consider the case of domesticated corn (maize). Its genes are indistinguishable from its wild ancestor teosinte, but corn looks amazingly different & can’t reproduce without human assistance. Before the discovery of epigenetics, this fact presented a problem for some theorists, but no more. It’s like the age of the earth issue before the discovery of nuclear radiation.

    Science marches on, & there is always less & less space of action for a divine designer or anything like it in biology. That’s why I think its wrong both theologically & scientifically to posit supernatural interventions where not needed. In that case, even if multiverses are found to exist, there will still space outside of spacetime for a mysterious Being. So, while the scientific jury might still be out on design of the universe, pending more observation & analysis, the case is closed against biological ID, unless & until some shred of supporting evidence can be adduced, which is highly unlikely, to say the least.

  141. It is not I that conflates intelligent design with biological ID. As a philosopher, I take the knowledge produced by science as a given. That’s what philosophers do. The people you are obsessed with do not.

    I’m going to have to curtail this somewhat; my wireless keyboard & mouse are acting up and I do not currently possess a standard wired keyboard, only a MS Natural and I’m not a touch typist. So I am going to quote the Wiki-bloody-pedia here:

    The fine-tuned Universe is the proposition that the conditions that allow life in the Universe can only occur when certain universal fundamental physical constants lie within a very narrow range, so that if any of several fundamental constants were only slightly different, the Universe would be unlikely to be conducive to the establishment and development of matter, astronomical structures, elemental diversity, or life as it is presently understood.[1] The proposition is discussed among philosophers, theologians, creationists, and intelligent design proponents.

    Physicist Paul Davies has asserted that “There is now broad agreement among physicists and cosmologists that the Universe is in several respects ‘fine-tuned’ for life”. However, he continues, “the conclusion is not so much that the Universe is fine-tuned for life; rather it is fine-tuned for the building blocks and environments that life requires.” He also states that “‘anthropic’ reasoning fails to distinguish between minimally biophilic universes, in which life is permitted, but only marginally possible, and optimally biophilic universes, in which life flourishes because biogenesis occurs frequently”.[2] Among scientists who find the evidence persuasive, a variety of natural explanations have been proposed, such as the anthropic principle along with multiple universes. George F. R. Ellis observes “that no possible astronomical observations can ever see those other universes. The arguments are indirect at best. And even if the multiverse exists, it leaves the deep mysteries of nature unexplained.”[3]

    The standard argument against the above invokes that there are many (an infinite number?) of universes and that we just happen to exist in the one that shows exquisite fine-tuning (apparent design). There is absolutely no observational evidence for the existence of these other universes and it seems to me that it’s just as big a leap of faith to believe in them as it is to believe in God.

    There is nothing in the fine-tuning argument to suggest that the creator/intelligent-designer/God [delete whichever is inapplicable] is required to be caught fiddling with or manipulating his/her/its creation. The only point at which the creator is required to “intervene” is at the creation. That is, he/she/it designed the universe we have and then either ignored it, went to sleep, or otherwise lost interest. As you say, there is no evidence that there has ever been any intervention post-creation. To claim that I do support such a proposition is absurd.

    Apropos the C4 process, there appeared at the time of investigation no evidence of the C4 process existing in any purported common ancestor of those thirty odd species. It could, one supposes, have been lurking, but that would amount to what Gould scathingly (and rightly so) called “a hopeful mutation”. CO2 levels were so much higher then that there would have been no selection pressure to favour such a process. It seems entirely reasonable to me therefore that HGT is a far more likely explanation for these unrelated species to share genes in common, than to invoke the standard argument that was all just coincidence that the random mutations in these species all hit upon the same genes at roughly the same time. I also fail to see why invoking HGT as an explanation is connected in any way whatsoever with creationism.

    I have read one of Behe’s books. He invokes what he believes to be a knockdown argument: evolution is irreducibly complex. What he fails to sustain is connecting the fact of irreducible complexity with biological evolution. Biologists attack the idea of irreducible complexity rather than Behe’s failure to connect the two concepts leaving those who know about the fact of irreducible complexity to wonder if the creationists might not after all be correct. It’s what’s called an own goal in soccer.

    I think it’s time I installed some touch-typing software. The last time I did so was in 1990 or thereabouts. When I suffered a computer crash, I discovered that the software would not install a second time unless the software had been uninstalled with the disk in the drive. One had to pay for a whole new license!

  142. The Pompous Git says:
    November 14, 2013 at 3:42 pm

    Condolences on the hardware & software issues. With every technology comes a price.

    A philosopher should never take what he or she assumes to be what science says as a given. Clearly, no one can become learned in every relevant discipline, but IMO Janice Moore’s heroes from the Discovery Institute must understand enough biology to know they’re lying.

    I’d at least like to separate the issue of a fine-tuned universe from biological ID. While some philosophers may be proponents of both design hypotheses, no biologist can defend ID on other than religious grounds. The deceased famous physicists you cite do not argue for the positions of Meyer, et al, the goon squad from the DI.

    Irreducible complexity is as far from a fact as is possible. It’s a made up, sciencey sounding scam in order to sneak creationism into schools. It is entirely without any basis in fact & lacks any scientific validity. It is Behe looking at bacterial flagella & saying, “Boy, those structures look little machines to me! I don’t know how they evolved, so God, oops, I mean an Intelligent Designer, must have poofed them into existence.” Why the big ID in the sky did that, he doesn’t conjecture. Maybe to help spread disease after the Fall of Adam & Eve.

    As noted, Behe’s anti-scientific belief (if he does really believe it) in “irreducible complexity” is a punt. He just throws up his arms & says, “I can’t explain bacterial flagella, so it had to be an Intelligent Designer!” But with every passing year the biochemical pathways through which the various types of flagella did or might have evolved are being elucidated. Behe could have participated in this program of real science, but instead chose to become a champion of back-door creationism. It pays better & he doesn’t have to do any real work. Same with DI’s philosophers.

    You must not have read the link on C4 plants I posted for you. Don’t blame you, as it’s long, as it must be to do what it does. It shows via standard molecular clock calculations that the C4 pathway arose independently in different lineages millions to tens of millions of years before the late Miocene explosion. I’ve mentioned this a number of times now. This is science, evidence from actual observations & time-tested calculations. The C4 explosion (funny, if you’re familiar with explosives) was no more magical than the Cambrian explosion of large animals with hard body parts. Plants that were effectively pre-adapted for drier, lowered CO2 Miocene conditions spread along with the environments that favored them over C3 plants, like trees. No Designer nor Director need apply.

    I’m not sure you understand what a “hopeful mutation” is, but the C4 plants were definitely lurking. No supposition required. The molecular clock data show that they were around in small numbers for a long, long time before the Miocene explosion.

    Even the Modern Synthesis wasn’t as dumb as you take it for. It recognized sources of variation besides mutation & types of inheritance other than Mendelian.

    Since you read up on the philosophy of biology in the 1970s a lot has happened. It’s hard for me to keep up, even with talking to workers in the field, reading as many papers as I have time for & getting invited to more seminars & Webinars than I can “attend”. For instance, in 1977, the year after Dawkins’ book which I’ve never read, introns & exons were discovered. This shook up thinking for a while. Since eukaryotes have them & bacteria & archaea don’t, some of the most rattled thinkers even posited two abiogenetic events. This hypothesis has been falsified, but other big surprises have occurred frequently since. To take but one example, it’s now known that “genes” don’t have to be on the same chromosome, for those organisms with more than one chromosome.

    So, I reiterate. There is no evidence in support of the anti-scientific religious doctrine of biological ID, & all the evidence to date in the word against it. However, feel free to inject God or a Designer into the history of life on earth wherever your fancy strikes. Just know that it’s not necessary. As for a universe designed so that elements, stars, galaxies & life could evolve in it, the jury is still out, according to some cosmologists, however angry that proposition makes a lot of other scientists.

    Good luck with the infernal machine issues.

  143. I may have typed too soon. Here’s a recent paper on the possibility of introns in the Domain Archaea:

    http://www.pnas.org/content/early/2011/02/28/1100862108.full.pdf

    “Evolution of introns in the archaeal world”.

    Archaea were first classified as a separate group of prokaryotes in that year of wonders 1977 by Carl Woese & George E. Fox based upon phylogenetic trees based in the sequences of ribosomal RNA (rRNA) genes.

  144. @ milodonharlani

    Irreducible complexity is as far from a fact as is possible. It’s a made up, sciencey sounding scam in order to sneak creationism into schools. It is entirely without any basis in fact & lacks any scientific validity.

    Try arguing that with Chaitin. Good luck!

    The Omega Number: Irreducible Complexity in Pure Math
    Gregory J. Chaitin
    Purchase on Springer.com
    $29.95 / €24.95 / £19.95*
    Abstract
    We discuss the halting probability Ω, whose bits are irreducible mathematical facts, that is, facts which cannot be derived from any principles simpler than they are. In other words, you need a mathematical theory with N bits of axioms in order to be able to determine N bits of Ω. This pathological property of Ω is difficult to reconcile with traditional philosophies of mathematics and with traditional views of the nature of mathematical proof and of mathematical knowledge. Instead Ω suggests a quasi-empirical view of math that emphasizes the similarities between mathematics and physics rather than the differences.

  145. The Pompous Git says:
    November 14, 2013 at 4:51 pm

    I meant the term as used by Behe in pseudo-biology, as I’d have thought was implied. Behe borrowed the concept from math. It doesn’t work in regards to biological structures.

    Behe’s prime example is a bacterial flagellum, although there are many. Had he decided to practice science rather than religious proselytizing, he might have helped find ways to fight disease by learning about the biochemical pathways that lead to the development of flagella in pathogenic bacteria.

  146. @ milodonharlani

    A philosopher should never take what he or she assumes to be what science says as a given. Clearly, no one can become learned in every relevant discipline, but IMO Janice Moore’s heroes from the Discovery Institute must understand enough biology to know they’re lying.

    I was taken to task for not taking what science (i.e. Dawkins et alia) says as a given! Pointing at recent discoveries was what got me labelled as a creationist. Funny when you think about it. That said, philosophers are not science researchers; philosophers ponder the logic and rationality of what is discovered and what is purported to have been. Most of that science is what makes it into academic texts, rather than the latest, greatest and frequently better forgotten papers. That said, many of my favourite philosophers are, or were, scientists.

    While some philosophers may be proponents of both design hypotheses, no biologist can defend ID on other than religious grounds.

    I doubt that. Perhaps you should distinguish between intelligent design and Stupid Design ;-) Just because people use the term Intelligent Design to describe their theory does not mean that they are intelligent.

    Sorry I haven’t had time to follow up the read on the current status of C4 in the depths of time. I am pretty busy. It’s not raining today. I have opened the link in a tab that may be perused when it starts raining again.

    Apropos the machine problem, I attempted to install the software I was given. It refused to install on my 64 bit Windows 7. Attempted to purchase the latest version from Amazon and discovered that only US citizens are allowed to purchase it! I have downloaded some free software in its stead. So it goes…

    And it’s not raining today! So it’s out to tend the plants, but no zea mays this year. It’s now too late due to weeks of inclement weather. We do not eat a lot, but the little we usually grow goes down a treat.

  147. @ milodonharlani

    Behe’s misappropriation of the term does not invalidate the term. That’s why I described biologists’ claim that there is no such thing as irreducible complexity as an own goal. Now I really must go for the day. Live long and prosper…

  148. The Pompous Git says:
    November 14, 2013 at 5:12 pm

    Whoever took you to task for doubting Dawkins apparently didn’t know that lots of biologists also had problems with his views.

    The only kind of design that exists in nature is stupid. Sometimes the results can be spectacular, but it’s never intelligently designed, but make do & slap dash with whatever odd bits are available. Over time the design can be improved, but it’s never intelligent from the start. You or I could design a better fish jaw bone than borrowing & adapting its gill arches. We could also design a better human foot, although maybe with aid of CAD.

    Here’s a shorter paper on C4 plants, with an excerpt also showing that they first evolved tens of millions of years before their Miocene-Pliocene “explosion” three to eight million years ago, & that their rise to ecological dominance occurred over millions of years:

    http://www.brown.edu/Research/Edwards_Lab/reprints/Edwards_etal_Science2010.pdf

    “Recent phylogenetic reconstructions show that C4 photosynthesis has evolved multiple times in
    grasses (16, 17). Time-calibration of these phylogenies using fossilized grass pollen and inflorescences places the earliest probable origin in the Early Oligocene (~30 to 32 Ma) (Fig. 2) and suggests that subsequent origins arose in clusters (for example, in the Middle Miocene). This timing has led researchers to hypothesize that the Early Oligocene drop in CO2 triggered evolution of the C4 pathway (16, 17). However, the proposal is challenged by the discovery of Late Cretaceous microscopic plant silica (phytoliths) diagnostic of grasses (Fig. 2), suggesting
    that this lineage may be much older than previously thought (18). A recalibration with these fossils would date the earliest C4 grasses to the Middle Eocene (17), a time of warm equable
    climates and probably of high CO2 (Fig. 2). Even more controversial are d13C records from leaf-wax molecules (n-alkanes) in marine sediments, indicating that C4 photosynthesis
    existed in Cretaceous land plants (19), albeit not necessarily in grasses.

    “New paleontological evidence also reveals crucial information about the Miocene environments that preceded C4 grasslands. Rather than being forested, as initially thought (20), it now
    appears that landscapes were relatively open. The evolution of ungulate grazers or mixed feeders (feeding on grasses and broad-leaved plants) and pollen data (21) supplemented
    by new, phytolith-based reconstructions of vegetation (22) document the emergence of savannas or woodlands with predominantly C3 grasses in the Early-Middle Miocene (11
    to 24Ma), several million years before C4 grasslands spread (Fig. 3). “This vegetation shift is evident in all of the studied cases, although its timing and pace seem to have varied among regions (Fig. 3).

    “C4 grasses occurred in the landscape soon after this transition. Phytoliths show that C4 Chloridoideae species were represented in North American grassland communities 19
    Ma (Fig. 2). Similarly, d13C records from fossil soils suggest that C4 grasses contributed 20 to 40% of local vegetation in several regions for many million years before C4 species completely dominated communities (Fig. 3) (23, 24). Spatially detailed sedimentological and isotopic
    reconstructions of the paleolandscape (25, 26) indicate substantial heterogeneity in vegetation structure, with tree-grass mosaics before and during the C3-C4 shift. C4 grasses seemed to
    have first invaded drier parts of floodplains, whereas C3 plants preferred moister habitats in
    topographic lows (25, 26).”

    Makes sense that C4 plants would have first colonized drier areas.

    Didn’t know that jingoistic fact about Windows 7. Take comfort from the fact that Windows 8 for mobile devices is worse.

  149. PS: If there were a way I could send you the Windows 7 upgrade you need, I would, but Mr. Softie seems to be hip to that trick.

  150. Well, Milodon Harlani. So you are STILL trying the spread the word about Neo-Darwinism. You do realize, don’t you, that in your almost daily promoting of the theory of evolution and of Darwin’s Origin of Species ideas as if they are fact and not conjecture, you are acting like one who is promoting ones’ religion? I am hopeful that your constantly pushing Darwinism is because you have some doubt as to its truth (perhaps, only subconsciously) and will open your mind to the possibility that you are mistaken. Your level of anger when confronted with Intelligent Design is, you know, quite telling… .

    It is nearly pointless to participate in a debate on this subject, because the Intelligent Design hypothesis requires some Bayesian prior assumptions that make the theory globally inconsistent and absurdly unlikely from the point of view of any sort of axiom of parsimony (e.g. Ockham’s Razor) or the actual evidence.

    I’ll try one time to address these points, although it is probably pointless because ID advocates without exception are inventing a hypothesis with the motivation of allowing for the participation of a beneficent deity that otherwise is completely invisible in any sort of statistical analysis of human affairs, usually (if they were honest) a specific beneficent creator deity from one specific world mythology. In the US and Europe, that deity is almost certainly “God” and/or “Jesus” in the Christian church.

    Any sort of argument based on teleology fails because if ID is true, there is an intelligent designer. Either the intelligent designer’s intelligence arose spontaneously — in which case intelligence and structure with the appearance of design can arise spontaneously and one cannot invoke the need for a designer to explain design — or that designer’s intelligence was itself designed by a still earlier intelligence. Since the Big Bang cuts off any sort of recursive chain without resorting to deity in some imagined external/parallel reality that we haven’t a shred of evidence to support, the argument is inconsistent.

    Given that one cannot say that ID is necessary when confronted with structures with purpose (because of the recursion problem), granting that ID is sufficient to explain almost anything, as is a theory that invisible fairies are the true cause of gravity, one has to invoke parsimony and look at the evidence. There is an absolutely enormous amount of evidence for evolution due to mutation plus natural selection. We see it happen all of the time in the laboratory. We combat it in the world of diseases. We have mountains of fossil evidence showing the evolution of species The theory is a sufficient explanation for species, diversity, intelligence, and structure.

    We then have two competing theories, both sufficient. Which theory has the preponderance of evidence? No evidence of structure counts in favor of ID, because evolution creates similar structures and we have direct laboratory evidence for it. What would count as evidence for ID is discovering direct scientific evidence of the designer. And there isn’t any. Not a shred. To invoke a designer, you have to explain how the designer got there or it is an incomplete theory. To claim “proof” of a designer, you have to produce direct evidence for the existence of a designer. The former requires an infinitely complicated explanation, all of it safely hidden — you might as well make your theory “I don’t know” because that’s all you will be able to say when asked about the nature or mechanism of the designer. The latter requires a measurement, a direct observation, of the designer. Otherwise you’re claiming to be able to infer a hidden cause when there is a much simpler explanation with direct evidence supporting it that is also sufficient.

    That’s why people don’t pay any attention to your silly videos. Show me the designer. That’s the only thing that counts as evidence of Intelligent Design.

    rgb

  151. @ milodonharlani

    First, thanks for the link to the paper on the origin of C4 grasslands. It is very interesting. It does not preclude, however, horizontal gene transfer and I still have no explanation from you as to how my belief that HGT plays an important role in evolution makes me an ID theorist in the Creationist sense.

    I must disabuse you of some things. While I did undertake a year of biology in 1969, the philosophy of biology course was in 2005. The biology was that current in 1999 plus whatever the grad students brought to the table.

    I subscribe to The Scientist (http://www.the-scientist.com/) having dropped my subscription to Scientific American some years ago when it began to fail to inspire me. Now it may well be that The Scientist is secretly a publication of the Discovery Institute, but I would need very strong evidence that this is so before believing it. HGT gets some coverage in that publication, as do evolutionary topic in general.

    Apropos Behe’s theory regarding bacterial flagellae, Four decades ago I was rather taken by Lynn Margulis’ theory that flagellae and the bacteria to which they are attached were a symbiosis between previously separate organisms. Ditto for mitochondria in eukaryotes. I still am. When I first came across her work, she was considered very infra dig. In the introductory geology course I undertook in 2003 I noted with some pleasure that her work is viewed much more favourably these days.

    You wrote:

    The only kind of design that exists in nature is stupid. Sometimes the results can be spectacular, but it’s never intelligently designed, but make do & slap dash with whatever odd bits are available. Over time the design can be improved, but it’s never intelligent from the start. You or I could design a better fish jaw bone than borrowing & adapting its gill arches. We could also design a better human foot, although maybe with aid of CAD.
    While it may be true that we might be able to come up with better individual designs for fish jaws, human feet etc, the more important observation is that it’s unlikely that we could design a better system than that which we observe in action. Life’s evolution appears to have run successfully for several billion years with no sign of obvious outside intervention.

    You wrote:

    Whoever took you to task for doubting Dawkins apparently didn’t know that lots of biologists also had problems with his views.

    There were several. The saddest was my best friend in high school and best man at my first wedding. He hosted Dawkins and Blackmore during a conference some years ago. My main antagonist was also a close friend for many years (originally an employee of mine). So it goes…

    Apropos the software issue, it’s not Windows 7 that needs updating, it’s the 32 bit software that was written more than a decade ago. My shift to 64 bit computing three years ago broke several applications. Thanks for your kind thoughts.

  152. Robert, I must take you to task for the following statement:

    There is an absolutely enormous amount of evidence for evolution due to mutation plus natural selection. We see it happen all of the time in the laboratory.

    Mutations occur at a rate of roughly one in a million replications. Most mutations are deleterious and are weeded out by natural selection. Note that last sentence. It’s vital to the issues here. Deleting errors is quite different to generating novelty, such as feathers instead of scales, or mammalian skin cells. Explaining the generation of novelty is a Big and Complex Problem.

    …molecular biologist, Barry Hall, published results which not only confirmed Cairns’s claims but laid on the table startling additional evidence of direct mutation in nature. Hall found that his cultures of E. coli would produce needed mutations at a rate about 100 million times greater than would be statistically expected if they came by chance. Furthermore, when he dissected the genes of these mutated bacteria by sequencing them, he found mutations in no areas other than the one where there was selection pressure. This means that the successful bugs did not desperately throw off all kinds of mutations to find the one that works; they pinpointed the one alteration that fit the bill. Hall found some directed variations so complex they required the mutation of two genes simultaneously. He called that “the improbable stacked on top of the highly unlikely.” These kinds of miraculous change are not the kosher fare of serial random accumulation that natural selection is supposed to run on. They have the smell of some design.

    Now the smell of design certainly does get those Discovery Institute types running around flapping their hands and saying “it must be God’s work”, but it does no one any good to call anyone who happens to notice that we are talking about the results of empirical research here a Creationist. There are other explanations. The most obvious one is that we don’t actually understand a very great deal of biology. I usually put it thusly. There are at least four possible explanations here:

    1. It’s all just down to an amazing long streak of lucky events. We Know The Truth. Live with it. [neoDarwinists]
    2. This is not the explanation for evolution. Evolution involves whole nucleotide sequences (horizontal gene transfer). [Panspermia advocates/Margulis et alia]
    3. There is some undiscovered mechanism/mechanisms operating to skew the odds. That is, the process is not random at all. [Prigogine et alia]
    4. God done it.

    The first explanation doesn’t really cut it. The number of possible random permutations of even a single gene sequence is impossibly huge to explore. The second has the benefit of support from the laboratory, but it’s also far from sufficient at this time. Prigogine’s observation that self-organising systems are involved is almost certainly true. Indeed, it would be surprising if they weren’t. That said, we don’t understand self-organising systems very well at this stage much beyond acknowledging their existence. The final one has, as you correctly point out, zero supporting evidence and any Bayesian argument requires “Bayesian prior assumptions that make the theory globally inconsistent and absurdly unlikely from the point of view of any sort of axiom of parsimony”. But then biology isn’t globally consistent either (not to mention science in general) and also generates many absurdities as David Stove pointed out in his excellent book of essays Darwinian Fairytales.

    Like nearly all philosophers, I am averse to entering into the ongoing food fight between creationists and biologists; it seems to consist mainly in mutual accusations of bad faith. What I am interested in are arguments that enable me to learn new things. Like the physicist Paul Davies (and others) I am interested in the question of why the universe is the way it is. And that definitely gets you into the issue of teleology. For an excellent overview of teleology including the fine-tuning argument which is what fascinates me, the Stanford Encyclopedia has an excellent, though longish piece here:

    http://plato.stanford.edu/entries/teleological-arguments/

    You correctly point out that a creator of the universe would be undetectable. Unfortunately, the current competing view appears to be that there are many if not an infinite number of universes. Is it not the case that these ever so many alternative universes are also undetectable? I do not expect an answer to that question.

    Thanks BTW for your many illuminating posts on this website. And I’m not sure if I thanked you directly for your excellent novel, but I found it very amusing.

  153. The Pompous Git says:
    November 15, 2013 at 9:30 am

    Margulis was right about endosymbiosis, wrong about the flagella, which have evolved independently repeatedly.

    Not sure what you disagree with me about HGT. Your “belief”, as I pointed out, is a commonplace in biology & has long been so. I didn’t say that your belief in it made you a creationist. You misunderstood me. What I said is that you seemed to think your learning about it was some great aha! moment that meant the Modern Synthesis was false, hence ID was possible.

    HGT is common in prokaryotes & happens, via different mechanisms, in eukaryotes as well. It seems you still miss the point. Variation arises from various sources. It doesn’t need to be just mutations occurring in the germ cells of a preceding generation.

    No biologist that I know of ever maintained that mutations from radiation or mutagenic agents was the only source of variation, even in the first iteration of the Modern Synthesis. You simply misunderstand what it maintained. Since the 1930s even more sources of variation have been discovered & we’ve learned a lot more about genomes & how “genes” work. It doesn’t mean that the Modern Synthesis was wrong as far as it went, any more than Einstein “proved” Newton wrong.

    Most mutations are indeed neutral or deleterious, but all organisms acquire them. Some are lethal, but most aren’t. Mutation is one means of accumulating variation but not the only one. It is an indisputable, factual observation that beneficial mutation can & do arise. We’re all the result of them. In each generation of humans, for instance, at least tens of billions of mutations occur in people who survive to reproduce, & they accumulate. They do indeed lurk & wait until conditions make them beneficial. But even if only one in a million of the latest mutations be beneficial in our current environment, that still leaves thousands to tens of thousands worldwide in each generation, even allowing for duplicate mutations. The sheer explosive number of humans is presently driving our evolution rapidly, despite our interfering with selective pressure through medicine & other cultural activities.

  154. The Pompous Git says:
    November 15, 2013 at 10:46 am

    Some physicists think that other universes are indeed detectable, have looked for them & indeed claim to have found evidence for them. Some of their colleagues aren’t so sure.

    http://arxiv.org/pdf/1012.3667.pdf

    http://arxiv.org/abs/1303.5090

    http://en.wikipedia.org/wiki/Laura_Mersini-Houghton

    You still don’t get how “randomness” applies to biology, & it sounds as if your (former?) friends failed to grasp it as well, maybe misled by their take on Dawkins. It’s not at all as you imagine, but I guess I’ve been unable to explain it, or maybe you don’t want to get it. I don’t feel any further attempt by me to do so can be worthwhile. If you think that biology as you understand it supports ID, I hope you gain from that belief whatever it is you desire.

  155. Oops, my bad. Forgot to reply to your citation of Cairns/Foster/Hall on adaptive mutation (AM). As I’ve commented repeatedly above, it has long been known that stresses can increase the mutation rate.

    The supposedly anti-darwinian “magic” of AM didn’t survive long, as is usual with such supposed mysteries. It was solved in 2000:

    http://www.pnas.org/content/97/12/6646.full

    “Abstract

    Upon starvation some Escherichia coli cells undergo a transient, genome-wide hypermutation (called adaptive mutation) that is recombination-dependent and appears to be a response to a stressful environment. Adaptive mutation may reflect an inducible mechanism that generates genetic variability in times of stress. Previously, however, the regulatory components and signal transduction pathways controlling adaptive mutation were unknown. Here we show that adaptive mutation is regulated by the SOS response, a complex, graded response to DNA damage that includes induction of gene products blocking cell division and promoting mutation, recombination, and DNA repair. We find that SOS-induced levels of proteins other than RecA are needed for adaptive mutation. We report a requirement of RecF for efficient adaptive mutation and provide evidence that the role of RecF in mutation is to allow SOS induction. We also report the discovery of an SOS-controlled inhibitor of adaptive mutation, PsiB. These results indicate that adaptive mutation is a tightly regulated response, controlled both positively and negatively by the SOS system.”

    If you were really interested in learning biology rather than promoting a teleological philosophy, it wouldn’t have taken you long to find this reference & others explaining how yet again the supposed ID magic is entirely explicable by biology. Same goes for the flagella of bacteria, archaea & eukaryotes. ID is just old creationist vinegar in a new bottle, using the same tired arguments of 19th century opponents of Darwin.

  156. @ milodonharlani

    You wrote: “Ohno was wrong about that. He didn’t know then what we know now, & was already shown wrong even before we found out as much as we have about genomics.”

    I quote here from the Wiki-bloody-pedia because it’s in electronic rather than paper form:

    Functional divergence is the process by which genes, after gene duplication, shift in function from an ancestral function. Functional divergence can result in either subfunctionalization, where a paralog specializes one of several ancestral functions, or neofunctionalization, where a totally new functional capability evolves. It is thought that this process of gene duplication and functional divergence is a major originator of molecular novelty and has produced the many large protein families that exist today.[1][2]

    Functional divergence is just one possible outcome of gene duplication events. Other fates include nonfunctionalization where one of the paralogs acquires deleterious mutations and becomes a pseudogene and superfunctionalization (reinforcement),[3] where both paralogs maintain original function. While gene, chromosome, or whole genome duplication events are considered the canonical sources of functional divergence of paralogs, orthologs (genes descended from speciation events) can also undergo functional divergence [4][5][6][7] and horizontal gene transfer can also result in multiple copies of a gene in a genome, providing the opportunity for functional divergence.
    Many well known protein families are the result of this process, such as the ancient gene duplication event that led to the divergence of hemoglobin and myoglobin, the more recent duplication events that led to the various subunit expansions (alpha and beta) of vertebrate hemoglobins,[8] or the expansion of G-protein alpha subunits [9]

    This reflects what I discussed with a friend who was far more into genomics than I am when I was in that philosophy of biology class in 2005. I do note that Ohno’s hypothesis regarding whole genome duplication (R2) appears to have fallen, but the part that interested me appears to still be currently accepted contra your statement above.

  157. @ milodonharlani

    Not sure what you disagree with me about HGT. Your “belief”, as I pointed out, is a commonplace in biology & has long been so. I didn’t say that your belief in it made you a creationist. You misunderstood me. What I said is that you seemed to think your learning about it was some great aha! moment that meant the Modern Synthesis was false, hence ID was possible.

    I don’t believe that I have ever stated that the Modern Synthesis is false. I have stated that Dawkins’ claims of diverging species being unable to ever exchange genomic information, i.e. HGT can’t happen, is false and that’s not the same thing. I have also stated that while ongoing ID might be possible, there is no evidence for it and that I have no intention of getting into the stoush between the creationists and biologists. Hardly a ringing endorsement for ID. And implying that I endorse ID in the very limited sense that you use the term seems tantamount to calling me a creationist.

    I have said that there are some legs in an argument for the universe being created by an intelligence, but that’s entirely separate from any arguments about God fiddling with his creation.

    And that I hope is that…

  158. @ milodonharlani

    Forgot to reply to your citation of Cairns/Foster/Hall on adaptive mutation (AM). As I’ve commented repeatedly above, it has long been known that stresses can increase the mutation rate.

    The supposedly anti-darwinian “magic” of AM didn’t survive long, as is usual with such supposed mysteries.

    So now John Cairns, ? Foster and Barry Hall are “anti-darwinian” creationist magicians, too. [sigh] At least I’m in good company…

  159. “If you were really interested in learning biology rather than promoting a teleological philosophy”

    From my notes ca. 2005:

    The teleological terms “function” and “design” appear frequently in the biological sciences.

    Examples of teleological claims include:

    A (biological) function of stotting by antelopes is to communicate to predators that they have been detected.

    Eagles’ wings are (naturally) designed for soaring.

    Biologists, despite frequently claiming to eschew teleological language, use such quite frequently. So it goes…

  160. Mr. Git:

    Cairns et al never made the philosophical leap you did. They knew there would be a natural explanation unlike your leap of faith.

    Your false examples are straight out of Answers in Genesis. I see you also doubt plate tectonics. Can you blame people for thinking you’re a creationist?

    You should study biology rather than philosophy thereof.

    I read about this thread on 350.org. Cannot say I was surprised to find Intelligent Design supporters here.

  161. You really cannot see the distinction between recognizing that adaptive behavior has a survival enhancing purpose so was selected for and believing that a supernatural power directs evolution in general toward some purposeful end such as humanity?

    Some philosopher! Pure sophistry!

  162. Diego Diaz said @ November 15, 2013 at 12:48 pm

    Dawkins does not say that about HGT. Search and find out what he really does say.

    From The River Out of Eden 1995 pp 7-8

    There are now perhaps thirty million branches to the river of DNA, for that is an estimate of the number of species on earth… Today’s thirty million rivers are irrevocably separate.

    Emphasis mine. If species are irrevocably separate as Dawkins states, then there is no possibility of HGT.

  163. Diego Diaz said @ November 15, 2013 at 1:09 pm

    Your false examples are straight out of Answers in Genesis.

    Since I have never read Answers in Genesis, I have no idea whether your statement is true or not. Please quote my words and provide a link. FWIW I am an agnostic on many things, most especially those I have never investigated. This is the very opposite of the faith you are alleging I possess.

  164. You did not search. Afraid of truth?

    He has written and spoken much on HGT. Your conclusion from out of context citation is unwarranted.

    Some philosopher! No logician!

  165. Diego Diaz said @ November 15, 2013 at 1:17 pm

    You really cannot see the distinction between recognizing that adaptive behavior has a survival enhancing purpose so was selected for and believing that a supernatural power directs evolution in general toward some purposeful end such as humanity?

    Please quote my words where you claim that I said I believe that a supernatural power directs evolution.

    I did write above “The [God done it explanation] has, as you correctly point out, zero supporting evidence and any Bayesian argument requires ‘Bayesian prior assumptions that make the theory globally inconsistent and absurdly unlikely from the point of view of any sort of axiom of parsimony’.” Emphasis added.

  166. 1. It’s all just down to an amazing long streak of lucky events. We Know The Truth. Live with it. [neoDarwinists]
    2. This is not the explanation for evolution. Evolution involves whole nucleotide sequences (horizontal gene transfer). [Panspermia advocates/Margulis et alia]
    3. There is some undiscovered mechanism/mechanisms operating to skew the odds. That is, the process is not random at all. [Prigogine et alia]
    4. God done it.

    This list is hardly exhaustive, and it isn’t clear at all how much luck is needed. I’m a bit of an expert on evolutionary algorithms, which are important in all sorts of optimization theories and search algorithms because they are literally the most efficient search algorithm we’ve been able to find for high dimensional spaces. Also (although my previous reply may have given the wrong impression) I’m not advocating only mutation plus natural selection, although that is a rather powerful process. There could be all sorts of ways that the dice are loaded, if you will. The world’s most successful species very probably evolved to evolve better than that — the algorithm itself is subject to tuning.

    I’m very fond of Prigogine’s general work, not specifically in the context of evolution. But it is indeed the case that there can be all sorts of things that skew the odds while still remaining “random”. They simply aren’t random on the original oversimplistic picture of mutation plus natural selection. As a single example, it is now known that species hybridization is not rare or nearly impossible, it is commonplace. Hybridization plus mutation plus selection is one of many possible skewing mechanisms.

    None of this affects the direct evidence we have of evolution in the form of a fossil record that — highly incomplete as it is (the odds of a dying animal being fossilized are poor indeed) — paints a clear and compelling picture of the evolution of species from common progenitor species, happening over and over and over again for nearly every species we look at. In our own family tree we can quite literally see where a break occurred in a chromosome comparing human and gorilla DNA, along with many other homologies:

    http://en.wikipedia.org/wiki/Human_evolutionary_genetics

    These genes are pure evidence for evolution. The leave lots of room (and the article discusses some of that room) for different mechanism for the changes, but there is little doubt that discrete changes occurred, and not much doubt when they occurred, to split the genetic line that became modern humans off from the line that became modern gorillas. There appear to be multiple mechanisms at work here — small changes that gradually are selected out according to benefit, and large changes that occur “all at once” (or in a comparatively short period of time), but both are arguably evolution, and neither one invokes an external intelligence making changes in Earth’s species over some 3 to 4 billion years.

    This is the critical issue, not the particular mechanism(s) of evolution. Is evolution the result of reasoned activity by an external entity or is evolution a naturally occurring process of genetic change due to all mechanisms plus the inevitable sorting out of living creatures on the basis some mix of luck and fitness to survive and reproduce (and yes, I’m well aware that “reproduce” is broader than just the individual as well, while even at the tribal or familial level it is still evolution)?

    The fossil record is absolutely overwhelming evidence for evolution, whether or not the evolution is precisely Darwin’s theory of evolution. Evolution best fits the observations. Evolution can be and has been observed in the lab. We use evolution as a tool — humans have evolved improved crops and animals for husbandry for thousands of years if not much longer by simply becoming an agent of natural selection, picking the biggest and best of animals to breed, picking the animals that were the safest to work with and best behaved according to our needs. Humans created the dog out of a wolf ancestor by means of pure evolution — breeding most the animals that exhibited (and continue to exhibit) the most desired traits. Perhaps, as you assert, mutation is too slow a mechanism to be able to create radical changes in appearance and behavior rapidly, but if so the differences between chihuahua and great dane are difficult to account for.

    Where I teach in the summers at the Duke Marine lab I can look out of my window and see the results of a mere 400 years of evolution. The so-called “Shackleford Ponies” live in comparative abundance on the outer bank islands just outside of my back door. They are the distant descendents of domesticated horses that made it to shore when ships foundered offshore in the sixteenth and seventeenth centuries. In a mere 400+ years, they have evolved to be much smaller (the islands have a severely constrained food supply), shaggier (they have to survive the winter), and most interestingly, they have evolved the ability to survive on brackish water, as the islands have almost no fresh water and what they have is inevitably far saltier than actual fresh water. The horse’s kidneys have significantly drifted due to mutation plus natural selection in only a few hundred years. The horses have other interesting traits — they have learned to read the tides, and know how to move between the islands when it is safe to do so, for example — but they are again direct evidence of natural evolution occurring on a fairly rapid timescale even in a small population.

    In the laboratory, every physician faces the challenge of successful evolution almost every day. Bacteria and other parasites are evolving resistances to the drugs and antibiotics we use to combat them. New genetic variants of diseases are constantly emerging and the successful ones can at any moment become the next pandemic. Bacteria or viruses that are not diseases mutate and become new species that are diseases — another source of potential pandemic. We observe evolution at every scale from microscopic to macroscopic, we use it as a tool, we use evolutionary algorithms in computational optimization theory, we have immensely powerful computer programs that can do statistical genetic analysis. While scientists are hardly a uniform group and are apt to disagree about all sorts of theories or the meaning of this or that bit of evidence, you will have a very difficult time finding credible scientists who don’t believe in evolution as the explanation for the diversity of species and as the best explanation for the natural history of the biosphere, even as I’m sure you can find that those same scientists are not at all in agreement on the precise details of the mechanisms involved (and could even all be right as there could be many mechanisms).

    God, of course, is a universal explanation, as are invisible fairies, solipcism, sufficiently advanced (and very, very patient) space aliens, pink unicorns, etc. One can always just make something up and explain away any inconsistencies by adding exceptions. This is not very reasonable — the more exceptions and inconsistencies you add, the lower the probability is that your “theory” is correct, especially without either supporting evidence or the ability to falsify a claim on the basis of evidence. As such it can never by purely logically or empirically refuted, any more than I can logically or empirically prove that I’m not a power unit in the matrix so that everything I think I know about the world is false. However, neither can it ever be logically supported until one comes up with direct observational evidence, and so far Gods and Pink Unicorns alike are scarce as hen’s teeth. So are super-intelligent space aliens or any other non-diety “intelligences” that ID advocates will offer up to prove that they don’t really mean God, it could be any old superhuman intelligence.

    This also applies to your semi-telelogical argument about the tuning of the Universe to “life” if not more specifically “human life”. There are a number of problems with this argument, as I’m sure you are aware. The first is that given direct knowledge only of the spacetime continuum in which we seem to live, we cannot speak of “probability”, as in “what is the probability of finding a Universe with the parameters our Universe has”. The answer is “unity”. Behold it. It Is. So far, we are unable to empirically demonstrate a hat full of Universes from which our Universe is drawn, nor can we postulate on the basis of any evidence a process that might have produced a “Universe tuned to life”. Worse, any attempt to do so will run into the teleological paradox. If you wish to assert that the Universe appears designed, and thereby infer a designer, that designer must be even more complex than the Universe, and hence must in an information theoretically precise sense be less likely. You are invoking a cause that is even less likely than the effect that you wish to claim is necessary because it is supposedly so very unlikely, in spite of the fact that the latter is manifestly real and the former pure supposition.

    Who designed the designer?

    If you postulate a designer that needed no designer, then surely it is far simpler to not bother, and postulate a Universe that needed no designer. You have the substantial advantage in the latter case that the Universe is not a postulate, it is an accomplished fact and every instant of your experience empirically affirms this. There is no evidence whatsoever for the undesigned designer.

    rgb

  167. Dr. RGB:

    Glad to see a real scientist among the ignorant crackpots here, casting pearls before swine.

    Good luck educating them.

  168. Diego Diaz said @ November 15, 2013 at 1:29 pm

    You did not search. Afraid of truth?

    I possess the following by Dawkins:
    Unweaving the Rainbow, Allen Lane 1998
    The Blind Watchmaker, Penguin 1998
    Climbing Mount Improbable Penguin 1996
    The Extended Phenotype Oxford 1989

    It would seem I am unafraid of Dawkins ;-) Tell me where in those pages I may find Dawkins contradicting his statement that I quoted above.

  169. In time it took you to comment, you could have searched “Dawkins horizontal gene transfer”. Why did you not? Scared of truth?

  170. Oh, and I do know, BTW, that you are not arguing for either ID or God per se — my arguments are against teleological arguments in general. I didn’t even point out the usual answer to the assertion — there could even be a hat from which separated, discrete Universes (or rather, spacetime continua as I dislike using the term Universe for anything but “everything that actually objectively exists”, the existential Universe) are “drawn”, or bubble out of, and their physical parameters could be completely random but it is a simple matter of fact that there won’t be any sentient beings that evolve to wonder about all of this in any of those Universes except the ones where the parameters are just right for this to occur.

    Indeed, this isn’t all that crazy an argument. Forget physical coupling constants. What is the probability that I exist, doing what I’m doing right now, in a Universe that is in exactly the state that this one appears to be (even with the right coupling constants)?

    Mathematics lacks enough zeros to put before the first nonzero digit… or, unity. Personally, I prefer unity, unless and until we find the hat and some sort of random process. I might even prefer unity afterwards. What’s the probability that I just typed the phrase “What’s the probability that I just typed the phrase “”What’s the probability that I just typed the phrase “””What’s the probability….””” (recurse indefinitely)? Apparently, it was unity.

    That’s the problem, those pesky Bayesian priors. Even with a hat, or urn, to draw from, you arrive at very different estimates for the probability of drawing a green ball from a large urn given only the evidence that you have drawn one green ball from it depending on how you think the urn was prepared! This makes e.g. Polya’s Urn type estimates so very interesting.

    rgb

  171. Dr. RGB:

    Glad to see a real scientist among the ignorant crackpots here, casting pearls before swine.

    Good luck educating them.

    Dear Diego,

    Real scientists try to avoid ad hominem, and there are quite a few non-crackpots on WUWT. That said, I’m sure there are indeed some crackpots, but they are more likely to be found on e.g. PSI than here. In fact, there it is more or less a sure thing. Pompous Git is actually a gentleman and a philosopher, and while we do not always agree, I would hardly call him ignorant or a crackpot. Can he be mistaken, or misinformed? Sure. So can I. So can you, if you’re honest.

    So far, he has said little that I would fundamentally disagree with except create a list of evolutionary theories that I think is a bit too narrow and give perhaps a bit too little weight to the ongoing work of evolutionary biologists. We’re way past the point where evolution itself can be (sensibly) doubted, and sure, there is lots of ongoing research with all of the usual trappings of well-done science — theories, experiments, observations, simulations — directed towards a better understanding of all of the mechanisms whereby evolution works. I doubt that any competent evolutionary biologist these days adheres to the strict mutation plus natural selection mechanism, simply because there is direct evidence of a lot more mechanisms at work. It’s not my field, so I am not going to be the best one to list all of the ones that are current best belief based on the evidence, but I’m guessing any good, current textbook in introductory evolutionary biology would have a survey, and even wikipedia probably isn’t too bad.

    As he pointed out, he most definitely did not advance the God hypothesis or any variant thereof, and if he did bring up one of the neo-teleological arguments, well, even I think that the observations are “interesting” at the same time that I recognize (and pointed out) that they cannot constitute statistical/empirical “evidence”.

    So please, be patient and polite. Calling people names is so very rarely productive. And bear in mind that the people who were pushing ID above are not, actually, particularly regular posters on WUWT. I don’t know what attracted them to this particular thread, but does it matter?

    rgb

  172. Lady with ID videos and man with literal interpretation of Genesis sound ignorant to me. I apologize but in Amazon Basin my work is hurt by fundamentalist missionaries.

    I see this is not a good site for me.

    Thank you for your excellent comments and you are right I was rude.

    Goodbye.

  173. @ rgbatduke

    We do not seem very far apart here. However, I think you may have missed my main point. Micro-evolution among dogs (for example) is manifestly not speciation, or at least not yet in any of the many accepted versions of biological species. Some speciation may be attributed to randomness, but this must take ever so much time given the size of the space of possibilities within one gene assuming one nucleotide substitution per million replications.

    Now I have never invoked God as a serious explanation for novelty arising in evolution, though ever so many seem to want to attribute that to me. What I have stated ever so many times is that there are some laws in the universe to which we are currently oblivious. Any claim to a complete answer must be predicated on knowing what we do not yet know. And the only being I have ever heard of that might know what we do not yet know is God which is rather funny when you think about it.

    Apropos the fine-tuning argument. It’s a bit much to attribute it to me, though I am flattered that you might think so :-) It’s an argument that’s actually been around a very long time, but really only gained its current status when Fred Hoyle did his work on nucleosynthesis in stars. I suspect that something akin to fine-tuning was in Einstein’s mind (for example), not just Paul Davies’. Yes, the probability that the universe has the properties it has is exactly one. But that’s IFF there are no mysterious other universes. I have an aversion to the concept of “other universes” when the universe is by definition “all that there is”. Invoking more than one “all that there is” would seem to violate simpliciter.

    I have never come across any explanation of what might be counted as evidence for God. Hume’s On Miracles effectively dispatches most of the arguments believers believe are valid and true. Conversely, I have never come across any explanation of what might constitute evidence against God’s existence. The argument you present: “Who designed the designer? If you postulate a designer that needed no designer, then surely it is far simpler to not bother, and postulate a Universe that needed no designer.” is the closest we can get. But it’s argument to the best explanation for an atheist. The believers say, as did Aquinas and Aristotle, there is an uncreated creator and for them that is an argument to best explanation. IOW ABE arguments heavily depend on what one’s presuppositions are.

    I find it far easier to state, as did Thomas Huxley: “I am agnostic.”

  174. It would seem Gregory Chaitin has recently written a book: Proving Darwin: Making Biology Mathematical and I have downloaded it to my Kindle. However, the sun is shining in a clear sky for the fist time in many weeks and farms do not take care of themselves so it isn’t going to be read by me today.

    http://books.google.com.au/books?hl=en&lr=&id=J8XG8Y5Ou5QC&oi=fnd&pg=PR7&dq=Proving+Darwin:+Making+Biology+Mathematical&ots=9NuHNx_Fl2&sig=SzF-NGUahndpPxZIUuk7jEKCflM#v=onepage&q=Proving%20Darwin%3A%20Making%20Biology%20Mathematical&f=false

  175. @ Diego Diaz

    There are many different kinds of people who post here. If you stick around long enough you might learn something. I constantly do so. And if you mistook me for Janice… well, what can an overweight 62 year old male say :-)

    Hint: there are likely some cultural differences at play here. My “God done it” statement above is not good English grammar. It is in fact a probably far too well veiled reference to a Monty Python sketch in which God says in a very prissy voice: “He done it!” about a character who was murdering archbishops or some such. Silly I know, but I then am renowned for silliness…

  176. I know you are not she nor ignorant prejudiced fundamentalist with no interest in truth like her or Genesis speaks of plasma and ions man but still this not a good site for me but thank you for saying “stick around”. I am Catholic but not crazy fundamentalist. My work is to help indigenous people and the nature of the Amazon, my home.

    So goodbye to you too sir as to Dr RGB.

  177. One other thing. I do not know the new maths book you have but there is much computer evolution already showing it works and even using evolutionary algorithms to make new software. Random more or less evolution is fact that can be demonstrated with maths.

  178. @ Diego Diaz

    You are (I imagine) referring to programs like Thomas S. Ray’s Tierra. While this emulates certain aspects of evolution, it does not generate novelty. This is the aspect of evolution that has me most fascinated and frankly, being so seems to get me into hot water every now and then. So it goes… I have always been keenly interested in the hard questions.

    Good luck with your work and your rainforest. It sounds like a fascinating place to work. The Git lives adjacent to a rainforest in a much cooler part of the world: Southern Tasmania. Our indigines are supposedly extinct which makes them justifiably angry. However, it’s probably better to be angry than extinct ;-)

  179. I am back again. Tierra I have not used. It is old and lacks.

    My work area is not rain forest. It is pampas, llanos and savannas of Beni, Bolivia from where come such crops as cassava, cotton, peanut, sweet potato, tobacco, vanilla, etc.

    Thanks for wishes.

  180. @ Diego Diaz

    I have long believed that the conundrum I face with the evolution of novelty in biology would eventually be solved computationally. Gregory Chaitin seems to believe the same, but estimates that it’s going to take a long time to achieve. IOW The Git will be dead when it happens. The problem with Tierra and its ilk is that information comes from outside. Dawkins’ example of evolution from a random string to “METHINKS IT IS LIKE A WEAZEL” presupposes the existence of the final string: “METHINKS IT IS LIKE A WEAZEL”. Also, IIRC, Dawkins acknowledged this and says something like “but evolution is very similar” or some such. This is arm waving to say the least.

    One question I remember asking all these many years ago was “Why would ‘junk DNA’ persist under natural selection pressure?” A few years ago I heard a geneticist on the radio saying how remarkably well conserved it was (more so than expressed DNA) and that it had been renamed ‘silent’ rather than ‘junk’. It is my belief, and this is not original with me, that the silent DNA is akin to a computer operating system and that the various organisms inhabiting Earth are running different software on essentially the same operating system. However, it’s vastly different to anything like what we currently run on our computers in that it automagically generates new stuff within an apparently closed system. There is no way that I can conceive of MS Word evolving into MS Excel gradually while retaining usefulness.

    Chaitin tips his hat to at least two panspermia (new information comes from outside) advocates: Fred Hoyle and Francis Crick. And that’s enough for him to be condemned by several biologists I have come across, but that’s life so to speak. He also notes how indebted he is to John von Neumann, Alan Turing and Kurt Gödel, three other thinkers who had a major impact on my thinking. And now I return to finishing his rather short book.

  181. milodonharlani said @ November 15, 2013 at 9:19 pm

    Dawkins talks with human genome entrepreneur Venter on HGT:

    http://www.edge.org/documents/dawkins_venter_index.html

    As it happens, Doctor Who had promised to take me to that event in August 2008 and return me to October 2005 which was when I wrote my piece. However, he has so far failed to turn up and fulfill that promise. It seems likely that he has been delayed (if that is the correct word in this context) in another part of the multiverse and will eventually do so and history might very well become instantaneously rewritten.

  182. rgbatduke said @ November 15, 2013 at 2:20 pm

    So far, he has said little that I would fundamentally disagree with except create a list of evolutionary theories that I think is a bit too narrow and give perhaps a bit too little weight to the ongoing work of evolutionary biologists.

    One of the problems I was having in the mid 2000s was being tasked for giving too much weight to current/recent work and that I should merely accept the older, simpler prescriptions of the modern synthesis (dare I say consensus). So it goes…

    You also write:

    if he did bring up one of the neo-teleological arguments, well, even I think that the observations are “interesting” at the same time that I recognize (and pointed out) that they cannot constitute statistical/empirical “evidence”.

    The ID argument as exemplified by Paley et alia is most decidedly based upon empirical evidence; it’s certainly not a priori. We just do not find it compelling or sufficient within the context that it is presented. For example, the creationists present the evidence of cnidarians (jellyfish) with well developed lenses, but no brain or retina to process the information from the gathered light. The creationist says: “God done it; The Git says: “The genes for lens formation did not arise in the jellyfish, they appear to have been transferred horizontally from some other organism; Dawkins said: “Retinas and brains precede lenses” (paraphrase from Climbing Mount Improbable). This latter is about as far from empirical as you can get.

    It is interesting though that these design arguments do not go away. “One possibility is that they really are better arguments than most philosophical critics (including The Git) concede. Another possibility is that design intuitions do not rest upon inferences at all.” But that then becomes another argument that I am loath to pursue.

    Thanks for your supportive comments Robert.

  183. rgbatduke says:
    November 15, 2013 at 1:35 pm

    A school of thought in canine evolution is that dogs originally domesticated themselves. It is hypothesized that outcast wolves scavenged the scraps & excrement left behind at human camps. These hang-around-the-camp wolves started following the people & became accepted by them not as threats but alarm systems against predators in the night. Later selective breeding occurred as people adopted the most tractable puppies. Later still, when the human diet came to include more grains, dogs evolved the ability to digest starches better than their wild ancestors, reliant primarily on meat.

    In experiments with foxes, domestication also produces up-turned tails & big floppy ears. Dogs retain adolescent wolf traits into adulthood, like barking. They are in this sense retarded-development wolves. As you note, they’re still the same species, but a distinct subspecies. For that matter, dogs interbreed with coyotes & produce fertile offspring (however there are some behavioral barriers to frequent mating). Although wolves appear to have arisen in NE Asia rather than North America, one hypothesis of their origin is that highly social wolves evolved from largely solitary coyotes, in order better to hunt bigger game of the Pleistocene. Genetics tend to support the hypothesis, so either coyote ancestors once ranged into Asia or fossil or molecular (rocks & clocks) evidence of earlier wolves hasn’t been found.

  184. The Pompous Git says:
    November 16, 2013 at 2:27 am

    That was just one of many hits I found in doing the suggested search. I realize that you wouldn’t necessarily keep up on developments in evolutionary biology after taking a course in the philosophy of biology, but as you’re interested enough in it to comment on it here, maybe so. However in a fast-moving discipline like evolutionary biology, 2005 was long, long ago, if not also far, far away. The Human Genome Project wasn’t even completed until 2003. And who knows how long your teacher had been giving the same philosophy lecture?

    As I said, I’ve not read Dawkins, 1976, but Kurland thinks he addresses in that book the issue of gene transfer, if not in depth:

    http://lup.lub.lu.se/luur/download?func=downloadFile&recordOId=146787&fileOId=625105

    http://www.embl.de/aboutus/science_society/conferences/conference_2000/participants/kurland/

    Dawkins was certainly aware of the latest developments in HGT, since recombinant DNA was a hot topic in the ’70s, especially at my then-university Stanford, where the 1947 discoverer of HGT, Lederberg worked. Recombinant DNA was first proposed by Lobban, graduate student of Kaiser in the Biochemistry Dept. at Stanford Med School. The first publications describing successful production & intracellular replication of recombinant DNA appeared in ’72 & ’73. Stanford applied for a US patent on recombinant DNA in 1974, listing the inventors as Cohen & Boyer.

    I have to agree that Dawkins should have discussed HGT in more detail than he apparently did. I never attended his lectures at Oxford while he was writing that book, but recall when his thesis adviser Tinbergen got the Nobel in 1973. Kurland above mentions Dawkin’s path-finder Hamilton, the adviser of Judson, whom you think has it all wrong on genes.

    The generation of novelty isn’t an issue in biology. It’s observable in the lab as well as in the field. It arises either by adaptation of an existing structure or process or by the sudden or gradual development of new structures or functions. It’s a commonplace both in the fossil record & the genome. Examples fill books. No intelligent guidance required. In fact, as I noted, an intelligent designer would rarely do it the way that nature has been forced to do.

  185. milodonharlani said @ November 16, 2013 at 10:25 am

    2005 was long, long ago, if not also far, far away. The Human Genome Project wasn’t even completed until 2003. And who knows how long your teacher had been giving the same philosophy lecture?

    [TIC]No, 650 Mya was long ago[/TIC] Our philosophy lecturer, as I have said before, knew nothing to speak of about biology prior to the commencement of the course. His first degree was in physics where he had worked on multi-value logics in quantum physics and his second degree was in philosophy. I cannot remember what his doctorate was in. What I do know is he was much younger than I and extraordinarily bright and an excellent pedagogue.

    The biology grad students in the class provided a lot of input on biology minutiae as needed, but the philosophy of biology is about broader issues, such as “what do we mean by species?” and I note you did not fundamentally disagree with our text’s conclusion that there are a flock of them.

    Another issue was the concept of memes, with Richard initially believing that they were a useful concept, though far less so when confronted by cogent argument from the class participants. This is in the nature of philosophy. Different positions on an issue are supported by argument (logic being prominent) and it’s the argument that is evaluated. That is, to take an extreme example, the proposition that God intervenes in his creation might be true, but nevertheless be deprecated on the grounds of lack of evidence (true propositions), or valid arguments (deduction or other inference). As I have said, interminably it seems to me, no-one has ever yet to my knowledge ever stated what might be considered grounds for belief in God. Certainly not the Discovery Institute, I have said that Richard Swinburne has demonstrated that God;s existence is more likely than not, but that is no more proof of God’s existence than the output of AOGCMs are proof of CAGW and is really only a coda to Aquinas’ Summa written over 700 ya.

    As it happens, the issue of novelty arising in evolution was not a topic in that philosophy class, or at least not important enough to receive any attention that I recall. That was a separate research project of mine and very much predated the class. Much juicier for philosophy is the issue of denial of teleology in biology, despite abundant use of teleological language in the discipline and how might biologists rid themselves of its use. Up until 2005, or thereabouts, every instance I was given of observed novelty arising either was not what I meant (think Galapagos finches, dogs and herring gulls), or it appeared to be the result of a pre-existing gene sequence transferred into the organism. You may fault me for not finding what I sought, but I refuse to take the blame for the impoverished, unsupportive examples given me when I requested them from people at the coalface so-to-speak. If they could not point me in the right direction, who would you suggest?

    Note that I did try very hard at the time and I am not at all accusing those I sought assistance from as acting in bad faith, or lacking sufficient erudition. It was as if they were blind to the issue of the difference between observation and inference. That in itself was an important learning in two regards. If someone is blind to something, no amount of request/badgering/pleading is ever going to result in generating a meaningful response. If the person you interrogate is blind to something, then what of oneself? Am I too blind to certain things? Perhaps something akin to this blindness prevented me from accepting the existence of God on faith and still does.

    Very early on in this private research I came across Tierra (and some other I cannot recall) and thought that this looked like a promising direction for research into how novelty might arise. I had decided very early on during my foray into evolutionary biology that this was probably a more rational approach than trying to decipher actual genetic code. The concept was supported by Dawkins’ approach in <The Blind Watchmaker, but disappointingly so. Dawkins, an apparently intelligent agent, was doing the selection. It was no further an advance than Darwin’s initial argument from artificial selection to natural selection by inference to the best explanation. My investigation of Tierra also disappointed.

    As a generalist/polymath/jack-of-all-trades [delete whichever is inapplicable] and having more avenues of learning to pursue before I die than I have time for, I decided to pursue some of those. Six years may be a long time at your age, but at mine it seems terribly short. I had also been offered part-time employment that would carry me through to retirement (I thought) and allow me to pursue my other interests. I make the observation that Chaitin’s proposed research project looks very interesting indeed, though I will (sadly), not be around to see it’s fruits.

    I end this with an amusing (to Pompous Gits) observation. Einstein is widely believed to have believed in God, mainly because he said he did. Dawkins disagrees and in his book The God Delusion declares him to have been an atheist. Conversely, Sir Fred Hoyle is widely declared to have been a believer in God and I have been told by a number of correspondents that he was a creationist. I possess several of Fred’s books wherein he asserts that he is an atheist. From this I draw the conclusion that no matter what one says, there are always those who will interpret your words to mean what they demand you ought to have said or written. It’s an interesting world to live in…

  186. Your Most Exalted Gitness:

    I’ll be 63 next month, if that matters.

    If your philosophy of biology course were taught by the physicist Dr. RGB of Duke, I’d say it was liable to be a highly worthwhile course. For a generic physicist, not so much.

    Hoyle was an atheist, no doubt about it, & never wavered, despite the disturbing to him implications of his study of life outside his area of expertise. Like many mathematicians & physicists who slide into ID territory, however, he erred in treating the emergence & evolution of life as strictly mathematical, probabilistic phenomena. One of the foremost such questioners in the 1970s was honest enough publicly to change his mind when he learned more about how the genetic code really works. When you actually look at the biochemistry involved, especially in light of advances in molecular biology & physical & organic chemistry of recent decades, both abiogenesis & evolution appear less & less against the odds & more & more inevitable, given the rules of our universe. Hoyle has been somewhat discredited for his opposition to the Big Band Theory, but IMO is still a thinker worth reading. Panspermia, his solution for the largely non-existent problems he saw, remains a defensible hypothesis. The latest discoveries of organic chemistry in the cosmos don’t necessarily support it, but don’t render it less likely either.

    Einstein was always coy about his theological beliefs. He may never have worked them out systematically to his own satisfaction. He definitely did not believe in a personal God guiding events on earth, let alone in individual human lives, counting the fall of sparrows & hairs on heads. Both he & Hoyle have been hijacked by creationists who twist their words, just as they lie about biology in general & Darwin in particular. They are shameless, paid liars.

    The proper study of novelty in evolution is biology, not a prior philosophy. The history of life on earth is the story of naturally accumulating innovations. We have only just started to be able to read the history book, but everything more science learns only reinforces the basic lesson already apprehended, ie that new “genes”, structures & processes arise naturally from preexisting building blocks.

    I know your time is limited, but here are some recent papers or summaries of present understanding dealing with novelty on both the genetic & organismal levels. Examples could be multiplied in both camps & all fields in between.

    A good survey of current knowledge of how variation & novelties accrue at the genetic level. It’s very good, IMO:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945180/

    An important example of how innovation rapidly increased in unicellular life in response to the greatest catastrophe & opportunity for “advancement” in the history of life on earth, ie the monumental Precambrian oxygenation event:

    http://www.ncbi.nlm.nih.gov/pubmed/21170026

    Moving far forward in time, how evolution adapted a preexisting structure to a novel use, ie the gill arch into the gnathostome jaw:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1571356/

    How, after some 300 million years of further evolution, the descendent of that first jaw evolved into a novel structure, the mammalian middle ear:

    http://www.ncbi.nlm.nih.gov/pubmed/21170026

    Which, interestingly, happened twice in mammalian evolution, both in monotremes & in the common ancestors of marsupials & placentals. That is, two different groups of proto-mammals who had both the “reptilian” jaw joint (which was increasingly used to augment hearing) & the mammalian joint at different times went the whole hog & moved the now little bones at the back of the jaw into the skull, mating them with the inner ear structure:

    http://evolution.berkeley.edu/evolibrary/article/evograms_05

    BTW, the otherwise nice graphic is marred by using the term “eutherian”, which included placentals but excludes marsupials. That’s a mistake. Our middle ear emerged in a common ancestor of both your continent’s wonderful pouched creatures & us placentals.

  187. @ milodonharlani

    Your most esteemed milodonharlaniness doesn’t quite roll off the tongue, so I’ll likely not use it again ;-)

    You should be aware that Richard’s class was at a fairly high undergraduate level being both a second year and third year class and marked according to which year one was in. The biology students were graduate students. Presumably they were either required to undertake further undergrad classes, or were there because of special interest. Given their enthusiasm for the topics, I’d plump for the latter.

    As for Richard, he may have been a little short of understanding key concepts in biology in the early stages of the course, but he seemed well up to speed by the end. As I wrote earlier, he is very bright. Note that we were discussing (and Richard’s lectures were closer to tutorials than classical lectures) keyconcepts, not minutiae. Philosophers of biology such as Sober, Ruse, Sterelny (who resembles me, not me him), Griffiths, et alia do not get bogged down in biological minutiae; they are usually far too busy getting bogged down in philosophical minutiae! But enough…

    Waaaay back then and a correction, seven years, not six, I came across Richard Lenski’s long-term e. coli experiment. Now according to my nemesis (and Gould) I should have expected Lenski to find divergence between his bacterial lines. When I reported my finding to my nemesis he wrote that convergence was exactly what would be expected. Now how something can be simultaneously divergent and convergent is beyond all except… post-modernist philosophers such as Derida and Foucault. I don’t believe I’ve mentioned yet that I am as far from being an admirer of their ilk as it is possible to be. And unlike those philosophy courses that people take “because you can’t fail” well, those who thought that and took any of Richard’s had a most unpleasant surprise. As that physicist turned philosopher Phil Dowe told first year students: “If your brain isn’t hurting, you are not doing philosophy!”

    Anyway, back to the farce. I revisited Lenski and his team’s work today and came across this juicy quote: “Natural selection is critical for the process of adaptation, yet its role in producing key innovations is less clear because, by fixing variants that improve existing functions, selection might strand populations on local adaptive peaks and thereby prevent them from discovering new functions.”

    http://www.sciencemag.org/content/335/6067/428.abstract

    I suspect we are at the stage of talking past each other. If I took you entirely at face value, then I would have to declare Chaitin’s proposal as p!ssing in the wind. I don’t think he is and I do believe that putting (naturalistic) evolutionary explanation on a genuinely secure footing is a very long-term project. I also note that if life is not irreducibly complex, then it will terminate in an ultimate organism/ecology and proceed no further. Sort of a biological version of Hawking’s belief in a “mind of God” equation. My intuition is that it is irreducibly complex and therefore must continue to evolve even unto the heat death of the universe. YMMV.

  188. Really crazy thought #64,348

    Suppose that this static organism that can no longer evolve (discover new things) at the end of a John Wheeler universe (serial big bangs and crunches) always says: we’ll design the next one to really be irreducibly complex! :-))))

  189. @ milodonharlani

    I just visited the Amazon page to read reviewers’ comments of Sterelny & Griffiths’ Sex and Death (there weren’t too many (any?) the previous time I looked). They are interesting and deal with the problems the evolutionary biology tackled in that the class I took all those many long years ago.

    I also just remembered you calling attention to my misunderstanding randomness in biology (entirely possible). Nevertheless, extensive discussion of randomness occurred in the cosmology class (same teacher and slightly more than the two dozen in the phil. biol. class). Despite the conceptual difficulties encountered by those unfamiliar with, for example, quantum physics, The Git was assessed as having an excellent understanding of underlying concepts. Perhaps physicists do have an entirely separate understanding of randomness than biologists… So it goes…

  190. @ milodonharlani

    I must admit to being utterly perplexed. You referred me to Henrik Kaessmann’s Origins, evolution, and phenotypic impact of new genes. On page two, I read

    At least since a famous monograph, authored by Susumu Ohno, was published over 40 yr ago (Ohno 1970), the word has spread that gene duplication may underlie the origin of many or even most novel genes and hence represents an important process for functional innovation during evolution. Essentially and consistent with earlier ideas (Haldane 1933; Muller 1935), Ohno emphasized that the presence of a second copy of a gene would open up unique new opportunities in evolution by allowing one of the two duplicate gene copies to evolve new functional properties, whereas the other copy is preserved to take care of the ancestral (usually important) function (the concept of neofunctionalization). Ohno also reviewed that duplicate genes can be preserved by natural selection for gene dosage, thus allowing an increased production of the ancestral gene product (Ohno 1970). Finally, it should be emphasized that it has been widely agreed for a long time that the most probable fate of a duplicate gene copy is pseudogenization (Ohno 1972) and that hence the majority of duplicate gene copies are eventually lost from the genome.

    and

    More generally, the convergent RNASE1 duplications are in line with several other recent reports that include other cases of new gene formation (see below) and therefore lend further support to the more general idea that adaptive genome evolution is, to some extent, predictable (Stern and Orgogozo 2009). Numerous other classical or recent examples from diverse organisms could be discussed here that illustrate the immense potential that DNA-based gene duplication has held for phenotypic evolution in different organisms (for reviews, see Li 1997; Long et al. 2003; Zhang 2003; Lynch 2007; Conant and Wolfe 2008).

    Yet you wrote: ““Ohno was wrong about that. He didn’t know then what we know now, & was already shown wrong even before we found out as much as we have about genomics.” The second quote above seems to echo what I have been saying; changes in the duplicated gene are not random. Indeed, something cannot be simultaneously predictable and random. What, precisely, makes Kaessmann correct, and The Git wrong when they are saying substantially the same thing?

  191. The Pompous Git says:
    November 16, 2013 at 11:20 pm

    Natural selection doesn’t ordinarily create innovation at the genetic level. It acts upon it. It could be said to create novelty at the organismic level, as in changing a gill arch into a jaw bone or jaw bones into ear bones. I don’t know why this would even be considered an issue.

    The processes that create novelty at the genetic level are those mentioned in my link on that, such as gene duplication (or multiplication), gene transfer & various kinds of mutation (which while more or less random result from natural processes operating all the time at more or less predictable rates in various environments or the whole planet).

  192. The Pompous Git says:
    November 17, 2013 at 9:00 am

    I’ll try again on randomness.

    That this or that base pair in a genome might be hit by a passing cosmic ray is more or less random. Yet the rate at which mutations by cosmic rays will occur is not random, but predictable based upon cosmic ray flux.

    The same applies to many if not most other mutagenic agents.

    The “accident rate” in transcription errors is also a statistical phenomenon. Its rate can vary based upon a number of parameters, but that such “random” mistakes will happen is predictable.

    Random “accidents” in biology result in predictable mutation rates. That such accidents will happen is a certainty, although of course there are other sources of genetic variation besides mutations. Organisms also effectively have some degree of control over their mutation rates because environmental stresses or changes subjecting a population to selective pressure can & do increase the accident rate. Conversely, a steady selective pressure in an unchanging environment can lead to maintaining a population’s genome more stable from generation to generation. That’s how you get “living fossils”, like the one-lunged Queensland lungfish, with the largest known vertebrate genome.

    I hope this helps.

  193. @ milodonharlani

    Since according to you Ohno was wrong about neofunctionalization and the document you referred me to says the opposite I do not believe it’s worth continuing with the conversation your majesty. Philosophers are averse to contradiction.

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