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?
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.
=================================================================
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.
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.
milodonharlani says:
November 13, 2013 at 8:38 am
Thanks. It is interesting that you find that the “splitters” have created their own problems.
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.
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
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.
Blog!
@ur momisugly 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:
And from Trends in Genetics a piece about corals and sea anemones:
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.
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.
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.
@ur momisugly 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”.
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.
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 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!
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.
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.
@ur momisugly milodonharlani
Try arguing that with Chaitin. Good luck!
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.
@ur momisugly milodonharlani
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.
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.
@ur momisugly 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…
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.
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.
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
@ur momisugly 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:
Robert, I must take you to task for the following statement:
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.
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.
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.
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.