NASA finds proof that amino acid components in meteorites originate in space.
This is exciting news. NASA-funded researchers have evidence that some building blocks of DNA, the molecule that carries the genetic instructions for life, found in meteorites were likely created in space. The research gives support to the theory that a “kit” of ready-made parts created in space and delivered to Earth by meteorite and comet impacts assisted the origin of life. We may all be immigrants on Earth.
By Bill Steigerwald
NASA’s Goddard Space Flight Center, Greenbelt, Md.
NASA-funded researchers have evidence that some building blocks of DNA, the molecule that carries the genetic instructions for life, found in meteorites were likely created in space. The research gives support to the theory that a “kit” of ready-made parts created in space and delivered to Earth by meteorite and comet impacts assisted the origin of life.
“People have been discovering components of DNA in meteorites since the 1960’s, but researchers were unsure whether they were really created in space or if instead they came from contamination by terrestrial life,” said Dr. Michael Callahan of NASA’s Goddard Space Flight Center, Greenbelt, Md. “For the first time, we have three lines of evidence that together give us confidence these DNA building blocks actually were created in space.” Callahan is lead author of a paper on the discovery appearing in Proceedings of the National Academy of Sciences of the United States of America.
The discovery adds to a growing body of evidence that the chemistry inside asteroids and comets is capable of making building blocks of essential biological molecules.
For example, previously, these scientists at the Goddard Astrobiology Analytical Laboratory have found amino acids in samples of comet Wild 2 from NASA’s Stardust mission, and in various carbon-rich meteorites. Amino acids are used to make proteins, the workhorse molecules of life, used in everything from structures like hair to enzymes, the catalysts that speed up or regulate chemical reactions.
In the new work, the Goddard team ground up samples of twelve carbon-rich meteorites, nine of which were recovered from Antarctica. They extracted each sample with a solution of formic acid and ran them through a liquid chromatograph, an instrument that separates a mixture of compounds. They further analyzed the samples with a mass spectrometer, which helps determine the chemical structure of compounds.
The team found adenine and guanine, which are components of DNA called nucleobases, as well as hypoxanthine and xanthine. DNA resembles a spiral ladder; adenine and guanine connect with two other nucleobases to form the rungs of the ladder. They are part of the code that tells the cellular machinery which proteins to make. Hypoxanthine and xanthine are not found in DNA, but are used in other biological processes.
Also, in two of the meteorites, the team discovered for the first time trace amounts of three molecules related to nucleobases: purine, 2,6-diaminopurine, and 6,8-diaminopurine; the latter two almost never used in biology. These compounds have the same core molecule as nucleobases but with a structure added or removed.
It’s these nucleobase-related molecules, called nucleobase analogs, which provide the first piece of evidence that the compounds in the meteorites came from space and not terrestrial contamination. “You would not expect to see these nucleobase analogs if contamination from terrestrial life was the source, because they’re not used in biology, aside from one report of 2,6-diaminopurine occurring in a virus (cyanophage S-2L),” said Callahan. “However, if asteroids are behaving like chemical ‘factories’ cranking out prebiotic material, you would expect them to produce many variants of nucleobases, not just the biological ones, due to the wide variety of ingredients and conditions in each asteroid.”
The second piece of evidence involved research to further rule out the possibility of terrestrial contamination as a source of these molecules. The team also analyzed an eight-kilogram (17.64-pound) sample of ice from Antarctica, where most of the meteorites in the study were found, with the same methods used on the meteorites. The amounts of the two nucleobases, plus hypoxanthine and xanthine, found in the ice were much lower — parts per trillion — than in the meteorites, where they were generally present at several parts per billion. More significantly, none of the nucleobase analogs were detected in the ice sample. One of the meteorites with nucleobase analog molecules fell in Australia, and the team also analyzed a soil sample collected near the fall site. As with the ice sample, the soil sample had none of the nucleobase analog molecules present in the meteorite.
Thirdly, the team found these nucleobases — both the biological and non-biological ones — were produced in a completely non-biological reaction. “In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water. This provides a plausible mechanism for their synthesis in the asteroid parent bodies, and supports the notion that they are extraterrestrial,” says Callahan.
“In fact, there seems to be a ‘goldilocks’ class of meteorite, the so-called CM2 meteorites, where conditions are just right to make more of these molecules,” adds Callahan.
The team includes Callahan and Drs. Jennifer C. Stern, Daniel P. Glavin, and Jason P. Dworkin of NASA Goddard’s Astrobiology Analytical Laboratory; Ms. Karen E. Smith and Dr. Christopher H. House of Pennsylvania State University, University Park, Pa.; Dr. H. James Cleaves II of the Carnegie Institution of Washington, Washington, DC; and Dr. Josef Ruzicka of Thermo Fisher Scientific, Somerset, N.J. The research was funded by the NASA Astrobiology Institute, the Goddard Center for Astrobiology, the NASA Astrobiology: Exobiology and Evolutionary Biology Program, and the NASA Postdoctoral Program.
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Dave Springer
Give me some examples of those “simpler forms” that often happen. I don’t know if you just made that up or are parroting someone who did.
Axolotls for example, amphibia who basically remain tadpoles all their lives. They must have evolved from some species who went through the usual amphibian metamorphosis from tadpole to grown individual, but somehow lost it on the way.
Any number of animals who live in caves or in the deap sea without light, who are blind with dysfunctional eyes, apparently evolved from creatures with functioning eyes.
Non-flying birds who must have evolved from flying birds, with now useless wings (ostriches, kiwis, but not penguins). Likewhise many insect species who lost their wings, the stubs still being discernible.
There are no examples of phyletic migration to much simpler forms.
I didn’t constrain my claim to entire phylums, so I don’t need to defend it. However I could mention viruses. The evolution of viruses is still under debate, but several theories assume they evolved from cellular organisms.
Eukaryotes don’t go backwards into prokaryotes. Multi-cellular forms don’t revert to single celled forms. Mammals don’t devolve into reptiles. Reptiles don’t devolve into fish.
That of course is not the claim. Evolution to simpler forms does not mean the exact ancestral forms reemerge. The likelihood of that happening are minuscule. It just means that organisms loses abilities their ancestors had, that organs become dysfunctional or degenerate, etc. Of course the new organisms will still be different from anything that existed before.
Ron Cram says:
Did any of you bother to read the paper I liked to “Darwinian evolution in the light of genomics?”
I had a glance just then. It’s a bit long and lacks a synopsis :). Also I know almost nothing about genetics (of which genomics is a specialised field), so I will have trouble understanding it. It would help me if you could state your main point in your own words.
About genetics, in the introduction (which I read) the paper rightly states that the understanding of evolution does not presuppose knowledge of the underlying microbiology. Evolution is a macroscopic process which we observe, regardless of our understanding of the genetic mechanisms. So I don’t see how a paper on genetics, whatever it might say, could refute evolution. Again, please reiterate in your own words.
In the meantime, I am willing to hear your thoughts on the other five evidences I have put forward.
This entire thread is getting more and more confusing. 🙂 What five evidences, in which of your posts (date, time)?
kuhnkat says:
August 13, 2011 at 7:10 pm
Yes, that’s pretty much it in a nutshell. If you have innate sense that love is preferable to hate, kindness preferable to cruelty, then the only question left is which of many religions which emphasize those things to choose for your wager. Christianity isn’t a bad choice provided you actually model your life after its founder who was man who wouldn’t harm a fly and whose most aggressive act in life that we know of was cursing a fig tree. Ghandi is another good example. Some branches of Buddhism are just as good. The bottom line remains that if whatever comes naturally to you is copacetic with some religion then you have little to lose and much to gain. A favorable risk/reward ratio is the essence of any good wager. Perhaps the chances of winning a lottery are slim but if the tickets are free then only a bonehead would refuse to hold one.
anorak2 says:
August 14, 2011 at 8:03 am
“Axolotls for example, amphibia who basically remain tadpoles all their lives. They must have evolved from some species who went through the usual amphibian metamorphosis from tadpole to grown individual, but somehow lost it on the way.”
must have evolved
That is a just-so story predicated on the logical fallacy of assuming that which is to be proven.
It also says nothing about whether the perpetual tadpole’s genotype is any less complex than the frog’s. It very likely isn’t and it’s just a change in gene expression rather than any actual step backward in complexity. I’ll give a counter-example. The domestic canine gets most of the attributes that makes it different from a wolf by arrested development. It retains many of the characteristics of puppies into adulthood. A Russian guy recently demonstrated this by domesticating foxes in a small number of generations by selecting those adults which exhibited kit-like trust of humans. Genotypically and phenotypically the dog and domesticated fox are no less complex than their wild cousins. Another example is cave fish which have underdeveloped eyes from many generations living in the dark. These fish rapidly regain their sight in the presence of light. These are simply examples of gene expression not a fundmental reduction in genotype complexity.
I realize you don’t have examples of real backwards evolution where a phylum regresses to a simpler phylum because there is absolutely no evidence that such a thing has ever happened. The radiation of life on this planet is a one-way street of increasing complexity. Your point about phylogenetic regression to some ancestral form is a straw man. I merely used those as examples of complexity. The only requirement is that the new phylogenic category be simpler than its progenitor.
FYI – viruses aren’t generally considered to be living things. They are not a kingdom of life and do not appear in any phylogenetic trees. They are simple machine-like constructions entirely dependent on more complex forms of life for their survival. In fact when someone asks how any “creator” might have guided the process of evolution I point out what a wonderful tool the retrovirus particle is for inserting or modifying a selected genetic payload into entire populations in a short space of time. Indeed, we use them for that ourselves in a purposeful manner.
@Dave Springer
Thanks for the genetics lesson, though I didn’t really need it. I have a Master’s in bioinformatics, which involves a lot of genertics, so I know all about MtDNA and the difference between mitosis and meiosis. I was trying to keep it simple for the sake of lay readers. Yes, of course, it is the whole organism that survives or not, but selection acts on individual mutations – itf the mutation is beneficial it spreads through the population, if not it doesn’t. Unless it is linked (i.e. is at a similar locus) to another mutation, in which case even a detrimental mutation might spread. And lots of other scenarios besides, but the main point is that individual beneficial mutations tend to spread across a population. Yes, I know all that stuff and a whole lot more. But thanks anyway.
And to answer Ron’s other 5 “evidences”:
“First, I would say it is rational to believe in the existence of God because the universe had a beginning at the Big Bang.”
Nonsense. Big bang theory simply describes that the universe expanded from being very hot and very dense. That is all!
“Second, it is rational to believe in God because life does not come from non-life. ”
Nonsense. That we have yet to produce life in the laboratory does not mean we never will. Everything we know about life, which is a lot, suggests it is nothing more than complex reproducing chemicals. Now consciousness is another story…
“Third, it is reasonable to believe in God because of Botany. ”
We covered that one.
“Fourth, it is reasonable to believe in God because of Genomics. See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/pdf/gkp089.pdf … ”
Nonsense. Of course we are post-Darwin, he died over a hundred years ago. Science progresses. The author is saying that horizontal transfer and neutral mutation may be more important that we previously thought. So what?
Fifth, it is reasonable to believe in God because he has acted in human history. The most telling and powerful action is the resurrection of Jesus Christ. It is the most well-attested event in ancient history.
OK, now you are talking specifically about Jesus, but anyway… Rubbish! There is not a single written account of the life of Jesus until around 40 years of his supposed death. The bible can’t even get it’s geography right. And the earliest non-biblical reports talk about Christians, not Christ. But even if the bible stories were based on a real person, so what?
“Sixth, it is reasonable to believe in God because I have a personal relationship with him. ”
My children had a personal relationship with Santa Claus, but they grew out of it.
Ron Cram says:
August 14, 2011 at 7:51 am
Dave Springer,
“I always enjoy reading your thoughts. I would also like to know what you think of the paper by Koonin. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/pdf/gkp089.pdf”
Horizontal gene transfer has been found to play a larger role than though in more complex organisms. I don’t find this surprising. Horizontal gene transfer is a way of life for bacteria. I’m not in the habit of denying capabilities that simpler organisms have to their offspring. Viruses routinely snag pieces of DNA from one organism and insert it into others. Our genomes are littered with the inactivated remnants of viral invaders. In fact commonality of retrovirus remnants by location and sequence is one of the most compelling bits of evidence in evolution of primates – i.e. that humans and apes once shared a common ancestor. We both have retrovirus remnants in exactly the same locations. Explanations for this other than the common ancestor infected with a retrovirus in a germ cell then passing that unique marker down to its progeny appear highly contrived to me.
Lynn Margulis is a prominent name in this area famous for formulation of endosymbiosis which places horizontal gene transfer as the principle mechanism underlying the radiation and diversification of life.
What I find even more interesting is what’s known as the global gene pool. This is the set of all unique genes from every living thing. Craig Venter recently circumnavigated the globe (a few times) collecting microbes from all the oceans at various depths and sequencing them aboard the ship as it travelled. He catalogued millions of new genes and is using that as a component library for construction of synthetic life forms.
What I wonder is that if you compared the global genome of a couple billion years ago when there was nothing but microbial life on the planet, before the evolution of multi-cellular forms emerged, would you get a global genome that was any smaller or larger than what you’d get today? The dogma is that you would get a smaller catalog but that’s just one more of the great many just-so stories that are found in the Darwinian narrative. It’s ruled out by nothing more than a priori rejection of the possibility that phylogeny was a predetermined process. That would require a plan and random evolution doesn’t make plans. Evolutionary dogma is a narrative where the forces directing is reactive-only. Evolution in that context can’t guess about what might be useful in the future. It’s a trial & error process where failures are erased from memory and successes preserved. In no case can it plan for the future it can only react to the present.
I recommend reading the following collection of papers I assembled in 2006 by one of the more vocal (and qualified, Emeritus Professor of Biology, University of Vermont, 50 years experience in comparative physiology) who proposes a hypothetical prescribed evolution:
http://www.uncommondescent.com/intelligent-design/collected-evolutionary-papers-of-john-a-davison/
He’s a cantankerous old coot but he knows an awful lot about experimental biology.
John B says:
August 14, 2011 at 8:55 am
“I was trying to keep it simple for the sake of lay readers.”
It wasn’t simple, it was WRONG. Individuals in obligatory sexual reproducers DO NOT inherit the entire genome of both parents. Man up and admit it was a mistake.
“Yes, of course, it is the whole organism that survives or not, but selection acts on individual mutations – if the mutation is beneficial it spreads through the population, if not it doesn’t.”
No John. That is patently false. It only spreads if it confers a differential reproductive benefit to the organism as a whole. Keep in mind such mutations occur by definition in a single individual and the process of fixation is a long one and requires more than a small amount of luck, especially in the early days, that some unconnected random evironmental insult like a flood, fire, drought, and so forth won’t wipe out the sub-population where it arose before it can become fixed.
Moreover there are few actual examples of progressive evolution by random mutation in obligatory sexual reproducers with large genomes and phenotypic plasticity. It’s recombination and up expression or down experession of pre-existing genes that causes changes in populations. You probably heard it called allele frequency. Random mutations where creating unique alleles, where we know about them, are almost always examples of trench warfare. Take the sickle cell mutation which is fixed in certain sub-populations of humans. It would quickly disappear if it wasn’t for a slight advantage in conferring some resistance to malaria parasites. Interestingly uncounted trillions of trillions of malaria parasites with extremely rapid response to selection pressure haven’t managed to mutate any ability to deal with the sickle cell mutation. This is trench warfare where the winner is determined by which can tolerate the greatest amount of injury.
The take home lesson from that is that the gene pool of any one species is very highly optimized as a whole and random mutations that create new improved alleles are exceedingly rare and the net benefit to an organism with regard to differential reproduction is so tiny that fixation is the result of a crap shoot where that original mutation in a single organism just happened to be one of the lucky ones whose genes spread for a whole host of reasons, some due to better luck in recombination with regard the environment and some due to better luck in not getting killed by some random external event. Fixation is a crap shoot with very little due to any discernable increase in survival value.
Insatiably curious, I read up a bit on these purported perpetual tadpoles used for an exceedingly weak example of devolution. It was weaker than I thought. My emphasis:
http://en.wikipedia.org/wiki/Axolotl#Axolotl.27s_neoteny
So they still retain the capability for metamorphisis. As I suspected it is supressed not absent and reemerges in individuals subjected to the right environmental pressures.
As for the other species without any known stimuli capable of causing metamorphisis there’s nothing at all that says their ancestors had the ability and they lost it. In any case they’re still salamanders. An immature salamander is still a salamander just as an acorn and an oak tree are no more or less genotypically complex than the other. It’s all a matter of gene expression not gene invention.
More on Axolotls… same source:
“The feature of the salamander that attracts most attention is its healing ability: the axolotl does not heal by scarring and is capable of the regeneration of entire lost appendages in a period of months, and, in certain cases, more vital structures. Some have indeed been found restoring the less vital parts of their brains. They can also readily accept transplants from other individuals, including eyes and parts of the brain—restoring these alien organs to full functionality. In some cases, axolotls have been known to repair a damaged limb as well as regenerating an additional one, ending up with an extra appendage that makes them attractive to pet owners as a novelty. In metamorphosed individuals, however, the ability to regenerate is greatly diminished.”
So upon metamorphosis they gain the ability to live on land but lose the ability to regenerate lost body parts. Seems to me like the ability to regenerate lost body parts can come in pretty handy for a salamander. I wouldn’t call that tradeoff either backward or forward with regard to complexity. It’s simply trading off one thing for another which may or may not be advantageous in any given circumstance.
I have to say this example is a FAIL with regard to it supporting the claim that evolution has no preference with regard to increasing or decreasing complexity. The claimant is going to have to do better. Much better.
Dave,
Yes, sexual organisms receive only half a genome from each parent. but since the full genome is paired up, they do receive a copy of each gene from each parent (X and Y chromosomes excepted). My point was that a reguloator from one parent can act on a gene inherited from the other. That’s all. I’ll admit what I wrote was misleading. On the inheritance of mutations, I said “if the mutation is beneficial it spreads through the population” and you said “It only spreads if it confers a differential reproductive benefit to the organism as a whole.” Same thing isn’t it? What else do you think I was referring to it being beneficial to?
I’m not sure what the point of the rest of your post was. Could you put it more succintly? I can’t work out if you are trying to make the case for intelligent design.
Tucci78 says:
August 10, 2011 at 11:50 am
“host Ben Stein asks Richard Dawkins, who is arguably the best-known living evolutionary biologist on the planet”
Has Dawkins actually published any papers in a peer reviewed journal in the field of evolutionary biology?
As far as I know he only writes books and never did a lick of original work in experimental biology, evolutionary or otherwise. All hat, no cattle, in other words.
So who ya gonna believe? Some pontificating Oxford windbag far more famous as the world’s most well known atheist, a man who never spent a day of his life outside undergraduate school in lab or doing field work or the greatest evolutionary biologists and paleontologists of the 20th century, men famous for their science not their religious convictions?
Gene Centric Evolution
Prominent opponents of this gene-centric view of evolution include evolutionary biologist Ernst Mayr, palaeontologist Stephen Jay Gould, biologist and anthropologist David Sloan Wilson and philosopher Elliott Sober.
Writing in the New York Review of Books, Gould has characterized the gene-centered perspective as confusing book-keeping with causality. Gould views selection as working on many levels, and has called attention to a hierarchical perspective of selection. Gould also called the claims of Selfish Gene “strict adaptationism”, “ultra-Darwinism”, and “Darwinian fundamentalism”, describing them as excessively “reductionist”. He saw the theory as leading to a simplistic “algorithmic” theory of evolution, or even to the re-introduction of a teleological principle.[17] Mayr went so far as to say “Dawkins’ basic theory of the gene being the object of evolution is totally non-Darwinian”.[18]
Gould also addressed the issue of selfish genes in his essay ‘Caring groups and selfish genes’.[19] Gould acknowledged that Dawkins was not imputing conscious action to genes, but simply using a shorthand metaphor commonly found in evolutionary writings. To Gould, the fatal flaw was that “no matter how much power Dawkins wishes to assign to genes, there is one thing that he cannot give them – direct visibility to natural selection”.[19] Rather, the unit of selection is the phenotype, not the genotype, because it is phenotypes which interact with the environment at the natural-selection interface. So, in Kim Sterelny’s summation of Gould’s view, “gene differences do not cause evolutionary changes in populations, they register those changes”.[20] Richard Dawkins replied to this criticism in a later book, The Extended Phenotype, that Gould confused particulate genetics with particulate embryology, stating that genes do “blend”, as far as their effects on developing phenotypes are concerned, but that they do not blend as they replicate and recombine down the generations.[10]
Since Gould’s death in 2002, Niles Eldredge has continued with counter-arguments to gene-centered natural selection.[21] Eldredge notes that in Dawkins’ book A Devil’s Chaplain, which was published just before Eldredge’s book, “Richard Dawkins comments on what he sees as the main difference between his position and that of the late Stephen Jay Gould. He concludes that it is his own vision that genes play a causal role in evolution”, while Gould (and Eldredge) “sees genes as passive recorders of what worked better than what”.[
@Dave Springer
Dawkins published plenty, but latterly moved on to become a scince communicator rather than a coalface scientist:
http://en.wikipedia.org/wiki/List_of_publications_by_Richard_Dawkins
@Dave Springer
I don’t understand why you’re getting so worked up about the axolotl thing. It seems you’re missing the point. I was explaining that evolution has no direction, it’s not towards “more complexity”. It has no purpose,it’s just what happens when natural processes do their thing. Therefore arguments which suppose it is directional or has a goal are moot. Hope that clears it up.
anorak2 says:
August 14, 2011 at 8:15 am
Ron Cram says:
Did any of you bother to read the paper I liked to “Darwinian evolution in the light of genomics?”
I had a glance just then. It’s a bit long and lacks a synopsis :). Also I know almost nothing about genetics (of which genomics is a specialised field), so I will have trouble understanding it. It would help me if you could state your main point in your own words.
Rather than put it into my own words and chance a mistake, let me quote a few selected passages I think are important to this discussion with a comment or two to explain how I interpret what he is saying:
From the abstract
Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An ade- quate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non- adaptive consequence of evolution under weak pur- ifying selection rather than an adaptation.
From pp 1011-1012
Now, 50 years after the consolidation of the Modern Synthesis, evolutionary biology undoubtedly faces a new major challenge and, at the same time, the prospect of a new conceptual breakthrough (15). If the Modern Synthesis can be succinctly described as Darwinism in the Light of Genetics (often referred to as neo-Darwinism), then, the new stage is Evolutionary Biology in the Light of Genomics.
He is saying neo-Darwinism is wrong and the current theory of evolution has to be modified.
Page 1013
The (nearly) neutral theory is a major departure from the Modern Synthesis selectionist paradigm as it explicitly posits that the majority of mutations fixed during evolution are not affected by Darwinian (positive) selection (Darwin seems to have presaged the neutralist paradigm by remarking that selectively neutral characters would serve best for classification purposes (1); however, he did not elaborate on this idea, and it has not become part of the Modern Synthesis).
Most mutations are not positive. The mutations which become fixed are usually nearly neutral (negative but not so negative the organism recognizes them as bad and eliminates them through purifying selection).
Page 1013-1014
In other words, from the organism’s standpoint, much of its genomic DNA should be consid- ered junk. This view of the genome dramatically differs from the picture implied by the selectionist paradigm under which most if not all nucleotides in the genome would be affected by (purifying or positive) selection acting at the level of the organism.
Page 1015
However, the advent of full-fledged genome sequencing qualitatively changed the entire enterprise of evolutionary biology. The importance of massive amounts of sequences for comparison is obvious because this material allows researchers to investigate mechanisms and specific events of evolution with the necessary statistical rigor and to reveal even subtle evolutionary trends. In addition, it is worth emphasizing that collections of diverse complete genomes are enormously useful beyond the sheer amount of sequence data. Indeed, only by comparing complete genomes, it is possible to clearly disambiguate orthologous (common descent from a single ancestral gene) and paralogous (gene duplication) relationship between genes; to convincingly demonstrate the absence of a particular gene in a genome, and to pinpoint gene loss events; to perform a complete comparison of genome organizations and reconstruct genome rearrangement events (68–71).
This is important because it explains the new data available.
Page 1015
Complementary to the advances of traditional genomics is the more recent accumulation of extensive metagenomic data. Although metagenomics typically does not yield complete genomes, it provides invaluable information on the diversity of life in various environments (78,79).
Beyond genomics and metagenomics, one of the hall- marks of the first decade of the new millennium is the progress of research in functional genomics and systems biology. These fields now yield high quality, genome-wide data on gene expression, genetic and protein–protein interactions, protein localization within cells, and more, opening new dimensions of evolutionary analysis, what is sometimes called Evolutionary Systems Biology (80–82). This new field of research has the potential to yield insights into the genome-wide connections between sequence evolution and other variables, such as the rate of expression, and to illuminate the selective and neutral components of the evolution of these aspects of genome functioning.
More on new information available.
Page 1015
A fundamental observation supported by the entire body of evidence amassed by evolutionary genomics is that the sequences and structures of genes encoding proteins and structural RNAs are, generally, highly conserved through vast evolutionary spans.
Not much evolution actually going on.
Page 1016
Conservative recon- structions of the gene sets of the common ancestors of the two domains of prokaryotes, bacteria and archaea, seem to indicate that these ancestral forms that, probably, existed over 3 billion years ago, were comparable in genetic complexity, at least, to the simpler of modern free-living prokaryotes (88,93). From an evolutionary biology perspective, it appears that the sequences of many genes encoding core cellular functions, especially, translation, transcription, replication and central meta- bolic pathways, are subject to strong purifying selection that remained in place for extended time intervals, on many occasions, throughout the 3.5 billion year history of cellular life.
Prokaryotes have the same basic gene set they had 3.5 billion years ago. Not much progress or increasing complexity there.
Page 1017
The observations of extensive, ubiquitous and occurring via multiple routes HGT (Horizontal Gene Transfer) outlined above lead to a fundamental generalization: the genomes of all life forms are collections of genes with diverse evolutionary histories. The corollary of this generalization is that the TOL (Tree of Life) concept must be substantially revised or abandoned because a single tree topology or even congruent topologies of trees for several highly conserved genes cannot possibly repre- sent the history of all or even the majority of the genes (146–149). Thus, an adequate representation of life’s history is a network of genetic exchanges rather than a single tree, and accordingly, the ‘strong’ TOL hypothesis, namely, the existence of a ‘species tree’ for the entire history of cellular life, is falsified by the results of comparative genomics.
Koonin here is discussing a possible total rejection of the LUCA (Last Universal Common (Cellular) Ancestor) and TOL (Tree of Life) concept. He is not yet committed to rejecting these (no doubt he is afraid of being ostracized by other evolutionary biologists), but he is raising the question.
The figure and caption on page 1018 is important. He is proposing a series of biological “big bangs” which start with LUCAS defined as “A pre-cellular Last Universal Common Ancestral State.” In essence he is proposing that life came from non-life not just once, but many times. He is forced to this position because he simply cannot support the view all life can be traced back to one living cell. He explains on page 1019.
Page 1019
However, the sets of genes assigned to LUCA in these reconstructions lack certain essential components of the modern cellular machinery. In particular, the core components of the DNA replication machinery are non-homologous (or, at least, non-orthologous) in bacteria, on the one hand, and archaea and eukaryotes, on the other hand (176). In another sharp divide, the membrane lipids have distinct structures, and the membrane biogenesis enzymes are accordingly non-homologous (non-orthologous) (177).
These major gaps in the reconstructed gene set of LUCA support the idea that different cellular systems ‘crystallized’ asynchronously and are suggestive of ‘phase transitions’ in the early phases of cellular evolution…In this case, the very concept of a distinct LUCA becomes ambiguous, and it might be more appropriate to speak of LUCAS, the Last Universal Common Ancestral State (181)
This appears to be highly contrived.
Page 1020
Considering the genome-scale study of evolution, the next series of important questions has to do with the dis- tribution of selection coefficients across genomes: how much of the non-coding DNA is actually junk, what is the pressure of purifying selection in different genes, and how common positive (Darwinian) selection actually is?
The evidence so far is that positive Darwinian selection is not common at all.
Page 1021
A genome-wide search for positive selection (measured as the gene-specific dN/dS ratio) in protein-coding genes from six mammalian species revealed 400 genes (2.5%) that seem to have experienced positive selection in at least one branch of the phylogenetic tree of the analyzed spe- cies; the values for most of the individual branches were very small (188). These estimates, although conservative, show that, at least, in mammals, positive selection affecting entire gene sequence is quite rare although many genes that are, generally, subject to purifying selection are likely to include positively selected sites.
Page 1023
The next big question that begs to be asked with regard to complexity, both organizational and genomic, is: was there a consistent trend towards increasing complexity during the 3.5 billion years of life evolution on earth? The most likely answer is, no.
This statement occurs in the section discussing the fallacy of evolutionary progress.
Page 1023
Furthermore, reconstructions for some indi- vidual groups, and not only parasites, point to gene loss and genome shrinking as the prevailing mode of evolution (249).
Actually gene loss and genome shrinking is usually thought of as devolution, not evolution.
Page 1023
Certainly, episodes of major increase in complexity are known, such as the origin of eukaryotes, and the origin of multicellular forms, to mention obvious examples. However, these seem not to be parts of a consistent, gradualist trend, but rather singular, more or less cata- strophic events triggered by rare, chance occurrences such as the domestication of the endosymbiont in the case of the origin of eukaryotes.
This observation seems to be the catalyst for Koonin’s ideas regarding biological “big bangs.” If Koonin advances a mechanism for these big bangs, I missed it. Are big bangs an evidence of design? Is there a big banger at work biologically? Is there an alternative explanation to why the usual path of devolution would be overthrown?
Page 1024
It appears that these findings are sufficient to put to rest the notion of evolutionary ‘progress’, a suggestion that was made previously on more general grounds.
I believe he is here rejecting the idea evolution occurs slowly.
Page 1028
Collectively, the developments in evolutionary genomics and systems biology outlined here seem to suggest that, although at present only isolated elements of a new, ‘postmodern’ synthesis of evolutionary biology are starting to be formulated, such a synthesis is indeed feasible. Moreover, it is likely to assume definitive shape long before Darwin’s 250th anniversary.
Here is Koonin statement of faith in evolution. He thinks it is possible to salvage evolutionary theory in a post-neo-Darwinist age. He does not yet know what form this new theory may take but he has faith it will happen in the next 100 years.
I tried to be fair to Koonin’s evidence and ideas. He is obviously committed to evolution and atheism, in spite of the evidence he presents. I think everyone will see it as interesting reading.
@Ron Cram
Found your six points, here’s my go at them
First let me say I’m not here to prove or disprove god. Personally I’m agnostic, but I have no intention to proselytize.
My intention is to protect science from intrusions by religion, including its camouflage called “ID”. Not because I’m against religion, but because I think the two deal with separate spheres who never intersect. Some of your points are of purely religious nature, to which I find it difficult to respond at all, as I don’t see the relevance to the subject of science. I’ll try to respond to them in a way that deals with the scientific aspect only.
First, I would say it is rational to believe in the existence of God because the universe had a beginning at the Big Bang.
That does not follow. There is no relation between the origin of the universe and the existance or non-existance of god. If it has an origin, it could have a natural cause. Likewhise an eternal universe does not exclude the existance of a god outside of it.
Besides we don’t currently know if the universe is eternal or had a beginning, but that is really irrelevant to the god question.
The beginning indicates there has to be a Cause, the Supernatural – an actor who is above the laws of physics. Even atheist and agnostic astrophysicists have agreed to this point,
This agnostic doesn’t agree to this point.
Second, it is rational to believe in God because life does not come from non-life.
Just because we haven’t observed the process doesn’t mean that life can’t originate from non-living things. We currently don’t know the origin of life on earth, because there are no fossils from that time and the time machine hasn’t been invented yet. The subject is open to research, and that research may produce results in the future.
Gaps in our current knowledge – of which there are undoubtedly many – do not prove god anyway. That fallacy has been put forward by the Christian curches over and over again, much to their chagrin after the gaps had been filled. They’ve abondoned that strategy meanwhile, and so should everyone else. Besides don’t you think it’s unworthy to reduce god to the role of a craftsman who fills in the gaps we can’t currently explain?
To believe it does is the same as believing in fairy tales. There is no evidence to support such a belief.
There currently is no evidence for any belief about the origin of life. I’m not giving any specific answer to the question, so I’m not guilty of the argumentum ad ignorantiam you accuse me of, while at the same time you’re committing it. 🙂 All I’m saying is we should not abandon the scientific method and insert “god did it” as a joker when it comes handy, because doing so would be unscientific. It would be straight back to the middle ages, where they did that all the time.
Third, it is reasonable to believe in God because of Botany. Food producing plants and trees have one main purpose, to produce food.
That is like saying noses have been designed for one main purpose, namely to support glasses. After all they do the job perfectly.
It’s completely the other way round. We adapted to eating plants. Plants were there first. Later creatures evolved who cannot feed on sunlight, but are reduced to eating other living beings. We call those newer creatures “animals”. They adapted to the food available around them, namely plants and other plant-eaters. Third stage is that some plants evolved to be eaten because it gives them certain advantages, we’ve already been through that.
There are even fourth and fifths stages, and probably more, it gets very complicated from then on, and it takes a biiiig imagination not to be tempted to see it as “designed”, even though it isn’t.
Chili pepper is an interesting example. Do you know why it tastes so hot? The purpose of its fruit is to spread its seed, but for some reason mammals destroy the seed in digestion, while birds don’t. So the plant evolved to synthesize a substance that mammals find painful in their mouths, but birds cannot taste. Unfortunately, for the plant, there’s a mammal who likes the taste of pain, namely us. We’ll have to wait and see how that influences chili pepper evolution.
Fourth, it is reasonable to believe in God because of Genomics.
If I understand you correctly, your point is that modern science has in part abandoned Darwin. That may be so. Certainly Darwinism has been expanded on, in parts modified, in some parts maybe even refuted. And if it hasn’t it may be refuted in the future. That is old news.
And irrelevant. Evolution does not rest on Charles Darwin, and his specific interpretation and explanation is not sacrosanct. Evolution itself may even one day be refuted, as it’s a falsifiable theory. Not very likely, but possible.
That is still not the point. The point is that whatever science knows, or says, or retracts, or where its knowledge has holes, there is never an excuse to put “god did it” in the equation, because that is always unscientific.
Fifth, it is reasonable to believe in God because he has acted in human history.
My goal is not to stop you believing in god, so that is off the point. If you think you have proof he exists you would be wrong though.
The most telling and powerful action is the resurrection of Jesus Christ.
For all we know it could be a legend.
It is the most well-attested event in ancient history.
Certainly not.
Do you believe Julius Caesar visited Britain?
Do you believe Beowulf fought a dragon? Do you believe Odysseus struggeld Skylla and Charybdis? So you think dragons and sea monsters are real?
There is far more evidence of Jesus rising from the dead than there is that Caesar ever lived.
Not really. Verification of sources is a vital part of historical research, and you failed to do that in your analogy. We know of Julius Caesar mostly from scribes whose goal was to report what went on and most of whom had no specific axe to grind, so those sources are for the most part trustworthy. Besides none of them tells Caesar was immortal or could perform miracles. He’s described as a regular human being.
99% of what we know about Jesus is from the bible, whose authors foremost aim was to proselytize. They wanted readers to admire Jesus and to believe in him as a deity. So they were not exactly neutral. As believers themselves they may have uncritically reported miracles they heard from elsewhere, or they might even intentionally have bent the truth a bit. Furthermore they report supernatural acts that stretch their trustworthiness quite a bit. It takes unusual evidence for such unusual claims, and some writing of a couple of missionaries doesn’t quite fit the bill.
We do have some sources outside of Christian scripture who report about Jesus, but miracles and resurrection are not mentioned in those source. The majority of historians agree that Jesus probably existed and that he was a Jewish preacher in Palestine with a large following. Everything else is still a matter of faith.
Sixth, it is reasonable to believe in God because I have a personal relationship with him.
For you only, and nobody here wants to stop you believing it.
C.S. LEWIS’ ARGUMENT FROM LOVE AND HUMAN KINDNESS
(1) Humans can love and be kind to each other.
(2) This doesn’t make sense in the nasty world of survival of the fittest.
Oh yes it does. Altruism can be beneficial for survival of the individual as well as his kin, especially in social species like us. It’s perfectly compatible with a scientific worldview, and specifically with evolution.
(3) The only possible source for love and kindness is God.
I surely hope not. On the contrary, I find it a bit depressing that some people only want to be kind to others because they believe god wants them to. I’d rather they be kind out of their own impetus.
Demonstrating yet again that one must necessarily be really, really stupid to push this creationist crap anywhere – much less in a forum purpose’d for the discussion of the sciences – at 11:06 AM we find the psychotic and morally depraved Dave Springer idiotically looking at my post from 11:50 AM on 10 August and writing that I’d said:
…continuing:
Obviously incapable of discerning the meaning of quotation marks or the HTML “blockquote” function which indents and italicizes marked sections to denote their status as quotations, this flaming Springer screw-up seems to think – does he think at all, we wonder? – that the line he’d recapitulated from that 10 August post of mine was my own assertion and not drawn from Ronald Bailey’s Reason magazine article (titled: “Attack of the Super-Intelligent Purple Space Squid Creators,” 15 July 2008) based on the remarks he’d given in the FreedomFest 2008 debate “Is There Scientific Evidence for Intelligent Design in Nature?”
Now, we’ve all seen how this Springer schmuck loves Wiki-bloody-pedia, sucking upon it for everything he knows (or will ever know) about the axolotl. Does anybody therefore conclude that the cement-headed lying bastich – that’s Springer, not the axolotl – might look into the article there concerning Richard Dawkins to satisfy what we’ll laughingly call Springer‘s curiosity about the fellow to whom Ronald Bailey was referring in the cited article? Had this willfully ignorant Springer putz bothered to do so, he might have found access to Dawkins’ full curriculum vitae, which includes a listing of the man’s publications and other works, to discover that Dawkins has, indeed, “published … papers in a peer reviewed journal in the field of evolutionary biology.”
So let us consider yet again not only the technical and scientific illiteracy of Dave Springer, so perfectly representative of the scum who are pushing “creationism in a cheap lab coat” within this forum, but also the smelly putz’s laziness.
And therefore to hell with Dave Springer, and every one of the other vicious religious fanatics clumsily fumbling to masquerade as honest disputants in this venue.
At 7:54 AM on 14 August, the “creationism in a cheap lab coat” blithering idiot Dave Springer pointlessly but diagnostically vomited up as his total contribution to discourse:
Inasmuch as the term “Nazi” refers to the Nationalsozialistische Deutsche Arbeiterpartei (NSDAP, or “National Socialist German Workers’ Party”) and – thus far – this Springer specimen hasn’t revealed himself to be adherent to the doctrines of that particular sociopolitical perversion – not that such would be all that surprising, given Springer‘s intellectual degeneracy – I have had no reason yet to classify him or his co-religionists as “Nazi.”
Lying religious fanatics, sure. Contemptible dolts incompetently second-handing the promulgations of genuine scientists, the contents of which neither Springer nor the rest of these fellahin have even the last desperate chance of apprehending, no question. But “Nazi“?
Nah. For one thing, it’s becoming possible to infer that this Springer nudnik couldn’t so much as march in step, even if his worthless excuse for a life depended on it.
Dave Springer,
I enjoyed your much more erudite and informed explication of the joys of genomics!!
“Christianity isn’t a bad choice provided you actually model your life after its founder who was man who wouldn’t harm a fly and whose most aggressive act in life that we know of was cursing a fig tree.”
Actually I would point to an incident in Jesus earlier life when he went to the temple where they had the money changing tables that may have included gambling. He blew his top telling off the priests and flipping stone tables estimated to weigh in the neighborhood of 200lbs based on archaeological work!! Matthew, Chapter 21, Mark, Chapter 11, and Luke, Chapter 19 are the tales.
I would also point to the night of Jesus’ arrest in the garden where he told his followers if they didn’t have money to sell their garments and buy swords. My belief is that he was saying he would no longer be around to protect them. Luke 22:35-38
I would also suggest that the command to turn the other cheek was on the basis of interpersonal relationships and other situations where it is simply better to reduce the intensity of the situation to allow the other person to calm down and give them the maximum chance to recover form their ire. I do not believe it was ever intended to be the response to a mob burning and raping the village… Mat 5:39 It is instructive to read the rest of the chapter to see the context in which it is stated as it would appear to be civil situations.
Finally Ghandi has an inflated reputation based on the civilization he was going against. Britain, while being money grubbing and expansionist was not particularly violent and brutal compared to less civilized or more focused groups. For example, what do you think might have happened if Ghandi had lain in front of a group of tanks led by the SS. Can we all say SQUIIIIIIIIIISH together?? I can even imagine a particularly brutal SS commander having the tank go as slow as possible to extend the lesson. Then there was Papa Stalin and Mousey Tongue who also would not have hesitated to erase this man on the spot and machine gun his followers with no hesitation from their soldiers to do the deed.
Thanks again for the excellent posts on genetics.
Tucci78 says:
“Oh, were we conducting a scientific investigation of kuhncat‘s duplicity, weaseling, moral depravity, and incompetence? Inasmuch as the dispassionate consideration of kuhncat‘s flagrant disregard for honest disputation was getting no response from him but more of the same stuff one might inadvertently squeeze out of a rabbit’s entrails while gutting it for the pot, we might as well keep adding a little napalm to the dissection of kuhncat‘s hideous pathology.”
“this flaming Springer screw-up seems to think – does he think at all, we wonder?”
Come on Tucci78. There you go calling names again. It seems this science stuff has you all worked up. I think a softer answer could have squelched Springer’s post easily enough. Being passionate about something is one thing, but I think your insults are not very helpful and they stand out more than any of your arguments. Your language, whether you mean it or not, infers superiority over others just because they misread a quote wrong, or do not hold the views you do (or the “consensus” if we must go there, which I think society has proven as well as this post there is no consensus on origin of life). I honestly think that the most important thing to learn here is some respect for others, even if they don’t deserve it (I speaking more of myself than anyone here). This will take you a lot farther in life than the arguments we’ve all been making on this post, at least I believe so, otherwise no one would listen to each other and learn anything. If you think I’m a fool and all for even posting this, then that is fine, I can take it; but I would recommend letting go of this post for your own sake.
Tucci78 says:
August 14, 2011 at 4:34 pm
Is 78 the year you were born, son? That’s the year I was honorably discharged from the United States Marine Corps at the rank of sergeant and enrolled in college under the GI bill. Your flames are lame and roll off me like water off a duck’s back. Grow up, son.
[snip]
Reply: Way too many bad words to deal with each one and preserve the comment. – Tone it down and try again. TB-mod
anorak2 says:
August 14, 2011 at 2:47 pm
@Dave Springer
“I don’t understand why you’re getting so worked up about the axolotl thing. It seems you’re missing the point. I was explaining that evolution has no direction, it’s not towards “more complexity”.”
I’m not worked up. It’s calle due diligence. I asked you for examples of evolution going backwards in complexity to support your claim that it has no general direction towards increasing complexity. You gave me Axotyl. I would be remiss if I didn’t look into it. As it turns out it wasn’t a very good example and I still believe that evolution has a trajectory from less to more complex as evidenced by the fossil record of life beginning as prokaryotes and gradually over the course of billions of years producing more and more complex forms with the pinnacle being the awesome complexity of the human mind. Evolution has a vector. Get used to it.
John B says:
August 14, 2011 at 10:57 am
“Yes, sexual organisms receive only half a genome from each parent. but since the full genome is paired up, they do receive a copy of each gene from each parent (X and Y chromosomes excepted).”
This is misleading. Genes aren’t split off and copied. The diploid number of chromosomes is split to haploid number from each parent in the creation of germ cells and then the two haploid numbers are recombined into diploid number upon fertilization. The paired chromosomes of each parent contain genes in the form of alleles which are variations on the gene, one variant on each chromosome in matching locii. The alleles may or may not be identical on each chromosome. The diploid daughter cell ends up with a copy of one variant from each parent. This explanation is not for your benefit but rather to make clear to readers unfamiliar with reduction division and recombination.
“On the inheritance of mutations, I said “if the mutation is beneficial it spreads through the population” and you said “It only spreads if it confers a differential reproductive benefit to the organism as a whole.” Same thing isn’t it? What else do you think I was referring to it being beneficial to?”
You were espousing gene-centric theory in my understanding. In that context the benefit goes to the gene. The gene propogates like an entity onto itself. As Gould said “The one thing you cannot give to an individual gene is exposure to natural selection”. Selection works on whole organisms.
The gene-centric theory dates back the days when the paradigm in molecular biology was “one gene, one function”. This was before we anything about things like transcription editing, introns, exons, polymorphism, polyfunctionality, reverse transcription of the same gene to yield a totally different product, reading frame shift to yield different products, and so forth. Fixation of new alleles is not so simple that you can view it as some kind of fitness improvement in and of itself. In many if not most cases it’s just carried along for the ride. Random mutation and natural selection is a conservation mechanism. Random mutations that produce an overall fitness improvement are rare as hen’s teeth. At best they are very near neutral and are far more often quite destructive. This huge imbalance between beneficial and catastrophic random mutations serves to keep the species from wandering too far off the reservation, so to speak. Indeed when we look to the fossil record we see a record of new species emerging fully formed and then enduring for an average of about 10 million years with little change then disappearing from the record as abruptly as they entered. Again as Gould stated “the trade secret of paleontology is that it disproves the very theory upon which it is based”. He was referring to gradualist theory, the accumulation of small changes which in toto over time lead to the emergence of new species. The fossil record is one of SALTATION. The prevailing theory of evolution cannot explain saltation and instead of questioning the dogma the fossil record was instead impeached first by Darwin and then carried on in that tradition through today. The theory of evolution CAN’T be wrong, thus the data must be wrong. A rather familiar refrain that echoes within the hallowed walls of anthropogenic global warming punditry.
Truth be told it appears to me that the chromosome is the basic unit of heritable change and that speciation is the result of very rare chromosomal reorganizations rather than the very common point mutations in individual genes. Rare chromosomal reorganizations would produce saltation of new species and explain why the fossil record has, in the past 150 years since Darwin first impeached it, been explored in far greater extent and detail and has still not told us a different story. The “incomplete record” excuse is wearing very thin.
“I’m not sure what the point of the rest of your post was. Could you put it more succintly? I can’t work out if you are trying to make the case for intelligent design.”
My position on intelligent design is that when you divorce it from the religious and anti-religious rhetoric and get down to actually asking whether design is something that can be reliably discriminated from non-design it has enough merit that we should at least pursue the question in the context of math, science, and engineering instead of fighting it out in pulpits and courtrooms.
Dave Springer,
Evolution has a vector. Get used to it.
I understand your point of view. But I am still very intrigued with the Koonin paper I asked you to look at because he discusses “the fallacy of evolutionary progress.” Genomics tells us most mutations/selections are not positive. Koonin thinks he sees biological “big bangs” which he thinks happen by chance to cause the progression. These “big bangs” are not selections in the normal sense. I really think his paper deserves more study. I excerpted a selection of his quotes above. The paper is about a lot more than just horizontal gene transfer and I would love to read what you think about it. My own reading is that Koonin’s biological “big bangs” are highly contrived. Evolution has a vector but it does not seem to have a mechanism.