…and this is a 
It's always amusing to see creationists try to explain why Charles Darwin was wrong, especially when they make up lists of reasons "Darwin's theory of evolution does not hold up to scientific scrutiny." These are always people who wouldn't know what scientific scrutiny was if it knocked them immobile with a carefully measured dose of Conus snail toxin, strapped them to an operating table, and pumped high-intensity Science directly into their brains with a laser. As I often wish I could do.
Anyway, some ignorant jebus-lover hacked together a list of 10 "mistakes" that Darwin made. Strangely, they completely miss his actual errors (probably because they've never read anything by Darwin and don't have enough knowledge of biology to recognize where he has been superceded) and babble on about what are actually creationist errors.
1. "Warm little pond" theory: There is no solid evidence of life arising spontaneously from a chemical soup.
Actually, there is. We know that organic chemicals arise spontaneously all the time in nature — they're even detectable floating about in space. We also know that biology is chemistry, and that every process driving biological phenomena is ultimately physical and chemical. We also know that life arose in a geologically brief period early in the history of the earth. It's certainly a better explanation than that some invisible guy said some magic words and poof, life appeared spontaneously with all the complexity of extant forms.
By the way, the "warm little pond" wasn't part of Darwin's theory. It was a brief speculation made in an 1871 letter to Hooker.
"It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, - light, heat, electricity &c.; present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed."
That's actually still an entirely reasonable hypothesis, and not a mistake at all, especially when you recognize that he was suitably cautious in his publications. Here's what he said in The Variation of Animals and Plants under Domestication, for instance.
"As the first origin of life on this earth, as well as the continued life of each individual, is at present quite beyond the scope of science, I do not wish to lay much stress on the greater simplicity of the view of a few forms, or of only one form, having been originally created, instead of innumerable miraculous creations having been necessary at innumerable periods; though this more simple view accords well with Maupertuis's philosophical axiom 'of least action.'"
2. Simplicity of the cell theory: Scientists have discovered that cells are tremendously complex, not simple.
Total fiction, but an oft-repeated lie by creationists. Scientists in Darwin's day had access to light microscopes with resolution as good as ours today; they were actively studying the structure of the cells, identifying and naming organelles, teasing apart the choreography of cell division. They were entirely aware of the mysteries and complexities of the cell's contents.
And again, there was nothing in any of Darwin's writings that presupposed that cells had to be simple.
3. Theory about the cell's simple information: It turns out cells have a digital code more complex and lengthy than any computer language made by man.
Wait, isn't this the same as #2? I'm seeing some padding going on already.
But no, the genome is not a computer program written in a complex computer language. The words "digital code" are not magic, nor do they imply any supernatural origin.
4. Theory of intermediate fossils: Where are the supposed billions of missing links in the evolutionary chain?
Oh, really? This is the most absurd creationist claim: we keep digging up transitional fossils and waving them in front of their noses, and they just close their eyes and chant "lalalalala".
5. Theory of the variation of species: Genetic adaptation and mutation have proven to have fixed limits.
They do? Where is this "proof"? When I can see from the molecular evidence that a fruit fly, a squid, and a human all share a common core of related genes, I have to say that if there are such limits, they are very wide — wide enough to encompass the entirety of life on earth.
If he means that there are limits such that a mouse will not give birth to an orangutan or a cabbage, I'd agree…but no biologist proposes any such ridiculously saltational view of evolutionary change. It's always the creationists who demand that a cat give birth to a monkey before they'll believe in evolution.
6. Theory of the Cambrian Explosion: This sudden appearance of most major complex animal groups at the same low level of the fossil record is still an embarrassment to evolutionists.
They are so embarrassed about it that they keep writing about it and studying it!
Remember, though, "sudden appearance" means over tens of millions of years…and it's a creationist who believes the whole of the earth's history is about a thousandth of the length of just this one geological period who is claiming that 20 million years is untenably sudden. It's also not true that that animals abruptly appeared: we have evidence of precursors, and even within the Cambrian we see patterns of change from beginning to end.
7. Theory of homology: Similarity of structures does not mean the evolution of structures.
This is the one case where this creationist has dimly caught a glimpse of a real argument within biology. We've been wrestling with the concept of homology for a long, long time — with problems of definition and implementation. These arguments, however, do not cast doubt on the evidence for evolution, so I'm not about to get into them here (this is where a philosopher of science would be much more useful!)
8. Theory of ape evolution : Chimpanzees have not evolved into anything else. Neither has man.
But a proto-chimp/human — our last common ancestor — evolved into both humans and chimps.
This is a very silly argument. It's like claiming that because none of my children have yet reproduced, it is impossible that my wife and I produced them.
9. Theory of the tree of life: Rather than all life branching from a single organism, evidence has revealed a forest of life from the very beginning.
Goddamn you, New Scientist! Ever since they ran their stupid, misbegotten cover, the creationists have been crowing about Darwin being proven wrong. The tree model is still largely accurate for multicellular life, but we have to add a component of horizontal gene transfer, and we recognize that at the root of the tree of life, in all those single-celled organisms, the profligate exchange of genes across species is much, much more common.
But this is still evolution! It's also an entirely natural mechanism; there aren't angels or gods mediating bacterial conjugation or viral transduction.
10. Rejection of an intelligent designer: This opened the door for many to reject God, the Bible and Christianity.
That's no mistake. You should reject gods, holy books, and various cults, because they're all bullshit.
That was a pathetic effort, so typical of creationists. I've seen many such lists of Darwin's errors, and there's a lot of overlap…but there's one thing I've never seen appear on any of them. Why don't they ever mention Darwin's biggest mistake, his theory of blending inheritance, pangenesis? It was completely wrong, it was even incompatible with natural selection, yet the creationists never seem to latch onto it as a tool for defaming Darwin. Is it because then they'd also have to understand that another natural mechanism, one that is intrinsically about chance and statistics, so thoroughly replaced Darwin's mechanism? Is it because they neither understand the theories Darwin proposed, nor Mendelian genetics?
(Also on FtB)
Life Science
Comments
Posted by: lavieintrus
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April 27, 2012 12:01 PM
A bit ranty, but an intelligent rant all the same. Yet, at this point how can you not rant about the silliness of the creationist trying to deny evolution? I know I can't, hahaha. This was a fun read, thank you.
Posted by: Amphiox, OM
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April 27, 2012 12:18 PM
I'll just point out here, even though it is obvious to anyone with half a brain, that regardless of whether the phylogeny of life is a single tree or a forest, it is still fully compatible with evolution. Evolution theory predicts trees (emphasis on the plural), and what is a forest made of if not trees?
Darwin himself presaged this when he talked about "from one form OR a few".
One primordial form gives a single tree. A few primordial forms gives a forest. And it doesn't even matter how many constitute that few - it could even be millions.
It just do happens that the empirical evidence right now suggests a single tree (or at least, a single remaining, still growing, tree) and we naturally incorporate this evidence into the modern understanding of the theory. But the theory is fully compatible with multiple trees.
Posted by: Owlmirror
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April 27, 2012 12:38 PM
But "forest" is not the right metaphor for early horizontal gene transfer. Indeed, "forest" plays into creationist conceptions of fixed species essentialism; it implies support for many different specially created "baramins".
Creationists seem to be generally OK with the "microevolution" of baramins to different breeds, but not to different species.
Of course, what they really really want is for the monkey and/or ape baramins to be distinct and utterly separate from humans.
What is inferred from early horizontal gene transfer is not a forest, but rather a web: a tree with many links connecting various branches, some more distant than others.
Posted by: Amphiox, OM
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April 27, 2012 2:00 PM
Yes indeed, Owlmirror, and if you actually read that New Scientist article, you find that the forest they refer to is not any old forest, but specifically an Aspen forest, with multiple individual clonal trees all interconnected by a web of roots underground-the whole thing being one organism with one original descent.
But of course the creationists miss this subtlety.
Posted by: 'Tis Himself, OM
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April 27, 2012 3:44 PM
Just once I'd like to see a new creationist argument. Biologists and allied trades keep finding new evidence which supports evolution. Creationists keep trotting out the old, already refuted arguments against evolution. I'm getting tired of the same old quote mining, arguments from ignorance and arguments from incredulity. I want some new stuff.
Posted by: Dev Null
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April 27, 2012 4:14 PM
Do you know, that would actually make a really interesting article: top 10 things that Darwin got wrong, written by a real biologist who actually knows.
Posted by: Michael Syvanen
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April 27, 2012 7:51 PM
Goddamn you, New Scientist! Ever since they ran their stupid, misbegotten cover, the creationists have been crowing about Darwin being proven wrong.
I actually blame those scientists who insist on referring to "the tree of life" and existence of a single root (Last Universal Common Ancestor). Amphioxus correctly points out that Darwin never strongly supported a "tree of life". His only figure in Origin of Species shows three trees of uncertain affinity. He repeatedly used the phrase "one or a few" origins.
It is a mistake to insist on using the term "the tree of life" because a tree is mathematically rigorously defined as a topology that lacks loops -- an aspen forest violates this definition. I am not just being pedantic here since every tree building algorithm used by evolutionary biologist have built into them the formal mathematical structure of what is called a Steiner tree.
In order to see biologically relevant evolutionary histories one must compare multipe trees that are based on different character sets and if they are incongruent use a netted diagram to summarize the result.
Posted by: Ichthyic
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April 27, 2012 8:34 PM
I actually blame those scientists who insist on referring to "the tree of life" and existence of a single root
then you're either an idiot, or intentionally want to introduce a red herring, since that has nothing to do with the paragraph you quoted, nor the Scientific American article, nor the creationist response to it.
In order to see biologically relevant evolutionary histories
Do you even know what that means?
Posted by: Amphiox, OM
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April 27, 2012 9:01 PM
The evidence for LUCA is pretty much unassailable. LUCA is the single root of the known living tree of life on earth. There may have been other roots at one time, but none of the others have any known descendant branches that are still alive.
It is important to remember that the prokaryotic "web" or "root network" (pick your preferred metaphor) occurs AFTER LUCA. LUCA was the original root. It produced branches in a treelike fashion. These branches then intermingled and connected to form a web. Then after the advent of eukaryotes, several trunks arose from this web and grew into trees, many with minimal or no merging of branches.
The whole thing is still accurately described as a tree. Aspens aren't the only trees to have this kind of structure.
Posted by: Michael Syvanen
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April 27, 2012 9:32 PM
Ichthyic I was quoted in that New Scientist (not Scientific American) article and the reporter for the article was in the audience for a talk I delivered at a Linnaen Society Meeting in 2008 -- a meeting celebrating that society's 150th anniversary of the publication of Darwin's and Wallace's theory of natural selection. So to a certain extent I added some fodder to the creationist's campaign that the absence of a single tree of life violated "Darwinism". That, in fact, is not true. In my talk I presented two slides showing that Darwin never endorsed a single tree of life, as amphioxus points out above. My interview with the reporter was made in that context. My point is that those misguided disciples of Darwin who equate a "tree of life" with "Darwinism" do not know what Darwin actually said about the subject.
You should avoid the ad hominum insult -- I suspect I have a much deeper understanding of evolutionary theory than you do.
Posted by: Michael Syvanen
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April 27, 2012 9:58 PM
Amphioxus says: It is important to remember that the prokaryotic "web" or "root network" (pick your preferred metaphor) occurs AFTER LUCA. LUCA was the original root.
Actually there is no evidence that LUCA ever existed. If you admit that since "LUCA" came into existence that relationships among life's kingdoms are highly reticulated, why is it so difficult to accept that LUCA itself is not the result of a reticulated process. If that is the case then it would seem obvious that "LUCA" (as it is commonly understood) was the result of multiple independent origins of life, i.e. we cannot trace life's origins to any single taxonomic group.
I will admit that this idea (that LUCA likely never existed) is very difficult for many to accept. I have been making this case for some time and it is not just educated amateurs but also professional biologists that have difficulty grasping this notion. I first put this out there in a TIG's piece in 2002 but even tried to float it at Panda's Thumb in 2006.
Posted by: Owlmirror
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April 27, 2012 10:19 PM
Or rather, Amphiox (no "us").
One of the things that creationists do, knowingly or unknowingly, is deliberately confuse "Darwinism" in the sense of evolutionary biology in general, and "Darwinism" in the sense of Darwin's original theory, unmodified by heredity, population biology, molecular biology, genetics, etc. This confusion has actually led to, among other things, creationists saying that Mendelian heredity proved evolution false, or words to that effect.
Generally, evolutionary biologists in the US would prefer to avoid the whole semantic mess by avoiding the term "Darwinism" when referring to modern evolutionary biology. I understand that in the UK, this is less of a problem, largely because creationists are less influential there.
Indeed, I note that it is only fairly recently that Richard Dawkins had the problems with the word "Darwinism" explained to him.
Posted by: Amphiox, OM
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April 27, 2012 10:51 PM
But that isn't the LUCA hypothesis. LUCA isn't, and never was claimed to be, the "origin of life". LUCA is the last universal common ancestor of all currently existing life on earth today.
It doesn't matter if LUCA itself arose from a reticulation of multiple independent origins of earlier lifeforms or not.
The question is whether or not LUCA represents a single organism (or population of organisms, or semi-unified gene pool) or not.
Posted by: northfox
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April 28, 2012 4:05 AM
PZ, Their point #1 is actually true. There is no experiment that can show that a living cell appears spontaneous in an organic soup. Presence of organics = life is not true.
Also, Darwin had much, much less knowledge about the complexity of a cell. Seeing a few organelles in a cell is not comparable with what we know today. Microscopy techniques (confocal, fluorescence, FRAP, depolarization, etc, etc) are new and not known to Darwin, or anybody at that time. Your secretary of Energy, Chu, did not become world-famous for FRET because it was a technique already used by Darwin to study the error-correction in the read-out of RNA information.
The Cambrian explosion did occur pretty sudden. 5 Million, not tens of millions as you say, is pretty sudden, also for biologists.
Etc., etc. Some of the ten claims seem to touch valid points.
Posted by: David Marjanović
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April 28, 2012 9:19 AM
First, as mentioned above, LUCA is the last universal common ancestor, not (necessarily) the first.
Second, lateral gene transfer is only possible between organisms that have compatible genetic codes carried by substances (like nucleic acids) that can hybridize with each other. That's almost the same as saying that lateral gene transfer is only possible between descendants of a single ancestor. If 3 different origins of life used 3 different sets of nucleotides, even if they all used RNA, gene transfer between them was extremely difficult or impossible.
So far!
</Homer Simpson>
What is life?
They have not, however, revealed a huge amount of drastically new information. They've filled in details.
The point remains: every time creationists claim that Darwin believed cells were uniform blobs, they're bullshitting.
No, fifty million – the entire duration of the Cambrian.
When the Cambrian began, there were no shelled mollusks; when it ended, there were cephalopods; the series of transitional fossils spans the Cambrian. And that's just one example off the top of my head.
Posted by: David Marjanović
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April 28, 2012 9:38 AM
...also, five million years is thirty thousand times the age of the Universe according to young-earth creationists.
Posted by: Amphiox, OM
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April 28, 2012 4:33 PM
That 5 million year length for the Cambrian Explosion is the old "rapid-fuse" hypothesis for it, and was based on older, incomplete understanding of the fossil record. New discoveries have debunked it.
The entirety of the cell complexity thing is a creationist red herring lie. Darwin is on record as saying he did not think the origin of life was a question answerable by science in his time. He conceived of evolution as happening AFTER the origin of life, ie the origin of the cell. The complexity of the cell is a question for abiogenesis theory. It's the standard creationist strategy of deliberately conflating evolution with abiogenesis.
How complex the first lifeform was is completely irrelevant to evolution, it will work the same regardless.
Posted by: Ichthyic
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April 28, 2012 4:48 PM
My point is that those misguided disciples of Darwin who equate a "tree of life" with "Darwinism" do not know what Darwin actually said about the subject.
and MY point was that this is irrelevant to what you were responding to.
Actually there is no evidence that LUCA ever existed.
citation please. I'm sure since you have convincing evidence that LUCA is a failed concept, you've published and are happy to provide the citation to your paper in the lit? I'm sure it would have been the subject of much discussion in the zoology departments I've spent time in, but somehow we must have missed it. Strange that.
You should avoid the ad hominum insult
you also apparently don't understand what an ad-hom is.
Posted by: Ichthyic
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April 28, 2012 4:54 PM
ah, yes. I think I remember you now.
Aren't you the one who was pushing the idea that horizontal gene transfer was more important than vertical historically?
now, who, exactly has more evidence for each side of that one again?
yeah, didn't buy it when you first proposed it, still not.
molecular data still does not support the idea that horizontal transfer has been a consistently significant part of evolution... even "biologically relevant" evolution. It's there, sure, but it simply isn't a large enough or consistent enough issue to think that standard lineages are overwhelmed by it.
I have been making this case for some time and it is not just educated amateurs but also professional biologists that have difficulty grasping this notion.
there's a reason for that.
anyone who cares to can read your CV via your link.
I did, many years ago.
Posted by: Ichthyic
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April 28, 2012 5:00 PM
...and lastly, not saying you are, but it seems if you'd like to start a debate wrt to historical importance of horizontal gene transfer, do you really think this is a good place to do it?
In a thread on creationism?
*shrug*
good luck with that.
Posted by: Owlmirror
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April 28, 2012 6:33 PM
Huh. I was wondering where that figure came from.
The WP article references a review by Simon Conway-Morris, from 2000:
So... even the most "explodey" ("principal events of evolutionary interest") parts of the Cambrian explosion still lasted 20Myr. Or at least, as understood 12 years ago.
I note, in contradistinction to the "≈45 Myr" given by SCM, that the length of the Cambrian appears to be 54Myr, per the 2004 and 2009 Geologic Time Scale.
Posted by: Michael Syvanen
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April 28, 2012 6:49 PM
I am not starting a debate here, but continuing one that I started in 1983. I am responding to a comment by one highly respected biologist.
That it happens at a place that questions creationism is easy to answer. I began to notice about 20 years back that creationists were citing my work as an argument against "Darwinism" and the fact of evolution. So sometime in the late 90s I began to refute those claims, mainly through comments at Talk Origins. One thing that made these discussions difficult is that many who defended evolution felt it was necessary to deny the importance of horizontal gene transfer in order to answer creationists claims. These are people that had reasonably good understanding of evolutionary biology but really lacked a good appreciation of the molecular genetics underlying the science of HGT.
BTW: I think I remember you now.
Aren't you the one who was pushing the idea that horizontal gene transfer was more important than vertical historically?
Not me. Not sure what you are saying here.
Posted by: Owlmirror
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April 28, 2012 7:16 PM
Really? Is there an example of this?
Maybe I'm confused because I don't see how horizontal gene transfer can be seen as helping support creationism in the first place.
Posted by: geometeer
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April 28, 2012 8:41 PM
Evolution of language, not of critters: Darwin has nowhere been superceded, because that is not a word (it would come from cedere, to withdraw, like concede). He has in some points been superseded (from sedere, to sit, as in sediment), or sat upon.
Between standing on the shoulders of giants, and sitting on the lap of Darwin, no contest.
Posted by: fancyflyer
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April 29, 2012 3:26 AM
#24: Orthography snobs, we. That one slowed my eye too. Blame it on the Tower of Babel, or some such supernatural operation. A fine post nevertheless. Thanks PZ.
Posted by: 'Tis Himself, OM
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April 29, 2012 5:32 AM
dictionary.com recognizes "superceded" as a variant spelling of "superseded".
Posted by: David Marjanović
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April 29, 2012 8:00 AM
That's all correct, but you must admit it makes remarkably little sense. It's really no wonder that so many well-educated people use the other spelling.
Posted by: https://www.google.com/accounts/o8/id?id=AItOawkZu7s43M5qM4ByJESkBudV2gViRSUTSVs
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April 29, 2012 9:55 AM
Every time we find a "missing link", it creates two new gaps where there used to be one. Besides, none of those fossils are actually changing before our eyes, so they are just different fossils - not evidence of anything we would reject no matter how much evidence there is.
Evidence doesn't matter against True Belief, whether those beliefs are about science or politics or race or whatever.
Posted by: Thorne
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April 29, 2012 10:30 AM
Try to remember, though. Creationists aren't really looking for evidence to SUPPORT Creationism. They already have that, in the Bible. They are looking for any tiny speck of evidence that doesn't support their shriveled concept of evolution, which they can then conflate into the newest "Proof That Darwin Was Wrong, Therefore God."Posted by: Owlmirror
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April 29, 2012 2:24 PM
Yeah... And I've seen them do that with Mendel's work (for pity's sake), as noted above.
I'm just wondering what form their idiocy took in this case.
Posted by: Stanton
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April 29, 2012 3:13 PM
There is a great deal of irony there, especially since Mendel's successor at the monastery thought that his hobby was unbecoming of an abbot, and had all of his notes burned.Posted by: David Marjanović
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April 30, 2012 8:49 AM
Circular irony: it's probable that Mendel actually wanted to disprove evolution by, basically, showing that mutations don't happen – that inheritance only combines and recombines the ever-same alleles and doesn't generate new ones. This may even explain why his numbers are (or so I've heard) slightly too good to be true.
Posted by: user-illusion.myopenid.com
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May 1, 2012 3:42 AM
"supersede" makes perfect sense. "supercede" makes no sense.
Not well-educated in what's relevant to properly spelling "supersede". As for "supercede" being in the dictionary, it's a concession to descriptivism, along with entries like "irregardless" -- but, as Merriam-Webster says, "It continues, however, to be widely regarded as an error.". Someday "lead" will enter the dictionary as an alternative spelling for "led" because so many "well educated" people can't manage to properly spell this three letter word.
Posted by: user-illusion.myopenid.com
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May 1, 2012 4:03 AM
A much more reasonable response to Dr. Syvanen than what he received here can be found at http://www.pandasthumb.org/archives/2005/08/the_last_univer.html
Posted by: stephen.trigg
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May 1, 2012 12:20 PM
The most fascinating aspects of creationists "forest of life" offensive is that either (a) proto-life emerged many times from the chemical soup or (b) speciation isn't nearly the boundary we'd imagined. In the first case, bio-genesis is commonplace (no gods need apply) and in the second that cats and monkeys can swap genes (well, the bacterial equivalent of cats and monkeys anyway). It is therefore a greater refutation of creationist nonsense than of evolution... as is almost anything that is factually correct.
Posted by: https://me.yahoo.com/a/6Y_kgetigd7xjEHMzt_AcLBRdzP6#24202
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May 1, 2012 6:15 PM
You know when Creationists tell me they do not "Believe" in the Theory of Evolution, My reply is; What makes you think you were given a choice?
To say that you Believe or do not Believe in a Scientific Theory implies that you are given a choice. If someone were to come up and tell you that they do not "Believe" in the Theory of Gravity does that mean Gravity ceases to exist and everything floats away? Nope. If they were to tell you that they do not believe in the Heliocentric Theory does that mean the Earth stops revolving around the Sun? Not a chance. Scientific Theories do not require nor allow Belief.
Scientific Theories are not a popularity contest and Science is not a Democracy. Scientific Theories happen whether people Believe in them or not. I tell them I don't believe in the Theory of Evolution, I understand it and accept it. No belief is necessary nor is it allowed.
How many times have you given facts to a creationist and they dismiss it by saying; "I don't Believe it." To me this is one of the Greatest crimes religion has ever committed against mankind, Teaching people that facts require belief or they are not facts.
So the next time a creationist tells you they do not "believe" in a Theory/Fact, Instead of going into an explanation of Evolution or whatever fact you are presenting instead ask them; "What makes you think you were given a choice?" Then sit back and enjoy the "Deer In the Headlights" look on their face.
Posted by: Michael Syvanen
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May 2, 2012 3:04 AM
Thank you user-illusion.myopenid.com for that link to the last time I presented my case against LUCA.
I just reread the comments there and even if they are 7 years old, they are the arguments that I would make today.
I continue to find it amazing how difficult it is for many people I consider quite rational in many respects will continue to adhere to ideas that are really no longer needed -- in this case the notion of LUCA.
Posted by: David Marjanović
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May 2, 2012 11:12 AM
"Move over", "steamroll over", makes more sense than "sit above". That's how the misspelling must have arisen and spread.
Cedere does not mean "move", it has a narrower meaning that wouldn't fit here. But few people are taught that much Latin anymore. What sense does it make that you need to study Latin for a year or two in order to be able to spell English?
Indeed. This example is a very good case for Opinion 16.
Thank you, I was unaware of most of that discussion. I now have a few questions for Dr. Syvanen:
1) Organisms that use the same genetic code, or perhaps very similar ones, can engage in HGT. The largest community of organisms that shares a genetic code can engage in the largest amount of HGT, which may be an advantage in many situations. When there are several such communities, it may therefore be expected that the largest one outcompetes all others. Fine. But if that has happened, don't all extant organisms descend from the last common ancestor of that one community, so there's again a LUCA? – Of course, the universal genetic code is optimal or nearly so, so it may have evolved several times separately. But this requires that the competition between the abovementioned communities only happened at such a late stage that the universal genetic code (or something very close to it) had already evolved at least twice, doesn't it? Because that would strike me as an unparsimonious assumption.
2) You say that the addition of arginine and tryptophan to the genetic code happened after Bacteria, Archaea and Eukarya diverged, and cite papers that tried to date these events by molecular divergence dating. How were those studies calibrated? Can they even be properly calibrated? Divergence dating requires both internal and external calibration points, which must have a wide distribution of ages, or it will suffer from systematic error. (I can provide references for this upon request.) And no, to use the divergence between plants and animals or that between fungi and animals as a calibration point is not good science, because the ages of these events can themselves only be estimated by molecular divergence dating analyses that themselves lack old calibration points. This is one of the main points of the famous "Reading the entrails of chickens" paper (Shaul & Graur, 2004 or so).
3) You ask repeatedly how it is possible to have two lysine tRNA ligases, unless they evolved in different lineages and were brought together by HGT. Well, that's easy: the same way chickens can have several albumins, one of which arose by gene duplication from a crystallin, an eye-lens protein. Both ligases apparently work equally well, so selection cannot act on them – there's no advantage in losing one.
Finally, does somebody have access to this paper?* Does it say that the universal genetic code arose from the fusion of two separate codes that evolved in two separate lineages? That still wouldn't mean the universal code arose more than once (in LUCA or one of its ancestors).
* My institution doesn't. That's rather baffling given what kind of institution it is, but not surprising given what kind of prices $pringer charges. They're the ones whose profits are 42 % of their revenue.
I like that. I like that a lot.
Well, frankly, you blundered in here assuming that everyone was familiar with your arguments. For better or worse – indeed, for worse –, that is not the case. You were inevitably misunderstood. :-|
Posted by: Owlmirror
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May 2, 2012 12:42 PM
Really?
I'm less than enthused.
It looks likes something designed to "win" by confusing the interlocutor ("Deer In the Headlights" look), rather than actually making a persuasive and convincing case that they need to re-examine their reasoning and understanding of the evidence.
I don't think that a lot of science is immediately obvious, and that includes evolution. People have a "choice" not to believe it, because there's no immediate penalty to not believe it, any more than there's a penalty to believing that the sun goes around the earth, or that gravity works by some other method than Newtonian universal attraction or Einsteinian space-time warping (I've seen a particularly perverse geocentrist argue for a fringe notion of "pushing" gravity -- no, I don't think it makes sense, but neither does it mean that he thought that gravity didn't exist).
It even seems possible to me that a quick-thinking creationist might well trot out, in response to the question asked, "Why, yes, we do indeed believe because we were given different choices, by God. I choose to believe in God, so I interpret everything through the lens of the Bible, and you choose not to believe in God, so you interpret everything through the lens of evolutionism." And so on, blah blah blah.
Creationism has gladly embraced some aspects of postmodernism. It needs to be argued with, not "defeated" with a single "zinger" question.
Posted by: Owlmirror
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May 2, 2012 1:04 PM
I'm not entirely convinced of the argument against LUCA. Do HGT events really render the question moot, rather than adding complexity to the model of inheritance?
Consider a bunny with GFP added, glowing greenly. While a tiny fraction of its genome was "horizontally transferred" (by humans) from jellyfish, does that completely render its descent from ancestral rabbits, Glires, and mammals, moot?
What percentage of the early genome results from HGT? Is it known? Is it even knowable?
I probably need to re-read the old Panda's Thumb article and comments, though, to make sure I understand the points. The answer (or answers) may be stated there, or implied, and I just didn't get it.
Posted by: Michael Syvanen
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May 2, 2012 10:17 PM
David Marjanović poses some interesting points and questions. I will try to address a couple of them.
His point #1. A scenario is presented that posits a LUCA that gave rise to the modern genetic code. That is quite plausible but there are many other scenarios that can have multiple lineages working in parallel that evolved the code (lineages that have in fact given rise to modern clades).
I cannot prove that LUCA never existed, my point is that it is not needed to explain life as we know it today.
His point #2. I agree with most of this argument that we cannot use the molecular clock to date events that happened that far back. My argument here about arginnine and tryptophan does rely on any absolute time calibrations. It was interpreting tree topologies, namely the significance of the star phylogeny.
His point #3. I am not sure of the significance of the chicken albumin story here. I did a quick google search and did not see what it was about those albumins make it relevant to this discussion.
Posted by: Owlmirror
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May 2, 2012 11:20 PM
David Marjanović @#38:
(emph mine)Michael Syvanen @#41:
He was responding to this part of your argument from the article on Panda's Thumb in 2005.
(emph mine) (emph mine)Or in other words, the non-homologous albumin genes are analogous to the non-homologous lysine tRNA genes. He's making an argument from analogy to answer the question you asked in 2005.
Posted by: David Marjanović
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May 3, 2012 8:42 AM
Of course. I didn't mean to suggest otherwise – I'd elaborate immediately, because without an explanation it would sound like I'm forcing them to believe something by sheer megalomaniac authority.
Fine, but is this more parsimonious than a single origin? If so, is it much more parsimonious?
I'm a phylogeneticist*, I'm used to not proving or disproving anything but just making parsimony arguments.
*of limbed vertebrates, so greater deviations from a tree than those found in this paper are unlikely.
Or indeed the 2002 paper in TREE.
Exactly. It's possible to evolve an albumin gene when you already have one, without replacing it; so I guess the same may hold for lysine-tRNA-charging enzymes.