First off I must apologize for doing another post on a subject that’s been done to death around here, but I’ve been meaning to make a post about this for a while but other stuff kept coming up. Anyway, things have quietened down at work where I now only have to maintain some cell cultures, so I have a bit of time duing the christmas holiday.
My post, which is a repost of something I also brought up in a thread on Larry Moran’s sandwalk blog, is about a chapter in Stephen Meyer’s book Darwin’s Doubt and what I can, if I’m being generous, only attribute to extremely shoddy scholarship.
Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:
“Axe had a key insight that animated the development of his experimental program. He wanted to focus on the problem of the origin of new protein folds and the genetic information necessary to produce them as a critical test of the neo-Darwinian mechanism. Proteins comprise at least three distinct levels of structure:4 primary, secondary, and tertiary, the latter corresponding to a protein fold. The specific sequence of amino acids in a protein or polypeptide chain make up its primary structure. The recurring structural motifs such as alpha helices and beta strands that arise from specific sequences of amino acids constitute its secondary structure. The larger folds or “domains” that form from these secondary structures are called tertiary structures (see Fig. 10.2).
Axe knew that as new life-forms arose during the history of life—in events such as the Cambrian explosion—many new proteins must also have arisen. New animals typically have new organs and cell types, and new cell types often call for new proteins to service them. In some cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins. But more often, proteins capable of performing new functions require new folds to perform these functions. That means that explosions of new life-forms must have involved bursts of new protein folds as well.”
In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiates that the cambrian diversification, or indeed any kind of speciation, or the that new cells types or organs, requires new protein folds. ZERO. Not one single reference that supports these claims. At first It reads like what I quote above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that attepts to address how hard it is to evolve new folds(and that work has it’s own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.
Meyer mentions Ohno:
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. When these molecules originated in Cambrian animals, they also likely represented a completely novel folded structure unlike anything present in Precambrian forms of life such as sponges or one-celled organisms. Thus, Axe was convinced that explaining the kind of innovation that occurred during the Cambrian explosion and many other events in the history of life required a mechanism that could produce, at least, distinctly new protein folds.”
No reference is given here either. The claim is simply made initially, so it’s hard to check. Is Meyer and Axe willing to bet that a preceding evolutionary history of, for example, Lysyl oxidase cannot be found in structure and sequence of related molecules? That there ARE no related molecules? Is that his claim? That the Cambrian explosion required tonnes of bona fide Orphan proteins with no preceding history? Where are the references that support this? Did Meyer or Axe look for homologues of Lysyl Oxidase and found none?
It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”
Well, much later in the same chapter, Meyer finally references Ohno:
“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21”
What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.”
What does that reference say? Let’s look:
“Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the
mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”
The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.
Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:
“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”
Where does he get this? His ass, that’s where.
How do I move this into the proper categories? Seems there is no option to edit once it’s been posted.
Rumraket,
Post-editing after publication is disabled. I’ll add a page break and categories if that’s OK.
PS if you need more editing PM me (or another admin).
And there’s a major crack in that source.
Glen Davidson
It’s interesting that the entire diversity of proteins in Life is accounted for by just 1282-1393 different folds (differences due to the classification method, but only a 4% error bar). It certainly doesn’t seem beyond the bounds of possibility that this ‘library’ was pretty much complete prior to the Cambrian (which is after all 85% of the way to the present era from the earliest cells). No new ones have been identified since 2008. I’d be interested to know which new folds have been identified in the animals, and whether any equivalent transition has been observed in any less self-centred groups – analysis of the distribution of these folds by taxonomic group would be useful. It’s probably been done; ain’t got time to look.
Interestingly, the same fold can be generated by apparently unrelated amino acid sequences. However, these do not have to arise independently in a ‘Hoyle-o-matic’ (TM) Amino Acid Randomiser. There is substantial lability at each individual site, provided the overall structure remains. Thus, acids can be substituted one by one, erasing the signal of common descent.
I recall some work by Axe where he substituted acids on the protein surface only, and showed that folding is rapidly inhibited by this targeted attack on the hydrophilic residues. However, there is no known evolutionary process that does this – mutation has no information as to where in the protein the residue will end up. There are far more potential pathways if you allow for amendment at any site. Eliminating evolution as a cause requires elimination of all paths.
The paper Petrushka has highlighted in this recent OP demonstrates that multicellular Eukaryota were well established at least 600 million years ago (there’s a reference in the paper to an earlier paper discussing evidence for sponge-like animals 800 million years ago). What strikes me about the organisms first seen in the Cambrian period is eyes and armour, suggesting a radiation of adaptive changes due to an “arms race” with some species adopting a predatory lifestyle while other species evolve ways to avoid predation.
Creationists draw lines in the sand and scientists ignore them when looking for evidence.
Allan Miller,
Interesting paper popped up which indicates viruses have many folds in common with cellular life, plus 66 unique to them. I predict we won’t see much about the implications of this for Intelligent Design.
While I have a certainly amount of respect for Dembski’s writing, I have none at all for Meyer’s. I don’t think he writes “in good faith”. He’s got a good enough brain and a good enough training in scholarship to do due diligence. That he doesn’t makes him simply lying in my view.
He must know how deceptive he was being in Darwin’s Doubt, even if he half believed what he was writing in Signature in the Cell.
Meyer: “The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures. “
There’s lysyl oxidase in yeast. For supporting bread and the head on a pint?
Try doing a protein blast for the amino acid sequence of lysyl oxidase. The protein has 3 billion year old homologues.
At one percent change per 10 million years, that’s a hundred percent in a billion years.
I know the math is bad, but nevertheless…
Bacteria had a long time to erase the origins of their protein codes.
Your complaint is that he fails to cite sources for certain of his claims. I think the charge of extremely shoddy scholarship could only be maintained if it could be shown that Meyer is utterly wrong and that he would know that if only he had done his homework. You’ve failed to show that is the case.
Moreover, I would think it obvious that new proteins would be required given all the new animals that appeared in the Cambrian, and that it is the claim that all the proteins already pre-existed in some hypothetical ancestor that is the extra-ordinary claim that requires evidence. Again, you have failed to make that case.
To borrow a quote from Alan Fox, “This OP is a waste of pixels.”
More Feature threads like this one please!
True or false?
Or is the complaint that Meyer failed to cite a source or sources for this claim?
As a general standard, good scholarship includes citations of the primary literature for all assertions about evidence (unless one has generated that evidence oneself), the scholarly and scientific views of others, etc. Secondary sources won’t do. No exceptions.
Its function is to permit readers to evaluate those sources directly rather than having to accept the author’s characterization of that literature.
So it’s not enough to get it right. Citations of the primary literature are required.
Standards are much more relaxed in the popular literature.
My understanding is that Meyer is claiming that a very large number of shiny new proteins appeared almost overnight. He’s writing about the Cambrian, not about the history of life. This is an extraordinary claim, not compatible with any broader understanding of the appearance rate of new proteins.
If you start making claims contrary to a well established understanding in a field, you probably need more sources for them, then if you are simply reciting what has been commonly accepted (and usually well researched).
I think it is revealing that he is completely wrong about the claim that is central to the book’s theme, and he fails to cite supporting evidence.
If one is attempting to overturn all of established biology and geology, it behooves one to get the facts tight. Or, if one is wrong, at least be in good company.
No points for quote mining.
What a scurrilous attack on Meyer.
Too bad for the IDiots every word about Meyer’s duplicity is true. Must make your moral compass go all haywire to know you’re supporting such a liar and con man.
It wouldn’t take many words or complicated words to disarm Meyer, if what he claims were true. Problem is, his books are garbage.
Some of the errors were known immediately. More of it unravels year by year as new findings appear.
Please do not discuss site rules or the awarding of points in general topics.
There is a thread for that, which the site owner occasionally reads and ignores.
False. According to Meyer’s one an only eventual source (Ohno).
How would you explain it then? Meyer goes on and on about the claim, then eventually cites a paper that argues the diametrically opposite.
False. According to Meyer’s one an only eventual source (Ohno).
What you find obvious is irrelevant. Meyers only reference makes the case, which is diametrically opposite to Meyer’s claim.
Taking Meyers example protein Lysyl oxidase, it’s present in bacteria with sequence similarities going below 40%.
I need say no more, he’s a rank amateur at best.
It’s my judgement. It’s harsh, but it’s the conclusion I draw from the evidence of his writing. I don’t think it’s unfair, therefore I do not agree that it is “scurrilous”.
Mung,
As it stands, he is just guessing. Add “I reckon” to the end of his sentence, to add force to the ‘must have’. There must have been …. oooh … loads!
It is possible to do a tree-wide analysis of the distribution of proteins and see which are (according to the method used) new to metazoa and which aren’t. So, which are? Lysyl oxidase isn’t for starters.
Yeah the funny thing is, we see the largest diversity of proteins in the class of “life” that evolve the fastest. This is just another line of evidence that supports evolution.
Here’s a curious paper btw: Divergence pattern of animal gene families and relationship with the Cambrian explosion.
Meyer, oh Meyer.
Mung,
So, Meyer states what is ‘obvious’, that new proteins ‘must’ have been involved, given all the new animals, and you accept it without demur. Anybody wishing to counter that claim (such as biologists, who know a thing or two about the protein requirements for ‘new animals’, and the taxonomic relations of proteins) must back it up! Priceless.
The vast bulk of the protein repertoire of animals with common ancestry in the Cambrian has homology in other groups outside of that clade. I’m not aware of an exception, though I’m sure there may be some. A reasonable inference is that the protein was also present in their common ancestor, and hence ‘pre-existed’.
Pick an ‘animal’ protein and I’ll let you know. Actin, myosin, haemoglobin, lysyl oxidase … ? [Pssst! try collagen!]
There’s more here: The importance of preadapted genomes in the origin of the animal bodyplans and the Cambrian explosion.
This paper Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes, shows no correlation between the origin of fold families and the cambrian explosion. Most folds seem to have originated in bacteria and early eucaryotes hundreds of millions of years prior to the cambrian, and subsequently shared and secondarily adapted for other functions later.
From the Miyata & Suga paper:
Of course, gene duplications aren’t strictly ‘new proteins’ anyway. I’m presuming that a new protein in Meyer’s terms is one with no homology anywhere. To identify a duplication, we must have some homology. When we add structural scoring, we can recover even deeper apparent homologies, where the digital signal has been erased but the constraint of structure remained constant.
Granted you can’t directly prove that two distinct sequences with the same fold are homologous, but I don’t see how Design would be the superior explanation of the commonality there. Especially when, with a rich enough dataset, you can virtually watch the sequence signal being eroded to nothingness, just the Cheshire-cat grin remaining.
Is this part of your campaign to increase participation here at TSZ and make it a friendlier place for theists and ID supporters?
You must support your claims or retract them.
“… it is the claim that all the proteins already pre-existed in some hypothetical ancestor that is the extra-ordinary claim that requires evidence. Again, you have failed to make that case.”
But, but, but, I found one, and that’s all I need. Good grief.
True or False?
So far I’ve seen one qualified false, which says that if we consult one source in the literature cited by Meyer then we have definitive evidence that it is not the case that as new life-forms arose during the history of life many new proteins must also have arisen.
Franky, I can’t believe that anyone would deny that as new life forms arose during the history of life that no new proteins must also have arisen. Are you all claiming that all known proteins already existed in the LUCA?
It’s the only example Meyer brought up. It was the first one Ohno mentioned, he apparently didn’t bother actually reading Ohno’s paper (it contains several other examples, and argues they all predate the cambrian).
You can’t fault me for simply using the same example Meyer does. You can’t fault me for correctly reading Meyer’s only reference.
Mung, please read the rest of the posts.
Mung,
You’re a funny guy, Mung. Who has claimed that ALL animal proteins pre-existed, and who claims that finding one supports the claim that most animal proteins have homologues?
Meyer has claimed that the Cambrian explosion ‘must have’ involved lots of new proteins – proteins with no homologues in sister groups, I take that to mean. And you agree. So I’m inviting you to find one. Lisyl oxidase, Meyer’s example, doesn’t work. It has homologues.
Mung,
Lizzie also thinks she knows more about biology than Meyer. Oh, and she also knows more about it than Cornelius Hunter. Heck, she doesn’t even need to study it.
You know when all the atheists here always tell their opponents to go study biology textbooks. Apparently they don’t actually believe that’s important.
Allan Miller,
I agree Mung is funny.
Mung,
There is no denying that, as evolution progresses, new proteins ‘must’, from time to time, appear. What is in dispute is that this has much to do with the Cambrian Explosion as opposed to any other 10-50 million year period of history. Meyer is asserting that the common ancestry of animals in the Cambrian is associated with a burst in protein novelty – that the change in the fossil record correlates with a significant step change in genomes. There is no evidence for this. We can look at Cambrian animals [eta – through their descendants, natch], and compare with sister groups, and we don’t see any such discontinuity.
Clearly and unambigiously false, as Meyers one and only reference showed already to begin with, using multiple examples of which Lysyl oxidase is merely the first. I have linked it, why haven’t you read it yet? Why hasn’t Meyer?
Mung, seriously. Read the fucking paper Meyer himself cites.
Yes, it shows this and you have not dealt with the arguments therein. Now you’re just pretending that because I’m seemingly the only person unambiguously saying it’s false, that serves as justification for shifting the burden of proof away from Meyer (and by extension you, who believe him) demonstrating the truth of his claims.
What you’re doing is functionally equivalent to saying “Meyer said it, I believe it, that settles it until you can prove him wrong to my satisfaction, which requires you to bring tonnes of literature before me, read it and spoon-feed me it in tiny digestible quotes”.
Please be an adult about this Mung.
Nobody is saying NONE arose during the cambrian, Mung. Now you’re moving the goalposts. Rather the claim is that the diversification of the cambrian explosion was overwhelmingly one of changes to cis-regulatory networks, instead of vast swathes of de novo protein evolution.
Please make an effort to understand the differences between words like “most”, “some”, “all”, “none” and so on. Meyer has turned the claim around, he’s saying the cambrian requires MOSTLY de novo protein inventions. READ WHAT I QUOTE:
Notice the bold (mine). That is OPPOSITE of the facts. Meyer is claiming the OPPOSITE of what is true. The OPPOSITE of what his one and only reference shows. It should read:
In most cases new proteins, while new in function, would perform them with essentially the same fold or tertiary structure as earlier proteins. And much less often, proteins capable of performing new functions require entirely new folds to perform these functions. That means the explosion of new life-forms would have mostly re-used already established protein-folds during the cambrian diversification.
That’s how it SHOULD have read if Meyer had bothered to actually read the Ohno paper he cites. And no, Ohno’s paper is by no means the only one. It is rather interesting, also, given how diverse the literature actually now is on regulatory evolution, that Meyer chooses to cite this rather old and single reference by Ohno.
No, I’m claiming the vast majority have arisen way before the cambrian, and that the cambrian is not at all correlated with an increased frequency of new folds evolving. Obviously new folds have arisen since 3.5 billion years ago, which you would know if you read all the references thus far discussed.
I don’t want to read you responding before you’ve read this, because right now what you’re doing looks like volitional ignorance. It’s like you’re trying to stay away from information that would force you to reconsider your views on Meyer and his book. I’d like to be wrong here.
If you read the Miyata and Suga paper, you will see that their evidence suggests that the Cambrian was not a time during which a great many new proteins arose and that Cambrian proteins appeared considerably earlier. That doesn’t mean they were all there in “the LUCA” (which isn’t a constant anyway- the LUCA of Cambrian organisms wouldn’t be the same as the LUCA of currently extant organisms. Did you mean the FUCA? The answer is also no.)
If criticising a published ID author makes TSZ unfriendly to theists and ID supporters, then there isn’t much point in even having a place to discuss ID ideas. It is my view that Darwin’s Doubt is either extremely incompetent or Meyer is dishonest. As I don’t think he is incompetent (even though the material is not his field, he has decent scholarship training and is not stupid), I can only include that he is dishonest.
Theists and ID supporters are free to point out that I am wrong.
It is supported by this OP for a start, coupled with the evidence that Meyer is a trained scholar. For my inference to be wrong, either Meyer is not as smart as I am crediting him as being, or the errors of fact and scholarship in his book are not as egregious as and others have claimed.
They seem pretty egregious to me.
I know more about some aspects of biology than both, yes. And yes, I have studied biology. I actually work and teach in a medical school.
I believe it’s important. I recommend that Meyer try to come to terms with the extant literature on the evolution and development of organismal form. Meyer might know more about biology than I do, but then that just raises some serious questions about why he’s got it so wrong in his book.
What is your explanation for that?
I’m not faulting you. I’m just saying you’re engaged in shoddy scholarship. 🙂
Okay, you’re free to say that.
But Rumraket is not engaged in shoddy scholarship.
So there’s that.
Right now I am trying to take this one step at a time, trying to figure out just where people think Meyer went off the rails. I’m doing my best to pretend I’m an adult.
The question is a very simple one. True or false:
… as new life-forms arose during the history of life … many new proteins must also have arisen.
I say it’s true. I haven’t seen a good reason to think it’s false. I think it would be an expression of good faith on the part of the Meyer critics if they agreed that it’s true.
Unless they want to insist it’s false.
We need a voting option here at TSZ. 🙂
I agree too, but I am definitely biased.
ok, cool. I’ll take that. If I want to say that Meyer is not lying or and not being dishonest, so far, I would be correct. So let’s move on to Meyer’s next statement.
True or false:
Just looking for where Meyer goes off the rails. Looking for where he starts lying and trying to deceive people.
It appears to be something in the water here at TSZ.
Let’s be clear about the context and use correct terminology, we are talking about the Cambrian Explosion, and new protein FOLDS. Not the entire history of life, and not just “new proteins” (it’s kinda hard to guess what is meant by a “new” protein, but Meyer’s actually talking about folds, so that makes it much more clear). So there’s a lot of missing context hiding in those ellipses.
With the added caveat to your quotes, that we are discussing the cambrian explosion, and the origin of new protein FOLDS – I claim it is false. I hereby arbitrarity define “many” new protein folds to mean 20 new protein folds. If we can find 20 or more new protein folds have arisen in the cambrian explosion, then indeed there has been “many” new protein folds arising. Do you protest this number?
That’s cute Mung. Try reading Meyer’s only reference. Try reading the additional ones I have brought, and the one Allan Miller linked.
I think it would be an expression of gullibility if we just agree it’s true, particularly when we are already in possesion of knowledge from actual research, that it is false.
If I knew nothing about biology I would probably agree with Meyer. It sounds intuitively plausible that the “new life forms” arising during the cambrian explosion, also come with “new protein folds”.
It’s just too bad that, in general, they didn’t. So my mere intuitions turned out to be of no value in determining what is true.
If calling someone a liar, dishonest, a deceiver, a con man, and claiming they are not posting in good faith are all valid forms of criticism, why are they against the rules here at TSZ?
You are engaging the the very sorts of activities that you frown on as detrimental to the goals of the site and now trying to defend them by saying discussion here would not be possible without them.
Well, I’d just like to express my skepticism about that. I think TSZ could get along just fine without you and others making such claims about ID authors and sticking to content and ideas.
I have a dream …
What do you mean with “so far”? You have not quoted Meyer here, you have quoted Allan Miller. And Allan’s statement diametrically opposes Meyer’s. Since Allan’s statement is supported by actual data, and Meyer’s is not and in fact is contradicted by the only reference Meyer himself gives, then no, it is not possible for you to be correct “so far”.
What do you mean by “next”? What was his previous statement that has not “so far” been shown to be false?
False.
To say that they “typically” have new protein folds servicing them is false, because it is actually a-typical. They usually don’t.
Right there where you actually quote him. The statement he makes is actually the opposite of the truth.
It SHOULD have read:
“New animals typically have new organs and cell types, but new cell types rarely call for new protein folds to service them. In most cases new proteins, while functionally new, would perform their different functions with essentially the same fold or tertiary structure as earlier proteins.”
He inverted the truth. He gave a single reference that argued the opposite of what he claimed. That’s either incompetent, or dishonest.