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.
Rumraket,
PhD-in-something-non-biological Torley remarks: “I don’t know what Rasmussen’s background is, so I’d be wary of assuming that he “gets” anything about new protein folds. “.
Snort!
Allan never-finished-his-PhD-but-at-least-his-degree’s-relevant Miller.
Exactly!
It’s supposed to be about new protein folds, or the lack thereof. At least that’s what I’m told. And it’s about the phylogenetics, or so I am told.
So the OP could have shown that all extant protein folds in animals pre-date the Cambrian animals.
Easy peasy.
Well, see, look on the bright side. Now you have a topic for your thesis.
Front Loading of Protein Folds Necessary for the Cambrian Animals Supports Theory of Intelligent Design
🙂
And just think. You can quote Meyer! You’re Welcome.
The problem with the OP is that the many claims of Meyer are called into question and dismissed on the flimsiest of excuses.
1. In chapter 10 of Darwin’s Doubt Meyer failed to cite a source for every claim he made in that chapter.
So freaking what. The book contains an extensive bibliography, and only here at TSZ is every author expected to cite a source for each and every one of their claims, except when they aren’t.
2. In chapter 10 of Darwin’s Doubt Meyer actually did cite a source for one of his claims, but that source contradicted his claim.
That source did not contradict Meyer. The Ohno paper had nothing at all to do with new protein folds.
Mung since you seem to be an expert on what Meyer thinks maybe you can clear up a few things.
Meyer says that around 530 MYA give or take the Intelligent Designer came by Earth. Then over the span of 5-10 MY the Designer created all the different phyla we first saw in the Cambrian. Right?
1. Life was on Earth for at least 2 billion years before the Cambrian, including at least 100 million years of multicellular life. Meyer’s explanation for where that life came from and how it diversified is…??
2. After the Cambrian there were at least 5 major mass extinction events including the Permian where 90% of all species went extinct. Meyer’s explanation for how the Designer planned for those events and how the intended future lineages survived is…?
3. After each mass extinction there were major re-radiations of life forms. Meyer’s explanation for the mechanisms that caused the re-radiation is…?
4. Anatomically modern humans didn’t appear on the scene until a few hundred thousand years ago. Meyer’s explanation for how that event is reconciled with his Biblical Christian belief that humans were created special is …?
Go ahead Mung, impress us with your knowledge.
Mung,
Actually, authors are supposed to cite a source for every claim they make in any scientific publication. Meyer’s out would be that his book wasn’t intended as a scientific publication but a popular treatment.
And Meyer does use Ohno as citation for a claim that’s the opposite of Ohno’s claims.
It is.
.. by the author who wrote it, so there’s no use pretending it’s about something else anymore. It would be nice for you if it was about something else Meyer could support, but since it’s about something Meyer can’t support, tough shit.
That would have been idiotic since I don’t actually believe that all extant protein folds in animals pre-date the Cambrian.
Now that your irrelevancies have been dealt with, you can start preparing yourself emotionally and intellectually for the intensely unpleasant experience it will no doubt be for you to concede that Meyer made a claim he not only didn’t support, but can’t support because it’s wrong. Specifically the claim that the cambrian explosion is associated with bursts of new protein folds having to emerge contemporaneously with it.
It is well past the time where you just admit that you have been mislead. You could also take this as an opportunity to show you have some integrity and don’t just play “your team” even when they’re wrong. That truth matters to you.
They’re dismissed because they’re not the point of this thread, and many of them are simply not in contention. For example, I do not contest the claims that animal diversification required new cell-types, new organs or new functions of cells. That’s why I’m not constantly writing about it, because it actually true according to what I know.
The very reason I’m focusing on protein folds, instead of all the other stuff, is because I happen to know that particular claim is wrong, and that Meyer’s one and only reference argues for a position opposite to Meyer’s.
Yes it did, in fact, contradict Meyer.
Meyer here clearly claims the protein folds emerged and had to emerge in the cambrain explosion.
Ohno argues they had to already exist.
Phylogenetics does not and cannot speak of a mechanism. That means no one can test the claim that natural selection, drift and/ or neutral changes can account for the Cambrian diversity
It’s true that phylogenetics isn’t about mechanisms. But after you do the phylogenetics you can reconstruct character evolution on the tree and estimate what changed and when. Then you can determine if that sort of event could plausibly occur by known processes. That doesn’t say it did, but it does say it could have. There are even phylogenetic tests (i.e. using character change on a tree) for natural selection vs. drift. So in this way one can indeed address, to a certain degree, mechanisms operating in the distant past.
John Harshman,
Matzke proved that phylogenetics would result in a tree even if a common design was involved.
Has anyone ever seen Meyer address these issues anywhere? I thought Mung would know since he’s an expert on Darwin’s Doubt but I guess he’s too shy to answer.
I want to see Meyer’s prediction of multicellular fossil discoveries that significantly predate the Cambrian. Where is Meyer’s tiktaalik? If Meyer didn’t anticipate micro fossils, what good is his philosophy of biology?
Mung,
‘Cept it doesn’t. There is simply a vacuous … uh … hypothesis that everything supports ID. Even eclipses.
Mung,
Uh .. isn’t it initially up to Meyer to support his contention? IDist says stuff, you swallow it whole and spend no end of time word-gaming what the OP is about. Now you seem to have finally conceded it is about protein folds, but seem to imply Meyer was under no obligation to support his original contention.
Because of course it ‘stands to reason’ that loads of new folds would be necessary. That’s all Meyer offers, and the only reason you seem to have for defending it. So now, it’s either loads of new folds or it’s front loading. IDist Grasps Any Straw Shock. I’m off to write an ID friendly book. Getting IDists to part with a dollar seems to be a piece of cake, long as you say what they want to hear.
Adapa,
Give him a chance! Been less than a day.
Just pulling a Mung. Those are the exact words he used to smear Nick Matzke over at UD when Nick didn’t answer a post the same day.
Mung isn’t a hypocrite now is he?
Especially eclipses.
heh. At first I thought you had written even ellipses. But that too.
Not that I am aware of. Can you cite him saying that?
Are you claiming that’s not the position Meyer put forward in Darwin’s Doubt? They what does Meyer say happened in the Cambrian?
Here is the description of the book taken directly from Meyer’s Darwin’s Doubt home page.
http://www.darwinsdoubt.com/book-preview/
What part did I get wrong Mung? Are you going to address the other questions about Meyer’s explanations for the life before and after the Cambrian?
I think you’re wrong. I don’t recall Meyer saying anything like what you attribute to him.
Here it is again:
As far as your other questions, let’s deal with this one first shall we? Can you cite Meyer as saying any such thing?
I cited his own webpage on the book FFS. Are you going to be an asshat like Gallien and play these childish “I don’t see any evidence” game?
What does Meyer give as the cause for the Cambrian explosion Mung? If you don’t know just say so.
An intelligent cause. It says absolute nothing about an Intelligent Designer coming to earth creating all the phyla.
LOL! I suppose that’s why the title of the book says “The Case For Intelligent Design”, because there was no Intelligent Designer of the Cambrian phyla. Or maybe the Intelligent Designer subcontracted out the manufacturing job to the Intelligent Builders.
Your stupid rhetorical games are an embarrassment to normal thinking adults Mung.
Adapa, perhaps you just need to be more clear about what it is that you claim Meyer said. In what sense of the word “created” do you say Meyer claims that “over the span of 5-10 MY the Designer created all the different phyla we first saw in the Cambrian”?
Do you mean “poofed” them into existence out of nothing?
No, Meyer never makes such a claim.
Yes, the title does not say The Case for the Creation.of the Phyla.”
IOW, it fails to support your claim.
Go ahead and tell us how you can have an Intelligent Design make its way into the genomes of all those Cambrian species without an Intelligent Designer / Intelligent Fabricator.
It’s pathetic that all you have are these juvenile words games but pathetic words games are the stock and trade of IDiots like Meyer.
From “Darwin’s Doubt”
As Mung explained, nothing about an Intelligent Designer coming by earth creating phyla.
Termite mounds are, by any reckoning, intelligently designed. They are air-conditioned, temperature regulated, masterpieces of construction which even improve the quality of the soil in their local environment. What intelligence is responsible for building such marvelous structures? Do we have to know or understand where this intelligence lies in order to deem these structures examples of intelligent design? No, we don’t.
From the Darwin’s Doubt Study Guide:
“As a science, ID does not address religious questions about the identity of the designer, but it opens the possibility that life was purposefully designed by an intelligent person that many would identify as God.”
Meyer won’t identify the Designer but he still says there is one and (wink wink) it just may be the Christian God.
You IDiots lost this fight about “if we don’t say who the Designer is then we’re scientific!” 10 years ago. No one falls for the bullshit anymore now than they did then.
Do you want to tell us how the Designs got into the genomes of all the Cambrian animals without a Designer putting them there, even if you don’t say Who it is? Or answer those four questions about the time before and after the Cambrian? Mung certainly lacks the courage to try.
Makes some sense, except that the “we can infer” part is untrue.
What Meyer is left with is an invisible, unnecessary sky fairy.
You can quibble about the nature of the sky fairy, but why bother. Its existence is unnecessary.
CharlieM,
If your aim is to prove to your own satisfaction that intellligence ‘must have’ been involved, you have done that. Do you have no further curiosity on the matter?
It is entirely possible that termite mounds are products of evolution, acting without internal or external intent. The standard ID response to this is a request for some mechanistic detail – the genes and steps involved. But when pressed for detail of their preferred alternative, they simply clam up. The old ‘pathetic level of detail’ gambit. It seems enough for ID to point to something a bit complex, and appeal to the ‘innit-obvious?’ response in readers. An independent observer might find that asymmetry somewhat shallow.
I deem these structures examples of evolution. My work here is done.
Oh, and the Cambrian. Evolution.
CharlieM, one of the frustrating issues in the whole ID debate is the lack of operational definitions. ‘Intelligence’ is one of the two key terms in ID and yet there are about as many different definitions for the term as there are ID supporters. This is a major reason why this debate gets so confusing.
There is a sidebar on Uncommon Descent with a Glossary. There they give this definition of Intelligence:
Using this definition it is incorrect to say that termite mounds are intelligently designed. The only criterion out of the list that would possibly apply is ‘to solve problems’. No case can be built for any of the others, and note the ‘and’ in the definition – it doesn’t say ‘or’, so all criteria have to be satisfied.
In other words, even using UD’s own definition, termite mounds are not intelligently designed. Ironically, using this definition it is actual impossible to detect Intelligence in anything unless one can directly investigate the designer! How else to establish that the designer has the capacity to reason, to learn, to use language?
What is your definition of Intelligence, and to what other things does it apply besides termite mounds?
fG
I don’t think there is any winking going on, Meyer makes no secret of his belief in the Christian God. How he thinks this God created the physical forms of the living world, I have no idea.
It is my opinion that throwing insults is a sign of an argument being lost.
Well firstly I do not believe that the designs are “in the genomes”. Genomes contain the means by which the living substance that is necessary for the further development of an organism can be assembled. The genome can bring about the production of proteins, but it must be under strict control if these proteins are going to contribute towards the development of a viable mature organism. Life begins with a seed or an egg, it does not begin with a bare genome.
As for your four questions, I could answer them from my perspective but that would be irrelevant, and as to how Meyer would answer them you would have to ask him personally. Meyer’s beliefs are of no particular interest to me, but gaining an interest and knowledge about the natural world does interest me.
Sky fairies may be unnecessary but what you are saying is that we already have the answers so we need look no further, or at least we must stay within self-imposed limits.
Well I believe that we have more questions than answers. Just imagine if physicists had said that atoms are the smallest parts of matter, we have no need to look further for anything hidden within them.
Progress in our understanding of physics forced us to look further. And I think that progress in our ability to look more closely at the living world is forcing us to look beyond the current, unsatisfactory, orthodox explanations.
I’ve forgotten the context (I’m supposing it was while looking at some ancient stone edifice), and I suspect I’m far from the only one to have heard such a remark, but someone once remarked to me that “they knew how to build in the old days”. I thought then that the truth is more nuanced. Most old buildings fall down but some (usually the most soundly constructed) survive and builders learn from past builders and past mistakes.
I’ve no difficulty in imagining the evolution of solitary insect to family group to full sociality. I can imagine the variation in types and extent of constructions of mounds and tunnels evolving over time by the process of trial and error. The most interesting question for me is how on Earth the extended phenotype of the termite mound is stored genetically and inherited.
The physical environment is a powerful designer. The physical properties of water, weather and the water cycle, the topography of the Earth and the effects of gravity result in rivers and river basins. Water runs downhill and erodes a river course. Who designs that?
The looking no further bit is both pathetic and funny. What is it you thing evolutionary biologists do? And what exactly do IDists do after they make their sky fairy inference?
And yet every time we pull back the curtain there is never any ‘Intelligent Designer’ there. Do you think it’ll be any different this time?
Of course I do. Do you? Anyone who believes that life is the product of blind, unguided, fortuitous happenings, need look no further. They are satisfied with their belief.
I think it takes a certain gullability to believe that termite mounds are fortuitous accidents. Engineers and designers are more and more looking to nature and copying the innovate designs they find there.
I deem these structures examples of intelligent design in evolution. My work here has not even scratched the surface.
I think of the process as environmental design. Aspects of the structure of termite mounds seem quite obviously at an optimum that could have evolved over time, especially the north-south orientation. How would this be incorporated in the germ line of termite populations intrigues me, as I said. (It also intrigues me that it doesn’t seem to intrigue anyone else here 🙁 )
Meyer’s whole argument is a classic God-of-the-gaps then. We don’t know the detail of how this happened so GAWDDIDIT! That line of reasoning was discarded by science three hundred years ago..
They are of great interest to the scientific community too. If Meyer wants his ideas to get serious consideration as a replacement for evolution then he needs a coherent explanation for ALL the data, not just the little bit he cherry-picked. That means the whole timeline of life on Earth, not just 10 MY in the Cambrian. Meyer won’t touch the questions because he has no handy bullshit answer that would stand up to the slightest scientific scrutiny.
Gaining knowledge about the natural world interests me greatly also. Part of that is keeping lying charlatans like Meyer away from science classrooms by exposing his intellectual mendacity.
I’m curious. Once you’ve decided for intelligent design of termite mounds, what is the next step in your research program, and how does it differ from the next step of a person who thinks they’re due to natural selection?
Just imagine if a non-scientist came out with a popular press book claiming everything science knew about the atomic structure of matter was wrong, and that matter was really held together by jebons. That’s exactly what Meyer is offering here.
CharlieM,
That is not what happens. People who ‘believe’ that way (more properly, see no sound reason to invoke intelligence) investigate where they can. They don’t let the matter rest. I don’t see a shred of such mechanistic investigation coming from your side. You stop dead at your suppositions. You have declared the termite mound intelligently designed. Full stop.
CharlieM,
I think you can shove your insinuations as to my ability to think on the matter up the nearest available orifice. We would need to be rather careful about how we characterised ‘fortuitous accidents’. Evolution is a product of variation and selection.
That hardly proves the copied design was itself designed.
Talk is cheap. Any day now you will start to demonstrate what lies beneath that surface, and go beyond the ‘duelling deems’ level. Any day now … that is, positive support for ID at the same kind of level that you expect evolution to provide.
Like “evolution”, “Intelligence” is one of those words that can never be fully described by a definition. Do you think that every ID proponent would agree with the definition provided at Uncommon Descent?
But without knowing anything about the designer we can still compare designs and judge which involved more intelligence. Take for example the British Comet airliner. Comets underwent a major modification. There were two types of window, one angular with ninety degree corners and the other in which the corners were rounded. Assuming you know nothing of the designers do you think you would be able to determine which is the more intelligent design?
I think that intelligence is innate throughout the natural world, not just in termite mounds.
CharlieM,
Are you suggesting that biology results from multiple designers of varying intelligence? Or one designer with off days?