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Friday, September 06, 2013

Darwin's Doubt: The Genes Tell the Story?

The main goal of Intelligent Design Creationism is to cast doubt on modern science, especially evolutionary biology. Most of the IDiot books are devoted to attacks on evolution. The underlying assumption is that if modern science is discredited then "god-did-it" becomes a viable alternative.

The latest book by Stephen Myer is no exception. The theme is that evolutionary biologists cannot explain the Cambrian Explosion; therefore, God must have created all the animals in the space of a few million years back in the Cambrian Era (about 530 million years ago).

Most of the book is about the lack of transitional fossils that document the slow transition from primitive worm-like creatures to modern phyla such as arthropods and chordates. Others have dealt with this and I'm not going to comment because it's outside of my area of expertise.1

There is strong evidence from molecular evolution that the major animal phyla share common ancestors and that these common ancestors predate the Cambrian by millions of years. In other words, there's a "long fuse" of evolution leading up to the Cambrian Explosion. Meyer refers to this as the "deep-divergence" assumption.

There are many versions of these trees. The one shown here is from Erwin et al. (2011). It's the one shown in the book The Cambrain Explosion by Douglas Erwin and James Valentine. It isn't necessarily correct in all details but that's not the point.

The point is that molecular phylogenies demonstrate conclusively that the major groups of animals share common ancestors AND that the overall pattern does not conform to a massive radiation around 530 million years ago. Also, it's very clear that the pattern is consistent with evolution and not with God creating all the animals at once.

Stephen Meyer has to address this evidence because it casts doubt on his main theme (God did it). I suppose I don't need to tell you what he says ... it's typical creationist denial. He claims that the evidence doesn't exist. Here are his reasons ...
  1. There are no fossils to support the earliest branches in the molecular phylogenies.
  2. There are many different molecular trees and they don't all agree with each other in terms of branching order and timing.
  3. Evolutionary biologists cherry-pick the data by only picking molecules that give reasonable trees.
  4. The trees rely on questionable assumptions; namely, that the molecular clock ticks at a constant rate and that there is a universal tree.
  5. The molecules being compared must be homologous but this is what is being tested so the argument is circular.
The conclusion is ....
Comparative genetic analyses do not establish a single deep-divergence point, and thus do not compensate for the lack of fossil evidence for key Cambrian ancestors—such as the ur-bilateran or the ur-metazoan ancestor. The results of different studies diverge too dramatically to be conclusive, or even meaningful; the methods of inferring divergence points are fraught with subjectivity; and the whole enterprise depends on a question-begging logic. Many leading Cambrian paleontologists, and even some leading evolutionary biologists, now express skepticism about both the results and the significance of deep-divergence studies.
I'm hoping to find time to go over each of Meyer's objections since they reveal a lot about IDiot misconceptions of evolution (and science) and a lot about how they employ strawmen, lies, quote-mining, and distortions in order to discredit an entire field (molecular evolution).2

1. Most IDiots are experts in everything. I'm not as smart as they are.

2. It always amazes me to discover that IDiots like Stephen Meyer think they know more than thousands of expert biologists who do this sort of stuff for a living.

Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [doi: 10.1126/science.1206375]


Newbie said...

You are such a character...
Are you bored? Let's have a couple of beers at the bar of your convenience and you can tell me all you want.... Which one do you like in Streetsville? I'm into the Spanish side if you like the wings...But I'm flexible

Mikkel Rumraket Rasmussen said...

Poor Meyer, he might want to try and deal substantively with studies such as these:
Beyond Reasonable Doubt: Evolution from DNA Sequences
W. Timothy J. White, Bojian Zhong, David Penny

We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10^−19 and combined over 8 datasets is ≈1×10^−132. By comparison, there are about 10^80 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 10^50 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution.

Newbie said...

Oh... Did you read the book? My wife got it for me even though I specifically requested Behe's "The Edge of Evolution"???. She could not explain why the Library system in Streetsville is a mess and gave her this... The Doubt?

Mikkel Rumraket Rasmussen said...

Funny thing is, Meyers book has been moved from Science to Religion on Amazon. AHahahaha... XD

Schenck said...

I feel like the creationist arguments so often amount to a bait and switch, along the lines of "Molecular phylogenies aren't perfect, we should be skeptical, there's a number of potential clearly they were designed and it was by god".

Robert Byers said...

Modern creationism purpose is to discover and teach the truth. not undermine evolution but simply it works out that way.

Molecular evidence is not scientific evidence for evolution. Its just a line of reasoning that one can extrapolate backwards from present molecular structures to past structures and so relationships .
Is it scientific evidence, a high standard of methodology, that is behind the idea of extrapolation??
I say it isn't.
Even if trur it still wouldn't be.
The problem with evolutionism has always been its illegitmacy in claims to having used scientific methodology. !
Evolution is not a scientific theory. Even if it was right as rain.

John Harshman said...

Mind if I play through?

Chapter 5: The genes tell the story? Meyer starts by attacking the molecular clock, which is admittedly an easy target. Estimates of the age of the bilaterian common ancestor vary widely depending on data and methods. To Mayr this means that all such estimates are meaningless, but that isn't necessarily true. We might, in fact be learning more about how to do it right. But I will agree that error bars should generally be wide. Meyer does however compound the problem by failing to clearly distinguish at least three separate nodes: Metazoa, Bilateria + diploblasts, and Bilateria. These all presumably have different ages, so randomly listing dates as if they all estimate the same thing is a problem. We now also believe there are multiple clades of both sponges and diploblasts, so lumping them conceals further nodes.

This, however, is perhaps the weirdest claim, which bears quoting: "Histones exhibit little variation from one species to the next. They are never used as molecular clocks. Why? Because the sequence differences between histones, assuming a mutation rate comparable to that of other proteins, would generate a divergence time at significant variance with those in studies of many other proteins. Specifically, the small differences between histones yield an extremely recent divergence, contrary to other studies. Evolutionary biologists typically exclude histones from consideration, because the times do not confirm preconceived ideas about what the Preambrian tree of life ought to look like." In other words, he's accusing biologists of cherry-picking data to fit (the irony of which escapes him). No that isn't why. It's because histones have an evolutionary rate (not, incidentally, equivalent to mutation rate) much slower than that of other proteins, and this can easily be shown by comparing divergences much more recent than the Cambrian. Though it may be that Meyer doesn't believe in different evolutionary rates, because he doesn't seem to believe in those recent divergences either, or in evolution of pretty much any sort.

In another part of the chapter, Meyer begins to doubt that there is such a thing as homology or phylogenetic relationships. While it's true that tree-building methods assume that there is a tree to build, there are also ways of testing whether the tree built is a better fit to the data than some other tree, or in fact than no tree at all (e.g. Theobald 2010). But to Meyer, phylogenetic analyses do not count as evidence of common ancestry. Conveniently.

And finally there is an attempt at Catch-22. A bilaterian ancestor must lack the special characters of descendant groups, so those characters must arise later. And he thinks that there can't be time for such characters to arise (because, as he tells us later, no amount of time, including the entire history of the earth, would be sufficient for even one of those characters to evolve).

The question of whether there was a bilaterian ancestor is of course separate from the question of its age. We end with a shameless quote-mine from Simon Conway Morris that doesn't at all say what Meyer wants to make it say, much less mean what he wants it to mean. "A deep history extending to an origination in excess of 1000 Myr is very unlikely", which Meyer takes to mean that Conway Morris thinks metazoan evolution must begin very close to the Atdabanian. How 1000 became close to 520 is unclear.

John Harshman said...

Chapter 6: The animal tree of life. Although Meyer doubted common ancestry in the previous chapter, it's necessary here to drive a stake through its heart by showing that phylogenetic analyses are invalid. And we do that the same way we dealt with the molecular clock: different analyses disagree! For this he goes as far back as the 1940s, never acknowledging that significant consensus has emerged more recently. Meyer falsely claims, though I'm not sure he realizes what he's saying, that phylogenetic analyses assume a molecular clock.

By the way, either the quote-mining is thicker in this chapter than in previous ones, or I've just read more of the papers. He cites a paper about conflicts among gene trees due to lineage sorting to claim that phylogenetic analyses are spurious. Of course it means nothing of the sort, only that the histories of genes may differ slightly from the histories of the species in which they are embedded. And he uses studies that claim extensive horizontal transfer to make the same point. Finally, he uses other studies that point to the possibility of very short branches that would be hard to resolve. In other words, if history is more complicated than a simple, single, obvious tree, it therefore doesn't exist. Oddly enough, though Meyer rejects the tree, he accepts affirmations based on it that the Cambrian radiation was quick.

Next he attacks the agreement between molecular and morphological phylogenies by pointing out that there are disagreements. Should have actually read Theobald's "29+ Evidences" instead of merely quote-mining it.

After that, we discover that morphological characters are not always in agreement with each other, and that some are quite labile. Therefore, of course, there is no real phylogeny.

We finish with repetition of an earlier point, that phylogenetic algorithms assume a tree; again, no mention of statistical tests. And anyway, convergent evolution (or, to Meyer, a hypothesis of convergent evolution, since he never accepts that evolution really happens) makes phylogenies invalid. Because hey, if there's any homoplasy at all, we can't trust anything, right?

Theobald, D. L. 2010. A formal test of the theory of universal common ancestry. Nature 465:219-222.

The whole truth said...

In case anyone is interested in comparing Meyer's new book to what Meyer, Marcus Ross, Paul Nelson, and Paul Chien published in 2004 about the Cambrian explosion, here's a link to a chapter in "Darwinism, Design and Public Education":

And here's a link to the press release for the book:

Mikkel Rumraket Rasmussen said...

"Oddly enough, though Meyer rejects the tree, he accepts affirmations based on it that the Cambrian radiation was quick."

This sums up how all of ID-creationism deals with the evidence for evolution. If they can bend it to suit their specious arguments, it's valid, otherwise it's not.

Diogenes said...

Lizzie Liddle has been deconstructing Stephen Meyer's bizarre assertions about about how evolutionary theory predicts that species should appear first, then genera later, then families, etc. and says Meyer, if evolution were true, phyla would not appear until quite recently-- like last Wednesday. Of course creationists show up to berate her and say, yes, that's what evolutionary theory predicts.

But what's interesting is that she reproduces figures from Meyer's book, specifically his Fig 2.11 (what evolutionary theory "predicts"-- species appear first, phyla appear last, with disparity increasing at a uniform rate) and his Fig 2.12, an appallingly poorly hand-drawn image that is supposedly of what we observe-- the 'real data'-- phyla appear and DO NOT CHANGE IN ANY MORPHOLOGICAL FASHION, no morphological changes at all (note the the horizontal axis on his hand-drawn graph is supposed to be morphology.) It's fraud: it's not real data, passed off as data.

Note that IDers Casey Luskin Stephen Meyer have been tossing around these fraudulent hand-drawn "pitchfork" plots (as I call them) since about 2003, maybe earlier. They're never based on real data, they are always called real data, and are sometimes fraudulently cited to references that say the opposite.

Maybe one of you cooler heads can coolly explain to me why Casey Luskin, Stephen Meyer, and possibly Jonathan Wells are not guilty of scientific fraud here.

Anonymous said...

Darwin's doubt should have started and ended with his first and the most important Darwin's doubt-the origin of life:

"There is grandeur in this view of life, with its several powers, having been originally breathed by Creator into a few forms or into one..."

I mean why bother about anything else? Why talk about anything else if the beginning of life is bleak or scientifically put-bullshit?

Why spend billions of dollars investigating the stuff that is past the most important and focus on something that doesn't matter if the origin of life can't be explained? How did we get here? How? Who is controlling this world? I have no idea but I have my suspicions...

Diogenes said...

Quest says: "How did we get here? How? Who is controlling this world? I have no idea but I have my suspicions..."

Uh... right. You're just an objective, neutral observer, right Quest? You're NOT a religious fanatic who already knows the answer, and is changing the facts and methodology to arrive at a predetermined conclusion. Naw, not you.

John Harshman said...


One odd thing is that Meyer repeatedly cites Budd & Jensen 2000, whose major takehome message is that supposed members of bilaterian phyla and and classes in the Chengjiang and Burgess are stem members of those groups, lacking at least some of the defining characteristics of the modern groups. That is, phyla do not appear suddenly, fully formed. At best, they're partially formed.

Budd, G. E., and S. Jensen. 2000. A critical reappraisal of the fossil record of the bilaterian phyla. Biological Reviews 75:253-295.

John Harshman said...

That was his previous book, Signature in the Cell.

And I agree totally: if we don't know everything, there's no point in knowing anything. Right?

John Pieret said...

Why spend billions of dollars investigating the stuff that is past the most important and focus on something that doesn't matter if the origin of life can't be explained?

That's about the dumbest thing I've ever heard. Just because we can't presently say with certainty how life began, we should not investigate how it developed over time? I can't imagine what the world would be like now if we all had your burning sense of curiosity.

Joe Felsenstein said...

(As you know) phylogeny algorithms do assume that there is a tree and they do find a tree. But the strength of the evidence comes not from the fact that it is a tree, but from the fact that many different parts of the genome find closely similar trees. And there is nothing in phylogeny algorithms that forces that. It sounds from your description that Meyer never grapples with that issue.

Mikkel Rumraket Rasmussen said...

Quest: What hole will you be shoehorning your god into when they solve the origin of life?

It's gap-theology all the way with creationists. Also sometime called edge-theology. God is always hiding just at the edge of scientific knowledge, where our understanding isn't yet complete.

This latest post of Quest's is interesting though, because it seems to concede that creationists know they've lost the evolution argument, so it's on to the next big "unknown" to hide god's deeds in.


SRM said...

Who is controlling this world?

I guess it is the inability to conceive that this is a nonsense question, is what dooms Quest to his permanent intellectual cul de sac.

One would think that just reading the means by which many people die prematurely every minute of the day on this planet would demonstrate that there is nothing controlling the vital logistics of our existence. Or maybe the controller has been on one long, long bathroom break.

Unknown said...

Why spend billions of dollars investigating the stuff that is past the most important and focus on something that doesn't matter if the origin of life can't be explained? How did we get here? How? Who is controlling this world? I have no idea but I have my suspicions...

How else do we find out about what happened at the beginning other than by studying what we have right in front of us and then working back? Without evidence, religious accounts of origins are just stories and they're a dime a dozen.

Faizal Ali said...

That is utterly flabbergasting, Diogenes. Is it really possible that Meyer, after spending his entire career trying to tear down evolution, still understands the theory so little? I guess it is.

Bill said...

Oh, I think Meyer understands the theory of evolution well enough to know the exact bridges and swampland he can sell his "base." Meyer isn't a butcher of quote mining, he's a surgeon.

Meyer deliberately and smoothly glides from "trilobites first appearing in Cambrian deposits" to "trilobites first appearing in the Cambrian." He leads his readers to believe that the Cambrian ancestors haven't been found because they didn't exist. Once this is established he can set about to discredit other pesky lines of research before revealing complete with trumpet fanfare the Intelligent Designer (rather the shadow, not the actual designer who is still a Big Secret)

Meyer has no shame, you can't insult him, he is impervious to criticism (except it makes him cry) and he's only responsible and accountable for raising money for the Discovery Institute. If he achieves that he's a success. Meyer may be an IDiot but he's not an idiot.

Strider said...

So, he's complaining about the lack of transitional fossil evidence and proposes to replace those theories with, what? Fairy stories? Does he *really* not see how ridiculous he is?

hank_says said...

The word "quest" is usually defined in dictionaries as a search, a journey, an attempt to understand, the act of seeking. It's the root word of "question", after all.

This makes Quest's choice of username red-hot with irony. He does not seek to know or understand anything - not if it doesn't gel with what he already purports to know or understand, anyway (that attitude is, of course, the polar opposite of knowing or understanding).

Given that, it's baffling why he turns up here (and why other fundamentalist trolls always turn up at other sites that discuss science) to decry evolution at every opportunity. Surely all this "bullshit" about evolution - if it actually is bullshit - doesn't affect him or his beliefs in the slightest because he's clearly right about everything, so why the hell does he turn up here to tilt at windmills? Why not be comfortably smug at home knowing he's right and will be proven right any day now?

JimV said...

I worked for a couple years at the start of my career with a nice fellow named Ron. I went into a different department and he became a program manager at Honeywell and I didn't see him for years, until one day I found him working at a Wendy's (fast-food franchise). Then I began encountering him on street corners as I walked home from work. He had become a fanatical Biblical literalist and argued with me against evolution and the Big Bang until my knees hurt from standing in one place and I had to go.

It turned out that in his early thirties he became bi-polar and was diagnosed as such (a diagnosis which he did not accept). He had lost his job at Honeywell and was divorced. He had a number of minimum-wage jobs but could not hold them long and now subsists on a Social Security Disability Pension. He told me that God had given him an IQ of 10,000 temporarily while debating the Devil in his presence and proving that every word of the Bible is literal truth.

The brain, like any other organ, is subject to malfunction. When the organ of reason and understanding malfunctions, the tragic victim may not be capable of recognizing his own plight. Symptoms are the inability to accept rebuttals of evidence and logic, and to respond with non-sequiturs and ad hominems. Besides Ron, I have heard of similar cases. A religious fixation is a common delusion in such cases.

I hope this not Mr. Quest's problem, but his behavior is similar to Ron's (who is still a nice fellow, underneath the delusions). If it is his problem, he deserves our utmost sympathy.

John Harshman said...

He grapples, in a way. He just denies that different parts of the genome find closely similar trees.

Diogenes said...

I asked: "Maybe one of you cooler heads can coolly explain to me why Casey Luskin, Stephen Meyer, and possibly Jonathan Wells are not guilty of scientific fraud here."

You are all cooler heads than I, yet none of you have tried to persuade me that Meyer's Fig. 2.12 is not scientific fraud.

John, you are right about the irony of any creationist citing Budd and Jensen 2000. Creationists say that all kinds of life appear "fully formed." By any reasonable definition, "fully formed" is precisely what stem groups are NOT.

So let's not dick around: the discovery of even a single stem group falsifies creationism. Budd and Jensen 2000 says the Cambrian is full of stem groups: therefore the early Cambrian falsifies CREATIONISM, not "Darwinism."

And when a creationist like Meyer cites Budd and Jensen, he either doesn't understand it, or-- or he's lying about its content.

hank_says said...

Meyer might see how ridiculous he is, and he might not.

If he does (or at least sees that others see it), he doesn't care because he's performing a function for the DI/ID/God. As anyone who's familiar with creationists knows, lying is A-OK when it's for God. Meyer knows exactly what he's doing when he performs his surgical quote-mines and glosses over/misrepresents the fossil record (and he knows just as exactly what his target audience will not do: check the quotes for context and the claims for veracity): snowing the rubes with big words (and never resisting a jab a C. Darwin) to spread the Word/bring the dosh. He's been doing it for years.

But if Meyer truly doesn't see how ridiculous he is, then he might justify our concern because such a lack of self-awareness, lack of willingness to critically analyse his own work, utter faith of his own correctness in the face of mountains of contradictory evidence (which goes back to and beyond "Signature"), such extreme denial etc might be an indicator of something more serious than simple, mundane, craven dishonesty in the service of God.

In either case his "work" is evangelism in a lab coat - religious fantasy with a veneer of scientific validity - and can be dismissed as such.

aljones909 said...

All that stuff about a 13,75 billion year old universe, quasars, dark matter, cosmic expansion, black holes, nuclear synthesis in supernovas etc. All completely pointless because we can't explain that first pico second.

SRM said...

Well said Jim V.

SRM said...

Right, this is seen in politics all the time. A politician makes a claim that is patently false (and almost always, he knows it is false). This politician may even correct or retract the statement at a later date.

But it doesn't matter: the falsehood has been successfully communicated to the target audience. That was the intended goal as a means to a political end, and it is all that matters.


“The main goal of Intelligent Design Creationism”
Confusing Creationism with ID – they are not the same.
“Most of the IDiot books are devoted to attacks on evolution.”
Ad hominem attack
“There is strong evidence from molecular evolution that the major animal phyla share common ancestors and that these common ancestors predate the Cambrian by millions of years. In other words, there's a "long fuse" of evolution leading up to the Cambrian Explosion. Meyer refers to this as the "deep-divergence" assumption.”
This is a mere assertion. You have not proven anything or answered any of the points.

“it's very clear that the pattern is consistent with evolution and not with God creating all the animals at once.”
Again, you are confusing evolution with Neo-Darwinism – they are not the same
“I'm hoping to find time to go over each of Meyer's objections since they reveal a lot about IDiot misconceptions of evolution (and science) and a lot about how they employ strawmen, lies, quote-mining, and distortions in order to discredit an entire field (molecular evolution.”
More Ad Hominem attacks and still no response and no proof of “the strawmen, lies, quote-mining, and distortions”. Only accusations and vitriol. And confusing an entire field of science (molecular evolution) with methodological materialism and the Neo-Darwinian paradigm.