Examining "Darwin's Doubt"

I explained why it’s a quote mine. Just read.

Yes, but that isn’t Meyer’s conclusion.

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Those two aren’t mutually exclusive. Just sayin…

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Their position of scientists is that evolution working from the bottom up is a hypothesis, and a well supported one.

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I agree with you. I guess the dispute, if there is one, is what the pattern of “bottom up” evolution should look like. I think the pattern should begin with organisms that look very similar gradually diversifying over time. What do you think the pattern should look like?

I agree. We see that, for example, in perissodactyls, where early members of the horse, rhinoceros, and tapir clades are hard to tell apart and were once all lumped under the name Hyracotherium. But taphonomy is the devil in the details here. Once we get a clear view at the evolution of animals, in the Chengjiang fauna, the bulk of that bottom-up evolution has already taken place with regard to the animal phyla. Still, we can see the classes still unformed, for the most part. We see primitive chordates, perhaps even some vertebrates, but the characteristics of chordate subphyla and classes have not yet appeared. We see arthropods, but the arachnomorphs are hard to distinguish from the crustaceans, and so on. The paper I referenced, Budd & Jensen 2000, has much more to say on this subject, and I recommend it.

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Hi John,

I have the Erwin and Valentine book you mentioned earlier. So if there’s anything in it you care to reference I’ll be able to look at that. It will probaby not come as a surprise that I did not find it to be much of a “corrective” to Darwin’s Doubt. :slight_smile:

I also have The Origin of Higher Taxa by.Kemp.

Has already taken place before the Cambrian? So would you agree that we do not see the bottom up evolution of the animal phyla in the Cambrian itself? That we do not see those precursors in the Cambrian itself? That we do not see the expected pattern if we restrict ourselves to the Cambrian?

Because if that is the case then at least one of Meyer’s premises is true. Right?

Evolution is descent with modification. Therefore, when you look at a clade you need to identify what the modifications are and what the ancestral traits are. We can approach this problem by looking at what the entire clade shares to figure out what the ancestral traits were. If we use the chordate clade as our example, the features shared by chordates include pharyngeal slits, dorsal nerve chord, notochord, and a post-anal tail. The modifications include a whole plethora of adaptations, everything from calcified bones to limbs. What do we see in the Cambrian? We see chordates with very primitive features that form the foundation of the chordate branch.

Would the very earliest chordates be very similar to other critters not in the chordate phylum? Yes. What causes these very similar critters to be the base of very large groups is time. During long periods of time these lineages have branched and branched, and in those branches you get different modifications which adds diversity to the lineage. This is the diagram that Darwin created to describe this process:

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It’s only a surprise because I’m used to your affection for Meyer, though I don’t understand it. Try Budd & Jensen.

Like Meyer, you are confusing the Cambrian with Cambrian Stage 3. Over 20 million years of the Cambrian happened before the visible appearance of the Cambrian explosion in the Chengjiang fauna.

No. I’m saying that we have a much poorer window into that evolution than we have of its end, though we do have the small, shelly fauna and trace fossils to provide a clue that it exists. Sadly, we have no lagerstätten of the proper age.

That isn’t the case, and none of Meyer’s premises is true.

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I do have a fondness for defending ID and ID authors from misrepresentation. That should not be mistaken for a fondness for the person or a willingness to overlook egregious errors.

…from what you perceive as misrepresentation. We disagree.

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We disagree about what? Have I said that anything you have written in this thread misrepresents Meyer? Let’s first figure out if we are talking about the same thing before we decide that we disagree!

If you haven’t, why are you bringing it up?

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Because I want you to understand where I am coming from. It has nothing to do with affection for Meyer. It has to do with affection for the truth. Something that you and I seem to share, and something I give you credit for, but that you can’t seem to give me credit for. The way you worded your comment it carries the insinuation that I am willing to be dishonest on Meyer’s behalf.

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One does have to wonder why so many different posters on different boards come to the same conclusion.

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Ignorance and stupidity is not the same thing as dishonestly. We usually don’t have enough information to tell the difference. I suspect it is often ignorance complicated by lack of trust. Our best approach is to default to non-judgmental education, until clear evidence arises that nefariousness is afoot.

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Do you match your fondness for defending ID from misrepresentation with a fondness for defending non ID scientists from misrepresentation? If not, there will be serious credibility deficits you will have to live with from everyone, including me.

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I try. It’s one reason I have so many books by evolutionists. I take seriously the idea that what they wrote could be misrepresented. BTW, there’s a post now at TSZ that I think misrepresented you and I said so.

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I thought I would jump in here belatedly and toss out a few more comments. First of which would be to thank @John_Harshman for a nice review of the first several parts of Darwin’s Doubt.

I hadn’t picked up the book for many years, and re-reading it was interesting. On a positive note, I believe this book is a reasonable summation of the progress, as it were, of the ID movement over the decades. It seems as if Meyer wanted to pull together most of the cogent arguments that ID proponents had raised against evolution over the years, and to tie these together into as coherent a train of thought as possible. I believe he did a credible job in this book.

Of course, in so doing, he has summarized, in one place, all of the time-worn and refuted arguments that has shaped the core of ID thought over the decades. The strange obsession that the ID camp has for the Cambrian Explosion is presented in full display, and the problems with their arguments are being hashed out quite nicely in this thread. I have nothing to add, mainly because better-qualified persons are doing such an excellent job here. My own interest has to do with molecular genetics and the like, which are subjects of Chapters 8-12 in this book. I won’t post a lengthy review of these chapters, since most of the issues raised are familiar and can be summarized fairly succinctly.

The title of Chapter 8, “The Cambrian Information Explosion”, is pretty self-explanatory, and tries to make the case that the Cambrian Explosion must have been heralded by some massive increase in information. This is a theme that recurs in the book. I believe this assertion has been discussed by others in this thread, and I don’t need to add anything.

The title of Chapter 9 is “Combinatorial Inflation”. A centerpiece of the chapter is the “legendary” Wistar Institute Conference of 1966, and deliberations that started to get at the matter of the ratio of functional sequences to all possible sequences. (One subsection is aptly titled “In Search of the Ratio”.) Favorable mention is made of the simplistic view (1/20^n) as well as some estimates borne out of sequence alignments that still yield vanishingly small numbers. To Meyer’s credit, though, some shortcomings are acknowledged, and he frames the work of subsequent ID proponents as seeking to address some of the problems with this naïve approach.

The title of Chapter 10 is “The Origin of Genes and Proteins”. The centerpiece of this chapter is Doug Axe, and his work that sought to better define the ratio mentioned in the preceding paragraph, namely that of function to all possible sequences. Put in this light, I would offer that Axe’s work was and is laudable. Other subjects are touched upon, but the emphasis is on the implications of Axe’s work, namely that protein function is rare in sequence space.

The title of Chapter 11 is “Assume a Gene”. The point of this contention is the matter of the origins of the many new genes assumed to be necessary for the appearance of new animals in the Cambrian Explosion. Initial focus is placed on a review article by Manyuan Long et al. entitled “The Origin of New Genes: Glimpses from the Young and Old”; this focus seems to derive from favorable mention of the review, and of the various mechanisms for the origins of new genes, by three thorns in the side of the Discovery Institute – Alan Gishlick, Nick Matzke, and Wesley Elsberry. These mechanisms deal with various ways by which gene duplication, exon shuffling, and other rearrangements might give rise to genes whose protein products encode novel activities. The feasibility of these mechanisms is argued against on largely theoretical grounds, based on ideas concerning protein folding, domain structures, and the like. (Ann has raised some of these issues in other threads.) Subsequently, Meyer raises the problem of the origins of so-called ORFans – genes and proteins with no apparent evolutionary ancestor. The likelihood that such genes might arise is discounted at least in part on the basis of Axe’s work.

The title of Chapter 12 is “Complex Adaptations and the Neo-Darwinian Math”. The general gist of the chapter is the need for complex adaptations, and therefore complex protein structures, during the unfolding of the Cambrian Explosion. These complex adaptations will require numerous coordinated mutational events, and thus run up against conceptual problems outlined in, among other places, a paper by Behe and Snoke and Behe’s book entitled “The Edge of Evolution”. Additional mechanisms involving co-option of extant proteins for new functionality are confounded by, among other things, research conducted by Gauger and Axe.

As John Harshman’s more extensive review here and the discussion show, there is a lot to talk about in this book, and this certainly holds for these four chapters. However, rather than a laborious (most here might prefer the descriptor excruciating) point-by-point takedown, I will try to convey my own overview and summation. As I stated above, this book is a reasonable overview of ID thinking circa 2013, something that (IMO) hasn’t changed much in 5 years or so. In the four chapters I have briefly described, Meyer lists several of the key pieces of research upon which are (still) based the core of Intelligent Design. Among these are:

Axe (Axe DD. Estimating the prevalence of protein sequences adopting functional enzyme folds. J Mol Biol. 2004 Aug 27;341(5):1295-315.) – the seminal study that purports to prove that functional sequences are impossibly rare in sequence space.

Behe and Snoke (Behe MJ, Snoke DW. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 2004 Oct;13(10):2651-64.) – the study that claims to have established that impossibly long times are required for even the simplest of mutational pathways to be “enacted”.

“ The Edge of Evolution: The Search for the Limits of Darwinism ” by Michael J. Behe – the book in which Behe immortalizes the number 10^-20 as a value representing the rarity of occurrence of appearance of a new protein functionality.

And Gauger and Axe (Gauger AK, Axe DD (2011) The evolutionary accessibility of new enzyme functions: a case study from the biotin pathway. BIO-Complexity 2011(1):1-17.) – this study has been discussed by @Agauger elsewhere in this forum, and she is welcome to briefly summarize its implications here. They basically have to do with the difficulty (impossibility?) of extant proteins acquiring new functionality by mutation.

(I would include here parts of Chapter 11 that, as far as I know, have not been formally published anywhere. These parts deal with objections to several of the specific mechanisms laid out in Long et al. that concern the evolution of novel function via gene duplication, domain addition or swapping, exon shuffling, and the like.)

This is a useful summary that Meyer gives us, as it connects some oft-discussed (and debated) studies with a foundational core of ID thought – namely, that macroevolutionary processes (as represented by the Cambrian Explosion) are beyond the reach of evolutionary processes. I would go so far as to say that the body of work given us by Meyer in these 4 chapters is central, foundational, essential to the ID movement. This was the case in 2012 (when, I suppose, Meyer was wrapping up the writing) and is, in my estimation, true today.

Which brings me to my point. ID proponents today treat this body of work as the last and final word on the matter of gene and protein evolution. However, as has been seen in this forum and elsewhere, each and every one of these works is fundamentally flawed, and in fact do not lead to the broad, sweeping generalizations and conclusions that are seen in the ID literature. What Meyer has in fact shown us is that the anti-evolution arguments that are part and parcel of the ID movement are based on studies that are fundamentally (I would argue fatally) flawed. Along with the service Meyer provides regarding the overview of the history of the ID movement, this latter outcome is one for which Meyer might be thanked.

(The review by Long and colleagues that occupies part of Ch. 11 - Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet. 2003 Nov;4(11):865-75.)

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All of us?

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Thank you for the thorough, collegial and gracious review of the arguments from the book, @Art and @John_Harshman !
It would seem that the charges of outright dishonesty or stumbling incompetence are belied by the extremely technical nature of the debate.
Sweeping generalizations rarely survive thorough scrutiny; there are, it would seem, exceptions to every rule that can truly and honestly be easily overlooked, given our own propensities to be too easily persuaded to one overarching view versus another.
This is another example of the kinds of productive dialogue we can have here, without having to resort to unkind characterizations of those who differ from us. Perhaps it’s time for an “Icons of ID” book from someone qualified to write it? Or, at least an “Icons of YEC?”
In any case, I continue to look forward to the lively dialogue here… naive as I might be about those prospects resulting in a new synthesis or even paradigm! : )

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