Examining "Signature in the Cell"

Within biological research, I think there is a great appreciation of the need for multidisciplinary approaches as the answers we’re now trying to address are getting very complicated. I’ve worked to help get engineering students exposed to biology early in their education. Their math and systems education can help create models for testing, among other things. Physicists and mathematicians have had a long history of making important contributions in the field. But you’ve got to immerse yourself in the basics of the field to make the strongest contributions.

And you’re right that almost nobody succeeds if they enter a field with the notion that everyone is wrong and “I’m here to set you straight”. 99+% of the time, that reliably identifies a quack, not a paradigm-changing genius.

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To be clear, it still might be true that 99+% of people are wrong on specific points. The really advantage of being from outside the field is that you are more likely to identify these errors, which can have very high significance. However, “winning” in the sense of changing the view of the field, takes great wisdom, carefully cultivated allies, and a bulletproof evidential argument. Sometimes it takes luck too.

I’ve been very lucky to have been part of shifts like this. If we are lucky, it can be a once in a career sort of contribution. Being in a field of rising importance and cross cutting application (deep learning), and having 9 years of graduate training (physician and scientist), I’ve been really lucky to “be in the right place and time” to see it more than once. I’d count the genealogical correction as on example of that, though the story isn’t fully played out yet. The other examples are far more obscure =), but perhaps with higher significance to human health.

@vjtorley might agree with you. I’m still a bit amazed how something that is self evidently true could be turned into such a long and controversial book.

Just to be clear, what are you claiming its basic premise is?

He is asking for an accounting, not only for the existence of coded information leading to functional metabolic activities in cells, but also in higher order morphology and a proliferation of adaptive body plans that serve to build whole interdependent ecosystems, etc. But, more fundamentally, he is asking about the elegant structure and complicated function of the code itself. It’s as if there are people who think that coherent music is the result of random dots falling on a page. We all know that’s not true. If I had the book with me at the moment, I could respond more closely.

Hi everyone,

A few quick responses.

I actually think Signature is by far the best work ever put forward by an ID proponent. It had it’s shortcomings and a lot of its claim have now been shown to be false with work coming from the Yarus and Zagrovic labs. But I felt like it was a good effort.

I agree. Whatever its faults, it was methodical, it tried to cover all bases, it set forth its central argument clearly and persuasively, in a manner that impressed even the acclaimed atheist philosopher Thomas Nagel, and it was modest in its conclusions: for instance, it made no claim to have proved the existence of God. It’s just too bad that two of its key factual premises were wrong: (i) the claim that the genetic code is a purely arbitrary code (see here for Dennis Venema’s refutation in 2016), which, if it had been true, would have ruled out any deterministic or law-governed account of the origin of life, and (ii) the claim that functional proteins (essential to life as we know it) are astronomically rare and very isolated from one another, among possible amino acid sequences, making their origin by chance practically impossible (see here and here for Venema’s reply, written in 2017). Had both of these assertions turned out to be correct, Meyer would have had a very solid scientific case against abiogenesis. Unhappily for Meyer, they both turned out to be wrong. But at the time when he wrote, they both appeared to rest on solid research.

Reading through Meyer’s book, it becomes apparent that his scientific case against abiogenesis rests critically upon the work of three scientists: Charles Thaxton (a chemist who strongly influenced his thinking about life’s origin and who got him philosophically interested in the question, during the mid-1980s), Dean Kenyon (a biologist who at one time espoused a self-organizational account of the origin of life, which he christened “biochemical predestination,” but who later came to reject it and espouse intelligent design) and Douglas Axe (a molecular biologist, upon whose research Meyer’s argument against the possibility of abiogenesis in chapter 9, “Ends and Odds,” is critically dependent). Meyer is not to be blamed for trusting these men. At the time when Meyer did his research which culminated in the publishing of his book, no-one on the “naturalistic” side was seriously engaging their scientific arguments against abiogenesis.

Before Venema’s series came out, Dr. Douglas Axe always seemed to be one step ahead of his critics: see his 2011 post here on the subject of protein folds, titled, “Correcting Four Misconceptions about my 2004 Article in JMB.” The only serious critic he had was a guy named Matheson, and from what I could judge (as a layperson writing for Uncommon Descent) it appeared to me that Axe had satisfactorily answered his arguments. Later, I came to revise that view, thanks to my interactions with a few scientists who assisted me, including @swamidass. But back in 2009, backing abiogenesis looked like backing a losing horse: a bad bet.

(1) Because Meyer is the author.
(2) Because I know how the publishing industry operates and how/why people choose to write endorsements for book jackets for many reasons.
Are you sure that you want to base your case on arguments like these?
I find myself almost speechless.

Blaming a philosopher of science for having been unintentionally misled by three scientists (two of them widely respected in their fields) who had done ground-breaking research in their fields sounds pretty harsh to me. Perhaps you’d prefer to leave science to the scientists, and let them fight it out in the pages of academic journals. But scientists are not always the best people at making arguments: philosophers often tend to be better at that sort of thing, and sometimes they can be better at communicating a message to the general public, too. Thaxton’s 1984 book, The Mystery of Life’s Origin, made a solid, highly technical and seemingly unanswerable case against abiogenesis on largely thermodynamic grounds, but it didn’t get on any best-seller lists. Meyer’s book, by contrast, was a huge success, and was much more accessible to the layperson. It got the message across, because it was written by a layperson who had nonetheless spent time talking to leading people in the field, including Nobel Prize winners. The guy might have been wrong, but he certainly did his homework.

I also happen to know for a fact that the people who wrote the blurbs for Meyer’s book meant what they said. I’ve been in touch with some of them, by email.

I find myself almost speechless that you would dismiss Meyer’s work (which you admit to not having read in years) as “just another lame ‘It’s too complex to have happened naturally so it must have been an intelligent designer’.” If he was wrong, he was at least nobly wrong, and excusably so.

Frankly, I’m very surprised that you are looking to the late Dr. Smalley to make your case.

The case against the possibility of abiogenesis rests upon an understanding of chemistry which was well within the grasp of a man like Smalley. I don’t know why he came to reject evolution, as I’ve never read Hugh Ross and Fazale Rana’s books, so I can’t comment on that. But if you look at Thaxton’s book, for instance, you’ll see that it doesn’t presuppose a deep knowledge of biochemistry, to make its case. Dean Kenyon, a former professor of biology who wrote the preface for the book, seemed to think that Thaxton, Bradley and Olson had put forward a pretty powerful argument: his only quibble was that they might have included a more detailed discussion of optical isomer preferences.

A passage from Kenyon’s preface is worth quoting:

If the author’s (sic) criticisms are valid, one might ask, why have they not been recognized or stressed by workers in the field? I suspect that part of the answer is that many scientists would hesitate to accept the authors’ conclusion that it is fundamentally implausible that unassisted matter and energy organized themselves into living systems. Perhaps these scientists fear that acceptance of this conclusion would open the door to the possibility (or the necessity) of a supernatural origin of life.

Finally, I will acknowledge that in my opinion, Darwin’s Doubt is a much less impressive work than Signature in the Cell. The former is an argumentative tour de force, while the latter displays a lack of solid mastery of the field. Meyer’s basic argument boils down to proteins (Axe again). I am therefore not surprised when you say that you found a lot of flaws in it. On that point, you are correct, although I do think that the scientists who Meyer’s book before it was published should have picked up on its failings. The fact that they didn’t suggests to me that there are major gaps in their expertise. Meyer would have been better off sending his manuscript to Nick Matzke or Bob Valentine, prior to publication. Cheers.

As for Smalley’s statements about Who Was Adam?, far from being a death blow to evolution, we have fairly definitively demonstrated the RTB model false. That was outside his area, and he was wildly wrong… Smalley was a phenomenal chemist, but that does not transfer over to biology, evolution, and population genetics.

You make a fair point abut evolution and the RTB model: Smalley was venturing outside his field here. I should acknowledge, by the way, that I know next to nothing about the specifics of the RTB model, except insofar as it relates to Neanderthals and modern humans.

The irony is that the basic premise of Signature in the Cell is correct: we just do not know how the first cell arose. It takes special talent to take such a concise and self-evident fact and turn it into a controversial book.

Meyer’s argument, as I see it, was not just an argument from ignorance. Central to his argument was the claim that even the most promising proposals for the origin of life were utterly unable to account for how the information which characterizes life - specifically, the genetic code, and the 250 proteins required by a minimally complex cell (according to Meyer) - came into being. When even the most promising naturalistic accounts of life’s origin are conceptually flawed, and when experimental data appears to suggest (as it did until a few years ago) that no remotely plausible chemical pathway to the first cell exists, then it is rational to infer, in the light of the limited information available to you, that life’s origin is not natural but artificial, and that intelligent guidance was required.

Meyer’s big mistake, as I see it, was to put a full stop where he should have left a comma.

I would strongly contrast his [Meyer’s] work from, for example, yours @vjtorley. You are engage people who disagree with you all the time, and are open to hearing what science shows us from points of view different than yours. That is part of why you and I got along so well, even when you were solidly in ID. If you, as a philosopher, can do that, why can’t Meyer?

I’ve never met or spoken to Meyer, so I can’t say how open-minded he is on the question of life’s origin. I do know that during his days at Cambridge, he rubbed shoulders with eminent scientists like Maurice Wilkins, Eugene Wigner, Fred Hoyle and Hermann Bondi, all of whom he spoke to, and two of whom expressed sympathy with the idea that life on Earth had an intelligent source.

As for why he hasn’t modified his views in recent years, I cannot say. All I can say is that it’s hard to change your views on a major issue when you’re 60 (as Meyer is, or will be this year), and when you’ve published a book strongly advocating a particular point of view on that issue. Not many people could do that. Cheers.


A post was split to a new topic: RTB’s Model and Smalley

That absolutely is his biggest mistake.

His other mistake, of nearly equal significance, is having not having a convincible computational biologist look at his work. In fairnesss, those are hard to find, and I myself was just graduating graduate school at the time, and therefore unknown and unavailable. Still, the mathematical errors are too difficult for me to over look. His case would have been much stronger if he had been more reserved.

I’m curious if you saw on the other thread on the origin of life where I mentioned I’ve been having private correspondence with Yarus. He was very impressed with Venema’s review of his work and was impressed with how up to date he was on other relevant experiments. He also recommended other work from other labs he thought was very important. Perhaps you would like the papers?

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A post was merged into an existing topic: Dabar Conference Paper Confidentially Available

Hi @T.j_Runyon,

I’m afraid I haven’t seen your remarks on the other thread. I’ve been a bit busy lately. And I would be interested in seeing the papers, thank you very much.

Meyer is 60!? Wow. Dude is eating his veggies. So the first link introduces you to Zagrovic and the kind of work he does. The second one is one of his papers that Yarus told me is one of many important ones. I have lots more. I’ll share here if people would like that or I can email them to you.

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I never said otherwise. I never questioned their sincerity. However, in re-reading my own statement, I can see my choice of words might give that impression. While in a hurry and being concise, I was unclear. So after reflection, I can understand your reaction. I should have chosen my words more precisely so as to remove that possibility of misinterpretation.

I find myself almost speechless [OK, I’m just being tongue-in-cheek to have fun with the dramatic phrase] that you didn’t read more carefully. But, seriously, you attributed my reaction to Meyer’s the words I had actually written about Signature in the Cell. That said, I’ve certainly heard Stephen Meyer make arguments which I would criticize similarly. (At my age and years later, I can’t be absolutely certain that I always remember which arguments Meyer made in Darwin’s Doubt and which arguments I’ve heard in his lectures and debates.)

By the way, one of the reasons why I am harsh on Signature in the Cell (and on Stephen Meyer) is because I was guilty of some of the same lame arguments early in my career. I am quite willing to admit that I have been guilty of multiple lame arguments. Far too many, in fact. Hopefully they became more rare as I lived and learned.

That is not an accurate representation of my position. On the other hand, I will be among the first to admit that my opinions (in general) on the aforementioned books are not all that important, especially considering that my disappointments in those books (and my reasons) are not all that atypical among academic reviewers of those two titles.

By the way, I have no beefs with abiogenesis—biological life from non-living ingredients—because that is what the Bible describes: “…from the dust of the ground” and “Let the land bring forth living creatures…” Whether or not a deity was involved is a theological/philosophical question and not a question which the Scientific Method can falsification test, or at least, not to this date. Whether or not an “intelligent designer” was involved, is a different question. [And yes, there are at least two popular definitions in use for the word abiogenesis in common discourse, where the one definition even assumes that abiogenesis is atheistic.]

And as I’ve said, I would be delighted to read a compelling comprehensive scientific theory of ID but thus far I’ve been disappointed.

Hi @T.j_Runyon,

Thanks for your response and for the articles. Here’s one I just came across regarding Zagrovic’s recent work on the stereochemical hypothesis for the origin of the genetic code:

The origin of the language of life (Phys.org, December 19, 2014, University of Vienna).

And here’s another:

mRNA/protein sequence complementarity and its determinants: The impact of affinity scales (In PLoS Comput Biol. 2017 Jul; 13(7): e1005648.)

If you have any more papers you’d like to share, I for one would be interested.

Hi @AllenWitmerMiller,

Thanks you very much for your response. I think I have a better understanding now of where you are coming from, and why you have criticized Meyer’s faulty arguments. Incidentally, I’d be interested in hearing more about how you transitioned away from creationism.

Incidentally, regarding abiogenesis, I agree that nothing in Genesis contradicts it. Cheers.


2 posts were merged into an existing topic: One Journey From YEC

@vjtorley This is one of the most closely argued, comprehensive and accurate assessments of the current situation with regards to ID that I have read; few people seem to know of the seminal nature of Thaxton’s book in all this, for example.
At root, @swamidass is correct that a driving force is the cogent critique that we simply do not know a fully viable abiogenetic explication of the inception of the first functioning cell, nor would solving that problem automatically validate the rest of the entire evolutionary explanation, for what is lacking in both cases is an answer to an unconscious process having some sense of what emerging problems there are, and what would work to solve them. I’ll be called unscientific for phrasing it this way, but a “natural process,” wholly devoid of any mechanism or organ of teleological acumen, simply cannot launch life, much less adaptible multicellular life. While the physical outcomes of evolution are undeniably true, once life has gotten started, the process itself is woefully inadequate (while not completely sterile) to account for what we actually find in the record of natural history.
Want me to prove that? I can’t. It is a candid assessment however, not merely a faith-informed ideology.
Waiting for the next clap of thunder… : )

@Guy_Coe, Related - I’m working on a topic about what Genetic Algorithms are capable of doing. It’s more of a project than a discussion at this point, and I hope to expand on it.


Looking forward to hearing more; sounds like possibly exciting research! Especially if you can find evidence that the algorithms are somehow encoded within the genome itself. Or, in whatever other manner you find to show how a cell can do, then apply, the math. That would be groundbreaking.

A post was split to a new topic: Examining “Darwin’s Doubt”