It’s a closely-guarded secret that can now be revealed – on Friday, May 14, Steve Matheson and I served as the critics for an event at Biola University the focus of which Stephen Meyer and his book “Signature in the Cell”. (Well, actually, this was the lead-in to some big hoopla about the release of a new Illustra DVD entitled “Darwin’s Dilemma”. But that will have to be the subject of someone else’s writing, since I didn’t go to the screening, nor did I bother to scarf up a DVD.)
It was probably against my better judgment to do this, but I folded this event in with some other, more professorial activities and managed to have a productive and agreeable visit to Biola.
But this blog entry is about the Signature in the Cell event. The format for this was a bit different from your usual debate – thus, after the glitzy Meyer presentation, a panel of hand-selected critics (chosen by the event organizers) would be given opportunities to grill Meyer. In other words, there would be no tit-for-tat here, but rather a one-way exchange of Q&A. This is roughly what transpired, but in a shorter period of time than I expected.
What follows is a recap (from memory – I didn’t bother trying to scribble down notes while everyone was talking) of the proceedings. This is intended as much as anything to convey my own impressions, and should not be mistaken for advice or instructions on how to approach things like this.
Rooting interests
Steve Matheson and I found out earlier in the day that the audience would be largely members of the surrounding community (as opposed to mostly Biola students). Although we perhaps didn’t deliberately plan along these lines, I think we were both (well, I sure was) anxious to establish a level of comfort on the stage. Those of you who know me know how I do this – I represent, for the Kentucky Wildcats, Boston Red Sox, Boston Celtics, Boston Bruins, and occasionally my kids’ school teams (Go Scots this week!). Moreover, Steve Matheson and I share the obsession for the Red Sox. So a few introductory remarks and a prominently-displayed logo on Steve’s slides helped to break the ice with the crowd. (Mention of the Celtics really gets a reaction in southern CA.) And it gave the following proceedings a rather friendly, if still adversarial, tone.
Questions
It turned out that we had only about an hour for questions – from myself, Steve Matheson, and a few selected ones from the audience or from Twitter. I had prepared six questions for this event, and only got to squeeze in three. My approach to these questions was to focus on specifics in his book, and to raise issues that Meyer likely had not prepared for (and thus would not be able filibuster away in a flurry of philosophical rhetoric, or to give a canned answer). In retrospect, this made for a somewhat confusing conversation, since Meyer often referred to my examples in ways that may have reflected my overly-concise (many would claim cryptic, I suspect) summations of the specific examples I wished to discuss. On the other hand, he was in no position to quibble with the facts. This was especially true for the first and third questions.
The first one was another ice-breaker of sorts – I mentioned my research interest (polyadenylation), my habit of going to the pages in books that deal with gene expression, and finding out what the text says about polyadenylation. Well, Meyer (and the audience!) understood where this was going – there is no mention of the most important process in gene expression in his book! This got some chuckles from the audience (to my surprise and delight) and served as a lead-in to the real question – one that flows from the disconnect between the possible information content of a poly(A) tail (as defined in Meyer’s book) and the multiplicity and significance of the functions of the poly(A) tail. (See footnote 1 for some pertinent links.) Meyer’s response was that the informational aspects of his ideas (which I will kindly call his theory from here on out) related to the digital code in DNA. The function-rich, information-poor poly(A) tail might be explained by some other level of organization or design in the cell. (The latter is a loose paraphrase, and may need correcting if and when a transcript comes out; to be honest, Meyer’s answer was fairly confusing and didn’t seem to me to connect the poly(A) tail with any cellular or design mechanism.)
My second question focused on another omission from the book, and an accompanying disconnect. Followers of the old ARN and ISCID boards know that a favorite subject of mine is the “garbage disposal”; it is a favorite because ID proponents choke on the notion that degradation, in essence throwing perfectly good proteins and nucleic acids away, is a deep-seated and fundamental foundation of life. I posed this for Meyer (and the audience) by explaining that cells throw switches by in essence ripping out the switch (as opposed to flipping it over and over); this is a fair and accessible description of how E3 ubiquitin ligases control gene expression (and many other processes). My “target” for this analogy were the several places in Meyer’s book that claim (or predict) that the machinery and circuitry in cells look like intelligently-designed machinery and circuits, and the subsequent “appeal to the best explanation” for the origins of these things. (Basically, the argument is that we only know of one means by which such complex objects can arise, and that is by design.) I suspect (although I do not know for a fact) that Meyer did not know the systems to which I referred, since his answer was pretty generic. He basically suggested that the analogy that I was attacking indeed may not be a perfect one for making the case for design, but that this wasn’t important because the central subject for the “appeal to the best explanation” was the digital code in DNA. (Meyer danced around this issue, to be honest, but this is what I got to be the gist of his response. It’s possible that his dancing hid a different intended answer.) Given that Meyer actually brings up the machine/circuitry/engineering analogy more than once in his book, I consider this to be a significant concession.
My third question returned to a subject that was raised first by Matheson and then repeated a few times by Meyer – the notion that functional proteins have lots of specified information. I returned to my comfort zone, the polyadenylation apparatus, and pointed out that several aspect of this complex (that I deliberately called irreducibly complex, but without drawing a response) completely contradict the notion that protein function is accompanied by large quantities of specified information. (See footnote 2 for more elaboration of this point.) This may be perceived by some as being a bit unfair – Meyer almost certainly would not know the details of the polyadenylation apparatus, and could not possibly argue about the specifics with someone who is an active researcher in the field. Nonetheless, it was a surprise (to me, at least) that he granted my assertions and intimated that, indeed, it was possible that protein function need not required lots of specified information. (IIRC, he actually stated this in the context of self-assembling systems; I don’t know why he did this, but I am willing to assume that he meant the same complex that I was talking about.) But he argued that some proteins and functions indeed would require lots of information. This seems to me to be another significant concession – if some protein functions do not require lots of specified information, then these should be quite accessible to what ID proponents would call “Darwinian mechanisms”. This concession has lots of ramifications – it renders Doug Axe’s suggestions about the isolation of functional proteins in sequence space somewhat less relevant, and it weakens the case (I suspect an important aspect of “Darwin’s Dilemma”) that a supposed requirement for new proteins during evolution (such as occurred in the Cambrian Explosion) makes such evolution improbable or impossible, at least without intelligent design. More generally, while it may be that absolute statements are not made by ID proponents, I think it important to have ID advocates backing down from claims or even hints that all (or even most) proteins have high specified information contents.
To close
That’s the recap. I haven’t tried to sum up Steve Matheson’s questions or impressions. But I must say that I very much enjoyed meeting Steve Matheson, and that we managed to squeeze in a lot of interesting, non-ID-related professorial and scientific discussions in this short stay.
Footnotes
Footnote 1: This, this, and this touch on many (but maybe not all) of the functions of the poly(A) tail.
Footnote 2: There are a number of studies and results that show that aspects of the polyadenylation complex contradict the “function requires lots of specified information” dictum. This essay discusses the involvement of an unstructured protein in the process of polyadenylation. This paper reveals that two functions of another polyadenylation factor subunit can be traced to relatively modest domains; the structure of the mammalian counterparts indicate that one of these (for sure) and likely both are small self-contained structures. (Sequence comparisons reveal significant dissimilarity in these domains and thus are indicative of a relatively low information content; I am helpjng to write a paper that will have this data, and readers will have to accept “in preparation” as the source for this assertion.) Finally, this paper (sorry about the paywall, email me and I will send a reprint) shows that one particular protein-protein contact involves a very small patch of amino acids, far too small to be possessed with lots of specified information.
A postscript
I mentioned some “professorial” activities that ended up making this trip quite rewarding. One of these was something I volunteered to do once I accepted Biola’s invitation to be on the panel of critics. I knew almost nothing about Biola, and I decided that one thing that would take some of the edge off of this experience would be to offer to give a seminar or lecture to the Biola scientific community. I decided that a lecture would be a better way to interact with students and Biola faculty outside of the adversarial, “us vs. them” atmosphere of the Meyer event. To my great and good fortune, the head of the Apologetics Program (that was organizing the event) forwarded my offer to the science faculty, and I was able to give a lecture to a large and diverse class. The lecture itself was a challenge, and I am not sure how well I pulled it off – the class was a collection of upper-level students who had a lot of biology course background, and younger science majors who had yet to take many (if any) biology classes. I chose to talk about some of the behind-the-scenes developments in plant biology that contributed to the unfolding of the small RNA story. This allowed me to talk about plant biotechnology (something that might interest a first-year student) and small RNAs.
Needless to say, the class reacted very well to my lecture, and I got several excellent and insightful questions throughout the talk. The following interactions I had with my two faculty hosts for the afternoon were also splendid. I was impressed, and I must ashamedly admit pleasantly surprised, by the students and my two hosts. I can only hope that this effort on my behalf allowed the students and their professors to see a “critic” in a different and more complimentary light.
The RNA Underworld 
I was hoping Stephen Meyer would have addressed his confused reply to the comments Professor Francisco Ayala made after reading “Signature in the Cell: DNA and the Evidence for Intelligent Design”:
“Again, I have to wonder whether Professor Ayala even cracked the pages of the book. My book is not about the origin of the human genome, nor about human evolution nor even biological evolution generally. It’s about chemical evolution, the origin of the first life and the genetic information necessary to produce it. In fact, I explicitly acknowledge in the epilogue that someone could in principle accept my argument for the intelligent design of the first life and also accept the standard neo-Darwinian account of how subsequent forms of life evolved. I don’t hold this “front-end loaded” view of design, but my book makes no attempt to refute it or standard accounts of biological evolution”.
So Stephen Meyer spends 90 pages discussing some of the theories of abiogenesis, certainly not all, and not even the most current ones, and thinks that that is adequate, and then pads out the rest of a 624 page book discussing inadequately DNA, which he says isn’t the actual argument he’s making, in spite of the book’s title.
His is a straw argument. He claims that first life had to have DNA, RNA and protein, which no one believes, with the exception of ID proponents, therefore life was intelligently designed. I don’t think that any reputable biologist would concede that.
Wayne–
To anyone who has read Signature in the Cell, it’s immediately apparent that you have not. Meyer does not argue that “the first life had to have DNA, RNA and protein”. He makes it very clear in the book that origin of life theorists do not propose that any longer. Thus, Meyer writes:
“By the mid 1980s many researchers concluded that both DNA-first and protein-first origin of life models were best with many difficulties. As a result, they sought a third way to explain the mystery of life’s origin. Instead of proposing that the first information molecules were proteins or DNA, these scientists argued that the earliest stages of abiogenesis unfolded in a chemical environment dominated by RNA molecules.” (Meyer, page 296)
Meyer then spends many pages critiquing the RNA world hypothesis. I’m not sure where you got your ideas about the book from (was it Steve Matheson’s misrepresentations of Meyer’s arguments) but either way, Meyer DOES critique the most current theories, namely RNA world.
No Will,
You’re wrong. The RNA-world scenario is NOT the most current model of abiogenesis. Any research from the 1980s is not cutting edge (it’s over 25 years ago, which is ancient history as far as this field goes). More recent theories include the hydrothermal vent theories, which are basically metabolism first, genetics later models, and also have the advantage that they are actually 21st century theories. Stephen Meyer is really just setting up his straw argument. Why else did he label the book “Signature in the Cell: DNA and the Evidence for Intelligent Design”? Why include DNA if he is actually conceding that there could have been something before DNA (and the RNA model is passe. Spending “many pages critiquing the RNA world hypothesis” is wasted space, hardly anyone (except perhaps Stephen Meyer in his attempt to create a straw man) accepts it as the first step.
Wayne–
My first point is this: strictly speaking, my prior comment refuted your claim that Meyer said “the first life had to have DNA, RNA, and protein,” because I documented from Signature in the Cell where Meyer made the exact opposite claim, namely that not all origin of life theorists require that DNA and proteins were present in the first life. Your other comments do not negate my refutation.
Now Meyer’s noted that RNA-world thinking started back in the 1980s. Most people familiar with the literature would just stop there, realize they made an error, and perhaps buy Meyer’s book and read it before critiquing it further. But unfortunately you used Meyer’s quote to misrepresent it and claim that somehow RNA-world thinking is “ancient history”.
Hmmm…again, to anyone familiar with the literature, it is immediately apparent that you are not familiar with origin of life thinking.
In fact, if you read Meyer’s book you’ll find that he cites some VERY RECENT papers from leaders in the field advocating the “RNA World” hypothesis, showing that this hypothesis is in fact quite relevant. Some of these papers Meyer cites include:
Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret E. Glasner, and David P. Bartel, “RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension,” Science 18 May 2001 292: 1319-1325.
Gerald F. Joyce and Leslie E. Orgel, “Progress toward understanding the origin of the RNA world” from The RNA WOrld (Cold Spring Harbor Press, 2006).
Jack W. Szostak, David P. Bartel, and P. Luigi Luisi, “Synthesizing Life,” Nature, 209:387-390 (2001).
There are plenty of other recent papers in the literature advocating the RNA world. Here are a couple of references if you’d like:
“Reconstructing the RNA World” (Science 27 February 2009)
Richard Van Noorden, “RNA world easier to make,” Nature (May 13, 2009)
Niles Lehman, “A ghost in the RNA machine,” Nature Chemical Biology 5, 73 – 74 (2009).
Finally–and this is perhaps a more debatable point–there are many problems with the volcanic vent hypothesis. (And its existence surely does not negate the fact that the RNA world hypothesis is the leading theory.” For example:
– Volcanic vents are EXTREMELY HOT and most organic molecules like amino acids or nucleotides break down at such high temperatures.
– Additionally, it’s virtually impossible to imagine how polymerization could occur via the necessary mechanism of dehydration synthesis in a fully aqueous environment required by the vent hypothesis.
– The existence of extremophiles has enthused vent proponents. While this is fascinating scientific find, it really says nothing about how life formed from non-life.
The vent hypothesis really has nothing going for it over any other hypothesis, and in fact has more problems than other hypotheses. The fact that it’s newer doesn’t make it any more viable.
So why does Meyer mention the DNA-first hypothesis? It’s simple: some have advocated it. He’s covering all his bases. And given that he also critiques current leading hypotheses like RNA world, nobody can fairly accuse him of advocating a straw man.
Might I humbly suggest that you familiarize yourself not just with Meyer’s book, but also other some of the relevant papers before commenting further on this topic. For someone who is so confidently asserting I’m “wrong,” I’ve sure cited a lot of evidence showing that you are wrong.
Signing off,
~Will~
Will,
You’re still wrong, when you claimed that Stephen Meyer discusses the most current theory of abiogenesis, the RNA-world, because he hasn’t. All your quibbling about recent papers being written on the RNA-world prove nothing. If hydrothermal vents are too hot for the development of life, then why is there such a rich ecology, including bacteria and animals, around “black-smokers” and the cooler “white-smokers” at depths of up to 3,000 metres? He’s still setting up a straw argument, because there is little point spending so much time discussing DNA unless he convincingly eliminates all, including ones that haven’t been thought of, that don’t require DNA initially. The DNA hypothesis is not simple, and I doubt that there is any biologist (except in the mind of an ID proponent) who thinks it is plausible.
“You’re still wrong, when you claimed that Stephen Meyer discusses the most current theory of abiogenesis, the RNA-world, because he hasn’t.”
So devoting a thirty page chapter on the RNA world doesn’t count?
“If hydrothermal vents are too hot for the development of life, then why is there such a rich ecology, including bacteria and animals, around “black-smokers” and the cooler “white-smokers” at depths of up to 3,000 metres?”
Probably because homeostasis within these living systems is efficacious for their survival. We’re talking about the ORIGIN of life prior to the arrival of such abilities, not the development of life.
“He’s still setting up a straw argument, because there is little point spending so much time discussing DNA unless he convincingly eliminates all, including ones that haven’t been thought of, that don’t require DNA initially.”
So do we eventually reach a point where we KNOW such proposals don’t work, or do we stay the course on abiogenesis and render it unfalsifiable?
Jeffrey Snipes,
Where is your reading comprehension? In writing 30 pages on the RNA world, Stephen Meyer hasn’t come even close to discussing the most current theory of abiogenesis. The wikipedia article on abiogenesis lists an entire page including many models, and Stephen Meyer confines himself to 2? What do you think is the ID explanation for life around hydrothermal vents at depths of up to 3000 metres if it didn’t actually develop there? And actually, the conditions aren’t all hot; within centimetres of the vent the temperature drops to quite a tolerable balmy temperature (if you could survive the enormous pressures of up to 3000 atmospheric pressures). The extreme low temperatures at that depth generally would provide the greater problem, were it not for the hydrothermal vents providing heat and food for bacteria such as hydrogen and hydrogen sulphide.
“In writing 30 pages on the RNA world, Stephen Meyer hasn’t come even close to discussing the most current theory of abiogenesis.”
So you no longer accept the claim that he never discusses the RNA world. You’ve also ditched that hypothesis in favor of something else. That’s a start.
“The wikipedia article on abiogenesis lists an entire page including many models, and Stephen Meyer confines himself to 2?”
Wayne, it’s really pointless to accuse me of having no comprehension skills while simultaneously making claims that contradict what Meyer actually wrote in SigCell. Meyer goes over a wide variety of proposals brought forth for the origin of life. These include everything from the protein world, DNA first, RNA world, etc. and explains why these are not sufficient. If Meyer or anyone else in the ID camp were forced to evaluate every crapshoot proposal brought up for the origin of life, they would probably never finish the book in question since new guesses are a routine way of keeping the hope alive.
In particular, you seem to think that all the problems Meyer highlights in his book, whether it’s acquiring functional protein folds, getting usable dna/rna sequences (not to mention getting the chemical constituents for cellular compounds to form at all) are no big deal if we simply place the scenario near oceanic vents. Just to clarify: I didn’t say life didn’t develop at deep-sea conditions, but I sure doubt that they started there on their own.
I think I should press you on a particular question I have brought up with other critics of ID before with regards to OoL. If the current scientific establishment intends to come up with a new guess for abiogenesis every time a prior one is proven untenable, then at what point do we know we’ve exhausted all possible hypotheses for non-telic proposals and can thus move on to other realms of explanation?
Hi Art,
If the garbage disposal system does not make good design sense, this counts against design.
But if it turns out that the garbage disposal system does make good design sense, does this count for design?
I would like to know before I waste my time figuring out why it”s a good engineering strategy, just to have you say, “Of course, evolution comes up with good designs, too.”
Jeffrey Snipes says:
“If the current scientific establishment intends to come up with a new guess for abiogenesis every time a prior one is proven untenable, then at what point do we know we’ve exhausted all possible hypotheses for non-telic proposals and can thus move on to other realms of explanation?”
Well, science has only been looking at the question for less than 58 years. Abiogenesis might be extremely improbable, but then again there are 100 billion stars in the Milky Way Galaxy and 100 billion galaxies in the visible universe, and abiogenesis only has to happen once, even if wildly improbably.
It’s also possible the exact question we need to be asking hasn’t actually occurred to us yet (but the answer is “42”). By the same argument, science hasn’t yet explained gravity in at least 330 years since Isaac Newton (?gravitons ?gravity waves). By the same argument, it would be reasonable to say that scientists should just say that “matter sucks.”
The Q and A was held to publicise the DVD “Darwin’s Dilemma”, a treatment of the Cambrian explosion, as further “evidence” of ID.
At one point in the DVD (the details are a little vague, I watched the video once only and I don’t want to watch it again as it was so painful), Jonathan Wells gave the illustration of a 24 hour clock, with 0 hours being the formation of the Earth (or perhaps first life on Earth), something like about 20:00 hours would correspond to the Cambrian explosion, happening over a period of 2 minutes on the clock (a blink of the eye).
So actually, what the ID proponents are saying is that the Intelligent Designer created bacteria and Archaea 3.8 billion years ago, basically did nothing for over 3 billion years, and then in a fit of creative energy over a period of 10 to 40 million years, decided to create trilobites and other marine animals. Trilobites which were so well-loved that they were very common for hundreds of million years, till most went extinct 350 MYA, and the rest 250 MYA in the “Great Dying” in the end of Permian mass-extinction, all to set the stage for the dinosaurs. Which incurred the wrath of the Intelligent Designer who smote them with a giant meteorite 65 MYA, just to smooth the path for mammals, and finally humankind, just 100,000 years ago.
So the Intelligent Designer had us in mind, 3.8 billion years ago (or perhaps 13.7 billion years ago, with the “Big Bang”), but just took a very long devious route to get to us?
If you won’t admit that Intelligent Design is bad science, then why won’t you admit that it is bad theology?
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Art, I see your Celtics are about to win game three. It lools like Celtics-Lakers in finals. There’s a novelty. 🙄
“Well, science has only been looking at the question for less than 58 years.”
And now for the big question: How long does it take before we know unintelligent causes lack efficacy in this area and thus intelligent causes can be invoked?
“Abiogenesis might be extremely improbable, but then again there are 100 billion stars in the Milky Way Galaxy and 100 billion galaxies in the visible universe, and abiogenesis only has to happen once, even if wildly improbably.”
The replicational resources you describe may be extremely massive, but then again there are 10 to the 130th power ways 100 amino acids could sequence and taking functional strands into account a 10 to the -65th power chance is in order. This assumes amino acids even have a chance to form in the first place and come into close proximity to possibly form peptide bonds while not being affected by interfering cross-reactions, face destruction by UV rays or hydrolysis, or just clump into non-functional proteinoids, or even manage after the fact to assemble together with lipids and a functional strand of nucleic acids of some sort along with other proteins (the current estimates I’ve seen state that at least 150 or so proteins would be needed to result in a self-replicating cell), which in turn has separate hurdles to cross which make the formation of RNA or DNA chemically impossible: http://www.evolutionnews.org/2009/02/origin_of_life_researchers_int.html
…I mean, come on. The denominator on just SEQUENCING a single functional protein on the early earth is probably as vast there are atoms in the entire known universe. I’m not holding my breathe on this one.
“If you won’t admit that Intelligent Design is bad science, then why won’t you admit that it is bad theology?”
Because I could care less about anything that could possibly resemble revealed religion. On this note though, is good theology supposed to entail a sky-daddy of sorts producing humans immediately?
Jeff,
Who says protein had to be the first biological structure formed? Science hasn’t solved what gravity actually is in over 300 years, but no one doubts that gravity exists. Is gravity a smaller or greater problem than abiogenesis?
“Because I could care less about anything that could possibly resemble revealed religion. On this note though, is good theology supposed to entail a sky-daddy of sorts producing humans immediately?”
I take it then, that you go for ID’s other idea of a super-intelligent extraterrestrial alien species which created life on Earth, without us in mind, so we don’t have it be theists at all?
Hi Bilbo,
You asked:
My point isn’t so much that the garbage disposal (E3’s, small RNAs, and the like) make bad design sense, but rather that this is not how switches are designed, period. As I said last Friday, you don’t shut down your computer by ripping out the power switch. You aren’t constantly tearing out transistors from the motherboard of your computer while it is running programs. Designers don’t design these things in this way.
The reasons why are quite different from “bad design”. They reveal fundamental dissimilarities between life and engineered (designed) objects.
A couple of notes about the OOL:
I think it is a mistake to take Meyer’s proclamations about OOL research at face value. It is a matter of fact that much progress has been made in 60 years or so, including a couple (at least) of foundational conceptual leaps. The field today is not so much about researchers bouncing from one failed idea to another; rather, it is about trying to sort out a number of viable hypotheses, each of which has significant positive experimental support.
As an example of how Meyer misleads in this regard, compare the discussion in this paper with Meyer’s badly-mistaken summary of the catalytic abilities of ribozymes.
As far as “replicational resources” and the matter of the origins and evolution of catalysts and functional proteins, the standard ID line is just plain wrong. I have expounded on this here, here, here, and here, among other places.
Hi Art,
We could design rip-out switches and transistors, but that woud be very bad design at the macro-level. Is it bad design at the nano-level?
Hi Bilbo,
Rip-out switches may seem to be bad design to you, but that’s only because cells (from whence the idea comes) are so unlike anything an engineer would create de novo. That is my point – when you adjust your eyesight, in essence going from 20-2000 (roughly the acuity of Meyer et al.) to 20-20, then the illusion of order, engineering, and design disappears.
I don’t know much about nanotechnology, other than that inspired by biology. But that sort of nanotech isn’t going to be much help in this discussion.
Hi Art,
I see Orlando isn’t giving uo without a fight.
No, rip-out switches at the macro-level seem like bad design because they would be highly cost ineffective.
So at the nano-level we need to ask if there would be a good design reason to have rip-out switches. I strongly suspect there is.
[…] Falk, Jeffrey Shallit, and Steve Matheson (I must also mention AG Hunt, who also has some great critiques…but got ignored by the DI). In particular, I recommend Shallit as someone who actually knows […]