Monday, November 16, 2009

Book Review: Signature in the Cell

An Open Letter (ok, a review) to Stephen C. Meyer, Author of Signature in the Cell:



Dear Stephen (you may call me Ben),



I believe what you do: In one God, almightly creator of heaven and earth, and Jesus Christ, his only son ... you know the rest. I have worked in science, too, and have a big interest in the questions of how life started. In both of these matters, I am on your side and am also theoretically predisposed to accept your arguments about Intelligent Design. I have no philosophical opposition to it, in fact, I believe, no, scratch that, I know that the creator stepped into creation as Jesus and gave us a glimpse of the future with the physical resurrection on Easter morning, an act of new creation unexplainable any other way.



So w/r/t this whole book you've just written, about how the Creator must be inferred to explain the origin of DNA? I very much wish you were right.



But you aren't.



I don't say this because I fear for my job. I have a feeling I could have a very nice job at the Discovery Institute if I pushed for it, speaking to churches and other groups across the land, defending Intelligent Design. After all, you're in town here, I could just commute. Here I've already got plenty of grant money and tenure, and I'm at a place where I could defend such a defense of ID as part of my job, even if all the rest of that was not true.



I say it because, as a scientist who prays and studies scripture, I do not buy your argument.



Let me offer some incoherent bullet points that I would organize and maybe will someday:



-- First off, if you want to convince someone like me, writing a 600-page book in which you take 200 pages to walk me through the Watson and Crick model of DNA and other details before you get into your argument is off-putting from the beginning. It's clear this book is not pitched to scientists who may have counterarguments. This book is pitched toward the general public who do not have counterarguments, which is fine for reporting, but does not work for the kind of close detailed argument you suggest is lacking. I have seen several sites that report the 600-page length of the book as if it were some kind of indication of its quality. But there's really about 200 pages of argument in it all. Of those 200 pages, about 100 pages or more were arguments that I've seen before in similar literature, repeated here without reporting on the context (some of which I provide below). I just read a 400-page book on the origin of life (see earlier review) that had me reading slowly and re-reading, making connections, illuminating other things I had read or learned earlier... this book, despite being longer, was read in about 1/10 the time (and only had, alas, 10 post-its compared to >100 for the other book!). It just didn't do what science does in that respect. Again, I understand, maybe the creator did it this way. It's just a bad sign when the length of the argument puts me off before I even get into the meat of it.



(So I'll basically go through the post-its now!)



-- The argument about the earth's early atmosphere is tantalizing but seems a case of cherry-picking, of finding old references that call things into question and leaving them at that. Whatever the low number of oxygen that started out, it was low and went up. There's a graph with more than 10 independent measurements of past oxygen levels vs. time, and though there is scatter, there's a line going up through it all. So oxygen was at least rather low, and it makes sense to a chemist that it reacted with a lot of the metals and non-metals to be absent from the early atmosphere, because oxygen is reactive, there's no getting around that. What kind of chemical reactivity do you propose for your assertion that there was some around, enough to interfere with the reduced chemicals? Why DIDN'T the oxygen react, if there was still some around? (Post it pg. 224)



-- Later you claim that DNA is information-neutral, that is, that there is no way one pair of base pairs will be favored over another. Of course, this is true, and is one of the reasons DNA actually works as an information-carrying molecule. But then you claim that because of this there can be no bias toward information in the bonding of DNA itself. Of course there can't -- DNA wouldn't carry as much information if there was a bias. But this doesn't mean DNA can't ever gain a bias in combination with other things. This tunnel vision on DNA shows up in the very way you structure your argument: you first argue it wasn't DNA, then it wasn't protein, then it wasn't RNA only. But what if DNA is brought together in triplets by another molecule -- then the other molecule confers its binding onto the information-neutral DNA template. Three DNA basepairs can be held together by another molecule in a triplet. This pattern holds through the book: the argument is made that it can't be this alone, or that alone ... but what about the recent findings that things can work together? That's a later bullet point. (Post-It Page 242)

-- There are frequent distortions of the biochemical facts. You write about "the discovery of seventeen variant genetic codes." But most of these are in mitocondria and they consist of a few exceptions to the hard-and-fast general rule. The writing implies that they are totally different codes, when actually they are a change in 1 to 6 out of 64 code units. The equivalent is that of an alphabet with one changed letter. Yet you imply that these are totally different codes. It is moves like this that highlight that you are not looking at the data and then coming up with an explanation (even one with God as a causal agent) but are rather starting with your explanation and then making thing fit into it. These are alternate codes that are exceptions that prove the rule: there is really one code and everything else is a slight variant of it, at most. Claiming that there are 17 different alphabets when you have 24 letters the same and 1 or 2 different, 17 times, is something that weakens your case rather than strengthens it. (Post-It pg. 248)

-- "Then again, it simulates a goal-directed foresight that natural selection does not possess." But the RJP Williams book I just reviewed, and my upcoming Weter lecture, are both about how chemistry gives biology a direction through the second law of thermodynamics! So if chemistry provides a "teleos" to biology is your argument undermined? I don't agree with the biologist's caricature of life as meaningless randomness either. But I think the rules for the emergence of life may be encoded, not in an irreducibly complex DNA molecule, but in the rows of the periodic table of the elements. You keep making the point that information must come from somewhere. Well, the pattern of bonding of the chemical elements (which influences the availability of each on Earth and the structures they can form) would provide some sort of information by this definition. The second law, not natural selection, would drive these chemical cycles. You use the second law only as a source of confusion, a Babel-like curse on the universe. But the second law can drive cycles of life, bringing life together, as described by Williams and as is a major point of my upcoming lecture. I can find no reference to the books and articles by RJP Williams and co-authors, and this is an unfortunate omission. (Post It pg. 284 also 336 and 332)

-- The claims that nucleotides are hard to assemble are outdated in one fell swoop by the recent paper in Nature by Sutherland's group that nucleotides form from a mixture of simple constituents, growing more complex with irradiation and cycles of wetting and drying like evaporation and "rain." Not only is this a problem for your argument because we now have a pretty good path by which nucleotides can form, but it also points out the failure in your "divide and conquer" reasoning. You attack DNA on its own, RNA on its own, protein on its own, for instance, and then you say because each of these is improbable we can just multiply the probabilities together and get a huge number. But that argument fails to account for the possibility of cooperation. This is what allows the nucleotides to form; that they mixed everything together in one big pot and these nucleotides spiraled out of it, self-assembling (by the chemical rules of bonding). I have a suspicion that a similar "working together" makes the other myteries work: that of the "central dogma" or the original (non-coded) cell itself. (Post-It pg. 302)

-- On Douglas Axe's work, I'm still a little annoyed that Axe spoke at the recent ASA meeting but no audio was posted for his talk. Do you want scientists like me to believe your work or not? Whatever the reason for that, the published work by Axe is fine enough on its own, and it does show up those who claim there are no peer-reviewed manuscripts in your libraries. But it misses something huge, something again from RJP Williams. You're only using one corner of the periodic table. You're arguing that a protein must be 150 residues long and made only of amino acids to work. I agree, that's improbable that something like that would just come together. But metals and metal ions can catalyze reactions by themselves! What about Fe or Fe-S or Ni or VO4 or whatever? One third of enzymes have metals in them, often for explicit catalytic use, in which the protein helps with binding but the metal does the chemical work. And even today some metal clusters (like nitrogenase's) will catalyze reactions without any protein at all. All Axe has proven is that proteins alone are unlikely to have been a beginning. But metals are better at chemistry and they could have been the starting point. There is no mention of this possibility anywhere in the 600 pages.

The bottom line is that I want your work to be in conversation with mainstream science. Your set of predictions is a good step forward (though you overstate your own success in the accuracy of the junk DNA predictions, you have an OK point). But reading this book after reading Williams is like reading Twilight after reading Lord of the Rings. It's just not in the same ballpark. Look, I want to believe, but you have to help my unbelief by demonstrating something, not by just taking the most difficult thing we can find, saying it's unexplained, and saying "now you have to believe what I say." No, actually, I don't.

I hope one day ID can publish a book that will get 100 post-its from me as I read it (and not from frustrations!). I will keep trying to read these books if you and your colleagues keep putting them out. I believe in your freedom of speech and, again, if I believe in a real God that really makes a difference I must allow for the possibility that you may be right. But you've got to do a better job if you're ever going to have a prayer of convincing me. And you've got to convince me if you ever want to convince someone who doesn't believe in any rationalities greater than their own.

But this book? This isn't it and I'm a bit frustrated at that.

This is not censorship or ignorance. It is grading an effort, and testing an argument, things I do every day. I gave it a chance and am beginning to think that the persistent effort of ID scientists to ignore the other developments (such as Sutherland's) that conflict with their views are seriously leading the church astray, and when you lead the church away from truth you are walking where angels fear to tread.

Yours (truly), BJM

25 comments:

Geoff said...

Hey Ben, I don't understand all the science, but as I'm reading this review, I'm thinking: You edit this and make it ready-to-publish (so to speak) and I think it would look great on Books & Culture or some website/journal... great job!

Jim Swetnam said...

Sir

Wonderful review. What is the name of the book by RJP Williams that you reviewed. The second law is so central to the origin of life, and life itself.

AIGBusted said...

Interesting book review. You might enjoy my blog, "Answers in Genesis BUSTED", which debunks creationism:

http://aigbusted.blogspot.com

Also, I've written a post on the junk DNA 'prediction' allegedly made by intelligent design proponents:

http://aigbusted.blogspot.com/2009/06/reply-to-jonathan-wells-part-1.html

BenMc said...

@Jim: The book is The Chemistry of Evolution and my review is at this link:
http://arrowthroughthesun.blogspot.com/2009/10/book-review-chemistry-of-evolution.html

ZDENNY said...

The Discovery Institute has to raise its own money so it has to always keep the wider audience in mind.

The Darwinians have effectively corrupted science through censorship. Climategate is providing a great example of how the godless censor, manipulate and destroy data that disagrees with their assumptions.

If we had an open system and real science, we need to end the censorship.

If funded, Discovery Institute could write to the scientific community only which is what it appears you are asking for without feeling the need to raise money all the time to keep their operation afloat.

Anonymous said...

Well this is an interesting critique. Thanks. I am looking forward to getting this book for Christmas. If nothing else I think the cover is groovy and will look nice in my bookcase :P

One note.. in your 'about me' section in left column. Why is "Christian" listed 7th? I am aware of your disclaimer stating they are in no particular order. But isn't "particular order" the most important part of being Christian? I'm just curious to know why you didn't state Christian first and foremost... reflexively..

Doppelganger said...

The 'Darwinians', eh?

So, is Meyer a Johnsonian? A Dembskiite? Before you start accusing the 'godless' of censorship, you may want to look up Giordano Bruno.
And perhaps if the DI was actually serious about presenting a scientific challenge to the ToE, they could shift some of the millions of dollars they have out of their PR budget into research. But I suspect that they are much more successful at PR stunts and giving talks in churches and such, why waste time on what they claim to be interested in?

Human Ape said...

I believe what you do: In one God, almightly creator of heaven and earth, and Jesus Christ, his only son ... you know the rest.

You might be pro-science, but apparently you're also a member of the asylum. You got any evidence for Jeebus? I didn't think so.

Anonymous said...

@Human Ape

I'm a former Christian turned atheist, and I just wanted to say that I don't find your mockery very helpful. If you asked him in person, I"m sure BJM would give you a carefully thought out answer (maybe there is one on this blog ... I'm new here). I'm sure I'd still disagree if I heard it, but I'm sure I would at least respect his answer even if I had very good reasons for disagreeing.

Here we have an academic Christian who admits he would like to believe in ID, but is holding back because of the evidence. That's all the more reason to respect his faith.

Anonymous said...

Ben,

I enjoyed your review of Signature in the Cell. After such a dramatic open – where you go out of your way to show how intellectually disposed you are to the idea – I was anticipating a real challenge to the evidence.

Unfortunately, you didn’t give one.

In fact, I read your review as rather manufactured and petty. I also found it somewhat interesting that you posted a 2000-word review, but spent well over 850 of those words setting up how open-minded you are, talking about yourself, and complaining that the author didn’t get to the point.

What was left of your critique seems trivial. It’s as if there was a need to be as uncharitable as possible in order to make up for the lack of anything resembling a real critique. For instance, on page 248 of the book the author writes “the discovery of 17 variant genetic codes” and then goes on to make the point that this offers rather conclusive evidence that there is not just a single set of codon-amino acid assignments. This conclusion flows directly from the evidence itself. But you return with “These are alternate codes that are exceptions that prove the rule: there is really one code and everything else is a slight variant of it, at most.”

I noted your use of the word “variant” as a descriptive term, and then noticed Dr. Meyer’s use of the word “variant” as the same descriptive term. I was left wondering what the big issue was.
You are of course welcome to characterize them as “alternate codes” if you wish (and I doubt anyone including Dr Meyer would disagree). Yet, it is these small potatoes you described as the author making “frequent distortions of the biochemical facts”. It truly makes one wonder who is offering up the distortions.

In another of your bullet points you write “Later you claim that DNA is information-neutral” and then you immediately agree with him on that claim. Then you write “But then you claim that because of this there can be no bias toward information” and then once again you immediately agree with him. Then the very next thing you do is deride him for the comments you just agreed with, and label it “tunnel vision on DNA”. This is another example of rather poor form on your part, and it characterizes most of what you had to say.

In yet another bullet point you say “The claims that nucleotides are hard to assemble are outdated in one fell swoop by the recent paper”. This is another comment of poor value. The group that synthesized an RNA molecule succeeded only after more than a decade of trying, and succeeded only by means of significant experimenter intervention at repeated steps along the process. Seeming to perhaps appreciate the issues better than you, Robert Shapiro (professor emeritus of chemistry at NYU) commented that “Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever”. He went on to say “The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely”.

(continued)

Anonymous said...

(continued)

Finally, in your closing remarks regarding Douglas Axe’s work you start by complaining “I’m still a little annoyed that Axe spoke at the recent ASA meeting but no audio was posted for his talk. Do you want scientists like me to believe your work or not?”

Once again, the pettiness comes through loud and clear, and one has to remind themselves that this is supposedly a book review – about a book.

You go on to say that Axe’s work is fine on its own merit, and then say “You’re arguing that a protein must be 150 residues long and made only of amino acids to work. I agree, that’s improbable that something like that would just come together”. But then you demand that Dr. Meyer should have explored the possibilities that metals could have played in the origin of life. You write “All Axe has proven is that proteins alone are unlikely to have been a beginning. But metals are better at chemistry and they could have been the starting point. There is no mention of this possibility anywhere in the 600 pages”

I am wondering why you feel it was incumbent on Dr Meyer to go off into pure conjecture and speculation about metals. I am certain he already had a thesis to put forward and was doing so.

And as a final dig at the author you say “Look, I want to believe, but you have to help my unbelief by demonstrating something, not by just taking the most difficult thing we can find, saying it’s unexplained, and saying “now you have to believe what I say.” No, actually, I don’t.”

This of course, is not just silly; it’s intellectually pathetic as well. First and foremost, there is not a single moment in the book that Dr Meyer says anything even close to resembling what you’ve ascribed to him. The quote you make doesn’t exist, you simply made it up. Not only does the comment not exist, but Dr Meyer went out of his way to say nothing like that, and in fact directly addressed your assertion on virtually every page of the book.

One might wonder…for someone who tries so hard to let it be known he wants to “believe”, what drove you to such low-brow means to show that you don’t.

It comes off looking a lot more like a simple refusal than anything else.

BenMc said...

@Anonymous, please note the format. It's an informal open letter on a rarely-read blog organized by the post-its I added to the book. It's in the context of a forum from ID promoters from a recent ASA meeting. Axe's speech was not made public and I wanted to listen to it. I don't know why but if it's not somehow made public I cannot interact with it. That IS frustrating. I wanted to establish my philosophical inclinations with the long windup (and I also wasn't tired of typing yet). I did not intend for this to be a cleaned-up argument. It's going to take more than quotes from professors emeriti to go against a detailed paper that interested me on each page. I'm still here. Convince me. The book didn't do it. That's just what this is ... a blog post. I'll keep reading but I have to say, I don't buy it, and, um, we haven't made any progress.

Anonymous said...

Ben,

I found your review unconvincing and it did not tackle any of the points that Stephen Meyer raised in his book.

My Points -

1. Yes his book was aimed at explaining the case of ID as the best causal explanation for the development of the cell. Yes its audience was the great unwashed masses. The wonder of his book is he succeeded in making it clear. Go read some Richard Feynman Ben. Richard Feynman, probably one of the greatest teachers that ever lived, understood that the object of teaching is to reach your audience not impress other academics.

2. You people remind me of Jesus's statement about the Pharisees. He said the Pharisees would say "We piped for you and you did not dance, we mourned for you and you would not mourn.
Stephen Meyer has produced academic papers ( we all know how that turned out for Richard Sternberg ) and popular books. If you are looking for an academic paper - go read his academic papers. When you read his book, accept that the audience it is aimed at, is not you.

3. I agree that the work of Doug Axe is a starting point. I am really interested in the problem of what does the phase space of protein formulation look like. If it is as sparse as Meyer believes it is, will that change your mind?

4. Arguments about chemical metabolism are irrelevant. Nothing counts until you get self replication of complex specified information. NONE yes that's right NONE of the RNA first or metabolism first models currently offered address this. I am a Physicist by trade. The arguments of OOL researchers are getting to sound too much like schemes for perpetual motion machines. A really clever designer can design a PMM that hides very well the introduction of an outside source of energy, but invariably it is there. The analogous thing happens in OOL schemes, whenever I read one, it just takes a small matter of time to see where intelligent manipulation of the pieces is introduced. ID still remains the best explanation for the cell. Deal with it.

Beaglelady said...

Great review... I suggest you post this at Amazon.com.

Doppelganger said...

So basically, because Ben did not cover the specific points that Anonymous found so special, the review is no good?

Talk about PETTY and absurd.

I found the review very informative, as one who has no intention of spending m,oney or time reading this latest repackaged collection of boilerplate gibberish.

Beaglelady said...

Will someone please contact Ben and ask him to post his excellent review on amazon.com? I can't find any contact information for him.

BenMc said...

@BeagleLady: Thanks for the compliment. I don't have an account on Amazon and haven't found the reviews to always be useful but I will think about it. I'll also do some posts in the future on this. Just not sure when ... back to grading ...

Beaglelady said...

No, reviews are not always useful, and sometimes get out of hand, but that's exactly why a really good review such as yours would be invaluable. You are a believer, a scientist, (and you've read the book!); I think those qualifications make you the best candidate to write a quality review for a book such as this one. (btw, Signing up for amazon.com is easy, and hey, they have good prices, etc.)

Thank you

harrykan said...

This review unsigned it seems. Who is the author? The small variations in DNA codes is interesting but it is also intuitively believable that an "engineer" would make slight modifications to implementations of the code. This is very common in software engineering.

BenMc said...

@harrykan: It's me -- the author. Because of the informal nature of the review I structured it as a letter and signed it with my initials. I wanted to make it so you'd have to look at other posts to find out more about me and see where I'm coming from, what science I've done myself, etc.

harrykan said...

ok Dr. McF. Do you agree that there may be some utility in modifying the DNA code in some implementations much as a programmer implements a java class differently via an interface. It's not intuitively jarring to see small variations while generally adhering to a sound design. This is what an intelligent agent can be expected to do.

BenMc said...

@harrykan -- one more comment and then I'll ask that we save back-and-forth for another post with fewer previous comments:

The argument does not depend on what a designer could have done. A designer could have done anything. Rather, the argument depends on what an "unfolding" system could NOT have done. Meyer's argument is that such a system could not have designed variant codes. My argument is that -- he's right. But what we see are not variant codes, they are <10% different across the planet, and even those variants are tucked away in mitochondria (also note WHERE the differences are: mostly in stop codons, which is the easiest place for an "unfolding" system to change. A designed code could vary anywhere.). As a biochemist looking for a designer, I would expect to see far more code variation (especially if DNA is truly information neutral that means the code can vary a lot!), but in fact I see hardly any variation at all. The one thing I think we can expect of a designer is that he is not capable of/intending to deceive. So when we see 99.999% of the codes being exactly the same it's fair to say there is one "universal" code and it COULD have "unfolded" from a single point. -- BJM

Dr. K said...

Minor point: There can be composition bias in DNA, due to effects associated with base stability and temperature (since GC pairs with 3 H-bonds are more stable that AT base pairs with 2 H-bonds).

Tom said...

Ink cannot author.

The medium cannot be the origin of the message.

It is fundamentally hopeless to look to the properties of chemicals to explain the origin of coding systems and encoded symbolic information, such as we find in cells. Chemicals don't need biology and they are not seeking to create symbolic information or the machinery and systems needed to implement it. It would not matter how much time was allowed.

Adding different combinations (i.e. your "things that work together") provides no help at all, since none of the combinations is seeking such a goal or showing any evidence of moving toward it.

Even if such a process could produce a suitable medium for information, it cannot create the translation systems required to actually encode and decode information. Until the coordinated system exists, the components are nonfunctional for information purposes. How does selection attach to a future effect?

The key point that perhaps you have missed is that it is not enough to make this or that molecule (e.g. "Three DNA basepairs can be held together by another molecule in a triplet."). None of the directions you hint at gives meaningful, encoded information that can also be decoded.

[About the matter of variant codes, that is a lesser side point, since the fundamental issue is that an undirected material process would not create any system for encoding information, let alone variations. But in passing... The variations are not just in mitochondrial codes, as you seem to suggest. Also, you seem to try to minimize the difference between a code for an amino acid and one that treats the codon as a stop code. However, that is the most disruptive type of difference -- one that would prematurely truncate the protein.]

On a positive note, I respect your declaration that you are approaching this scientifically, not for the sake of philosophical/theological commitments. And you are right that this is about what undirected natural processes can vs. cannot do.

Best to you.

Anonymous said...

Spiritual realities are always foundational to the natural.

Scientists can't create 1 living cell of anything.

The true complexity of the living cell lies not in the biochemistry, though this is wonder enough. Rather, in the spiritual base.

This is undiscoverable. God holds the keys. This can be very irritating to the sin defender.

Scientists want REAL answers on their deathbeds. They realize that "fun with science" times are over. If fact, their decease is due to a spiritual reality.

And he is before all things, and by him all things consist. (Col 1:17)
:-)