Stephen Meyer, a founding member of  Discovery Institute, and cause celebre for the brouhaha generated by his peer reviewed paper on ID, has just come out with his best argument in a book. To recap the ID arguments: Dembski argued on the basis of mathematics, Behe argued for "irreducibly complex" biological mechanisms, and Johnson argued for legally coherent logic. Meyer bases his argument on the digital information system of the cell. His book hit the shelves last month, and while I have only read the front matter (as well as Meyer's previous essays) here is my response to a hostile review of his book by a biology major.

I received Signature in the Cell by Stephen C. Meyer in the mail today. That's 600 pages to kill in less than two weeks, but I'll do my best. I've started reading it already. I was momentarily surprised to recognize the name of the author. And while was involved in the scandal at the Smithsonian, I don't believe he is guilty of much beyond doing poor science.

This is kind of you, but whether he is guilty of manslaughter or not really makes no difference to the arguments he presents. You will have to stop moralizing about the motives of scientists and address their purported claims. Ad hominem is not and never was, a scientific response.

The real breach of ethics came from Robert Sternberg, who by-passed the peer review process in order to sneak on Meyer's article into the journal the Proceeding of the Biological Society of Washington.

No, that is NOT what a blue-ribbon congressional committee concluded. It would do you good to read what the lawyers say, because scientists make really poor legal eagles. Take my 30-year-experience word for it, no peer review operates the way a journal claims. No ethical breeches were made, merely the breech of publishing something that was deemed a priori blasphemous, which is generally where the good science is located. Read Thomas Kuhn's "Structure of Scientific Revolutions" if you want more details on what was really going on in the debate. But more importantly, ad hominem rebuttal does not actually address the science in the article. If you are going to attack ID for what it says, you should not attack it for who says it.

There is a lot of misinformation about the events surrounding this episode.

Indeed there is. It would do you good to get Sternberg's opinion too. Watch the "Expelled" movie and you will see the interview with him discussing this "scandal".

In fact, the book's prologue spews lies and misinformation starting on the first page. Luckily for the author, this early dishonesty is independent of the intellectual work he purports to have conducted, which I have taken time to evaluate.

Hmm. Once again, attacking the irrelevant details of a story is just another method of ad hominem, for it really doesn't matter who your mother is, frankly, when evaluating scientific debate. And when you research the "lies and misinformation" I guarantee you will be astounded how the story you've been told has been twisted as well. Best not to argue over irrelevant points, you can't win, but you can lose.

I would like to note that Meyer states that he published an article in a respected peer-reviewed journal. While this is technically correct, the peer-review of his particular article was never carried out.

You're nit-picking at irrelevancies. It was peer reviewed by three reviewers, despite what you may hear otherwise, both Stephen Meyer and Richard Sternberg will tell you how. And as I told you before, peer-review is a murky enough process that you really don't want to get into a debate of what constitutes valid "peer-review". The stories are quite spicy, and I have an evening full of them.

It is also important to note that there has not been a publication of a pro-intelligent design article in any peer-reviewed scientific journal since (nor was there before).

Um, quite the contrary (and you can go to Discovery Institute and check out their list). But you have made a claim in the form of a universal negative, which everyone since Aristotle has pointed out is extremely difficult to validate. I don't think you can exhaustively prove this claim until you have read every peer-reviewed article ever published and asked if it supported design. But if you did, you would find many more than you just stated. (Yockey's 1992 paper comes to mind, though the man himself eschews ID, his papers support it.)

So in general you are quite right, there are not many peer-reviewed articles, but there have been two dozen or so that have been highly influential. But you might ask why this is an important point to make? Were there any publications of the inverse square law of gravity before Newton? Did that invalidate his theory?

Meyer makes the point that truly innovative work doesn't fare well in the peer-reviewed journals, simply because one can't make a lengthy argument in that brief format, and abbreviated papers are too incomplete for reviewers to approve. After all, even Darwin had to publish his innovative work in a book. So whether there have been one, two, or a dozen peer-reviewed articles doesn't make a theory any more valid or invalid. Science is NOT consensus, politics is.

My very first point of contention is that there seems to be a radical misunderstanding about what evolutionary theory claims to explain and what it does not.

You are catching on to the whole problem with this debate. When there are different definitions for the main terms, then how can any consensus be achieved? But the problem is worse that that, the problem is that multiple definitions are used and interchanged causing ambiguities that are intentional; a method known to students of Aristotle as "equivocation". Once again, lawyers are all over these rhetorical shenanigans, while scientists seem oblivious. That's why Phillip Johnson, a lawyer, got involved in ID, because without knowing the science, he got very suspicious of the equivocation he saw in the defence of Darwin.

Meyer's point about intelligent design does not necessarily conflict with evolutionary theory, though it is closely related. Meyer argues about origin of life, which evolution technically does not address.

No, if you read Meyer carefully, he objects to both Evolution (as a deterministic system of speciation) as well as origin of life (OOL). The point is that if bacterial life is designed, then why isn't invertebrate life, vertebrate life, mammals and primates? There is no a priori reason for terminating design with the first bacterium. The same principles that detect design in OOL, can detect it in transitional forms as well. Which is why Darwinists see OOL as the camel's nose, as well they should.

But your technicality for evolution is just that, an equivocating technicality that is easily dismissed. The problem is that there are 5+ definitions for evolution, and when someone brings an argument against one, then retreat to another definition is pure and simple equivocation. I don't have space to enumerate the many definitions of evolution, here are just a few:

1) evolution-1: change over time. -- Both ID and Darwinists accept this.
2) evolution-2: change over time caused by random chance.-- Both ID and Darwinists accept this.
3) evolution-3: change over time caused by random chance leading to fundamentally greater complexity -- Darwinists accept this, ID doesn't.
4) evolution-4: absemce of change over time due to any other process than chance and law (physics) --Darwinists accept this, ID doesn't.
5) evolution-5: Non-existent, impossibility of any forces in nature except those due to material causes (physics) --Darwinists accept this, ID doesn't.

OOL problems fall into the category evolution-4, which is a subset of evolution-5. Claiming that OOL is a mystery to evolution (and therefore not defended) would still permit miracles and ID, so that despite not wanting to talk about OOL, no Darwinist will abandon evolution-4 and evolution-5. That's why it is an equivocation to say evolution is technically not about OOL.

(We could say a great deal about -4 and -5 and metaphysics, but it would distract from the science right now.)

Evolution by natural selection describes a mechanism to explain how lines of organisms change over time. It is used to elucidate the mechanism by which, from generation to generation to generation, organisms gradually change. We know from incredible amounts of data, fossil and genomic evidence to cite two sources, that organisms do change over time. We can see this very clearly in bacterial evolution today because bacteria reproduce so quickly.

You are defending evolution 1, and evolution-2. There is no debate here. There is, however, a debate whether evolution-3 has ever been observed even in bacteria. See Michael Behe's "The Edge of Evolution" for a recent discussion of the malaria parasite by a microbiologist. The problem is the that all observed evolution in bacteria (notably anti-biotic resistance) is devolution, not evolution. The resistant species is less robust in the wild than the original, which cannot be an argument for "progress".

The issue of origin of life, or abiogenesis, has implications for evolution but in no way can call evolution into question.

Indeed it can. Because if instead evolution was caused by--as I have peer-reviewed published papers describing--bacterial transport on a comet, then the whole scenario of "descent with modification" is called into question. If life arrived from outside the Earth, then we aren't seeing "change over time", but "transport over time", making evolution no more correct than saying your old neighbors mutated into that new family with kids.

It is origin of life that Meyer claims to address. However, what he actually does is address origin of information of life. These are two closely related but subtly different claims. Essentially, he constructs a straw man by saying that DNA has information in the form of the genetic code and that since we see code today in the form of digital, which is man-made, the genetic code must also be made by some intelligence which he terms a "designer."

Look, it is a rhetorical device to insist that your opponents arguments are "straw men", when you cannot refute them. Whether or not DNA==Life or merely DNA-->Life is an irrelevant distinction. Or as they say in rhetoric, "a distinction without a difference". There are no examples of life without DNA/RNA. If you want to call prions "life", then you have most of the biology community against you. So it is perfectly within the purview of science to replace a mushy biology word with a concrete physical analogue, and then draw conclusions from that physical analog.

But what he fails to adequately address is the fact that DNA is not the only material that can store information.

Again, this is a distinction without a difference. Information is stored in countless ways on your laptop, in the RAM, in the buffers, in the monitor, but if it evaporates when you turn it off, it isn't the kind of information that is important to your thesis. DNA is the permanent record of info in the cell, and everything else derives from it. None of the other information storage devices are relevant to the question of speciation. In fact, Darwin formally disallowed information flow backwards from the environment into the genome, condemning Lamarck's thesis, (which is now being supported as the newly discovered "epigenetic" information). Biologists even give this one-directional information flow a name, "The Central Dogma" is that the DNA holds the info, and everything else derives from it. If your complaint about other sources of info were valid, you would have to erase the "central dogma" from the textbooks.

Further, he asserts that any assemblage of information must be artificially created. Both these statements are false. Proteins, RNA, clay, and many other pre-biotic molecules can store and replicate informaiton, especially if all these materials are allowed to interact with each other, which is almost definitely the case.

Okay, we now have two T/F issues that you think are central to Meyer's thesis. He says:

(1) DNA is the central information storage of life, and hence to OOL. You say no. Let's examine the evidence:

a) Do proteins contain information? Yes. Can they replicate that information? Not very well. Can they store that information for any important length of time (say, 100 years, the lifespan of tortoises and some people.) No. Can they store it for 1 year? Not without enormous error rates. Can they store it for 1 day? Not at the part-per-billion error rates of DNA. Why? Because the peptide bonds get hydrolyzed, and several of the amino acids that make up proteins are unstable. They are nearly useless an information bank, with cellular lifetimes on the order of seconds or minutes.

b) RNA. Can it replicate? Not really, it is 99% the product of a cell that has DNA in it. Does it have information? You bet. Can it store information for 100 years? No, it is much less stable than DNA. Typical lifetimes in the cell are again seconds to minutes. Does this invalidate Meyer's thesis? No, he specifically mentions that DNA and RNA are considered the same in principle, but the "Central Dogma" says that RNA is produced from DNA. So Meyer is merely going by the book here, and if you want to argue a "RNA-world" hypothesis, you will have to take a controversial thesis. But you called this pre-biotic, which is ridiculous. RNA is as biotic as DNA.

c) Clay. Can they replicate? No, they are formed from bacterial interaction with silicate rock. This is not replication anymore than feces replicate. Do they have information? No. Then what are we arguing about? Someones half-baked speculation on OOL from clay. Why are you then so sure that there is information involved? Because you relied on faulty information sources, who needed this as a way to solve the OOL problem for evolution-5.

d) If you have "many more" pre-biotic information molecules then let the world know, it would really help the discouraged OOL community.

So your objection turns out to be another distinction without a difference. There may be other ways to store information, but none of them turn out to be important. Perhaps what Meyer said was that DNA was the only important one, and I believe you are in agreement with him.

(2) Meyer says that any assemblage of information must be artificially created.

Is clay artificially created? Yes, by bacteria. Is RNA? Yes, by DNA.
Are proteins? Yes by RNA and ribosomes.

So once again, you are in complete agreement with him. Find me some information that was created by chance or by physical law. That is what would prove Meyer wrong. Crystals are made by physical law, but they lack information. Constellations are made by chance, but they don't encode any message. Until you offer an alternative, I think you are in complete agreement with Meyer here.

Next he tries to play games with large numbers, again employing a straw man.

I hate straw men as much as the next guy, but you will have to explain why these are straw, and why real men don't obey the same laws of physics that dominate these number problems. Sir Fred Hoyle, an ardent atheist and materialist, did the numbers for evolution and arrived at nearly the same calculation. See his 1987 book "The Mathematics of Evolution". It isn't a straw man argument, and it has never been satisfactorily solved.

He is also guilty of using what wikipedia call "weasel words." Here is a link explaining them. Weasel words are sometimes a problem in wikipedia articles when a person wishes to put spin on an otherwise largely objective article. Meyer uses words like "random" and "chance" in sometimes inappropriate ways to create the illusion of clarity while actually attempting to make use of the common connotations of the words to manipulate the reader's opinion.

We are descending into ad hominem again. I mentioned that you yourself used equivocation earlier (the British use vocabulary where an American uses idiom), so be careful whom you accuse. If Meyer is guilty of equivocation, then carefully distinguish between the two meanings and see if his argument depends on confusing the two. If not, then he is no more guilty of "weasel words" than the "pro-lifers and the anti-aborts" are. Face it, words have connotations along with denotations. Get used to it, because one day someone will do it to you, and calling them names doesn't really pack the same persuasive punch. (BTW this is why newspapers and dead-tree media are going the way of the dinosaur--they decided weasel words were necessary in reporting the news the right way. Morality crusades and ad hominem have a way of destroying their messengers.)

Meyer misdefines a scientific theory, calls it the "chance hypothesis," and attacks an idea that no serious scientist really endorses. The "chance hypothesis" that he describes was tossed out more than 40 years ago, way before much of the really robust and insightful work in pre-biotic chemistry was performed.

Umm, just because an experiment was declared "old-fashioned", doesn't mean that the results aren't still cited as evidence. The Miller-Urey experiment and the Oparin hypothesis remain in every textbook despite the fact that they are not considered valid mechanisms for OOL. The point Meyer is making, is that these hypotheses lie at the foundations of biology, and when they are overturned, there is a serious problem with the super-structure built upon them. Calling them out-of-date, does nothing to uphold the logical superstructure. It is the status-quo biologist who has to find a replacement for the chance hypothesis, or the entire Darwinian edifice is endangered. (As every serious Darwinist along with Darwin readily admits.)

Below is one example of hundreds of papers published in well-respected, peer-reviewed scientific journals (which didn't by-pass the peer-review process).

Quantity is no substitute for quality, and the sheer quantity of papers pushing weird OOL theories does not make them believable or even make them probable. I can tell you the funniest I've heard, about hydrogen-peroxide based life on Mars. Simply hilarious. Remember, quantity is not quality, consensus is not science.

This is a link to a podcast from Nature magazine that interviews the author of a paper that identifies mechanisms for the spontaneous formation of pyrimidine RNA nucleotides in the conditions of the early earth.

I am peripherally involved in the OOL debate, because I wrote some papers on cometary transport of life, and listened to various OOL arguments against comets and supporting an Earth-origin. So having listened to these people come to the Astrobiology conference and attack my friends, I can only laugh when I hear their arguments. Since you take this so seriously, let me point out a few relevant issues the paper seems to overlook. Here's some of the abstract:

Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis—cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate—are plausible prebiotic feedstock molecules and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

a) The first point is the admission of the impossible
From a colleague's blog:

"The first point worth making is that new advances are often shown to be significant by referring to the lack of progress that had earlier characterised the field. This is often a surprise to the general public, who are typically fed a story that the problems are largely cracked and abiogenesis researchers (OOL) are confident of tying up the loose ends in the near future. Wade's report refers to the solution of "a problem that for 20 years has thwarted researchers trying to understand the origin of life - how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth."
Van Noorden explains the problem like this:
"An RNA polymer is a string of ribonucleotides, each made up of three distinct parts: a ribose sugar, a phosphate group and a base - either cytosine or uracil, known as pyrimidines, or the purines guanine or adenine. Imagining how such a polymer might have formed spontaneously, chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide. But even in the controlled atmosphere of a laboratory, efforts to connect ribose and base together have met with frustrating failure."
Abiogenesis researchers adopt either 'law' or 'chance' as causal explanations. They have rejected 'design' (not because it does not work, but because they insist on all causation being material). The new research is driven by a confidence in 'law'. The researchers are chemists. For them, the origin of life is a matter of chemistry. Thus, Sutherland, the lead author, is quoted as saying:
"My ultimate goal is to get a living system (RNA) emerging from a one-pot experiment. We can pull this off. We just need to know what the constraints on the conditions are first." [and] "My assumption is that we are here on this planet as a fundamental consequence of organic chemistry, so it must be chemistry that wants to work."
What, then, has been achieved? The researchers have synthesised both pyrimidine ribonucleotides (but not the purine ribonucleotides). As Van Noorden described it, they have "shown that it is possible to build one part of RNA from small molecules". They havenot formed RNA molecules; they have not addressed the chirality problem, they have not generated any biological information and they have not made RNA do anything of biological significance, let alone become clothed with a membrane and undergo replication.
Nevertheless, what they have done can be applauded as an elegant example of systems chemistry. A specific bond was needed between the Ribose and the Nucleobase, and a decade of research proved that the bond was not going to form directly. So what the researchers did was to create the bond and then turn the components on each side of the bond into the desired building blocks of the Ribonucleotide. Phosphate, which previously caused problems for OOL researchers, becomes a catalyst. Szostak's News and Views essay draws attention to the elegance of their approach:
"But in a remarkable example of 'systems chemistry', in which reactants from different stages of a pathway are allowed to interact, Powner et al. show that phosphate tames the combinatorial explosion, allowing oxygenous and nitrogenous reactants to interact fruitfully."[. . .] "The penultimate reaction of the sequence, in which the phosphate is attached to the nucleoside, is another beautiful example of the influence of systems chemistry in this set of interlinked reactions. The phosphorylation if facilitated by the presence of urea; the urea comes from the phosphate-catalysed hydrolysis of a by-product from an earlier reaction in the sequence."

b) The second point is the redefinition of the "Plausible"
As you know, Miller-Urey tried to start with a plausible reducing atmosphere, added electricity, and found amino acids. The whole argument they made was that this was a plausible composition for a plausible atmosphere. Unfortunately, both assumptions have been challenged, and the Miller-Urey experiment is no longer used as OOL evidence (except in biology textbooks!) Not because it doesn't work, but because it is implausible. But compared to Miller-Urey, the compounds and concentrations of "cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate" are totally and completely implausible! Not only so, but the plausible introduction of water and oxygen completely poison the reaction. So the RNA-world hypothesis is watering down the word "plausible" to mean "anything that we can do in a lab".
Here's a more erudite description from the same colleague's blog:

"It is good chemistry, but does it achieve a major advance in abiogenesis research? Questions can certainly be raised. The researchers argue that they are not starting with any unrealistic initial conditions: "We don't use any way-out scenarios - all the conditions are consistent with what we know about early Earth." However, this is disputed.
"The flaw with this kind of research is not in the chemistry. The flaw is in the logic - that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro, a chemist at New York University. [and] Dr. Robert Shapiro [. . .] said the recipe "definitely does not meet my criteria for a plausible pathway to the RNA world." He said that cyano-acetylene, one of Dr. Sutherland's assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth "could be considered a fantasy." [and] "But while this is a step forward, it's not the whole picture," [James] Ferris [of the Rensselaer Polytechnic Institute in Troy, N.Y.] points out. "It's not as simple as putting compounds in a beaker and mixing it up. It's a series of steps. You still have to stop and purify and then do the next step, and that probably didn't happen in the ancient world."

c) The third point is the unintentional support of ID.
But "anything we can do in a lab" is done by intelligent agents, chemists, who control the temperature and composition to get the result they need. Since this is unlikely to occur by chance in the pre-biotic Earth, what this experiment really reveals is just how much ID is required to make ribonucleic rings in the absence of life. Here's my colleague's blog again:

"It can be argued that the chemical reactions documented actually yield products that are intelligently designed. The experimental conditions are engineered to selectively accumulate some reaction products (by fractional crystallisation) and selectively destroy others (by the influence of UV radiation). These conditions are considered more plausible in Darwin's hypothetical "little warm pond". Indeed, Wade's report says: "Dr. Sutherland's report supports Darwin". This is significant because the emphasis in abiogenesis research has shifted in recent years to other scenarios - notably at mid-ocean ridge locations. Those who find themselves impressed with the potential of this research would do well to reflect on the way the chemistry is engineered to achieve the outcomes and the associated fine tuning of environmental factors. These are not Darwinian emphases!

d) The fourth point is the failure to address the problem: what makes RNA special.
All this work is just on the pyrimidine rings! We haven't even discussed the bases that line the RNA, which is where the real information is found. We're debating the abiotic manufacture of the machinery and haven't even gotten to the primary evidence of ID, the information coded on the RNA. Nor have we discussed peculiarities of living RNA versus the RNA of this reaction, namely, the chirality of life versus the non-chirality of chemistry. We still haven't figured out the machinery, and likely never will. The blog again:

"Of the other limitations mentioned above, the chirality problem is noted in Wade's report: "A serious puzzle about the nature of life is that most of its molecules are right-handed or left-handed, whereas in nature mixtures of both forms exist. Dr. Joyce [an expert on the chemical origin of life at the Scripps Research Institute in La Jolla, Calif.] said he had hoped an explanation for the one-handedness of biological molecules would emerge from prebiotic chemistry, but Dr. Sutherland's reactions do not supply any such explanation."

e) Conclusion
Does any of this discussion give me confidence that we are on track to explain RNA-World? No, because if anything, these "advances" admit just how far away we are from getting even one aspect of the RNA-world to function, much less the coding and the self-enzymatic activity. Miller-Urey was wrong about a "protein-first" OOL solution, but the RNA-first solution is even more implausible and difficult to imagine.

Furthermore, Meyer also "takes on" other scientific theories by the same misrepresent and attack method.

Attacking is the nature of science. Misrepresenting isn't. So if he is guilty of misrepresenting, then you are duty bound to make it clear what is being misrepresented. Sure, you can quote PZ Myers at Pharyngula who claims all sorts of misrepresentation, but my point is that after the ad hominem name calling and accusations are finished, no one is able to clarify the precise misrepresentation nor demonstrate which logical error was committed. In other words, it wasn't a misrepresentation that was at fault, but a disrespection problem; it wasn't the science but the religion that was violated. Calling blasphemy a misrepresentation is a category mistake.

If he were to appreciate the common sense of evolution, he would understand why his attacks don't make sense.

Science is not common sense. This is rule #1 in every text book on the philosophy of science. Otherwise we could all be arm chair scientists. The only reason for scientific experiments is that science violates common sense. Metaphysically stated, nature is external to us, and therefore we can never predict what nature will do without an experiment.

He uses highly evolved macromolecules and asserts that this huge complex couldn't have come together by random chance. Well duh! Evolution says that it would have been the result of 4 billion years of small changes and gradual additions. Further evolution asserts that each form along the way had to have served some purpose in the cell, though that purpose could change as other elements also evolved to shift structure and function.

I'm glad we are in agreement about the mathematics of evolved macromolecules. But you are taking on faith two further assumptions: (a) that 4 billion years of small changes will accomplish the big changes; (b) each change had a beneficial function at that time. Both assumptions can be tested. Yes, evolution really is a theory and not religion if it can be tested. And both experiments reveal the opposite conclusion.

a) Not billions, not trillions, not even quadrillions of years are sufficient to account for the information changes between bacteria and humans, or OOL. The simplest bacteria still has more information in it than the probabilistic resources of every hydrogen atom in the universe (10^80) rearranged at their vibrational speed (microseconds=10^-6s) for the age of the universe (10^15 seconds) = 10^(101) combinations. Because the amount of information is closer to (10^10,000) which is Hoyle's estimate. Hubert Yockey, another non-ID atheist, gets 10^40,000 information bits, I believe.

b) Most mutations are not beneficial. In fact, most beneficial mutations involve 2 or 3 changes, which have probabilities that become vanishingly small, because they have to happen simultaneously if the organism is to survive. Considering that there are fatal mutations between the beneficial ones, you need to recognize just how difficult it is to evolve a change in a protein. The only reason it has been stated as an easy problem is because people wanted the conclusion, but didn't want the experiment. Once again, the science-is-not-common-sense problem.

Meyer also rudely dismisses the criticism of Kenneth Miller, a professor of biology at Brown University and a devout Christian.

Miller is neither polite, nor devout. But this is an ad hominem argument. Most importantly, he is wrong.

If you would like a Christian's take on evolution, I suggest reading one of his books--Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution or Only a Theory: Evolution and the Battle for America's Soul.

Such views are by Theistic Evolutionists, who are really not theistic at all, they are deistic, which either out of ignorance or malice, they do not differentiate. That is, they are much closer to Unitarians than Christians. This includes Frances Collins too, and the former Calvin College prof, Howard Van Till. But once again, this is all ad hominem, and irrelevant to the question at hand.

It is not until chapter 14 that Meyer even addresses any chemical or biological questions at all. He attempts to discredit the RNA world hypothesis with 5 "problems." The first problem he highlights is being solved right now, piece by piece. The link to the podcast above addresses one of the issues with prebiotic chemistry, and issue which is commonly known in that field of study as the biggest problem with the RNA world hypothesis. And look, we've just figured it out. So, so assume that we won't figure out how the rest of it works is defeatist.

Umm, I think the claims to victory are a bit premature (see my earlier comments on the Nature paper). Not only so, but human history tells us that hubris is a bigger problem than humility. I would say that RNA world has so many compelling and orthogonal counter-arguments, that there really is no chance that it will survive, say, even 10 years. It is less compelling than Oparin in his day, or Miller-Urey in theirs.

The second problem isn't actually a problem. He just states that a highly evolved system functions more efficiently than a less evolved one. By "evolved" I mean several things, not simply complexity. Specificity is a major part of it. There are an ever increasing number of papers that identify RNA functioning as enzymes in a range of critical roles. To say that RNA can't do this function well enough is just silly.

On the contrary, it isn't silly because it is based on experiment. The fact of the matter is, that RNA is not the primary component of life, DNA is. I may sound like a broken record, but it is the Central Dogma for a reason. One would have to assume that OOL began with RNA, and then magically converted to DNA later, wiping out all traces of RNA life. So the first problem is how RNA-first could have evolved and then vanished.

Likewise, DNA holds more data than RNA, so the second argument is that one would have to assume that the less info-rich molecule created the more-info rich molecule, which is like saying heat flows from colder to hotter. And I could go on. The logic is so strained as to make one wonder what RNA has going for it at all, that it should have become the OOL favorite.

The third problem makes a big jump in logic and again forgets that evolution occurs by a series of small changes rather than giant leaps.

I think we are dealing with the gambler's paradox here. The fact that rolling snake-eyes 100 times in a row is unlikely, cannot be made more likely by breaking it down into 100 separate rolls of the dice. You cannot make evolution more likely by talking about intermediate steps. Statistics won't let you. But more importantly, biology won't let you.

He also asserts that there is only one way for a coding system to have evolved, which is quite absurd. Explaining all the problems with his logic on this point would take a very long time.

Nevertheless, it would be quite instructive. Because as you take your opponents argument seriously, you will discover the weaknesses in your own. His logic, along with his education, is more extensive than your own, which means you really have no reason to dismiss him, other than the "argument from authority" of your teacher's unsubstantiated opinions.

The fourth problem again misapplies "chance" and statistics, among other things.

I have yet to meet a Darwinian biologist who can do statistics. I would wager 10:1 odds that his statistics are better than yours. Check out Michael Behe's blog on the errors made by biology PhD statistics.

The fifth complains that we haven't figured out how to make a specific RNA enzyme. This is perhaps a challenge for scientists to figure out, but is not sufficient to toss out the RNA world theory unless you subscribe to Michael Behe's motto "This is too hard for me to figure out, so I'll just say God did it." Behe, btw, has claimed for years that the bacterial flagella couldn't have evolved. The problem is that some scientists found not just one, but several plausible mechanisms for its evolution. Behe, predictably, maintains that he is right.

Well, your profs, predictably, claim that Behe is wrong. Being able to predict a scientist's biasses does not, I repeat myself, invalidate his arguments. But Behe doesn't say what you just claimed he said. This is another one of those equivocation problems. Behe claims that there are three causes for an action: law, chance and design. Design is not a "gap theory", it is not the absence of law and chance that defines it, though certainly it is a strong argument for its existence. Rather, it is the presence of a certain quantity, which Dembski calls "complex specified information", that defines design. Behe demonstrates why bacterial flagella are complex, he demonstrates why they are specified, and he demonstrates why they possess information, from that he infers design.

Now materialists only allow for two explanations: law and chance. This means that they have no explanation when flagellar motors are highly improbable and no law defines their construction. They fall back on either speculation (Darwin's speciality) casting about for some law that will derive this result, or they rely on some incredibly impossible accident. But unfortunately, speculation is not science. It is not experimental. It is not data. It is merely that, speculation. So just because Darwin can "imagine a warm pond" for OOL does not make it any more likely, nor imagining a "injection mechanism" for flagellar motors, makes it any more probable. Not until an experiment demonstrates OOL, or demonstrates the evolution of flagella from some less intelligent precursor, are we left with anything more than pure speculation. This is why Behe doesn't have to accept their "plausibility" arguments because there's nothing there to see. See the discussion of "plausibility" above.

Most of these criticisms are what can be termed an "argument from ignorance."

Au contraire, pierre. Argument from ignorance requires there to be a lack of evidence to make a case. On the contrary, as I said earlier, design is a positive evidential argument from observation of complex specified information. Darwin and the evolutionary biologists are the ones making speculative arguments from ignorance.

In chapter 17, Meyer attempts to state that he has not been arguing from ignorance. However, if we are to read him literally, he seems to be arguing that aliens designed life on earth.

And why not? We have comets with fossilized life on them, some of which we have never seen on Earth. I refer you to spie04.pdf, as well as spie05, spie06, spie07 and spie08. (I didn't have the money to attend SPIE this year, though I was planning to describe magnetite framboids as a bacterial adaptation to cometary living.)

Even so, his argument puts aliens and God on equal footing as being the agents of creating life on earth. Actually, I take that back, he actually gives aliens a slight advantage.

And this is a problem for an atheist? What exactly do you find objectionable about this?

Further, his justification for not accepting that in the future science may be able to give a more complete picture of how life began through natural means is dubious. He asserts that science makes similar assertions all the time. However, this is another misrepresentation.

Again, I think this is clear and obviously true. So be careful about calling blasphemy a misrepresentation, that's a category mistake.

For instance, the conservation laws of thermodynamics say that matter and energy are never created or destroyed.

No, actually they don't. Materialists (from 500BC until 1904 AD) used to say that matter is neither created nor destroyed, but Einstein demonstrated that they are convertible. So now some materialists say that the sum of matter+energy is constant, but again, string theorists and multiverse cosmologists disagree. In neither case did thermodynamics have anything to say about it.

The reason for this is that if matter or energy were created or destroyed the universe could not exist given the known laws of physics.

On the contrary, Fred Hoyle wanted a materialist universe with chance evolution, but knew that it was too improbable. So he suggested that the universe has lasted forever, constantly creating matter out of nothing and expanding so as to maintain a constant density. He kept the physics the same, even with a small rate of ex nihilo hydrogen creation. It was the most popular cosmology among astrophysicists from 1930 to 1960. Read about it in Robert Jastrow's "God and the Astronomers" [1978].

However, he is not justified in saying that we will never figure out the origin of life because doing so is 1) possible, 2) increasingly likely, and 3) would violate well established laws of physics.

I don't know quite what you meant to say with this sentence. The OOL problem can be solved, since obviously there was a beginning to everything, it just may take aliens to solve it. It is the a priori elimination of all intelligence and aliens from the set of potential explanations that cannot be justified.

I stopped reading after chapter 17 due to time constrictions, but also because he stops talking about anything scientifically relevant.

That's a pity.

This book cites no experimental science in support of its thesis.

I found all kinds of scientific support. I'm not sure why you said this.

It avoids most recently published scientific work, mostly because it would cast doubt on his assertions (something he admits to having done before).

No, a book has to be finished sometime, and that means publishing something that is at least a year out-of-date (given the lead times for publication). Nor has there been any progress in OOL or DNA research in the past few years that has changed any of the standard models, as your own citation of RNA-world demonstrates. He's as relevant today as he was 2 years ago.

He misrepresents current scientific understanding and misrepresents the criticisms that have been raised against him, albeit cleverly.

You're making a category mistake again.

The author, whose PhD is in a humanity discipline, not a science discipline, argues just as I would expect him to given his degree, which is in History and Philosophy. Thus, he gives long accounts of history and trivia and recites lots of well-accepted philosophical thought to establish rapport with his readers (though he bored me with long-windedness) before pulling a sort of bait and switch by getting the reader to keep agreeing with him and then making an assertion that is poorly supported. And he did this repeatedly.

I fail to find the "poor support" that you cite. Unless you mean "blasphemy" again.

It's one of the more cleverly written pieces in a long line of intelligent design and creationist dogma. Still, it is written to make a political or religious point rather than a scientific one.

There is no such thing as a purely "scientific point", all objective arguments have subjective presuppositions. Read Kuhn. Really read Kuhn. His advisor was a logical positivist who expected that sociology would support this myth you are citing about a "scientific view". Kuhn's scientific data did not support the myth. Read Berger and Luckman on the sociology of knowledge. You really need to interact more with the liberal arts faculty who have been saying this for 50(!) years to the deaf ears of biologists. Even physicists are beginning to catch on, albeit slowly.

This is not surprising because intelligent design is by definition not science.

By whose definition? Biologists? And how, precisely, does one do an experiment to find the definition of science? Isn't definition, by definition, a non-scientific activity? So then, since definition is by definition not empirical, we must not let unscientific definers define what scientists can do. If, on the other hand, science is defined by what scientists do, than ID is a truly wonderful scientific field, pursued by Aristotle on up to the present. It is materialists who are in a minority.

Our scientific understanding a vast range of disciplines advances weekly (with peer-reviewed publications) and we gain a deeper understanding of the natural world. There is still a vast amount we do not yet know or understand. There is much left to discover. But to arrive at a conclusion and then try to argue and manipulate the public understanding of science for personal reasons is not ethical.

Agreed! So you should never use ad hominem arguments, or let statements about the "lack of peer-reviewed papers" stand in the way of doing science.

It should be recognized as such and discarded.

Isn't this conclusion at odds with the previous sentence?