14 February 2010

Signature in the Cell: Chapters 4 and 5 - errors and problems

Meyer's basic idea in chapters 4 and 5 is reasonably coherent. But I find further evidence in both chapters that Meyer is careless and underinformed on the subjects he addresses. (I explained before why I think this matters. If you think I'm not being nice enough to Meyer, consider providing me with the Rules of Engagement that apply when criticizing culture warriors who are proposing world-shifting new ideas.)

1. A bizarre paragraph in chapter 4 makes me wonder if Steve Meyer is terribly confused about bacterial transformation. On page 104, he writes:

Oswald Avery correctly determined it was DNA, not bacteria living or dead, that caused the mice to die. But when scientists established that DNA directs protein synthesis, Avery's results were viewed in a new light. DNA caused the mice to die, all right, but it did so by directing the production of proteins that were toxic to the mice (though, obviously, not to the bacteria from which the DNA was derived).
This is really strange talk. What Griffith had established was that one strain of bacteria could be converted – transformed – into another strain through direct contact. What Avery and colleagues showed was that DNA was the chemical agent that could transform bacteria. It was, in fact, living bacteria that killed the mice, and the key difference was not a toxic protein – it was a sugar-based coat called a capsule. I wonder if Meyer, portrayed as an eminent philosopher and historian of science, has actually read the work of Avery et al. If he had, he would know that those scientists wrote this on page 140 of their historic 1944 paper:
Transformation of types has never been observed to occur spontaneously and has been induced experimentally only by the special techniques outlined earlier in this paper. Under these conditions, the enzymatic synthesis of a chemically and immunologically different capsular polysaccharide is specifically oriented and selectively determined by the specific type of S cells used as source of the transforming agent.
Translation: we can induce one strain to transform into another, and we know that this occurs when a certain enzyme (a protein) creates a certain sugar-based capsule in the transformed strain. The enzyme appears when cells are exposed to the "transforming agent." And of course Avery et al. identified that transforming agent as DNA.

2. Meyer attempts to construct an analogy between CAD-CAM and protein synthesis on pages 120-121. It's a failure, because there's little analogy between the two processes, and Meyer wisely abandons the analogy after that. The main purpose seems to be a plug for Expelled and a pointer to free animations at the Signature in the Cell website.

3. On pages 125-126, Meyer briefly discusses introns and RNA splicing. In that paragraph, he does immense damage to his credibility as a scientific thinker or even commentator. There are two errors in the paragraph. One is merely embarrassing. The other is devastating. On page 126, Meyer writes this about the process of RNA splicing:
This process requires the existence of other specific enzymes – exonucleases, endonucleases, and splicesomes, for example – that can correctly identify and excise the nonprotein coding text from the initial RNA transcript and then splice together the resulting fragments of coding text in the correct order.
This statement shows that Meyer did not understand the two pages in Lodish's Molecular Cell Biology textbook that he cites there. RNA splicing is accomplished by a huge multi-part molecular machine called the spliceosome, which is made mostly of RNA and is not known to include either exonucleases or endonucleases. Meyer did mention the spliceosome, but spelled it wrong. (He got it right in the one other place he mentions splicing.) Did he not consider having a real biologist look at this book at some point before it was published? (I've seen the acknowledgements, and the answer appears to be "no" but I don't know all the folks mentioned there.) But the real mistake is on page 125:
...the original DNA text in eukaryotic organisms has long sections of text called "introns" that do not (typically) encode proteins. Although these introns were once thought to be nonfunctional "junk DNA," they are now known to play many important functional roles in the cell.
This is the discredited creationist "junk DNA" ploy. It signals the presence of some combination of ignorance, sloth, and duplicity. I've written elsewhere about the layers of dishonesty in the this ploy, and was hopeful that Meyer would either avoid using the tactic or would at least attempt to tell the truth about non-coding DNA. Here's a short explanation for why Meyer's statement is ludicrous.

The human genome contains at least 190,000 introns (though it's been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That's 768 million base pairs. And biologists have identified "important functional roles" for a handful of them. How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they're snipped out of the transcripts and discarded before the darn things even leave the nucleus. We might return to this topic, since it's interesting and there are more layers of duplicity in the "junk DNA" fairy tale that Meyer has included in his book. But Meyer has done significant damage to his credibility by including it. In my view, he showed his cards. It looks to me like this isn't a book about science. It's a book using science to advance an agenda, and rigorous scientific truth-telling is secondary to that goal.

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