Bane

Anyone read this:

<a href="http://www.gregbear.com/A55885/Bear.nsf/pages/300067" target="_blank">The New Biology</a>

He has a different view on ID. I found it quite interesting.

ohwilleke

Sounds like Bear is proposing a debate between a "Gaia" model of intelligent design, in which the biosphere is viewed as a single intelligent organism that acts rationally, and "sophisticated randomness" . . . a view of the forces of genetic change as lacking a central guiding force, yet involving considerably more complexity, interplay and detail than a casual notion of "random" mutation would entail. He still, of course, rejects young earth creationism, and even heavier handed versions of ID.

bluefugue

I read Darwin's Radio. It certainly attributes to evolution far greater power than the generally supposed blind, in-the-moment natural selection. One can talk about "evolution of evolvability" and higher-level mechanisms, but the mechanism Bear proposes in DR seems to go further and actually be able to predict a species' adaptive requirements millennia in advance. I don't buy a word of it, but then what do I know...?

Bane

Yep, I knew it seemed familiar.

I was aware of that. That's why I took the article more seriously. He's not interested in shoving a specific theology down our throat. He believes in a god though.

I always thought the guy was a biologist?


I haven't. I was looking for a good scifi book to read and stumbled upon his site. Is it a good read?

bluefugue

It's pretty good, although I just don't buy his mechanism for evolution. However Greg Bear (along with Gregory Benford) is one of the best "hard sci-fi" writers around. He really does his research; his books are always good food for thought.

theyeti

I don't buy it either. For one thing, it requires genes to be dormant for huge stretches of time without degenerating into noise. No explanation for that. And of course, it begs the question of why those genes are there in the first place. However, his focus on endogenous retroviruses is interesting, in that these suckers do have a great effect on our genome (though unlikely in any great adaptive effect). But I didn't like the book at all. I thought the writing was terrible.

theyeti

pz

He's a science-fiction author. He really doesn't seem to know very much biology, but he's very, very good at presenting an illusion that he does.

I found his essay ignorant and pretentious. When he says things like, "The paucity of hypotheses in biological science may be something of an intellectual crime, perpetrated by academics protecting their own fiefdoms against assault by barbarian unbelievers-hardly an atmosphere in which to raise and tutor new generations of biologists", he's making a rather nasty accusation based entirely on his own lack of knowledge. Biology is rich in hypotheses in this subject, quite contrary to his assertion. The thing is that for such hypotheses to generate much interest or attention, they also have to provide a reasonable basis for further work, and not contradict existing observations.

The hypothesis he makes in his science fiction novels fail in both regards.

He may resent the fact that biologists aren't falling all over themselves in excitement at his glorious science-fiction ideas, but that's not our fault: the problem is that his ideas are just plain bad biology.

theyeti

Oh my. I just read the essay. This guy is more clueless than I thought -- he's not just a crappy writer.

He completely misunderstands what the Central Dogma is, confusing it with the one gene, one protein hypothesis. He claims that RNA editing "shatters" the notion that DNA is responsible for phenotype, apparently oblivious to the fact that RNA editing enzymes come from DNA. He claims that insertions and rearrangements don't count as random mutations. And then there's my favorite:

Uh, why is it of great difficulty to describe this as a random event? Retrotransposition of genes happens all the time, and it is known not to be directed. This is why it usually creates processed pseudogenes. I suppose those were produced deterministically?

Later on he says that coevolution would have been thought ridiculous in the recent past -- apparently "recent" means prior to Fisher.

The whole thing reminds me of the much-too-often observed layman who has been burdened with a caricatured, over-simplified, and obsolete view of biology, who then, upon getting a tiny glimpse of what's been going on in the last few decades, suddenly realizes that things are more complex than he thought. Having had this sobering revelation, instead of realizing that he's been ignorant all this time, he blames the scientific establishment for adhering to old views that it has not adhered to for a very long time. Fancying himself the revolutionary, he proudly proclaims the scientific community, whose workings he does not understand, close-minded and dogmatic for not jumping onto his own uninformed, silly ideas. I see this all the time. Arrgghh!

theyeti

pz

He also says, "The sidebar to this dogma, which claims that DNA is read-only-implying that the genetic material changes only through random mutations, not through insertion or rearrangement of genetic material-collapsed some time ago with the discovery of mobile genetic elements such as transposons and retroviruses." This is muddled nonsense. Insertion and rearrangement are just other ways of generating random mutations; there's nothing new or unusual about that. Those mechanisms are also not the reason DNA is considered modifiable, which was due to the discovery of retroviruses -- and "write-only" was not part of the central dogma, anyway.

Molecular biologists will be very surprised to learn that a property which is central to many of their most commonly used tools is somehow revolutionary and destroys our vision of how biology works.

Retrotransposition is also not a necessary mechanism to generate a gene duplication; I don't know if there is any evidence that primate trichromacy is specifically a product of retrotransposition, either. I think he just threw that in because it is a nifty six-syllable word that makes him sound knowledgeable.

Of course, whether it was a retrotransposon-mediated event or just a unequal crossing over doesn't matter -- As you say, nothing in that suggests that it was a non-random event. Those things happen all the time.

Exactly! Mr. Bear needs a good dose of humility, and a little remedial education in basic biology. Maybe he should take my cell biology and genetics courses.

All this does make me considerably less inclined to ever pick up one of his books, though.

theyeti

I couldn't find the reference. Though I do have a copy of Patthy's Protein Evoution chapter on the "birth of new genes". Bear is referencing this book which references another book which references the original research. That might tell you something about his scholarly habits. The chapter has commentary about retrogenes and lists a couple of examples -- phoshoglycerate kinase and preproinsulin I. Trichromatic color vision is not listed there, but it might be listed as being caused by retrotransposition event elsewhere in the book.

Of course, you're right that unequal crossing-over is a much more common way to duplicate genes. I suspect that he's unaware of this though, and only knows about retrotransposition because he researched it for a book he wrote that makes no sense and is boring as hell. Retrogenes are cool because they leave some good evidence of their specific history, but they're rare because retrotransposition usually results in a 5' truncation, due to the reverse transcriptase falling off before completion -- and of course no regulatory elements get carried along. So the vast majority end up as non-functional pseudogenes. But for some reason, these "can be described as a random event only with great difficulty."


theyeti