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Some reader rants

I've been horrible about posting reader feedback. This will change. Maybe someday we'll even open up the blog and let people slap stuff onto the page without my imperial approval. Democratize the operation. I'm not sure how to make that happen, and in fact I need to learn how to use this blogging tool better (like, is it possible to post a photograph? And how can I get rid of that wimpy, goofy, doofy picture of me at the top? That was taken years ago. I look nothing like that now and frankly didn't ever look like that).

Tom Shroder's post about Intelligent Design has inspired a great deal of reaction. Just to recap, I wrote something about life at the bottom of the sea and rhapsodized about the powers of evolution, and Tom thought I hadn't adequately summarized one aspect of the Intelligent Design argument.

Pavel Litvinov writes:

I have a problem with Tom Shroder's " So maybe there is something else - as yet unknown - at work in evolution besides simply random mutation and natural selection". It is amazing that in 150 years (or so) since the publication of "Origin of Species" everything we learned only confirmed precisely that seemingly simple but very deep idea, and it seems unlikely that this basic fundamental fact will change, although we have learned amazing facts since and no doubt will learn even more about actual mechanism of evolution and there are still many unanswered questions. Enemies of Darwin's Theory have been trying to use new discoveries in genetics and other sciences to try to find anything to overturn it, but failed every time! It is especially amazing because Darwin had no idea and did not try to hypothesize (as far as I know) anything about actual mechanism at work .

Gary Oxford, who has a blog of his own, writes:

I too am in solo dad mode this week, with my wife off doing something called "Chowder Society." Having been charged with maintaining vegetable consumption by our two sons, Captain Entropy and Impulse Boy, I have discovered 2 solutions compatible with my hectic, ESPN watching lifestyle. One approach is the little pop-top cans of carrots and green beans. The other is pizza. Even cheese pizza, which my boys prefer, has tomato sauce rich in lycopene, helping to protect their inactive little prostates from future cancer. And isn't oregano a vegetable?

On a more serious note, I must jump on the Malcolm McGowan bandwagon wondering what your editor was smoking when he posted on Intelligent Design. Let me make 4 additional points:

1. If we're going to have a discussion about evolutionary aspects of the immune system, can we do a better job defining terms? What are these "highly complex structures in the human immune systems that would require millions (or billions?) of individual mutations to come into being?" Are we talking about antibodies, MHC molecules, T cell receptors, complement, all of the above?
I can't discuss this any further without some guidance.

2. You may want to talk to some comparative immunologists, who study the immune systems of other organsims, before you say that there is no adaptive value to any of these mutations by themselves. Here's a name to get you started: Martin Flajnik, in the Department of Microbiology, University of Maryland School of Medicine. That's a local call.

3. If ID proponents get the benefit of the doubt, why don't evolutionary biologists? Is it because their ideas are more complicated, require more thought to analyze, are more than simple bromides calculated to make the uneducated feel good about their ignorance?

4. There are more things going in evolution than mutation and natural selection. Such as genetic drift, horizontal gene transfer, endosymbiosis, transposons, alternative splicing, prions, gene duplication, and the major generator of antibody and T cell receptor diversity, gene rearrangement. Believe or not, we biologists have continued learning since Watson and Crick. Is it too much to ask the same of science journalists and their editors?

Sorry about the rant, Joel....If you get a chance, come by my blog, http://corndoggerel.blogspot.com to nominate a Worst Cover Song Ever.


Josh Munger writes:

These "millions of mutations" that occur in the hypervariable regions of
various immune system proteins were not selected for on an individual basis,
the system itself that produces the variability in the genes -- was selected for -- this system is a result of a number of genes, i.e. there are genes responsible for creating this hypervariability which are definitely evolutionarily favored (under the control of natural selection) so that our immune system can handle most anything thrown at it. Hope this is clear.

Russ Acker joins in:

Who says, "there are highly complex structures in the human immune
systems that would require millions (or billions?) of individual
mutations to come into being, yet no amount of those mutations alone
would have any adaptive value at all. You need all of them, working
together, to get the benefit..."???

According to http://evolution.berkeley.edu/evosite/evo101/VIICComplexity.shtml,
there are several ways to explain that: some intermediate stages can
provide partial advantages over nothing at all; a feature that acts as
an intermediate stage of one adaptation might be the well-adapted stage
of something else entirely; and natural selection can duplicate
important features so that one version is still available to do
whatever it does, while the other version gets to diverge into
something else.


Tom Michels writes about Tom Gold, a legendary scientist who died not long ago:


Your recent blurb "Adaptation" got me thinking about the intriguing theories of Thomas Gold -- the twice Nobel-ed astronomer who died last June, after his book "The Deep Hot
Biosphere" had roiled many feathers. Had Gold not already secured an ironclad
scientific reputation, his book would never, ever have seen the light of day. His basic thesis is
that the organic matter found in oil that had led people to think of oil as a fossil fuel, is not the source of oil after all. Instead, oil is bubbling up from the earth's core. A rich subsurface biosphere feeds on oil and associated gases such as methane and helium, and this is the source of the organic matter
in oil. The methane ice worms and critters that feed on oil seeps would support this, as would the life that has been found at the bottom of the Marianas Trench and other inhospitable environments.
Furthermore, if you follow the oil business at all, the biggest thing in the Gulf of Mexico is "Deep Gas" -- reserves of natural gas that are found at depths of 15,000 to 35,000 feet below surface (and maybe greater, we just don't have the technology to get at it). There are so many iconoclastic thoughts in Gold's theory that I certainly don't have the space or expertise to go into them. But the one most relevant to your column would be that the organisms in the Challenger Deep may have evolved from the sub-surface up, not from the surface downward. You can find an abstract of Gold's book at the
link below. Very interesting stuff.

http://people.cornell.edu/pages/tg21/DHB.html

Also, here's a link about Deep Gas:
http://www.gomr.mms.gov/homepg/whatsnew/newsreal/031119.html

My quick response: I had the pleasure once of interviewing Gold at Cornell, and found intriguing his theories on oil and the deep hot biosphere (I will try to dig up a Why Things Are link about this). But in the case of the recent foraminifera (sp?) at the bottom of that trench, the scientists found genetic links to organisms living at shallower depths and even on land. I suppose they could have "evolved toward the surface," but that's just as remarkable as doing it the other way around.

By Joel Achenbach  |  February 16, 2005; 12:40 PM ET
 
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