The genome is not a computer program

The author of All-Too-Common Dissent has found a bizarre creationist on the web; this fellow, Randy Stimpson, isn’t at all unusual, but he does represent well some common characteristics of creationists in general: arrogance, ignorance, and projection. He writes software, so he thinks we have to interpret the genome as a big program; he knows nothing about biology; and he thinks his expertise in an unrelated field means he knows better than biologists. And he freely admits it!

I am not a geneticist or a molecular biologist. In fact, I only know slightly more about DNA than the average college educated person. However, as a software developer I have a vague idea of how many bytes of code is needed to make complex software programs. And to think that something as complicated as a human being is encoded in only 3 billion base pairs of DNA is astounding.

Wow. I know nothing about engine repair, but if I strolled down to the local garage and tried to tell the mechanics that a car was just like a zebrafish, and you need to throw a few brine shrimp in the gas tank now and then, I don’t think I would be well-received. Creationists, however, feel no compunction about expressing comparable inanities.

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Bisexual flies and the neurochemistry of behavior

Blogging on Peer-Reviewed Research

On the one hand, this is a strange tale of mutant, bisexual, necrophiliac flies, and you’ve got to love it for the titillating nature of the experiments. But on the other, much more interesting hand, it’s a story about drilling down deeply into the causes of a complex behavior, and tracing it to a single gene product — and it also reveals much about the way the chemicals sloshing about in the brain can modulate responses to stimuli. Work by Grosjean and others on a simple Drosophila mutant, genderblind, which causes flies to be indiscriminate about gender in their courtship, opens up a window into how sexual responses are shaped and specified.

Think about human sexual responses. Some of us, when we see an attractive woman, are at least mildly aroused; others are have their sexual interest picqued when they see an attractive man; still others might feel sexual urges when they see a shoe, or a plush animal, or a pot of baked beans. No matter what the stimulus, these are all biological responses, with something in the environment matching some trigger in our brains and initiating a cascade of neural, neurochemical, and hormonal activity that leads to sexual behaviors. The question we want to address is what every step in the biology is doing; unfortunately, human behaviors are both too complex and not amenable to ethical experimentation, so we turn instead to simpler organisms that allow us to find simpler causes and carry out thorough experiments to probe the behavior.

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Dubious parentage

It would seem like sweet poetic justice if James Watson were found to be 1/8th African, but I’m afraid I don’t quite believe it. This is news coming from a company called deCODE genetics, an Icelandic outfit that analyzes an individual’s racial background on the basis of various genetic markers. While I can buy the claim that they can assess the distribution of various alleles in populations, I really dislike the game of trying to work in reverse and assign the fraction of a race to an individual.

I don’t think Larry is much impressed with them, either. Here’s another article that brings up the flaws.

The problem is compounded by the increasing improbability of the company’s claims. Watson is also 9% Asian. He’s got a 31% lesser chance than average of getting asthma, and a 2% greater chance of prostate cancer. These kinds of numbers are meaningless when applied to individuals. We don’t even know all the genetic factors that contribute to the various diseases listed, so it’s ludicrous to pretend they can quantify the total risk for a single person that way. While I’ve got no problem thinking there are shared alleles percolating through African and European populations, there are much more reliable ways of determining that a person has an African great grandparent.

(via Accidental Blogger)

Student Post: Immortalized Mules

I spent a summer working on an Arabian horse ranch when i was 17. I loved that place and am crazy about Arabians but… let’s face it. We’ve severely inbred horses for show. Exhibit A:
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It’s not uncommon for an Arabian pedigree to boast seven lines of relation to one horse. Bask, for instance, was a famous Arabian stallion and today a large percentage of Arabs are his decendents including my horse, Rebel, of whom I’m foolishly fond:

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Well, I learned some interesting news at today’s Senior Seminar. Why inbreed when you can clone! It’s all the rage among mule racing enthusiasts. Don Jacklin, president of the American Mule Racing Association, almost single-handedly funded cloning research at the University of Idaho of his champion mule line. Cloning champion horses has been made into a very lucrative business in France. Cryozootech turns a large profit cloning gelded or aged horses so that their clones can be used for breeding. If I had 300 grand I could clone Rebel.

It will be really interesting to see what happens to these animals as they age. The mules are reported to be healthy and competitive racers but concerns over telomere length have yet to be addressed.

…And yes. I did just want to use the phrase “mule racing enthusiasts.”

Gay Genes? Genetics?

While reading Jonathan Weiner’s book – Time, Love, Memory, I ran across several topics that are quite controversial. I thought that the book did an excellent job of presenting the science of these subjects while remaining neutral. One such topic is the genetic component of homosexuality. Studies have shown a tenative link between certain genes and homosexuality. Other studies have shown no such link. The thing about genetics is that genes interact with one another in very complex ways. It has taken decades to work out the mechanism of genes involved in circadian rhythm, and new discoveries are still being made. Working out the genetic component of homosexualiy is going to be difficult, and until more is known about how genes influence sexual orientation I am going to withhold judgment as to how much of a role they play.

Nobel in Medicine goes to…

I’ve known for years that this was going to happen: Mario Capecchi, Oliver Smithies and Briton Martin Evans have won the Nobel Prize in Medicine for their work on targeted gene mutations. If you’re interested in what kinds of work they’ve done, I described one paper on Hox regulatory evolution, and this work on the evolution of the Hox code wouldn’t have been possible without their knockout techniques.

Tandem repeats and morphological variation

Blogging on Peer-Reviewed Research
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All of us mammals have pretty much the same set of genes, yet obviously there have to be some significant differences to differentiate a man from a mouse. What we currently think is a major source of morphological diversity is in the cis regulatory regions; that is, stretches of DNA outside the actual coding region of the gene that are responsible for switching the gene on and off. We might all have hair, but where we differ is when and where mice and men grow it on their bodies, and that is under the control of these regulatory elements.

A new paper by Fondon and Garner suggests that there is another source of variation between individuals: tandem repeats. Tandem repeats are short lengths of DNA that are repeated multiple times within a gene, anywhere from a handful of copies to more than a hundred. They are also called VNTRs, or variable number tandem repeats, because different individuals within a population may have different numbers of repeats. These VNTRs are relatively easy to detect with molecular tools, and we know that populations (humans included) may carry a large reservoir of different numbers of repeats, but what exactly the differences do has never been clear. One person might carry 3 tandem repeats in a particular gene, while her neighbor might bear 15, with no obvious differences between them that can be traced to that particular gene. So the question is what, if anything, does having a different number of tandem repeats do to an organism?

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Luskin on gene duplication

Casey Luskin has to be a bit of an embarrassment to the IDists…at least, he would be, if the IDists had anyone competent with whom to compare him. I tore down a previous example of Luskin’s incompetence at genetics, and now he’s gone and done it again. He complains about an article by Richard Dawkins that explains how gene duplication and divergence are processes that lead to the evolution of new information in the genome. Luskin, who I suspect has never taken a single biology class in his life, thinks he can rebut the story. He fails miserably in everything except revealing his own ignorance.

It’s quite a long-winded piece of blithering nonsense, so I’m going to focus on just three objections.

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Brains feeling stretched…

Cosma has to go and show off with a magisterial demonstration of why he is the smartest man on the internet: he’s written an exceptionally thorough description of heritability and IQ. It’s not a light read (statistics and genetics!), but it’s probably the most informative thing I’ve read in a month or more.

I’m sure I’m going to have to read it a few more times before I’ve absorbed it all.