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.

The Hox code

Blogging on Peer-Reviewed Research

The Hox genes are a set of transcription factors that exhibit an unusual property: they provide a glimpse of one way that gene expression is translated into metazoan morphology. For the most part, the genome seems to be a welter of various genes scattered about almost randomly, with no order present in their arrangement on a chromosome — the order only becomes apparent in their expression through the process of development. The Hox genes, on the other hand, seem like an island of comprehensible structure. These are all genes that specify segment identity — whether a segment of the embryo should form part of the head, thorax, or abdomen, for instance — and they’re all clustered together in one (usually) tidy spot.

Within that cluster, we see further evidence of order. Look at just the Drosophila part of the diagram below: there are 8 Hox genes in a row, and their order within that row reflects the order of expression in the fly body. On the left or 3′ end of the DNA strand, lab (labial) is expressed in the head, while Abd-B (Abdominal-B) is expressed at the end of the abdomen.

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Schematic of relationship between Drosophila and mouse Hox genes. Hox genes are shown as colored boxes in their order on the chromosome. Orthologous genes between Drosophila and mouse, and paralogous mouse genes are shown color-coded.

Knocking out individual Hox genes in the fly causes homeotic transformations — one body part develops into another. These genes are early actors in the cascade of interactions that enable the development of morphologically distinct regions in a segmented animal — the activation of a Hox gene from the 3′ end is one of the earliest triggers that leads the segment to develop into part of the head.

Now look at the mouse part of the diagram above. We vertebrates have Hox genes that are homologous to the fly Hox genes, and they’re also clustered in discrete locations with 3’→5′ order reflecting anterior→posterior order of expression. There are differences — the two most obvious that we have more Hox genes on the 5′ side (these correspond to expression in the tail—flies do not have anything homologous to the chordate tail), and vertebrates also have four banks of Hox genes, HoxA, HoxB, HoxC, and HoxD. This complicates matters. Vertebrates have these parallel, overlapping sets of Hox genes, which suggests that morphology could be a product of a combinatorial expression of the genes in the four Hox clusters: there could be a Hox code, where identity can be defined with more gradations by mixing up the bounds of expression of each of the genes.

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FunGenEvoDevo

I got some email today with lots of constructive suggestions (See? Not all my email is evil!) for how we ought to change the education of biology students — such as by giving them a foundation in the history and philosophy of our science, using creationist arguments as bad examples so the students can see the errors for themselves, etc. — and it was absolutely brilliant, even the parts where he disagreed with some things I’d written before. Best email ever!

Of course, what helped is that I spent my summer “vacation” putting together a new freshman first semester course for biology majors that I’m teaching for the first time right now, and it’s exactly the course he described. It was eerie, like one of my future students had invented a time machine and come back into the past to tell me what to do. A lot of the course content is locked up behind a password-protected firewall, I’m afraid, but just to show you what I’m talking about, I’ll put the course schedule below the fold.

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