Sandwalk: Testing the Macaque Genome

Friday, April 13, 2007

Testing the Macaque Genome

We've already been looking at the macaque genome for several months but now that the genome paper is being published I thought some of you might be interested in how the preliminary data stacks up to what we expect.

I'm interested in a family of gene known as the HSP70 gene family. The genes encode the major cellular chaperone that's responsible for correct protein folding. HSP70 is the most highly conserved gene known [Evolution of the HSP70 Gene Family].

We know how many genes there are in mammalian genomes so we can search the macaque genome at Rhesus Macaque Genome Resources to see if the expected genes are present. Here's the result.

HSPA1A: not present, probably due to incomplete sequence or annotation

HSPA1B: correct gene/protein

HSPA1L: correct gene/protein + one incorrect isoform that's really a splicing artifact

HSPA2: not present, probably due to incomplete genome or annotation

HSPA5/BiP: correct gene/protein + one incorrect alternatively spliced isoform that's really an artifact

HSPA8: one single correct gene/protein

HSP9B/mtHSP70: correct gene/protein + three incorrect isoforms generated by EST artifacts

That's not too bad for an initial draft sequence. Two genes are missing and so are several pseudogenes. I assume they'll turn up later when the genome sequence is being finished. Most of the splicing artifacts have been ignored by the annotators but a few have slipped through. They'll be deleted later on when the annotators are informed that the isoforms don't exist.

All in all, this is much better than most genome sequences at this stage. It's a bit better than the chimp genome but still a long way from the quality of the human genome. The mouse genome is almost as good as the human genome. Keep in mind that dozens of labs have been working on the human genome annotation for over six years since the sequence was first published. The cow, dog, frog and several fish genomes are in much worse shape and the chicken and sea urchin genomes are practically useless.

Horse, opossum, rat, pig, rabbit, cat, sheep, tree shrew, guinea pig, hedgehog, elephant, and platypus genomes are still at the assembly stage [Ensemble Genome Browser].

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

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Friday, April 13, 2007

Testing the Macaque Genome

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