September 2005 Archives

My mother grew up in Americus, GA because my grandfather was a professor of chemistry at Georgia Southwestern College. My mother is in the process of moving back to Americus and is already teaching school in Sumter Country. Meanwhile, my step father is living in Athens until they sell their house.

You may recall that Plains, GA is the home of former president and Noble prize laureate, Jimmy Carter. Plains is also in Sumter County and is about about nine miles from Americus. Until my mother and step father buy a house in Americus, my mother is living in Plains with her childhood friend, whom we visited a lot when I was little.

Guess what they are doing on Sunday?

Throwing Jimmy Carter his 81st birthday party. How cool is that?

(Of course, Clinton’s party would be more entertaining.)

Creation Seminar in Athens

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Yesterday, if I were not busy grading ~200 essay exams for “Evolutionary Biology”, I could have attended a whole day of creation seminars by Grady McMurty of Creation Worldview Ministries, a “full-time international creation emissary, biblical scientific creationist, and apologist.” They were held in Athens at Cornerstone Church of God, which some members of Tiffany’s family want her to attend. (She grew up in a small Church of God, but now attends a progressive, United Methodist congregation.)

Grady McMurty held the following seminars:

  • Noah’s Ark to the Cross (Teens & Adults) – “God’s divine hand is seen from the Ark of Noah to the Cross.”
  • Foundations – “The contrast of two worldviews, the relevance of creation.”
  • Dino-Mania – “The dinosaurs, the Bible and the fossil record.”

Given that I was inundated with grading for evolutionary biology, the evolutionist conspiracy kept me from hearing the truth about evolution. For instance if I had attended I may have heard about

  • the implications of the “Laws of Science” like the first and second laws of thermodynamics
  • how photosynthesis and metamorphosis could not possibly come into existence by random chance
  • out of order geologic layers and polystrate fossils
  • hoaxes and frauds: “Piltdown Man, Java Man, Peking Man, English Peppered Moths, the Horse Series, Pithecanthropus alalus, Galapagos Finch Beaks, embryonic recapitulation and the Monera.”
  • how the acceptance of evolution is the foundational justification to promote: human racism, homosexuality, abortion, euthanasia, lawlessness, pornography, and all the other immoral and unethical activities within our society

“Katrina/Bush is the fault of evolution, Teach the controversy.”

McMurty isn’t done he has thirty reasons why evolution is wrong. (McMurty has to be right; he has a Doctorate of Divinity from an unaccredited correspondence school.)

Use Dawg Online

I’ve now set up a web interface to Dawg.

http://scit.us/cgi-bin/dawg/

an example output – this is the example given in my paper.

More Dawg News

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I got an email today from Eran Elhaik that their paper using Dawg has been published by Molecular Biology and Evolution.

Elhaik, Sabath, and Graur (2005) The “Inverse Relationship Between Evolutionary Rate and age of Mammalian Genes” is an Artifact of Increased Genetic Distance with Rate of Evolution and Time of Divergence. Molecular Biology and Evolution Advance Access Sept. 8

Abstract: It has recently been claimed that older genes tend to evolve more slowly than newer ones (Alba and Castresana, 2005). By simulation of genes of equal age, we show that the inverse correlation between age and rate is an artifact caused by our inability to detect homology when evolutionary distances are large. Since evolutionary distance increases with time of divergence and rate of evolution, homologs of fast evolving genes are frequently undetected in distantly related taxa and are, hence, misclassified as “new.” This misclassification causes the mean genetic distance of “new” genes to be overestimated, and the mean genetic distance of “old” genes to be underestimated.

Papers Papers

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My Dawg paper is complete and will be published by Bioinformatics in early November to coincide with the GT conference.

I got a suprise earlier this week when I was offered a coauthorship on a nearly-finished paper because of some posts I made on this blog. That is definately a nice outcome of my blogging.

Busy Busy

The semester is heating up, and I probably will not be bloggin much until I get several things done.

My Department is Hiring

Two Faculty Positions In Evolutionary Biology

As part of a long-term commitment to building strengths in evolutionary biology, the Department of Genetics at the University of Georgia plans to hire five new faculty in evolutionary biology over the next three years. This year, we invite applications for two tenure-track positions in evolutionary biology at the Assistant Professor level. For one position, we have a preference for a scientist working in the field of molecular evolution. For the second position, we are looking for an evolutionary biologist whose work includes a strong theoretical component. Future faculty lines will be in the areas of ecological genetics, evolutionary genomics, and evolution & development.

Applications should be sent by email as a single PDF file that includes a cover letter, CV, statements of research and teaching interests, and representative publications, by October 14, 2005 to the appropriate e-mail address below. Three letters of recommendation should be sent by the references, either in PDF format to the appropriate e-mail address, or in hard copy, to the Molecular Evolution Search Committee or the Evolutionary Biology/Theory Search Committee, Department of Genetics, University of Georgia, Athens, GA 30602-7223. Applicants interested in applying for both positions should send two separate applications.

For information about the department, see http://www.genetics.uga.edu. For the molecular evolution position, please send applications to: [Enable javascript to see this email address.]. For the evolutionary biology/theory position, please send applications to [Enable javascript to see this email address.].

The theory position is to fill the void left in the department after my advisor, Dr. Marjorie Asmussen, was tragicly killed while riding her bike. Maybe I can get myself appointed as the student rep on the theory search committee.

NY Times Editorial

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Waiting for a Leader

Published: September 1, 2005

George W. Bush gave one of the worst speeches of his life yesterday, especially given the level of national distress and the need for words of consolation and wisdom. In what seems to be a ritual in this administration, the president appeared a day later than he was needed. He then read an address of a quality more appropriate for an Arbor Day celebration: a long laundry list of pounds of ice, generators and blankets delivered to the stricken Gulf Coast. He advised the public that anybody who wanted to help should send cash, grinned, and promised that everything would work out in the end.

We will, of course, endure, and the city of New Orleans must come back. But looking at the pictures on television yesterday of a place abandoned to the forces of flood, fire and looting, it was hard not to wonder exactly how that is going to come to pass. Right now, hundreds of thousands of American refugees need our national concern and care. Thousands of people still need to be rescued from imminent peril. Public health threats must be controlled in New Orleans and throughout southern Mississippi. Drivers must be given confidence that gasoline will be available, and profiteering must be brought under control at a moment when television has been showing long lines at some pumps and spot prices approaching $4 a gallon have been reported.

Sacrifices may be necessary to make sure that all these things happen in an orderly, efficient way. But this administration has never been one to counsel sacrifice. And nothing about the president’s demeanor yesterday - which seemed casual to the point of carelessness - suggested that he understood the depth of the current crisis.

While our attention must now be on the Gulf Coast’s most immediate needs, the nation will soon ask why New Orleans’s levees remained so inadequate. Publications from the local newspaper to National Geographic have fulminated about the bad state of flood protection in this beloved city, which is below sea level. Why were developers permitted to destroy wetlands and barrier islands that could have held back the hurricane’s surge? Why was Congress, before it wandered off to vacation, engaged in slashing the budget for correcting some of the gaping holes in the area’s flood protection?

It would be some comfort to think that, as Mr. Bush cheerily announced, America “will be a stronger place” for enduring this crisis. Complacency will no longer suffice, especially if experts are right in warning that global warming may increase the intensity of future hurricanes. But since this administration won’t acknowledge that global warming exists, the chances of leadership seem minimal.

Chimps are Laughing at You

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Given Nature’s publication of the chimp genome, I figured that I’d share one of my all time favorite figures from a scientific paper. It is from Gagneux et al. (1999) Mitochondrial sequences show diverse evolutionary histories of African hominoids. PNAS 96 (9): 5077.

Fig. 1. Unrooted phylogram of the neighbor-joining tree of 1,158 different CRI sequences before (A) and after (B) after topiary pruning to level PL = 8 to remove homoplasies. Bootstrap values >= 50% for the primary internodes are shown. Position of the midpoint root is indicated by arrow. Different colors indicate species (humans, bonobos, and gorillas) and subspecies (chimpanzees). Symbols indicate individuals belonging to the same social group.…

What is very obvious from this paper figure is how genetically homogenous we are compared to our closest relatives. I’ve heard it stated that a single chimpanzee tribe has as much genetic diversity as is found in the entire human species. So next time you feel fit to make fun of us southerners for kissin’ cousins remember that chimps are laughing at you.

More on Gas Rumor

This is the story from today’s Athens Paper:

Athens motorists jammed local filling stations Wednesday afternoon as gas prices surged to more than $3 a gallon.

The lines mirrored similar panic buying across Georgia as word of possible shortages and even rationing spread, but the situation was exacerbated in Athens by a widespread rumor that local retailers would stop selling gas by 3 p.m. Wednesday.

Regular unleaded was just under $3 a gallon when University of Georgia student Lindsey Phillips got in line at the Quick Stop on Lexington Road and Winterville Road. Half an hour later, as she began pumping gas at about 3:15 p.m., the station raised the price to $3.39 a gallon. The price Wednesday morning had been $2.71.

The rumor that local retailers would stop selling at 3 p.m. may have created an area gasoline shortage, said wholesalers like Bobby Tweedell of Tweedell & Van Buren Oil Co.

Before Wednesday’s panic, the supplier had about a five-day supply of gasoline on hand, but Wednesday afternoon’s stampede meant the supply could run out late Friday or early Saturday, Tweedell said.

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