December 2005 Archives

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Well, Tiffany and I are back home for the evening from Christmas trips. We’ve been at her parents since Thursday and drove by my Dad’s for dinner before coming home for the night. We go to her Aunt and Uncle’s tomorrow in Augusta.

We are also heading up to Raleigh on the 30th or 31st for a few days. I have to be in Athens on the 4th.

It’s going to be hard to find time to get some research done and upgrade PT before the semester starts again.

Christmas Tree


Tiffany and I put up our Christmas/Solstice/Yule/Saturnalia/Holiday tree tonight. Prof. Steve Steve was a big help in decorating.


Santa Tease



Wells’s has his pathetic 10 Questions to Ask Your Biology Teacher, and I wanted to post some of the questions we asked our biology students this semester. Since I’m in the middle of grading 170+ final exams right now, I am going to post the review questions for the exam. These questions cover the second half of the course, Evolutionary Biology (Gene/Biol 3000).

How many of you know the answers? How many of you even know what is being asked? How many of you think that Wells would have no clue?

  • What is the difference between cladogenesis and anagenesis?
  • What is the phylogenetic species concept?
  • How do the biological species and phylogenetic species concepts differ?
  • Give an example of a premating isolating barrier and explain how it works.
  • Give an example of a postmating isolating barrier and explain how it works.
  • What do measurements of genetic identity (and distance) tell us about the speciation process?
  • Define sympatric taxa and give an example.
  • Define allopatric taxa and give an example.
  • What is known about genes affecting reproductive isolation?
  • What is epistasis and why is it important to reproductive isolation?
  • Give an example of postzygotic reproductive isolation caused by chromosomal differences.
  • How is mating choice measured in Drosophila fruit flies?
  • How are Drosophila fruit flies collected in nature?
  • Why is reproductive isolation so important in speciation?
  • What is allopatric speciation by vicariance? Be sure to include in your answer an explanation of vicariance.
  • How does peripatric speciation differ from allopatric speciation by vicariance?
  • What is the distinction between selection OF and selection FOR?
  • What are two major mechanisms can lead to reproductive isolation?
  • What are the Dobzhansky-Muller incompatibilities that may cause hybrid sterility?
  • How is reproductive isolation reinforced?
  • How did experiments in my own laboratory bring about selection for stronger reproductive isolation?
  • What is parapatric speciation?
  • Why is sympatric speciation thought to be rare?
  • How does speciation by polyploidy occur?
  • What is the difference between autopolyploidy and allopolyploidy?
  • What is the basic idea of a “web of life” instead of the classical “tree of life”?
  • Give an example of each of the two mechanisms that bring about gene exchange between two species.
  • What are the three major domains (or empires) of the current phylogenetic tree of life? Include an example of a species in each of the three.
  • List 7 major levels of classification in taxonomy.
  • Name 5 levels of taxonomic classification for humans.
  • Why are synapamorphies important in building phylogenies?
  • What is homoplasy?
  • Give an example of homoplasy.
  • What is the central feature of the method that Hennig proposed for building phylogenies?
  • Name 2 methods for inferring phylogenetic relationships.
  • How is the molecular clock used to estimate actual dates of divergence in phylogenies?
  • What is the difference between a gene tree and a species tree?
  • Do gene trees and species trees always agree? Why?
  • What is a polytony?
  • What are paraphyletic taxa? What did Hennig say about them?
  • List at least 3 kinds of evidence for evolution that come from systematics.
  • What is convergent evolution? Give an example.
  • What is meant by mosaic evolution?
  • What is adaptive radiation? Give an example.
  • What is Wegener’s Theory of Plate Tectonics?
  • What is the basic of concept of radiometric dating?
  • In what era did dinosaurs arise and diversify? When did this era start?
  • Name the era, period, and epoch in which Homo sapiens evolved.
  • Give 3 reasons why the fossil record is often incomplete.
  • Name a missing link and explain which groups it links.
  • Explain the concept of punctuated equilibria.
  • What are 2 lines of evidence that there is a single common ancestor of life?
  • How old is the first evidence of life?
  • Our domain of life carries descendants of organisms from another domain of life. Name these descendants and the domain from which they originated.
  • In which era and period did most modern phyla appear in the fossil record?
  • When was the K/T extinction, and what is thought to have caused it?
  • Explain the terms adaptation and exaptation and illustrate them with examples from the evolution of tetrapods from fish.
  • In “At the Water’s Edge”, Zimmer talks about homeotic genes and how they might be involved in morphological evolution. Give a brief account of how this might occur.
  • What is biogeography?
  • What is convergent evolution? Examples?
  • What did Darwin say about biogeography?
  • Who was Wallace and how did he divide the earth into biogeographic realms?
  • What role does vicariance play in speciation and in biogeography?
  • What role do phylogenetic methods play in biogeography? Examples?
  • What do the terms allochthonous and autochtonous mean, and how are they used in biogeography? Examples?
  • What is phylogeography? Example.
  • What was the most significant element missing from Darwin’s theory of evolution? Who introduced it later?
  • How do microevolution and macroevolution differ?
  • What is the major difference between exponential and logistic models of population growth?
  • What do the statistical techniques of regression and correlation measure?
  • What is the “Red Queen” Hypothesis?
  • When did mass extinctions occur?
  • What are the major causes of extinction?
  • What are the 3 “Tiers of Evolutionary Change” proposed by Gould? Give evidence for them.
  • What are the basic components of a “life table”?
  • How is fitness related to natural selection?
  • What does r, the Malthusian parameter of demography, define?
  • In a population growing in size, which counts most, reproduction early in life or reproduction later in life? Why?
  • In a population with stable population size, which counts most, reproduction early in life, reproduction later in life, or neither? Why?
  • Is there any advantage to life beyond reproductive age in humans? Explain.
  • What is the concept of tradeoffs among fitness components?
  • What is Lack’s concept of optimal clutch size in birds?
  • What is “net reproduction” in a demographic model? How is related to fitness?
  • What are r and K selection?
  • Explain why figs and wasps are used as an example of coevolution.
  • How do commensals differ from competitors?
  • What are “brood-parasite” birds? Example?
  • How can you explain the fact that bill sizes (bill depth) in G. fuliginosa and G. fortis are more different when the two species share a habitat than when they live alone?
  • How have rabbits and myxoma virus coevolved in Australia?
  • How does Batesian mimicry differ from Mullerian mimicry?
  • Which contributors to the “Modern Synthesis” of evolutionary theory wrote principally about macroevolution?
  • What are some reasons that living fossils might remain relatively unchanged morphologically for very long periods of time?
  • What is relaxed selection? What evidence is there for it?
  • What are three key events in human evolution?
  • What does the term “Hominin” refer to?
  • Where are human fossils are most commonly found?
  • Which molecular marker is best used to trace male dispersal, and why?
  • Which molecular marker is best used to trace female dispersal, and why?
  • What is the concept of coalescence?
  • On the basis of genetic data, when did humans move into South America?
  • What is the difference between the “multiregional” and “replacement” hypotheses for the origin of modern humans?
  • How have these hypotheses been tested? Which is favored?
  • What evidence did the Grants and their colleagues obtain about natural selection on Darwin’s finches?
  • What role did the Grants find for hybridization in Darwin’s finches?
  • Give 2 lines of evidence showing that humans are still evolving.
  • What is the evidence that humans are evolving by genetic drift?
  • What kind of selection is still operating on humans? Examples?
  • What is eugenics, and why are many biologists concerned about it?
  • What is molecular evidence for evolution of eyes in flies and mice? What bearing does it have on the general thinking about the evolution of complex structures?
  • What have homeobox genes told biologists about developmental aspects of evolution?
  • What is co-option and how does it figure in our understanding of molecular-developmental aspects of evolution?


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What do you call a bear that is sometimes happy and sometimes sad?

A bipolar bear.

ID and Assault

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It is interesting to watch ID activists act skeptically towards the reported beating of a recently controversial KU religion professor. If, as many critics now believe, the police will eventually conclude that the report is a hoax, they will do so based on the naturalistic and materialistic constraints of their worldly occupation. However, ID supporters don’t suffer from such constraints and are freer to follow the evidence wherever it leads.

Clearly, it is in the realm of possibility that the professor was attacked not by “rednecks,” but by angels sent by The Almighty to punish the professor for upsetting His chosen people, Kansas’s Religious-Right Republicans. In fact, this explanation is actually better than all others currently under consideration because it can explain any and all evidence uncovered during the investigation. Even the lack of evidence can be explained by the angels’ magical powers.

As with all other Intelligent Design explanations, this explanation’s correctness is plainly obvious to its supporters, who thus have no interest in proving it. Critics bear the onus to prove it wrong. Unless any critic can produce an infinitely detailed naturalistic explanation (down to the position of every sub-atomic particle in the universe) for the time of the assault, then Assaulting Angels are clearly the best explanation for what happened to the professor. Critics who ignore this explanation are dogmatic materialists wanting to remove God from police investigations.

(Hat tip to Wesley.)

Georgia Earns a B

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Well the grades for the state science standards have been released and our state has improved its score from an F to a B. Our new standards are now 12th in the nation.

Our standards were going to be much worse when the state superintendent, Kathy Cox, decided to gut evolution education in the standards. (See previous post.) She not only wanted the word “evolution” removed from the standards but also removed roughly 70% of the material pertaining to evolution. Other controversial subjects like the age of the earth were also redacted from the standards by her. (Unlike Minnesota’s (now Florida’s) Yecke, I don’t think Cox was intentionally trying to promote creationism but rather was honestly trying to avoid classroom controversy. Woops.)

Public outrage over her move, especially comments by Jimmy Carter (a nuclear engineer, former President, and Nobel laureate) forced her to add the material back in. However, these shenanigans left little room to improve the standards further, which is why we didn’t manage an A.

One interesting thing to note is that Georgia scored well on its treatment of biology. It’s the other science that made us loose points.

By far the best feature of these standards is their handling of life sciences. Introduction of the important ideas of modern biology begins early, and their development is steady and carefully sequenced. High school work is a real advance over what has preceded it in the primary grades, yet it is solidly based on the acquired background. The treatment of biological diversity and evolution is straightforward and comprehensive; but for unnecessary parsimony on molecular biology, it would be outstanding. (We understand that the intelligent design creationists are very active in Georgia, too, but so far it appears that they haven’t succeeded in mutilating the state standards.) Grade: “B.”

None of this would have been possible without the diligence of Georgia Citizens for Integrity in Science Education.

Evolution Letters

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There’s been some letters in recent weeks to the Athens Banner-Herald about evolution. Here are as many as I could find.


Pat Hayes asks:

If teaching evolution causes people to act like apes, then what excuse, we wonder, do conservatives offer for the religious fundamentalists who beat Prof. Mirecki along a rural Kansas road, yesterday.

Well, if you believe that people came from dirt, then you begin to treat them like dirt.

It’s Tiffany’s Birthday

SEC Champions


I’m sure most of you have realized that I’m a big fan of the Georgia Bulldogs. (Not a rabid fan like my friend Sam, but a big fan nonetheless.) Well my Dawgs came through last night and took LSU to the woodshed. Texas and USC had pretty routs, and FSU squeaked by, but Georgia took down the biggest opponent, dominating the #3 team in the country in all areas of the game.

For all those people who thought that Tennessee, Florida, Auburn, LSU, or Alabama was going to win the SEC, I guess you look stupid now. (Some more than others, *cough*UT*cough*.)

We were one injury from being undefeated, but I guess it is better that we had some losses because I prefer to end the regular season on a high note, than complaining about being shafted by the BCS.

I’m picking Texas to beat USC for the national championship, based on the difference in their defenses.


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