Wednesday, June 29, 2005

Random Mutation and Natural Selection

A common argument from the anti-evolution crowd is that random mutation plus natural selection cannot result in the complexity of life we observe on earth. This, of course, ignores all of the other evolutionary forces that work on natural populations and represents a general ignorance of the modern theory of evolution. Furthermore, some people are unclear as to what biologists mean when referring to random mutations. In this post I explain the statistical definition of random, some different classes of mutations, and the random nature of genetic mutations.

1. What it means to be random
In order to understand the statistical meaning of random one must first have some familiarity with probability. Probability is just a mathematical way of describing how likely a certain event will occur relative to all alternative events. For example, there are two possible outcomes when flipping a coin: heads and tails. Assuming the coin is fair (i.e., heads and tails are equally likely), we have a 50% chance of flipping heads and a 50% chance of flipping heads. Another way to describe this is the probability of heads is 0.5 and the probability of tails is 0.5. Notice how the probability of heads plus the probability of tails is equal to one (0.5 + 0.5 = 1); we refer to this as a complete set as it includes all possible outcomes, and the sum of the probability of all those outcomes is equal to one.

The result of a coin flip is random NOT because we have no idea how it will result, but because we cannot say for certain how it will result. We have some idea what will happen – half of time we’ll flip heads, and half of the time we’ll flip tails. The coin flip is said to be random because we cannot say for certain what will happen, but we can determine the probability of each result. Random is another way of saying “not directed” (i.e., there is nothing determining absolutely the result of a particular trial or run).

Now, imagine if the coin is not fair and the probability of heads is 0.6 and the probability of tails is 0.4 (i.e., 60% of the time you will flip heads and 40% of the time you will flip tails). Flipping the coin will still be a random process, but you will flip heads more often than tails. A common misconception is that all results are equally likely in a random process; this is not the case. A random process only implies that every possibly outcome has some assigned probability, and that probability is the only thing that influences whether or not a particular event occurs.

2. Genetic Mutations
Before I get into the random nature of genetic mutations, I think it’s necessary to describe some different types of genetic mutations. Readers familiar with molecular genetics can probably skip this section. If I become unclear at any point, I suggest referring to this excellent summary of mutations.

Your genome is made up of DNA which is composed of four different nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C). These nucleotides are arrayed in a linear fashion, much like the words on this page. We can write out the order of nucleotides in a gene like we write out letters of a word (e.g., ACGTACCGT). If we change a particular letter to a different letter (an A changing to a T, for example) we say that a “substitution” has occurred.

The adenine (A) molecule is similar in structure to the guanine (G) molecule (they are referred to as purines), and the thymine (T) molecule is similar to the cytosine (C) molecule (T and C are pyrimidines). Purines are more likely to change to another purine (A => G or G => A) than they are to change to a pyrimidine (A => T, A => C, G => T, or G => C). The same is true for pyrimidines – they are more likely to mutate to another pyrimidine than to a purine. Purine to purine (A <=> G) and pyrimidine to pyrimidine (C <=> T) mutations are referred to as transitions, whereas purine to pyrimidine and pyrimidine to pyrimidine mutations are transversions.

Now that I’ve got you totally mixed up with the jargon of substitutions, I’d like to add a couple more types of mutations to your lexicon. We can add or remove a letter or multiple letters from a particular sequence resulting in an insertion or deletion event (indel). These events can be small (only one or a few nucleotides) or fairly large (an entire gene can be duplicated into another part of the genome resulting in an insertion on the order of thousands of nucleotides). Large deletions are thought to be extremely deleterious, but the fitness cost of smaller indels is still unclear and greatly depends on whether or not they are located in coding sequence or noncoding sequence. Gene duplications resulting in large insertions allow for existing biochemical pathways to evolve new functions and for the appearance of new pathways.

Finally, we will consider a few types of large scale chromosomal mutations. These types of mutations affect the structure of a chromosome or the makeup of the genome in a major way. Chromosomal duplications result in the duplication of a single chromosome, whereas genome duplications result in the duplication of an entire genome. Chromosomal inversions result in a large segment of a chromosome reversing in order. Chromosomal fusions occur when two chromosomes join to form a single chromosome, and fissions are when one chromosome splits into two. A fusion event combined with a fission event is referred to as a chromosomal translocation – a large part of a chromosome is removed and attached to another chromosome. Inversions, fusions, fissions, and translocations do not result in any new information in the genome, but they restructure the existing information which could have important evolutionary implications.

3. The Random Nature of Genetic Mutations
Once you are comfortable with random sampling and probability as well as the nature of genetic mutations, it’s clear what biologists mean when they say, “Mutations are random.” We will start by following a single nucleotide from parent to offspring, and then move on to looking at the entire genome.

Let’s assume the probability of a substitution at a particular nucleotide is 10-9 (a very small number). We will only consider two possible outcomes: substitution (mutation) and no mutation. If you’ve followed me up to this point, you can see that this is analogous to the coin flipping example. We do not know if a particular nucleotide will or will not mutate in one generation, but we do know how likely a mutation event is. Whether or not this nucleotide mutates is a random process, with the probability of one in a billion (10-9) that it does mutate. One out of a billion times that nucleotide will mutate in the process of going from parent to offspring.

This line of thinking can be extended to an entire genome, made up of millions of nucleotides. Each nucleotide has the probability of 10-9 that it will undergo a substitution event in one generation. We can also assign probabilities to other mutational events (indels, duplications, inversions, etc) that can be estimated from natural populations or laboratory experiments. We can use these probabilities to calculate the expected number of mutations in the entire genome going from one generation to the next.

It’s important to understand that when biologists say the mutational process is random, we mean that it is not directed. There is nothing determining definitively that a mutation will occur at a particular nucleotide. Mutations provide the raw material on which natural selection acts. Natural selection is a deterministic process; a beneficial mutation will always reach fixation in an ideal population (i.e., natural selection will cause it to replace all the other alleles), and a deleterious mutation will always be lost. We have no way of saying for sure whether or not a particular nucleotide will mutate because mutation is a random process – we can only assign a probability that it will mutate.

Monday, June 27, 2005

It's MIT so it must be good.

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Sunday, June 26, 2005

CSI: Little Kids

The CSI shows have become an amazing marketing tool for the forensics industry. This article in the NYTimes talks about forensics camps springing up around the country:

"The National Science Teachers Association and the American Academy of Forensic Sciences have reported a surge in interest among students, and many schools now include some aspects of forensics in science curriculums."
Penn State just started a forensics major and hired the director of forensic biology in New York City's Office of Chief Medical Examiner to head the program. The forensics program is described as an "interdisciplinary program incorporating basic science courses with courses from anthropology; entomology; veterinary science and toxicology; crime, law and justice; ethics; statistics and psychology." Let's hope genetics (specifically molecular population genetics) are included in the "basic science courses." With so much talk about DNA testing in criminal cases it would be a shame for someone to graduate with a degree in forensics and not be able to explain the difference between mitochondrial and nuclear DNA or how we can determine the probability a particular banding pattern on a gel belongs to a random individual from the population.

The article goes on to discuss the difference between real forensics and forensics as it's portrayed in prime time TV:
"The American Academy of Forensic Sciences has sponsored conferences for middle school and high school teachers since 2002 to show them how to present forensic techniques in an accurate way because the television portrayal is not always the way it is done in reality."
You mean there isn't a machine that I can put a blood sample into, and it will genotype that individual at 12 marker loci in less than one minute? Are you telling me I still need to purify DNA from my sample, PCR the DNA, and run out the products on a gel or in a chromatography machine? Yeah folks, it really takes about an entire day (at the very least) to genotype an individual (assuming everything goes right) . . . and that's only if the markers are already designed.

Friday, June 24, 2005

Friday Random Ten (24 June 2005)

Dinosaur Baseball Edition

Carl Everett, Major League Baseball's foremost expert on paleontology, offered up his sage wisdom on the topic of evolution in July of 2000:
"God created the sun, the stars, the heavens and the earth, and then made Adam and Eve. The Bible never says anything about dinosaurs. You can't say there were dinosaurs when you never saw them. Someone actually saw Adam and Eve. No one ever saw a Tyrannosaurus rex."
Five years later he's expanding his realm of expertise. Recently appointed to Major League Baseball's committee for public relations, Everett offered his plans for alternative family days at the old ballpark:

"Gays being gay is wrong. Two women can't produce a baby, two men can't produce a baby, so it's not how it's supposed to be. ... I don't believe in gay marriages. I don't believe in being gay."

He doesn't believe in dinosaurs or gays (what about gay dinosaurs?) and doesn't think baseball fans know jack-shit about, get this, baseball:

"Fan is short for fanatic -- he's crazy about something he really doesn't know about. And it's proven that 99 percent of baseball fans have no idea what they're watching."

Everett's study, slated to be published by the Society for American Baseball Research, proves once and for all that baseball fans are uninformed bigots. Bill James, who was unavailable for comment, is rumored to be working on two new statistics with Everett -- for batters they propose a metric known as OPTI (Offensive comments Plus Total bases per Inning) and for pitchers they suggests the new stat OPRI (Offensive comments Plus Runs allowed per Inning). Some believe that this will revolutionize Moneyball and possibly revitalize the career of former Braves closer John Rocker.

Am I being too tough on Carl Everett? Well, I may not be able to tell the difference between a curve, a slider, and a slurve, but I can explain the infield fly rule, and I'd say I understand closer to 50% of what's going on during a game than the one percent Everett claims. Leave the biology, the sociology, and the statistics to the experts Carl, and focus on hitting the little white ball really hard.

Without further delay, I give you this week's Friday Random Ten:
  1. Unwritten Law - Harmonic
  2. Beastie Boys - Paul Revere
  3. Specials - Pressure Drop
  4. Greatful Dead - Friend of the Devil
  5. Lagwagon - The Kids Are All Wrong
  6. David Bowie - Young Americans
  7. Foreigner - Cold as Ice
  8. Hot Hot Heat - Elevator
  9. Tilt - Pious
  10. Mike Ness - Dope Fiend Blues

Wednesday, June 22, 2005

Coyne versus Carroll

The stage is set. The arena is packed. The two men enter the ring. In one corner, Sean Carroll, the developmental biologist. In the other corner, population geneticist Jerry Coyne . . .

OK, maybe that's a bit over-dramatic, but Jerry Coyne has a critical review of Sean Carroll's Endless Forms Most Beautiful in this week's issue of Nature. After the customary praise of Carroll's accessible writing and mentioning the importance of evo-devo, Coyne questions Carroll's thesis: that the majority of important phenotypic evolutionary innovations are due to changes in gene expression rather than protein sequence. Coyne critiques Carroll's position as mere inference:

"Carroll first notes that dissimilar species can in fact be genetically similar: 'Mice and humans have nearly identical sets of about 25,000 genes' and 'chimps and humans are almost 99 percent identical at the DNA level. Since the sets of genes are so widely shared, how do differences arise?' His answer is the evolution of non-coding regulatory elements: whether you are a man or a mouse apparently depends solely on your promoters and enhancers. But the underlying statistics are deceptive; even a 1% difference in DNA sequence implies a substantial difference in protein sequence. We now know that humans and chimps have different amino-acid sequences in at least 55% of their proteins, a figure that rises to 95% for humans and mice. Thus we can't exclude protein-sequence evolution as an important reason why we lack whiskers and tails."
What can we make of this obvious difference in opinion between two very well respected researchers? Well, for one thing, they are approaching biological evolution from two drastically different perspectives. Carroll is trained as a developmental biologist, and has been extremely influential in the burgeoning field of evo-devo. Coyne, by contrast, studies the genetics of speciation and tends to favor selectionist explanations for the origin of species (as opposed to neutral or population structure type hypotheses). Coyne's work is much more quantitative, whereas Carroll tries to unravel developmental pathways. I am not saying one approach is better than another, only that they are different and lead to different ways of thinking about the similar questions.

Also, Carroll seems to bring this criticism onto himself when he "presents his vision of the field without admitting that large parts of that vision remain controversial." If this is the case (now may be a good time to mention that I have yet to read the book), it may appear to the general public, to whom this book is intended, that a consensus has been reached and Carroll's view is universal.

While I definitely think that some evidence points to the importance of regulatory changes in evolution, we do not know what the relative roles of gene expression and protein sequence play in the evolution of development. Even untangling these two aspects of development can be difficult as changes in the protein sequence of a transcription factor can lead to regulatory changes in genes in downstream pathways. I'd say it's definitely an area of active research, and I do intend to read Carroll's book.

As a point of contrast, check out this review by PZ Myers.

Slate Profiles Skeptics

Read this Slate article if only to see the publication redeem itself for William Saletan's crappy treatment of the anti-evolution movement by lumping Intelligent Design in with fakes like Uri Geller and psychic surgeons.

Something (kinda) interesting

It appears the infamous John A. Davison has discovered my blog. I was wondering if I should acknowledge him, as he is just making the same tired comments he became famous for at the Panda's Thumb. I've written about Davison before (mostly in awe of his ignorance of the relevant literature), and you can get a little bit of background here and here.

I was all set to ignore him until he mentioned that he's been getting support over at John Rennie's blog, SciAm Perspectives. I had to go check it out; John Rennie is hardly someone who would endorse Davison's prescribed evolution hypothesis. Well, it turns out the support isn't coming from Rennie, but rather a hijacked comments thread.

Davison and Jianyi Zhang have discovered each other. I don't have the time nor the energy to describe Davison's hypothesis or Zhang's speciation mechanism, but I can say they have nothing in common other than existing on the fringe and having no outside support. The two do a little back-patting in the comments section of Rennie's blog and applaud each other for going against the Darwinian establishment, and Davison calls this support.

I'd like to take this opportunity to point out that evolution does not happen by random mutation and natural selection alone, as the anti-natural-selection crowd likes to present the mainstream position. I have never claimed this to be the case, and I would question any biologist who believes that these are the only two legitimate evolutionary forces. I have blogged about alternative evolutionary forces. I have also blogged about stupid ways to detect natural selection. Basically, no one in the mainstream establishment thinks in such simple terms such that they disregard all other evolutionary mechanisms. We are open to alternative explanations such as neutrality, meiotic drive, niche construction, and the effects of genome structure.

When your pet theory doesn't get accepted by anyone, don't blame the "Darwinists." It may be time to rethink your hypothesis and consider some of the criticism you're receiving. There is a rich history of building on our understanding of evolution by accepting novel ideas into the modern synthesis. There is no Darwinian establishment bent on excluding all non-selective explanations, so don't paint that us versus them picture.

Oh yeah, happy summer solstice!

Tuesday, June 21, 2005

What's Going On

What's Going on in the World Wide Web

I just got out of my committee meeting, and boy are my arms tired . . . I don't get it?? Said committee meeting is one of the reasons blogging's been light recently. That and the fact that NOTHING INTERESTING IS HAPPENING.

The meeting went well; my committee was both supportive and encouraging, all the while offering suggestions for improving my projects. What more could you want out of a thesis committee? We'll wait and see if they feel the same way when I take my comps soon.

I lied about nothing interesting happening -- there are a couple of things I noticed while surfing the internet. I'll take this opportunity to briefly blog on them, returning to the original incarnation of the blog as a collection of links.

Science as politics: The NYTimes has a particularly dated review of the Kansas Kangaroo Kourt (hereafter referred to as the KKK, which reminds me of Krusty's Komedy Klassics, wherein I lose all of my non-Simpsons literate readers). Other than the fact that it came out a couple of weeks too late, the article is fairly readable. The article focuses on Ken Miller, of Finding Darwin's God fame, and how Miller and other real scientists refused to participate in the KKK because "the outcome of the hearings was a foregone conclusion, and that participating in them would only strengthen the idea in some minds that there was a serious debate in science about the power of the theory of evolution." You can't sum it up better than that.

My favorite aspect of the review were the quotes from John West, a Discovery Institute (DI) fellow and political scientists. You know the DI is bogus when the use a political science to argue biology. Here is Dr. West in a shining moment of irony:

"The majority of biologists obviously support Darwinian evolution in its full-fledged view. The question is, are there legitimate, peer-reviewed criticisms? If there are, students should know about them."

Because there are no "legitimate, peer-reviewed criticisms" (at least none that mention Intelligent Design as a viable alternative) can we call the whole "teach the controversy" thing off and move on to more important topics?

Politics as science: Also from the NYTimes comes this discussion of a study in The American Political Science Review. Using data from twin studies the authors conclude that political beliefs are heritable. I'm not interested in figuring out if the research is legitimate or not, I just find it amusing that the study is described as "the first on genetics to appear in the journal." Pretty soon we'll see political scientists writing papers on the implications of tissue specific alternative splicing on voter turnout in non-presidential year elections. You can read the original actual article here.

Bad religion as science: I watch way too much TV. I'll watch TV when I wanna see my favorite shows and sporting events. I'll even watch TV when there's nothing good on, which is how I discovered my new favorite show (warning, hardcore Christian fundy fake-science behind this link), OriginsTV on Cornerstone Television. If you thought the Discovery Institute was a barrel of monkeys, check these guys out. They take literalism to the extreme.

That's all for now. Hopefully I'll have some more posts in the coming days, provided something interesting happens.

Friday, June 17, 2005

South Carolina, welcome to the club!

A bill has been proposed in the South Carolina State Senate containing Santorum language (aka, the crap one of my US Senators tried to put into the No Child Left Behind Act). The bill seems harmless enough:

In the promulgation of policies and regulations regarding kindergarten through twelfth grade education, the State Board of Education shall implement policies and a curriculum that accomplish the General Assembly's desire to provide a quality science education that shall prepare students to distinguish the data and testable theories of science from religious or philosophical claims that are made in the name of science. Where topics are taught that may generate controversy, such as biological evolution, the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society.
The one major problem I see is that it singles out biological evolution as a controversial topic, whereas other subjects such as physics and chemistry are not mentioned. The wording seems uncontroversial, but we must question the motivations of such legislation.

The lead sponsor of the bill (Sen. Mike Fair, R-Greenville) is described as a “dominant voice advocating for S.C. schools to teach more than Charles Darwin’s theories of evolution.” I’m all for teaching more than Darwin’s theories of evolution. South Carolina students shouldn’t just learn about an outdated theory from the mid 19th century. They should also be exposed to Dobzhansky, Mayr, Wright, Fisher, Haldane, and the rest of the great minds behind the modern synthesis. It shouldn't stop there, either. They should also learn about the advances in evolutionary biology that came about due to developments in molecular techniques such as DNA sequencing. They should learn about the neutral theory, evo-devo, and molecular phylogenetics.

Of course, spending so much time on evolutionary theory wouldn't allow one to devote as much time to other subjects, like bible study . . .

Friday Random Ten (17 June 2005)

Robbing the Cradle Edition

The evolgen Friday Random Ten promises:

Keeping it random, here are ten songs that popped into my mp3 player this morning:

  1. Cream - White Room
  2. Jurassic 5 - Improvise
  3. Me First and the Gimme Gimmes - Wild World
  4. Bob Dylan - Hard Rain's A-Gonna Fall
  5. Less Than Jake - Welcome to the New South
  6. Rolling Stones - Angie
  7. Bob Marley and the Wailers - Simmer Down
  8. Descendents - When I Get Old
  9. Long Beach Dub Allstars - Wonders of the World
  10. Living End - Problem

Thursday, June 16, 2005

Three Cheers for Y-chromosome Bearing Sperm

From Science Blog:

More boys than girls born in U.S. -- again

For the 63rd year in a row, the number of boys born in the United States outnumbers births of girls – in 2002 94,232 more boys than girls were born. This is the central finding of a new Centers for Disease Control and Prevention (CDC) report that examines total sex ratios at birth for over six decades. The total sex ratio is the number of male births divided by female births times 1,000.

I wonder if anyone has taken a close look to see what causes this sex ratio distortion. It seems to me it could occur any time from spermatogenesis to birth. There could be segregation distortion during meiosis, differences in sperm success, effects on implantation in the uterus, or developmental differences.

By the way, to learn more about human fertilization check out this movie by Planned Parenthood (via Pharyngula).

Spam of the Day.

As I emptied my Junk folder this morning, the subject line of one of the emails caught my eye:
Horny pills - low price
This could mean one of two things:
  1. These pills really wanna get their groove on. In that case, I'd be nervous to swallow them in the off chance that they try to hump my esophagus.
  2. These pills look something like Onthophagus beetles. Ouch! That would really hurt going down the old food chute.

Or maybe I'm missing something . . .

Wednesday, June 15, 2005

Tangled Bank hits the big three-0.

The Tangled Bank turned 30 today. Go read some excellent science writing over at the Geomblog (that blog name always looks like they mis-spelled "genome" to me). It's a bit heavy on the math side -- but that's what you expect from a blog dedicated to " Ruminations on computational geometry, algorithms, theoretical computer science and life" -- so make sure you bring your copy of Discrete Multivariate Analysis.

Takin' it to the rack.

This picture (via Sean Carroll -- the physicists, not the developmental biologist) was too odd to pass up.

The photo was taken at an Islamic school in Illinois. More pictures are available here. I wonder if they'd ever consider this uniform once the season begins.

Tuesday, June 14, 2005

Racist Drug Development.

UPDATE (22 June 2005): Nature has a news item on this drug with some good insights from Francis Collins. Collins suggests, "We should move without delay from blurry and potentially misleading surrogates for drug response, such as race, to the more specific causes."

An important point that needs to be brought up is that race is a somewhat subjective classification. Someone who identifies himself as African-American may be of less than 25% African ancestry. While there is real genetics behind the differences between Africans, Europeans, and Asians, sometimes ethnicity seems to overpower those differences in a cultural setting. Do we prescribe a drug that only seems to work in people of African ancestry to a patient who identifies himself as African-American even if he's mostly of European ancestry?

I know razib will bring this up, so I will point out that the majority of African-Americans are mostly of African ancestry.

African-Americans are the result of admixture between Africans, Europeans, and Native Americans. Furthermore, Africans are a paraphyletic group containing more genetic diversity than all other human populations combined. That's why this bothers me a bit:

This Thursday, eight years after the drug [BiDil] was rejected for use in the general public, an F.D.A. panel will consider whether BiDil should become the first drug intended for one racial group, in this case, African-Americans.

A study of 1,050 African-American heart failure patients showed that BiDil significantly reduced death and hospitalization, prompting the American Heart Association to call BiDil one of the top developments of 2004. BiDil increases levels of nitric oxide, which widens blood vessels.

The drug's maker, NitroMed Inc., says its decision to test and market BiDil as a drug for African-Americans is based on solid science. But BiDil's application has engendered controversy, with many scientists convinced that race is too broad and ill-defined a category to be relevant in determining a drug's approval, especially since geneticists have failed to identify a biological divide separating one race from another.

. . .

"My criticism of the African-American Heart Failure Study is that they only studied African-Americans," he [Dr. Joshua Hare, a cardiologist at the Johns Hopkins University Medical Center] said. "To really test the hypothesis is to study both populations and then show, aha, the African-Americans did respond better. They didn't do that."

. . .

Jonathan Kahn, a medical ethicist at Hamline University law school in St. Paul, said BiDil's approval as a black-only drug would give an official ring to the discredited idea that race is a biological category.

The scientist in me says that there is very little reason to suspect a drug would work differently in African-Americans than in European-Americans because of genetic difference between the two ethnic groups. There may be some environmental differences, however, that cause the drug to perform differently in the two populations.

The commie pinko bastard in me notes the "historical inequities in medical treatment for African-Americans" and wonders if this is an example of social justice.

Smoking Your Telomeres Away.

Here's another reason to give up smoking:

"Tim Spector, director of the twin research unit at St Thomas' Hospital in London, and his team have shown that telomeres shrink dramatically in patients who are obese or heavy smokers."

So, put down the Camel lights and hit the gym or else no more telomeres for you. Interestingly, Drosophila can tolerate polymorphisms for telomere length and gene content (I believe this is an unpublished result, so no link). Of course, Drosophila are far advance compared to humans in that they have evolved telomerase independent mechanisms for the maintenance of telomeres.

What Evolution Is

In my continuing pursuit to publish the entire contents of Dobzhansky and Pavlovsky's "Indeterminate Outcome of Certain Experiments on Drosophila Populations" on my blog, I present you with some more gems from one of the foremost researchers of the modern synthesis.

First, I give you an excerpt from the introduction, in which Dobzhansky describes how biologists study evolution:

"Repeatability of observations and experiments is taken for granted in science. If experiments on similar conditions fail to yield similar results, one suspects that some variables in the materials or in techniques have escaped detection. Yet, some natural processes happen only once; history, either on the biological or on the human level, does not repeat itself. There is, of course, nothing mysterious in this uniqueness. Evolutionary processes in nature are influenced by usually very numerous internal and environmental variables. It is unlikely that the whole constellation of variables can remain constant for long, or that it can recur in the future. The elementary components of the evolutionary process, the mutational and selectional steps, are both repeatable and reversible; evolution is however unrepeatable and irreversible. Geneticists and other experimentalists concentrate their attention chiefly on the elementary components, and are consequently reproached by those who study evolution by other means for not being able to observe evolutionary changes of any consequence. This reproach fails to take into account that historical events and trends become comprehensible only through understanding of the unspectacular everyday events which bring them about." (The emphases are my own.)

How about that!? It's a bit wordy, but a nice refutation to the anti-evolution movement of today -- and it was written in 1953. No, we cannot recreate the major evolutionary changes that resulted in the diversity of life on earth that we observe today. This is not because evolution did not happen, but because so many damn parameters go into each step in evolution to try to understand every detail would be akin to assembling an adult human in a laboratory cell by cell. You wouldn't argue that because we cannot describe the process of human development taking the trajectory of each and every cell into account that biochemistry and molecular and cellular biology should not be taught. Well, the same goes for evolutionary biology. We can, however, try to understand the processes that underlie evolution (mutation, natural selection, genetic drift, gene-environment interactions, etc) in order to get a clearer picture of how it occurred.

The paper from which this quote is taken deals with laboratory experiments in which changes in allele frequencies over time are repeatable and can be described using simple mathematical functions. In essence, the authors show that certain rules govern evolutionary change (i.e., the repeatable/reversible processes) and they contributed to the wealth of knowledge developing at the time.

The article concludes with a distinction between micro- and macro-evolution. While I have a particular distaste for those terms, Dobzhansky makes an important point:

"Even though these new adaptive genotypes were compounded from pre-existing genetic elements, the changes observed in populations of mixed origin surpass the scale of the changes observed in populations of geographically uniform origin. In the former, new adaptive genotypes arose and became established, while in the latter the alterations involved chiefly the relative frequencies of certain previously available genotypes. If the latter changes are labeled microevolution, the former may perhaps be referred to as mesoevolution. The words macroevolution and megaevolution would, then, be reserved to designate emergence of new types of body structure and function, requiring time in geological scale, and usually leading to formation of new genera, families, and still higher categories. Needless to say, these four words refer only to the dimensions of the changes which they describe, while most evolutionists regard it as probable that the essential genetic mechanisms are similar throughout." (The emphases are my own.)

When a biologist describes an evolutionary change as microevolutionary or macroevolutionary he/she is only referring to the scale of the change itself and not to the processes underlying that change. We can gain an understanding of the large scale irreversible/unrepeatable evolutionary events through studying the small scale repeatable/reversible events. Both processes are governed by the same mechanisms such as meiosis, natural selection, population level phenomena, and environmental effects.

In fact, where we draw the line between micro and macro is somewhat arbitrary. If we say that speciation is a macroevolutionary process, then recent results indicate that population level phenomena are responsible for macro level changes.

A Fate Worse Than Death

In a previous post, I may have come across as dissing Dobzhansky. This is not the case at all. I have utmost respect for the man and his often unappreciated sense of humor. For instance, check out this gem from the paper entitled, "Indeterminate Outcome of Certain Experiments on Drosophila Populations":

"It can be seen in figure 3 that most of the lines intersect at values of W1 between 0.25 and 0.50, and at values of W2 between 0.85 and 0.95. These variations are well within the limits of sampling errors. Only the lines F, G, and H intersect at values of W1 below 0, which is biologically impossible, since a negative W would mean that carriers of a certain genotype would suffer a fate worse than death."

This reminds me of The Princess Bride when Westley was "MOSTLY dead."

Monday, June 13, 2005

Holla Back At Me.

I'm back from North Carolina. The combination of sitting behind the wheel of my car for 16+ hours and sitting in uncomfortable chairs for 20+ hours in the past few days has left my back in tangles. I spent the good part of Sunday laid out on my couch trying to recover -- although, the two hours of playing ultimate frisbee on Sunday probably didn't help much. Who the hell has lower back problems in their mid-twenties? It just ain't right!

In the process of looking over some old data (not my own data -- really old data from the 1950s) in preparation for a committee meeting in a couple of weeks, I rediscovered a journal article by Dobzhansky entitled, "Indeterminate Outcome of Certain Experiments on Drosophila Populations." This title left me almost as confused as the lyrics to "Hollaback Girl." Why publish indeterminate results? What experiments? Which Drosophila populations? Could an article this vague be accepted for publication in today's competitive scientific environment?

Dobzhansky was notorious for publishing a lot of papers and often criticized for his style of doing science. Some have gone so far as to say he performed half-assed experiments and never analyzed his data with the rigorous attention it deserved. I can neither confirm nor deny such reports and leave the discussion to the experts. While I sit here, my back screaming at me for putting it through hell the last few days, I can only wonder if I could get a paper published entitled, "Unclear Results of Some Analysis of a Drosophila Genome."

Wednesday, June 08, 2005


It has been pointed out to me that the commenting feature has not been working. I'm not sure if this was Blogger's fault or my own, but it appears to be ok now. Please let me know ( if you're having trouble.

Tuesday, June 07, 2005

I now know where I don't ever want to live.

I just drove down from Pennsylvania to North Carolina for a short workshop on coalescent theory. Throughout Pennsylvania, Maryland, West Virginia, and Virginia, the weather was near perfect: sunny, but just a bit too warm for my taste. Then I reached North Carolina. After driving for about a half an hour I reached some wet pavement and though to myself, "This is odd." I then drove through some of the hardest rain I've ever seen only to emerge 15 minutes later into clear skies and dry pavement. It was as if there was a major rain cloud sitting over a small stretch of highway. When I reached Raleigh, I got out of my car and into the most oppressively humid air I'd ever experienced. After I got to my room and set my things down, I considered going out and exploring the North Carolina State Campus. It was then that I heard multiple pounding claps of thunder followed by a rain storm that has persisted for nearly an hour. Remind me to never move south of the Mason-Dixon line -- I could never survive it.

If I learn anything amazing while I'm down here, I'll try to post on it. Chances are, however, the material is too specialized to be of general interest. Of course, that hasn't stopped me before.

Monday, June 06, 2005

Alabama in the Middle/I hate Netscape 8

I hate Netscape 8 . . . ok, I should have saved my post in Word before uploading it to Blogger.

Netscape crashed in the middle of me writing about another school board in Pennsylvania planning to add intelligent design (ID) to their curriculum (via Red State Rabble). Well, you should go read the article yourself and learn why, as James Carville said, Pennsylvania is "Philadelphia in the east, Pittsburgh in the west, and Alabama in the middle."

Also included in the original post that I lost when Netscape 8 crashed:
  • This has happened before in Dover and the PA State Legislature.
  • Why won't Phil Skell shut up already?
  • Why did they interview a science instructor at Penn State when there are plenty of faculty studying evolution?
I'm honestly contemplating switching back from Netscape 8 to Netscape 7. The features in Netscape 7 were supperior to what Firefox, IE, or Netscape 8 offer. Why did they overhaul the Netscape browser (essentially building it around Firefox and IE), when they could have updated the far supperior Netscape 7 program?

Sunday, June 05, 2005

Old Faulty Arguments Rearing Their Head Again

Via Red State Rabble:

Students should be told that some respected scientists find Darwin's theory inadequate because it is based on 19th-century science, which does not account for the 21st-century science of molecular structure of life. Study of the molecular structure of complex systems will help students understand how life works and see the shortcomings of Darwin's theory. Students should be told that irreducibly complex systems, such as the blood-clotting system, disprove Darwin's theory.

Students should be told about intelligent design and creationism. They can learn the science behind each theory and become better students.

-- Vonderlear Fields , Clinton

This uninformed opinion was published in response to the Washington Post's request for their readers' answer to the question, "What should students be told about the origins of life?"

First off, none of the five letters address the topic of the origins of life; they're all concerned with evolution/creationism/intelligent design in some manner. Evolutionary theory says nothing about the origin of life.

Secondly, it is bad judgment and professionally negligent to publish Fields's uninformed letter. Fields's arguments are tired, old hat from the ID movement. The blood clotting pathway is Michael Behe's pet example, but there are multiple rebuttals posted all over the internet. I won't deal with this specific example as it has been beaten to death, resurrected, then killed again.

What bothers me most is Fields's treatment of evolutionary theory. It seems as if this reader's only exposure to evolutionary biology comes from Darwin's Black Box and some media coverage of the evolution-creationism debate. Modern evolutionary theory is not based on 19th century science. During the 20th century, the neo-Darwinian synthesis brought together ideas from the developing fields of genetics and systematics to create a more comprehensive theory of evolution. Over the last century (and into the 21st century) molecular biology has played a critical role in the development of evolutionary theory. Evolution does account for the 21st-century science of molecular structure of life; intelligent design fails to account for advances in molecular biology by parroting disproven argements.

Saturday, June 04, 2005

It's everywhere . . .

. . . so it must be designed.

Everyone is chiming in on the Wells Rivista article. Stranger Fruit interprets the relevence of the journals the IDists publish in. John Rennie questions the logic of the argument. And you didn't think PZ Myers would stand by without comment either, did you?

So, what can we make of the Discovery Institute and their propaganda machine? As John Lynch points out at Stranger Fruit, the journals publishing the ID tripe are not exactly at the level of Science, Nature, Cell, PNAS or any of the other upper echelon publications. In fact, Lynch gives us their incredibly low impact factors:
  • Rivista 0.500 (for 2003)
  • Proc Biol Soc Wash 0.506 (for 2003)
Impact factors are defined as "a measure of the frequency with which the 'average article' in a journal has been cited in a particular year or period" by Thomson Scientific (the group in charge of impact factors). They calculate it by "dividing the number of current year citations to the source items published in that journal during the previous two years." Essentially, it is the expected number (mean) of citations in the current year for an article published in the last two years.

Publications in journals with impact factors less than one should not expect to be cited in the next year as the average article appearing in those journals has less than one citation in the year following its appearance. Because the importance of a particular publication is measured, in part, by the number of citations it receives, we can see how insignificant both Rivista and PBSW are in the world of biological research.

Please don't take this as an attack on people who publish in low impact journals (although, John Lynch points out that Rivista is more than just a low impact journal -- it has a history of endorsing anti-evolution and creationism). I merely am saying that it is not worth trumpeting a publication in a journal with an extremely low impact factor. If the DI could get their "scientists" to publish original research (which neither ID article has been) in important journals, we may have to take them seriously -- and it would also indicate they've gone out and done some real research. Until then, they will twiddle away in obscurity.

Of course, not everything exists in obscurity. Take, for example, the ubiquitin proteins. As the name suggests, they are everywhere. Because these proteins are ubiquitous and highly conserved, they must be designed. This is, of course, a continuation of Wells's centriole hypothesis and is essential for the success of the ID movement. Without wasting any more time (or doing any real research or data analysis) I must publish my ubiquitin theory immediately.

Friday, June 03, 2005

Data!? We don't need no stinking data!

Red State Rabble pointed me toward an editorial in the Albuquerque Tribune on an attack on science that hit a bit too close to home:
"The latest attack is right here in Albuquerque, where the Southwest Region director of the U.S. Fish and Wildlife Service has arbitrarily decided to limit the use of genetics in making official decisions on protecting endangered animals and plants.
"In essence, he announced that advances in conservation biology and scientific understanding and classification of species and sub-species should be ignored, in favor of only what was known at the time a species was listed as endangered or threatened.
"Human understanding of species, genetics and evolution has grown dramatically since the Endangered Species Act was adopted. The enforcement of this law should not be limited to some artificial point three decades ago, when science has advanced our understanding and knowledge exponentially since then - and continues to do so."
Apparently Dale Hall (the Southwest Region Director mentioned in the piece) hasn't heard about the use of molecular markers in ecological research (a burgeoning field known as molecular ecology). This is not just an attack on conservation or reluctance to appreciate what genetic tools can contribute to related fields; this is an outright attack on science:
"Science, which is based not on belief or desire but on factual, repeatable and sustainable evidence, should be the rock-solid foundation for environmental and conservation laws and regulations."
Thankfully, not everyone at the Fish and Wildlife Service shares Hall's view:
"Hall's counterpart in Denver, Mountain-Prairie Region Director Ralph Morgenweck, also challenged Hall, citing the need to broadly apply genetics to species at risk of extinction. To do otherwise, he says, 'could run counter to the purpose' of the law and appears to contradict the agency's long-standing policy of applying 'the best available science.'"
Someone needs to buy Dale Hall a copy of Avise and Hamrick's Conservation Genetics.

Friday Random Ten (3 June 2005)

Gay Drosophila Porn Edition
(this should do wonders for my site's search-ability)

This recent paper in Cell contains the following image:

Those of you who have stared at Drosophila under a microscope will recognize that as a female fly courting another female (HOW UNATURAL!!). I will join my allies on the religious right in condemning such behavior as immoral and wrong. To read what those pinko commies at the NYTimes think about it, click here. They also seem to endorse this disgusting behavior:

The results are certain to prove influential in debates about whether genes or environment determine who we are, how we act and, especially, our sexual orientation, although it is not clear now if there is a similar master sexual gene for humans.

We all know that homosexuality is a disease that can only be cured through worshipping Jesus and donating lots of money to the 700 Club. Apparently this type of immoral behavior has been going on in Drosophila labs for over 4 decades. How gross! And if you thought the lesbians above were disgusting, check out what these guys are doing:

Oh, yeah. Don't call them fruit flies. They may be fruitless, but they sure ain't fruity. This abomination must be cured.

Without further ado, here's today's Random 10:
  1. 311 - Beautiful Disaster
  2. Mike Ness - House of Gold
  3. Don Henley - The Boys of Summer
  4. Outkast - She Lives in My Lap
  5. Tilt - Want To Do
  6. Kid Rock - Cowboy
  7. Descendents - Descendents
  8. Bouncing Souls & Anti-Flag - Ever Fallen in Love (With Someone You Shouldn't Have Fallen in Love With)?
  9. Me First and the Gimme Gimmes - Don't Cry For Me Argentina
  10. My Chemical Romance - I'm Not Okay

Wednesday, June 01, 2005

Tangled Bank #29.

The Tangled Bank

Tangled Bank #29 has been posted at Organic Matter. There are 40 entries, so make sure to devote a fair chunk of your time if you plan to read them all.