Friday, January 21, 2005

Evolution -- Creation Course.

The following was posted on EcoLog and EvolDir:
Dear friend,

Do you know about a good discussion list on evolutionary
biology ? I interested in a list to discuss the evolutionary
mechanisms, the history of evolutuionary biology, creation
versus evolution and also about teaching material !

Also, I am interested in real articles (not websites)
discussing the creation X evolution debate! I need real
published material to use with my students.

Could you help me plase ?

Thanks !!


Grupo de Estudos em Ecologia de Mamiferos (ECOMAM)
Universidade de Taubate - Departamento de Biologia
Taubate, SP. 12030-010.

Currículo Lattes:

I replied to him with the following email:
If you are looking for an evolutionary biology listserve similar to Ecolog, check out EvolDir.

The Panda's Thumb is an online discussion of the evolution/creationism issue -- I know you don't want websites, but the links and articles on The Panda's Thumb are an excellent resource.

As for published material, you'd be hard pressed to find such discussion in research journals since there is no real debate amongst evolutionary biologists. I can think of a couple of pseudo-articles that may be of interest to you. First, there is this "article" which, though not published in a peer review journal, is written in a manner similar to a critical review article. It is a rebuttal to the Intelligent Design article (Meyer S. 2004. The Origin of Biological Information and the Higher Taxonomic Categories. Proc Bio. Soc. Wash. 117(2):213-239) that caused a bit of a stir due to its illegitimacy as a primary research article. There were a couple of comments on that in Nature (431, 114 & 431, 897)

As I mentioned earlier, there is no serious debate amongst biologists regarding evolution and creationism, so there is very little published material in scientific journals on the topic. Of course, there is plenty of news coverage and legal work on the subject if that's what you're interested in.

Other websites that may interest you:

Hopefully this is of some assistance,
I would encourage anyone who can add anything else to email him.

Tuesday, January 18, 2005

Cryptic Species

I've been meaning to write about this article in Nature for about a week now. I started writing about a half-hour ago, got about halfway through, then accidentally deleted the post. Now, I'm off to start again. I'd like to point out that this is an essay, not a research article, and I've learned that it's a lot harder to comment on essays and reviews than on primary research.

The authors deal with the problems associated with cryptic species. I've taken cryptic species to mean, "morphologically indistinguishable to the researcher examining the population." This definition leads me to conclude that cryptic species are not a true biological phenomenon, but a byproduct of the study of natural populations. They are only called cryptic because we cannot tell them apart, just like we have categorized all Drosophila species into a single genus, when we could have put them in an order or family if we so desired.

I will use the biological species concept (BSC) for my discussion since it is the most widely accepted species concept for dealing with sexually reproducing species -- I'll ignore asexually reproducing species for now even though they make up the majority of life on earth. The BSC states that two populations (or lineages) deserve species status if they cannot form viable and fertile hybrids. Conversely, all populations within a single species are capable of exchanging genetic information in a process known as gene flow, which can be diagnosed using molecular markers and used to infer species status if hybridization cannot be observed or studied in the lab or the field.

Getting back to the essay, the authors describe a scenario whereby cryptic species are found:
[A] number of individuals belonging to a morphologically recognized species are sequenced (or otherwise genetically characterized), normally at several points (loci) within the genome. Then, often unexpectedly, the various genotypes will cluster in reciprocally monophyletic groups, with no signs of genetic exchange between them. Similar evolutionary scenarios are evident at each locus, suggesting that the corresponding populations are reproductively isolated from each other, yet the sampled populations are not geographically isolated.
This type of pattern is expected for geographically isolated (allopatric) populations, but a single population of a species is expected to be randomly mating so that monophyletic groups are not consistently observed at multiple loci. The pattern described by the authors is a telltale sign of two distinct populations -- determining species status is a whole other process.

All one can conclude from monophyletic groups are distinct evolutionary lineages. It is important to determine how genetically differentiated the two groups are, and if they truly are sympatric. They may appear sympatric (i.e., collected in the same geographic area), but if their mating patterns are asynchronous or their mating ranges do not overlap, they have an excellent potential to speciate (if they haven't already) because of their extrinsic reproductive isolation. This is similar to problems we encounter when defining niches because we are limited by what we can observe and describe. Just because it looks like the two evolutionary lineages inferred from the molecular markers are sympatric, does not necessarily mean they are -- we may be missing something, as nature is a very complicated place.

In my opinion, the most interesting questions are those that deal with the mechanisms of speciation. Determining whether two indistinguishable groups are cryptic/sister/true-species is only the first step in the study of speciation. By examining closely related species (for instance Drosophila pseudoobscura and D. persimilis) we may be able to detect the remnants or current processes involved in creating complete reproductive isolation between these close relatives. The authors miss the boat on this key point, as they conclude we should be
looking for the conditions in which cryptic species will thrive — pursuing their causes whilst decrypting their nature
Since cryptic species is an artifact of the scientific process being used, simply identifying, describing, and characterizing patterns of cryptic species is not sufficient in itself. These are excellent initial observations that should then lead to many questions regarding the process of speciation (this is going from the what/observation to the how/hypothesis). Only by examining pairs of taxa at different points in the process of speciation can we fully understand how speciation works in sexual organisms.

Intelligent Design Creationism

A recent opinion piece in my local paper inspired me to write the following essay. Also, see these other letters here and here. The public opinion, judged using this small sample, is split. Hopefully we can work to straighten out the creationists among us.

The recent flurry of opinions published in this newspaper -- capped off with Richard S. Brown's longwinded and misguided piece -- show a fundamental misunderstanding amongst the general public regarding evolutionary biology. Within the field of biology, there is no serious debate over biological evolution, and there is no faith involved in evolutionary biology. Furthermore, scientific consensus is not determined by a popular vote of an uninformed public, but instead by support from those actively involved in a research area and exposed to the undistilled data firsthand.

Intelligent design (ID) advocates like to point out that the believers in their camp include approximately 300 scientists. They fail to mention that many of these scientists are experts in fields other than biology, and of those that are biologists (such as Dr. Michael Behe, a Biochemist at Lehigh University) all are experts in fields other than evolutionary biology. Typically, when scientific revolutions occur, they are spearheaded by researches with a fundamental understanding of the subject matter they are revolutionizing. This is not the case for Intelligent Design, and, in contrast to the small minority of scientists who support ID, the National Center for Science Education has collected signatures from 513 PhD scientists who oppose creationism (about two thirds of which are biologists), and that's just the ones named Steve.

The claim that evolution is based on faith is tantamount to declaring that hundreds (if not thousands) of biologists, whose graduate degrees involved research in evolutionary biology, did not collect and analyze real data according to proper scientific procedures, but rather simply believed in a dogma and were given an education under false pretenses. I find the assertion that evolutionary biology is a faith based doctrine insulting, considering the massive amounts of evidence in support of the theory relative to the minute amount that intelligent design advocates point to. The so-called "holes in the fossil record" do nothing to take down the theory of evolution -- fossilization is an uncommon event that requires many conditions to be met (the proper body type, environment, geological conditions, etc.), not to mention the difficulty in finding new fossils. It's too bad for creationists that there is overwhelming support for evolution from other fields, such as genetics, developmental biology, molecular biology, cell biology, biochemistry, anatomy, behavior, and ecology. For instance, all organisms on earth (viruses, bacteria, plants, animals, and fungi) share the same genetic code based on nucleic acid molecules. This genetic material encodes genes, and when genes from different species are compared they reveal evolutionary relationships. These evolutionary relationships can be inferred between closely related species (such as humans, chimpanzees, gorillas, and other primates) or between extremely divergent organisms (like humans, wheat, and E. coli). The amount of genetic relatedness is reflected in developmental, anatomical, and physiological similarities. Taking the massive amount of published evidence into consideration, the scientific community has come to the conclusion that biological evolution is the most logical and most heavily supported explanation for the diversity of life on earth and presents most rewarding opportunities for future scientific study.

A referendum or school board decision cannot determine whether evolution is fact, but we do have the power to chose whether we would like to educate the next generation of researchers in the proper way to do science. It is impossible to ignore the fact that biological evolution is an extremely supported theory amongst biologists, and that Intelligent Design is nothing but a political movement lead by a fundamentalist group bent on including biblical teachings in science curricula. I agree with Lee Cuddy in his letter to the editor that science should not remain static; that is why the biblical story of creationism was replaced by the scientific theory of biological evolution (it would be a disservice to negate the modern renaissance of biology by teaching outdated ideas). Richard Brown has "observed over the years that it is the evolutionists who obfuscate the ever-changing details of their theory." Sadly, Mr. Brown does not realize that as more information is obtained, scientific theories change to accommodate the growing wealth of knowledge -- this not obfuscation, it is adaptation. As opposed to evolutionary biology, which has theories that can be disproved, intelligent design offers no testable hypotheses.

Supporters of intelligent design and creationism are guilty of ignoring the abundant amount of evidence in an attempt to support a conclusion that they have made prior to collecting and analyzing data; their process is an example of bad science. Imagine how difficult it would be to identify the causes of lung cancer if, before we began examining anything, we decided that it was due to a voodoo curse and looked for evidence for that curse at every step of our examination. As the amount of biological research has increased exponentially over the past few decades, scientists have continuously gathered evidence that supports biological evolution and learned more about the rules that govern this process, all the while basing their conclusions and future research on previous findings as opposed to belief or dogma. That is how science is done.

Thursday, January 13, 2005

Dover Dimwits.

PZ Myers at Pharyngula comments on an OpEd in the York Daily Record that is absolutely, staggeringly, ridiculously (and the adverbs keep rolling in) misinformed. Two alleged scientists (a husband and wife team that is the ID doppelganger of Peter and Rosemary Grant) support ID and come to the conclusion that evolution is just a theory and not worthy of the status of scientific law. I try to break down their horrible argument below.
We, as two trained, field experienced scientists, wish to clarify these issues.
James Bogart is an adjunct faculty member at York College studying mechanical engineering. And Cheri Bogart has a bachelors degree in biology (scroll to the bottom). Now if that doesn't make them authorities on evolutionary biology, I don't know what does.

They go on to poorly define theories and laws, which Pharyngula tackles quite well, so I won't get into here. The gist being they make up their own definitions, then say that gravity, electromagnetism, thermodynamics, etc are all laws, but evolution is just a mildly supported theory. Yeah, and phylogenetics doesn't tell us anything -- I'll get to that later.

But here's one of the gems of their argument:
There have been several famous theories that were agreed upon by most of the world’s scientists and philosophers that were later proven to be false. A very prominent example of these is the theory that the earth is flat. The scientists could stand on a boat and see for long distances in every direction so of course the world had to be flat — their observations proved it! We all know that this is not true yet people several hundred years ago were ridiculed for believing otherwise.
Guess what also fits this definition: CREATIONISM!!! Yes, two hundred years ago most Europeans believed that God created the earth and all life on it in the past few millennia. Then, over the past couple of centuries, we have accumulated enough evidence to determine that life on Earth has evolved over billions of years. Charles Darwin came up with the theory of Natural Selection to explain how that life evolved and other scientists have updated Darwin's theory and added new theories, but they all explain how evolution happened without the aid of supernatural powers.
[E]volution and intelligent design, rely upon a considerable amount of wishful thinking to back up their claims.
I would love to see the wishful thinking that goes into understanding evolution. In fact, evolution and ID are not even competing views, as the authors try to argue. Rather, ID is another explanation for how evolution occurs. It's a bad (make that, terrible) theory, but it's a theory of the HOW. What happened (evolution over billions of years) is hardly debatable. IDist try to argue that God did it, but real biologists try to come up with more scientific explanations.
If humans evolved from the lower primates (chimps, monkeys and gorillas), then where are the “in-between” specimens? Where are the chimps that can use verbal language? Where are the chimps that can reason well enough to negotiate the price of an item? Where is the chimp that understands sarcasm and jokes? All of these intermediate specimens are missing from the evidence. Yes, we can find fossils of something that looks similar to both humans and the lower primates, but if they were superior to the chimps, then why are they gone while the chimps remain?
Humans did evolve from monkeys, but so did chimps and gorillas. These idiots need a lesson in primate systematics, and I'm hardly the one to give it them, but I'll try. Apes (e.g., chimps, gorillas, orangs, and even humans) evolved from old world monkeys. Then, the apes began to diverge, and over millions of years resulted in what we see today. We did not evolve from chimpanzees -- instead we evolved from our common ancestor with chimps, which may have been chimp-like, but it still wasn't a chimp. Those "missing links" that they describe, they're in the fossil record and no, we cannot study behavior directly from the fossil record, morons. Also, when we use DNA data to reconstruct phylogenies (some of the best stuff for this purpose when it's available), we can see the relatedness of primates in the trees (this works for all life on earth, not just primates). We're related at the genetic level, and the percent identity of the DNA sequence reflects our relatedness.

They argue that evolution violates the second law of thermodynamics, which has been shown to be fallacy here. Of course, they also think ID is reasonable:
However, because of the significant gaps in the pure evolutionary theory, the concepts [ID] are as reasonable as any offered by the proponents of evolutionary theory.
Aside from the fact that most evolutionary theory (aside from ID) is scientifically testable and is presented by real biologists and published in peer review journals, yes ID is reasonable. WTF?? ID is not reasonable, it's the greatest Just So Story of them all.
We are both scientists and we both are Christians who lean toward the ID theory as being more plausible because there are just too many flaws in the data used to support evolutionary theory.
Flaws in the data??? When is data ever perfect? What you must look at is flaws in the interpretation of the data, and all evolutionary theory (aside from ID) offers scientifically testable claims. ID is not scientifically testable, therefore it is not science.

You are Christians who are interweaving their faith and their science. It's fine if you want to believe in God (or Gods), but keep those beliefs separate when you try to make objective, logical decisions. Look at the data, and see that biological evolution is as strongly supported as gravity among scientists, and see that among the theories to explain evolution, ID is an infant (and one born with severe birth defects at that). Hey, I kind of like that: ID is a retarded baby. Maybe it's a bit too mean, and not fair to all people with major birth defects.

Wednesday, January 12, 2005

Tangled Bank.

Tangled Bank (2005), Vol.2, No.19, p.1, has been published.

Sunday, January 09, 2005

Vytorin Gets it Wrong

Merck has been running commercials for it's new cholesterol drug Vytorin. The advertising campaign talks about how you can have high cholesterol because of your diet as well as your family history. This is nothing new -- any phenotype is shaped by genetic makeup and environment -- but it's how it's presented in the commercial that's so bothersome.

The adwizards that came up with this one (SNL reference for those who aren't big Adam Sandler fans) keep pushing the idea that family history can shape cholesterol levels, an idea so ludicrous it must be squashed. First off, family history can be a good indicator of cholesterol levels (as well as a good indicator of height, weight, eye color, hair color, and many other characteristics). Family history does not shape any of these characters. Saying you get high cholesterol because of your family history is like saying I will be persecuted for being Jewish in Eastern Europe because my grandparents were persecuted for being Jewish in Eastern Europe. It's mixing up correlation, causation, and association.

You see, us scientists use correlation and association to make inferences. You are not more likely to have high cholesterol because Grandpa Sid had high cholesterol, but you are more likely to have high cholesterol if you inherited a predisposition to high cholesterol from Grandpa Sid. It may seem like a subtle difference, but it's preposterous to say that there are two sources of cholesterol: the food you eat and that produced by your body based on family history. Cholesterol does come from the food you eat and it is produced by your body, but the cholesterol produced by your body is based on your genotype, which is inherited from your ancestors and inferred based on family history. Yes, we can determine your predisposition to many diseases and ailments based on family history, but family history is NOT THE CAUSAL SOURCE -- it's the genes stupid!

Biomed Thinktank

A few weeks ago there was a post on EvolDir for a "Biology, Medicine, and Society" thinktank. I don't have much to say on this, but it seems like a great idea if it's setup and run properly. Science has become incredibly specialized and it's hard to see the applications of many areas of research. That does not mean that they are not useful -- pure science can be quite rewarding and the accumulation of many "non-practical" areas of research make up the wealth of knowledge that leads to innovations that many people can take advantage of. For instance, without evolutionary genetics theory, much of the disease gene mapping done using the human genome sequence would not be possible! At the very least, laypeople should understand the scientific process (even if they don't understand all of the terminology and technicalities) so that they don't get fooled by bad science such as Intelligent Design (to use an overused example).

Evolution of Phenotype and Genotype.

I went to the National Academy of the Sciences' meeting in honor of Ernst Mayr. The general topic was "Systematics and the Origin of the Species," the title of Mayr's publication from 1942. There were talks by Howard Ochman, Allen Orr, Jody Hey, among many other prominent biologists studying speciation, but one talk by Mary Jane West-Eberhard stood out to me.

Dr. West-Eberhard's talk, entitled "Developmental Plasticity and Evolutionary Innovation," was particularly interesting. She used quadruped mammals that have learned to walk bipedaly due to injuries that prevented them from using the front limbs as an example of developmental plasticity. She argued that these learned behaviors could have evolutionary implications if they provided a benefit to those individuals that were able to learn them. In a way, she was speaking about memes (learned rather than inherited behaviors) sweeping through a population.

Needless to say, this produced quite a stir among a few folks who viewed this as an example of Lamarckian evolution -- the evolution of acquired characteristics. But Dr. West-Eberhard's point was not that inheritance of genetically encoded traits is unimportant, rather that these learned characters could shape the organism's environment and, therefore, alter the selective landscape and lead to genetic evolution.

It's a rather innovative way of looking at drastic phenotypic evolution that avoids "hopeful monster" type mutations in favor of behaviors that can drastically change phenotype. I assume (I am not entirely familiar with the model and my only exposure to it comes from the one talk I attended) that when an individual acquires a new (successful) behavior and other individuals mimic it, natural selection will favor alleles that are more fit with this novel behavior. It's almost like a population moving to a new environment with different selective pressures, so that natural selection changes the allele frequencies from that in the old environment to the new one (remember, fitness is only relevant in relation to the environment and the other alleles present in a population).

As an example, one can think of primitive bipedal primates (our ancestors) moving out of the trees in the African rain forest and into the flatlands. It may be possible that a population learned to walk upright without any drastic mutations, and they were able to exploit an open niche on the jungle floor. Next, either new mutations or existing alleles were selected for that increased the fitness of these bipedal individuals, and, over time, there was a strong genetic component to bipedal locomotion that initial arose through purely environmental/behavioral means. Pretty neat, huh?

I may be getting some of the details wrong (I'm not an expert on the subject), but I wanted to get these ideas down since they seem pretty cool. Also, it's a nice F.U. to those intelligent design/creationists who argue that evolutionary biologists are constrained by their dogma and unwilling to accept new ideas. This hypothesis (unlike ID) is testable and scientifically workable, which means it's worthy of publishing in peer-reviewed journals and worth discussing and scientific meetings. And it looks like Lamarck may not have been entirely wrong after all!