Tuesday, March 11, 2008

The deep history of genes and irresponsible reviews

For reasons I won't go into, I was looking up an old review of a paper of mine, that is now published (after originally being rejected a few times). I don't know if I have bad luck, or bad technique, but most of my papers are rejected several times before they are published. I do believe strongly that I've gotten my share of incompetent and irresponsible reviews. One example of an incompetent review is quite relevant, and related to other posts.

In the manuscript in question, I reported finding multiple opsin visual pigment genes in ostracod crustaceans. I concluded that these genes were the result of gene duplications. The reviewer, who admitted not being a molecular biologist, took issue with concluding that multiple genes were due to gene duplication, writing:

"...while humans indeed have 3 opsin genes, it is not certain that they all arose from duplication - the rod, blue, and red/green lines have been separate for millennia, and it is possible that some have entered the genome by other mechanisms."

When I get reviews back, I often take notes (meant only for myself), such that I summarize the reviewers comments, and can understand and remember them later more easily. In response to this reviewer's comments, I wrote:

"True, aliens just MIGHT have come down and put opsins in our genome. Short of that ALL GENES ARISE BY DUPLICATION!!! (He did say he was not a molecular biologist)."

As I wrote on a previous post the dogma among evolutionists now is that most genes originate by duplication. My reviewer had a pre-1950's view of gene evolution. He failed to understand, as Ingram had done as early as 1961, that genes likely have a long history, and a deep common ancestry. The reviewer has failed to come to grips with the common ancestry of genes. Just as pre-Darwinian biologists believed that each species was created independently, my incompetent reviewer, and pre-Ingramian biologists believed that genes may be independently created. I wonder how many other people fail to understand the deep common ancestry of genes.

I wonder how many people fail to grasp the deep common ancestry of all biological entities, united by a deep history, diverging through new combinations, and through specialization of duplicated entities.

Thursday, March 6, 2008

Questions about evolution

I just had a student ask me some questions about evolution. Since I spent a little time on this, I thought I would post it here, in case someone else might find it useful. I left the student as anonymous.

Hi professor Oakley, I had your Macroevolution course last year, and am now in Ken Kosik's Neurobiology course this quarter. We've been talking a good deal about the evolution of the nervous system, and I had a few questions I figured you would be most qualified to answer.

Professor Kosik brought up your research on the genes conserved from sponge to human that, in humans, are important in the formation of eyes. I remember you mentioned this during Macro, too, and that, despite being used by Creationists as evidence for Creation, it is, in fact, further evidence for evolution.
Well, the bottom line is that creationism is not science, it is a faith. My own philosophy is that faith and science are completely separate, "non-overlapping magisteria". One can have faith in a creator and also accept the scientific facts of evolution; I know several people who fit this precise description. (I personally am agnostic, I don't care if there is some sort of creator or not, I don't see any reason why it should matter to my life).

Creationism is simply not a science, it does not present testable hypotheses, because one can always say "that is how the designer made it". I prefer to use the term "anti-evolutionists" to describe people who twist logic to call into question the scientific facts of evolution. My goal is to distinguish the magisteria - divine creation is not impossible, but it is unscientific.

See this article for what I mean by non-overlapping magisteria, in SJ Gould's words:

In contrast to creationism, science presents hypotheses. One hypothesis of evolution is global common ancestry, the hypothesis that all life is derived from a single common ancestor. This hypothesis is supported when we find highly non-random similarities among organisms - like a nearly universal genetic code, for example. We could find scientific facts that contradict universal common ancestry, such as a non-DNA form of life - therefore it is a testable hypothesis.

There are many other testable hypotheses in evolutionary biology, such as "natural selection is a primary mechanism driving evolutionary change". We talked in macroevolution about how people test for the requirements of natural selection (variation, super-fecundity, heritability, and differential survival due to or correlated with the heritable trait). We also talked about inferring selection on genes using neutral theory as a null model.

Why is this? Also, where can I find your paper on this topic online?
Here is a good blog about our eye research:

Here is the paper:

and a news story that was in many newspapers:

Regarding the synapse research, that Ken probably talked about in your class, here is a news article:

Here is the original paper for that:


We covered the topic of "exaptation" in Neuro and this, too, makes me wonder about evolution. If we don't know the original purpose of a gene that eventually helped us make an eye, who's to say that it ever had a purpose?

We can make inferences about the functions of genes using phylogeny and comparative biology. If two genes share the same function, then likely their ancestral gene had the same function. There are statistical models for working out more complicated cases, too.

So, in the case of our eye research, we do have a good idea of the previous function. Eyes use phototransduction, which is a GPCR-based transduction pathway. We can see by inferring the history of genes used in eyes, that they are closely related to other GPCR pathways. GPCR pathways very generally transmit signalls from outside cells to inside cells, and "tell" that cell to do something. In the case of vision, a gene (called opsin) evolved light sensitivity. But opsin is related to other GPCR genes that transmit signals, but not light signals. In this way, we can see that light perception evolved from other signaling genes.

It seems like assuming that the gene DID once have a purpose implies evolution - isn't this a circular argument?

In the case of opsin visual pigment genes, we can infer that the ancestral gene did have a function.

I'm not sure I've worded this incredibly clearly, but I'm sure you get a lot of questions like this, so you probably have a good feeling for the problems people tend to have with evolution. Evolution, since taking your course, has pretty much become the entire basis on which I understand biology, but in these cases I'm not so sure it makes sense.

Your thoughts on the centrality of evolution are shared by some great scientists (I didn't know he was Russian Orthodox Christian, supporting my point above): Theo. Dobzhanski