Applications of Evolution 3 - tradeoffs in resistance.

Someone just emailed me a copy of an interesting press release. Some time back, a particular mutation known as CCR5delta32 was identified as conferring greatly increased resistance to HIV in individuals who had two copies of that particular gene (in geek terms, those are individuals homozygous for that particular allele). According to the press release, a group of researchers have discovered that this resistance to HIV comes with a price. The individuals who are homozygous for the CCR5delta32 allele do have greatly increased resistance to HIV, but they also have greatly decreased resistance to the West Nile Virus.

This is interesting (to me, anyway) for a number of different reasons.

First, it shows that whether or not a particular mutation is beneficial, neutral, or harmful doesn't just depend on what the mutation does. It also depends on the conditions that the organism lives in. If this mutation is found in someone who lives in an area where West Nile is absent but HIV is common, then this is a beneficial mutation. If the same exact set of genes are found in someone living in an area where West Nile is common and HIV rare or absent, then the mutation is harmful. The environment is almost always important in determining the net effect that a particular mutation is likely to have on the organism.

I should probably stop for a second to make clear what I mean when I use the word "environment." In this case, I'm not just talking about the climate, or pollution, or the effects that humans are having on the natural world. In evolutionary biology (and ecology and other contexts), the "environment" that a particular organism lives in includes everything outside of the organism that has an effect on it. This includes the climate, of course, but it also includes things like predators, competition with other members of the same species, the presence or absence of alternative food sources, and a host of other such things.

In our case, as a species, our environment includes the various disease-causing agents that we are exposed to. As is the case with other environmental factors, like average temperature and rainfall, this factor can vary widely from one geographical location to another. This is true at both large and small scales. On a large scale, for example, leptospirosis is relatively common in Hawaii, but it is pretty much absent in the Northeastern US. On a smaller scale, strains of bacteria that are resistant to multiple antibiotics are more common in hospitals than they are in most homes.

If you want to look into this further, it gets more complex and more interesting, because pathogens are organisms too (that's arguable with viruses, but for these purposes they act like organisms so we'll treat them as such). Anyway, pathogens are organisms, and whether or not a particular mutation in a pathogen is beneficial will depend on the pathogen's environment. For pathogens that impact humans, humans are an environmental factor. Let's say that a strain of HIV mutates in a way that lets it attack people who have the CCR5delta32 resistance. Is that mutation beneficial? Maybe, but maybe not. It's going to depend on whether or not this gain comes with a corresponding cost, and whether the cost is worth the gain. That's going to depend in part on how common people expressing CCR5delta32 resistance are in that area.

Situations like this are things to keep in mind when you hear creationists and ID proponents making arguments like, "almost all mutations are harmful." Life is complex, environments are complex, and the relationships between organisms and environments are extrordinarily complex. The effects of a mutation will depend on an enormous range of factors, and a change in just one external factor can make a harmful mutation beneficial, or a beneficial mutation harmful.

In this case, this mutation was pretty clearly beneficial in North America just a few years back. Anyone who had two copies of the gene with this mutation was resistant to HIV, and until fairly recently West Nile wasn't present here, so the lack of resistance to West Nile wasn't a big problem. Now, it is entirely possible that the mutation is more harmful than helpful. Both HIV and West Nile are relatively uncommon in the US, but HIV transmission can largely be prevented as long as care and common sense are used, while West Nile transmission takes place through an insect vector, and is much harder to prevent. With West Nile now present in almost the entire country, we may well have seen this mutation change from being beneficial to harmful within just a couple of years.

Whether or not a particular mutation is helpful or harmful is very important to evolutionary studies, because it helps determine whether or not that particular mutant form (allele) of the gene is likely to spread, and whether it is likely to spread through the entire population or just certain geographic areas. If the allele is helpful in some locations and harmful in others, it can actually lead to a situation in which you get genetic differences in different areas of the population. That's cool, because it is one of the many scenarios that can lead to one species dividing into two.

This is a pretty cool finding, even if it isn't good news for the HIV research and treatment community. It has definitely taught us some things that are going to be really important to infectious disease specialists - not least, that the CCR5-inhibitors that are currently being tested in clinical trials may have a really big down-side - but also because it can give us some insight into the complex nature of the interactions between our genes and the environment, and how that impacts evolution.

This is interesting...

...apparently, yesterday's post about Casey Luskin's attempt to have his cake and eat it too may have actually been illegal. The only question is whether or not this blog qualifies as "anonymous." I don't use my name here, but I do over on Panda's Thumb.

Spinning creationism back into the classroom

It didn't take long for the Discovery Institute to try to call "Darwinists" intolerant for attempting to keep religious advocacy out of the schools. Casey Luskin discusses, over at the Discovery Institute's Media Complaints Division, the lawsuit that Americans United for the Separation of Church and State just filed against a California school. (Ed Brayton discusses this suit in depth over at Dispatches from the Culture Wars.)

According to Casey, because the course is listed as a philosophy class, objecting to it, "represents the true heart of these Darwinists: they don't care about keeping religion out of the science classroom, their goal is to censor any non-evolutionary views in ANY venue regardless of whether or not it is religion or science!!" This misrepresents the actual situation.

The title of the course is "Philosophy of Design," but even Casey admits that there are some problems with that title:

"The course is misnamed--it actually advocates for young earth creationism and teaches out of the Bible. Such a course would have been more aptly titled something like "Philosophy of Origins" -- but not "Philosophy of design" because intelligent design has nothing to do with young earth creationism or Biblical views."

Strangely, though, after admitting that the course doesn't meet the DI's party line on definition of Intelligent Design, he goes on to castigate "Darwinists" for trying to exclude ID from schools:

Rev. Barry Lynn, who leads Americans United for the Separation of Church and State, apparently doesn't want ID even in a philosophy course, because it's too dangerous for young minds to learn about regardless of the venue.

Consistency is clearly not a hobgoblin of Casey's mind, regardless of its size. As Casey admits, this is a class that advocates for Young Earth Creationism and which teaches out of the Bible. Casey says that those positions aren't related to Intelligent Design, so why on earth would he think that objecting to a course that does such things is the same as objecting to a class on Intelligent Design?

Near the end of his diatribe, Casey poses a question, "What objection could one possibly have to having students learn about material some people consider religious in a philosophy course?" Casey clearly thinks that this question has a clear answer:

The answer is simple: Darwinists aren't interested in keeping non-evolutionary views just out of the science classroom, they want non-evolutionary views out of students minds completely. If anyone ever doubted the full measure of Darwinist dogmatism, this lawsuit should dispell those doubts.

Casey's answer is indeed clearly stated and simple. It is also wrong.

First, let's be clear about one thing: this is not a class that is having students "learn about material that some people consider religious." As Casey admits, this is a class that "advocates for young-earth creationism and teaches out of the Bible. [emphasis mine]" Advocating for something is not the same as teaching about it.

Second, the young-earth creationist position is not "material that some people consider religious." It is a religious position. You need look no further than the various statements of faith that the different young-earth groups support to see that.

Casey tries to squirm around the separation of church and state issue with a couple of quotes, neither of which actually applies in this case. In the first, he quotes a passage from a Supreme Court decision: "education is not complete without a study of comparative religion." I actually agree with that, but unless Casey can somehow manage to explain how a class that "advocates for young-earth creationism and teaches out of the Bible," is comparative religion. In the second, he quotes Barry Lynn, the head of Americans United: "when it comes to matters of religion and philosophy, they can be discussed objectively in public schools, but not in biology class." Here, again, Casey needs to show how this course manages to be "objective".

Objecting to having young-earth creationism taught in a public schools isn't a sign of dogmatism about "Darwinism," or about evolution, or about anything to do with science. This is about keeping the state from sponsoring any specific set of religious views at the expense of others. If that's dogmatism, than I guess this is an area where I get dogmatic.