Tag: Evolution

As an evolutionary biologist with a 50% appointment in a medical school (in the Med. Micro. and Immunology department at U. C. Davis – my other 50% is in the Section of Evolution and Ecology on the main campus) I am somewhat dismayed by the lack of attention evolution receives in Medical Schools.

So I am starting a new thread here on my blog about why medical professionals need to understand evolutionary biology. First, there is a great site out there for people who want to learn more called the “Evolution and Medicine Network” which has links to courses, articles, books, etc.

Here are my top 10 picks for reasons medical professional need to understand evolution

1. Antibiotic resistance. The emergence and spread of antibiotic resistance is one of the most vexing issues in medicine right now as well as one of the best studied topics in the evolution of microorganisms. Understanding how antibiotic resistance originates and spreads is fundamentally a question of evolution. The more medical professionals understand this issue the better they will be at preventing spread in hospitals and in convincing patients and the community to stop abusing antibiotics in human and animal care.
2. Origin and spread of virulence. Not all pathogens are equal. Some are minor annoyances. Others produce really nasty outcomes. And importantly, organisms can change these virulence properties on the short term. Even more importantly, behavior of medical personnel can both influence the spread of virulent strains (can anyone say – wash your *$&% hands) and can unintentionally select for more virulent strains. Understanding the evolution of virulence is critical for making sure health care does not make things worse (see papers by Ewald for example).
3. Vaccine use and development. Vaccines involve altering the evolutionary arms race between pathogens and hosts. It is not an intelligent design arms race. If you do not get the difference, stay out of vaccine work.
4. Cancer origins. Cancer is in essence a analog of natural selection operating among cells within the body. Unfortunately for us, the “winners” of this selection process are those that have uncontrolled growth. Thinking of cancer in this way can help understand how to both prevent and treat it.
5. The human microbiome. Beneficial microbes are all over us and play fundamental roles in human health. Unfortunately they are very hard to study because, well, they are small, and many cannot be grown in culture in the lab. The current ways to study them primarily involve indirect DNA based assays involving evolutionary and ecological analyses of the data.
6. Understanding the human genome. The human genome is done (well, almost, but close enough for most uses). Now what? Well, the best way to learn about the genome sequence itself is through “phylogenomic” analyses comparing to other genomes.
7. The relevance of animal and other models. Mouse is a useful model for some aspects of human biology but not all. Drosophila too. And even yeast and E. coli? Which aspects of human biology can be modelled by each model organism? Understanding their evolutionary history and evolutionary processes helps figure this out.
8. Aging. Aging is in essence an unfortunate side effect of natural selection maximizing fitness by futzing with health and reproduction in the early years. Since there is little fitness cost to mutations that lead to deleterious effects when we are old, well, we are kind of screwed. But understanding the ailments associated with aging is best done with this knowledge of the efficiencies and inefficiencies of selection.
9. The immune system. See #3 above. But this is bigger than that. The whole process of how the immune system (both the innate and the adaptive components) works both at the level of an individual and at the level of a population is an exercise in population genetics and natural selection.
10. Pluses and minuses of high mutation and recombination rates. Many medical professionals know HIV has a high mutation rate. And some might know that recombination rates are high in some pathogens. What are the consequences of this on the pathogen biology? Read Evolution 101, or my new textbook.
11. A bonus one. Epidemiology of infectious diseases. One of the best tools in studying the spread of infectious diseases is phylogenetic analysis – which can show how different strains are related to each other.

Just a brief tour of some of the areas that evolutionary biology informs medicine. More on this later.

Well, in my last post I asked if people were committed to “Evolution” and I confess I got a bit worried that this might be misinterpreted by some as “We believe in evolution regardless of the facts.” And in fact there was one flame-like comment posting that I deleted from the comments.

But now apparently the Pope has read my blog (or maybe someone told him about it) and he has come out in full support of evolution as a science and the facts of evolution as we evolutionary biologists know then (i.e., natural selection, macro and microevolution, etc).

As reported on MSNBC the Pope said

the debate raging in some countries —particularly the United States and his native Germany — between creationism and evolution was an “absurdity,” saying that evolution can coexist with faith.

In addition, he said

They are presented as alternatives that exclude each other,” the pope said. “This clash is an absurdity because on one hand there is much scientific proof in favor of evolution, which appears as a reality that we must see and which enriches our understanding of life and being as such.

Furthermore, and more importantly, the Pope has re-stated his belief that everyone must do something about global change and environmental destruction:

“We cannot simply do what we want with this Earth of ours, with what has been entrusted to us,” said the pope, who has been spending his time reading and walking in the scenic landscape bordering Austria.

I know I said recently that biology had a good day in the Bush administration. Unfortunately, that was mostly genetics and biochemistry. Evolution and environmental stewardship never seem to have good days there. Maybe just maybe, the Pope will have some impact around the world on both issues even as the U.S. sticks its head in the sand. NOTE – SEE COMMENTS – THE POPE IS PRETTY CLEARLY NOT DOING EVERYTHING HE COULD TO PROTECT THE ENVIRONMENT.

Peggy Farnham at the U. C. Davis Genome Center sent me this picture. apparently of a real tattoo. After a google search I found at least an early source for it here.

This inspires me to ask everyone out there – are you committed to Evolution? What have you done to show your commitment?

What have I done? I think the biggest example of my commitment, though boring, is that I worked six years on a new evolution textbook which was just published a few weeks ago (which you can find out about here or order from Amazon here).

Less boring – I once stood on a street corner in New Orleans with Owen White and handed out altered forms of a pamphlet someone else was handing out in which we added some information about evolution.

So – rather that spout off about what I have done .. what has anyone else done? Are you committed?

Well, I was interviewed yesterday by the AP (see the AP article here) relating to an article in Science on Genome Transplantation by John Glass, Craig Venter, and crew and the Venter Institute. Their article is coming out in tomorrow’s Science. Though this was not published in an Open Access journal, I think this one is definitely worth talking about and looking at.

Here is what they did, in a nutshell. Took one mycosplasma species (mycoplasma are bacteria that do not have cell walls and have very small genomes) and very carefully removed its chromosome. They then mixed this with a recipient mycoplasma that had some detectable genetic differences. And they then selected for cells that had a antibiotic resistance function found only in the “donor” genome. And they got some growth. And surprisingly, many of the cells that grew up appear to have COMPLETELY replaced the endogenous genome with the donor genome. Thus they use the term genome transplantation.

It seems like a pretty solid paper, although I still am not 100% convinced that these are not some relics of the original donor cells that simply made it through the genome extraction processes intact (this is very unlikely given their controls but still possible). Assuming that they really have genome transplantation, it is a pretty cool result.

Why? Well, it means that at least in some sense, they can use this as a tool in synthetic genomics. One of the big limitations of synthetic biology right now is how one would make a genome in vitro of a bacteria and then get this genome to “boot up” into a cell. For viruses, they can make genomes in the test tube and get the virus to be created because viruses are cellular parasites and all they have to do is get the DNA for the virus to be packaged in the right way into a cell or viral capsid. But for a bacteria, things are much different. The challenge has been how to get a recipient cell to boot up a new genome and delete its own or at least silence its own. And without going into all the gory details, this has proven challenging.

So – now genome transplantation. On the one hand, it can serve as a way to boot up a new genome. However, it probably has limited potential in many ways since to get the new genome to effectively replace the old one, it has to not only be replicated, but the machinery of the cell present in the recipient has to work well enough on all the key components of the donor genome to get the booting up to work. For example, all the promoters in the donor genome must be transcribed efficiently by the recipients machinery, at least for the RNA and protein synthesis machinery genes, so that the donor stuff can get made. And of course the replication origin and other replication features must all work as well. What this means is that I think genome transplantation will only work if the donor and recipient are very similar to each other for most of the housekeeping genes and functions. So this is not yet ready to work for all of synthetic biology. But it still seems pretty cool.

OK

I know I am a little dim (well, maybe a lot). And maybe something was lost in the translation of putting this on the web. But WTF? Can someone explain to me what the point of the NY Times “story” entitled “Evolution is” with a bunch of quotes?

And again, WTF? Why did they pick these quotes?

Like this one by Gould

“It touches all our lives; for how can we be indifferent to the great questions of genealogy: where did we come from and what does it all mean? and then, of course, there are all those organisms: more than a million described species, from bacterium to blue whale, with one hell of a lot of beetles in between – each with its own beauty, and each with a story to tell.” – Stephen Jay Gould

and this one by Maynard Smith

“As an evolutionary biologist, I have learned over the years that most people do not want to see themselves as lumbering robots programmed to ensure the survival of their genes.” – John Maynard Smith

Anyone out there have the inside scoop on this?

Congrats to Southwest Airlines. On a recent flight coming back to Davis from San Diego I saw a nice 1 pager in their Spirit Magazine promoting the Darwin exhibit currently on display at the Field Museum in Chicago. Many places shy away from saying anything about evolution for fear of antagonizing ID supporters. In fact, I cannot recall ever seeing anything on evolution in anyother airline magazine. Kudos to Southwest. Another reason to fly them. For those airlines that shy away from topics like evolution in their magazines, do they also shy away from physics and math in their engineering departments?

Just a quick post suggesting people check out the slashdot story on a field trip to the creation musuem. Thanks to Doug Rusch for pointing this out.

The New York Times is reporting that Darwin (and by Darwin, they mean evolution by natural selection) is getting more and more support within the conservative community in the US.

Basically there appear to be two camps emerging. The anti-science group (not what they called them in the Times article but that is what they are) who cannot reconcile Darwinism (or many other scientific tenets) with their religious beliefs. And on the other side are conservatives who not only accept evolution by natural selection as a fact, but embrace it as supporting many of their conservative ideals. This second pro-evolution conservative clade includes fundamentalist types who, like Francis Collins, believe that evolution by natural selection is indirectly the hand of God. The pro-evolution clade also includes political and social conservatives, who are not particularly religiously conservative.

I found the article fascinating in many ways because finally philosophical conservatives are taking a stand against the religious right. For example:

“I do indeed believe conservatives need Charles Darwin,” said Larry Arnhart, a professor of political science at Northern Illinois University in DeKalb, who has spearheaded the cause. “The intellectual vitality of conservatism in the 21st century will depend on the success of conservatives in appealing to advances in the biology of human nature as confirming conservative thought.”

Also — from the article

What both sides do agree on is that conservatives who have shied away from these debates should speak up. Mr. Arnhart said that having been so badly burned by social Darwinism, many conservatives today did not want “to get involved in these moral and political debates, and I think that’s evasive.”

Yet getting involved is more important than ever, after “the disaster” of “President Bush’s compassionate conservatism,” he said, because the only hope for Republicans is a “fusion of libertarianism and traditionalism, and Darwinian nature supports that conservative fusion.”

So I say to all you social or political conservatives who think that anti-evolution talk is not necessary and potentially damaging, come out come out wherever you are. The time is now for evolutionary biologists to embrace these conservatives. Not because they agree or disagree with their politics. But because evolutionary biology does not itself make ANY moral judgements nor force one to make any political decisions. It is science. Just as quantum physics does not support the right or the left, evolutionary science is apolitical. That is not to say that evolutionary science cannot be used to inform political and social and moral decisions. It is just that evolutionary science is not about those things. It is about studying the way the world works.