The Untimely Passing of Chris Comer

In our enlightened country, it appears the forces of darkness have another victory. The state of Texas director of science curriculum has been forced to resign (when did we stop calling it being fired?) as reported here. The reasons behind her firing "appear" to be several fold, however in my estimation there was one reason for her firing and several piss ass justifications because the fire-ers knew they were morally bankrupt and were trying to cover their respective asses.

The impetus behind Ms. Comer's firing, I mean forced resignation, you ask? She sent out an email letting some people on her mailing list know that there was a local lecture coming up soon by Dr. Barbara Forrest a Professor of Philosophy at Southeastern Louisiana University. Dr. Forrest was a witness in the Kitzmiller vs Dover trial (which found Intelligent Design to be creationism repackaged). In case you were wondering Dr. Forrest testified for the plaintiffs.

"But but but she was fired for a number of reasons!" You say?
"Is it difficult breathing with your head up your ass in the sand?" I respond.

The call to fire Comer came from Lizzette Reynolds, who previously worked in the U.S. Department of Education. She also served as deputy legislative director for Gov. George W. Bush. She joined the Texas Education Agency as the senior adviser on statewide initiatives in January.
Reynolds, who was out sick the day Comer forwarded the e-mail, received a copy from an unnamed source and forwarded it to Comer's bosses less than two hours after Comer sent it.
"This is highly inappropriate," Reynolds said in an e-mail to Comer's supervisors. "I believe this is an offense that calls for termination or, at the very least, reassignment of responsibilities.
"This is something that the State Board, the Governor's Office and members of the Legislature would be extremely upset to see because it assumes this is a subject that the agency supports."

One of the problems is that Comer's email may give the impression that the state of Texas science curriculum board may actually support and endorse the position of the speaker. You know the position that intelligent design is a strategy used by right wing christians to get creationism, and ultimately their narrow minded interpretation of christianity, into schools. God forbid, the science curriculum board supports, you know, things associated with science. God forbid the people of the state of Texas actually get the idea that the science education committees support science and science education.

This all stems from Don McLeroy's (state board of edekashun chairman and vocal creationist) new policy of "tolerance." In other words, we'll tolerate evolution, for the moment, but you need to tolerate my beliefs as science until such time as we can redefine my belief as the one true revealed science of god.

This could not come at a better time for the Texas fundies, as the state is reviewing their science standards in the next few months. Mark my words, Texas/ID will be an issue in the near future. The creationist (aka fundamentalist christians) have removed yet another roadblock in their quest to get their religion promoted in schools and all the while the decry themselves as victims. When will we stand up for ourselves and send them back to the fringe where they belong?

Translational research, is it worth the hype?

For disclosure: I am a basic biomedical scientist

Currently, biomedical research is categorized as either basic or translational. Basic research, in the biomedical world, is that which is focused on understanding some system or process related to human health. This could be trying to elucidate how a pathogen grows and carries out its nefarious plan of attack on the human host, learning how distinct types of human cells arise and what their function within the body is, learning how a drug affects a given target cell in an attempt to predict the ramifications of said affects. In short, basic research in biomedicine is focused on increasing our basic knowledge of something related to human health.

Translational research, often referred to as bench to bedside research, is that which is focused on solving a specific problem essentially from scratch. This could be developing a new antibiotic against some pathogen or curing some non-infectious disease. In general, this type of research is superficially important and warrants significant funding. However in practice, this type of research is in general a failed approach to problem solving and results in large expenditures of research dollars without necessarily providing new information.

The problem with translational research is that it is immediately goal driven, we need to prevent autoimmune disease XYZ (I made this name up for the sake of example in case you thought it was a real disease). Obviously, preventing autoimmune disease XYZ is a worthy goal, but that does not mean a soluton is readily apparent.

A basic biomedical research program would focus on determining the cause of disease XYZ and establishing the specific difference(s) that distinguish a healthy individual from a patient with XYZ. Once these differences are identified approaches can be taken to prevent, correct, or otherwise intercede with the onset of XYZ. In short, basic biomedical science is goal driven but is more imbedded in the biology and idea of generating new information. For example, determining the cause of autoimmune disease XYZ will almost certainly provide new information about the immune system and how it functions. Identifying differences between healthy individual and patients can provide molecular, biochemical, cell biological, and genetic insights into human biology. Going to get a cure using this approach, I do not know. But I can essentailly guarantee we will know a lot more than we do now. "Well so what?" you say. Remember this information does not exist in a vacuum, other researchers doing fundamentally different research on cancer ABC may greatly benefit from the studies done on autoimmune disease XYZ and develop a new therapy.

A translational researcher program needs to focus on getting to the beside, in other words a treatment. So how do we go about developing treatments? Well if much is known about the disease (in other words much basic research has already been done) then there are likely approaches to be found in the literature. So a translational researcher could develop projects from the available body of literature. However, if these approaches were tried and failed to work, they may not have been published so our would be translational researcher may be wasting their time and your money. Hell, an approach may actually be suggested in the literature but not followed up on for any number of reasons, the researchers were pursuing other approaches they thought were more viable, it was not an area the researchers were trained in, etc. This would represent a reasonable use of translational research. Its also possible that the translational researcher would make an educated guess and essentially take a shot in the dark at an approach. The problem here is that if the approach does not work, we often have not learned any meaningful biological information in the process. Remember what I discussing now is based on a disease we know a lot about. What if we know squat? Well, now we are left with the shot in the dark approach and we generally learn nothing about the disease in the process.

Another shot against "translational" research. In previous interations it was termed "applied research" to contrast with basic research. It was flawed as a major thrust then as it is now, the name change did not alleviate the problems.

Now with all that I have just said, I do not have an inherent problem with translational research. It is an important, nay essential, part of biomedical research. The entire field of diagnostics is translational. My problem lies in the funding priorities that are swinging tremendous amounts of money towards translational research and by definition away from basic research. This may result in more therapies in the short term (although I extremely doubt it), it will certainly slow down progress on improving human health in the long run as these resources are often lost without at least the gain of basic biological understanding.

Why are these funding priorities changing? Easy. Translational research is sexy to the average Joe. Congressman JP Assclown can understand needing a cure for cancer, so lets throw more money at it and stop wasting time studying the cell cycle in some irrelevant fungus (see Noble prizes for 2001) However, the honorable Assclown doesnt realize that this is not a viable approach. Its like saying we need cars that get 150 miles per gallon, knowing what your goal is does not tell you how to get there. Research is not like a maze where you can start at the end and work your way back.

An eminent scientist I was talking to over this issue made the point that in any good basic science program the applications should be clear. I think that sums up my feelings on the subject well.

Pluses and minuses

Just a brief note to highlight that the day PBS airs the Nova episode Judgement Day, Bush vetoes the bill funding the NIH. I have not yet watched Judgement Day, its taped, everything I've heard makes it sound like it is a great documentary summarizing the trial. I'll post something once I've watched the whole thing. Conversely, our president, his holiness, has in his infinite wisdom decided to veto bill H.R.3043 stating that Congress was "acting like a teenager with a new credit card". What a fucktwit. Sure, let's start 2 (maybe 3 wars soon), cut taxes, and throw the bill at our children and grandchildren and then engage in name calling like a high school quarterback berating the smart kids. I got news for you commander and chief, a cheerleader is not a quarterback.

You know it is becoming clearer to me that there is not a war on religion (we'll hear much of this during the coming season) but a war on education, intelligence, rationalism, and critical thinking. Maybe this shouldn't be surprising, if you want to maintain personal power and you are wrong, it helps if the people don't know any better.

And by the way, I am not a staunch defender of the weak ass democrats leading Congress. They still refuse to take the president to task for his abuses and deriliction of duty. Of course, one has to wonder if this is in part because they believe they'll have the white house next and then his power will be theirs?

In Science We Trust

Referring back to the Speaking Science 2.0 discussion I attended back in October, there was another point raised by PZ Myers I wanted to discuss. PZ, responding to a question I believe, explained that he wanted to educate society into how science works. He wants the general public to understand how we know what we know and how we deal with what we do not know. PZ would not be satisfied with the public simply buying it because scientists said it.

First, I am completely in agreement with this philosophy. Only when the public truly understands how science works can they make rational decisions regarding a variety of topics. For example, gay marriage is a devisive issue in national politics. Can a scientific approach solve it? No, but it can address specific aspects of the issue. Many people are still under the impression that a homosexual lifestyle is a choice similar to choices you make at a fast food restaurant...."Can I take your order?" "Yes, I'll have a cheese burger and large fries with a diet pepsi." For here or to go?" "Here, umm wait a second, make it to go. I think I'll check out that new gay bar." Here's where science can provide some insights. Are there genetic components related to homosexualiaty? Are there developmental (in utrero, psychological, etc) considerations that impact the "decision"? Do gender roles fall into a simply binary function? or is there reason to believe gender roles are better explained as two overlapping curves? In this way, science can add something to the discussion. Science will not affect bigotry, intolerance, or a particular -ism, but it can provide greater understanding to an issue that is generally framed by both sides to a point preventing any discourse.

All that being said, I do not believe this philosophy reflects an attainable goal. I do not believe we can educate the public as a while into how science works. First, people are busy and have other things going on. What I think is important and critical, others find superfluous to paying the bills and enjoying life. Second, science is hard....or at least it isn't easy. You don't always get a firm answer, people dislike grays, they like black and whites. Statistics are misunderstood (misunderestimated by our president).

Thus, I favor an Increased Trust Philosophy. It is immediately sufficient for the public to trust the scientific process. Basically the public does trust science, as evidenced by creationists, politicians, and industrial interests using psciense (it sounds the same but means something different) to bolster their preconceived positions. Much like we trust our pharmacist to accurately fill our prescriptions (unless you're getting birth control or retrovirals, then you might be concerned), our auto mechanics, etc, public trust in scientists would do much to offset some of the problems that have become apparent the last 10-20 years. No it will not necessarily fix a problem, but at least we can have informed rational discussions.
•Smoking is bad for you, yet many smoke. No rational person is smoking without that knowledge, they have made an informed decision.
•Vaccines are good for you, yet many do not vaccinate. Many people have mis-information regarding vaccines and autism, they have made an uninformed decision. In part, because these people do not trust the scientists/doctors, but do trust the charlatans.

So how do we increase trust? Difficult question, more science and the scientific process being explained is important. More head on critique/assault of psiense also good. Playing nice is important, but when assaulted for the forces of ignorance, playing nice is the kiss of death. Framing is a nice tactic, but does not truly deal with the problem. Science vs psience is not like Pepsi vs Coke and a matter of marketing. Its like milk vs a bucket of fermented cow shit, one could kill you.

My Course

While exceedingly time consuming, I truly enjoy teaching. I currently teach a course called Eukaryotic Microbiology that is in its second iteration. In other words, this is the second time Im teaching it and is the second time this course has been offered. Last year, I taught this course with a colleague, but he has moved on leaving the course in my hands.

This series of events has been particularly stressful because the course is still in its infancy and I had to essentially double the content of the course. I say essentially, because I can draw on some of the things done by my colleague last year. Regardless, this is, in my opinion, a great course. (Obviously, the students may disagree...I am interested in this year's evalutions). The course is geared for advanced undergraduates and some beginning graduate students. Further, there are no good textbooks that cover eukaryotic microbiology (mycology, parasitology, plant biology are just some areas that need to be included)....You know maybe this could be a sabbatical project, but I digress....

So how do I deal with the lack of a textbook? While I may be an expert in some areas of mycology, I am not an expert in eukaryotic microbiology. Further, it would be impossible to cover eukaryotic microbiology in any depth over the span of time we have. Thus, this course was designed to discuss important areas of biology and important eukaryotic microbes. We use review articles and primary peer reviewed articles as the focus of our discussion. We dedicate one week to each topic/organism. For example, this week we focused on the parabasalids, a deeply rooted branch of the eukaryotic lineage which is best known for harboring the sexually transmitted pathogen Trichomonas vaginalis and a variety of termite gut protists that are required for termites to be able to digest wood. First, I give a lecture introducing the organism(s) being addressed and the topic we are focusing on. The students, presumably, have read several reviews to get them up to speed. During the second class, two students present an assigned research article (one article per student) focusing on one aspect of their paper. Finally, the third class is a discussion, led by me, based on questions/issues that arise from the lecture or papers. We use the awesome power of the internet to post questions on the course website, an advantage being students can respond to each other and a dialog can begin before this third class.

What I appreciate most about this class is that I realize these students are generally not going to remember jack about these organisms or topics. However, I do believe they get a better appreciation for how science and the scientific process actually works. We spend time talking about why a given paper is better than another, how papers are peer reviewed, what are the limitations to a given experiment, etc. Further, some of my students make extremely insightful comments on specific issues I had not considered, so I find I learn as much if not more than my students.

It will be nice to have this course completely under my belt at the end of the semester, so I can begin to refine those topics that did not work as I had hoped or completely change those topics that I believe failed. Sadly, one of the papers I chose for this weeks student presentation was a bust. While the paper had many limitations, I thought that the novelty of it would be appreciated (I primarily pick papers with a heavy duty molecular genetic focus, so I figured I would throw the students a bone). Alas the novelty could not outweigh the limitations. So I have already identified an aspect to be adjusted for next year.