The Science of Biblical Literalism

Welcome to America! Home to (arguably) the largest population of people who view the bible as inerrant. These people often say that they take the bible literally. They don't, but they do use the word "literal" incorrectly.

For example, if the bible were literally true, there could be no parables.
Anyone of those people who espouse biblical literalism want to disagree with this point? If Jesus told a parable, you know a made up story to make a point, then the words in the bible reflecting that parable are NOT literally true. Those words are fiction, make believe, allegory, etc. So if you believe the parable is not literally true, then you are not a biblical literalist. By the way, if you happen to agree with me here, but are one of those jackasses people who believe the world is 6000 years old because of Genesis, then please refrain, in the future, from saying the bible is literally true. What you want to say is that the bible is inerrant. You are still a moron, but at least by being precise I won't think you're a fucking moron anymore.

So what is the problem with biblical inerrancy? It would be easier to start with what isn't the problem with biblical inerrancy, so let's start there....

1. Biblical inerrancy allows me to be a mindless dolt. I do not have to think, critique, analyze, or otherwise use any part of my brain above the brain stem to be a functional member of my church. It allows me to simply accept what I am told by those who affirm they know what they are talking about as long as they have previously cloaked themselves in some biblical context.

2. ??? I guess I only have the one.

OK, lets see about some of the problems with biblical inerrancy and by problems I do not mean specific issues but the overall problems with this line of "reasoning."

1. Translation. The bible is not read in the language it was written. The old testament was written in Hebrew and the new testament in Greek. These were then translated through Greek (in the case of the old testament) and Latin and ultimately into English. This is not completely true, for example we have some old Greek texts of the new testament which can be translated directly into English. Regardless, you have to believe that there is a 1:1 or 1:1:1 or 1:1:1:1 word for word translation between these languages. Anyone who is fluent in more than one language understands the absurdity of this position. Look at the English language: take the words LARGE, HUGE, GIGANTIC, HUMONGOUS do these all convey the exact same meaning? If these words were being translated into Japanese what would the corresponding words be? More importantly if we asked 100 Japanese-English speakers would they translate these to the same corresponding words?

"Fine" you say, "this is just a triviality it doesn't change any fundamental meaning thus the bible is inerrant." Indeed, the example of BIG synonyms is susceptible to that rationale. However, the fact is that translations are subject to interpretations and these interpretations affect the meaning of the text. How many sermons have you been to where the focus is on a specific word in a verse? If the original text had the word LARGE and through several translations it became GIGANTIC, then your pastor may incorrectly focus a sermon on the "fact" that the bible states it was a gigantic whatever and not simply a large whatever.

2. Source. There are no original texts of any part of the bible, no original verses, chapters, words, etc. None. Nada. Zip. Zero. Jack Squat. Thus, you have to assume that the translation you are reading is in fact based on a valid copy of the original. Not just a copy, a copy of a copy of a copy of a copy of a copy and nowhere during this genealogy can a scribe have changed the text (see below). Seem likely? Remember this was before the printing press so there were very few copies of any text.

3. Editing. Here you true believers just need to jam your head in the sand. It is clear that the biblical text has changed over time. In fact biblical scholars (not the ones whoring themselves on Sunday morning TV, but actual people of education and intellect that read and study the ancient manuscripts) have long known this fact. I will reference Bart D. Ehrman's Misquoting Jesus for a more thorough analysis of this point (and point 2 to a lesser degree), its an easy read and comes in at an simple to get through 200 pages. Also, you can go to your local study bible (not bible study which is less about study and more about ideological justification) and look at the various translations and difficulties with the text. Here's a fun fact for the biblical inerrancy campers still following along....John 7-8: verses therein regarding the adultress brought before Jesus by the Pharisees: NOT ORIGINAL it was added well after the fact. "Let he who is without sin cast the first stone," not written by John, more like the John Grisham of the time.

Please, before you throw out the "god had it added later to complete the bible" argument. Remember you will have to accept that the bible wasn't correct before that point or undergo some type of logical fallacy that should cause your brain to explode if there was a god.

4. Inclusion/Exclusion. How did the decision regarding which books and letters to include get made? There are numerous writings that were left out. The Gospel of Judas, the Gospel of Thomas, the Apocalypse of Peter, etc. Why are these left out? and why are the others in? Note the new testament as we are familiar with it didn't originate until ~350 and even then it was not uniformly accepted as is for hundreds of years. So was the bible wrong for most of the first 500 or so years of christianity?

Summary:
There are at least 4 lines of reasoning that demonstrate the position of biblical inerrancy is absurd. The one contradictory position is that biblical inerrancy is easier. This is true, but so is life after a lobotomy.

Science Debate 2008

I have joined ranks with Mooney and Kirshenbaum in my support of a presidential debate on science and technology policy. I see important reasons for this debate. Sciencedebate 2008

First, science and technology are either at the forefront of many current issues (global warming an embryonic stem cells) and are an underlying aspect of many addition issues (cost effective pharmaceuticals for the elderly). Here is where I see the greatest benefit from this type of debate. Determining where the candidates stand on certain issues and most importantly why they have that stance.

Second, I want to know how these candidates view science. Currently, our society has, at least a tolerance in, the idea that facts are akin to beliefs. There is an undercurrent of antagonism towards science, rationalism, intellectualism etc. In a variety of speeches, the candidates have reinforced this view in my mind. When 3/9 republican candidates raise their hands in response to the question "Which of you DO NOT believe in the theory of evolution?" without a show of embarrassment or subsequent backpedaling you know there is a problem. From this kind of debate we can find out who answers questions related to science and technology policy accurately or who answers in such a way as to appease the religious right.

When I joined I posted a question that will never get used, though I am sure many are posting something similar. I do not have the quote but it was approximately...."All of the candidates have expressed the importance of faith in their lives and policy decisions. My question is what will the candidates do if they learn that the best available science directly contradicts one of their beliefs, one current example could be the intelligent design-evolution issue. (Obviously there are a plethora of examples global warming, nukes in Iraq, abstinence-only sex education, etc.)

Sign up, tell your Congressional representatives, teachers, university officials, religious leaders, etc. to support this debate as well.

Lewis Black Shoots on Faith Via Creationism

Says "I have thoughts." Watch the whole thing, but focus on the 45 second mark for the previous quote.


Now before some of you get your panties in a wad, note this is not a dig on religion in general or christianity. It is a dig on a specific version of christianity in this country (if you follow this version, go ahead and wad up your panties now). I am not opposed to faith overall. Hell, I have faith. I have faith that most people won't act like psychopaths, I have faith you won't change lanes into my car while driving. However, this faith is based on experience. I have faith in other things as well, if you tell me you have the simple cure to some medical problem that the AMA doesn't want me to know about, I have faith you are an asshole, idiot, or both. If you tell me some product you are selling is safe, despite all these medical reports, I have faith you are more concerned with the health of your stockholders wallets and not my health. Again faith based on experience. I freely admit I could be wrong, but 9 times out of 10 I bet I'm right.

That being said I am concerned with "faith" as it is currently being bandied around. "Faith" these days means, to me, a belief in a fundamentalist version of evangelical christianity (FVEC). The nice thing about this version is that normal christian practitioners (of which I believe represent most christians) won't contradict it. When a FVEC says their faith tells them abstinence only education is the moral course, what christian is comfortable saying "I think your faith is wrong," when the data says abstinence only education is a failed policy.

Mostly my concern is all the talk by the presidential candidates on both sides about their faith. I care not-a-whit about your beliefs in the supernatural. Actually, to hear them talk about it scares the shit out of me. These people will have the potential to affect my life, and the lives of my family, in profound ways, I don't want to hear about their favorite fucking ghost story and how it may guide their decisions. I want to hear about their policies, how and why they came to have them, how they plan to support them, and what these policies mean to all the people of the US, not just the specific sub-set that hails from the same regional denomination. I want to know what it would take for a leader to abandon a policy. I want the next leader to think with their head and let their guts focus on digestion and not thinking. I want our leaders to make the best possible decisions using the information they have available and let them have faith in the fact they are doing the best they can.

Hit tip to Pharyngula

Clever science is fun science

From the day-to-day questions we ask, experiments we do, papers we read, and what we think about in my lab, things often seem dull. The breakthroughs and insights made by myself and members of my lab offset this and do make the work exciting, inspiring, and fun. However, sometimes I read a paper that fascinates me often from the new information perspective. Occasionally I find a paper that I classify as fascinating from the cleverness of the scientists who did the study. These tend to be the paper I read and think "Why didn't I think of that!"

The November 30th issue of science had just such an article.
The paper by Sorek et al discusses the issue of horizontal gene transfer in bacteria. Horizontal gene transfer (HGT), the acquisition of new genes from unrelated sources, is widespread throughout the bacteria and is found within eukaryotes as well. HGT is behind the epidemic of antibiotic drug resistance in previously susceptible organisms. We have known for quite some time that genes that encode diverse functions could be transferred horizontally, but the limits of what could and could not be moved has not been definitively studied. Sorek et al set out to answer this question.

Here is the clever bit...The authors used currently available genomic sequence information to get a idea about what was going on. To understand this you need to understand how genomes are sequenced.

In short, you purify genomic DNA from the organism you are interested in studying. This tremendously long genomic DNA is broken into much smaller fragments containing on average 1-3 distinct genes, This fragmented DNA is cloned into a vector (a DNA backbone that can be stably moved into 1 or more organisms) and the resulting vector + fragmented DNA (plasmid) is recovered in the bacterium Escherichia coli. Any given E.coli cell will get one plasmid, so 10s -100s of thousands of E.coli cells need to be recovered to get enough individual fragmented DNA molecules to ensure you have the entire genome of organism of interest represented. These plasmids are then recovered and sequenced. In general terms researchers want to have 10x coverage, that is every piece of DNA is sequenced 10 times on average. Despite this 10x coverage there are always regions of the genome that are not recovered.

Back to the clever bit, the authors realized that putting these plasmids into E.coli represents HGT. These vectors are in fact derived from natural E.coli strains and are transferred naturally between strains. So, through the process of obtaining genome sequence for a variety of bacterial species, Sorek et al realized that the scientific community had inadvertantly set up an experiment to determine the limits of HGT. They simply (and by "simply" I mean anyone with a computer and knowledge of these systems could have done it, it is not meant to diminish the work or insights of the authors) took available genome sequence information from 79 distinct species and looked to see what was not sequenced using the process described above. Again, the idea being if a region was not sequenced, it must not have been propagated in E.coli (the gaps in a genome sequence are obtained using other more labor intensive methods). Indeed, the authors found regions from these species that were not able to be propagated in E.coli. Interestingly, these regions that could not be propagated were not random, but contained genes encoding specific types of proteins. However, the authors noted a given gene could be recovered in E.coli from at least some of the 79 species, thus it seems like no specific protein encoding genes always fail to be transferred into E.coli.

This in and of itself is interesting and important information, but the authors did not stop here. They actually took this bioinformatic data and conducted some biological studies (something done too little in the bioinformatic field in my opinion). The authors wanted to know why some genes were not readily transferred to E.coli. They went on to show that these underrepresented genes are toxic in E.coli. Interestingly, it was an innate property of the gene product's activity because they observed the same toxicity if the used an extra copy of the E.coli gene.

So here we have a paper in which the authors learn some interesting biology primarily because they were smart enough to come up with and follow up on a good idea.

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.

Controls

In order to conduct an experiment to test a hypothesis, controls are the most important aspect. Controls are the tests/assays that let you know an experiment is working correctly. In other words, a control lets you know the results of your tests are valid.

Using a trivial example of a standard technique in molecular biology: lets say you want to amplify (make many copies of) some bit of DNA using the polymerase chain reaction (PCR). In PCR, you add DNA to be amplified (copied), primers (short DNA sequences that specify the DNA to be amplified, a buffer containing various salts, dNTP (the building blocks of DNA), and Taq (a DNA polymerase).

After running your PCR, you find that you obtained no product. Why? There is a cornucopia of reasons why...your template (the DNA to be amplified) was no good, your primers are not correct, the dNTPs are bad, the machine that the reaction was run in was not set up correctly, etc. etc. etc.

Now in some cases, such as you are amplifying a known target using standard conditions, the failure is due to some technical difficulty, in other words user-error. Here, controls are often overlooked because these "standard" conditions work so often, people cut corners. The problem with not having controls here is that it takes you longer to trouble shoot the problem. Here, the controls are straightforward: 1. Use primers that "always" work, to test that your template DNA is good; 2. Use your primers on template DNA that is known to work; others (but lets keep it simple with these two). If your test PCR failed but control reaction 1 worked and control reaction 2 failed, then the problem likely lies with your primers....maybe they are at the wrong concentration. If your test PCR failed and control reaction 1 failed, but control reaction 2 worked, then your problem likely lies with your template DNA....maybe it was degraded during purification. If your test PCR failed and control reactions 1 and 2 also failed, then the problem likely lies in your dNTPs, Taq, or machine. The take home message here is that if your experiment fails the controls help you determine what is wrong so you can correct the issue and make progress faster.

In other cases, such as you are testing for the presence of specific DNA in an unknown sample, failure could be due do the absence of the specific DNA (IMPORTANT) or a technical difficulty (TRIVIAL). Why does this matter, lets say you are testing for the presence of a pathogenic organism in a sample using the PCR. A negative result (failure) would lead to the conclusion that said sample was not contaminated with said pathogen. (If you are about to eat or buy for your child said sample, you want to be sure a negative result means the sample is pathogen free, not that the technician who did the study forgot to add Taq). Here controls serve to establish the veracity of some result. Without the control the results are, at least, suspect but to me it means the results are useless.

So controls are important for two reasons. First, they provide technical assistance for day-to-day protocols. Second, they demonstrate that a given result is meaningful.

Does this matter in general for scientists? Absolutely! To take a recent example, in our departmental journal club we discussed a paper that looked at the interaction of a bacterial species with the surface cells (epithelial) of a mouse lung. The pictures presented showed a three bacterial cells next to the host epithelial cells. Based on this, the authors conclude that these bacteria interact with the host cells. However, there are no controls. The lung alveoli are very small spaces, thus there is not much extra room within them. So as a skeptical scientist, I want to know what a non-interactive bacteria would look like. Based on the space available, it seems that by raw chance most bacteria, regardless of interaction, would be in close proximity to the epithelial cells.
This issue of experimental weakness is often dealt with using independent approaches. However, in this manuscript the authors used this "result" as the reason for all their additional studies. Thus, the entire work was dogged by the idea that the "interaction" the authors mention was an artifact (not real).

In memorium: Dr. Danny Brower

There are those people who make a significant difference in your life. Danny Brower was one of the people who had a major role in my life and it is with great sadness that I learned he passed away Oct 5th. Dr. Brower, a professor in the departments of Molecular and Cellular Biology and Biochemistry and Molecular Biophysics, was one of my Ph.D. thesis committee members when I was a graduate student in MCB. Danny was a rigorous scientist who always conveyed the highest of standards. He was considered one of the "hard" professors by my colleagues, which was odd considering that Danny was never aggressive or mean-spirited. My sense was that he simply expected from the students as much care in their approach to scientific thought as he had. I specifically sought out Danny as a committee member and remember our initial discussion. First, he wanted to know why I wanted him on my committee (scientific thought, increased breadth for my committee, and a desire to push myself with a rigorous committee come to mind). This is an important question and I use it myself when asked to serve on thesis committees. Second, he told me he had no problems failing a student regardless of what the other committee members thought. This was not said in a mean-spirited way, but I believe Danny wanted to ensure that a student truly wanted him on the committee and was not simply finding a warm body. Again, I take the same tack and can honestly say that I have also been the only committee member to give a student a failing grade. As with Danny, this is not a spiteful decision but a way to maintain the rigor of the program, keep expectations high, and push the students to their full potential.

While I do not know for sure, I believe Dr. Brower had a major impact on my career. My graduate school tenure can not be considered a success by any quantifiable metric. However, I was able to land an extremely good post-doctoral position. This was due, in part, to my letters of recommendation which were written by several committee members including Dr. Brower. Without a good post-doc position, I would have ended up doing a run of the mill post-doc, not pushing myself, and likely would not be an associate professor. Who is to say what would have happened if, but suffice it to say because of Dr. Brower, I am one of those he touched who is able to continue his legacy of mentorship.

Finally, I want to note that Danny was not just a mentor, he was a friend. During an extremely difficult part of my life after receiving my PhD, Danny and his wife Sharon opened their home to me. They were kind and caring and I am truly appreciative of all they did. I have not touched on the work Danny did nor how the aspects of his work in Drosophila contributed to the field. Science is an incremental process and those of us who do it realize that if we hadn't done something, someone else would have. Danny's impact is more than the research he did, it is his affect on others that is unique and has truly lasting value.

Framers vs Educators

The other night (Friday), I was fortunate enough to attend the Bell Museum's Speaking Science 2.0. The speakers discussed the issue of framing science, which I have commented on and posted numerous responses on other blogs. On the pro-framing side was Chris Mooney and Matt Nisbet, the two authors of a policy forum on Framing science in the journal Science a few months ago. On the pro-education side was PZ Myers and Greg Layden, two scientists who have been critical of the framer's message.

The discussion, while advertised as a cage fight, was much more sedate. (Needless to say I would have taped Smackdown if I had known how pleasent this forum would be.) The framers took the stage first and gave a well-oiled presentation outlining their main points. After a couple of days reflection, my recollection of their points are: 1. Scientists suck at communicating science, 2. The public is stupid and will always be stupid, 3. The right-wing has embraced this stupidity and taken a marketing approach to get the public to think about issues from their perspective, 4. The scientists need to use this marketing strategy if they want to compete, 5. If we take the framers' advice, magic will happen and we will win.

The framers left much unsaid to avoid some problems with their position, but Layden and Myers were kind enough to state the unstated, more about that later.

First, I want to go through my responses to my rather snarky interpretation of the framers' position.

1. Scientists suck at communicating science. Well this time I am not being snarky. This stereotype is well propagated in the framing debate and, as far as I can determine, just accepted without any real information to back it up. I asked the first "question/long winded statement" after the panel presentations, and one point I wanted to make was this stereotype is bullshit. Sure, there are bad science communicators who are scientists, but by and large I think scientists are pretty effective. Currently, we are getting hosed by the right-wing, is this due to scientists being poor communicators or the army of right-wing non-scientists being effective. When industry (with an economic bias) or religion (with a self-preservation bias) gets involved, they can use dedicated resources to promote their viewpoint. Scientists actually have jobs, its hard to find time to disseminate information (lies in the case of the right-wing) when we have to teach, do research, write manuscripts, write grants, etc. So I will agree we do not get our message across as effectively, but this is not IMO due to poor communication but to being outnumbered.

2. The public is stupid and will always be stupid. Snark #1. Mooney and Nisbet obviously did not say this, but the conclusion is distilled from the following points that were made. First, people are "intellectual misers." I won't disagree with this in general terms, but I will disagree with the defeatist attitude it instills. You know people don't want to think about hard stuff too much, so there's no sense trying to educate them. Better is coming up with a 15-30 second sound bite that is vacuous and trite but pulls at some emotional heart string. Second, popular science isn't working. The traditional approaches like magazines such as Popular Science, Discover, etc aren't cutting it. While the subscription rates to these mags may be dropping, I expect this is true across the board. Thank the internet not mental miserness. One person (panelist or audience member, I forget which) noted that there are a number of dedicated sience channels on cable, this means at least some % of the public is tuning in. So the current attention span of the public may be short, but that doesn't mean the public is not educatable. Mooney and Nisbet basically said that science education through the popularization of science is a good thing, but then turned around and noted how it doesnt work and basically cant work, so just resort to framing.

3. The right-wing has embraced this stupidity and taken a marketing approach to get the public to think about issues from their perspective. Well, I can't disagree with this one. The marketing/resources used by the right-wing is profound and works pretty well. Sadly, I do not know an adequate response to this. Lawsuits, by the general public, do not seem to work, case in point the tobacco industry. There really are no reprecussions for lying, presenting false information, etc. After the Dover trial, it was not the Discovery Institute and Michael Behe that paid, it was the school district that paid and is still paying in massive legal fees. I think the only approach is to teach the public how science works, skepticism and critical thinking skills are a powerful tool that only serve to help our side. Of course, the framers have given up on this approach and ask us to follow suit. Actually, they pay lip service to the education approach but immediately follow up with why it won't work.

4. The scientists need to use this marketing strategy if they want to compete. Here is where the framing position truly sits. Layden and Myers both acknowledged that the framing strategy can be a short-term band aid on a problem and I concur there is a place for framing. When the discussion is on global warming, it is useful to note the ecomonic ramifications, the loss of polar ice (polar bears as well), potential climatic changes, etc. This really goes hand in hand with point 1 and during my oration I noted that the reason we have a clean water act is because the frame was made that no one really wants to drink poison. The point I want to make is that we have always been framing. However, here is where I think one of the biggest problems with the framing position lies. When it comes down to framing, both sides do it. So the result is who has the most compelling sound bite? Who has the biggest star representing their message? Is Oprah on our side (global warming is a pressing issue episode) or theirs (everyone in the audience gets a new car!!)?

5. If we take the framer's advice, magic will happen and we will win. Again, if we go with the frame perspective, it comes down to who makes the best sound bite. There is no magic here, if our frame is stronger, we win; if there's is stronger, they win. Notice there is no mention of where the truth lies.

The educators' position was about education and religion. The montrosous brachiosaur sitting in the room that Mooney and Nisbet didnt notice.....maybe the stage lights were too bright?

Layden made some extemporaneous remarks noting the problems in K-12 education which were carried on by Myers. Layden pointed out that there is, in fact, a culture war going on in this country whether the framers want to admit it or not. Myers went on linking the power of the religious right to affect education, thus generating more stupid people who are easily swayed to become religious, increasing the clout of the fundamentalists, who are now able to further affect education, generating more stupid people, repeat until schools are more about indoctrination and not education.

I will note Mooney and Nisbet had more elegant slides; Myers had informative slides.

While Mooney and Nisbet were talking, I realized a problem with their idea of framing is that they have a one size fits all approach, this was the crux of my question/statement. In the case of global warming, environmental issues, etc, the framing position holds water. Here is a good way to get the scientific ramifications out to the public, of course the other side has their frame, but at least there are messages that can be put-forth. However, with evolution the frame perspective fails IMO. The other side has the frame "If you believe in evolution, you will go to hell." What is our frame? Nisbet took the teach evolution in schools specific issue and gave me three possible frames.

1. Teaching evolution will make our town more attractive to economic development. No way does this hold water in my mind. Im sure Dell computer is not setting up their next assembly factory in Dover because of the 21st century monkey trial. Frames need to appeal directly to your audience. You do not connect evolutionary biology with industrial development directly.

2. Trying to get ID-creation "science" in school will make us look bad. Bad to who? The secularists? I mean come on, frame it the other way, if we succeed in our efforts we will be a beacon of light to other oppressed schools in our christian nation. Who cares, if the supreme court will strike it down, that's far down the road and god will be happy.

3. Trying to get ID-creation "science" in school will waste public resources in the legal fight. Yeah, the fundies are worried about wasting public resources (can you say Iraq war). Your pretty scientific talking head says, this is a bad idea because the law is against you and it will waste huge quantities of resources, sounds good. You go to church and your pastor says, we can't have these liberal elitists who don't live here tell us we must expose our children to this heretical teaching. Resources, schmesources, what resources will help you in hell? In heaven you'll have all the resources you want including 50 virgins oops, wrong fundies. The fundie leaders are the ones who, on accident, say we don't need to worry bout the environment because the rapture, its a comin'. They can generally keep that vitriol off the pulpit when engaging the sheep masses and the masses are more than happy to overlook any slips.

So what it comes down to is our frames in this issue are not remotely sufficient or appropriate. The framers want the educators to back off and not offend the religious. You hurt our message they say. In an odd sense, the framers are correct, the educators could cause damage. The fundies have cast the argument as science vs religion, not the educators. The educators are more than happy to smack them down, and rightly so. When a fundie says if you believe in the science of evolution, you are going to hell, the fundie made it science vs religion not the scientists. If your personal message is dealing with global warming, great! If you want to embrace the religious in your message, I say Great again, you are doing the right thing. If you want us to shut up about our message so yours doesnt suffer, I say you are putting a gun to your own head and just asking someone to pull the trigger. If evolution falls to the fundies, then biology becomes meaningless classification, biology is science, if one entire branch of science is now suspect, why not all the other areas? Why is physics immune to a christian perspective? Why is geology immune?

Summary statement. Framing in specific issues is warranted and done. More is always better, and more scientists should be encouraged to get involved to offset the army of darkness. Suggesting that the religious want to be on our side is false, the religious, by definition, cannot tolerate science (not everyone of course, there are scientists who are religious, but it should be clear to those with neuronal function Im talking about the fundies). I do not want them excluded from the global warming issue, I want them helping to deal with any problems we have. However, I will not cow tow to those fundies. If they decide that we have to choose between their belief based on a suspect book (Ill blog about it later) and the evidence, then Ill choose the evidence. If they try to get the evidence suppressed, Ill state that their religion is a bad thing that has no true merits. If it did, suppression would not be necessary. There is no frame available to deal with fundies, only education.

The Scientific Method: Facts

Science is an approach, a methodology. In short, it is a way to study the world around us. In that sense, it is philosophy. Science is not a set of knowledge, although it is often confused as such. Science is the knowledge generated using a specific method. Here, the term "specific method" is not the most definitive, because different areas of scientific research depend on different approaches. The power and limitations of the methods associated with spectral analysis of distant galaxies is distinct from the power and limitations of the methods associated with transcriptional profiling analysis of organismal responses.

Regardless, there are terms associated with science and terms dissociated with science. Here, are my thoughts.

Associated with science:
Fact: This is a point of reality. A fact is something that is. Generally, scientists do not use the term fact in articles, but do use the term observation or data. Facts are objective. "The basketball hoop is high." While this may seem like a fact, it is not because it is subjective. From my vantage point the hoop is high, but from Manute Bol's perspective it is not. Now if we say "The baskbetball hoop is 10 feet off the ground." That is a fact. This leads to another aspect of facts, they must be verifiable and/or reproducible. If I say the basketball hoop is high, you cannot confirm that because the term high is subjective. However, if I say the hoop is 10 feet high, we can measure it and check. You do not have to take my word for it.

One thing to realize, regardless of whether you care about science or not (and you do even if you dont know it), is that people often speak about facts or in a way that sounds factual without that being the case. For example, "Our intelligence shows Sadam has weapons of mass destruction." (verifiability issues) or "Men are better in math and science than women." (objectivity issues) "4/5 dentists surveyed prefer Dentyne." (reproducibility and objectivity issues).

My personality defect results

Your Score: Smartass

You are 100% Rational, 57% Extroverted, 71% Brutal, and 71% Arrogant.

You are the Smartass! You are rational, extroverted, brutal, and arrogant. In fact, you could very well be the anti-Christ, as you are almost the exact opposite of everything Jesus was supposed to be. While Jesus says love your enemy, you say love beating the crap out of your enemy. While Jesus raises the dead, you raise hell. While Jesus walks on water, you tend to sink. You probably consider people who are emotional and gentle to be big pussies who are obviously in lesser stature than you. You have many flaws, despite your seeming intelligence and cool-headedness. For instance, you aren't very nice. In fact, you're probably an asshole. And you are conceited and self-centered. Not only that, but you are very loud and vocal about all this, seeing as how you are extroverted. There is no better way to describe you than as a "smartass", I'm afraid. Perhaps just "ass" would do, too. But that's a little less literary and descriptive. At any rate, your main personality defect is the fact that you are self-centered, mean, uncaring, and brutally logical.

To put it less negatively:

1. You are more RATIONAL than intuitive.

2. You are more EXTROVERTED than introverted.

3. You are more BRUTAL than gentle.

4. You are more ARROGANT than humble.

Compatibility:

Your exact opposite is the Emo Kid.

Other personalities you would probably get along with are the Capitalist Pig, the Braggart, and the Sociopath.

If you scored near fifty percent for a certain trait (42%-58%), you could very well go either way. For example, someone with 42% Extroversion is slightly leaning towards being an introvert, but is close enough to being an extrovert to be classified that way as well. Below is a list of the other personality types so that you can determine which other possible categories you may fill if you scored near fifty percent for certain traits.

The other personality types:

The Emo Kid: Intuitive, Introverted, Gentle, Humble.

The Starving Artist: Intuitive, Introverted, Gentle, Arrogant.

The Bitch-Slap: Intuitive, Introverted, Brutal, Humble.

The Brute: Intuitive, Introverted, Brutal, Arrogant.

The Hippie: Intuitive, Extroverted, Gentle, Humble.

The Televangelist: Intuitive, Extroverted, Gentle, Arrogant.

The Schoolyard Bully: Intuitive, Extroverted, Brutal, Humble.

The Class Clown: Intuitive, Extroverted, Brutal, Arrogant.

The Robot: Rational, Introverted, Gentle, Humble.

The Haughty Intellectual: Rational, Introverted, Gentle, Arrogant.

The Spiteful Loner: Rational, Introverted, Brutal, Humble.

The Sociopath: Rational, Introverted, Brutal, Arrogant.

The Hand-Raiser: Rational, Extroverted, Gentle, Humble.

The Braggart: Rational, Extroverted, Gentle, Arrogant.

The Capitalist Pig: Rational, Extroverted, Brutal, Humble.

The Smartass: Rational, Extroverted, Brutal, Arrogant.

Be sure to take my Sublime Philosophical Crap Test if you are interested in taking a slightly more intellectual test that has just as many insane ramblings as this one does!

Link: The Personality Defect Test written by saint_gasoline on OkCupid Free Online Dating, home of the The Dating Persona Test

Well not too surprising there, realizing and accepting that it is statistically likely I could also fall in the sociopath group. Glad to have my deep antipathy for emo kid.

Surgeon Private

Well who can say they are surprised at this point (more Bullshit-R-Us).

Just for a point of reference the Surgeon General of the United States is charged with the following (this from the Surgeon General's website)

The Surgeon General serves as America's chief health educator by providing Americans the best scientific information available on how to improve their health and reduce the risk of illness and injury. The Surgeon General is appointed by the President of the United States with the advice and consent of the United States Senate for a 4-year term of office. In carrying out all responsibilities, the Surgeon General reports to the Assistant Secretary for Health, who is the principal advisor to the Secretary on public health and scientific issues.

Let me rephrase the salient point in bold "The Surgeon General serves as America's chief health educator by providing Americans the best scientific information available on how to improve their health and reduce the risk of illness and injury."

Seems reasonable enough but apparently Dr. Richard Carmona was prevented from expressing sound justifiable scientifically supported opinions regarding issues that President Bush's policies are at odds with. Take for example sex education and abstinence. His holiness, president Bush, has embraced an abstinence only policy, a carry over from his gubernatorial days in Texas. Dr. Cameron states that he was not allowed to promote comprehensive sex education that only included abstinence. In Texas, abstinence only policies that were initiated have since been shown to be failed policies. But never one to take data and evidence over blind faith, Bush has tried to push national and international abstinence only poicies. Worse, he has inhibited professional discussion of sex education by his own Surgeon General. Bush doesnt want to surround himself with the best, get the best possible advice, make hard decision, and live with the results of those decisions. No, Bush surrounds himself with yes-men (either voluntary yes-men or coerced yes-men), gets advice that confirms he is right, makes the decision he was going to make anyway, and makes sure the results of those decisions are always good at least in his own mind. I have said it before and Ill say it again: Bush is not a leader, Bush is a coward. Anyone who has to hide contradictory evidence and suppress dissent does not have good policies. Even if reality was wrong and Bush was right, by being unwilling to stand tall in the face of opposition he is not fit to be president. In fact, those qualities are better suited for anonymous blog trolls than president.

So, I can almost understand how this ideologue got reelected, I cannot understand why this country isnt at the door of the white house protesting for his resignation. Bush is a crank in every sense of the word (I would use the term fanatic, but Bush is beyond that at this point) and sadly his actions affect directly and indirectly every person in this country and many people globally. Even sadder, his actions will continue affecting people for years after this fiasco of an administration is gone.

Damn Atheist had it Coming!

This just in atheists are the same as everyone else! It turns out there is no reason for athiests to be concerned about civil rights, because unlike women, African Americans, and gays and lesbians we got it easy.

But do unbelievers really suffer comparable harm? Atheists are not denied equal access to housing for lacking belief in god, nor are they kept from seeing their partners during life-threatening scenarios in hospitals. Atheists don't earn sixty-five cents for every dollar earned by believers, nor are they prevented from voting. To our knowledge, there is no such thing as "atheist bashing." If there were cases of such harm, one would expect to hear about them in the media and the courts, or at least in the common knowledge of unbelievers. So, where are the cases? On many occasions we have put this question to leaders in the nonreligious community and have never been presented with a single compelling example.

Well there you go. Atheists have not been evicted, nor has there been reason to believe atheists could lose their jobs.

Sure, it would be hard to be elected to higher office in America as an avowed unbeliever, but it would also be impossible for a socialist or a Mother Earth spiritualist. And being barred from the Boy Scouts hardly affects one's basic life prospects. Besides, most experts agree that Scouting is not a "public accommodation" in which everyone has a right to be included.

Hard? Did they actually say hard? Well, I guess this would make it hard in Arkansas Constitution Of The State Of Arkansas Of 1874. You'll notice no mention of socialists or Mother Earth spiritualists. Its good to see Grothe and Dacey did the fact-checking you expect when making such sweeping statements, too bad they didnt try google.

I should point out there is the flip side viewpoint published by the Council of Secular Humanism two issues after one in which the Grothe Dacey article appeared.

Hat tip to Framing Science, which brought this to my attention. And an especially big thank you to Nisbet for raising my bloodpressure 20 points just before bed with his offensive support of the original article and flippant dismissal of dissenters in the comments. I particularly enjoyed "If there were cases of such harm, one would expect to hear about them in the media and the courts, or at least in the common knowledge of unbelievers. So, where are the cases?" Look up any prayer in school law suit, creationism/ID law suit like the recent Dover trial, "under god" law suit, etc these are all separation of church and state issues, but I think it is pretty easy to see how state sanctioned religious favoritism is effectively discriminatory. Also, while you're looking up those cases, try and find out about the fall-out and abuse the plantiffs inevitably had

Final snark coming, Hey Grothe and Dacey, with a large proportion of the country religious and even more afraid of offending the few most virulent of the religious, are you surprised this isnt getting more press? When a homosexual man gets dragged to death behind a Texas pick-up truck its big news, but those who actually survive an assault are generally not making headlines. Similarly, when a Kansas professor is hospitalized after being beaten by ID proponents it is news....I guess Grothe an Dacey forgot because Mirecki lived.

Although based on his defensiveness on the "Framing Science" debate, Im not surprised.

Books....My must reads

Alright I thought I would spend some time discussing books I love or those that have had a lasting effect on me. At least initially, these books will be about biological science, including the history of science, philosophy of science. However, I will also include other books that have had an intellectual effect on me. So you won't hear about Crichton's Jurassic Park, only impact was some spectacular special effects in the movie.

The Growth of Biological Thought: Diversity Evolution and Inheritance. Ernst Mayr.

Today's installment is a rather thick book by the late great Ernst Mayr. This epic book is really the history of biology. It is broken up into 4 parts, the first is really a 131 page introduction in which Dr. Mayr discusses the how he approaches writing the history of science, discusses the scientific method and how the scientific method impacts on biology, and discusses the brief intellectual history of biology. This latter issue is recurrent in the other 3 parts, so its helpful to lay out the intellectual history and contributors early in broad strokes.

The second section discusses Diversity, although it is truly a discussion of the history of taxonomy and the species concept. Ultimately this is a mystery with no resolution as the species concept is still a moving target. The criteria used to define a mammalian species is not sufficient to define a bacterial species. Further, what a molecular biologist may define as a species, an ecologist may defnie as multiple species. This is not to suggest the species concept is not useful, simply that it is extremely complex.

The third section discusses Evolution. This section should be read by all creationists as the history of evolutionary thought significantly predates Darwin and many of the foundations were worked out by Christian "scientists" working to demonstrate the existance of their god. The growth of evolutionary thought and its culmination with molecular biology are discussed as the impact of evolution in speciation.

The final section discusses Variation and Its Inheritance. Here Dr. Mayr describes early thoughts on inheritance, Mendelian genetics, and the identification of DNA as the source of variation and inheritance. Again this is from a historical perspective, and was the section I was least impressed with. My diminished enthusiasm had more to do with this being an area I was already quite familiar unlike the earlier sections.

Word of Warning....The is not an exciting read and my addition comes in at >990 pages. I do not suggest you read it before bed (I did, but admittedly I am off.) It is clear amd well-written, including many notes and references for each section. These are real references from original works published in the 1700, 1800, and 1900s. This always lends a bit of intellectual honesty in my opinion. Also, I expect it was exceedingly difficult to write. The sections do not lend themselves to be separate entities as there is much overlap between them and these areas are heavily intertwined.

The important thing is that these areas are intertwined with all areas of biology and having knowledge of these areas is important to have a strong appreciation of the other areas. Myself, I never took an evolutionary biology course in college, although I was a Biochemistry major and obtained my PhD in Molecular and Cellular Biology. (I am not saying we never discussed evolution, simply that I never took it as an entire course.) This, I think is a mistake, and maybe the requirements have changed since I was a student (doubt it), however understanding evolution, species, variation are central to all areas of biology. I spend a good chunk of my time bashing genes for a living. Do these areas really help me intellectually? Absolutely. Understanding evolution allows me to compare my work with that of other organisms to either generate novel hypotheses or suggest explanations to distinct results. Variation? Well, my organism is found in people all over the planet, do they all behave the same? are the genes Im interested in doing the exact same thing at the exact same time in all of these isolates? (Maybe, but is alcohol dehydrogenase expressed the same in all people on the planet?) What about species? Interesting question, how is my organism classified as a species? It is an asexual (as far as we know) organism, so there is no meiotic recombination that we know of. It can scramble its chromosomes and handle aneuploidies (a different number of copies of its chromosomes from the "wild-type") quie well. My point is, knowing about these issues does not hurt my research and makes me a better scientist because I can think about these issues in relation to my work.

Finally, Dr. Mayr wanted to write a second compendium on the area of molecular biology. Sadly, this never was completed. However, another of my favorite books The Eighth Day of Creation by Hoarce Freeland Judson does just that, but we will leave that until next time.

(BTW alcohol dehydrogenase is expressed less in many people of Asian decent hence their ability to enjoy Friday nights a lot more cheaply than I can. Another word of warning, never hang out with a friend that overexpresses alcohol dehydrogenase unless you have nothing to do the next day.)

What kind of Atheist am I?

You scored as Scientific Atheist, These guys rule. I'm not one of them myself, although I play one online. They know the rules of debate, the Laws of Thermodynamics, and can explain evolution in fifty words or less. More concerned with how things ARE than how they should be, these are the people who will bring us into the future. Scientific Atheist 100% Apathetic Atheist 83% Militant Atheist 67% Angry Atheist 58% Spiritual Atheist 42% Agnostic 25% Theist 0% What kind of atheist are you? created with QuizFarm.com

Well damn, I took this quiz yesterday and scored 83% as an angry atheist compared to a militant atheist also rolled in at 7% theist. Less angry and less godly today...Must need more coffee this morning.

The Great Frame debate

A few weeks ago Chris Mooney and Matt Nisbet published a policy forum article in Science, a major scientific journal published by the American Association for the Advancement of Sciences (AAAS) (Framing science). The result of this essay has been an ongoing discussion between those who agree with Nisbet and Mooney and those who think they are over-the-top, at the best, and hurting the cause of science, at worst. Basically, the point of contention is around the idea that Nisbet and Monney’s want atheist scientists need to sit down, shut up, and let the god fearing scientists talk to the public. I wrote at length in response to a blog Mooney wrote, which is essentially an elementary school whine about his name being used poorly here. I decided to post my response here, albeit with additional comments to maintain some coherence.

The "framing" debate will not die. So at least I am not kicking a dead horse here. My take on this debate is that Chris Mooney and Matt Nisbet are not hearing what their critics are saying. First, most (all even) of the critics have clearly and repeatedly stated that many scientists could be better communicators to the general public (which is what I think was the main point of their policy forum). Others have pointed out that many scientists actually are good communicators since we often teach at colleges at various levels, but also talk at high schools and to younger audiences at various times, although improvements are always possible and warranted.

The issue leading to the backlash is in their attacks on atheism and science in a religious society. In recent history Debbie Schussel and other right-wing, dare I say, nut jobs are telling atheists to shut up and keep out of sight. Now Mooney and Nisbet are essentially taking up that rallying cry. They may disagree, but I think if you read their Science piece, Washington Post Op/Ed, and blog comments here, and here that conclusion becomes clear. I guess that approach worked in the past. Richard Dawkins, PZ Myers, and Larry Moran, all vocal atheist scientists who are the target of Mooney and Nisbet, could be subject to house arrest, without internet hook-up of course, until the American theocracy no longer deems evolution a threat....say the year 2250? Worked for Galileo.

Will atheists like Dawkins etc. make the thin-skinned religious people walk away from the table as warned by Mooney and Nisbet? Maybe, but I would argue that the vitriol spewing members of the other side, Pat Robertson comes to mind, should be pushing them right back to the table for the same reasons. I mean if these people actually are reachable, then all the "damage" Dawkins does by insulting their religion should be offset by the "damage" caused by the other side insulting their intelligence. I rather doubt a significant portion of the religious community in this country actually expected god to throw a meteor at Pennsylvania after the Dover trial, despite Pat Robertson’s orgasmic (try to find it, you’ll see) predictions. By the way, it wasn't Dawkins et al that caused the Dover trial, nor was it an atheist that caused the Scopes trial. It troubles me greatly, when these partners in scientific advancement suggest that these cultural divides are caused by or due to the likes of Dawkins and company.

They want to keep religion out of the debate with science. Fine, I agree, lets do that. Of course scientists did not bring religion into the evolution debate, which is the core matter Dawkins et al are dealing with. It was not a scientist saying: look god is dead, vive l'evolution. It was the religious saying: if evolution, then god is dead. This is the same argument used to discourage the acceptance of the sun as the center of the solar system or that the fossil record is flawed because animals cannot be extinct. So they bought it up, not us. Should we ignore it and just go for a better PR campaign? Maybe, but I don't like our odds...us: better quality of life; them: eternal damnation.

I guess I see this culture war as a pendulum. They have their pit-bulls and we have our german shepherds, and there are all the non-aggressive dogs in the middle. If Dawkins et al shut up, as some would like, then the pendulum automatically swings more towards their side. And damnit, we have facts on our side. Mooney and Nisbet confuse facts with “data dumps”. However, that is just a piss poor stereotype, ie strawman, which allows them to group together and discount scientists as communicators with a stroke.

In short, albeit long at this point, making sure we communicate the benefit of science to individuals and society and communicate the risks to individuals and society if we ignore science is a good use of the framing concept that I doubt anyone would argue with. However, in the evolution debate all bets are off, because we lost that "frame" decades ago. In fact, I doubt our side was ever in the game in America. So at this point evolution is ingrained in the American psyche as a religious issue. We do not need to discuss religion or tread on it harshly. However, when religion says us versus them, I will then I agree (what other choice do I have?), pick up the gauntlet and slap them in the face with it.

I really wonder what advice Mooney and Nisbet would give to Copernicus, Galileo, Scopes, etc. "Ok, we agree that what you say is correct, but you may irritate important people or even break the law. How would that look to the public, seeing you arrested or worse? How about you write some nice letters to the cardinals, pope, legislature explaining things to them, without scaring their beliefs in any way. Then, once they agree, you can talk about the solar system or teach evolutionary theory. However, until then please play nice and don't do anything to ruffle any feathers. Sincerely your partners in scientific advancement."

Post-script: In case you were wondering german shepherds are much smarter, better, loyal, useful, and allaround way cooler than pit bulls.

Jobs and morals

There has been much discussion lately regarding the "rights" of pharmacists and doctors to not fulfill prescriptions/treat patients depending on their personal morals. Inevitably this comes down to religion not ethics not philosophy not rationale thought. Just religion. (While this is a relatively new blog you will find a recurrent theme.........wait for it......Religion sucks)

Now this topic has been addressed by others (for example see PZ Myers) and I am probably stating thoughts that have been expressed by others. However, hearing things a different way can be informative. Regardless I find the whole issue to be, in a word, bullshit and here is why:

The slippery slope approach. Real example: 1. a fundamentalist christian pharmacist chooses NOT to fill a prescription for the morning after pill. Has happened and in fact several states are considering legislation to protect the right of these “healers” to not only not provide a legal service, but to also allow them to not provide accurate information. For example, one deciding not to provide service would not have to recommend a physician/pharmacy that does provide said service.
So lets consider several other hypothetical examples in increasing insanity; 2. A roman catholic pharmacist decides not to fill birth control prescriptions. 3. A roman catholic pharmacist decides to fill birth control prescriptions with placebo. 4. A fundamentalist (pick a religion) refuses to fill prescriptions for an HIV+ patient. 5. A klu klux klan pharmacist decides to not fill any prescriptions for a black or any other disparaged patient. 6. A fundamentalist refuses to fill antibiotic prescriptions to a 10 year old child. 7. A religio-nazi only fills prescriptions to members of their specific faith.
First, I consider scenario 1 (the one that’s happened) and scenario 6 equally insane. I made the list by increasing absurdity in today’s culture, but in practice are these scenarios are all absurd. Some people are in favor of example 1, which is why short-sighted legislators are voting in favor of it. Example 2 is a direct extension of example 1, thus not a stretch. I mean if your religious convictions can allow you to not fill morning after pill prescriptions, why can’t your religious convictions allow you to not fill a birth control prescription. Example 3 is a variation of example 2 but more extreme. Obviously, swapping a prescription with placebo is illegal. But really, in this day and age in this country, I can envision this happening and the pharmacist getting a free pass because he/she did not directly endanger the life of the patient and were only acting on their deep seated beliefs. Example 4 is simply due to the belief that AIDS is the sky god’s punishment on a given lifestyle, a view expressed on the floor of Congress during the AIDS epidemic. Example 5 is absurd, the repercussions would be extreme, although I expect the issue would be washed over by the resignation of said pharmacist and the presentation that said patient could have gone somewhere else to get the prescription filled. Examples 6 and 7 are even more absurd and won’t happen in this country unless the theocrats truly take over and suspend (read burn) the Constitution. The point is, if we allow someone to decide which prescriptions to fill or which patients to treat based on religious beliefs, where do we draw the line? who do we want to draw the line? Religious beliefs have no logical frameworks, yet we allow them to guide major decisions on those who do not share those beliefs.

Is it the pharmacist’s place do decide when a morning after pill is given? What if a 14 year old girl is raped by her father?
Pharmacist: “I’m sorry dear, but my personal belief in god, means I cannot in good conscience fill this morning after pill prescription. You should have saved yourself for marriage.”
Girl: “But I didn’t have sex.”
Pharmacist: “Look god will forgive you for being a little whore, but not if you kill a child and I am not going to assist in jeopardizing your soul.”
Girl (whispering): “But I was raped”
Pharmacist: “Well that’s too bad dear. But that isn’t the fault of your potential fetus. Further, you shouldn’t have put yourself in that situation, were you at a rave or drinking, you just bring it on your self. (To passing customer) “Hi Ellen, we seeing you at prayer meeting tomorrow?”
Girl: (whispering even softer): “It wasn’t my fault.....my dad....my dad raped me.”
Pharmacist: “Well, that would be different if it was true, but how can I know. If you could prove it I guess I could fill your prescription. If you haven’t already, report it to the police and if there is enough evidence to convict your father, Ill fill your prescription.”
Girl: “But, but that would take months!”
Pharmacist: “Maybe, maybe not.....I’ll pray for you dear.”

The slippery slope part II. Since pharmacists and doctors have begun meting out services based on religious convictions, why not other professions. Police will only serve and protect the majority religious group in that community. Serving people of other or no religious faith may be seen as accepting or taking other gods and the primary sky god in America don’t play that. Same for firefighters. Teachers will only have to teach that which is in keeping with their religious beliefs....a big boon to the creationists.

Here’s a thought, you don't want to fill legal prescriptions because of superstition and perverse beliefs.....GET ANOTHER FUCKING JOB!

Welcome

So how to start.....Welcome and thanks for coming. I'll start by answering a few questions regarding who I am and what the purpose of this blog is and is not

Who am I? Tough question. Most relevant is I am a family guy (not The family guy), husband and father. I am a scientist, assistant professor of microbiology at a major research institution. I am also an opinionated bastard or at least have been called that. I am not politically correct, or at the very least, I do not actively try to be. I am happy to call a spade a spade and will not pussyfoot around an issue because someone will get offended (and I promise you that someone will get offended). If you are easily offended go read another blog. I do not tolerate stupidity and I expect much from people (yes I am generally disappointed). I am not perfect and will admit to a mistake if I make one, though it doesnt happen often. I do not know everything and enjoy learning new things and ideas.

What is the purpose of this blog? Well in short I think a lot about many issues and want to share those thoughts with others. Over the last 10 or so years, I have thought much about science and the impact of science on society as a whole. One thing I have decided is that scientists, as a whole, suck at interacting with society. We have our champions, notably Carl Sagan and Stephen J, Gould and Richard Dawkins, but by and large, we live in our labs, talk with our colleagues, and go on our merry way. At one time, I think this probably worked well, because society (of course I am specifically refering to American society) had a healthy respect and appreciation for science. I think that has fundamentally changed over the last few decades for a variety of reasons we can explore at another time. Now I think a good proportion of society does not understand the power of science, does not appreciate science, nor does it have respect for science. In short I see a real backlash against science by our society and firmly believe this is ultimately a very bad thing for us all.

What is not the purpose of this blog? Hmm not sure. Because many of my blogs will be about religion and pseudoscience I will attract people who disagree with me or as I like to call them, idiots. This will immediately lead to flames from said idiots which may lead to rebuttal flames from non-idiots. I do not want this blog to become a perpetual flame war. So, feel free to comment but I would like to end with a quote, whose source I have forgotten, "I'll be less mean, if you be less stupid."