Field of Science

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


Apathetic Atheist


Militant Atheist


Angry Atheist


Spiritual Atheist






What kind of atheist are you?
created with

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 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.