Molecular biologists don't understand molecular biology, but Creationist engineers do?

Via Pharyngula I heard about these thoughts by a Creationist engineer musing on the contents of a molecular biology textbook (the link is to All-Too-Common Dissent, a pro science blog written by a scientist, where you can find the link to the original Creationist post):

"My hypothesis is that the field of molecular biology is simply not understood by the majority of biologists and thus pretty secure from rational debate by laymen. By claiming that this discipline (which they probably don't understand either) proves Darwinism and that Darwinism is vital to understanding molecular biology, the Creationists can be silenced, humiliated and put in their place by simply invoking superior knowledge. More malpractice?"

And there's this gem:

"It [this molecular biology textbook the guy was looking at] has a considerable Physical Chemistry and Organic Chemistry component which would make it intimidating for the large majority of biologists, but this subject is really foundational to understanding the molecular foundations of genetics"

Eh? The field of molecular biology is not understood by the people who are actually doing professional research on the subject, but it is understood by a fundamentalist Christian engineer?

So biologists don't know enough math, chemistry and physics to understand what they're doing? I hear comments like this every so often, like the guy who told me that his chemist friend doesn't consider biochemists real chemists. Another example is the first comment to the All-To-Common Dissent post where one guy says this:

"I'm an engineer but also did biology at university for one year. Let me say that the math and physics done at the university level by biology students nowhere approaches real math or physics; it's barely beyond grade 12 level. That said, the only biology you get in engineering is a few things about bacteria when it came to municipal water engineering, so not a whole lot, and certainly less than what biologists got in math and physics."

One year of freshman biology does not really give you an idea of the kind of quantitative training biologists get. I definitely think that biologists these days need more quantitative training to deal with some of today's most exciting research questions (and the educational trend is going in that direction). However, as Scott showed in the original post on All-To-Common Dissent, undergraduate biology curricula require plenty of math, physics, and chemistry - enough to truly grasp molecular biology as well as it's understood today, and usually much more chemistry than engineers are required to learn (chemical engineers excepted of course).

Biochemists get serious chemistry training - as an undergraduate, I had 5 semesters of chemistry (plus labs) before I took a year's worth of biochemistry; I also had 4 semesters of physics, including a class on quantum mechanics where we practiced solving the Schroedinger equation (admittedly just the easier time-independent form). Most biochemistry programs require 1-2 semsters of physical chemistry as well (I didn't major in biochem, so I didn't take p-chem). Anyone who has taken an upper-level undergrad course in physiology can vouch for the quantitative nature of that field. (The course I took involved more math than was in my chemistry classes.)

It's true that biologists generally don't go beyond two semesters of calculus and maybe introductory linear algebra, but frankly you don't need more than that to be a successful molecular biologist who understands the field. (Also, most of us learn much of our math in physics and chemistry courses, not math courses.)

At the graduate level, almost all programs require anyone in biology to take a graduate-level biochemistry course, which involves a lot of homework problems dealing with kinetics and thermodynamics (physical chemistry) and enzyme reaction mechanisms (electron-pushing organic chemistry) - maybe intimidating, as the Creationist engineer claims, but the fact is, all of us biology PhDs had to take and pass it.

And I'm not even getting into genetics, which has its own quantitative foundation.

Engineers and physicists like to pretend that biologists stop their quantitative training as soon as they finish high school. As we've seen, that's not true, but there is another important point - nobody, not even engineers and physicists, has really figured out (yet - I'm still hopeful) how to effectively, compellingly, use more sophisticated math to produce a deeper understanding of biology. Computer scientists and statisticians have contributed a lot to genome sequence analysis, but we have not yet produced very predictive theories or models of cellular behavior that are rooted in the physical behavior of the components of the cell. That may require more math than what biologists are using now. However I doubt that biology (or engineering, for that matter) will ever require the kind of math used by today's theoretical physicists. For the time being, most biologsts know enough math and chemistry to understand the discipline they work in.

Best Science Books

Once more, it's the most commercial time of the year, and every one is coming out with their Holiday Book recommendations. While the NY Times and the Washington Post put out the most well known best books list (and I'm peeved, but not surprised, that Thomas Pynchon and Richard Powers didn't make these top 10 lists), Discover Magazine has put out a list of the best 25 science books of all time.

The blog for the National Book Critics Circle notes that this list "is more about scientific umph than readability." Frankly, I don't even think that's true - I really can't see what bizarre criteria would generate a list that includes Newton's Principia (not that readable), Lovelock's Gaia (not much scientific umph), and Watson's Double Helix (very readable, but not a scientific milestone like the Principia). "Scientific umph" is frankly a bad criterion for a list of great scientific books, because major accomplishments in science are generally not first presented in book form (with a few obvious and older exceptions - Newton's Principia, Darwin's Origin. Sheer literary value is not a good criterion either, because you can have well-written 'science' books where the science itself is not really that substantial, but the writing is so good they're worth reading anyway. (Some people are going to hate me for this, but I find Lewis Thomas's books to be in this category. Personally, I don't find them as insightful about science as the books on my list below, but I know others disagree.)

A list of great books should have both scientific umph, and literary value, but in this sense: they should be compelling, well-written books that convey something deep about science - how it works, how its practitioners think, or about a specific concept. They should make a serious contribution to how we (scientists and the public) think about some aspect of science.

So I've put together my (currently partial) list of what I think are the best science books (in English), books which should be readable (though not necessarily easily readable - understanding science does take effort) by people who aren't professionals in the subject dealt with:

The Making of the Atomic Bomb, Richard Rhodes (1986) (and the 'sequel', Dark Sun, about the hydrogen bomb). This is the most amazing scientific history I've every read. Rhodes writes in absolutely stunning prose, and gives the best current historical account of the development of nuclear physics. Along with the elements of scientific history and biography, Rhodes also develops other themes, like the relationship of science to war, the state, and secrecy. Science writing doesn't get any better than this.

The Character of Physical Law, Richard Feynman (1965). I have fantasies about some day teaching an Intro to Science course using these incredible lectures about scientific reasoning. Feynman was a master lecturer (keep in mind that essentially all of Feynman's books are edited transcriptions of lectures). So while the prose, in a literary sense, may not be Pulitzer material, as lectures, Feynman's language is superb. This book provides very deep insight into scientific thinking, with (naturally) a large slant towards physics.

On the Origin of Species, Charles Dawrin (1859) (Also, The Descent of Man, which I think is a better second Darwin book to read than the Voyage of the Beagle.) One of the few books of the last 200 years to be in itself a major scientific contribution. The Origin is still popular because it is one of the most readable original scientific contributions out there. Darwin was apologetic about his writing style, but hey, in general those Victorians were pretty damn literate, so it's a good read. Actually, Darwin's style is quite good - he usually avoids the pathologically florid style which other scientific writing of that era often succumbed to. This book is substantial because it lays out a major scientific discovery and is an excellent example of scientific reasoning.

Feynman Lectures on Physics, Feynman, Leighton, and Sands (1964) (In principle, this should be generally readable, since it begins with Freshman physics; in reality, it's very tough. Lay readers can do almost as well with the subset of the lectures contained in 6 Easy Pieces and 6 Not So Easy Pieces.) Why am I giving this a separate entry, when I've already included The Character of Physical law? These lectures, while providing similar insight into general scientific reasoning, give an excellent presentation of specific scientific content - of what we have actually learned through scientific reasoning. If you're a person whose willing to plow through dense books by people like Kant, Wittgenstein, or James Joyce, the same effort with the lectures on physics will be well worth the payoff. In terms of language, again keep in mind that these are edited lectures - from this perspective, the language is very well crafted.

The Double Helix, James Waton (1968) This is a well-written account of one of the major discoveries in biology.

The Selfish Gene, Richard Dawkins (1976) This is sort of a popular book, sort of an original contribution, but like Darwin's Origin, a well-written exposition of one way of reasoning using evolutionary concepts.

What is Life, Erwin Schroedinger (1944) This is somewhat dated, and some of the ideas presented have been rejected. However, this book single handedly pushed many physicists into biology, some of whom turned out be major figures in the development of molecular biology. This book is valuable for more than just historical interest though - Schroedinger raises unsolved issues about the Origins of Life.

Genius, James Gleick (1992) (Chaos is another great Gleick book that I think is at the same level.) This is my favorite scientific biography of all time. Gleick, like Rhodes, is a superb writer. I almost didn't put this book on this list though, because I don't think Gleick effectively conveys the content of Feynman's scientific work. (In Gleick's defense, quantum electrodynamics is incredibly abstract and tough to convey.) But, as a work about what makes a scientist tick, and how a great scientist develops, this book ranks among the best.

Goedel, Escher, Bach, Douglas Hofstadter (1979) A great big, substantial meditation on math, music, and logic, composed in vivid, well-crafted language.

A Brief History of Time, Stephen Hawking (1988) A classic discussion of some of the big questions facing physics.

I'm going to stop the list here (out of sheer laziness, and to leave room for other great authors I haven't read yet), but obviously there are many more that can be included. There are a bunch of other books that are some of my personal favorites, but don't, for one reason or another, quite have the timeless/universal quality of the books above:

The Road To Reality, Guns, Germs, and Steel, Ahead of the Curve, The Demon-Haunted World, Human Natures, The Triumph and Tragedy of J. Robert Oppenheimer, The Creationists (this is a really well-written book about people trying to cope with their faith and the progress of modern biology), This is Biology, Boltzmann's Atom, Silent Spring... - this list can go on for awhile.

My favorite science book published in 2006 was Nicolas Wade's Before the Dawn, about human evolution. Wade is a skilled writer who can effectively convey scientific content in accessible language. On the downside, I don't think this book does enough to distinguish hypotheses and speculation from widely accepted scientific conclusions, always a tough issue when you're describing science at the frontier of a given field.

There's a lot of good stuff to read out there.

UPDATE 12-4-06: I forgot to include one major book that should have been on Discover's list: The Eight Day of Creation, by Horace Freeland Judson (1979) This is one of the most insightful histories of science. It deals with the molecular biology revolution, and is full of excellent material about how the founding molecular biologists chose their questions, thought about them, and largely solved them. There is no better book on molecular biology.

Sequencing technology and the Neanderthal Genome

You've probably read about the two recent papers in Science and Nature reporting the sequencing of portions of the Neanderthal Genome. (Subscription required for full text of the Nature and Science papers. Check out Google for the many news stories on this.) This is exciting work, but I'm not really going to comment about the signficance of the results - I think it's worth understanding how new sequencing technology enabled researchers to sequence 1 million bases of 38,000 year-old DNA.

Each group used a different sequencing technology, and as a result, their coverage of the genome differed widely: the Nature group got about 1 million base pairs of sequence, while the Science group got about 65,000 base pairs. (Recall that the human genome contains about 3 billion base pairs, and the Neanderthal genome was undoubtedly similar.) The Neanderthal genome is a challenge because, obviously, any DNA remaining in the 30,000-40,000 year old bones we have is highly fragmented, and the amount of contaminating DNA from microbes (not to mention scientists) is significant. To eventually cover the entire genome, we need a method that can generate lots and lots of sequence without being prohibitively expensive.

The Science group used a more traditional method, which works well for most large-scale genome sequencing efforts, but is not really well-suited for getting huge chunks of Neanderthal genome. As a result, this group obtained only 65,000 base pairs of DNA sequence (which is still a significant accomplishment.) The big problem with this method is that the fragments of DNA isolated from Neanderthal bones have to be cloned before they can be sequenced. (In layman's terms - the DNA fragments have to be placed inside circular pieces of DNA called plasmids, which can be then grown in large quantities inside bactieria.) Many fragments of Neanderthal DNA fail to be cloned at this point, meaning that you lose much of the sample that was painstakingly isolated from the ancient bones.


The Nature group used something called pyrosequencing, which is done on machines called 454 sequencers. Crucially, this technique does not require a cloning step, which means much more of the isolated sample gets sequenced. Pyrosequencing also produces lots and lots of sequencing data very quickly. (One major downside is that each sequence is much shorter than what you get using traditional Sanger Sequencing, by a factor of ten at least. But in this case, the Neanderthal DNA fragments are so short this doesn't matter.)

You can read a really nice explanation of how pyrosequencing works at 454's web site. (For more technical coverage, look here.) Without this technology, a Neanderthal genome project would not be feasible. With this technology, we can now consider all sorts of sequencing projects that would not have been financially or technically feasible before - not just Neanderthal sequencing, but also large scale studies of gene varation in natural populations, including humans. Such large-scale sequencing could help up close in on the genes involved in complex diseases.

I said I was going to talk about sequencing, but I can't resist making a plug for completing the Neanderthal genome. It's interesting to learn about the changes in the genome that took place during evolution, but it's also extremely useful to have a more closely related genome as we try to find and understand the functional portions of the human genome. Having multiple genomes of close species has helped enormously in flies, worms, and yeast (for examples, check out this, this, and this). As is usual in almost any genome-level study of human biology, you can't get far without using an understanding of evolution.

Where did all these scientists come from?

It's no secret that it's now more difficult than ever to get funded by the NIH, in spite of the fact that Congress doubled the NIH budget between 1998 and 2003. Researchers have been frustrated and wondering, over coffee and in print, where all the money has gone.

NIH director Elias Zerhouni explains what's going on in the November 17th issue of Science. Grant applications have nearly doubled since 1998 - from 24,151 in 1998 to an expected 46,000 applications in 2006. And this isn't just because individual scientists are applying for more grants - in 1998, 19,000 scientists applied for grants, while in 2006, there were 34,000 scientists who applied.

Where did all these people come from? (I should note that I'm one of these people - I just submitted my first NIH application this summer.) When Congress announced its intention to double the NIH budget, universities started expanding - adding new graduate programs, hiring new faculty, and building new core facilities. All this happened amazingly fast, and now we're feeling the crunch. It doesn't help that the NIH budget hasn't kept pace with inflation since 2003, but Zerhouni presents the numbers that lay to rest other explanations for the funding crunch that have been tossed around - such as an excessive investment in large clinical trials or big, Manhattan project-style science at the expense of smaller, innovative projects initiated by individual researchers.

Is this a good thing? The down side is that with more people we'll get more fraud, more mediocre science, and more fragmentation of the scientific community. It's already barely possible to seriously keep up with the literature in one's own field - which means it will be harder to find people on review committees who understand each other. It's much, much harder for a young investigator to get started - in the past, scientists in their 20's and early 30's have been among the most innovative and creative scientists, but young scientists today have their motivation and creativity squashed by the high barriers to independence, barriers which are only overcome when some of your best years are over with. Sure, older scientists are still damn good researchers, but if the start of your scientific career is creatively stunted, it can hobble your thinking later on.

In spite of these drawbacks, the fact is that there is still a hell of a lot of good scientific work to do, even if all of it isn't the most pathbreaking or innovative science. There are a lot of useful details to be worked out, enough to keep people busy for a long time. Money invested in new scientists will be money well spent - much more well spent than much of billions of dollars we lost in the attempted reconstruction of Iraq, money which did more to enrich the already bloated pockets of Dick Cheney's friends than it did to benefit the Iraqis.

The investment in research infrastructure made by US research universities and biotech companies in recent years has helped keep the US at the forefront of an increasingly competitive world-wide scientific community. If we want to stay there, we need to pay for it.

As Zerhouni put it:

"Since 1945, United States success in scientific research and development has been the result of the implicit partnership that exists among academia, the federal government, and industry. In this model, research institutions take the risk of building and developing our national scientific capacity; the federal government, through a competitive peer-review process, funds the best science; and industry plays the critical role of bringing new, safe, and effective products to the public. This strategy is the keystone to sustaining American competitiveness, and must be preserved."

How should we teach our kids math?

The NY Times is reporting on the lagging math skills of US kids and efforts to change, yet again, how we teach math. I'm sympathetic to the desire to teach math in a way that doesn't turn people off. Too many people (including some people who grow up to be biologists) go through their education feeling very, very insecure about their ability to do and understand math.

What's tough about this problem is that you just can't teach the concepts and let kids figure out for themselves how to solve the problems. Understanding is good, but in math, understanding is not a substitute for the ability that comes with lots and lots of practice. This is different from many other fields of study, where if you understand the basic ideas and arguments you can work out a lot for yourself. To actually do math well, you need regular, sometimes mind-numbing practice - you can't just reinvent the wheel (i.e., derive your results from first principles) every time you need to solve a problem.

Gaining proficiency in math is similar to being able to do the NY Times crossword puzzle or play arpeggios on the piano - you simply need a lot of repetitive practice. You may know what an arpeggio is, but that's different from being able to play them over the entire keyboard, in all major and minor keys at a fast tempo.

Just like with the piano, kids will like math more when they are actually reasonably good at it. And there is no reason that most kids can't be fairly good at the kind of basic math we'd expect every educated person to know. Our teaching needs to reflect that - it's good to encourage understanding, but proficiency will never come without plenty of practice.