The Futile Cycle

Since when do universities write press releases for review articles? Is it really necessary?

Via Pharmalot, apparently Pfizer is going to court to try to force the NEJM to release its confidential reviews of articles on Celebrex and Bextra, two of Pfizer’s products that have been targeted for lawsuits on their side effects.

Now, I’m not saying either way whether Pfizer is guilty of misinformation and such on Celebrex and Bextra, but this subpoena is just wrong. The scientific peer-review process has traditionally depended on confidentially to ensure candid and honest statements about the quality of research without fear of repercussions or retribution. It’s not perfect, but it’s sure a hell of a lot better than going without a peer-review system, and trying to break the confidential review system is like trying to force journalists to open up their sources. It stops the flow of good journalism, and it stops the flow of proper science.

Pfizer isn’t doing itself or the rest of the drug industry any favors, either. For whatever reason, people hate drug companies even more than they hate other companies (except maybe Big Tobacco), perhaps because they think that drug companies are evil machines sucking money out of sick and desperate people. That’s not true, and there are many noble people, including doctors and scientists, working hard out there in the drug industry to find the latest drugs to help people, but these kinds of antics from the top are just awful. I don’t envy the researchers at Pfizer, as they don’t deserve society’s scorn for all of this.

Lately, genome-wide association studies are popping up everywhere. Just scanning through the latest Nature Genetics, almost half of the articles are such linkage studies. The studies represent one of the greatest convergences of population genetics, fundamental molecular biology, the human genome project, the HapMap project, disease biology, and microarray technology.

Leonid Kruglyak has a great review article out in Nature Reviews Genetics on the history and development of such genome-wide studies.

I think these kinds of studies will eventually have the potential to revolutionize medical diagnostics and drug therapy, since it’ll become easier and easier to figure out risk factors for disease and tailor drug therapies to the specific risk categories a patient falls into. I’m really excited to see how this field progresses, especially when newer technologies arise for rapid sequencing of genomes!

I was sitting in my lab reading through the PNAS early online publication articles when I come across a letter to the editor with the title: “Going beyond the genetic view of cancer.” (PDF) Intrigued, I read it, and to my horror, I find a letter filled with words like this:

Dynamic protein-based phenomena–for instance, (insulin-driven) “oncoprotein metastasis” explicable by an extension of physical string theory into (sub)cellular biology…

The fact that the author (a one “Razvan Tudor Radulescu”) cites an arXiv “pre-print” that he wrote himself is quite suspicious. His contact information, of course, is with non-institutional, free email address.

To me, this can mean only: HE’S A CRANK.

What is PNAS doing publishing letters from cranks? I get spam in my email from this gentleman in Nicaragua, should I publish those in a journal, too?

Perhaps I’m leaping to conclusions. Let’s take a look at the arXiv pre-print, which would be more fleshed out than a single letter to the editor:

Here, a new scenario is put forward on the spreading of the neoplastic process across cells and tissues that may prove seminal both for our future understanding and treatment of malignancies.

First sign of crank-dom: exceedingly high opinion of one’s own work, describing it as “seminal.”

In this context, my peptide string theory (10-12) is likely to represent a significant addition [to the field]. It rests upon the assumption according to which major biological processes concerning distinct, yet related proteins are the result both of (long-distance) attractive forces in the sense of the physical string theory (13,14) and of “emergent properties” inherent to the same proteins whereby the term “emergent” is to be understood as employed by John Searle in his book entitled “The Mystery of Consciousness.”

The sentence continues, but the point is rather obvious. Crank. What are the citations to? Let’s see…citations 10-12 are self-citations (one to yet another arXiv preprint). Citation 13 is to a popular science book, The Elegant Universe, and citation 14 is to an editorial by Ed Witten.

Now, I’m no expert in string theory, but I doubt that these second two works have much biological insight to offer. String theory, after all, is about understanding how all the various laws of physics might be unified. Sorry, but general relativity? Not all that relevant to what goes on in the body, since biology doesn’t really go near the speed of light. Quantum mechanics is more related, in that it’s the foundations of chemistry and of molecular-level phenomena, but even then, we’re not pushing the boundaries of our knowledge of sub-atomic processes in looking at biology.

Why is this letter being published by PNAS? All I know is, this kind of stuff makes real scientists look bad. Does the National Academy not vet letters to the editor before publishing them?

Pure Pedantry links to an awesome paper on visualizing the cell cycle in mice using fluorescent markers. They can even look at the cell cycle state of cells in histological sectionsof mice! Check out the blog post, because Jake Young highlights the coolest picture and the coolest video in the paper; the movie at Cell and ScienceDirect seem to be down, so you can see the video at Pure Pedantry or at Google Video.

One of my biggest fans got me a copy of The Eighth Day of Creation, which I’d been wanting to read for some time now. In the first chapter, check out this old-timey maxiprep (i.e. large-scale DNA isolation and purification) protocol, courtesy of Avery, MacLeod, and McCarty from their historic 1944 paper demonstrating that DNA was the carrier of genetic information in cells:

To get [DNA], they grew virulent Type III pneumococci at blood heat in twenty-gallon vats of broth made from beef hearts, spun out the bacilli in an iced centrifuge, suspended them in brine, and brought the “thick, creamy suspension of cells” quickly to a temperature hot enough to kill the cells and to inactivate “the intracellular enzyme known to destroy the transforming principle” [DNase]… They then washed the cooked pneumococci in three changes of brine to remove capsular sugar as well as whatever protein would come away, extracted the bacteria by shaking them for an hour in a solution of bile salt to break the cell walls (and then threw away the cell residue), and reprecipitated the extract with pure grain alcohol.

“The precipitate forms a fibrous mass which floats to the surface of the alcohol and can be removed directly by lifting it out with a spatula,” the paper said. This was now washed several times with chloroform to remove protein, and suspended yet again. A digestive enzyme was put in to eat away any remaining capsular sugar. Removal of protein was repeated, “until no further film of protein-chloroform gel is visible at the interface.” Pure grain alcohol was added again, “dropwise to the solution with constant stirring.” At a concentration where the alcohol nearly equalled the extract, “the active material separates out in the form of fibrous strands that wind themselves around the stirring rod. This precipitate is removed on the rod and washed….The yield of fibrous material obtained by this method varies from ten to twenty-five milligrams per seventy-five liters of culture.”

Wow, and I thought maxipreps take too much time now! Compare the above to a more modern DNA isolation protocol, courtesy of Black Knight.

Reading back over the posts that I made for Just Science week, it seems like I had a theme going (unintentionally), which is that biology is a lot more random than most people seem to think.

For one thing, molecules don’t act like robots. They don’t whir and click into perfectly aligned machines that do everything smoothly. Molecules jiggle, they backtrack, they pause, they drift away, they snap apart, they even do things wrong. A lot. A ton of our evolution has been oriented towards controlling (or harnessing) the randomness of the molecular world in which we live. Though we speak in the language of determinism, that is simply a metaphor for a much more random reality. I think biologists sometimes do the world a disservice by hiding behind these deterministic metaphors.

On a larger scale, not everything in biology need be from adaptation. Evolution is quite random; it is a tree of historical accidents that has been pruned and shaped by natural selection.

Sometimes random is just random. Our bones aren’t white for a good reason; it just so happens that white is the color of the molecules and minerals in our bones. In the same way, I’ve tried to argue that some phenomenon in cell biology and molecular biology may just be historical accidents with no adaptational or functional meaning. I think that that should be the default theory for any phenomenon that biologists discover.

After all, if the intelligent design community is pushing for a default theory of a purely functional world, in which everything was specifically made by a greater being for a purpose, then (since they’re wrong) the default theory for real science is the opposite: the history of any species is a series of historical accidents, a tree grown with its roots buried deep in the rich soil of randomness.

I was rereading a classic paper by Francis Crick, the one in which he describes how they discovered the triplet nature of the genetic code. [Crick et al. (1961) Nature 192, 1227-1232.] It’s an absolutely fantastic paper – extraordinarily well written, clear in logic, and with no lack of charm – but this time through, something else caught my eye (emphasis added):

¹¹Feynman, R. P.; Benzer, S.; Freese, E. (all personal communications).

This, of course, refers to the rather famous Richard P. Feynman, the bongo-playing, womanizing theoretical physicist of quantum electrodynamics fame.

Apparently, Feynman took a summer off and did work on phage T4 genetics, specifically on the rII region. During his work, he figured that he was isolating multiple mutations in the same gene - a mutation and its suppressor. It’s neat that he was so close to getting to the fundamental nature of frameshift mutations, but alas, he returned to theoretical physics soon afterwards. Thus, it was up to another physicist-turned-biologist (Francis Crick) to discover the real nature of reading frames and the triplet code.

But in any case, a really neat historical crossover between fields.

I have yet to take my general exam (a.k.a. qualifying exam), which is what I need to pass in order to get to the next stage of my Ph.D. studies. Up until now, I’m basically a masters’ student, doing some research, taking classes, attending seminars, and basically learning my way around being a research scientist. After generals (assuming I pass…), my department expects us to teach and focus on completing my thesis.

I know some schools don’t do this, but in my department, the general exam is basically an oral exam — we present our thesis proposal, as well as one paper that is on a related (but different) field. The prospect of it frightens me to no end, but it’s still about a year away.

Of course, the main thing that I’ll be judged on is my science, but humans are humans, and since the exam is quite subjective, I’ve got to use every edge I’ve got, including improving my speaking skills.

At MIT, there’s a famous annual lecture given by Prof. Patrick Winston called “How to Speak.” This year, a blogger managed to take some notes from the lecture, for those less fortunate of us who don’t have a chance to see it. There are even some tips on speaking specifically for oral exams. I like this one:

3. Practice. Ask your friends to listen to your talk. Tell them to try to make you cry.

In an earlier post a two days ago, I mentioned that recently people have been speculating about the existence of “transcriptional factories”, because they saw that some genes might move to different parts of the nucleus when they’re turned on. They propose theories like this:

My answer: maybe nothing?

A new paper in Molecular Cell attempts to find evidence that genes don’t need to relocate in order to be activated; that is, it tries to disprove the notion of the “transcriptional factory.”

The problem with looking at how DNA is organized in the nucleus is that DNA is very small and hard to see, especially in a cell that’s alive (as opposed to killed, fixed, and stained with various dyes). DNA is invisible under a normal light microscope except when the cell is going into mitosis, when the DNA gets wrapped into chromosomes that get separated. Normally, though, the DNA is in this diffuse mass throughout the nucleus, and thus completely invisible.

The authors here get around this problem at first by using a trick called “polytene cells”; in the salivary glands of fruit flies, certain cells will accumulate a huge number of copies of DNA, leading to these really fat bundles of DNA called “polytene chromosomes,” which are actually visible under a microscope! The cool thing is that these chromosomes have different densities along the DNA, causing it to have distinctive stripes. Biologists can use these stripes to figure out where genes are on chromosomes, and then follow those genes by sight!

Here’s a picture of polytene chromosomes from that paper:

Another neat thing is that when genes turn on in polytene chromosomes, the bundle of DNA opens up to let proteins bind and start reading the gene sequence, causing the chromosome to “decompress” or “puff” (and thus become invisible). The authors here track the puffs with the labeled RNA polymerase II in order to see where heat shock genes go in the nucleus when they are turned on.

In polytene cells, the authors couldn’t find any sign that the heat shock genes moved around a lot, and the genes that did respond to heat shock did not move to the same place. But these are polytene chromosomes; maybe in normal diploid cells, that doesn’t happen?

So the authors also use “FISH” (fluorescent in situ hybridization) in order to see where specific genes are located in normal, non-polytene cells. Basically, one takes a piece of fluorescent DNA and sticks it into a fixed cell, hoping that the piece of DNA will base pair with its complementary partner DNA inside the nucleus. Using this, the authors saw very little change in the location of most genes when they turned on, although one gene did move a little.

Thus, the authors don’t find, at least for heat shock genes, that it’s necessary for them to move around the nucleus in order to get transcribed. In the end, perhaps the aggregates of proteins and such in the nucleus are just that: aggregates.

The simplest explanation may sometimes be the best one, even if it’s a little boring. I’m excited to see how the research in this field develops, and whether this paper turns out to be horribly wrong (it can happen to the best of papers), or whether the idea of transcriptional factories becomes outdated.

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Yao, J., Ardehall, M.B., Fecko, C.J., Webb, W.W., Lis, J.T. (2007). Intranuclear Distribution and Local Dynamics of RNA Polymerase II during Transcription Activation. Molecular Cell, 28(6), 978-990.