The Futile Cycle

The internet allows people to produce some amazing things. Go see! Twitter as it was meant to be seen.

Every two weeks, I look forward to my copy of Cell (yes, I’m a big dork that way). This week, I found Cell had a really surreal cover: a drawing of a phoenix.

Curious, I turned to look at the cover description. It was, to say the least, quite cheesy:

Cover art…depicts CASK kinase as the Phoenix, presumed dead in the fires of evolution, resurrecting in an unanticipated active form.

A little purple much? It was apparently drawn by the second author of the corresponding paper. A good drawing…but “cheeserific” symbolism (to quote a friend of mine).

Another cheesy cover I saw a while ago was this Nature cover, hearkening back to pulp science fiction:

Awesome retro-nerd-ness!

Sorry for the lack of posts, but alas, science (especially biology) does not wait, and things die when neglected.

Meanwhile, I have around three weeks left in my final laboratory rotation before I have to choose my thesis lab, and I’m having a hard time deciding. Coincidentally, Nature Reviews Molecular Cell Biology just published a two-part article called “How to succeed in science: a concise guide for young biomedical scientists.”. There are some interesting tidbits in here, and it gives an interesting, biology-centric perspective on how to look on one’s career. Part I is focused on choosing a field and a lab for graduate school and post-doctoral work. Part II focuses mostly on how to generate ideas and make discoveries. I thought both were excellent reads.

I also recently found Dent Cartoons, which is the home of the famous Nine Types cartoon trilogy. Check it out; very amazingly true!

Dr. Free-Ride over at Adventures in Ethics and Science has written a post on a topic near and dear to my own heart: the boundaries between science and belief. Her position is that there is no conflict in the mind of a scientist who believes in a supernatural deity. It’s a topic that I’ve been mulling over for the past 10 years or so.

In some ways, it is very easy to fall into the strict regime in which “if one believes that the scientific method leads to truth, that is the methodology to be applied in all beliefs of truth, public and private.” I think many scientific atheists hold to this sort of belief very often.

There is, of course, that very crucial “if” in that sentence that many philosophers will jump on. Does the scientific method lead to truth, exactly? Maybe not. No truly introspective scientist says that they know the entire truth; all we have are models that work well enough. Where does the photon “go” when it’s absorbed by an electron? Well, we don’t know; we don’t even really know what “absorbed” means, but as long as we do good bookkeeping on the energies and momenta of all the particles, it seems to work out pretty accurately, at least as far as we can tell.

In addition, can I know that my senses are the same as others’? What makes a schizophrenic’s reasonings about the truth of the world less “true” than mine? Does the fact that I have to wear glasses make a difference on my conclusions about how something looks? So truth is, perhaps, more a social construction, especially truth based on scientific observation. “Truth” needs to be verifiable to someone else, and based on some standard that others can replicate, not based on my unique, idiosyncratic senses.

But I feel something fundamentally wrong with simply saying that the scientific doesn’t lead to some sort of generation of knowledge. After all, the keyboard under my fingers feels real enough. I can hit it with other things, to ascertain its existence. Is the possibility that I’m some sort of “brain in a vat” really going to bar me from asserting the truth that my computer exists? Though Dr. Freeride might characterize my belief in the reality of the world I sense as a scientifically unjustifiable metaphysical commitment, can it really not be? Am I not justified in asserting that the world is real until I have reason to believe it’s not? (Being unplugged from the Matrix might do it.)

Is there, then, truth other than this sort of knowledge?

From Uncertain Principles comes this gem of a sentence:

My opinion, in the end, is that a lot of what people find objectionable about fraternities and sororities is not an inherent property of the organizations, but rather an emergent property of large groups of 18-22 year old Americans.

A lot of news stories are once again talking about breakfast and its connections to weight and obesity. Consider this BBC article as one example. This Reuters article hypes breakfast as magically keeping teens skinny. The original Pediatrics journal article is here.

What’s wrong with all of this? The research doesn’t say whether eating breakfast makes someone lose weight. All it says is that skinnier teens eat breakfast more often than more obese teens, on average. That doesn’t mean that suddenly eating breakfast more will make you lose weight.

Consider, these details in the paper. People who eat breakfast more also: “more likely to be white, to come from a higher [socio-economic status], and to engage in higher levels of physical activity.” Hmmm, breakfast-eaters do more exercise, huh? I wonder if that has anything to do with the difference in weight…hey, will eating breakfast also make me white and wealthy? Awesome!

Sure, the authors try to correct for the physical activity differences in their regression, but no regression is perfect, and since all of the data is essentially self-reported, it’s hard to tell whether hours spent per week in “strenuous, moderate, and mild exercise” is really a good reflection of lifestyle choices. Maybe they take the stairs more often, or bike and walk more than those who don’t eat breakfast. Is running a mile moderate, strenuous, or mild exercise?

In addition, there are the classic correlation-versus-causation arguments: perhaps people who eat breakfast are just those who tend to have a higher metabolism naturally, and so they have the energy in the morning to get up early enough to eat breakfast. Or perhaps breakfast eaters are just more conscientious of their life choices, including sleeping, planning ahead, being less stressed, and so on, which might contribute to their lower BMI. Their eating breakfast in the morning could then be just one more symptom of their conscientiousness.

Though this article was published in the journal called Pediatrics, really this is just a sociological or economic study, not a medical study. Researchers and the news should stop hyping it as some sort of recommendation for preventing obesity. Breakfast isn’t a therapy just yet.

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Timlin, M.T., Pereira, M.A., Story, M., Neumark-Sztainer, D. (2008). Breakfast Eating and Weight Change in a 5-Year Prospective Analysis of Adolescents: Project EAT (Eating Among Teens). PEDIATRICS, 121(3), e638-e645. DOI: 10.1542/peds.2007-1035

There are two interesting new papers out in the newest issue of Molecular Cell, and one from Science a week back that’s online early:
An Important Role for the Multienzyme aminoacyl-tRNA Synthetase Complex in Mammalian Translation and Cell Growth: Seems that the two different forms of Arginine tRNA synthetase have different roles in the cell, one to make tRNAs for synthesizing proteins, and to make tRNAs for degrading them via the ubiquitin pathway!

Human Alu RNA is a Modular Transacting Repressor of mRNA Transcription During Heat Shock:
Non-coding RNAs have been shown to have transcriptional regulatory properties, but this particular paper discusses one that looks a lot like a protein, in the sense that it seems to have modular “domains.” Pretty neat work!

Selective Blockade of MicroRNA Processing by Lin-28: The main discovery of the paper is, of course, nicely summarized in the title. The idea is that Lin-28 prevents the biogenesis of let-7, one very well-studied (though not well-understood) family of microRNAs, by binding to the RNA and preventing Drosha and Dicer from gaining access to it.

Day to day, I work a lot with clear, colorless drops of liquid, shuttling them back and forth between small plastic vials. I also work with cells, but they just look like cloudy suspensions in strange-smelling liquids.

But every time I look at cells under a microscope, I can’t help but gaze in wonderment. Cells! Under a microscope!

Even better are images and videos online from the American Society for Cell Biology, which I found via Bitesize Bio. Make sure to check out the videos, some of which are absolutely spectacular and inspiring. Some of my favorites include watching rat heart cells beating in a Petri dish, seeing fish cells zooming across slides (especially check out how fragments of cells without a nucleus can still move around! Movement is thus, at least in the short term, independent of transcription), the movement of mitochondria within a cell, seeing chromosomes divide in real time using just light microscopy, and watching Drosophila embryo syncytial division (where all of the nuclei divide simultaneously, without cytokinesis).

Biology is an absolute wonder, and I hope you find these videos as inspiring as I do.

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

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!