The Futile Cycle

This morning I came across a short blog post that talks about pollution and environmentalism; the first sentence just irritated me:

The theory of evolution describes life forming and emerging billions of years ago from the slimy shores of a chemical soup.

This is not the theory of evolution. The origins of life are a completely different topic! Basically, evolution assumes that life already exists, somewhere, somehow, and describes how one species change over time. Evolution explains why bacteria and humans fundamentally share some similar biology, it explains why mitochondria look like bacteria, and it explains the diversity of traits within and between species. It does not talk at all about where life came from.

Origins of life studies are much harder and more controversial than evolution, basically because we have to speculate about things like the composition of the Earth billions of years ago, how likely life is under those conditions, and so on. For evolution, we have solid evidence, experiments, and well-thought-out quantitative predictions, regardless of what the “intelligent design” folks like to claim. For origins of life studies, mostly these are missing, save for a few prominent experiments (prominent because, well, there really aren’t that many, and so the couple that we do have get a lot of notice).

The theory of evolution is not controversial to those who know what they’re talking about. Theories of life origins are quite controversial. Very different.

Nature has published online some of the most prominent scientific breakthroughs that they’ve published in the last century, and the subjects span archaeology and biology to physics and astronomy. They’ve released for free commentaries that explain the significance of the accompanying papers.

I particularly enjoyed Ginés Morata’s commentary “The blueprint of animals revealed” (PDF), which explains Christiane Nüsslein-Volhard’s and Eric Wieschaus’ extraordinary paper in fruit fly genetics, for which they, along with Ed Lewis, received the Nobel Prize in 1995.

Also making an appearance is Sydney Brenner’s commentary on Watson and Crick’s double helix paper (PDF), which gives a short history of the context for the discovery, and how much it was overlooked at the time.

These days, the papers just make up little boxes and such in textbooks, and it’s hard to really appreciate the time and effort that went into these discoveries. Nüsslein-Volhard and Wieschaus, for example, screened thousands upon thousands of matings to get their short list of genes! Flies ain’t bacteria, and screening mutations in flies – especially embryonic lethal mutations that have to be maintained heterozygously in diploid – is a lot harder than looking at a plate of colonies, that’s for sure!

Happy Holidays to all of you. And to those of you still in lab over the holidays, cool (and gross) seasonal Petri dish art! (h/t Miya)

Via Marginal Revolution, apparently Harvard has a policy for Ph.D. students, which is that for every 5 graduate students in their eighth or higher years of a Ph.D. program, the department will lose a slot for new admits. This is a great idea! No Ph.D. student needs to take longer than 8 years, and this policy makes sure that professors are motivated to keep the pipeline flowing instead of simply accumulating students.

The film adaptation of No Country for Old Men is the Coen Brothers at their finest.

It reminds me of Harold Bloom’s reaction to Blood Meridian: he started reading, threw it across the room because he was so angry at how violent it was, picked up, finished, and proclaimed it the greatest modern American novel.

“No Country” was one of the most brilliant, but also one of the most sickening, films I’ve ever seen. When the credits started rolling, I felt tired, overwhelmed, and wrung out. The film reminds me of the end of The Mission, where Father Gabriel tells Rodrigo that he isn’t strong enough to live in a world in which violence is the right answer. Except in this case, there is no question, there is just violence. Though the film did have its black humor interludes, one only laughed because, as the sheriff says at one point, what else can you do? The humor here is blacker than Fargo; in fact, the tone of the film is really Fargo with all the happiness sucked out of it. No happiness and no relief.

(spoilers follow)
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One things that still astounds me is how fast the field of biology changes. If one looks back even just ten years, the human genome was yet to be sequenced (as was the genome of a vast number of organisms), and microarrays were just being invented. Lester wrote recently about how medical knowledge gets obsolete every 5 years, but individual fields in biology and medicine move much faster than that, and the pace is only growing faster.

Even in the past year, the number of things that I’ve learned that have gone out of date is pretty amazing, especially on the fundamental ways in which life works. For example, my knowledge of RNA export, the basic redundancy of duplicate ribosome genes, and the “fact” that miRNA downregulates translation, have all become obsolete, even though just last year, I took a class on the regulation of gene expression that incorporated all the latest research in the field. Actually, this isn’t the advancement of the field in the last year; it’s the advancement of biology in the last month!

I have no idea how professors manage to keep up with the changing face of biology year after year after year! Just think about all the scientists around who lived before the days of BLAST, PCR, and PubMed, to list three tools indispensable to any working molecular biologist.

The fast pace is exciting, though! Research science is like white-water rafting through through a river of knowledge; the challenge here is to keep from drowning!

Apparently, now more people live in cities than in farms. Via the Freakonomics Blog, this is, according to Ed Glaeser (and I agree with his massive intellect), a Good Thing:

A central paradox of the twenty-first century is that declining communication and transportation costs have made cities more vital than ever. In the developing world, cities are the intellectual gateways between the human capital of India and China and the markets of the West. In the developed world, cities have enjoyed a remarkable resurgence over the last 25 years as the density that once made it easier to move hogsheads onto clipper ships now serves to spread knowledge in finance and new technology. Globalization and the death of distance increased the returns for being smart, and you become smart by hanging out with smart people. As such, cities remain important because they create the intellectual connections that forge human capital and spur innovation.

….

Humans are a social species, and our greatest achievements are all collaborative. Cities are machines for making collaboration easier. Thus, I am delighted that our planet has become increasingly urban.

I love cities. I’m currently living in a giant, semi-rural-ish suburb with farmland five minutes from my room. I do love the green, massive trees that bury my university, especially during the fall when it all turns a spectacular gold, and I love having star-filled nights, but I also miss the bustle of people, the soaring skyscraper skylines, having friends, family, and fun in walking distance, and just the sheer energy that comes from the city.

Not to mention all the brilliant science that was happening in Boston. My department is great, but there are just so many more people in Boston doing science; there are always exciting talks to go to and new discoveries coming out just down the street. I miss that very much.

In an interesting paper by John Hawks which has been making waves, HapMap studies have found that the evolutionary rate in humans has accelerated over the last 40,000 years or so, starting from the middle of the last Ice Age which ended about 10,000 years ago.

Pretty cool stuff! John Hawks has a pretty brief explanation on his blog, but Razib has a much more extensive explanation at Gene Expression which helps to tease out the population genetics involved in understanding the HapMap human genetic variation data.

Human population genetics is an amazing thing, both for medicine and for understanding our societies. Anthropology of this kind is cool!

I recently came across this section from Current Protocols in Molecular Biology on gene expression analysis of a single or few cells. I was intrigued, so I skimmed it a bit. There is one conclusion I came to: the only molecular biology technique more painful than RNA extraction from cells is RNA extraction from one cell. Consider:

Contamination can be reduced by working under a laminar-flow clean bench that has never been exposed to PCR-amplified DNA or cloned DNA, and that is preferably located in a room apart from laboratories where DNA is handled…Unfortunately, contamination might still occur since many enzymes (in particular, reverse transcriptase) contain traces of bacterial DNA/RNA that will be co-amplified with the desired single-cell mRNA….RNase inhibitors are not added because they are frequently derived from human placenta and might therefore be contaminated with human nucleic acids.

Gosh, I hope I never have to do this (knock on wood).

I’m excited to be starting my next rotation on Monday! I just found out today that my next lab is one that studies quiescence, which is basically how cells in our body “hibernate” until they need to wake up to do something. In high school biology, you might have learned about mitosis, where cells copy DNA, separate out the chromosomes, and divide to create two new cells. Well, cells aren’t always constantly dividing, and there’s a specific “hibernation” state (called quiescence) that cells go into when they aren’t needed. Fibroblasts hibernate until you get cut, at which point they start responding to the wound by dividing and turning on genes that help with healing. I’m very excited, as I’ve never worked with mammalian cells or tissue culture before. It’ll be an experience, and hopefully really productive!

I really enjoyed my last rotation, which was in a yeast cell biology lab. I did a lot of microscopy to find out some mechanisms by which yeast cells have sex. I don’t want to get into the specifics too much, but basically no one knows how the specific mechanisms of yeast sex happens, especially how the two cells fuse together to become one cell. It was a really great project to start with this year, as it involved some very basic biological techniques, it wasn’t too hard, and I was able to start generating data right away while working on other side projects that were harder and riskier.

So overall, am I happy in graduate school? Yes, I think so. I’m learning a lot, which I always find awesome, I’m discovering new stuff, which is neat, and there’s something quite satisfying with the bench work in biology.