Saturday, November 16, 2013

What is the best text editor?

Ah, why a post on this, when there are probably already something like 17,000 posts being written on the topic at any given time? Well, it’s a topic we often debate in lab, usually as a cool down from some protracted Python vs. MATLAB vs. Perl vs. R argument. Gautham likes vi, as do many programming junkies. I used to use Emacs for a while, then migrated to a little known text editor called Smultron, and now I use some combination of the IDEs incorporated in MATLAB and R and TextWrangler for everything else. And you know what? It works! I can actually edit text this way! I can save the changes, and the run the program! Amazing. What’s even more amazing is that virtually every text editor does this. The conclusion I came to is that it just doesn’t much matter how many fancy key codes your editor can handle (looking at you, Emacs!), nor how complex or simple the interface is (to a point, and once you get used to it), because unless you’re working with punchcards, your programming is much more likely to be limited by your mind than your choice of text editing program. I used to think more about text editors back when I was in graduate school, and I remember one day stopping by the office of Boyce Griffith, who is one of my academic “brothers” (i.e., we had the same advisor). Now, Boyce is one of the most incredible scientific programmers I’ve ever met, having written literally millions of lines of hard core C and C++ to implement very complex simulations of fluids, including these amazing simulations of the human heart. I saw Boyce was programming away using some fairly primitive text editor, and I was like “Man, you don’t use Emacs or something?” Boyce said “No”, and I said “Why not?” and he said “Whatever, it doesn’t matter.” Amen. In the end, I think the best text editor is, you know, one that edits text.

Tuesday, November 12, 2013

some thoughts related to "The Frustrated Gene: Origins of Eukaryotic Gene Expression"

- Gautham

Chris forwarded this interesting essay to the group:
The Frustrated Gene: Origins of Eukaryotic Gene Expressionby Hiten D. Madhani.

The arguments are not airtight, but how could they be anyway? A friend of mine has said that these efforts are necessarily a connect-the-dots exercise with the dots spread very far apart. It is not at all easy to figure out how these ancient devices came about. Nevertheless, the presented idea that the complexity of gene regulation was created to temporarily ward off selfish DNA makes more sense than it having arisen primarily to actually enable complexity. I think that the perspective still leaves open the possibility that we've kept all those adaptations because they do enable complexity, but I am nowhere near qualified to judge that for sure.

What is clear is that looking at every aspect of gene regulation in eukaryotes and thinking that it has to create a net benefit to the organism at the present, rather than maybe resulting from a prior bottleneck, a prior arms race with a parasite, or even the defeat at the hands of a parasite, may be a mistake. It is terrifying how natural selection is rather helpless in preventing the spread of even damaging transposons in a sexual population. Biology is supposed to make sense in light of evolution, but it may be that no organism may make sense if we require it to be in all aspects evolutionary optimal.

I recall one of Marc Kirschner's book saying that it was at the time an ongoing embarrassment to evolutionary biologists that they don't have a solid explanation for why sexual reproduction is advantageous. They give us the simple story that it enabled complexity and evolvability, but they themselves are not convinced that the numbers work out, or at least they weren't a decade or two ago. It is hard for us to even make a case for sexual reproduction, and yet some of us are losing sleep trying to explain things like apparent gene redundancy.

It is possible that us larger eukaryotes at least operate in too big a variety of circumstances, and perhaps we compete more on the basis of behavior than on the basis of physiology. Perhaps our environment changes too rapidly, and we reproduce too slowly, to allow us to reach our biochemical evolutionary pinnacle. I've been watching "The Life of Mammals" series from BBC. It seems far easier to explain the extraordinary diversity in behavior and shapes of animals on evolutionary grounds, than it is to explain even basic things like their wildly different DNA content.