notageek

And it’s almost dead week again. The air is full of pollen. My eyes are hot and dull, dark and weepy; my head is full of thermodynamics.

Yesterday I stood up and talked about co-adaptation of gene complexes, antibiotic resistance and the improbability of descending an adaptive peak. I did not faint, but I did note that we’re seriously screwed on the antibiotics front, and I might post notes later.

I am rushing up against the end of everything–this term, this degree, this era of triumph over pathogenic microbes–and when I think about it I would love to believe in the teleological ends of evolution the physicist proclaimed last night.

Then I think about the stability of antibiotic resistance, and 30-year studies of darwin finches, and widow bird tails, and the adaptive significance of infanticide. What god we want is not in evolution, nor yet illumined through this mode of inquiry; this joy of symmetry, evolution and moleclar movement is to be found in Mycobacterium leprae as much as in humans, as much in adaptive infant abandonment as in tender extended parental care. To call it beauty or joy, actually, is probably a profound mislabelling, and a subset of the naturalistic fallacy.

Biological systems are so, and function so, and change at certain behest; to draw religious conclusions is dangerous, and does a disservice to the literature. I do not know if the stars sing in their courses, or the atoms we split cry out, but such songs have no relevance to evolutionary concepts of “Nature”–not red in tooth and claw, not loving and benevolent, but utterly changeable, and still alive.

Usually there’s a lot to be gained by cross-pollination. Sometimes, though, the structures just appear to be too specialised, and then the audience goes home thinking that people should stick to their own fields. Tonight I listened to a physics professor

• expound on the ends towards which evolution is progressing

• argue from a naturalistic fallacy
• state that the main form of selection on organisms is at the species level

I was willing to entertain the “quantum wave of possibility” collapsing with a decision. But then he talked about the use of child past-life recall and other past-life regression data as evidence for reincarnation, and I could feel my mind snapping shut. Right about the time the guy in the beard stood up for the third time to talk about UFOs.

Ok, so you hate going to the gym. Fair enough; it’s full of sweaty people who are thinner than I’ll ever be, and people who sit on the weight machines between sets, and there’s no curtains on the shower stalls.

That’s nothing new. If you really like climbing stairs to nowhere, or lifting random heavy objects, it’s a small price to pay, I guess, but remember, when you hear that nobody looks at you when you’re naked in the locker room, IT’S A LIE.

I’m sure there’s people who don’t; I’m sure most people try to not be obvious about it. But the lesbian and bi girls are probably checking you out, the women younger than you are are wondering how well you’ve aged, and everybody–for values of everybody that are “me”–is comparing her body to somebody else’s. On snarky days it’s a competition thing, but mostly it’s just to see.

What I have learned:

• It’s pretty uncommon to have a genuinely ugly ass.

• even women who look great in snug workout clothes don’t look much like porn stars in the shower
• “great” has a much broader definition than you might think
• other people DO pee in the shower

If I have scared you, remember that

• You don’t have to get completely naked when changing

• You can take a perfectly good shower without exposing any under-swimsuit bits besides your bum
• after so many years of checking out other women’s bodies, we probably won’t look for very long
• clean fluffy socks after a workout can remedy any number of minor indignities

“This” being my argument that any selective advantage noncoding DNA regions confer is not because they sop up mutations due to faulty copying mechanisms.

Suppose two genomes of length L1 and L2, in base-pairs. Suppose a mutation rate r, in mutations/bp–say 1/n. Suppose that the composition of L1 is C, a coding region of length L1, and that the composition of L2 is a coding region of length C and a noncoding region of length N.

L1=C
L2=C+N

The mutation rate for each genome is constant at r. The number of likely mutations in L1 is

r*L1 = r*C = C/n

number of likely mutations in L2 is

r*L2 = r*(C + N) = r*C + r*N = C/n + N/n

in either case, the number of mutations likely in the coding region is constant.

The argument made in class was that a genome with no noncoding material is guaranteed to have any mutations happen in a coding region. Ok, duh. That then proceeded to “so a genome with some noncoding material might have the mutation happen in a noncoding region”, and i think that’s bunk. Here’s why:

Suppose you have two genomes, both of length L1, suppose constant rate r = 1/n bp, suppose composition of L1=C1, composition of L2 = C2 + N2.

C1=C2 + N2; C2 = C1 – N2; C2 < C1 for all N2 < 0

mutations in L1 = r*L1 = C1/n
mutations in L2 = r*L2 = r*C2 + r*N2 = C2/n + N2/n

we already showed that C2 < C1, so yes,
r*C2 < r*C1 and C2/n < C1/n, but only because C2 < C1.

Rather; yes, there are fewer mutations in the coding region of the genome that has a noncoding region, but only because that coding region is smaller. The proportion of mutations in the coding vs noncoding regions (in this polymerase-based argument) varies only with the proportions of the lengths of each type.

I am not discounting any advantage extra DNA might confer in different mutational circumstances, like the UV radiation one (one I had already made, I might note), but to argue that a noncoding region will sop up mutations from polymerase errors seems spurious to me.

Addendum:
Someone In class kept saying “look at the ratios”, so let’s look at the ratios.
The proportion of mutations in the coding region will be C/(C + N); as the proportion of noncoding DNA increases, the proportion of (this type of) mutations in the coding region will be smaller, true, but only because as noncoding DNA is added, the total number of mutations increases.

Supposedly, since I’ve had a course in microbiology, I know a fair bit about prokaryotic life.

That’s silly. I can juggle redox respiratory half-equations, and I can calculate the number of ATPs phosphoryalted for each molecule of whatever metabolised, and I can talk at length about autotrophy and nitrogen fixation, and a bit about different sorts of pathogens and toxins, but that doesn’t really mean anything.

A Winogradsky column has some cellulosic material at the bottom, buffered with calcium sulfate. The rest of the jar is filled with mud to within an inch of the mouth, topped with water and left in front of a convenient light source. Mine lives in the windowsill. The bottom layer usually turns black; sulfidogenic bacteria eat the cellulose and make hydrogen sulfide. This diffuses upwards to the phototrophic green and purple sulfur bacteria and the green and purple non-sulfur bacteria (which actually do use the hydrogen sulfide). Mine is from the Millrace pond, and appears to also have a lot of iron oxidisers. Iron oxidisers, and similar microbes, are part of the reason strip mines get those acidic buildups. They may also be the reason I don’t have many purple bacteria.

Floating around the top, oblivious to the anaerobic sulfur-based drama below, are some cyanobacteria. They seem pretty happy in their little oxic environment.

I could write you the redox equations for all of those colonies, the change in standard free energy, the ATPs hydrolysed, the bizarre thermicities of some microbial communities, and it would not matter. I know of but do not know these microbes; the Winogradsky column, after all, is named after someone who did both. All I did was put some paper towels and mud into a jar and leave it in the windowsill.

The bacteria appear unchanging. Their jar holds a stable community, a dynamic equilbrium of life unaware of its confinement, a clonal colony of clonal colonies from a pond across town. The microbes sit in my window, and, when I remember, I love them.