I should be grading last week’s lab assignment for the class I’m teaching, or reading the papers for Tuesday’s journal club, but instead I’ve pissed away most of the day avoiding Real Work, and now I’ve decided that I just must clean out my bookmark queue. I’m probably going to regret this tomorrow, but here goes…

Last week, Hal asked me about some work on mitochrondrial DNA (mtDNA) mutation rates. (It’s towards the bottom of the linked page.) He was asking about this report, which found mtDNA mutation rates in C. elegans that were about 100 times greater than previously observed. I still haven’t had time to read the original research article, and I’m not really an evolutionary biologist anyway, so take the following with a big grain of NaCl. Several questions seem to be unresolved, to me: First, since the animals were under no selection whatsoever, is there any chance that they were accumulating other mutations that could increase the mtDNA mutation rate? (This could be answered by looking at the rate of accumulation of mtDNA mutations over the 200 generations used by the scientists.) Second, is 200 generations enough time to get a decent sample? Were multiple populations grown for 200 generations, or is this based on one group of worms? How recently were they isolated from a real “wild type” population? (Animals can accumulate mutations when living under lab conditions — leading to infamous deaf-blind strains of lab mice, because they’re more likely to be grabbed by the scientist looking for one to breed.) Finally, why is the mutation rate of mtDNA assumed to be constant across evolutionary time? I know it probably makes a lot of the math easier, or solvable in the first place, but I can’t think of any reason why it has to be the case. Anyway, hopefully that answered Hal’s question, sort of.

Oh, and good luck to Hal on the thesis — hurry back, y’hear?

Reason Online had an article about animal research last week. Unfortunately, in their desire to tar the animal rights crowd, the authors choose an unreasonably large brush. There is a place for animal research in science, but I also think that there are some species that do deserve some additional protection — great apes among them. While the move to grant constitutional rights may be overstepping the case, I think the success in teaching ASL has shown that there is something not unlike intellect in some primates, and that probably deserves protection of some sort.

The National Review hatchet piece on Judy Blume is seriously off base. Is there something about the process of childbirth that causes all parental memory of childhood to be wiped away?

Texas principal institutes no-hug policy.

“Really, in junior high, they just don’t need to put their hands on each other because they can get into trouble,” [Robbins] said.

Maybe, just maybe, this issue here is with a grown man unable to deal with the idea of non-sexualized touching between peers. Maybe, just maybe, this grown man shouldn’t be in a position of authority over children.

Nice summary of some current theories about aging.

Great. I’ve moved from the land of the hantavirus to the land of West Nile virus. On the other hand, maybe this will have a positive effect, if it gets people to be more careful about leaving potential mosquito breeding grounds (e.g., buckets of water) lying around their yards.

James Lovelock — formulator of the Gaia hypothesis — says that nuclear power is the way out of the fossil fuel crisis. I also get a bit of a giggle out of the idea of dropping reactor waste into the rain forest as a way of restricting development.

Le Tigre should probably go onto the “To Buy” list, if I ever get around to reviving it.

Salon covers the bioethics lawsuit. It’ll be interesting to see this play out in the courts; it’s an interesting complex case.

Beauty. (Warning: naked bits behind that link.)

Since I got to NCBI, I’ve been reading a bunch of bio-computational method and technique papers, trying to get a feel for the way people think about the big problems in the field. It’s a lot more math than I’ve been used to, and a lot of that math is statistical. Bayesian methods are fairly popular, but until I read the linked article, I didn’t realize how controversial their use is.

There was a new bioperl release last week — get it here.

The 1998 Perl Quiz Show Questions, with answers. Should kill a good hour or so, if you’re looking for something to do.

ISMB2000 papers are up, for those of you (like me) not lucky enough to attend.

In Praise of Sloppy HTML, my ass. Look kids, getting it right isn’t that hard. Being sloppy because it “saves time” and “isn’t that important” doesn’t make me think an organization is closely managing it’s resources, it makes me think they hired amateur wankers to do their coding. Of course, my opinion isn’t worth much, as I’m part of that unimportant “small minority” of techies. Feh.

As you probably know unless you’re living in a cave, the 2000 Ig Nobles happened. Winner list here.

Thanks to Monkey Fist for summarizing my thoughts about political content carried on broadcast media.

Boy howdy, do I ever love that War on Drugs. Yes siree Bob, no two ways ‘bout it.

Unfortunately, the online version of a quilting story in the Washington Post doesn’t have the nice pictures that were in the dead tree version. The Renwick Gallery page doesn’t appear to have any either. (This link especially for the quilting side of the family; we’re keeping a warm thought for y’all.)

Most of you have probably heard of Kary Mullis, the, ummmm, rather eccentric kookball researcher that won the Nobel for inventing the polymerase chain reaction (PCR), which has made most modern molecular biology possible. Most of you probably haven’t heard of Michael Smith, who shared the Nobel with Mullis, and who recently died. In contrast to some of Mullis’s actics, Smith put on a class act:

On learning that he had won the Nobel Prize, Dr. Smith invited 12 co-workers with him to Stockholm to share in the glory and the festivities, picking up the entire check. The party included all research assistants, post-doctoral fellows and graduate students who had worked on projects that led to his prize.

Follow-up on last entry’s request for DC area traffic info on the web:

(First from Rafe; other two from Mike.)

Ahh, hell. I was getting all set to wrap this up, when I got mail from Lyn about a new Medley entry, which lead me to a new All Too Cozy entry about engagement rings (and rituals, in a bigger sense). I had some of the same feelings back when Lor and I had been dating for a while — and I guess maybe the best way to explain is just to tell the story…

So, like I said, we’d been dating for a while — a bit over a year, if memory serves. Everything was good, we were happy, and at that relationship point where we technically had separate addresses, but were in fact living together — you know, the “where are we sleeping tonight?” stage. It was getting to be That Time. Those of you who are married know what I’m talking about; we both pretty much knew we were going to be moving on to the next stage, but we hadn’t actually formalized anything yet. At one point, being my essentially lovable yet irascible self, I told Lor that I wasn’t ever going to ask anybody to marry me, because the odds were that, as the man, I would have taken the initial step in the relationship, by asking the woman out. In my opinion, I continued, it was only fair that the woman should pop the marriage question, so that she too would have to experience the possibility of rejection. Actually, I might have done that little schtick a couple times — I don’t remember. I wasn’t really serious — some of it was my ambivalence about gender equity in relationships, but mostly, I was just trying to pull her chain a little bit. So, of course, I was pleasantly surprised when she took me at my word, and popped the question. She bought a ring for me too; the whole nine yards. Clearly, I said yes, and it was one of the better decisions I’ve ever made.

So, anyway, that was my personal solution to the engagement ring quandary. (And hopefully I don’t come off like too much of a schmuck in the telling of it.) We ended up using my engagement ring as her wedding band, which also has a nice cyclic quality to it, I think. Plus, having the guy wear the engagement ring is a pretty good way to head trip some of the more up-tight people in your life. 8^)=

Anyway, I think I’ll wrap it up with that little story. It’s going to be a long week; I should probably get to bed now.

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