2010: FTSOS in review, January to March

Posted on December 28, 2010 by Michael

Yes, this is one of those lists. And there are going to be four parts. Deal.

January:
There was some good stories from this month, but I can only focus on a couple. One of my favorites was the discovery that pushed tetrapod evolution back 18 million years. This was a quantitative change – not a qualitative one. That means that the discovery did nothing to change the relations scientists have constructed for species at and around that time (397 million years ago); it only increased the time frame in which we recognize tetrapods to have lived.

This was also the month when I was attacked by a bunch of caricature feminists. The whole issue arose over my position that a picture of two fat women on CNN was an objectification of fat people (because it accompanied an article about fat women). The caricature feminists took this to mean that I hate women, don’t think they should have any rights, and as I recently saw in an unrelated thread on an unrelated blog 11 months after the fact, that apparently I’m also racist.

And then there was the first threat of the Maloney Mess. It is not clear how the maker of that threat knows Maloney, but she apparently knows him well enough to be aware of the profession of his wife. (Everyone now knows she’s a lawyer since she amateurishly issued a cease-and-desist request, but that happened only recently.)

February:
The big hubbub during this month was the suspension of FTSOS. The reason had to do with Andreas Moritz and Christopher Maloney. I hardly need to go into great detail at this point, but briefly: I made a post criticizing Moritz nearly a year earlier. I later made a post criticizing Maloney. The two got in contact with each other as a direct result. Moritz emailed WordPress with information provided to him by Maloney. The claim was that Maloney was a doctor (not true) and I said he was not a doctor (true). Since there was a threat of a lawsuit, WordPress demanded I change or delete my statement. I did. But I was suspended anyway. As it turns out, Maloney is a naturopathic doctor, not a real doctor, so I was always in the right. But that wasn’t important to anyone at the time. Well, except Simon Singh, Richard Dawkins, PZ Myers and a number of other defenders of real science who helped publicize the censorship. And presto, I am back.

This was also the month when FTSOS hit the arbitrary mark of 100,000 views. I have always been open about the fact that I am fortunate to have images show up in Google Image, but the vast majority of views come from posts with substance. And really, that has always been the trick: Put up content that interests people and they will read it.

One of the biggest non-Moritz/Maloney posts was the one about circumcision. I always feel the reactions to these sort of posts end up very skewed because much of the absurdly vehement opposition is just that – absurd and vehement. It is a vocal minority being vocal. But they do have legitimate concerns. In fact, I suspect if I wrote that article again, it would go through some significant revision. But I do not see myself ever sharing the inane passion against circumcision that the anti-snip crowd displays.

March:
My favorite post from this month was the one on mitochondria and microsatellites. I wrote about the difference between how the two are utilized in studies on populations and evolution. Mitochondria is good for the long-term, but microsatellites can be very useful over short periods, perhaps over a few thousands generations. In the post I cited one study on the spatial and temporal structures of populations of Atlantic cod off the coast of Canada and Maine, extending to Nantucket Shoals.

There was also the heartbreaking story of Constance McMillen. Her bigoted southern school would not allow her to attend her prom with her girlfriend because, well, it was a bigoted school. A judge ruled as much, but the school then encouraged parents to create a private prom to which Constance would not be invited. Constance has since moved on, receiving scholarships from celebrities and others who respect her for being a human being who matters.

Another heartbreaker comes from the post about Kelly Glossip. Kelly was in a relationship with Dennis Engelhard, a police officer who died while on duty. And even though they had long shared their lives together, Kelly was not allowed to receive any sort of survivor benefits because the two were legally prevented from entering a same-sex marriage. I think if more people bothered to realize how their anti-gay, pro-bigot stances hurt real human beings, we would start to see a lot less opposition to equality.

Finally, I have to break with the short-lived tradition of only featuring three posts per month because I just have to mention my article about the reasonableness of absolute uncertainty. I wanted to explain what atheists mean when they say “There’s probably no God” since so many people seem to think atheism is the same as certainty. It is not.

Expect April to June tomorrow.

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Corrections, corrections

Posted on March 31, 2010 by Michael

In my post about microsatellites and mitochondria there were a few errors. Fortunately, the author of the paper that formed the basis for a large portion of what I wrote also happens to be my professor. I petitioned him for review:

I stated that mtDNA is powerful as a tool for determining relations within a species. It should have read that mtDNA is useful for determining certain evolutionary patterns. There’s little excuse for this mistake.

I said genetic variation as determined by microsatellites is an indicator for population health. This may be true, but it isn’t possible to really be sure. If natural selection is acting upon these points, then populations with more variation may have better fitness.

I stated that populations are managed via arbitrary geographical lines. I actually meant political lines, but it’s unclear if that is true. This depends upon the level of coordination in management and conservation between the U.S. and Canada, and precisely where the borders fall. More on this later. Update: The political lines largely follow the geographical divides. There is some overlap, but it is minor.

I’ve also corrected some minor language here and there, as well as a citation (the paper I used was from 2004, not 2003). All the updates can be reviewed on the original post.

Thanks to Chris for his help.

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Microsatellites and mitochondria

Posted on March 24, 2010 by Michael

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mitochondrial DNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out.

The sequence indicates the hominin’s line diverged about a million years ago from the line that gave rise to both humans and Neanderthals and that split about 500,000 years ago.

That makes it younger than Homo erectus, the pre-human that spread out of Africa to much of the world about 1.9 million years ago.

“It is some new creature that has not been on our radar screen so far,” said Svaante Paabo, a colleague of Krause’s who specializes in analyzing ancient DNA.

And it would have lived near to both modern humans and Neanderthals. “There were at least three … different forms of humans in this area 40,000 years ago,” Paabo said.

The article goes on to state that more research is needed to determine just where it qualitatively sits on the evolutionary tree. My point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals. At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.

Update: Thanks to Chris Lage for offering his advice and corrections on this.

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