Friday Posts

Workout notes: rest day; I might get in 2-3 miles after writing this and stretch, and maybe a swim tomorrow.

Politics

Fred Thompson: rejected by James Dobson (right wing Christian leader). Part of the reason is that Thompson won’t “talk about his faith”. Ok, so that is a good thing in my eyes.

Of course, he doesn’t know about Hillary Clinton’s proposed health care plan; he falsely claimed that she would make health insurance a requirement to get a job. Of course, she didn’t say that, and neither did her plan.

Mitt Romney: in 2002 he (along with John Kerry) enthusiastically supported a gay pride parade. Yes, that is a good thing, but will hurt you if you are courting the wingnut vote as he is!

Hillary Clinton: made an outrageous statement, comparing Dick Cheney to Darth Vader. Mr. Vader demands an apology!!!

Republican Senators: manage to get sniveling Democrats to support their idiotic “let’s condemn MoveOn.org for their attack ad on General Petraeus. (The ad itself). Of course, not all Democrats went along; Boxer and Durbin stood up admirably. Hillary Clinton and Chris Dodd voted “no” and Obama had better things to do with his time (though he voted yes on the competing Boxer amendment).

Nevertheless, there are those of us who are disappointed and ashamed of how spineless our political leadership is; frankly we aren’t trusted with political power because we don’t deserve to be. Some of us (including myself) won’t give any more money to organizations such as the DCCC and the DSCC, but will instead give directly to the candidates that we like. Of course, given my finances, that isn’t much of a threat.

And, there are some, including this Obama supporter, who think that we are overreacting.

‘m talking to you, wingnuts, for caring more about a stupid newspaper ad (and yes it was stupid) than you do about the well-being of US soldiers.

I’m also talking to more than a few people in the progressive blogosphere.

Why?

Because you’re talking about the wrong vote today.

There was a vote today that was important and had direct relevance to ending the Iraq war.

But, if one paid attention to the blogosphere’s self-interested whining, one would think that the big news was the Moveon vote.

The vote you SHOULD be talking about described below.[...]

Then he talks about Feingold-Reid.

his is the vote on refusing to fund the Iraq debacle except to fund the withdrawal.

While a bunch of people were going nuts over a symbolic vote on a bullshit sense of the Senate resolution, there was a vote to try to end the Iraq debacle

Unfortunately, that vote ended in defeat.

We did get 28 Democrats to vote the right way on that legislation.

Wow. We supposedly control the Senate and manage 28, count them, 28 votes. That sure makes me feel better!

More politcs: Ann Coulter caught spreading a falsehood. She attacked lawyers (as a whole, ok, she has a law degree) and said that there was no such thing as a “Lawyers without Borders” group (as there is for doctors, and yes, I’ve given money to the doctor’s group).

Ok, to be fair (only a liberal would try to be fair to their enemy; perhaps that is what is wrong with us!), Ann Coulter was merely popping off about something she knew nothing about; so it probably wasn’t really a lie. Nevertheless, this shows that you can’t trust what she says.

Disclaimer: my whine about liberals being fair to their enemies is a joke. I try to be, but so do some conservatives.

Iraq: interesting graphs on opinion polls as to whether our presence in Iraq is making things better or not. Read the text (it is brief) and telling, as are the polls themselves. This article (written by a scientist) does make a good point about how to label one’s graphs.

War Protest: turns ugly when a parent of a son who was killed in action is beaten by pro-war protesters. Note: they guy who was beaten has a reputation himself for losing his temper as a few months ago, he burned a vehicle driven by Marines who went to notify him and his son’s mother of his son’s death. From what I read, this guy was provoked when the pro-war protesters tried to steal a photo of his son that was taped to a memorial.

Academia: sometimes zealots get carried away and bar people from speaking for no good reason. Cosmic Variance weighs in; I applaud his evenhanded manner.

Evolution: Professor Moran talks about the usefulness and the limitations of using models. He also talks about robustness of mutations and its role in biological innovation.

When I first read the paper by Ciliberti et al. (2007) I was disappointed. On the surface, the paper seems to be addressing an important issue in evolutionary theory; namely, how can you get significant innovation in light of the fact that most biological systems resist change? On closer reading, however, it seemed more complicated than that. The authors were actually dealing with a phenomenum called “robustness.” This is a popular description of a simple fact—the fact that many mutations are neutral so that there can be many variants of a protein that all carry out the same function. This has been known for decades.

The people who use the word “robustness” tend to elevate it to a level of significance that makes me nervous. Furthermore, they rarely use the term “random genetic drift” or “accident” in their papers, giving the impression that “robustness” is an adaptation that favors evolution.

There’s much to criticize in the field of evolutionary developmental biology or evo-devo. Some of the “theories” are little more than wide-eyed speculation. I’m thinking particularly of The Plausibility of Life by Marc Kirschner and John Gehart.

That’s one of the problems I have with this paper. The other problem is that it’s a modeling paper. The authors create a model of evolution and demonstrate that their model produces systems that evolve. I have a problem with these models. While a mathematical model is useful to show that a mechanism can work, it does not prove that it does work.

Let me give a quick example to show you why I’m skeptical of claims by modelers. It is possible to model a Lamarckian process where species inherit acquired characteristics. The result will be evolution but that does not mean that the inheritance of acquired characteristics is a real mechanism of evolution. This point is not always made clearly in papers that describe mathematical models of evolution. To often, the fact that the model produces evolution is taken as evidence that the assumptions in the model are correct and it is an accurate representation of real biological evolution. [...]

[...]The paper describes a model of an evolutionary system. It happens to be gene regulatory networks but it could be just about anything. Ciliberti et al. (2007) show that if you have a single system with no variation then the possibility for innovative change is limited. On the other hand, if you have a robust system where there are many different variants—in different species—then there are more pathways to innovative change. Seems like a pretty trivial conclusion to me. It’s the sort of thing Sewell Wright was talking about (Wright, 1932).

The course of evolution through the general field [adaptive landscape-LAM] is not controlled by direction of mutation and not directly by selection, except as conditions change, but by a trial and error mechanism consisting of a largely nonadaptive differentiation of local races (due to inbreeding and by occasional crossbreeding) and a determination of long time trend by intergroup selection.

The paper doesn’t mention Wright, random genetic drift, or neutral mutations; although it does talk about neutral networks.

Actually, now I want to read (or at least skim) that paper!

The paper:
S. Ciliberti, s., Martin, O.C. and Wagner, A. (2007) Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. (USA) 104:13591-13596. Abstract.