Category: Science

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Oh, the Gall!

Back when I TAed physics, I used to tell the students that a huge chunk of physics was simply having the gall to believe that you could get the answer. In other words, “confidence is key!” (Of course this probably also leads to the well known problem of extralusionary intelligence)
In this spirit, here is an article in the Washington Post about gender stereotypes and scores on a math test. In the 90s a series of experiments showed that if you made students identify their sex (or race) on an exam then this would cause their scores on math tests to change, causing, for example, females scores to fall. The thinking here, of course, is that recalling your gender might also recall the negative stereotypes which are place on females in math. Well what the Washington Post article describes is what happens if you do the opposite. What happens if you ask questions before the exam which remind the students of their postive attributes. Well, the WaPo reports that a recent study found that in fact in this case the male test scores stayed the same and the female test scores increased such that they were indistinguishable from the male test scores! Having the gall to believe you could possibly be smart is, indeed, it seems very important. (I had an English teacher in middle school who used to berate the students for making fun of people who were doing well in class. “Why wouldn’t you want to get good grades?” she would ask. Thanks Mrs. Perry!)

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The Tao of Tao

Terence Tao, in a UCLA press release about his Fields medal:

What are Tao’s secrets for success?
Tao, who was raised in Australia, offered some insight. “I don’t have any magical ability,” he said. “I look at a problem, and it looks something like one I’ve done before; I think maybe the idea that worked before will work here. Nothing’s working out; then you think of a small trick that makes it a little better but still is not quite right. I play with the problem, and after a while, I figure out what’s going on.
“Most people, faced with a math problem, will try to solve the problem directly,” he said. “Even if they get it, they might not understand exactly what they did. Before I work out any details, I work on the strategy. Once you have a strategy, a very complicated problem can split up into a lot of mini-problems. I’ve never really been satisfied with just solving the problem. I want to see what happens if I make some changes; will it still work? If you experiment enough, you get a deeper understanding. After a while, when something similar comes along, you get an idea of what works and what doesn’t work.
“It’s not about being smart or even fast,” Tao added. “It’s like climbing a cliff: If you’re very strong and quick and have a lot of rope, it helps, but you need to devise a good route to get up there. Doing calculations quickly and knowing a lot of facts are like a rock climber with strength, quickness and good tools. You still need a plan — that’s the hard part — and you have to see the bigger picture.”
His views about mathematics have changed over the years.
“When I was a kid, I had a romanticized notion of mathematics, that hard problems were solved in ‘Eureka’ moments of inspiration,” he said. “With me, it’s always, ‘Let’s try this. That gets me part of the way, or that doesn’t work. Now let’s try this. Oh, there’s a little shortcut here.’ You work on it long enough and you happen to make progress towards a hard problem by a back door at some point. At the end, it’s usually, ‘Oh, I’ve solved the problem.'”
…
What does Tao think of his success?
“I’m very happy,” he said. “Maybe when I’m in my 60s, I’ll look back at what I’ve done, but now I would rather work on the problems.”

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Awards

Fields Medals: Okounkov, Perelman, Tao, Werner. I was excited to see Terence Tao win because I’ve actually read and understood one of his papers. Not the stuff he’s winning the Medal for, of course. See Michael Nielsen (rising from his deep silence 😉 ) for connections of Tao’s work to quantum information science (by Hayden, Daftuar, and Klyachko.) Perelman has, apparently, declined the Medal and the arxiv is stressed by people downloading his papers:

22 Aug 2006: arXiv.org servers are currently under very heavy load due to demand for Grisha Perelman’s papers, published only as arXiv.org e-prints, which are available below. We encourage you to use a mirror such as lanl.arXiv.org or aps.arXiv.org, and we thank you for your patience as we try to accommodate the demand. Perleman was named a Fields Medalist at the opening ceremony of the International Mathematical Union.

Nevanlinna Medal: Jon Kleinberg.
Gauss Prize: Kiyoshi Ito. And the quants rejoice!

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Quantum Doctor

Here is an interesting article by Dominik Janzing and Thomas Beth, both from Karlsruhe, Germany. The jist of the article is that if the world were more quantum, doctors would have to learn Bell inequalities!

On the potential influence of quantum noise on measuring effectiveness in clinical trials
ABSTRACT:To test the effectiveness of a drug, the medical researcher can instruct two randomly selected groups of patients to take the drug or not to take it. Each group should comply with the instructions exactly or else the causal effect cannot be identified satisfactorily. This holds true even when those who do not comply are identified afterwards, since latent factors such as patient’s personality can influence both his decision and his physical response. However, one can still give bounds on the effectiveness of the drug depending on the rate of compliance. They are described by 16 inequalities. Remarkably, the proofs for these bounds given in the literature rely on models that represent all relevant latent factors influencing patient’s behavior by hidden classical variables. In a strong analogy to the violation of Bell’s inequality, half of the inequalities fail if patient behavior is influenced by latent quantum processes (e.g. in his nervous system). Quantum effects could fake an increase in the recovery rate by about 13%, although the drug would hurt as many patients as it would help if everyone took it. We show that the other eight inequalities remain true even in the quantum case. We do not present a realistic model showing the above effect. We only point out that the physics of decision-making could be relevant for the causal interpretation of every-day life statistical data. Our derivation of the remaining eight inequalities suggests how to avoid problematic hidden-variable models in classical causal reasoning by representing all latent factors by quantum systems.

I’m guessing that this won’t help in the battle physicist’s have when teaching premed students (“Ooooh, but please just give me one more point on this quiz. Pleeeease!”)

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Beyond DNA?

Just got an email with the following article. A big deal?

Scientists Say They’ve Found a Code Beyond Genetics in DNA
By NICHOLAS WADE
Researchers believe they have found a second code in DNA in addition to the genetic code.
The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.
The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.
The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues.
There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length.
Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.
Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms.
The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.
Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.
But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.
The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, “We think that for the first time we have a real quantitative handle” on exploring how the nucleosomes and other proteins interact to control the DNA, he said.
The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested.
Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning.
“I think it’s really interesting,” said Bradley Bernstein, a biologist at Massachusetts General Hospital.
Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was “a profound insight if true,” because it would explain many aspects of how the DNA is controlled.
The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.
In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.