# blueollie

## 11 August 2010 posts

Science and Mathematics

Here is an announcement of a paper which claims that P is NOT equal to NP. What does that mean? First, “P” means “polynomial time”; things that can’t be solved in polynomial time take longer than those that can. Now as far as “P” and “NP”, very roughly speaking it means this: “P” means that a task (say, finding the prime factors of an integer) can be completed in polynomial time. “NP” means that an answer can be checked in polynomial time.
So this result, if true, says that being able to check an answer in polynomial time does not mean one can FIND it in polynomial time. (I am being simplistic here).

Astronomy: here is a cool show-off photo. I’ll reproduce the NASA photo; surf to the article for the explanation.

Abiogenesis How did life begin? Could there be life elsewhere in the universe? Here is yet another article on some clues:

Researchers have found millions of “super” bacteria thriving inside the oxygen-starved Lake Diamante, in the center of a giant volcanic crater located over 15,400 feet above sea level.

The bacteria’s habitat is similar to primitive earth, before living and breathing organisms began wrapping a protective atmosphere of oxygen around the planet.

The conditions — which include high arsenic and alkaline levels — could also shed light on life beyond Earth.

“This is of great scientific interest as a window to look to our past and also for a science called astrobiology, the study of life on other planets,” said Maria Eugenia Farias, part of the team that discovered the life-forms in Lake Diamante earlier this year.

If bacteria can survive here, the theory goes, it could also survive somewhere like Mars.

So-called “extremophiles” have been found in other parts of the world — and they can have significant commercial value. Bacteria that break down lipids are used in detergents for example.

But Farias said these bacteria, called “polyextremophiles” are exceptional because they flourish in the harshest of circumstances.

“What we have here is a series of extreme conditions all in one place. And this is what makes this place unique in the world,” said Farias, a microbiologist at the National Scientific and Technical Research Council in Tucuman province.

The lake sports levels of arsenic 20,000 times higher than the level regarded as safe for drinking water and its temperature is often below freezing. But because the water is so salty — five times saltier than sea water — ice never forms.

The bacteria’s DNA mutates to survive the ultra-violet radiation and low oxygen levels found at such high altitudes, which could make it of interest to the pharmaceuticals industry, Farias said. It could also have future commercial applications in products such as sunscreens, she added.

Fractals: they appear in many surprising places…including in superconductors.

Medicine This is bizarre:

People getting cosmetic surgery in India have brought back to Britain a new gene that allows any bacteria to become a superbug, and scientists are warning this type of drug resistance could soon appear worldwide.

Though already widespread in India, the new superbug gene is being increasingly spotted in Britain and elsewhere. Experts warn the booming medical tourism industries in India and Pakistan could fuel a surge in antibiotic resistance, as patients import dangerous bugs to their home countries.

The superbug gene, which can be swapped between different bacteria to make them resistant to most drugs, has so far been identified in 37 people who returned to the U.K. after undergoing surgery in India or Pakistan. […]

Almost as soon as the first antibiotic penicillin was introduced in the 1940s, bacteria began to develop resistance to its effects, prompting researchers to develop many new generations of antibiotics.

But their overuse and misuse have helped fuel the rise of drug-resistant “superbug” infections like methicillin-resistant Staphyloccus aureus (MRSA).
[…]

In other words, this gene helps current bacteria become resistant to antibiotics. The evolutionary arms race continues unabated.

Politics
Interestingly enough, the right wing/conservatives seem to delight in attacking science. I can sort of understand this one; the Republicans need the religious right and there are many more of them than they are of scientifically minded folks. But there have to be millions of people who like science and favor conservative economic and foreign policy views.

But we have been yucking it up over the right wing attacking….relativity theory? (yes, conclusions from relativity theory has to be accounted for in things like satellite assisted communications and GPS calculations).

This is lampooned in a cartoon and by Rachel Maddow:

The Gibbs flap

White House spokesman Robert Gibbs stirred up some intra-party controversy this week when he expressed frustration at the “professional left” in an interview with The Hill newspaper.

From The Hill:

During an interview with The Hill in his West Wing office, White House press secretary Robert Gibbs blasted liberal naysayers, whom he said would never regard anything the president did as good enough.
“I hear these people saying he’s like George Bush. Those people ought to be drug tested,” Gibbs said. “I mean, it’s crazy.”

The press secretary dismissed the “professional left” in terms very similar to those used by their opponents on the ideological right, saying, “They will be satisfied when we have Canadian healthcare and we’ve eliminated the Pentagon. That’s not reality.”

Of those who complain that Obama caved to centrists on issues such as healthcare reform, Gibbs said: “They wouldn’t be satisfied if Dennis Kucinich was president.”

The White House, constantly under fire from expected enemies on the right, has been frustrated by nightly attacks on cable news shows catering to the left, where Obama and top lieutenants like Chief of Staff Rahm Emanuel have been excoriated for abandoning the public option in healthcare reform; for not moving faster to close the prison at Guantánamo Bay; and for failing, so far, to end the ban on gays serving openly in the military.

Reaction has been swift.
Here is Rep. Alan Grayson (who I like…and yes, I am now on his donor list, though most of my money will go to Illinois Senate and Governor races):

Here is another “we knew it all along” type of reaction. Paul Krugman (a frequent liberal critic who I often agree with) wonders if it is the Obama aides that are the most upset; he wonders if they are angry that the President will now listen to a wider variety of opinion:

But I think people are missing an important point: what’s good for Obama is not necessarily good for his aides.

Think about it: Complaints that the administration should have pursued a bigger stimulus, or fought harder for the public option, or taken a different position on Afghanistan aren’t going to matter in the midterms. But they might hurt White House aides who argued against a bigger stimulus (to the point of not even passing the option on to the president), or argued against a harder push on health reform (perhaps even calling for retreat after Scott Brown), or have argued that continuation of Bush foreign policy is a political winner. The point is that the president might actually take those criticisms to heart, and rethink who he listens to.

Greenwald summarizes Gibbs’ rant:

(1) The Professional Left are totally irrelevant losers who speak for absolutely nobody, and certainly nobody in Real America who matters; but (2) they’re ruining everything for the White House!!! And: if you criticize the President, it’s only because you’re such a rabid extremist that you harbor a secret desire to eliminate the Pentagon — that’s how anti-American you are! You’re such a Far Left extremist that Dennis Kucinich isn’t far enough Left for you, you subversive, drug-using hippies! You’re so far to the Left that you want to turn the U.S. into Canada. As David Frum put it today: “More proof of my longtime thesis, Repub pols fear the GOP base; Dem pols hate the Dem base.”

Of course the Republicans got to 41 Senators from fearing their base and may well blow a huge opportunity to make massive gains in 2010; we’ll need to see how it goes.

And I should point out that…yes, even President Franklin Roosevelt, who is now considered to be the model for liberalism…drew fire…from his liberal base!

Assorted Political Stuff
Sarah Palin: too much for some conservatives:

Will Bunch talking about his excellent book on President Reagan

No, this is not an attack on President Reagan; in fact, Bunch argues that Reagan was smarter than many of his critics realized (and yes, I was one of about the 100 people in the US who didn’t like President Reagan). But Bunch does argue that President Reagan’s record (e. g., actual policy positions) has been misrepresented by today’s conservatives; in fact, he was more of a pragmatist than today’s conservatives will admit.

Mosque near ground zero: I agree with Christopher Hitchens (who, like me, is an atheist who doesn’t see much good in Islam). I think that a mosque should be treated the same way as a church, temple or whatever.

August 12, 2010

## Posts for 11 July 2010

Yes, part of it was that I was very tired and snippy (didn’t sleep well last night) and the pain killer (which I haven’t had in about 12 hours) has an unfortunate side effect. For those who aren’t bothered by TMI, think “clay”. I found this product to be useful.

But, on the good side, I can put more weight on the leg and can bend the knee even more; tomorrow the big bandages come off. 🙂

What I have to remember is that my last operation was in 1984 (25 years old at the time) and I had far less done and I had spent overnight in the hospital. But the difference between Saturday and Friday was huge and I’ve made another great “leap” (metaphorical, not physical!) so I see myself climbing onto the exercise bike by the end of the week and maybe even the water for some easy stroke drills.

I hope to get caught up on research this week as I am not as loopy as I was before. People tell me that hydrocodone is addictive; I don’t see it. I can’t wait to get off of it!

So, to my posts of the day:

Mathematics: tough mathematics is its own reward. This is an interesting post on the Poincare Conjecture and the person who solved it (who turned down the Fields Medal!) (via Jordan Ellenberg in Slate):

[…]he entities we study in science fall into two categories: those which can be classified in a way a human can understand, and those which are unclassifiably wild. Numbers are in the first class—you would agree that although you cannot list all the whole numbers, you have a good sense of what numbers are out there. Platonic solids are another good example. There are just five: the tetrahedron, the cube, the octahedron, the dodecahedron, and the icosahedron. End of story—you know them all. These mathematical objects behave something like the chemical elements, which are neatly classified by Mendeleev’s periodic table. Many properties of an element are determined by its place in the table. For instance, we knew a lot about how metals like germanium and gallium would behave before they were actually discovered in nature!

In the second class are things like networks (in mathematical lingo, graphs) and beetles. There doesn’t appear to be any nice, orderly structure on the set of all beetles, and we’ve got no way to predict what kinds of novel species will turn up. All we can do is observe some features that most beetles seem to share, most of the time. But there’s no periodic table of beetles, and there probably couldn’t be.

Mathematicians are much happier when a mathematical subject turns out to be of the first, more structured, type. We are much sadder when a subject turns out to be a variegated mass of beetles. (But have a look at Fields Medalist Timothy Gowers’ beautiful essay “The Two Cultures of Mathematics” for a spirited defense of mathematical enterprises of the second sort.)

So, where do three-dimensional shapes, the subject of the Poincaré conjecture, fit in? To simplify, let’s think about two-dimensional shapes first. These fall firmly in the “periodic table” category. The only such shapes are the surfaces of “doughnuts” with multiple holes. The number of holes is called the genus of the surface and plays the role that the atomic number does for chemical elements. (Here is a picture of the surfaces of genus 0, 1, 2, and 3.) Geometer William Thurston (another Fields winner) made the daring conjecture that three-dimensional shapes, too, can be classified in a more complicated but equally structured way. Perelman has proved this conjecture, which has Poincaré as a straightforward corollary. That means, in turn, that we can think about proving general statements about three-dimensional geometry in a way that we can’t hope to about beetles or graphs.

Perelman’s work isn’t important because of its applications. It won’t help anyone build a bridge, aim a rocket, crack a code, or privatize Social Security. Mathematicians, no dummies, like to point out that, in some unspecified future, Perelman’s theorem might pitch in to help with these problems in ways that aren’t obvious now. But its real significance is like that of the fact that a times b is equal to b times a; it’s a basic structural statement about how the world is organized. If you prefer order to chaos, that’s something worth caring about.]

Now for those who are interested the Poincare Conjecture says the following: a 3 dimensional object that has the “algebraic information” of a sphere is a sphere (in terms of homotopy groups). This is false at the level of homology: one can do surgery on a knot in $s^3$; that is, scoop out a solid torus neighborhood of a smooth knot, do that again in another copy of $s^3$ on an inequivalent knot, and then identify the torus boundaries where the meridian of one “missing solid torus” is identified with the longitude of the second and visa versa. Then the meridians bound a Seifert surface in the “other” $S^3$. That forms what is known as a “homology” sphere; right homology, wrong fundamental groups.

Medicine Recently I had talked about the case where an Olympic caliber athlete had her sex challenged. This article deals with those who naturally have sexual ambiguities and how the fetus can be treated to prevent this. Of course, there is some fear in the gay community that this is some sort of program to keep gay people from being born.

It’s happening to crops in the United States, too. In 2004, Donald Davis, PhD, a former researcher with the Biochemical Institute at the University of Texas, Austin, led a team that analyzed 43 fruits and vegetables from 1950 to 1999 and reported reductions in vitamins, minerals, and protein. Using USDA data, he found that broccoli, for example, had 130 mg of calcium in 1950. Today, that number is only 48 mg. What’s going on? Davis believes it’s due to the farming industry’s desire to grow bigger vegetables faster. The very things that speed growth — selective breeding and synthetic fertilizers — decrease produce’s ability to synthesize nutrients or absorb them from the soil.

A different story is playing out with organic produce. “By avoiding synthetic fertilizers, organic farmers put more stress on plants, and when plants experience stress, they protect themselves by producing phytochemicals,” explains Alyson Mitchell, PhD, a professor of nutrition science at the University of California, Davis. Her 10-year study in the Journal of Agricultural and Food Chemistry showed that organic tomatoes can have as much as 30 percent more phytochemicals than conventional ones.

But even if organic is not in your budget, you can buck the trend. We polled the experts and found nine simple ways to put the nutrient punch back in your produce. […]

Surf to the link to see these 9 ways.

More science
An advance in quantum computing: we can now trap the light from a single ion (electrically charged atom).

Evolution and biology
Jerry Coyne on the “evolving by getting an entirely new genome” paper:

A new paper by John Jaenike and his colleagues in Science, however, shows a form of biological evolution by natural selection that isn’t based on changes in genes. It’s based on changes in the presence of symbiotic bacteria that protect a species from parasites.

The species in which the nongenetic evolution has occurred is the mushroom-feeding fruit fly Drosophila neotestacea in North America:
[…]
Some flies also carry another organism: the bacterial symbiont Spiroplasma, which is found in many insects. In D. neotestacea, however, the presence of Spiroplasma protects the fly from the sterilizing effects of nematodes. While flies with worms and no Spiroplasma are virtually sterile, the presence of the bacteria confers almost normal fertility on worm-ridden flies. It’s not yet clear how this works, but worms in flies with Spiroplasma are much smaller than those without the bacteria. Presumably the bacteria does something to the worms (or to the flies) that makes the worms grow much more slowly.

So this is a good setup for natural selection. First, there is variation in a trait—some flies have Spiroplasma, others do not. That trait is heritable, for Spiroplasma are transmitted directly from mother to offspring in the egg (there’s no “horizontal” adult-to-adult transmission). And there’s an environmental factor—the parasitic, sterilizing worms—that cause differential reprodution of flies depending on whether or not they carry Spiroplasma. Those flies who carry Spiroplasma can still produce offspring, and hence pass on the Spiroplasma to the next generation; those flies who don’t carry the bacteria don’t get protection from nematodes, and leave no (or very few) offspring. In the presence of worms, then, there’s a huge selective advantage in flies to carrying bacteria.
[…]

There is much more there.

He also talks about the evolution of single celled organisms to multi-celled organisms paper:

So how did multicellularity come about? How much genetic change was needed to get those single cells on their own to form colonies, with some of them specializing in reproduction and the others in locomotion, nutrition, and the like? Did it take a wholesale restructuring of the genome?

That was the question that Simon Prochnik and his colleagues asked—and partially answered—in a new paper in Science. They had a clever approach: look at two species that were fairly similar, but one of which was multicellular, showing some differentiation among cells, and the other was not. Here are the species they used. The “simple” one was the unicellular alga Chlamydomonas reinhardtii, which has flagella, threadlike organelles that can be whipped about to move the cell though the water. This species has been used extensively in studies of movement and organelle differentiation. Its genome was sequenced in 2007. […]

Does the initial evolution of multicellularity require many new types of genes, or will a few simple changes suffice?

The answer seems to be the latter. Comparing the V. carteri genome with the already-published C. reinhardtii genome, Prochnik et al. showed this:[…]

Surf to the link to find out. 🙂

Social/Political
Facts have often little to do with what one believes in politics:

It’s one of the great assumptions underlying modern democracy that an informed citizenry is preferable to an uninformed one. “Whenever the people are well-informed, they can be trusted with their own government,” Thomas Jefferson wrote in 1789. This notion, carried down through the years, underlies everything from humble political pamphlets to presidential debates to the very notion of a free press. Mankind may be crooked timber, as Kant put it, uniquely susceptible to ignorance and misinformation, but it’s an article of faith that knowledge is the best remedy. If people are furnished with the facts, they will be clearer thinkers and better citizens. If they are ignorant, facts will enlighten them. If they are mistaken, facts will set them straight.

In the end, truth will out. Won’t it?

Maybe not. Recently, a few political scientists have begun to discover a human tendency deeply discouraging to anyone with faith in the power of information. It’s this: Facts don’t necessarily have the power to change our minds. In fact, quite the opposite. In a series of studies in 2005 and 2006, researchers at the University of Michigan found that when misinformed people, particularly political partisans, were exposed to corrected facts in news stories, they rarely changed their minds. In fact, they often became even more strongly set in their beliefs. Facts, they found, were not curing misinformation. Like an underpowered antibiotic, facts could actually make misinformation even stronger.

What is going on/ Well, some of it is that people don’t believe inconvenient facts, sometimes because these aren’t facts:

This effect is only heightened by the information glut, which offers — alongside an unprecedented amount of good information — endless rumors, misinformation, and questionable variations on the truth. In other words, it’s never been easier for people to be wrong, and at the same time feel more certain that they’re right.

Oh, and we’ve seen this too:

People ignorant of the facts could simply choose not to vote. But instead, it appears that misinformed people often have some of the strongest political opinions. A striking recent example was a study done in the year 2000, led by James Kuklinski of the University of Illinois at Urbana-Champaign. He led an influential experiment in which more than 1,000 Illinois residents were asked questions about welfare — the percentage of the federal budget spent on welfare, the number of people enrolled in the program, the percentage of enrollees who are black, and the average payout. More than half indicated that they were confident that their answers were correct — but in fact only 3 percent of the people got more than half of the questions right. Perhaps more disturbingly, the ones who were the most confident they were right were by and large the ones who knew the least about the topic. (Most of these participants expressed views that suggested a strong antiwelfare bias.)

Studies by other researchers have observed similar phenomena when addressing education, health care reform, immigration, affirmative action, gun control, and other issues that tend to attract strong partisan opinion. Kuklinski calls this sort of response the “I know I’m right” syndrome, and considers it a “potentially formidable problem” in a democratic system. “It implies not only that most people will resist correcting their factual beliefs,” he wrote, “but also that the very people who most need to correct them will be least likely to do so.”

The article talks about our brains being wired to seek consistency. In fact, consistency and tradition is part of the moral framework for conservatives.

But liberals are prone to this too:

New research, published in the journal Political Behavior last month, suggests that once those facts — or “facts” — are internalized, they are very difficult to budge. In 2005, amid the strident calls for better media fact-checking in the wake of the Iraq war, Michigan’s Nyhan and a colleague devised an experiment in which participants were given mock news stories, each of which contained a provably false, though nonetheless widespread, claim made by a political figure: that there were WMDs found in Iraq (there weren’t), that the Bush tax cuts increased government revenues (revenues actually fell), and that the Bush administration imposed a total ban on stem cell research (only certain federal funding was restricted). Nyhan inserted a clear, direct correction after each piece of misinformation, and then measured the study participants to see if the correction took.

For the most part, it didn’t. The participants who self-identified as conservative believed the misinformation on WMD and taxes even more strongly after being given the correction. With those two issues, the more strongly the participant cared about the topic — a factor known as salience — the stronger the backfire. The effect was slightly different on self-identified liberals: When they read corrected stories about stem cells, the corrections didn’t backfire, but the readers did still ignore the inconvenient fact that the Bush administration’s restrictions weren’t total.

Note: this (sticking with “false facts”) isn’t only a problem with the politically ignorant:

And if you harbor the notion — popular on both sides of the aisle — that the solution is more education and a higher level of political sophistication in voters overall, well, that’s a start, but not the solution. A 2006 study by Charles Taber and Milton Lodge at Stony Brook University showed that politically sophisticated thinkers were even less open to new information than less sophisticated types. These people may be factually right about 90 percent of things, but their confidence makes it nearly impossible to correct the 10 percent on which they’re totally wrong. Taber and Lodge found this alarming, because engaged, sophisticated thinkers are “the very folks on whom democratic theory relies most heavily.”

This article goes on to suggest that the media do their jobs and hammer those who lie in public.

July 11, 2010

## Scifri Videos: Rumble In The Jungle

Science, technology, environment and health news and discussion from the makers of the NPR public radio program Science Friday with host Ira Flatow.

Vodpod videos no longer available.

more about "Scifri Videos: Rumble In The Jungle", posted with vodpod

Jerry Coyne has more here: he thinks that this will be some sort of mating call (a ‘froggy flirt”) and goes on to talk about scientific papers and how to “sell” your work to the journal.

May 30, 2010