links for 2008-03-26

• Building the ivory tower: Network effects in academia - Vox EU
• Homeowners Who Won’t Cut the Price - New York Times
• St. Louis Fed Taps Successor for Poole (Good choice) - WSJ Economics Blog
• Lessons learnt from Great Depression - Times Online
• What a Rodent Can Do With a Rake in Its Paw - New York Times
• Bear: Did the Fed and Treasury Push Too Hard? - naked capitalism
• John McCain's plan to ignore the economy - Andrew Leonard
• McCain-onomics: A tax cut in every corporate pot - Andrew Leonard
• Evolving the Wow! Factor - Olivia Judson
• 3 Theories That Might Blow Up the Big bang - Discover

Comments

[anne]

http://judson.blogs.nytimes.com/2008/03/25/evolving-the-wow-factor/index.html

March 25, 2008

Evolving the Wow! Factor
By Olivia Judson

Here are two pieces of bizarre natural history:

One. The crab spider Thomisus onustus. Some individuals are a most unspiderly color: they are hot pink. This allows them to hide in hot pink flowers — and ambush unwary bees. Other individuals are yellow, and hide in yellow flowers. Even more surprising, their colors are not fixed: move a pink spider to a yellow flower, and she can change her color to match.

Two. In the center of the Atacama desert in northern Chile, it rains less than five millimeters (less than quarter of an inch) a year, yet there are bacteria living inside quartz pebbles. Like plants, these bacteria make energy from sunlight. (The quartz is translucent, so it lets in some light, but at the same time, shields the organisms from the worst of the ultraviolet radiation.)

I mention these oddities because this week, I want to resume my obsession with mutations, and look explicitly at a type that I've so far mentioned only in passing: beneficial mutations.

All mutations are accidental changes to DNA. Beneficial mutations are those accidental changes that in some way improve an organism's chances of surviving and reproducing. Obvious examples from recent decades would be a mutation that confers antibiotic resistance on bacteria that cause disease in humans, or one that confers poison resistance on a rat. Less obvious are mutations that produce hot pink spiders and quartz-dwelling bacteria. But the point is that such mutations allow organisms to evolve to fit their environments better — a process known as adaptation.

Adaptation is the "wow!" factor of nature: when we see something spectacular or exquisite, we are typically looking at an adaptation. And what underpins adaptation is the appearance and spread of beneficial mutations: the process is not possible without them. Yet despite their central role in adaptive evolution, beneficial mutations have — until recently — received surprisingly little attention.

As a result, crucial questions remain open. For instance: is it the case that most beneficial mutations have small effects — and how often do beneficial mutations with large effects happen? And: can we predict which kinds of beneficial mutations will spread through the population by means of natural selection — and which will appear and almost immediately vanish?

The answers hold the keys to understanding how fast organisms can evolve to fit new environments — and thus to practical matters like the appearance of drug resistance in hospitals, as well as a more general view of how likely different populations are to go extinct when the environment changes.

There are several reasons for this neglect of the benign. One — dare I say it — is fashion. In the late 1960s, the geneticist Motoo Kimura proposed the neutral theory of molecular evolution. According to this idea, most mutations are either harmful (and will quickly disappear from the population because those bearing them die) or irrelevant. If this is the case, most genetic variation has no impact on fitness — the technical term for how good an organism is at surviving and reproducing. Kimura's development of the neutral theory was enormously influential, and prompted a flurry of work investigating whether most genetic variation is irrelevant.

Then it was the turn of deleterious mutations, which became trendy in the late 1980s and early 1990s. Deleterious mutations have been hypothesized to play a central role in a variety of evolutionary phenomena, including (and most prominently) sex. The argument is that organisms with a deleterious mutation rate above a certain threshold must reproduce sexually.

The reason is that sex purges deleterious mutations from the population: sex generates new gene combinations, and thus in each generation it creates some individuals with relatively few deleterious mutations and some with lots. Those with lots die; those with relatively few go on to have large numbers of children....

[anne]

Thanks to B.W. Lilly:

There are some great color photos of these spiders at

http://www.nicksspiders.com/nicksspiders/thomisusonustu s.htm .

[hari]

@ Anne - Obsession with Mutation.

The DNA is indeed the key to how mutation takes form and replicates itself. I must confess, as a medical student ( 1959-60), I ventured into a "test tube" experiment to replicate my ideal of future in our genetic lab. The lady Prof was against my thought process but allowed the experiment to go forward (accompanied by a molecular biologist). I wanted to create an "olive brown" female of distinguished features which I'd sort of found in my investigations of old Europe....My test was a dismal failure indeed and the centrifuge didn't wait to tell the results.
The moral of the story is still useful for me because I married a Swede with a view to a similar (DNA) mutuation. My two children don't like to hear my story (how I got to the idea!). But the result of mutation are discernable; more so in my son. I'm beginning to recognize the differences in cognition when he gets into a debate with me and so on.

The other thing you have to acknowledge is that mutation is a means to genetic survival - in our globalized world today.

[anne]

http://judson.blogs.nytimes.com/2008/03/11/stop-the-mutation/index.html

March 11, 2008

Stop the Mutants!
By Olivia Judson

This week, I'm going to do an impossible experiment.

I'm going to wave a magic wand and reduce the mutation rate to zero, instantly, in all species, and forever. Then I'm going to watch to see how long it takes for evolution to stop.

I'll report back in several millennia.

As I've mentioned in previous columns, mutations — accidental changes to DNA — provide the raw material for evolution. They make the difference between fur that is black and fur that is golden; between pink petals and blue ones; between the ability to fly over the Himalayas, as bar-headed geese do, and being able to stay underwater long enough to drown prey, as crocodiles can. Mutations are the ultimate cause of all the genetic differences we see around us; the ultimate cause of the differences between a human and a banana, between a starfish and a toadstool.

Actually stopping mutations is a physical impossibility — hence the need for a magic wand. But if they were to stop, so would raw invention.

But evolution would not. Not for a long time.

Although we often think of evolution in grand terms — a lineage of fish turning into frogs, or monkeys becoming apes — the technical definition is more humdrum. It's simply a change in the frequencies of different versions of a gene in a population over time.

To see how this can work, imagine a population of mosquitoes. Suppose most of them are sensitive to insecticide, but a few harbor a version of a gene that confers resistance. If you suddenly start spraying insecticide, you'll kill many of the mosquitoes that are sensitive; those that are resistant will be much more likely to reproduce, and will tend to leave more offspring. In the next generation, the frequency of the gene for resistance will have increased, and the population will have evolved a little. (For this article, I'm ignoring the possibility of evolution through non-genetic means, such as culture, which though important for humans is irrelevant for most other organisms.)

In short, a supply of genetic variation is all that's necessary for evolution to continue. And in most populations, genetic variation is already abundant.
Just look at us. Genetic differences among humans include differences in the ability to taste different flavors, digest alcohol or milk, or resist malaria or HIV; they include differences in skin, hair and eye color; in predispositions for heart disease or breast cancer; in amount of chest hair, the ability to grow a beard, the tendency towards baldness; the list goes on and on.

Nor is it just humans and our entourage of cats, dogs, sheep and company, that have lots of versions of lots of genes. Wild organisms in a given population vary genetically, too. Oak trees a few feet apart differ in the size and shape of their acorns. Male guppies from the same stream come in different colors, and with enormously different patterns of spots. Fruit flies from the same species differ in the number of bristles on their bellies; stalk-eyed flies differ in the lengths of their eye stalks. Galápagos finches, famously, differ in the shapes of their beaks.

Indeed, one of the great surprises of the past decades has been how much genetic variation there is, for there's far more than anyone expected. Some of this variation (exactly how much is the subject of debate) is meaningless, or "neutral" — it has absolutely no effect. But the rest can play a role in how well organisms survive and reproduce. Moreover, the utility of a gene depends on circumstances. Insecticide resistance genes are useful when there's insecticide about, but not when there isn't: then, they can be detrimental. In areas where insecticide is not sprayed, mosquitoes without the resistance gene do better. For some reason, having the resistance gene makes you less likely to survive the winter....

[anne]

http://judson.blogs.nytimes.com/2008/02/05/a-mutant-obsession/index.html

February 5, 2008

A Mutant Obsession
By Olivia Judson

This week I'm introducing the first article in what will be an occasional series about mutation. And yes, I admit it: I'm obsessed with mutation (which is why I've already alluded to it in a couple of earlier articles). The reason is that mutations to DNA form the raw material for evolution. It's wondrous to think that mutations, accumulated over billions of years through the action of natural selection and the other forces of evolution, have produced such diverse life forms as vampire squid, coconut palms, death cap mushrooms, giant Gippsland earthworms, Etruscan pygmy shrews, E. coli — and us.

First things first: what are mutations? They are accidental changes to an organism's DNA; they typically happen when the cellular machinery makes a mistake as it copies DNA from one cell to the next. Once a mutation happens, it may or may not be preserved down the generations — whether it is depends on a variety of factors, not least natural selection.

A fruit fly. Photo Credit: Richard T. Nowitz/Photo Researchers Inc.Early geneticists didn't know about DNA, so they thought of mutations in terms of how they changed an organism's appearance — a fruit fly with white eyes instead of red, or no bristles on the insides of its legs, peas that were wrinkly rather than smooth. But these days, mutations are typically classified by the effect they have on DNA. It turns out that there are many different types of mutation, with many different kinds of effects — and they contribute to the evolutionary process in surprisingly diverse ways.

Some are more common in plants; others, in animals. Some are more likely to occur in eggs; others, in sperm. Some have immediate effects; others don't — but instead have a substantial impact on long-term evolutionary potential. And in my view, it's only by appreciating the full diversity of mutations that the evolution of countless different life forms becomes comprehensible. The aim of the series, then, is to survey the mutational landscape.

The canonical mutation — the one everyone learns about in biology class — alters the part of a gene that contains the instruction to make a protein. In case you don't have an intuitive feeling for what proteins are, the easiest way to think about them is as small objects, each with a shape and a function — just as a teacup has a shape for holding tea. Proteins are built out of a kind of molecular Lego; the bits of Lego that are required are listed in the gene. So a mutation to the protein-coding part of a gene often has the effect of altering the protein's shape — like substituting a big Lego brick for a small one, or one with a hinge for one that's rigid. Such shape changes often affect how a protein does its job.

Mutations of this type tend to have an immediate effect on the organism, affecting its health, behavior, or looks. For instance, if you compare oldfield mice (Peromyscus polionotus) that live on the Florida mainland with their cousins that scamper around the sand dunes on the nearby Santa Rosa Island, the first thing you notice is that mainland mice have dark fur, and beach mice have pale, sandy-colored fur. A significant part of the difference in fur color has been traced to a single alteration in the DNA sequence of a gene called Melanocortin-1 receptor. The mutation alters the shape of the corresponding protein, and this interferes with the mouse's ability to produce a dark pigment. (To pick up last week's theme of evolution repeating itself at the genetic level, mutations to Melanocortin-1 receptor are also implicated in changes to hair and skin color in humans and (probably) Neanderthals, and to feather color in the lesser snow goose and the Arctic skua.) ...

[hari]

Aldous Huxley's "Brave New World" was partly a journey into the world of mutation. He came from a renowned family with background in Chemistry. Amazing stuff when he appeared at our high school (on our island!) and spoke about his musings which included bits and pieces of his experiments with drugs and whatnots....I was hooked!

[anne]

These are the 3 essays on mutation in the midst of what is Olivia Judson's current series of weekly essays. All the essays are footnoted, which is a pleasure. The work sets a new standard for such easily accessible science writing.

Now, to consider Swedes mutating....

[anne]

http://shakespeare.mit.edu/Comedy/tempest/thetempest.5.1.html

1611

The Tempest
By William Shakespeare

Act V. Scene I.

Before Prospero's cell.

Here PROSPERO discovers FERDINAND and MIRANDA playing at chess

MIRANDA

Sweet lord, you play me false.

FERDINAND

No, my dear'st love,
I would not for the world.

MIRANDA

Yes, for a score of kingdoms you should wrangle,
And I would call it, fair play.

ALONSO

If this prove
A vision of the Island, one dear son
Shall I twice lose.

SEBASTIAN

A most high miracle!

FERDINAND

Though the seas threaten, they are merciful;
I have cursed them without cause.

Kneels

ALONSO

Now all the blessings
Of a glad father compass thee about!
Arise, and say how thou camest here.

MIRANDA

O, wonder!
How many goodly creatures are there here!
How beauteous mankind is! O brave new world,
That has such people in't!

PROSPERO

'Tis new to thee.

[hari]

My three grandchildren (a girl and two boys) remain to be taken through the likes of an extended orientation to origin of life, renaisance, and what became of civilization.

[hari]

My three grandchildren (a girl and two boys) remain to be taken through the likes of an extended orientation to origin of life, renaissance, and what became of civilization.
My son is still a bachelor...suppose he's waiting for the right mate.

[anne]

http://www.huxley.net/bnw/index.html

1932

Brave New World
By Aldous Huxley

A SQUAT grey building of only thirty-four stories. Over the main entrance the words, CENTRAL LONDON HATCHERY AND CONDITIONING CENTRE, and, in a shield, the World State's motto, COMMUNITY, IDENTITY, STABILITY.

The enormous room on the ground floor faced towards the north. Cold for all the summer beyond the panes, for all the tropical heat of the room itself, a harsh thin light glared through the windows, hungrily seeking some draped lay figure, some pallid shape of academic goose-flesh, but finding only the glass and nickel and bleakly shining porcelain of a laboratory. Wintriness responded to wintriness. The overalls of the workers were white, their hands gloved with a pale corpse-coloured rubber. The light was frozen, dead, a ghost. Only from the yellow barrels of the microscopes did it borrow a certain rich and living substance, lying along the polished tubes like butter, streak after luscious streak in long recession down the work tables.

"And this," said the Director opening the door, "is the Fertilizing Room."

Bent over their instruments, three hundred Fertilizers were plunged, as the Director of Hatcheries and Conditioning entered the room, in the scarcely breathing silence, the absent-minded, soliloquizing hum or whistle, of absorbed concentration. A troop of newly arrived students, very young, pink and callow, followed nervously, rather abjectly, at the Director's heels. Each of them carried a notebook, in which, whenever the great man spoke, he desperately scribbled. Straight from the horse's mouth. It was a rare privilege. The D. H. C. for Central London always made a point of personally conducting his new students round the various departments....

[anne]

http://www.nytimes.com/2008/03/26/science/26rodentw.html

March 26, 2008

What a Rodent Can Do With a Rake in Its Paw
By SANDRA BLAKESLEE

Degus are highly social, intelligent rodents native to the highlands of Chile. They adorn the openings of their burrows with piles of sticks and stones, have bubbly personalities and like to play games.

But in a laboratory setting, degus can do much more than play hide-and-seek, according to a study in the online journal Plos One (www.plosone.org). They can learn to use tools.

Specifically, degus have been trained to reach through a fence, grab hold of a tiny rake and pull their favorite food, half a peeled sunflower seed, close enough to reach with their mouths. After two months of practice, researchers say, the degus can move the rake as smoothly and efficiently as croupiers in any Las Vegas casino.

This is first time rodents have been trained to wield tools, said Atshushi Iriki, a neuroscientist, who led the experiments at the Laboratory for Symbolic Cognitive Development at the Riken Institute in Tokyo. But other species may soon join them.

While it has long been thought that tool use is a hallmark of higher intelligence, Dr. Iriki said, the brain structures that underlie such abilities may lie dormant in many animals with good hand-and-eye or paw-and-eye coordination. Training them to use tools in captivity provides insights into the plasticity of their brains, he said, and may shed light on how early humans evolved tool use in the first place.

“There’s an interesting push-pull to this demonstration of the use of an artificial rake by a rodent,” said Richard Morris, a neuroscientist and expert on animal behavior at the University of Edinburgh, who was not involved in the study. “The push is that if rodents no less than primates can learn to use tools, interesting questions arise about the nature and components of intelligence. And the pull part is that the observation sets the stage for a new neurobiological approach to this fundamental facet of mind, of brain.”

In the wild many animals use simple tools. Chimpanzees and crows actually create them. But an underlying question is, What changes take place in an animal brain when tool use evolves?

To find out, Dr. Iriki initially conducted experiments with Japanese macaques, monkeys that do not tend to use tools in the wild. In the laboratory, he trained them to use a rake to reach out and retrieve their favorite treat, raisins. Later the animals learned to use a short rake to pull in a longer rake, which could then be used to fetch more distant raisins.

As the monkeys developed these skills, their brains showed signs of gene activity in a brain region that integrates vision and touch. The same was likely to be true of the degu, Dr. Iriki said. The rodent has superb paw-and-eye coordination and a pad on its paw that can act like a thumb.

In the experiments, six degus stood behind a fence with gaps wide enough to let their forelegs pass through but not their mouths. A rake-like tool was placed within easy reach. The animals had to grasp the rake and pull seeds in close enough to eat.

As the degus became more adept, the experimenters placed the seeds further away. The animals had to push the rake around the seed, twist it and pull.

The degus did not hesitate to use rakes of different sizes, colors and shapes. They were reluctant to use a tool that had no teeth....

[hari]

...Mankind is beautious...and you have to find it.

Incredible from where ALdous chose the title of his book!

[ddt]

Housing Activists Protest At Bear Stearns (Video)
http://dealbreaker.com/2008/03/housing_activists_protest_at_b.php

Over 200 protesters from a housing advocacy group made it inside Bear Stearns corporate offices at 47th and Park Avenue. The protest was organized by the Neighborhood Assistance Corporation of America, which was founded by union activists. (They were the ones in the yellow shirts.) After being ejected from Bear’s lobby, they headed over to JP Morgan Chase. And, a few moments ago, they seem to have wandered off to do whatever it is demonstrators do after a demonstration. (We're guessing: wait in TKTKS line for Xanadu tickets.)

The protesters object to the Fed-led rescue of Bear Stearns by JPMorgan Chase and demand what they call “real solutions” to mortgage difficulties faced by homeowners. They advocate the implementation of a homeowners initiative which would stop all the interest rate increases, roll back the interest rate increases to the initial qualified rate, impose a moratorium on all foreclosures and require the mortgage servicers’ to pursue a loan restructure that reduces the interest rate and/or outstanding mortgage to a mortgage payment the homeowner can afford for the remaining term of the loan.

Update: Reuters now has a story on the protest up on its wires and CNBC has video of the protest.

[ddt]

from Reuters:

"Bear Stearns employees were alternatively amused and perplexed, taking pictures on their cell phones."

haha

[Patricia Shannon]

http://discovermagazine.com/2008/apr/25-3-theories-that-might-blow-up-the-big-bang/article_view?b_start:int=1&-C=

The cyclic universe directly solves the problem of before. With an infinity of Big Bangs, time stretches into forever in both directions. “The Big Bang was not the beginning of space and time,” Steinhardt says. “There was a before, and before matters because it leaves an imprint on what happens in the next cycle.”

Not everyone is pleased by this departure from the usual cosmological thinking. Some researchers consider Steinhardt and Turok’s ideas misguided or even dangerous. “I had one well-respected scientist tell me we should stop because we were undermining public confidence in the Big Bang,” Turok says.

I don't doubt that there are people dumb enough to think that evidence for an infinity of big bangs would somehow give evidence that the big bang existed.
The cyclic universe is not a recent idea. Barring solid proof otherwise, I've always believed it made the most sense, given evidence of the big bang. It doesn't make sense the universe would go on for infinity acting one way, then all the sudden do things differently one time with a single big bang.

It is almost as if our universe were fine-tuned to start out far from equilibrium so it could possess an arrow of time.

That makes as much sense as saying human beings are fine-tuned to provide an suitable environment for tapeworms.

Barbour’s arguments are complex, but his core idea remains simplicity itself: There is no time (pdf). “If you try to get your hands on time, it’s always slipping through your fingers,” Barbour says with his disarming English charm. “My feeling is that people can’t get hold of time because it isn’t there at all.”

So time doesn't exist because humans can't explain it? Typical silly hubris.

[Patricia Shannon]

Correction "that the big bank existed" should have been "that the big bank did not exist"

[Patricia Shannon]

Ok, another correction : "bank" should be "bang"
Maybe the current economic problems are affecting my spelling :)

[Patricia Shannon]

The argument is that organisms with a deleterious mutation rate above a certain threshold must reproduce sexually.

The reason is that sex purges deleterious mutations from the population: sex generates new gene combinations, and thus in each generation it creates some individuals with relatively few deleterious mutations and some with lots. Those with lots die; those with relatively few go on to have large numbers of children....

Of course, this doesn not mean that these organisms will develop sexual reproduction. Some will, some won't. The ones that don't become extinct.

The same in human behavior, whether economics, environment. or any other aspect of life. We may know that we need to take certain actions to avoid severe danger, but that does not guarantee we will take those actions, any more than all, or even most, individuals will change their lifestyles in ways that are helpful to their health and life expectancy.