Regenerating mice? I don't believe it

The Australian: It's a miracle: mice regrow hearts [August 29, 2005]

The web is alive with news of a gen-engineered mice that can regrow organs (except, most interestingly the brain -- as though the brain has a deep commitment to unaltered structures). It smells like cold fusion to me. Too incredible, too unanticipated, too revolutionary.

We have experimented with amputating or damaging several different organs, such as the heart, toes, tail and ears, and just watched them regrow," she said.

"It is quite remarkable. The only organ that did not grow back was the brain.

"When we injected fetal liver cells taken from those animals into ordinary mice, they too gained the power of regeneration. We found this persisted even six months after the injection."

Professor Heber-Katz made her discovery when she noticed the identification holes that scientists punch in the ears of experimental mice healed without any signs of scarring in the animals at her laboratory.

The self-healing mice, from a strain known as MRL, were then subjected to a series of surgical procedures. In one case the mice had their toes amputated -- but the digits grew back, complete with joints.

In another test some of the tail was cut off, and this also regenerated. Then the researchers used a cryoprobe to freeze parts of the animals' hearts, and watched them grow back again. A similar phenomenon was observed when the optic nerve was severed and the liver partially destroyed.

The researchers believe the same genes could confer greater longevity and are measuring their animals' survival rate. However, the mice are only 18 months old, and the normal lifespan is two years so it is too early to reach firm conclusions.

I'd bet my $10 there's something funny here.

Human evolution: fascinating things that won't be taught in Kansas

In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times

This discussion of the evolution of the Y chromosome is fascinating, but I was more struck by some off-handed comments about current hypotheses on human and chimpanzee evolution (none of which will be taught in Kansas). Chimpanzees, are closest relatives, are monsters -- or at least the males are. They slaughter infants of other males, they kill one another frequently, they are murderous to outsiders, their transgender relationships make human males appear enlightened.

Six million years ago, what was our common ancestor like? Did chimpanzees become nastier over time, or did we become (hard to believe) "nicer" -- or is the truth more complex than we can imagine? Was neandertal gentle, and cro magnon viscious (it appears we ate the neandertals)? Six million years is a long time -- even if it is a tiny fraction of the history of large animals.

Incredibly, genetic data and studies of ancient skeletons may combine to give us some clues to a story of a 300,000 generations...

Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.

The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago....

... The chimp Y chromosome has lost the use of 5 of its 16 X-related genes. The genes are there, but have been inactivated by mutation. The explanation, in his view, lies in the chimpanzee's high-spirited sexual behavior. Female chimps mate with all males around, so as to make each refrain from killing a child that might be his.

The alpha male nonetheless scores most of the paternities, according to DNA tests. This must be because of sperm competition, primatologists believe - the alpha male produces more and better sperm, which outcompete those of rival males.

This mating system puts such intense pressure on the sperm-making genes that any improved version will be favored by natural selection. All the other genes will be dragged along with it, Dr. Page believes, even if an X-related gene has been inactivated.

If chimps have lost five of their X-related genes in the last six million years because of sperm competition, and humans have lost none, humans presumably had a much less promiscuous mating system. But experts who study fossil human remains believe that the human mating system of long-term bonds between a man and woman evolved only some 1.7 million years ago.

Males in the human lineage became much smaller at this time, a sign of reduced competition.

The new result implies that even before that time, during the first four million years after the chimp-human split, the human mating system did not rely on sperm competition.

Dr. Page said his finding did not reach to the nature of the joint chimp-human ancestor, but that "it's a reasonable inference" that the ancestor might have been gorillalike rather than chimplike, as supposed by some primatologists.

The gorilla mating system has no sperm competition because the silverback maintains exclusive access to his harem.

Frans B. M. de Waal of the Yerkes National Primate Research Center in Atlanta said he agreed with fossil experts that the human pair bonding system probably evolved 1.7 million years ago but that the joint ancestor could have resembled a chimp, a bonobo, a gorilla, or something else entirely.If ourcommon ancestor was gorilla like, then chimps have taken the nasty road ...

Poisoned soils of New Orleans 8

Extraordinary Problems, Difficult Solutions

It may be that the final blow to New Orleans won't be the floodwaters, but rather what the waters turned up ...

...Louisiana, a center of the oil, gas and chemical industries, "was known for its very weak enforcement regulations," Kaufman said, and there are a number of landfills and storage areas containing "thousands of tons" of hazardous material to be leaked and spread...

...Given New Orleans's desperate straits, recovery teams will not be able to do anything with the toxic mess except pump it into the Gulf of Mexico, ensuring that the contamination will spread to a larger area, he said. "There's just no other place for it."

Once the water is gone, environmental officials will likely undertake a "grid survey," sampling the formerly flooded areas to get soil profiles and determine how safe it is for residents to move back or rebuild.

The survey is likely to take six months. "If it were me, I wouldn't go back until there was a solid assessment of contamination of the land," Kaufman said. And even then, he added, authorities will be monitoring levels of water toxicity along the coastline for years: "There is no magic chemical that you can put in the Gulf to make heavy metals or benzene go away. You're stuck with it."

Toxic soils might end up being what turns much of what was city into undeveloped lands or nature reserves.

Update 9/4/05: Happily, this may not come to pass.

How a foreign policy wonk gets their themes

Obsidian Wings: Formative Experiences: Foreign Policy

This ends up being a remarkably readable and interesting overview of foreign policy errors. It doesn't mention what we got more or less right (Kosovo, it seems) or where we had good intentions (Somalia). It's a set of experiences and principles of interest to anyone who favors a rational approach to governance.

The enlightenment is in full retreat in America

First this: NYT 8/30/05: One adult American in five thinks the Sun revolves around the Earth...

then this:

NYT - Teaching of Creationism Is Endorsed in New Survey

... 42 percent of respondents held strict creationist views, agreeing that "living things have existed in their present form since the beginning of time ... 18 percent said that evolution was "guided by a supreme being" ... 26 percent said that evolution occurred through natural selection ... 38 percent favored replacing evolution with creationism...

It's easy to see why McCain has endorsed teaching creationism in the schools. Whatever his personal beliefs may be (and he's no scientist), no Republican could get nominated without supporting creationism. Noone could be elected without supporting it.

America's retreat from reason is starting to resemble Soviet mysticism. My Soviet era textbook on Atlantology may soon have an increased retail value. At some point all American rationalists may have to seek some Randian retreat -- or move to China. Or just give up.

The politicization of the american military

From two directions, ongoing evidence of the politicization of the American military:

Military Wrestles With Disharmony Among Chaplains

"When we were coneheads -- missile officers -- I would never, ever have engaged in conversations with subordinates aligning my power and position as an officer with my views on faith matters," she said. Today, "I've heard of people being made incredibly uncomfortable by certain wing commanders who engage in sectarian devotions at staff meetings.

and the demotion of an officer that dared to speak up.

David Brin has been blogging on this. I don't think we need assume the deliberate conspiracy of a purge. The modern military has long had a Republican bent, but as the country becomes increasingly polarized, and as evangelical christianity becomes a de facto state and martial religion, it makes sense that those who think Bush is a dolt will leave. In short order the balance tips so only the loyalists remain -- a curious and unanticipated side-effect of a volunteer army.

It is a somewhat worrisome thing to have a military closely aligned with a theocratic right wing government that also controls the House, the Senate, the Supreme Court and much of the media. Fortunately the history of this sort of thing is so reassuring ...

Is Econbrowser being converted to Peak Oil?

Econbrowser: Supply factors in the 2005 oil price surge

World oil production increased 4.2% during 2004, leading many analysts to conclude that demand increases, not supply disruptions, were the story behind last year's rise in oil prices. As data for 2005 become available, I'm forced to conclude that the reason that oil prices have continued to surge above their values from 2004 is not further increases in demand, but rather concerns about the ability of supply to increase significantly above the 2004 levels.

Econbrowser (Hamilton) has been a cogent and insightful critic of simplistic Peak Oil mania. He's not yet ready concede that we may be nearing the Peak Oil zone, but he's getting there.

At the moment he feels the problem is recent past underinvestment in refining and processing, but I've read him for a while. He's clearly shifting his thinking, and lately is tending towards structural production issues as a component.

If we have hit Peak Oil, prices will rise until world consumption falls or stabilizes. Inflation adjusted prices still put us well below the early 1980s, but we're getting up there. I suspect US citizens will make serious changes to their practices when oil passes $7 a gallon, but that China will decrease its consumption earlier (by going into major recession).

If we've really hit Peak Oil that could happen within 1-2 years. Stay tuned to Econbrowser for updates, I'm not willing to bet either way.

The speciation of modern man

The History of Chromosomes May Shape the Future of Diseases - New York Times

Twenty-three chromosomal rearrangements separate man and macaque -- except for some humans it's 24:

... But scientists have also documented some rearrangements that are not hazardous or that are even beneficial. This year, for example, scientists discovered that some Northern Europeans carry a large inverted segment on one of their chromosomes. This inversion boosts the fertility of women who carry it.

How many such flips before you have a new species?

Teaching the controversy: genetics from 1968

The Chromosome Shuffle: Corante - The Loom

Teaching the Controversy: Part XVIII (emphases mine)

The Intelligent Design crew wants to pit the science of 1968 against the science of 2005.

One of the most interesting features of our chromosomes, which I mention briefly in the article, is that we’re one pair short. In other words, we humans have 23 pairs of chromosomes, while other apes have 24. Creationists bring this discrepancy up a lot. They claim that it represents a fatal blow to evolution. Here’s one account, from Apologetics Press:

If the blueprint of DNA locked inside the chromosomes codes for only 46 chromosomes, then how can evolution account for the loss of two entire chromosomes? The task of DNA is to continually reproduce itself. If we infer that this change in chromosome number occurred through evolution, then we are asserting that the DNA locked in the original number of chromosomes did not do its job correctly or efficiently. Considering that each chromosome carries a number of genes, losing chromosomes does not make sense physiologically, and probably would prove deadly for new species. No respectable biologist would suggest that by removing one (or more) chromosomes, a new species likely would be produced. To remove even one chromosome would potentially remove the DNA codes for millions of vital body factors. Eldon Gardner summed it up as follows: “Chromosome number is probably more constant, however, than any other single morphological characteristic that is available for species identification” (1968, p. 211). To put it another way, humans always have had 46 chromosomes, whereas chimps always have had 48.

1968. That's the science the creationists favor? If this were a matter of reason they wouldn't be on the playing field, but of course it's not. Any nation capable of reelecting GWB can readily convince themselves that green is red, and that science in 1968 is as robust as science in 2005.

Of course, on further reflection, that makes perfect sense. Faith based writings in 1210 are just as relevant as those written in 2005. Why should biology be any different?

Love explained

Talk to the Animals - New York Times:

Sure sounds like love to me ...

Functionally, I suspect love is an often temporary chemical imbalance of the brain induced by sensory stimuli that causes us to maintain focus on something that carries an adaptive agenda. Love is an adaptive feeling or emotion - like hate, jealousy, hunger, thirst - necessary where rationality alone would not suffice to carry the day. Could rationality alone induce a penguin to trek 70 miles over the ice in order to mate and then balance an egg on his toes while fasting for four months in total darkness and enduring temperatures of minus-80 degrees Fahrenheit and gusts of up to 100 miles an hour? And bear in mind that this 5-year-old penguin has just returned to the place of its birth from the sea, and thus has never seen an egg in its life and could not possibly have any idea what it is or why it must be kept warm. Any rational penguin would eventually say, 'To hell with this thing, I'm going back for a swim and to eat my fill of fish.'

And to those with particularly challenging children, a not-so-temporary imbalance. If one loves long enough in the face of selfish logic, it would not be surprising were the brain to change fairly permanently.

This is a fascinating essay. Does the necessity of love indeed bound rationality? I don't quite agree. I think the author is confusing 'rationality' with 'self-interest'. Rationality is the capacity to reason, self-interest is one end to which reason is put. One may be exceedingly capable of logic, extrapolation, creativity and problem solving, and yet dedicate those ends to comrades, children, friends, society, or mate.

From the perspective of pure reason, I suspect a worm or even a rock is loved neither more nor less than one's self. Reason alone has no goals nor ends, any more than today's computers have goals or ends.

Excellent discussion of extended warranties or service contracts

To Buy or Not to Buy: The Quandary of Warranties - New York Times

1. The length of a manufacturer's warranty (assuming, unlike Samsung air conditioners, one can find a service center) is a marker of quality. Extended warranties or service contracts are pure insurance plans.

2. The margin on electronics is 25%, the margin on a service contract is 45%. That's why sales people push service contracts.

3. Consumer reports has some specific recommendations:

Consumer Reports generally advises against buying extended service contracts because 'the cost of repair is probably equal to the cost of warranty, so you should probably just keep that money in your pocket,' a spokeswoman, Lauren Hackett, said. One Consumer Reports survey found that three years after purchase just 5 percent to 7 percent of televisions needed repair, and 13 percent of vacuums (not counting belt replacements). But 33 percent of laptops had been sent to the shop or the recycle bin.

The consumer group does recommend extended service policies on three items, Ms. Hackett said: laptops, treadmills (they are too cumbersome to take to the shop, she said, and service calls are expensive) and plasma TV's, because the technology is new and 'if you are spending $5,000 for a TV set, you might want to get a warranty.

A very nice summary, except they forgot that many high end credit cards offer one year extensions to the manufacturer's contract. Once you factor in that option any service contract becomes much less interesting -- even on a laptop.

Another twist: sometimes the manufacturer's service is not the best. Apple's service contract (AppleCare) requires devices be serviced by Apple, and they apparently use psychopathic inmates as their labor force. There are advantages to finding non-Apple service if it's available.

Strategic errors: creating CD DRM schemes that shut out the iPod

Apple, Digital Music's Angel, Earns Record Industry's Scorn - New York Times

This is a great business article. Apple and the record labels are fighting about Apple's online music store pricing and Apple's iPod only DRM scheme (FairPlay).

Why does Apple have any leverage at all in this fight? Because the alternative to Apple is illegal file sharing -- and there's no revenue there at all.

That's why BMG's DRM protected CD scheme is suicidal:

... BMG in particular has taken steps that may apply pressure to Mr. Jobs to make Apple's software compatible with that of other companies. The company has issued dozens of new titles - including high-profile CD's from the Dave Matthews Band and the Foo Fighters - with software to limit the number of copies that can be made from the disc. The software is compatible with Microsoft's music software, but not Apple's, and as a result music from those Sony BMG albums cannot be transferred to iPods that are hooked up to Windows-based PC's. EMI has been test-marketing similar software with a handful of titles.

So what will a BMG customer do now? Will they give up iTunes, their iPod, and the music they've purchased online? Or will they get the MP3s from friends or strangers? Just guess.

Phone company posted rates are completely meaningless

A Monthly Mystery - New York Times

Well, not completely meaningless. You know the monthly fee will be higher than whatever is published. I've blogged on this before and sent letters of complaint to our state attorney general. At last the New York Times has noticed:

Although surcharges have been around for a while, they have been growing and more consumers are complaining that such fees have become a backdoor way for phone companies to raise prices while keeping advertised rates low.

The carriers might promote flat-rate phone plans for, say, $49.99 a month, but once the many indecipherable fees are larded into a bill, a customer may actually pay $10, $20 or more a month.

"The proliferation of these charges is happening because the carriers are playing a shell game, plain and simple," said Thomas Allibone, an independent auditor and a former member of the consumer advisory committee at the Federal Communications Commission. "They'd rather weather a customer's complaint because they are making $20 or more in surcharges."

...The phone companies say that the surcharges are legal and that they have the right to keep them out of the advertised price of calling plans as long as they are explained on Web sites and in service contracts.

I wrote my letter to our attorney general about Sprint when I tried to get a copy of contract that explained their pricing. Oddly enough, they couldn't find one. I tried quite a bit.

In our increasingly libertarian world, caveat emptor is a slogan to live by.

Alas, the fundamental problem is that, in a sufficiently complex environment, we are all stupid. There is some point at which we can't keep up and we simply surrender all hope. Cheap computing power is enabling scams of great complexity, such as intricate ways to disguise true prices. We could negotiate one such scam, but not a hundred. How many people have thought through the full implications of various Digital Rights Management schemes, and how those schemes decrease the value of DRM protected media?

Bottom line, barring regulatory action, this will only get worse.

First United Church of the Flying Spaghetti Monster

Open Letter to Kansas School Board: Teachng the Controversy

If one is going to teach intelligent design as science, then one ought to be able to litigate to include other approaches, such as 'incompetent design' or 'accidental creation' or 'silly design' ...

...I’m sure you now realize how important it is that your students are taught this alternate theory. It is absolutely imperative that they realize that observable evidence is at the discretion of a Flying Spaghetti Monster. Furthermore, it is disrespectful to teach our beliefs without wearing His chosen outfit, which of course is full pirate regalia. I cannot stress the importance of this enough, and unfortunately cannot describe in detail why this must be done as I fear this letter is already becoming too long. The concise explanation is that He becomes angry if we don’t.

You may be interested to know that global warming, earthquakes, hurricanes, and other natural disasters are a direct effect of the shrinking numbers of Pirates since the 1800s. For your interest, I have included a graph of the approximate number of pirates versus the average global temperature over the last 200 years. As you can see, there is a statistically significant inverse relationship between pirates and global temperature...

...In conclusion, thank you for taking the time to hear our views and beliefs. I hope I was able to convey the importance of teaching this theory to your students. We will of course be able to train the teachers in this alternate theory. I am eagerly awaiting your response, and hope dearly that no legal action will need to be taken. I think we can all look forward to the time when these three theories are given equal time in our science classrooms across the country, and eventually the world; One third time for Intelligent Design, one third time for Flying Spaghetti Monsterism, and one third time for logical conjecture based on overwhelming observable evidence.

Yo ho ho and a bottle of rum.

Has the social security crisis been averted? Klotho protein for aging

Life-Lengthening Hormone Found in Mouse Research

We can extend the lifespan of mice 20% by injecting a peptide produced by the Klotho gene:

The discovery was triggered by a study Kuro-o and his colleagues published in 1997. That study identified a gene in mice that, when damaged, caused the animals to experience all the hallmarks of aging in humans -- hardening of the arteries, thinning bones, withered skin, weak lungs -- and to die prematurely. They dubbed the gene Klotho, for the Greek goddess who spins the thread of life.

Suspecting the gene may play a role in regulating life span, Kuro-o and his colleagues genetically engineered mice with overactive Klotho genes. In the latest experiments, they found that these animals lived an average of 20 to 30 percent longer than normal -- 2.4 to 2.6 years vs. a normal life span of about two years -- without any signs of ill effects, according to the new report.

'The extension of life span is widely accepted as a reliable marker for the suppression of aging,' Kuro-o said. 'This shows the Klotho gene regulates aging.'

The researchers then identified a small protein component, called a peptide, that the gene produces and found it circulating in the animals' blood at double the normal level.

After isolating and purifying the substance and reproducing it through genetic engineering techniques, the researchers injected the substance into normal mice. Tests on those animals, combined with experiments involving cells in the laboratory, indicate that the substance modulates a crucial biological pathway involved in an array of basic metabolic functions that has become the focus of aging research in recent years.

'It's a pathway that has been conserved by evolution that has been found to play a key role in regulating life span for flies, worms, mice and probably humans,' Kuro-o said.

Studies, for example, suggest that damping down this pathway -- known as the insulin/insulin-like growth factor-1 signaling pathway -- may be the mechanism that extends longevity in animals that are fed an ultra-low-calorie diet.

This may be very important for persons with the very rare disease of Progeria. (Yes, this has occurred to others.)

Would a purified protein of this sort slow aging in humans and thus avert the social security crisis? Ahh, there's the catch. Given the advantages to human communities of long-lived women, and the the extent to which males have mostly female genomes, I'd guess we find three things:

- It doesn't work on females -- we'll find their Klotho peptide levels are already pretty high.
- It does add 5 years of life to newborn males if given for the entire lifespan, but has no significant benefit for middle-aged males.
- It has a big impact on a subset of the the population that turns out to have a faster basal aging rate (maybe as high as 30% of our population).

The third of these might indeed avert the "social security crisis". (We already know how to avert it really -- more selective immigration policies (wealthier immigrants -- follow Canada's model) and making payouts more progressive.)