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RNA activation of genes

Thursday, November 30, 2006

The subject of RNA has come up in a number of scientific developments recently. It seems that RNA occurs in more forms and plays more roles within cells than scientists have previously supposed.

Some of the important forms that RNA can take have been known for some time. The oldest of these are messenger RNA (mRNA), which is an intermediate stage in the translation of genetic information from DNA to proteins, and transfer RNA (tRNA), which assists in the making of proteins in a ribosome. Further, ribosomes themselves are made up of some proteins and another type of RNA, ribosomal RNA (rRNA). Besides that, RNA is the genetic material of the type of viruses known as retroviruses, which include HIV.

In the 1980s, forms of RNA, called ribozymes, that act as catalysts in cellular chemistry, were discovered – and the discovery led to a Nobel Prize.

All of the forms of RNA found in cells, except for tRNA, are known collectively as non-coding RNA (ncRNA) because they do not directly encode the information in genes. Within the past 10 years a number of additional types of ncRNA have been found, including microRNA (miRNA) and small interfering RNA (siRNA).

Small interfering RNA is a big deal, big enough that the discovery has already lead to the awarding of a Nobel prize this year, though the discovery occurred less than 10 years ago:

Nobel prize for genetic discovery
Two US scientists have been awarded the Nobel Prize for medicine for their pioneering work in genetics.

The work of Dr Andrew Fire and Dr Craig Mello could lead to new treatments for a range of illnesses, including viral infections and cancer.

They discovered a phenomenon called RNA interference, which regulates the expression of genes.

The process has the potential to help researchers shut down genes which cause harm in the body.

The breakthrough has also given scientists the ability to systematically test the functions of all human genes.

The process by which siRNA can interfere with the expression of certain genes is known as RNA interference (RNAi). The process can occur by at least two mechanisms and has been thoroughly verified.

Now there is a surprizing, and controversial, claim that similar short RNA molecules can boost the expression of some genes:

How to get your genes switched on
The latest twist on the Nobel prizewinning method of RNA interference, or RNAi, could prove to be a real turn-on. Whereas standard RNAi silences a target gene, switching protein production off, the new technique boosts gene activity, providing a genetic "on" switch.

RNAi can silence genes in two ways. It can block the messenger RNA that is the intermediate between gene and protein and it can also interfere with "promoter" sequences that boost a gene's activity. It was while investigating this second phenomenon that Long-Cheng Li of the University of California, San Francisco, and his colleagues stumbled on the new method, dubbed RNA activation.

There's more detail in this article from Science (subscription rqd):

Small RNAs Reveal an Activating Side
This surprising skill--dubbed RNAa, because the RNAs activate genes--is described this week in the online edition of the Proceedings of the National Academy of Sciences. If the claim is sustained, RNAa would be a powerful biological tool and could lead to new therapies for diseases such as cancer. But some scientists say the results may reflect an indirect outcome of RNAi, rather than a new way to activate genes. "It's going to be a question of whether this holds up," says Erik Sontheimer, an RNA researcher at Northwestern University in Evanston, Illinois.

At this point, it seems that the gene activation could occur because the production of an inhibitory protein is blocked by conventional RNAi.
One key question is whether Li's RNAs are activating genes by silencing others, which would just be RNAi by another name. For example, proteins called negative transcription factors can prevent genes from being transcribed; silencing the genes for these proteins could activate genes they control.

But there is evidence that something different might be happening.
No one yet knows how small RNAs could turn genes on, especially for so long. RNAi typically silences genes for 5 to 7 days, but RNAa boosted gene activity for up to 13 days. The molecular machinery underlying RNAi appears to be involved in RNAa, raising the question of how the same enzymes can sometimes turn genes off, and sometimes on. "What makes one siRNA [small interfering RNA] a silencer, and what makes the other one an activator?" asks Sontheimer. "No clue."

Additional information:

Small dsRNAs induce transcriptional activation in human cells – original research paper (subscription rqd for full access)

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Stuff I forgot to mention about memory

Wednesday, November 29, 2006

And speaking of memory here and here, there's recent research I forgot to mention. Oh, the irony. (Damn! I sure hope someone comes up with a memory pill, and fast.)

First up is a gene named Kibra. It's expressed in the hippocampus, and has been found to be associated with memory performance.

Research Team Identifies Human 'Memory Gene'
The impact of the study is that it gives the research community a new and important handhold into truly understanding the process of memory. The ramifications of this report are ultimately developing new and effective medicines that can combat memory loss, and that might also help improve memory in people with memory disorders like Alzheimer's disease.

The team has already begun working on new drugs to restore memory function in age-related memory loss and diseases that have a memory loss component.

What this press release doesn't make clear is that discovering exactly what the protein corresponding to this gene does in neurons of the hippocampus will help us understand memory better. And that in turn may help find ways to augment memory even in people who don't have memory disorders.

In the meantime, while we're awaiting such a breakthrough, research has found ways to make the best use of the memory we have. First:

Asleep at the Memory Wheel
Going a night without sleep may cause your hippocampus to go on strike. A new study has caught this crucial memory-encoding brain region slacking off in college students the day after they've pulled an all-nighter. The study is one of the first to investigate how sleep deprivation interferes with memory mechanisms in the human brain.

Unfortunately, you need a subscription to Science in order to see the full article, but the key point is this:
To find out which part of the brain was responsible for this forgetfulness, the researchers repeated the experiment with a different group of undergrads, but this time used functional magnetic resonance imaging (fMRI) to monitor brain activity while the students viewed a set of emotionally neutral photographs. The fMRI scans revealed lower activity in the hippocampus of sleep-deprived students than in well-rested students. This suggests that just as sleep is important for consolidating new memories after they're learned, as other studies have shown, it's equally important for preparing the brain to learn new things the following day.

This work was done by Matthew Walker and his colleagues at Harvard. Here are several reports of releated work they've done previously.

One last item – if you want a good memory, lay off the weed:

Marijuana wreaks havoc on brain's memory cells
Smoking marijuana often causes temporary problems with memory and learning. Now researchers think they know why.

The active ingredient in the drug, tetrahydrocannabinoid (THC), disrupts the way nerves fire in the brain’s memory centre, a new study shows.

David Robbe at Rutgers University in New Jersey, US, and colleagues gave rats an injected dose of THC, proportional to the amount inhaled by a person smoking an average-sized marijuana joint.

The team monitored the drug’s effect using wire probes placed in a memory centre in the animals’ brains – the hippocampus. The probes monitored the nerve impulses as they fired.

Normally, cells in hippocampus fire in sync, creating a current with a total voltage of around 1 millivolt. But THC reduced the synchrony of the firing. The drug did not change the total number of firings produced, just their tendency to occur at the same time – and this reduced the combined output voltage of the nerve signals by about 50%.

Abnormal firing occurs because THC binds to a receptor on the surface of the nerve cell, and so indirectly blocks the flow of current, Robbe believes.

See also: Marijuana's High Times Not Memorable with Neurons Out of Sync

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Folate and cancer

Monday, November 27, 2006

I must admit I don't really understand all the hubbub about folate and cancer. First we have this strange business where some say that low levels of folate in one's diet either increase the risk of colon cancer, or else decrease it. Take your pick.

And now we read that, as far as breast cancer is concerned, it doesn't have anything to do with risk:

Dietary Folate Intake Not Associated With Breast Cancer Risk
Folate, a vitamin that is abundant in fruits and vegetables, helps maintain DNA integrity, and a lack of it has been associated with DNA strand breaks and disruptions in DNA repair. Previous studies have suggested that increased folate intake may be associated with a reduced risk of breast cancer, but this association was not replicated by large studies that followed study participants prospectively. In addition, a common genetic change in the gene encoding a key enzyme in folate metabolism, called MTHFR, can lead to low folate levels in the body and therefore could be associated with breast cancer risk.

OK, so folate somehow is good for DNA integrity in the petri dish. Fair enough. Evidently, however, there's more to the story when folate is ingested with one's food. Like, maybe, it has a hard time reaching one's cells where it can do some good. Looks like we have a drug delivery issue here.

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High energy cosmic rays

Astrophysicists have wondered for a long time where cosmic rays come from, especially the most energetic ones.

A couple of recent research reports identify two different sources. The first of these is our old friend, Cassiopeia A:

Chandra discovers relativistic pinball machine

New clues about the origins of cosmic rays, mysterious high-energy particles that bombard the Earth, have been revealed using NASA's Chandra X-ray Observatory. An extraordinarily detailed image of the remains of an exploded star provides crucial insight into the generation of cosmic rays.

For the first time, astronomers have mapped the rate of acceleration of cosmic ray electrons in a supernova remnant. The new map shows that the electrons are being accelerated at close to the theoretically maximum rate. This discovery provides compelling evidence that supernova remnants are key sites for energizing charged particles.

This situation is described as a "pinball machine", because the electrons making up the cosmic rays (in this case) are accelerated by being bounced back and forth between magnetic fields and the expanding shock wave generated by the supernova:
"The electrons pick up speed each time they bounce across the shock front, like they're in a relativistic pinball machine," said team member Glenn Allen of the Massachusetts Institute of Technology (MIT), Cambridge. "The magnetic fields are like the bumpers, and the shock is like a flipper."

There are other accounts of this research here, here, and here.

Meanwhile, in another part of the universe, another team has identified a completely different source:

'Big bang gas' in cosmic particle-accelerator shock
Giant shockwaves around a distant cluster of galaxies could be generating some of the mysterious cosmic rays that strike Earth. They could also give us a clue as to why the universe is threaded with magnetic fields.

The cluster, called Abell 3376, is a swarm of galaxies about 600 million light years away. On either side of this swarm are two huge arc-like structures, each about 3 million light years across, that are sending out radio waves.

However, interestingly enough, apparently it is still the combination of magnetic fields and shock waves that is responsible for the particle acceleration – even though Cassiopeia A is 10,000 light years distant from us, while Abell 3376 is 60,000 times further away. The latter is also several million light years across, while Cassiopeia A is only about 10 light years wide. So there remains a major mystery about what produced such huge shock waves in Abell 3376:
Then what created the shocks in the first place? There are two possibilities. It may be that roughly a billion years ago, two clusters crashed into one another to form Abell 3376. The collision could have sparked a shockwave that travelled out through the cluster gas, whose remnants we are now seeing.

But there is a more intriguing possibility. Primordial gas, untouched since the big bang, should be constantly pouring into all galaxy clusters. Computer simulations of the cosmos show that gravity tends to pull the gas into stringy structures called filaments.

Abell 3376 could be threaded on one such filament, and the two shockwaves could mark where this cool ancient gas smacks into the super-hot gas of the cluster.

Other accounts of this research: here, here.

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Biological basis of aggression

Saturday, November 25, 2006

Is it typical in animal species that there are significant, genetic differences between males and females in common behavior? The answer is yes, apparently, for fruit flies. And there is even a single gene whose slightly different forms in males and females produces differing behavior typical of each sex:

Fighting Like a Girl or Boy Determined By Gene in Fruit Flies
Fighting like a girl or fighting like a boy is hardwired into fruit fly neurons, according to a study in the Nov. 19 Nature Neuroscience advance online publication by a research team from Harvard Medical School and the Institute of Molecular Pathology in Vienna. The results confirm that a gene known as “fruitless” is a key factor underlying sexual differences in behavior. The findings mark a milestone in an unlikely new animal model for understanding the biology of aggression and how the nervous system gives rise to different behaviors.

This gene was already known to control courting behavior, which (unsurprisingly) differs between males and females. But the differences go beyound courting:
The fruitless gene is known for its role in male courtship. The large gene makes a set of male-specific proteins found exclusively in the nervous system of fruit flies, in about 2 percent of neurons. The proteins are necessary for normal courting. Males missing the proteins do not court females, and they sometimes court males, other research groups have shown. Females with a male version of the gene perform the male courting ritual with other females.

The same gene directs another sex-specific behavior – fighting patterns, the new study shows. Female fighting, for example, largely involves head butts and some shoving. Males prefer lunges; they rear up on their back legs and snap their forelegs down hard – sometimes nailing an opponent that is slow to retreat.

The flies undergo a major role reversal when the male and female gene versions are switched. With a feminine fruitless gene, male flies adopt more ladylike tactics, mostly the head butt and some shoving. With the masculine fruitless gene, females instinctively lunge to the exclusion of their usual maneuvers.

Can such results be extrapolated to more complex animals like, say, humans? Of course not, at this early stage. But it's a start. The next step is to investigate just how the fruit fly gene tweaks the fly's nervous system to yield specific behavior:
The findings provide a welcome guidepost to help enable future research to track down the underlying neural circuitry, said Bruce Baker, a biology professor at Stanford who first linked the fruitless gene to male-specific courtship behavior. “That’s a pretty big thing,” Baker said. “We can think about understanding in molecular detail how we go from the initial genes and the proteins they encode to the nervous system that causes our body to respond in certain ways.” More generally, he said, such studies form a potential bridge between systems neuroscience studies of behavior and modern molecular neuroscience research into individual neurons and synapses.

Once that is understood in fruit flies, researchers can approach analogous behavior in more complex animals. As another account of the research explains,

Gender-bending boy fruit flies fight like girls
It is important to learn about such complex behaviors in a simple organism, and then apply this knowledge to higher and higher forms while ultimately trying to gain insight into human behavior, Kravitz said.

People do not have an exact equivalent to the "fruitless" gene, Kravitz added, but probably have other human genes serving similar functions.

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NASA's Spitzer Peels Back Layers of Star's Explosion

Wednesday, November 22, 2006

NASA's Spitzer Peels Back Layers of Star's Explosion

Astronomers using NASA's infrared Spitzer Space Telescope have discovered that an exploded star, named Cassiopeia A, blew up in a somewhat orderly fashion, retaining much of its original onion-like layering.

Cassiopeia A – click for 800×800 image

Cassiopeia A, or Cas A for short, is what is known as a supernova remnant. The original star, about 15 to 20 times more massive than our sun, died in a cataclysmic "supernova" explosion relatively recently in our own Milky Way galaxy. Like all mature massive stars, the Cas A star was once neat and tidy, consisting of concentric shells made up of various elements. The star's outer skin consisted of lighter elements, such as hydrogen; its middle layers were lined with heavier elements like neon; and its core was stacked with the heaviest elements, such as iron.

Earlier (2004) press release on Cassiopeia A, with images: Deepest Image of Exploded Star Uncovers Bipolar Jets

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This is pathetic

Snap judgments about candidates are the best way to pick winners, study suggests
After watching ten-second silent video clips of competing gubernatorial candidates, participants in the study were able to pick the winning candidate at a rate significantly better than chance. When the sound was turned on and participants could hear what the candidates were saying, they were no better than chance at predicting the winner. For the study, Benjamin and Shapiro showed 264 participants, virtually all Harvard undergraduates, ten-second video clips of the major party candidates in 58 gubernatorial elections from 1988 to 2002.

Researchers found that the accuracy of predictions based solely on silent video clips was about the same as or greater than the accuracy of predictions based on knowledge of which candidate was the incumbent and information about the prevailing economic conditions at the time of the election, including the unemployment rate and any changes in personal income for the year prior to the election.

I understand that "leadership" is important for forming consensus and hence getting things done. And charisma is a large part of what makes some people seem like "leaders".
The findings also underscore the importance of charisma as distinct from policy positions or party affiliations in winning elections.

But what if the policy positions of the candidates with more charisma in fact stink out loud? Happens all too often...

Given candidates who lack principles and ethics, is there much difference between having charisma and being a good con artist?

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Alternative splicing

Tuesday, November 21, 2006

Not so very long ago it used to be that molecular biologists thought that for every protein in the body there was a specific gene, and every gene contained the instructions for making just one protein. Then, when the human genome was completely mapped several years ago, it was found, to everyone's embarrassment, that there were a lot fewer than 25,000 different genes in the genome. This is in a genome of 3.12 billion base pairs. And the human genome is far from the largest. Ordinary corn has 5 billion base pairs and 50,000 genes. The trumpet lily plant (Lilium longiflorum) has 90 bilion base pairs in its genome, and the marbled lungfish (Protopterus aethiopicus) has 139 billion – but apparently nobody has had the patience to sit down and count their actual genes. (Reference; see also here.)

Anyhow, it's estimated that humans use at least 100,000 different proteins, maybe a lot more, so the point is that some genes must be capable of coding for a lot more than just one protein. It's now understood that this is accomplished by the process known as alternative splicing. As you know, genes are not simple, uninterrupted sequences of base pairs. They have within them several subsequences known as exons and introns. In a nutshell, the exons are eventually transcribed into messenger RNA, while the introns are discarded.

Except there's a little more to it than that. In order to produce different proteins, it's necessary to select a subset of exons to code for each particular protein. So how does this actually happen? Some new research has figured this out in one specific case:

RNA Map Provides First Comprehensive Understanding Of Alternative Splicing
It's biology's version of the director's cut. In much the same way that numerous films could be stitched together from a single reel of raw footage, a molecular process called alternative splicing enables a single gene to produce multiple proteins. Now a new RNA map, created by a team of researchers at Rockefeller University and the Howard Hughes Medical Institute and announced in the journal Nature, shows for the first time how the specific location of short snippets of RNA affects the way that alternative splicing is controlled in the brain.

Though scientists have begun to appreciate how alternative splicing adds a layer of complexity to brain processes that enable us to think and learn, exactly how alternative splicing is regulated during these processes -- and in some cases is uncontrolled (or dysregulated) to cause disease -- has remained elusive. The map provides the first comprehensive understanding of how alternative splicing works throughout the genome. The results have implications for a better understanding of such brain functions as learning and memory, neurological diseases and cancer biology.

To make a long story short, there is a brain protein called Nova that was known to be capable of binding to 50 different sequences of RNA. The study found that there were actually 30 different exons which contained those sequences, and whether or not a given sequence had been bound by Nova could cause the exon to be either included or excluded (depending on circumstances) from a final transcript.

This is of more than just theoretical interest. Errors in the transcription process can cause a variety of disease conditions:
By offering a global understanding of how alternative splicing works across the genome, the map has implications for the treatment of a growing list of human neurologic diseases in which RNA regulation, and particularly RNA splicing, has been implicated as the primary cause, including certain types of cancer and a number of brain and muscle disorders.

"Given that the complexity of the brain is orders and orders of magnitude more complex than the number of genes we have, one of the intriguing things about alternative splicing is that a relatively small number of regulatory splicing factors acting in concert on a single transcript can potentially generate a large number of different protein variants," says Darnell.

"There is a converging set of observations indicating that as neurologic diseases are better understood, alternative splicing is going to play an important role in generation of disease and therefore an important role in normal generation of cognitive function," he adds. "Our new work lays out an approach to developing a global understanding of how alternative splicing is regulated by one disease-associated protein, Nova, offering a route by which scientists may now be able to approach a number of diseases with a fresh start."

It's interesting, also, that this process is being observed in the brain. Because, as Antonio Damasio has just predicted for New Scientist as one of the most likely discoveries of the next 50 years, we should learn how relatively few genes can create such complexity in the brain:
Most of what I regard as exciting in recent neuroscience has concentrated on two broad areas: molecular neurobiology and an understanding of the systems related to cognition and behavior. The future will no doubt promote advances in those two areas. On the molecular side, it will be possible to know how so few genes (relatively speaking) create so much complexity in the human brain.

It would be a good guess that the use of alternative splicing is pretty common in brain tissue.

Update: And in fact, I wrote about this very topic a year ago: RNA splicing occurs in nerve-cell dendrites. The interesting thing is that in most cells, splicing is known to occur only in the nucleus. In neurons, however, it occurs in dendrites, the part of a neuron to which other neurons form connections.

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Improving your memory

Sunday, November 19, 2006

Who wouldn't like to have a better memory? Probably nobody, except maybe Solomon Shereshevskii or the fictional Ireneo Funes.

Neuroscientists are coming up with various small steps towards better memory:

Scientists Use Gene Therapy To Improve Memory And Learning In Animals
Stanford University neuroscientists have designed a gene that enhances memory and learning ability in animals under stress. Writing in the Nov. 8 issue of the Journal of Neuroscience, the Stanford team says that the experimental technique might one day lead to new forms of gene therapy that can reduce the severe neurological side effects of steroids, which are prescribed to millions of patients with arthritis, asthma and other illnesses.

"Steroids can mess up the part of the brain involved in judgment and cognition," said neuroendocrinologist Robert Sapolsky, co-author of the study. "In extreme cases it's called steroid dementia. Ideally, if you could deliver this gene safely, it would protect the person from some of these cognitive side effects, while allowing the steroid to do whatever helpful thing it should be doing elsewhere in the body."

Unfortunately, gene therapy is (at least presently) rather a drastic technique:
[T]his type of gene therapy will not be medically available until scientists figure out a way to safely deliver the chimeric gene to humans, Sapolsky said. He also noted that the treatment should be used to prevent severe neurological side effects caused by medication and should not be given to those who simply want to enhance their short-term memory and learning skills. "You can't drill into people's heads and inject a virus just because somebody has a big exam coming up, " he said.

OK, so maybe it's back to the drawing boards. Here's something that, at least, doesn't require a Black & Decker:

A Stimulating Slumber
Each night as you sleep, your brain buzzes with electrical activity. Neuroscientists suspect that that this activity helps solidify memories formed during the day. Now, they've bolstered their case: for the first time, researchers have shown that electrically stimulating the brain during sleep can enhance memory performance the following day.

We might call that a "proof of concept". Looks a little better, but still sort of cumbersome. However, if you're taken with the idea there are more references on the study here and here.

OK, guys, let's try once more. Can't we do just a little better? Maybe:

Hopkins researchers discover how brain protein might control memory
Researchers at Johns Hopkins have figured out how one particular protein contributes to long-term memory and helps the brain remember things longer than an hour or two. The findings are reported in two papers in the Nov. 9 issue of Neuron.

The protein, called Arc, has been implicated in memory-linked behaviors ranging from song learning in birds to rodents being aware of 3-D space.

It turns out that this Arc protein works indirectly by controlling a couple of other proteins:
To figure out what Arc was doing, the Hopkins team looked for what other proteins Arc "plays" with. Using Arc protein as bait, they went on a molecular fishing expedition in a pond filled with other proteins normally found in the brain and hooked two known to be involved in transporting materials into and out of cells.

"Moving things in and out of cells is critical for normal brain cell function. We were extremely excited that Arc might somehow be involved in this transport because it links transport to memory formation," says Worley. "This brings us one step closer to understanding how the brain saves memories."

According to Worley, memories form when nerve cells connect and "talk" to other nerve cells. It's thought that the stronger these connections are, the stronger the memory.

Bueno. Muy bueno. Unfortunately, proteins don't work very well when delivered in pill form. (The stomach tends to digest them.) But perhaps we're getting closer to something that will help you pass that bar exam.

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Hubble Finds Evidence for Dark Energy in the Young Universe

Thursday, November 16, 2006

NASA's Hubble Finds Evidence for Dark Energy in the Young Universe
Scientists using NASA's Hubble Space Telescope have discovered that dark energy is not a new constituent of space, but rather has been present for most of the universe's history. Dark energy is a mysterious repulsive force that causes the universe to expand at an increasing rate.

Investigators used Hubble to find that dark energy was already boosting the expansion rate of the universe as long as nine billion years ago. This picture of dark energy is consistent with Albert Einstein's prediction of nearly a century ago that a repulsive form of gravity emanates from empty space.

So, that's the big cosmology news for today. It's very closely releated to what's discussed in the Beyond Einstein article of a couple of days ago.

Actually, in a way, it's kind of boring, since the findings are pretty much what "conventional wisdom" (of the last 6 or 7 years) has expected. No apple carts have been upset as a result of this. But further confirmataion of accepted theories is in its own way very important too.

The take-away is that NASA now has even better justification for the JDEM kind of mission to obtain better supernovae data in order to put tighter limits on the w parameter in the "equation of state" for dark energy.

I've written a lot about this stuff before in much more detail here, but perhaps I'll revisit that to highlight the most important ideas as they relate to the present news.

There are some presentation materials here from today's NASA press conference.

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What makes humans smarter than chimps?

Wednesday, November 15, 2006

Why have geneticists considered complete sequencing of the genomes of a variety of species so important? One reason (of many) is what we learn by comparing these other genomes with the human genome. And if you consider the genome of a close relative of humans, such as our closest relatives, chimpanzees, the comparison may be particularly enlightening.

The complete sequencing of the chimp genome was announced in August 2005. In May of this year, some results from comparing human and chimp genomes started to emerge:

Chimpanzee study reveals genome variation hotspots
Researchers believe that dynamic regions of the human genome - "hotspots" in terms of duplications and deletions - are potentially involved in the rapid evolution of morphological and behavioral characteristics that are genetically determined.

Now, an international team of researchers, including a graduate student and an associate professor from Arizona State University, are finding similar hotspots in chimpanzees, which has implications for the understanding of genomic evolution in all species.

That's an interesting clue, but it still doesn't tell us much about what accounts for the difference between human and chimp brains. More specifics about this came out three months ago, in August:

Scientists Find Brain Evolution Gene
Scientists believe they have found a key gene that helped the human brain evolve from our chimp-like ancestors. In just a few million years, one area of the human genome seems to have evolved about 70 times faster than the rest of our genetic code. It appears to have a role in a rapid tripling of the size of the brain's crucial cerebral cortex, according to an article published Thursday in the journal Nature.

Study co-author David Haussler, director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, said his team found strong but still circumstantial evidence that a certain gene, called HAR1F, may provide an important answer to the question: "What makes humans brainier than other primates?" Human brains are triple the size of chimp brains.

But that's only the beginning of the story:

Scientists Identify Gene Difference Between Humans and Chimps
Although this research does not definitively link this region to brain differences between humans and our closest relatives, it is intriguing. "We don't know what it does, and we don't know if it interacts with reelin, but the evidence is very suggestive that this gene is important in the development of the cerebral cortex, and that's exciting because the human cortex is three times as large as it was in our predecessors," notes team leader David Haussler of the University of California, Santa Cruz. "Something caused our brains to evolve to be much larger and have more function than the brains of other mammals."

And, of course, this is just the first of the 49 rapidly evolving regions to be studied. "Now we have to go through the other 48," Haussler says.

Sure enough, other interesting things are being found in other regions of the human genome that have evolved rapidly. This came out in October:

DNA trail points to human brain evolution
The human brain may have evolved beyond that of our primate cousins because our brain cells are better at sticking in place, researchers say.

A new study comparing the genomes of humans, chimps, monkeys and mice found an unexpectedly high degree of genetic difference in the human DNA regions that influence nerve cell adhesion, compared with the DNA of the other animals.

Accelerated evolution here allowed human brain cell connections to form with greater complexity, enabling us to grow bigger brains, the researchers suggest.

Ah ha. So enhanced adhesion between neurons facilitates bigger brains. That makes sense. But the story gets even more interesting, because apparently it's not only specific genes that play a role in this, but certain noncoding DNA regions between genes do also:

Looking for Smarts Between the Genes
The strongest evidence for accelerated evolution on the human line was found in noncoding sequences next to genes involved in helping neurons adhere to each other. The team found 69 such sequences, suggesting that changes in these regulatory elements may have contributed to the evolution of uniquely human cognitive talents.

Neuronal adhesion molecules play a major role in wiring the brain, Rubin says, such as the formation of connective synapses between nerve cells. These processes, he adds, are important in early brain development and also crucial for learning, memory, and cognition in adults. For example, Rubin says, one of the noncoding sequences is next to a gene called CNTN4, which appears to be involved in the development of both verbal and nonverbal communication abilities in humans, while another is adjacent to CHL1, which is linked to cognition in both humans and mice.

So this links up with another famously intriguing question: why is it that more than 90% of the human genome is made up of gaps between genes, gaps that don't seem to code for any proteins? Researchers have begun to suspect that some of this noncoding DNA consists of regulatory sequences that can affect, in different ways, when different genes are "expressed" and actually able to produce specific proteins. Looks like some of this noncoding DNA is important enough to help account for the rapid evolution of human brains.

I have the feeling we're just seeing the beginning of research findings in this area, and we're about to be hit by an avalanche of it. Here's another study reported just this week. It involves not just single genes, but entire networks of interconnected genes:

Unraveling where chimp and human brains diverge
By evaluating the correlated activity of thousands of genes, the UCLA team identified not just individual genes, but entire networks of interconnected genes whose expression patterns within the brains of humans varied from those in the chimpanzee.

"Genes don't operate in isolation – each functions within a system of related genes," said first author Michael Oldham, UCLA genetics researcher. "If we examined each gene individually, it would be similar to reading every fifth word in a paragraph – you don't get to see how each word relates to the other. So instead we used a systems biology approach to study each gene within its context."

The scientists identified networks of genes that correspond to specific brain regions. When they compared these networks between humans and chimps, they found that the gene networks differed the most widely in the cerebral cortex -- the brain's most highly evolved region, which is three times larger in humans than chimps.

Secondly, the researchers discovered that many of the genes that play a central role in cerebral cortex networks in humans, but not in the chimpanzee, also show significant changes at the DNA level.

Since there are probably scores of genes implicated in human-chimp brain differences, organized in different networks, I expect we're going to see research on this come out for some time to come.


Additional information:

Accelerated Evolution of Conserved Noncoding Sequences in Humans
This is the abstract of the article in Science which describes the research about the importance of noncoding DNA for human brain evolution. (Subscription rqd for access to full text of the article.)

Scientists Explore Function of 'Junk DNA'
Via Evolution Research, this is a recent (like, last two days) news item on research into noncoding DNA that works by coding for microRNA.

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Low folate diets and colorectal cancer - WTF?

Tuesday, November 14, 2006

Folates are a type of B vitamin. Some studies show that a deficiency of folates is associated with an increased risk of colorectal cancer:

Low folate diets found to increase risk of colorectal cancer

Interestingly enough, a deficiency of folates also decreases the cancer risk:

Low folate levels may curb colorectal cancer risk

Low folate levels may cut bowel cancer risk

Maybe someone should study the risks of high levels of folates? Or just say "the heck with it"....

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Beyond Einstein

Monday, November 13, 2006

Here's the second article in a series I'm going to do on NASA's advanced astrophysics and cosmology science program, which they've called "Beyond Einstein". The first in the series is here. It provides background on the Bush administration's lamentable intentions to delay indefinitely or even abandon most of the more advanced of NASA's pure science programs, including Beyond Einstein.

My purpose in writing about this is to stimulate interest in the program among that part of the U. S. public that pays attention to basic science, especially advanced studies of the universe at large. Because, you see, as a result of last week's elections, the character of the U. S. Congress is going to change significantly next year. There's reason to hope priorities can change. When NASA's science budgets are discussed in future years, we can advocate that Congress reinstate funds for the missions that make up the Beyond Einstein program.

The main purpose of this post is to present background information on the program. But of course, a few words need to be said first about what the Beyond Einstein program is. Fortunately, NASA's home page of the project does a really great job of providing both an overview and detailed background information. See especially the science page, the mission descriptions, and additional resources.

In a nutshell, the various missions together and separately will investigate four of the most mysterious phenomena that we know of in the universe: black holes, gravitational waves, dark energy, and cosmic inflation. These phenomena are grounded in Einstein's general theory of relativity. Yet there's a great deal we don't understand about each one – hence the name "Beyond Einstein".

This graphic from the project site sums it up (click for full-size image):

If you go to this page, you'll be able to click on individual parts of the graphic for more information. The items at the far left are space missions that have already been launched (except for GLAST, whose launch is scheduled for late 2007) or ground-based facilities (LIGO) that are currently working on different parts of the puzzle. Immediately to the right of those are two missions (LISA and Constellation-X) that are well-along in planning – but not yet approved and funded. They (as well as everything else to their right) are missions that were ditched, at least for the present, in NASA's 2007 budget.

LISA will use interferometry techniques, as does LIGO, to search for gravitational waves. But because the separation of the three observation points will be millions of kilometers, instead of a few thousand in LIGO, it will be vastly more sensitive. LISA should be able to detect gravitational waves resulting from supernovae or black hole collisions.

Constellation-X is to consist of four X-ray telescopes on a single spacecraft. It is a successor to previous space-based X-ray observatories, such as Chandra. Constellation-X will be able to study phenomena that are energetic in the X-ray part of the spectrum, such as physics in the vicinity of black holes and very hot gas found in large galaxy clusters.

The missions in the center of the chart are less far along in planning. Of the three, the dark energy probe appears to be farthest along. In fact, there are actually three possible designs in competition. In August, NASA authorized a comparative analysis of the three designs in order to identify the "best". Each of them will measure the effects of dark energy over the history of the universe by locating and studying 1000 or more Type 1a supernovae. They differ in the additional kinds of measurements they can make. However, the status of this mission (as well as the others discussed here) has recently been thrown into further uncertainty, as we'll explain in a minute.

The purpose of the inflation probe is to gather stronger evidence for the process of inflation that appears to have occurred beginning a mere 10-35 seconds after the big bang. (As discussed here and here, back in March NASA announced that an analysis of WMAP data in fact gave preliminary evidence for inflation.) In addition, the probe will seek data that can discriminate among the many possible models which can describe inflation. There are different ways that the probe can study the problem, including a more detailed analysis of polarization in the cosmic microwave background, and a study of the evolution of large-scale structure in the universe.

The black hole finder, as the name implies, will be designed to locate and study black holes (both stellar-mass supernova remnants and supermassive black holes) in order to learn more about how they form and grow. As such, it will build upon work done by Constellation-X.

As for the two "vision missions", it's really too early for scientists and engineers to define them in any detail. Much will depend on phenomena that are better understood from the results of earlier missions, and most likely phenomena we don't even know of yet. Understandably, these missions (and certainly others like them) are decades in the future.

And this brings us to the latest news. It should be clear enough that there are plenty of overlaps and interdependencies among the various missions. The capabilities of later missions will depend critically on what we learn from earlier ones. After all, until 1997, no one seriously suspected that dark energy even existed. (And some experts still doubt its existence.)

Because of this, as well as because of the severe present constraints on NASA's science budget, The National Research Council (NRC) of the National Academies has formed a committee – at the request of NASA and the U. S. Department of Energy – to conduct an assessment of the Beyond Einstein program. The first meeting of the committee was held last week (November 6-8). The agenda is here. Further information on the committee, including its membership and staff, is here.

This is the committee's task statement:
1. Assess the five proposed Beyond Einstein missions (Constellation-X, Laser Interferometer Space Antenna, Joint Dark Energy Mission, Inflation Probe, and Black Hole Finder probe) and recommend which of these five should be developed and launched first, using a funding wedge that is expected to begin in FY 2009. The criteria for these assessments include:

a. Potential scientific impact within the context of other existing and planned space-based and ground-based missions; and

b. Realism of preliminary technology and management plans, and cost estimates.

2. Assess the Beyond Einstein missions sufficiently so that they can act as input for any future decisions by NASA or the next Astronomy and Astrophysics Decadal Survey on the ordering of the remaining missions. This second task element will assist NASA in its investment strategy for future technology development within the Beyond Einstein Program prior to the results of the Decadal Survey.

As of right now, I haven't seen any accounts of what happened at the meeting last week. If anyone out there has some actual information about the meeting, or has seen reports of it, please let me know.

What I do know is that some people are pretty worried that the real purpose of this committee is to narrow down the Beyond Einstein program to just one mission, or possibly two, because of NASA's budget problems. This might entail not merely postponing other missions, but essentially killing them altogether. The problem is that, if some level of misson activity cannot be funded on an ongoing basis, then many researchers and their institutions will have to find other things to do, and it could be very difficult to bring teams back together when, or if, funding becomes available. See two posts here and here, from Steinn Sigurðsson for examples of the kind of speculation going around.

Oh yes, there is one other thing. Along with the announcement on October 31 (before the NRC committee meeting), that a final service mission will be flown for the Hubble Space Telescope, there were strong hints that other astronomy missions are on hold. The report on this printed in Science: Hubble Gets a Green Light, With Other Missions on Hold is available only to subscribers, but says at the end:
Griffin's decision means that NASA will spend most of its astronomy budget on three major missions--the Hubble servicing flight, construction of the James Webb Space Telescope, and the Stratospheric Observatory for Infrared Astronomy (SOFIA). Technical troubles, schedule delays, and cost overruns plague the latter two. But Weiler [director of NASA's Goddard facility] says that the Webb is back on track after a rough couple of years, while SOFIA--which Griffin initially canceled only to revive in July--is slated to begin operations in 2009. Those large projects leave little room for smaller or future missions. For example, NASA halted work earlier this year on the extrasolar planet-seeking Space Interferometry Mission (SIM) in order to cover SOFIA's cost overruns. Those pressures worry some astronomers, who fear that the three missions will limit new efforts.

"Is the astronomy program with just [Webb], Hubble, and SOFIA a good astronomy program? You betcha," says Weiler. Although he acknowledges that there is a gap in smaller missions for the next few years, he notes that the cost of building the Webb will peak in 2008 and then decline over the next 5 years. "The big issue now is what to do with that wedge."

The four leading contenders appear to be the Joint Dark Energy Mission with the Energy Department, a mission called Constellation-X that features a bevy of x-ray telescopes, the Laser Interferometer Space Antenna to study black holes and the early universe, and SIM. NASA had intended to fund all in this decade and the next, but budget constraints likely will make for a competitive race.

Make of that what you will, but it certainly doesn't sound too good.

On the other hand, it certainly looks like the task of the NRC committee is to select at least one of the Beyond Einstein missions. Further, NASA is going ahead with other new astronomy projects. In addition to GLAST (launches late 2007), on October 13 there was an announcement that the Wide-field Infrared Survey Explorer will be launched in 2009 to do infrared sky maps, which would capture both nearby planetary systems undergoing formation as well as very distant galaxies – news report, further information.

So here's the bottom line I see for now: The NRC committee will take a year or so to ponder the situation. They may pick one project to go forward with initially. (Betting seems to be on the dark energy probe, because of the involvement of the Department of Energy.) Other missions in the advanced planning stage (LISA and Constellation-X) may wind up on hold, or one may be slotted as well.

The important point: there is plenty of time to make the argument before the appropriate Congressional committees that the NASA science budget should be increased enough so that the Beyond Einstein program can go forward, without having to sacrifice planning that has already been done and disrupting teams that are already in place.

Fortunately, as a result of last week's elections, Congress will have new people in charge who should be inclined to place a higher value on basic science than those they are replacing.

Update 1 (11/13/06): According to a comment by Steinn, LISA and Con-X have been "approved", but only minimally funded.

Update 2 (11/14/06): Now Steinn says funding was cut off. In any case, they're going noplace fast at this point.


Additional information:

Beyond Einstein: From the Big Bang to Black Holes
This is a 110 page document you can download in PDF format, and it's very much worth the effort. It's profusely illustrated (full color) and describes all of the missions and gives a good overview of the underlying science. Only problem is it was published in January 2003. But the additional science that has been learned in the last four years mostly confirms the premises of the program.


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NASA 2007 science budget

Saturday, November 11, 2006

This is old news. The main purpose of this post is to provide historical references for something I'm going to write more about, and to give a general flavor of the controversy over NASA's science budget.

On February 6, 2006 the Bush administration delivered NASA's 2007 budget to Congress – and there were substantial cuts in the science programs. I wrote a little about that here, as part of a general discussion of a variety of NASA problems at the time. (See the section on "NASA's 2007 budget".)

You most likely don't want to plow through all these articles, so I'll just summarize. Some of the science missions that were cut back or eliminated from the budget included probes to Mars and Jupiter's moon Europa, and a telescope to search for Earth-like extrasolar planets (Terrestrial Planet Finder).

Two other missions, which I will write more about, involved advanced astrophysics: the Laser Interferometer Space Antenna to search for gravitational waves and Constellation-X to study black holes.


Philosophia Naturalis #3 has been published

Thursday, November 9, 2006

And you can find it right now, at geek counterpoint. Don't miss it – it's really good.

Thanks, Lorne, for a fine job.

Inflation and the cosmic microwave background

Sunday, November 5, 2006

About three weeks ago I wrote a little about the cosmic microwave background (CMB), and talked about writing more. So here's a little more. The CMB is microwave radiation we can (almost) literally "see" even though it originated only about 350,000 years after the big bang. (I'll explain more in a minute about what "originated" means in this context.)

There are a number of things very wonderful and remarkable about the CMB. Not only is it one of the major pieces of evidence supporting the big bang theory in general, but it also gives us much information about things as diverse as the relative proportions of ordinary matter and dark matter in the universe, the overall curvature of the universe ("flat", "convex", or "concave"), and the ratio of the number of baryons (protons and neutrons) to photons in the universe.

Further, of particular concern here, the CMB provides a means of testing a theory – the theory of cosmic inflation – that describes a much different period of time than that of the CMB itself, a period of time that began only about 10-35 seconds after the big bang itself. The theory of inflation comprises a range of models describing what may have happened at that time. If there is any truth at all to the theory, the CMB can help narrow the range of acceptable models.

I have a couple of older articles on this from back in March/April here and here. These deal with the announcement back then of analysis of data from the Wilkinson Microwave Anisotropy Probe (WMAP) that, among several other things, gave the first reasonable evidence for inflation.

Rather than dive right away into further explanation of that, I'm going to refer you first to this excellent recent article on the subject by Sean Carroll: Reconstructing Inflation.

What's that, you say? It sounds impressive, but you don't quite follow the details? OK, let's step back for a moment and review the basics. The picture below is a graphical representation of the main data obtained from WMAP:

This picture shows slight variations in temperature across the entire sky, at microwave frequencies, where blue represents coolest and red represents warmest. The variations are actually very small: the whole range is ± 200 microKelvins (millionths of a degree K).

Temperature differences correspond directly to differences in matter density – because a gas under higher pressure is warmer and denser than the same gas under lower pressure (the "combined gas law"). So what we see here are minute ripples of higher and lower pressure in the matter of the universe at roughly 350,000 years after the big bang. What has caused these pressure waves? Carroll's article explains

The same basic mechanism works in both cases — quantum fluctuations (due ultimately to Heisenberg’s uncertainty principle) at very small wavelengths are amplified by the process of inflation to macroscopic scales, where they are temporarily frozen-in until the expansion of the universe relaxes sufficiently to allow them to dynamically evolve.

The spots and blotches you see in this picture are shadows on the wall, as it were, of quantum fluctuations that actually occurred 10-35 seconds after the big bang. At first, in a period that lasted perhaps only 10-33 seconds, these fluctuations were inflated at an incredible rate. Thereafter, they continued to expand along with the rest of spacetime itself, until we see them projected on the CMB wall 350,000 years later.

To be more precise, we should note that this metaphorical CMB "wall" did not form at some single precise time. Instead, the CMB itself is a result of most of the hydrogen and helium matter in the early universe making the transition from an ionised plasma to an ordinary gas of neutral atoms, as free electrons were "captured" by the hydrogen and helium ions. Consider, for simplicity, just the hydrogen. It takes 13.6 eV (electron volts) of energy to separate an electron from a hydrogen atom. In the early universe when the typical photon had much more than this energy, atomic hydrogen could not exist for long, as most passing photons could "liberate" the electrons. But when the energy of the typical photon dropped, as the universe expanded, to the equivalent of around 13.6 eV, hydrogen atoms became stable for longer periods of time. This is known as the period of "recombination" (even though prior to this, protons and electrons had never been in a "combined" state). Once there was a lot of atomic hydrogen, photons of the most common energy levels "scattered" from the atomic hydrogen, and the universe was somewhat opaque to those photons.

But as the temperature dropped further, most photons did not have enough energy to liberate electrons from hydrogen atoms. So most photons ceased to scatter from atomic hydrogen, and the universe effectively became transparent again. Although this happened over a relatively short period of time, it was not instantaneous. By the time that most hydrogen was in an unionized state, a typical photon never again scattered off a hydrogen atom. So around any present observer, there is a "surface of last scattering". Assuming what are currently considered the most likely cosmological parameters, this corresponds to a time about 13.3 billion years ago (equivalent to a red shift of about 1100), about 350,000 years after the big bang. This surface of last scattering is what we see today as the CMB. The temperature of the universe at this time of last scattering was about 3000° Kelvin, but due to the subsequent expansion of the universe, the CMB photons now have an energy that peaks around 2.725° K, in the microwave part of the spectrum.

There is another way to represent the WMAP data for the CMB. You've probably seen it in some form. (It's in Carroll's article, if you read that.)

The vertical scale on the left is a measure of the amplitude of temperature fluctuations. The top and bottom scales are measures of angular size. 90°, for instance, is one fourth of the whole sky. The "multipole moment" (l) is an integer that corresponds to an angular measure of 180°/l. So, for instance, the peak on the above graph occurs around l=200, which is slightly less than 1°. For comparison, the angular size of the full moon viewed from earth is about .5°. What the graph is saying, roughly, is that strongest temperature fluctuations (spots in the picture above the graph), if you could see them with your naked eyes, are almost twice the angular size of a full moon. (Astrophysicists use multipole moments, since they are the relevant identifiers of "spherical harmonic" functions that are used to construct a series representation of the function which describes theoretical temperature variations, similar to the way that a Fourier series can represent a function of one real variable.)

The small dots on the graph are WMAP measurements for various values of l. They come with error bars, which are mostly too small to see, because the WMAP measurements were mostly pretty precise. The red line through the measured values is the theoretically predicted values, assuming that the temperature variations are actually the result of quantum fluctuations that occurred in the inflationary period. The locations of the two peaks to the right of the main peak are especially important, and they correspond fairly well to theoretical predictions.

Carroll's article explains how there are actually two kinds of perturbations we might potentially observe in measured quantities: "scalar" and "tensor", reflecting the fact that Einstein's equation describing gravity waves (which result from the inflation-era quantum fluctuations) is a tensor differential equation. Further, all that we can readily measure from the WMAP data are scalar perturbations:

To date, we are quite sure that we have detected the influence of scalar perturbations; they are responsible for most, if not all, of the temperature fluctuations we observe in the Cosmic Microwave Background. We’re still looking for the gravity-wave/tensor perturbations. It may someday be possible to detect them directly as gravitational waves, with an ultra-sensitive dedicated satellite; at the moment, though, that’s still pie-in-the-sky (as it were). More optimistically, the stretching caused by the gravity waves can leave a distinctive imprint on the polarization of the CMB — in particular, in the type of polarization known as the B-modes. These haven’t been detected yet, but we’re trying.

Problem is, even if the tensor modes are there, they are probably quite tiny. Whether or not they are substantial enough to produce observable B-mode polarization in the CMB is a huge question, and one that theorists are presently unable to answer with any confidence.

The WMAP experiment was capable of studying polarization of CMB microwaves only rather crudely. But a new experiment is due for launch very soon (early 2007) in the form of the European Space Agency's Planck mission. Considering that it took several years to analyze WMAP data, we may not have better information right away – but it won't be too long, if everything goes reasonably well.


Further information about CMB:

Wilkinson Microwave Anisotropy Probe
NASA web site of WMAP, containing background information, images, and graphs.
Wayne Hu's Home Page
One of the best collections of CMB information, including an introduction, explanation of the physics, and discussion of CMB polarization.


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Dawkins vs. Haggard

Ted Haggard is the evangelical mega-star currently in the news because... well, you know. Everyone knows who Richard Dawkins is, but he's currently in the news because of his new book The God Delusion.

So it's interesting that Dawkins interviewed Haggard not so long ago as part of a documentary on the mad, mad world of hyper-religion. See the YouTube video of it here. Notice how Haggard's lips are twisted into a vicious snarl during the 1-on-1 interview with Dawkins. Guess T. H. was needing a meth fix, or at least a "massage".

On a lighter note, check out the Dawkins interview with Stephen Colbert here.

And then, since this is a science blog, check out Sean Carroll's review of The God Delusion.

Lastly, I might as well mention my own article on Steven Pinker's essay on Dawkins.

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Why blue-eyed men prefer blue-eyed women - but not vice versa

Saturday, November 4, 2006

Most people learn in high school (if they're paying attention) that human eye color is a genetic trait which follows fairly simple rules. The primary gene that controls eye color exists in several forms, called alleles. The protein produced by one of the alleles causes the eyes to be brown, while a variant allele producing a slightly different protein does not. Since the human genome contains two copies of each gene, if even one of these copies is the allele for brown eyes, brown will be the resulting color, regardless of the other allele. Such an allele is said to be "dominant". Another eye color (e. g. blue) will result only if both copies of the gene are non-brown alleles. Such alleles are said to be "recessive".

Children receive one copy of each paired chromosome from each parent. It follows that if one parent has two copies of a dominant gene, every one of their children will receive at least one copy, regardless of what the other parent has. All children of this mother and father will have brown eyes, if even one parent has two brown eye alleles, and even if the other parent has two blue eye alleles.

If both parents have one brown and one blue allele, then for any particular child, there's a 1 in 4 chance of receiving two brown alleles, a 1 in 4 chance of receiving two blue alleles (the only case that will result in blue eyes), and a 2 in 4 chance of receiving one brown and one blue allele (hence brown eyes). If one parent has blue eyes, and the other has both a brown and a blue allele, then the odds are 50/50 for each of their children to have either brown or blue eyes. So if one or both parents have brown eyes, it's possible for them to have blue-eyed children. But when both parents have blue eyes, so all of their alleles are for blue eyes, all of their children will have blue eyes. In that case, if any child has brown eyes, it must be the case that one parent – most likely the male – is not the biological parent. Oops.

So a blue-eyed man has an interesting advantage over men with brown eyes – a very dependable way of knowing that he is not the father of a particular child, provided he mates with a blue-eyed woman. Further, a blue-eyed man who regards blue-eyed women as more attractive than women of other eye colors is more likely to mate with blue-eyed women. And so such a blue-eyed man has a selective advantage over other blue-eyed men who have no such preference (or a preference for brown-eyed women).

This would be advantageous, at least in prehistoric times, if in addition such a man was less inclined to provide for a child without blue eyes – even if there was no conscious recognition that the child could not be his own. Some recent research has indicated that blue-eyed men sometimes actually, if unconsciously, do have a tendency to regard blue-eyed women as more "attractive", and hence (presumably) are more likely to choose them as mates:

Blue Eyes -- A Clue To Paternity
Eighty-eight male and female students were asked to rate facial attractiveness of models on a computer. The pictures were close-ups of young adult faces, unfamiliar to the participants. The eye color of each model was manipulated, so that for each model's face two versions were shown, one with the natural eye color (blue/brown) and another with the other color (brown/blue). The participants' own eye color was noted.

Both blue-eyed and brown-eyed women showed no difference in their preferences for male models of either eye color. Similarly, brown-eyed men showed no preference for either blue-eyed or brown-eyed female models. However, blue-eyed men rated blue-eyed female models as more attractive than brown-eyed models.

Since a mother almost always can be sure a given child is hers (except for rare events like accidental switching of infants), a mechanism that provides a way to recognize that a child isn't her own provides little additional advantage. And so, blue-eyed women do not have an evolutionary advantage from a tendency to regard blue-eyed men as more attractive than others. So they do not, in fact, have that tendency.

If you're looking around for an example of specific, and unexpected, behavior for which evolutionary psychology offers the simplest explanation, this may be a good choice.

Update 8/3/08: There is more recent news on this subject here and here.

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Big Bang Theory Saved

From the title you might think that the theory was in serious peril. But it wasn't, really.

Big Bang Theory Saved
An apparent discrepancy in the Big Bang theory of the universe's evolution has been reconciled by astrophysicists examining the movement of gases in stars.

Professor John Lattanzio from Monash's School of Mathematical Sciences and Director of the Centre for Stellar and Planetary Astrophysics said the confusion surrounding the Big Bang revolved around the amount of the gas Helium 3 in the universe.

The issue arises from what is actually one of the greatest successes of the big bang theory – quantitative calculations of the relative abundances of a few light element produced within the first 5-10 minutes of the universe by the process of "big bang" nucleosynthesis.

Detailed calculations depend on vaious factors, such as the temperature and rate of expansion of the universe during the time in question, as well as the densities and relative abundances of the "raw materials" (mostly protons, neutrons, photons, and neutrinos) when nucleosynthesis begins. The calculations are complex due to the dependence on so many factors, but they're no real sweat with modern computers. Even before modern computers, the first physicists to make the computations (George Gamow and associates) in the late 1940s were able to come up with surprisingly good results, all things considered. (They predicted a mass fraction of about 50% helium-4, when the correct figure is more like 25%.)

The objective is to compute the abundances of the light elements deuterium (hydrogen-2), helium-3, helium-4, lithium-6, and lithium-7 (relative to protons – ordinary hydrogen). In order to check the correctness of the calculations, the numbers have to be compared with actual measurements of the relative abundances of these elements, either at the present time, or at some known time in the past.

And that's where the difficulties lie. In the first place, it's necessary to be sure the relative abundances can be measured accurately. This is nontrivial, since, in the most extreme case, the predicted abundance of lithium-7 is a minuscule mass ratio on the order of 10-10. (Lithium-6 is an even smaller ratio, too small to measure.)

The second problem is that there's no way to observe the relative abundances right after nucleosynthesis is complete. At best, the measurement could be made a billion years or so after the big bang. And in practice, the best measurements are made on nearby objects, corresponding to more than 13 billion years after the big bang. So you have to make allowances for any changes that could have occurred in that time span, due to incremental production or destruction of isotopes (in stars, for example).

The most problematic case has been with helium-3. Until the research just reported, there has been much less helium-3 detected than should be expected, because this isotope can be produced in low mass star like our sun. But the discrepancy can now be accounted for, since this helium-3 should be destroyed near the end of a star's life:
Near the end of a star's life there is a 'core flash' and it was at around this time that the computer models revealed a small instability in the movement of the gases in the star. "When we looked at this in 3D we found this hydrodynamic instability caused mixing and destroyed the helium 3 so that none was released into space," Professor Lattanzio said.

Additional information:

Deep Mixing of 3He: Reconciling Big Bang and Stellar Nucleosynthesis – original research report in Science (subscription rqd for full access)

On the case of the "missing" helium – PhysicsWeb

Scientists crack open stellar evolution – Lawrence Livermore National Laboratory


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