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Top five nanotech breakthroughs of 2006

Sunday, December 31, 2006

Here's an interesting top-something list, from Forbes – nanotechnology:

Top Five Nanotech Breakthroughs Of 2006
This year saw a slew of remarkable nanotech breakthroughs, and narrowing down the top five was no easy task. One major theme of 2006 was the intersection of computing and biology--integrated circuits were used to study everything from neural activity to tissue dynamics, and disposable bio labs-on-a-chip became a reality.

As usual, one can take issue with some of the citations or suggest others. But what's especially interesting here is that in each item, there are actually multiple instances of progress in the same general area. Allow me to illustrate this with several examples.

1) DNA ORIGAMI

There are reports on the work in question here, here, here, and here. This work involves constructing nanoscale objects out of DNA molecules. There is, in fact, a whole subfield of nanotechnology centered around the use of DNA. It's called, DNA nanotechnolgy (unsurprisingly). Prof. Ned Seeman of NYU has been a leader in this field. Some of his references are here (with some nice graphics), here, here, and here. Seeman's laboratory most recently reported a "nanorobotic arm" using DNA – see here, here, and here.

And here's some additional news this year related to DNA nanotechnology:


2) NANOMAGNETS TO CLEAN UP DRINKING WATER

This research obviously has immense real-world importance. But it isn't so much an example of a major area of nanotech activity. Anyhow, here's an overview of the work: Cleaning Up Water with Nanomagnets. The original work was published in Science (November 10, 2006): Low-Field Magnetic Separation of Monodisperse Fe3O4 Nanocrystals.

3) ARRAYS CONNECT NANOWIRE TRANSISTORS WITH NEURONS

Nanowires of various kinds have been big news this year. For examples, see here, here, here, here, here, here, and here.

Similarly, there have been a number of results with interfacing electronics and neurons, for such things as controling prosthetic limbs and playing computer games. One of the more interesting examples is the recent report of a small robot controled through a neuro-electronic interface. Carbon nanotubes have also been used for neuro-electronic interfaces.

But the work mentioned in the Forbes article, where silicon nanowires only 20 nanometers wide can detect signals at as many as 50 places on a single neuron, is certainly impressive. See here, here, or here for details.

Other research into interfacing neurons and carbon nanotubes: here.

4) SINGLE NANOTUBE ELECTRICAL CIRCUITS

Research involving carbon nanotubes is probably the most active area in the whole field of nanotechnology. The examples are far too numerous to mention individually.

Reports on the research referred to in the Forbes article can be found here, here, here, here, here, here, here, here, here, and here.

Other uses of carbon nanotubes in electronics are reported here, here, here

5) NANOPARTICLES DESTROY PROSTATE CANCER

There's a general problem with uses of advanced drugs as therapeutics, especially for cancer and in gene therapy – delivering the drugs as specifically as possible to the organs or tissues where the drug should be active, while avoiding tissues where the drug could be unnecessarily harmful. Chemotherapy is perhaps the principal example of this problem. It is possible to design nanoparticles which gain entry only to certain types of cells, so encasing a drug inside such a particle may solve the problem.

Research involving chemotherapy for prostate cancer was reported in April of this year, and is a noteworthy example of this approach. Reports about the research can be found here, here, here, here, here, here, and here. An especially long and informative article about MIT cancer research, including the nanoparticle work, is here. Here's a more general overview: Tumor-Seeking Nanoparticles.

Nanoparticles can also be used to deliver imaging or contrast agents to cancer cells in order to make them easier to detect. There have been a number of other research results reported this year involving nanoparticles for drug delivery or imaging. A few recent examples, just since October:


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For another review of important nanotechnology results this year, with many links, take a look at: The Year in Nanotech – Dazzling displays, handheld sensors, cancer killers, and nanotube computers.

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Clues to the origins of life

The question of how life originated on Earth is one of the really big open questions for science. Right up there with questions like how the universe itself started and how the human mind works.

Questions about how life began have been asked for a long time, of course. But only within roughly the last 50 years, since DNA and related biochemistry began to be understood, has it been possible to address such questions scientifically.

DNA, and its very close relative RNA, provide the framework for one essential of life: the storage of information, which allows for "blueprints" that describe a living organism to be conveniently encoded, so that individual organisms can be duplicated and, ultimately, evolve into more complex organisms. We now understand pretty well how DNA and RNA work, so one key question now is – how did DNA and RNA, the carriers of genetic information, come about?

DNA and RNA are made up of relatively simple organic molecules – sugars and phosphate groups that can polymerize to form a backbone, and a small number of bases which encode information by the way they are ordered in their attachment to the backbone. The information encoded in DNA details how to make proteins, which are also polymeric organic molelcules, consisting of amino acids attached to each other in a sequence specified (mostly) by the DNA. It is the proteins that make up the bulk of the cellular machinery that constitutes a stand-alone single-celled organism, or by grouping together makes a multi-celled organism. So a large part of the question of life's origins comes down to that of how these various organic chemicals came to exist.

In addition to the organic chemicals that make up an organism, another necessity of life is the ability to utilize energy that is ultimately obtained from the environment. In most cases, this energy is derived from sunlight, although in a few rare cases it can come from radioactive elements. Either way, an organism needs to tap into the environmental energy in order to drive chemical reactions which power cellular mechanisms that enable reproduction, locomotion, and (in multicellular organisms) growth. (More complex organisms can also derive their energy from "food", in the form of simpler organisms that have stored up environmental energy obtained more directly.) So another key question is: when and how did these energy-management processes come about?

There have been recent research findings that are relevant to various of these questions.

Let's consider the origins of organic compounds first. One line of thinking is that organic compounds were primarily synthesized from inorganic compounds in natural processes here on Earth. The names Aleksandr Oparin and J. B. S. Haldane are associate with this idea. The classic experiment testing the idea is known as the Miller-Urey experiment, after Stanley Miller and Harold Urey, and was first conducted in 1953, the same year that the structure of DNA was identified by Francis Crick and James Watson. As yet, this is still just a conjectural possibility.

An alternative scenario for the origins of organic compounds is that some simple ones formed in space, which is known to happen, and that some of the basic building blocks of life, such as amino acids, were introduced to Earth on meteorites. This possibility has gained more plausibility from the recently announced finding of apparent "organic materials" in a meteorite that fell in 2000.

NASA Scientists Find Primordial Organic Matter In Meteorite
In a paper published in the Dec. 1 issue of the journal Science, the team, headed by NASA space scientist Keiko Nakamura-Messenger, reports that the Tagish Lake meteorite contains numerous submicrometer hollow organic globules.

Because the meteorite immediately became frozen in ice after it landed, the possibility of contamination from terrestrial material was minimized. Further, the isotopic composition of hydrogen and nitrogen in the globules is quite unlike what is normally found on Earth. It also appears that the material in the meteorite formed at least 4.5 billion years ago – before the Earth and the other planets themselves.
"The isotopic ratios in these globules show that they formed at temperatures of about -260° C, near absolute zero," said Scott Messenger, NASA space scientist and co-author of the paper. "The organic globules most likely originated in the cold molecular cloud that gave birth to our Solar System, or at the outermost reaches of the early Solar System."

Additional references:

Just about two weeks later, results from a completely different souce appeared that also showed the existence of organic compounds in primorial solar system material. This was from the Stardust mission to retrieve grains of matter from the comet 81P/Wild-2:

Comets hold life chemistry clues
Scientists studying the tiny grains of material recovered from Comet Wild-2 by Nasa's Stardust mission have found large, complex carbon-rich molecules.

They are of the type that could have been important precursor components of the initial reactions that gave rise to the planet's biochemistry.

Unlike the case with the Tagish Lake meteorite, it was possible to identify many of the organic compounds in the returned material:
These Wild-2 compounds lack the aromaticity, or carbon ring structures, frequently found in meteorite organics. They are very rich in oxygen and nitrogen, and they probably pre-date the existence of our Solar System.

"It's quite possible that what we're seeing is an organic population of molecules that were made when ices in the dense cloud from which our Solar System formed were irradiated by ultraviolet photons and cosmic rays," Dr Sandford explained.

"That's of interest because we know that in laboratory simulations where we irradiate ice analogues of types we know are out there, these same experiments produce a lot of organic compounds, including amino acids and a class of compounds called amphiphiles which if you put them in water will spontaneously form a membrane so that they make little cellular-like structures."

Additional information from the special Stardust issue of Science (December 15, 2006 – sub. rqd. for full access):

Although these results indicate that organic material formed in or before the earliest stages of the solar system might have seeded organic chemistry on Earth, there is as yet no evidence that this actually is how it happened. An even more radical possibility is that actual living carbon-based organisms that originated outside of our solar system "transplanted" life to Earth. This idea is known as panspermia, but so far, there's little or no credible evidence for it. Short of that, we know at least that the organic compounds for life either originated on Earth or arrived from outside.

So let's move on and turn to the question of how the earliest organisms managed energy supplies in order to reproduce and move. Every organism on Earth that produces energy from the chemical processing of carbohydrates, fats, and proteins uses, a complex series or reactions known as the citric acid cycle (also known as the Krebs cycle). (There are other energy-producing processes, of course, such as photosynthesis.) The question to be answered is how this complex series of reactions first arose:

New Insights Into The Origin Of Life On Earth

In an advance toward understanding the origin of life on Earth, scientists have shown that parts of the Krebs cycle can run in reverse, producing biomolecules that could jump-start life with only sunlight and a mineral present in the primordial oceans.

The Krebs cycle is a series of chemical reactions of central importance in cells -- part of a metabolic pathway that changes carbohydrates, fats and proteins into carbon dioxide and water to generate energy.

Since the cycle can run backwards, it is possible to identify an inorganic compound that may have kickstarted the process:

Nature's Jump-Starter
Reporting in next week's Journal of the American Chemical Society, researchers at Harvard University say they may have found at least one of the original players. Called sphalerite, the compound is a mix of zinc and sulfur ejected from hydrothermal vents and known to have been plentiful in Earth's early seas. Geochemist and co-author Scot Martin says the team's new lab experiments show that when immersed in sterile water and exposed to sunlight, sphalerite can create three of the five basic organic chemicals necessary to start the Krebs cycle in relatively quick fashion. Further research is needed to isolate the other compound or compounds that could have produced the remaining two Krebs ingredients, he notes. If scientists can find their sources, then they will know that the five chemical foundations of the Krebs cycle were being manufactured easily and routinely in Earth's early oceans.

In addition to relatively simple organic chemical building blocks and chemical reactions that can release energy to make an organism that is "alive", there is a third prerequisite for life: some method of storing information about an organism's composition and structure so that the organism can replicate itself, instead of simply disappearing after each generation. In other words, genetic material.

Today, that genetic material consists of DNA and RNA, which in turn are made up of a handful of bases that act as symbols encoding the genetic message and are arranged along a linear backbone of simple sugar and phosphate groups. But are these the only possible chemical entities that can perform this kind of function?

In the past, other possibilities have been suggested, such as peptide nucleic acids (PNAs). A PNA has a backbone formed of simple molecules consisting of carbon, nitrogen, hydrogen, and oxygen. These are liked together by peptide bonds, which form when H- and OH- units from two molecules combine to form H2O, leaving the original molecules joined to each other. Such peptide bonds also form the backbone of proteins. But unlike proteins, PNAs have DNA-like bases attached to the backbone instead of amino acids. However, PNAs do not occur naturally, so they do not seem to have played a role in life on Earth.

If there are other ways of structuring a backbone, perhaps comparing them to what is actually used in RNA (the sugar known as ribose) and DNA (the sugar deoxyribose) would suggest why the latter proved to win out. That was the idea behind this research:

Uncovering DNA's 'Sweet' Secret
“These molecules are the result of evolution,” said Egli, professor of Biochemistry. “Somehow they have been shaped and optimized for a particular purpose.”

“For a chemist, it makes sense to analyze the origin of these molecules.”

One particular curiosity: how did DNA and RNA come to incorporate five-carbon sugars into their “backbone” when six-carbon sugars, like glucose, may have been more common? Egli has been searching for the answer to that question for the past 13 years.

Recently, Egli and colleagues solved a structure that divulges DNA's “sweet” secret. In a recent issue of the Journal of the American Chemical Society, Egli and colleagues report the X-ray crystal structure of homo-DNA, an artificial analog of DNA in which the usual five-carbon sugar has been replaced with a six-carbon sugar.

It was found that homo-DNA is more stable that DNA/RNA and it allows a wider variety of bases to be attached. So why didn't it prevail?
[D]espite homo-DNA's apparent versatility in base pairing and its thermodynamic stability, other features of the molecule's architecture probably preclude it from being a viable genetic system

For example, it cannot pair with other nucleic acids — unlike DNA and RNA which can and must pair with each other. Also the steep angle, or inclination, between the sugar backbone and the bases of homo-DNA requires that the pairing strands align strictly in an antiparallel fashion — unlike DNA which can adopt a parallel orientation. Finally, the irregular spaces between the “rungs” prevent homo-DNA from taking on the uniform structure DNA uses to store genetic information.

The findings suggest that fully hydroxylated six-carbon sugars probably would not have produced a stable base-pairing system capable of carrying genetic information as efficiently as DNA.

So that variation didn't work out. But what about the possibility of using a different set of bases than the purines and pyrimidines which actually occur? That was investigated in this study:

Origin Of Life: The Search For The First Genetic Material
To find the right track in searching for the origins of life, the team is trying to put together groups of potential building blocks from which primitive molecular information transmitters could have been made. The researchers have taken a pragmatic approach to their experiments. Compounds that they test do not need to fulfill specific chemical criteria; instead, they must pass their “genetic information” on to subsequent generations just as simply as the genetic molecules we know today—and their formation must have been possible under prebiotic conditions. Experiments with molecules related to the usual pyrimidine bases (pyrimidine is a six-membered aromatic ring containing four carbon and two nitrogen atoms), among others, seemed a good place to start. The team thus tried compounds with a triazine core (a six-membered aromatic ring made of three carbon and three nitrogen atoms) or aminopyridine core (which has an additional nitrogen- and hydrogen-containing side group). Imitating the structures of the normal bases, the researchers equipped these with different arrangements of nitrogen- and hydrogen- and/or oxygen-containing side groups.

Unlike the usual bases, these components can easily be attached to many different types of backbone, for example, a backbone made of dipeptides or other peptide-like molecules. In this way, the researchers did indeed obtain molecules that could form specific base pairs not only with each other, but also with complementary RNA and DNA strands. Interestingly, only one sufficiently strong pair was formed within both the triazine and aminopyridine families; however, for a four-letter system analogous to the ACGT code, two such strongly binding pairs are necessary.

The conclusion was that the critical factor affecting the composition of modern genetic material was the structure of the bases rather than the structure of the backbone. It was necessary to have only certain bases which are capable of pairing up in specific ways, as occurs in double-stranded DNA and DNA-RNA combinations.

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Nature's review of 2006

Tuesday, December 26, 2006

Nature is one of the world's two premier science journals, the other being... Science. Sadly, their review of this year's science developments is, to this observer at least, simply underwhelming.

Oh, they mention Perelman's work on the Poincaré conjecture, and a couple of developments in biology (stem cells, and genetics). But as far as fundamental science is concerned, that's about it. Their emphasis is predominantly on stories that made big newspaper headlines for social/political reasons, such as global warming and natural disasters.

Sure, that stuff is very important for its human impact. No argument about it. But it's been covered endlessly in the popular media. Does Nature think they've added much to what you could read in, say, the New York Times? Or Newsweek, for that matter.

My advice to Nature, not that they've asked: Put the main emphasis on the fundamental science – in some serious depth we can't find elsewhere – instead of the yakety-yak one can hear from any talking head on the news shows.

That said, if anyone reading this still wants to read a little more from Nature's editors about what they considered scientfically important in 2006, here are some of their top 10 lists:

Editor's choice stories
A "vegetative" patient who showed signs of consciousness. That was number 1! A social scientist who could glibly discuss gravitational waves. (Number 3.) The world's smallest vertebrate. (Number 4.) Demise of the world's "most infamous" iceberg. (Did you know there was one?)

Reader's choice stories (most clicked on)
This list is better than the editor's choice. But not by much. Example: "Sexy pictures and lacy underwear take men's minds off getting a good deal."

Most commented on stories from Nature's news blog
This is probably the most interesting list. Lots of good arguments here, if you care for that sort of thing. Does gender matter? Islam and science. Delusions of faith.

Longer news features
Ranges from the genuinely important (climate change) to the "why did they bother?" category. And you'll have to buy a subscription to read most of them. Betcha no one does.


For the record: here's the home page for Nature's "review of the year's top stories and pictures".

Science's top 10 "breakthroughs" of 2006

Science Magazine's selection of the top scientific developments of the year is basically the grand prix of scientific competition. And the editors usually make pretty good calls, though in truth there are many, many important scientific developments over the course of a year. Recognizing only 10 just leaves out too much. But it seems like a limitation we have to live with. Fortunately, there are other, if less prestigious, commentators who offer similar lists on science in general or on specfic fields. Taken all together, we get a more comprehensive picture of what happened during the year.

Anyhow, you can find an index of Science's articles on the top 10 (from the December 22 issue) here. (Access is free, though you will have to register at the site.)

Their choice for top breakthrough of 2006? It's the proof of the Poincaré conjecture. It is rather unusual for a development in mathematics to rate so much attention, but then this is no ordinary breakthrough. Something like this comes along in mathematics only every 10 or 20 years. It was written about on this blog here, here and here. (And in a few other articles besides, which you can find by searching the archives.)

Science's choices for runners-up were interesting too, of course. Among those are some that have been discussed here, such as macular degeneration (this), memory (this, this, and this), and small RNA (this). There's a steady stream of developments in the latter two areas, in particular, so stay tuned for more.

Just as interesting as the list of this year's breakthroughts were Science's list of areas to watch in 2007. Prominent in this list are the areas of planetary science (both our own solar system and others) and genome mapping and comparison.

It's also interesting to note areas that are not on the list, for either this year or next. Where, for instance, are topics in cosmology, astrophysics, and extragalactic astromomy – such as dark matter, dark energy, black holes, the cosmic microwave background, and gamma-ray bursts? Some very fundamental results have been obtained this year, with more surely to come in 2007. They've been discussed extensively here – search the archives for plenty of examples. Just goes to show how much has to be left out of a "top 10" list.

Additional references:

Maths solution tops science class – from the BBC

Beautiful politicians win more votes

Wednesday, December 20, 2006

This is sort of in the same vein as a recent post here:

Beautiful politicians win more votes: study
Beautiful politicians win more votes, according to Australian National University research released today that asked an independent group of ‘beauty raters’ to assess the looks of 286 major party candidates who ran in the 2004 federal election.

The study, conducted by ANU economist Dr Andrew Leigh and University of South Australia student Amy King, found that voters tend to opt for the better-looking candidate.

“Compared to the average-looking political candidate, a candidate at the 84th percentile of the beauty distribution, as judged by our independent raters, receives an extra 1½ to 2 per cent of the vote. In some seats, this is the difference between winning and losing,” Dr Leigh said.

And it isn't really news, is it? After all, people learn at an early age to treat elections as popularity contests. And who is it that wins student elections in high school anyway?

Unfortunately, that's not a good way to judge competence or good government policy. Never has been, but now that televised coverage of politicians and elections is so pervasive...

Perhaps it's worth thinking about the value placed on "beauty" and "good looks" for elected public officials. Here's one thing that Wikipedia says about physical attractiveness:
Prototypicality as beauty

Besides biology and culture, there are many other factors determining physical attractiveness. It is seen that when many faces are combined into a composite image (through computer morphing), people find the resultant image as familiar and attractive, and even more beautiful than the faces that went into it. One interpretation is that this shows an inherent human preference for prototypicality. That is, the resultant face emerges with the salient features shared by most faces, and hence becomes the prototype. The prototypical face and features is therefore perceived as symmetrical and familiar. Apparently, this reveals an "underlying preference for the familiar and safe over the unfamiliar and potentially dangerous"

In other words, people who are considered attractive within a population are those who are most "typical" or "average". Or inversely, least atypical, least different from the largest number of people in the population. People who are considered less attractive have facial features that vary a lot from the norm, such as lips that are too thin or too thick (compared to the average), eyes too far apart or too close together, eyebrows that are too sparse or too bushy.

And what makes these "unattractive" is that they are "unfamiliar and potentially dangerous".

Surprising? Nope. Just not a good way to judge things like competence, ability, common sense, etc. Funny thing is, our culture has sensible maxims like "you can't judge a book by its cover."

But everyone has some tendency to judge by the cover anyhow. It's a decision-making heuristic based on understandable factors.

Just not a good heuristic, because it's based on unanalyzed assumptions that aren't appropriate.

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Do carbon nanotubes present a health hazard?

Monday, December 18, 2006

Perhaps not:

Nanotubes Tracked In Blood And Liver: Study Finds No Adverse Effects
In the first experiments of their kind, researchers at Rice University and The University of Texas M. D. Anderson Cancer Center have determined that carbon nanotubes injected directly into the bloodstream of research lab animals cause no immediate adverse health effects and circulate for more than one hour before they are removed by the liver.

The findings are from the first in vivo animal study of chemically unmodified carbon nanotubes, a revolutionary nanomaterial that many researchers hope will prove useful in diagnosing and treating disease.

Of course, there needs to be much more research than that. Like long-term exposure, for example. But this is a promising start.

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Is pot a gateway drug?

Sunday, December 17, 2006

Apparently not:

No 'Smoking' Gun: Research Indicates Teen Marijuana Use Does Not Predict Drug, Alcohol Abuse
Marijuana is not a “gateway” drug that predicts or eventually leads to substance abuse, suggests a 12-year University of Pittsburgh study. Moreover, the study’s findings call into question the long-held belief that has shaped prevention efforts and governmental policy for six decades and caused many a parent to panic upon discovering a bag of pot in their child’s bedroom.

Of course, as we just noted here, cannabis doesn't do any good for your memory.

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Top 10 Health Stories of 2006

Saturday, December 16, 2006

Having recently posted a note on physics stories of 2006, I guess I should do health/medicine news next. So there's this: The Top 10 Health Stories of 2006.

I won't quibble with inclusion of any of the choices, but I do have comments on some of them (numbers keyed to items in the article):

  • 1. HPV vaccine – This isn't exactly a vaccine "against cancer". Cancer vaccines are under active development, but they're a different animal. This is a vaccine against human papillomavirus (HPV), which is responsible for about 70% of cervical cancers. I've written about it here.

  • 4. Treatment for macular degeneration – Since macular degeneration is caused by misplaced and uncontrolled growth of blood vessels in the eye, any drug that can inhibit angiogeneisis may be a potential treatment for the problem. It just so happens that anti-angiogenesis drugs are also possible treatments for solid cancers, since the drugs can inhibit blood supply to a tumor. Such a drug, with the trade name Avastin, was approved by the FDA in 2004. Avastin is a monoclonal antibody developed by Genentech, and may become a blockbuster drug for many types of cancer.

    Not coincidentally, the new macular degeneration drug, Lucentis, that the FDA approved this year is also from Genentech. It consists, essentially, of a portion of the Avastin antibody. Avastin has actually been used off-label to treat macular degeneration, and there is some controversy about the fact that Genentech hasn't run clinical trials of such use, even though Avastin is sold for a considerably cheaper price than Lucentis.

    Both Avastin and Lucentis target a protein called vascular entothelial growth factor (VEGF). A number of other drug companies are working on anti-angiogenic drugs that target VEGF. Some of them may be much more powerful than Avastin and Lucentis, such as one called a VEGF trap, from Regeneron Pharmaceuticals. (More information about that.)

  • 6. Vaccines – Vaccines are of two kinds: preventive and therapeutic. Both types work by conditioning the immune system. The former, more familiar, type wards off infectious diseases by stimulating the immune system to attack the agent of infection (usually a virus). Therapeutic vaccines are designed to mobilize the immune system in order to treat an existing disease condition. Of course, vaccines of both types are aggressively being sought to combat AIDS and cancer. But there's also a lot of research and development going into vaccines for conditions you might not expect, such as nicotine addiction and alcoholism. See this news article for an example dealing with nicotine.

  • 10. Vitamin D – The article mentions reports of beneficial effects of vitamin D for cancers of the breast and pancreas. This has been suspected for some time, as this story from 2004 indicates. Other studies have shown beneficial effects in prostate cancer (see here, here, here), ovarian cancer (see here, here), and colon cancer (see here, here).


There's one thing I think that the article misses. Even though it discusses cancer in relation to HPV and vitamin D, there has actually been an absolute flood of new research results on cancers of all types. Much of the research has dealt with the basic biology of cancer, such as the roles played by many different genes, the process of metastasis, and the involvment of stem cells in the onset of cancer. Although such research hasn't yet led to clinical trials of new drugs and therapies, I see this as a very important sign for the future. I'll try to write about "top stories of 2006 in cancer biology" some time after the new year.

Also related to cancer, there have been some new drugs approved for bone/blood cancer-like diseases such as multiple myeloma and myelodysplasia (e. g. Revlimid).

There has also been a lot of progress in understanding the biology of Alzheimer's disease. Not enough, yet, to fully understand the disease mechanism, but quite a lot is being learned. There may be some breakthroughs here before too long.

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Holiday gifts for science folks

Sorry to mention these so late, but I just came across this site – Bathsheba Sculpture – from a talented artist. I won't violate the artist's copyright by putting some pictures here or hotlink them – just have a look at the site. The artist, Bathsheba Grossman, does sculptures of mathematical forms using 3D printing technology, and also creates images laser-etched inside glass. The technology is quite interesting too.

For folks who are more into biology than math, the artist also does protein models etched in glass, shown at her other site: Crystal Protein. If you happen to have a PDB code for a favorite protein of yours, you can even get a custom model made.

I don't know whether Bathsheba's work is unique, as I'm not very familiar with the art world. All I can say is that I'd certainly feel proud to give this kind of gift, or surprised and fortunate to receive such.

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Physics Story of the Year

Thursday, December 14, 2006

'Tis the season for articles with titles like "Story of the year," "Notable achievements of 2006," and so forth. Here's the first one I've seen so far. And with almost 4 weeks to go (from when it was posted), it's jumping the gun a little. Who knows what might happen on the remainder of our world line before the 2007 mark?

The Physics Story of the Year
The physics story of the year 2006 was, we believe, the new high precision (0.76 parts per trillion uncertainty) measurement of the electron’s magnetic moment by Gerald Gabrielse and his colleagues at Harvard University. Then in a second paper the same experimenters used the new moment in tandem with a fresh formulation of quantum electrodynamics (QED) provided by theoretical colleagues to formulate a new value for the fine structure constant (denoted by the letter alpha), the pivotal parameter which sets the overall strength of the electromagnetic force. The new value has an uncertainty of 0.7 parts per billion, the first major revision of alpha in 20 years. A comparison between this new value and values determined by other methods provides the best test yet of quantum electrodynamics (QED).

OK, that one didn't get much play in the general press, but some additional physics stories did achieve more prominence. Here are some of my favorites, with links to additional information:

  • The observation of many more supernovas at redshifts of 1, thus establishing the idea that dark energy was around even in the early universe. [More: here, here, here, here, and here. I wrote about it here.]
  • New WMAP measurements of the cosmic microwave background, including polarization information, help to sharpen cosmological numbers such as the age or the flatness of the universe. [More: here, here, here, here, here, and here. I wrote about it here.]
  • Advances in plasmonics, or "two-dimensional light". [More: here, here, and here.]
  • Advances in the study of graphene, including the discovery of a new form of the Hall effect. [More: here and here.]
  • Progress at several labs in modeling gravity wave transmissions from black hole mergers, the kinds of events which LIGO or LISA would possibly detect. [More: here.]
  • Measuring the presence of virtual strange quarks inside protons.[More: here and here.]
  • Heaviest baryons discovered. [More: here, here, here, and here.]
  • Investigating whether the electron/proton mass ratio changed over time. [More: here and here]
  • Telecloning. [More: here, here, here, and here.]


Whew. Quite a list. But I think it leaves a lot out, too. There have been a number of interesting discoveries related to black holes. I've written about some of them. There have also been many advances in the related fields of spintronics, quantum information, and quantum computing. (I still haven't written about those.) Some other areas where there's been quite a lot of progress: carbon nanotubes, dark matter, and laser wakefield accelerators. And that's not the end of it.

Perhaps, if Santa puts an abundance of time under the tree for me this year, I'll tackle writing about what's happened in some of those areas.

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A starburst galaxy

Sunday, December 10, 2006

VLT Image of Starburst Galaxy NGC 1313 (11/23/06)
This FORS image of the central parts of NGC 1313 shows a stunning natural beauty. The galaxy bears some resemblance to some of the Milky Way's closest neighbours, the Magellanic Clouds. NGC 1313 has a barred spiral shape, with the arms emanating outwards in a loose twist from the ends of the bar. The galaxy lies just 15 million light-years away from the Milky Way - a mere skip on cosmological scales. The spiral arms are a hotbed of star-forming activity, with numerous young clusters of hot stars being born continuously at a staggering rate out of the dense clouds of gas and dust. Their light blasts through the surrounding gas, creating an intricately beautiful pattern of light and dark nebulosity.

But NGC 1313 is not just a pretty picture. A mere scratch beneath the elegant surface reveals evidence of some of the most puzzling problems facing astronomers in the science of stars and galaxies. Starburst galaxies are fascinating objects to study in their own right; in neighbouring galaxies, around one quarter of all massive stars are born in these powerful engines, at rates up to a thousand times higher than in our own Milky Way Galaxy.




NGC 1313 - Click for 1280×1157 image

Philosophia Naturalis #4 has been published

Friday, December 8, 2006

Daniel Collins at Down to Earth has posted the 4th edition of Philosophia Naturalis. It's your gateway to interesting science reading, right here.

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.


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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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