The Perimeter Institute along with the University of Waterloo together form probably the largest concentration of the theorists in quantum computing in the world. And they just keep growing! So, in the past few years, I have been calling those two institutions “the black hole of quantum computing.” When I told this to Andrew Landahl at a meeting I was just attending in San Diego, he came up with a great correction to my description. Really I should have been calling it “the blackberry hole of quantum computing!”
Beyond DNA?
Just got an email with the following article. A big deal?
Scientists Say They’ve Found a Code Beyond Genetics in DNA
By NICHOLAS WADE
Researchers believe they have found a second code in DNA in addition to the genetic code.
The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.
The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.
The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues.
There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length.
Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.
Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms.
The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.
Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.
But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.
The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, “We think that for the first time we have a real quantitative handle” on exploring how the nucleosomes and other proteins interact to control the DNA, he said.
The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested.
Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning.
“I think it’s really interesting,” said Bradley Bernstein, a biologist at Massachusetts General Hospital.
Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was “a profound insight if true,” because it would explain many aspects of how the DNA is controlled.
The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.
In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.
UFOs
Something for me to look for next time I’m back in Yreka, Unidentified Fossil Objects:
Geologists have discovered strange disc-shaped features in slate deposits in California. The features, at Yreka, are between 2 and 7 centimetres across and 2 to 4 millimetres thick; some have centres stained with iron oxides. One geologist, Nancy Lindsley-Griffin of the University of Nebraska, has already dubbed the saucer-shaped features, ‘unidentified fossil-like objects.
Geologists discoverd the UFOs in bedding planes of the slate, formed from ocean bottom that was deposited between 400 and 600 million years ago. The objects are puzzling because they lack the symmetry that fossils of living organisms usually display. They are also too large to be the droppings of any creature alive at the time, and do not look like concretions, such as agates, formed by natural chemical processes. Lindsley-Griffin says they resemble very tiny bicycle wheels, with a central core and an outer rim, but with most of the spokes missing.
Einstein Meandered
Via Three-toed Sloth, I find out that Titan has meandering rivers. Did you know that there is an emperical relationship between the width of a river and the wavelength of its meander? Einstein did and was one of the first to explain the reason for this relationship. I wonder if the meanders on Titan obey the same law?
Yreka, I Have Found It!
I grew up in a small town in northen California called Yreka. Eureka? No Yreka! Yreka (population around 7000) is located about fifteen minutes north south of the border between Oregon and California on Interstate 5 which runs inland down the west coast. Just to confuse things, Eureka is also located in northern California, but is on the coast about two hours south of the California and Oregon border. From this description you might think that these two towns are close to each other. In fact it takes something like five hours to drive from Yreka to Eureka. (By the way, for those of you who are interested, northern California does NOT include the San Francisco bay area. Look at a map and judge for yourself!) Want to remember how to spell Yreka? “Yreka Bakery” backwards is “Yreka Bakery” (One of Herb Cain’s favorite palandromes palindromes.)
Anyway, back on topic (there is a topic to this post?) Last night I watched the premeire episode of the SciFi channel’s new “Eureka” show. The jist of the show is that Eureka is actually the site of a top secret research laboratory and as such the town is populated by a large number of eccentric scientists/shadow government characters. The show is pretty amusing, as such shows go (a judgement which is purposefully vague), and includes such great lines as “But Dr. [whose name I can’t remember] was our best quantum physicist!” I’ll probably get suckered into watching it again, in large part as an act of solidarity for the part of the world I grew up in.
But watching “Eureka” reminded me of a false impression I had about being a scientist when I was growing up. One of my favorite books growing up was “A Wrinkle in Time” by Madeleine L’Engle. In this story, the protaganist’s parents are scientists. Who live in an old house in the country. Huh? Scientists making a living in the rural world? Being a rural kid this seemed perfectly reasonable to me at the time and made, I think, becoming a scientist seem not so incompatable with living in a rural town. But, alas, I think the real world is much different. Unless of course “Eureka” is more than a T.V. show and there turns out to be a top secret research lab in Eureka. If there is, could the relevant people please send me an application?
His Experience as a Woman in Science
This interview with a Stanford professor (of neurobiology) about his experience as a woman in science is an interesting read (via Angry Physics.)
New Pynchon
Jud writes in to tell me that there will be a new Thomas Pynchon novel out this December. Here is a link to Amazon.com’s page. There is a blurb in the comments section on Amazon.com describing what this book is supposed to be about. However, the authenticity of this blurb is currently in doubt.
Sweeeeet!
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Comment preview fixed. Anyone having problems with it, let me know.
No Comment on Qubit
A previous article on the meeting at Bell labs that I attended. Notable:
The National Institute of Standards and Technology and the super-secret National Security Agency are backing U.S. quantum projects.
NSA spokesman Ken White declined to elaborate, “given the sensitivities about our work to understand the secret communications of our foreign adversaries while protecting our own communica tions, and given our desire to preserve our nation’s unique advan tages in these pursuits.”
Ack. Quick, better shut down quant-ph!
Quantum Eve
Turns out that of the mother and father protocols which have helped illuminate the field of quantum information, only the mother is necessary: quant-ph/0606225:
Title: The mother of all protocols: Restructuring quantum information’s family tree
Authors: Anura Abeyesinghe, Igor Devetak, Patrick Hayden, Andreas Winter
We give a simple, direct proof of the “mother” protocol of quantum information theory. In this new formulation, it is easy to see that the mother, or rather her generalization to the fully quantum Slepian-Wolf protocol, simultaneously accomplishes two goals: quantum communication-assisted entanglement distillation, and state transfer from the sender to the receiver. As a result, in addition to her other “children,” the mother protocol generates the state merging primitive of Horodecki, Oppenheim and Winter, a fully quantum reverse Shannon theorem, and a new class of distributed compression protocols for correlated quantum sources which are optimal for sources described by separable density operators. Moreover, the mother protocol described here is easily transformed into the so-called “father” protocol whose children provide the quantum capacity and the entanglement-assisted capacity of a quantum channel, demonstrating that the division of single-sender/single-receiver protocols into two families was unnecessary: all protocols in the family are children of the mother.