science snippets

I’ve been fooling around with the Bloglines blog feature, and considering turning it into a sidebar feed for this site. But then again, why not just make a second MT blog? In the meantime, I thought I’d recycle a few entries here.

scissors icon Developmental patterning: this one’s for PZM. Double-segment periodicity underlies ‘odd’ segment generation in centipedes
Apparently, centipedes have between 15 and 191 pairs of legs, and the number is always odd, and we don’t know why. The paper to which this story refers indicates that segments are defined in pairs in the developing centipede embryo, and each segment develops a pair of legs. So why odd, and not even? The authors speculate that development of the forcipules (“poison claws”, which are modified legs) reduces the resulting even number by one, resulting in an odd number. So the actual mystery mechanism in question is, what programs the forcipule development?
Bah. I just read the abstract, and the real story is how the co-ordinated expression of two different genes lays down a pattern of single-segment periodicity. That’ll teach me to blog from the report not the paper.
Heh. Update to the update: the single segment periodicity is probably laid down in cycles that generate two segments each, and the generation of odd numbers of leg pairs may indeed be due to the extension of this process as far as the segments containing forcipule, genitals and so on. So the report was right, but (I found it) confusing. That’ll teach me to trespass on Prof Myers’ territory.

scissors icon German science newsfeed. If you read German, this newsfeed, which I found by browsing science-related feeds at, is quite often well ahead of the English language feeds on my blogroll. For instance: yawning chimpanzees (German feed July 24, English feed July 26), the oncomouse patent (German feed July 6, English feed July 26) and the world’s smallest fish (German feed July 7, English feed July 21).
Note that this works even for pretty feeble values of “read German”. I can get the gist of most stories without help, but need translation help and/or a dictionary to actually understand what’s going on. In fact, I originally added the feed to motivate me to pick up learning German again.

scissors iconColour perception is not innate, but acquired after birth.
The abstract is here. Monkeys raised for a year under monochromatic lights showed clear differences in their colour vision compared to those raised under normal conditions. I wonder how this relates to colour-related learning in humans with colour deficient vision (like, say, me).

scissors icon Gene therapy reaches muscles throughout body, reverses muscular dystrophy. The paper will be in the August Nature Medicine, the abstract is available here.
Researchers at the Muscular Dystrophy Cooperative Research Center at the University of Washington School of Medicine have built an adeno-associated virus vector which specifically, and without eliciting an immune response, delivered an engineered dystrophin gene to every skeletal muscle, and the heart, of adult dystrophic mice. (Disruption of dystrophin production causes Duchenne muscular dystrophy in humans; without reading the paper, I assume the mouse is a knockout/similar model of the same disorder.) One injection of the viral vector caused a “dramatic improvement” in the animals’ dystrophy.
Not only is this an important proof of principle for muscle-targeted gene therapy, it may be useful in other genetic disorders which do not even involve muscle tissue but simply require widespread expression of the therapeutic gene.
Something else that’s good to see: the director of the MDCRC stressed that “the paper represents one discovery on the long path to any clinical applications in people [and] that there are a number of scientific challenges and regulatory requirements along the way, so any tests on humans are many years in the future” — and the reporter included those quotes.

scissors icon Chagas parasite invades genome (abstract here).
Trypanosoma cruzi kinetoplast DNA sequences end up in the host genome, opening up the possibility of some pretty freaky horizontal transfer of genetic information, plus influence on host evolution via mutation and creation of recombination hotspots. The article doesn’t say “first time ever documented outside of retroviruses” so I guess other instances are known — but I’d never heard of them.

scissors icon ET first contact ‘within 20 years’
Heh. Bullshit. Publicity seeking bullshit. (Don’t get me wrong though, I *love* SETI and related goals/ideas; if this guy can bring in funding, more power to his bullshit generator.)

flexcar, schmexcar

What the spousal unit said. Flexcar is aware of the problem, admits it’s a problem, and yet doesn’t fix it (they’ve been around since 1999, and I don’t suppose that this summer is the first one in which the card readers have crapped out). That doesn’t sound like a company that wants my business, which is just as well since they won’t be getting any more of it until they can guarantee me I won’t be left stranded if I park the damn car in the sun.

zooming out

Surprising Degree Of Large-scale Variation In The Human Genome (the Science paper is here).
Researchers at Cold Spring Harbor Labs using ROMA (representational oligonucleotide microarray analysis) to investigate the differences between tumour and normal cells included a normal-normal control to establish lower limits of variability. What they found was that the genomes of normal individuals vary not just at the level of the individual nucleotide or even gene, but also on a much larger scale, with deletions and duplications from 100,000 b to 1 Mb (b = base, or more accurately base pair, a single “rung” on the familiar twisted rope ladder image of DNA).
What ROMA does (there’s a good explanatory paper here) is to compare reduced-complexity representations of two genomes. The current average resolution is one probe every 35 kb. The authors say that 10-15 kb is feasible, but the more granular comparison may be more interesting, at least initially, because it shows the “big picture” — like zooming out on a map. (There is some tradeoff, of course; earlier lower-resolution studies found far fewer polymorphisms.)
So, how big is 100 kb – 1 Mb? The entire genome is about 3000 Mb, and contains about 30,000 genes, so the “average gene” is about 100 kb. This is a bit misleading since a typical gene is a few hundred to several thousand bases of coding sequence, which may be spread out across hundreds of kb but is more usually contained within, say, a few tens of kb. So, 100-1000 kb is easily big enough to encompass a whole gene, or even quite a few entire genes. Indeed, the authors found variation in some 70 genes, including the gene which causes Cohen syndrome and genes known to be involved in neurodevelopment, leukaemia, drug resistance in breast cancer and body weight regulation.
The team compared twenty individual genomes and found 76 unique CNPs (copy number polymorphisms, the authors’ name for the large deletions/duplications they are screening). The average CNP was 465 kb (median 222 kb) and individuals differed from each other by an average of 11 CNPs, so if the sample is representative (and the subjects were from a variety of geographic backgrounds) people differ from each other by around 4-5 million bases out of 3 billion, or 0.13-0.16%. The authors give multiple reasons to expect the observed CNPs to represent only a subset of the total, which they estimate to be 226 CNPs covering 44 Mb, or around 1.5%.


My “blog this” folder was getting a bit full, so here’s a random assortment of stuff that caught my eye. Much of it came from MetaFilter.
scissors icon Dammit! If lemurs can do it, and I am descended from lemur-like primates, why can’t I aestivate?
scissors icon In my place is “a series of entries about living with HIV”. It’s also a stone cold display of courage.
scissors icon This would piss me off too. “Every time one of my Aequorea photos is used in someone else’s story, something bad and wrong happens.”
scissors icon Knock on wood, not for luck but for functionality.

French physicists have figured out how to rap on tabletops to communicate with CD’s, lights or most other nearby electric or electronic devices. The inexpensive new technology has the potential to turn kitchen tables, desks, windows or other rigid surfaces into remote control panels with hundreds of touch-sensitive spots.

scissors icon The Last Word. Well, not really, but this Q&A section of New Scientist online is great. Why are the ends of your fingernails white? Are men always taller than their mothers? If your eyes were popped out and put back in the wrong way, would you see upside down? How far does the average mole tunnel in its lifetime? Why do tornadoes have the shape of an inverted cone? Why do old rubber bands go all icky? What percentage of the world’s population is flying on airplanes at any given time?
Caveat lector, though: I think the first answer to this one is bollocks, so other answers may be less than reliable. (Relax, there’s a search function so you can find those questions without links.)
scissors icon Ubuweb’s 365 day project is a collection of outsider audio. This is some of the weirdest stuff you will ever hear.
scissors icon In 1853-4, Commodore Matthew Perry led a mission to, er, convince Japan to open its doors to the rest of the world. Artists on both sides of the encounter did what artists do, and Black Ships and Samurai presents 200 graphical representations, both “looking East” and “looking West”, together with a vivid historical narrative by MIT Prof John W. Dower.
scissors icon First we have “driving while black”, now it’s “taking pictures while brown”. Ian had a bullshit run-in with the Patriot Act, but rather than give in to intimidation he went online to make some real trouble. Good for him.
scissors icon Now this is cool. Creepy, but cool.

The hollow, talking tombstone will include a flat touch screen and will house a computer with a microchip memory or hard disc. It will be powered by electricity from the cemetery’s lighting system.[…] “It’s history from the horse’s mouth.”

My first thought was, why not solar power? My second was, since I want to be cremated rather than buried, why not use this website as a virtual tombstone? I could even add video. I have seen a few websites maintained after the author’s death by their friends or family, and I wonder whether it will become common to leave provision for one’s website in one’s will. The more I think about it, the more I like the idea.
scissors icon Sent is an art project built on phonecam pictures. There’s a gallery of public submissions and another for invited artists. The best thing about gadgets is the neat things people do with ’em.
scissors icon 100 years’ worth of War of the Worlds cover art.
scissors icon Galleries of “found photos” from public p2p directories. Betcha can’t stop at one.
scissors icon The Basic Laws of Human Stupidity. As the footnote says, there is genius at work here. No attribution, for reasons you’ll discover if you find the post that led me to it.

speak out

A Senate vote on the Federal Marriage Amendment is expected in early July, and the Human Rights Campaign is providing a quick, easy way for you (that is, US residents) to contact your representative(s) on this issue.
This is the letter I sent (the first paragraph is part of the form):

As your constituent, I urge you to oppose any amendment that would write discrimination against gay, lesbian, bisexual, and transgender Americans into the Constitution.
The FMA is an attempt to lend to naked bigotry the force of law. It is wrong, and vile, and I write to assure you that extraordinary circumstances will be required before I will support in any way any public figure who does not oppose it. I seldom make this statement in contacting my political representatives, as I am a meliorist by nature and experience and do not believe in delivering ultimata, or burning bridges. This is a time for exceptions, though, and I am making one. I would greatly appreciate hearing from you on this issue.

Seriously, it takes all of five minutes to send a letter; if you can do this and you don’t, I hope your asshole catches fire. Via Republic of T.