Posted: 24 Jul 2008 08:54 PM CDT
Today’s PRS.B sees the publication of a supertree of 600 Dinosaur species. Awesome. ScienceDaily has more information here. Here’s a picture of it:
The abstract says:
Posted: 24 Jul 2008 05:50 PM CDT
Guest post by Paul Jaffe, MAADDSG@aol.com; coordinator, Manhattan Adult Attention Deficit Disorder Support Group; New York, NY, USA. [7/17/08]
Recently, gene-therapy researchers — who have had their ups and downs — scored a point: the restoration of some vision to patients with retinal degeneration [1,2].
To effect this, they used a generally harmless adeno-associated virus (AAV). The goal was to deliver, to the retina, a functioning copy of a defective gene thought to trigger the illness. This viral “vector” was injected through a surgical procedure deemed reasonably safe.
Within gene therapy, AAV vectoring – which may soon turn a corner  — is now standard. This includes a well-publicized effort [4,5,6] — and a less-publicized effort  — to treat Parkinson’s Disease.
Unlike the above, which might be termed corrective gene therapy, the PD applications are closer to compensatory gene therapy. Here, the aim is to alter the brain so as to mimic a treatment several steps removed from an underlying pathology.
In each PD clinical trial, a gene has been inserted to encode a specific enzyme. These are:
The vectors are known, respectively, as the AAV-GAD and the AAV-AADC.
The PD research might — or might not — succeed. (One vector is in US Phase II testing; the other, in Phase I.) The question here is: might either be used elsewhere? (more…)
Posted: 24 Jul 2008 01:52 PM CDT
DNA Diagnostics Center (DDC) has done it again—the world's largest private DNA testing laboratory has achieved another perfect rating after a surprise inspection by AABB, the organization that sets industry standards for family relationship testing in the United States. Last week, the lead assessor from the AABB carefully examined DDC's performance in the many crucial areas [...]
Posted: 24 Jul 2008 12:16 PM CDT
Dr. Ken Garson, lab ninja and science overlord extraordinaire, (here is a picture of his lab bench), and I recently had a discussion about musical theory. I have taken a fair bit of musical theory over the years and I remember very little. However, I was certain that Ken was wrong when he stated that in certain scales a C# is different than a Dflat.
Don't mess with Garson. Turns out that while I was correct when using the modern tuning of equal temperment, back in the day of musical geniuses like Bach, instrument tuning was not so crude and was specific to the key in which it was being played. Intervals in musical scales are defined by frequency ratios, and they aren't always so pretty. C# is not Dflat according to that definition.
Ken has done some fine research on this subject in order to point out my infiroirity. Equal temperment is used so that an instrument like the piano can be played in any key. However, from a great summary on the history of tuning and temperment:
* Our first written instructions for setting equal temperament come from Giovanni
Maria Lanfranco in 1533:
Posted: 24 Jul 2008 12:04 PM CDT
Wii Fit, for the Nintendo Wii, recently hit store shelves, touting itself as a fun fitness product claiming
By playing Wii Fit a little every day, you, your friends, and your family can work towards personal goals of better health and fitness.Perhaps the game Rock Band should take a similar tack in advertising.
A story at BBC News equates rock drummers to top athletes. These conclusions were reached by tests on Clem Burke, drummer for Blondie, who was hooked up to a heart monitor and other equipment during a performance. An hour in concert can burn up to 600 calories and tests on Burke showed his heart averaged 140-150 bpm, peaking at 190 (see this chart for Fox and Haskell's exercise zone formula). These rates, the article claims, are comparable to Premier League football (soccer) players.
I don't doubt that you can get a workout playing the drums - I've certainly broken a sweat hammering away at Rock Band (sorry, not a musician here) - but the BBC piece seems to go a bit far in it's comparison to top athletes:
"Footballers can normally expect to play 40 to 50 games a year - but in one 12 month period, Clem played 90-minute sets at 100 concerts.This quote, combined with the previous comparison to professional football players, seems to imply that drumming is more physically demanding. Instead, I would read it as going against their thesis that "rock drummers are top athletes"; that is, drumming isn't nearly as strenuous as professional sports.
Enjoy your drumming, and feel good knowing that you're burning some calories, but if you're planning on leaving your pick-up soccer league to go pro there are probably better ways to get in shape.
Any thoughts from drummers out there?
Posted: 24 Jul 2008 12:03 PM CDT
I can't say that have often been called "brassy" but I sure do prefer that to some other descriptions that I have seen lately like irreverent
or disingenuous or in the case of my latest Research Proposal "denied".
So I was pleased that Andrew Leonard of Salon used that lovely word in his July 16th post in regards to my proposal that the best way to ensure a safe food supply with the least amount of damage to the environment is to integrate genetic engineering with organic farming.
Here is the good part:
... Ronald was even brassy enough to cite "Silent Spring's" Rachel Carson as a potential muse for those who aim to merge the latest biotechnology with sustainable agriculture.
After all, in 1962 she said:
"A truly extraordinary variety of alternatives to the chemical control of insects is available. Some are already in use and have achieved brilliant success. Others are in the stage of laboratory testing. Still others are little more than ideas in the minds of imaginative scientists, waiting for the opportunity to put them to the test. All have this in common: they are biological solutions, based on understanding of the living organisms they seek to control, and of the whole fabric of life to which these organisms belong. Specialists representing various areas of the vast field of biology are contributing -- entomologists, pathologists, geneticists, physiologists, biochemists, ecologists -- all pouring their knowledge and their creative inspirations into the formation of a new science of biotic controls."
....But the quote that really seemed to sum up an approach to farming (and just about everything else) that this blog can get behind also came from Ronald, quoting a farmer friend of hers:
As Mike Madison, a fellow farmer, neighbor and writer says, "In dealing with nature, to be authoritarian is almost always a mistake. In the long run, things work out better if the farmer learns to tolerate complexity and ambiguity... Having the right tools helps."
Leonard indicates that our books have joined his "endless queue". Does that mean he will buy them but not read them- or worse yet, just jot the names down on a long list?
Posted: 24 Jul 2008 10:25 AM CDT
Well, sorry for the lack of posting recently. Out sick thanks to a fun antibiotic resistant bacteria. In honor of that here are some tips to staying clean:
A Germ-Zapper's Guide to Clean (from the Washington Post
hat tip to Doug Rusch for pointing this out and giving me something to do other than worry about bacterial infections)
Posted: 24 Jul 2008 09:51 AM CDT
Tuesday, I posted on Bt Corn as an example of a “good” genetically modified (GM) crop whose benefits vastly outweigh its risks, risks which are akin to the development of antibiotic resistance in the health sector. Here, I thought I’d mention Pharma Corn as an example of a “bad” GM crop, in my opinion at least.
The PLoS Biology article from last time touches on Pharma Corn as well, but only for a short summary. Check out the Journal for Agrobiotechnology Management and Economics (2005) for a more comprehensive article on Biopharming and the Food System.
For Pharma Corn, gene flow *is* a serious concern, and extensive measures are required to contain Pharma Corn. Just think of the consequences of hybridization between corn engineered to manufacture drugs and corn intended for human consumption. What happens if you inadvertantly consume a drug to which conflicts with your body’s chemistry or your correct prescriptions, just by eating an ear of corn.
But okay, the FDA is known for tight regulation of such things, and Pharma Corn doesn’t require much acreage, making containment easier. But look at the situation:
Clearly, “prodigious obstacles” summarizes the situation for Pharma Corn as a agricultural product of the future.
Posted: 24 Jul 2008 09:33 AM CDT
Posted: 24 Jul 2008 08:27 AM CDT
OSCON is a very interesting meeting. Apart from opportunities to meet old friends and acquaintances, and talk to people like Damian Conway and Toby Segaran, and having a very productive conference, one also gets to get a pulse on some trends, more on this in a bit.
Also please to find some life science types here, including people from Pfizer and 454. I still feel that one sign that academia and even commercial life science companies don’t quite get it when it comes to software development and engineering is that while we are quick to travel to any number of scientific conference, the attendance at programming and technology-centric conferences is limited. Which means you miss out on talks about XMPP and how it can be use to power and scale web services, and learn about the open web, etc.
XMPP is definitely making its presence felt at OSCON. I only got a chance to attend one talk, where XMPP was essentially presented as an alternative to REST, assuming that SOAP was so bad that you wanted to avoid it and REST had limitations. I won’t go into that argument (other than agreeing on the SOAP bit), but twitter chatter suggested that there was a lot of discussion around XMPP.
It’s also interesting to see the level of interest in things like memcached and the importance of community. I also found it interesting to observe the differences between the crowd at OSCON and at other geek-tech conferences. There’s a number of people here, not a large number, but enough, who are not quite web aware. That surprised me a little.
Anyway, all I have time for right now. More later.
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Posted: 24 Jul 2008 06:37 AM CDT
According to Peter Olson of the Natural History Museum in London, "All free-living organisms host one or more parasites". This can be taken two ways, both of them generally true: a) that each individual multicellular organism hosts at least one individual parasite within its body, and b) that each free-living species plays host to at least one species of parasite that attacks it exclusively. Consider this second point for a moment. For each free living species there is one or more (usually several more) parasite species -- that is, as a category (polyphyletic, obviously), parasites may very well be the most diverse types of organisms on the planet.
On the other hand, most parasites are much smaller than their hosts, and so it has typically been assumed that they contribute a negligible fraction to any particular ecosystem's total biomass. Nuh-uh. In a report published in Nature this week, Kuris and colleagues presented five years' worth of analyses of estuaries in California and Baja California in which they measured the amount of biomass made up of parasites and free-living organisms.
In sum, Kuris et al. (2008) examined 138 species of infectious agents, 199 species of free-living animals (including invertebrates as well as fishes and birds), and 15 species of free-living plants in their study. They found that plants contributed the most biomass to all three of the estuaries they studied, followed by groups such as snails, bivalves, and crabs. Parasites made up only about 0.2% to 1.2% of the animal biomass of each environment, and on average parasite groups had biomasses 1000 times lower than the average free-living group. However, as Kuris et al. (2008) report,
Certain parasitic groups dominated the parasite biomass, reaching levels similar to those of common free-living groups. For instance, the biomass of trematode worms was comparable to that of the fishes, burrowing shrimps, polychaetes or small arthropods. In all estuaries, trematode biomass exceeded bird biomass by threefold to ninefold.In other words, parasites make up a larger fraction of the living matter in these environments than do the top predators. In particular, parasites that castrate their hosts (i.e., prevent them from diverting resources into reproductive effort) were the most abundant. The world is not fishy or feathery, it is fluky.
So, whereas the famous quote attributed to J.B.S. Haldane that if there is a creator he must have "an inordinate fondness for beetles" still applies, it may be that he has an even more pronounced affection for parasites. Especially the castrating sort.
Kuris, A.M., R.F. Hechinger, J.C. Shaw, K.L. Whitney, L. Aguirre-Macedo, C.A. Boch, A.P. Dobson, E.J. Dunham, B.L. Fredensborg, T.C. Huspeni, J. Lorda, L. Mababa, F.T. Mancini, A.B. Mora, M. Pickering, N.L. Talhouk, M.E. Torchin, and K.D. Lafferty. 2008. Ecosystem energetic implications of parasite and free-living biomass in three estuaries. Nature 454: 515-518.
Posted: 24 Jul 2008 05:42 AM CDT
I can't agree more. I heard sometimes the claim that within 5-10 years, more than 95% of the scientific literature is going to be read by computers only. Possible. However, the converse alternative might be interesting to consider: what if 95% of scientific papers could be 'written' by computers? Even if this formulation is obviously provocative and unrealistic, the point is that harnessing the 'network effect' of the web may have two complementary components, one community- the other computer-driven. On one hand, web 2.0 functionalities enable community-driven commenting, rating and even writing of scientific publications. On the other hand, semantic web technologies are expected to facilitate computer-driven integration of scientific data from multiple sources, which is likely to play an increasingly important role in science. Rather than mining thousands of unread papers, the scientist of the future may rather search the web for relevant data first and integrate it to generate – or 'write' – novel insight. In fact, integration of large datasets already represents a major field of research in systems biology (see Chuang et al 2007, Xue et al 2007 or Mani et al 2008 as recent examples published in Mol Syst Biol).
It seems thus that, in addition of being web 2.0 enabled, new publishing models should 'embed' more structured data into online publications. In short, 'papers' could progressively transform into hybrid online objects that resemble more to database records (see Timo Hannay's post on this topic) or highly structured documents. At the extreme, one could even imagine to publish 'naked' datasets, without any 'stories' around them. Of course, efficient data integration will require the data to be in a standard and structured format and its quality will have to be well characterized. These are all far from trivial qualities.
The good old-fashioned papers are probably not going to disappear as publication units, in particular for high-impact studies reporting novel and deep insights. It is also not the point here to propose dumping every scientist's hard drive into the web. Data-rich publications would be published only when the authors would feel it appropriate. There might thus be some equilibrium to find between papers that will never be read except by a text mining engine and pure datasets, published as a resource, easier to search, to mine and to integrate. This dialectic may ultimately boil down to the issue of how well will text mining and data integration technologies perform in the future.
In any case, within the context of the current debate about the saturation of the peer-review system, I wonder whether a data-centric form of scientific publishing could help to release somewhat the pressure. Reviewing of datasets might be quicker and could rely more on standardized evaluation parameters. If assorted with proper credit attribution mechanisms and metrics of impact, data-rich (or even data-only) publications may represent an alternative model complementing the traditional 'paper' format. It would prevent the loss of useful data otherwise buried in verbal descriptions and, most importantly, would hopefully stimulate web-wide integration of disparate datasets.
Posted: 24 Jul 2008 04:14 AM CDT
I’m linking to a Danish page here, sorry to those of you who do not quite master that language yet.
It concerns the age old question of whether you prevent a shaken beer can from spilling when you open it, if you tap the can on the top first. A lot of people do this, but does it have any effect?
Klaus Seiersen — incidently an old drinking buddy of mine from the physics department — did an experiment with 30 cans and didn’t see any correlation with tapping and amount spilled.
You spill your beer when it foams out of the can, and the foam is caused by the CO2 in the beer. When you shake the can, the CO2 gets mixed with the beer, and the beer foams. To prevent this, all you have to do is to wait until the CO2 settles in the top of the can again…
Posted: 24 Jul 2008 03:50 AM CDT
I guess the squeaky weel gets the oil. After complaining about the access to CLC bio’s whitepaper, Lasse Görlitz send me an email explaining how they are capitalists and that should explain why I need to fill out a webform to download a paper… anyway, he attached this logo and all is forgiven.
Yes, I am that easy to buy off!
Posted: 24 Jul 2008 03:33 AM CDT
According to this press release, CLC bio has released a whitepaper describing their assembly algorithm. I’m very interested in reading it. The speed sounds impressive, and assembly is an interesting algorithmic problem. There’s just one problem: the link to the paper isn’t a link to a paper at all! It’s a web form that lets you apply for it … and after filling out the form the kindly tell you that they’d get back to you.
Sorry guys, this is too lame! Just give me the damn paper!
Posted: 24 Jul 2008 02:00 AM CDT
Posted: 24 Jul 2008 12:08 AM CDT
Looks like ABI has begun releasing more tools to their user community...see their new site (I really like the color scheme they chose for the site.. ) A variety of assembly and mapping tools are available...as far as I can tell they are parts of the pipeline already present on the instrument..."corona" and "matoGff" are built in tools that do the automated secondary analysis. Now they are provided as standalones with fairly detailed documentation...which is always helpful. Also there are...
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