The DNA Network

The original post calls this ethanolomics, but I’d like to think of it as a particularly interesting branch of cladistics. [Synthesis]

Mr. Gunn — Wed, 14 May 2008 20:37:27 -0500

I also thought most Belgian ales were produced by spontaneous fermentation.

This post is about beer, cladistics, phylogenetics

Canada Wide Science Fair [Bayblab]

noreply@blogger.com (kamel) — Wed, 14 May 2008 20:23:17 -0500

For the past two days, I've been a judge at the Canada Wide Science Fair here in Ottawa. The students and their projects have been extremely impressive. For those in the Ottawa area who want to see some of the future stars of Canadian research and innovation, there is a public viewing this Saturday, May 17th between 9am and noon in Montpetit gym at the University of Ottawa.

Octane Rating [Bayblab]

noreply@blogger.com (rob) — Wed, 14 May 2008 18:14:13 -0500

Just a little FYI. I was stumped today on what exactly an octane rating on gasoline meant.
The octane rating is based on results using a test engine. It is the resistance to autoignition that is being measured. Autoingition is undesirable in a gasoline engine as this produces knocking. It is called an octane rating as iso-octane is defined as 100 and n-heptane is defined as 0. So a mixture of 87% iso-octane and 13% n-heptane would have an octane rating of 87%. However that doesn't mean that a fuel with a 97 octane rating has 97% octane, it just has characteristics as if it was 97% octane and 3% n-heptane.

Response to Doug Gurian-Sherman, senior scientist with the Union of Concerned Scientists [Tomorrow's Table]

noreply@blogger.com (Pamela Ronald) — Wed, 14 May 2008 17:32:50 -0500

Thanks to Doug Gurian-Sherman, senior scientist with the Union of Concerned Scientists) for his thoughtful comments. My response here:

1. In our book, we make the point that sometimes GE is the most appropriate technology to solve a particular problem but not always. Geneticists, breeders and farmers are endlessly innovative and there are often many approaches to tackle a particular problem. There are cases where GE is the most appropriate technology. Case in point: GE papaya. There was no other tool available to combat papaya ringspot virus, nor is there now. Please see previous blog on this subject.

2. Doug says that it is not simple to find and commercialize a GE trait. I agree. All new varieties (GE or otherwise) need to be rigorously tested for their agronomic properties. This takes time and resources. This doesn't mean we should stop developing new varieties (GE or otherwise) though.

3. I agree that “the rising problem of herbicide resistant weeds and its consequences, for example, are a significant environmental (and practical) problem”. But this is a problem anytime an herbicide is used extensively and is not an environmental consequence of GE. The same result would occur if the crop is GE or non-GE (and many such herbicide tolerant non-GE crops have been generated). GE crops themselves have had had no negative environmental or health effects after over 1 billion acres have been planted.

4. In some of its commercial forms, glyphosate is mixed with a compound called a surfactant that allows it to be more eff ective. Although glyphosate is nontoxic to freshwater fish, there is evidence that a surfactant called POEA, used in some formulations, is more toxic than glyphosate alone to aquatic species. If the surfactant or herbicide creates environmental problems then it makes more sense to simply regulate the surfactant or even the herbicide itself.

5. Bt has had some real benefits in reducing chemical insecticide use. The recent analysis by Cattaneo et al (2005) clearly shows that there is similar biodiversity (ants and beetles) in GE cotton fields vs non-GE cotton fields. In contrast, broad-spectrum insecticides (which are used on the vast majority of non-GE cotton fields throughout the world) significantly reduces ant and beetle species richness.

6. Although BT-cotton in China has been dramatically effective in reducing pesticide use, after 7 years some farmers started spraying again to control secondary insect pests that are not controlled by Bt. This points to the need to integrate GE crops into organic farming systems that also use crop rotation and beneficial insects to control secondary pests. Please see this article for more details.

7. “I don’t see how you would fit herbicide tolerance into organic in any case”. I agree. Herbicide tolerant crops were developed for conventional farming systems in the US and do not benefit organic farmers or most farmers in less developed countries that cannot afford the herbicide. Each new GE crop variety must be evaluated on a case by case basis.

8. As to negative health effects, while there may be none from current crops, we really don’t have the data to know with much certainty. Please see article by Engber.

9. “The FDA process is voluntary, with no required tests and very few recommended ones”. As far as I know all US companies that have released transgenic crops have submitted their new variety to the FDA process.

10. “The claims by many of your more vocal colleagues that these crops are more stringently regulated than any others is moot because the standard of comparison for many of these crops is nothing! I.e., other crops are not regulated at all for safety, so of course ANY regulation, even the weakest, is by comparison more stringent!” I agree that GE crops are regulated whereas other crops are not. Doesn't this kind of regulation indicate much greater stringency?

11. “ The question should not be whether a few current transgenic traits out of dozens or hundreds are harmful, if the technology goes forward as many would like, but whether the regulations are adequate to reliably detect those that may be harmful”. I agree. Although there is wide consensus here in the US and abroad that all GE crops currently on the market are safe to eat, all future crops must be evaluated on a case by case basis.

12. “Although you have alluded to some of the big issues around GE in your other posts, you don’t deal with them head on (again, apologies if you do that in you book)”. Please see chapters 10 “who owns the seed?” and chapter 11 “Who owns the genes?” in Tomorrow's Table.

13. “Finally, you do not address the very important issue of opportunity costs when pursuing GE. In a world of limited resources, we need to put those resources where they can do the most good.” Current interventions to combat vitamin A deficiency rely mainly on pharmaceutical supplementation, which is costly in the long run and only partially successful. The most recent estimates indicate that golden rice is expected to save lives of thousands of children. This is a golden opportunity to use GE. Lives of children are at stake.

23andme is Shaking up Clinical Research [Retail Genomics: The Science and Business of Consumer Genomics & Consumer Bioinformatics]

noreply@blogger.com (Simon Lin, MD) — Wed, 14 May 2008 17:15:50 -0500

It is coming.

Yes, 23andme is challenging the traditional way we are conducting clinical trials. In a press release today, 23andme is announcing a partnership with the the Parkinson's Institute to discover genetic and environmental factors of Parkinson's disease.

Six months ago, my colleagues and I send out a grant proposal arguing the potential efficiencies of combining consumer genomics with clinical trials. Although I am frustrated to learn a week ago that our proposal was not funded, I am very happy to see the press release today from 23andme, which essentially validated our proposal.

Bottlenecks of Traditional Clinical Trials	23andme's Innovative Solutions
Patient recruiting	Social network
Cost of SNP scans	May do cost-sharing with participants

Similar to the early days of sequencing and bioinformatics development, I would expect to see the industry driving the innovative applications, instead of the academics.

There are "2.0" hypes on everything recently, including the "Research 2.0" in the press release. Even though there are a lot of details to be worked out, I am still very positive on it.

Dr Watson's Genetic Counselor: Witty or Insulting? [PredictER Blog]

noreply@blogger.com (PredictER) — Wed, 14 May 2008 16:42:03 -0500

Today's issue of Nature [subscription required] includes a letter responding to Wheeler DA, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (17 April 2008) | doi:10.1038/nature06884. The author of the response, a genetic counselor, lifts a layer off the science publishing hype that surrounds anything about the human genome in this era. Also see the very insightful and witty table comparing two potential personal genome and genetic counseling clients: "Dr. Watson" and a "lay patient".

Here's a sample:

- Dr. Watson: Thinks the $1 million cost is a good deal - Lay Patient: Worried about the cost of a - consultation
- Dr. Watson: Brings in sequence data on a hard drive - Lay Patient: Brings in records about sinus infections
- Dr. Watson: Chose to have Apo-E sequence redacted - Lay Patient: Expects to learn blood type
- Dr. Watson: Shares 1.68 million SNPs with Craig Venter - Lay Patient: Googles SNPs to find out who they are

Well said! But gee, the "lay patient" must be a real dimwit ... if I ever need a genetic counselor, I'm going to do my homework first! - J.O.

Source: Roche MI. A case of genetic counselling for Dr Watson. Nature 453, 281 (15 May 2008) | doi:10.1038/453281a; Published online 14 May 2008.

How is a starving, mutant yeast like a cancer cell? [adaptivecomplexity's column]

adaptivecomplexity — Wed, 14 May 2008 15:11:45 -0500

When yeast are starving, they do what any rational microbe would do: they stop dividing and hunker down, trying to conserve resources until the good times return.

Well, I'm a Doctor [evolgen]

Wed, 14 May 2008 14:00:00 -0500

I can officially claim myself as a member of the ivory tower elite. At least, that's what they tell me.

Read the comments on this post...

X-Prizes for Health and Medicine? [ScienceRoll]

berci.mesko@gmail.com (Bertalan Meskó) — Wed, 14 May 2008 12:21:44 -0500

Have you ever heard about the Ansari X Prize that resulted in constructing the world’s first privately developed spacecraft?

Source

Have you ever heard about the Archon X-Prize for Genomics? It will lead us to a new generation of genome sequencing methods.

What about an X Prize for Health and Medicine? Students at the Massachusetts Institute of Technology came up with some interesting ideas.

Of the specific proposals, one team suggested a prize for a major milestone in dealing with the problem of TB, which remains endemic in 22 nations and costs 1.7 million lives every year. Effective treatments exist, but the testing is relatively expensive and often misses active cases. So they proposed a $10 million prize for a new cheap, fast and accurate diagnostic system that could reach most of the 50 percent of cases that now go undiagnosed. Winning the prize would require not just laboratory demonstrations but field tests on 1,000 patients to show that it really works under difficult conditions.

The second proposal was for a simple, portable system that could be used by community health workers to carry out initial diagnostic evaluations for the 10 most widespread fatal, transmissible diseases. Such screening could lead to prescriptions of drugs or treatment for some conditions or referral to a doctor or nurse for conditions that require skilled care or more difficult diagnosis.

What do you think? An X Prize for Health and Medicine would be a good idea? Which medical specialty would be your choice?

Sequence and Ligation Independent Cloning [Bitesize Bio]

Nick — Wed, 14 May 2008 07:31:43 -0500

Regular readers will know about the advantages of T4 DNA polymerase-mediated ligation independent cloning. The fact that it is faster, more efficient and allows easier parallel cloning than conventional cloning has made it my method of choice in the lab.

But the technique does have it’s downsides - not least the requirement that existing vector multiple cloning sites be modified to convert them into ligation independent cloning vectors.

This paper by Li and Elledge recently flagged up in a comment by Max (thanks Max!) looks like it could change all that. It turns out that no sequence modification is required at all and LIC (or sLIC - sequence and ligation independent cloning as the authors call it) can be performed at any site in any vector of your choice.

If you are familiar with T4-mediated ligation independent cloning you will know that the vector sequence needs a specific LIC site containing restriction site flanked by regions that lack one of the nucleotides (e.g. adenine) for a 13-14nt stretch (read this first if you are not familiar with it). After linearising at the restriction site, the vector is incubated with dATP + T4 DNA polymerase, which chews back the 3′ end of the DNA until it stops after 13-14 nucleotides due to the presence of the dATP. This creates a single-stranded region to with a similarly treated insert can be annealed.

In this paper, Li and Elledge showed that the specific vector LIC site was not required. Treating the vector with T4 DNA polymerase and no dNTPs for a certain length of time (30 minutes was optimal for them) was sufficient for vector preparation. The single stranded stretch this creates is longer than required for annealing an insert, but single stranded gaps like these are apparently repaired very efficiently by E.coli after transformation so this is not a problem.

They also demonstrated that inserts prepared in one of three ways could be successfully annealed and transformed, which considerably increases the versatility of the process. The insert prep methods were:

1. T4 DNA polymerase treatment. Just like the vector, the insert could be subjected to T4 DNA polymerase treatment (without dNTPs) to create single stranded regions that will anneal to the prepared insert.
2. iPCR. Non-treated PCR fragments could also be annealed to prepared vectors, albeit with much lower efficiency. They showed that this is because a subset of fragments were synthesised incompletely, resulting in 5′ overhangs. Although this is was relatively in efficient, the authors found that it was robust and recommend it for routine cloning.
3. Mixed PCR. This was the most efficient method. It involves amplifying the insert using two separate reactions. In the first reaction, the forward primer has a 30nt tail homologous to the vector ss region, while in the second reaction, the reverse primer has the homologous tail. After amplification the two reactions are mixed, denatured and annealed to yield a subset of inserts that have both the forward and reverse primer single stranded tails that can be annealled into the prepared vector.

The authors showed that efficient annealing needed only 20-30 nt (single stranded) regions of homology at each end of the vector and insert. Amazingly, the homologous regions didn’t even need to be at the ends of the insert - the authors showed that non-homologous regions of up to 20 nucleotides could be tolerated as the branched products produced after annealing are efficiently trimmed and repaired by the cell.

I have not had a chance to try out this method yet, but it certainly looks very exciting. It looks to me like once this I have this protocol is up and running there will be no need at all for restriction enzyme-mediated cloning… which is a day I long for!

When I have some results of my own from this I’ll publish them, and my protocol here so watch this space.

Genetic Manipulation [Sciencebase Science Blog]

David Bradley — Wed, 14 May 2008 07:00:08 -0500

Are you happy to eat genetically modified foods? What about your friends and colleagues? Do the GM pros outweigh the cons?

I asked a few contacts for some answers by way of building up to a more formal response to those kinds of questions that will be published soon in the International Journal of Biotechnology (IJBT, 2008, 10, 240-259).

Plant geneticist Dennis Lee, Director of Research at mAbGen, in Houston, Texas, suggests that GM crops have several significant advantages. “Total cost per acre can actually be significantly less for GM crops,” he says. This is particularly true for crop species, such as maize, that have been modified to produce natural toxins that fend off insect pests or protect the crop from the herbicides need to keep weed growth at a minimum. However, he points out that, “In practice, this is often not the case - farmers tend to err on the side of caution and continue to use significant amounts of pesticides and herbicides.”

That said, crops can also be modified to grow in substandard conditions, such as strains of tubers grown in Kenya that are capable of surviving both drought conditions and high-salt soils. “Obviously, this is beneficial to yield - you can actually get some food out of places where you previously could not,” adds Lee. In addition, it could be possible to modify some crops to have greater nutritional content, such as the so-called “golden rice” project by Ingo Potrykus then at the Institute of Plant Sciences of the ETH Zurich.

One of the biggest perceived problems regarding GM crops is the possible contamination of other species. What if
herbicide-resistant
genes could
jump into weed speciesWhat if herbicide-resistant genes could jump into weed species, for instance? Lee points out that this putative problem can be overcome by using terminator technology to jumping genes. “However, in doing so, it creates a different problem,” Lee adds, namely that farmers must buy seed from the agbiotech company each year rather than save seed for planting.” One might say that this is an exploitative industry focused purely on maximizing profits, but at the same time it solves a serious technical problem that has been seen as one of the biggest stumbling blocks to the acceptance of GM crops.

Jeff Chatterton, a Risk and Crisis Communications Consultant at Checkmate Public Affairs, in Ottawa, points out that the pros are well documented: increased yield per acre, ease of use and perhaps, some day, increased ‘consumer level’ benefits such as higher nutritional values. But, echoes others’ comments on the hidden con of farmers the world over potentially being locked into the agbiotech company’s seed and having no recourse to produce their own from one year to the next.

“As traditional family farms are increasingly moving towards “Roundup Ready” corn or soybeans, you’re increasingly seeing a change in the business model of farming,” he says. “Rather than ‘family farms’ using traditional farming practices, agricultural operations are increasingly becoming factory farms.” It might be said that the emergence of factory farms is occurring outside the realm of GM crops, but with pressure being applied to produce more and more crops for non-food purposes, including, biofuels, unique polymers, and other products, the notion of a factory farm that doesn’t even feed us could become an increasing reality.

Lee also mentions an intriguing irony regarding the public perception of risk-benefits concerning GM crops and that is that the toxins produced by modified Bt maize is exactly the same toxin produced by the natural soil microbe Bacillus thuringiensis (Bt) itself and this is same Bt toxin that so-called “organic” farmers are usually allowed to use instead of “synthetic” pesticides.

Information Technology and Services Professional Bill Nigh of Bluenog, based in New York, provides perspective as a lay person. “We’ve been engaged in genetic manipulation for a long time now,” he says, “but it was limited by the technology at hand. With recombinant DNA it’s a remarkably more vast
field of
play and a
whole new ball gameWith recombinant DNA it’s a remarkably more vast field of play and a whole new ball game.” He stresses that his main concern regarding GM crops is that, “We seem to be just smart enough to make drastic breakthroughs and inventions, and are driven by the dynamics of the marketplace and ego to produce a lot of new things quickly. However our systems of governance, oversight and coordination are not mature enough to work through the implications of those new things in a timely fashion, especially the unforeseen synergies the breakthroughs can unleash.”

All that said, an international team has now investigated the various issues and has assessed the public’s Willingness to Accept (WTA) GM foods based on experimental auctions carried out in France, UK, and USA. Lead author of the IJBT paper Wallace Yee now at the University of Liverpool, worked, while at Reading University, with colleagues in various disciplines, from agricultural and food to business and economics in Italy, New Zealand, UK and US to explore perceptions of risk and benefits, moral concerns and attitudes to the environment and technology.

“Trust in information provided by industry proved to be the most important determinant of risk/benefit perceptions,” the researchers conclude, “willingness to accept followed general attitudes to the environment and technology.” They also found that educational level and age could also enhance perceived benefits and lower perceived risks of GM foods. “Our research suggests that trust-building by industry would be the most effective approach to enhancing the acceptance of GM foodstrust-building by industry would be the most effective approach to enhancing the acceptance of GM foods,” the team says.

“If the industry could educate people that GM technology does not pose any threat to the environment, but provides benefits to society as a whole and consumers as individuals, the attitudes of the public towards GM in food production would be favourable, and in turn increase their willingness to accept,” they conclude.

Computing professional Paul Boddie of Oslo, Norway, coming at the issue of GM crops from an indirect angle provides an allusion to computer programming that seems quite pertinent and was originally attributed to Brian Kernighan, which Boddie suggests readily transfers to other disciplines including genetic engineering: “Everyone knows that debugging is twice as hard as writing a program in the first place. So if you are as clever as you can be when you write it, how will you ever debug it?”

A post from David Bradley Science Writer

Genetic Manipulation

What does DNA mean to you? #5 [Eye on DNA]

Hsien-Hsien Lei, PhD — Wed, 14 May 2008 03:03:00 -0500

What does DNA mean to you?

Reader jhay of The Four-eyed Journal says:

DNA means a lot to me. It’s the reason for my being, from its hundreds of codons and sequences I am what I am today. I also believe that it will definitely shape the future because in this age where Information is a vital resource, what better source of information could you work on to advance human civilization than DNA itself! The possibilities are just exciting!

TED talks: Space [Mailund on the Internet]

Thomas Mailund — Wed, 14 May 2008 02:00:36 -0500

I’m a bit of a space exploration enthusiast myself, so of course I have to list a few TED talks on that as well…

The future of space flight

Exploring Earth and the solar system

I would love to see this happen… This might be my favourite talk of them all. I was almost applauding myself at the end.

Project Orion

This was a really cool project that never happened (for good or bad… atomic rockets are a bit risky but very powerful).

Our place in the cosmos

…and really a lot more than cosmology…

World wide telescope

I wasn’t sure if this should be under the heading “Space” or “IT”, but here it is…

Table of contents for TED Talks

Previous in series

Ubiquitous computing [business|bytes|genes|molecules]

Deepak Singh — Tue, 13 May 2008 20:10:46 -0500

Nat Torkington has a thoughtful post up on the O’Reilly Radar where he writes about ubiquitous computing (or ubicomp as he calls it).

I want to cast that problem a little differently. Let us assume we have a scalable cloud that we can tap into, perhaps with databases that easily scale to support streaming data. Let us imagine a lab, with instruments streaming out data, with devices consuming those data, and systems that can make decisions based on the data they are receiving. Such an interconnected work, a world with pervasive, ubiquitous computing might sound like science fiction, but over the past few years, we have slowly but surely built up the beginnings of an infrastructure that will make this scenario possible, perhaps a lot faster than we thought. The iPhone, the Chumby, the Bug, these are just early examples, as are streaming video services and communication platforms like Twitter and XMPP.

Of course, before we get there, we really need to develop systems that are smart about making decisions and filtering information, otherwise, we’re just going to get buried in a deluge of data that will make our heads spin, individually and collectively.

Update: On a semi-related note, here’s an Ignite talk from Where 2.0 that is an example of where we are headed (via O’Reilly Radar)

Ignite: Health In the Real World - Steven Hammond
By opening a geospatial window on patient-entered medical information, PatientsLikeMe is changing the way patients and researchers look at diseases and treatments in long-term illnesses like ALS, MS, and HIV.

Further reading
Research Streaming

Image via Wikipedia

Technorati Tags: Ubiquitous Information, Streaming Data

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Book Review: Beyond Genetics by Glenn McGee [Think Gene]

Andrew Yates — Tue, 13 May 2008 20:07:25 -0500

Read: (yes | maybe | no)

Beyond Genetics is a core of a few short essays fluffed into a book. Everything about this book screams “move my consulting career” including:

the stated mission to write Negroponte’s “Being Digitial” for genomics
forced introduction of cliche vocabulary like “geneware” and “genomic generation”
rheumy calls for “ethics” and “oversight” —like some middle-manager who always suggests “further meetings” or “forming a committee”
bombastic announcements like “gene therapy will be as common as aspirin in ten years” —like some overenthusiastic “sales consultant” behind an expo booth
slovenly adherence to political correctness and unwelcome cultural and personal anecdotes —like some high school principle giving a speech. Perhaps half the text is dedicated to fluffing potentially problematic statements.

Some of the book I liked. For instance, McGee does a good job of discussing the gene patent debate. But this book was clearly written to sell in popular bookstores and boost McGee’s stature in a fledgling industry. As such, Glenn is controversial only enough to be noticed, and he strokes every political group in the genomic industry without assuming any thoughtful responsibility for his genomic vision because “hey, it’s the future, right?” So if he’s wrong, this book will be safely forgotten without offending anyone, and that’s what’s already happening.

If you liked “The World is Flat,” you may like this book. Otherwise, let this one collect dust at the Barnes and Nobles.

Scientific Research and Medicine in Second Life [ScienceRoll]

berci.mesko@gmail.com (Bertalan Meskó) — Tue, 13 May 2008 16:35:46 -0500

David Pescovitz at BoingBoing had an interesting post about scientific research in Second Life, the virtual world:

This week’s Science News discusses several real scientific research projects inside Second Life. For example, Drexel University neurobiologist Corey Hart is building a virtual frog to study the neural pathways involved in hopping. Meanwhile, Robert Amme, a physicist at the University of Denver, is modeling a nuclear reactor as a training tool. Indeed, many research institutions are leveraging the simple sim tools of SL to create immersive science learning experiences.

This is a great example about how to close the gap between real science and the virtual world. You may also know about our medical exercises at the Ann Myers Medical Center where they train medical students (just like me) with case presentations. Now here is a tool with serious potential that could help us do it even better:

Text files, images and videos in one place. The aim is to create virtual patients with virtual medical conditions. Why is it beneficial for medical students?

The entire medical education is about case presentations. We move forward clinic by clinic during our studies and listen to case presentations all the time. That’s what we can do in Second Life but with even more educational material and without time or geographical restrictions.

According to DusanWriter, there are pharmacy patient case studies as well in Second Life.

The school has started to use SL as a training module, and has created a virtual version of Greensboro’s Moses Cone Family Practice Center, a local medical center. Students create an avatar and move through the center either as a student interviewing a patient, or as a patient. At the end of the simulation, the student takes a quiz to test his knowledge of the case history and of the practice center.

If you want to know everything about Second Life & Virtual Worlds for Academic Healthcare & Education, check out the slideshow of Patricia F. Anderson.

And if you don’t have a computer at home, let’s use a mobile to enter Second Life:

DDC Helps Unite Family Through DNA Testing for Immigration [The DNA Testing Blog]

DDC Panel — Tue, 13 May 2008 15:59:34 -0500

This year, DDC helped make Mother’s Day very special for one Ohio family. The Ezenagus are originally from Nigeria but now live together in a Northern suburb of Cincinnati, and it has taken over a decade for all members of the family to secure their visas, or “green cards,” and immigrate to the United States. For [...]

X2, a hypothesis aggregator, is surprisingly interesting and engaging. [Synthesis]

Mr. Gunn — Tue, 13 May 2008 15:34:58 -0500

My colleague Attila pointed me to X2, an effort by the Institute for the Future to collect and collaboratively rank hypotheses about future directions of science. When I read about it, it sounded interesting, but coming from futurists, I rather expected it to be all style and no substance.

I was pleasantly surprised to find a substantial amount of interesting content on the site, and it seems like the core functions all work as expected. Instead of being just another pawn in my attempt to own the first page of Google results for my name, William Gunn, (I dominate Mr. Gunn already ) I might actually spend some time there.

The basic function of the site is similar to Scintilla, in that users submit content and you can rate it and find related content you may not have seen, but instead of being fed by a collection of RSS feeds
(though there are user-suggested feeds as an input source), users submit “signals”, which are short essay-style blurbs about an idea or concept whose time is coming. “Hypotheses” can be written about the proposed meaning of a signal, and “forecasts” combine a set of signals which illustrate a trend. Because the types of content aren’t just blog posts parsed from a feed, the site isn’t overrun with noise, such as the scienceblogs.com blather that has troubled my use of other recommendation engines. Interestingly, the “Add a feed” link simply goes to a project info blurb, so perhaps they’re working on that very problem.

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This post is about future, hypothesis, prediction, recommendation, science

cyclone Nargis: do we let them stand alone? [the skeptical alchemist]

noreply@blogger.com (steppen wolf) — Tue, 13 May 2008 15:06:54 -0500

If you are a fan of the Lord of the Rings, you might just remember that moment when you see the Elves arriving at Helm's Deep, at a time when the Rohirrim thought that nobody would ever come to help in the fight against Saruman. I remember well, because so many things happen in this world when that moment comes again and again, and nobody ever decides not to let people in need stand alone. Rwanda and Darfur come to mind. Man-made wars.

But now, here comes this case. This case is, in most people's minds, so unequivocal, that our inability to react to it will be perceived by most as deeply unethical. Here comes a time when, struck by the force of nature, a government fails an entire nation...and we stand here to watch and pontificate on whether it would be legal for the UN to send troops to Myanmar. Too bad we know exactly why Russia and China voted against a UN resolution in favour of stronger UN intervention in Myanmar (two words: Tibet and Chechnya).

Burma continues to reject help

Burma's military rulers still oppose foreign aid workers helping the many thousands left destitute and in danger of disease by Cyclone Nargis.

Vice-Admiral Soe Thein said Burma was grateful for an aid shipment from the US, which arrived on Monday, but said there was no need for aid workers.

The UN has warned of the risk of a "second catastrophe" unless a massive aid operation is put in place rapidly.

The organisation is calling for a "transport corridor" to be set up.

The UN's humanitarian chief, Elisabeth Byrs, reiterated the international community's exasperation with Burma's ruling junta.

"We are only seeing the peak of the iceberg, and the situation risks becoming a lot more dramatic if there isn't an acceleration of humanitarian aid," she told journalists in the Swiss city of Geneva.

'Haphazard' delivery

The official death toll from Cyclone Nargis is approaching 32,000 - but observers fear the final count will be much higher.

Ms Byrs said 55,000 tonnes of rice would be needed to feed the 750,000 people estimated to be in danger for three months. Half of the rice would need to be imported.

So far, she said, the World Food Programme had been able to send only 361 tonnes of food aid - and distribute just 175 tonnes.

Emergency help has been held up by Burma's rulers, who have accepted the aid but refused to allow experts from overseas to co-ordinate its delivery.

Aid agencies say much of the food and equipment arriving in the country is not getting to those who need it because the junta does not have the organisation to transport it.

A BBC correspondent inside Burma says aid delivery is haphazard and private citizens have begun to distribute water and cakes from the backs of their cars rather than waiting for the soldiers to help.

French news agency AFP reported that the military had imposed a curfew in some of the worst-affected areas in the Irrawaddy Delta region over fears that rice rations would be stolen.

"You can't go out after 7pm because the soldiers will shoot," a 60-year-old man from the village of Pyin Ka Yaing told an AFP reporter there.

Apparently, it can also take about 3 hours for a European national on Burmese ground to get a tourist visa, but if you happen to be a relief worker, you will simply not be allowed in.

I guess this is what the ruling junta wants, ahead of the upcoming constitutional referendum which could keep them in power for a very long time still. Which makes me wonder whether the area struck by the cyclone would have voted, before the events, against or in favor of the junta remaining in power.

Never underestimate a bureaucracy's instinct for self-preservation.

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Research is a money pit [Bayblab]

noreply@blogger.com (Anonymous Coward) — Tue, 13 May 2008 12:11:37 -0500

Do you ever get the sense that research money often goes wasted? Even if you ignore all the research dead-ends and the discoveries which have limited implications, and just concentrate on what you can get for your tax money. How often does an expensive machine get used for only one experiment, how often do we throw out stuff that still works. And not to mention the price gouging that suppliers are guilty of. I don't understand how a ice pack for a western apparatus can be 10 times more expensive than a regular one, or why a research fridge is four times the price of a regular fridge. It's certainly not for the reliability, from what I've seen of our fridges. Some of the kits you can get now are ridiculous, especially considering the hourly wage of the person using it. It begs the question: should we hold the researchers accountable for the money they use? Between two researchers who produce the same work, should we choose the one who will do it for cheaper, or do we risk stifling innovation? Just take this example of a researcher who used his grant money for chrome wheels and big screen TVs. It sounds like he got off easy:

"Another $123,703.20 in expenditures appeared to be "inconsistent" with his research grant proposals, the documents say. But university investigators gave him the benefit of the doubt saying the nine computer monitors and other items "might have been related" to his research from a "general scientific perspective."

The university then made an arrangement with the researcher that in the "event of timely repayment" of $24,767.33, it would not ask for the rest of the money back.

The university returned $21,485.67 to NSERC. The documents indicate the other $3,000 refunded by the scientist was sent back to other agencies that had also financed his research."

Everything You Wanted to Know About the Human Genome But Were Too Lazy to Figure Out [Bayblab]

noreply@blogger.com (Bayman) — Tue, 13 May 2008 11:37:48 -0500

This new book sounds cool. "A Short (173pp) Guide to the Human Genome", by Stewart Scherer. Probably a great one for your bathroom or outhouse collection. Such a reference is drastically needed - everyone in biology should know the human genome inside out, but who has the time to fish out all the info? Now we don't have to. Sweet.

The Epi-Genomic Canary [The Gene Sherpa: Personalized Medicine and You]

noreply@blogger.com (Steve Murphy MD) — Tue, 13 May 2008 08:51:00 -0500

So many people talk about guniea pigs as the research subject. I think this is a disservice for the pigs. Personally I think the Shaft Canary is a much better analogy. You see, the subtle changes...

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Post-Modernism versus Science [Bitesize Bio]

Dan — Tue, 13 May 2008 05:44:57 -0500

A few months ago I mentioned about how people shouldn’t take science, on faith, but instead on data. Put another way, this is about post-modernism, or anti-modernism, where facts and their interpretations are all relative, at least to some degree.

I came across an outstanding essay on the subject by Daniel Dennett over on Butterflies and Wheels: Postmodernism and Truth. There are a few excerpts below the fold [Emphasis mine]. Yes, there’s still Kuhnsian sociology of science, although I’ve always read Kuhns as agreeing with the bit from the last quote that I have below the fold: “The methods of science aren’t foolproof, but they are indefinitely perfectible. Just as important: there is a tradition of criticism that enforces improvement whenever and wherever flaws are discovered.”

[T]hose fields where the stakes are higher–and more direct–there is a longstanding tradition of being especially cautious, and of taking particular responsibility for ensuring that no harm results (as explicitly honored in the Hippocratic Oath). Engineers, knowing that thousands of people’s safety may depend on the bridge they design, engage in focussed exercises with specified constraints designed to determine that, according to all current knowledge, their designs are safe and sound. Even economists–often derided for the risks they take with other people’s livelihoods–when they find themselves in positions to endorse specific economic measures considered by government bodies or by their private clients, are known to attempt to put a salutary strain on their underlying assumptions, just to be safe. They are used to asking themselves, and to being expected to ask themselves: “What if I’m wrong?”

Granted, scientists are still human and falliable. But yes, the whole of the endeavor of scientific research, to say nothing about other technical occupations, are centered around scrutinization of results, and “bootstrapping our way to ever greater accuracy and objectivity,” to refer to the next quote. I would just change accuracy to precision there, because accuracy implies a pre-defined target, whereas precision instead implies the reproducibility of results. As I found out early on in grad school, trying to fit your results to your expectations is bass-ackwards.

Is the line really straight? How straight is it? In response to these questions, we develop ever finer tests, and then tests of the accuracy of those tests, and so forth, bootstrapping our way to ever greater accuracy and objectivity. Scientists are just as vulnerable to wishful thinking, just as likely to be tempted by base motives, just as venal and gullible and forgetful as the rest of humankind. Scientists don’t consider themselves to be saints; they don’t even pretend to be priests (who according to tradition are supposed to do a better job than the rest of us at fighting off human temptation and frailty). Scientists take themselves to be just as weak and fallible as anybody else, but recognizing those very sources of error in themselves and in the groups to which they belong, they have devised elaborate systems to tie their own hands, forcibly preventing their frailties and prejudices from infecting their results.

In case you haven’t noticed from reading scientific papers, researchers, amongst themselves, are notoriously conservative (not in the political sense) in how they make inferences based on available data. If you claim something in a manuscript, the peer-review process is supposed to call you out on it - and if the initial reviewers miss such overstatements, someone somewhere will probably notice, sooner or later. Funding requests are another thing, of course, but even there a scientist is judged on their ability to collect and interpret data which matches reality. If they fail to meet expectations in terms of data-driven research, then they’re in trouble.

What inspires faith in arithmetic is the fact that hundreds of scribblers, working independently on the same problem, will all arrive at the same answer (except for those negligible few whose errors can be found and identified to the mutual satisfaction of all). This unrivalled objectivity is also found in geometry and the other branches of mathematics, which since antiquity have been the very model of certain knowledge set against the world of flux and controversy. In Plato’s early dialogue, the Meno, Socrates and the slave boy work out together a special case of the Pythagorean theorem. Plato’s example expresses the frank recognition of a standard of truth to be aspired to by all truth-seekers, a standard that has not only never been seriously challenged, but that has been tacitly accepted–indeed heavily relied upon, even in matters of life and death–by the most vigorous opponents of science.

Platonism may have been greatly flawed in some respects, but in mathematics, he and his fellow Ancient Greeks were very perceptive fellows. They noticed that quantification was as objective a way of interpreting reality as you could get. And such quantification is excactly what the precision of science is built on - exemplified best by the calculation of the value of Pi. We still don’t have an accurate or perfect number that equals Pi, only an astoundingly precise estimate for that number. The same is true for all of science - again, we are bootstrapping our way to better and better approximations of reality.

The methods of science aren’t foolproof, but they are indefinitely perfectible. Just as important: there is a tradition of criticism that enforces improvement whenever and wherever flaws are discovered. The methods of science, like everything else under the sun, are themselves objects of scientific scrutiny, as method becomes methodology, the analysis of methods. Methodology in turn falls under the gaze of epistemology, the investigation of investigation itself–nothing is off limits to scientific questioning.

Indeed. And this epistemology is how knowledge is acquired (as opposed to certainty*).

* = Science has proof without any certainty. Faith has certainty without any proof.