The DNA Network

List your favorite science books [adaptivecomplexity's column] Posted: 29 Aug 2008 04:39 PM CDT Via Cosmic Variance I see that it's blogger book-list time again. Cocktail Party Physics gets us started with a list of the best popular science books. Great science books are always neglected in lists of the world's best books, so browse these lists for a smorgasborg of the best science writing out there. Here's my contribution, which is based on two main criteria - the quality of the prose, and the substance of the science. A good science book should effectively convey the ideas involved in the story, or something about how science itself works as seen through the life of a successful scientist. The list does not include many old books - for some reason, popular science books can quickly seem very dated. Read More...

Let's talk about facts this election - Part IV - Soft Power [The Daily Transcript] Posted: 29 Aug 2008 02:59 PM CDT One of America's strengths was that people looked up to the US. In WWII soldiers would give up to the US on purpose, because they knew that they would be treated fairly. How do I know this - my grandfather who fought for the Italians was one of them. Imagine that power. You are so highly regarded that your enemies would rather give up to you than fight you. But we've squandered that. In the name of fighting terror, we torture. In the name of justice, we invade a country without justification. And it's worse then that - we actually bombed a country and then fail to build it back up again. Hundreds of thousand dead for what? I was against the Iraq war, but even worse than this misguided adventure was the fact that we failed to rebuild the country after we got rid of the regime. Why did we fail? All the talking heads would say that we didn't have enough of a military presence there, but lets face reality, the GOP just doesn't understand that the government has a role to play in building society. Instead of sending experts to rebuild Iraq, we sent cronies who were experts at chanting right-wing mantras and little else. Iraqis were angry. All of the good will that some Iraqis had for the US evaporated. Thankfully the Iraqi insurgents have figured out that Al Qaeda is worse than the US and are now fighting on our side to rid their country of religious zealots. Yes, fanatics can ruin your neighborhood. In the midst of all this, the world's collective jaw dropped. The US was first irrational and then appeared incapable of doing anything right. I'm glad that these guys weren't the ones to face the post WWII world, they would have wrecked it with their free-market government-is-good-for-nothing ideology. So America's ability to convince its allies that it held the moral high ground evaporated. People around the world were sickened and disgusted with the Bush administrations policies and as a consequence world opinion of the US dropped. Now why is this important? Well as a non-American I'm telling Americans that the world wants, and needs an enlightened and strong America. Why do you think that so many flocked to hear Barack Obama's speech in Berlin? Because he's a celebrity? Germans, Europeans and most of the world wants a America that spreads fairness, peace, equal opportunity and democracy. Obama, the candidate opposing McCain and the GOP, opposed the war and wants to reestablish US's status in the world as a leader for justice and opportunity. That's why. So the title of this post has the word facts, and so here are some to backup what I'm saying. First this graph of world opinion from the BBC: Here's a snapshot of how one country (this case Portugal - just for you evil gomez) views the US (source): A majority of Portuguese (55%) sees the US influence in the world as mainly negative, while just 29 percent believes it is mainly positive. Disapproval of US foreign policy is widespread in Portugal, with very large majorities disapproving of US treatment of detainees at Guantanamo (84%), the handling of the Iraq war (83%), global warming (79%), and the Israel-Hezbollah conflict (72%). The Portuguese also tend to view US handling of rising nuclear tensions negatively, with 57 percent disapproving of the situation with Iran and 51 percent disapproving of the situation with North Korea. More than three in four (77%) in Portugal see the US military presence in the Middle East as instigating more conflict than it prevents, and just 15 percent see the US as a stabilizing force in the region. If you want some really disturbing numbers, see this report by Gallup. Note that these numbers are not the product of "jealously" or any of the crap that right-wing pundits spout. The Portuguese, just like many others, expect more from the US. And that's why Barack Obama, the candidate opposing McCain and the GOP, is so popular throughout Europe. So what are the numbers? This is from the Pew Research Center: Even Aussies prefer Obama by a wide margin (and there is no way that Aussies are jealous of the US - trust me). So will the act of electing Obama increase America's stance in the world? Probably. Will it increase America's soft power? Very likely. Read the comments on this post...

SEQanswers Registers 1000th member! Traffic/posts continue to grow! [SEQanswers.com] Posted: 29 Aug 2008 02:27 PM CDT SEQanswers has marked a major milestone this morning, with the registration of it's 1000th member, in just over 10 months of existence. Membership and activity have continued to grow rapidly, totally outstripping my expectations. I had some fun looking at some statistics from the database and Google Analytics this morning, and I thought I would share. From the above graph, the rate of new registrations continues to climb. In the month of August to date, over 160 new members have... Read more and join the community...

Canadian Health Concerns [Bayblab] Posted: 29 Aug 2008 02:13 PM CDT There have been a couple of items in the news recently regarding Canadian health issues. Both of them have been touched on before (which should come as no surprise - we're visionaries here at the Bayblab). The first is Listeria which began with an outbreak which left one dead and several others ill and the subsequent product recall and shutdown of the Toronto Maple Leaf production facility. We've tackled Listeria before, and discussed some of the strategies companies use to minimize contamination - mainly sanitary design and proper cleaning. In the US, bacteriophage are also used for Listeria management. In Canada, we have yet to adopt these measures: [Retired Health Canada microbiologist and food inspector Bill] Riedel said Canada needs a system like one approved in the United States two years ago, in which bacteriophage therapy is used to combat Listeria monocytogenes found in foods. Bacteriophages are viruses that infect and destroy bacteria. As of Wednesday, the number of deaths caused by the outbreak was 6, with 10 others under investigation. Major fast-food chains McDonalds and Mr. Sub were affected by the recall. I wonder if bacteriophage technology would have prevented this outbreak, and if the death toll and economic impact will accelerate a move towards it. Second up is the mumps outbreak in western Canada. I've written about disease resurgance before, usually measles. This time it's mumps. Close to 200 cases have been reported in the Chilliwack region of British Columbia - a province that typically sees no more than 5 cases per year (according to CBC.ca). Of the 191 cases reported so far since the outbreak began in Chilliwack in February, 10 to 20 are still active. Half of the people who have been infected have not been immunized, a quarter have had at least one shot and a quarter do not have vaccination records, Dr. Brodkin said. One person developed meningitis, nine suffered hearing loss and 26 had swollen testicles or ovaries. It is not clear how many of those cases will result in permanent deafness or sterility. Officials fear that up to two-thirds of cases are going undetected and continue to spread the virus. The outbreak has been linked to religious groups in the area who are opposed to vaccination due to their beliefs.

Insulin without the stem cells [Mary Meets Dolly] Posted: 29 Aug 2008 11:46 AM CDT Stem cells are supposed to cure everything, if you buy into the media frenzy. First we were told that embryonic stem cells were the best. But because of Bush's very right but very unpopular stance on funding ESC and cloning research, scientists have been looking for alternatives. Induced pluripotent stem cells, or iPS, came from looking at alternatives to riping open existing embryos or cloning new ones to obtain pluripotent stem cells. iPS cells are adult stem cells that have been "reprogrammed" back to a pluripotent or "embryonic" state. Scientists at Harvard have used nuclear reprogramming technology to take normal pancreatic cells, not stem cells, and program them to produce insulin. From the LA Times: Harvard study may ultimately shift treatment options away from stem cells for a variety of diseases. Injecting a cocktail of proteins directly into the bodies of diabetic mice, researchers have converted normal pancreas cells into insulin-producing cells -- a genetic transformation that could pave the way for treating intractable diseases and injuries using a patient's own supply of healthy tissue. The Harvard University scientists activated a trio of dormant genes that commanded the cells to transform themselves, much as a person might upload a new operating system onto a computer to change a PC into a Mac. Within 10 days, the pancreas cells ceased their normal function -- making gut enzymes to digest food -- and instead produced insulin to regulate blood sugar, according to a study published online Wednesday in the journal Nature. Doug Melton, co-director of the Harvard Stem Cell Institute and the study's senior author, said the same approach could be used to generate motor neurons for patients with amyotrophic lateral sclerosis, to make cardiac muscle cells for heart attack victims or to create other crucial cells that can repair damage wrought by a range of illnesses. "We were able to flip the cell from one state into another," Melton said, adding that the approach should be useful in treating disorders in "any case where there's a cell type missing and there are neighboring cells that are still healthy." This is really great news for diabetics. And as the headline suggests, this announcement may shift the focus away from embryonic stem cell research and even stem cell research altogether. This made me wonder how the pro-cloning-embro-destructive research crowd are reacting to this development. I needed to look no farther than a press release from the California Institute of Regenerative Medicine or CIRM. In case some of you are not familiar with CIRM, it is the regulatory body that oversees the $3 billion dollars of California taxpayer money that is earmarked for cloning and embryonic stem cell research. Californians were told that if they funded cloning and embryonic stem cell research, cures would come. And even during a state budget crisis, Californians bought it. This press release is more about how CIRM is still relevant, than it is about the amazing work of these Harvard scientists: CIRM applauds the creativity and value in the research reported and shares the excitement in the promise it might hold. However, it emphatically refutes assertions by opponents of embryonic stem cell research that this new study proves embryonic stem cell research is not necessary. In fact, the Harvard study poignantly points out the value of embryonic stem cell research. This maybe true, but this seems like a super desperate attempt to make sure everyone still believes that embryonic stem cell research is still king. Case in point, this section describing the limitations of nuclear reprogramming: The research reported in Nature is a major advance but it has significant limitations. It can be considered a type of gene therapy and has many of the same limitations and concerns that have been identified in the field of gene therapy. The genes that reprogrammed the cells were carried into the cells by adenoviruses, which have caused severe immune reactions and triggered cancers in gene therapy. The mice in this study were immune compromised mice, so that complication was not seen in this model, but to-date has proven difficult to overcome in humans. Huh, last I checked, immune response and tumor formation were "significant limitations" to embryonic stem cell research as well. Funny how that is not mentioned. I love the last paragraph which basically screams "we are still important and by-gum people still love us": CIRM was established in early 2005 with the passage of Proposition 71, the California Stem Cell Research and Cures Act. The statewide ballot measure, which provided $3 billion in funding for stem cell research at California universities and research institutions, was overwhelmingly approved by voters, and called for the establishment of an entity to make grants and provide loans for stem cell research, research facilities, and other vital research opportunities. To date, the CIRM governing board has approved 229 research and facility grants totaling more than $614 million, making CIRM the largest source of funding for human embryonic stem cell research in the world.

Bioinformatics as mashup [business|bytes|genes|molecules] Posted: 29 Aug 2008 08:54 AM CDT bioinformatics: acquiring, collating and rearranging information already available elsewhere? That is from a Tweet by Neil. My reaction was somthing along the lines of “boy that sounds like the definition of a mashup”. Bioinformatics is a broad field, but part of it, a good part of what a bioinformatician does is exactly what Neil describes. The work of a bioinformatician is built on data collected by many people around the world and deposited in a variety of data bases. A lot of what we do is take information from one and try and match it up to information from a second source, presumably with the goal of getting additional insights. It might sound crude to call it that, but I think if we start thinking of bioinformatics as a mashup, we could start thinking about making those mashups available to others, and perhaps even new ways to present the information. Disclaimer: This post was written early in the morning before any intake of caffeine Related articles by Zemanta A global informatics collaboratory Paul Watson talks about CARMEN

September is Now Ovarian Cancer Month [The Gene Sherpa: Personalized Medicine and You] Posted: 29 Aug 2008 08:38 AM CDT In one fell swoop of the pen on the 26th. President Bush signed into proclamation, September is now Officially Ovarian Cancer Month. This is a very big deal for those families who have been affected... [[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Let's talk about facts this election - Part III - Health Insurance [The Daily Transcript] Posted: 29 Aug 2008 08:30 AM CDT I'm Canadian. Back when I lived in Canada, health insurance was never a worry. Sure you might have to wait a bit before you got it, but you could always count on being sen by a doctor when ever something is wrong. If you want you can get additional health insurance that will pay for upgrades, but almost all Canadians will never let go of Universal Healthcare. But what is the situation down here in my adopted land? (I've lived in the US for ten years) The Democrats want to change things, they recognize that the system is broken. In contrast the GOP claims that the status quo is just fine, that the free market will solve all of our problems, but the numbers tell a different story. Let's look and see what the free market has done: Source: NPR Health Care Back in the National Spotlight Note that the break in the line in the above graph was caused by an adjustment in how the numbers were tallied. And look at how the cost of both health insurance and education are skyrocketing. We will soon become a country where only the rich can afford a trip to the doctor or a decent education. The GOP and free market preachers always chant that the market is more efficient than socialized programs. But when short term profits are the goal, sometimes you need to spend a whole lot more on management in order to screw your clients. So what are the stats on overhead? This is from a NEJM article: Background: A decade ago, the administrative costs of health care in the United States greatly exceeded those in Canada. We investigated whether the ascendancy of computerization, managed care, and the adoption of more businesslike approaches to health care have decreased administrative costs. [...] Results: In 1999, health administration costs totaled at least $294.3 billion in the United States, or $1,059 per capita, as compared with $307 per capita in Canada. After exclusions, administration accounted for 31.0 percent of health care expenditures in the United States and 16.7 percent of health care expenditures in Canada. Canada's national health insurance program had overhead of 1.3 percent; the overhead among Canada's private insurers was higher than that in the United States (13.2 percent vs. 11.7 percent). Providers' administrative costs were far lower in Canada. Between 1969 and 1999, the share of the U.S. health care labor force accounted for by administrative workers grew from 18.2 percent to 27.3 percent. In Canada, it grew from 16.0 percent in 1971 to 19.1 percent in 1996. (Both nations' figures exclude insurance-industry personnel.) Conclusions: The gap between U.S. and Canadian spending on health care administration has grown to $752 per capita. A large sum might be saved in the United States if administrative costs could be trimmed by implementing a Canadian-style health care system. Ref: Steffie Woolhandler Costs of Health Care Administration in the United States and Canada NEJM (03) 349:768-775 So who's in touch with reality? Those who believe in invisible hands, or those looking at the situation on the ground? Read the comments on this post...

Zen and the Art of Global Maintenance [Sciencebase Science Blog] Posted: 29 Aug 2008 07:00 AM CDT A discussion a while back, over a few beers, with a Buddhist friend about life, the universe, and everything (what else?) got around to the subject of null physics and the notion that the universe may always have existed and may exist for eternity to come. Sciencebase regulars will know that this concept is covered in a rather bizarre book I mentioned a few posts back entitled How to Discover Our Universe. While there is certainly room for improvement in current cosmological models this notion of an always having existed universe is not to everyone’s taste, at least in terms of conventional Western ideals. Indeed, it positively reeks of pseudoscience in the eyes of many of us raised on the conventional cyclic observation-explanation-prediction rote of modern science. Anyway, it was almost inevitable that a paper with a Zen, or should I say, Daoist, inclination would land in my inbox. And so completing the circle in drops a paper from Philosopher of Science Anthony Alexander. Alexander is currently Director for Studies and Research at a structural engineering, conservation and urban design consultancy that is apparently pioneering sustainability in the built environment. But, that is not the focus of his paper. He notes that the physics of the 18th century Western world was fundamental in establishing the basic concepts for the study of economics and our understanding of the fledgling Industrial Revolution. However, industry and physics have moved on, not least as a product of the almost exponentially increasing pace of technological change. It is perhaps this seeming progress and our need to consider a passage through time that many people cannot contemplate a universe without a beginning. But, before you run to the hills or roll into a potential energy well, this post is not about to go all mystical and misty eyed. There are no implications or allusions to an Ayurvedic notion of quantum mechanics. There is no incense burner on my deskThere is no incense burner on my desk. And while there might be a yoga teacher working on my accounts as I type, there is certainly no ambient crystal and phoenix rising yoga therapy session planned for this evening in a padded room with all-natural oxygen bubbling through gently illuminated vials of dihydrogen monoxide. Anyway, back to Alexander’s technique… He suggests that 18th century physics has been “comprehensively displaced by progress within Western science. The new larger field of understanding encompasses the complex, the chaotic, unpredictable and the fluid aspects of the real world. Unfortunately, the institutions of the modern world, the industries, the money movers, the pen pushers, remain firmly entrenched in a clockwork Newtonian world view whereas science is all about non-linearity of systems, probability of sub-atomics, and duality of energy and matter. This staid view considers the world to be stable and ordered, and human activity to be somehow fundamentally distinct from nature. While environmentalism and green economics have the grand aims of redressing the balance it is actually globalisation, according to Alexander, that has raised our awareness of other cultures and their disparate world view that could provide us with the means to reconcile the Newtonian industries with modern physics and systems theory. Alexander turns to one of his leanings - the martial arts - for inspiration as to how this might happen. The martial arts, kung fu, karate, judo, and their Daoist counterparts, invert the logic of Western combat. Training in the kicks, punches and locks of these various martial arts are aimed not at causing pain or injuring one’s training partner but in providing health benefits to both. A Western perspective might see an arm lock as a route to pain, whereas a practitioner of a particular martial art will see it as a way to build muscular stretch, for instance. Alexander sees parallels between this inverted logic of the martial arts not only with the concepts of modern physics but with the green economics. The status quo of 20th century Western economics [which persists even now] can be challenged by green economics, [but] does not seek harm to anyone or anyone’s interests. It seeks to promote harmony and longevity - values that are at the heart of common sense, sustainable development and [martial arts] culture, which all parties stand to benefit from. There really is no mysticism here, we are plunging head-first into global environmental crises. Physics underwent a paradigm shift to shake of Newton’s clockwork universe, perhaps, as Alexander suggests, we should work through his analogy and see green economics as the new paradigm for industry across the globe. Alexander, A. (2008). Different paths, same mountain: Daoism, ecology and the new paradigm of science. International Journal of Green Economics, 2(2), 153. DOI: 10.1504/IJGE.2008.019997 a Zen and the Art of Global Maintenance

The impact of web 2.0 on medicine and healthcare (SMIT 2008) [ScienceRoll] Posted: 29 Aug 2008 06:12 AM CDT I’m currently writing from Wien, Austria, where I’m attending the 20th International Conference of the Society for Medical Innovation and Technology (SMIT2008) and just presented my slideshow in the e-health section. The feedback was quite good here, but I would love to hear your thoughts on this. Of course, I will present a rather different slideshow in Toronto at the Medicine 2.0 Congress next week.

MyNetResearch: The newest addition to the squad [ScienceRoll] Posted: 29 Aug 2008 04:41 AM CDT The newest addition to the List of Community Sites for Scientists and Physicians is MyNetResearch. Our purpose is to assist you in maximizing your research productivity through global collaborations. We all have outstanding colleagues, yet have felt the disappointment of these colleagues not sharing our research interests and passions. This is not modern research-at least it’s not what research should be in the 21st century. Why be limited to local research collaborations when there are hundreds or even thousands of research experts across the world with whom you could have highly productive collaborations?

What’s on the web? (29 August 2008) [ScienceRoll] Posted: 29 Aug 2008 04:31 AM CDT A list of major scientists with blogs. That’s why I love using Friendfeed… What if journal current contents were tag clouds? (What You’re Doing is Rather Desperate): Genome Research Medicine 2.0: Social Networking, Collaboration, Participation, Apomediation, and Openness: A unique publication from Gunther Eysenbach just before the Medicine 2.0 Congress. Please nominate the 3G Project launched by Rima Bishara, MD:Teach health ed to pre-school age kids living in disadvantaged homes while parents and/or grandparents are present to also learn in a non-threatening setting. If Science was an Olympic Sport… (O'Really? at Duncan.Hull.name)

Scientific Identity [business|bytes|genes|molecules] Posted: 29 Aug 2008 12:34 AM CDT I have been thinking a lot about distributed identity lately and what it means for scientists. This was fueled by a bunch of things, including the recent news about OAuth, and discussions around social networks in science. We keep talking about how to connect information together. In the general web world, you have various services that, with varying degrees of success, bring things together into a common namespace. What we need to do in the scientific space is something similar. We have standards in place to make sites and services talk to each other. If we could figure out how to move our scientific identity, i.e. our collaborators, our communications (formal and informal, peer reviewed or otherwise), and our interests across services, while maintaining control over the communications, we would be in a very good place as we redefine how we communicate and practice of science. Personally, I’d like to see journals and scientific “networks” adopt OpenID, OAuth, and other web standards and along with DOIs and perhaps something like SciFOAF. Another paradigm to look at is laconica, which allows you to communicate across communities (and makes good use of OAuth), in essence giving you a distributed identity. In true internet meta-fashion, you can sign up using OpenID. On a parting note, a key success factor will be abstraction. We need to have the tools, etc in place that all the underlying complexity is abstracted away, otherwise there will always be too much friction to get started Related articles by Zemanta It’s Official: Mashup Privacy Protocol OAuth Is Fair Game

I see PLoS in everything #2 [The Tree of Life] Posted: 28 Aug 2008 10:26 PM CDT OK - I cannot help it. Whenever I see this little train letters in stores everywhere I spell something related to PLoS. If you support OA, please continue the conspiracy and spell something OA-related wherever you find letters like this. PS - Vaughn this is for your kid. This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist at the University of California, Davis.

Let's talk about facts this election - Part II - The Federal Budget Deficit [The Daily Transcript] Posted: 28 Aug 2008 09:46 PM CDT Again here's a simple graph that says it all. And they say that Democrats are fiscally irresponsible. Read the comments on this post...

Fat gene demonstrates role in cognitive development [biomarker-driven mental health 2.0] Posted: 28 Aug 2008 09:07 PM CDT Sometimes we humans tend to think we’re pretty sophisticated, but let’s face it, once we’ve got a fridge full of food and a partner to mate with, most of us - like every other species - are pretty content.  So it may seem reasonable, from an evolutionary standpoint, that a gene that regulates food intake and metabolism - leptin - would have wide-ranging effects on almost every physiological system in the human body including: immune, reproduction, endocrine, skeletal and CNS. A new PLoS ONE paper entitled, “Leptin Replacement Improves Cognitive Development” reports that administration of recombinant leptin to a 5-year-old boy with a nonconservative missense leptin gene mutation (Cys-to-Thr in codon 105) yields dramatic improvements in neurocognitive function. The open access paper describes the many known effects on leptin on neuronal plasticity and it is wonderful indeed to see its success when used as a therapeutic agent.  That the development of so-called ‘higher’ cognitive function in humans is regulated by a small peptide secreted by fat cells may be an affront to some, but not me.  “Honey, pass the chicken wings !”

You are subscribed to email updates from The DNA Network To stop receiving these emails, you may unsubscribe now.	Email Delivery powered by FeedBurner
Inbox too full? Subscribe to the feed version of The DNA Network in a feed reader.
If you prefer to unsubscribe via postal mail, write to: The DNA Network, c/o FeedBurner, 20 W Kinzie, 9th Floor, Chicago IL USA 60610