agribusiness

Spliced feed for The Science Network

2008-12-17T05:08:00.001-08:00

Spliced feed for The Science Network

Skepticality #092 - Numb3rs - Cheryl Heuton and Nicolas Falacci creators of Num3rs [Skepticality - Science and Revolutionary Ideas]

Posted: 16 Dec 2008 04:43 PM CST

Rarely is mathematics a major plot component on AmericanÂtelevision.ÂThe exception, of course, is the current hit prime time CBSÂtelevision drama Numb3rs.Â "We all use math every day: to predict weather, to tell time, to handleÂmoney.ÂMath is more than formulas and equations: itâs logic. Itâs rationality. Itâs using your mind to solve the biggest mysteries we know." So begins every episode â astonishingly â ofÂone of the consistently highest rated programs in its time slot.ÂNow in its fifth season,ÂNumb3rsÂhas helped pave the way for a whole new generation of science-basedÂprogramming on American television. This week Swoopy talks with Cheryl Heuton and NicolasÂFalacci (the creators and Executive Producers of Numb3rs) about the challengesÂof creating a fictional TV drama chock full of real science andÂmathematics.

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Spliced feed for The Science Network

2008-12-14T05:07:00.001-08:00

Spliced feed for The Science Network

Skeptics Guide #177 - December 10th, 2008 [The Skeptics' Guide to the Universe]

Posted: 13 Dec 2008 06:25 AM CST

News Items: Age of the Sphinx with Dr. James P Allen, Supernova Reflections and Milky Way's Black Hole with Phil Plait, Searching for Dyson Spheres; Your Questions and E-mail: Skeptical Authority; Randi Speaks: Cold Reading; Science or Fiction

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Spliced feed for The Science Network

2008-12-10T05:07:00.001-08:00

Spliced feed for The Science Network

Skepticality #085 - Why Magic is Important - Panel Discussion with James Randi and D.J. Grothe [Skepticality - Science and Revolutionary Ideas]

Posted: 09 Sep 2008 05:38 PM CDT

The hosts of Skepticality are recovering from their spectacularlyÂsuccessful "Skeptrack" events at Dragon*Con 2008: four days of livelyÂdiscussion featuring guests from some of the most prominent skepticalÂorganizations around the world. Included were James Randi and Dr. Phil PlaitÂfrom the JREF, Dr. Michael Shermer of the Skeptics Society, BenjaminÂRadford and D.J. Grothe from the Center for Inquiry, and Richard Saunders andÂcrew from the Australian Skepticsâto name only a few. For those who participated in this groundbreaking weekend, we look forwardÂto hearing your stories. For those who could not attend,ÂSkepticalityÂbrings you the first of several recordings from last week's panelÂdiscussions, beginning with James Randi and D.J. Grothe discussing "Why MagicÂis Important to Skepticism." This in-depth discussion of the entwined histories of magic andÂskepticism reveals how creating illusions can illuminate the truth.

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Skeptics Guide #163 - September 3rd, 2008 [The Skeptics' Guide to the Universe]

Posted: 06 Sep 2008 07:25 AM CDT

SGU Live from DragonCon 2008 with special guests James Randi, Pamela Gay, and Derek Colanduno; News Items: The Milky Ways Supermassive Blackhole; Live Questions; Science or Fiction

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Skeptics Guide #162 - August 26th, 2008 [The Skeptics' Guide to the Universe]

Posted: 01 Sep 2008 07:25 AM CDT

Interview with Richard Saunders; News Items: WTC-7 Collapse, Neanderthal Tool Making, Rainbow Lady Follow Up; Your Questions and E-mails: Teleportation; Science or Fiction

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Skepticality #084 - What's The Harm? - Interview: Tim Farley [Skepticality - Science and Revolutionary Ideas]

Posted: 26 Aug 2008 10:55 PM CDT

Misinformation is everywhere, but nowhere more prolific than on the internet. A Google search for "homeopathy" or "UFO" returns a landslide list ofÂmystery-mongering websites. Yes, there are a few skeptical web resources too âÂbut a non-skeptic can be easily misled online. On this episode,ÂDerek & Swoopy talk with Tim Farley, aÂskeptic applying his 20-plus years ofÂsoftware development experience to the creation of advanced tools and techniques for fighting the battle against misinformation on the World WideÂWeb.Â Tim's popular websites include the Skeptical Software Tools blogÂ"Skeptools" (which uses Web 2.0 techniques to aid the spread of criticalÂthinking information online), and WhatsTheHarm.net, which has collected theÂstories of over 225,000 people who have been injured or killed as a resultÂof supernatural andÂpseudoscientificÂpractices from alternative medicine to hypnosis to faith healing.

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Skeptics Guide #161 - August 20th, 2008 [The Skeptics' Guide to the Universe]

Posted: 23 Aug 2008 07:25 AM CDT

Interview with Adam Savage from Mythbusters; News Items: Remembering Perry, Monkey Eludes Dragnet, Bigfoot Body Hoax Revealed, Robot with Biological Brain, The Future of Doping; Special Report: JREF Psychic Challenge Report; Science or Fiction

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Skeptics Guide #160 - August 13th, 2008 [The Skeptics' Guide to the Universe]

Posted: 16 Aug 2008 07:25 AM CDT

Interview with Captain Disillusion; News Items: Bigfoot Body Claim, Invisibility Cloak, Prince Charles on GM Food, Sprinkler Rainbow Lady; Science or Fiction

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Skepticality #083 - Watch this Space - Interview: Dr. Phil Plait, The Bad Astronomer [Skepticality - Science and Revolutionary Ideas]

Posted: 12 Aug 2008 10:37 PM CDT

Long-time listeners may recall thatÂSkepticality's very firstÂinterview guest was Bad Astronomy author and popular science bloggerÂDr. Phil Plait.Â This past week the James Randi EducationalÂFoundation (one of the leading organizations to promote critical thinkingÂand examination of pseudoscience) announced that The Bad Astronomer himself will be the newÂJREFÂPresident. Now, Dr. Plait returns to SkepticalityÂto tell Derek & SwoopyÂnot only aboutÂinteresting advances in privately-funded space travel and theÂfuture of NASA under a new presidential administration, but also aboutÂexciting developments in his own career â including his new role at the JREF,Âchanges for Bad Astronomy, and Phil's impending trips to the Galapagos andÂDragon*Con 2008.

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Skeptics Guide #159 - August 6th, 2008 [The Skeptics' Guide to the Universe]

Posted: 09 Aug 2008 07:25 AM CDT

Interview with Phil Plait and James Randi; News Items: James Doohan Ashes Lost, Solar Power Breakthrough, China Weather Control, The Montauk Monster; Your Questions and E-mail: Where Does Matter Come From; Science or Fiction

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Skeptics Guide #158 - July 30th, 2008 [The Skeptics' Guide to the Universe]

Posted: 02 Aug 2008 07:25 AM CDT

Interview with Banachek; News Items: Edgar Mitchell UFO Claims, UFOs and Terrorism, Gas from Garbage; Your Questions and E-mail: House and the Therapeutic Diagnosis; Science or Fiction

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Skepticality #082 - Rationalist Rap - Interview: Greydon Square [Skepticality - Science and Revolutionary Ideas]

Posted: 29 Jul 2008 10:07 PM CDT

The mainstream rap and hip hop communities are known not only for a way with words and penchant for controversy, but also for occasional drama. Rapper Greydon Square is no exception.Â On this week's episode of Skepticality, Derek and Swoopy hang loose with Greydon and talk about his musical influences, being embraced by the atheist community â and why this Compton native (raised as a legal orphan by the Department of Children & Family Services of California) refuses to be a product of the system.

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The DNA Network

2008-12-08T18:45:00.001-08:00

The DNA Network

Aphid-bacterial symbiosis in more detail, and in the New York Times [The Tree of Life]

Posted: 08 Dec 2008 07:41 PM CST

Nice little bit in the New York Times tomorrow about aphids and their symbionts. Henry Fountain writes (Observatory - How Tiny Insects, With a Little Help, Survive on Plant Sap - NYTimes.com) about a new article by Angela Douglas, one of the true pioneers of endosymbiont research. In her study she dissects in fine scale detail which essential amino acids are missing from the aphid sap only diet and which ones are made by the symbionts. Interestingly, the research apparently shows that the aphids may have figured out how to make methionine by themselves. I say apparently since I have been unable to track down the paper which I assume is coming out soon.

I should note, in one of the symbioses like this that I have studied with Nancy Moran we found that there were two symbionts contributing to the nutrition of the host. We found that one of the symbionts was likely making amino acids for the host (an insect called the glassy winged sharpshooter which eats only xylem sap) and the other symbiont was likley making vitamins. Nancy showed later with John McCutcheon that the symbiont that was making vitamins also was predicted to be making methionine for the host. So it seems possible there might be a missing symbiont in the aphid study? Although it would be cool if the aphid has figured out how to make an amino acid most animals are not able to make.

Hat tip to Max Lambert for pointing this out.

Nils Reinton (SciPhu) relaunches site: BIOpinionated [Think Gene]

Posted: 08 Dec 2008 06:23 PM CST

Nils Reinton has relaunched his site, SciPhu, as BIOpinionated. Nils is a molecular biology scientist working in medical diagnostics, and his blog is consistently interesting and insightful. Check it out!

Tree of Life Gift Recommendation - Climate Kits [The Tree of Life]

Posted: 08 Dec 2008 05:33 PM CST

Just a quick recommendations for a gift for this holiday seasons that seems cool (metaphorically and literally). It is the climate kit. It comes from a friend of mine from college, Kathy Washienko and this is some of their text:

Kits are convenient collections of tools and tips that will help your family and friends reduce your environmental impact. By grouping what you need in one handy package, a kit makes it easy and fun to take energy-saving steps. Each kit is ultimately a gift to our environment, but will also save you money in reduced energy costs.* And every kit comes with our innovative "rebate." Check them out!

Sounds good to me. And given that I am trying here to promote trees (albeit phylogenetic ones, not real ones) I like that they are planting a tree and trying to be green.

Save babies, break the law. [Think Gene]

Posted: 08 Dec 2008 04:52 PM CST

This was such a “good idea” that I had to share. Maybe some radical Ivy grad student can pick up the ball here.

If you want to put your money where you mouth is, email Josh here at Think Gene, and maybe he’ll tell you how to buy the supplies and make the primers to do these tests for free / at cost. You could drive around in a van providing free genetic tests to save babies —”liberating the science”— for probably less than a few thousand dollars US. It sounds like a good trustafarian grad student project. Fight the man, save babies, hide behind the family trust when your antics piss off powerful people who would crush you otherwise… yah. Much better than “saving the Earth” by smoking organic pot or whatever.

Originally posted as a comment by Andrew Yates on Think Gene using Disqus.

The genetic architecture of metabolic traits: a data explosion [Genetic Future]

Posted: 08 Dec 2008 03:07 PM CST

Nature Genetics has just released six advance online manuscripts on the genetic architecture of complex metabolic traits. The amount of data in the manuscripts is overwhelming, so this post is really just a first impression; I suspect I'll have more to say once I've had time to dig into the juicy marrow of the supplementary data.

The general approach of exploring the genetic architecture of quantitative disease-associated traits (often called intermediate phenotypes or endophenotypes) rather than categorical case-control analyses of disease status raises some interesting questions, but I'm going to save those for another time and focus instead on the results.

Executive summary
For those who don't want to wade through the details, here's the gist: these papers use genome-wide association data from very large numbers of individuals to analyse the genetic architecture of disease-associated traits like blood lipid and glucose levels (rather than looking for associations with disease status itself). They find a bewildering array of new variants associated with these traits, and indications of many more genes still to come as sample sizes increase. However, for most traits, despite very large sample sizes the majority of the variance is not explained by the identified variants.

For those who are interested in more details, I've tucked them below the fold:

Citation:
Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, Mark I McCarthy, Mark J Daly, Marjo-Riitta Järvelin, Nelson B Freimer, Leena Peltonen (2008). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population Nature Genetics DOI: 10.1038/ng.271

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TripAnswers or Twitter? [ScienceRoll]

Posted: 08 Dec 2008 03:00 PM CST

Twitter is a microblogging tool that allows us to post 140 charachter-long messages and we do have a huge medical community there so it’s quite easy to ask medical questions and get relevant answers from doctors from around the world.

TripAnswers is a site where clinicians can ask questions.

TRIPanswers is a repository of clinical questions and answers drawn from a wide number of sources around the world and builds on TRIP's ten years experience of answering clinical questions. Ultimately, we want to create a resource where clinicians can easily find answers to their question and, who knows, create a clinical Q&A 'space' where users can share their own Q&As (it's always struck us as wasteful that clinicians around the globe answer questions and this effort is never shared!)

Which one would you use to ask questions?

Futher reading:

National physician group MDVIP partners with Navigenics [The Navigator - Navigenics Blog]

Posted: 08 Dec 2008 03:00 PM CST

Vance Vanier, M.D.

Navigenics is pleased to announce a new relationship with a national network of physicians who practice proactive, personalized medicine. Through the collaboration, the Navigenics genetic testing service will be made available to their patients, who number more than 100,000 nationwide. I'd like to share some of the information about this collaboration, as described in a news release issued today:

National Physician Group MDVIP Partners with Navigenics to Provide Personal Genetic Tests for Preventive Medicine Practice

Boca Raton, FL and Redwood Shores, CA – December 8 2008 – MDVIP, Inc., a leading national network of physicians dedicated to preventive and personalized healthcare, and Navigenics, Inc., a leading personal genomics testing company, today announced a first of its kind collaborative effort to integrate genomic-based preventive healthcare in physician offices. Through this initiative, Navigenics' genomic testing service will be available to MDVIP affiliated physicians to help patients understand their genetic risk factors for disease and work with their doctors to develop individualized prevention plans.

Navigenics will provide MDVIP patients and their affiliated physicians with insight into their personal genetic predisposition for developing certain medical conditions where primary or secondary prevention could improve health outcomes. The Navigenics test will identify individuals' genetic markers for developing such conditions as type 2 diabetes, cancer, heart attack, and celiac disease. Working with their personal MDVIP physician and Navigenics' board-certified Genetic Counselors, individuals can chart and implement a personalized wellness course to help decrease their overall risk, delay disease onset or prevent it altogether.

"We have for many years been closely watching the field of genomic testing evolve into a tool that can enhance and inform the practice of preventive medicine," said Edward Goldman, M.D., CEO of MDVIP. "We believe that Navigenics' preventive genomics service has the potential to be an innovation that could significantly enhance patient care."

Next-Generation Sequencing Statistics [ScienceRoll]

Posted: 08 Dec 2008 02:52 PM CST

Have you ever wondered about the typical run time of a next-generation genome sequencer? PolITiGenomics has the answers:

Read more about next-generation sequencing in the Trends in Genetics article: The impact of next-generation sequencing technology on genetics.

Salary prospects for biology majors [Bayblab]

Posted: 08 Dec 2008 01:08 PM CST

This may or may not surprise you, but who do you think has the highest median starting salary and mid-career salary between those three: History graduate, philosophy graduate, biology graduate? When it comes to salary you're actually better off with an undergrad in history, philosophy, geography, any engineering, or any science other than biology. If it makes you feel better, it still beats drama and is about equivalent to an English major with $38.8K starting and $64.8K mid-career. Why is that? I'm not sure, but It probably is a consequence of supply and demand. Not much demand for biologists, and way too many graduates.

Leaf Camouflage Pictures and Videos [Bayblab]

Posted: 08 Dec 2008 12:59 PM CST

I ran into a collection of awesome leaf mimicry pictures and videos I origonally ran into on boing boing. Definitely worth checking it out. The blog that is hosting these pictures, The Conservation Report, seems to have an ongoing thing with pictures of impressive animal camouflage. While I would love to get some of the leaf mimicing fish for my aquarium, looks like they'd eat my neon tetras!

Finnish population structure won't persist much longer [Genetic Future]

Posted: 08 Dec 2008 12:45 PM CST

In my previous post on Finnish population clustering I should have emphasised that the map was constructed only from individuals who had both parents from the same geographic/linguistic region; this obviously provides a lot more power to detect a correlation.

The close match between genetic and geographic ancestry in these selected individuals indicates that there hasn't been a huge amount of long-range admixture between Finnish populations over quite a long period of time - if there had been, there would be no reason to expect much correlation between the two maps. However, data in the supplementary section of the paper show that there has been substantial mixing over more recent history:

This graph shows the number of individuals from the cohort that had both parents from a single region. You can see immediately that the single largest category is the "mixed" category indicating parentage that crosses region boundaries. It seems likely that many of these individuals come from border areas between the regions (in which case excluding them from the map will have resulted in a rather artificial increase in the separation between clusters), but no doubt there are also many examples of long-range admixture resulting from increases in population mobility during the 20th century.

As mobility continues to increase the correlation between geographical location and genetic ancestry will decline rapidly. We really are in a brief and privileged moment in time: a moment when we have the tools to perform genome-scale analyses of ancestry, but before globalisation [and urbanisation] begins to erase information about historical population structure.

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Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, Mark I McCarthy, Mark J Daly, Marjo-Riitta Järvelin, Nelson B Freimer, Leena Peltonen (2008). Genome-wide association analysis of metabolic traits in a birth cohort from a founder population Nature Genetics DOI: 10.1038/ng.271

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Congrats to Pamela Ronald et al. for Award for Flood Resistant Rice [The Tree of Life]

Posted: 08 Dec 2008 11:00 AM CST

Congrats to Pam Ronald, colleague, Davis faculty member, and fellow science blogger for receiving a USDA Discovery Award for helping develop a flood resistant rice variety. For more on this see

deCODE to Integrate New Genetic Risk Factor for Type 2 Diabetes into its deCODEme™ Personal Genome Scan Service [deCODE You]

Posted: 08 Dec 2008 10:25 AM CST

Prince Joachim of Denmark and Princess Marie of Denmark along with deCODE scientist Unnur Thorsteinsdottir during an official visit to deCODE laboratories earlier this year.

Reykjavik, ICELAND, December 8, 2008 – deCODE genetics (Nasdaq:DCGN) today announced the discovery by an international consortium of scientists from deCODE and major European and US academic institutions of a single letter variation in the human genome (SNP) that is associated with increased fasting glucose levels and risk of type 2 diabetes (T2D). deCODE will employ its CLIA-registered genotyping laboratory and existing testing platform to swiftly integrate the finding into its deCODEme™ personal genome scan, and to assess the addition of this new variant to the company's deCODE T2™ reference laboratory test for assessing individual risk of type 2 diabetes.

The multinational study analyzed a number of SNPs that had been suggestively linked with fasting glucose levels in several major studies involving some 36,000 individuals from Europe and the United States.The analysis identified a version of single SNP within the gene encoding melatonin receptor IB (MTNR1B) that was associated with notable increase in fasting glucose levels. The deCODE team then demonstrated in its Icelandic cohort that this SNP also associated with an increased risk of T2D, a finding that was then replicated in a meta-analysis of data from more than 80,000 cases and controls from Europe and the US. Approximately 10% of the participants in this study carry two copies of the at-risk version of this SNP, putting them at more than 15 percent greater risk of type 2 diabetes than individuals who carry no copies. The paper, entitled "Variants in MTNR1B influence fasting glucose levels," is published today in the online edition of Nature Genetics, and will appear in an upcoming print edition of the journal.

"This finding is another step towards rounding out our understanding of the genetic factors that underpin glucose regulation and risk of type 2 diabetes. This variant does not confer sufficient risk to be of clinical utility on its own. But when measured in addition to our TCF7L2 variant that is the anchor of the deCODE T2™ test, it may, like other common variants conferring modest risk, enable the test to capture an even larger proportion of inherited risk. We are currently evaluating its integration into deCODE T2™, because understanding genetic risk of T2D enables individuals and their physicians to focus, personalize and improve prevention. In the meantime, we will be enabling our deCODEme subscribers to check their profiles for this new variant, keeping them at the cutting edge of human genetics" said Kari Stefansson, CEO of deCODE.

Type 2 diabetes: A major public health problem
T2D is a chronic condition that develops when the body either becomes resistant to or doesn't secrete enough insulin. Diabetes affects nearly 200 million people worldwide and, according to the American Diabetes Association, some 21 million in the United States. The vast majority of these have T2D, and as many as one third of Americans with diabetes may not even be aware that they have the disease. More than 50 million Americans have pre-diabetes, a condition characterized by elevated blood glucose levels and which puts these individuals at high risk for developing T2D. T2D can be managed and – most importantly – prevented. If losing weight, eating better and getting adequate exercise aren’t enough, there are also medications that can help to manage blood sugar levels and insulin response to reduce the likelihood of developing diabetes. For more information on T2D and how to prevent it, you can go to the American Diabetes Association's website.

23andMe offers family discount, just in time for Christmas [Genetic Future]

Posted: 08 Dec 2008 09:45 AM CST

Personal genomics company 23andMe is now offering a discount of $200 for customers who buy three or more kits before December 31st.

In a press release the company explains the reasoning behind the price cut:

By offering this discount, 23andMe hopes to encourage families, in particular, to explore the unique features of the 23andMe Personal Genome Service™ that are of special interest to people who are related. These features allow family members to learn how genetically similar they are and how genes were passed down from grandparents to grandchildren.

Still unconvinced? Just imagine the heart-warming sound of your entire family spitting into plastic tubes on Christmas morning. Now that is the sound of the 21st century Christmas...

Example photo only. Results of buying a 23andMe kit for your children may vary from the scenario depicted.

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Genetics and geography in Finland [Genetic Future]

Posted: 08 Dec 2008 08:35 AM CST

Here's a figure from a brand new paper on the genetics of metabolic traits in a large Finnish cohort (which I'll be posting about in more detail shortly):

On the left is a map of the counties the samples were collected from, colour-coded by geographical/linguistic group; on the right is the genetic clustering of the samples using the same colour scheme. For anyone who's been reading Razib's posts on genetic maps of Europe and East Asia, the clear message here won't come as a surprise: once you have a sufficiently large sample of markers, genes correlate with geographic ancestry with satisfying precision even within countries. And of course this precision will continue to improve with analyses that involve markers with lower frequencies (using large-scale sequencing data), which are likely to be much more informative about fine-scale geographic ancestry.

The Finns are an interesting group, being clear genetic outliers relative to most of the rest of Europe. No doubt Razib will have more to say about this map given his notorious attitudes towards the Finnish people.

Added in edit: It's worth emphasising that the individuals plotted here were only those who had both parents from the same region; see my follow-up post.

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I'll be hosting the 4th Molecular and Cell Biology Carnival on December 14th [The Daily Transcript]

Posted: 08 Dec 2008 08:18 AM CST

Send in your entries before the weekend using this form or by emailing me directly.

You can visit the MCB Carnival homepage by clicking on the badge/button:

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Advice for doctors on dealing with personal genomics customers [Genetic Future]

Posted: 08 Dec 2008 06:52 AM CST

Think Gene's Andrew Yates has posted generic responses for medical professionals to use when dealing with patients who come armed with their results from 23andMe or Navigenics.

They're probably quite useful little tools for busy doctors without the time to brush up on the field of personal genomics, but - seeing as this is Andrew Yates - they're also a dig at the careful "medicine but not medicine" stance of personal genomics companies.

An excerpt:

Thus, applying 23andMe to your health care would be a violation of the 23andMe terms of service and, as stated, it "cannot be relied upon at this point for diagnostic purposes." We think 23andMe is a great educational tool, and we are excited about its future potential, but we cannot use the test results to provide any medical services. Further, you consented to "not change your health behaviors on the basis of [23andMe]," so for us to counsel otherwise would be unethical.

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Calling fellow bloggers! [Genomicron]

Posted: 08 Dec 2008 06:40 AM CST

Calling fellow bio bloggers -- help get the word out for the special issue of Evolution: Education and Outreach all about eye evolution. The content is free to access online and the authors include many of the world's top eye evolution researchers. A handy table of contents with links is provided below for easy copy and paste maneuvers.

Evolution: Education and Outreach
Volume 1 Issue 4

Editorial

351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)

352-354. Introduction by T. Ryan Gregory (PDF)

355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)

Original science / evolution reviews

358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)

390-402. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)

403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)

415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)

427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)

439-447. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)

448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)

463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)

476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)

487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)

493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)

Curriculum articles

498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)

505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)

509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)

Book reviews

548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)

Genetics of gene expression in African-Americans: ominous news for personal genomics? [Genetic Future]

Posted: 08 Dec 2008 06:00 AM CST

I was planning to write a long article on this recent paper in PLoS Genetics, but p-ter at Gene Expression and G at Popgen ramblings have both covered the central message very well.

So if you haven't read those articles, already, go and do so now - when you come back, I want to talk about the potentially worrying implications of this paper for the future of personal genomics.

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Spliced feed for The Science Network

2008-12-08T05:07:00.000-08:00

Spliced feed for The Science Network

Dioxins in Pork [Sciencebase Science Blog]

Posted: 07 Dec 2008 07:02 AM CST

Dioxins Before Swine - Irish pork is off the menu, according to the BBC.

The UK’s Food Standards Agency is monitoring pork products in the Irish Republic because of fears of contamination with dioxins. “Tests showed some pork products contained up to 200 times more dioxins than the recognised safety limit.” Interestingly, dioxin levels in soil have been declining in recent years, according to another BBC report from 2007. The alert over dioxins followed an alert after PCBs (polychlorinated biphenyls) were found in Irish pork on 1st December.

So, what are dioxins and should we be worried about them?

Dioxins are organic compounds formed when a huge range of materials, particularly chlorinated polymers (PVC plastics) burn and in some industrial processes. They are ubiquitous in the environment and became the focus of environmental activism because of their reputation for being among the most toxic compounds known. Colloquially “dioxin” is talked of as if it were a single compound rather than a class of compounds, but the most usual reference is to the chlorine-containing compound 2,3,6,7-tetrachlorodibenzodioxin. Dioxins should not be confused with the compound 1,2-dioxin and 1,4-dioxin, which are heterocyclic, organic, antiaromatic compounds.

2,3,6,7-Tetrachlorodibenzodioxin can have some nasty effects such as irritation to the eyes, allergic dermatitis, chloracne, porphyria; gastrointestinal disturbance, possible reproductive, teratogenic effects, liver, kidney damage, haemorrhage, and occupational carcinogenicity. But, does that long list of problems mean anyone eating any of the food products from Ireland - bacon, ham, sausages, white pudding and pizzas with ham toppings - were or are in any danger. “The UK’s Food Standards Agency said it did not believe at this stage that UK consumers faced any ’significant risk’,” reports the BBC. Seems like fair comment, only serious chronic exposure to low levels of dioxins or acute high level exposure are of real concern.

No member of the public has ever died from dioxin poisoning, despite the fact that for several decades industry has been inadvertently releasing these materials into the environment as impurities in hundreds of products and that countless burning materials release the same supposedly deadly compounds across the globe continuously. Occupational exposure has led to probably at most four deaths from industrial accidents involving release of dioxins, according to John Emsley writing in The Consumer’s Good Chemical Guide.

Don’t forget to grab the Sciencebase email newsletter or newsfeed for a more complete update on the porcine dioxin story soon.

Dioxins in Pork

The DNA Network

2008-12-07T18:43:00.001-08:00

The DNA Network

Stock Navigenics Patient Response [Think Gene]

Posted: 07 Dec 2008 05:52 PM CST

For your own use —at your practice, institution, or otherwise.

Regarding Navigenics and our genetic medical services, please note the following excepts from the Navigenics Terms and Conditions and the Navigenics Form to which you agreed while purchasing your Navigenics test:

Navigenics Terms and Conditions
http://www.navigenics.com/policies/TermsAndConditions/

“The contents of our Site … are for informational purposes only…

You should seek the advice of a physician … regardless of any information contained within Your Report. You should not ignore professional medical advice or delay in seeking it because of Your Report or any other Content. Furthermore, you should not interpret Your Report or any other Content as recommending any specific treatment plan, product or course of action…

…THE [Navigenics] CONTENT IS INTENDED SOLELY FOR YOUR INFORMATIONAL PURPOSES AND IS NOT INTENDED AS MEDICAL ADVICE, OR TO BE USED FOR MEDICAL DIAGNOSIS OR TREATMENT, FOR ANY INDIVIDUAL PROBLEM.”

Navigenics Informed Consent
http://www.navigenics.com/policies/InformedConsent/

“It is important to realize that although your genome-wide scan will analyze approximately 900,000 SNPs in your DNA, information about clinical significance is not yet available for most of these SNPs.”

Thus, to use Navigenics while providing health care would a violation of Navigenics Terms and Conditions as the test is not “to be used for medical diagnosis or treatment, for any individual problem.” Further, The Terms and Conditions specify that on the basis of the Navigenics test, one should not ignore or delay any existing medical advice, nor should one interpret the results to recommend any other action. Thus, for us to counsel otherwise would also be a violation of the Terms and Conditions, and it would be unethical since you agreed not to change your behavior on the basis of Navigenics. Finally, as stated in Navigenics Informed Consent, “information about clinical significance is not yet available for most of [the Navigenics test].” Medical practices like ours are ethically and legally obligated not to recommend or apply any test or that is not known to be clinically significant while providing health care.

Navigenics does state that its test results are “merely an indication that you may be genetically predisposed to that condition and may wish to consider further independent testing, consult your physician or pursue genetic counseling.” However, any medical advice or genetic counseling services that we would provide for a patient with the Navigenics test would be the same as for a patient without the Navigenics test.

We would be honored to be caring for you and your health. However, we are unable to use the Navigenics test in our medical practice. We sincerely apologize on behalf of the medical community if you were led to believe otherwise.

war on Xmas – the Atheist Anthem Competition [the skeptical alchemist]

Posted: 07 Dec 2008 04:24 PM CST

Not that atheists are declaring war on Xmas, but you can imagine the reaction of the crazies if they only found out...

...that Q Transmissions, a weekly skeptical call-in talk show in Edmonton, Alberta, Canada, has started a singing contest for a new atheist anthem!

You can find the music and lyrics on their website, and send them your best rendition of the anthem.

So keep those submissions flowing, and your atheism glowing!

View blog reactions

TwitFitter: Twit for Your Health [ScienceRoll]

Posted: 07 Dec 2008 02:35 PM CST

One of the most interesting or funniest ideas of the week is TwitFitter, a place for fitness enthusiasts and fitness professionals to motivate each other to work out, stay healthy, and get fitter.

Have you got any experience with it?

Anyway, nowadays Twitter is really on fire. I started to use Tweetdeck to track my twits and I just found a post on How to got to web 2.0 mentioning two practical examples why Twitter can be useful for medical professionals.

A colleague here at the hospital told me about this one. What is happening here is a Doctor in South Africa is at bedside asking a Doctor in India for real time assistance with a diagnosis. From other correspondence he has with this doctor in India, it is clear that he knows him personally and/or professionally, so he is a trusted source from the requestor’s position.

Web 2.0 timeline and future: Slideshow [ScienceRoll]

Posted: 07 Dec 2008 02:26 PM CST

Richard Akerman from Science Library Pad published this interesting slideshow about history leading up to Web 2.0, characteristics of Web 2.0, Twitter, Facebook and FriendFeed.

Emergency Training in Second Life [ScienceRoll]

Posted: 07 Dec 2008 02:16 PM CST

Everybody must know what basic life support means. This virtual tool may help you to learn more about such an important procedure.

Now I’ve got a huge list of useful Second Life medical sites and islands on Webicina, but here is the newest addition. The Italian Resuscitation Council (IRC) is starting to explore the possibilities to use Second Life like an environment for training. To teleport there, click here.

Excerpt from their mission statement:

One of the great advantages of Second Life environment is the possibility to create various training simulations, improving and testing teamwork, leadership, and technical skills. Simulations can be used simultaneously by a group of trainees connected from world different locations.

IRC headquarters in SL should became a place were instructors can be trained and re-trained. We are planning to build a CPR training platform in SL to maintain and update knowledge after a traditional BLSD course. Finally, IRC headquarters would become a site where avatars/layperson can afford to the cardiac arrest prevention knowledge and basic life support information.

It’s also possible to organize meetings at this great place.

Cooking & Science with Ferran Adria: Webcast Tuesday Dec 9th 6:30PM [The Daily Transcript]

Posted: 07 Dec 2008 09:54 AM CST

Here is some info:

The world acclaimed chef of El Bulli, Ferran Adria, will discuss the fascinating relationship between modern science and modern cuisine.
Adrià, called by Gourmet "the Salvador Dalí of the kitchen," will trace the birth of molecular gastronomy, manipulating the physical and chemical processes of cooking, and then discuss his own adventures in what he calls "molecular cooking."

In particular, he will explore the use of hydrocolloids, or "gums" that enable a delicate fruit puree to be transformed into a dense gel, and deconstruct techniques like sferificacion, creating a resistant skin of liquid (as in a pea soup held in a pod of nothing more than itself).

Considered one of the most creative individuals in any profession, Adrià views preparing food as a language "to transmit impressions, feelings, sensations, and experiences." He says, "Cooking is a language with its own special alphabet. From one alphabet, each cook creates his or her own unique conversation. Our role as chefs is to expand this dialogue, offering the world new forms of culinary expression."

Ferran Adrià is the head chef of the restaurant El Bulli, located on the coast of Catalonia near the city of Barcelona. Perhaps best known for creating "culinary foam," Adrià's stated goal is to "provide unexpected contrasts of flavor, temperature and texture. The idea is to provoke, surprise and delight the diner." El Bulli has 3 Michelin stars and is considered among one of the best restaurants in the world.

If you are in the Boston Area here's what you need to know:

Cooking & Science with Ferran Adrià: A Conversation on Creativity
Hosted by the Harvard Physics Department & Harvard SEAS
Tuesday, December 9, 2008
6:30pm - 8:00pm
Harvard University, Physics Department, Jefferson Hall 250
17 Oxford Street
Cambridge, MA

If you're not in the Boston Area, or simply can't make it, you can watch the lecture live by following this link.

Read the comments on this post...

Sherpa on Vacation [The Gene Sherpa: Personalized Medicine and You]

Posted: 07 Dec 2008 09:39 AM CST

Keep Climbing. I'll be out for seven days....and when I return, I am going to change the game for DTC testing, Research on Personalized Medicine, and finally show everyone where they can set up...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Dioxins Before Swine [Sciencebase Science Blog]

Posted: 07 Dec 2008 07:02 AM CST

Irish pork is off the menu, according to the BBC. The UK’s Food Standards Agency is monitoring pork products in the Irish Republic because of fears of contamination with dioxins. “Tests showed some pork products contained up to 200 times more dioxins than the recognised safety limit.” Interestingly, dioxin levels in soil have been declining in recent years, according to another BBC report from 2007.

So, what are dioxins and should we be worried about them?

Don’t forget to grab the Sciencebase email newsletter or newsfeed for a more complete update on the porcine dioxin story soon.

Dioxins Before Swine

What is Science 2.0? HHMI's Take [adaptivecomplexity's blog]

Posted: 06 Dec 2008 06:34 PM CST

Via Larry at Sandwalk, the Howard Hughes Medical Institute is excited about Facebook, YouTube, and Blogs.

What does this have to do with science? Like Larry, I'm still skeptical of what impact this has on what I do in the lab:

Spliced feed for The Science Network

2008-12-07T05:05:00.001-08:00

Spliced feed for The Science Network

Skeptics Guide #176 - December 3rd, 2008 [The Skeptics' Guide to the Universe]

Posted: 06 Dec 2008 06:25 AM CST

News Items: Early Earth, Turtle Missing Link, Search for the Ivory-Billed Woodpecker, Power from Sound; Your Questions and E-mail: DNA from Hair, Magic Water, Starting a Skeptics Group, Carbon Footprint; Name That Logical Fallacy; Science or Fiction

This posting includes an audio/video/photo media file: Download Now

The DNA Network

2008-12-06T18:38:00.001-08:00

The DNA Network

Genes predict the ancestry of African-Americans [Genetic Future]

Posted: 06 Dec 2008 03:55 PM CST

I'm in the middle of a longer post on a recent paper on the effects of genetics on gene expression differences in African-Americans, which has also been well-covered by p-ter at Gene Expression. I wanted to post this section separately to avoid detracting from the issues in that post.

This figure will not provide any big surprises for those who have been following developments in human genetics over the last five years - but it still provides a compelling illustration of the power of genetics to predict individual ancestry:

The figure shows the results obtained when the European, Nigerian and East Asian samples from HapMap and 100 African-American samples are clustered using principal component analysis based on data from ~600,000 genetic markers.

The European, Nigerian and East Asian samples form strong clusters that are extraordinarily well-separated, demonstrating how easy it is to distinguish between members of these groups with sufficiently large numbers of markers. However, it should be emphasised that adding additional populations from other parts of the world would fill most of the gaps between these clusters, since human geographic variation is largely continuous rather than discrete.

The most interesting aspect of the figure is the distribution of the African-Americans, who almost all fall on a remarkably clean line stretching between the European and Nigerian clusters, with some individuals being pulled towards the East Asian cluster (presumably due to admixture from South or East Asia). Using these data each individual's relative level of European and African ancestry can be estimated with high precision. After removing four outliers (the three samples falling furthest from the European-African line, and one individual falling very close to the European cluster) the European admixture levels of individual African-Americans fall between 1 and 62%, with an average of ~21% - a figure consistent with previous studies.

Subscribe to Genetic Future.

Alkes L. Price, Nick Patterson, Dustin C. Hancks, Simon Myers, David Reich, Vivian G. Cheung, Richard S. Spielman (2008). Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans PLoS Genetics, 4 (12) DOI: 10.1371/journal.pgen.1000294

Read the comments on this post...

MCB Carnival is coming – need a host! [the skeptical alchemist]

Posted: 06 Dec 2008 03:41 PM CST

Work is taking over my life lately. Not that it's a bad sign, but it's been keeping me away from my blog a little too much. In the meantime, that time of the month is coming – yes, the Molecular and Cell Biology Carnival is approaching fast, and I am on the lookout for a host!

There are two easy ways to become a host: you can contact me at the e-mail on the right hand column of this blog, or you can leave a comment on this post. Make sure you read more about being a host at the MCB website. The carnival will take place on December 14, so make sure you contact me soon!

While I am looking for a host, I would also like to invite you to submit your post for the Carnival – you can e-mail me directly, or use this submission form.

Last but not least, I cannot leave you without something funny and, of course, Prop 8-related. I am quite sure this clip, found through a friend, is going to make your day.

See more Jack Black videos at Funny or Die

P.S. The latest Skeptics' Circle edition is up!

View blog reactions

Online Communities: Diabetes [ScienceRoll]

Posted: 06 Dec 2008 01:59 PM CST

I’ve already written about a few diabetic community sites such as D-Life and TuDiabetes.Now I would like to share two other sites with you:

Juvenation: A Type 1 Diabetes Community

Diabetic Connect:

If you want to know more about the role of web 2.0 tools in diabetes management, check my interview with Kerri Morrone.

Please let me know if you happen to know or use other diabetes communities.

Medicine Meets Virtual Reality 17: Virtual Reality Therapy [ScienceRoll]

Posted: 06 Dec 2008 01:44 PM CST

I write a blog for the Medicine Meets Virtual Reality 17 conference and publish a series of interviews with famous participants. The third interviewee is Dr. Dennis Wood and the topic is virtual reality graded exposure therapy. Check it out!

Spliced feed for The Science Network

2008-12-06T05:06:00.001-08:00

Spliced feed for The Science Network

Flu Structure, Mp3s, and Magnetic Minestrone [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

You can read my latest science news updates in spectroscopynow.com:

One flu over - X-ray studies have revealed details of the structure of a protein used by the avian influenza, H5N1, that allows it to hide its RNA from the infected host’s immune system. The structure could provide a new target for the development of antiviral drugs against this potentially lethal virus

Minestrone and magnetic resonance - Researchers in the US and France may have overturned decades of theory in magnetic resonance studies by spotting a discrepancy in the way nuclear spins behave. Their new mathematical model of the process improves our understanding of atomic behaviour and could lead to better NMR spectra, sharper magnetic resonance images, and perhaps one day a fully portable MRI machine.

Organic soil matters - Could the earth beneath our feet hold the key to climate change? According to scientists at the University of Toronto Scarborough their NMR results show that global warming is changing the molecular structure of organic matter in soil.

Battery capacity is full of holes - Researchers in Korea have developed a novel material for the anode in rechargeable batteries, which they say could make them much more efficient and extend significantly the length of time between charges.

And on ChemWeb for science news with a chemical element:

First on the list in this week’s Alchemist, more on the new anode material, which is potentially good news for the iPod generation. In analytical research, HPLC has been used to spot dummy tequila and in medical chemistry US radiologists suggest that a dose of modified vitamin D could protect citizens from a dirty bomb attack. Next up, a new approach to addressing qubits allows for faster measurements that could take us a step closer to a quantum computer, while Yorkshire chemists are working out the best mix of starting materials to get the maximum height yield on their tasty products. Finally, this week’s award is a record breaker in the State where big is everything.

Flu Structure, Mp3s, and Magnetic Minestrone

Top Ten SNPs [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

If you ever thought genetics was only about disease, then check out the popular SNPs list on SNPedia. A SNP (pronounced “snip”) is a single nucleotide polymorphism, which in BradSpeak(TM) is basically a difference in a bit of your DNA that makes you different from the rest.

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

rs1815739 sprinters vs endurance athletes (I reckon I lack both)
rs7495174 green eye color and rs12913832 for blue eye color
rs6152 can prevent baldness (this was discovered far too late for me)
rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

rs9939609 triggers obesity (not a genetic excuse for eating too much)
rs662799 prevents weight gain from high fat diets (ditto)
rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Top Ten SNPs

The DNA Network

2008-12-05T18:40:00.001-08:00

The DNA Network

If only I’d commissioned a tango on the RET proto-oncogene… [genomeboy.com]

Posted: 05 Dec 2008 04:24 PM CST

Maybe I’m a sucker for methylation, but when it comes to interpretive dance as a means of explaining one’s dissertation, my vote goes to “The role of folate in epigenetic regulation of colon carcinogenesis” by Lara Park of Tufts University.

http://www.youtube.com/watch?v=_IUVkMXd_c8

You can see the rest here.

My First Twitter Interview [ScienceRoll]

Posted: 05 Dec 2008 02:22 PM CST

Diariomedico.com, a Spanish medical site, kindly asked me to do an interview through Twitter. 15 short questions, 15 fast answers in the well-known 140 character-long format.

It will take place on the 10th of November (Wednesday) at 12:00 EST.

You can check it out if you visit my Twitter page.

Feel free to follow me, join the health 2.0 discussions or just check the links I publish on Twitter.

Radical Sharing Transforming Science [ScienceRoll]

Posted: 05 Dec 2008 02:16 PM CST

Cameron Neylon published another unique slideshow. The main question: Does science need transforming?

Healthcare in Second Life: Youtube Playlist [ScienceRoll]

Posted: 05 Dec 2008 02:13 PM CST

I just found a playlist on Youtube that is dedicated to healthcare in Second Life, the virtual world. Numerous videos about tools for medical education and sites for patient support.

An example:

When physicists try to talk genetics... [adaptivecomplexity's blog]

Posted: 05 Dec 2008 01:09 PM CST

...the result is never pretty. I made this point in a comment, but I've hoisted it up here because this issue deserves more visibility.

Physics professor Steve Hsu makes this argument:

Overview of NGS platforms [Next Generation Sequencing]

Posted: 05 Dec 2008 09:10 AM CST

David Dooling over at PolITiGenomics has compiled a nice table with some important metrics of the three most prevalent NGS platforms - go check it out!

CNN Shuts Down its Science Journalism Department [The Daily Transcript]

Posted: 05 Dec 2008 08:54 AM CST

CNN, like most other MSM outfits have been sacrificing reporters, foreign correspondents in favor of pundits (aka political operatives), fancy gizmos (verging on a reenactment of Star Wars) and fluff. The canceling of their science journalism department is just the latest decision that underscores the decay of private-sponsored journalism in this country. Is it the MSM's fault or does it say something about the whims and wishes of the general public?

Sad. PZ says it best.

Read the comments on this post...

Flu Structure, Mp3s, and Magnetic Minestrone [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

You can read my latest science news updates in spectroscopynow.com:

And on ChemWeb for science news with a chemical element:

Flu Structure, Mp3s, and Magnetic Minestrone

Top Ten SNPs [Sciencebase Science Blog]

Posted: 05 Dec 2008 07:00 AM CST

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

rs1815739 sprinters vs endurance athletes (I reckon I lack both)
rs7495174 green eye color and rs12913832 for blue eye color
rs6152 can prevent baldness (this was discovered far too late for me)
rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

rs9939609 triggers obesity (not a genetic excuse for eating too much)
rs662799 prevents weight gain from high fat diets (ditto)
rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Top Ten SNPs

Portuguese DNA database gets green light [My Biotech Life]

Posted: 05 Dec 2008 06:18 AM CST

Trying to keep up with the rest of Europe, Portugal is now ready to setup a DNA database of convicted criminals that receive sentences of 3 years or more. Basically the bad guys get booked and swabbed and the database should allow authorities to solve more crimes and convict the right people.

As I had stated a few months ago, the 3 years penalty rule is an iffy situation because there are some crimes like copyright infringement that can land you up to 3 years in jail.

The 3 year sentence aka "serious crime" rule is an obvious attempt to avoid the abusive DNA indexing of every criminal infraction. Sort of contrary to what takes place in the UK where anything except traffic infractions get you "tagged".

Keep in mind that the penal system in Portugal is way more bland than that of the US. Here, the maximum prison sentence is 25 years (No such thing as life in prison or death penalty).

The Portuguese authorities are doing their best to keep things as transparent as possible and have ensured that all will be done to guarantee the privacy of the data. Moreover, unlike the UK, criminal suspects will not be included in the DNA database and those that are acquitted will be immediately removed.

Not only criminal DNA information will be stored in the database. Anyone that wishes to be included in the database can do so. This can and has been found to be helpful in identifying missing persons and unidentified corpses.

Other countries like Spain and Greece have also recently began to maintain DNA databases.

[Image: Wikipedia:DNA]

Portuguese DNA database gets green light

Around the Blogs [Bitesize Bio]

Posted: 05 Dec 2008 04:58 AM CST

Three story highlights from related blogs:

All Graduate Student Supervisors Take Note
“This lovely piece has been circulating of late, but Sonke has been kind enough to allow the SCQ to present his “Advice for Potential Graduate Students” as a handy dandy pin-up, suitable for pinning up in some visible area of your lab.”

FDA Interested in Collaborating with Personal Genomics Companies
“[Genetic Future] describes an intriguing twist in the ongoing struggle between the nascent personal genomics industry and regulatory bodies: apparently the FDA is exploring the possibility of collaborating with consumer genomics providers to track adverse drug reactions”…

Increased Secretion in Senescent Cells, and Chris Patil on the Campisi Lab’s New PLoS Biology Paper: Cellular Senescence, Protein Secretion, and the Aging/Cancer Paradox
Chris Patil (Ouroboros) co-authors an interesting new paper in PLoS Biology, and bloggers discuss.

Gate Keepers for Genetic Information [The Gene Sherpa: Personalized Medicine and You]

Posted: 05 Dec 2008 04:48 AM CST

A recent set of comments came to me from a Genetic Counselor. They were well thought out, but I think she may have misinterpreted me... I pray that your attitude changes before you have a practice of...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Stock Response to “How 23andMe May Be Used In Medicine” [Think Gene]

Posted: 04 Dec 2008 10:56 PM CST

For your own use —at your practice, institution, or otherwise.

Regarding 23andMe and our genetic medical services, please note the following excepts from the 23andMe Terms of Service and the 23andMe Consent Form to which you agreed while purchasing your 23andMe test:

23andMe Terms of Service
https://www.23andme.com/about/tos/
“23andMe Service Is For Research and Educational Use Only. We Do Not Provide Medical Advice, And The Services Cannot Be Used For Health Ascertainment or Disease Purposes”
…”cannot be relied upon at this point for diagnostic purposes”

23andMe Consent Form
https://www.23andme.com/about/consent/
“You should not change your health behaviors on the basis of this information.”

Thus, applying 23andMe to your health care would be a violation of the 23andMe terms of service and, as stated, it “cannot be relied upon at this point for diagnostic purposes.” We think 23andMe is a great educational tool, and we are excited about its future potential, but we cannot use the test results to provide any medical services. Further, you consented to “not change your health behaviors on the basis of [23andMe],” so for us to counsel otherwise would be unethical.

Again, we would be honored to be caring for you, but any medical advice or genetic counseling services that we would provide would be exactly the same as for a patient without the 23andMe test.

Cancer Research Blog Carnival #16 [Bayblab]

Posted: 04 Dec 2008 10:47 PM CST

Welcome to the 16th Edition of the Cancer Research Blog Carnival, the monthly carnival of cancer-related blogging. This month's edition has a healthy dose of cancer stem cell news, and we'll kick it off right here at the Bayblab with a post from Rob on that very topic.

Rob describes a recent paper in Nature that casts some doubt on the cancer stem cell hypothesis - or at least the scarcity of these cells - though he doesn't think it's that serious a blow.

Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.

Alexey at Hematopoiesis follows that up with a pair of research blogging posts also about stem cells and cancer. First off, he describes the complexity of the cell cycle and stem cell self-renewal, how disruptions in these processes can lead to hematological malignancies and how the complexity adds a layer of protection

So, on one hand, downregulation of those genes promotes stem cells to exit from a quiescent state and enter into cell cycle, leading to their expansion, exhaustion and cancer development, but on the another hand, the involvement of multiple genes could protect them from it.

This is followed with a post about age related changes in gene expression. Cancer is fairly well recognized as a disease of aging, but Alexey takes a closer look at specifics

Now, let's get close to cancer. Bmi-1 is known as a tumor promotor, and genes that it repress - Ink4a/Arf are tumor suppressors. Hmga2 is anti-aging, but is a tumor promotor. So, aging of adult stem cell system actually protects us from cancer.

Abel Pharmboy at Terra Sigillata has another piece about the link between aging and cancer. This one focuses on a recent PLoS Biology paper discussing senescence-associated secretory phenotype and how it may complicated therapies taking advantage of the senescence pathways.

Cells induced to undergo senescence with DNA-damaging agents exhibit a secretory phenotype, termed the senescence-associated secretory phenotype (SASP), whereby molecules involved in inflammation and metastasis are released into the local environment. In younger individuals, this
mechanism could prevent the development of cancer but in older individuals could increase the risk of cancer. In cancer, for example, therapies that causes cellular growth arrest and senescence may be of limited utility unless those senescent cells are removed. My takehome message from this paper is that we may have to rethink the benefit of cancer therapies that are cytostatic.

Abel Pharmboy was also able to talk to one of the authors directly about the significance of the paper.

While on the topic of unintended consequences, Philip Smith has sent us a story by dsantore at Sociology Eye. The brief piece describes the story of a New York Times editor taking testosterone suppressants as cancer treatment and found them gender blurring.

Among the more notable side effects are Jennings' shrinking testicles, hot flashes, and potentially enlarged breasts. The gendered implications of these bodily changes are not lost on Jennings

The original story in the NYT is an interesting cap on the month of Movember, and a reminder of some of the lesser thought of aspects of prostate cancer.

With that concludes the 16th edition of the Cancer Research Blog Carnival. The next one will appear Jan 2, but is still in need of a host. If you're sick of seeing it here at the Bayblab all the time, send us an email and we'll set you up as a future host. In the meantime, start writing posts for the next edition and submit them here. You can check out previous editions here.

Body-Swapping with a Mannequin [adaptivecomplexity's blog]

Posted: 04 Dec 2008 10:22 PM CST

If you need more proof of how easy the human brain is to fool, hop over to Scientific American's 60 second science and read about how a group of mad scientists used virtual reality goggle to get subjects to 'body-swap' with a mannequin.

I'm waiting for the Wii version.

European ancestry associated with higher breast cancer risk? [Yann Klimentidis' Weblog]

Posted: 04 Dec 2008 09:28 PM CST

Latinas have been found to have a lower incidence of breast cancer than other ethnic groups. Indigenous Americans have the lowest incidence. This meta-review paper from a few months ago finds that ethnic disparities in breast cancer can be explained by SES, except for the lower incidence among African Americans.

So what do they find in this new paper (see abstract below)? It's a case control study with a pretty large sample size (440 cases and 597 controls, matched for age) of Latinas in the SF Bay area to determine whether genetic differences between groups account for differences in breast cancer incidence. They used 106 AIMs (ancestry informative markers). Interestingly:

"Breast cancer among Latinas presents a particularly
interesting case because the main ancestral components of the Latino population (European and Indigenous American) have the highest and lowest breast cancer incidence (1)."

They control for a suite of known breast cancer risk factors
(including education, but unfortunately, not income). Surprisingly the cases and controls differed significantly for many of the measured risk factors.

The main findings:

"In unadjusted models, we found a strong association between genetic ancestry (continuous) and breast cancer risk. Higher European ancestry was associated with increased risk, with an odds ratio (OR) of 1.79 [95% confidence intervals (95% CI), 1.28–2.79; P less than 0.001] for every 25% increase in European ancestry. When known risk factors and place of birth were adjusted for (Table 2), the association with European ancestry was somewhat attenuated but remained statistically significant (OR, 1.39; 95% CI, 1.06–2.11; P = 0.013). When African ancestry was included in the adjusted model, the association with European ancestry became stronger [OR for European ancestry, 1.54 (95% CI, 1.11–2.52; P = 0.004), and OR for African ancestry, 2.05 (95% CI, 1.00–7.56; P = 0.055)]."

They also looked at the association using genetic admixture and "using parent/grandparent European origin instead of genetic ancestry."

"We observed a significant association between the number of European-born parents/grandparents and breast cancer risk, with higher number of European ancestors being associated with increased risk (OR, 1.21; 95% CI, 1.02–1.44; P = 0.025, adjusted model)."

Although their results suggest that there may be some genetic risk factor specific to individuals with higher European ancestry, they are careful to acknowledge the possibility for residual confounders. It's too bad they didn't control for income and/or some other SES variables.

Genetic Ancestry and Risk of Breast Cancer among U.S. Latinas
Laura Fejerman, Esther M. John, Scott Huntsman, Kenny Beckman, Shweta Choudhry, Eliseo Perez-Stable, Esteban González Burchard and Elad Ziv
Cancer Research 2008;68(23):9723–8

Abstract: U.S. Latinas have a lower incidence of breast cancer compared with non-Latina White women. This difference is partially explained by differences in the prevalence of known risk factors. Genetic factors may also contribute to this difference in incidence. Latinas are an admixed population with most of their genetic ancestry from Europeans and Indigenous Americans. We used genetic markers to estimate the ancestry of Latina breast cancer cases and controls and assessed the association with genetic ancestry, adjusting for reproductive and other risk factors. We typed a set of 106 ancestry informative markers in 440 Latina women with breast cancer and 597 Latina controls from the San Francisco Bay area and estimated genetic ancestry using a maximum likelihood method. Odds ratios (OR) and 95% confidence intervals (95% CI) for ancestry modeled as a continuous variable were estimated using logistic regression with known risk factors included as covariates. Higher European ancestry was associated with increased breast cancer risk. The OR for a 25% increase in European ancestry was 1.79 (95% CI, 1.28–2.79; P less than 0.001). When knownrisk factors and place of birth were adjusted for, the associationwith European ancestry was attenuated but remained statisticallysignificant (OR, 1.39; 95% CI, 1.06–2.11; P = 0.013).Further work is needed to determine if the association is dueto genetic differences between populations or possibly due toenvironmental factors not measured.

The DNA Network

2008-12-04T18:46:00.001-08:00

The DNA Network

Sweet news about a spoonful of sugar [The Navigator - Navigenics Blog]

Posted: 05 Dec 2008 12:15 AM CST

Michael Nierenberg, M.D.

"All natural sweetener."

"Just like sugar."

"Zero calories."

Artificial sweeteners have been billed as the perfect alternative to sugar – a way for weight-conscious adults to have their cake and eat it, too. Yet more and more, a modicum of restraint is certainly advised when reaching for those packets of aspartame or sucralose.

While it's true that sugar alternatives are much sweeter than table sugar, requiring smaller amounts to achieve the same level of sweetness, they won't necessarily help you lose weight and keep it off. Simply taking the sugar out of a slab of chocolate cake doesn't miraculously transform it into a low-calorie, high-nutrient food. At the end of the day, it's still a slab of chocolate cake, with calories from flour, shortening, eggs, and other ingredients like nuts. So if you eat too much of it, your body will be the worse off from the encounter, regardless of which sweetener is used.

In fact, a growing body of evidence suggests that, when compared with sugar, no-calorie sweeteners may actually make it harder for people to control their body weight.

Scientists a step closer to understanding AIDS immunity [My Biotech Life]

Posted: 04 Dec 2008 08:06 PM CST

I don’t usually get my science news from the Portuguese paper but this article caught my eye. Amazingly I didn’t pick this up in the huge amount of science and immunology feeds I subscribe to but I digress.

It seems that researchers are a step closer to understanding how HIV seropositive individuals can live with the virus for years with out taking antiretroviral drugs and contracting AIDS.

This small population of under 0,2 percent happens to have a way to keep their CD4+ count at a normal level while the CD8+ lymphocytes stick to their job maintaining viral levels as low as 50 viruses per milliliter of blood. Normally this is not the case and CD8+ lymphocytes can’t keep up with the viral activity.

I have always thought that the key to understanding how to overcome or prevent HIV/AIDS was to study these individuals that seem to be immune. This is not a simple virus but I do think science is making progress, one small step at a time.

[Image: Wikipedia:HIV]

Scientists a step closer to understanding AIDS immunity

Statistics on next-generation sequencing platforms [Genetic Future]

Posted: 04 Dec 2008 05:37 PM CST

David Dooling from PolITiGenomics has put together a handy little table for genomics nerds like me: statistics on the output of the various iterations of the three major competing second-generation DNA sequencing platforms (Roche's 454, Illumina's Solexa/Genome Analyzer and ABI's SOLiD).

It's probably a little inscrutable for non-genomicists, but it helps to provide some insight into the sheer scale of the DNA sequence data currently being produced by large-scale sequencing facilities. A single Illumina GA II machine, for instance, churns out on the order of 8 gigabases of sequence (that's almost three human genome equivalents) every week. Now consider that my workplace as of this week has 37 Illumina machines, all running hot pretty much 24/7 (well, most of the time), and you have some sense of the quantity of sequence currently being generated - and of the informatics infrastructure required to store, manage and process that volume of data.

Read the comments on this post...

Going (pro)Rogue [Bayblab]

Posted: 04 Dec 2008 01:59 PM CST

With a recent election overshadowed by Obamamania to our south, the Canadian government decided to draw some attention to itself with a recent parliamentary crisis. In that election, the Conservative Party earned more seats than any other single party, but not enough to command a majority of the 308 seats in the House of Commons. Still, they were asked by the Governer General, to form a minority government with Stephen Harper as Prime Minister. This is what normally happens, and what everybody expected (read: took for granted) based on the distribution of seats after the election. Typically for a minority government to last, they have to play nice with the other parties to reach compromises in order to get a majority of votes in the house. Mr. Harper somehow didn't realize he didn't have a majority and pushed an economic statement that was sure to not sit well with the Liberal, NDP and Bloc Quebecois members that make up the majority of the seats in parliament. They didn't like it, decided "hey, we're in the majority, if we band together we topple this government and try to replace it with a coalition made up of the majority of MPs". This was to happen Monday in a vote of confidence on Harper's ability to lead.

So, less than two months after a federal election, and even less time sitting, Harper saw the writing on the wall and decided instead of letting government, you know, govern (during this worst economic downturn since the Great Depression, yadda, yadda) to take his ball and go home, suspending parliament (called proroguing) to buy time to figure a way out of this mess. The Governer General agreed to his request this morning. So until Jan. 26, this parliamentary showdown has been averted, as well as the ability of parliament to do anything. But it has made for interesting times, one of the most interesting parts being the revelation of how few Canadians understand how their government works. Hopefully this has been an opportunity for learning. Larry Moran at Sandwalk has been following what he calls Conservative Lies more closely, and hopefully we can also clear up some misconceptions here at the Bayblab. First an explanation of our parliamentary system (from a Sandwalk commenter):

Let me refresh your memory as to how a Westminster-style Parliamentary system works. The people of Canada do NOT elect a government; they elect members of the House of Commons. The members of the House choose the government. By tradition, the legal Head of State (the Governor-General, in our case) asks the leader of the party with the most seats in the HoC to form a government; that is, to form a cabinet to try to pass laws.

If the majority of the members of the HoC lose confidence in the ability of the minority, they have the right to express this through non-confidence votes or votes against bills that deal with government's ability to spend money.

In this case, the Prime Minister must ask the GG to dissolve Parliament and call an election (remember, the GG is our head of state, and the only one who can call an election). The GG has the legal option to ask another party or parties to form a government, if he or she feels that this party or parties has the confidence of the majority of the HoC (for instance, if a majority of the legally elected members of parliament got together and forged a formal agreement...).

This proposed coalition is absolutely in keeping with Parliamentary law and tradition. It has been forged by people who have been legally elected by the people of Canada. Of course, the GG is completely within her rights to call an election at the request of the Prime Minister. She will have to decide whether it is in Canada's best interest to hold the 4th election in 4 years, and second election in 3 months, or if it is in Canada's best interest to bring in a duly-elected government that has the pledged support of the majority of the HoC, and has proposed specific measures to rectify certain issues currently facing us.

Some of the misconceptions that have been repeated during this debacle:
I voted for Stephen Harper for Prime Minister.
In Canada, a federal election is a series of local elections. Unless you live in a specific riding you never cast your vote for Harper (or Dion, Layton, Duceppe). Yes, many people vote based on party affiliation and pretty much all the time the Prime Minister is the leader of the party with the most seats but the reality is that you vote for a parliament, not a governement.

The Liberal/NDP/Bloc coalition...
The Bloc Quebecois would not be part of a coalition governement (they would have no cabinet positions, for example). They have simply agreed not to bring down a proposed coalition government within 18 months (which some reservations, I would imagine). Furthermore, the accusations of the coalition 'being in bed with separatists' are divisive, offensive appeals to emotion. It suggests that the duly elected officials from Quebec shouldn't have a role in government and that votes from that province shouldn't carry as much weight as from the rest of the country.

A coalition government is undemocratic
Which is more undemocratic: a broad, cross-party agreement between elected MPs who represent the majority of Canadian voters, or shutting down government and locking them out? A coalition government (common in many other democracies where minority governments are the norm) or a PM going (pro)rogue?

Read the coalition agreement here and their economic plan here [pdf]

McClendon: Home for the Holidays Thanks to DNA Testing [DNA Testing Blog]

Posted: 04 Dec 2008 01:53 PM CST

Robert McClendon, exonerated by DNA testing performed by DDC, is home for the holidays for the first time in 18 years. He was released August 11 after DNA evidence cleared him of a child rape charge. McClendon is the 7th Ohio exoneree (read about the other six in this Columbus Dispatch article) and his is the [...]

Photo session [Mailund on the Internet]

Posted: 04 Dec 2008 01:45 PM CST

Hi, sorry I haven’t written anything in ages. I’ve been completely swamped in work on a genome project, but one I don’t think I can write about until the paper is out, and since I haven’t thought about much else the last couple of weeks I’ve been silent here.

Don’t worry, I’ll tell all about it when we are getting closer to publication.

Anyway, a few days ago I had a photo session related to the project (and a previous project) and you can see some of the pics below.

(Photographs by Jesper Voldgaard).

As you can no doubt guess from the pictures, some abes are involved in the project…

Science nerds can't score [Bayblab]

Posted: 04 Dec 2008 12:49 PM CST

A recent study in the journal of sexual health (castration or institutional subscription required) looking at the prevalence of chlamydia screening uncovered some interesting facts about university student sexuality:

"Arts students were younger, more likely to be sexually active and to report having little or no knowledge of chlamydia. Males in the study were less likely to have had sex as a group compared to the group of females in the sample. Science students were also less likely to have had sex compared to their counterparts in other faculties."

So why are science boys unable to seal the deal? According to the authors:

"Boys also start having sex later than girls, [...] And who are the people at unis that go to the rave parties and the bar? ... it's not the nerdy boy science students. They're carrying on doing their experiments, going to the library or doing their assignments."

Ouch. Is that true? I thought that was only the engineers!

Also while you're there, you can check out these papers on understanding oral sex or on how impotent males feel vibrators, in the same issue of the journal.

"Free" large scale sequencing for Department of Energy related projects ... [The Tree of Life]

Posted: 04 Dec 2008 12:19 PM CST

Interested in Department of Energy-related missions such as global carbon cycling, alternative energy production, and biogeochemistry? And want some genomes, metagenomes, or other things sequenced that are relevant to these topic areas? All you have to do is write a proposal to the Joint Genome Institute (JGI) Community Sequencing Program, get it selected by the review committee, and then the JGI will do the sequencing and some analysis for you.

Go to this web site to learn more ....JGI - CSP Overview.

Doubts on the Cancer Stem Cell Hypothesis [Bayblab]

Posted: 04 Dec 2008 10:46 AM CST

The cancer stem cell hypothesis states that a tumour consists of a subpopulation of cells that give rise to all the heterogeneity found in the cancerous tissue. These cells have some common markers and characteristics of normal stem cells. These, the hypothesis suggests, give rise to the tumour and are therefore the best target for cancer therapeutics.
A recent paper in Nature seems to have caused a bit of a stir in the cancer stem cell field. (first born child or expensive subscription required). Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.
A wired artcle on the work really tries to stir the pot:(free)
"The controversial idea that all tumors are created by cancer stem cells received a setback Wednesday."
There are also some great summaries of what the impact of this paper may be in this field of research in Nature. News and Views. Nature News. Again you will have to sell organs or have an institutional subscription.

I can't say that I know much about cancer stem cells, only that I find the hypothesis interesting. As the summaries suggest, I would not find it surprising that some cancers do indeed consist of a subpopulation of cancer stem cells wereas others do not. I also don't know if specifically targetting cancer stem cells is going to cure a patient since these cells, while capable of causing a recurrance don't cause the symptoms of cancer.
I also don't follow the logic that the cancer stem cells are the reason that chemoresistance occurs, and other hypothesis that have come out of the cancer stem cell hypothesis.
That being said I certainly don't find this study to be blow to the cancer stem cell hypothesis.

ABRF 2009 is just around the corner [FinchTalk]

Posted: 02 Dec 2008 09:11 AM CST

Karen Jonscher said it best, "Reminder - register now for the [ABRF] Satellite Educational Workshops!" In her email to the ABRF email forum, Karen reminded us that the ABRF Education Committee is...

Spliced feed for The Science Network

2008-12-04T05:07:00.001-08:00

Spliced feed for The Science Network

Shedding Light on Neon Signs [Sciencebase Science Blog]

Posted: 03 Dec 2008 07:00 AM CST

As regular readers know, I like to keep a fairly close eye on what Sciencebase visitors are searching for so that I can put together new posts that provide answers to the questions readers want answering. Recently, there has been a spate of search queries related to neon signs. Perhaps not the most exciting of subjects, but there is some nice chemistry to be learned from all the different colours available, so I thought I’d shed some light on the subject of noble gas illumination.

Incidentally, for those unaware of the history of noble gases, they were at one time known as inert gases because chemists though their full outer shell of electrons made them unreactive. As more and more reactions for these so-called inert gases were discovered, it became necessary to give them another label, hence noble.

A neon light is not really much more than a fluorescent tube (actually, it’s less as it needs no phosphor coating on the inside), but instead of containing mercury vapour to give a bright “white” light, neon tubes contain the noble gas neon, surprise, surprise. Pass an electric discharge through a tube containing low pressure neon and it will glow with that familiar orange-red glow, so evocative of late-night bars and sleazy movies.

A neon light uses a very high voltage to propel an electric current through a low-density gas of neon atoms held in a glass tube. Charges from the electrode at each end of the tube fly through the gas colliding frequently with neon atoms and transferring some of their energy to the neon atoms. This kicks the neon atoms into a higher energy, excited state, with an electron in a higher orbital than normal. This excited state does not last and as the electron loses energy the atom drops back to a lower energy state and releases a photon of light. The energy of this photon is equivalent to the energy fall and for neon atoms that coincides with an energy that produces a reddish glow.

Many people, unfamiliar with the noble gas group of the periodic table - the p-block, assume that all coloured fluorescent tubes used in signage are neon signs. However, there are two ways to produce other colours - paint a standard mercury tube with the colour you want or far more effectively use a different noble gas in the tube instead of neon, perhaps together with mercury vapour to give a stronger glow. Here’s a break down of the discharge colours for each noble gas.

Helium (He) - Orangey white, usually
Neon (Ne) - Orange-red glow
Argon (Ar) - Violet, pale lavender blue
Krypton (Kr) - Grayish dim off-white
Xenon (Xe) - Blue-grey
Radon (Rn) - radioactive, not used in lighting

Of course, it is not only the noble gases and mercury vapour that can be added to lighting tubes. Nitrogen produces a slightly pinker glow than argon, oxygen glows violet-lavender but dimly. Hydrogen glows lavender at low currents, but pinkish magenta above 10 milliAmps, while carbon dioxide produces a slight bluish-white. Mercury can be made to glow in the ultraviolet, and is used in so-called black lights. Sodium vapour at low pressure glows the bright yellow of street lighting, particularly in England. And, even water vapour produces a glow similar to hydrogen, only dimmer .

Shedding Light on Neon Signs

The DNA Network

2008-12-03T18:45:00.000-08:00

The DNA Network

Gene for the placebo response? Not even close. [Genetic Future]

Posted: 03 Dec 2008 07:45 PM CST

New Scientist trumpets the discovery of "the first placebo gene". The study in question is here.

I usually don't comment on this type of study, but this time the hype is just too much for me: New Scientist describes the study as "a milestone in the quest to understand" the placebo effect; an article in ScienceNow quotes a psychiatrist saying that "the findings could have major implications for research design". The article itself certainly doesn't talk down its results, with the first sentence of the discussion stating:

The present study demonstrates that the magnitude of the placebo response [...] is tied to attenuated amygdala excitability, which in turn is linked to serotonergic genetic variation.

The problem? The study examined just 25 subjects, and if there's one clear lesson from the history of candidate gene asociation studies it's that such tiny studies are essentially worthless: systematic reviews of the field (e.g. here, here and here) have consistently found that the majority of such associations are never replicated, suggesting that positive results in small studies are substantially more likely to arise through a combination of chance, error and publication bias than through a genuine causal link.

It's only relatively recently that genetic association studies have come of age, with the advent of agnostic genome-wide association studies, massive sample sizes, rigorous statistical frameworks and the use of independent replication cohorts. Unfortunately, it appears that such novelties haven't yet permeated Uppsala University's Department of Psychology - but that hasn't stopped their study from generating media attention, in publications that should really have known better.

So don't believe the hype: as a good rule of thumb, if a genetic association study contains fewer than 100 subjects, it's not a "milestone" with "major implications" - in fact, you might as well simply pretend it doesn't exist at all. (Many studies with more than 100 subjects are also crap, but at least there's a chance they're capturing a genuine causal variant.) I'm deadly serious about this. The field is so littered with the stinking carcasses of unreplicated candidate gene associations that it's a reasonable default to simply assume that any small, unreplicated study is false.

Now, if only there was a way to get some science journalists to internalise that little rule of thumb...

Read the comments on this post...

Paralogous genes and disease alleles [Yann Klimentidis' Weblog]

Posted: 03 Dec 2008 06:38 PM CST

I don't quite fully get this, but the point of the method that they propose is to look at paralogous genes to more efficiently pinpoint the actual causal variants from among the many "hits" that pop up in GWASs.

Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations Are Correlated in Paralogous Proteins
Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, Martin G. Reese
PLoS Comput Biol 4(11): e1000218

Abstract: The millions of mutations and polymorphisms that occur in human populations are potential predictors of disease, of our reactions to drugs, of predisposition to microbial infections, and of age-related conditions such as impaired brain and cardiovascular functions. However, predicting the phenotypic consequences and eventual clinical significance of a sequence variant is not an easy task. Computational approaches have found perturbation of conserved amino acids to be a useful criterion for identifying variants likely to have phenotypic consequences. To our knowledge, however, no study to date has explored the potential of variants that occur at homologous positions within paralogous human proteins as a means of identifying polymorphisms with likely phenotypic consequences. In order to investigate the potential of this approach, we have assembled a unique collection of known disease-causing variants from OMIM and the Human Genome Mutation Database (HGMD) and used them to identify and characterize pairs of sequence variants that occur at homologous positions within paralogous human proteins. Our analyses demonstrate that the locations of variants are correlated in paralogous proteins. Moreover, if one member of a variant-pair is disease-causing, its partner is likely to be disease-causing as well. Thus, information about variant-pairs can be used to identify potentially disease-causing variants, extend existing procedures for polymorphism prioritization, and provide a suite of candidates for further diagnostic and therapeutic purposes.

Mendel's Garden [Genetic Future]

Posted: 03 Dec 2008 06:04 PM CST

Chris over at A Free Man has done a great job putting together the latest issue of genetics blog carnival Mendel's Garden - check it out.

Read the comments on this post...

Activating a gene through pioneer transcripts [The Daily Transcript]

Posted: 03 Dec 2008 05:47 PM CST

First up read yesterday's entry on Genomic Organization.

Now that you've done that, let's talk about a paper that appeared in Nature about a month ago. The article is entitled:

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs (link)

Superficially you would look at this title and exclaim Wow another function for non-coding RNAs! Well not exactly. It would seem that everyone is going ga-ga over these non-coding RNAs, but if you dig deeper, something else is going on. Note that I'm not saying that the paper is crap, in fact the results are VERY interesting, but you have to keep in mind that this paper is describing is how the act of transcribing non-coding RNA affects genomic organization.

But before we begin, let's dust off our lexicon. Here are some definitions that I did not bring up yesterday. Chromatin can be thought of as the configuration of DNA with its associated proteins, mainly nucleosomes. Chromatin remodelling refers to alterations in the packaging of this DNA so that the tightness and location of nucleosomes have been altered. As I described yesterday, these changes will affect how DNA binding proteins associate with the genome, which in turn modifies what regions are transcribed into RNA.You'll also remember that the theme of that post was that RNA Polymerase II (aka Pol II) and nucleosomes have a strange relationship. In fact Pol II can directly alter the modifications found on histones and can also influence how DNA is bound to its nucleosomes. So there is a constant conversation between chromatin structure and Pol II.

The Nature paper illustrates this principle nicely. It demonstrates how one gene, fbp1, is activated in response to glucose deprivation. Strangely, Pol II plays a big part in initiating gene activation by allowing the chromatin to be remodelled.

You see it would seem that when the gene is "inactive", Pol II transcribes very long RNAs that start well before the fbp1 gene. These "pioneer" transcripts cover a whole section just before and then continue past the gene and end at the normal termination site. These long mRNAs are even polyadenylated at their end. But they are weird. These RNAs are neither spliced nor translated into protein. The transcripts are found at a very low level and seem to be unstable (I'm inferring that the transcripts have a short half-life from some of their gels, but unfortunately the authors don't measure this parameter). When glucose levels are lowered, the long transcripts disappear and instead new shorter RNAs are made by Pol II molecules. These shorter RNAs begin at points closer to the gene's start site but again end at the gene's termination site. The short guys are however much more numerous as compared to the initial pioneer transcripts. Eventually very short transcripts are made. These transcripts start at the "consensus start site" of the fbp1 gene and are not only properly spliced but are translated into protein.

Now here is the cool part, if you genetically modify the yeast genome so that a transcriptional terminator is introduced in front of the fbp1 gene, you not only prematurely truncate these long pioneer transcripts but you prevent the production of all the shorter transcripts. Yes you prevent the stepwise activation of the gene.

So what is happening?

Read the rest of this post... | Read the comments on this post...

Ethics of Genetic Testing: Part 1 [Mary Meets Dolly]

Posted: 03 Dec 2008 04:02 PM CST

I have found that many Catholics are confused about genetic testing and the ethical issues that surround it. So I have decided to write a two part series on the ethics of genetic testing.

Part 1: Genetic testing is not all bad.

DNA11.com

And yet many Catholics are wary of the Human Genome Project (HGP) and genetic testing, and the knowledge they provide. Of course, there are serious ethical implications, but the HGP has provided a wonderful opportunity to prevent and even cure disease. As genetic testing becomes more commonplace, we will have more information on diseases that one may be at risk to develop. If discovered early enough, we can make choices to help prevent or delay the onset of that disease.

A colleague's battle with cancer is a good example of the use of genetic testing to prevent disease. We now know that mutations in the BCRA1 or BCRA2 gene put a woman at high risk of developing breast or ovarian cancer. My colleague's mother, aunts, and cousin had breast or ovarian cancer. She, herself, was an ovarian cancer survivor. When the test for mutations in the BCRA1 gene became available, she found that she did have the mutation. Her sister was also tested, had the mutation, but had yet to develop cancer. Knowing she was at high risk, the sister underwent preventive surgery and now regularly gets screened for tumors. Hopefully, she will never develop cancer, but, if she does, it will be caught early, increasing her chances for survival.

Doctors often use genetic testing to help treat their patients. A good example is the test for a mutation in the Factor V Leiden gene. Factor V Leiden is the most common hereditary blood coagulation disorder in the United States. Patients with a mutation in this gene are at greater risk of developing potentially deadly blood clots. If a doctor knows that a patient has an increased risk of developing a clot, they can prescribe medication or monitor the patient closely after surgery.

Genetic testing also provides information on Hereditary Hemochromatosis (HHC), the most common form of iron overload disease. HHC is an inherited disorder that causes the body to absorb and store too much iron. If the disease is not detected early and treated, iron will accumulate in body tissues and may eventually lead to serious problems. Mutations in the HFE gene are the thought to be the cause of HHC. A genetic test can identify patients who are at risk for developing HHC before they begin to have symptoms. In fact, there are countless such conditions and diseases, linked to genetic factors, that will be positively impacted by genetic testing, including diabetes and Alzheimer's disease.

Genetic testing has also created an exciting new field called pharmacogenetics. Pharmacogenetics is the study of how

DNAStore.com

people's genetic make-up affects their response to medicines. Because each person metabolizes drugs differently, it can take a lot of trial and error before a doctor will find the right drug or combination of drugs and dosage(s) for a particular patient. Scientists continue to find genes that regulate the metabolism of drugs. Discovering the genetic profile of how a patient may react to a class of drugs will facilitate the doctor's decision on which drug and what dosage is appropriate for that patient. Recently, a sales representative showed me a microarray DNA chip that tests the genes responsible for the metabolism of psychiatric drugs. This test will provide psychiatrists with valuable information, so they can better prescribe medications, increasing effectiveness and reducing side effects.

Prenatal diagnosis of the unborn, using genetic testing, is always an ethically sticky subject. There are several immoral uses of prenatal genetic testing that I address in Unethical Uses of Genetic Testing, but, as Catholics, we cannot automatically assume that prenatal genetic testing is immoral. An obstetrician opposed to abortion once told me that, in his observation, genetic testing has often prevented a couple from aborting their child. He said that not knowing is often more scary than knowing, and couples may be more likely to abort if they do not have all of the information available. In the future, with the perfection of surgery on the unborn in the womb, prenatal genetic testing may actually save unborn lives. The Vatican Congregation of the Doctrine of the Faith has made a statement on prenatal diagnosis:

"Is prenatal diagnosis morally licit? If prenatal diagnosis respects the life and the integrity of the embryo and the human fetus and is directed toward safeguarding or healing as an individual, then the answer is affirmative."

All of the benefits of genetic testing are too numerous to list here. The Catholic Church welcomes genetic testing when its function is to improve sound medical practice. The possibilities of genetic testing prompted John Paul II to make the following statement:

Indeed, the biomedical sciences are currently experiencing a period of rapid and marvelous growth, especially with regard to new discoveries in the areas of genetics. But if scientific research is to be directed toward respect for personal dignity and support of human life, its scientific validity according to the rules of each discipline is not enough. It must also qualify positively from the ethical point of view, and this presupposes that from the outset it endeavors to promote the true good of human beings as individuals and as a community. This happens when efforts are made to eliminate the causes of disease by putting real prevention into practice, or whenever more effective therapies are sought for the treatment of serious illnesses.

Stephen Hawking coming to Ontario. [Genomicron]

Posted: 03 Dec 2008 03:57 PM CST

Check this out...

Hawking plans long commute to Canada

JoVE: Video-publication in Medicine and Psychology [ScienceRoll]

Posted: 03 Dec 2008 01:50 PM CST

JoVE is the Journal of Visualized Experiments, a journal of videos indexed by Pubmed as well. Now, they expanded their video-based model of scientific publishing to include medicine and psychology protocols. We had to wait for this improvement, but now it happened.

The first two videos:

College Tuition is a Scandal [adaptivecomplexity's blog]

Posted: 03 Dec 2008 09:52 AM CST

College tuition has increased 439% since 1984, and the net yearly cost of college at a 4-year public university is 76% of the median family income, according to a story in today's NY Times. Even community colleges don't end up being a much better deal. It's a scandal. We're pricing most people out of college at a time when middle-class income is stagnating and education is more critical than ever for career success.

Sing this! [ScienceRoll]

Posted: 03 Dec 2008 09:25 AM CST

Shedding Light on Neon Signs [Sciencebase Science Blog]

Posted: 03 Dec 2008 07:00 AM CST

Shedding Light on Neon Signs

Increased Secretion in Senescent Cells [The Daily Transcript]

Posted: 03 Dec 2008 06:57 AM CST

I just read a paper that features fellow science blogger Chris Patil as an author (although he would be the first to state that he was second on the author's list). The manuscript, which appeared in yesterday's edition of PLoS Biology, describes senescence-associated secretory phenotype (aka SASP), a phenomenon that is associated with cancer cells treated with chemotherapeutic reagents that cause DNA-damage and with cells undergoing senescence. From the paper:

Despite support for the idea that senescence is a beneficial anticancer mechanism, indirect evidence suggests that senescent cells can also be deleterious and might contribute to age-related pathologies [10,23-25]. The apparent paradox of contributing to both tumor suppression and aging is consistent with an evolutionary theory of aging, termed antagonistic pleiotropy [26]. Organisms generally evolve in environments that are replete with extrinsic hazards, and so old individuals tend to be rare in natural populations. Therefore, there is little selective pressure for tumor suppressor mechanisms to be effective well into old age; rather, these mechanisms need to be sufficiently effective only to ensure successful reproduction. Further, tumor suppressor mechanisms could in principle even be deleterious at advanced ages, as predicted by evolutionary antagonistic pleiotropy. Consistent with this view, senescent cells increase with age in mammalian tissues [27], and have been found at sites of age-related pathologies such as osteoarthritis and atherosclerosis [28-30]. Moreover, in mice, chronically active p53 both promotes cellular senescence and accelerates aging phenotypes [31,32].
How might senescent cells be deleterious? Senescent cells acquire many changes in gene expression, mostly documented as altered mRNA abundance, including increased expression of secreted proteins [33-41]. Some of these secreted proteins act in an autocrine manner to reinforce the senescence growth arrest [37,38,40,41]. Moreover, cell culture and mouse xenograft studies suggest that proteins secreted by senescent cells can promote degenerative or hyperproliferative changes in neighboring cells [35,39,42,43]. Thus, although the cell-autonomous senescence growth arrest suppresses cancer, factors secreted by senescent cells might have deleterious cell-nonautonomous effects that alter the tissue microenvironment.

It turns out that SASP is responsive to oncogenic forms of RAS and loss of p53, two of the most important genetic contributors to cancer.

It will be interesting to tease out whether SASP is solely due to an increase in transcription of a select group of secreted proteins or whether some other aspect of mRNA metabolism is altered (such as a decrease in mRNA turnover). After all, there seems to be a tight connection between stress and mRNA metabolism (see this post). Also it is likely that the secretory potential of the endoplasmic reticulum has to be upregulated and this clearly requires certain branches of the UPR gene regulatory program (unfolded protein response - again another stress response pathway - see this post) to be activated.

Abel Pharmboy has a great post on the article, that I strongly encourage you to go over and check it out.

I should also add that one of the benefits of blogging as a scientist is that it gives you a forum to discuss your published results. In this spirit, I encourage you to head over to Ouroboros and ask Chris about SASP and his latest findings.

Read the comments on this post...

Top 10 Innovations In Life Science [Bitesize Bio]

Posted: 03 Dec 2008 05:30 AM CST

The Scientist magazine has published a list of the top 10 innovations in life science in 2008, as judged by their panel of expert judges.

Among the chosen highlights are:

An in-vivo multispectral imaging system that provides fluorescence, luminescence, and radioisotopic imaging overlayed onto anatomical X-ray, which can be used to view molecular movement in small animals in nearly real time.

A Fucci (Fluorescent ubiquitination-based cell cycle indicator)-based system that allows real-time, in vivo imaging of the cell cycle.

A service that allows end users to order customised zinc finger proteins to snip genomic DNA at the precise location they desire for knocking-out, or in, genes.

And a low-cost DNA sequencing system that can sequence the entire human genome for just $60K… and they aim to reduce the cost to $10K by the end of 2008.

Check out the whole list at The Scientist Magazine.

Is It Heritable? Twin Study Evidence Suggests Eyeball (aka Intraocular) Pressure is Substantially Affected by Genetics [DNA and You]

Posted: 03 Dec 2008 01:14 AM CST

As I've previously mentioned, twin studies allow an estimation of the heritability of a trait by comparing the degree of concordance in a given phenotype between MZ (identical) twins and DZ (fraternal) twins.

I recently came across a fascinating study looking at the heritability of intraocular pressure - that is -the pressure on the inside of the eyeball that ophthalmologists and optometrists measure when screening for glaucoma. Carbonaro and colleagues, from the Twin Research and Genetic Epidemiology Unit at King's College London School of Medicine, performed a classical twin study to estimate intraocular pressure (IOP) heritability¹. Although there was some modest variability in the heritability estimates depending on which of 3 instruments was utilized to measure IOP, the results suggested that genetic factors explain about 62 percent of the variation in IOP, with individual environmental factors and/or stochastic factors accounting for the remainder.

62 percent is impressively high, but of course does not tell us anything about the genetic architecture of the trait. Although some progress has been made in understanding the genetics of congenital glaucoma, we have much further to go with adult glaucoma/IOP elevation. Despite the existence of a few clues^2-4, much work remains to be done.

Photo: By ninjapoodles via Creative Commons.

Cited References

1. Carbonaro F, Andrew T, Mackey DA, Spector TD, Hammond CJ. Heritability of intraocular pressure: a classical twin study. Br J Ophthalmol 92:1125-8, 2008.

2. Duggal P et al. Identification of novel genetic loci for intraocular pressure: a genomewide scan of the Beaver Dam Eye Study. Arch Ophthalmol 125:74-9, 2007.

3. Wiggs JL et al. Genome-wide scan for adult onset primary open angle glaucoma. Hum Mol Genet 9:1109-17, 2000.

4. Nemesure B et al. A genome-wide scan for primary open-angle glaucoma (POAG): the Barbados Family Study of Open-Angle Glaucoma. Hum Genet 112:600-9, 2003.

A few questions for Governor Palin [Omics! Omics!]

Posted: 02 Dec 2008 11:03 PM CST

It's hard to believe that it's been a full month since the historic election. Well, depends on how you count a month, but today is the first Tuesday after the first Monday in December.

I was more of a political junkie in my youth, but I haven't sworn off the habit. Only in the last few days was I attempting to handicap the electoral college. TNG was a huge Obama fan, asking every adult in sight whether they would be voting for him. On the flip side, the other ticket had Miss Amanda quite charged up -- the idea of a Canino-American being one heartbeat from the presidency was too much to resist (though she has declared she will nip any groomer who attempts to apply lipstick to her!). Her disappointment that night was quickly salved by Obama's first major policy declaration in his celebratory speech. Alas, her closest kin have not been mentioned as in the running for the White House staff position.

Speaking of Governor Palin, it seems she will not be fading from the limelight. No, indeed it looks like her personal Iditarod will be going for the nomination in 2012. Alaska's chief executive made a number of comments during the campaign which induced consternation in the scientific community. Granted, the fruit fly remark was specifically about research on a totally different bug than Drosophila in a completely agriculturally-targeted setting, but it didn't endear her to the fans of Morgan & Bridges. Given she has four years to prepare, it wouldn't hurt to start now. And, in the spirit of reuse, should she not run it would seem the majority of these queries would apply to the majority of other Republicans who went for the high office this year.

1) You have publically taken stands that some views held by a minority (or less) of the scientific community should be accepted and used as the basis for policy decisions (e.g. the existance and/or cause of global warming trends) and/or taught in public schools as viable alternatives to the majority view (e.g. creationism). How do you choose which 'maverick' scientific theories have merit and which do not?

2) Which of the following maverick theories, relevant to major issues in this country today, should be taught in public schools or used to guide policy:

2.1) Healthcare (research priorities, Medicare/Medicaid reimbursement policy)

2.1.1) Childhood vaccines cause autism

2.1.2) AIDS can be treated more effectively with vitamin combinations than antiretrovirals

2.1.3) AIDS is caused by lifestyle factors and not the virus HIV

2.1.4) High cholesterol levels do not cause heart disease; cholesterol lowering using drugs risks cancer & depression

2.2) Physical sciences

2.2.1) Petroleum is not a limited supply of fossil remains of ancient lifeforms but rather is constantly created by processes deep in the earth (clearly an area where Ms. Palin has declared as in her sphere of expertise)

2.2.2) Manned space travel through the van Allen belts is guaranteed to be lethal; funding an attempt to land on the moon should be cancelled.

2.2.3) Einstein's Theory of Relativity is clearly wrong, as the concept of time dilation is so opposed to normal experience as to be laughable.

3) Should the U.S. government ever fund research outside its borders? Under what conditions should such operations be funded, if ever?

4) To what degree should non-expert politicians alter the research funding priorities set by experts in the field?

5) What, if any, useful science has come from studying fruit flies? Should the U.S. fund any further research? What other organisms do you also feel are not worth researching?

This is just a draft; readers are invited to submit further questions via the comments

Mendel’s Garden #26: A Few of My Favorite Things [A Free Man » Science]

Posted: 02 Dec 2008 10:28 PM CST

I’m quite pleased to host this month’s Mendel’s Garden - a blog carnival featuring the best genetics writing on the internets for the last month. Since it’s my party, I’ve picked out a few of my favorite topics to feature. But in the way of introduction for the neophytes in the crowd, let’s define our terms. The first question I ask my students on their first exam is “What is a gene and how is it regulated?”. I’m looking for them to talk about Mendel’s description of units of inheritance and the modern DNA based definition. Well, RPM of Evolgen thinks that it’s time to expand our definition or throw the word out entirely. He makes a solid argument, based on the fact that a lot of things that are transcribed in the genome wouldn’t be considered ‘genes’ by most of us. But if we trash the word, what would geneticists call themselves?

For a perfect example of the beautiful complexity of genetics illustrated, check out this father-son photo from Not Afraid To Use It. About says it all. Without further ado, a few of my favorite things genetical:

I found a couple of great posts about the genetics of autism. Now, to clarify, I’m not a big fan of autism per se, but I got embroiled (in a minor way) in the controversy with this post on the autism-MMR vaccine sham. Since then, I’ve followed the new research on autism with some interest. A post over at Highlight Health describes two genome-wide genetic analyses that identified five genetic loci that contribute to autism susceptibility, lending more support to the argument that autism is largely a heritable disorder. Kristina Chew, of AutismVox, thinks that geneticists sometimes go a bit far, however. Her response to a “sweeping” new theory that an evolutionary tug-of-war between parental genetic contributions is astutely skeptical. And of course, As is the case with any genetic disorder, there is an environmental component to consider. Reviewing an odd study out of Cornell, the Great Beyond details an assertion that autism rates are higher in rainy parts of the world. Take of it what you will, folks.

I’ve become increasingly fascinated with human evolution and in the genomic era research into our roots is just burgeoning. This month, Daniel McArthur at Genetic Future writes about one of the new tools available to evolutionary geneticists and gives an example of its use to look at positive selection at certain human genetic loci. One of the more interesting stories from this field is of the pair of skeletons found in a mass grave in Germany locked in an intimate embrace. The Great Beyond describes the DNA analysis that revealed that the 4600 year old remains were of a parent and child and appear, with fractured skulls and an arrowhead in the spine, to have been unfortunate victims of humanity’s penchant for genocide. Of course, none of this may matter according to UCL’s Steve Jones (as reported on Dick Dawkins dot net) who says that human evolution is done due to a dearth of older fathers. Jones argues that genetic variation comes, in part, from mutations that men accumulateas they get older. Don’t worry, Steve, I think there are plenty of toxins about to keep us mutating.

Speaking of junk science, there was some new junk on junk DNA released as a press release from the Genome Institute of Singapore. As Bayblab points out, this is a new and disturbing way of publishing your results - skip all the hassle of peer review and editing and just throw it out there to the mainstream press. Shame really, because this is my third topic of choice - epigenetics. Yann Klimentidis, on his blog, recounts some recent research looking at epigenetic changes in utero brought on by environmental stress. Zamp Bionews has more about epigenetic control of offspring fertility, which in this case is regulated by small RNAs apparently passed on maternally. Alex at The Daily Transcript has RNA, if not epigenetic, regulation in his post describing how each RNA binding protein in yeast tends to associate with mRNAs of a particular type. He hypothesizes that the expression of entire classes of genes may be subject to coordinated regulation at the level of mRNA metabolism.

And finally this month, a technical brief for those of you doing the hard work of science rather than just writing about it. Sandra, who blogs at Discovering Biology in a Digital World, tells us about a new BLAST feature that allows users to create a custom database. Sandra goes through a step-by-step tut and generates a viral phylogeny. For those Ph.D. students out there in the “Nothing Works Doldrums”, Nick at Bite Size Bio has some reassuring words for you - sometimes things just don’t work. That’s biology.

Next month’s Mendel’s Garden will be hosted by Another Blasted Weblog. If you’re interested in submitting, you can do so here.

This posting includes an audio/video/photo media file: Download Now

How Transcription Affects Genomic Organization and Vice Versa [The Daily Transcript]

Posted: 02 Dec 2008 06:15 PM CST

Recently there has been a flood of press about epigenetics and non-coding RNA. What is lacking from these articles is a description of how DNA is packaged and what DNA elements such as promoters and enhancers do. Today I would like to touch upon all of these subjects with a post on how DNA is organized and how this affects the turning on or off of genes.

OK here we go ...

One of the biggest findings over the past couple of years is how the act of transcription feeds back onto the organization of DNA.

What do I mean by that?

Read the rest of this post... | Read the comments on this post...

UC Davis giving further props to blogs (mine that is) [The Tree of Life]

Posted: 01 Dec 2008 06:34 PM CST

Hey - thanks UC Davis. Thanks for promoting blogs on your front page (under the Blogs, iTunes and Facebook section) and thanks for promoting my "Things Scientists should be thankful for"posting.

Spliced feed for The Science Network

2008-12-03T05:09:00.001-08:00

Spliced feed for The Science Network

Skepticality #091 - Skeptics Undercover - Kate Holden and Tiana Dietz visted The Discovery Institute (and so should you)! [Skepticality - Science and Revolutionary Ideas]

Posted: 02 Dec 2008 02:00 AM CST

Over the past several episodes, Skepticality has endeavored to showcase an eclecticÂrange of skeptical activism.Â Our recent guests haveÂoverwhelmingly agreed that everyone has something to offer â and that "activism"Âcomes in many flavors.ÂÂ This week, Derek & Swoopy talk with bloggers Kate Holden andÂTiana Dietz, who recently had an unorthodox adventure at theÂwell-knownÂIntelligent Design think tank The Discovery Institute.ÂTheseÂunapologeticÂrabble-rousersÂdiscuss the controversialÂtactics that took themÂwhere few skeptics have gone before.

This posting includes an audio/video/photo media file: Download Now

The DNA Network

2008-12-02T18:45:00.001-08:00

The DNA Network

Finding a New Gene Behind Language Disorders [adaptivecomplexity's blog]

Posted: 02 Dec 2008 11:54 AM CST

Why can humans talk while chimps can't? The answer is more than just vocal cord anatomy; our brains have a lot to do with our ability to learn and use language. One 'language gene' is FOXP2. Mutations in FOXP2 lead to a rare but dramatic language disorder. Characterized by an inability to use grammar. We all know people who are grammatically challenged (stemming from illiteracy, for example), but this disorder is not the same thing - the affected people have a strong genetic barrier that prevents them using grammar, no matter how hard they work at it.

This disorder is a dramatic example of a language development disorder, but millions of children have much more mild language disorders. Many of these kids outgrow their language problems but not all. A group of researchers working in the UK and the US asked whether some of these relatively mild language disorders are somehow connected to the FOXP2 gene, which so far has only been found to be involved in dramatic speech disorders. Sure enough, they found that variants in a gene regulated by FOXP2 are strongly correlated with mild language disorders.

ABRF 2009 is just around the corner [FinchTalk]

Posted: 02 Dec 2008 09:11 AM CST

Karen Jonscher said it best, "Reminder - register now for the [ABRF] Satellite Educational Workshops!" In her email to the ABRF email forum, Karen reminded us that the ABRF Education Committee is...

Interview with Robert Green about Presidential DNA [The Personal Genome]

Posted: 02 Dec 2008 06:37 AM CST

Last week I featured a recent NEJM article by Robert Green and George Annas about presidential DNA and its role in public elections. Co-author Robert Green (pictured right) agreed to share more about his views on the issue, in the following Q&A:

TPG: Both presidential candidates released information about their personal medical history during the recent election. Why do you believe genetic information should be treated differently? Why is DNA exceptional?

RG: There is a great deal of debate about whether DNA information warrants the ‘exceptionalism’ that has attached to it. The risk information provided by most genetic tests is currently less specific than family history and other risk factors can provide, putting it squarely into the domains of disease risk that health workers regularly communicate to patients. When discussing common diseases, the “exceptionalism” of genetic testing is amplified by the incorrect public perception that most genetic markers provide highly predictive information, when in fact, this is true for only a few.
Yet for some situations, there are undeniably special features to genetic testing. DNA is a highly specific identifier for forensic purposes and the occasional revelation of non-paternity can create upheaval in families. Genetic tests for highly penetrant diseases may provide reliable predictive information far in advance of symptoms, and providing such information to one family member may inadvertantly provide it to another who does not wish to receive it. And in situations where highly penetrant disease information is available far in advance of symptoms, there is greater potential for both prevention and for discrimination or unnecessary psychological distress.
Since much of the aura of ‘exceptionalism’ surrounding genetic testing is a byproduct of misunderstood notions of determinism, some of it should fade and normalize as the population learns more about genetics in the coming decade.

TPG: Both Obama and McCain have potentially serious conditions in their family medical histories (prostate cancer and heart disease, respectively). Do you believe genetic information could have helped voters in the last election evaluate the health status of the candidates?

RG: Most of us would agree that health information is relevant to a candidate’s fitness for office, particularly an office like the Presidency. Therefore, health information that could affect fitness for office seems undeniably relevant to voter decisions. So while the public does not have a right to know every detail of a candidate’s medical history, those facts relevant to fitness should be public information. Health information related to fitness may be misunderstood, exaggerated or minimized and therein lies the problem. The public is not particularly skilled or rational at sorting out the probabilities associated with health risks from whatever source… be it prior illness, lifestyle habits like smoking, cholesterol levels, family history information or genetic testing results. In the last election, I do not believe that any genetic information currently available woudl have been sufficiently predictive to warrant sharing with voters. However, if a highly predictive genetic test for recurrence of melanoma were available, that would arguably have been relevant and thus, would warrant dislosure to voters.

TPG: In your article you argued that the fierce political environment that surrounds elections, combined with our limited ability to understand genetic information, might lead to “genetic McCarthyism”. Is this a temporary circumstance?

RG: As we pointed out, there is a clear potential that someone might try to use genetic markers to smear another candidate, particularly in the realm of behavioral of psychiatric genetics. Certain conditions, such as mental illnesses, are so psychologically loaded that such smears might even be effective, even if quickly countered by experts explaining the predictive limitations of the science. But as your question suggests, as the general population becomes more familiar with genetic information and the limitations and complexities of such information, there should be less of a potential for distortion. Whether you call it “Genetic McCarthyism” or “Genetic Swiftboating”, and whether it occurs in presidential politics or in other contentious situations (lesser elections, custody cases), all of us in genetics should be prepared for it and prepared to combat it when it occurs.

–
Green, Robert C., Annas, George J. The Genetic Privacy of Presidential Candidates. N Engl J Med 2008 359: 2192-2193.

Dr. Robert Green is a professor in the Departments of Neurology, Medicine (Genetics), and Epidemiology at the Boston University Schools of Medicine and Public Health.

Networking with LinkedIn and LabRoots [Bitesize Bio]

Posted: 02 Dec 2008 04:56 AM CST

You may have seen some of the different websites around for networking. I'm not talking about Facebook or Myspace, which are for social networking. Facebook and Myspace are great for keeping up with friends and sharing more personal details about your non-work life.

For scientific networking, you want to be able to connect with people on a professional level. Networking is critical because biotech and bioscience in general are very small worlds.

The people you are meeting and working with today may very well be the ones that help you get a job 10 years from now. The sales rep that you pissed off yesterday because he interrupted you at your bench might be the vice president of a company you would die to work for years later. Believe me – it does happen.

So start building your network of associates and colleagues now and you will reap the benefits when you need it the most.

Ok, so which site to use? We've given an overview of social networking sites for scientists here before. But I'd like to focus on the two networking sites I currently use for keeping in touch with my contacts and helping me to build my network.

The first one is LinkedIn and the other is a brand new site called Labroots.

LinkedIn

On LinkedIn, your profile is professional and is basically your CV or resume. You can embellish on your profile to highlight your achievements and advertise your marketability, if you are looking for a job.

There are a very large number of recruiters using LinkedIn so you can almost guarantee that you will be contacted by potential employers if you are looking for work.

A nice feature specific to LinkedIn is that you can leave a recommendation on a colleagues profile and they can recommend you. This is especially great to have unsolicited reviews about you if you are looking for employment and also it's just nice to receive positive feedback.

Another unique feature of LinkedIn is that once you have entered your information on your graduate schools and former companies, it alerts you when people from your previous schools or companies are registered. It proactively helps you to re-connect with old friends and colleagues. And LinkedIn also gives you updates on your network's network so you can check out new people and see if you have common interests.

What I love about this site is that there are a huge number of professional using it. Their website says that over 30 million professionals are members of LinkedIn. That may be an underestimate.

Virtually everyone in the biotech industry can be found on LinkedIn and I am noticing more and more that academic researchers are using it too.

But it is not strictly for biotech and scientists, in fact it is not career specific at all so every industry is represented on LinkedIn.

I highly recommend this site to everyone because of it's depth of members and the ability to easily build a network for your current or future career.

Labroots

Labroots is a brand new networking site specifically for the scientist. It was started by Greg Cruikshank in March of 2008.

At first I was skeptical about whether or not I really needed another site besides linkedin.com for networking. But after playing on the site and with my profile for the last few weeks, I have to say it is a really cool.

The profile information is also similar to a CV or resume except unlike linkedin.com, it is basically the dates and places where you studied or worked and doesn't have the option to go into major detail about your skills or experience. It seems to be more focused toward the academic researcher because they providing space to list posters, papers, grants, presentations, and honors and awards.

The difference between LinkedIn and Labroots is that the profile information is just the facts without the fluff.

The features I like best about the site are the news articles, events, and publications and the ability to personalize your homepage with widgets such as an RSS feed, the weather, the encyclopedia, a dictionary, a calculator, a clock, and a language translator.

It makes the page more your own and something you might want to keep open all day long. You get the latest scientific news headlines and publications along with the fun stuff you selected for your front page. This makes the site more unique and more customized so its more than just a networking site but it is also a great resource for information.

Because this site is new, membership is still ramping up so although there are many interesting discussion groups to join (I started two myself), there is not much discussion at the moment. I hope this changes as people find out about labroots.com and register.

I think as scientists we sometimes become very introverted because of the depth of focus required in our projects and the intense singularity of lab life. Networking sites provide a way for scientists to connect and meet people that you would normally never interact with and all from the safety of a computer. No actual human physical interaction is necessary.

Now all we need is for these networking sites to send us free t-shirts and we'll be all set!

oh great Ceiling Cat... [the skeptical alchemist]

Posted: 01 Dec 2008 11:56 PM CST

View blog reactions

What’s on the web? (1 December 2008): Top 10 Medical Innovations for 2009 [ScienceRoll]

Posted: 01 Dec 2008 01:37 PM CST

Top 10 Medical Innovations for 2009 (Digital Pathology Blog): For the third year in a row, Cleveland Clinic doctors and consultants have picked the medical innovations they think will rise to the top next year.

MetaCarnival: Volume One, Number 2 (Emergiblog): The blog carnival of all the biomedical blog carnivals is up.

Web 2.0 … Health 2.0 … Research 2.0?

You don't nor need to own your data (liako.biz)

Vadlo:

Vadlo is brought to you by two biology scientists who wish to make it easier to locate biology research related information on the web.

Vadlo search engine caters to all branches of life sciences. VADLO allows users to search within five categories: Protocols, Online Tools, Seminars, Databases and Software.

Monday Video: Amateur Transplants [ScienceRoll]

Posted: 01 Dec 2008 01:25 PM CST

No comment:

Top 10 Amazing Biomedical Videos [ScienceRoll]

Posted: 01 Dec 2008 01:24 PM CST

Wired Blog published a list of 10 amazing biomedical videos featuring some really great animations, but they missed a few others:

And many more at MolecularMovies.org:

World AIDS Day 2008: Bloggers Unite! [ScienceRoll]

Posted: 01 Dec 2008 01:00 AM CST

December 1 is the World AIDS Day so it’s time to dedicate a post to this important disease. From Wikipedia:

Acquired immune deficiency syndrome or acquired immunodeficiency syndrome (AIDS or Aids) is a set of symptoms and infections resulting from the damage to the human immune system caused by the human immunodeficiency virus (HIV). This condition progressively reduces the effectiveness of the immune system and leaves individuals susceptible to opportunistic infections and tumors. HIV is transmittedmucous membrane or the bloodstream with a bodily fluid containing HIV, such as blood, semen, vaginal fluid, preseminal fluid, and breast milk. This transmission can involve anal, vaginal or oral sex, blood transfusion, contaminated hypodermic needles, exchange between mother and baby during pregnancy, childbirth, or breastfeeding, or other exposure to one of the above bodily fluids.

Check AIDS.gov for more reliable information. And please visit the Bloggers Unite site:

Bloggers Unite is an attempt to harness the power of the blogosphere to make the world a better place. By asking bloggers to write about a particular subject on 1 day of the month, a single voice can be joined with thousands to help make a difference; from raising awareness for cancer, to an effort to better education systems or supporting 3rd world countries.

Cyberchondria and Health 2.0 News [ScienceRoll]

Posted: 29 Nov 2008 02:51 PM CST

I should study psychiatry for my next exam, but I must share a few articles with you first:

Monitoring your vices online (TheStart.com): Featuring Dr. Gunther Eysenbach, the organizer of Medicine 2.0 Congress.

Health 2.0 Through the Eyes of a Diabetic - One Year Later (Read/Write/Web):

One year ago, I discovered that I had contracted Type 1 Diabetes. I was 36 at that point and it’s relatively rare for someone of my age to suddenly get Type 1 Diabetes - indeed they used to call this form of diabetes “juvenile diabetes”, because it mostly occurs in children. So it was quite a shock to discover that I had it! Immediately I looked to the Web to find out all I could about this condition. I discovered a thriving community of ‘health 2.0′ apps and social networks, which I then wrote about in this blog.

Trends in Health 2.0: Mark Bard - Manhattan Research (HealthDot)

Internet diagnoses: Trust them or toss them? (Wickedlocal)

But in the world beyond the television screen, many physicians have come to recognize the value of their patients' use of the Internet.

And, if you are like most people, you turn to the Internet for health. Eighty-four percent of adult Internet users in the U.S. go online for medical information, according to a 2007 Harris poll. Some of them, like Diana C., believe the Internet saved their life.

Microsoft Examines Causes of 'Cyberchondria' (NYTimes.com)

MyGeneticist: I want to know about my DNA [ScienceRoll]

Posted: 29 Nov 2008 02:30 PM CST

Steve Murphy, our gene sherpa, informed us about a new site, MyGeneticist.com which

…is a service that empowers you to understand the information stored in your DNA, so you can use this knowledge to make healthy life choices. Founded and operated by scientists, myGeneticist’s mission is to complement existing healthcare systems and to make a positive impact on society by helping people make informed decisions. myGeneticist will be launching soon.

We need such services… I can’t wait to see how it actually works.

Genome Island in Second Life [ScienceRoll]

Posted: 29 Nov 2008 02:12 PM CST

Do you remember my post mentioning Genome Island, a unique educational place in Second Life? I also made an interview with Max Chatnoir, the creator. Now you can explore the island through a video:

Spliced feed for The Science Network

2008-12-02T05:07:00.001-08:00

Spliced feed for The Science Network

The Future [Sciencebase Science Blog]

Posted: 01 Dec 2008 07:00 AM CST

Pundits are predicting that the first computer that will be at least as intelligent as a human will be built in 2010 and by 2049 a $1000 computer will outsmart the entire human race. But, this video is about more than that.

It tracks the shifts that are occurring today and extrapolates them into implications for those currently in high school and higher education. Think about it, if you start a technical degree this year, half of what you learn in that four-year course will be outdated before you reach the end of the third year. After all, it took radio 38 years to reach a 50 million audience, television 13 years, the internet 4 years, and Facebook achieved a market penetration that size in just 2 years.

In 1984, the year I started university, there were 1000 internet devices around the world (I certainly didn’t send an email till more than four years after that). By 1992, that number was 1,000,000. Today, there are at least a billion internet devices and that number will inevitably rise as people with at least one personal computer augment their connectivity with more and more mobile devices. Incidentally, you can get Sciencebase on your mobile here.

The video was produced by the zyOzy Foundation, which believes that the themes in the “Did You Know?” video are global in nature and apply to schools and children around the world.

The Future