Thursday, August 7, 2008

The DNA Network

The DNA Network

Want To Popularize Science? Here's the gadget for you! [The Daily Transcript]

Posted: 07 Aug 2008 07:12 PM CDT

TravelBlogue, or How to live vicariously through one's student. [Genomicron]

Posted: 07 Aug 2008 04:34 PM CDT

The very first post here was called "My grad student made me do it", and explained that a then-newly-arrived PhD student in my lab was a blogger and got me interested in blogging. He is still a blog author, and most recently has posted a very enjoyable series about his travels from more or less the bottom to the top of the USA/Canada parts of North America looking for aquatic creatures. I personally did not get to go anyplace exciting this summer, but it has been great having the option to live vicariously, especially as he was most recently at one of the coolest (literally?) places on Earth: Devon Island in the high Arctic. Follow his adventures:

Florida to Guelph:

Guelph to Thompson:


Resolute and True Love
  • Coming soon

Book review: "The Animal Research War" [Discovering Biology in a Digital World]

Posted: 07 Aug 2008 04:27 PM CDT

"Did you know," my friend whispered, "that the Humane Society funds terrorists?"

I was stunned. What? That's crazy! I've adopted pets from there. No way! How could those be the same people??

My friend and I were suffering from "brand confusion." In business, this happens when different companies use similar names for their products in order to confuse the marketplace. In the animal rights movement, brand confusion is used to misdirect the funds that would otherwise help groups who do genuine humanitarian work.

418eP%2BP3kAL._SL210_.jpgAs I learned in "The Animal Research War" by P. Micheal Conn and James Parker [published by Palgrave Macmillan, ISBN-13:978-0-230-60014-0], there is an animal rights group that goes by the name of the Humane Society of the United States (HSUS). But this is not the group that runs animal shelters. The HSUS takes the money that well-meaning people think they're giving to shelters and uses it to fund propaganda campaigns.

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

Why It’s So Hard to Quit Smoking [Epidemix]

Posted: 07 Aug 2008 02:55 PM CDT


Let’s assume that pretty much every smoker in the U.S. knows cigarettes are bad for them. And let’s that assume that “bad for them” is understood as likely to kill them. Someday. But in the meantime, before that”someday” happens, millions of people continue to smoke, until for more than 400,000 Americans, someday becomes today. And that’s just death - according to the CDC, about nine million Americans suffer some 13 million smoking-attributable health problems every year. No wonder the U.S. spends more than $75 billion in smoking-related health costs every year.

What we’re left with, then, is a very clear picture that people continue to smoke even when they know it’s bad for them - yet more evidence that, as I’ve said before, behavior change is hard.But what’s especially surprising is when the harms caused by smoking hurts not just the smoker, but others. I’m not talking second-hand smoke. I’m talking real dangers. Dangers not evident someday, but very much in the here and now.

Today, the CDC offers some staggering evidence on that score: Two reports in the MMWR that demonstrate just how hard it is to quit smoking - even when it’s somebody else’s health at risk, not your own.

First, there’s a study on smoking prevalence among women of child bearing age in the U.S. Aside from the familiar yet unsettling statistic that 22.4% of women 18 to 44 years old are smokers, there’s this unnerving stat: among smokers aged  18 to 24 years old, a staggering 68% have tried to quit. But only 26% have been successful. Ouch. That means that even when these potential mothers are trying to stop smoking, they have only a 1/3 chance of success. That success rate gets better among older groups - by ages 36 to 44, about 46% of smokers manage to quit. But even so, that’s a horrible success rate. And one can presume that the flip side - the majority of smokers can’t quit - means that there are a whole lot of women smoking right through their pregnancy. When, one imagines, they’re most motivated to quit, because it isn’t their health on the line, it’s their unborn child’s as well.

If that’s bad, this is worse: another study in the MMWR carries the gripping title, “Fatal Fires Associated with Smoking During Long-Term Oxygen Therapy.” Yes, that’s right: a study about how many oxygen tanks exploded because the people using them couldn’t keep from lighting up. The study looks at fires in four states (Maine, Massachussetts, New Hampshire and Oklahoma), and finds some 38 fires from 2000 to 2007 can be attributed to exploding oxygen tanks due to cigarettes. Remarkably, only 37 people died in these fires, and only three of those weren’t the smokers themselves. Nonetheless: can there be a more clear sign that cigarette addiction drives people to act in self-destructive ways - not only by continuing to smoke, but to do so at the risk of blowing themselves up? (I should note, these fires are a mere subset of  the number of fatal fires caused by cigarettes - which are the leading cause of residential fire deaths in the U.S., according to the CDC report).

Here’s why I keep on about behavior change, and why smoking is a central illustration of the challenges involved: There’s a lot of talk out there these days, including by me and here on this blog, about preventive medicine. The line goes that once we learn our risks - genetic, environmental, and otherwise - we’ll be able to take action and change our lives, adjusting our behaviors to ward off those risks. It sounds good, and I continue to believe that preventive medicine will bring us to a more efficient, more effective, and more responsive healthcare system. We’ll live smarter and longer and better.

But if we want to know the stakes involved in expecting millions of Americans to start living better, smokers offer perhaps the clearest example of how challenging this will be. After all, no behavior has better evidence for negative repercussions, no group is better informed about the health risks involved in their behavior, and no activity carries such a clear upside for the public health. 400,000 people die every year when they needn’t have, if they’d just acted differently. And yet: the evidence shows that it isn’t easy. People will still misbehave when they know it’s against their own interests. People will misbehave when they’re putting their children’s health at risk, too.

And - holy cow - people will misbehave even when they’re going to blow themselves up.

Photo courtesy Larry Taylor.

The five little Boogers and how they grew [Discovering Biology in a Digital World]

Posted: 07 Aug 2008 12:31 PM CDT

Leave it to those wacky Korean cloners. In December, scientists from Gyeongsang National University gave us fluorescent kitties. Now, we have cute little puppies!

These aren't the first cloned pets on the market, we have stores that sell glowing fish. But these clones have a bit higher price tag. For $50,000 Bernann McKinney got 5 new "Boogers" from RNL Bio; "Booger McKinney," "Booger Lee," "Booger Ra," "Booger Hong and "Booger Park." That's $10,000 a Booger!

Still, who can resist these cute little boogers? I have a picture of the puppies below the fold and as you can see, they're adorable!

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

A way to break out of the pyramid scheme [The Daily Transcript]

Posted: 07 Aug 2008 11:30 AM CDT

I was going to write something about the latest analysis of NIH funding in Science, but DrugMonkey did the work for me so go read his post. The bottom line is that NIH funding goes through boom-bust cycles that cause instability throughout the biomedical fields. In boom times the biomedical research fields recruit lots of grad students and postdocs (many of these recruits being foreign), after all the PIs need the work force and they now have funds to pay them. Then when these junior scientists go looking for their own lab and their first R01, the lack of funds forces many out of academia. To prevent this scenario from happening the NIH would need a 6% annual increase, which in all practical terms is impossible. Michael S. Teitelbaum calls this a "positive-feedback loop", but I tend to think of it as a pyramid scheme. And recently the NIH has been getting a whole lot less then a 6% increase - it's been flat. You can imagine the consequences.

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

Health 2.0 and Medicine 2.0: Tensions and Controversies in the Field [ScienceRoll]

Posted: 07 Aug 2008 11:24 AM CDT

Benjamin Hughes; Indra Joshi and Jonathan Wareham just published an article in the Journal of Medical Internet Research: Health 2.0 and Medicine 2.0: Tensions and Controversies in the Field. They cited Scienceroll when defining medicine 2.0.

An excerpt:

The terms Medicine 2.0 and Health 2.0 were found to be very similar and subsume five major salient themes: (1) the participants involved (doctors, patients, etc); (2) its impact on both traditional and collaborative practices in medicine; (3) its ability to provide personalized health care; (4) its ability to promote ongoing medical education; and (5) its associated method- and tool-related issues, such as potential inaccuracy in enduser-generated content. In comparing definitions of Medicine 2.0 to eHealth, key distinctions are made by the collaborative nature of Medicine 2.0 and its emphasis on personalized health care. However, other elements such as health or medical education remain common for both categories. In addition, this emphasis on personalized health care is not a salient theme within the academic literature. Of 2405 papers originally identified as potentially relevant, we found 56 articles that were exclusively focused on Medicine 2.0 as opposed to wider eHealth discussions. Four major tensions or debates between stakeholders were found in this literature, including (1) the lack of clear Medicine 2.0 definitions, (2) tension due to the loss of control over information as perceived by doctors, (3) the safety issues of inaccurate information, and (4) ownership and privacy issues with the growing body of information created by Medicine 2.0.

In my opinion, health 2.0 focuses on healthcare and patient support while medicine 2.0 focuses on medical education and communication.

DNA Testing for Surrogacy or ART Scenarios [The DNA Testing Blog]

Posted: 07 Aug 2008 08:59 AM CDT

Editor’s Note: This article was originally written for the Guest Blog on Adoption Under One Roof’s website. Adoption Under One Roof is an organization dedicated to covering adoption from every angle, every view, for everyone. When surrogacy or Assisted Reproductive Technology (ART) is used to bring a life into the world, it is always a good [...]

rs4675690 C-allele steers my left insula away from angry old farts [biomarker-driven mental health 2.0]

Posted: 07 Aug 2008 08:22 AM CDT


Indeed, learning how to manage one’s response to the negative emotions of others and stay out of trouble is an important life skill. At some point, most of us learn to just avoid angry, mean or melodramatically negative people and save ourselves the strife.  Roy Perlis and colleagues, in their recent paper, “Association of a Polymorphism Near CREB1 With Differential Aversion Processing in the Insula of Healthy Participants“, show how the transcriptional regulator CREB might exert an influence on this learning process. By having subjects view images of various facial expressions, the investigators found that individuals with the TT genotype at rs4675690 (C/T) showed less negative activation in the left insula, a brain region that is known to activate when subjects feel disgust, but not happiness, desire or fear.  Subjects with the TT genotype have been shown to require more effort in the management of negative emotions and are at greater risk for suicide when being treated for depression.  In the Perlis et al., study, TT subjects showed less of an effort (as measured in key presses) to avoid viewing emotionally distressing pictures. The known role of CREB in neural plasticity suggests that this gene may facilitate neural changes associated with memory. Unfortunately, 23andMe does not cover this SNP, so I’ll just have to hope that (during the upcoming election) my insula keeps me on the path to enlightenment.

Joined Up Fuels [Sciencebase Science Blog]

Posted: 07 Aug 2008 07:00 AM CDT

cars in snowThe green morals of UK motorists are currently being held to ransom by the government. The government hopes to increase vehicle taxes based on how much pollution a car produces - it’s a green tax, a carbon tax, call it what you will. Some drivers will end up paying twice as much each year to keep their car on the roads. The bigger the car, the theory goes, the more fuel it will use and so the more polluting it will be in terms of pumping out carbon dioxide and so the more vehicle tax you, the driver, must pay.

Apparently, big cars (4×4s, MPVs, big estates, and anything over 2.1 litre engine capacity, built before 2001, will be exempt from the approximate doubling of vehicle road tax that is imminent. And, that’s certainly a good thing. Not least because our family seven-seater has a 2.3 litre engine and was made in 1998. It all seems to make sense, at first glance. Who could argue with that? Such a tax increase will force drivers of big gas guzzlers to swap their Kensington Tractors for something a little more environment friendly.

But, it is not as if CO2 were the only pollutant, it’s not as if global warming were the only issue, and it’s not as if actually building new cars is a green process in itself. All those old-ish MPVs, are going to be sold on and new smaller cars bought, this drives the market, of course, and with an alleged recession pending, that might be a good thing in terms of economies. But, a quick back-of-the-envelope calculation will show that building a new car to replace that suddenly unwanted Kenny Tractor will expend far more energy and waste far more resources than continuing to drive it guzzling gas or not.

It seems to me that there is very little joined-up thinking when it comes to environmental issues. No one ever sits back and says, hold on a moment, when plans to potentially scrap millions of potentially serviceable vehicles for the sake of a tax saving comes up in discussion.

More to the point, the school-run of supersized vehicles, queuing up and belching out fumes while darling Jocasta and Joshua are delivered obesely to school without having to walk, is to some extend a tabloid a stereotype. Some people rely
the extra
seats and space
afforded them
by the bigger car
people rely on the extra seats and space afforded them by the bigger car. One car transporting six or seven people, at an albeit lower mpg, is surely better than two cars wearing out the tarmac even at 10-20% lower total fuel consumption. Hummers and sports utes excepted, of course, but you don’t see many of those on British streets.

Karl Hillman and Björn Sandén of the Department of Energy and Environment, at Chalmers University of Technology, Sweden, seem to recognise this need for complete Life Cycle Assessments (LCA) including so-called Well-to-Wheel studies as they apply to the transport sector in general.

They have investigated how well decisions are being made as we strive to reduce pollution and to meet climate-change targets. They suggest that rarely are time and scale related factors given any attention, which I read to coincide with my points about swapping big vehicles for small at least in terms of energy wasted in the process and the splitting of transportation into ever smaller units.

Writing in the International Journal of Alternative Propulsion, the Chalmers team discusses how road transportation is currently responsible for 20-25% of world carbon dioxide emissions and is almost entirely (99%) dependent on fossil oil, despite the occasional hybrid siting.

To reduce oil dependence and greenhouse gas emissions, different policies are now being implemented to increase the share of motor fuels based on renewable energy. In the short term, the European Union directive on the promotion of the use of biofuels or other renewable fuels for transport forces the member states to set targets for the minimum use of renewable fuels.

Perhaps the UK government plans to use the extra tax it raises from gas guzzlers to develop renewables for transport so that it can meet EU and international targets more effectively. Somehow I doubt it, with deficits on every table, state-adopted banks heavily in the red, and a media-inspired recession just round the corner, I suspect every last penny will have been accounted for before you could say rapeseed methyl ester.

Hillman, K.M., Sanden, B.A. (2008). Time and scale in Life Cycle Assessment: the case of fuel choice in the transport sector. International Journal of Alternative Propulsion, 2(1), 1. DOI: 10.1504/IJAP.2008.019689


Joined Up Fuels

New Search Engine for Biology [Bitesize Bio]

Posted: 07 Aug 2008 05:19 AM CDT

Here’s something that I’m sure all our readers will find interesting, if they haven’t heard it already: there’s a web search engine out now for specifically designed for biologists, called VADLO.

I heard about it via Pharyngula, and first impressions seem to be good, for the most part. Particularly, VALDO enables users to search by category: protocols, online tools, seminars, databases, and software.

The emphasis appears to be entirely on weeding out non-credible sources, leaving behind peer-reviewed articles and textbooks. In this respect, it resembles Google Scholar, but by introducing the mentioned categories, it is better tuned to the computing needs of biologists.

If that’s not enough, there’s a “Life in Research” cartoon series. Who doesn’t like lab humor??

Another star with cancer. [The Gene Sherpa: Personalized Medicine and You]

Posted: 07 Aug 2008 05:07 AM CDT

I am crawling out of bed to comment on another person who has breast cancer. Christina Applegate diagnosed at 34 years of age with Breast Cancer. She apparently had received an MRI which caught this...

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

Book Review: A Short Guide to the Human Genome [Think Gene]

Posted: 07 Aug 2008 04:45 AM CDT

A Short Guide to the Human Genome

A Short Guide to the Human Genome

Author: Stewart Scherer

Publisher: Cold Spring Harbor Laboratory Press

Read: (yes | maybe | no)

“A Short Guide to the Human Genome” (or SGHG) is a book by scientists, for scientists. It’s not for laypeople, and while condensed, it’s an advanced text best read by molecular biologists comfortable reading scientific papers about genomics. For this, SGHG is a “maybe” read.

But, as a useful book for scientists, SGHG is quite good. Laudably, its stated purpose is to present facts to flesh academic work. With its simple question-to-answer format and well-summarized tables and graphs, it does so well —without sacrificing scientific thoroughness. However, don’t expect any explanations, editorial insights, or appeals to the “bigger picture.” Which Genes Have the Most Exons? Scherer states the facts: TTN has the most exons. It has 312 exons. You are expected to provide your own context.

This book is for you if:

  • You need to pepper your powerpoint presentation with “relevant interesting facts” about the genome. In fact, if you teach a university lecture about genetics or molecular biology, BUY THIS BOOK. You will not regret it, and your lectures will be better for it.
  • You have or may ever write a scientific paper with a string of “ATCG” anywhere in the text.
  • You are a huge nerd for factiods, and hey, you read all those journals anyways…

This book is NOT for you if:

  • You find Nature Genetics to be unintelligible.
  • You find Nature Genetics to be uninteresting.
  • You’re James Watson.

I eagerly anticipate the contents of this book to appear on Wikipedia.

Fun Genome Facts!

(see? You can’t resist peppering your work with these snackable factiods. Just think how easy this could make your work when you need some plug-and-play ideas?)

  • The blood type of reference human genome is “O” (pg. 135)
  • A mouse has 19 autosomes, plus the XY sex chromosomes. While similar, its genome is about 10% smaller than a human’s. (pg. 146)
  • The Y chromosome is by far the least sequenced chromosome, with only 44.4% sequenced (as of release 36.2). This is because the Y chromosome contains large blocks of repeated sequences, and the “shotgun” approach to used to sequence the reference human genome does not resolve repeated sequences accurately. (pg. 6)
  • How big is the largest protein? 33,423 amino acids (titin, which is encoded by the TTN gene). The smallest? 25aa (product of gene RPL41). The smallest predicted? 13aa (LOC644929 and LOC727721). (pg. 68)

Myostatin inhibitors may improve recovery of wartime limb injuries [Think Gene]

Posted: 07 Aug 2008 03:22 AM CDT

Kevin: Myostatin inhibitors are going to be extremely useful drugs once they reach the marketplace. Other uses include farming animals with more meat and treating muscular dystrophy, plus a very large potential market of people who want more muscle without having to exercise.

Inhibiting a growth factor that keeps muscles from getting too big may optimize recovery of injured soldiers, researchers say.

They are studying two myostatin inhibitors in mice with limb injuries, first to see which works best and then to identify the best delivery mechanism, says Dr. Mark Hamrick, bone biologist in the Medical College of Georgia Schools of Graduate Studies and Medicine.

“Fifty to 60 percent of the injuries occurring in Iraq are to the limbs, and the average injury requires five surgeries,” Dr. Hamrick says. “Myostatin inhibitors are known to improve muscle regeneration and we have evidence that they also increase bone formation. We believe these inhibitors will result in a stronger, more rapid recovery for these soldiers and other victims of traumatic limb injuries.”

A $1.2 million grant from the Office of Naval Research to Dr. Hamrick is enabling laboratory studies of two experimental myostatin inhibitors: a decoy receptor and a binding protein, both developed by MetaMorphix, Inc. of Beltsville, Md. Both inhibitors have been shown effective in muscle regeneration, but this is the first trial that looks at their impact on bone. (more…)

VCU Massey Cancer researchers find gene therapy that kills pancreatic cancer cells [Think Gene]

Posted: 07 Aug 2008 03:03 AM CDT

Josh: Normally, I would say it’s probably not the best idea to give gene therapy to cancer patients as a treatment. The reason being that current gene therapy delivery systems have the tendency to cause cancer. However, in this case, which such low survival rates, I think any treatment is worth trying.

Researchers at the Virginia Commonwealth University Massey Cancer Center and the VCU Institute of Molecular Medicine have published findings that implicate a new chemoprevention gene therapy (CGT) for preventing and treating pancreatic cancer, one of the most lethal and treatment-resistant forms of cancer.

In the July issue of Molecular Cancer Therapeutics, the researchers showed that combining a dietary agent with a gene-delivered cytokine effectively eliminates human pancreatic cancer cells in mice displaying sensitivity to these highly aggressive and lethal cancer cells.

Cytokines are a category of proteins that are secreted into the circulation and can affect cancer cells at distant sites in the body, including metatases. The cytokine used in this study was melanoma differentiation associated gene-7/interleukin-24, known as mda-7/IL-24. (more…)

Esther Dyson on the Digital Health Revolution [The Personal Genome]

Posted: 06 Aug 2008 09:29 PM CDT

Scribe Media’s Peter Cervieri interviews Esther Dyson, board member of 23andMe and one of the PGP-10.

Esther Dyson Video Scribe Media

In the interview, Esther gives her views on the history of commerce on the internet, problems with health care as we know it in the U.S., and the future of genetics.

No comments: