The DNA Network

Posted: 14 Jul 2008 05:35 PM CDT

Maq (Mapping and Assembly with Quality) is an algorithm, developed at the Sanger center, for assembling Next Gen reads onto a reference sequence. Since Maq is widely used for working with Next...

Personalized Genetics: Selfome [ScienceRoll]

Posted: 14 Jul 2008 04:52 PM CDT

It’s not about genomes and proteomes any more. Personalized genetics leads to a strange field called selfome where an individual is in the focus. Just take a look at the Quantified Self project, the first personal genome user group.

There are some quite interesting opinions in the blogosphere I would like to share with you. Allie Janson thinks there should be a distinction between recreational and medical genetics.

There is no harm in learning that you have a genotype that makes your pee smell after eating asparagus (a much cheaper option: eat some asparagus, wait a couple hours, and pee). And you certainly don't need a physician to interpret that information for you. On the other hand, learning that you are predisposed to certain diseases requires a little more foresight and follow-through.

Tim O’Reilly, the father of web 2.0, also has something to say about personal genomics companies selling tests directly to consumers:

I have to say I find myself doubtful about the urgency of this regulatory move. It smacks more of the hand of the AMA, an entrenched industry trying to make sure that the new tools of genetic testing remain under the thumb of doctors, than of true consumer protection.

You have only to walk into Whole Foods to encounter a multi-billion dollar industry of supplements making all kinds of dubious health claims, which is completely unregulated. Why pick on personalized medicine, which has way more substance, and at least so far, way more care in the types of claims it makes?

Jennifer Mccabe Gorman and Matthew Holt attended the US DHHS Meeting on Consumer-Direct Genome Sequencing. Conclusion: We need a high-tech patient advocate service. Yes, and we need doctors who are trained to understand the main problems of personalized genetics. We need a whole generation of doctors who can tell the patients properly about their risks for diseases.

To show you a peer-reviewed article as well, here is a recent publication of NEJM, Polygenes, Risk Prediction, and Targeted Prevention of Breast Cancer.

And do you know how much data your genome is?

Why Health or Medicine 2.0? [ScienceRoll]

Posted: 14 Jul 2008 03:32 PM CDT

Some interesting statistics have recently been published. According to Pharma 2.0:

99% of physicians are online for personal or professional purposes
85% of offices have broadband
83% consider the Internet essential to their practice

At The Deloitte Center, you will find even more details about the web usage of health consumers. Yes, there will be much more patients who seek health-related information on the web and who want to communicate with their doctors via e-mail or Skype.

And if a doctor thinks like that:

being absent from the Web is the surest way of avoiding disclosure of personal information on the Web.

How will he answer the questions about reliable medical online resources?

No, the basics of practicing medicine will never change dramatically due to new technologies or the web. But it will change the way it is practiced. Not because it is so important or so overhyped, but because patients will need this kind of knowledge and expertise. This will happen either you like it or not. And physicians of the 21st century must be ready and qualified to meet these expectations.

And yes, we have innovators who can show us new ways, such as Jay Parkinson.

We have tools to work with:

And we have concepts.

I believe, with opportunities of web 2.0, we can totally change medical education; we can build careers and we can develop a more efficient communication.

Health 2.0 will reform healthcare itself; medicine 2.0 will do the same with education. Or is already doing…

Do you still believe it is just a bubble?

Experimental Physics a la Canadien (or Canuck Anthropology?) [Bayblab]

Posted: 14 Jul 2008 02:52 PM CDT

OK, so we don't always get the calculations right. But you can't say we don't give it our all. This video of Kenny Powers' attempted cross-border "Superjump" over the 1 mile wide St. Laurent river is classic Canadiana all the way. As are the sweet custom mods on his pimped-out, jet-powered, Lincoln Continental. You can bet this idea was conceived after way too many cases of Labatt's 50. And it's certainly a cultural relic you won't find the likes of in post-NAFTA Canadia!

Popular Science has a breakdown of the physics:

"If, as the narrator informs us, the car achieves a takeoff speed of 280 mph, then using the equations of projectile motion, we can easily calculate that without air resistance (estimating a launch angle of about 30 degrees) the maximum distance the car could achieve is around 1500 meters, or just short of a mile. (I'll leave it to those of you with a little physics background to confirm this is true.) However, at speeds of this magnitude, air resistance will have a major effect on the flight of the car. The force of air resistance is proportional to the square of the velocity, so if you double the speed you quadruple the air resistance. Incorporating the effect of air drag into the calculations we find that Kenny won't even make it a quarter of a mile before falling ignominiously into the river."

Ooo. A little harsh. Come on guys, hind-sight's 20-20 right? Anyway, check out the video and judge Kenny's physics for yourself:

Further reading: For those unfamiliar with the psychology of the male Canadien and/or interested in further exploring Canadian anthropology through the miracle of YouTube Video, see also The Best Of Ron Hextall, Canadiens vs Nordiques 'Good Friday brawl' 1984, The Never-Ending Bench Clearing Brawl of Canada vs Russia 1987 at the World Juniors, the seminal National Film Board of Canada mockumentary "FUBAR", and Canadian television favorite "The Trailer Park Boys".

Things to update on Genomicron -- what dontcha like? [T Ryan Gregory's column]

Posted: 14 Jul 2008 02:50 PM CDT

Scientific Blogging is a work in progress and lots of neat features (some of which are visible, some are not) are being incorporated continually. As things move forward, it is helpful to bug the powers that be to fix things that we don't like and to include things that we do. So, in this comment thread, please NICELY point out things that you would like to see updated or changed.

Posted: 14 Jul 2008 08:37 AM CDT

After Paris we flew to Munich on Airberlin (20Euros per ticket, 50Euros after taxes and airport fees.) There we met up with some former colleagues (Julia and Michael) and a current member of the Rapoport Lab (Briana) who will be leaving us soon to start her own lab in the MCB department at Harvard's Main Campus. Also in attendance was Briana's husband and my wife who snapped this picture of us in the English Garden.

Munich is a beautiful city. For anyone who enjoys the music, Munich might as well be the world capitol of classical music. The number of great performers who currently live in-and-around the city is astonishing.

Another stop worth mentioning is Ludwig Maximilian University of Munich. Here is where many of the founders of Quantum Theory studied (examples include Pauli and Heisenberg). Thomas Mann also lectured here.

The university is also known for the White Rose, a non-violent anti-Nazi group. They waged a campaign against Hitler's policies and were eventually caught. Beneath the fold I'll describe a famous and tragic event.

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

Young Scientists [Sciencebase Science Blog]

Posted: 14 Jul 2008 07:00 AM CDT

Young scientist Children are so bright these days. Allegedly. It seems that not a week goes by without some juvenile prodigy whizzkid, or child genius solving an engineering problem, revising some scientific data or inventing some world-saving gadget.

You probably saw the recent news about a 13-year old boy from Germany, taking part in a science festival, who corrected NASA calculations on the likely impact of asteroid Apophis, shortening the odds of a killer collision with Earth. Agence France Press reported it as follows:

NASA had previously estimated the chances at only 1 in 45,000 but told its sister organisation, the European Space Agency (ESA), that the young whizzkid had got it right.

Prior to that there was the case of the 17-year old Ottawa high school student who, while contributing to a science fair, apparently invented a way to identify and cure influenza. A team of ten students, won second prize for identifying genes that help plants thrive in salty soil, while third prize went to a 15-year-old in the same competition for her discovery of a human gene variation that may help in dealing with bipolar disorder. (More on science comp here).

Then there was the Manitoba student who received the first-ever Triple Crown for high school science with a project finding alternatives to chemotherapy in the fight against cancer, winning first-place finishes in biotech-industry sponsored national challenge. There’s the teen inventor who came up with a new way to make biodegradable plastic bags.

And, of course, who could forget the 11-year old who invented a diabetic dress for her sister. Then there’s the six-year old who discovered rare pterosaur bones on the Isle of Wight. One student even won a major science fair prize for a project entitled: “Identification, Characterization, and DNA Sequencing of the Homo Sapiens and Mus Musculus COL20A1 Gene (Type XX Collagen) with Bioinformatics and Polymerase Chain Reaction (PCR)”, which makes squeezing an egg into a bottle seem a little trivial to say the least.

Schoolboy boffin beating cancer, cracking computer codes, finding life on Mars? You got it!

The list goes on. There are so many teenage geniuses out there.

Now, is it just me being a cynical old hack with an insider’s view of the media and public relations industries, or does this strike anyone else as odd? All these instances of child prodigies in science, have seemingly achieved what international research teams with industry and academic funding cannot seem to, all for the sake of a science fair or with some direct link to another organisation seeking publicity. Indeed, many of
these
junior scientific
discoveries get reported
widely across
all mediamany of these junior scientific discoveries get reported widely across all media and internationally too. And, therein lies the rub.

While I don’t wish to disrepect the efforts and achievements of any of the students taking part in science fairs and working hard to put together a great project, I wonder just how many of these so-called breakthroughs ever come to anything more than a framed certificate and a nice fat payout from the industry sponsor. Of course, one might level the same criticism at countless science projects being undertaken by adults on a professional basis the world over.

Meanwhile, Jessica Shepherd writing in The Guardian reports that science exams really are more difficult than the arts and humanities exams, and researchers at the UK’s Durham University have the data to prove it. Apparently, there were “substantial differences in the average grades achieved by the same or comparable candidates.”

But, according to the Royal Society of Chemistry, “There is now clear evidence of an alarming gap between the high-quality teaching and curriculum material presently available for science lessons in schools in the UK , and the corresponding simplistic questions being set in national examinations for 14 year-olds.” RSC spokesman Brian Emsley gave me several examples of just how tough the science questions can be at this age, for example:

Why is copper used for wires in a circuit?
(a) Copper does not stick to a magnet
(b) Copper is a brown metal
(c) Copper is a good conductor of electricity
(d) Copper if a good conductor of heat
Some stars are bigger than the Sun but they look smaller. Why do they
look smaller than the Sun?
(a) They are brighter than the sun
(b) They are further away than the Sun
(c) They are the same colour as the sun
(d) They are nearer the Sun
What is hot melted rock called when it is UNDERGROUND?
(a) Sand
(b) Magma
(c) Lava
(d) Mud
In very cold weather, why is a mixture of salt and sand is spread on roads (choose two options from a-c and i-iii
(a) Salt makes the roads white
(b) Salt makes water freeze
(c) Salt makes ice melt
(i) Sand dissolves in water
(ii) Sand increases friction between car tyres and the road
(ii) Sand makes water freeze

One final question Emsley showed me, reminded me of a silly anecdote about vermin and compost heaps and asked: What powers a solar-powered mole-scarer?

“Vast sums of money are being spent by government, industry and other educational bodies to enhance the excitement and delivery of STEM subjects, covering science, technology, engineering and mathematics,” according to the RSC, “but this is being negated by examiners who are reinforcing low expectations, and setting the standards that the weaker schools teach to.”

So, one the one hand, we have a global public relations system marketing high school students as geniuses because they use some big words in a science fair project and yet, there is a major disparity between what these children are learning at school and how they are being tested. So, who are the geniuses here? Answer (a), (b), or (c).

A post from David Bradley Science Writer

Young Scientists

The Chinese are Coming… to Grad School [Bitesize Bio]

Posted: 14 Jul 2008 05:39 AM CDT

Did you know that it is more likely that the next graduate student you meet in the US is from one of two Chinese alma mater’s than from any other U.S. university, including UC Berkeley, Cornell University, and the University of Michigan, Ann Arbor? That’s a striking figure, the topic of a tiny comment in last week’s Science: Top Ph.D. Feeder Schools Are Now Chinese.

While I may not have known that statistic however, it’s not surprising, as any past or current graduate student will tell you. There are a lot of non-American’s in American grad schools. Props to those non-Americans - they worked hard and have earned it.

At the same time, as I said, that statistic is striking. It really makes me wonder why, exactly, is a Ph.D. looked upon so much more highly in other countries than the U.S., yet the U.S. somehow maintains the reputation of its universities. How can American universities maintain themselves at all as major research institutions in a country indifferent or even hostile to higher learning?

Not that I blame American students for the lesser interest in graduate school - it’s a lot hard work without much likelihood of appreciable pay afterwards. There isn’t much incentive for individuals looking out for No. 1, and in search of the American Dream. The only Americans going into academic research are those interested in esoteric careers and intellectual fulfillment.

People from the developing world however, view advanced education of the sort obtained with a Ph.D. as more of a means to the American Dream than Americans do, I think.

I also think that the education level of a population is a strong indicator of its long-term posterity. This is why I am concerned, as an American. The level of interest in advanced degrees may very well be a bellwether for decades to come, when the current generation of American undergraduates become its leaders.

Or maybe I’m over-reacting, overvaluing the Ph.D. sheepskin on my wall and the walls of my colleagues. What say you?

When you know the Books are Cooked [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Jul 2008 03:38 AM CDT

I finally had a chance to sit down and review Genetics in Medicine for the month of June. Yes, I am a month behind.....leave me alone. I have been doing some other things for the last few...

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Telehealth at Home with Genesis DM [ScienceRoll]

Posted: 14 Jul 2008 02:46 AM CDT

Genesis™ DM telehealth device from Honeywell HomMed (Brookfield, WI), one of the winners of 2008 Medical Design Excellence Awards, aims to help people living with long term health conditions, such as COPD or chronic heart failure, to maintain and monitor their health. In addition, the device was designed to help patients keep track of medical appointments and other important events.

Web-based and content-rich, the new Genesis™ DM is the latest generation of the industry's best-selling monitor. With over 40,000 monitors in service worldwide, we provide the most complete remote biometric and symptom evaluation available.

Genesis DM is seamlessly integrated into the innovative new Honeywell HomMed LifeStream™ telehealth platform, providing web-enabled, on-demand access to disease-specific symptom management (DSSM), customizable by diagnosis and symptoms.

This telehealth device measures heart rate, blood pressure, and weight, and provides customizable subjective disease-related queries for a more complete picture of an individual's health. Automated set up and automatic patient engagement with a friendly voice and easy-to-use interface guide the patient at every step.

Product page: Honeywell HomMed Genesis™ DM remote patient care monitor…

This is a cross-post with Medgadget….

Doggie ancestry [Yann Klimentidis' Weblog]

Posted: 13 Jul 2008 11:06 PM CDT

I heard about this, but never saw the details:

From the website of Doggie DNAPrint:

For example, in 2004 Parker et al. sequenced 75 SNP and 96 microsatellite loci in 85 dog breeds and showed that modern dog breeds are distinct genetic units and that breed can be accurately determined from dog DNA. Looking back relatively far in the dog family tree, Parker et al. noted that there appear to be 4 main dog breed types:
The wolf-like (yellow in the K=4 part of Figure 1)
The Herders (green in the K=4 part of Figure 1)
The Hunters (red in the K=4 part of Figure 1), and
The Mastiff (blue in the K=4 part of Figure 1)

Figure 1 (above) shows some of their data (Figure 3 of Parker et al., 2004), where dog breeds are clustered based on their affinity with the founders or parental dog populations for each of these 3 ancestral groups. Dog breeds such as the Akita, Chow Chow and Siberian Husky fall into the Wolf-Like group, Collies, Greyhounds, Borzoi etc. fall into the Herder group, Beagles, Pointers and Terriers (etc.) fall into the Hunter group and Bulldogs, Mastiffs, Boxers (etc.) fall into the Mastiff group.You will note that, due to the history of their origins, each breed is characterized by a unique ratio of admixture among these families.

Seed Magazine Cribsheet #16: Synthetic Biology []

Posted: 13 Jul 2008 10:46 PM CDT

Probably the single most useful page we’ve ever seen for a quick understanding of the potentialities of Biotechnology. We love it. Seed Magazine is an awesome publication. Quote: “The Key Question of Synthetic Biology: Can we learn to program DNA and living organisms as well as or better than we currently program computers?”

Stanford - Promoting open access while selling access to "closed" journals [The Tree of Life]

Posted: 13 Jul 2008 10:34 PM CDT

Some people may have seen the press Stanford got a few weeks ago regarding the Open Access initiative of their School of Education. For some more information on this see

Stanford's Education School Requires Open Access

Stanford University School of Education's Open Access Mandate—Harvard Medical School Next?

Science Commons » Blog Archive » A new open access mandate at Stanford

Certainly sounds like a good move on their part. And then I got an interesting thing in the mail from the Stanford Alumni Association (I earned my PhD from Stanford) trying to get me to join the association (see letter below). What was the selling point? If I joined I would get access to newspapers, periodicals and even scientific journals, through their library. So Stanford is all for OA in some places. But while they have access to closed journals, they will use that as a recruitment tool to join the Alumni Association. Seems to me like a better way to push for Open Access would be for all of Stanford to take the School of Education's position and for the university to immediately cancel all subscriptions to completely closed access journals.

“Love more” [genomeboy.com]

Posted: 13 Jul 2008 09:35 PM CDT

“Our genes are not our fate,” he says. I couldn’t agree more.

But do I have to eat kale?

Saving Money and Gas and the Planet by Not Travelling [The Tree of Life]

Posted: 13 Jul 2008 07:00 PM CDT

A UC Davis professor has been getting some local press for NOT going to a meeting . Well, OK that is not exactly the point. He (Timothy Morton) gave his talk remotely by video taping it and then having the people in Scotland watch the DVD and then talk to him. The reason for the news coverage is that by doing this this saves both money and carbon output. Given that I have been canceling trips left and right recently for some medical reasons, I like this idea.

I even gave a talk over iChat to a metagenomics gathering in Berlin that was organized by Dan Falush. I was supposed to go to to this workshop last week as a run up for the International Congress of Genetics (which I have also bailed on but they did not offer to let me speak remotely).

I might add that doing a talk by iChat worked out OK ... we probably needed speakers for the computer on the other end and microphones so I could hear the discussion. And not sure my talk was any good. But technically, iChat worked out fine.

So what I am now going to say is that I am canceling the trips for environmental reasons ...

agribusiness

Monday, July 14, 2008

The DNA Network

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