Friday, October 17, 2008

The DNA Network

The DNA Network

Uploading your data to iFinch [FinchTalk]

Posted: 17 Oct 2008 02:05 PM CDT

iFinch is a scaled down version of our V2 Finch system for genetic analysis.  Unlike our larger, industrial strength systems, iFinch is designed for individual researchers, small labs, or teachers...

Customize Medical Search with ScienceRoll [ScienceRoll]

Posted: 17 Oct 2008 01:44 PM CDT

The recent relative lack of posts is due to my upcoming neurology exam. Only a week left, so fingers crossed…

But here is a new post mentioning Scienceroll Search, our personalized medical search engine.

Advancing medical search for health professionals is a hot topic. We have already reviewed SearchMedica, GoPubMed, Hakia PubMed and Semantic Medline Cognition -now we turn our attention to ScienceRoll Search Engine.

Personalized search home pages such as BuildaSearch, Rollyo and Samfind are not new to the search genre, but well structured medical search engines with credible sources are hard to find. Science Roll is a medical blog run by Bertalan Meskó who, with the help of has created a well structured medical search database.



Direct-to-consumer genetic testing in trouble [ScienceRoll]

Posted: 17 Oct 2008 01:26 PM CDT

Have you seen the new FDA warning letter?

Last week, the FDA made a positive move. A warning letter sent to the Laboratory Corporation of America, the nation’s second-largest clinical laboratory company, states that the company’s OvaSure test is illegally marketed and poses a potential public-health risk. Introduced in June, the test measures six proteins in blood to assess whether or not a women has ovarian cancer. Because the test was not designed, developed, and validated by the company, and since it is intended for use as a diagnostic tool, the FDA states that the product requires proof of efficacy.

Although critics worry that overregulation might impede innovation, most agree that genetic testing is in its infancy and needs further validation in reproducible large-scale clinical studies. The long-term hope is that genetic testing will change medicine from treatment to prediction and prevention. Now is the time for a broad debate to decide the appropriate level of regulation for direct-to-consumer genetic tests, so that the results of such tests can truly inform care.


Further reading:


Punished with grandchildren [Mary Meets Dolly]

Posted: 17 Oct 2008 12:29 PM CDT

When Barack Obama said he didn't want his daughters to be "punished" with an unwanted baby, he lost my vote.  I had a crisis pregnancy in college and a baby is never a "punishment."  Ever.  This ad takes it even further.  Thanks Pro-life Blogs.

Visit the Galápagos for free! (as an avatar) [Discovering Biology in a Digital World]

Posted: 17 Oct 2008 11:18 AM CDT

The Galápagos islands rank high on my list of places that I really, really, really want to visit. But for many reasons, it's always looked like a trip to the Galápagos would be at least a decade or two away.

Now, I'll be able to go in January and so will all of you.

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

Blocked Access Bummer #1 [The Tree of Life]

Posted: 17 Oct 2008 09:37 AM CDT

I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work).  Today's bummer is I wanted to read an article by Joel Sachs on "Resolving the first steps to multicellularity" but I could not get it because I do not have access to Trends in Ecology and Evolution at home.  Bummer.  Looks like it could be good. 

The cloning conundrum [Mary Meets Dolly]

Posted: 17 Oct 2008 08:07 AM CDT

Science Books [Sciencebase Science Blog]

Posted: 17 Oct 2008 07:00 AM CDT

technology-writingOnce again, I have a stack of great books sitting on the Sciencebase desk ready for review.

First up is Go Green - How to Build an Earth-Friendly Community, which you will be pleased to learn has been published on apparently sustainable paper. The author, Nancy Taylor, is an environmental columnist and teaches a course on the art of green living. Her book does what it says on the tin (also recyclable, other metals are available), offering advice for those who want to change the way they live to be more in line with a sustainable future. Homeowners, students, professionals could do well to take a look and learn how to live greener lives. Politicians should also take a look, as at the bottom line, Taylor could show them how to save money.

And, speaking of green, fuel cells are apparently the future. Gavin Harper, in Fuel Cell Projects for the Evil Genius explains how they work and how you could make and test a simple fuel cell.

Next up is Ad Lagendijk’s Survival Guide for Scientists. In a scientific world, steadily growing virtual, it’s reassuring to know that some of the old principles of good writing, preparing a research paper, putting up a poster presentation, corresponding with fellow scientists, and giving a talk, are still valid. It’s not all flickering comments on Twitter and Feedfriend after all. The Guide is aimed primarily at undergraduates, grad students, and postdocs in the natural sciences and offers a practical howto on the foundations of writing, presenting and researching science.

A Short Guide to the Human Genome from Stewart Scherer attempts to answer some of the basic questions about genetics. How many genes are there in the human genome? Which genes are commonly associated with disease? What are the biggest genes? How close is the human genome to the mouse, yeast, bacteria?

Stem Cells, Human Embryos and Ethics edited by Lars Ostnor attempts to define whether it is acceptable from an ethical, as opposed to scientific standpoint, to use stem cells harvested from human embryos for biomedical research or as treatments for sick patients. This advanced book provides a brief introduction to the emerging technologies and a basis for wider debate.

From inner space to nearby outer space, Ralph Lorenz and Jacqueline Mitton take us on a tour of Saturn’s mysterious moon in Titan Unveiled. This is the first authoritative book to look at the data from the Cassini-Huygens probe sent to observe one of the largest moon’s in the solar system, Titan.

Staying with astronomy, but taking a much broader cosmological view, Leonard Susskind tells us of his battle with Stephen Hawking to make the world safe for quantum mechanics in The Black Hole War. With nothing less than an understanding of the entire universe at stake it was essential that the argument over the true nature of black holes between Susskind, Hawking, and Gerard ‘t Hooft be won, one way or the other, so that we can know what happens ultimately to someone sucked into a black hole.

Finally, just arrived is this year’s Best of Technology Writing, edited by Clive Thompson. If this is anything like the previous two editions then it is a feast of great technology writing from my peers across the pond. It carries a fascinating mix of topics from a molecular recipe for the perfect gin & tonic to an ancient Greek artifact that may have been the world’s first laptop computer.

Science Books

Well, at least I got a lot of traffic out of the deal… [Mailund on the Internet]

Posted: 17 Oct 2008 03:44 AM CDT

That’s the most hits I’ve ever had in a day, and I’ve already hit more than average for a day only this morning…

Update on my swapping woes [Mailund on the Internet]

Posted: 17 Oct 2008 03:35 AM CDT

I feel a bit embarrased about the ranting and complaining about Linux yesterday, ’cause as it turned out and as suggested by most of the commenters, on Linux you actually have the tools to fix the system when it is broken.

And broken it was, but only on my box.

The comment that sent me down the path to solving the problem was this one:

Marc Paradise Says:

You can reduce linux's annoying tendency to swap out too fast:

Here are some instructions on how to do this for ubuntu:

See, at the time I thought my problem was that the system was swapping way too much, to the point where I couldn’t get in contact with it.  That is how it behaved.  It would run out of RAM, the disk would be spinning, it would slow down to the point where I couldn’t interact with the machine.

So reducing swapping might crash some programs if they run out of memory, but at least I would be able to interact with the system.

Sounded like just the thing to go for.

Well, when I followed the instructions I came to this command, with this troubling error:

$ sudo swapoff -a swapoff: cannot canonicalize /dev/disk/by-uuid/d00bfdb4-c541-4d56-8448-b0a13ce352a8: No such file or directory

Ups, something is wrong here.  Could it be that the system doesn’t know where the swap partition is?  I checked the system monitor and to my horror found that it uses 0 bytes of swap, even when I am trying to fill up the RAM with all the applications I can fire up.

Yep, something is wrong here.

I googled for “swapoff: cannot canonicalize” — I find that googling the error message usually leads me to the answer faster than actually thinking about it — and then I hit this thread:

I followed the advice there and update /etc/fstab and viola, my swapping is back up (well, after running swapon -a).

If I stress the system now, of course some tools slow down as they are swapped out, but the behaviour is no where near what it was earlier.

Why the symptoms earlier looked like swapping rather than crashing applications I don’t know, but I don’t really care either.  I’m just happy to have a stable system back.

Sorry for ranting, Linux, in the end you came through for me :)

Thinking big, thinking long [business|bytes|genes|molecules]

Posted: 16 Oct 2008 11:37 PM CDT

The real big opportunities are changing the infrastructure of society

Vinod Khosla

Venture Hacks highlights an interview with Vinod Khosla, where he talks about big opportunities, multi-billion dollar markets. The kind of change that literally impacts how we live.

Wait, there’s more

We are an investor that tries to build companies. We make money by building entities over the long term. We're not in the business of transacting or doing deals. We don't even allow that word here. It's not buying and selling, that's a transaction. You don't invest in something and say I can sell it tomorrow or next year. We take a five year, ten year view and say we can build a company that can significantly change the landscape. Now if you happen to do that, you build companies of lasting value, make a large impact and if you do, you're going to have a valuable company that you can make money on. So it's a long term versus short term perspective.

You know what. Those who fund science could learn a thing or two from Mr. Khosla

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Larry Moran on Phylogenomics, my new paper, and species [The Tree of Life]

Posted: 16 Oct 2008 09:50 PM CDT

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

Using Evolution to Predict Disease Mutations [adaptivecomplexity's column]

Posted: 16 Oct 2008 09:36 PM CDT

As many readers here know, evolution isn't just some esoteric topic disconnected from the rest of biology. It's a core theory that is underlies all of biology. Today our department heard a talk from Dr. Sudhir Kumar, a U of Arizona scientist who is using evolutionary theory to improve our ability to predict which mutations are likely to cause disease (PDF).


Life is for the living? [Mary Meets Dolly]

Posted: 16 Oct 2008 06:23 PM CDT

This movie is misnamed.  It is called "Life is for the Living".  It should be called, "Life is for Those Deemed Worthy to Live."  Embryos are living too, just not worthy of finishing out their lives according to those who made this film. Once again it seems embryos have a duty to die.

UN reconsiders human cloning [Mary Meets Dolly]

Posted: 16 Oct 2008 11:03 AM CDT

In 2005, the United Nations said "NO" to human cloning for any reason.  They rightly saw that human cloning, even for therapeutic reasons was "incompatible with human dignity and protection of life."  According to the UN website they are reconsidering their stance:

The permissibility of therapeutic cloning will be the focus of a United Nations ethics panel later this month when it considers whether a non-binding General Assembly declaration calling on Member States to ban all forms of human cloning should be reassessed in light of scientific, ethical, social, political and legal advances....

"Recent technological developments and new prospects for the use of stem cells in the therapy of human diseases have once again raised the issue of adequacy of international regulations governing this research," an IBC working group set up at the request of UNESCO Director-General Koïchiro Matsuura said in a report in September.

I am sure they got it right the first time.  But if the UN wants to revisit the issue, fine.  But the real issue is why they want to revisit human cloning.  Let me give it to you again:

"Recent technological developments and new prospects for the use of stem cells in the therapy of human diseases have once again raised the issue of adequacy of international regulations governing this research."

What developments?  In the last three years what significant "advances" have been made in the field of therapeutic cloning treating patients?  So someone in Southern California finally cloned a human embryo and extracted stem cells.  No patient is any closer to getting treated with stem cells made from human cloning.  Patients are much closer to getting treated with their own stem cells with no cloned embryos and no human eggs needed.

Considering the Pandora's Box that therapeutic cloning may open, including the exploitation of poor women for their eggs, I am surprised the UN would reconsider their stance with no evidence that human cloning will ever surpass adult stem cells in treating patients.

This may be once again prove that if the politicians, special interests and the media repeat that therapeutic cloning is the "most promising stem cell research" enough, then it suddenly becomes a reality.  I sure hope the UN does not fall for it.

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