The DNA Network

Dinosaur: it’s what’s for dinner [genomeboy.com]

Posted: 23 Sep 2008 08:02 PM CDT

Munger, who writes the Progressive Alaska blog, told me Palin is not just a creationist, but a “young Earth” creationist who believes that man and dinosaurs once shared the planet, and that the world will end in her lifetime.

Palin-tology, you might call it.

Munger claims she tried to stock the local school board with creationists several years ago, which caused him to quiz her on her beliefs.

“She doesn’t believe in science, and her father was a science teacher,” Munger said. “She told me she felt she would see Jesus in her lifetime.”

May He deliver us all.

Urine match heads [Bayblab]

Posted: 23 Sep 2008 06:28 PM CDT

We discussed at lunch if you could survive, drinking your own urine. It was lunch so drinking other people's urine wasn't discussed as it seemed unappetizing.
In any case I can't really figure out how long you could repeatedly drink your own urine to stave off dehydration. However you could distill your urine. Of course, I wouldn't bother with digging a pit ect. like the link suggests when you could just do it on your stove.
In any case this reminded me that urine contains the element phosphorus, which has an interesting history. Check out a great synopsis on the history the discovery of phosphorus. Also there is an entire book out about phosphorus. Here is a review of The Shocking History of Phosphorus by John Emsley by the Naked Scientists.

What does privacy mean to you? Please complete this survey [The Tree of Life]

Posted: 23 Sep 2008 06:21 PM CDT

ThePrivacyPlace.Org Privacy Survey is Underway!

Researchers at ThePrivacyPlace.Org are conducting an online survey about privacy policies and user values. The survey is supported by an NSF ITR grant (National Science Foundation Information Technology Research) and was first offered in 2002. We are offering the survey again in 2008 to reveal how user values have changed over the intervening years. The survey results will help organizations ensure their website privacy practices are aligned with current consumer values.

The URL is: http://theprivacyplace.org/currentsurvey

We need to attract several thousand respondents, and would be most appreciative if you would consider helping us get the word out about the survey, which takes about 5 to 10 minutes to complete. The results will be made available via our project website (http://www.theprivacyplace.org/).

Prizes include
$100 Amazon.com gift certificates sponsored by Intel Co.
and
IBM gifts

On behalf of the research staff at ThePrivacyPlace.Org, thank you!

Open Access Under Attack [The Daily Transcript]

Posted: 23 Sep 2008 05:09 PM CDT

I'm back from Toronto. And now I'm just trying to keep up with all the crap I haven't dealt with in the last few days. Tomorrow we have an RNA Data club meeting (info here) and then I got this interesting email about some terrible legislation that might actually come to a vote tomorrow:

On September 11, 2008, the Chairman of the House Judiciary Committee (Rep. John Conyers, D-MI) introduced a bill that would effectively reverse the NIH Public Access Policy, as well as make it impossible for other federal agencies to put similar policies into place.
The legislation is HR6845: "Fair Copyright in Research Works Act". You can read more about the intentions of this legislation here.

Please contact your Representative and Senators no later than September 24, 2008 to express your support for public access to taxpayer-funded research and ask that he or she OPPOSE HR6845.

Especially important are members of the House Judiciary Committee and Senate Judiciary Committee.

For more, read what Bora had to say.

Read the comments on this post...

Gene-geography video [Mailund on the Internet]

Posted: 23 Sep 2008 04:32 PM CDT

A youtube video about this paper:

You might also want to check out this paper.

Identifying irresponsible dog owners by DNA testing dog droppings [Discovering Biology in a Digital World]

Posted: 23 Sep 2008 04:10 PM CDT

Every fall, we had to confront it. People would let their dogs run around on the field in the morning and by the time soccer practice started, the field would be full of deadly doo.

There's nothing that hurts soccer practice more than a soccer ball or shoes that went through a pile of dog poo.

That's why I'm so exciting to see this new application for DNA testing. That's right. Kids will be able to play soccer without worry and dog owners will be held responsible for cleaning up after their pets.

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

Google Founder, Parkinson’s Disease and Good Marketing? [ScienceRoll]

Posted: 23 Sep 2008 03:39 PM CDT

Sergey Brin, the co-founder of Google, wrote about his genetic predisposition for Parkinson’s Disease on his personal blog. Of course, he shared information from his 23andMe account, what else. His wife, Anne Wojcicki is the co-founder of 23andMe, a personalized genetic company.

Because there are only a small number of genes which are known to have a very substantial effect on health (e.g. 10 times the average risk), I felt the possibility of discovering something very important to my health was just a hypothetical exercise. So, when my wife asked me to look up G2019S in my raw data (23andMe scientists had had the forethought to include it on their chip), I viewed it mostly as entertainment.

But, of course, I learned something very important to me — I carry the G2019S mutation and when my mother checked her account, she saw she carries it too.

Well, he didn’t analyze properly his genetic results as Steve Murphy, our gene sherpa and the clinical genetics fellow at Yale, pointed out some days ago. First, the gene Brin mentioned (LRRK2) is not the most important gene in the story of Parkinson’s and second, his risk cannot be 80%. According to Steve:

Parkinson Disease affects approximately 1% of the population by age 65% and 4 to 5% by age 85 years. Therefore the lifetime risk is 2-5%. So a 1.2 to 2.1 Odds ratio would be 4% to 10% roughly. Not 80%!

LRRK2 is not one those genes that increases your risk by tenfold…

LRRK2 mutation accounts for 5 to 6% of familial PD and 1-2% of sporadic PD. Not exactly what I would call useful for a screening test. Mind you this is given for North Americans and Europeans.

Kevin Fischer had some comments about it as well.

Why was it a fantastic marketing trick?

Now everybody is talking about it and the misinterpretation of his genetic data.
23andMe is getting a huge media attention.

Which means Brin is a good husband and knows how to promote her wife’s service efficiently.

Any Happy Navigenics Customers Yet? [Week printf("%d",i++)!] [Think Gene]

Posted: 23 Sep 2008 03:33 PM CDT

We here at Think Gene are still waiting for a report of least one person who will vouch as a satisfied Navigenics customer. To qualify:

You paid full price for the Navigenics service.
You are willing to vouch as a “satisfied” customer of Navigenics over the Internet using your full name and email address. (in lieu of a full name, we will accept a web domain)
You are not an employee of Navigenics nor have any affiliation with Navigenics or its employees.
You are not a member of the press. (blogs are OK)

There is no prize for identifying oneself as this happy Navigenics customer because we feel that the joy of being a happy customer of Navigenics would be its own reward.

A running tally of identified satisfied Navigenics customers will be kept below for your convenience:

Identified Satisfied Navigenics Customers: 0

Leave reports in the comments.

ScienCentral Channel: Genetic Genealogy [ScienceRoll]

Posted: 23 Sep 2008 03:19 PM CDT

I’ve been a subscriber of the ScienCentral channel in Youtube for a while and there are really great videos about important topics such as genealogy (Blaine will certainly like it).

Genes don’t just tell whom you’re related to or why you look a certain way; now, they can also tell you where you came from. Researchers have created a genetic map of Europe, and they hope to expand it globally, as this ScienCentral News video explains.

Potential new treatment for cystic fibrosis? [ScienceRoll]

Posted: 23 Sep 2008 03:12 PM CDT

I just found an interesting article at the PHG Foundation about a new potential treatment for cystic fibrosis, a genetic condition affecting the exocrine (mucus) glands of the lungs, liver, pancreas, and intestines. It is caused by a mutation in the CFTR gene. The product of that gene is a a chloride ion channel that plays role in creating digestive juices and mucus. If there is no normal copy of the gene, the person will be affected by CF.

The new drug VX-770 was developed by the Cystic Fibrosis Foundation in collaboration with Vertex Pharmaceuticals; it targets the defective CFTR protein to improve chloride transport. The Cystic Fibrosis Trust supports a group at the University of Bristol in investigating how new drugs restore function to defective CFTR proteins; group leader Dr David Sheppard reported results at the BA Festival of Science indicating that the new drug could cause a near 50% reduction in salt levels in sweat and a 10% improvement in lung function in cystic fibrosis patients. He said: "The early results with VX-770 suggest that drug therapies which target defects at the root of the disease have the potential to improve greatly the quality of life of CF patients"

Here is a video describing the symptoms:

Sub-Zero Bioprospecting: Tip Of The Iceberg []

Posted: 23 Sep 2008 02:45 PM CDT

It’s not just the tropics generating all the genetic diversity and commercially promising compounds. Nature responds to environmental extremes in all sorts of biotechnologically-leverageable (ouch. syllabic train-wreck.) ways. The Canadian Press reports on how DNA from arctic organisms can be applied: new antifreeze compounds in food products, new medical therapies for stroke victims, and more. International issues loom: “Canada may not be taking advantage of its extensive Arctic ecosystem. Of 31 known patents concerning products derived from Arctic organisms, two-thirds are held by U.S. companies. None are Canadian.”

Examining the Medical Blogosphere: An Online Survey of Medical Bloggers [ScienceRoll]

Posted: 23 Sep 2008 01:34 PM CDT

Some months ago, I was asked to take a survey focusing on the habits of medical bloggers. The research was conducted by Ivor Kovic et al. and they published the results in the Journal of Medical Internet Research (JMIR).

We approached 197 medical bloggers of English-language medical blogs which provided direct contact information, with posts published within the past month. The survey included 37 items designed to evaluate data about Internet and blogging habits, blog characteristics, blogging motivations, and, finally, the demographic data of bloggers.

Medical bloggers are highly educated and devoted blog writers, faithful to their sources and readers. Sharing practical knowledge and skills, as well as influencing the way other people think, were major motivations for blogging among our medical bloggers. Medical blogs are frequently picked up by mainstream media; thus, blogs are an important vehicle to influence medical and health policy.

Advancing science through blogging [Mailund on the Internet]

Posted: 23 Sep 2008 11:40 AM CDT

There’s a paper in the latest issue of PLoS Biology about blogging: Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy

The topic is how blogs can be used as an outreach from scientists to the public. That sounds fair enough. There’s also a bit about how this can be formalised.

I’m not sure I would appreciate that much. I like my blogs informal. For formal stuff, I’ll stick to journals.

There’s a detailed comment on the paper at DrugMonkey. By and large I agree with the comments there…

Dick Eastman Interviews The Genetic Genealogist at FGS 2008 [The Genetic Genealogist]

Posted: 23 Sep 2008 11:36 AM CDT

On September 5th at the 2008 Federation of Genealogical Societies Conference in Philadelphia, Pennsylvania, I was interviewed by Dick Eastman. In the interview we discuss my blog, DNA testing in general, and my free ebook, “I Have the Results of My Genetic Genealogy Test, Now What?” (which is available for download in the sidebar of the blog).

If the player doesn’t appear in the post, the interview is available here (http://rootstelevision.com/players/player_conferences.php?bctid=1811559654). It was a pleasure to meet and talk with Dick, and I hope you enjoy the interview.

You Know You Want a Yeast Biochemical Pathways Wall Poster [adaptivecomplexity's column]

Posted: 23 Sep 2008 11:23 AM CDT

Who wouldn't want a map of all the known yeast metabolic pathways on the wall? Download your copy here (PDF). The catch is you have to print it out yourself.

Psyco and JIT compiling

I had hoped that I could gain the speed I needed using Psyco. I’ve been lucky with that in the past, getting about x10 in speed.

It is a JIT (just-in-time) compiler that actually compiles (generate machine code) the code rather than interpret it.

With languages such as C++ you need to compile the code more or less manually before you can run it. That translate the high-level code into machine code that can actually run on the machine.

In Java you also compile the high-level code, but there you compile it into something called byte code that cannot actually run on the machine. Instead the byte code can be interpreted in a Java Virtual Machine (JVM). This is how you get their “compile once, run everywhere”.

This is actually also what Python does, you probably just haven’t noticed, because Python does it automatically. When it loads a script, it first translates it into byte code and then it interprets it. If you load a module, you might have noticed a .pyc file. That is the byte code for that module. But you only see these files for modules, ’cause Python doesn’t write the byte code to file for your scripts.

For modern virtual machines, like JVM, the byte code is not just interpreted. The machine will analyse how the program executes and compile important functions — the hot spots — into machine code for faster execution. This is what is called just in time compilation (sometimes just too late, but that is a bit cruel).

This, by the way, is also the technology running under the hood of Google’s chrome browser. There, the virtual machine runs Javascript, but the idea is essentially the same as for the JVM.

Lars Bak, the lead engineer behind that virtual machine, explains it here:

To stray a bit from the main point I can mention that I had a class some years ago taught by Lars here in Aarhus. Many of the people now working with Lars had the same class, so that was a successful class. He is going to give it again this year, so don’t you just wish you were studying computer science at our university right now? ;-)

Anyway, back to Python. Here you can also get JIT compiling using the module psyco. All you have to is add these two lines to your program:

import psyco

psyco.full()

You can get finer control over the JIT compilation by doing a little more, but this is the simplest way to get it going, and usually it pays off nicely. It is a bit memory hungry, so it isn’t always the thing to do, but more often than not, it is.

You get the most out of it when your code is actually doing something serious. Lots of loops and branches and such. Typical algorithmic code.

If you are mainly calling built in functions, you do not gain as much. Those are already compiled, typically, so they are pretty optimised as it is.

For my scripts, I am mainly scanning through the alignment and updating statistics in a bunch of tables, and I didn’t gain more than maybe a factor of two from psyco. Not really enough for the speed I need.

Profiling Python

Before you go ahead and paint “go faster stripes” on your code, you should always profile it. You will be surprised at where the majority of time is spent.

In Python you have three modules for profiling: profile, cProfile and hotshot. The first two have the same functionality, but cProfile is written in C and is faster.

I typically use cProfile. The hotshot module is not maintained (according to the Python documentation) and the documentation certainly isn’t, so I have never quite figured out how to use it. I don’t have to either, though, ’cause cProfile does all I need it to.

With cProfile you can load the module in and have fine control over what you profile, but I find it the easiest just to profile the entire script. You can do this by loading the module directly when you call your script, like this:

python -m cProfile your-script.py

After your program has finished, cProfile will write a summary of where the time was spent in the run.

If you want to analyse the result in more detail, you can write the profiler’s analysis to a file

python -m cProfile -o profile.report your-script.py

that you can then read into Python using the module pstats

>>> import pstats

>>> p = pstats.Stats('profile.report')

and you can then sort the report using various criteria. For example, to get the top 10 runtime sinners, you can do:

>>> p.sort_stats('time').print_stats(10)

Tue Sep 23 15:09:35 2008    profile.report

         7932274 function calls in 23.290 CPU seconds

   Ordered by: internal time

   List reduced from 119 to 10 due to restriction <10>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)

        1   10.303   10.303   23.276   23.276 extract-statistics.py:2(<module>)

  1314684    7.036    0.000   11.282    0.000 extract-statistics.py:47(is_singleton)

  5258736    4.246    0.000    4.246    0.000 extract-statistics.py:50(<genexpr>)

   377622    1.187    0.000    1.215    0.000 /usr/lib/python2.5/site-packages/bx_python-0.5.0-py2.5-linux-i686.egg/bx/align/core.py:125(column_iter)

   862137    0.391    0.000    0.391    0.000 extract-statistics.py:40(is_informative)

     9991    0.028    0.000    0.028    0.000 {range}

    39960    0.022    0.000    0.022    0.000 /usr/lib/python2.5/site-packages/bx_python-0.5.0-py2.5-linux-i686.egg/bx/align/core.py:193(__init__)

        1    0.014    0.014   23.290   23.290 {execfile}

    10989    0.014    0.000    0.014    0.000 extract-statistics.py:53(windows)

     4995    0.010    0.000    0.013    0.000 extract-statistics.py:28(<genexpr>)

Here the topmost line is the entire script, and that is using all the time. Not really a surprise. The next three or four lines tells me where I should put my optimisation efforts.

(If you are now wondering why I bother optimising something that takes 23 CPU seconds then congratulations for paying attention to the report and being sceptical about when to bother optimising. I am only running my scripts on a very tiny fraction of my data for the profiling — anything else would take much too long — so that is why. For the real data, optimising really is needed).

Small World Competition Open for Voting [Bitesize Bio]

Posted: 23 Sep 2008 05:30 AM CDT

Popular voting is open for the Nikon Small World competition. This thing is great, revealing the beauty of the extremely small in images such as the above one from last year’s competition.

Small World is regarded as the leading forum for showcasing the beauty and complexity of life as seen through the light microscope. For over 30 years, Nikon has rewarded the world’s best photomicrographers who make critically important scientific contributions to life sciences, bio-research and materials science.

It looks as though every imaging technique, from photon- or electron-based to computer generated images, has at least one representative entry. I figure that most people will vote for something related to their field (or major). Or am I wrong - is there a particular imaging technique that people find more aesthetic, regardless of background in science?

Image: Dr. Eric Hwang at The Scripps Research Institute, La Jolla, CA, USA - Retinoic acid-induced P19 neuronal aggregate (40x)

Protein evolution switch-off fluorescent proteins (and on) [Reportergene]

Posted: 23 Sep 2008 02:39 AM CDT

Canonical fluorescent proteins (FPs) emit light once excited by appropriate irradiation. In a peculiar group of them, the reversibly switchable fluorescent proteins (RSFPs), irradiation converts the protein from the fluorescent on-state to the non fluorescent off-state. Then, a subsequent exposure with UV light brings back the protein to the on-state. Intriguingly, switchable fluorescence allow for sub-diffraction resolution microscopy (nanoscopy) as previously explained, so any RSFP is important for new microscopy development. Unfortunately, known RSFPs share more or less the same switching features and properties: this is a limitation for scientists aimed at developing new imaging schemes with different RSFPs.

After seven rounds of directed molecular evolution from the RSFP Dronpa, Martin Andresen and colleagues from the Max Plank, report in the September issue of Nature Biotechnology, the generation of two new bright RSFP with unique absorption and switching characteristics. These new proteins, called Padron and bsDrompa will allow for the implementation of monochromatic, multilabeled imaging and dual color far-field fluorescence nanoscopy.

Let me give a personal perspective: I bet in a near future someone will exploit the on/off properties of those reporters to get a tomographical solution of fluorescence (and bioluminescence) imaging in living mice.

Martin Andresen, Andre C Stiel, Jonas Fölling, Dirk Wenzel, Andreas Schönle, Alexander Egner, Christian Eggeling, Stefan W Hell, Stefan Jakobs (2008). Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy Nature Biotechnology, 26 (9), 1035-1040 DOI: 10.1038/nbt.1493

New forum: Next Gen Sequencing Service Providers [SEQanswers.com]

Posted: 22 Sep 2008 10:37 PM CDT

Per the suggestions of a few people, I've created the to discuss all aspects of third-party next gen sequencing service companies. With the explosion of service providers I've seen in the past year or so, I think this could be a very valuable resource to make sure we're spending our research dollars wisely. So as always...feel free to post questions, reviews, or anything regarding this topic.

Read more and join the community...

Steven Weinberg, Ralph Waldo Emerson And The Impact of Science on Religion [adaptivecomplexity's column]

Posted: 22 Sep 2008 10:15 PM CDT

Emerson looked forward to the day when America would be self-reliant and not second rate in its scholarship. In science, the U.S. has fulfilled Emerson's ambition, but at what cost to religion?

Physicist Steven Weinberg muses on religion's fate in the West as science has come to dominate our culture:

Let's grant that science and religion are not incompatible—there are after all some (though not many) excellent scientists, like Charles Townes and Francis Collins, who have strong religious beliefs. Still, I think that between science and religion there is, if not an incompatibility, at least what the philosopher Susan Haack has called a tension, that has been gradually weakening serious religious belief, especially in the West, where science has been most advanced. Here I would like to trace out some of the sources of this tension, and then offer a few remarks about the very difficult question raised by the consequent decline of belief, the question of how it will be possible to live without God.

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Tuesday, September 23, 2008

The DNA Network

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Psyco and JIT compiling

Profiling Python

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