Saturday, August 30, 2008

The DNA Network

The DNA Network

Open Data, Open Visualization and a new blog [business|bytes|genes|molecules]

Posted: 30 Aug 2008 03:21 PM CDT

A reviewer at the National Institutes of Healt...Image via Wikipedia I discovered a new blog today, FlowingData, at least I don’t recall having seen it before. The blog is all about the meaning of data. How did I find it? One of my Google alerts took me to a post on How Open Should Open Source Data Visualization Be. The part that I went straight to was the part on the three aspects of open source data visualization; Open Tools, Open Code, Open Data.

I don’t necessarily agree with some of the discussion in the post, at least from a scientific perspective, where data visualization is a key to data interpretation, although it’s possible I am misinterpreting the author who seems to be favorable of openness. Again, it’s not always possible to satisfy all three. While R does achieve that, but you can’t always use R (it has it’s performance limitations).

In science, code, data, and data interpretation all go together. The value lies in the interpretation of the data, the hypotheses underlying the interpretation and the presentation of the interpretation. The openness is important, not because it is our duty to give back, but because it is good science. Andrea, in the comments, makes some interesting points. By the way, if you include links to your MyExperiment Workflows, you get super extra brownie points. In particular

However, I believe there's more potential benefit than risk in sharing my so-called intellectual property. Open science ideals (as exemplified by sharing data, analysis, and results) are highly congruent with the values of the open source communities that I study, and I can't help but conclude that the institutionalized incentive systems for academics that make us hesitate to share knowledge are overdue for revision.


I share my work on principle; science is supposed to be about truth and knowledge, not hoarding data and hiding tools from others for our own personal benefit, to the potential detriment of the greater community.

What we need to spend time figuring out as a field is to take this discussion beyond academia. How can we allow people to make money from good ideas, on top of an open science backbone. Too much of the discussion centers around publishing, peer review, etc, but perhaps that’s where the initial discussion should take place.

The good news, I think most scientists are pre-disposed to open science, it’s just a case of the system that discourages them to go in that direction.

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Another medical chumby … cool [biomarker-driven mental health 2.0]

Posted: 30 Aug 2008 02:38 PM CDT

Just saw this on engadget … fun and useful - just like chumby but with a medical twist.  Who knows, it may someday make housecalls (see link below).

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Private eyes []

Posted: 30 Aug 2008 09:04 AM CDT

NEW YORK (GenomeWeb News) – Large amounts of aggregate human DNA data that the National Institutes of Health and other groups made open to researchers around the world is being locked up from public view due to privacy concerns that arose this week when a new forensic DNA method was announced that could conceivably leave people vulnerable to identification.

So that’s it? After all the elaborate mechanisms put in place for investigator applications, data submission, data access, data monitoring, data oversight, and governance…now we just pull the plug on sharing of GWAS data because it can’t be protected?

poisonous mushrooms? use real-time PCR! [Reportergene]

Posted: 30 Aug 2008 08:59 AM CDT

Boletus edulis or Amanita muscaria? Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system, as reviewed by Elio at Small thing considered. Don't forget the thermocycler into your wild mushrooming trails!

Let's talk about facts this election - Part V - Science Funding [The Daily Transcript]

Posted: 30 Aug 2008 08:41 AM CDT

And I won't even talk about the whole Global Warming issue. Governmental funding of science is fundamentally important to our economic future.

First let's look at funding for the National Institutes of Health, the main source of money for biomedical research in the US:


Joseph j7uy5 @ Corpus Callosum points out:

I can't help but notice that the funding leveled off the same year that the Iraq War started.

How about the Physical Sciences, Engineering, Math & Computer Sciences? They have all flat-lined since GWB came to power:


On the biggest issues of our time, energy, the story is no better. Money for alternative energy research has been flat through both Democrat and Republican Administrations. You would think that after 9/11 there would be a push for this type of research. Here's the data:


One of the most ambitious ideas is to develop fusion power, but is it being done in the US? Try Southern France. So if our future relies on a strong support for Science, who do you trust?

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BLI and cancer #2 [Reportergene]

Posted: 30 Aug 2008 08:25 AM CDT

Read also BLI and cancer #1

This is the post topic selected in the first Reportergene poll. Enjoy it!

Within a cell, ATP is both the energy currency inside and an extracellular messenger outside. Recent data show that adenosine concentration is much higher in the insterstitium (outside) of solid tumours compared to healthy tissues, and this information corroborates the growing awareness that tumour cells build up a "self-advantage" microenvironment that reduces effectiveness of anti-tumour immune response. Understanding ATP concentrations outside the cells in vivo is a must for uncoming cancer research.
The italian researcher Patrizia Pellegatti and colleagues from Ferrara University, have engineered a chimeric plasma membrane-targeted luciferase that allows in vivo real-time imaging of extracellular ATP. With this novel probe, they have measured the ATP concentration within the tumour niche of several experimentally-induced tumours. How they did it?

They previously engineered a chimeric luciferase-folate receptor construct in which they appended to luciferase cDNA the targeting sequences (leader sequence and GPI anchor) derived from the folate receptor. This novel probe, named pmeLUC (plasma membrane luciferase) is in fact targeted to and retained at the plasma membrane thus detecting ATP in the aqueous layer close to the cell surface.

So-called "reporter genes" are in fact reporting more than transcriptional activity, and some companies are exploring this new market.

Pellegatti, P., Raffaghello, L., Bianchi, G., Piccardi, F., Pistoia, V., Di Virgilio, F., El Khoury, J. (2008). Increased Level of Extracellular ATP at Tumor Sites: In Vivo Imaging with Plasma Membrane Luciferase. PLoS ONE, 3(7), e2599. DOI: 10.1371/journal.pone.0002599

Saturday Morning Video [The Daily Transcript]

Posted: 30 Aug 2008 07:18 AM CDT

This one is dedicated to the residents of New Orleans who for the past three years have been rebuilding that beautiful city.

Long live The Big Easy.

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What is it with Republicans and Creationism? [adaptivecomplexity's column]

Posted: 29 Aug 2008 09:30 PM CDT

Why is it so hard to find national Republican leaders who don't espouse creationism? Why does opposition to the very successful science of modern biology have to be part of today's definition of a conservative? When you hear that someone is a creationist and a politician, it's a safe bet today that this person is a Republican.

Why is a major American political party in the 21st century so in bed with one of the most anti-intellectual movements out there?

U.S. Vice Presidential candidate Sarah Palin on teaching creationism to public school children of all faiths (or none):


Sarah Palin on EvolutionCreationism [The Tree of Life]

Posted: 29 Aug 2008 09:20 PM CDT

Well, it seems McCain has further embraced an anti-science agenda with his pick as Sarah Palin as his running mate.

The Science Bloggers are a bit up in arms over this. I think there is some hope that she/McCain will drift back to the middle on this at some point but they both now seem to fall in the camp of the Intelligent Design supporters. It is the "independent" streak both do seem to show occasionally that gives me hope that if they do get elected, they will not be as tied to the ID supporters as they will be during the election.

Anyway, here are some things I found on the web about Palin's evolution views:

NewMiner.Com: in response to written questions in a 2002 election ...
Q: The education section of the Republican Party of Alaska's platform states "We support giving Creation Science equal representation with other theories of the origin of life. If evolution is taught, it should be presented as only a theory." Do you support this position? Why?

A: I support this plank in the Republican Party's platform. I believe society can have healthy debates on scientific theories, so equal representation of creation and evolution shouldn't be an offense.
Anchorage Daily News in 2006 reported
The volatile issue of teaching creation science in public schools popped up in the Alaska governor's race this week when Republican Sarah Palin said she thinks creationism should be taught alongside evolution in the state's public classrooms.

Palin was answering a question from the moderator near the conclusion of Wednesday night's televised debate on KAKM Channel 7 when she said, "Teach both. You know, don't be afraid of information. Healthy debate is so important, and it's so valuable in our schools. I am a proponent of teaching both."
Most other thigns I have seen are rehashing these two stories in some way. If anyone has any other detail I would love to see it.

Examples of blog posts on this issue include:

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