The DNA Network

The Scientific Method Rules [adaptivecomplexity's column]

Posted: 11 Sep 2008 08:14 PM CDT

Razib at Gene Expression and Andrew Sullivan at the Daily Dish discuss science vs. scientists.

Razib:

I bring this up because many scientists believe that because science is such a superior method of extracting information about the world around us, and constructing predictive models which have been shown to have great utility, that that means that they as scientists can simply transfer their godlike powers to other domains with the greatest of ease. But as the above should make clear I believe this is a false perception, because the power of science arises from the intersection of the communal wisdom of tens of thousands of individuals over decades with the nature of the subject at hand. Granted, there are individual geniuses of great brilliance such as the great Isaac Newton, but the outcomes of his dabbling in alchemy and scriptural hermeneutics should go to illustrate that cognition applied to a fool's errand only results in glorious foolery.

Jurassic Beer! []

Posted: 11 Sep 2008 08:08 PM CDT

Okay, this is the kind of thing we live for here at Aminopop. Biotech has been slinging some pretty tough talk in recent years about the necromantic revivification of extinct species — the Dodo Bird, T-Rex, the Tasmanian Tiger – with precious little to show for all the bluster. Which is why reviving 25-million-year-old yeast — and then making beer out of it – gets us so excited. Rarely do you find an opportunity to connect with Biotech on such a visceral level… and over Buffalo hot wings, no less.

The critics rave: “William Brand, the Oakland Tribune beer critic, says the ancient yeast provides the wheat beer with a distinctively ‘clove-y’ taste and a ‘weird spiciness at the finish’” while “The Washington Post Style section’s summer beer critic pronounced it ’smooth and spicy, excellent with chicken strips.’”

Data friction [business|bytes|genes|molecules]

Posted: 11 Sep 2008 07:41 PM CDT

it's just striking how some very basic kinds of data friction keep getting in the way of ever-more-amazing possibilities for analysis and insight. – Jon Udell

I don’t think I need to add anything to this line (at the end of a typically great post by Jon)

I wonder what kind of data friction life scientists have to fight through. Back in the day, it was all the non-standard terms and slight changes that used to show up in the PDB. In recent times, I have heard of datasets (same kind of data) from different groups that had one column of different with no directions on what the different column meant. Try designing a schema for that.

Of course, the need to come up with yet another data format is the favorite pastime of most life science data creators.

The World Bank Opens API to Key Global Data

don't crack down bioluminescence imaging [Reportergene]

Posted: 11 Sep 2008 04:48 PM CDT

The laboratory that discovered leptin have recently reported a BAC transgenic mouse line that express luciferase under the control of leptin promoter elements. They showed that bioluminescence imaging faithfully recapitulates regulation of leptin mRNA in different condition of fasting/fed regimens in normal/obese background with/out leptin withdrawal. So, by in vivo imaging they now strive to characterize the still unknown cellular program responsible for restoration of adipose tissue after weight loss. Best wishes. I'm a strong supporter of reporter imaging in animal research (here, here and here). However, this latter model pose me some doubts. Even if I recognize the finest quality to study gene expression chronology in a living animal, I wonder about the necessity and the economy to make research with surrogate markers (luciferase) of a single gene expression (leptin). Signalling networks are so robust and redundant!

In my humble opinion, luciferase reporter mice are better exploited to track responsive elements of critical transcription factor, in that case the photon emission would be a surrogate marker of the final result of one/more signalling cascades and not just the mirror of one of our 30,000 genes. That's much informative. Of course, then you need some deconvolution, but you can reasonably get the dissection of your pathway by crossing your reporter mouse into a KO background. Definitively, to study mRNA expression in a tissue, I prefer a hierarchical clustering of quantitative PCR dataset (of different genes), chiefly with new technologies (here and here). Yes, this is just my personal naive opinion, feel free to fill my gaps.

K. Birsoy, A. Soukas, J. Torrens, G. Ceccarini, J. Montez, M. Maffei, P. Cohen, G. Fayzikhodjaeva, A. Viale, N. D. Socci, J. M. Friedman (2008). Cellular program controlling the recovery of adipose tissue mass: An in vivo imaging approach Proceedings of the National Academy of Sciences, 105 (35), 12985-12990 DOI: 10.1073/pnas.0805621105

this is another example of BLI crack down

“First we sequence ‘em, then we club ‘em!” [genomeboy.com]

Posted: 11 Sep 2008 03:59 PM CDT

Cognitive dissonance, for lack of a better term:

According to Alaska’s 2009 catalog of earmark requests the state’s sea life are in great need of federal money. As Politico points out, Palin’s office requested $2 million in federal monies to study crab mating habits; $494,900 for the recreational halibut harvest and $3.2 million for seal genetics research.

Those requests for the study of wildlife genetics and mating habits seems pretty antithetical to the long-standing views of Palin’s running mate, John McCain.

“We’re not going to spend $3 million of your tax dollars to study the DNA of bears in Montana,” McCain said earlier this year, referring to a request from Montana for federal money to study the endangered grizzly bear. “I don’t know if it was a paternity issue or criminal, but it was a waste of money.”

Let's talk about facts this election - Part VII - More Family Values [The Daily Transcript]

Posted: 11 Sep 2008 02:22 PM CDT

In a comment to yesterday's post Rev Matt stated:

There is also a correlation between teen pregnancy and religion.

I tried to look up the stats for the US and couldn't find any. What I discovered (mostly from this study) was that in the US religiosity correlates with a lower rate of contraception use (not surprising), a delay in the age of a person's first sexual experience (not that surprising) and a decrease in abortion. So in the US it is not clear what the correlation is between teen pregnancy and religiosity. (If any one can find that data, let me know.)

ON THE OTHER HAND there does exist quite a bit of data comparing the stats between different countries. Here the story is quite clear, the more religious a country is the higher the incidence of teenage pregnancy, teenage abortion, infant mortality (<5yrs old), teenage suicides, and homocides.

Here's a few graphs where teen pregancy is ploted against various measures of religiosity.

If you are interested in other cross-national stats, check out Google's Gapminder.

Ref:
Gregory S. Paul
Cross-National Correlations of Quantifiable Societal Health with Popular Religiosity and Secularism in the Prosperous Democracies
Journal of Religion and Society (05) Vol.7

Sam A. Hardy, and Marcela Raffaelli
Adolescent religiosity and sexuality: an investigation of reciprocal influences
Journal of Adolescence (03) 26:731-739

Read the comments on this post...

The marriage gene [Mary Meets Dolly]

Posted: 11 Sep 2008 02:21 PM CDT

You knew this was coming. Scientists have reported that they have found a "marriage" gene. From the Baltimore Sun:

Scientists at Sweden's Karolinska Institute reported recently that for the first time, they have found a direct link between a man's genetic makeup and his aptitude for marriage. Their research showed that men who lack a particular variant of a gene that influences brain activity are more likely to be devoted, loving husbands and more likely to be involved with women who praise them as emotionally close and available.

By contrast, men who possess the gene variant, called an allele, are more prone to marital discord and divorce, and the women who put up with them are more likely to describe them as distant and disagreeable. If marital fidelity and contentment are hard-wired into some men's brains, there's certainly a temptation for women to try to increase their chances of a happy union by screening potential spouses' genetic codes.

Of course, genetics is rarely 100%. Which means just because you have a genetic variation doesn't mean a whole lot unless you also take other factors like environment, morality, promises made before God, etc. into account.

I don't need to test my hubby for this one though. I know he doesn't have the "distant and disagreeable" variant. But, I sure would like to know about these others that the writers at the Baltimore Sun talk about:

Brides-to-be with a human-engineering turn of mind surely also will want to check out the possible presence of a gene for taking out the trash, folding the laundry and picking up stuff off the floor - not to mention the all-important money-making gene. None of these crucial but elusive fragments of DNA has been detected yet in the lab. Scientists should keep digging.

Too late for me, but keep on digging cause I have three daughters!

Medicine 2.0 Congress in Spotlight [ScienceRoll]

Posted: 11 Sep 2008 01:54 PM CDT

Some days ago, Slideshare.net featured the slideshows of the successful Medicine 2.0 Congress:

I also uploaded my presentations:

And one more example that I liked a lot:

Check all the great slideshows out here.

New Youtube Channels [ScienceRoll]

Posted: 11 Sep 2008 01:43 PM CDT

I wanted to share two new, medicine-related Youtube channels with you. The first one is managed by the Detroit Medical Center and focuses on medical animations, educational materials.

The second one was launched by Mark Senak, the blogger of Eye on FDA and focuses on:

The eyeonfda channel is an extension of my Weblog www.eyeonfda.com and is designed to collect video of interest to the pharmaceutical, biotech and public health communities and meant to aggregate health care videos along disease and issue specific lines.

600$? [ScienceRoll]

Posted: 11 Sep 2008 01:32 PM CDT

My dear friends, I told you before… You just lost 600$ for being less patient than us. 23andme lowered the price of their service from 999$ to 399$. Even if I still think it’s not worth it, more patients will get access to their genetic background because of the lower barriers. An excerpt from the New York Times report:

The move might touch off a price war in the nascent business. The company's main competitors, Navigenics and deCODE Genetics, charge about $2,500 and $1,000, respectively.

Mari Baker, chief executive of Navigenics, said the company would not be reactive to what its competitor did, saying that "cheapest wasn't always best." She expressed some surprise at 23andMe's new price, saying, "I know what our costs are. They are many times greater than that."

Read more about it on the blog of Steve Murphy, our gene sherpa.

MyFoodAdvisor: What to eat? [ScienceRoll]

Posted: 11 Sep 2008 01:21 PM CDT

Regarding some medical conditions (diabetes, kidney and heart disease), it’s even more important to know what we actually eat. So The American Diabetes Association came up with a useful tool, MyFoodAdvisor, that can help patients to know more about nutrients, recipes and dishes.

MyFoodAdvisor provides food information to people with diabetes, heart disease, kidney disease and those looking to lose weight. This interactive tool compares foods by 22 different nutrients, suggests healthy alternatives, and analyzes what you currently eat. Portion sizes are standardized, based on the American Diabetes Association and American Dietetic Association exchange lists so all carbohydrate-containing foods are shown in servings of about 15 grams of carbohydrate.

Expectations of a Grad Student [Bitesize Bio]

Posted: 11 Sep 2008 12:46 PM CDT

Graduate Survival Guide:

The ultimate goals of graduate students are to obtain a Ph.D. and to become prepared for a professional career in science. A “professional career in science” can be a great many things, e.g., a professor in a research university, a professor in a small liberal arts college, a career in industry, a position in a non-governmental organization, government work or entrepreneurship. Anyone who is admitted to the graduate program at Utah already has all the raw material to obtain a Ph.D. However, self-motivation, self-discipline, and guidance from faculty and peers are also necessary ingredients. The purpose of this guide is to outline the general steps in graduate school and to reassure you that the attainment of this goal is both possible and rewarding.

Graduate school in Biology is very different from undergraduate education, Medical School, Law School, or other professional graduate training programs. In graduate school, you will become your own teacher and your own motivator. There are few formal courses; most training is done informally in laboratories and/or in the field rather than in the classroom. You will have few quantitative assessments of your performance (e.g., exam grades, course grades), however each assessment is of critical importance. Your advisor will help guide the overall course of your project, especially at the beginning, but your rate of progress will depend largely on your own initiative and hard work. The relatively free-form nature of graduate education, the necessity to become a self-motivator, and the diverse challenges can cause stress, anxiety, and self-doubt. Experiencing self-doubt is typical, and is best countered by keeping the lines of communication open between yourself and fellow students, and between yourself and your advisor.

Basic concepts, but a topic that is probably on the minds of a lot of students who are thinking about grad school (or just started grad school). “What is expected of you once you become a graduate student?,” is at the heart of the matter.

I’ve put it differently in the past, but the three skill sets that the Utah Biology Department article has up nicely covers it. Grad students will need (a) communication skills, (b) analytical skills, and (c) experimental skills.

Alternatively, you could say that the outstanding grad student should be able to write and talk about their field clearly and concisely. That sounds easy, but don’t take it for granted - molecular biology, for instance, can be a mish-mash of complexity for someone fresh out of undergrad. Just getting by isn’t an option, you have to really know your stuff (you’re becoming a scientist, afterall).

Going hand-in-hand with communication is the analysis. Molecular biology as a whole is extremely competitive, and you have to ask the right questions (and design the right experiments) before your competitors.

And finally, the outstanding grad student should have “good hands.” This is probably the most important, at least for experimental fields of biology such as molecular biology. The ability to collect data often can make the analysis obvious, even if it makes the communication not so obvious.

Iron Maiden and "Déjà Vu" [Bayblab]

Posted: 11 Sep 2008 12:19 PM CDT

In a recent Nature Podcast (I think?) I heard a short interview with the blogger running Mind Hacks who was attending the first European science blogging conference . He mentioned that his favorite post was this story about Iron Maiden lyrics being cited in a paper as a description of deja vu. I just had to share the paper and lyrics:

here is the paper that started it all:
the déjà vu experience is a subjective phenomenon that has been described in many novels and poems. Here we review over 20 literary descriptions. These accounts are consistent with the data obtained from psychiatric literature, including various phenomenological, aetiological and psychopathogenetic aspects of the déjà vu experience. The explanations, explicitly formulated by creative authors, include reincarnation, dreams, organic factors and unconscious memories. Not infrequently, an association with defence or organic factors is demonstrable on the basis of psychoanalytic or clinical psychiatric interpretation. The authors recommend that psychiatrists be encouraged to overstep the limits of psychiatric literature and read prose and poetry as well.

And somebody submitted these lyrics as a comment in the British journal of psychiatry quoting the song:

When you see familiar faces
But you can't remember where they're from
Could you be wrong?

When you've been particular places
That you know you've never seen before
Can you be sure?

'Cause you know this has happened before
And you know that this moment in time is for real
And you know when you feel déjà vu.

Chorus:
Feels like I've been here before (rpt. four times)

Ever had a conversation
That you realise you've had before
Isn't it strange?

Have you ever talked to someone
And you feel you know what's coming next
It feel pre-arranged.

'Cause you know that you've heard it before
And you feel that this moment in time is surreal
'Cause you know when you feel déjà vu

Chorus

You can listen to it here...

Genomics: A Megatrend Revisited [Genome Blog]

Posted: 11 Sep 2008 11:30 AM CDT

I was in the Horse Store earlier in the week looking around at all the neat stuff they have for the horse lover. As I was standing at the till, I noticed a little freebee booklet called “The Gatepost” self described at the Greatest little horse magazine. How could I resist?

The magazine seemed to flip open automatically to a page with a beautiful stylistic drawing of a DNA molecule and an article titled “Turn on Your Horse”.

As we prepared for the 21st Century, there seemed to me to be a whole trend of predicting and forecasting what would be the trends of the future. On the list of the best sellers was the book, Megatrends 2000 by John Naisbitt and Patricia Aburdene. They examined ten new directions. One of them was “The Age of Biology”

While much of what they speculated about the importance of biology, biotechnology and genetics has come become a reality, I don’t believe that they could have had any idea of how much genomics would become a part of our culture.

A Genetically Engineered Swat that is clean and green [Tomorrow's Table]

Posted: 11 Sep 2008 10:44 AM CDT

Olivia Judson just published an article describing an interesting approach to controlling Dengue fever.

Dengue is caused by any of four related viruses transmitted by mosquitoes. So far, nothing has proved sustainable. Hence the interest in genetic engineering.

As with humans, viral diseases of plants are some of the most difficult to control in an effective and sustainable manner.

In plants, papaya engineered for resistance to papaya ringspot virus has been tremendously effective in virtually eliminating the disease from the islands. After release of GE papaya to farmers in May 1998, production rapidly increased with a peak of 40 million pounds in 2001.

Combating viral diseases will likely be the most effective use of genetic engineering that we will see in the near future.

Thanks to Jonathan Eisen for directing my attention to this article.

Open Science Required Reading: MSNBC on "Era of scientific secrecy nears its end" [The Tree of Life]

Posted: 11 Sep 2008 08:08 AM CDT

There is a must read out there about Open Science. Robin Lloyd has a excellent article on Open Science (Era of scientific secrecy nears its end) posted at MSNBC. I am not sure whether this was originally written for MSNBC or not nor the whole history of the piece. But the article discusses some of the issues associated with Open Science.

It has some good sections like:

The openness at the technological and cultural heart of the Internet is fast becoming an irreplaceable tool for many scientists, especially biologists, chemists and physicists — allowing them to forgo the long wait to publish in a print journal and instead to blog about early findings and even post their data and lab notes online. The result: Science is moving way faster and more people are part of the dialogue

It also lists some of the aspects of Open Science including

Blogs where "scientists can correspond casually about their work long before it is published in a journal";
Social networks "that are scientist friendly such as Laboratree and Ologeez"
Sharable sites like "GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents"
Citation sharing sites like "Connotea that allows scientists to share bookmarks for research papers"
Preprint servers "such as Arxiv, where physicists post their "pre-print" research papers before they are published in a print journal"
OpenWetWare "which allows scientists to post and share new innovations in lab techniques"
Video sharing sites like "The Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work"
Sequence databases like "GenBank, an online searchable database for DNA sequences"
"Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles";
"Online open-access (and free) journals like Public Library of Science"
"Open-source software that can often be downloaded free off Web sites"

Sure the article gets a few things a little mixed up. For example, software can be free even if it is not open source. And not all open access journals are the same. But the article is overall very good and has some of my favorite Open Science advocates in it like Cameron Neylon and Jean-Claude Bradley.

A lot to chew and then spit! [The Gene Sherpa: Personalized Medicine and You]

Posted: 11 Sep 2008 06:39 AM CDT

As my friends and I work furiously to get the Sherpa's Plan to public(BTW it will be released in parts, and no I didn't spend a T.Boone Pickens like 1.2 billion dollars on it.) , some things have...

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9rules for Highlight HEALTH [Highlight HEALTH]

Posted: 11 Sep 2008 12:40 AM CDT

We are entering a revolutionary period of medicine, one in which medicine is predictive, personalized, preemptive and, most importantly, participatory [1].

Predictive medicine: genomics, DNA sequencing, family history
Personalized medicine: individual genetic variation prescribes treatment
Preventive medicine: focus on disease prevention (i.e. wellness)

Participatory medicine requires voluntary, intelligent participation, not passive acceptance. It is based on the understanding that treating an individual patient with optimal care is often beyond any single individual’s ability.

Participatory Medicine: a patient-centric and proactive model of healthcare that includes e-patients, patient groups, health-focused social networks, the entire health care team and clinical researchers in a collaborative relationship based on education and communication.

One of the goals of Highlight HEALTH is to promote health literacy for improving self-management in health. For e-patients and healthcare professionals to take active roles in evidence-based healthcare, there must be online resources that offer credible health information and provide references for further study. My hope is that Highlight HEALTH is one of those resources.

I spend a great deal of time researching biomedical literature and reviewing health resources for articles here on Highlight HEALTH. It’s quite gratifying when my efforts are recognized. With that said, I’m pleased to announce that Highlight HEALTH is now a member of the 9rules community of bloggers.

What is 9rules?

9rules is a prominent, online social content network that aggregates hand-picked blogs, representing some of the best content from the independent web. 9rules is a place where members and readers can find quality content, learn new things and connect with other like-minded people from around the world.

The 9 Rules of 9rules

Love what you do.
Never stop learning.
Form works with function.
Simple is beautiful.
Work hard, play hard.
You get what you pay for.
When you talk, we listen.
Must constantly improve.
Respect your inspiration.

Each blog that applies for membership is reviewed for quality, value and contribution to the blogosphere. Although the exact number of websites submitted isn’t being reported, at least 2,200 blogs applied for membership (greater than 1,100 submissions for Round 6, twice as many for Round 7). Highlight HEALTH is one of the 73 currently accepted sites listed on the 9rules blog. That puts it in the top 5% of websites reviewed.

Many websites I read and/or subscribe to, such as Zen Habits, business|bytes|genes|molecules, Think Artificial, The Genetic Genealogist and Wise Bread, are 9rules members and I’m honored to be ranked alongside of them. As Highlight HEALTH explores biomedical science, you can find it in the Science Community of 9rules.

My thanks to the 9rules triad — Paul Scrivens, Mike Rundle and Tyme White — for accepting Highlight HEALTH.

References

Strategic Vision for the Future. From Curative to Preemptive Medicine. Elias A. Zerhouni, M.D. Director, National Institutes of Health. 2008 Mar 5.

Thank you for subscribing by RSS or email. I work hard to make the articles on Highlight HEALTH engaging and I truly appreciate your interest and readership!

This article was published on Highlight HEALTH.