Friday, November 21, 2008

The DNA Network

The DNA Network

What could be worse than snakes on a plane? [Discovering Biology in a Digital World]

Posted: 21 Nov 2008 07:37 PM CST

Neural circuits for personality … genetic insight follows … marriages everywhere saved ! [Biomarker-driven mental health 2.0]

Posted: 21 Nov 2008 06:50 PM CST

Flash circuit

Image by cibomahto via Flickr

A recent paper from Andreas Heinz and colleagues (doi: 10.1038/nn2222) provides more neuroimaging evidence in humans for a a circuit that regulates our responsivity to stimuli that evoke emotional responses.  The basic circuitry involves the amygdala (a place in the brain where emotional memories are registered), the prefrontal cortex (a part of the brain that is involved in making decisions and assessing threats) and the cingulate cortex (a place in the brain where expectations are compared to sensory inputs & outgoing responses).  These 3 brain regions are interconnected in a loop through various synaptic contacts and the responsivity of these synapses can be modulated by neuomodulators such as dopamine, serotonin and noradrenaline.  It turns out, that several neuroimaging studies have begun to demonstrate that this (relatively) simple circuitry underlies human personality and temperament. In the Heinz study, the level of dopamine that was released into the amygdala was correlated with levels of functional activation to emotional stimuli as well as a dimension of temperament known as negative affect.

I recall once having taken the Meyers-Briggs assessment in graduate school and had a blast comparing my results with my wife - who was almost my polar opposite. Now, the latest neuroimaging and imaging-genetic research has begun to explain the complexities of human personality in basic neural circuitry where genes such as 5HTT and MAOA ‘turn up’ or turn down’ the gain on various synaptic contacts in this circuit - leading to the immense, yet systematic variation in personality and temperament that makes our social lives so interesting.  As I navigate my way through marriage and parenthood, I’m often glad I took the personality test with my wife many years ago.  It always helps to see things from the other person’s perspective.  Now, as she obtains her 23andMe profile, perhaps we will begin to compare our genomes together - the ultimate form of marriage counseling !!  Click here for more personality tests.

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23andMe Always Has Destroyed Saliva After Testing and Data on Demand! [Think Gene]

Posted: 21 Nov 2008 04:47 PM CST

As clearly stated in the Consent Form at 23andMe:

Genetic Data: The laboratory processing your saliva sample will analyze your DNA to determine your genetic information. The laboratory will not analyze your saliva for any biological or chemical components, markers or agents other than your DNA. The laboratory will not have access to your name or your other personal information. A unique bar code will allow 23andMe to link genetic data derived from your sample to your account. After analysis, your remaining DNA and saliva samples will be destroyed.

Account Deletion: You have the right to delete your genetic information from our systems. Within thirty (30) days of receiving your written request, we will delete your account, and your information will not be included in any future research, including future research by other organizations. Any research conducted prior to the end of the thirty (30) day period following receipt of your request will not be altered or halted. Once your account is deleted it will not be retrievable. For purposes of clarity, any user-generated content you contribute will not be deleted and your genetic information associated only by barcode may be retained at the laboratory. Click here for more information.

Given all the angst in the community, I assumed that there must have been some recent clarification, because I have written records here of my own confusion, and it is a common sentiment in the community that somehow 23andMe is unethically hoarding user DNA.

Nope. I bought my 23andMe kit sometime in winter 2008 and received my kit in March 2008. At the time, I photographed and scanned all the pieces of the kit —including the Consent Form— which I then emailed to my gmail account for safekeeping. Here you can see the same statements above printed in the Consent Form from at least March 2008.

This is an alarming oversight on behalf of me and the community. However, I would also like to highlight two more statements from the Consent Form:

You should not change your health behaviors on the basis of this information.

Furthermore, 23andMe’s service is not a test or kit designed to diagnose disease or medical conditions, and it is not intended to be medical advice.

I hope 23andMe’s marketing and PR is very very careful about misrepresenting their product in the media, which of course, they quite clearly hope to be a health company, so of course they are misrepresenting their product to some degree. However, I’m really feeling too cynical right now to make a call one way or the other. Everybody incessantly talks, but nobody ever says anything, and it’s getting to me.

Using the MRSA database to teach students about data analysis and public health [Discovering Biology in a Digital World]

Posted: 21 Nov 2008 03:50 PM CST

There's no question that the ability to work with information is one that will be required and valued for a long time to come. I think it's imperative for teachers to have students practice this skill whenever an opportunity comes about. The problem for many teachers is finding the time to identify good data sets.

MRSA stands for Methicillin-resistant Staphylococcus aureus (MRSA), a serious problem for hospital patients. Six of out seven people who become infected with MRSA, get it from some kind of health-care facility. In 2007, the CDC issued a report claiming that 18,000 people die every year from invasive MRSA infections, a higher number than US deaths from AIDS.

Luckily, the Seattle Times has put together a nice database on MRSA infections that can be freely used by anyone and can serve as a nice teaching resource as well.

Having students work with information from the MRSA database would be useful for instructors who teach graphing skills, statistics, microbiology, nursing, epidemiology, or any area of public health.

Here's how.

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Evolution in Detail: The Grants' Study of Darwin's Finches [adaptivecomplexity's blog]

Posted: 21 Nov 2008 12:43 PM CST

Yesterday our department hosted Peter and Rosemary Grant, who spoke about their 30+ years studying natural selection and finches in the Galapagos. (If you're interested in the book version of their work, check out Jonathan Weiner's Pulitzer Prize-winning The Beak of the Finch.)

While the Grants give a great presentation, full of pictures the Galapagos finches in action, my first impression was that none of this was really groundbreaking. As the Grants mentioned multiple times in the talk, Darwin anticipated so much of what they observe in the Galapagos. In an age of molecular genetics, a long-term, non-molecular field study is bound to seem a little old fashioned, although the Grants have recently been taking DNA samples and incorporating the tools of molecular genetics into their work.

In the end, I came away from the talk satisfied. This work may not be conceptually groundbreaking, but I find it important for at least one reason: this is evolution in detail, in the wild.

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Dancing your PhD [Bayblab]

Posted: 21 Nov 2008 12:10 PM CST

The AAAS had its annual science dance contest, and the results are in! The idea is to use body movement and art to communicate the findings of your first-author publication, so that you may perform in February at the AAAS meeting. Clearly they are taking cues from the evermore popular IgNobel. This will appeal to the subset of people who like both "So You Think You Can Dance" AND are members of the AAAS (judging by my lab, it may be greater than you'd think). Of course they are not the first to create this overlap, it's been done before, but never in a competitive setting. .

Here is the winner for the graduate Student category: "The role of vitamin D in beta cell function"

'Tis the Season [Bayblab]

Posted: 21 Nov 2008 12:07 PM CST

Christmas season is almost upon us - and if you're to believe the mall displays, it has been since mid October. With it comes office parties, rum-laced egg nog (marrow rum?) and gift exchanges. And with family gift exchanges, often come Santa 'wish lists'.

The Christmas list remains something of a puzzle to me. Sure it removes much of the stress of gift giving (What should I buy? Will they like it? etc.) but it seems to fly in the face of the conventional "It's the thought that counts" wisdom, since they're meant to take thought out of the equation.

But conventional wisdom is often wrong and a more fitting aphorism would be "It's the act that counts". And in fact, the act may be as (or more?) important for the giver as the receiver. Families that cut back on gift giving by doing a "Secret Santa" type exchange may be doing themselves a disservice, the New York Times reports:
But while it's reasonable to cut back on spending during the holidays, psychologists say that banning the gift exchange with loved ones is not the best solution. People who refuse to accept or exchange gifts during the holidays, these experts say, may be missing out on an important connection with family and friends.
Of course retailers are probably thrilled with that idea. Gift giving is a social interaction and by not participating either by not giving or declining gifts you miss out on social cues and opportunities to strengthen bonds
"[Not participating in gift exchange] doesn't do a service to the relationship," said Ellen J. Langer, a Harvard psychology professor. "If I don't let you give me a gift, then I'm not encouraging you to think about me and think about things I like. I am preventing you from experiencing the joy of engaging in all those activities. You do people a disservice by not giving them the gift of giving."
Psychology Today explains further. Giving a gift forces the giver to reflect on the relationship (at least subconsciously). It focuses the giver on who their important relationships are, and the nature of those connections (the nature of the gift, the effort willing to be made, etc.) and answering these questions is satisfying. And gift giving reinforces itself through these feelings in a sort of feedback loop:
We usually think that the more we care about someone, the more we want to give to them. This is probably true. But what is even more interesting is that the more we give, the more we come to care about the person to whom we are giving. We feel alive in the activity. And it is the receiver who has provided the opportunity for us to feel this good, so we feel loving in return. Moreover, as social psychologist Daryl Bern, Ph.D., has taught us, we deduce our attitudes from our behavior. "I must really care or else why would I have given such a meaningful gift?"
A recent paper in Science supports the idea that giving is good for the giver. The authors show, through both survey and field study, that spending money on others is predictive of happiness. While one might think that happier people are more prone to giving (which may be true), the authors also showed that people randomly assigned to give to others reported more happiness compared to those told to spend on themselves.

So on that count the old wives may have got it right: It is better to give than to receive.

Support ESC research? Stop calling yourself Catholic! [Mary Meets Dolly]

Posted: 21 Nov 2008 12:04 PM CST

Support embryonic stem cell research? "Stop calling yourself Catholic. You're not." What a hoot! From

IVF babies 2 to 4 times more likely to have birth defects [Mary Meets Dolly]

Posted: 21 Nov 2008 11:10 AM CST

I have long said that I believe that in vitro fertilization (IVF) is human experimentation without the consent of the one being experimented on.  In other words, does anyone really think about the effects on a child of being conceived in a dish?  I think the wants of the parents and their so called "reproductive rights" override any real thought about the health or well being of the child.  God forbid, in our society someone actually stand up and say, "It is not okay to conceive a child in anyway possible just because Joe and Sally want a genetically related child."

This is not the first study that confirms that children produced by IVF are more likely to have birth defects that those conceived the way God intended: in a womb, not a laboratory.  It probably will not be the last.  From Medical News Today:

A nationwide US study found that babies conceived with Assisted Reproductive Technology (ART), such as in vitro fertilization (IVF) were between 2 and 4 times more likely to be born with certain defects than babies conceived naturally.

The study was conducted by researchers at the US Centers for Disease Control and Prevention (CDC) and was published early online in the journal Human Reproduction on 16 November.

Compared to babies conceived without ART, the CDC study found that among pregnancies that resulted in single births, ART was linked to twice the risk of certain heart defects, over twice the risk of cleft lip (with or without cleft palate) and more than four times the risk of some types of gastrointestinal defects.

So drinking coffee or alcohol, or smoking while pregnant is a cardinal sin in our society, but deliberately putting a child at greater risk for serious birth defects is fine.  Does not make any sense to me.

A Doctor is now in the House... [adaptivecomplexity's blog]

Posted: 21 Nov 2008 10:48 AM CST Redneck Genetics. It's now Dr. Redneck Geneticist. Justin successfully finished his PhD this week - head on over and congratulate him, now that he's sober again.

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23andMe [Think Gene]

Posted: 21 Nov 2008 09:56 AM CST

Update: oh wow, it turns out that the 23andMe contract always has stated that 23andMe destroys the sample after testing and will delete data on demand (at least, since March 2008). Full story coming. A lot of people have a lot of explaining to do…

Quickly: a few people have asked me to update my opinions about 23andMe. My previously stated opinions have not changed (I’m a customer of 23andMe, and I like it). Further, I don’t have strong ethical ideas about consumer products. 23andMe is a nerdy toy —like a novelty x-ray— not medical advice, and as long as 23andMe continues to organize and present good scientific information, I’m happy. Generally, I think that 23andMe sets a high standard for transparency, scientific tool usability, and responsiveness. Particularly, Andro Hsu, the Sci-tech liaison has been great, and 23andMe continues to make responsible adjustments. For example, I suggested a few months ago:

…Keeping the saliva sample violates medical research conventions, and that offends the ethical standards of others in the medical research community….

Solution: Add account deletion to the main FAQ and promise to destroy the saliva sample on account termination.

Apparently, 23andMe agreed and now destroys the saliva samples.

I think that there will be issues in the near future as “geeky toy” evolves to “obvious medical advice,” but I expect 23andMe to handle these growth issues responsibly.

What I don’t like about 23andMe is its wholehearted embrace of the American marketing culture and its media games. Unfortunately, that’s how business has to be done today, and I’d probably do something similar if I ran 23andMe (though my approach would be significantly less… estrogen-y…). Startups don’t have the luxury of non-commercialism, and most news media isn’t anything more than a marketing expense a few companies removed, so relax.

What I don’t like about the community response to 23andMe is when people seize on some tiny detail and spew some diatribe without actionable rational discourse. Transparency is so vital to good medicine, and attacking a company for every statement not prepolished by some PR shill strongly discourages transparency. That is wrong. Really, not every off-the-cuff statement by a company officer is a medical emergency. Significant medical misinformation must be corrected, but transparency is much more important to the future genomics industry. The significant medical misinformation I see doesn’t come directly from 23andMe, it comes from the parade of media bots swarming about the celebrity of the company. I can’t say the same for other genomics companies…

I certainly have my complaints about 23andMe, but I try to keep them to myself until I have something intelligent to say about them. And yes, I have willfully “picked a side” in the interest of pragmatism, though my real alligance goes to Coriell whom nobody knows much about, but that is the cost they incur because they don’t play the stupid media games. They are also less driven to “capture a market” because they have been a medical research institution for several decades, and judging from their huge warehouse of nitrogen-preserved cell lines, they expect to exist forever.

Genetic test as a Christmas present [deCODE You]

Posted: 21 Nov 2008 09:03 AM CST

Pam Bale is going to get her three grown-up children a deCODEme genetic test for Christmas

Pam Bale is going to get her three grown-up children a deCODEme genetic test for Christmas

Pam Bale knows what she wants to get her three children for Christmas. Two of Pam's children are in their 20s and the other is 30. In other words, a little too old for video games. So they're not getting a Wii or Guitar Hero. Instead, Pam wants to surprise her kids on December 25th with a genetic test.

"I think the kit would open up all sorts of doors to their future," says Pam. "They are young adults, and at their ages the test can show them what medical concerns they might face down the road. They are young enough so they can take the steps to avoid those concerns. It would make their whole future happier and healthier and extend their lives. I think it's a great gift to give to my kids. So don't tell them. I don't want to ruin the surprise."

For the whole interview with Pam Bale go to deCODEme Customer Stories.

This week's paradigm shift: a single-celled organism can also leave tracks. [Genomicron]

Posted: 21 Nov 2008 07:07 AM CST

My displeasure with media stories continues today with another over-the-top, speculative, and tailor-made-for-quote-mining article from Discovery News. The gist of it is that some people saw a very large, single-celled organism leaving tracks in the sand. Therefore, we need to "revolutionize" the way we think about evolution because maybe this is the sort of creature that left trace fossils in the Cambrian.

The choice bits:
Single-Celled Giant Upends Early Evolution

Slowly rolling across the ocean floor, a humble single-celled creature is poised to revolutionize our understanding of how complex life evolved on Earth.


The finding could overturn conventional thinking on a mysterious time in the evolution of early life known as the Cambrian Explosion. Until about 550 million years ago, there were very few animals leaving trails behind. Then, within ten million years an unprecedented blossoming of life swarmed across the planet, filling every niche with hard-bodied, complex creatures.

"It wasn't a gradual development of complexity," Matz said. "Instead these things suddenly seemed to burst out of a magic box."

Recycled Virgins, Nano, and Trigger Points [Sciencebase Science Blog]

Posted: 21 Nov 2008 07:00 AM CST

virgin-oilMy latest science news is now online in the spectroscopyNOW ezine. This week:

Recycled virgin - Recycled engine oil has high levels of organic impurities, heavy metals, and carcinogenic compounds, according to work carried out by researchers in Jordan. They have used atomic absorption (AA), inductive couple plasma (ICP) and Fourier transform infrared (FTIR) analyses to spot the differences between virgin and recycled engine oil.

In a spin over nanomaterials - Researchers at Rensselaer Polytechnic Institute, New York, are hoping to spread the word far and wide of a new analytical technique that can help scientists and technologists working with nanomaterials. They say that their discovery could help accelerate the development of materials for the next generation of solar energy conversion and computer data storage.

Deadly proteins and trigger points - US researchers have used NMR to identify a previously undetected trigger point on a naturally occurring “death protein” that helps the body get rid of damaged or diseased cells. The researchers suggest that their findings may offer a novel target for new drugs that could be used to treat cancer by forcing malignant cells to undergo apoptosis, or cellular suicide.

Finally, a rather technical item that will appeal to that specialist niche working on time-resolved laser-induced fluorescence spectroscopy. German researchers have found a new way to fit a statistical model to TRLFS spectra that could reveal hidden details and remove background noise, much more effectively than before. The method could allow samples containing various radioactive elements to be analysed effectively despite the interferences from the different ions present.

Recycled Virgins, Nano, and Trigger Points

Open Genomics: Genome Evolution Simulator [The Tree of Life]

Posted: 21 Nov 2008 03:21 AM CST

Quick post here.   Cool new paper (and the software could be cool too but have not tried it yet) on simulating genome evolution.  The paper is from Ian Holmes and others at Berkeley (see his lab page on BioWiki here) and the paper can be found here in Genome Biology. Here is the abstract:
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at

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