Posted: 11 Sep 2008 08:14 PM CDT
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.’”
Posted: 11 Sep 2008 07:41 PM CDT
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.
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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
Posted: 11 Sep 2008 03:59 PM CDT
Cognitive dissonance, for lack of a better term:
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.Read the comments on this post...
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:
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:
Too late for me, but keep on digging cause I have three daughters!
Posted: 11 Sep 2008 01:54 PM CDT
Posted: 11 Sep 2008 01:43 PM CDT
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:
Read more about it on the blog of Steve Murphy, our gene sherpa.
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.
Posted: 11 Sep 2008 12:46 PM CDT
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.
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
When you've been particular places
'Cause you know this has happened before
Ever had a conversation
Have you ever talked to someone
'Cause you know that you've heard it before
You can listen to it here...
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.
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.
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 dialogueIt also lists some of the aspects of Open Science including
Posted: 11 Sep 2008 06:39 AM CDT
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 .
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.
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
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.
This article was published on Highlight HEALTH.
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Posted: 10 Sep 2008 11:05 PM CDT
23andMe has dropped their price by $600, and some have cited this and me as harbingers of doom.
First, when I say that an industry is “dead,” that doesn’t mean that all businesses shut down overnight and nobody buys anything ever again. It means that the assumptions of a business model seemed flawed with reasonable confidence. So, by that model, new businesses are unlikely, and existing businesses will evolve or fade away. Fly-by-nights may vanish overnight, but that’s why they’re called fly-by-nights.
Second, everybody knew that 23andMe would drop their price from day one. The test was too expensive. The science was getting cheaper. Everybody said so; everybody knew this. BEHOLD! 23andMe’s new product is marginally better and 60% cheaper. If you paid $1000 for 23andMe.v1, and you are pissed, and you demand a refund —you are a fool.
So, as expected.
Yes, I’ve heard the chatter. “But you know, DTC genomics really makes their money from selling the results to pharma…” But that’s speculative revenue from a product that doesn’t quite exist, not cash flow from paying customers now, and companies pay expenses in cash, not VP BIZDEV! “partnerships.” If investors actually believed this story, they would fund companies that sold tests for much less than thousands of dollars to build this database and sell it. They don’t believe this, so instead they funded companies that sold tests for thousands of dollars, hoping that the brand and operational experience built in the meantime would give them an advantage if a market for genomic databases materialized.
The story is that Coriell is building that genomic database. GO PAY ATTENTION TO CORIELL. They offer real medicine and do real science!
Not relevant to the “database sale discussion” is deCODE Genetics, a genomics research company, who probably trusts itself to use its own deCODEme genomic data for its own genomic research
Now: The faerie tale about DTC startups selling data to pharma is dead; let’s talk like adults about real customers who pay cash money for real products.
Which startup can make sales?
Which startup has the best product?
Which startup has the best brand?
Which startup has money and talent to operate and evolve despite an increasingly skeptical investor community and a dead business model?
Which startup is so loved by the media that Rupert Murdoch will smell his own piss to be in their blog?
Which startup was founded by one of the most powerful, richest families in the world?
Haha, I was just kidding. Real customers paying for real products doesn’t matter in this business.
People, 23andMe isn’t going anywhere. They are the Bill & Melinda Gates Sergey & Anne Brin Foundation, Silicon Valley style. Anne Wojcicki is married to Sergey Brin, so 23andMe has access to all the talent, connections, and capital 23andMe would ever need to make 23andMe work. Thus, assuming 23andMe doesn’t do anything egregious, they will exist for as long as Mrs. Anne Wojcicki Brin pleases it to be so. If 23andMe shuts down, it won’t be for some mundane reason like the bills weren’t paid, it will be because Anne felt like it. One thousand Coriells wouldn’t change that.
What, does that offend your meritocratic, democratic, American dream sensibilities? Too bad. Go get an Ivy+ degree and marry your own richest man in the world.
People like 23andMe. I like 23andMe. People buy 23andMe tests. I bought a 23andMe test. They’re the best, they can make sales, they have the best product, and someday, they might even “sell” their database to Google. So what? Doesn’t matter. All of that is just something plus infinity.
End of story.
History Remembers Navigenics:
Navigenics thought that they could be Internet Doctors, but they sell premium commodity non-medical medical information, exclusively available to everyone on the web. What do medical specialists charge? Durrr, let’s put a picture of a doctor on our website charge that!
If anybody in medicine was ever going to take Navigenics seriously, Coriell quite clearly dispelled that idea. They don’t have customers, doctors hate them, scientists don’t trust them, Navigenic’s product sucks compared to 23andMe, and unicorns carried their database-pharma-sale story back over a rainbow to happy magic land. Who cares what Navigenics thinks anymore?
As for consumers? I am a fan and customer of 23andMe. You found me. We exist. I challenge anyone to find a single happy customer of Navigenics.
Navigenics: at least they didn’t commit insurance fraud.
History Remembers deCODEme:
I really want to like deCODEme. I do. Not because deCODEme is so great, but because they flew me to Iceland once for a job interview, and I appreciate that. Sure, too many people gave me the “run away unless they pay” speech, but they still have a special place in my heart because, let’s face it, Iceland is kind of a cool country. Maybe the Icelandic government will bail them out, or maybe Kari will hop into a viking ship and raid England or something. But, sorry, deCODEme is just not competitive with 23andMe, and until I’m convinced otherwise, when I say DTC genomics, I mean 23andMe. But, they’ll continue to exist as long as deCODE does someway or another. Running a Ruby-on-Rails website is cheap.
deCODE did start a new blog, though. Check it out! deCODEyou
NOTE: “VP BIZ DEV!” is to be read as if you are barking a college football slogan while chugging a natty and wearing a jersey featuring no less than one food stain.
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