The First Cell with a Synthetic Genome

The big news in biology last week is the creation of a viable, replicating cell with a wholly synthetic genome. The work was done at the J. Craig Venter Institute and you can hear Venter himself talk about the breakthrough at TED:


Or, if you want more of the nitty-gritty, you can read the paper published last week in Science (free access).

And, of course, there are plenty of reactions. Nature has collected the opinions of a handful of experts, as has Edge.org. That something like this can be done, conceptually, is unsurprising. We've seen viable cells with exogenous genomes - albeit not synthetic genomes - before. (Think Dolly or the resurrected ibex) Technologically, though, the successful synthesis and transplantation of a Mbp genome is pretty exciting, particularly if synthesis costs follow the trends of gene sequencing. The implications for genetic engineering are obvious, and with the publication of the Neanderthal genome earlier in the month the imagination really gets going.

Naturally there are some confused objections, fears and doomsday predictions as well, which are dutifully taken-down by P.Z. Myers.

What is it like to be a new PI?

I found this blog post from a recent Harvard Prof who discusses the realities of becoming a PI. A few highlights:

-"I guess that I spent about 40% of my time chasing after funding"
-"These days, funding rates are abysmal: less than 10% for some NSF programs, and the decision on a proposal is often arbitrary. "
-"the biggest predictor of success as a junior faculty member is how much of your life you are willing to sacrifice"
-"Most of my days are spent in an endless string of meetings"

Things may seem bleak but there is a silver lining:
"The main reason to be an academic is not to crank out papers or to raise a ton of money but to train the next generation. I love working with students and this is absolutely the best part of my job."

(H/T Ben Ferguson)

Next Up: An Irony Meter...

One tricky part about internet (or any written) communication is the lack of visual and audio clues that help impart intent or meaning. Sarcasm, in particular, is difficult to convey. Israeli researchers have tried to tackle that problem and have unveiled SASI: a Semi-supervised Algorithm for Sarcasm Identification.

SASI, a Semi-supervised Algorithm for Sarcasm Identification, can recognize sarcastic sentences in product reviews online with pretty astounding 77 percent precision. To create such an algorithm, the team scanned 66,000 Amazon.com product reviews, with three different human annotators tagging sentences for sarcasm. The team then identified certain sarcastic patterns that emerged in the reviews and created a classification algorithm that puts each statement into a sarcastic class.

77% is better than some people I know!

[via Omni Brain]

DCA Patient Trials

You may remember a few years ago, there was buzz out of the University of Alberta about a simple molecule, dichloroacetate (DCA), that was effective at inhibiting aerobic glycolysis and slowing the growth of cancer cells in vitro and in mouse models. This was hailed in some quarters as a miracle cure, others claimed it would never see the light of day because Big Pharma would keep it down, unscrupulous peddlers seized a money-making opportunity and more sensible people took the data for what it was and awaited further investigation and proper trials.

The first patient trials have now been done, and the results are in. Surgically excised glioblastomas showed signs of reversal of the Warburg effect and increased apoptosis.

The clinical trial was quite small, involving 5 patients with neuroblastoma being treated with various standard therapies plus DCA. Three showed regression of their cancers, though it's not certain whether it was the DCA or the existing treatment responsible for the change.

Both Abel Pharmboy [Dichloroacetate not yet an effective treatment for aggressive brain cancer] and Orac [Dichloroacetate (DCA) and cancer: Déjà vu all over again] have excellent descriptions of DCA, how it works and analysis of the trial on their respective blogs. The bottom line seems to be that DCA remains interesting, but needs to benefit from more research and well-designed trials before moving to a real treatment.

Wind Power

The recent blogging about the Gulf oil leak (both here, and around the web) reminded me of this great commercial for alternative energy.

Double Jeopardy?

The oil spill in the Gulf of Mexico is an environmental disaster, and cleaning it up takes more than simply plugging a leak and mopping it up. Photo galleries try to capture the extent and degree of the damage. But what of the hundreds of thousands of gallons of chemicals being dumped into the Gulf as a chaser? The New York Times has a piece about this necessary evil.

Even in the best cases, dispersants are applied in what might be termed a lose-lose strategy. Scientists make the calculation that it is better to have the ocean filled with low concentrations of the dispersant chemicals — which are in themselves mild to moderate poisons — than to have dense oil on the surface or washing up onshore, places where it is most likely to harm wildlife.

Companies are protective of their dispersant formulas, and in some cases these chemicals have had their approval pulled in other countries. Speakeasy Science has some details on a few of the chemicals in use, based on MSDS information. Right now, this is preferable to a vast, suffocating oil slick but it will be important to continue to monitor the area long after the clean-up is complete. As the NYT describes it, this is "one of the largest and most aggressive experiments with chemical dispersants in the history of the country, and perhaps the world."

Human Migration

The recent discovery that humans with ancestors outside of Africa have Neanderthal DNA definitely made me think about Guns, Germs and Steel (by Jared Diamond) again and made me question my knowledge of ancient human migration. In an effort to educate myself a bit better about human genetic history I found this interactive map of human migration based upon genetic data. It is definitely worth a quick run through if you are at all interested. There are some interesting bottlenecks and I find it amazing how far humans got before agriculture was developed.

Drill Baby, Drill

This comes from the blog Fake Science ("For when the facts are too confusing") which is full of 'educational' posters like this one, some of which are quite funny. They seem to have missed Step 3.5 though: wring the oil out of waterfowl and other marine life.

Awesome AACR video: "it's our time"

Cancer Carnival #33

It's that time of the month again: Cancer Research Blog Carnival time! Kicking things off, we have some research blogging from the Mad Lab Rat about mathematical modelling of cancer virotherapy.

Which was why the first thing that struck me when a certain jazz-playing poetry-writing philosopher-doctor sent this paper my way was that it was involved in developing a mathematical model for treatments. Not to replace animal testing, obviously, but to cut the tests down to those that were more likely to work, reducing the need for animal use.

The paper is exploring glioma virotherapy, which uses synthetic viral capsules to target cancer cells and kill them, while not harming the surrounding normal cells.

The paper models a variety of factors, including immune response and the effects of immunosuppressants and their effects on oncolytic virus propagation.

What does the eruption of Eyjafjallajökull have to do with cancer? The Thoughtful Animal explores a link between volcanic ash, intelligence and cancer

Put most simply, a teratogen is something in the environment that messes with a developing fetus. Specifically, teratogens are environmental agents that are relatively harmless to an adult, but that can result in birth defects and developmental disorders of varying severity in the child.

He does note that health-wise there isn't much to worry about with this particular eruption.

Over at Aetiology, there are a couple of student guest posts exploring causes of various cancers. First, a look at existing data examining a link between alcohol-based mouthwash and oral cancer. A second post explains how common gut bacteria may be involved in development of colon cancer. On the subject of colon cancer, Healthcare Hacks briefly discusses some research describing the health effects of fruit skin pigments (specifically anthocyanins) - colon cancer and obesity effects in particular.

In a bit of a change of pace, Life, Death, Cancer is a thoughtful post about the emotional experience of participating in a cancer race and the effectiveness of those types of fundraising efforts.

Finally, if you're interested in pretty data presentations (read: infographics), The Web Nurse has a collection of 25 such infographics related to smoking.

That's it for this month's Cancer Research Blog Carnival. For older editions, visit the Carnival Homepage. Don't forget, the CRBC has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available. For a broader collection of science-related blog carnivals, sign up for the Science, Medicine, Environment and Nature Blog Carnival Twitter Feed

Rats eating high-fructose corn syrup get obese.

This is actually a bit old and covered by many others in a more timely manner. The title says it all. Research on rats at Princeton University indicates that high-fructose corn syrup (HFCS) get fatter than rats fed equivalent calories of other sweeteners. HFCS is the sweetener of choice in North America and is in many different foods, including many you don't think of. One that surprised me was mayonnaise.
This is probably the punchline of the article for lawyers:

"Our findings lend support to the theory that the excessive consumption of high-fructose corn syrup found in many beverages may be an important factor in the obesity epidemic," [emphasis mine]

We still drink too much soda, its not the fault of companies that sell it that we are all fat. (I use the term soda because it is what many Americans, the fattest nation on earth, call pop). I don't have access to the full article at this time and don't understand how it was established that the HFCS consumption was excessive.

In case you think that the pictures in the article of test tubes full of orange soda are strange, as I did initially, let me point you to the relevant quote in one picture caption:

"The concentration of sugar in the sucrose solution was the same as is found in some commercial soft drinks, while the high-fructose corn syrup solution was half as concentrated as most sodas, including the orange soft drink shown here."

Rats don't prefer orange crush over Coca-Cola, that is a ridiculous notion. The picture was taken by someone who watches CSI and likes science eye candy and really, it's the people that matter anyways.

Of Alcohol and Intelligence

Over at Gene Expression, Razib Khan has done a quick analysis of alcohol consumption demographics. In one chart, he shows a correlation between alcohol consumption and vocabulary. As a dipsomaniac and sot, this comes as no surprise. He writes:

I was expecting it. That is, that the more intelligent, who scored high on a vocabulary test, would drink more than the dumb, who scored low. Look at the other correlates above. But I’ve rarely seen such a stark near-monotonic trend with Wordsum.

I mean, just look at Hemingway. But Razib also warns about findings like these:

Anyway, just be careful of studies extolling the virtues of alcohol unless they control for confounds. It’s just a fact that stupid people tend to die earlier, because they often make life decisions in keeping with their nature.

Haldane and Hybrid Bears

Haldane's* Rule:

When in the offspring of two different animal races one sex is absent, rare, or sterile, that sex is the heterozygous (heterogametic) sex.

This rule is almost universally true (see table**) and is supported by the observations that among hybrids such as ligers, zonkeys and mules the males (XY) are all sterile while females (XX) may be fertile (though often poorly so, due to mismatched chromosome numbers, discussed briefly here). The reverse observation - sterile females - is true in species where the male is the homogametic sex such as birds and butterflies. Hypotheses explaining the genetic basis of Haldane's Rule and its challenges are explained nicely here.

Recently, a new fertile hybrid was discovered. The grizzly-polar bear hybrid has been seen before, as discussed here, and with changing habitats and more grizzly-polar bear encounters we'll likely see more. The Toronto Star is reporting the first offspring of a hybrid bear.

Researchers in the Northwest Territories say they may have found the first recorded offspring of a hybrid female polar-grizzly bear in the wild. [...] Officials with the territorial government say those test showed that the dead bear was the offspring of another hybrid bear — a female polar-grizzly mix who had mated with a male grizzly.

Given Haldane's Rule, that the hybrid parent was female isn't surprising, but it remains to be seen whether the males are sterile or if this becomes the first mammalian exception.

---
*In addition to being one of the founders of population genetics, Haldane also wrote poetry about rectal cancer, a disease he succumbed to in 1964.

**Table source: Nature 355, 511-515 (1992). Ref. 41 refers to Coyne, J.A. and Orr, H.A. in Speciation and its Consequences (eds Ott, D. and Endler, J.) 180-207 (Sinauer, Sunderland, Massachusetts. 1989)

Stem Cell Blogging

I've just started a new gig writing for the Stem Cell Network, where I'm part of a team of bloggers writing about stem cell news, research and related topics. My first post is up now:

In Britain, a young boy is currently recovering from a remarkable surgery to replace his windpipe. Tissue transplantation itself is hardly a routine thing, but there are a couple of things that make this case, reported in the British Medical Journal, particularly interesting.

Read more

The Glucose Song

Something silly for Sunday... (but who doesn't love The Archies?)



[via Dr. Isis]