KR Sridhar and the BloomBox - must see video!

Watch CBS News Videos Online

Can this really be true? The "beach sand" is obviously SiO2, but I wonder what's in the green and black paints... at $3000/box, he is right, this will revolutionize the way we produce energy. Can't wait to read more on this. And a desi geek to boot! Yay!!!

Speaking of Stats... Check out Nate Silver

I'm sure you will have heard about the recent study that said that only 2.8% of Oklahoma High school kids passed a basic civics (citizenship) test.

Well, Nate Silver (or Poblano, as we used to know him) has a superb take-down of the statistics, and his analysis strongly suggests that the entire study was fabricated. You may know Nate from his electoral statistical wizardry - he got almost everything right, and he shows up every so often on MSNBC. "Are Oklahoma students really this dumb?" is WELL worth a read. This is how a stats dork should write.

Of course, this IS the deep red state Oklahoma, so I wouldn't be surprised if there's a bit of, ahem, an IQ issue here, but still...

Update: Apparently StrategicVision, the pollsters behind this study, is a REALLY shady outfit, and is taking some serious heat from all around.

Indian Ancestry on Nature's cover. Awesome!

I just got this week's Nature magazine. (Yes, I have a personal subscription. There are copies of Nature and Science on my TV tray. Yes, I am a dork.)

And this is what is on the cover:

The actual article by Reich, Thangaraj, Patterson, Price and Singh (and a really neat "News and Views" section written by Aravinda Chakravarti at Hopkins) basically looks at the variation in genomes of individuals from India. Without getting into the weeds, what they did was to analyze DNA from 25 different groups in India, from different geographical areas, from different castes and language groups, and then do some statistical heavy lifting to look at how similar/dissimilar simple variations in sequences (SNPs) are across these groups.

What these studies reveal is something that anyone (myself included) may have intuited just by growing up in various parts of India. There is an amazing breadth of established groups/communities. I mean, anyone who has seen Indian currency will know that we have 15 national languages, and it is quite commonplace to cross state lines and have absolutely no idea what the hell is being spoken (upon which broken English and furious gesticulation will work). But what this study says is that there are basically "Ancestral North Indians" (ANI) and "Ancestral South Indians" (ASI) who have two distinct lineages (Indo-European and Dravidian, respectively), and current day Indians are basically a melange of these two lineages, with ANIs strong in the North and fading towards the South, and vice-versa with ASIs (the other language groups - Austro-asiatic, Tibeto-burman, and Andamanese are sub-variants of ANI and ASIs). This spectrum is reflected in skin color (light to dark), languages, and even caste structure. (Upper and middle tend to be more ANIs, lower castes tend to cluster with ASIs.

The group also makes a case for "founder effects" (basically, genetic bottlenecks) well AFTER 3000 BC when the Dravidians showed up, and 1500 BC when the Indo-European speakers showed up, suggesting that many dispersed communities were established and then they stayed put. The paper also reveals little nuggets - the Santhal and Kharia tribes, which are Austro-asiatic, are descendants of people that arrived 60,000 years ago? Yep, sixTY thousand. The groups also makes the case for marriages within communities (endogamy) has been happening for many centuries, resulting in some interesting disease predispositions.

Overall, this is one really cool study, which you should read (even if the stats may be somewhat inaccessible). As Chakravarti points out, this is only the start - many more detailed analyses should be done on the Indian population to get a true picture of the genetic tapestry that is India.

But that being said, the concept of ANIs and ASIs brings me back to something I have always said : North and South India are two different countries, man...

Lab retreats are fun - in a really sad masochistic way

Here's the deal, apparently. If you are in a lab that is big and well funded and sufficiently hard-core (which big and well funded labs tend to be), your boss will sometimes decide that the best way to get group morale up is to go for a little lab retreat. Now this isn't the kind if retreat that your corporate types will relate to. No fancy yacht, champagne and strippers.

What we do is ensconce ourselves a secluded place and talk science amongst ourselves for two days straight. Which, if you really think about it, is like any other two days at work. Except with less comfortable chairs, unbearably cold air conditioning and catered food (to be paid for, thankyouverymuch).

Of course, the formality of the entire occasion demands that you actually prepare for a good week or so in advance, so you don't make a damn fool of yourself. And then your presentation gets ripped anyway with glee, either because it's way too ambitious or it isn't ambitious enough or the controls aren't quite right or the time line for experiments are incomplete. In other words, its almost exactly like a thesis committee meeting, except with more thesis committee members and no threat of failure. Of course, in this case, you just get fired for incompetence. Still, the whole thing while being incredibly tiring, was surprisingly fun (yes, yes, that means I'm a gigantic dork. I know)

Anyway, all of this is to explain away the absence for a week. And the incredibly hungover feeling this past weekend.

Like you all care. But still, there you have it.

Moon Rock? Naah. Tree bark? Ooooh yeah.

So, we went to the moon and got back a bit of, ahem, a very much terrestrial tree?

I'm sure there'll be a fantastic explanation for this. Plus of course I'm sure you heard that NASA recently admitted that they lost the original tape of the moon landing because it had been "written over". So they had to take the TV video tapes and had it restored by Hollywood. I'm no conspiracy crank, but that's just a bit convenient, no?

Here come the machines...

Scarily awesome.

Groundwater Tables in India - a dire situation indeed

Did you read about this? The ground water is falling DRAMATICALLY in India. I mean, I knew that India's water resources are under some serious strain, but FIFTY FOUR CUBIC KILOMETERS LOST EVERY YEAR?????? ARE YOU KIDDING ME????

You can read Richard Kerr's article about it here ; the Original article is by VM Tiwari et. al., but I can't link to it right now. It includes some very cool satellite imaging that records very small localized changes in Earths gravity, and uses it to track water content at or below the surface.

Here is the money chart.



Green is OK; means the water tables are more or less stable. Not bad for most of central India and some of the west (which gets poured on every monsoon season). The blues indicate some trouble; unsurprisingly, Tamil Nadu in the south east is shaded blue; the state is always just that bit short on water (the North east monsoons yield less that far south; Bangladesh gets dumped on during that cycle).

But you see that GIANT swathe of dark blues, purples, and hot pinks?

Yeah, those people are FUCKED.

When you have 600 million or so people living in the plains of the Ganges and drawing on groundwater for irrigation to feed themselves, you're bound to run into problems. But 10 or more centimeters a year????

Oh Jeez. Oh Jeez. This is not going to end well.

Update: Reader Pzau points out that the states currently worst-hit by drought are in Central India, and therefore should be darker pink. Not quite. This graph shows you the rate of water table decline, which is independent of the current water table levels in any particular area. In fact, it is quite likely that areas that are already arid would have a small drop (if any) in the water table because the levels are already so low, they can't go any lower, either because the aquifiers have dried up, or because the satellite can no longer pick up changes in signals.

This man ran for President of the United States of America...

I know, he lost, but he was a serious contender. Presenting to you Tom Tancredo, wanker from Colorado.

Scientists boycott Louisiana

Wow, nice to see scientists showing some spine. Now as you may know, the governor of Louisiana, Bobby Jindal, is a thoroughly misguided, anti-evolution republican (what else?) politician. (Both his voting against the stimulus and the legislation that he signed into law that will allow for "supplemental materials" that "provoke debate" in science classes are topics that deserve their own detailed post, but that comes later).

But now, The Society for Integrative and Comparative Biology has decided to back out of their annual conference, which was slated to be held in New Orleans, as a result of this legislation. That's a lot of money that the city and the state can ill-afford to lose. Though the city is taking the punishment for some pretty backward political thinking (you should read the comments section in the nola article to see how people in the area think. It's illuminating), the protest is great, in my opinion. Not that science should be political - it shouldn't - but when we are up against a systematic program to undermine a very basic tenet of Biology for no real reason other that religious bigotry, the least we can do is let our voices be heard.

More Stupidity from the "Vaccines cause Autism" folks

You may have already heard about the landmark ruling by a special court, where judges given the quaint title "Special Master", ruled that vaccines indeed, do NOT cause autism. This is something that we knew for a while in the scientific community, but we have had respectable scientists have their lives turned into a living nightmare by a small but vociferous group that somehow tapped into public sentiment and insisted that vaccination indeed caused autism. For those of you who don't know, THIS ENTIRE CONTROVERSY WAS KICK-STARTED ALMOST SINGLE HANDEDLY BY A NOW THOROUGHLY DISCREDITED SCIENTIFIC PAPER BY ONE MAN - ANDREW WAKEFIELD. (Seriously, follow the link for a thorough debunking of the paper).

Now, I understand why parents of autistic kids would want to know what causes their child's symptoms - I understand that they may want to search for something to pin blame on. But this was more than just calling into question the efficacy of vaccines. This campaign by the anti-vaccine group has immunologists and epidemiologists genuinely concerned. Why? Because it makes a whole generation now susceptible to diseases that we should have eradicated long back. The crucial concept to understand here is "herd immunity"; basically, when a significant fraction of a population (herd) is vaccinated, it is more difficult for a bug to be transmitted from one individual to the next, and it eventually runs out of people it can infect, leading to its eradication. And when the crazies convince people not to vaccinate their kids, shit like this happens (yep. Measles - endemic again). Or this.

And then there was a gem from the spokeswoman of this group (and I can't find the link now for the life of me), AFTER the ruling - I'm paraphrasing: "... until we know what causes autism we cannot definitively say what cannot cause autism."

So while we don't know what caused the plane crash at Buffalo, we can't say that my peanut butter jelly sandwich lunch yesterday didn't cause it?

The antarctic ice-sheet IS warming. Why does the right wing still have a problem with this fact?

You may have already read the article in this week's Nature: The data (don't take my word for it - the views are pretty much unanimous on this) is solid. The antarctic ice sheet has been warming pretty much at the same rate as the rest of the globe in the last 50 years.

So why does the right take such glee is misrepresenting facts? It's easy: if you read drudge, just watch his headlines when there's a heat surge. Silence. I can guarantee it. If there's a winter storm, snow, a cold front, ANYthing that is not a five degree spike in average temps, you'll see it given pride of place on the website. Or you'll get supposedly snarky, but in reality really stupid shit like this (from today):




I also saw Bill O' Reilly today (yes, yes, I do, every once in a while. It gets my blood pumping, so I look at it as therapeutic. Have to be careful to limit myself to 5 minutes though...), and he quoted an NYT article about the Nature paper; He said something like this: "Well, look at their title; it says that a study finds new evidence of warming. But go a few lines down, and they say that weather stations in other locations, including the one at the South Pole, have recorded a cooling trend. Sounds like that's a misleading headline, eh?" And then he gives his trademark patronizing smirk and head shake.

NO YOU ASSHOLE, IT ISN'T A MISLEADING HEADLINE. The FACT is that the overall sheet HAS indeed been warming, and the tmeps from East Antarctic are noisy - NOTHING remotely like a cooling effect, as BillO was insinuating.

I mean, we KNOW BillO is an awesome guy, but this is either incredibly stupid or especially cynical/misleading. And since he apparently not an idiot (jackass: yes, mentally deficient: no), you have to go for the latter option. The same is true for the even bigger jackass, Sean (vomit) Ha... Han... sorry, I just can't bring myself to type his name.

And that then begs the question:

What do these right wing jackasses stand to gain by denying a scientific fact? See, I can understand the whole anti-evolution fight: the more you can invoke god in our creation, the better you can control gullible folk; its a power thing. You can always threaten people to behave because otherwise they'll get fucked in the ass by some dude with a trident, but you can't say "Hey you better do this or evolution will turn you back into a chimp." So that's you they demonize/deny scientific fact that evolution does indeed work. But what the hell do you gain by denying global warming???

Someone, help me out.

Horribly dorky Limerick

Of Charles Darwin I'm no fan.
What he theorized, I too, can.
A little transversion,
mutation and selection;
ape, pea, pen, pan, man!

Ulimate Dorkiness/Awesomeness

So what you see in the background is a Ion Abrasion (Dual Beam) Scanning Electron Microscope fitted with a Kleindiek micromanipulator and Platinum Gas Injection System. There are maybe half a dozen of these in the world, and this one's sitting in our basement. We use it to do cool shit with cells.

What you see in the foreground is the controller device for the robotic arm that my lab mate installed in the machine. Look at it closely.

Yep, that's a video game controller that's been yanked out of a PS2.

I think I'm dying

I just realized today what a good thing it is that bleach smells the way it does. Now, some genius (at Pfizer I think) decided to make an equally noxious disinfectant called Roccal - that kills at least 23 different types of microbe, they proudly proclaim - which smells like, uh, Roccal. It doesn't quite smell like roses, but the point is, it doesn't feel god-awful as you BREATHE IN LUNGFULS of the shit.

I used it today in a closed room today. Didn't smell anything except for the mild aroma of Roccal. So I continue to do my work, and then it starts feeling as if some one's scratching the insides of my lungs. First its a gentle itchy feeling, and then it's Oh-Jesus-my-lungs-are-on-fire. I mean, this thing very soon felt like it was liquifying my lungs from the inside out. It sucked big time. My pleural cavity feels like its been through a meat grinder. I'm somewhat better now, but I can't help thinking I've shaved off a good ten years off of my life.

Yeah, moral of the story: Don't stick around too long when you're disinfecting something in a closed room.

Gallo just got bitch slapped

Big news - The 2008 Nobel Prize for medicine has been awarded to Luc Montagnier and Barre-Sinoussi for their discovery of HIV (or as they called it back then, LAV). The committee didn't even mention Robert Gallo during the citation.

For those of you interested in some of the history of the discovery of HIV, here is a nice little account of the race to find the virus that caused AIDS, and the controversy that ensued; here is another. The fracas soured diplomatic relations between the US and France for a while. (Well, not that the two countries have been the best of buddies ever, but still...)

Two things:
1. I'm glad that the scientific community went this way; despite all the hype, the French group *did* isolate and characterize the virus first.
2. Gallo was a dick about it. If you came in second dude, no amount of shouting will make you first.

Obama vs. McCain - Science Advisors

This from last week's Nature magazine. A quick scan will tell you how the candidates think. Obama has Harold Varmus, who is a Nobel Laureate and was head of the National Institues of Health, and a bunch of, well, scientists. The list also includes two other Nobel laureates - Bob Horvitz (MIT) and Peter Agre (Hopkins). McCain has a bunch of old hands from government, and corporate heads. Including our friend Carly Fiorina who walked away with $42 million after bringing HP to its knees and was McCains very public on-TV supporter until this.

Plus of course, McCain will have Sarah Palin by his side, who has this to say about Evolution vs. Intelligent design.

Good times.

update: More of Sarah Palin's views on all this + abortion + the gay in her interview with Katie Couric. Watch her talk about how she "didn't make the choice to be gay" (towards the end of the clip).
(h/t pushupdad)