Friday, 30 July 2010

Der Spiegel interview

While some of us are off tasting the newest batch of home-brew, I was reading this great Der Spiegel interview with Craig Venter - decoder of the Genome, creator of the first artificially produced genome. Craig Venter is a fascinating character. His arrogance allows him to tackle projects that most people would feel are unworkably hard and complex. Is it still arrogance if you and your team is really that good? Between the two central 'characters' of the human genome sequencing project, Venter and Francis Collins, I much prefer Venter because he talks no-nonsense Science, while Collins has the tendency to slip into generalities, speak in hyperbole, and mostly has been a one hit wonder. Venter comments on him, accurately in my estimation,
SPIEGEL: So you don't consider Collins to be a true scientist?

Venter: Let's just say he's a government administrator.
A good administrator, in my estimation, for managing the behemoth government run genome project, but not the gee wiz scientist who cracked the genome that everyone seems to think he is. There's this tendency to introduce him as 'the man who sequenced the human genome.' What bothers me the worst is that he rarely, in my experiences, corrects this mistake.

This is how the interview starts, and it only gets better and better:
SPIEGEL: Mr. Venter, when the elite among gene researchers undertook the decoding of the human genome, you were their greatest enemy. They called you "Frankenstein," "blood sucker," "Darth Venter" and even "asshole." Why do you attract so much hostility?

Venter: Well, nobody likes to be beaten -- by superior intelligence, planning and technology. That gets people upset.

SPIEGEL: Every area of science is competitive. But it doesn't lead to that kind of hostility in all areas.

Venter: The human genome project was completely different, it was supposed to be the biggest thing in the history of biological sciences. Billions in government funding for a single project -- we had never seen anything like that before in biology. And then a single person comes along and beats scientists who have been working on it for years. It is no wonder they didn't like that.

SPIEGEL: Wasn't it more the case that your opponents were afraid that you, as a profit-oriented entrepreneur, would make the human genome your own private property?

Venter: That is totally absurd; and you know it. Initially, Francis Collins and the other people on the Human Genome Project claimed that my methods would never work. When they started to realize that they were wrong, they began personal attacks against me and made up these things about the ownership of the genome. It was all absurd.
I strongly encourage you to read the full thing. Der Spiegel did a bang-up good job on this interview!

Wednesday, 28 July 2010

Saying what we suspected

If you're in the north, this time of year you don't get a very good look at the stars for another month or so. Actually, today is the last day of the year without dawn or dusk, where the sun goes a specific number of degrees below the horizon. Thus ends our 24 hours of daylight. But if you can see the stars now, or if you could see the stars in a few months, you might look up and wonder if anyone is looking back. It's a question as old as it gets: are we alone? Does earth have the only life in our galaxy, or universe, or are there others like us out there, with alien hopes and dreams, alien struggles, on alien planets?

For the longest time, it was assumed that we could never know the answer to this question. After we started measuring the distances to the stars, we realized how mind-bogglingly vast the galaxy was, and it sort of crushed the hope for exploration of those stars. This was before we knew about other galaxies, which are even mind-bogglingly further. Hopes for interstellar exploration are dim, barring the discovery of exotic things like "Negative matter" or energy on the scale of Plank Energy. But Frank Drake realized that using probabilistic statements, he could estimate the number of alien civilizations in existence. It's very non-controversial, and just a bit conservative:

N = R* x fp * ne * fl * fi * fc * L
or the Number of civilizations in our galaxy is equal to the rate of star formation in our galaxy, the fraction of those stars that have planets, the number of planets that can potentially support life per star, the fraction that go on to _develop_ life, the fraction that go on to develop intelligent life, the fraction of intelligent life that develop technology, and all this times the length of time that civilizations will release detectable signals.

It's difficult to estimate fl, fi and fc, but thanks to exciting work on the moon Titan, as well as Mars, the percent of planets that develop life, or are capable of developing life might not be as low as we thought - that is fl. R* is considerably easier to measure, and is estimated to be around 7 stars per year, averaged over the life of our galaxy. This leaves fp and ne - fraction with planets, and number of earth like planets - as the last of the parameters we have an honest chance at getting a great estimation of.

That's where Kepler comes in. The Kepler satellite is a stellar observatory launched by NASA 2009, with the goal of finding earth-like planets. The problem with detecting planets in space is two-fold. A) they're tiny, and b) they don't really glow. Imagine you're on a boat, on a clear night, trying to look at another boat with a pair of binoculars. You can see the other boat - it has lights on - but you can't see the people because they don't glow, and they're too far away. Occasionally, one might pass under some light, and you could get a glimpse of them for a short moment they're fully illuminated but you have to be very lucky to see this, and it doesn't work from a greater distance away. Or they might pass in front of the light, and though you can't see them, you know they're there because they blocked the light. It's easier to see them from a greater distance, since you're inferring from the dip in light reaching you, not by directly imaging them.

The Kepler mission similarly uses this 'transit' method for looking at stars, looking for tiny dips on light as the planets pass in front of them, temporarily blocking some of the light. Previously, our methods were constrained to looking for planets so massive that their gravity causes their mother star to wobble. Unsurprisingly, most of the planets we've found are massive and close to their mother star - definitely not candidates for life supporting planets. The Kepler mission can spot much smaller planets using the transit method, and will let us (among other things) narrow down the window on how many earth like planets there are.

A screen capture from Dimitar Sasselov's presentation at the TEDGlobal conference.
Dimitar Sasselov, of the Kepler mission, let a massive bombshell at the TEDGlobal conference in the UK, ahead of schedule, and presumably without permission from NASA. Buried in his slides, and casually mentioned, is the number of earth like planets they've found so-far. The number is staggeringly huge. Suddenly, the super-massive planets we've been finding thus-far are back to being weirdos, and non-normal, as the majority of planets they discovered were earthlike. You can watch the presentation at the bottom of my post; I strongly recommend you do. It's worth throwing a huge amount of caution in here, saying that this is not peer-reviewed science, and was not authorized. It's quite possible that Dimitar was horribly wrong, and his facts and figures are incredibly erronious.

I'm not an astronomer, so I can't generalize this to a rate and a number for the purposes of the Drake Equation, but it's pretty dang clear to me that the new values will be high. This, holding the rest of the estimated values of the Drake Equation steady, raises the number of other civilizations out there. As a biologist, I can't help but feel life is almost inevitable (although intelligent life rare). I have more than gut reasons for holding this view, and maybe I'll elaborate on them later. I strongly suspect within my life-time, we'll find proof of life on Titan (before Mars - I'll even gamble money on it), which will widen the niche that life is show to be able to cling to. In reality, I strongly suspect we will find that life, though not cheap, is abundant and resplendent.

You can read more at discovery news, and And pretty soon, I suspect, everywhere else.


Tuesday, 27 July 2010

Dr Erich Follmann

Yesterday, at 8:30am, Dr. Erich Follmann passed on. Erich was a superior friend, colleague, teacher and scientist, and is already sorely missed. He was a warm, inherently likeable man, known for being level-headed and under-spoken. It is hard to find someone who would speak a word of ill against him, as he was not the sort to make enemies. I could learn so much about how he dealt with people.

Though sometimes he felt a bit like an anachronism, I soon found that it was because I failed to see the subtlety of his view of scientific topics. His understanding of wildlife diseases and epidemiology was impressively broad, and he helped greatly deepen our understanding of Rabies in the wild. He passed on so much knowledge to the newest generation of wildlife biologists through thoughtful, deliberative teaching process, both here at the university, and through outreach to the public at large. His knowledge of, and passion for Arctic Foxes was greater than any cliché could encompass.

It's not for his achievements as a scientist I will remember Erich, but as a fundamentally decent human being. I wish I could remember the first time I met Erich with any clarity, but from the beginning, I know I couldn't help but admire and respect the man. He had a warm personality, and was patient enough to always make time for people. More than once, Erich gave me invaluable advice that not only made me a better scientist, but I feel helped me realize what I need to do to become a better human. If I just knocked on his door (the one with the 'immunize your coyote' sticker on it, and the poster from his long time in Barrow), I knew that  he would make time for me. It's this I will maybe miss the most.

Erich, you were a great mentor and colleague. You are desperately missed.

Monday, 26 July 2010

Assorted Links

This is not how you get kids to sit still for their shots.
If someone used one of those on me when I was young, I would be terrified of rodents in addition to needles.

To quote the DNM:

JUNEAU, Alaska — Perhaps Sean Parnell’s greatest accomplishment so far as governor is that he’s not Sarah Palin.
I don't think they could be more spot-on. Yes, she's definitely not him. He's definitely not Sarah Palin. In fact, I have a scoop for the News Miner: Sean Parnell is also not Mister T. I pitty the foo who don't prioritize gasline development!

I'm a bit late with this, since everyone and their uncle is linking it now. But my computer was on vacation, is my excuse for not having it posted last week. But if you haven't seen it, a really cute porcupine:

Aaaand, we're back!

I got a new power-supply for my decrepit laptop just in time for my blogaversary! In 2007 I decided to try blogging about something other than me (since I'm very boring), and opened this one up to ramble about Alaska, Science, and things that hit my fancy. 3 years is nothing in person time, but in blog-time it's forever. Alas, I haven't hit the big-time yet - I've the same 30ish readers from a years ago, though I get a lot more hits from India these days. Hi India! But despite this, my total traffic has gone up a bit, thanks to Research I get a nice little spike in traffic whenever I do a story as part of that collective, and sometimes people give me later link-backs.

I haven't tapped a co-blogger, though I keep meaning to. I'm thinking of looking for someone who does a branch of Science I don't know much about (though, maybe I'd have to change the name). But that's harder than finding a roommate! What if they leave the milk out, and forget to close their HTML tags? Anyhow, I've gone and freshened up my blog a bit in terms of layout and so forth. The most noticeable change is my icon - I've finally ditched the old one I didn't take for one of UAF's handsome reindeer!

Will I still blog a year from now? Aipaagni! Maybe I will, maybe I won't. I don't know the future. But I do know I'm going to have another beer tonight.

Happy Birthday, Blog!

Thursday, 15 July 2010

Will we ever catch up with Cuba?

Marginal Revolution, a wonderful economics blog, reproduces this following graph.

I'll take it down if they want me to - it's their work. Two things strike me when I look at this. First, the bulk of the wold is around the gender parity mark for education. Except for one massive exception, which is India. India has a large population, and falls on the left side of the parity line, meaning that females have less than males. You could move all the other outliers over into the main cluster, and you wouldn't budge the world average much.

Secondly, Muslim Countries are at one some of the best and worst nations when it comes to parity. Pakistan isn't some third world nation - it's a major political and economic player. The quality of living is fairly high there. And yet they're very low in terms of parity. On the other hand, Iran is not known for its womens rights (although it is no Afghanistan), and Palestine there are systematic abuses of women in the name of Moral policing. And yet they're both healthily above the parity line.  I wonder if culture is a major cause of variance in this graph... I'd do the analysis myself, but I wouldn't know how to lump the countries.

Wednesday, 14 July 2010

Computer blahs

I'd love to hammer out a few more posts, but my computer is developing new broken parts all the time. The latest one is the power supply - I shouldn't be shocked, I suppose. This is a 4 year old computer! Here's two things to keep your attention for a few

Kangaroos fighting!

Apparently, I write like this guy:

I Write Like by Mémoires, Mac journal software. Analyze your writing!


Monday, 12 July 2010

Cry me a river

Nutraceutical companies are screaming bloody murder over European Union regulations that are beginning to give them the squeeze. You see, in the United States it's easy to sell whatever horse-anaq you want, making just about any claim you want, so long as you include the Quack Miranda warning:
"These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure or prevent any disease."
When I see that, I do not walk away. I run. Far far away. Basically, you can get away with whatever fairy tale you want if you throw that in your ad somewhere. There are few exceptions, such as specific medical claims, but woo-peddlers know how to dance around those requirements deftly. That's why you can buy all sorts of horrible substances as "Nutritional Supplements" in the United States, including ones that turn you blue.

Not so in the EU, under some new regulations coming into effect. Now you have to, Gasp! prove your statements. Thus, the wailing and the gnashing of teeth from the garbage-salesmen. BBC writes,
The Nutrition and Health Claims Regulation was adopted back in 2006 "to ensure that consumers are not misled by unsubstantiated, exaggerated or untruthful claims about foodstuffs", but it is only now that it is beginning to bite.
European Union member states have together submitted over 44,000 'general function' health claims on the part of manufacturers. These were boiled down to 4,637 claims for consideration by the Parma-based European Food Safety Authority (EFSA). Of around 900 claims so far examined, a massive 80% have been rejected.
80% sounds generous. There's a whole lot of stuff out there, from magic bracelets with magnets to sticks of wax you apply to the forehead. Sounds like they need to tighten their regulations a bit, because I promise you, the remaining 20% has some real garbage in there.
"It can take three years to get these kinds of human studies together but in the meantime the claims are going to be wiped away," he said. "The regulation is killing this industry and the job losses are already being felt."
Oh boo hoo. You have to actually prove the stuff actually works? The pharma industry has had to deal with more serious regulations for decades, and aside from the criminally insane, few people would recommend we go back to the days where a snake oil salesman was a real active player in medical world. Derek Lowe of the excellent blog "In the Pipeline" writes,
Cry me a procreating river, dude. Or come over here to where you can't get near the market without going through the clinic first - and for a lot longer than three years, I might add. And where every claim you make for your product is hammered out with the regulatory authorities, and if they catch you stretching out past them you can get fined out the wazoo. So they won't even let you keep running the ads while you go fetch some evidence, eh?
I would be slightly sympathetic to the nutraceutical sellers if it weren't for the fact that so many of their sales people encourage people to only take their products, causing unnecessary death. Homeopathy, and other forms of this anaq, kill.

Thursday, 8 July 2010

Spot the changes

Would you notice if I was switched with another person while we talked? What a silly question, you might reply. You can't get swapped out in a conversation, and if you were talking to someone, and not asleep, surely you'd notice if your conversation partner was changed for a new person. Oh, but you'd be oh so very wrong. Watch this short video, as a man asking for directions is changed out before two people's eyes, and neither of them notice that the person they were talking to is gone.

The problem is our brain is too good at filling in the gaps, and ignoring things it thinks are irrelevant. Much of what we see in our day to day life is a broadly painted picture, with our brains filling in the blanks with patterns from our previous experience. This makes eye-witness testimony some of the most unreliable and weakest of the forms of evidence. It's ironic that in law, eye-witness evidence is considered some of the strongest.

Edited to add: I forgot two things. First, I want to hat-tip Neuroskeptic for an article that had the video. Second, I want to link this other, more amusing video. In it, the person is not just swapped out for another White male with a similar hair cut, but by a bald White male, Black male, a much shorter Asian female, and a variety of other people. You'd think people would notice when the appearance and gender of the person they're talking to radically changed!

Tuesday, 6 July 2010

Impossible things

I regret that I haven't read as much "Classic" literature as I should. I've read modern books, but not much from before 1950. I find it hard to be interested in anything written before the invention of super glue or power steering, as people bereft these inventions would invariably have little of interest to say.

Still, I found this passage from Chapter 5 of Through the Looking Glass. I've italicized the bits I find the most interesting:
"Only it is so very lonely here!" Alice said in a melancholy voice; and, at the thought of her loneliness, two large tears came rolling down her cheeks.

"Oh, don't go on like that!" cried the poor Queen, wringing her hands in despair. "Consider what a great girl you are. Consider what a long way you've come to-day. Consider what o'clock it is. Consider anything, only don't cry!"

Alice could not help laughing at this, even in the midst of her tears. "Can you keep from crying by considering things?" she asked.

"That's the way it's done," the Queen said with great decision: "nobody can do two things at once, you know. Let's consider your age to begin with - how old are you?"

"I'm seven and a half, exactly."

"You needn't say 'exactly'," the Queen remarked. "I can believe it without that. Now I'll give you something to believe. I'm just one hundred and one, five months and a day."

"I can't believe that!" said Alice.

"Can't you?" the Queen said in a pitying tone. "Try again: draw a long breath, and shut your eyes."

Alice laughed. "There's no use trying," she said "one can't believe impossible things."

"I daresay you haven't had much practice," said the Queen. "When I was your age, I always did it for half-an-hour a day. Why, sometimes I've believed as many as six impossible things before breakfast.
There goes the shawl again!"

The brooch had come undone as she spoke, and a sudden gust of wind blew the Queen's shawl across a little brook. The Queen spread out her arms again and went flying after it, and this time she succeeded in catching it herself. "I've got it!" she cried in a triumphant tone. "Now you shall see me pin it on again, all by myself!"

"Then I hope your finger is better now?" Alice said very politely, as she crossed the little brook after the Queen.

Monday, 5 July 2010

It's the new Cornell

I heard this on the radio, and it's too funny not to pass on: Glenn Beck is starting his own "University!"

Now I'm absolutely positive that his scholarly credentials are impeccable, and Universities will be falling over themselves to recruit Beck-U graduates for graduate school.

I find it curious that he thinks the Federalist Papers are a mandate for limited government. I thought the Federalist Papers were actually advocating the larger government, and it was the Anti-Federalists who were wary of the expansion of governmental power. But they largely lost that argument (though they got a few concessions in the mix known as the "Bill of Rights") and nobody likes the losing team, not the least TV pundits.

Is it just me, or does "Beck-U" Sound like a curse? "Beck-U buddy!" "Oh yeah, well "Beck-U in the face!" I think we can all agree that this kind of profanity needs kept away from children (won't somebody think of them?)

This post is a metaphore for something

From the always excellent XKCD. I love this one because growing up, I didn't understand the difference between a simile and an analogy, which they teach you in year 3 or 4 or school (or so I seem to recall). I always thought language is a bit of a funny thing.

I hope you all are having a great 4th Holiday - unless you're not in the US, in which case I hope you're having a nice Monday the 5th. :) I need to get my behind to work, though, to get some things done!

Friday, 2 July 2010

Beer Notes on Samuel Smith's Imperial Stout

Samuel Smith's Imperial Stout by Samuel Smith Old Brewery, UK
The label on the stout 55cl bottle is a tad tacky, trying to look olde timey too much. When you open it, you're immediately slammed with fruity smells. This is only intensified as the coffee-black beer pours, leaving a dark tan head. In the goblet the lesser odour of yeast, and something faintly peppery peeks through. You definitely taste the peppery notes of the beer, a complex flavour almost like the offspring of coffee and banana. There are definitely bitter chocolates mixed into this mix. The carbonation is moderate, giving the beer a bit of a sparkling quality in the mouth. It's very reminiscent of Obsidian Stout by Deschutes, in a way, but with a sweet middle. In all, a pleasant though heady beer.
4.2 of 5, A-

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