Tuesday, March 27, 2007

Tangled Bank #76 at balancing life

Science, they say, is a way of life. Now, I don’t know when I started living the scientific life, but I surprisingly can remember some of my earliest experiments as a little child. As a toddler some three years old, I loved mangoes, knew that mangoes came from mango trees, knew mangoes had seeds, and knew that trees grew from seeds. So I thought it would be simplicity in itself to eat a mango, save the seed, and plant it so that it would become a tree and give me as many mangoes as I could possibly gorge. I took the mango seed to my backyard and dug a little hole in the mud where I planted it. And every morning for the next four days, I watched and waited for a mango tree to grow.

Nothing happened.

And then I learnt that seeds need water and care, and trees take years to grow. I loved learning how things worked, and especially how the natural world functioned. So, without any more ado, here’s a tribute to that mango seed’s lessons in a mangolicious edition of The Tangled Bank.

(Mangoes, like all fruits, have dozens of distinct species, each with a taste, smell, shape, texture and history of its own, and to me are more than just fruit).

Alphonso pickings:

Mike from 10000 birds is down in Texas, stalking the golden cheeked warbler. That little bird is as beautiful as a juicy golden alphonso. Unlike their golden-yellow cousins the leopards, the clouded leopards are small, dark, and perhaps more elusive than the golden cheeked warbler. But they’re just as beautiful. Grrlscientist writes about the clouded leopards of Borneo, which are now officially a separate species, distinct from other clouded leopards found across South Asia. This edition of the Bank is particularly good for rare animal species. Grrlscientist also writes about a rare bird, the long-whiskered owlet, being seen in the wild. Apparently, this sighting is the first in years. Now, if only the long-whiskered owlet would audition for the next Harry Potter.

Dasheri days:

While still talking about animals, it’s time to visit Greg Laden’s blog where he has an absolutely fascinating post on cloned wolves, wolf behavior, wolves as social animals, and why wolves won’t breed in zoos. On the other hand, Matt at the Behavioral Ecology Blog is interested in sex and the single fur seal, as he sums up studies on polygyny and the laziest males who get some action.

There’s little from the world of fossils this week, but Matt Celeskey at the wonderful Hairy Museum of Natural History writes a fascinating post about a 95 million year old fossil of a lizard which has taken limb shortening to extreme levels. It’s almost a snake. Speaking of fossils, there’s good news from what I think is one of the most impressive organizations in America, the Smithsonian. Joshua, thinking from Kansas, keeps a close eye on happenings at the Smithsonian, and talks about the long overdue resignation of Lawrence Small, the secretary of the Smithsonian. Good riddance, that.

We’ve talked about animals and birds and even fossils, so let’s not leave out plants. Over at the agricultural biodiversity blog is an excellent post on mapping underutilized genomes, and the sequencing of the taro genome, and why it can be tremendously useful. Taro, mango, all good.

Langda in space? Why not?

There’s always room in the Tangled Bank for odd science, and the great outdoors (space). Mark Rayner at the skwib talks about tracking and destroying asteroids with lasers. If you’re worried that the end of the world is near, thanks to a rogue asteroid headed for earth, head over there. Over at Daylight atheism is a beautiful post reminding us that the Earth is not at the center of the universe, and there’s a universe out there to explore.

Bainganapalli in winter? I think not.

Perhaps thanks to Al Gore’s recent effort in Washington there are a good number of posts this week on climate change, global warming, conservation and consumerism.
Jeremy Bruno over at the Voltagegate wonders aloud about celebrities endorsing conservation, and consumerism.
Phil for humanity has some facts about global warming that even a kid can understand. I think he does kids a disservice. They’re smart, and learn. It’s us adults who refuse to believe facts.
Over at the bioblog is an excellent post on the constantly changing definition of drought and the effect of human action on the amount of water around. Wyatt at foggy bottom lantern thinks Al Gore’s description of global warming in terms of a fever is a great idea, and goes on to describe fevers and global warming.

Sweet Chausa and spicy Totapuri slices:

Over at A blog around the clock Bora summarizes a recent paper which shows the importance of glucocorticoids (cortisol) in the regulation of circadian cell cycle rhythms. Bora’s summary is excellent. Meanwhile, at Fight aging, there’s a nice summary of recent interest in microglia, and their role in degenerations of aging, as well as emerging putative roles of nitric oxide in aging. I’m particularly fond of nitric oxide, so, go read that post!

Ourobros has a fascinating post on longevity vs evolutionary fitness and describes why traits that might shorten the lifespan of an organism might be positively selected for if it improves reproductive fitness.

I dream of mangoes:

To finish off this edition of the Tangled Bank are some posts that are lost or are almost philosophical. At The price of rice, Barry asks if death is really necessary, talking of Kurzweil’s prediction that we’ll reverse engineer our brain some day, and overcome death. Meanwhile, over at sharpbrains, Jeffery Gonce, a high school psychology teacher, shares one of his student’s essays titled “Tis better to give than receive”: oxytocin and dopamine. The Ominouscomma seems to have a rather talkative subconscious mind, which responds to the conscious mind. At OhCash are his observations and thoughts on why dogs love people.

And to end the Tangled Bank, here’s some advice from Paddy K on understanding women. It’s a doomed effort, but some readers might want to try.

That’s it for this edition of the Tangled Bank. The next one should be up in two weeks, at Tara Smith’s Aetiology.

Help! Feeds messed up

For some reason, I was tinkering with the labels of my older posts, and that seems to have messed up my feeds on feedburner (and now a whole bunch of older posts are showing up as recent posts).

Does anyone, ANYONE, know how to fix this? If you have any ideas, please let me know.

Sunday, March 25, 2007

Science on TV

Growing up in India as a kid, the television was reserved mostly for Saturday evening or Sunday morning entertainment. Those were the glory days of Doordarshan, the state-run TV station that had one (and later, two) channels during the height of socialist repression. That was it. One channel, with a couple of soap operas, a Kannada movie on Saturday, cartoons on Sunday morning, and a Hindi movie on Sunday. By the time cable TV made its appearance and started becoming popular (with Star TV, and some 10 other channels), I was practically through high-school.

Anyway, that’s digressing from the point.

In spite of being the sole channel on television, there surprisingly were a reasonable number of rather decent shows. And in one area, the state-run channel did rather well. They took their role as “educators of the nation” rather seriously, and so there were some very good science shows that we ended up watching.

As a kid, the first science show I watched (on the much-abused Doordarshan) was the wonderfully evocative Cosmos. I remember Carl Sagan’s voice, though at that time I had no idea who Sagan was, and probably didn’t even fully comprehend the series. The shoddy state run TV station continued to surprise, broadcasting a number of films from The National Geographic’s enviable collections. On Saturday mornings (I think), a series of films called Expeditions to the animal kingdom were aired, and as a kid, I could name and correctly identify more animal, bird, insect, crustacean or fish species than the rest of my family combined. Then there were the movies from Project tiger, the Indian government’s focused (and at the time successful) effort to save the tiger from extinction due to poaching and habitat loss.

On Saturday afternoons, the Universal Grants Commission (UGC) would air dull, amateur, but very informative documentaries on various topics of science and education. And perhaps the finest science show that was ever aired on Doordarshan remains the always enjoyable Turning point. I would wait with eager anticipation every week for Girish Karnad and Prof Yash Pal to show up and host that show, and watched with rapt attention as the great discoveries of science were unveiled and explained. To me, all those years ago, Prof. Yash Pal seemed like the most astounding mind on the planet. He seemed to know everything, and science as a career option almost seemed irresistible.

I mean, imagine being a fountain of knowledge talking science on TV!

It seems like kids today, thanks to a glut of sports, music, cartoons, entertainment, sitcoms, movies and the like, have less time to watch shows like these (that we “had” to watch, since there was nothing else on TV). It’s a pity. But, as I now continue to watch my favorite show on TV, Nova, I often nostalgically remember those old days, and thank Doordarshan for its science shows.

Tuesday, March 20, 2007

A mosquito for fighting malaria

There’s been some buzz in the news recently, about genetically engineered mosquitoes that can no longer transmit the malaria causing plasmodium parasite to humans. The idea now is to now potentially introduce these mosquitoes among populations of normal mosquitoes. Over time, as the mosquitoes mate with each other, the normal mosquitoes would pick up the gene that would prevent infection by the plasmodium parasite, and so if the plasmodium can no longer infect mosquitoes, the mosquitoes would no longer be able to transmit the parasite to humans.

There are two angles to this story that interest me. First, there is the science itself, which is fascinating. Understanding the mechanisms of how the plasmodium parasite infects mosquitoes, and enters their gut and propagates is interesting in itself. There is also the other side, the “practical” side which proposes making these engineered mosquitoes as tools to control and prevent malaria, which at a first glance seems reasonable. So, I thought I’d post my thoughts on both these aspects.

I heard of the research itself some three years ago, when the research group published an interesting paper in Nature. Now, for those of you unfamiliar with malaria, the disease is caused by a parasitic protozoan called plasmodium. The disease is transmitted to humans by mosquitoes, which have simplistically described as the “insect vector” for the parasite. In reality, the plasmodium is a parasite of both humans and mosquitoes (and the mosquito is a parasite of humans), and needs both in order to go through its full developmental cycle. In mosquitoes, the parasite (in a specific life cycle stage) needs to go through two epithelial regions of the salivary gland and the midgut, and only then can it complete its development. Now, researchers had identified a small peptide, called SM1 that bound these two epithelial regions, and inhibited the crossing of this region by the malarial parasite. After doing some rather challenging experiments, they were able to now genetically engineer mosquitoes that expressed this SM1 peptide on their own. The big finding in this study was that when these mosquitoes ingested the malarial parasite, the parasite was not able to cross the epithelial region, and so could not complete its development. So, these mosquitoes would not pass on the parasite to mammals (and us).

The authors then suggest that it might be possible to use these mosquitoes, and introduce this gene in wild mosquitoes. This could be another way of disease control. However, those early studies did not show if these genetically engineered mosquitoes were really fit for breeding, and if they could be used to control infective mosquito populations. Contrastingly, it is also known that mosquitoes that are infected with the plasmodium parasite have decreased fertility. So, the authors carried out some follow-up studies (which are now in the news), where they hypothesized that if the genetically engineered mosquitoes (where the plasmodium could not complete its life-cycle) were fed with infected blood, they would be more fit and reproduce better than normal mosquitoes. If this were so, then if there were two equal starting populations (of normal or genetically engineered mosquitoes), the engineered mosquitoes should survive and proliferate better than the normal “wild-type” mosquitoes. They found exactly that.

The two groups of mosquitoes were allowed to feed on mice which were infected with the plasmodium parasite. Over time the mutant engineered mosquitoes began to rapidly outbreed the normal mosquitoes, and soon became the majority population. For a control, the researchers used normal, uninfected mice as food. In this control, the two groups of mosquitoes proliferated at the same rate, with no advantage for any group.

All this is nice from a scientific perspective. There’s no doubt that the researchers have proven their two main points. They’ve shown that you can engineer mosquitoes that won’t be fully infected with plasmodium and these mosquitoes can no longer transmit the parasite to mammals. They’ve also shown that these mosquitoes have a growth advantage over normal mosquitoes when infected with the parasite, so will outgrow normal, infected mosquitoes.

What I am far more skeptical about is the use of these mosquitoes in controlling and perhaps helping to eradicate malaria. The idea is that if these mosquitoes were released in the wild, they would soon become a dominant population. So, not only will they no longer be able to transmit malaria, but the plasmodium parasite itself will find itself without a host, and so over a long time will not be able to propagate.

Sure, it might work. But the thing about malaria (and a bunch of other infectious diseases) is that it isn’t impossible to control or diminish malaria. It’s just that in the places where malaria now still persists, there isn’t an infrastructure in place to really combat the disease. The disease goes along with breeding mosquitoes, poor sanitation and lots of stagnant water, poor hygiene, and poverty. Malaria was very common in the United States about 70 years ago. Systematic efforts on mosquito population control, dredging stagnant water pools and good sanitation pretty much wiped out malaria from the States (in less than 20 years). It’s possible to control the disease without releasing mutant mosquitoes (though I personally do not have too many ethical issues on starting trials with these engineered mosquitoes to see if they’ll help). And by just keeping it simple, it will actually improve the lives of many people along with controlling the disease.

But the world isn’t simple, is it?

(references: Nature 417, 452-455 (23 May 2002) | doi:10.1038/417452a, Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0609809104)

Sunday, March 18, 2007

Tangled Bank here on Balancing life

The Tangled Bank

The next edition of Tangled Bank is going to be right here on Balancing life, on the 28th of March. If you write any post broadly in the areas biology, medicine or science in general relating to the workings of the natural world, and would like to participate in the Tangled Bank, or have read someone else's post you really like, go ahead and nominate it (only one post per person, please).

Email them to host[at]tangledbank[dot]net , with Tangled Bank somewhere in the subject line. You could also email them to me directly at linuslax[at]yahoo[dot]com

Do try to send in your entries by the 26th.

Wednesday, March 14, 2007

Jesus camp

A little late, but I finally got to watch last year's exceptional film, Jesus Camp.

If a documentary film could ever be called "chilling", this would be it. If you haven't seen it, go get the DVD.

Till then, here's a trailer for you:

Saturday, March 10, 2007

Be fat, the wonder drug will save you

I’ve often blogged about the fascinating field of calorific restriction leading to longer life spans. Some of the most spectacular work in the field has been from David Sinclair’s group at Harvard (along with work from his former boss, now competitor, Lenny Guarente at MIT), starting with work on the sirtuin (Sir) genes, which are deacetylases credited to causing the increased survival during calorific restriction.

The knowledge that calorific restriction (which is not starvation or malnutrition, but just highly restricted calories, more than 30% less than normal diets) led to a substantially increased lifespan in all organisms from yeast through flies to mammals is quite old now. However, the discovery of the sirtuins by Sinclair really changed the way we looked at the field. Now, we had a molecular target that seemed to control the beneficial effects of calorific restriction. This gene appeared to regulate processes like fat metabolism, glucose and insulin production and cell survival. Not surprisingly, the group started to look for small molecules, drugs, that could increase the activity of Sir genes, and thereby potentially provide the benefits of calorific restriction without actually being on a restricted diet. After all, let’s face it. We’d all love to gorge ourselves like the proverbial pigs, avoid all exercise, but still live healthy, long lives. In earlier studies, Sinclair’s group did find a group of compounds that appeared to do just that; activate Sir genes, and provide the benefits of calorific restriction without the need for a restricted diet.

That study though was in yeast. Sure, it’s all well and good for yeast to live longer, and perhaps brew more beer, but we really care about humans. So, the question was would these compounds work in mammals?

I got to hear Sinclair talk at a department seminar a couple of weeks ago, and heard him talk about just that. It’s one thing reading a paper about a study, and another thing altogether to hear it from the people who found it. The personality, enthusiasm, “humor” and everything else about people make it often more interesting to hear about their work, rather than just reading about it.

David’s talk was excellent, and he had little trouble engaging the (rather large) audience. Their “star” drug, the molecule that worked best in yeast and worms, was resveratrol. They now carried out tests in mice, which were put on a super high fat and calorie diet, and then fed resveratrol. Their goal was to see if resveratrol might result in the mice on a high-calorie diet living as well and as healthily as mice on a normal diet. Effectively, they wanted to see if the mice could gorge themselves and still live well.

Their results were nothing less than dramatic. The mice on a high calorie diet would normally die far earlier than mice on a normal diet. However, when the high calorie diet mice were fed resveratrol, they went on to live completely normal lives, similar to mice on a normal diet. What’s more, when these researchers analyzed the mice in greater detail, they found that resveratrol improved insulin sensitivity in mice (which would decrease blood glucose levels). Also, the high calorie fed mice became rather fat, with huge livers, but resveratrol prevented the increase in liver size, keeping it normal. Resveratrol also improved heart function in these mice. One of his most striking pieces of data was an array study, where they studied the expression pattern of numerous genes in normal mice or high calorie mice. The expression patterns were dramatically different. But, when the mice on high calorie diets were fed resveratrol, their gene expression patterns almost exactly mirrored mice on a normal diet.

David calls the mice on resveratrol the “Lance Armstrong” mice. Their muscles looked more like the muscles you’d expect on athletes, even though they were rather chunky. In a hilarious video, he showed a short movie where mice fed on a fat rich diet were put on a treadmill. The fat mice struggled to stay on the treadmill. Guess what the resveratrol fed mice did? They practically (and effortlessly) outran the treadmill, to reach the wall and then tried to jump over it.

So, even though the mice on a fat-rich diet became fat (in spite of steady doses of resveratrol) they were super-healthy. Obviously, some of us asked him what happened to normal mice that took resveratrol, and he said they were just superbly fit. What’s more, his company is now carrying out trials for resveratrol (and other drugs developed from resveratrol, that target Sir’s) in people, and the results, in his words “were very, very encouraging”.

The future drug of choice for performance enhancement, anyone?

I thought the whole concept was fantastic, starting from finding an activator for an enzyme (which is much harder than finding an inhibitor) to the fact that it actually worked.

You can read all about it in more detail on the Nature website if you want to.

Postscript: Resveratrol is found naturally in grapes and in wine. But don’t try to drink too much wine, though it might be delicious. You’d need to drink a massive amount of wine to get enough resveratrol to do you any good, and by then you’d probably be dead from cirrhosis of the liver.

Tuesday, March 06, 2007

Hot stuff

Given how hot South Asian and South East Asian food is, it almost seems incredible that chili peppers originated in the Americas. The old world, and India in particular, were famed for their spices, including black pepper. But the good red and green stuff was introduced to Asia only after Columbus stumbled upon America (and the fool still wanted to prove that he’d reached India). Anyway, it’s needless to say that a whole bunch of people across the world are addicted to the hot stuff.

But how long has it been since the humble chili made it to our (at least the native American) plates?

It looks like the chili’s been on our plates perhaps even before humans made plates (or pottery technologies developed). They’ve been cultivated and eaten for over 6000 years. At least that is what some researchers from the Smithsonian have discovered. And their discovery was almost accidental.

For many years, researchers had found well preserved starch granules in specific sites (I cannot even imagine how people go around looking for almost fossilized starch grains). Most of these were identified as starch grains from maize or squash, which were probably staple food for the Americans then. However, many of the starch grains were not identified and remained a puzzle. Apparently, no one tested chili peppers, because they assumed that early farmers would concentrate on growing staple food, like maize or squash. To make things harder, chili peppers don’t leave microfossils, and pollen (or most other organic matter, really) doesn’t preserve all that well in the wet, hot tropics.

But these researchers found some starch grains embedded in some stone tools and cookware, and were confirmed to be chili pepper starch grains (using a number of techniques). The archeological site where these were found, and the tools themselves were over 6000 years old, in a very early human settlement in Ecuador. What’s more, similar starch grains were found in a few other sites, across South America.

This really amazes me, partly because I think the “hotness” of chili peppers were evolved by plants ostensibly to protect themselves from predators. When we bite into a chili, there is that moment of pure, indescribable anguish, as the sinuses are cleared and the eyes water (while the tongue, throat and bowels quiver in terror). Why do we keep going back to chili peppers? And why, why did people 6000 years ago decide to start domesticating and cultivating pepper? (Someone needs to go and test if eating chili peppers releases endorphins, and gives us an addictive “high”).

(You can read the original paper here, in Science 16 February 2007:Vol. 315. no. 5814, pp. 986 – 988. Picture from Nature doi:10.1038)

Saturday, March 03, 2007

The power of assumptions

This is an old one, so bear with me.

A farmer, a biologist and a theoretical physicist meet to discuss how cows could give more milk.

The farmer thinks, and says we need to improve the food content, nutrition and living conditions of cows. Then they'll give more milk.

The biologist thinks, and says we could make a genetically engineered cow that would make much more milk.

The physicist thinks, pauses for a second, and then says....

"Assume the cow is a sphere......"

Ah, the power of assumptions! I remember plenty of physics classes in high school, where we had a bunch of problems to solve, and had to start off our solutions with reasonable assumptions.

Only, not all assumptions I made were reasonable. After all, isn't reasonable a subjective word? I distinctly remember knowing so little in my JEE entrance exam that I solved every single problem with mostly ridiculous assumptions. Assumptions can be powerful starting points to solve problems, but only when accompanied by sound reasoning. If you do solve a problem with an assumption, it is imperative to now go back and test your assumptions to see if they would hold true under varying conditions.