Friday, September 09, 2005

Everything Scientific Vol. 1

In an earlier post of mine, there was a comment which asked Are the scientists not doing a good enough job of taking science to the people. There is some truth to that statement. Also, mainstream media (with exceptions like the New York Times science page) does a shoddy job of reporting scientific breakthroughs. Most scientific journals require subscription for access, making even editorials difficult to reach. Science bloggers do however write exceptionally about science, and the Tangled Bank is a great, fortnightly science Carnival.

I thought I’ll start a fortnightly feature with my own breakdowns and synopses of recent scientific breakthroughs I read over that time (spreading news of the scientific breakthroughs in a nutshell). So, here’s Everything Scientific Vol. 1. (Please comment on whether this is a good idea, and if so, what areas of science are interesting).

Chimps and us:
One of the biggest breakthroughs since the Human Genome project is the recently unveiled primary draft of the Chimpanzee (Pan troglodytes) genome). Now, this is a big deal for a number of reasons.

A genome, simply speaking, is the complete genetic material in an organism. The two genomes show (without any doubt) that they are over 98% identical. What makes us so different from Chimps? Because a genome contains BILLIONS of nucleotides (the nucleic acids that make up DNA, the genetic material), this small percent difference amounts to millions of base differences between chimps and humans. Other highlights include variations in different genomic regions. For example, the male Y-chromosomes show the greatest divergence, while the female X chromosome shows the lowest (but still substantial, so no bad jokes please) divergence between chimps and humans. The three most prevalent hypotheses about human-chimp differences are protein evolution (proteins are the “business end” of genes), the “less is more” hypothesis (loss-of-function changes, like loss of body hair), and changes in gene regulations. The genome will go a long way in addressing and understanding these differences. Additionally, Chimps and humans are prone to different diseases (for example, Chimps are pretty resistant to cancers), and these differences in the genomes can help us understand why this is so, and perhaps (years down the road) lead to therapeutics.

Another major breakthrough is the discovery of chimp fossils. There are tons of hominid (human predecessor) fossils, but early chimp fossils hadn’t been found. Well, now they have been unequivocally found, and all from the same part of central Africa where some of the oldest hominid fossils have also been found.

More reading (with subscription): Timeline, Chimp genome issue of Nature, PZ Myer's take.

Smoking makes you blind:
We know that smoking is bad for us, and messes our lungs up, and gives us cancer. But here’s strong Scientific evidence that smoking increases age related macular degeneration (AMD). Basically, AMD is jargon speak for severe and irreversible vision loss in the elderly. Bad enough being old and somewhat blind, but going blind faster than you need to? Bad mojo, that.

Rapid and cheap genome sequencing:
There were a number of interesting breakthroughs reported in Science, but one that caught my eye was a new and cheap way to carry out Genome sequencing (subscription required). In a nutshell, traditional methods (which involve amplifying fragments, and separating them by a process called electrophoresis) needed lots of expensive reagents and equipment, which only a few research institutes have (mostly in the US, Japan or Europe). But these new methods just use common epifluorescence microscopes and beads on immobilized gels (that most small labs have). So, to me the exciting thing is that this can easily be used in smaller universities (including teaching universities in India), and students in these labs might actually do more than learn theory.

Too much information?:
A major problem confronting scientists is the sheer volume of information that’s coming out. Even in specialized fields, there are dozens of specialized journals that a researcher has to follow. Little wonder then that the public rarely gets to see breakthroughs in newspapers. Below is an excerpt from the perspective of a geneticist (talking only about Genetics journals), which remains true for almost ALL research areas, and separating wheat from chaff is pretty hard (but it’s all wheat in this post):

Before the Second World War, there were only two North-American journals exclusively devoted to genetics — the Journal of Heredity and Genetics. In the late 1940s, Genetics spawned two progeny — the American Journal of Human Genetics and Evolution………… It emphasizes the contrast between those years, when a reader had a realistic chance of keeping up with the whole field, and the current plethora of journals that makes it impossible to keep up with even the tables of contents.

Pain is all in the head:
Perhaps you’ve experienced severe pain, and felt much better immediately after taking a painkiller. But not all of that effect is necessarily due to the medicine. There’s something called a placebo effect, where people often report feeling better if administered a pill (even if the pill isn’t really a drug). One of the funniest placebo effects I’ve seen is the placebo effect seen in Viagra’s drug trials (it was pretty large, and it was not the guys, but their partners who were surveyed!). An excellent recent paper in the Journal of Neuroscience clearly shows that upon administering placebos (when the patients were NOT told that it was placebo), the activity in regions of the brain that are involved in natural opiate activity (called endorphins, the same stuff that often gives runners a high) substantially increased. This might explain why homeopathy is so successful in treating minor ailments.

Nanoparticles go beyond carbon:
Chemical and Engineering news (subscription required) has a cover story on inorganic nano-materials (83(35), August 29,2005 ). Even the nanotechnology world, just like our own, is driven by carbon. Carbon remains king, but in applications where high loads, temperatures or pressures are required, these inorganic materials are making a mark. Fullerene (an organic compound) like inorganic molecules (WS2, MoS2 etc) are now increasingly being studied for their lubricant properties, and they just might be the future of the automobile industry.

Free access to scientific breakthroughs:
Most scientific journals remain “subscription only” (especially the high profile ones, which have the big stories). But there has been a recent effort to make information more available to the public. One fantastic effort is the Public library of Science and their two present journals (PlOS biology and PlOS medicine) look like they’re going to be high profile, high impact journals, FREE for readers. Their goal is to make science more accessible to people around the world, and it’s a super effort.

That's all folks:
Finally some humor, and what it takes to be a hostel warden at IIT (could apply to ANY university hostel). Not really science, but oh well!

Happy weekend reading!


Anonymous said...

I think it is a great idea.

Anonymous said...

It's a great idea. And an excellent first volume.

L said...

Hey keep them coming...a much better digest than me roaming all over for it..!! But only nature..?? I mean only Bio???

Abi said...

Hi Sunil,

This is an absolutely wonderful idea, and I am glad you have chosen to implement it. The first volume is excellent, and I am sure the future volumes will get only better.

Just one suggestion: please try to provide links to free online resources in addition to the original sources that may not be free. For example, I am sure other bloggers (such as P.Z. Myers) have commented on the Chimp genome, and linking to them would add great value.

Great idea, excellently done! Yeh dil maange more!

Anonymous said...

hullo! why is this not a nomination for my scian melt?! have included it anyways. check it out later...
good show !

Sujatha Bagal said...

Great idea Sunil. Many of these completely escape my attention on a regular basis. Would it be possible to include space-related info? Especially the hunt for other solar systems.

Sunil said...

Thank you all....

This one definitely had a biology/medicine/nanotechnology/chemistry bias, but this was just a starter. "I", I will definitely start including areas of astrophysics, paleontology, physics (except string theory, which I cannot understand), more chemistry in subsequent editions.......this was just a sampler to see if any one thought it was a good idea.

There will definitely be LOTS of space stuff (with the astrophysics stuff).....there's always some interesting news out there in the major science magazines.

Soultan of Swing said...

Awesome idea! I'm going to cancel my subscription to Discover/Popular Science!

Anonymous said...

Good job, Sunil! The warden piece was awesome, too.

Anonymous said...


I got the link to this post from Abi. It is truly wonderful. You might also want to check this site:
Most of the stories read like the reports in the Science & Technology supplement of the Hindu, though.


Sunil said...

thanks Vikram, Vishnu. Bala.....I think you should continue your subscription to Discover...that's a great mag. And you should perhaps become a student member of the american chemical society (it's pretty cheap, and you'll get free Chem & Engg news, which is a nice mag also!).

Guru.....that scienceblog link is very nice indeed, and good fun to read!

Anonymous said...

great idea.
on the smoking makes you blind part - i have come to the conclusion that smoking has probably caused every known human disaster since the fall of man:) the snake probably tempted eve with a cigarette shaped like an apple !
The kauravs and the pandavs went to war over a tobacco field and
of course ravan whacked ram's special blend of cigars!

i was an ex smoker btw :)

Michael Higgins said...

This is a nice idea. It gives people like me who tend to focus to much on econ or other specialized areas a opportunity to see other scientific breakthroughs.

Anonymous said...

Sunil, this is a GREAT idea; I really hope you plan to follow up with it :)

I was excited to read about the cheap genome sequencing methods. You're right, as a Life Science STudent in Bombay, it was frustrating not to be able to practically experience all the interesting stuff we were taught in lectures.

Sunil said...

Harini....yup...even though nicotine is extremely effective in reducing stress, the overall effect of smoking is waaaay too much into the negative side. Glad it's "ex smoker" now.

Michael, thanks. That was the basic idea, to bring out reports to people who otherwise wouldn't have time to follow them.

Ash, thanks. Yes, will follow up with it, every two weeks. Yes.....that to me might be the best thing to come out of this sequencing method (even though now conventional sequencing prices have come down substantially. But most small universities in India don't even have PCR machines, so, there's a long way to go there).

gawker said...

I'm not sure whats the point of carrying out research on the ways in which smoking can kill you. If the picture of a tarred lung does not convince a smoker to quit, why would the procpect of going blind do that?

nina said...

many thanks sunil!

it makes such a difference reading a summary written by someone who understands the source material, as opposed to the arbitly truncated versions passed off in the newspapers.

looking forward to the next installment.