GNR

Vijaysree Venkatraman has a nice article on Prof. G.N.Ramachandran's work at the University of Madras in the fifties and the sixties: How a Madras scientist won the global race in the ’50s to crack the structure of collagen. An excerpt:

First, he needed to find a source of collagen. The shark fin collagen from the biochemistry department on campus didn’t yield great images. Good quality pictures were essential to cracking the collagen puzzle, he knew. Leather, it occurred to GNR, was largely collagen.

Not far from the university campus was a new institute – the Central Leather Research Institute. GNR decided to pay his neighbours a visit. As he made his way there, the leather choices in GNR’s mind were Kangaroo Tail Tendon or Beef Achilles Tendon. The deputy director of CLRI turned out to be a kindred soul, happy to help a fellow scientist. The beef sample was easy to obtain locally. But if kangaroo collagen was going to yield the best diffraction images – as the scientific literature said – the deputy director promised to get GNR samples from Australia.

Thus, GNR found himself some purified marsupial collagen to work with.

The only information available on the fibrous protein collagen was this: one-third of its total amino acid content was glycine. Using this fact, looking at the pictures he had taken, GNR made an intuitive leap. [...]

What if Facebook was actually called Policebook?

Apparently, a serial murderer and rapist was identified by the police when they used a DNA database (called GEDmatch, which appears to be a site meant for helping people find their relatives) to which he had voluntarily provided his DNA data. Science has an interview with Yaniv Erlich, a Columbia University geneticist, who had alerted to possible uses of a site such as GEDmatch in 2014.

An excerpt where Erlich makes a key point:

Q: There’s a lot of concern about privacy being compromised here, but people voluntarily put their data into GEDmatch.

A: It's not like people fully understand the consequences of putting their DNA into a public database. They think, “So many people use the website, so it’s OK.” Or: “Oh, it’s a website for genealogy.” What if it was called Police Genealogy? People wouldn’t do it. We don’t think about everything. We think about the most likely thing. [Bold emphasis added]

Links

• Avery Thompson in Popular Mechanics: 5 Simple Math Problems No One Can Solve. "Easy to understand, supremely difficult to prove."
• Jordana Cepelewicz in Nautilus: The Social Physics of Trump Tactics. [Published a couple of weeks before the US elections, its title could very well have been "Phase Diagram of Bad Ideas"].
• Joanna Rothkopf in Jezebel: Here's What Happens to Your Body When You Die [video; 10 minutes].

Links

1. Harvard University press release: Cooperation, considered. "New model reveals how motives can affect cooperation". This is based on an interesting game -- a variation of the cooperation game by adding a twist that conveys some information about the first player's motives to the second player.

2. Emily Singer in Quanta: Game Theory Calls Cooperation Into Question. "A recent solution to the prisoner’s dilemma, a classic game theory scenario, has created new puzzles in evolutionary biology."

3. Clive Thompson in Smithsonian: How the Photocopier Changed the Way We Worked—and Played. A very interesting excerpt about how the US lawmakers viewed "xeroxing":

   “It was really a great moment in the late ’70s when it was a wonderful loosening of copyright,” says Lisa Gitelman, professor of English and media studies at New York University. These days, Congress is working hard­—often at the behest of movie studios or record labels—in the opposite direction, making it harder for people to copy things digitally. But back in the first cultural glow of the Xerox, lawmakers and judges came to the opposite conclusion: Copying was good for society.

Auctioning of Jim Watson's Nobel Medal

There are just too many bizarre twists in this sequence: James Watson auctioned off his 1962 Nobel Medal; the highest bidder, a Russian multi-billionaire, bought it and returned it to Watson. Read more about Watson's peevish motivations here, and about the aftermath of the auction here.

Links

1. On this the World Elephant Day, you should enjoy this cute overload video shared by Sanjeeta in our Institute's Ecological Students Society blog. Institute.

2. Andy Thomason in CHE: How Did the Federal Government Rate Your College a Century Ago?

3. Another bit of historical curiosity: Did Srinivasa Ramanujan fail in math? A. Venkatachalapathy clarifies with some documentary evidence.

4. Amir Alexander in SciAm: The Glory of Math Is to Matter.

   ... [M]ost fields of higher mathematics remain as they were conceived, with no practical application in sight. So is higher mathematics just an intellectual game played by exquisitely trained professionals for no purpose? And if so, why should we care about it?

Bias in Biology

Update: Vijaysree Venkatraman's Science Careers article does a good job of placing the PNAS study within the larger context of recent discussions about gender bias in STEM fields [Thanks to Madrasi for the comment-alert].

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Scott Jaschik in Inside Higher Ed: Are the Stars Sexist. The 'stars' in the title are the academic elite of the male kind in biology departments in US research institutions.

... Men are less likely than are women to hire female graduate students and postdocs. And of particular concern, men who have achieved elite status by virtue of awards they have won -- in other words, the men whose labs may be the best launching pads for careers -- are the least likely to hire women who are grad students and postdocs.

Loneliness

On 24 June 2012, Lonesome George -- the last member of his subspecies of giant tortoises of Galapagos island -- died. The last years of his alone-ness attracted quite a bit of news coverage -- see, for example, this and this.

Lonesome George has been on my mind for several days since our 13-year old son has been researching the Galapagos tortoises for his holiday homework project (what a shitty concept!). And along comes this moving piece by Robert Krulwich the lone known survivor of a plant species in Namibia:

So What If It's Ugly? It Just Keeps On Going ...

Far, far, far away is a great place to be — if you want to stay marvelous. There is a plant, called Welwitschia mirabilis (mirabilis being Latin for marvelous), found only one place on Earth. You can get there, as artist/photographer Rachel Sussman did, by driving through the vast emptiness of the Namibian desert, the Namib Naukluft, in Africa.

Welwitschia, when you finally get to see one, sits apart. It's very alone. All its relatives, its cousins, nieces, nephews have died away. It is the last remaining plant in its genus, the last in its family, the last in its order. "No other organism on earth can lay such a claim to being 'one of its kind,' " writes biologist Richard Fortey. It comes from a community of plants that thrived more than 200 million years ago. All of them slowly vanished, except for Welwitschia. It has survived by doing very little, very, very slowly — sipping little wafts of dew in the early mornings, otherwise minding its own business, as the big, busy world goes by.

Helminths

Thank FSM the elections are over! Any guesses on who will head the HRD ministry? And the S&T ministry?

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In an on-going effort to keep this blog going, let me start with a link.

An informative Q&A on the state of science behind helminthic therapy, or "the deliberate infection with helminths, or parasitic worms, by swallowing them or letting them crawl through the skin."

Caution: the article is infested with gross pics of worms.

Alberts et al: "Rescuing US biomedical research from its systemic flaws"

The long-held but erroneous assumption of never-ending rapid growth in biomedical science has created an unsustainable hypercompetitive system that is discouraging even the most outstanding prospective students from entering our profession—and making it difficult for seasoned investigators to produce their best work. This is a recipe for long-term decline, and the problems cannot be solved with simplistic approaches. Instead, it is time to confront the dangers at hand and rethink some fundamental features of the US biomedical research ecosystem.

That's the abstract of the PNAS paper entitled Rescuing US biomedical research from its systemic flaws by Bruce Alberts, Marc W. Kirschner, Shirley Tilghman,and Harold Varmus, each of them a biggie in science and in US science policy.

Link via DrugMonkey who has also penned a critique of this article; his post starts with a very perceptive tweet from Jonathan Gitlin: "This should be read as a mea culpa, given the authors’ roles in creating this problem in the first place."

Links

1. Wildlife photographer, author of Secret Lives, and IISc alumna Natasha Mhatre writes about the hard work that went into the wonderful potter wasp pic that won the first prize in the National Wildlife Federation photo contest. Key quote: " I didn't click it, I didn't snap it, no, no, I stalked it and I made it."

2. Mathematical eye-candy: John Baez has an animated picture of the Enneper Surface drawn by Greg Egan.

3. Vi Hart: How I Feel About Logarithms: "I like the number 8. I like the way it smells like 2 and 4 with a hint of 3 in a cubic sort of way ..."

Novartis judgment: Myth and Reality

In a must read write-up, Debunking Big Pharma's canard against Novartis judgment: Myth and Reality, Prof. Brook K. Baker, Professor of Law at the Harvard University and Senior Policy Analyst Health GAP, explains the essentials of the recent Indian supreme court verdict -- a landmark one that stood India up. Here is a sample to get you going.

Myth 8: The Novartis decision undermines the global search for new medicines.

Fact: Of all the canards, this is probably the most ludicrous. Big Pharma makes the vast majority of its profits on sales to rich patients in rich countries. Nearly 75% of global drugs sales by dollar volume in 2011 was in Europe, North America, and Japan. Indian sales comprised less that 2% of global sales. Drug giants do not make R&D decisions or shut down promising drug candidates because they didn't squeeze a little extra profit out of small market.

To the contrary, drug companies waste a lot of research dollars now trying to evergreen existing medicines instead of focusing on truly innovative medicines. They spend nearly 2 1/2 times on marketing and administration as they spend on R&D. Despite the "risks" of R&D they still retain more in profits than they actually spend each year on R&D.

Read more...

[Thanks Prof. Guhan Jayaraman for email share]

The Story of Vitreous Circulation

Several months back my father noticed black spots in his vision in the right eye. After a thorough check-up at a premier eye hospital in Chennai, he was diagnosed with a 'retinal tear'. Read more in wikipedia, under retinal detachment. Why does this happen? Remedy? What has this got to do with the title story of vitreous circulation?

The human eye is an imperfect sphere, about 24 mm (just about an inch) thick in the major axis, from the cornea on the front side to the retina on the back side. In between we have the lens supported on the front side by two tubular 'hooks' containing the aqueous humor fluid. As the name implies, this fluid is aqueous and can even circulate within the tubular 'hooks'. The retina, on which the lens focuses the images of what we see, is separated from the lens by a vitreous humor. This vitreous humour, by default, is not aqueous; it is jelly-like, what is known technically as a Non-Newtonian fluid. It maintains the shape of the eye, keeping the distance between the lens and the retina. As we age, the vitreous gel loses its aqueous nature and hardens. Unfortunately, as it hardens and contracts, confined between the retina and the lens, it 'pulls' on the walls. In effect, for some of us as we age, the retina is pulled in -- a retinal 'tear'.

The remedy is to stick the retina, figuratively, back in its place. For this, first we need to slice open the eye behind the lens and scoop off the jelly-like vitreous humour. Then, the retina is stuck back in its place by cauterizing it with targeted laser heating. Then the eye is stitched in place and closed. Within few weeks, bodily fluids ooze into the region between the retina and lens to replace the original hardened vitreous humour that was scooped off. Hopefully, when the eye patch is taken off, the vision should be minus those black spots and become normal. These things went on fine and let us say my father regained his normal vision.

But all of this is only background information for a short story that took off in between, which (obviously?) involves me and my research.

Links

This has to be among the best blog commentaries on open peer reviews of a published article: Another just-so story, this time about fists by T. Ryan Gregory at Genomicron is about a recent study that attracted tons of attention and coverage in news media:

To sum up, this is a paper that presents a small dataset of biomechanical analyses. It used an inappropriate sampling of subjects, and the only conclusions that can be drawn from the data are that the fists of trained martial artists are buttressed better than other arrangements of the hand. There is absolutely no information that is relevant to the question of why the human hand evolved as it did. (Note that this was not published in an anthropology or evolutionary biology journal). Moreover, to connect these observations with the evolutionary origin of human hand morphology requires some very unrealistic assumptions and a rather poor grasp of how one actually studies trait evolution.

The most impressive thing about this study is that it managed to gain so much attention with so little substance.

While we are on the topic of evolution, here are a couple more links:

1. P.Z. Myers has started a series on αEP (or, Anti-Evolutionary Psychology; apparently, the symbol α is used in the sense of "anti" in immunological circles), and two posts are already up: αEP: Shut up and sing!, and αEP: The fundamental failure of the evolutionary psychology premise.

2. Carl Zimmer has a nice summary -- in Of men, navigation and zits -- of a recent paper about sex differences in spatial abilities, and the proposal that "male spatial ability is not an adaptation so much as a side effect."

3. These two short videos are noteworthy for their use of vivid physical metaphors for describing how a lot of evolution is due to just plain "dumb luck".

IITM Research Highlights

In an inspired move, IIT Madras website now carries a separate section on their research highlights. This is an idea proposed by Prof. S. K. Das, our current Dean - Academic Research; and was executed by Dr. Phanikumar and his team.

The main page would show a catchy image that leads to a short write-up about the research intended for the general reader. A separate link can be provided there for more technical details. Each 'research highlight' would stay on the main page for about two weeks, before going into an archive, subsequently ready for recycle in a future time.

Now for the shameless plug part (you saw it coming miles ahead, didn't you?): One of my recent research project happens to hog the main page for these two weeks.

Check it out.

From the Annals of Longest Gramatically Correct Sentence

... that made a spectacularly wrong assessment.

"I believe he has ideas about becoming a scientist; on his present showing this is quite ridiculous. If he can't learn simple Biological facts, he would have no chance of doing the work of a Specialist, and it would be sheer waste of time both on his part, and of those who have to teach him."

From the 1949 school report card of Sir John Gurdon, 2012 Nobel Prize in Physiology or Medicine, when he was 15.

Here is an image of part of that report card.

Read more from this Telegraph article.

Links

1. Rahul Siddharthan's op-ed in The Hindu, The Real Questions from Kudankulam, drew a response from Atul Chokshi, a colleague in our Department. Rahul has posted his reply on his blog.

2. Subhra Priyadarshini has a good piece at the Nature India portal on research on social wasps being carried out in Prof. Raghavendra Gadagkar's group at IISc. Prof. Gadagkar is the author of articles with such cool titles as We Know that the Wasps 'Know' and A Subaltern View of Eusociality.

3. New Prof at the Academic Garden: Are You a Student? A hilarious story (with a pretty nifty twist in the tail), parts of which must be familiar with faculty members blessed with youthful looks.

4. Annie Zaidi: Smoke That! A column about issues raised by recent utterances of Justice Bhaktavatsala and Senior Advocate v. Shekhar [see also this recent post: Stuff Indian Government Says].

Mammalian, fleshy, inflatable cylinder

Because Arunn started it, and because we were just talking about a deceitful professorial dude wanting to stiff students, I just couldn't resist posting this one:

Penises of the Animal Kingdom

Do you know Jim Knowlton, won the IgNobel'92 for his anatomy poster "Penises of the Animal Kingdom," a portion of which is reproduced here.

[left to right: Whale, Elephant, Giraffe, Bull, Horse, Pig, Porpoise, Ram, Goat, Hyena, Dog, Man]

Read more at the Improbable Blog (check also this link for a video on how penises work; not as simple as you would snigger).

As a bonus, Jim Knowlton gets to teach courses with cool titles, like the Human Gross Anatomy at the Indiana University. The closest cool (or hot?) homophone that I get to teach is the 'Pennes' bio-heat equation, which looks like this:

;-(

Impact(!) of Mathematical Equations in Biology Papers

... The density of equations in an article has a significant negative impact on citation rates, with papers receiving 28% fewer citations overall for each additional equation per page in the main text. [...]

That's from the abstract of a recent PNAS paper: Heavy use of equations impedes communication among biologists by Tim W. Fawcett1 and Andrew D. Higginson of the University of Bristol.