Tangled bank #87

Welcome to another edition of the Tangled Bank, the blog carnival broadly about the natural sciences. My original idea was to get creative, and trace the history of logic while threading through another edition of the Tangled Bank. But these are busy days, so we’ll keep it short and sweet (and please excuse any typos or errors, this was put together rather quickly).

Here goes.

Critters everywhere:
Starting with archer fish, Andre at Biocurious writes about animals that intuitively know and use very advanced concepts in physics, but then, can they write equations? And I had absolutely no idea that those garden destroying squirrels were immune to rattle snake poisons. Read all about that, infrared body temperatures and tail flagging over at Grrlscientist’s. She also has another post on the deadly Marburg hemorrhagic disease, which is incurable and is transmitted by a virus. Apparently the the source of this virus is a fruit bat. At the Invasive Species Weblog, Jennifer writes about the common periwinkle snail, which we first thought was an invasive species, then were told that it has been in North America for 8000 years, and now it is back to being an invasive species. And what’s a “tangled bank” without mention of the Galapagos islands and the fabled finches? Mike of 10,000 birds writes about the unique birds of the Galapagos. That island has such an amazing concentration of diversity, it even has four endemic mockingbirds (and there’s just one in all of the rest of North America).

Pure, unadulterated science:
Veo Claramente has an excellent post on the damage response framework of microbial pathogenesis. That’s some very good science writing on a fascinating topic. At the wonderful world of Archaeozology there is a post on the diversity and origins of cattle. If you ever wondered how and when the wild, cud-chewing bovine was domesticated, here is your answer. In some more excellent science writing, Aaron at Synapostasy has a three part mini-review on the evolution of X and Y chromosomes, so here are links to Part I, Part II and Part III. At Cotch.net, Joe, writing about evolution and cancer, neatly summarizes a review on DNA check points, tumors and the loss of apoptosis. And over at Ouroboros, there is an interesting post on delayed aging via increased Arf and p53, discussing if tumor suppressor genes are beneficial or detrimental with respect to ageing and lifespan.

Religion and science:
There’s surprisingly little about religion and science this week. But there’s still some good stuff. At the Primate Diaries, Eric lucidly explains The feeling of what happens: Science, faith and Nature’s error. He also has an excellent post on sexual equality, double standards and social scale.

Odds and ends:
Andrew the Sexy Secularist is making a sales pitch for some rather nice looking jewelry. Except that these are DNA double-helix bracelets! Go buy some.

Its midnight, and you can’t go to sleep? Do you look at those early sleepers and early risers with utter disbelief? Don’t worry, you aren’t an unnatural freak. You fall into the group Paddy K calls the B-team, and your tribe is large.

Sharp brains links to a number of research articles on “Computer based cognitive training (or “brain fitness”), and some of the links are fascinating. Also worth reading are the ten habits of highly effective brains. I’m going to practice positive, future oriented thoughts everyday, starting now.

From Omnome comes the story of an inventor who claims to have invented injectable heat generating nanoparticles which will cure tumors. Omnome doesn’t think a cure for cancer is going to come from here. Finally, from my own blog, here’s a little bit of history, on standing on the shoulders of Giants.

That’s it for this edition of the Tangled Bank. The next edition will be in two weeks, at The behavioral ecology blog.

Book review: The scientists

I have to start off by admitting that it had been quite a while since I read any book that was over 500 pages long, with the words neatly typed in a small font size. The Harry Potters don’t count, and their pleasing illustrations and tween-friendly, reassuringly large, bold font and plenty of action make them rather easy to read. But when I saw the exquisite cover of John Gribbin’s The Scientists: A History of Science Told Through the Lives of Its Greatest Inventors I knew it was a book I had to read.

Gribbin, of course, is a formidable science writer, and his In search of Schrodinger’s Cat once taught me more about quantum physics than high school and college did together (admittedly, even after reading the book, I still knew next to nothing about quantum physics). So, when I noticed that he was the author, I expected The Scientists to be creative as well as highly readable. This book sets out to do much more than describe the history and facts behind one (or even a group) of discoveries. The book attempts to describe the past 500 odd years of scientific discovery, starting during the later part of the European renaissance, where a burst of human creativity eventually laid the foundations of the modern scientific method, and progresses to the present times of frenetic scientific activity and discovery by the minute.

Any book that sets off to describe 500 years of discovery takes the risk of being excessively descriptive or tedious, burying the reader in scientific fact or jargon. Constantly talking about great discoveries can effortlessly kill any interest the reader has in science, a fact neatly attested by my own high-school science text books (which were well meaning, but failed to capture our attention). But Gribbin beautifully weaves a tapestry of the stories of the discoverers, the scientists themselves, and through these stories brings out the great scientific discoveries that ushered in the modern world of science. Everyone likes reading stories about people, their lives, their problems, their inspirations, their animosities and their transgressions. But a purely historical account of the great scientists of the past, without describing their discoveries, is meaningless. Gribbon manages to perfectly balance both aspects, and walks through the lives of the scientists who shaped modern science, while beautifully describing (in considerable detail) their contributions not just to that aspect of science, but to scientific thinking and future discoveries as well.

The first chapters of the book are aptly titled Renaissance men and The last of the mystics, starting with the likes of Copernicus, Bruno, William Harvey and moving quickly to Tycho Brahe and Kepler. It is both fascinating and incredible to read about the times in Europe then, in a world deeply clouded by superstition, and where religion (in Europe it was the Catholic Church) had a vice-like grip on all knowledge. The earliest scientists weren’t really called “scientists”, and most of them did quite a bit to ruffle the feathers of those in authority, particularly the church, for which many of them suffered. It is equally interesting to read about their lives, and how many of them were themselves deeply influenced by the church (or were clergymen themselves). While here, Gribbin describes Galileo as the “first scientist”. While describing these early giants, Gribbon subtly but surely brings out the concept of the Scientific method, which was slowly beginning to develop and starting to leave an imprint. In the first few chapters, Gribbon devotes much of the space to a description of the times and the lives of these pioneers, rather than their discoveries alone. This allows him to elegantly establish a historical context from where the modern scientific schools of thought were allowed to emerge from.

It also allows Gribbon to steadily build the pace of the book. The fascinating stories of these scientists draw the reader deep into the book, and allows the reader to paint a picture of these people and their times (the only annoying thing is that I keep picturizing Pope Urban VIII with a bald head, sunken jaws and gleaming schrew-like eyes, while Galileo describes his Dialogue Concerning the Two Chief World Systems, and I just can’t get that out of my head). By the third chapter you are engrossed in the book, and are ready to jump into the world of the “founding fathers”, Descartes, Huygens, Boyle and the subsequent “Newtonian revolution” (while Newton was undoubtedly a giant amongst giants, it is without doubt that numerous pioneers like Halley and Hooke played almost as significant a role in ushering the scientific “revolution”). Gribbon also points out that the “scientific revolution” didn’t really happen the way we think “revolutions” happen (giant rumbles and the falling of the Bastille), but slowly churned and grew, with each generation of scientists building upon the work of the preceding one. And from the era of Newton, there was no looking back for the world of science.

After Newton, the face of science changed for ever. The foundations laid by astronomy and classical physics (culminating in the Principia allowed scientists (or “gentlemen scientists”, as they were in those days) to start thinking of simple laws by which the universe worked. The steady discoveries of astronomy and geology meant that geologists and biologists would have to confront the fact that the earth was far older than traditional Biblical interpretations, something that would have substantial ramifications on society. By the time Gribbon finally describes Charles Darwin and his life, he has already described the prior foundations that helped Darwin formulate his theory of natural selection; the substantial work on understanding the age of the earth, the work of Charles Lyell, the earlier work of Hooke and Leeuwenhoeke in describing biological cells (and their similarities), the superb work of Carolus Linneaus (who classified organisms based on similarity, breaking them down from species all the way to phylum and kingdom), and finally the brilliant work of Alfred Wallace, who independently proposed a theory of natural selection, which prompted Darwin to complete and publish his own (more well developed) theory. Given this complete historical context, we understand how it was but inevitable that Darwin (or someone else like Wallace) would naturally have to put all the pieces together.

As the book nears modern times, the pace dramatically starts to increase. After all, by the late 19th century, science was poised to explode. It was the end of the amateur gentleman scientist, and the beginning of the professional scientist. The fields of chemistry, physics and biology started to become distinct. And then with the discovery of radioactivity and the beginnings of quantum physics, the world of science pretty much changed for ever. The chapters describing the work of the likes of Thomson, Rutherford, Plank, Pauli, Heisenberg, Schrodinger and the innumerable contributions of Albert Einstein, all move along at a frenzied pace. There are now too many characters around, and Gribbin can no longer linger on the lives of one or two alone. Yet he manages to squeeze in little anecdotes or stories that keep us, the reader, lapping it all up. Nuggets, like Rutherford being greatly amused when awarded the Nobel prize for Chemistry (since at the time the atom was under the purview of chemistry), since Rutherford thought of himself as a physicist and didn’t think too much of chemists, or the story of the Curies, and Marie Curie’s notebooks are to this date still so radioactive that they are kept behind a leaden safe (both Marie and Pierre Curie suffered seriously due to radiation, something they didn’t know about then. So they literally died because of their science). Near the very end, we reach the spectacular discoveries of genetics, DNA, the genetic code and finally, the realm of outer space.

I can only describe this book as a superb effort. It is one of those books that appeals at different levels. A reader can open any chapter and read it independently, enjoying the stories in them. The writing is tight and vividly descriptive, and is simultaneously written for scientists, amateur scientists, science aficionados, historians and everyone who likes a good yarn. The book serves as an outstanding reference for the past 500 years of western scientific thought. There are some books we never buy (but sometimes “borrow”), others we buy just to read once and then forget. But some books are keepers, which we keep going back to again and again, discovering or relishing a new nugget each time we dig into it. This is one of those books.

The joy of questioning

Selva, who publishes TheScian.com and blogs as the Scientific Indian on scienceblogs had asked me to write a guest essay for his publication, TheScian.

My essay, titled "The joy of questioning" is now online on TheScian. What's more, Selva has taken the effort to make an audiocast out of it, with some snazzy background music to boot.

Quite flattering.

Read or hear the essay here.

A history of Indian mathematics

As many readers of this blog know, I’m fascinated by the history of discovery. While you certainly can be a good scientist without a knowledge of the history of discovery, there is much to learn from not just what is known, but also how it was discovered. Usually the stories behind discoveries are almost as fascinating as the discoveries themselves. Additionally, reading about the stories behind the discoveries also sometimes are humbling experiences; and makes you realize how much work might have gone into some findings, or how much some other discoveries was based on a collective work many individuals preceding the discoverer.

Additionally, reading about the history of discovery also makes you realize that knowledge or discovery was never restricted to one group or place alone, but different civilizations at different times had bursts of creativity, resulting in important discoveries. From there you can begin to understand how some societies progressed more rapidly than others. For example, Jared Diamond in his Guns, germs and steel uses this knowledge to understand how western societies managed to reach their current level of domination.

Anyway, coming to this post, I have always been a little disappointed in the way Indian history was taught to us in our schools. This is particularly true about the history of discovery (in science and mathematics) in India. There was the old colonial school of thought (which some people still have) that the foundation of all knowledge came from the west (starting with Egypt, Greece and Rome). Yet any historian knows that in the ancient world, there were thriving civilizations in Persia, India and China, and more importantly, there was not just trade, but well established and vibrant exchange of ideas and practices across these regions. This automatically suggests that there must have been some good ideas and discoveries in all these regions, in order for them all to be advanced (for the time) societies. There’s also the opposite (and rather amusing) view that comes from an excessively Indian nationalistic prism, which more or less states that all knowledge that exists in the world was discovered in India first (come on, tell me you’ve heard this one). Again, given the evidence (about vibrant civilizations in contact with each other across Europe and Asia), this isn’t likely to be true either. That said, there was nothing worthwhile that was ever taught to us about Indian science and mathematics.

As I read more about Indian mathematics in particular, I was fascinated by how rich the field was, and how much it has contributed to the field of mathematics in general. Some contributions are quite well known; and many of us are aware of the modern numeral system and the use of zero, first developed in India. This number system was later adopted (and improved) by the Arabs and Persians, from whom it reached Europe, and is now called the Hindu-Arabic numeral system. Some other contributions, like the development of the decimal system are also well known.

Anyway, here is a fantastic article by J.J. O’Connor and E.F. Robertson, on the excellent Mac tutor, on the history of Indian mathematics. This briefly mentions contributions like the numeral system, but also describes (or links to more articles about) major contributions and discoveries in algebra, trigonometry (including an independent discovery of the Pythagoras theorem at about the same time as Pythagoras), quadratic equations, the invention of the “Taylor” series, the value of pi, and much more, all of which makes absolutely fascinating reading.

I found it well worth my time to read more about it here (Indian mathematics, The sulbasutras, Indian numerals). Fascinating.

Tangled bank and Mendel's garden

It was an incredibly busy week so blogging has been a little slow, but things should be back on track sometime next week.

Meanwhile, here's an important announcement. Two absolutely wonderful carnivals are coming here to Balancing life.


Another edition of Tangled bank will be hosted right here on Balancing life on the 29th of August. If you have recently written something in the broader areas of biology, medicine, science in general, or about the natural world in general,go ahead and send in your posts. Send in your entries BEFORE the 28th, to host[at]tangledbank[dot]net .


The second carnival,the September edition of Mendel's garden will be hosted here on Balancing life somewhere in the first week of September. Mendel's garden is about all areas and aspects of genetics. "Everything from transcription to evolution to genetic counseling and social implications of genetics research are welcome." If you have never participated in Mendel's garden, this is a good time to do so. Send in your nominations by September 7th. You can use the Blogcarnival submission form to send in your entries.

On the shoulders of giants

I’m presently reading an absolutely fascinating book called The Scientists by John Gribbin (I’ll have a detailed review of this one of these days). This book discusses the development of modern science, starting with the beginnings of modern scientific thought in the west, about 600 years ago. This book is really about the different personalities that shaped science, as much as it is about the discoveries themselves.

Not surprisingly, over time our ideas about the scientists themselves become clouded by myth, urban legend and the force of their discoveries themselves. We start to imagine scientists in a certain mould, and typecast them into wrought-iron personalities, just like we do to most famous people. Soon, the myth becomes so large that it is impossible to even think that these people had any other sides to their personalities. Of course, we see this all the time with important political and historical figures, like religious leaders or kings or presidents and the like, where it is often impossible to say anything that goes against popular perception.

Anyway, Isaac Newton and Albert Einstein are probably the two scientists who have absolutely captured popular imagination. They were each a colossus of their times, and their scientific achievements are towering (and that would be my understatement for the day). When I was in high school, I had a thoroughly entertaining chemistry teacher who would regale us with stories in most of his lectures, usually to inspire us, and would end up struggling to finish the syllabus. Chemistry was an afterthought. Anyway, one of his stories was about Newton and his famous “shoulders of giants” saying.

In case you haven’t heard that one before, Newton wrote in a letter to Robert Hooke that said

“If I have seen further it is by standing on ye shoulders of Giants.”

To the casual reader, it might seem like Newton was being rather modest and respectful, and suggesting that his towering achievements were built on the work of pioneers before him. Anyway, that was what my chemistry teacher told us. Now, my chemistry teacher was an outstanding yarn spinner, and in an earlier time in India would have achieved great fame and fortune as the village story teller. But for all his ready wit and imagination, he unfortunately was a terrible historian, and thought that actual facts were just trifling inconveniences that needed to be put in their place, ignored when justified. He had done so with this famous quote as well.

So, coming back to Gribbon’s book, I thoroughly enjoyed reading the parts about the lives and contributions of Hooke and Newton. Newton was undoubtedly one of the greatest scientists of all time, but contrary to popular modern imagination, was hardly the paradigm of virtue some make him out to be. He was petty, vindictive, churlish (I’ve never used that word, churlish, in a sentence before), and extremely influential as well. If he decided to dislike someone, that poor sod was toast. Unfortunately for Hooke, that was exactly what happened to him.

Hooke, in terms of pure scientific achievement, really contributed almost as much to science (if such things are really quantifiable) as much as Newton, even though he is mostly remembered for one of his minor contributions, Hooke's law of elasticity. Hooke had made substantial contributions to the field of optics (particularly through his epic book, Micrographia), and in planetary motion. In a series of letters about planetary motion, Hooke had suggested conceptual links between attractive forces and forces decreasing with the square of distance (the inverse square law that later became a foundation of the concepts of gravity that Newton mathematically proved). Hooke also had suggested at various times that planetary orbits could be elliptical (again, it took the mathematical genius of Newton to actually prove this), and furthermore, Hooke had also independently observed what are now famous as Newton’s rings. Now, from all surviving accounts of Hooke (and there are few surviving accounts, the reasons for which we’ll talk about in just a few minutes), Hooke was a first rate experimental scientist (though not a mathematical genius), and was also someone who loved to share his ideas and discuss them freely. Newton was quite the opposite. Anyway, Newton published his masterpiece, Philosophiae Naturalis Principia Mathematica, but in it he did not acknowledge or even mention Hooke’s contributions at all. While Hooke was as excited and amazed by the brilliance of Principia he was very disappointed that Newton did not give him any credit at all. What is more, Newton decided to take great offence when Hooke brought up the subject.

He then used his considerable power (Newton held many powerful positions with patrons from the royal family and nobility of England) to diminish or expunge all accounts of Hooke’s numerous contributions. Hooke made many attempts of rapprochement which Newton spurned. It was in one of these numerous letters that the two exchanged where Newton made the famous quote on standing on the shoulders of giants.

Why shoulders of giants, you ask? Well, Hooke was a physically weak man who suffered from numerous ailments (from childhood), was short in stature and had a severely crooked back. Newton, in all his spite, was mostly mocking Hooke, as if to say that Hooke’s own contributions were tiny.

While none of this takes away anything from Newton’s astounding scientific achievements, it does make the person behind them so much more human, and not perfect. We need to learn to dissociate the person from the achievement, but often fail to do so.

So much for the stories of my chemistry teacher. Now I need to check on one of his other favorite stories, that of Kekule. I’ll wager right now that my teacher had no idea what he was happily talking about.

What’s for dinner tonight?

Life has plenty of problems. Some are dark and depressing, some urgent but negotiable. Some go away when solved, and others persist. Some can be solved, and others just cannot. But there is one problem that never fails to bother me. It is said that an army marches on its stomach. And living in the States, I’ve been told enough times on TV that it is an Army of One. Well, in that case, I am an army, and my marching stomach comes home hungry every single night after a hard day’s work, and unfailingly asks

“So, what’s for dinner tonight?”

Thousands of years ago life was simpler. Humans were simple hunter-gatherers, and the evening meal depended on the ability of the group to manage to find some food. If they found and killed a mammoth, it was mammoth a la carte for dinner. If all they found during their quest were some gnarly roots, bitter berries or rotten carcasses, well, that was for dinner.

Then humans began to prosper as they learnt agriculture. Before you knew it, thousands of years had passed, fruit, grain and livestock had been domesticated, salt and spices painstakingly researched and then, finally, there was real food. With real food and prosperity came the joy of choice, and people the world over (at least those who could afford it) could choose what they wanted to eat every day.

Which brings us back to the problem at hand; that of my dinner.

Life growing up in India was exceedingly good. Mom was always there toiling away to provide the best she could manage for dinner. She would select the choicest of vegetables everyday, and bring them back from the market. Then, each day a different dish would be painstakingly prepared for dinner, with rice and lentils on one day, or spinach and chapattis on other days. A South Indian spread on some days, or a North Indian effort on another. All I had to do was to come back from school, finish some homework, show up on the dining table, consume unimaginably large quantities of a delicious dinner and then complain that I would have preferred puris and chole to rasam and cabbage. My poor mom.

But now life’s not easy for us. We’ve got to come back home after impossibly long and tiring days and then decide what to make for dinner. The body, mind and heart all insist that the only reasonable place to be is the couch, but that rascal stomach wills us on towards the kitchen. And here is where being an epicure really, really sucks (I’ve always wanted to use that word, “epicure”. Almost sounds sophisticated). As far as calories go, there is never a problem. There’s always the option of eating a sandwich or opening a box of macaroni and cheese or consuming some ever reliable Maggi or Ramen noodles. Pizza or takeout? Naah. Unfortunately, those are just calories. If they were ever used to describe food, food would wrinkle its nose and walk away. Sure, I can eat sandwiches or cereal on one night, but if I ate that two nights in a row, that dictatorial tongue and stomach just do not permit it.

And this puts me in a quandary. If I want good food, I’ve got to (to use an American cliché) make it happen. Now, don’t get me wrong here, I love cooking. But the problem is that I like it so much that it has to be done well. The tomatoes have to be lovingly sliced, and the onions perfectly chopped and laid out on the cutting board, and then caramelized to perfection. Simple rice and lentils don’t do it for me, but fried lentil balls, now that is something. The tongue demands a different taste every night, from spicy and tangy to mild and sour. These things require time and energy, and that, on weekdays, is like the proverbial Mastercard, priceless.

So here is the quintessential dilemma. I need to eat good food. In order to eat good food I need to make good food. In order to make good food, I need time, readily available groceries and energy. I don’t have all three of them.

But I still need to eat good food.

Can there ever be a solution for this? Can the stomach ever stop saying “what’s for dinner tonight?”

Grant writing 101

(Since many of my readers are scientists/academics/students, I thought this post might be useful for them. I wrote this as part of my own notes after attending a short grant writing workshop).

A big part of the rat race in science is all about money. After all, science and research don’t come cheap, and research in the biological/biomedical sciences cost small fortunes. Anyway, there are a lot of scientists out there who seem to be both fantastic scientists, and fantastic at raising money for their research. But there are just as many (in my opinion) lousy scientists who seem to have no problem in raising money, or superb scientists who struggle to get enough grant money to even stay afloat.

My own personal hope of course is to be successful in raising money AND be a really good scientist. But I do need to learn about the do’s and don’ts of fundraising. I had the opportunity of attending one of those workshops for postdocs on grant writing, and I must say it was a very good learning experience. So, I thought I’d share some of the things I had learnt there from the PIs who were conducting the workshop.

The focus of the workshop was to outline how a senior postdoc or an early investigator would go about writing a first significant grant. The main bread and butter grant for most researchers is an “RO1” from the NIH, typically worth ~1.2 million dollars spread out over 5 years, and the idea of this workshop was to outline what went into making a successful RO1 grant (and could be easily modified for any other grant of course).

Before I get into the details; here’s one general point that I liked. Stick to the page limits of the grant, and don’t try to fudge it by decreasing font size to 8 or margin limits to 0.1 cm. Be concise and stay under the limit. If you cannot stick to the word/page limit, there’s something wrong with your grant.

1) The background and specific aims: Start by stating your specific aims clearly, and keep it under one page. Ask the right questions: do you want to do it? Do you care? Will the reader care? Will your institute care? Can you do it?

Divide the problem into well defined components. And once you get going on the grant, get advice from people who are successful in getting grants. In the specific aims, it should be clear to the reader on why you’ve chosen this problem and why anyone should care. Don’t fish where everyone else is fishing, unless your bait is very, very special.

Of course, the proposal needs a good hypothesis. But importantly, it should also be well stated, in one or two concise sentences. The hypothesis should be both testable and significant. And end with something like “to fulfill these goals, we propose the following 3 aims”, all of which are arranged in a nice, sequential order. The goals of the entire proposal (and particularly this first part) should be clarity, cohesion, competence and curiosity. Don’t neglect the abstract, because that’s the first thing anyone reads. In fact, put a lot of effort into it.

2) Preliminary data: these days, the amount of “preliminary” data that goes into a grant is just a little less than what will go into a Cell paper. But the purpose of this section is to convince reviewers that you can do all the proposed preliminary aims. So, in the specific aims, it is important to at least have the first 2-3 that you absolutely CAN do, and perhaps one that is speculative. Any more that is too speculative, and you are toast. Expectations in a grant are very high, and funding is very tight.

3) The research plan: First of all, you cannot have too much depending on the success of one set of experiments. Which also means that your specific aims should have some independence from each other. If your first aim fails, your entire proposal should not sink. And, this is something many scientists forget, appearance counts a lot. So, however brilliant you are, don’t be sloppy in the writing. Write concise sentences, spell check your document, write in PARAGRAPHS (and not endless pages), leave page breaks, and make nice figures. Highlight key points.

Finally, there are all the other “hidden” factors that you need to highlight. If you are proposing experiments where you don’t have demonstrated expertise, see if you can get letters of support from other people in your department who are experts in that area. If your department/institute has certain core facilities or resources that you can use, highlight that.

After all of this, there is one area that will remain a crapshoot. The reviewers themselves. But sometimes (or often) it is possible for you to find out who might be in your review committee (particularly with NIH study sections). You may be able to find out what their pet peeves are, and can make it a point to address those areas carefully in your grant proposal.