Keep It Simple, Silly

Random, caught-my-eye post of the day from http://science.slashdot.org/story/14/09/22/1312251/how-our-botched-understanding-of-science-ruins-everything?sdsrc=popbyskid

An anonymous reader writes

"Pascal-Emmanuel Gobry writes at The Week, "If you ask most people what science is, they will give you an answer that looks a lot like Aristotelian 'science' — i.e., the exact opposite of what modern science actually is.

Capital-S Science is the pursuit of capital-T Truth. And science is something that cannot possibly be understood by mere mortals. It delivers wonders. It has high priests. It has an ideology that must be obeyed. This leads us astray. Countless academic disciplines have been wrecked by professors' urges to look 'more scientific' by, like a cargo cult, adopting the externals of Baconian science (math, impenetrable jargon, peer-reviewed journals) without the substance and hoping it will produce better knowledge.

This is how you get people asserting that 'science' commands this or that public policy decision, even though with very few exceptions, almost none of the policy options we as a polity have have been tested through experiment (or can be). People think that a study that uses statistical wizardry to show correlations between two things is 'scientific' because it uses high school math and was done by someone in a university building, except that, correctly speaking, it is not.

This is how you get the phenomenon ... thinking science has made God irrelevant, even though, by definition, religion concerns the ultimate causes of things and, again, by definition, science cannot tell you about them. ... It also means that for all our bleating about 'science' we live in an astonishingly unscientific and anti-scientific society. We have plenty of anti-science people, but most of our 'pro-science' people are really pro-magic (and therefore anti-science). "

END of Article

At least for now, this holds true, the deluge of jargon in a publication is quite unwarranted, in my humble opinion. However, we are in a vicious cycle that starts with papers getting rejected because they are too "easy to understand" or are doing "simple experiments" that a 12 year old could do. The reviewers think that if it is too simple then it doesn't behoove them to publish it in their journal, "what is the big deal?" they ask.

The question of "what is the big deal?" gets answered by academics in the form of massive amounts of data generated from high-throughput experiments using expensive and cutting edge equipment followed by an application of every form of statistical testing procedure known to man. If there isn't a hypothesis then we'll let machine learning algorithms loose on the data. Something will have to bunch up, cluster or have significance somewhere. We can make up the story after we have the results in front of us.

Why do we do it? because everyone else is doing it and we won't get publications and the grants that follow them if we don't do what "everyone else is doing".

What does this lead to eventually? A flood, thousands of papers buried under thousand others. Filled with jargon, complex mathematical notation, statistical tests that were probably cherry-picked because they gave the answers that were what the investigators wanted.

Finally, you the science newbie has to enter this world, you pick a topic and are rewarded with a deluge of papers. How does one get around to reading all of this? A FeedReader helps, but only in aggregating papers from topics that you would like to read. They still have to be read by you, understood, comprehended and the methods have to be tried out to see if they work.

Then you stumble upon all the limitations of the published method when you start to work on it. It will be quite some time before you realize that the best stories that could be told using the method are already published and that you are looking at the dregs. It's too late to back out, you've spent a considerable amount of time trying to understand it and get it working and you can't abandon all the work just like that. You try to mix and match different things to see if something comes, anything at all. Your desperation colours your perception and you attempt to justify any result by bending your "unbending scientific principles". Then it becomes an exercise in torturing the data with statistical tests until you get the answer that you want, even a hint of it supported by a P-value cut-off that you chose after the the application of the statistical test and the P-values came. Then you try to wrap it up into a story and get it published.

Why bother? I don't know...maybe because we have nothing better to do.

Shathranj ke Khiladi (Experts of Chess)

TLDR;
Random musings about Chess and Life, The title of this post is from a story by Premchand, a Hindi writer who wrote pithy, wry and direct stories about aristocracy and the life of poor men under them. Experts of Chess briefly is a story of two chess players so engrossed in games of chess that they ignore the fall of their king and his kingdom and the decimation of soldiers, later they have an argument about the game and duel each other and are both mortally wounded which is the end of the story. This post has little to do with that story though and more about the game of chess and an analogy to life.

#include<chess.h>
#include<musings.h>
void main()
{

I’ve taken to playing chess about 4 months back. I was introduced by a friend to the game again (I used to play real lousy when I was a kid). She is good at it and has me beat all but 2 times out of the 12 games that we’ve played, there was a vodka fueled game where I was beaten really badly and I can’t still say it was because I was inebriated. Then I’ve played against the computer on Chess Titans on Windows 7. Started with Level 5, the first game lasted two hours with plenty of Undo Moves and a reversal from a checkmate (which according to the game statistics is counted as a loss even if you undo), played from there and won by checkmate. 

While I played I realized that early in the game there was no way to predict the future moves of my opponent to more than 3 moves as the number of possible combinations were insane. However, shit could get real very fast if you played fast and loose.

There is quite a bit of breathing room in the beginning and this is when you should prepare the layout of your pieces such that they back each other up. If you play a move just for the heck of it without an idea of what strategy that move benefits to, then you’ve wasted your move. A move that could tighten your offence or strengthen you defence is what you should always be on the lookout for.  Also no point taking out the big guns early when the board is full and you have no space to move. When the opponent is clever enough, even if you have them defended you will lose them to the pawns, which is never a good deal. Use the Knight early on, it can jump over pieces and on a choc-a-bloc board, it is a good way to pick out defensive pawn positions, avoid losing the Knight if you can help it. The computer always tries to get my Knights in exchange for its own and considers it a fair trade. I wonder why it would do that considering it could have used them just as well.

There are no spare moves towards the middle of the game. You have to play everything with a purpose and exactly right keeping all the pieces backing each other up while breaching into the enemy lines.  The middle of the game is when the pieces start going off the board and you have to start weighing your options. Would you mind losing a Knight for saving a rook or a bishop? A pawn threatens both your Knight and your bishop, which one do you choose? The Queen, yes you have to save her and you could end up sacrificing quite a bit just to save her. The computer always goes for your queen so never put it up-front with a lesser piece defending it. Send the Rook in for an attack if you have to and then defend the Rook with the Queen but never vice-versa because the computer will just take your Queen and not care what it loses in return. In other scenarios you will notice it putting its Queen head-to-head with yours and then losing its Queen to take yours. But this is a pre-meditated calculation that assumes that a Pawn from the computer is already half-way across the board and will reach the end of the board and promote itself to a Queen which will make your King a sitting duck.

The end of the game is a little anti-climactic. I’m told that towards the end, the game is predictable, so predictable that in fact the computer stores look-up tables for the moves that can result in the fastest check-mate. The irony is that, despite the board being largely empty, there is not much space to run around to and you will eventually be trapped into a corner and check-mated. Hope or horror also exists when a pawn goes over to the other side of the board and gets promoted, mostly to Queen. That is mostly the end, if you have just the King and other odd-end pawns, it could also be the end for the opponent if you have a bishop or another Queen on a largely empty board with the other King in the corner.

It seems to be quite a useful analogy for life. Play for a strong defense, build your fundamentals. When the attack comes you should have your defense ready otherwise it will be decimation. No point taking out the big guns first. Play the small battles with the pawns and weaken the defense of the enemy, then start moving in for the kill with the big guns

Recently I happened to play Level 6. It is very hard for me and this particular game lasted 2 hours or more. I got check-mated in at least 6 different ways and kept undoing the game to see what the point of no-return was. I played a variety of endings which were ending in check-mate. Finally I found an undo point where it seemed I was able to smuggle my Queen bang in the middle of enemy territory. It already had its Queen and kept troubling my King in an oscillating check series where I stayed put in a, for the lack of a better word, fortress of Pawns in a triangle. Then began my series of check moves, I had my Queen backed up with a Rook and that Rook backed up with another Rook just so that the computer Queen wouldn’t dare kill on the diagonal. Then a sudden check by the computer Queen which came and stood right behind my King and I took the Queen for nothing. Then there was nothing to do but to use my Queen as soon as possible for a check-mate and that was it. I had won Level 6 for the first time ever. I had drawn it previously but a win always has a nice warm fuzzy feeling to it. To beat a machine, well maybe not the best chess engine but a fairly decent one.

However if I were to stretch the analogy of chess for life far enough, is it possible that you could have made a series of moves from where there is a point of no return? It would not be really possible to know because I knew that until I did about 9 undoes (10 moves back more or less) I was not able to get to the point in the game where I was able to save my power pieces and also move in for the kill. I repeatedly lost my Rooks and the Queen in exchanges where the computer retained a Rook, lost the Queen and managed to promote a Pawn to Queen in the next 3 moves to give me a check-mate. Out of the 9 variants of the undo games I played (they all ended in check-mate for me differently) only one of the games was where I managed to defend as well as move in for the kill simultaneously.

Is it possible that I may have reached that point in life as well, where I may have just made the best of the positions I had set out initially but now it is just a few moves to check-mate? There is no Ctrl Z to the moves you make in life and there is of course no going back to play a different variant. Is the late 20’s, the middle game of academia-chess? Have the choices that determine the closing moves of the endgame been made? I guess I will know 5 years down the line and it will be too late to do anything by then. All I know is that going from one day to the next, I always make sure I always know more than what I started out with and knowledge has always been power. By a check-mate I mean the glass wall you hit up against and you just can't go higher than that, a win would be a place where you do the science you like and you live it too. Also when you realize that academic hierarchy like a lot of others in the world, is a little lop-sided, and you definitely don't want to be at the bottom of a pyramid of incompetents.

As to the question of if it ends in a check-mate for me, your guess is just as good as mine.

}

Science Humour

In the first 2 years of my Ph.D, I happened to educate myself on how to write scientific text that can be horrifyingly obfuscating as well as technically impressive while looking scholarly enough to pass for publishable writing. Sometimes however there has been un-intended humour that comes only when you read it aloud. On the other hand, I try not to pass up the opportunity to crack a subtle joke in an institute seminar or lab meeting. So here are a couple.

For instance we had this hypothesis that exhaled breath would contain organic compounds that would help us detect the constitution of the microbiome of the gut. Basically the relative proportion of sulphur containing gases, methane and other gases would indicate what sort of bacteria were present in the gut. Being in an omics institute, we gave this collective parameter the name "gas-ome".

If that wasn't funny enough, in a proposal that I ended up writing, we had figured that different bacteria could emit the same gases so gas production alone couldn't be used to determine constitution. So we wrote, "Since gas production is degenerate among different species" to peals of laughter on recognizing the un-intended pun. By degeneracy we implied that different species could produce the same gases (like same codons being produced by different tri-nucleotides), however the social implication of that sentence wasn't clear until we wrote it and read it aloud.

My seminar jokes have been subtle. One which I never made was this one

 "As much as you think that this is a scene from the movie "Kill Bill Vol I", it is not. It is a correlation of epistasis values between FBA and SGA for 97000 double knockouts."

Of course this wasn't going to go well with an audience that may not have watched the movie so I let it pass.

Another one, which I didn't crack but was there for everyone to see was a slide on using mathematical models to construct a minimal genome. See if you spot it, it is a calculus joke.

Hint: Top left corner, math expression is a joke.

Speaking of calculus jokes, here is one from my favorite (although slightly irregular) science comic at www.abstrusegoose.com

That's all for the random blog entry of the day folks!

Winston Churchill quotes

From here:
www.tehelka.com/remembering-indias-forgotten-holocaust/

1. “the starvation of anyhow underfed Bengalis (was) less serious than sturdy Greeks” 
2. “I hate Indians. They are a beastly people with a beastly religion.”
3. (Another time)“the beastliest people in the world next to the Germans”

Okay I think that I won't be quoting this guy ever, and neither should well-fed Bengalis.