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Friday, September 28, 2012

Molecular Biology Primer: The Central Dogma

The science of molecular biology is found in the latest cancer treatment, behind the development of antiviral and antibiotic drugs, and even in today's superhero movies (where the hero's DNA is altered through a lab experiment, spider bite, etc). But just what the heck is molecular biology? Do you need a degree in biology or chemistry to understand and appreciate what occurs on the smallest scale in every living organism?

This is part of a primer written for readers with very little knowledge of biology. I have compiled this brief explanation of biological information, as well as some resources for further studies, so that such readers will still be able to access and digest any future posts with commentary on scientific topics.

In the rest of the post, I hope to accomplish a few things. First, through a musical analogy of the journey from sheet music to sound, you will learn the so called 'central dogma' of molecular biology, the flow of information which is at the very heart of life. This will lead into an explanation of how this information is ultimately expressed in the form of the function of proteins, how this expression is controlled, and some of the consequences of protein function.

My depiction of the central dogma and the flow of information from genetic material to protein function. For the aficionado, I attempted to make this as accurate as possible: the mRNA sequence translates to the protein shown, and the protein is folded in order to shield the hydrophobic residues A, V, and L.

In a future post, I will describe in more detail some of the methods researchers use to study molecular biology. As a teaser, I highlight here some typical questions posed by molecular biologists. (Note: these questions are probably more typical of academic scientists. This is another product of that axiom, 'write what you know'). Finally, I will provide some resources for further study (in particular, check out of the videos from the Dolan DNA Learning Center. They are really cool!).

Tuesday, September 25, 2012

Combating Anti-Sicilians with ..e5: Anti-Rossolimo

This post is a continuation in a larger series, providing here some opening analysis, statistics, and games. Please see the previous post for an introduction to the topic of meeting the Anti-Sicilians with an immediate …e5

1.e4 c5 2.Nf3 Nc6 3.Bb5 e5

White has several plans in this position. They can try to exploit the d5 square with Nc3, or the d6 and d5 squares with Na3-Nc4, possibly followed by Nc4-e3-d5. They can try to achieve the pawn break c3 and d4, hoping for a trade that will undermine Black's structure. Some players will attempt to trade on c6, and others still will rely on a slight lead in development by playing O-O, delaying selection of one of the above plans until Black commits.

Out of 259 games starting from this position, White scores ~61% (128 wins, 58 draws, and 73 losses). A more telling statistic, however, is the average rating of each player and their performance; if the White players from this sample are consistently stronger, then it is to be expected that the will win more often.

Average ratings and performance

White rating: 2285 (200 games); White performance: 2330 (59% vs 2265)
Black rating: 2265 (195 games); Black performance: 2190 (37% vs 2285)

The performance differential is also in White's favor. One should keep in mind, however, that this is still a fairly small sample size of games, and even if the statistics are unfavorable, it doesn't indicate that the line is unplayable. Furthermore, quite of number of the Black losses occur late in the game, after Black has already equalized (that assessment is my own, coupled with confirmation from SCID's engine).

You can download the full SCID opening report (in PDF format), which includes a theory table, as well as the PGN file containing the games. In addition, I've condensed the lines presented here (with annotations) into one single PGN file, available for download.

In most of the variations below, I will include statistics and reports on those specific lines, despite the fact that the small sample size for some makes them almost meaningless. Again, keep in mind that statistics aren't everything.

These variations will be split up into 4 different sections:
A) Miscellaneous 4th moves from White
B) 4.Bxc6
C) 4.c3
D) 4.O-O

This is my first large analysis post, and so you can expect updates to the lines (as mistakes are found) as well as updates to the format. Read ahead, and make sure you check back often!

Friday, September 21, 2012

Combating Anti-Sicilians with ..e5: Introduction

To paraphrase Vizzini, one of the villains from the Princess Bride, most people think twice about going against the Open Sicilian (as White) when death is on the line. This is true in the ranks of amateurs and when playing games in blitz or online; often, this will leave Black facing various Anti-Sicilian setups, such as the Rossolimo and Moscow variations, the Alapin Siclian, the Closed Sicilian, the Grand Prix, and a variety of gambits (Morra, Wing).

Fortunately, there are a number of ways Black can successfully combat these openings, and usually can chose a setup that is similar to their favorite line in the Open Sicilian (Dragon players can fianchetto, Taimanov players can play ..e6 and ..d5, etc). Players who employ the Sveshnikov variation (A group of which I am an occasional member) are often at a loss to achieve similar play versus the Anti-Sicilians as they do when playing the Open Sicilian. 

Wednesday, September 19, 2012

Chess Primer: Calculating Moves

If you have read the other Chess Primer posts on this blog, "Basic Rules" and "Understanding Chess", then you will know how to move the pieces and how to judge (at a very simple level) the effectiveness of a move. In order to play good chess, and follow the games of experienced players, it is also necessary to be aware of several common attacking patterns and combinations, and to be able to calculate if certain moves will lead to an effective attack or a dead end. Chess players refer to a series of moves which require concrete calculation (move by move analysis) as tactics.

Calculating Moves 

Section I: The Double Attack
Section II: The Pin
Section III: Tips on calculating combinations

Tuesday, September 18, 2012

Chess Primer: Understanding Chess

This post is intended to be read after Chess Primer: Basic Rules

Now that you know how the pieces move, and how to read chess gamescores, you will be able to play through recorded games, watch live ones, and of course play your own. When spectating however, the reasons behind the moves, and whether or not they are good moves, might not be clear. Who is winning and why? Unfortunately it is not easy to determine the answer to these questions watching a chess game, at least compared to more popular sports.

After all, you don't need to be a professional football player to know which team is winning a game; all you need to know is how to read the score. With chess, this is more difficult. Here, I'll show you some features of a chess position which often indicate one side is winning. These are things you should look for when you are looking at chess games. These positional features don't always confer an advantage, but they often define the struggle in the game.

Warning! The following two sections is my attempt to distill down a lot of chess knowledge into a handful of paragraphs. Despite my attempts to make this as concise as possible, I do apologize for the remaining verbosity and the length. In addition, the experienced player will recognize rampant generalizations. Keep in mind that this section is to be used only as a guide, and further study is encouraged.

Understanding Chess
Section I: Piece Power, Current and Potential
Section II: Pawn Structure

Chess Primer: Basic Rules

Welcome! If you are reading this, then it is likely that you don't know much about chess, but are eager to learn. Hopefully this crash course will leave you with the following knowledge

1) How the pieces Move
2) How to read chess games (PGN gamescores)
3) How to understand a game between more experienced players (In other words, what are the important features of a chess position), and improve your own play
4) How to calculate chess moves (tricks and tips for playing good chess)
5) Avenues for further study

I've tried to make this guide as simple, straightforward, and practical as possible. However, in taking this approach there is much I have had to oversimplify and omit. Hopefully this information will do enough to spark your interest to learn more about Chess, and develop a deeper understanding of the game. Who knows, you may even one day become a grandmaster!

Basic Rules
Section I: The starting position in chess
Section II: How the pieces move
Section III: The object of the game
Section IV: Portable Game Notation

An introduction to Chess, for the biochemist

Due to the wide scope of this blog, and the split audience it is likely to generate (something that is not recommended for blogging, I should add), I thought it would be prudent to provide some introduction to chess for the uninitiated. Eventually, this post will be followed by a complementary entry, "Biochemistry for the Chess Player", to make any commentary I have on science more accessible to my fellow pawn pushers.

You can take a look at my crash course for the game to get you started. It is broken up into three sections: Basic Rules, which covers piece movement and recording games; Understanding Chess, which explains how to judge the value of pieces and positions; Calculating Moves, covering a few common attacking patterns and tips on how to spot them. 

The guide that I have assembled aims for brevity, and does generalize quite a bit. If you are more serious in learning how to play, or how to improve your play, I would recommend looking at some of the following sites. They are roughly in order, although the list is by no means comprehensive. Another useful list is found, not surprisingly, in a post at the excellent Kenilworthian blog. 

In the list below, you will find links for learning the basic rules, how to read chess notation, as well as sites for learning and practicing simple checkmate patterns, attacking themes, and chess strategy.

Basic Rules

Rules of chess -Wikipedia, the free encyclopedia 
Very straight forward and complete description of the rules.

How to Play Chess: Rules & Basics - 
Similar to Wikipedia entry, but interactive / animated

The Chess Comic
Piece Movement
Starts with the movement of the pawn

Sunday, September 16, 2012

Square One: An Introduction

Chess is everything: art, science, and sport.  -  Anatoly Karpov

For me, chess is at the same time a game, a sport, a science and an art. And perhaps even more than that,. There is someting hard to explain to those who do not know the game well. One must first learn to play it correctly in order to savor its richness.  -  Bent Larsen

Chess is a unique cognitive nexus, a place where art and science come together in the human mind and are refined and improved by experience.  -  Garry Kasparov

Welcome to Science on the Squares, a blog about Chess and Science, and everything in between.

I've heard on occasion the cliche "Write what you know". In some ways, it is through this phrase I arrive at this blog. I am an avid chess player (although not particularly strong, only USCF 1666 at time of writing), and I am also currently drawing my doctoral studies in molecular biology to a close. Thus, I am in position to comment on both worlds. As the quotes above (grabbed from suggests, these worlds may intersect in some ways.