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Wednesday, December 19, 2012

Book Review: Thinking with Chess


You can find another one of my book reviews at Chesscafe.com. (Previously, I reviewed Walter Browne's "The Stress of Chess".)

This time around, I took a look at "Thinking With Chess", by Dr. Alexey Root. This book is more or less a teaching guide for chess coaches or parents. My review is entitled "Teaching with Challenges", named because the most interesting and valuable part of Dr. Root's book are the challenges. These are essentially mini-games used to exercise a particular chess skill.


Image taken from www.brooklyncastle.com

The book is put together nicely, but unfortunately I couldn't bring myself to give it a great rating because of the limited amount of material (the size of the book). This is reflected in the concise nature of the review; there was simply not a whole lot to talk about! (My apologies to Dr. Root for any offense, but I'm just trying to deliver an honest opinion.)

Did you read this book? If so, what did you think? What is your favorite book on chess instruction?

Evolutionary Biology and Education


The internet is perennially abound with discussion over evolutionary biology. It is a topic that surfaces repeatedly in the news, either in the form scientific dispatch describing a new species or in political news concerning the friction between science and religion. The latest iteration of the latter debate concerns recent remarks by Florida Senator Marco Rubio when answering a question about the age of the earth. The Senators somewhat ambiguous and confused (but understandable and unsurprising) answer has found both critics and apologists. He eventually qualified his answer, and I think made a good point that I will echo later in the post: the age of the earth has nothing to do with his tasks in the Senate. Even this point has been criticized, but I think it rings true in a subtle way).  Many of these debates, however, usually filter back to the opposition between creationism and evolution (as well as geology, embryology, or any other science that touches on the same points).


(Taken from Joyfully Battle Worn's blog without permission. Interesting post, you should definitely check it out. Echos some of the sentiments I expound here, although approached from a more religious perspective.)

The astute reader may be queuing up their groans and moans (or cheers, if they are into this debate). "Will this blog also devolve into a debate over evolution?" While I thought it would be appropriate to weigh in on the subject (after all, this blog is partly devoted to science, and biology in particular), you need not fear that these pages will transform into another blog taking on evolutionary biology. After all, there are many fine sites that primarily focus on this topic. I am especially familiar (and fond of) some of the more popular ones maintained by other scientists, such as PZ Meyer's Pharyngula. There is even a blog, aptly named EvolutionBlog, that focuses on both evolution and chess!

What then, does Science on the Squares have to offer to the evolution blogosphere? I am trained in molecular biology, not evolutionary biology (although I am well-read on the subject), and thus I will leave the discussion of the finer points of this science to others. However, I would like to add a voice to the debate over the proper placement of evolution in the classroom.

I've beaten about the bush long enough; my point is that neither creationist science, intelligent design, or evolutionary biology (as I understand it to be currently taught) belongs in the science classroom. No, you don't need to adjust your screen or check your glasses: I did indeed call for the partial removal or reform of evolutionary biology from the Science curriculum. 

Now that I have your interest, please select 'Read More' to read this article in its entirety. I'll give you a preview: the evolutionary explanation of the origin of species is more history than it is predictive science, and thus is not critical to the education (or future competitiveness) of our youth.

The position I've taken is one that is sure to stir up controversy, and will probably have the somewhat unique distinction of angering proponents of both evolution and creationism. Please feel free to add to the discussion by leaving a comment below, but try to keep it civil!

Monday, December 10, 2012

The Science of Chess: Moving to the (heart) beat


Recently a team of researchers published an article (PDF format) in which they monitored the heart rate of Chess players during a game (Aptly titled The tell-tale heart: heart rate fluctuations index objective and subjective events during a game of chess. Published in Frontiers in Human Neuroscience, 2012, Vol 6, No 273). 

The same authors of that study have summarized their work for chessbase news in a report also aptly titled: "Psychology: The Heart of Chess". Naturally, I was interested, as I have posted before about the intersection of science of chess and I check PubMed occasionally for such work (although I must have missed this particular study).

Picture reposted (with modifications) from Chessbase. I do not own the rights to the above picture (or for that matter, any of the pictures used in this post).

The article is interesting and thought provoking. There have been many studies that examined some psychological or mental aspect of the game, but there are much fewer (to my knowledge) that studied the physiological manifestations of a chess player's mind. As the article reminds us, Chess is fertile ground for studying all of these phenomenon. 

What did you think of the article? Select 'Read More' to see my full opinion. Please share your thoughts in the comment box below!

Saturday, December 1, 2012

Introduction to Scrambled Chess Puzzles


Here, I will describe a new type of chess puzzle, which I call Scrambled Chess. This is going to be a small example puzzle; I will commence a larger series (Scrambled Sundays!) which will feature full puzzles posted biweekly. (The first one will be posted tomorrow, Dec 2nd!)

Image from http://sp.life123.com/bm.pix/scrambled-eggs1---eggs-on-plate.s600x600.jpg


Like Freeze Chess and ChessWords, I think Scrambled Chess is a good tool for visualization. In fact, they are probably even better, since they can test visualization skills in several different ways. Also, unlike Freeze Chess (which I developed independently, but are very similar to Bruce Alberston's Chess Mazes), it seems that Scrambled Chess is completely novel. They are also somewhat difficult to explain, but hopefully the example below will make the objective and rules clear.

As an introduction, here is a smaller version of one of these puzzles. (The rules / how to play is described below).



Introduction / Example Puzzle. Movement is Rook by Knight (The notation used for these puzzles will be RxN). Starting Square: A4. Target Square: B1

This is a smaller, 4x4 board (the real puzzle would be a standard 8x8 board). As you can notice, each square is inscribed with the coordinates of another square. The goal is to make piece movements that are legal for both, according to the pieces specified. 

In these puzzles, two pieces will be specified, from the choice of Knight, Bishop or Rook. The first piece dictates the movements that should be taken on the board, while these movements must correspond to legal moves in within the scrambled coordinates.

If the puzzle is Rook by Knight (This one is, as specified by RxN), this means that only Rook moves are allowed, but the correct moves are those to squares with written coordinates that correspond to a Knight move.

The goal is to go from the starting square (shown in brick red) to the target square (shown in blue), making moves that conform to the above rules.

As mentioned above, I will be posting a puzzle every other week, on Sunday (starting tomorrow). Some of these puzzles can be complex, and can be any combination of Rook, Knight, or Bishop moves (RxR, RxN, NxN, NxB, etc). Remember, the first piece dictates movement on the puzzle board, the second piece corresponds to the coordinates inscribed within each square. In this same notation, I have developed puzzles such as Rx2N; what this signifies is that the moves must be with coordinates that correspond to a two move hop of the Knight. 

In the above example, a Rx2N move would be A4-A3, since this uses the inscribed coordinates E4-D5. This corresponds to a two move route of the Knight; E4-f6-D5, or E4-c3-D5. In this particular example, however, that would be a dead end (you cannot read the target square under those conditions). 

What do you think of Scrambled Chess? Please share your thoughts by leaving a comment below!

Stay tuned for a full puzzle tomorrow!

Please hit 'Read More' for the solution to the above puzzle, explained. For now, I've suddenly got an appetite for some scrambled eggs....

Friday, November 30, 2012

My Excel "FEN to Diagram" Tool



Every Chess blogger and publisher must at one time grapple with the same issue: how to create and display diagrams and games. I have explored and tried a few options, including the pgn4web and chessup.net tools (at time of writing chessup.net server is down). A more detailed list is provided by Michael Goeller's Kenilworthian, among others. Here, I will recount how I came to develop my own, offline solution, an Excel file that converts FEN to chess diagrams.

For a time, I thought I had settled upon using the Chessup.net server, in which I could simply put a FEN string into the URL for the image, and viola, I would have chess diagrams on my site. However, it was unsettling to realized that when their servers went down, so did all the diagrams on my site. I should have saved each image and uploaded them. Even if I had done this, however, the failure of their service would mean that I would need to change the style of diagrams on my blog.

I value consistency when it comes to the appearance of these blog posts. Thus, I began to search for a more reliable, offline solution. However, since I use a Mac. I was found wanting for programs to quickly turn FEN strings into diagrams. My solution: make my own tool to accomplish the same end. I'm a bit of an excel guru, if you might have guessed from my Mutual Information articles (part 1 and 2). Naturally, I chose this program to craft my solution.



Here, I will make available the excel workbook that I have setup to generate all the new diagrams on the site. In order for this tool to work, you must have the Chess Cases font. I will provide the workbook in two different Excel formats: .xlsx, and .xls

Feel free to use this tool as you see fit. I would appreciate a mention if you use it for your site. If you do use it, experience problems, or have suggestions for improvement, I'd love to hear from you. Just drop a comment below!

Read on for more detailed instructions on how to use the Excel Chess Diagram tool. If you are trying to accomplish something special, or need some additional help, I may be able to give you a hand; simply post your inquiry as a comment.

Thursday, November 22, 2012

Mutual information in Chess


In a previous post, I introduced the topic of mutual information. This is a statistical analysis technique that can be used to determine if there are a connection between two variables.



Mutual information finds many applications, including analysis of biological sequences (this is the use I am most familiar with). Last time, I questioned whiter or not this technique can be applied to chess in any meaningful way. I think the answer is a partial yes, and here I will share with you my initial exploration of this idea.

Happy Thanksgiving

I'd like to wish all of my readers a Happy Thanksgiving! 

Stay well, trade the lab work for family time, eat Turkey, and play chess!





Also, I should take this moment to apologize to you, dear reader. I had been relying on ChessUp.net for creating the diagrams for this site. Unfortunately, the server for that site is down, hence the disappearance of all the diagrams from this site! I will work this weekend to resolve this problem.

Time for some Turkey,
And a Thanksgiving Haiku.
Happy Holiday!

Tuesday, November 13, 2012

Introduction to Mutual Information


Despite the vague sounding term, the concept behind Mutual Information is a rather simple one. It is essentially a measurement of the dependence between two random variables. Huh? Put simply, it describes a sort of correlation between the outcomes for two different varying quantities.



Below, I try to introduce the concept and some uses of Mutual information. Since my experience in using this statistical technique has been one focused on bio-informatic analysis, most of the examples and uses I describe relate to biology and sequence analysis. There are a multitude of other uses! To read the rest of this article, select the 'Read More' Link below.

What ways have you used mutual information, or what problems do you think it can be applied to? Please share below by leaving a comment.

The image above (and some below) is from Wikipedia (I claim no rights to them)

Monday, November 12, 2012

Opening Lanes looks at the ...e5 Anti-Anti-Sicilian


International Master Gary Lane runs a very informative, interesting, and entertaining column at ChessCafe.com called Opening Lanes, in which he answers reader questions about various chess opening variations. 

In this month's column, he answered a question I posed, about the variations 1.e4 c5 2.Nf3 Nc6 3.Bb5 e5 and 1.e4 c5 2.Bc4 e5. I was excited to see a titled player look at these variations, especially a Bishop Opening's specialist like IM Lane (Since 1.e4 e5 2.Bc4 c5 transposes).

You can read his analysis in PDF format.



I have been posting analysis on meeting Anti-Sicilians with ..e5. There were not many games to be found featuring this move, and very little freely available analysis. I already have surveyed 1.e4 c5 2.Nf3 Nc6 3.Bb5 e5, and will return to this line in more depth in the future. I am also going into more depth with 1.e4 c5 2.Bc4 e5 (which could also arise from the Bishops Opening).

I may eventually pen a larger response to IM Lane's analysis, although I doubt there is much to be critical of (after all, he's hundreds of rating points stronger than I, and probably has more time and resources to boot!). That being said, after 1.e4 c5 2.Bc4 e5 3.f4, the only third move he analyzed for White, I would prefer 3…exf4 over either 3…d6 or 3…Nc6 (the options he covered in his article).

My analysis on 1.e4 c5 2.Bc4 e5 3.f4 will be posted in the near future, since it is anyway the next option in my series of 1.e4 c5 2.Bc4 e5 (It will be line D).

Please check out IM Lane's column, and let me know what you think!

(The pictures above are from Chesscafe.com; I claim no right on them, providing them only for aesthetic pleasure.)

Wednesday, November 7, 2012

Combating Anti-Sicilians with ...e5: Anti-Bc4 (Line C)


This post is concerned with the line 1.e4 c5 2.Bc4 e5 3.Nc3, or Line C in the series. See the introductory post for this series for Line A, as well as an explanation of the entire variation and some database statistics. 




This is part of a larger series on meeting anti-Sicilian lines with …e5. In a previous post, I covered how this move can successfully be employed against the Rossolimo Siclian (1.e4 c5 2.Nf3 Nc6 3.Bb5).

In the introduction to this series on ..e5 against the anti-sicilians, I point out that Black needs to take care of d5, anticipating moves from White such as Nc3-d5, Na3-c4, and c3 followed quickly by d4. The move Bc4 also introduces pressure against f7. Black should be on guard for moves like Ng5 (which in the initial position is not possible due to Qxg5).

1.e4 c5 2.Bc4 e5
C) 3.Nc3
D) 3.f4
E) 3.b4
F) 3.Nf3 (Followed by c3, O-O, d3, or b4)

Click 'Read More' below to see the analysis. Stay tuned for continued analysis of this variation, from Lines D through F (Links will be activated once the posts are up.) 

I try to provide as comprehensive and accurate analysis as I can, but as a class player with limited time and computer resources, I've probably missed quite a bit. 

Please let me know what you think, and add any of your analysis in the comments section!

Wednesday, October 31, 2012

My Book Review at Chesscafe.com

I have recently reviewed a book, Walter Browne's "The Stress of Chess", for the excellent chesscafe.com website. You can check out my review, which I titled "A sometimes stressful read" at their site (now archived; 11/12/12).




Since I live on the East Coast, hurricane Sandy has interrupted my blogging efforts. Now, I am up against a deadline for a very important meeting with my thesis committee on November 6th (after which I will exercise my civic duty and vote). So, dear reader, please excuse the dearth of posts in the coming week. 


Wednesday, October 24, 2012

Combating Anti-Sicilians with ...e5: Anti-Bc4 (Line B)


This post is concerned with the line 1.e4 c5 2.Bc4 e5 3.c3, or Line B in the series. See the introductory post for this series for Line A, as well as an explanation of the entire variation and some database statistics. 



This is part of a larger series on meeting anti-Sicilian lines with …e5. In a previous post, I covered how this move can successfully be employed against the Rossolimo Siclian (1.e4 c5 2.Nf3 Nc6 3.Bb5).

In the introduction to this series on ..e5 against the anti-sicilians, I point out that Black needs to take care of d5, anticipating moves from White such as Nc3-d5, Na3-c4, and c3 followed quickly by d4. The move Bc4 also introduces pressure against f7. Black should be on guard for moves like Ng5 (which in the initial position is not possible due to Qxg5).

1.e4 c5 2.Bc4 e5

A) 3.Qh5
B) 3.c3
D) 3.f4
E) 3.b4
F) 3.Nf3 (Followed by c3, O-O, d3, or b4)

This post has been vastly expanded, as part of blog renovations described in an earlier post. If you would like to see the original analysis, please email/contact me.

Tuesday, October 23, 2012

Shake up at SOTS!


Warning! Grab a hard hat, because I am doing some renovation! 



OK, thats an exaggeration no safety equipment is necessary. But I am making a few changes to how I post games, as well as to the style of the site.

To my regular readers, I thank you for your audience; I hope you enjoy the new site design. I have to apologize, however, for some redundancy that will result.

Not only are the colors different, but I am doing away with the java replay applet. It was cool and stylish (thanks pgn4web!) but ultimately I felt that the annotations were presented in a clumsy format. I decided, therefore, to go to an more throw-back style and present annotations in text with scattered diagrams. Now, if you'd like, you can print out these posts and read them on the train/bus/plane/etc.

To those itching to replay the games, I will still provide PGN files. If you don't know what PGN is, or how to read it, you can view my primer on PGN (portable game notation) from an earlier post. There are a bunch of free viewers on the web and for download. Here are a select few:


Due to this change in format, the opening articles I had posted previous would become unwieldy. Therefore, I decided to break these up into a number of smaller posts.

This, I think, affords several advantages. For starters, different lines can be linked together, and you can explore different variations without wearing out the scrollbar. Secondly, it will allow me to post the analysis of individual lines, instead of entire systems at once. I'll be able to make each post more detailed, and you won't have to wait so long for an update.

So, in what will seem like a flurry of posts, I will be reposting the analysis of the lines starting 1.e4 c5 2.Nf3 Nc6 3.Bb5 and 1.e4 c5 2.Bc4. There will be some updates, and the analysis will be more in depth in some lines. Soon to follow will be my long-promised work on 1.e4 c5 2.Nc3 e5

It's a shake up at SOTS! (Science on the Squares; I think the acronym has a nice ring to it). I welcome any an all reader suggestions on the site's format.

Occam's Razor in Science and Chess


Somewhere along their education, most scientists learn about Occam's razor. This principal, attributed to the 14th century logician William of Ockham, is usually stated as the preference for a simpler theory over a more complex one (as long as both are supported by the facts). When formulated this way, it might also be called the law of parsimony or economy, or just the rule of simplicity.



Occam's razor does not only apply to the hard sciences. This rule has been applied, sometimes in a modified form, to many fields. Even chess players may utilize Occam's razor. After all, while scientists use experimentation to falsify competing hypotheses, chess players engage in a similar activity by evaluating competing moves through analysis (often with computer help). Just as two different hypotheses may explain the facts, two candidate moves may appear (at first blush) to be playable. In either case, experimentation or analysis is used to find the correct choice between the alternatives.

I would suspect, however, that many scientists  do not appreciate the rationale behind this razor, as well as it limitations. They may be in danger of over estimating the power of this principle. In fact, I'd wager that chess players are more aware of the proper use of Occam's razor. Some of the original justifications for the razor where aesthetic (simpler theories and more elegant moves must be better), but this rationale is quite simply irrational. There is no good reason to believe a priori that either the inner workings of the cell or the strategy on a chess board must be simple. Even if many successful theories rely on simplicity, this does not preclude a phenomenon (or a position) being studied that requires a complex explanation.

Select 'Read More' to see the complete article, in which I discuss the justifications for Occam's razor using examples, and exceptions, from the chess world. The law of simplicity is more of a guideline, a way of prioritizing experiments and guarding against circumstantial theories. 

As Sherlock Holmes might say, understanding Occam's Razor is "Simplicity itself!"

Monday, October 15, 2012

Bryant Park Blitz: An Einstellung loss?



A few weeks ago, I was in the city on a Sunday, killing somme time while my girlfriend was recording some music (Check out her itunes page!). Naturally, I took the opportunity to get in a game of chess, and headed down to Bryant Park. There I found a player, sitting smugly with sunglasses on (it was a nice September day) taking on various opponents. Most of the opponents he played were crushed, making fairly simple mistakes and dropping pieces to simple tactics as the bespeckled player jokingly taunted them. I noticed, however, some errors in his play (both tactical and positional), and his tendency to underestimate the counterplay of his opponent.


I have posted the game below for your enjoyment. It was played with the time control of 5-0 (5 minutes each side, no increment). In hindsight, I think that this game might be a good example of the Einstellung effect. This effect is essentially when you become fixated on only certain moves or ideas, miss the optimal continuation in a position. I recently posted about some research concerning the Einstellung effect on chess players (it is a more generally phenomenon), and it brought this game back to my mind. In fact, I otherwise would have not posted the following game, because it contains some really rather sloppy play (I'm usually sharper that this tactically, I swear!), but is nonetheless instructive on several points.




In particular, I became fixated on the pressure my opponent was exerting on my King in the above position, and missed an excellent resource on move 21; I played the awkward 21.Bf4, when a combination of 21.fxg6, Rf7 and Rh7 would have easily secured the win.


Select 'Read more' or the following link to view the whole game.


The time pressure of blitz can sometimes highlight our tendency to overlook important possibilities. What examples of the missed possibilities and the Einstellung effect do you have in your own games?



Tuesday, October 9, 2012

The Science of Chess: Fernand Gobet and the Einstellung effect


Since this blog is about Chess and Science, it is only natural to discuss the nexus between the two: scientific studies that examine some aspect of Chess. The game of chess is used by some social science, psychology and neuroscience researchers as a model or tool to examine memory, expertise, decision making skills, or some other process that two combatants engage in over the chessboard.




A few chess players may be already familiar with an example of this type of work, perhaps the highly cited studies by Adriaan de Groot. In some of the studies conducted by de Groot, chess players of different skill levels were tasked with position recall and were told to analyze a position while thinking out loud. This has led to conclusions about the way expert players organize their memory, and how they search and evaluate a position. (I'll probably revisit de Groot in a future post)


A contemporary researcher in this field is Fernand Gobet, a professor at Brunel University, West London. (See his professional homepage). Gobet has dual qualification to study chessplayers, since he is both a cognitive psychologist and an international master (a qualification not unique to the researchers in this field). He has published a number of interesting articles on a variety of aspects of the game, ranging from memory, visualization skills of chess players, and even gender differences between players. Of particular note, Dr. Gobet has attempted to simulate certain aspects of expert memory and skill using commuter models.


Below, I'll give you my reaction to a paper by Dr. Gobet that deals with the interesting Einstellung effect. While I am scientist, cognitive psychology is not my field, so the experts will have to forgive me if I do not assess the work correctly. Also, I provide below only a brief sketch of the work; I might someday blog about the individual topics in more detail, as I learn more about them.


I'd love to hear from you, dear reader, if you have some insight onto to the work of Dr. Gobet or others. In particular, please feel free to let me know if I have gotten something wrong. You can do so by leaving a comment.



Saturday, October 6, 2012

Combating Anti-Sicilians with ..e5: Anti-Bc4 (Line A)


In this post, I'll begin to look at answering either 1.e4 c5 2.Bc4 or 2.Nf3 Nc6 3.Bc4 with …e5. This is part of a larger series on meeting anti-Sicilian lines with …e5. In a previous post, I covered how this move can successfully be employed against the Rossolimo Siclian (1.e4 c5 2.Nf3 Nc6 3.Bb5 e5).




Where the move ..e5 against the Rossolimo drew parallels with the Ruy Lopez, the reply …e5 against the Bc4 attack will appear similar in some lines to the Guicco Piano (1.e4 e5 2.Nf3 Nc6 3.Bc4 Bc5). However, the presence of a pawn on c5 instead of the Bishop, together with the weakness of the d5 square, makes for some important differences.


In the introduction to this series on ..e5 against the anti-sicilians, I point out that Black needs to take care of d5, anticipating moves from White such as Nc3-d5, Na3-c4, and c3 followed quickly by d4. The move Bc4 also introduces pressure against f7. Black should be on guard for moves like Ng5 (which in the initial position is not possible due to Qxg5).


Unlike the line with Bb5, the Bishop on c4 may prove to be a target for Black, and White needs to watch out for a6-b5, which may threaten to capture the Bishop. Furthermore, the Bc4 move does less to put pressure on the Black e-pawn, and gives the second player more flexibility in their response.


In this post, I will only cover line A. In subsequent posts, I will consider several other variations. Lines A through E concern with the immediate 1.e4 c5 2.Bc4 e5, while Line F considers a delayed version 1.e4 c5 2.Nf3 Nc6 3.Bc4 e5.

1.e4 c5 2.Bc4 e5


A) 3.Qh5

B) 3.c3
C) 3.Nc3
D) 3.f4
E) 3.b4
F) 3.Nf3 (Followed by c3, O-O, d3, or b4)

It is worth noting that, if Black can successfully meet 2.Bc4 with ..e5, then he has a defense not only against a rare anti-sicilian, but to the Bishop's Opening as well (Replying to 1.e4 e5 2.Bc4 with …c5). Even if White can secure a space advantage or some initiative, it makes a good surprise weapon against a weaker opponent, if you are prepared to suffer a bit!


Out of 29 games that open with 1.e4 c5 2.Bc4 e5, White is winning 70% (W19 D3 L7). Download the full opening report. Remember, with these small samples sizes, the numbers may not have much significance! As always, they can be skewed by some games in which Black lost for reasons unconnected with their opening play.


Also, remember to check back to this post occasionally; I will continue to do analysis and update the post if necessary (I wasn't able to complete the survey at the time of the posting). If you spot an error in my analysis, or think you have a better idea then what I came up with, please post your moves and lines in the comment section!


This post has been updated and is still under construction!; for an explanation, see my post describing the blogs renovation. If you would like the original, truncated analysis on all of these variations, please email/contact me.  The full analysis of remaining lines will be posted eventually.


Wednesday, October 3, 2012

Molecular Biology Primer: Obtaining and Interpreting Data


As mentioned in the previous post in this series, molecular biologists are primarily concerned with studying the expression, structure, and function of proteins in the cell (sometimes this necessitates the study of the genetic material which encodes the protein, particular when the proteins expression is being questioned). 

How do scientists go about answering these questions? What are their tools of the trade, how are they used, and what are their limitations? Here I explore some of the broad limitations common to many techniques used in molecular biology. If you'd like to learn more about some of the more common techniques, I have provided at the end of the article short descriptions and ample links for more information.


I'd also like to hear from you! What experimental limitations have I omitted or underestimated? If you know of some cool new techniques, please help me grow the list I have compiled by adding a comment.


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!