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.

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!).

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

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 - Chess.com 
Similar to Wikipedia entry, but interactive / animated

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