Tuesday, June 5, 2012

Steal This Book! Computer simulation and scientific theory

Abbie Hoffman
In the riotous protest times of the '70s, leading protester Abbie Hoffman published Steal This Book, "a manual of survival in the prison that is Amerika."  Of course, one must assume that Hoffman wasn't too opposed to the system to decline any royalties, nor that he really meant for copies to be stolen: presumably the idea was to read the book and understand the realities of society at the time.  Then you could choose to accept or fight the system, or at least understand it and what it's doing to you.

We devote a lot of effort in MT to commenting on and, yes, criticizing what we believe are deserving targets in contemporary science, especially as relates to genetics and evolution. We premised MT on ideas in our book of the same name, because we think evolution and an over stress on simplified genetic causal thinking diverts attention from many aspects of biology that we feel are at least as important.

People resist learning some lessons we think they should learn, perhaps largely out of ignorance (though in many ways intentionally not facing what might dampen various vested interests). 

With Brian Lambert, I have developed a highly general and flexible computer simulation program called ForSim, for simulating genetic causation and its evolution.  Its dual major purposes are first, to generate simulated, but realistic, data to test various theories and detection methods for complex phenotypes--such as those so intensely being pursued by GWAS and other methods.   Users can simulate the data and then sample it in various ways (families, case-control studies, etc.) to see how much and how one can find of what is known (because the simulation generates all the data required) to be the truth.  Secondly, the evolution of that genetic architecture within and between populations can be simulated, to understand how genetic effects change.

ForSim is a net-effects program, that omits many important aspects of genetic + environmental causation, such as those that make up the bulk of the book MT.  Thus, it greatly oversimplifies reality. But it tries to be natural in many ways (future additions will explicitly allow simulation of gene networks, developmental biology, and episodic traits like some diseases).

ForSim is a complex, intricate program and most readers of this blog would not be interested in or attempt to use it.  Fine, that's not our point. Our point in mentioning it is that just to see what is involved in complex traits and their evolution is a sobering lesson in why we object to simplistic ideas and rosy promises. 

ForSim execution flow
If one absorbs the message, one should be less sanguine or naive about what is being promised and found (or not) in the real world.  And one can get a sense of why we say what we do!  We did not invent biological complexity or the reasons why gene mapping (GWAS and similar approaches) are struggling as they are (as reflected rather clearly in the flood of papers aggressively praising their dramatic success).

We don't expect you to use ForSim, but if you're interested in seeing just what is involved in even a restricted evolutionary simulation, read the ForSim book!  You don't have to steal it, because the Manual can be downloaded here.  It's free (as is the program for any MT reader who might want to try it).

Again, we're not advertising anything from which we make any monetary or other gain.  We use the program, but just reading the Manual can be very instructive.  We wrote the program, and use it, and talk about it, because one way or another we think everyone, scientists and public alike, should be made aware of the realities of the causal complexity that so often is an inherent part of life.

But....wait!  What exactly is computer simulation?  Can't you simulate anything you want, the way a video game simulates Dungeons and Space Fighters?  Isn't what we really need an improved actual theory, some laws of life that really work well in terms of relating your genes to your traits?  Surprisingly, the answer is yes, you can simulate anything you want, but no, simulation isn't inferior to other kinds of theory even in this same respect.  We'll explain that next time.

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