DNA study challenges basic ideas in genetics

The Boston Globe ^ | June 14, 2007 | Colin Nickerson

[Sopater]

A massive international study of the human genome has caused scientists to rethink some of the most basic concepts of cellular function. Genes, it turns out, may be relatively minor players in genetic processes that are far more subtle and complicated than previously imagined.

Among the critical findings: A huge amount of DNA long regarded as useless -- and dismissively labeled "junk DNA" -- now appears to be essential to the regulatory processes that control cells. Also, the regions of DNA lying between genes may be powerful triggers for diseases -- and may hold the key for potential cures.

The research, published in a set of papers in today's editions of the journals Nature and Genome Research, raised far more questions than it answered -- and in a sense was a rallying cry for more and deeper research into the functioning of the genome, often referred to as the "blueprint" for life.

"The instruction manual for life is written in a language we are only just beginning to understand," Francis Collins, director of the federal government's National Human Genome Research Institute , said at a news conference yesterday.

[js1138]

If you understand the language that MS Windows was written in, and understand the syntax required to get the code to perform in the manner intended, then you are justified in making such a comment. However, to call the genome "spaghetti code" when you neither understand the language nor the syntax is both presumptuous and ignorant.

I've worked with Windows code, and I've done maintenance on twenty year old systems. I know what spaghetti code is.

The characteristics I refer to are the intertwining of codes for disparate functions, so that a change to any function results in unexpected changes in unrelated functions. In systems having millions of lines of code developed over several decades, where no one person ever sees the entire system, you get situations where making changes to some small part of the system causes changes or errors in unexpected places. Often these effects are hidden for months or years.

In living things, changing one characteristic often results in changes to many features. For example, a fifty year project to breed tame Siberian foxes was successful, but the resulting animals do not retain their valuable pelts. Their coats are more like dogs' coats. This seems also to have happened when wolves were bred into dogs. Genes have multiple functions that cannot be separated. Hence the term spaghetti code.

[SuziQ]

Genes, it turns out, may be relatively minor players in genetic processes that are far more subtle and complicated than previously imagined.

So it is true, we are fearfully, wonderfully made.

[SuziQ]

I remember my major professor refusing to call it that, rather he called it “non-coding” and added that, just because we did not know what it did, that did not make it “non-sense”

Sounds like a very wise man.

[Elpasser]

Oh my. It seems that the basic unit of life is growing ever more complicated and difficult to explain from the aethist’s self-creation perspective.

[Inquisitive1]

the very last sentence will say something like "WHAT TOOK YOU SO LONG?" :-)

Actually, the last word will be '49'.

[Sopater]

Genes have multiple functions that cannot be separated. Hence the term spaghetti code.

My point was that just because you don't understand the functional complexity of a written language, doesn't make it "spaghetti code". The term is pejorative in nature and intended to belittle the programmer or to imply a great deal of inefficiency in the code. Until you can specifically show the code could be improved upon from it's original design, you have no basis for calling it "spaghetti code".

[js1138]

I’m commenting on an objective, quantifiable characteristic of the code.

Why, for example, is hair style functionally related to behavior? Whic is the more likely explanation: it is impossible to have expensive fox fur on a tame creature? Or the functions governing behavior and fur quality are linked by accident?

[Sopater]

Why, for example, is hair style functionally related to behavior?

Who says it is? Selective breeding is a crap-shoot.

[js1138]

Who says it is? Selective breeding is a crap-shoot.

Selection, whether natural or artificial, works with whatever variation presents itself.

[Sopater]

Selection, whether natural or artificial, works with whatever variation presents itself.

Absolutely, and unless you have control of ALL of the variables, you really have no idea what undefined variations are inadvertently being selected out. When you're talking about something with the complexity of a Siberian fox, the end result, therefore, is a crap-shoot.

The only variables that were in any kind of control were the traits that were intentionally being selected for and against. The endless list of traits not considered and understood up front are going to be impossible to control.

[Ethan Clive Osgoode]

Selection, whether natural or artificial, works with whatever variation presents itself.

So the eugenists say. I take it you don't believe in somatic variations.

[js1138]

Do you have a point?

[sphinx]

But that would imply deliberate design, and that thought is not permitted.