The logic of life brings order to our genes

[Guest guest]

The logic of life brings order to our genes

01 Dec 2004 http://www.medicalnewstoday.com/medicalnews.php?newsid=17109

It is tricky enough to get a soccer team of eleven players to cooperate

and work as one - but what would it be like if there were 25,000 players

on the field? What would the rules be like, and how many referees would

it take to make sure that the rules were followed? As it happens, our

genomes consist of networks of roughly 25,000 interacting genes, and

these networks are obviously very stable and resilient to changed

conditions. Out of billions of cells, not a single one falls into chaos.

How can order be maintained? A question that scientists have been

pondering since the 1960s may now have been answered by theoretical

physicists at Lund University.

In the most recent issue of the Proceedings of the National Academy of

Sciences USA, professor Carsten and his collaborators Björn

sson and Carl Troein demonstrate how this is possible. The

American physician and scientist Stuart Kauffman - a pioneer in the

field, who formulated and attempted to solve the problem as early as

1967 - is their co-author.

At any given time, each of the 25,000 genes in a cell may or may not be

producing a protein - each gene is 'on' or 'off', to use language from

the world of computers. A gene can affect other genes, turning them 'on'

or 'off'. A simple case is that two genes are controlling a third gene.

To activate this third gene, both the controlling genes might need to be

active, or maybe only one or the other.

" In such a simple subsystem, sixteen different rules are possible in the

interaction between the genes, and a large number of different solutions

can emerge for the entire network, " says professor . It was

systems like this that Dr. Kauffman started working with; he assumed

that the different solutions corresponded to different cell types. This

would also explain how the DNA can be the same in all types of cells.

Unfortunately, real systems are vastly more complicated. More than two

genes may be involved in activating a single gene. In the case of three

controlling genes, there are already 256 different rules. And in a

system of 25 genes, the number of possibilities is greater than the

number of atoms in the known universe...

To find those solutions that would produce stable systems, and

his collaborators have primarily used literature knowledge from the

foremost guinea pig of genetics: the fruit fly. More is known about the

details of the genetic network here than in humans.

" In the fruit fly one can find almost 200 rules that are canalyzing, and

this property is most likely general and applicable to genetic networks

in other organisms, " Carsten notes. " With 'canalyzing' we mean

that there is a controlling gene that decides the value of the gene it

activates by being either on or off. In that case, other controlling

genes don't have any effect on the activated gene. It doesn't matter

whether they are on or off.

With canalyzing rules, it turns out that the networks become stable

regardless of the number of controlling genes, the size of the networks

and the initial state of the system. " It might be added that when Stuart

Kauffman first started working on this problem, he was using punch

cards. Now that the problem has been solved, it was not thanks to

simulations on a powerful computer - it has been sufficient with

observations, logical thinking and mathematical labor.