Thread: "irreducible" complexity predicted in 1918

The information that I've been able to find so far on how to construct those graphs says:

"Each gene, each input, and each output is represented by a node in a directed graph in which there is an arrow from one node to another if and only if there is a causal link between the two nodes."

I'm a little confused. I guess we should stick to unicellular organisms. So an input is a state of the environment, an output is the production of a protein and a gene is the genetic material for a protein?

Is that right?

Also, will the graph be cyclic in general? That is, are there positive feedback loops or not?

Originally Posted by PhilosopherStoned

The information that I've been able to find so far on how to construct those graphs says:

"Each gene, each input, and each output is represented by a node in a directed graph in which there is an arrow from one node to another if and only if there is a causal link between the two nodes."

I'm a little confused. I guess we should stick to unicellular organisms. So an input is a state of the environment, an output is the production of a protein and a gene is the genetic material for a protein?

Is that right?

Also, will the graph be cyclic in general? That is, are there positive feedback loops or not?

That is a transcription network. It describes how products of certain genes influence expression of other genes.
Gene is defined as information needed for a functional protein (or non-coding RNA). In order to function, apart from the coding sequence, a gene must have other features as well.
One of these features is a promoter, a regulating sequence found upstream of the coding region.

Transcription factors (TFs) are proteins that bind to promoters and influence the transcription of those genes. They can either activate them or repress them. Some genes are also controlled by multiple TFs. Each TF has its own target sequence, but they sometimes overlap causing TFs to compete for binding (competing TFs would have opposite effects on that gene)

Interesting to note: around 10% of all human genes are thought to be TFs

Most TFs are, abstractly speaking, intracellular representations of extracellular conditions.
E.g. nutrient concentration drops, TFs that regulate starvation response become active and turn on (and turn off) their respective gene targets.

(discovery of this mechanism earned Jacques Monod a Nobel prize, google "Lac operon" if you're interested in more details)

In the graph nodes represent genes and edges represent interaction.
X------>Y means: "the product of gene X is a transcription factor for gene Y"
Hubs are genes that code for TFs involved activation and repression of many proteins.

To answer you other question: out of all possible 3-node motifs, the positive feedback loop is the only one that's significantly overrepresented in transcription networks. It can function as AND or an OR logic gate, depending on other parameters.

Also, a lot of genes regulate their own expression. I'm not sure, is a node connected to itself a cyclic subgraph?

Originally Posted by SnakeCharmer

Also, a lot of genes regulate their own expression. I'm not sure, is a node connected to itself a cyclic subgraph?

Yes. Thanks for the info. This is very interesting stuff. I've only ever studied evolutionary biology from the perspective where a gene is defined to be "the genetic matter which codes for a heritable phenotypic trait." That definition gets used by ethologists I suppose. I've been getting curious about going deeper recently though.