#patrick forber

[empiricaldaily]

By classifying proteins as interactors, we can clearly identify the specific DNA fragments that qualify as replicators. Now, one property that replicators must possess is a consistent phenotypic effect on their interactors, as Dawkins elegantly showed in The Extended Phenotype. Strikingly, genes do not have this crucial property. Through the amazing set of posttranscriptional mRNA processing mechanisms uncovered in the last 40 years (including alternative splicing and RNA editing), transcription of a single gene often results in the production of many distinct protein isoforms with very different functional roles. DNA fragments coding for individual protein domains, however, do have a consistent phenotypic effect, since protein domains are functionally independent parts of proteins that play the same role no matter which isoform they appear in. So proteins are an example of what we are calling the fundamental interactors, the interactors that experience the consistent phenotypic effects of corresponding replicators. Notice that it then becomes straightforward to picture how the phenotypic features of the fundamental interactors came about, in glorious molecular detail: small variations in the sequence of domain-coding fragments that allow protein domains to perform their function particularly well are selected for over thousands of generations, enhancing cooperation and expanding the range of cooperative opportunities available between fundamental interactors and ultimately contributing to the fitness of the organism. Of course, domain-coding fragments are not the only replicators in eukaryotes; the differential selection for regulatory elements and transposons is just as important for understanding how the features of organisms came to be. This extra layer in the hierarchy of interactors helps show how a molecular developmental toolbox can mix and match gear to assemble organisms, and potentially fills the gap that the evo-devo crowd has been saying was slighted by the gene's-eye view, integrating the beautiful details of molecular biology with Dawkins' vision of life.

Daniel Dennett, Patrick Forber, Nikolai Renedo. 2015. (Title: A Vision of Life, in Molecular Detail [edge.org])

[empiricaldaily]

We would like to propose a friendly amendment that will allow for more accurate identification of these two entities, the replicator and the vehicle. The vehicle concept is slightly too restrictive, but in both directions: By adopting David Hull's term interactor, we can identify not only the extended phenotypes, but phenotypes that are cohesive entities smaller than the individual organism, sets of phenotypic products that interact with their molecular environment to cause the differential selection of replicators. Individual proteins, for instance, interact with other protein interactors in the cellular environment, cooperating with each other to build functional cells and organisms. The success of the replicators that build proteins does not depend on whether the protein survives to reproduce, as in the case with vehicles, but rather on how well the proteins cooperate with the surrounding proteins to build an organism with a fitness advantage.

Daniel Dennett, Patrick Forber, Nikolai Renedo. 2015. (Title: A Vision of Life, in Molecular Detail [edge.org])

[empiricaldaily]

Dawkins' brilliant distinction in The Selfish Gene (1976) between replicators and vehicles provided a clear framework for understanding how the wonders of life arise in a world dominated by the tedious laws of physics, and in the light of all we have learned subsequently about the details at the molecular level, his 1976 language strikes us as sometimes wonderfully prescient—anticipating "selfish DNA" or genomic parasites, for instance—but not perfect, of course. He acknowledges the slack in a few phrases here. The concept of gene has undergone some transformations, for instance, so are replicators genes? "Let's call them 'genes' because nowadays they pretty much all are genes." And he himself, in The Extended Phenotype (1982), showed that the set of phenotypic products that combine to enhance the futures of the replicators are not all in the organismic vehicle.

Daniel Dennett, Patrick Forber, Nikolai Renedo. 2015. (Title: A Vision of Life, in Molecular Detail [edge.org])