Why Stylus?

Stylus is an unique in silico model of gene→protein→function mapping in biology that provides a way to test evolutionary scenarios. This is because Stylus reflects the way mutation and selection work in biology.

Mutation (genetic causation) acts at a low level to produce changes to individual genes or segments of the genome. Selection (evolutionary causation) then evaluates the functionality of the resulting organism, i.e. the sum of all interactions between genes and proteins that affect the organism’s functional capability.

In Stylus, changes to the genome produce variations in the vector traces drawn by the program. Those traces are then compared to a standard Han character set to determine if their meaning is damaged or changed. Because the genome is linear and continuous, and includes sequences that control start and stop, domains that are used in multiple contexts, signals that control operon regulation etc., many of the kinds of sequence evolution proposed by biologists as a way to get new functional proteins or pathways can be tested in Stylus. 

As the paper describing the Stylus genome states, 

…the contribution of Stylus  is to make evolutionary experimentation possible in a model world where low level genetic causation has the essential role that it has in the real world. Combined with the free Stylus software, the complete Stylus genome made freely available with this paper paves the way for analogy-based studies on a wide variety of important subjects, many of which are difficult to study by direct experimentation. Among these are the evolution of new protein folds by combining existing parts, the optimality and evolutionary optimization of the genetic code, the significance of selective thresholds for the origin and optimization of protein functions, and the reliability of methods used for homology detection and phylogenetic-tree construction.

(Source: biologicinstitute.org)

Stylus encodes a compact self-descriptive proteome

Stylus is an in silico model of the relationship between genetic sequence (genotype) and the ensemble of functional proteins encoded by the sequence (phenotype).  The Stylus genotype  specifies vector traces that reproduce Chinese Han characters. Those characters are then assembled into a functional proteome whose function is to describe key terms in the Stylus program (much like our genome specifies the protein building blocks necessary to asemble us.)

Shown above is a representation of the nine key terms of the Stylus proteome with their meanings in English. The bracketed terms present in abbreviated form how the genome and its proteome specify the genetic code. Although smaller than even the smallest known bacterial genomes at 70,000 bases, Stylus is similar in complexity in terms of numbers of proteins and protein domains encoded. Characters that are used multiple times are similarly colored, along with their meanings.

(Source: biologicinstitute.org)

Comparing Stylus with other computational models of in silico evolution

The key sequence to structure to function relationship found in biology is missing from nearly every other computational model of evolution, but present in Stylus. In addition, only Stylus uses a codon-based sequence to structure map like the one found in life.

For the peer-reviewed article describing the program see here.

(Source: biologicinstitute.org)

Miniature Molecular Power Plant: ATP Synthase (by DiscoveryScienceNews)

Just when you thought you knew everything, life comes along and blows your mind. The picture above is of 4-strand DNA; for more see the article in Nature. Even if 4-strand DNA proves to be artifactual in living cells, it still looks really cool.