Informatics

(it’s designed to) These are some thoughts prompted by the recent article Arrival of the Fittest: Robustness and flexibility are basic design principles. We design modules so that they are robust against minor damage, bad inputs and changes in other parts of the code. This aids ‘evolvability’ of the whole by untangling the knots so that parts of the design can be worked on independently. Think of Dawkins’ METHINKSITISLIKEAWEASEL parable. The string of text can evolve because each letter is selected independently. The system is designed to evolve. By contrast, in an undesigned bag of chemicals or genes you would have all kinds of cross interaction which means a change in one chemical could have wide-ranging unpredictable effects. The chemical/genetic Read More ›

Mutations are used to explain evolution but also cause cancer. Biologists have discovered conditions for multiple mutations. Can we therefore infer that evolution via mutations is more likely? or that enhanced mutations will cause faster species degradation and extinction?

Biologists describe mechanism promoting multiple DNA mutations

DNA mutations—long known to fuel cancer as well as evolutionary changes in a living organism—had been thought to be rare events that occur randomly throughout the genome.

However, recent studies have shown that cancer development frequently involves the formation of multiple mutations that arise simultaneously and in close proximity to each other. . . .Anna Malkova, associate professor of biology in the UI College of Liberal Arts and Sciences, notes that the DNA repair pathway, known as break-induced replication (BIR), can promote clusters of DNA mutations.

“Previously, we have shown that double-strand DNA breaks, which can result from oxidation, ionizing radiation and replication errors, can be repaired by BIR,” says Malkova.

“During BIR, one broken DNA end is paired with an identical DNA sequence on another chromosome and initiates an unusual type of replication, which proceeds as a migrating bubble and is associated with the accumulation of large amounts of single-strand DNA,” she says.

In the Cell Reports study, researchers subjected yeast cells undergoing BIR to alkylating (cancer cell-killing agents) damage. “We found that the single-stranded DNA regions that accumulate during BIR are susceptible to damage that leads to the formation of mutation clusters,” explains Cynthia Sakofsky, postdoctoral fellow at the UI and one of two co-first authors on the paper. “These clusters are similar to those found in human cancer,” she says.

Importantly, say the researchers, the paper provides a mechanism to potentially explain how genetic changes form in human cancers. Thus, it will be critical for future research to determine whether BIR can form clustered mutations that lead to cancer in humans.

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The UK Independent is noting how Stephen Hawking says of the Film on AI, Transcendence — plot summary here at wiki, that ‘Transcendence looks at the implications of artificial intelligence – but are we taking AI seriously enough?’ First off, I think “implications” is probably over the top — we seem to be more looking at materialist yearnings for eternity, resurrection and paradise. (As in, on the presumption that intelligence boils down to evolutionarily written software running on wetware neural networks, then we can upload ourselves to a machine of sufficient sophistication, and reconstitute our bodies as we will, then amplify intelligence and create paradise. Anyone who understands why power tends to corrupt will understand why even were that possible, Read More ›

In my first post I discussed the concept of information, in particular whether information is contained in a physical object by its mere existence.  In this post I would like to consider an additional issue relating to information, namely, the point at which information arises or comes into existence. Information is often closely associated with meaning – meaning that is transmitted from a sender to a receiver.  As a result, some have suggested that information only exists when there is both a sender and a receiver who have a prior agreement about the protocols to encode the information and after there is a successful transmission, receipt and understanding of the information. However, viewing information as existing only after it has been transmitted Read More ›