Re: computer virus

Scott Chase (
Mon, 08 Nov 1999 00:45:39 -0800

Date: Mon, 08 Nov 1999 00:45:39 -0800
From: "Scott Chase" <>
Subject: Re: computer virus


On Mon, 08 Nov 1999 10:13:46 John Wilkins wrote: >On Sat, 6 Nov 1999 14:24:43 -0800 (Stephen Danic) wrote: > >>> If a molecules is deformed, it will still probably bind to >>> or act as a substrate to *something*. Hence, gene products are able >>to >>> vary a lot and still function, while machine code tends to be much >>more >>> restricted - the only code that can vary randomly and still work is >>code >>> that doesn't get executed. >> >>Even so, biological genetic mutations are usually fatal. So it is with >>computer programs. Some GP researchers have suggested that mutations >>are >>more likely to be succesful if the gene has been accidently duplicated >>first. The product of the duplication (in biological systems) can then >>mutate freely, because the correct gene is still being expressed. > >Most mutations are neutral. They have little or no effect upon >phenotypic viability. > I think the neutral mutations might be the ones that occur in regions of a molecule that are not functionally constrained (eg- the active site of an enzyme would be constrained). Mutations might be more tolerable in regions devoted to structure removed from important parts of a protein. Here we get into the nasty territory of allozymes or electromorphs and also if the mutation is conservative (ie- whether a change in amino acid has an effect on the protein molecule such as a change in charge). Some molecules are more constrained *in toto* than others too, which is taken into consideration IIRC when doing molecular phylogenetic work (I think they call it calibration of molecular clocks).

There are also silent mutations which relate to third base wobble and the redundancy of the genetic code where several codons might correspond to the same amino acid. The genetic code is degenerate (but not ambiguous). Everything I know about molecular evolution could fit on the head of a pin, so I could be off a bit. > >Gene duplication, particularly of tandem repeats >and microsatellite sequences, does provide an enormous opportunity for >the evolution of novel function, and such genes are called "paralogous", >that being the form of molecular homology where the homologs are not in >the same locus. > Yes, in the context of multicellular animals you are correct. There are gene families which have resulted from duplication/divergence events outlined by the master Susuma Ohno in his classic _Evolution by Gene Duplication_. Genetics texts cover this topic and its basis in unequal crossover events during meiosis. This is a churn for gene redundancy. There is repetitive junk too (which IIRC explains some of the C-value paradox). Some amphibians are really strange with regard to this extra junk.

In the context of molecular viruses, I'm not sure how much genic redundancy there is. Viruses are known more for efficiency than redundancy. They tend to squeeze as much as they can out of a limited genome space, some employing overlapping reading frames. There might be some redundancy in viruses, but I think metazoans and their gene families are the epitome of redundancy and facilitated sloppiness. There could be tolerance for changes in aa or nucleotide sequence for viral proteins, but this might come down to wobble, conservative aa changes, and/or the consideration of constrained versus non-constrained regions within a protein.

Now, if we were to consider memes as mind viruses and tweak the analogy to its fullest capacity, maybe the consideration of antigenic shift/drift could apply. > >> >>I'm not sure how work is progressing in Computer Genetic Programming, >>but >>some analogy should apply. As long as the original function is retained >>in >>some form, the copy will be free to mutate without killing the system. >> >>In a computer program, if a mutation occurs that causes a function to >>report >>an incorrect value, the product may still be succesful. It shouldn't >>always >>generate a system crash. I'm tempted to believe that computer programs >>are >>More resilient to mutations than biological systems. > >Obligatory quip: you do not use either Windows NT or MacOS 8, then... > >Seriously, a single bit error in, say, the address register, can cause a >massive failure in a very short time. Almost *no* point mutations cause >that sort of catastrophic reaction or collapse in biological organisms, >unless they are very simple to begin with (ie, viruses, stretching the >point to include viruses as organisms). > > > I have no clue what the mutation rates are like in viral genes or DNA, but I do recall that one problem with HIV is its capacity to change and the problem with flu viruses is that they come in different strains each year, so those in charge of constructing vaccines must think ahead or consult their psychics.

I *could* be wrong, because it's been a while since I've been exposed to some of the nitty gritty of viruses and then then only superficially, but maybe one might consider the ability of viral antigens to change.

I'm not sure how any of this carries over to computer programs or computer viruses as an analogy.

Scott Chase

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