Extinction on the desktop

One reason I’ve not posted for a few days is that my computer blew up. Quite spectacular – smoke and bangs and everything. A failing power supply took out much of the rest, requiring a new system. The old one lasted nearly ten years, so I can’t complain. But even in that time updates to Windows and so on created headaches in keeping the thing functioning. I’ve had to update drivers for hardware rendered obsolete, buy new compatible programs and so on. I frankly dreaded trying to start again from scratch.

And with justification. I do a lot of sound recording, previously using a decent built in soundcard and audio interface (new drivers for which I had to find from Russia a couple of years ago when Microsoft improved my operating system and the maniufacturers didn’t bother to update), to power software that I had to renew at the same time because the old stopped working. Now people favour external sound modules, and the one I have bought actually had drivers for the new Windows OS (though I had to download them specially). However it stubbornly refused to work at all until I changed back to older drivers for the Firewire connection I’d bought for the computer, and adjusted everything I could to save memory (like shutting off the Windows sounds, even though compared to my last machine the new one has a memory the size of a planet).

Even after all that I keep getting clicks, stoppages and delays that make it unusable. The manufacturer reckons that I need to get a different Firewire connection as certain kinds tend not to be compatible. We shall see when it arrives – different systems respond to different types, even though they’re all made to the same standard. Thankfully the Internet is full of forums for people with these kinds of problems – but equally full of suicidal victims who’ve spent months trying to solve their compatibility problems and are reduced to cursing the manufactuers and, indeed, the whole creation. Aspiring recording stars have become unproductive gibbering wrecks.

I haven’t mentioned that my music keyboard is no longer compatible, requiring a cunning fix I thought of myself (one rapidly becomes a geek in this business). Nor have I noted that the sound programs I always use (especially my self-manufactured drum soundfonts, which have attracted admiration from my musical peers) couldn’t find a way to cooperate until I downloaded a special synthesiser, which in turn needed the download of some enthusiast’s modified component to play more than one sound at a time. And I certainly won’t trouble you about my having to buy a new printer and scanner because – guess what – they’re not compatible with the new stuff. Oh yes, and a new wireless card…

It’s hard to believe that a month ago, with an ancient system, I could go into my study, switch on and record whatever masterpiece I wished. Now I’m suffering the effects of evolution, or in Gregory’s careful and excellent terminology, “extension” (because it was all done more or less deliberately by clever people). It’s fascinating that, despite all that human ingenuity, not only is all my own ingenuity required to make anything work, but the helpful experts who manufacture it are reduced to advice like, “Try replacing X – that sometimes works, but we can’t guarantee it.”

Now as this paper shows, the genome of even a simple bacterium is directly comparable to computer software. And, of course, the proteins it encodes are equivalent to the hardware. Systems biology is even beginning to compare the equivalent elements of biological and computer systems, as this article demonstrates nicely.

As I have laboured over my recalcitrant technology, one thought has repeatedly occurred to me. All this rubbish happens when intelligent engineers plan to improve domestic computer systems and use their best efforts to achieve clear objectives. And yet the biologists are telling me that the equivalent living systems are achieving better results cheerfully from the bottom up by random mutation and natural selection. As a sound system, my computer would already fail to survive natural selection despite my concerted efforts. If I’d tried to make changes at random, extinction would have come even sooner. And it won’t be trying stuff at a venture that puts it right either – it’s just too complex a system for that to be other than a laughable fantasy.

But hold on – if you read the article, you’ll see that its contribution to knowledge is to show the distinction between the bacterial transcriptional regulatory system and the computer’s regulatory control network (or between their respective operating systems, to put it more simply). Computer systems are top-heavy, using many master- and  mid level – controllers on a relatively small number of generic “workhorse” functions. So for cost-effectiveness, generic functions are preserved – at the price of robustness. Or, when push comes to shove, at the price of the sanity and hard-earned cash of the buying public.

Bacteria, on the other hand, have a large number of specialised “workhorses”, and fewer mid level- and master-controllers, giving a “bottom up” appearance, and functionally a bigger number of more independent “modules”. The authors argue that this suits the process of random mutation and natural selection – a deleterious mutation is only going to damage a limited number of modules, rather than ruining the whole shebang as computer changes do.

Well. Maybe that’s the answer to my heretical thoughts. Here is evidence that living systems are actually substantially different from my computer, despite the analogical similarity. Random changes might be terminal for my Dell, but life and health for my dog and his progeny. I still find it difficult to credit at an emotional level, but maybe someone will eventually be able to fill in the detail and show it to be so. Maybe. Were it not for the note at the end of the discussion section of this paper, which says this:

Previous studies have made the related finding that as one moves towards more complex organisms, the transcriptional regulatory network has an increasingly top-heavy structure with a relatively narrow base. Thus, it may be that further analysis will demonstrate the increasing resemblance of more complex eukaryotic regulatory networks to the structure of the Linux call graph.

Bacteria, then,  might not be like a computer. But, equally, they are also not like you, me and all of us eukaryotes. We’re more like the Desktop Demon, as far as our systems go. And our operating systems appear to be pretty species-specific, if chomosome structures and repetitive elements are anything to go by. Somebody still has to explain how chimps on Windows Vista upgraded to humans on Windows 7 without the whole undirected project going belly up.

Jon Garvey

About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
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