Junk DNA, Junk Memes, Recombination, and Art

[drscott]

One of my research projects in the late 80s dealt with genetic algorithms. This means you design a simulated system that mimics evolution by natural selection: select an encoding that can be cranked through a constructor to produce a virtual organism, set up an initial population of these organisms and a simulated environment for them to interact with, and let them compete, grow, reproduce sexually, and transmit their more successful combinations of characteristics to the next generation. Over many generations these systems are capable of creating very skillful populations, and the sum of the activities of the population gets more and more optimal in extracting resources from the virtual environment. I learned quite a bit about population genetics from these experiments, and the simplifications inherent in these systems compared to real biology can make apparent what is not so obvious in real life.

Many popular treatments of the topic imply that mutation ( a random change in the DNA caused by radiation or chemical accident) is the critical factor in gradual change of the genome over time. This is not really true; as life evolved on Earth, almost all of it using the same encoding (four bases ATCG) and similar constructors, by far the most common source of change became recombination. Within a species population vast changes can occur using only the DNA sequences present in the population as they are sexually recombined in different sequences, changing both in frequency and in function as fragmentary sequences are combined in new ways. But there's more: viruses can transfer chunks of their DNA into cell nuclei, and vice-versa, and bits and pieces of DNA from one species can be transferred to another this way, sometimes ending up in the mainstream population. So the population of DNA fragments is a sea of words that is shared among all life forms, and we are all related, not only to other humans, but to all life, down to the bacteria. The meanings of these fragments depend on the context in which they occur, and when put together in a new way, the "sentences" of life can say something completely new even when created from old parts.

An organism typically has far more DNA than appears to be in actual use to encode proteins or participate in gene expression. The "unused" DNA is often called Junk DNA, and it was thought to be accumulated in unused areas of the genome over time. But some significant part of this at some point in the past was useful material, which has been swapped by accident into a place where it is masked and dormant. For example, a moth species adapted to a snowy environment is primarily light-colored, but has unexpressed (recessive or switched out) genes for pigmentation remaining from a long-ago era when it was adapted to a dark forest environment. If the territory occupied by this species suddenly changes climate (as has happened many times in the past), the population may find itself struggling to survive when its individuals are now easily picked out against a darker background, and thus subject to a much higher rate of predation. Natural recombination via sexual reproduction will produce a few individuals who are darker, and the much higher survival rate for those individuals means the next generation will have many more of the old pigmentation DNA fragments, will produce even more dark and darker individuals, and by this process over a very few generations can re-express the species' previous character as a dark-pigmented group suitable for survival in a forest. In this way recessive, and to a lesser extent "junk," genes are a species memory, providing a library of characteristics from which the species can draw to evolve to suit its changing environment.

Now we bring in a bit of jargon. In complex systems work, we often abstract the system of relationships between parts of a complex system and apply them to a system made up of different parts that, because it is similarly connected, has similar behaviors. The meta level expresses the commonality of behavior of the systems even though they are built on a different substrate.

The term meme was popularized by Richard Dawkins to mean a basic unit of cultural DNA, a fragment of an idea which, when strung together with others in meme-complexes, are the basic units of cultural transmission and replication. He pointed out the similarities between transmission of cultural ideas and genetic information; slightly inaccurate copying, recombination, survival of the fittest, and reproduction leading to similar population "memetics." As the body of knowledge carried by the population of the world grows and evolves, it, too, carries a lot of "junk memes," formerly adaptive fragments of knowledge and belief which no longer appear to have value, yet are carried quietly along with the body of the culture.

Some of these memes can do great harm in the modern world - racism, xenophobia, superstition, mercantilism. Those cultures that express them in harmful ways tend to be overwhelmed and die out over time, but still they show themselves over and over again. It is reasonable to say that under some environmental conditions not currently present in most of the world, they were all useful ideas in that they helped a population survive under a set of conditions no longer present.

The myths and false beliefs of our time were the common wisdom of some earlier era, as some of our common wisdoms of today are destined to be deprecated to become the superstitions of the future. But this past body of cultural fragments are the shiny shards we put together to create new things that are useful and valuable. When we write or paint or create, we take bits and pieces from diverse sources and put them into a new relationship with each other, and say something never before said.

So while it's important not to let fools and misguided mystics do actual harm to the world or damage its future, it's also important to keep that junk pile of useless and false ideas, no matter how harmful they may once have been. Those who practice these ideas to the detriment of others are to be pitied and kept from decisionmaking posts, and (where possible) gently educated away from their fixations. But a combative stance toward them can do more harm than good by cementing their belief that they are being persecuted, and the group cohesion so produced can actually make the people holding these ideas more dangerous.

Here's the intro to a recent special section of The Economist, one of the best short overviews I've ever seen of modern social evolutionary thinking:



The story of man

Dec 20th 2005
From The Economist print edition

Modern Darwinism paints a more flattering portrait of humanity than traditionalists might suppose

IN THOSE parts of the planet that might once have been described as “Christendom”, this week marks the season of peace on Earth and goodwill towards men. A nice idea in a world more usually thought of as seasoned by the survival of the fittest. But goodwill and collaboration are as much part of the human condition as ill-will and competition. And that was a puzzle to 19th-century disciples of Charles Darwin, such as Herbert Spencer.

It was Spencer, an early contributor to The Economist, who invented that poisoned phrase, “survival of the fittest”. He originally applied it to the winnowing of firms in the harsh winds of high-Victorian capitalism, but when Darwin's masterwork, “On the Origin of Species”, was published, he quickly saw the parallel with natural selection and transferred his bon mot to the process of evolution. As a result, he became one of the band of philosophers known as social Darwinists. Capitalists all, they took what they thought were the lessons of Darwin's book and applied them to human society. Their hard-hearted conclusion, of which a 17th-century religious puritan might have been proud, was that people got what they deserved—albeit that the criterion of desert was genetic, rather than moral. The fittest not only survived, but prospered. Moreover, the social Darwinists thought that measures to help the poor were wasted, since such people were obviously unfit and thus doomed to sink.

Sadly, the slur stuck. For 100 years Darwinism was associated with a particularly harsh and unpleasant view of the world and, worse, one that was clearly not true—at least, not the whole truth. People certainly compete, but they collaborate, too. They also have compassion for the fallen and frequently try to help them, rather than treading on them. For this sort of behaviour, “On the Origin of Species” had no explanation. As a result, Darwinism had to tiptoe round the issue of how human society and behaviour evolved. Instead, the disciples of a second 19th-century creed, Marxism, dominated academic sociology departments with their cuddly collectivist ideas—even if the practical application of those ideas has been even more catastrophic than social Darwinism was.

Trust me, I'm a Darwinist

But the real world eventually penetrates even the ivory tower. The failure of Marxism has prompted an opening of minds, and Darwinism is back with a vengeance—and a twist. Exactly how humanity became human is still a matter of debate. But there are, at least, some well-formed hypotheses (see article). What these hypotheses have in common is that they rely not on Spencer's idea of individual competition, but on social interaction. That interaction is, indeed, sometimes confrontational and occasionally bloody. But it is frequently collaborative, and even when it is not, it is more often manipulative than violent.

Modern Darwinism's big breakthrough was the identification of the central role of trust in human evolution. People who are related collaborate on the basis of nepotism. It takes outrageous profit or provocation for someone to do down a relative with whom they share a lot of genes. Trust, though, allows the unrelated to collaborate, by keeping score of who does what when, and punishing cheats.

Very few animals can manage this. Indeed, outside the primates, only vampire bats have been shown to trust non-relatives routinely. (Well-fed bats will give some of the blood they have swallowed to hungry neighbours, but expect the favour to be returned when they are hungry and will deny favours to those who have cheated in the past.) The human mind, however, seems to have evolved the trick of being able to identify a large number of individuals and to keep score of its relations with them, detecting the dishonest or greedy and taking vengeance, even at some cost to itself. This process may even be—as Matt Ridley, who wrote for this newspaper a century and a half after Spencer, described it—the origin of virtue.

The new social Darwinists (those who see society itself, rather than the savannah or the jungle, as the “natural” environment in which humanity is evolving and to which natural selection responds) have not abandoned Spencer altogether, of course. But they have put a new spin on him. The ranking by wealth of which Spencer so approved is but one example of a wider tendency for people to try to out-do each other. And that competition, whether athletic, artistic or financial, does seem to be about genetic display. Unfakeable demonstrations of a superiority that has at least some underlying genetic component are almost unfailingly attractive to the opposite sex. Thus both of the things needed to make an economy work, collaboration and competition, seem to have evolved under Charles Darwin's penetrating gaze.

Dystopia and Utopia

This is a view full of ironies, of course. One is that its reconciliation of competition and collaboration bears a remarkable similarity to the sort of Hegelian synthesis beloved of Marxists. Perhaps a bigger one, though, is that the Earth's most capitalist country, America, is the only place in the rich world that contains a significant group of dissenters from any sort of evolutionary explanation of human behaviour at all. But it is also, in its way, a comforting view. It suggests a constant struggle, not for existence itself, but between selfishness and altruism—a struggle that neither can win. Utopia may be impossible, but Dystopia is unstable, too, as the collapse of Marxism showed. Human nature is not, to use another of Spencer's favourite phrases (though one he borrowed from Tennyson, his poetical contemporary), red in tooth and claw, and societies built around the idea that it is are doomed to early failure.

Of the three great secular faiths born in the 19th century—Darwinism, Marxism and Freudianism—the second died swiftly and painfully and the third is slipping peacefully away. But Darwinism goes from strength to strength. If its ideas are right, the handful of dust that evolution has shaped into humanity will rarely stray too far off course. And that is, perhaps, a hopeful thought to carry into the New Year.

Comments

[malcarne.livejournal.com]

Now I'm curious as to your responses to Greg Bear. Have you read his Blood Music, the Eon series: specifically Legacy, or his Darwin books?

[dr-scott.livejournal.com]

I've read all of them, at the time they came out, but that was a long time ago. I loved Blood Music and it probably started me down a road of paying attention to bio-nano-computing issues, but I suspect the premise is implausible knowing what I know now; creating AI-containing nanites is a much harder problem than either AI or nanofabrication alone, and the apocalyptic singularity model (which requires a world which is metastable and implodes on contact with a mere organizing principle or geometrically expanding change agent) isn't much more likely than Vonnegut's Ice-9. The similar fears of GMO are foolsh, since nature has made every possible effort to create successful parasitic organisms by recombining pieces of code; gray goo is fungus, and its success is limited. Only injection of AI or some spot source of energy could change the constraints on current natural system to allow some kind of bio-singularity, and it won't be easy or sudden.

Bear seems to have lst his creative touch. I like some of his recent work (Kiln People was decent) but he's not breaking any new ground.

[malcarne.livejournal.com]

I lament Bear's taming of his once wild imagination, see: his last three sci-thrillers. I brought him up because your post resonates a bit with his meta-themes
of goopy bio-diversity and evolution...also I was just reading his short story, "Mandala," which, if you're familiar with his early work, clearly illustrates the aforementioned themes later to be expounded upon in Blood Music, Legacy, etc. This with a veneer of biblical extrapolation.

Anyway, I appreciate your assertion that a truly complex system will shrug off(or subsume) any infection. It's like "ecology fascists" bemoaning presidential policy; the threat's in their minds. The "ecology fascists" are, themselves, the paltry infection.

[dr-scott.livejournal.com]

Much later note: I am an idiot (or neurons are decaying ) -- Kiln People is David Brin, not Bear. Duh. Still true, wrong example; I should have cited Darwin's Radio. Not bad, but not seminal.

agree about the Darwin duo

[malcarne.livejournal.com]

Kiln People didn't sound right, but there's so much Bear(!) out there. I've just started reading Brin, specifically the Uplift novels.