Sunday, 27 August 2017

The scientific neglect of filtering and sorting

In computer science, filtering and sorting are big topics. Donald Knuth devoted volume 3 of his epic The Art Of Computer Programming to these two topics. That's a reasonable indication of their importance in computer science.

However, science in general took a different route. Filtering is dealt with partly as "selection" - which is covered most comprehensively by evolutionary biology. However filtering is a much broader topic, which extends well beyond biology. As a result, the science of selection is fragmented:

Because the science involved is fragmented there are also a number of areas where it could be applied, but currently isn't - because its influence is not understood or recognised. When small coins accumuate in your wallet, that's a type of selection. Similarly selection results in unpalatable goods accumulating in your refridgerator. Selection is also important in many common physical phenomena, such as erosion, crack propagation, catalysis, crystal growth and electrical discharges. However, its influence often goes unrecognised there as well.

In 1971, George Price called for a theory of selection, writing:

A model that unifies all types of selection (chemical, sociological, genetical, and every other kind of selection) may open the way to develop a general ‘Mathematical Theory of Selection’ analogous to communication theory.

Price continues with:

Selection has been studied mainly in genetics, but of course there is much more to selection than just genetical selection. In psychology, for example, trial-and-error learning is simply learning by selection. In chemistry, selection operates in a recrystallisation under equilibrium conditions, with impure and irregular crystals dissolving and pure, well-formed crystals growing. In palaeontology and archaeology, selection especially favours stones, pottery, and teeth, and greatly increases the frequency of mandibles among the bones of the hominid skeleton. In linguistics, selection unceasingly shapes and reshapes phonetics, grammar, and vocabulary. In history we see political selection in the rise of Macedonia, Rome, and Muscovy. Similarly, economic selection in private enterprise systems causes the rise and fall of firms and products. And science itself is shaped in part by selection, with experimental tests and other criteria selecting among rival hypotheses.

If the situation with filtering in science is bad, the situation with sorting is surely worse. At least selection is championed by evolutionary biologists. Sorting is also very common. You can see its results while looking at stones on a beach or clouds in the sky. Shaking your breakfast cerial makes the biggest lumps rise to the top - a simple sorting operation. I have talked about "natural sorting " before - but most people have never heard of it. If the science of filtering is fragmented, the science of sorting is positively obscure.

There have been efforts to build a general science of selection. Proponents of universal Darwinism have been working on it. There's Zukav's "Without Miracles". There's Hull's "Science and selection". There's Fog's "Towards a universal theory of competition and selection". There's Campbell's "Epistemological roles for selection theory". It is probably fair to say that most of the pieces are out there, but the topic is far from penetrating the scientific mainstream. It seems as though more work in the area remains to be done.

Saturday, 19 August 2017

The inheritance of acquired sexual preferences

I've long been interesed in the idea that acquired sexual characteristics can be inherited - as part of my more general interest in Lamarckian inheritance. Here is how I have previously described the idea:

The author argues that surgical breast enhancements are inherited, and tend to produce offspring with larger breasts. A mechanism is provided: those with breast enhancements tend to attract mates who prefer larger breasts, and some of that preference will have a genetic basis. Genes in men for a preference for larger breasts will tend to be statistically linked to genes whose expression produces bigger breasts when in women, due to their shared evolutionary history. So: we can expect breast enhancement patients to have offspring with larger breasts than would have been produced if no enhancement surgery had taken place. The reasoning here can be applied to most sexually-selected traits.
I notice that the same logic applies to acquired sexual preferences. A similar example can be used to illustrate this idea. Imagine someone acquires a preference for large breasts - perhaps via exposure to pornography. Their offspring are likely to inherit this preference. How? They are likely to mate with individuals with large breasts, who are in turn more likely than average to carry genes coding for a preference for large breasts.

The fact that the idea also applies to acquired preferences expands its scope. I think that this idea has not been investigated very thoroughly. We don't yet have good theories or models about it. That makes it challenging to judge its overall significance. Another thing that needs doing is empirical testing and quantification. So far, the idea is armchair philosophy. However, the effect should be fairly simple for scientists to measure. It ought to be reproducible with fruit flies or mice, for example. Possibly, data sets suitable for testing the idea may already be out there somewhere.

Defending Lamarck

I think most proponents of cultural evolution acceot the idea that it has a Lamarckian component. I have writen about the topic before - e.g. see: On Lamarckism in cultural evolution. I know many critics accept the role of Lamarckian evolution in culture as well, since one of their refrains is that cultural evolution is not Darwinian, it is Lamarckian.

Lamarck's most famous doctrines these days are the inheritance of acquired characteristics, and the principle of use and disuse. Those are the ideas he is most criticised for holding these days. Textbook orthodoxy says that Darwin's ideas were vindicated while those of Lamarck were rejected. Experiments by August Weismann involving chopping the tails off while mice and observing whether this "acquird characteristic" was inherited are often cited inthis context. The so-caled "Weisman barrier" prevents "acquird characteristics" from finding their way into the DNA of the descendants.

The problem with this is that other traits are inherited. If Weismann had chosen to focus on other traits - such as stress, food preferences or parasite load - he would have found that there was an inherited component. Human examples show the inherited of acquired characteristics most clearly. Jews inherit their missing foreskins from their parents. Tattooed individuals have tattooed offspring. Piercings are inherited. Foot binding, tongue plates, extended necks are all passed down the generations. The inheritance is cultural, not genetic, but Lamarck never confined his views to particular inheritance mechanisms. These were, generally speaking, not known in his day.

There are plenty of examples that don't involve culture too. Dogs inherit their fleas from their parents. Gut bacteria and tooth decay are also acquired characteristics that are inherited. Examples can also be found of Lamarck's principle of "use and disuse". Muscles are a famous example of this principle. With use, muscles grow, and with disuse they shrink. The question is: do offspring inherit their parents muscle distribution? The answer is: yes, sometimes, a bit. The changes are not primarily inherited via DNA - though of course DNA can affect how much you use your muscles. Instead, diet and exercise-related factors that influence muscle size are inherited culturally and through a shared environment.

This is all fairly simple and should be uncontroversial. Nontheless, modern critics of Lamarck refuse to accept that his ideas have any merit. What do they have to say for themselves? Science blogger Jerry Coyne provides a recent example in his article "Aeon tries to revive Lamarck, calling for a “paradigm” shift in evolution". Coyne starts off with a reasonable characterization of the inheritance of acquired characteristics, saying:

Lamarck, of course, was the French biologist and polymath who proposed that animals could stably inherit modifications of their body, behavior, and physiology that were imposed by the environment.
However, then Coyne rapidly goes off the rails, with:

The problem with this idea, and why Lamarck hasn’t become any kind of evolutionary hero, is that it doesn’t work. While the environment can play a role in sorting out those genes that their carriers leave more offspring, there’s no good way for environmental information to somehow become directly encoded in the genome. For that would require a kind of reversal of the “central dogma” of biology

This is, of course a mistaken view. When A mother acquires AIDS, and passes that "acquired characteristic" on to her offsping, no violation of the central dogma is involved. Coyne is totally missing two other possibile ways acquired characteristics can be inherited by offspring: non-DNA inheritance and symbiosis. The idea that DNA modifications must be involved is a very blinkered conception of evolutionary change.

With this, I think, Coyne's critique of Lamarck collapses. The modern vindication of Lamarck doesn't really detract from Darwinian orthodoxy very much. Darwin's ideas still remain very important. I would not describe Lamarckian evolution as much of a "paradigm shift". Darwin himself believed in the inheritance of acquired characteristics, and proposed an elaborate (though mistaken) theory about how they could be inherited. Lamarckian inheritance is more like an extra wrinkle to Darwinian evolution.

Sunday, 13 August 2017

Mutations and recombination in cultural evolution

Another claim in the recent Creanzaa, Kolodny and Feldman document (Cultural evolutionary theory: How culture evolves and why it matters) is my topic today. They say:

Unlike in genetics, where mutations are the source of new traits, cultural innovations can occur via multiple processes and at multiple scales
To start with, this is rather obviously not true: classically, mutations and recombination are the source of new traits in evolutionary theory. However, are the authors correct to claim that these processes need augmenting in cultural evolution? The answer, I think is: not if you conceive of them properly in the first place. Let me explain.

To start with, let's look at what the authors claim are the new processes that go beyond mutation in the cultural domain. They give two examples. One is individual trial-and-error learning. They also say that:

New cultural traits can also originate when existing traits are combined in novel ways
This is cultural recombination - the parallel in cultural evolution of recombination in the organic realm. Do the authors really not know that ideas have sex too?

What about trial-and-error learning, though? Surely there is no leaning in genetics. Trial-and-error learning is a composite process. It starts with trials, which are often mutations of previous trials. Then there is the "error" part, which does not involve generating new variation at all, but rather is based on discarding information based on its success. In other words, it is selection, not mutation or recombination. By breaking trial-and-error learning down into its component parts, it is found to be a composite product of mutation, recombination and selection - not some entirely new process demanding fundamental additions to evolutionary theory. Skinner realised this, by formulating his learning theory while using evolutionary terminology (such as "extinction"). Many others have followed in his footsteps, conceiving of learning in evolutionary terms.

Isn't this a matter of terminology? With these author's definition of 'mutation' they are right, but with my definition of 'mutation', I am right? Yes, but terminology isn't a case of words meaning whatever you want them to mean. Scientific terminology should carve nature at the joints. Definitions of 'mutation' and 'recombination' that apply equally to both organic and cultural evolution are useful, I submit. Less general ones are not so useful.

To summarize, it is possible to conceive of mutation and recombination in a way that make them encompass all sources of variation. Mutations are sources of variation based on one piece of inherited information. Recombination is a source of variation based on two-or-more pieces of inherited information. In theory, it might appear that there's one other possible process: creation - variation based in inherited inforation which comes out of nowhere. One might give the origin of life as an example of genes arising from non-genes. However, we don't really need this proposed 'creation' process. Information never really comes out of nowhere. There's a law of conservation of information - parallel to the laws of conservation of energy and conservation of charge. We can see this in the microsopic reversibility of physics - information is neither created nor destroyed.

I claim then, that mutation and recombination have it covered. The additions to evolutionary theory proposed by these authors are not necessary. They are unnecessaary complications, which evolutionary biologists should soundly reject as not contributing anything to the basic theory.

Saturday, 12 August 2017

Diagram showing where cultural evolution in academia goes wrong

Creanzaa, Kolodny and Feldman have a recent document out titled: Cultural evolutionary theory: How culture evolves and why it matters. It has a nice diagram which is useful in illustrating where academia goes wrong in its study of cultural evolution. Here is the diagram:

The caption reads: "Cultural transmission is more complex than genetic transmission and may occur on short timescales, even within a single generation."

This diagram is profoundly misleading. It is based on a view of cultural evolution that doesn't include symbiology. A genes vs culture diagram that includes cultural symbionts on one side, but not genetic symbionts on the other is not showing the whole picture. Humans share DNA between individuals - in the form of bacteria, viruses, yeasts, fruits and vegetables - very much as they share culture between individuals.

Framing the diagram as "Human genes" vs "Human culture" is not comparing like with like. Bacterial and viral genes are not part of the human genome (unless you count the 10% of the human genome that is descended from viral genomes) - but human culture isn't part of it either. On the left, symbionts are excluded, while on the right they are included. It is an unfair comparison which leads to the confusion propagated by the caption. In fact parasite evolution can happen within a single host generation in both the cultural and organic realms. Contrary to the spirit of the diagram you can get genes from peers in both cultural and organic evolution. They are parasite genes, or symbiont genes in both cases. Cultural evolution does not differ from organic evolution in this respect. The idea that in culture you can get genes from many sources, while in organic evolution you only get them from your parents is a popular misconception about the topic.

The whole document has a whole section on "Culture and Microbes". However there is no mention of the idea that culture behaves similarly to microbes and other symbionts. The man-machne symbiosis, for example is not mentioned. Yet symbiosis is the very basis of the whole field according to memetics, one of the very few symbiosis-aware treatments of cultural evolution out there.

The neglect of symbiology in academic cultural evolution mirrors its neglect in the study of organic evolution - until the 1960s. However, cultural evolution's scientific lag means that cultural evolution is far behind, and few academics have even a basic understanding the relevance of symbiosis to the evolution of culture. Maybe these folk never read Cloak (1975) and Dawkins (1976).

I think the history of this misconception of the whole field in academia is fascinating. Why has it lasted for so long and why has it not yet been corrected? I don't have all the answers but I think the origin is fairly clear. Anthropologists wanted a complex theory of cultural evolution, to signal their skills to other academics and prospective students. They may also have wanted to distance themselves from previous attempts to marry evolution and culture. Any mention of biology turns most anthropologists off. Artificially weakening the influence of biology in the theory may have made the theory more palatable to other anthropologists. Still, science is a self-correcting enterprise. Eventually, the truth will out.

Friday, 4 August 2017

The tautology criticism yet again

It's frustrating:: critics keep repeating the same long-debunked objections to memetics. Jerry Coyne is one of the latest to raise the objection that memetics is an empty tautology:

“Memetics” is a weak analogy to natural selection that adds nothing except tautology to our view of how human culture evolves. Memetics boils down to this: memes spread because they have properties that allow them to spread.
As any scientific historian will tell you, Darwin's theory faced exactly the same bogus criticism. Critics argued that "survival of the fittest" was a tautology because fitness was defined in terms of who survived. Any evolutionist should be able to explain what is wrong with that argument: "fitness" can be taken to refer to "expected fitness" - as opposed to fitness measured after the fact. Then it isn't a tautology any more.

The exact same reply works for cultural evolution: to make testable predictions, use expected fitnesses.

I have seen much the same objection raised to the Price equation and Hamilton's rule. These have been criticised as tautologies by Martin Nowak and Edward Wilson among others. This criticism ought to be dead these days, but like a zombie, it refuses to lie down.