Sunday, 29 December 2013

Subfields of genetics

The science of heredity could be usefully subdivided into:

Symbiotic genetics is probably an unfamiliar concept. It would deal with the "genetics" of symbiotic unions. Basically this largely consists of studying when symbiotes are gained or lost from such unions.

Symbiont gain should be called "symbiogenesis" (though, in fact, that term is often used to refer to something else). Much of the symbiology literature addresses this topic.

There's an interesting book about symbiont loss: The Ghosts Of Evolution Nonsensical Fruit, Missing Partners, And Other Ecological Anachronisms by Connie C. Barlow.

In a previous article I offered a classification scheme for mutations. It is interesting to think how the various types of mutation apply to symbiotic genetics and population genetics.

Symbiotic genetics is particularly relevant to students of cultural evolution - since cultural evolution is heavily based on symbiology.

Mutations classified

Arbitrary document modifications can be modeled as a series of insertions and deletions.

This sort of scheme works pretty well as the basis for a mutation classification scheme - in both organic and cultural evolution.

Sometimes it is useful to model a combined insertion and deletion as a replacement.

With insertions and replacements, the source of the introduced information can be used to sub-classify. The most obvious sub-classification involves whether the inserted information comes from self or other. A replacement of material from yourself could be classified as a rearrangement.

An insertion of material copied directly from yourself would be a duplication. A movement of material is commonly called a translocation.

This scheme is similar in some respects to the existing one used to classify organic mutations - though my proposal is substrate neutral.

An orthogonal classification scheme is whether the mutations are accidental or deliberate. Deliberate mutations are seen in the immune system, for example. They are also a common feature of cultural evolution.

Mutations can also be classified by their effect on function, by their effect on fitness and by whether they are inherited. These classification schemes work equally well in the organic and cultural realms.

Sunday, 22 December 2013

The sciences of memory and copying

A possible alternative to having a science of heredity is to have a science of memory and a science of copying (since memory and copying are the main components of heredity). In a number of respects, this would be good - since memory and copying are pretty different phenomena.

We already have a science of memory: "mnemology". This is named after Richard Semon's fine concept of the "mneme" - which was great, but ultimately lost out to the "gene". Unfortunately, mnemology does not seem to be a well-known subject area. There are also "memory studies" and "memory theory" - which don't quite seem to be the same thing. The science associated with memory seems to be a bit fragmented. Animal memory seems to have been assimilated into psychology and cognitive science - and not given a name of its own. The topic of "genetic memory" has been assimilated into genetics.

If you look for a science of copying, there doesn't seem to be much out there - except for evolutionary theory, biology, genetics and "epigenetics" [sic]. There is information theory - perhaps that is the nearest thing.

A science of copying would probably have two foundations: the concept of mutual information - from Shannon information theory - and the concept of causality. I've gone into this in more detail in my article: What are inheritance and copying?

Since one way for patterns to persist is via copying, we could have the science of memory including the science of copying. That way we could still call it the "science of heredity", "science of persistence", or "genetics". Persisting without copying is a topic unto itself - but perhaps one that is not worthy enough one to have its own separate field.

This whole situation seems rather unfortunate. The sciences of persistence and memory seem fragmented, while the science of copying barely seems to exist - outside of biology.

Perhaps my perspective on this is a bit different from other scientists. For me, storage and copying are fundamental operations. They are certainly fundamental operations inside computers. If you think about it, they are pretty fundamental operators in the rest of the world as well. To have a science of memory and a science of copying seems like a natural way to carve the world up to me. However, what we currently have seems to be a long way from this.

Saturday, 21 December 2013

Universal Darwinism and the origin of life

One of the more coherent critiques of universal Darwinism I am aware of comes in the first part of the book Genetic Takeover: And the Mineral Origins of Life by A. G. Cairns-Smith. The author argues in some detail that there's no such thing as "prebiotic evolution", or "chemical evolution" - and the origin of life represented the dawn of the era of adaptation. He rejected the idea that you could draw on the concept of adaptation before the first self-reproducing agent existed.

We now know that this idea is wrong. There was copying with variation and selection before the origin of life. Evolutionary theory applies to a variety of non-living systems that preceded the first living things. The concept of "adaptation" also applies to such systems.

The rest of the thesis in this book seems little-affected by these more recent developments. Crystals still look as though they are the most likely candidate substrate for the first living things. The idea of a genetic takeover still seems to be highly significant.

Probably, universal Darwinism makes the probability of the origin of life seem larger - since invoking adaptation before the origin provides new paths and mechanisms via which life could arise.. However our main evidence relating to the likelihood of life's origin still consists of observations about its history on the planet and astronomical observations of other worlds - rather than arguments from physics or chemistry. So perhaps this doesn't make much difference.

However, universal Darwinism might help to illuminate possible pathways towards the origin.

Video: Richard Dawkins On Meme

I can't embed this video. It's called "Richard Dawkins On Meme".

Dawkins is promoting his autobiography here - and he describes the role of memes in The Selfish Gene.

The video is dated November 2013.

Friday, 20 December 2013

Against phenogenotypes

The term "phenogenotype" has been proposed to refer to a mixture of cultural and genetic traits - originally by Marc Feldman, I think.

Robert Aunger was critical of this concept - saying that such combinations tended to be transitory.

Herbert Gintis once wrote:

He shows that culture cannot be identified with phenotype or behavior. It follows that we must drop the term 'geno-phenotype'. In its place we can use the term 'geno-memotype.'

I don't like the term "phenogenotype". It's a confusing mixture of two different kinds of thing. Phenotypes include genotypes - so a "phenogenotype" would be just a phenotype. Instead, "phenogenotype" is used to refer to combinations of traits - or to combinations of genes.

In practice, "phenogenotype" is generally used to mean something close to a "geno-memotype". This name is better - but the concept is rarely needed, since memes and genes typically have different inheritance paths, and lumping them together in this way confusingly suggests that they are closely associated.

The proposed concept of a "phenogenotype is on my mind today because I read A Cooperative Species" recently - and the authors use this terminology.

I notice that Marcus Feldman was still teaching the "phenogenotype" terminology in 2014 here.

Tuesday, 17 December 2013

The domain of the science of heredity

I more-or-less take it for granted that:

  • We should have a science of heredity;
  • That this science should be called "genetics";
There seem to be a fair number of people who think that the term "genetics" is best reserved for the study of nucleic-acid-based heredity - but that seems like an extremely parochial and out-dated perspective to me.

Nor do there seem to be other sensible proposals for the name of a science of heredity. In my "Against Replicator Terminology" essay, I propose "replicatology" as the name for a possible alternative science of heredity. However, it doesn't seem very likely that "replicatology" will get anywhere. We already have a science of heredity. It's called "genetics".

This post is about another topic, namely: what is the proper domain of the science of heredity. If you look up "genetics" you'll see that it is often defined as the science of heredity in living organisms. This would make it part of biology. However, heredity, like evolution, is not confined to living things. Both of these concepts apply to all kinds of things that are not conventionally considered to be alive - electrical discharges, drainage basins, propagating cracks - and so on.

Do we really need a science of heredity for living things - and another science of heredity for non-living things? I am sceptical. I'm pretty sure that the domain of the proposed science of heredity should not be limited to things that are alive. This proposal means that genetics would not be a sub-discipline of biology.

Monday, 16 December 2013

Parallels to universal Darwinism

Alex Mesoudi's recent book was titled: Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences.

However in Universal Darwinism, evolutionary theory also applies to physics, chemistry and computer science. This expanded scope of Darwinian explanation means that it has the potential to unify all the sciences - extending even beyond the physical laws of our universe into the realms of mathematics.

Parallels seem inevitable. Statistics also penetrates all branches of science. Thermodynamics (in the form of statistical mechanics) describes processes that aren't confined to universes with physics like ours. Universal Darwinism is a lot like statistical mechanics. Another case that springs to mind is complexity theory. Complexity theory deals with systems on an abstract level. Systems theory and cybernetics have similar potential for generality. Computer science and mathematics are also very general. Let's list these items as follows:

  • Mathematics;
  • Statistics;
  • Computer science;
  • Systems theory;
  • Complexity theory;
  • Statistical mechanics;
  • Cybernetics;
Conventionally, Universal Darwinism describes a set of processes. It doesn't seem as broad as mathematics, statistics or computer science (which are pretty process agnostic). However, its precise scope has yet to be fully elucidated. Some argue for a very general version of Darwinism that applies to all non-miraculous change. Such an expansive conception of Darwinism would put it on the same level as computer science - which studies computable processes.

However, overall, statistical mechanics looks like the best parallel to me.

In the 1930s Fisher noted resemblances between some aspects of population genetics and statistical mechanics, writing:

It will be noticed that the fundamental theorem proved above bears some remarkable resemblances to the second law of thermodynamics. Both are properties of populations, or aggregates, true irrespective of the nature of the units which compose them; both are statistical laws; each requires the constant increase of a measurable quantity, in the one case the entropy of a physical system and in the other the fitness, measured by m, of a biological population.

For me, that pretty-much captures the spirit of universal Darwinism.

Universal Darwinism seems to be in the process of being born into a storm of controversy. Complexity theory offers the nearest parallel here, I think - but the advent of complexity theory seems like a relatively mild revolution - in comparison to the one that universal Darwinism heralds.

Sunday, 15 December 2013

Rupert Sheldrake on memetics

In my last blog post here, I wrote:

I'm actually secretly pleased when such folk criticise memetics. If only Roger Penrose, Rupert Sheldrake, John Searle, Deepak Chopra and Al Gore could be persuaded to say some bad things about memetics!

I just checked: Rupert Sheldrake has said some bad things about memetics! In Morphic Resonance: The Nature of Formative Causation he says:

Richard Dawkins coined the word meme to refer to “a unit of cultural transmission, or a unit of imitation. He deliberately chose a word that sounded rather like gene to stress the analogy between genes and memes as replicators. But one of the problems with this term is that it is atomistic: it implies that memes are independent units, at the same level as each other. By contrast, thinking of cultural inheritance in terms of morphic fields has no such implication: morphic fields are organised in nested hierarchies.

So: memes are "atomistic" - and the answer is "morphic fields"!

For anyone unfamiliar, Rupert Sheldrake is a card-carrying pseudoscientist. His writings are full of parapsychological nonsense. Sheldrake's concept of "morphic resonance" is sheer pseudoscience.

So: would I like to replace cultural Darwinism with a bunch of mystical phoney baloney? Thanks - but no thanks!

Of course, just because some ignorant folk criticise memetics, it doesn't mean that it is true. However, from the perspective of an advocate, the more of the opponents are idiots, the better. One of the historical problems with memetics is that its prominent supporters have been folk other scientists don't want to associate with. That's not a problem with the theory, it's more of a sociological problem. However the "other side" isn't too great either. Rupert Sheldrake is the tip of an iceberg of undesirables.

Velikovsky on criticisms of memetics

I've spent some time going through the criticism of memetics from the memeophobes. I do this on my web site, on my blog, and in my 2011 book on the topic.

Others have spent time on this too - including Dennett, Blackmore and Hull. However I felt that more effort was needed in some places.

Another recent defender of memetics has been Sylvain Magne. Now, Joe Velikovsky is making some welcome contributions. Thanks, Joe!

Replies to some critics of “Memetics as a pseudo-science”

These articles seem to be promoting Velikovsky's paper on the topic - but that's fair enough.

I'm not sure all these critics are worth bothering with. Benitez-Bribiesca (2001) is an oft-cited critic of memetics - but the associated paper is totally hopeless. I rarely bother with addressing such nonsense. I feel much the same about Lanier. Lanier has lots of opinions, but a large proportion of them seem to be worthless nonsense.

I'm actually secretly pleased when such folk criticise memetics. If only Roger Penrose, Rupert Sheldrake, John Searle, Deepak Chopra and Al Gore could be persuaded to say some bad things about memetics!

Friday, 13 December 2013

Defenders of neoDarwinism

The "modern synthesis" - though vague - was too specific and must now be considered to be toast.

However it still continues a zombie existence in the minds of some researchers. Here's Joe Feldstein:

the Modern Evolutionary Synthesis has been challenged by people who invoke epigenetics, phenomena of evo-devo, punctuationism, and a variety of other existent and nonexistent phenomena. the Synthesis has survived all these. It has turned out that some of these phenomena either do not exist (as in the case of neo-Lamarckian mechanisms). Other such as epigenetic mechanisms have little long-term effect. The rest can be considered to be examples of the workings of the mechanisms of mutation and selection, as in the case of evo-devo phenomena.
Here's Jerry Coyne:

I’m constantly puzzled these days by how often people argue that the neo-Darwinian synthesis is wrong, and that we need a new paradigm. Genetic assimilation, epigenetics, horizontal gene transfer—all of these buzzwords are evoked as reasons to jettison our “conventional” view of evolution. But always, when you look at the data, the evidence that these phenomena will overturn neo-Darwinism is nonexistent. I’ve already written a lot on the epigenetics hype, and have shown that there’s no evidence that a single adaptation in nature involves the fixation in the DNA of an epigenetic alteration of the genome that isn’t initially inherited. Yet people keep banging on about epigenetics. I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis-is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon.
The modern synthesis was missing symbiology and universal Darwinism. It was so vague that its possible to argue that these things have been - or could be - incorporated into it - but it seems better to say that we're now in a new world that the founders didn't see coming - rather than siding with those defending these outdated and misleading dogmas.

Sunday, 8 December 2013

Richard Dawkins - on the definition of the term "meme"

Richard Dawkins recently wrote - in an AMA on Reddit:
  • Q: How do you feel now that memes, first discussed in your book The Selfish Gene, have become ubiquitous in internet culture? [...]
    • A: I'm pleased that the concept of meme has become widely understood, but the true meaning is a bit broader than the common understanding. Anything transmitted with high fidelity from brain to brain by imitation is a meme. [...]
Of course, that is true. However, to briefly recap why this sort of definition of a meme is not very useful scientifically:

Cultural elements spread from one human to the next irrespective of their copying fidelity. Essentially the same math applies to cultural elements that are copied with high fidelity and poor fidelity. Of course poor fidelity copying typically leads to a mutational meltdown - and acts against adaptive evolution. However, it does not always do so. There are ways of applying error correction to systems that exhibit poor copying fidelity. Some of these are used in real life cultural situations. Copying the most popular variant can stabilize even poor fidelity copying systems - and prevent a mutational meltdown. It is basic information theory that you can preserve signal fidelity even if you have poor quality data transmission channels.

There's little point in having a science of high fidelity copied cultural elements. It's would be a subset of the science of all copied cultural elements.

Also, there is no good reason to mention "imitation". Imitation is a type of social learning. A science of all social learning is at hand. This covers imitation, teaching, local enhancement - and other types of social learning. Being specific when you can so easily be general is not the scientific way.

In my opinion, Dawkins isn't helping memetics with this kind of material.


Self-confessed memetic hijacking victims

Memetics suggests that we might observe individuals so infested with memes that the interests of their genes are overridden. I refer to this as memetic hijacking. Susan Blackmore proposed we call such creatures "meme fountains" - which sounds remarkably positive to me. I've previously use the term "meme shedding" for the way in which such creatures leave a trail of memes wherever they go.

One of the most famous examples of memetic hijacking involves chaste priests who devote their energy to prosletysing. They tend to produce copies of their memes, not copies of their genes.

Theory suggests that memes might adapt in ways that divert host reproductive success towards meme replication - as is seen in the organic realm - where some parasites sterilize their hosts - in order to make use of their reproductive resources.

Of course many necrotrophic memes also reduce the fertility of their hosts by shortening their lifespan. Suicide bombers - who are sterilized by their memes in a most dramatic fashion - are an obvious example of this.

Not many memetic hijacking victims are "self-confessed". However we do see a few. Richard Dawkins recently volunteered that:

as for me, I'd rather spread memes than genes anyway.

He had previously said:

I'm unlikely to be among those who turn out to be ancestral to all. But I'd rather spread memes than genes anyway.

Richard does have a daughter, though. Similarly, Steven Pinker famously wrote in How the Mind Works:

I am happy to be voluntarily childless, ignoring the solemn imperative to spread my genes. And if my genes don't like it, they can go jump in the lake.

There are probably many other self-confessed memetic hijacking victims out there. I'll try to add them to this page as I track them down.

Saturday, 7 December 2013

Coyne gets heredity wrong

Popular science blogger (and meme critic) Jerry Coyne seems to be in a terrible muddle about the basic biological concept of heredity these days.

Here he is on his blog:

All heritable differences between species, in fact, must reside in the DNA; we know of no cases in which they don’t. Where else could they be?
Heritable differences between species can also reside in culture or the environment. The fact that modern humans have rocket-ships and Neanderthals did not is due to cultural variation - not genetic variation. It just isn't true that heritable differences "must reside in DNA". The idea that "we know of no cases in which they don’t" is just bunk. About 20-40% of variation in modern humans is due to cultural inheritance. That's not as much variation as DNA is responsible for - but it is a non-trivial amount.

Heredity can also reside in the environment. For instance, most marsupials over the last million years have inherited their position on the Australian continent from their parents - along with their DNA. Position is inherited too.

This is similar to the last time - where we had:

Geneticists now know the genetic basis of dozens of adaptive traits that differ between populations and species. All of them reside in the DNA. If non-genetic adaptive change was common, we would have found it.
Coyne has a long history of misunderstanding cultural evolution. One wonders when the penny is finally going to drop with him.

Sunday, 1 December 2013

The limits of evolutionary theory

The quest for the edge of evolutionary theory has been pursued by many. Often they conclude that morality - or some other aspect of human nature is "beyond the edge of evolution".

My search for the limits of Darwinism is a bit different. It's obvious that Darwin's theory of evolution covers all living things. However, it is now also now clear that the same theory applies to a range of inorganic systems - drainage systems, propagating cracks, electrical discharges - and so on. I discuss this in more detail in various places - including:

So: what are the limits of evolutionary theory? One solution is to have a theory that covers all change. I've briefly discussed this possibility in:

Such a complete theory of evolution has also been proposed by Nathalie Gontier. However, notoriously a theory that predicts anything also predicts nothing. This is not necessarily a fatal flaw - Turing's theory of computers applied to the universe in the form of the Church, Turing, Deutsch principle also predicts nothing. However, not making concrete predictions is not a very positive feature. This motivates the search for more easily falsifiable evolutionary theories.

Evolutionary theory usually involves a reproducing population undergoing mutations and subject to selection. However, this leaves open the issue of what counts as a "population", what a "mutation" is and what qualifies as "selection".


One classical way of constraining the predictions of evolutionary theory is to insist that mutation occurs at random. Obviously unconstrained variation can't be permitted - since otherwise you can explain any form of change by saying: "that's just a macromutation". Random mutations represents the opposite extreme.

The problem with the "random mutations" solution is lack of realism. Mutations aren't really random. Variation isn't really undirected with respect to fitness. The idea may be a pillar of neo-Darwinism, but it's just a confused mistake.

I think that Donald Campbell nailed the nature of the constraints on variation in 1974 - by saying that they depended on existing "knowledge" - where "knowledge" is intended in a broad sense that includes the accumulated "wisdom" stored in organisms' genomes.

Donald Campbell's solution might have been technically correct, but it isn't very neat. To apply it one must know what counts as "existing knowledge" - which is a non-trivial problem. Modelers typically tend to stick with random mutations - since these are more tractable.


A population is a clearly defined concept in the case of sexually-reproducing organisms. In most other cases it isn't so clear. I generally advocate that a broad conception of what counts as a population be used: any collection of one or more entities.


Selection takes the form of production and elimination. Entities are produced and eliminated. Production and elimination are a bit like creation and destruction - except that production could take the place of revealing an existing thing - while elimination could just hide something - rather than destroying it.


A clue about the domain of universal Darwinism is that it appears to cover the same domain as maximum entropy thermodynamics - whose application domain is fairly well established.

Another clue is that it appears to underpin all goal-directed systems and all adaptations.

Most systems that are macroscopically reversible are not usefully modeled by universal Darwinism.


The options for falsifying theories based on universal Darwinism are mostly based on evolution taking place too fast - and insufficiently gradually. Insisting on random (or undirected) mutations is the classical way of doing this. However, even if you relax this notion - and only insist that the mutations are based on existing knowledge - that still provides reasonable possibilities for falsification.