Sunday, 22 July 2018

The non-randomness of mutations

Sometimes people contrast organic and cultural evolution by saying that in cultural evolution, mutations are not random, they can be the result of "intelligent design". IMO, the most correct response to this is is to say: "mutations are not random in organic evolution either". I haven't written about the "random mutations" issue too much because others have been capably handling the issue. One exception was here, where I complained about goalpost moving by proponents of random mutation.

Here I want to concentrate on here is explaining the case for mutations being biased towards being adaptive in the organic realm in simple terms.

The basic idea is that the mutations used in evolutionary models are themselves often the product of selective processes. A simple example of this is mutations in multicellular organisms. The differences in organisms between one generation and the next are what shows up in evolutionary models as having a mutational component. However, the mutations are actually the product of a selective process - namely the repeated production and selection of germ-line cells during development.

What about mutations in single-celled organisms? Even measuring these across a single generation introduces selective bias. Some mutations kill their owners. Those muatations won't be found in immediate descendants because they are selectively filtered out.

Another perspective comes from Perry Marshall, who writes: "Damage is Random. Repair is Not". Gene repair mechanisms are common and selectively bias mutations is adaptive directions.

A possible response to these types of claim is to say that it is mixing up selection and mutation. Mutations are not biased towards being adaptive before selection acts on them. That argument represents a declaration of victory by definitional fiat, but that is not its only problem. In many of the cases described so far, the mutation and selection involved are causally separate and take place at different times. The mutation happens first, and then selection happens later. In such cases, defining mutation as changes in the absence of selection seem viableHowever, there is no rule saying that mutation and selection can be so separated. As an example consider mutations that arise during copying. Imagine that somer sequences are more prone to mutation than others. There, mutation and selection occur at the same time and are entangled. Even stereotypically random sources of mutation - such as cosmic rays are vulnerable to this type of entanglement, for example if DNA sections can be shielded or reinforced by methylation, or in other ways.

Since defining adaptive mutations out of existence fails, what other avenues of retreat are available for the "random mutation" proponents? There are probably some involving redefining "randomness". Proponents already redefined this term to mean "not adaptively biased", maybe they could redefine it further to mean "not adaptive". Most mutations are still deleterious, so that position seems more defensible. It would be an enormous retreat, though.

Another defense against the type of argument given above might consist of insisting on empirical evidence. If biased mutations are so common, then we ought to be able to find them empirically. That's a reasonable request. Looking at the existing experiments that have been performed, I don't see an obvious case that decides the issue. So, this seems like a hole in the case for adaptive bias to me. On the other hand, I think the theoretical case is pretty watertight, and isn't likely to be overturned by experiments.

Another response could be to claim that the effects of adaptive bias are minor, and mutaions being random are a good approximation, and one that simplifies things considerably. I could cope with that. I can think of some circumstance where random mutations are not a very good approximation - such as genetic engineering - but they are also currently fairly rare. Randomish mutations might well be the rule inside cells for moost of evolutionary history.

I've been living with an understanding of adaptive mutations for over a decade, and my testimony is that Darwinism survives reasonably well without them. Darwin didn't believe that mutations were random - he know that variation existed, but "mutation" wasn't really a significant concept back then. The concept of "equivocal mutations" came in with the neo-Darwinian synthesis. Random mutations are still available as a theoretical approximation, should they be required. Mutations necessarily being non-adaptive is a dead concept in my book. Its defenders come across as being defenders of out-dated dogma.

The whole idea of mutations being different in cultural evoilution and organic evolution still has merit. Brains are a different environment from cells, and different types of change can happen in them. There are still bounds and limits to what can hapopen inside a brain, though. It isn't the case that anything goes, and so cultural evoiolution becomes an unfalsifiable theory that is compatible with any observations on the grounds that it could be a macromutation. However, the idea that mutations are directed in cultural evolution, but not in the organic realm is mistaken and has to go.

Saturday, 21 July 2018

Cultural kin selection vs better communication

I have previously argued that cultural kin selection explains a wide range of common phenomena. Among these were cooperation between computers and printers, and cooperation between people who share a language.

I have long been aware that other explanations have been proposed for some of these phenomena. In particular one such explanation is that shared memes involving communication make it easier for the parties involved to communicate and communication fosters cooperation. I was hoping that a critic would make this point, so that I could reply and cite them, but there's little harm in being proactive.

I have a few separate points to make in response. Firstly these really are examples of cultural kin selection. They do involve shared memes resulting in cooperation, and part of the reason why they spread is that copies of them in one body has the effect of selectively favoring copies of them in other bodies.

Secondly, the case for cultural kin selection does not rest in any way on cases where communicaton between the parties involved is fostered because the shared memes help to establish a communication protocol. Take money for example. A shared currency facilitates cooperation, but it is hard to make a case that it does so by fostering communication between the parties involved. That is just not how it works.

Thirdly, shared memes fostering better communication is another explanation for cooperation that does not invoke the logic of kin selection, and yet is clearly involved in some of these phenomena. To the extent that I claimed that cultural kin selection is the reason why computers cooperate with printers, I misspoke. There's more than one mechanism involved in the correct answer to that. I don't know if I did actually write that. I did write (in 2012):

Shared memes are also a big part of why your computer cooperates with your printer

I hedged my bets a bit back then, but even what I wrote might still be an overstatement. Shared memes resulting in cooperation via cultural kin selection is involved in a complete explanation for why your computer cooperates with your printer - but I wouldn't like to defend it being a "big" part of the explanation.

Now that I have thought about this in a bit more detail, I am wondering about interactions between the two mechanisms. Shared memes can produce cooperation via cultural kin selection and shared memes can produce cooperation via facilitating communication between the parties - which often results in improved cooperation between them. However, to what extent does cultural kin selection promote this other effect? Does its effect frequently come first? What about interactions the other way around? Better communication could easily promote meme transfer between the parties involved resulting in more shared memes and more cultural kin selection. How about interactions with genetic kin selection? You learn your language from your parents initially. The shared genes result in shared memes, which foster communication, and promote meme transfer from the parents, turning genetic kin into cultural kin. These interactions are fascinating, and researchers with awareness of cultural kin selection should be peering in.

Monday, 9 July 2018

Bonduriansky and Day: Extended Heredity

Bonduriansky and Day's book Extended Heredity: A New Understanding of Inheritance and Evolution is now available. The topic area has a big overlap with the topic area here. The Amazon blurb reads:
For much of the twentieth century it was assumed that genes alone mediate the transmission of biological information across generations and provide the raw material for natural selection. In Extended Heredity, leading evolutionary biologists Russell Bonduriansky and Troy Day challenge this premise. Drawing on the latest research, they demonstrate that what happens during our lifetimes--and even our grandparents' and great-grandparents' lifetimes―can influence the features of our descendants. On the basis of these discoveries, Bonduriansky and Day develop an extended concept of heredity that upends ideas about how traits can and cannot be transmitted across generations.

By examining the history of the gene-centered view in modern biology and reassessing fundamental tenets of evolutionary theory, Bonduriansky and Day show that nongenetic inheritance―involving epigenetic, environmental, behavioral, and cultural factors―could play an important role in evolution. The discovery of nongenetic inheritance therefore has major implications for key questions in evolutionary biology, as well as human health.

Extended Heredity reappraises long-held ideas and opens the door to a new understanding of inheritance and evolution.

The book looks interesting and it is certainly a welcome contribution to the literature on the topic, but it fairly quickly aroused my critical faculties. Check out page 19, to start with. The authors present a classification scheme for heredity, listing, genes, self-regenerating factors, non-self-regenerating factors, structural inheritance and epigenetic inheritance. It seems half-baked to me.

The authors seem rather obsessed with biological systems. If they are "extending" heredity, are they extending it to physics and to inorganic systems outside biology? Apparently not. In which case the authors are not really embracing the "extension" part of their thesis very well. Darwinian evolution, properly understood, applies to a range of inorganic physical systems and is not limited to biology.

The authors bemoan the dominant "gene-centric" view of heredity apparently without considering the possibility that all inheritance is mediated by genes by definition of the term "gene". If the gene really is the unit of heredity, then the "epigenetic inheritance" category they apparently favor becomes an oxymoron.

I searched for "memes": 1 hit. I searched for "universal darwinism": 0 hits. Universal Darwinism pioneers Blackmore, Plotkin and Dennett each get 0 mentions. It all seems like pretty poor coverage to me.

Here is one author's page about the book.

Sunday, 8 July 2018

George Christos: The Memetic World

I recently became aware of the book draft of The Memetic World. This is a book by George Christos. In 2017, George described the work as follows:

my unpublished book called "The Memetic World", which was basically written in 2003

George goes on to say:

I do not want to edit what I have previously written so there are bits that are incomplete. There are also ideas I wanted to work into the text at some stage. I am not sure I agree with everything I wrote then, but it is what it is.

The draft is clearly incomplete, with missing figures, notes to the author about where to insert more material, mysterious red sections. Also, the draft peters out into sketchy notes, and there's no index or references.

Book length treatments of memetics are fairly rare, so my attitude is to gratefully treasure what we have. So, I am pleased to find this manuscript. This book is clearly heavily inspired by Blackmore's 1999 book. George references Blackmore 146 times - more than all the other authors he mentions combined, I think. The themes tend to follow Blackmore's interests. That's mostly good, but it means that there's too much material about the self and consciousness for my taste. The book is a fair bit more amateurish than Blackmore's, even after accounting for its unfinished nature.

I'm not done analysing the contents so far, but so far I have learned at least one interesting thing from the book - to do with human longevity. Recent increases in human longevity are clearly memetically driven. My "background" theory would blame this on medical advances. However, as George points out there's a meme's eye view on this, which suggests that memes may divert resources away from DNA reproduction into maintenance processes that help the host to live longer as part of their strategy to get into more brains. Maybe this is a fairly obvious idea, but I don't recall having thought of it before reading The Memetic World.

To close, here's a recent promotional video for the book:

Tarrifs in evolutionary economics

In classical economics, targeted tarrifs are bad because they cause absolute harm both parties involved. Preventing win-win deals harms both sides. Much the same argument suggests that most conflicts are also costly and bad. In evolutionary economics, things are a bit different because fitness is relative. Paying a cost to harm another actor is then explicable - if they are a main rival.

Of course the actors involved should posture and dispaly their strength to each other first, but if neither side will back down, then they can be expected to fight. Do tarrifs damage yourself as much as them? Maybe, but maybe not if you pick the list of tarrifs and your plan factors in their capacity for retaliation. Even if the damage is equally distributed on both sides, there's also the capacity to endure damage to consider.

Targeted tarrifs are in the news at the moment due to the ongoing US-China trade war. I won't go so far as to argue that that trade war is rational, but it has some of the attributes that you might expect from a rational conflict. In particular, the US and China are fairly direct rivals. They are two of the largest players in the world and so maybe they are not worried that conflict between them will increase the relative strength and power of other parties not directly involved in the conflict. Also, America is currently is a strong position, but it is widely forecast that a business-as-usual strategy will result in China gradually overtaking the US in the next century, mostly due to its larger pool of human resources. It is not hard to imagine that the US feels it needs to switch things up a bit.

Sunday, 1 July 2018

Filtering, sorting, copying, mutation

One of the most popular schemes to classify evolutionary processes is based around the idea of selection. Evolutionists distinguish selection from genetic drift and then subdivide selective processes into kin selection, group selection, natural selection, artificial selection, sexual selection, divergent selection - and so on.

I'm not opposed to the idea of selection, but do think that the popularity of the concept has pushed alternative classification schemes into the shade. One of my preferred subdivisions is to start by ignoring the distinction between drift and selection and to divide initially by whether the process involves death or reproduction - or more broadly subtraction or addition. For example, here is an article on the topic adapted from my 2011 book: Natural production and natural elimination.

A closely-related classification scheme involves some other topics which I have promoted: sorting, filtering and copying. "Filtering is now my preferred term for evolutionary processes that subtract. "Sorting" refers to processes that neither subtract not add entities, but instead rearrange them. A focus on frequencies leads to sorting processes being ignored. However, in practice, sorting is common and influences evolution as a precursor to filtering.

One of the things I like about "sorting", "filtering" and "copying" is that they are pretty crisp computer science topics. One of the problems with selection is that is is so general. Saying "selection did it" is a very weak explanation because almost everything counts as a form of selection. Yes, genetic drift exists, but that's just a form of noise. If almost everything counts as being a form of selection, selection becomes difficult to falsify as an explanation.

While filtering obviously coveres "selection by death", it also crosses over into the realm of reproductive processes as well. Males are frequently sorted on "leks" and then the genes of the worst males are filtered out of the gene pool by females. While that is a form of subtraction, it is one which is pretty closely linked to reproduction - and what is commonly described in terms of "sexual selection".

Filters can vary in the time of their application, or filtering that takes place at different times can be modeled as a series of filters. These two approaches are equivalent.

"Filtering" is close to what Dawin originally meant by "natural selection". Darwin argued that "sexual selection" was not a form of "natural selection". The modern meaning of "natural selection" was introduced after Darwin's death. It pictures "sexual selection" as a type of "natural selection".

The picture here leads to the following classification scheme for evolutionary change:

  • Entity count changes
    • Filtering (subtraction)
    • Copying (addition)
  • Entity count remains the same
    • Sorting (rearrangement)
    • Mutation (in-place change)

Organisms moving around is not normally considered to be a form of evolutionary change - so "rearrangements" are mostly omitted or ignored. However, rearrangements are important. They are not completely ignored, but they are downplayed, I claim.

The left-hand labels in this classification scheme are all the information theory / computer science ones - except for the "mutation" category. That one has gone the other way - when the concept is used in computer science the biological term is often used.

Friday, 22 June 2018

Positive and negative feedback in evolution

Evolutionary theory has its own historical tradition and has developed its own terminology. However I sometime wonder what it would look like if it was (re)discovered by 21st century engineers. This post consists of some musings on that theme.

If evolution was (re)discovered by modern engineers, one concept that would probably be more extensively employed is "feedback". Feedback is the name for systems whose outputs are "fed back" into their inputs. Of course, this happens all the time in biological systems in various ways. The term "homeostasis" is often used in biology, and this is just a type of negative feedback. In particular, gene pools typically have their outputs fed back into them. From this perspective, favorable selection is a type of positive feedback acting on trait frequences (or gene frequencies), while unfavorable selection is a generally similar type of negative feedback.

Framing natural selection in terms of positive and negative feedback seems useful to me. The "feedback" terminology seems more general, and that is often a virtue in science.

Another piece of biological terminology that might be framed differently by engineers is "fitness". "Fitness" is an overloaded term, but "inclusive fitness" could plausibly be replaced by "utility" - the more general term from economics which refers to "that which is optimized". The common term "expected fitness" would become "expected utility" - another standard concept. One slight difference is that "fitness" is usually though of as being "relative", while "utility" is usually thought of as being absolute. It's a minor issue because there are usually many players and so the distinction doesn't make much difference. Anyway, IMO, the way to resolve this is to say that economics has got this wrong.

Saturday, 16 June 2018

Andres Gomez Emilsson's pure replicators

This post is about Andres Gomez Emilsson's proposed concept of "pure replicators". First, I'll let Andres introduce the concept:

I will define a pure replicator, in the context of agents and minds, to be an intelligence that is indifferent towards the valence of its conscious states and those of others. A pure replicator invests all of its energy and resources into surviving and reproducing, even at the cost of continuous suffering to themselves or others. Its main evolutionary advantage is that it does not need to spend any resources making the world a better place.
Conventionally, a "replicator" is something which copies are made of. Agents and minds aren't really replicators, they are large complicated things which can't easily be copied. "Reproducer" might be more appropriate terminology from this perspective.

Evolution optimizes for survival and reproduction. However, that does not mean that it builds creatures that are uniformly devoid of compassion. The evolutionary function of compassion may not be obvious or easy to explain, but it is likely to exist because compassion is widespread among humans. Probably, compassion promotes social cohesion and encourages acts of reciprocal altruism.

Andres warns against becoming a "pure replicator", but he defines this as an agent indifferent towards suffering, and most humans care act as though they care about the suffering of themselves or others - because compassion is built into them by evolution as a proximate goal. Becoming free of compassion does not seem as though it is a likely fate in the first place.

Andres apparently agrees, writing: "Most animals do indeed care a great deal about the valence of their own consciousness". He goes on to explain that "pure replicators" are mostly a future threat. There follows a bunch of speculation about how future intelligent machines might not use the pleasure-pain axis in their motivational systems.

I think that part of the problem here is a failure to properly distinguish between proximate and ultimate goals. A hypothetical agent with the sole goal of maximizing the number of their great grandchildren might still have proximate goals of minimizing the suffering of themselves and others. Many kinds of personal suffering are likely to be negatively correlated with the number of great grandchildren produced. Concern for others could well be adaptive too, though that's a bit harder to understand. That is how evolution can build compassionate creatures.

Andres apparently thinks that compassion is a useless spandrel. That seems tremendously unlikely to me.

However, my number problem is not with the science, it is with the terminology. You can't just hijack the "replicator" terminology and load it up with qualia for no good reason. The proposed termiology is simply ridiculous.

Friday, 15 June 2018

Carl Zimmer on heredity

Carl had a small but nice section on memes in his "Evolution" book. Carl's latest book on "Heredity" is out now. It is called "She Has Her Mother's Laugh: The Powers, Perversions, and Potential of Heredity". It has a section related to cultural evolution, called "The Teachable Ape". Memes get mentioned, but pretty dismissively.Carl cites Ehrlich and Feldman saying that: "The most recent attempts using a 'meme' approach appear to be a dead end".

Carl does cover attempts to expand the concept of heredity to culture, but he avoided citing most of the literature on the topic. Carl managed to convey that he knew something about cultural evolution, but it didn't seem as though he had very much understanding of the topic. I thought the chapter was quite disappointing. It seemed like a step backwards from his 2006 effort.

Wednesday, 13 June 2018

Counter-memes

"Meme, counter meme" is the title of a 1994 Wired article by Mike Godwin. Mike tells the story of how he combatted Nazi comparison memes on usenet by using counter-memes generated using memetic engineering. I don't know if "counter-meme" saw much use before 1994, but Mike Godwin either coined or popularized the phrase.

I think that "counter-memes" is a useful concept. Fighting bad memes with good ones is a common and obvious technique, and "counter-memes" seems like an appropriate name for the concept.

"Counter-memes" are part of the memetic immune system. Some are most effective before exposure to the memes they counter - those are like vaccines. Others are typically used after exposure - those are more like antibiotics.

I think that "counter-memes" is one of the bits of memetics that has the potential to go mainstream and enter the common vocabulary. It's fairly useful and fairly catchy. It could pretty easily happen that people start responding to posted memes with "counter-meme: <blah>". If explicitly saying "counter-meme" when responding to a meme with a corrective meme signals that you are up on the latest internet lingo, it could become quite common. I find this fantasy pleasing and would like to help make it a reality.