Little Changes: teaching evolution, one rhyme at a time

Today, I was catching up with some old podcasts. One was the Naked Genetics podcast from last January, which featured a book that I had never heard of but sounded rather cute. It’s called Little Changes and was written by Dr Tiffany Taylor from the University of Reading as a way to introduce evolution (by Natural Selection) to under 11s - and their teachers. I’ve not got it - I don’t have any under 11s - but the preview on Amazon looks fun and the illustrations look sweet too.

I won’t reproduce any sample text here as it is all copyrighted but you can “look inside” on Amazon if you are interested. Apart from someone who (ambitiously) got it for their three year old, the customer reviews are good too.

Some Darwin quotes for Darwin Day

Today is Darwin Day, so why not visit DarwinDay.org and see if there are any activities in your area? Alternatively, you can follow Darwin's adventures on HMS Beagle in blog or tweet form. I've been reading the blog of his diary but I think he was too seasick to mention his birthday in the entry for 12th Feb 1832:

There has been a little swell on the sea to day, and I have been very uncomfortable: this has tried and quite overcome the small stock of patience that the early parts of the voyage left me. Here I have spent three days in painful indolence, whilst animals are staring me in the face, without labels and scientific epitaphs.

Of course, another great Darwin Day activity is to read/browse On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life? As well as the PDF linked there, you can also get it free on the Kindle. I've not read it for some time but whenever I dip into it I am struck by how much he seemed to understand the process of Natural Selection despite no one having a clue at that stage about the biology underlying heredity.

The term "Natural Selection" comes in for some criticism because, it is argued, there is no real selection taking place. Nature is not actively picking and choosing - it is a passive selection process. Such criticisms are, I think, ill-founded and usually just a semantic ploy born out of desperation when faced with the inescapable reality that Natural Selection is very real. When you read the Origin, it seems clear to me why Darwin chose the term "Natural Selection":

"From these considerations, I shall devote the first chapter of this Abstract to Variation under Domestication. We shall thus see that a large amount of hereditary modification is at least possible, and, what is equally or more important, we shall see how great is the power of man in accumulating by his Selection successive slight variations. I will then pass on to the variability of species in a state of nature ... As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form." [Introduction]

This is still a good summary of the general principle and process of Natural Selection even in 2013. Darwin recognised that Artificial Selection and Natural Selection are essentially the same thing. We have filled in a lot of the details but Darwin really did get the basics largely right, which is one of the reasons he is still honored by evolutionary biologists. It is re-stated more clearly in Chapter XIV, Recapitulation and Conclusion, in a way that I like because it really lays out the challenge that stands before Creationists to this day - how could Natural Selection not happen?:

"If then we have under nature variability and a powerful agent always ready to act and select, why should we doubt that variations in any way useful to beings, under their excessively complex relations of life, would be preserved, accumulated, and inherited? Why, if man can by patience select variations most useful to himself, should nature fail in selecting variations useful, under changing conditions of life, to her living products? What limit can be put to this power, acting during long ages and rigidly scrutinising the whole constitution, structure, and habits of each creature,--favouring the good and rejecting the bad? I can see no limit to this power, in slowly and beautifully adapting each form to the most complex relations of life. The theory of natural selection, even if we looked no further than this, seems to me to be in itself probable."

And similarly in Chapter IV, Natural Selection:

"Can the principle of selection, which we have seen is so potent in the hands of man, apply in nature? I think we shall see that it can act most effectually. Let it be borne in mind in what an endless number of strange peculiarities our domestic productions, and, in a lesser degree, those under nature, vary; and how strong the hereditary tendency is. ... Let it be borne in mind how infinitely complex and close-fitting are the mutual relations of all organic beings to each other and to their physical conditions of life. Can it, then, be thought improbable, seeing that variations useful to man have undoubtedly occurred, that other variations useful in some way to each being in the great and complex battle of life, should sometimes occur in the course of thousands of generations? If such do occur, can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection. Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element, as perhaps we see in the species called polymorphic."

The other great thing about this paragraph is the last line. Another unfair criticism leveled at "Darwinists" is the idea that we think that Natural Selection explains everything. It never has and never will. Right from the outset, Darwin alluded to what we now know as Random Genetic Drift - the "fluctuating" evolution of neutral variants in traits that are "neither useful nor injurious".

Another thing that stands out is how little Creationist arguments against Natural Selection have progressed in the last 150 years. Like the good scientist that he was, Darwin outlined a number of potential difficulties to his theory. In the final chapter, however, he summarises the objections thus (my emphasis):

"Such is the sum of the several chief objections and difficulties which may justly be urged against my theory; and I have now briefly recapitulated the answers and explanations which can be given to them. I have felt these difficulties far too heavily during many years to doubt their weight. But it deserves especial notice that the more important objections relate to questions on which we are confessedly ignorant; nor do we know how ignorant we are. We do not know all the possible transitional gradations between the simplest and the most perfect organs; it cannot be pretended that we know all the varied means of Distribution during the long lapse of years, or that we know how imperfect the Geological Record is. Grave as these several difficulties are, in my judgment they do not overthrow the theory of descent with modification."

Creationists and Intelligent Design Creationists still go after these zones of ignorance. The big difference is that we often now have a very good idea of "how ignorant we are" and can say with great confidence that the remaining objections "do not overthrow the theory of descent with modification" and are, indeed, wholly consistent with it.

Evolution is a population-level phenomenon

An argument I have been encountering a lot recently is one that goes something along the lines of:

"Natural Selection cannot be the source of novel adaptations because it only works on what it already present. It does not generate anything and therefore a novel trait cannot be the product of Natural Selection."

These claims are then used to support the primacy of mutation as the driving force behind evolution, often coupled with (unsubstantiated) claims that these mutations are not random. In other words, Natural Selection is a myth and goal-directed mutation is responsible for the evolution of adaptations.

On face value, this can seem like a convincing argument. Natural Selection does only act on existing variation. New variants do have to arise by mutation (for a given definition of mutation), which is independent of selection. However, extrapolating that to mean that adaptive evolution occurs through the source of the new variants, mutation, and not selection is a classic case of confusing individual traits with population/species traits. I suspect that this confusion is the source of misunderstanding for many people who champion directed mutation and denigrate the power or potential of Natural Selection.

We have a tendency to draw phylogenetic trees as single lines for the branches. It is important to remember, however, that these branches - representing the evolution of species of gene sequences - are actually representing whole populations of organisms or molecules.

Evolution is a population-level phenomenon: individuals mutate but they do not evolve. It is true that new variants have to arise in an individual, independent of selection. However, we do not say that a trait has "evolved" until it reaches a high frequency or even reached (effective) fixation in the population.

For example, certain mutations cause polydactyly (extra fingers and toes) in humans but we do not say that humans have "evolved six fingers". For humans, a mutation usually has to reach a frequency of 1% before being considered a polymorphism. This is somewhat arbitrary but it needs to be in at least two generations; otherwise, lethal or sterilising mutations would constitute a polymorphism and this would make the concept pretty useless. Likewise, it would be pretty silly to say that something had "evolved sterility" because a single individual had a sterilising mutation.

Evolution does not need Natural Selection. Random processes are sufficient for a neutral (or nearly neutral) trait to "drift" its way through a population to fixation. However, without invoking an external agent, Natural Selection is the only process that drives a trait through (or from) a population, resulting in adaptive evolution.

Population-level change is still change. A population or species acquiring a new trait is still evolution of a new trait. A novel evolved trait can be the product of Selection.

Differential survival, (inclusive) fitness, selection and evolution

In my last post about Multi-level selection and The Selfish Gene, I neglected probably the most famous and important aspect of the "Group Selection" debate: "inclusive fitness", which (along with its specific form, "kin selection") can potentially give rise to counter-intuitive adaptive behaviours such as altruism and self-sacrifice. To understand inclusive fitness and how/why (a) it works, and (b) it is important, we have to revisit the importance and meaning of heritability in selection.

The key point is that "fitness" and selection are about more than just differential survival. Differential survival is sufficient for evolution - the population will change with time - but without the heritability aspect, this is not selection and there can be no adaptation.

It's easiest to think about this in terms of purely random events. Imagine two populations of beetle (there sure are a lot of beetles!) living in two trees who, by chance founder effects have different frequencies of an allele that causes melanism (a dark colour morph). Now imagine that one of those trees experiences a rare catastrophic event - perhaps a meteor-strike, or it is on a cliff-top and collapses into the sea - that wipes out its entire beetle population. The frequency of melanic colour morphs in the beetle population has changed - there has been differential survival - but because it was totally unrelated to the causal reason for the differential survival, this is not selection.

Evolution without selection happens all the time and can easily lead to certain traits becoming fixed in a population, even if they have no direct (or only a very weak) fitness effect on those with the trait relative to those without. (Fitness is always relative.) Most changes at the molecular level, for example, are neutral changes occurring through random genetic drift. This is still evolution, it is just not selection - it will not give rise to adaptation. (Although a change of environment - and the environment for genes is never static - could render a previously neutral trait as good or bad.)

So where does kin selection and inclusive fitness come in? Well, a key - and sometimes confusing - point about fitness and selection is that the individuals expressing the heritable trait and the individuals benefiting from the heritable trait do not have to be the same individuals. This is critical because it reinforces the special place that genes have in multi-level selection.

In the last post, I wrote:

Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen.

This is the difference between "replicators" (in Dawkins parlance) and mere reproducers. The crucial thing about genes is that they make copies of themselves, which are then carried by different members of the population. A particular genetic variant will increase in frequency if the sum total of all its effects is to the collective benefit of carriers of that genetic variant, even if some of its effects are detrimental to some of its carriers. Hence altruism can still spread if it has a genetic basis and the net product is increased survival/reproduction of carriers of the altruism "gene(s)".

There are two more important points about inclusive fitness:

1. Kin recognition is not required. Crucially, there does not need to be a conscious awareness by the altruistic individual; it does not need to be able to recognises its kin or fellow gene-carriers. (Although, clearly, if it can then it will be even more successful.)

2. All fitness is inclusive fitness. Inclusive fitness is one of the few unifying principles of biology that, as far as I can tell at least, applies across the board. Whether you are talking about Artificial or Natural Selection, Individual or Group Selection, it all comes down to inclusive fitness. Even when all of the phenotypic effects of gene are limited to its carrier - pure "Individual Selection" - inclusive fitness comes in to play: as long as it benefits more individuals than it impairs, it will still spread. (The same gene can have different effects in different individuals.)

The nice thing about inclusive fitness is that it works irrespective of the nature by which the sum total of its effects benefit its carriers. These effects can occur at any level of biological organisation and may, indeed, have effects at multiple levels; thanks to inclusive fitness, far from being in conflict, multi-level selection and The Selfish Gene are one and the same.

Multi-level selection and The Selfish Gene

Yesterday, I attended a seminar run by the University's Institute for Complex Systems Simulation by Samir Okasha, a Professor of Philosophy of Science from the University of Bristol and author of the book "Evolution and the Levels of Selection" (among others). The talk was entitled 'Individuals versus Groups in Evolutionary Biology' and Prof. Okasha gave a very interesting presentation about some of the history and issues surrounding the discussions (and sometimes arguments) about "Group Selection" and its modern incarnation, "multi-level" selection.

It looks like an interesting book too and is on my ever-growing reading list. I'd particularly like to ponder some more his thoughts on emergent group properties - something I do not currently have the time, space or philosophical nonce to explore further in this post.

There was one key aspect of the debate that, in the interests of time, was not covered in detail in his talk: the issue of heritability and what that means for "Units of Selection". The more I think about it, the more I think it is a real barrier for people understanding the problem and, in my opinion, leads to all sorts of confusion about how evolution and selection work.

This is a quote from an Amazon review of his book that sums up the key issue quite nicely:

So often we are bombarded with 'scientists' giving us their metaphysical views as if they were 'scientific fact'. It is therefore refreshing to find a philosopher looking at a science and seeking to clarify the various concepts in that science.

Okasha observes that the various life forms are arranged in a hierarchy:
Ecosystems
Species
Colonies
Organisms
Cells
Chromosomes
Genes.

Generally reproduction occurs at the same level in the hierarchy: organisms reproduce to give organisms; chromosomes divide to give chromosomes; colonies divide to give colonies, and so on. According to the logical formulation of the theory of `natural selection' a) variation, b) differential fitness (different rates of survival and reproduction) and c)heritability (parent - offspring correlation) are required to produce evolutionary change. All these may be present at each of the levels in the hierarchy so there is nothing that necessarily restricts selection to any one level, say at the level of the gene. To claim that selection always occurs at the level of the gene is to confuse the result of selection (the proportion of the various genes in the gene pool) with the process of selection (where in the hierarchy the winnowing actually occurs). [My emphasis]

This is an argument that I have come across a few times on internet forums and like - often by non-biologists. (I'm not sure why the reviewer puts quotes around 'scientists' - perhaps this is an unfair dig at Dawkins. When these arguments appear, they are often accompanied by a barrage of anti-Dawkins nonsense about dogmas and how our old, flawed understanding of evolution is being overthrown etc. At best, this is a gross exaggeration. In my opinion, it is utter hogwash.)

Quite simply, I don't think this argument works because it overlooks something very important. I have highlighted the key phrases in bold. This review has the matter utterly backwards. To say that selection is occurring at a level other than the gene and not the gene (and "gene" in this context must have the correct evolutionary meaning not the biochemical meaning) is to confuse the agent of selection, which can be gene, cell, organism, family, whatever, and the target of selection - the "gene". This is because, for selection to work, there has to be heritability and this heritability is not simply "parent - offspring correlation".

(At this point, I would like to make it clear that I do not think Samir Okasha makes this mistake. I've not read his book yet but in his talk he was very clear to make the distinction between causality in selection - what we call direct and indirection selection, which correspond to causal and correlative changes in gene frequency. He also pointed out that there is no conflict with multi-level selection and "The Selfish Gene".)

For selection to work, there has to be a causal link between the heritable trait and differential fitness. Mere correlation is not enough. It is enough for evolution - there will be a change over time - but it is not enough for natural selection. And this is where genes are special. Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen. Reproduction in the important sense - heredity - does not occur "at the same level in the hierarchy".

Has anyone actually demonstrated non-genetic inheritance of any higher-level trait? I'm not aware of any and whenever I have raised this in online discussions, I am normally just met with a barrage of anti-Dawkins nonsense or some vague notions about epigenetics, behaviour and "emergent" properties (which I advocate in general, by the way,) without any specific demonstration or model as to how these higher levels reproduce and pass on their traits to the next generation. Crucially, you have to do more that demonstrate that it could work mathematically or in a computer simulation - you have to demonstrate that there is a corresponding biological reality.

Which brings me to another important point. I would also question the notion of "fitness" at some of these higher levels. Ecosystems do not reproduce at all. There can be competition between groups of organisms, certainly, and long-term differential survival, which will result in evolution - just as random events such as floods and meteor strikes can influence long-term evolution through differential survival. But this is not selection. The ecosystem is changing because of individual success or otherwise and individual success is being influenced by the environment - the changing ecosystem - but an ecosystem is not directly spawning a new ecosystem that inherits its properties and goes off into the world to compete with different ecosystems. (It seems to me that there is one higher level entity capable of non-genetic inheritance - something championed by Dawkins himself. The cultural replicator, or "meme". This is not what multi-level selection is about, though, as far as I can tell.)

A final problem for non-genetic multi-level selection is that many of these "levels" don't really exist in a fashion that makes selection possible - they are part of continua rather than discrete entities. An ecosystem, for example, does not really mean anything specific. I am an ecosystem from the perspective of my gut microbes. The whole planet is an ecosystem. It is useful to drawn the boundaries at different points for specific study but we should remember that these distinctions are arbitrary. Even an "individual" is a woolly concept thanks to symbiosis - and we are probably all symbionts at the end of the day.

The only thing that is absolute is that you can break everything down to genes (genetic information) and their environment. The flow of information is one way. Genetic information is modulated - but not created - by the environment. (Even accounting for epigenetics, which modulates the environment but not the genotype, though this is for another post.) The Selfish Gene (and its Extended Phenotype) still wins.

Or does it...?

There is one problem that remains for the "Selfish Gene" and it is the same one that plagues almost all of biology. Just like all the levels above it, a "gene" (in the evolutionary sense) is just a mirage. In many ways, there is no such thing as a gene. There is just genetic information. We like to talk about a "gene for X" but really what we mean is "heritable genetic information that has a causal but environment-dependent tendency to produce X". This is just a problem of conception and language, though, not the underlying mechanism and theory. Selection is still ultimately acting on genetic information, and it is still selection at this level that gives rise to adaptations, but how you package this genetic material up into genes is, again, context-dependent and (thanks to recombination and mutation) can be complicated.

It fascinates me how we love to try and split continua - life, species, development, genes - into discrete packets even when no such packets exist and then tie ourselves up in knots because we can't let go of those arbitrary (and false) divisions we have made. Ultimately, I think the issue of Individual versus Group Selection might just be this problem, taken to another level.

Artificial Selection versus Natural Selection

One of things you will probably encounter quite quickly if you ever discuss evolution with a Young Earth or Intelligent Design Creationist is a deep confusion about Natural Selection. Often this is as simple as claiming that it doesn't exist and explains nothing, which is clearly and demonstrably utter nonsense. Recently, I experiences a more unusual extension of this claim:

"Natural Selection does not exist. It is all Artificial Selection."

This is usually an attempt to discredit experimental evidence for Natural Selection that comes from direct laboratory manipulations, such as the long-term experimental evolution of bacteria in the lab of Richard Lenski and colleagues.

A less extreme position is to claim that lessons learnt from artificial selection, generating different breeds of dogs, for example, are cannot be extrapolated to nature because Natural Selection is fundamentally different. Both variants of the argument are utterly wrong.
[Image credit: Science Museum.]

So, what is the difference between Artificial Selection and Natural Selection?

Philosophically, I think it is the difference between being directed or undirected. This is different to it being a case of directional versus undirectional. All selection is directional - that's the point. Evolution without any direction happens - neutral evolution and Random Genetic Drift - but this does not give rise to adaptations. Selection, on the other hand, imparts directional constraints to the evolutionary trajectory because some variants do better or worse than others.

This is most clear with "Negative" or "Purifying" selection, in which certain directions are closed because carriers of those variants are less competitive. This is what produces a signal of evolutionary conservation. More dramatic are the cases of "Positive" selection, in which particular variants have increased "fitness" compared to the population (i.e. the genetic material for that variant is more likely to be passed on to the next generation than a random bit of DNA in an individual without that variant) and thus it "sweeps" through the population. (Contingent on the strength of the effect and the population size.)

The point is, though, that while Natural Selection has direction it is not directed - it has no goal it is striving towards. The direction is imposed by the environment that a particular variant finds itself in at the time. This environment includes all the other variants in the population: fitness is always relative.

The direction of selection can also change from generation to generation, even within a generation. (Think of adaptations to hot or cold weather and consider climate variability, for example.) This means that populations can evolve themselves into an evolutionary dead-end, or lose a gene/trait that could prove useful in the future. Evolution by Natural Selection reacts to the now, it does not predict the future. The bills of Darwin's finches are specialised for certain foods they have encountered during their radiation - they have not all remained versatile generalists, ready to adapt quickly to changing food availability.

I think this is the real reason that many religious people have a problem with evolution by Natural Selection: there is no goal, no target, so humanity cannot be the goal. We are not the pinnacle that evolution has been working towards, we are just a by-product of past selection and chance events. (There are, of course, ongoing discussions about the predictability of evolution but this is really a question as to whether, if evolution were re-run, something like us (i.e. intelligent life) would inevitably appear. I can't imagine that any evolutionary biologist would seriously entertain the notion that we would re-appear if life were restarted.) The root of the argument against Natural Selection (but accepting Artificial Selection) is born of the belief that all evolution is directly governed and directed by some kind of deity. (Even if this deity is dressed up as an "Intelligent Designer".) Often, this is coupled with claims along the lines of "there is no such thing as random mutation" and other such arguments, which simply do not account for observations of the world around us. (Not unless, for reasons unclear to me, you postulate a deity who is deliberately out to deceive and make things look random and undirected. I'll save this one, and the randomness of mutation, for another post!)

The directed/directional distinction is just one aspect of the difference, however. To really qualify as Artificial Selection, I think that the directing agent has to be directly choosing (selecting) who reproduces and who does not. This is distinct from Natural Selection, in which the differential breeding success is just a consequence of reactions to the environment. This is why claims that experimental evolution in the lab are Artificial Selection are normally wrong. Laboratory evolution is normally directly studying Natural Selection, albeit with a tightly controlled environment. (One of the key approaches in science is to try and remove as much random variability and simplify the system as much as possible.)

In some ways, it is easy to see this by examining the spectrum of selective regimes used in the lab. Some can be quite complex in terms of responses, such as changes in temperature or the addition (or removal) of certain common or key nutrients. Others are much more defined, such as the addition of an antibiotic resistance, in which a very specific trait - resistance - is being sought. This is still Natural Selection: the environment being controlled and the organisms are surviving differentially based on their genotypes in response to this environment.

It could be - and sometimes is - argued that this is actually Artificial Selection and that the specific antibiotic regime is merely the mechanism by which the human is artificially selecting. It could be argued - blurring the boundaries between the two, which I'll get back to - but it shouldn't be argued, for I think it is a wrong (if forgivable) position to take. Even antibiotic resistance experiments are not purely selecting one trait. There will also be more subtle selection pressures due to the choice of media or growth conditions. As well as resistance, there will still be pressure to grow fast. There may even be complex biotic interactions where a subpopulation protects the rest of the population, such as biofilm formation. Even though the desired outcome might be antibiotic resistance, the experimenter is not (normally) actively selecting individuals. (S)he is not manually screening individuals and picking which ones to propagate.

This is quite different to selective breeding in dogs, for example. Here, a breeder is picking a particular trait - such as the ridge in a Rhodesian Ridgeback and selecting specific individuals with that trait to breed from. This is so powerful as a selective force that it can over-ride normal fitness considerations and evolve a trait that is otherwise downright detrimental to the individuals concerned. A number of pedigree dogs have severe health problems, for example.

This distinction of active versus passive selection of individuals with specific traits is certainly one way to view the Artificial Selection versus Natural Selection issue. There is another way, however, which I tend to err towards and makes the statement that there is no Natural Selection and only Artificial Selection even more erroneous: Artificial Selection is actually just a special case of the more general process of Natural Selection: one end of the continuum. Far from there being no Natural Selection, it is all Natural Selection!

The fact is, philosophy aside, there is no real biological difference between the two. Yes, it's easier to spot and define the selection when it's directed and tightly controlled - which is why it is so useful in the lab - but the basic mechanism of differential reproduction of heritable variants holds true for both. Furthermore, there is a direct analogy for Artificial Selection in nature, in which decision-making agents actively choose which individuals get to reproduce based on specific traits - Sexual Selection. (Intersexual selection, specifically, in which mate choice (as opposed to direct intrasexual competition) is a determining factor in reproductive success.) Sexual selection and mate choice abound in nature and can produce some quite absurd phenotypes that, like the products of artificial selection, are not necessarily healthy. From the perspective of the organisms experiencing the selection, a human imposing Artificial Selection is just part of the environment in just the same way as a choosy mate might be.

One possible example of this is the antlers of the (now extinct) Irish Elk. The photo above (from WEIT) shows male (right) and female (left) Irish Elk skeletons from the Museum Building in Trinity College Dublin. The sexual dimorphism - only the males have the monstrous antlers - is a clear sign of sexual selection and the antlers of male Irish Elk are so massive that it is thought they probably contributed to their extinction.

It's not actually the best example, to be honest, because the initial sexual selection on antlers was almost certainly intrasexual selection between fighting males and even though the Irish Elk antlers are too big for such behaviour, their monstrous size could be linked to increases in body size rather than intersexual selection for big antlers. That said, there must have been some force maintaining such impractical ornamentation and female mate choice is a prime contender. I mainly picked it because my brother works in the Museum Building and I used to see these elk quite regularly when I lived in Dublin. There's also an alternative YEC explanation for their extinction (right, also from WEIT; cartoon by Chris Madden)! If you don't like the elk as an example, there is always the peacock. (Whole books have been written about it if you want to know more.)

So, in conclusion: not only do Artificial Selection and directed evolution provide good tools for investigating aspects of Natural Selection, in very real terms they are Natural Selection. Anyone who claims that Natural Selection does not exist and everything is Artificial Selection has got the situation entirely backwards.

Is evolution random?

In a recent perusal of The Blogosphere, my eye was caught by a post at A Tippling Philosopher entitled Far from random, evolution follows a predictable genetic pattern, Princeton researchers find. As I suspect most evolutionary biologists would, I got rather annoyed by this title. I should point out, however, that the Tippling Philosopher is not to blame - this is the title of the original Princeton press release.

Unfortunately, my VPN is playing up so I cannot access the original article (Zhen Y, Aardema ML, Medina EM, Schumer M & Andolfatto P (2012). Parallel molecular evolution in an herbivore community. Science 37(6102):1634-7) but I am a bit short of time anyway and don't want to do an in depth study. I suspect the press release actually does a fairly good job of summarising the main points as does the abstract:

Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na+,K+-ATPase (ATPα), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPα with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.

This is all very interesting and very cool - the power of evolution by Natural Selection demonstrated in replicate. The thing that irked me, though - and the focus of this (probably too hasty) post - is the title and the first paragraph of the Princeton press release:

Far from random, evolution follows a predictable genetic pattern, Princeton researchers find

Evolution, often perceived as a series of random changes, might in fact be driven by a simple and repeated genetic solution to an environmental pressure that a broad range of species happen to share, according to new research.

Evolution is not a series of random changes. At least, adaptive evolution, which is the subject of this paper, is not. Neutral evolution largely is random but that's only one part of evolution as a whole and to imply otherwise is rather misleading. The raw material for evolution is indeed random mutation but this is not the full picture. There was a clever chap who realised that heritable random variation in a trait, if it produced differential survival and/or reproduction, could result in the non-random change of that trait. Good ("fit") traits would increase in frequency and eventually dominate the population, while bad traits would be removed. He realised this over 150 years ago and called it Natural Selection. His name was Charles Darwin and his book is free on Kindle if you want to read it. (Yes, I know, this is a gross simplification of history!)

This is compounded by the title: "Far from being random, evolution follows a predictable genetic pattern, Princeton researchers find". Well, yes, sometimes it does (and in this case) but we've also known that for years. The argument about the predictability of evolution is one that has been going on for a long time. (Read Gould's "A Wonderful Life", for example.) If you were to rewind the clock and let evolution run again, how much would history repeat itself? We know the answer is not "always" and we know the answer is not "never" but we do not know where on the continuum between "always" and "never" reality lies. (Major catastrophic events notwithstanding. These are another role of chance but somewhat different to the one determining evolutionary trajectory.)

In evolution, the opposite of "predictable" is not completely "random". One has to be clear that even if we cannot predict a precise evolutionary trajectory due to the complexity (and, yes, randomness) in the system, trajectories that give rise to exquisite adaptations always have a large non-random component (selection). This may seem like a trivial thing but it's not, for this is the kind of language that feeds the misconceptions spread my advocates of Intelligent Design and other forms of Creationism. (Of course, this study also nicely blows such nonsense out of the water.) If it is "often perceived as a series of random changes", it is only because of misconceptions like this being repeated.

For me, it is the last line of the abstract that is most intriguing and possibly the big discovery:

"Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy."

The authors cite "the large number of potential targets for modulating cardenolide sensitivity". It seems that they think that the other possible target genes are more prone to affect other systems as well in a bad way. (I am not sure how they rule out the possibility that the selective advantage of changes in this particular pump are just much, much greater than the other genes and its just driven by the probability and rates of positive selection.) If this turns out to be a widespread phenomenon, it could indeed have implications for the predictability of future adaptation, which could be useful in our changing world!

This is just one example, of course. Another recent paper on parallel and convergent evolution in Proc. R. Soc. B (free this time), "The probability of genetic parallelism and convergence in natural populations" by Gina Conte, Matthew Arnegard, Catherine Peichel and Dolph Schluter, looked at a bunch of studies and concluded that "estimates [of the probability of gene reuse in parallel and convergent phenotypic evolution in nature] using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies".

I'm sure there's a bit of ascertainment bias towards traits under strong selection (as these are more obvious and thus more studied) but it confirms the Andolfatto study that in the right circumstances convergent evolution can make use of the same gene(s). (They also cite counter-examples, so be quite clear that this is not universal.) It's not a surprise that it happens but given the amount of diversity between genomes - and numbers of genes affecting many traits - the level is possibly surprising. To be honest, I can't decide if I am surprised or not as it is so hard to generate a reasonable a priori expectation.

I still don't think that all this means that evolution in general is predictable (we still need more studies) but it certainly does hammer yet another nail in the coffin of the old Creationist chestnut about evolution being random. Natural Selection is NOT random - that's the whole point!

Footnote: I must concede that in writing this post I realised that explaining the role (and meaning) of "random" in the context of evolution is not quite as simple as I thought. "Random" commonly does mean a lack of predictability but I maintain that it is not helpful to use this language for evolution without some serious explanation of what you mean by random. Random mutation plus Selection means that we are talking about a lack of determinism, not a lack of direction. (This was also supposed to be a quick/short post!)

h/t: A Tippling Philosopher and WEIT

Natural Selection: a mechanism, a theory AND a fact

There are a bunch of science/research social/professional networking sites these days, vying to become the Facebook or LinkedIn of Academia. One of these is ResearchGate, which looks like it might be one of the better ones. (One day, I might do a proper comparison.)

One of the features of ResearchGate is the ability to pose questions to the community. Occasionally, when it's an interesting topic or I think I can help, I chip in. Unfortunately, ResearchGate is not devoid of Creationist trolls it seems, and in a discussion about random mutation as the source of biological innovation I responded to comments that

"Natural selection does not explain anything. It is not a scientific theory."

and

"Darwinism is an ad hoc narrative that lacks both quantization and predictive power."

Responding was possible ill-advised (don't poke the crazy!) but, as evolutionary biologist, it saddens and offends me to see such nonsense in what is supposedly a scientific forum. I responded thus:

Natural Selection is a well documented fact of nature. It is an inevitability given a certain set of circumstances (heritability, variation, competition and non-random differential survival) and those circumstances are all individually and collectively documented both in the lab and in nature. (Read "Why Evolution is True" for some examples of both.) It is not the only, or even necessarily the main, driving force of evolution as most change at the genetic level is neutral. However, it remains as the primary mechanism of ADAPTIVE evolutionary change. It explains in general terms how exquisite adaptations can be ultimately caused by random events (mutations) through non-random survival. To call it an "ad hoc narrative" is just plain wrong unless you are trying to applying it to specific PAST events, in which case there is usually a great deal of speculation (and lack of certainty) involved. When used in laboratory (and field) experiments using fruit flies or bacteria, it is most certainly NOT an ad hoc narrative and has great predictive power. I am not sure that it can be "quantized" but it can certainly be quantified, as population geneticists have been doing for years.

This then elicited a very strange response and a complaint about the term "Natural Selection" that I have seen before but did not expect to find in a supposedly serious discussion:

OK, Richard, Natural Selection is a well documented fact of nature. It may be so.

Then also i agree that " It remains as the primary mechanism of ADAPTIVE evolutionary change.". It may be too.

The problem then is that Natural Selection does not explain anything. A fact does not explain,. Neither does a mechanism.

You need to decide whether Natural Selection is a fact, a mechanism or a theory. Theories are not facts, nor mechanisms. Using the same word for a fact, a mechanism and a theory is just creating confussion.

For me, the only thing confusing here is how anyone can seriously claim that "Natural Selection does not explain anything". "Natural Selection does not explain everything" would be fair enough but "anything"? Really‽ Even Creationists seem to be happy that Natural Selection can account for "microevolution" (ewww!) and antibiotic resistance! In case anyone else out there is also confused, I thought I would re-post my reply here:

Natural Selection is a mechanism by which random heritable variation is shaped through time through non-random survival to produce non-random evolutionary change. That the mechanism of Natural Selection is responsible for adaptive evolutionary change is a fact. (The big unanswered question is how much observed evolutionary change is actually adaptive.) It is also a scientific theory as it has been subject to scientific scrutiny and repeatedly confirmed through experiments and observation. I do not understand how this can be confusing. It explains how you can get non-random evolutionary change (adaptation) from random heritable variation. This is a BIG explanation and rightly rates among one of the top scientific theories/discoveries of all time. If you think it explains nothing, then try SCIENTIFICALLY explaining adaptation without it.

Natural selection is one of the most beautiful and elegant explanations/mechanisms/theories/facts in all of science. There is a reason that Darwin is so famous!