How Evolution Works - Part 1 - Chance and Necessity

The main driving force behind evolution is understood to be natural selection acting upon genetic mutations. Each organism has slight genetic differences to their parents and so there is variation in a population at any one time. Often there are variations which improve fitness of an individual.

Key term - Fitness: In evolution fitness does not mean "faster" or "stronger", but "better suited to the current environment". In this sense the fitter individual may actually be the smaller, weaker and slower organism. Fitness is entirely dependent on context.

Natural selection acts when there is variation in a population, especially in populations where organisms produce more offspring than are able to reach maturity. Individuals in a population compete over resources, whether it is food, water, space or mates. In some species, competition, especially in males, is often direct, resulting in combat. Competition can also come from other species which require the same resources.

The fitter members of the population are most likely to breed and pass on their genes to the next generation, thus passing on their own favourable variation. Natural selection concerns the organisms which are more able to pass on their genes. Success in breeding is often more important than success in survival, though the two are connected (a short life with lots of breeding can be a more successful strategy than a long life with little breeding).

A point to remember is that natural selection has no foresight and cannot select variation which are favourable in future environments; it can only select for the current environment. A change in the environment changes the context for fitness. Sometimes a trait which is fortuitous in the current environment is useful after the environment changes, sometimes for a new purpose, this is known as abaptation or preadaptation.. 


When there is continuous phenotypic variation (the phenotype is the outward appearance of an organism) there are three ways in which natural selection can act on a population: stabilising, directional and disruptive.

In stabilising selection the existing mean of the distribution of inherited variability is favoured. In other words, variance is reduced as extreme variants are selected out. For example, in a population both the largest and smallest individuals may be selected against, maintaining a mean between the two. This is often seen with birth rates in populations.

During directional selection the mean shifts as selection favours one extreme of the inherited variability distribution. This sort of selection is most common when a change in environment occurs. The famous peppered moth experiment demonstrated this as environmental change caused a shift in the mean colour of the moths from pale to dark.

Disruptive selection splits a population in two by favouring both the extremes of the variability distribution. From one phenotype emerges two distinct phenotypes. This process may be instrumental in the evolution of many new species as a population splits and adapts to new environments.

Some key points to remember about natural selection is that it is a non-random process and that it acts on very slight changes in phenotype. The chance aspect of evolution is genetic variation as mutation is a random process; natural selection does not act randomly but is instead differential reproduction, something which can be easily predicted. Changes which are too large in an organism most often result in being selected against as they are more likely to be poorly suited to the environment. Small changes do not stray far from the already favoured phenotype and so natural selection can favour those which provide even a tiny advantage, refining the adaptation.

When discussing natural selection it sometimes helps to make a key distinction. Natural selection acts on any phenotypic trait, whether it is heritable or not. Evolution requires heritable variation to be selected. The selection of a trait can also result in the selection of other connected traits, such as when a gene has multiple functions (pleiotropy).

Natural selection acts at all stages of the life cycle, the image below is useful in distinguishing the different types of selection at work:

As natural selection works on small changes it can take a long time. Each change it favours is a successful increase in fitness which accumulate bit by bit. Natural selection is a cumulative process and is therefore very important in the construction of complex adaptations in evolution.

Part 2 will go on to discuss speciation. Natural selection is a heavily studied phenomenon for which a lot can be found. I recommend The Blind Watchmaker  by Richard Dawkins for any who want to know more, particularly with regards to natural selection being cumulative.

Does Natural Selection Drive Evolution?

Natural selection is widely accepted as the driving force of the evolution of complexity, but the question is whether or not it is the only explanation. It would be naive to suggest that it was the only force, so the question should be rephrased as to whether or not it is the most significant. Connected to this is the importance of chance in evolution. The following are a selection of proposed mechanisms:

Genetic Drift


This is accepted as an evolutionary mechanism and can be very important in population dynamics. Genetic drift occurs when there are different alleles of a gene in a population which have equal survival value. Drift can cause one to be favoured over another. This is the key mechanism debated as an alternative to natural selection as it has potential to be important during speciation events. However, drift alone cannot construct a complex adaptation. With regards to adaptations drift can facilitate natural selection on occasion by randomly favouring an allele which may have future possibilities; the adaptation is still due to natural selection, but with a slight helping hand from drift. For more see here.

Neutral Evolution


Neutral theory states that areas of the genome are free from selection and can evolve at a steady pace. It is the theory underlying the molecular clock technique in dating evolutionary events. Neutral evolution cannot drive the evolution of complexity, though it is very important at the molecular level.

Epigenetics and Neo-Lamarckism


Epigenetic factors are not currently well understood so to rule them out as insignificant would be premature. Epigenetic factors appear to be too transient to be effective in the evolution of adaptation, however, they can be manifested in the phenotype and can hide genetic effects which natural selection would normally work on. It seems so far that it cannot explain complexity, but may be able to elucidate the workings of natural selection and may complicate matters. See here and here for more.

Phenotypic Plasticity


Organisms can adapt within their own lifetime due to the flexibility to change physical appearance. The important aspect of phenotypic plasticity occurs during development as it can determine the phenotype for the whole life of the organism. These phenotypic differences are not genetic, though the range of plasticity may well be and is open to be selected for. Again, this will not construct complex adaptations, but is a source of key variation that may aid in the survival of a species. For something similar, see here.

Self-organisation


Both biotic and abiotic systems have examples of self-organisation. Protein folding and viral self-assembly are two insightful biological examples. These have an underlying selectable genetic basis, but their phenotypic variability (one could say plasticity) may provide more variation, thus facilitating natural selection in constructing complex adaptations.

Most of the answers, it seems, will come from studies into embryological development. The processes which translate genotype into phenotype still need some elucidation and may unlock the secrets of evolution. As is shown, my view is that none of these other processes can construct complex adaptations, natural selection does that, however, they can facilitate it through their alteration of the variation available for selection (whether by muting it as with epigenetics, or by bringing more diversity as with plasticity). To say natural selection is the only driving force is to be too simplistic, though it does seem to be the most important.

For more on natural selection  I recommend The Blind Watchmaker  by Richard Dawkins. He champions it in a lot of a detail and discusses neutral theory as well. For more on the topic of other mechanisms see here.

Disagreeing With Dawkins?

I wrote this a while ago but only recently typed it up. The font is probably going to go crappy on me, but ah well.The picture I have chosen contains a gorgeous ammonite fossil which is clearly from the Mesozoic. It has quite well developed sutures so came quite late during the period which is often seen as the age of the dinosaurs when it was equally the age of the ammonites, particularly in the oceans.

Professor Richard Dawkins (1941-) is a world renowned author and scientist from Oxford university who has increased public awareness of evolution over the years. Studying under the eminent Niko Tinbergen, as a scientist he is an ethologist who studied the adaptive significance of animal behavioural patterns such as "Selective Pecking in the Domestic Chick". With this as his basis he has written some of the best popular science books expounding evolution, with selection and adaptation being prominent topics. He has, in recent years, shot to fame in wider circles due to his book "The God Delusion". I have decided to take a little time to show where I agree and disagree with Dawkins.

It barely needs stating that we both agree that all life has evolved over the last 4 billion years from a common ancestor which probably resembled bacteria. Dawkins' books make it clear that evolution is a distinctly non-random process and that it occurs in a very slow, incremental fashion; we are again in agreement. We both clearly agree on the main concepts in the theory of evolution, but when looked at deeper some differences occur.

Much of Dawkins' work focuses on the power of natural selection. He rightly states that selection is the only mechanism which can construct adaptations (though some recent evidence suggests that drift can give it a little helping hand). Genetic drift and neutral theory are not ignored as 'pluralists' would claim, but are both acknowledged as occurring but with no adaptive advantage.

"The Selfish Gene" and subsequent books presented his gene selection views, which are perhaps what e is best known for in evolutionary biology. It is not always obvious that this is not a case of overzealous reductionism. Dawkins talks frequently of gene complexes and of bodies as vehicles or 'robots' of the genes; these are not to be ignored. He eloquently argues that selection must act on agents which persist over generations with a degree of conservation; only genes satisfy this replication criterion.

Gene selection overlooks some key issues. One issue with the statement that selection requires a degree of conservation is that phenotypes do fit this if it is viewed broadly. Although the individual phenotype is broken down by recombination with each generation, the differences between each generation are most often very small; enough perhaps for selection to be at work.

It also overlooks the concept that selection acts upon interactors, which is fulfilled by selection on the individual organism. Genes go through complex processes before being expressed phenotypically, the web of development can make gene selection seem implausible. Moreover, Dawkins has occasionally made it appear that gene selection is synonymous with selection on the individual. This is not to say that gene selection does not occur, for outlaw genes are proving increasingly common and there are genes with direct phenotypic expression (likely the exception to the rule and often deleterious). I also do not know Dawkins' views on epigenetics, as some experiments have shown epigenetic factors altering phenotypic traits, effectively muting the voice of the genes. I therefore reject gene selection as most prominent and appear to be more open to other levels of selection. I view it as predominately on the individual, though modular selection is also an attractive prospect. My mind is open to group selection, though I do not feel I have sufficient mathematical knowledge to judge it properly.

Species selection is an interesting concept which remains difficult to test. Dawkins does not often talk about species selection, though his views appear to be that it is plausible in determining which lineages diversify or go extinct, but with little to no effect on adaptation. Species have emergent properties not found in individuals such as geographical range and diversity, though such traits are arguably not passed on. My views are similar to this, though it is a difficult one as we run the risk of zooming in too close and not seeing the species as a whole, or conversely zooming out too far and seeing only species as individuals; balance is required.

Evolutionary arms races are one of Dawkins' insightful contributions which aid understanding in evolution and have evidence to back (though it must be noted that there are circumstances where it can be drowned out by other occurrences). It is a solid explanation for many evolutionary trends and adaptations. He also famously promotes the idea of extended phenotypes, a useful model for understanding the interaction of organisms with environments, particularly parasites.

"Extrapolationism" is a term which was often used by Stephen Jay Gould when referring to scientists like Dawkins who view large scale evolution as simply local events scaled up over longer time. I do not disagree with such  a view, but find it deficient as it cannot easily take mass extinction into account and tends to ignore fossil trends which need explaining. Simple speciation mechanisms coupled with genetic change in local populations cannot account for the variety of patterns found in the fossil record. For example, phyletic gradualism and punctuated equilibrium both occur on large scales; these are not plausibly extrapolated from microevolutionary trends in local populations, the bigger picture is a necessity.

Dawkins once dared to write about evolvability, almost taboo at the time, though since his effort many others have taken up the torch on this subject. I find Dawkins' case for the evolution of evolvabilityevolvability involved watershed events, Dawkins describes segmentation, which raised the upper bound of complexity and enabled lineages to become more able to diversify and adapt. Other examples include multicellularity and sexual reproduction. Interestingly this may open the door for selection of an entire clade (though then the issue would be whether the crown or stem groups are selected).

I enter shaky ground when I attempt to discuss contingency and convergence. Dawkins speaks more positively of convergence and my own position is not yet firm. I sit somewhere in the middle, finding some aspects seem inevitable whereas others seem almost to be pot luck. I don't feel that there is sufficient data to judge what would happen with a replaying of the tape.

Dawkins appears to believe that selection has a large range of variation to act upon and that the plausible variations which we do not see were selected against. This ignores the possibility that certain variation did not occur and thereby naively removes the need for an explanation of how much variation can occur. Constraints are found not only from the physical laws of nature but also from changes frozen into our lineage which cannot be reversed. Historical changes effect developmental possibilities, narrowing the variation available for selection.

Richard Dawkins had a very prominent and vocal rival in the late Stephen Jay Gould. Gould's main contribution to the theory of evolution was punctuated equilibrium. Dawkins dismissed 'punk eek' as a minor yet interesting empirical observation demonstrating different "gears" (presumably stasis, bradytely, horotely and tachytely). His dismissal was perhaps too rash, though in retrospect it was not completely out of order. Punctuated equilibrium was almost unnecessarily hyped as it carried a lot of potential which had not stood the test of time. Dawkins was clearly correct that it is still a form of gradualism, but ignored the overall pattern which had the potential to uncouple micro and macro evolution as well as bringing prominence to species selection. It necessitated a wider view of evolution, not just gene changes in a population. In recent years it is seen as one palaeontological pattern among many and appears to be a lot more than simple "gear" changes in response to environmental pressures.

An area I rarely discuss is psychology and cultural evolution, unlike Dawkins who confidently states his opinion. Evolutionary psychology clearly has value, but perhaps too much is given to it. A behavioural trait should not simply be given adaptationist explanation, for the brain is an organ which is full of possibilities for non-adapted traits to occur. Scrutiny and caution are of the utmost importance.

Dawkins kick started the field of memetics, used to explain cultural evolution. It strays close to pseudoscience, embracing 'just-so' stories and ignoring other possibilities in favour of an ideology. The only plausible place for memes to exist is the internet, or so it seems to me.

In conclusion, I agree with Dawkins on many issues within the theory of evolution. Some differences occur, though many are subtle and some are simply due to a different degree of scepticism. Unlike Dawkins I have not had a long, fruitful career allowing m to think about and test these ideas, so I am open to the possibility that our disagreements may slowly vanish as I delve deeper and deeper into the wondrous theory. On the other hand, palaeobiology may lead me closer to the views of Gould as opposed to Dawkins' ethology of the gene! Who knows?

A New Type of Selection?

Another interesting article I found on PhysOrg.com was titled A new type of genetic variation could strengthen natural selection.  This article immediately attracted my attention and provides interesting support for a concept which does not get much attention and is even considered controversial.

The study shows that not only are individual genes and whole organisms selected for, but also gene networks. The study looked at the genomes of variations of yeast within the same species and found that gene networks had been preserved even though the genes are inactive in one variant. Balancing selection allows two variants of the same gene to exist in a population and has normally been observed with individual genes; it has now been found to work on gene networks. It is not yet known whether this is a rare case or whether selection on networks is common.

The concept which comes to mind from reading about this study is modular selection, a controversial view about the level of selection. At which level(s) selection acts often attracts heated debates and the two extremes tend to be gene selection and hierarchical selection (where natural selection occurs on many levels). Current views tend to hold that gene selection and individual selection both occur, but which is more dominant is still often the key issue (other levels are getting a resurgence in popularity, such as group selection). As genes are selected for indirectly (they are not interactors) the idea of gene complexes is used to explain how genes can be selected for in groups. The main argument in favour of gene selection is that a gene is reliably transmitted from generation to generation and so selection has time to act on it. Phenotypes are broken down at the genotype level by recombination with each new generation and so it is argued that the phenotype is not selected for (though it should be kept in mind that phenotypic variation from generation to generation is often so small that natural selection will not "ignore" subtle changes).

Modular selection bridges the gap between these two levels. Selection on a gene complex cannot explain why the gene network has been selected for in the yeast example. It would be wrong to label this modular selection for semantic reasons which should not be ignored (modular selection applies to complex multicellular organisms which form in a modular fashion; gene networks cover modular selection but are not exclusive to it).

In Lu et al (2009) modules are described as "tightly integrated complexes of characters with discrete, semi-independent and temporally persistent histories" and that these "were the principle focus of natural selection and played a leading role in evolutionary transitions".  This places modular selection midway between gene selection and selection on the individual. Modules are both interactors (unlike genes) and have potential phylogenetic longevity (more so than phenotype) which circumvents the issues with each other type of selection. Schlosser (2002) states that "modules tend to be more important in delimiting actual units of selection than either organisms or genes, because they are less easily disrupted by recombination than organisms, while having less context sensitive fitness values than genes".

West-Eberhart (2003) described modular selection as a subunit of evolution. She states "[the] notion of the phenotype as a nested hierarchy of modular subunits implies both semi-independence and connectedness among subunits." This is what is found in this study using yeast, supporting the idea that modular selection is not only valid but to be found in more than just pterosaurs and other vertebrates.

This to me is exciting news and will influence our understanding of how natural selection works, particularly on which level. Sadly PhysOrg.com do not provide a link to the papers they discuss or even a reference, so I struggled to track down the paper.

References:

Hittinger, C.T. Goncalves, P. Sampaio, J.P. Dover, J. Johnston, M. and Rokas, A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature. 464, 54-58.

Lu, J. Unwin, D.M. Jin, X. Liu, Y. and Ji, Q. 2009. Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proceedings of the Royal Society B. 


Schlosser, G. 2002. Modularity and the units of evolution. Theory in Biosciences. 121: 1-80.

West-Eberhard, M. J. 2003. Developmental Plasticity and Evolution. Oxford University Press, Inc. New York, pp. 56.