Monday 14 March 2022

Evolution News - Evolution of Evolvability

Capturing the many facets of evolvability | Science Linx News | Science LinX | University of Groningen

Imagine, if you can, being a creationists who has swallowed the absurd idea that the scientific theory of evolution is a 'theory in crisis' which is about to be overthrown by a superstition from the fearful, ignorant infancy of our species in the Bronze Age, from a time when a bunch of nomadic pastoralists and hill farmers in the Middle East though Earth was small, young, flat and had a dome over it to keep the water above the sky out. You've been waiting excitedly for most of your adult life for this momentous event - the first time an established scientific theory has been replaced by a mystical, supernatural one involving unproven entities and magic - and so proving that you know better than all those clever scientists without having bothered to learn any science!

Then along comes a bunch of those clever scientists from Groningen Institute for Evolutionary Life Sciences at the University of Groningen in the Netherlands and not only presents a detailed discussion paper on how evolution works, but on how evolvability itself evolved, with no hint whatsoever that they have any doubts about evolution being the reason for all the biodiversity.

Copyright: © 2022 The authors. Published by Elsevier Ltd.
Open access
(CC BY-NC-ND 4.0)
And to cap it all, they even explain the notion of 'punctuated equilibrium' that was invented by the evolutionary biologist, Stephen Jay Gould, to try to explain the fossil record which appears to show that many species have long periods of stasis when their morphology changes very little, followed by a burst of rapid evolution, then another period of stasis, etc.

Many creationists like to imagine this somehow refutes Darwinian evolution, although Gould never proposed a mechanism for it and other biologists have explained that Darwinian gradualism doesn't imply a constant rate of evolutionary change, especially at the phenotypic level and that what can appear to be a sudden change in phenotype in the geological columns can take tens or hundreds of thousands of years. Or the record simply shows that one species was replaced by another closely related species over that part of its range, as happened in the UK where the more robust introduced grey squirrels have replaced the slighter native red squirrels in less than a hundred years. In the geological column in, say, 10,000 years, this will look like a case of 'punctuated equilibrium' and an unexplained sudden change to a more robust form. The explanation is that newly evolved evolvability enables a species to radiate into new niches to give a relatively sudden increase in new species or to more quickly evolve in response to environmental pressures.

So, what do you do if you're a creationists and a paper like this is published?

Well, what most creationists will do is ignore the paper and handle the resulting cognitive dissonance in any one of several rehearsed ways: dismiss it with the wave of a hand; tell themselves that the scientists must be wrong because they disagree with the scientists, and they know best; declare it to be part of the massive world-wide conspiracy to turn people against god (even though intelligent design is definitely not a religion, it's real science! Got that!); and anyway, Piltdown Man and Bible!

Sadly, for creationism however, reality is that thing that is still true even when you don't believe it, and, as these scientists show, evolution is very much part of reality and underpins all of biology. As the Groningen University new release which accompanied the paper explains:
All life evolves: microorganisms can become resistant to drugs, viruses evade our vaccines, and species may adapt to climate change. Even the ability to evolve can evolve. If we were to understand how this happens and which mechanisms play a role, it may be possible to predict evolution to some extent. This is why the concept of evolvability is now very popular in various areas of the life sciences. However, it turns out that this concept is used in very different ways within the scientific community. Theoretical biologists from the University of Groningen have now written a paper that should create some order in discussions on evolvability. It was published online in Trends in Ecology and Evolution on 10 February.

It all started with a journal club, organized by three PhD students in evolutionary biology. They could not always agree on whether a paper under discussion was really about evolvability and eventually realized that this could be due to their different backgrounds: the emergence of antibiotic resistance, the evolution of gene networks, and the evolution of vertebrates living in social systems. ‘The confusion that we experienced is also reflected in the literature,’ says Jana Riederer, joint first author of the paper together with journal club members Stefano Tiso and Timo van Eldijk. ‘We wanted to sort this out for ourselves at first,’ she continues. ‘But then we thought that it might be useful to others too.’

The result of their discussions is a paper that describes different facets of evolvability. ‘We identified three types of mechanisms underlying evolvability,’ explains Van Eldijk. These are determinants providing variation, determinants shaping the effect of variation on fitness, and determinants shaping the selection process.

Cartoon showing the three types of mechanisms underlying evolvability
Each one contributes to evolvability in a different way. This can be compared with the process of baking a cake: the end result depends on several fundamentally different aspects – the amount of ingredients, the quality of ingredients, and the baking process. We suggest that evolvability is analogously affected by three different classes of determinants: those providing variation (‘the amount of sugar’), those shaping the effect of variation on fitness (‘the type of sugar’), and those shaping the selection process (‘the baking process’). An example of a determinant providing variation is the mutation rate, where mutation encapsulates a wide variety of phenomena ranging from point mutations to genome rearrangements. Developmental biases are examples of determinants that shape the effect of variation on fitness. Consider, for instance, the developmental system underlying the eyespot pattern on the wings of the butterfly Bicyclus anynana. This system is organized in such a manner that mutations can easily change the colour composition of the two wing eyespots in the same direction, while mutations changing the colour composition in opposite directions are extremely rare (depiction based on [40.]). Depending on whether the selective pressure favours eyespots with the same colour composition or not, this bias may facilitate or impede evolvability. Finally, an example of a determinant that shapes the selection process is generation time: a shorter generation time allows faster adaptation – in absolute time, bacteria evolve faster than elephants.

Furthermore, evolvability depends on the timescale. Pathogens, such as bacteria or viruses, often reproduce asexually by cloning themselves, while many hosts, such as humans, reproduce sexually. Therefore, questions regarding the arms race between hosts and pathogens are closely related to a longstanding debate in evolutionary biology: which type of reproduction facilitates evolution best? Riederer: ‘We concluded that they each work best at their own time scale.’

Sexual reproduction
Asexually reproducing organisms evolve fast, which is better in the short term but they typically do not reach the highest level of adaptation. In contrast, sexual reproduction slows down evolution but allows for a more thorough exploration of all options and, in the long-term, achieves a higher level of adaptation. Van Eldijk: ‘Evolutionary scientists often choose an endpoint for their studies and will, for example, look at which bacterial strain is best adapted after a hundred generations. But they might get a different outcome if their experiment were to continue for a thousand generations.’

A final aspect of evolvability is a difference in scope: some mechanisms work for many different environments, for example an increased mutation rate. Others, such as the presence of a specific enzyme that could evolve to confer resistance to a particular antibiotic, are limited in their scope. But both mechanisms can help to shape evolvability.
In the Highlights section of their paper, the scientists explain more:
Evolvability, the capability to undergo adaptive evolution, is determined by a staggering diversity of mechanisms and organismal features. When discussing evolvability, it is useful to distinguish three categories of determinants: those providing variation, those shaping the effect of variation on fitness, and those shaping the selection process.

Some determinants of evolvability have a broad scope in that they affect adaptive evolution across many different environments; others have a narrower scope in that they impact evolvability only with respect to particular challenges. Being explicit about the scope of evolvability determinants would largely facilitate communication across disciplines.

On different timescales, the comparison of organisms regarding their evolvability and the comparison of mechanisms regarding their effects on evolvability can lead to very different conclusions.

‘Evolvability’ – the ability to undergo adaptive evolution – is a key concept for understanding and predicting the response of biological systems to environmental change. Evolvability has various facets and is applied in many ways, easily leading to misunderstandings among researchers. To clarify matters, we first categorize the mechanisms and organismal features underlying evolvability into determinants providing variation, determinants shaping the effect of variation on fitness, and determinants shaping the selection process. Second, we stress the importance of timescale when studying evolvability. Third, we distinguish between evolvability determinants with a broad and a narrow scope. Finally, we highlight two contrasting perspectives on evolvability: general evolvability and specific evolvability. We hope that this framework facilitates communication and guides future research.

Riederer, J. M., Tiso, S., van Eldijk, T. J., & Weissing, F. J. (2022).
Capturing the facets of evolvability in a mechanistic framework.
Trends in Ecology & Evolution
, 10 February 2022. DOI: 10.1016/j.tree.2022.01.004

Copyright: © 2022 The authors. Published by Elsevier Ltd.
Open access
Reprinted under a Creative Commons Attribution – NonCommercial – NoDerivs license (CC BY-NC-ND 4.0)
Again, we see science refuting creationism without any effort or intent, simply by telling the truth. These three scientists have not only shown there is no doubt that evolution is the best available explanation for biodiversity but that the ability to evolve is itself an important biological trait that is selected for by an organism’s environment. The evolution of this trait also explains the pattern seen in the fossil record which shows periods of morphological stasis interspersed with periods of rapid evolution. The evolution of evolvability also explains the otherwise puzzling evolution of sexual reproduction which is ubiquitous even though, on the face of it, less efficient than the more primitive vegetative reproduction. Sexual reproduction increases evolvability by frequent remixing of genes.

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