LUCA latest: Shapiro redux (Introduction)

by David Turell , Thursday, July 06, 2023, 17:59 (506 days ago) @ dhw

A giant new essay by Shapiro:

https://aeon.co/essays/why-did-darwins-20th-century-followers-get-evolution-so-wrong?ut...

This failure to take account of alternative modes of change has been foundational to popular and scientific misconceptions of evolution.

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During the past century, discoveries that have challenged the gradualist view of evolution have been sidelined, forgotten, and derided. This includes the work of 20th-century geneticists...Their findings were ignored or ridiculed to convey the message that the gradual accumulation of random mutations was the only reasonable explanation for evolution...However, it’s an absence that’s particularly conspicuous because alternatives to random mutation have not been difficult to find.

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These arguments about symbiotic cell fusions, despite being vigorously championed by the evolutionary biologist Lynn Margulis in later years, did not find a place in evolutionary textbooks until they were confirmed by DNA sequencing at the end of the 20th century. And yet, even though these arguments have now been confirmed,...symbiotic cell fusions have still not been incorporated into mainstream evolutionary theory.

An absence that’s perhaps even harder to explain is why the pioneering work of the cytogeneticist Barbara McClintock, one of the giants of 20th-century genetics, has not been accepted as posing a viable alternative to dominant theories of evolution. McClintock won the Nobel Prize in 1983 for her discovery during the 1940s...of rapid genetic changes in maize plants that were definitely not random – changes found not only in maize but, we now know, across all forms of life. After confirmation by molecular geneticists in the 20th century, discoveries like hers should have inspired a radical rethinking of evolution. Instead, these ideas were accepted only among a small circle of geneticists.

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McClintock found that unstable loci carried insertions of genetic material that were unlike any previously discovered. She demonstrated that these ‘controlling elements’,...Controlling elements were not fixed at a specific site in the chromosomes and, unexpectedly, were able to move or ‘transpose’ from one place to another in the genome. When they arrived at a new location in the genome, they could alter the expression of nearby genetic material. This discovery revealed an entirely new mechanism of genetic regulation and variability: maize plants were rapidly changing their own genomes through transposable controlling elements (TEs). And moreover, TE changes were nonrandom in two ways. Firstly, the same DNA element could insert repeatedly at new target sites; and, secondly, TE mobility and mutagenic activity was activated by specific organismal stress conditions.

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The fact that TEs respond to stress indicates that they are regulated biological entities that play a sensory-guided role in survival and reproduction. The notion of controlled biological processes at the core of organic evolution is plainly incompatible with a purely physicalist explanation, such as random mutations plus natural selection.

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Eukaryotes appeared around 2 billion years ago, and we know from DNA sequencing that this important step in biological evolution included a cell fusion, or ‘symbiogenetic’ event, between a particular kind of aerobic bacterium and a particular kind of anaerobic archaeon. The bacterium was the ancestor of the mitochondria that allow our cells and those of other eukaryotes to efficiently generate energy in the presence of oxygen, known as aerobic metabolism.

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Horizontal DNA transfer occurs across all taxonomic boundaries... For a horizontal transfer to occur, a DNA sequence has to be extracted from one organism and taken up by another. There are multiple biological mechanisms involved in these horizontal DNA exchanges, including viruses, parasites and the uptake of DNA from the environment.

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Like horizontal DNA transfer, ‘domain shuffling’ involves inserting extended segments of protein-coding DNA in various locations in the genome. This means that cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’.

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The rapidly expanding catalogue of functions shows that, through ncRNAs, genomes encode biologically functional molecules other than proteins. It is possible that ncRNAs even represent a higher level of biological control than proteins...the discovery of functional ncRNAs in the genome completely undermines arguments for evolution by Dawkins and similar thinkers that rely on random mutation and natural selection.

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In many cases of hybrid speciation, the novel hybrid genome undergoes a whole genome duplication (WGD), involving the duplication of all chromosomes. WGD does not take place through random mutation but rather by control over cellular reproduction.

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By turning evolutionary variation from random accidents to biological responses, 21st-century molecular genetics and genomics have revealed that living organisms possess tremendous potential for adaptive genome reconfiguration.

Comment: I have eviscerated a 5.000-word essay. Read it all with pleasure.