Evolution: more genomic evidence of pre-planning (Evolution)

by David Turell , Monday, February 22, 2021, 18:29 (1153 days ago) @ dhw

DAVID: What new requirement? Each next stage of human development starting at Lucy (or similar) grew 200 cc average until it stopped at sapiens with 1,200+cc alj due to frontal and prefrontal enlargement. Very full use of big brains started only in the past 10,000+ years when we left caves. Each anticipatory enlargement forms the same pattern since Lucy. Are you proposing new chance small requirements each time? Doesn't the pattern fit a plan? I chose God's agency.

dhw: I don’t know how often you want me to repeat that NOBODY KNOWS what caused brain expansions, which is why we have different theories: new artefacts, new discoveries, changing conditions providing new problems to solve or opportunities to grasp. All we know for sure is that the modern brain changes when acquiring new skills or meeting new requirements, but now it has stopped expanding and complexifies instead. So maybe in the past, when brains were smaller, they expanded once their complexification capacity had been exceeded. It’s a theory – as is your belief that your God kept popping in to perform operations on sleeping groups of hominins and homos – but you have never yet explained why you find it inconceivable.

You are arguing for natural expansions, but cannot explain why each expansion is so large it exceeds all current needs and has to be used until complexification is all used up and then requires enlargement. This can obviously be interpreted as enlargement in anticipation of future need, the same as my theory. In my view such a response must come from a mind that can anticipate the future, not by natural chance. Therefore, I say God does it.

Behe

DAVID: Yes, new genes happen, but loss of genes is also observed, and your question to me is is it chicken or egg first. New adaptation with loss of genes means loss of genes caused the adaptation as the authors imply in the article.

dhw: It "means" no such thing. Please tell us why it is impossible for new adaptations (and the acquisition of new genes) to make certain existing genes redundant.

DAVID: That is not my impression of the article's import, having reread it.

dhw: I am not asking about the article’s “import”. I am asking you to respond to my argument.

You constantly scurry around to protect Darwin. The article mainly discusses loss of genes, but does note new genes also contribute to changes. I've said that.

From the article showing major import:

"The existence of a category of alleles distinguished by a derived loss of biochemical function has been described by various names: “amorphic” (Muller 1932), “loss-of-function” (Jones 1972), “nonfunctional” (Nei and Roychoudhury 1973), “knockout” (Kulkarni et al. 1999),”null” (Engel et al. 1973), “pseudogene” (Jacq et al. 1977), or simply “gene loss” (Zimmer et al. 1980). Total gene loss is the most obvious case of loss of function. Comparisons of gene content between distantly related species have revealed considerable evidence for adaptation via complete deletion of genes or even entire sets of functionally related genes (Wang et al. 2006; Blomme et al. 2006; Will et al. 2010; McLean et al. 2011; Griesmann et al. 2018; van Velzen et al. 2018; Sharma et al. 2018; Huelsmann et al. 2019; McGowen et al. 2020; Baggs et al. 2020). Pangenome analyses have revealed extensive gene content variation segregating within species. For example, the average Brachypodium distachyon genotype is missing almost half of the genes observed in the species pangenome (Gordon et al. 2017). Yet total gene loss is not the only means by which loss of function can occur. In their review of evolution by gene loss, Albalat and Cañestro (2016) point out that single mutations and many mutation types such as premature stop codons, frameshifts, splice site disruptions, and elimination of regulatory regions required for gene expression can have effects that are functionally indistinguishable from complete gene loss. Here we will discuss how the phenomenon of allelic heterogeneity—that numerous types of mutations can produce the same functionally analogous allele—is important for understanding the evolutionary dynamics and implications of adaptation by loss of function."