Return to David's theory of evolution PARTS 1 & 2 (Evolution)

by David Turell , Thursday, April 07, 2022, 16:06 (959 days ago) @ David Turell

Does common descent come from a single ancestor. No support from biochemistry:

https://evolutionnews.org/2022/04/sara-walker-and-her-crew-publish-the-most-interesting...

"For Dobzhansky, as for all neo-Darwinians (by definition), the apparent molecular universality of life on Earth confirmed Darwin’s prediction that all organisms “have descended from some one primordial form, into which life was first breathed” (1859, 494) — an entity now known as the Last Universal Common Ancestor, or LUCA. So strong is the pull of this apparent universality, rooted in LUCA, that any other historical geometry seems unimaginable.

"Theoretician Sara Walker and her team of collaborators, however, are looking for an account of what they call the “laws of life” that would apply “to all possible biochemistries” — including organisms found elsewhere in the universe, if any exist. To that end, they wanted to know if the molecular universality explained under neo-Darwinian theory as material descent from LUCA (a) really exists, and (b) if not, what patterns do exist, and how might those be explained without presupposing a single common ancestor.

"And a single common ancestor, LUCA? That’s what they didn’t find.

***

"A strikingly similar pattern obtains with the critical (essential) components of all organisms. Gagler et al. 2022 looked at the abundances of enzyme functions across the three major domains of life (Bacteria, Archaea, Eukarya), as well as in metagenomes (environmentally sampled DNA). What they found was remarkable.

***

"The lesson that Gagler et al. 2022 draw from this discovery? The pattern is NOT due to material descent from a single common ancestor, LUCA. Indeed, under the heading, “Universality in Scaling of Enzyme Function Is Not Explained by Universally Shared Components,” they explain that material descent from LUCA would entail shared “microscale features,” meaning “specific molecules and reactions used by all life,” or “shared component chemistry across systems.” If we use the CPU / laptop analogy, this microscale commonality would be equivalent to finding CPUs from the same manufacturer, with the same internal logic circuits, in every laptop we examine. (read article to understand analogy)

"But what Gagler et al. 2022 found was a macroscale pattern, “which does not directly correlate with a high degree of microscale universality,” and “cannot be explained directly by the universality of the underlying component functions.” In an accompanying news story, project co-author Chris Kempes, of the Santa Fe Institute, described their main finding in terms of functional synonyms: macroscale functions are required, but not the identical lower-level components:

“'Here we find that you get these scaling relationships without needing to conserve exact membership. You need a certain number of transferases, but not particular transferases,” says SFI Professor Chris Kempes, a co-author on the paper. “There are a lot [of] ‘synonyms,’ and those synonyms scale in systematic ways.”

"As Gagler et al. frame the point in the paper itself (emphasis added):

"A critical question is whether the universality classes identified herein are a product of the shared ancestry of life. A limitation of the traditional view of biochemical universality is that universality can only be explained in terms of evolutionary contingency and shared history, which challenges our ability to generalize beyond the singular ancestry of life as we know it. …Instead, we showed here that universality classes are not directly correlated with component universality, which is indicative that it emerges as a macroscopic regularity in the large-scale statistics of catalytic functional diversity. Furthermore, EC ( Enzyme Commission Classification), according to their designated EC numbers. universality cannot simply be explained due to phylogenetic relatedness since the range of total enzyme functions spans two orders of magnitude, evidencing a wide coverage of genomic diversity.

"It is interesting to note that this paper was edited (for the PNAS) by Eugene Koonin of the National Center for Biotechnology Information. For many years, Koonin has argued in his own work that the putative “universality due to ancestry” premise of neo-Darwinian theory no longer holds, due in large measure to what he and others have termed “non-orthologous gene displacement” (NOGD). NOGD is a pervasive pattern of the use of functional synonyms — enzyme functions being carried out by different molecular actors — in different species. In 2016, Koonin wrote:

"As the genome database grows, it is becoming clear that NOGD reaches across most of the functional systems and pathways such that there are very few functions that are truly “monomorphic”, i.e. represented by genes from the same orthologous lineage in all organisms that are endowed with these functions. Accordingly, the universal core of life has shrunk almost to the point of vanishing…there is no universal genetic core of life, owing to the (near) ubiquity of NOGD.

"Universal functional requirements, but without the identity of material components — sounds like design."

Comment: Simply, following genes and biochemistry there are too many changes to find a steady pattern of simple steps, one following the other. A designer at work would explain all the jumps and discontinuities.