Updates
October 26, 2019: this is quite interesting. I did not realize this until tonight. I have the "original" book on this subject. From wiki:
The theory of facilitated variation demonstrates how seemingly complex biological systems can arise through a limited number of regulatory genetic changes, through the differential re-use of pre-existing developmental components. The theory was presented in 2005 by Marc W. Kirschner (a professor and chair at the Department of Systems Biology, Harvard Medical School) and John C. Gerhart (a professor at the Graduate School, University of California, Berkeley). [The book I have was c. 2005.]
The theory of facilitated variation addresses the nature and function of phenotypic variation in evolution. Recent advances in cellular and evolutionary developmental biology shed light on a number of mechanisms for generating novelty. Most anatomical and physiological traits that have evolved since the Cambrian are, according to Kirschner and Gerhart, the result of regulatory changes in the usage of various conserved core components that function in development and physiology.
Novel traits arise as novel packages of modular core components, which requires modest genetic change in regulatory elements. The modularity and adaptability of developmental systems reduces the number of regulatory changes needed to generate adaptive phenotypic variation, increases the probability that genetic mutation will be viable, and allows organisms to respond flexibly to novel environments. In this manner, the conserved core processes facilitate the generation of adaptive phenotypic variation, which natural selection subsequently propagates.
Original Post
This is how Marc and John introduce us to the ancestor of all extant life.
We do not know whether life originated with RNA- or DNA-based heredity, or whether in fact heredity preceded or followed the evolution of proteins.
Because all recent life forms contain DNA as the stable repository of the sequence of information of proteins and use RNA as an intermediate interpreter of the DNA sequence, we can assert that around three billion years ago bacteria-like organisms were present that had DNA, RNA, a genetic code for 20 amino acids, and ribosomes as factories for making proteins under the direction of RNA.
The basic processes of DNA replication, transcription into an RNA copy, and translation into protein had been established. [Why do the authors say "basic processes"?]
The organism must also have been a self-replicating cell enclosed by an impermeable membrane of two layers (a bilayer) of lipids.
It must have contained several hundred kinds of enzymes for synthesizing the major components of the cell, including the 20 amino acids, the cell membrane lipids, and the DNA bases.
An energy metabolism based on the breakdown of sugars must have been established at that time. The synthesis of cofactors, which later became vitamins, would have been established as well. [Co-factors first, then vitamins? How would they know that?]Reminds me a of Rudyard Kipling "just-so" story.
The organism of course [of course] would have had other attributes not commonly shared by its descendants.
Everything above would be part of the "big question of how life arose," but again, the authors in this book will look at the "little questions of how life evolved." After all, once you have the basic recipe and ingredients, there are a gazillion ways to modify the final product.
A critical component of Darwinism is "common descent." If Marc and John use the term, I have not yet seen it. They allude to it but they don't mention "common descent" as an important component of Darwinism. But I digress.
Having said that, they do have an excellent graphic showing the "evolution" or "progress" or "relationship" between prokaryocytes and modern eubacteria and archaea; between prokaryocytes and eukaryocytes; between eukaryocytes and protists; between eukaryocytes and multicellularity; multicellularity and plants, fungi, and animals; between multicellularity and body plans; between body plans and 30 phyla of animals (p. 49).
They admit no one can explain how the last ancestor of all extant life came to be. Disappointingly, they waste space on Francis Crick's suggestion that the LAOAEL was extraterrestrial. That simply wastes time moving the issue back one (gigantic) step. It would have been just as easy to say that God created the LAOAEL. [By the way, most refer to this last common ancestor as the "last universal common ancestor" or LUCA.]
Once you have the LUCA, then there can be a gazillion explanations of how things played out, most of which are stymied when Michael Behe starts asking questions.
The writers directly address Michael Behe near the end of the book but, for me, do not make their case.
Marc and John do a great job showing how various life forms developed, but at the end of the day, they could have been describing how various computer operating systems all evolved from the Turing machine.
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Re-Reading
October, 2019
Darwinism:
- survival of the fittest
- heredity
- method of heredity: mutations; molecular basis for mutation
If that is correct, that the method of heredity is mutations, the question that is raised, is that enough. Is "random mutation" adequate to explain evolution.
1940s: The Modern Synthesis (p. 28)
The three great disciplines had split (p 29):
genetics
developmental biology
evolutionary biology
"... [t]his fact was of only hypothetical interest in evolutionary biology until the molecular revolution. With the advent of huge depositories of information from genomic sequence, it now seems possible to reconstruct the molecular ancestry of extinct forms from the gene sequences of living forms." -- p. 41.
"... the major inventions of evolution, such as those that supported the first complex cells or the first multicellular animals." -- p. 41
"This association between similarity in function and similarity in DNA sequence has help up even in distantly related organisms." -- page 44. Function and genes tracked together. If did not have to happen this way; one could have preceded the other. But function and protein structure were conserved together in the core processes. -- p. 44
Evolution: conservation and diversification. Most folks overlook conservation. Authors argue that conservation is perhaps more important than diversification. "Conservation must be a selected property, not simply a residue of properties that have not had time to change. Given the robust pace of evolution, conservation apparently doe snot impede diversification. The observation most demanding of further explanation is the stasis of core processes in the face of rapid change and divergence of anatomies and physiologies. -- p. 46
This is what amazes me. On one day, nothing that resembles life, only dead rock, and the next day, geologically speaking:
... we can assert that around three billion years go bacteria-like organisms were present that had DNA, RNA, a genetic code fo 20 amino acids, and ribosomes as factories for making proteins under the direction of RNA. The basic processes of DNA replication, transcription into an RNA copy, and translation into protein had been established. This organism must also have been a self-replacing cell enclosed by an impermeable embrane of two layers (a bilater) of lipids. It must ahve contained several hundred kinds of enzymes for synthesizing the major components of the cell, including the 20 amino acids, the cell membrane lipids, and the DNA bases. An energy metabloism based on the breakdown of sugars must ahve been established at that time. The synthesis of cofactors, which later became vitamins, woudl have been established as well. Teh organism of course would have had other attributes not commonly share by its descendants. -- p. 46 - 47.Wow, one day, there was nothing. The next day, all of that. Any one of those attributes would have been amazing, but all of that, literally overnight.
It will be interesting if the authors explore what happened in those 24 hours, or whether they start at that point and move on. Since this is a book on evolution and Darwinism, I assume they will move on from this point.
But there's more:
Even if some of the sources of energy were different from those of modern bacgeria, they would have already been very complex. Repeat: they would have already been very complex. Overnight. From nothing, to "very complex." Most of the biosynthetic pathways for making the 60 or so building blocks of cells would have been identical to those that now exist in all life forms. -- p. 47If today's professors of biology accept this without some deep thinking / deep questioning, one could argue that today's biology professors are the Druids of our day.
Page 50: the authors answer the question I asked above -- the authors will start with life as we know it and will not venture to explore how life began in the first place. -- p. 50.
Tree of life:
The universal ancestor that arose 3 billion years ago split into two major lines of bacteria-like organisms:
- modern eubacteria ("eu" - true)
- modern archaebacteria (modern, but ancient)
- Modern eubacteria: a dead end; they are today what they were 3 billion years ago
- archaebacteria: ancestors of eukaryotic organisms, including humans
- most archaebacteria now inhabit extreme environments (a question to explore: why?; possible answer: last niche in which they survived; all other niches, overcome by eubacteria; the question is why eubacteria survived and archaebacteria did not survive in 99% of the earth?)
- archaebacteria, three large groups
- methanogens: produce methane
- salty environment group
- hot springs group
- I believe morphologically the two lines look almost identical; it's their biochemistry that is very, very different, and that biochemistry comes from their DNA; DNA sequencing that separates them ... but that was discovered much, much later
- all of these forms, eubacteria and archaebacteria are called prokaryotes and lack a defined cell nucleus
- it took a billion years to get to this step after life originally appeared on the scene
- cyanobacteria: "invented" oxygen-geneating photosynthesis
- then the archaebacterial line split into two lineages
- one line led to modern archaebacteria
- the other line led to eukaryotic organisms (organisms which contain a nucleus)
- eukarotes
- single-celled protists (used to be called protozoa [small animals])
- great multicellular kingdoms of plants, animals, fungi
- Huge evolutionary shift, 1.5 to 2.0 billion years ago when ancient archaebacteria split into those two lineages (one lineage conserved themselves; the other lineage spun off what would be come karyotes)
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