Maybe dissent from Darwin can’t kill a career any more?

3 Replies to “Maybe dissent from Darwin can’t kill a career any more?”

1. 1
   PavelU says:

   February 23, 2019 at 4:41 pm

   ID fans should start looking for another club to switch to. Your time is up. Here’s the game changer:
   Evolution Since Coding
   Cradles, Halos, Barrels, and Wings
   Book • 2018
   Zachary F. Burton
   https://doi.org/10.1016/B978-0-12-813033-9.00001-9

   Description
   Evolution since Coding: Cradles, Halos, Barrels, and Wings describes genesis of metabolism, transcription, translation, cell structure, eukaryotic complexity, LUCA (the last universal common (cellular) ancestor), the great divergence of archaea and bacteria, LECA (the last eukaryotic common ancestor), extinction, and cancer in very simple ways. The work (almost) “synthesizes life from scratch” (since coding) and describes the tools for readers to check the author’s work. As a result, readers understand living systems and their evolution in a conceptual way and are empowered to utilize powerful but accessible tools in computer-based biology.
   The work serves as foundational reading for a variety of researchers, academics, and students in life sciences, for example in evolution/evolutionary biology, biochemistry, genetics/molecular genetics, molecular biology, cell biology, and microbiology, as well as disciplines beyond biological science. Its approachable style makes the book accessible for introductory students and educated laypersons. Evolution since Coding is suitable to supplement college courses that mix computers, evolution, and biology from freshman to senior level.
   Key Features
   . Provides a simple, hands-on, conceptual route to understanding ancient evolution and the diversification of life on earth
   . Offers a conceptual understanding of biology, evolution, protein structure, RNA synthesis systems, protein synthesis systems, signaling systems, genesis of the three domains, and cell structures
   . Approaches ancient evolution via code-breaking protein and RNA sequences and motifs

   Chapter 1 – Big Questions

   What are the big questions about how life evolved on earth? How did an RNA-protein world diverge to cellular life? How did the three domains of life diverge?

   Chapter 2 – What This Book Is About

   The intention of this book is to provide a simple, verifiable understanding of evolution of life on earth. The argument, at its core, is frighteningly simple: (1) our “designs” are surprisingly simple and not obviously “intelligent”; (2) RNA synthesis describes evolution; (3) evolution describes RNA synthesis; and (4) evolution of seemingly overly complex protein synthesis systems can be simply modeled. Therefore, evolution can be viewed by understanding mechanisms of RNA and protein syntheses. Before DNA genomes, life passed through a strange RNA-protein world. RNA-template-dependent RNA polymerases of the two double-?–?-barrel types (described in detail in this book) became the dominant enzymes for RNA synthesis. As life evolved into the DNA-template world, these enzymes evolved to become DNA-template-dependent RNA polymerases and spread to all cellular life. RNA, therefore, was and is the central coding molecule of life on earth and remains the intermediary between DNA genomes and protein catalysts. Because life comes from an RNA-protein world, mechanisms for RNA synthesis remain at the heart of life processes, and understanding RNA synthesis is a key to understand evolution.

   Chapter 3 – Scientific Acronyms

   If, for any reason, the reader is disappointed by a paucity of incomprehensible scientific jargon or unfamiliar acronyms in this book, the author sincerely apologizes. Where necessary, I shall try to provide subtitles to science speak. If the reader finds words or phrases that seem incomprehensible, Wikipedia can provide a description. Otherwise, please be assured that the author knows many arcane scientific acronyms and strange words that I shall try to refrain from using. That being said, there is significant complexity to RNA synthesis systems and their networks, making some jargon unavoidable. Please, however, look beyond the language and relate to proteins from their structures and core motifs. Proteins are Frankenstein’s monsters, and parts are parts. There are many and striking protein family resemblances that, using molecular graphics, anyone can see.

   Chapter 4 – Molecular Graphics

   The story of genesis cannot be appreciated unless the reader utilizes molecular graphics. Molecular graphics programs are freely available and easy and rewarding to use. Using tutorials, you can teach yourself to use these programs in about an hour.

   Section I: The Old Testament of Gene Regulation
   Chapter 5 – Evolution as a Cutout Doll Problem I

   Protein structure/function may seem to be an arcane branch of human knowledge, but I assure you it is not. Protein structure and function can be understood and analyzed by anyone. The evolution of protein structures and functions can also be understood in significant detail.

   Chapter 6 – Evolution as a Cutout Doll Problem II

   The core concept of this book is that last universal (cellular) common ancestor (LUCA) and the RNA-protein world, ancient though they be, can be viewed in extant core protein motifs. By any human standard, core protein motifs are immortal. Core protein motifs go back to LUCA and beyond to the RNA-protein world. Astoundingly, ancient core protein motifs are ?4 billion years old on an ?4.6 billion year old earth.

   Chapter 7 – The Best Art

   Molecular biology, genetics, and biochemistry have the best science. To fully appreciate this book, you must learn to make molecular art.

   Chapter 8 – Intelligent Design

   Protein structure/function does not support the concept of intelligent design. Protein design follows a different set of rules: the rules of gene fusion, evolution, genetics, and protein folding.

   Chapter 9 – Polymers

   RNA and DNA are linear polymers of four nucleic acids. Compared to RNA, DNA tends to function as more chemically inert but more stable double-stranded structure. As such, DNA is a more reliable repository of genetic information than RNA.

   Chapter 10 – LEGO (Trademark) Life

   The story of genesis of life on earth is preserved as written history. The remarkable story remains written in genetic code, protein secondary structure, and protein tertiary structure. This is a language that can be read by anyone (no PhD necessary, although perhaps helpful). The story has now largely been decoded.

   Chapter 11 – ?/? Proteins

   I wish for you, with your newfound, immense skill in protein structure analysis, to consider ?/? proteins. We shall consider TIM barrels, Rossmann folds, TOPRIM domains, ATPases, and kinases. Many more examples are available than we shall cover.

   Chapter 12 – The Inevitability of ?/? Folds

   Stephen J. Gould, eminent evolutionary biologist, indicated that if evolution were to occur again, it would look quite different. Maybe so, particularly for intact animals. Given rules of genetics and the genetic code and rules for protein structure, solubility, and function, it is very difficult to conceive of life on earth without a primary role for (?–?)n repeat proteins.

   Chapter 13 – Evolution Puts the Y (Why) in Biology

   OK. So it is a dumb pun, even dumber written than spoken, but that is my favorite kind: dumber the better. In studying ancient evolution, think of genetic mechanisms: ligations (linking two RNAs), duplications, multimerizations, purifying (negative) selection.

   Chapter 14 – Evolution Is Not Anti-Religion

   Evolution is no more antireligion or anti-Bible or anti-Islam than jet airplanes or wristwatches. It is simply a modern understanding of biology. Without evolution, nothing in biology makes sense, and everything is stamp collecting.

   Chapter 15 – Computers in Biology

   To appreciate protein structure/function/evolution/dynamics, you need a computer: a PC or Mac will do. You do not need a supercomputer initially. This is the best art and science. Perusing a protein structure is like visiting Mars, only more alive, more essential, more human.

   Chapter 16 – The Old and New Testaments of Gene Regulation

   In one of my scientific studies, I indicated that evolution of life on earth divides naturally into an Old Testament and a New Testament of gene regulation by two double-?–?-barrel-type RNA polymerases. I repeat the analogy in this chapter because I think it is helpful to understand the central importance of RNA synthesis in the evolution of life on earth.

   Chapter 17 – Evolution as a Cutout Doll Problem III

   Multi-subunit RNA polymerases evolved around two double-?-?–barrels, the bridge helix and the trigger loop. Cradle loop barrels include RIFT barrels, double-?-?–barrels and swapped-hairpin barrels. Naming of double-?-?–barrels is based on the pattern of crossing peptide chains.

   Chapter 18 – Multi-Subunit RNA Polymerases Book I

   Multi-subunit RNA polymerases of the two double-?–?-barrel type are among the most beautiful, complex, and dynamic proteins in the human biosphere. Furthermore, multi-subunit RNA polymerases, their general transcription factors, and promoters form the core of the narrative of evolution of life on earth. In this chapter, I use a bacterial RNA polymerase–initiating complex (PDB 4XLN) interacting with promoter DNA to describe some of the features of these essential enzymes. So, this chapter is an attempt to look under the hood and partly disassemble the perplexing RNA polymerase motor. The RNA polymerase structure I selected is from Thermus thermophilus, a bacterial hyperthermophile. A bacterial RNA polymerase was selected because it is slightly simpler than archaeal and eukaryotic RNA polymerases in subunit structure and has fewer zinc (Zn) atoms. Otherwise, because of evolution, features of bacterial RNA polymerase are also features of archaeal and eukaryotic RNA polymerases.

   Chapter 19 – Multi-Subunit RNA Polymerases Book II

   Multi-subunit RNA polymerases of the two double-?–?-barrel-type are found in all living organisms. In archaea and bacteria there is one RNA polymerase. In eukaryotes, there are three. The carboxy terminal domain (CTD) of eukaryotic RNA polymerase II evolved at LECA (the last eukaryotic common ancestor). Eukaryotic complexity can partly be ascribed to the three RNA polymerases and the CTD on RNA polymerase II.

   Chapter 20 – The Chemical Synthesis of Life

   The many necessary transitions from chemistry to energy transduction to polymers to coding to protocells to DNA genomes to cellular life are mostly unknown but appear to have occurred rapidly over a few hundred million years on earth. Harnessing redox power and chemical energy was essential. Generation of polymers and then coding and replicating polymers was essential.

   Chapter 21 – The RNA World

   The presumed RNA world was a time largely dominated by RNA and ribozymes before evolution of the tRNA cloverleaf, the ribosome and RNA-directed protein coding.

   Chapter 22 – Ribosomes

   Ribosomes and cloverleaf tRNA connect the RNA world to the RNA-protein world. The peptidyl transferase center of the ribosome is considered to be a ribozyme but not an efficient one. In evolution, ribosomal protein cofactors failed to assume peptidyl transferase center function. Ribosomal RNA sequences, which are highly conserved, are often used to generate evolutionary trees, but, because rRNA remains so unchanged, other metrics may be more informative to understand the major signposts in evolution relating LUCA and the three domains.

   Chapter 23 – The RNA-Protein World

   The RNA-protein world requires RNA-based protein coding, so mRNA, tRNA and ribosomes evolved. RNA genomes are volatile and chaotic with RNA fragments of limited size. Expect mixtures of multi-copy RNA gene colonies with gene independence and with individual gene copies potentially in competition. RNA ligations, necessary for RNA replication, link gene copies together to form multimers, generating repeating sequences and leading to evolution of barrels, sheets and other common repeat folds. The RNA-protein world was a time of remarkable gene diversity before evolution of rapidly replicating DNA genomes took over and partly suppressed mechanisms of innovation.

   Chapter 24 – Transfer RNA

   Cloverleaf transfer RNA (tRNA) is the ancient molecule (>3.5 billion years old) around which translation systems evolved. The first cloverleaf tRNA was formed by ligation of three 31 nucleotide minihelices and two symmetrical internal 9 nucleotide deletions. The anticodon loop and the T-loop are homologous sequences and are very similar in structure. The D-loop is derived from a truncated UAGCC repeat. Acceptor stems are derived from a truncated GCG repeat and its complement. Five nucleotide segments surrounding the anticodon loop stems are remnants of acceptor stems. Because of its stiffness, tRNA is an effective translation adapter. Cloverleaf tRNA generation was a revolutionary evolutionary innovation that allowed standardization to the 3 nucleotide genetic code. tRNA evolution, therefore, is an example of iteration of simple sequences and motifs forming a molecule of enduring value.

   Chapter 25 – The Three Domains of Life on Earth and Scientific Working Hypotheses

   A model for evolution of the three domains must explain the following: (1) the transition from the RNA-protein world to the last universal common (cellular) ancestor (LUCA); (2) the great divergence of archaea and bacteria from LUCA; and (3) fusion of archaea and bacteria to form eukaryotes. This chapter outlines defining characteristics of LUCA, archaea, bacteria, and eukaryotes in order to frame arguments about the major transitions. The great divergence of archaea and bacteria from LUCA is mostly attributed to changes in promoters, general transcription factors, and transcription systems. Evolution of eukaryotes is attributed to endosymbiotic fusion of archaeal and bacterial cells and genomes.

   Chapter 26 – LUCA

   LUCA was the last universal common (cellular) ancestor of archaea, bacteria, and eukaryotes. LUCA diverged to archaea and bacteria. It can be considered to be the first cellular life and the first DNA genome–based life. DNA is a more stable repository of genetic information than RNA.

   Chapter 27 – General Transcription Factors and Promoters

   The last universal common ancestor (LUCA) promoters and general transcription factors evolved via iteration of a small number of simple DNA sequences and interacting protein motifs. Divergence of archaeal and bacterial transcription systems from LUCA describes why archaea and bacteria became separate domains. Archaeal transcription factor B (TFB) and bacterial ? factors are homologs that include homologous helix-turn-helix domains that locate to homologous regions of archaeal and bacterial promoters. TFB-? homology appears, therefore, to root the “tree of life” at LUCA.

   Chapter 28 – Archaea

   The archaeal promoter includes a BREup (BRE upstream of TATA), a TATA box, a BREdown (BRE downstream of TATA), and an initiator element (recognized as the transcription start by RNA polymerase). Essentially, the modern archaeal promoter can be generated from the LUCA primordial promoter through the coevolution of RNA polymerase, TBP, TFB, and promoters. TFE, with two winged helix-turn-helix domains and a Zn finger, was recruited to help support accurate initiation.

   Chapter 29 – Bacteria

   To recognize promoters, bacteria utilize ?-factors. ?-factors are 4 HTH units and HTH2 and HTH4 are most important to recognize the Pribnow box (–10 promoter region) and –35 promoter region. HTH3 interacts with the extended –10 promoter region, which is located at the upstream edge of the transcription bubble.

   Chapter 30 – Methane and Oxygen

   Photosynthetic cyanobacteria caused the Great Oxygenation Event, reducing atmospheric methane and resulting in snowball earth. The biosphere can control the atmosphere.

   Section II: The New Testament of Gene Regulation
   Chapter 31 – LECA

   Eukaryotes are a complex fusion of many archaea and bacteria. Eukaryotic cell organelles are relics of archaeal and bacterial endosymbionts. Introns in eukaryotic genes were generated by hopping of ?-proteobacterial group II intron elements. Eukaryote complexity results from defenses against genetic fusions and intron invasions.

   Chapter 32 – Eukaryotic Multi-Subunit RNA Polymerases, General Transcription Factors, and the CTD

   With many additions, eukaryotic transcription systems evolved from archaeal transcription systems. Eukaryotes have RNA polymerases I, II, and III, with a carboxy terminal domain (CTD) repeat (YSPTSPS) on RNA polymerase II. Beginning with the intron-splicing apparatus, an extensive interactome evolved to function with the CTD. Tracking RNA polymerase II through the transcription cycle requires the CTD and the CTD interactome, and the eukaryotic cell cycle was evolved from the RNA polymerase II transcription cycle. Much of eukaryote cell and organism complexity and intricate eukaryotic signaling evolved from RNA polymerase II transcription systems.

   Chapter 33 – Patchwork Eukaryotic Phylogenomics

   Eukaryotic genomes are a strange and complex patchwork of archaeal and bacterial genes with many eukaryotic innovations. Eukaryotes appear to have evolved via multiple nested endosymbiotic fusions.

   Chapter 34 – Plants

   Plants evolved via endosymbiosis of a primitive alga and a photosynthetic cyanobacterium. The capacity for photosynthesis was transferred horizontally via Matryoshka endosymbiosis.

   Chapter 35 – The Permian–Triassic Extinction

   The biosphere can control the atmosphere. Toward the end of the lush and verdant Permian age (?252 million years ago), a horizontal gene transfer event occurred between bacteria and an archaeal methanogen. Genes encoding cellulase enzymes were transferred to the methanogen to degrade plant matter (cellulose), providing a huge new store of food to a methane-generating archaea.

   Chapter 36 – The Triassic–Jurassic Extinction

   The Triassic–Jurassic Extinction occurred about 201.3 million years ago about the time of the breakup of Pangaea.

   Chapter 37 – The Cretaceous–Paleogene Extinction

   The Cretaceous–Paleogene Extinction resulted largely from a huge asteroid impact on earth ~66 million years ago.

   Chapter 38 – The Paleocene–Eocene Thermal Maximum

   The Paleocene–Eocene Thermal Maximum occurred about 55.8 million years ago. Global warming rose by about 5°C and ocean pH dropped by about 0.5 units.

   Chapter 39 – Promoter Proximal Pausing and the CTD Interactome

   The promoter-proximal pausing mechanism, found in only complex animals, is an evolutionary innovation in the RNA polymerase II CTD interactome. Because promoter-proximal pausing allows nuanced and complex gene regulation, this system helps direct development of complex body patterns. Not surprisingly, cancers and viral infections target the promoter-proximal pausing mechanism.

   Chapter 40 – Human Evolution

   From the point of view of ancient core protein motifs, humans are not particularly unique. For the most part, compared to other mammals, unique human characteristics can be attributed to differences in gene expression, which are likely to evolve via the jumping of retrotransposable elements.

   Chapter 41 – Human Cancer

   Cancer is caused by accumulation of multiple mutations, therefore cancers evolve. Cancers target complex human gene networks. To learn about human cancers, utilize online cancer databases.

   Chapter 42 – Homology Modeling and Cryoelectron Microscopy

   Cryoelectron microscopy is a means to obtain very large, dynamic atomic structures of molecules. Homology modeling allows threading of homologous amino acid sequences to existing structures obtained by cryoelectron microscopy or X-ray crystallography. Homology modeling demonstrates evolution.

   Chapter 43 – Human Extinction

   The human species races into the Great Anthropocine Extinction. Catastrophic man-made global warming is now essentially irreversible. Catastrophic ocean acidification is now inevitable. Evolution works via purifying (negative) selection of poorly adapted organisms.

   Chapter 44 – Evolution Versus Faith

   Evolution is not antireligious. In contrast to religion, however, evolution is strongly predictive for analysis of biological systems. Evolution is strongly supported by conservation of protein and RNA motifs for ~4 billion years.

   Chapter 45 – Concept in Biology

   So, does biology have concept or is it stamp collecting?

   Chapter 46 – Other Books and Studies

   This chapter provides a guide to further reading.

   Supplementary Materials
   Index
2. 2
   jawa says:

   February 23, 2019 at 4:44 pm

   Oh, no! This guy again?
   Who let the dogs out?
3. 3
   PeterA says:

   February 23, 2019 at 8:38 pm

   “Have they never heard the phrase non sequitur? As strange as it may seem to people outside the charmed circle, many Darwinian biologists find it difficult to distinguish the question of what occurred in biology from the question of how it occurred.” —Dr Michael Behe

   https://uncommondescent.com/intelligent-design/michael-behe-responds-to-the-hit-pre-publication-review-at-science/