Enlarge the diagram to see that pheromones are linked to longevity via signaling and chromatin modifiers.
The longevity of worms and flies can be modulated by the opposite sex82,123,124 a process that can involve pheromone production and/or sensing82,124
As secondary metabolites are evolutionarily conserved, the potential links between pheromonal signalling, chromatin and ageing deserve further exploration in other species.
My comment: The stability of organized genomes is nutrient-dependent and controlled by the physiology of reproduction. That fact has been placed into the context of evolution and longevity.
The link from metabolic network to genetic networks is easy to understand in the context of ecological variation that links pheromones to the physiology of reproduction and ecological adaptation via RNA-mediated events.
What does “evolve” mean outside the context of what is known about physics, chemistry, biology, and the RNA-mediated events that link epigenetically-effected gene duplication and amino acid substitutions to nutrient-dependent cell type differentiation and biodiversity via the physiology of reproduction in all living genera?
‘When I use a word,’ Humpty Dumpty said, in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’
My comment: Here’s what “evolution” means to Jerry Coyne. It means that all species evolve.
There are no “laws” in evolutionary biology comparable to those in physics, except perhaps that “all species evolve”…. — Jerry Coyne (Why Evolution is True)
My comment: Coyne claims that the laws of physics do not apply to evolutionary biology. His claims cannot be linked to anything serious scientists know about physics or about chemistry or about biology. You must simply accept his claim that “all species evolve.”
In Coyne’s world, if you observe something that looks like what you can claim is evolution, you can remove everything else you observe about physical relativity in everyday life.
See for example: 4 Ways You Can Observe Relativity In Everyday Life
For an electron to jump to a higher energy level it needs to absorb a specific wavelength of light.
My comment: In the context of neo-Darwinian theory, a definition linked nutrient-dependent energy jumps to biodiversity via mutations. See: What is Life?
… in the offspring even of thoroughly pure-bred stocks, a very small number of individuals, say two or three in tens of thousands, turn up with small but ‘jump-like’ changes, the expression ‘jump-like’ not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries’s mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule.
Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)
My comment: De Vries quantum jumps should have been attributed to the sun’s biological energy. Please consider that fact before you accept the claim that “evolution is true” because evolutionary theorists defined “evolution” outside the context of the Laws of Physics. They will tell you evolution is true, so you must first realize that your acceptance of their theory means you need not accept anything known about physics since, I repeat, “There are no “laws” in evolutionary biology…”
If neo-Darwinian evolutionary theory could be placed into the context of physics, the energy jumps linked to differences in the color of gold would be called mutations. The mutations that give the gold its color could be linked to the color of skin.
The claim that skin color arises in the context of beneficial mutations eliminates any need to explain how the sun’s biological energy is linked to the nutrient-dependent energy jumps that link RNA-mediated events from atoms to vitamin D and nutrient-dependent ecosystems in the context of everything known to serious scientists about biologically-based top-down causation.
Instead, evolutionary theorists start from the bottom up. That’s what a special issue of the journal “Cell” did. See the table of contents of the special issue (below) with links that allow you to read the abstracts.
These articles were supposedly written by experts in their disciplines. All the experts ignore the Laws of Physics and the chemistry of nutrient-dependent RNA-mediated protein folding. What’s worst is that the experts ignore everything known to serious scientists about biologically-based cause and effect, which requires some knowledge of how atoms are linked to ecosystems.
In what may have been intended as comic relief, the articles appear to include information on everything known about the origin of eukaryotes (organisms with a cell nucleus and mitochondria), the Cambrian explosion, the origin of terrestrial flora, and even the evolutionary history of birds.
After learning everything these experts know about the history of life on earth, The RNA World as a Model System to Study the Origin of Life reveals that they made it all up. They forced their claims to fit neo-Darwinian theory.
Only then are we told there must be a model that links the theory to facts. The model that is required links atoms to ecosystems via RNA-mediated events. We can ignore that model if we agree to believe in evolutionary theory. Watch how it explains the history of life outside the context of any model — before you are told that a model is required.
In the end, you will see that these experts “…care less about how our particular life arose and more about the possible ways life could arise under a variety of conditions.” Simply put, they care more about their ridiculous theories than facts.
They “…see the RNA World as a particularly tractable model system for studying the emergence of biological complexity during an origin of life.”
Serious scientists do not claim that biological complexity automagically emerged.
History of life on Earth – Geoffrey North
Excerpt: As living things have evolved and diversified…
The tree view of life – Florian Maderspacher
Excerpt: Maybe it is enough to know that “we’re related to the grass”.
How life shaped Earth – Michael Gross
Excerpt (with my emphasis): …life has changed our planet and made it a more complex, diverse, and life-friendly place, but on the other hand it is no stranger to positive feedback loops that lead to mass extinctions and could in principle wipe out all life.
Archaea – Laura Eme, W. Ford Doolittle
Excerpt: Whether anything unites Archaea with Bacteria as ‘prokaryotes’, and whether or not any such shared features are primitive (present in the common ancestor of all extant life) or derived (arrived at convergently through streamlining, or by lateral gene transfer between the two domains) remain open questions.
Photosynthesis and early Earth – Patrick M. Shih
Introduction: Phototrophy has sustained life on Earth, possibly since the dawn of life.
Insect evolution – Michael S. Engel
Excerpt: When such a powerful combination of factors is permitted to run over hundreds of millions of years, the natural byproduct is unrivaled diversity.
Lobopodians – Javier Ortega-Hernández
Excerpt: Thus, onychophorans, tardigrades and euarthropods are all technically extant lobopodians, even though the latter have arthropodized rather than lobopodous limbs.
Phylogenomic Insights into Animal Evolution – Maximilian J. Telford, Graham E. Budd, Hervé Philippe
Conclusion: More sophisticated methods for mapping characters are necessary (Box 2) but the potential for convergent evolution on the one hand and for character loss or character state reversion on the other is not easily overcome (especially given that, as we have underlined, simplification is an evolutionary driving force). The next step of mapping homologous characters onto trees will require the collaboration between morphologists, developmental biologists, comparative genomicists, palaeontologists and phylogeneticists.
The Origin and Diversification of Birds – Stephen L. Brusatte, Jingmai K. O’Connor, Erich D. Jarvis
Conclusion: The flurry of recent work on avian evolution is a prime example of how fossil, morphological, genomic, phylogenetic, and statistical data can be combined to weave an evolutionary narrative, and explain how some of the modern world’s most familiar species became so successful.
The Evolutionary Origin of a Terrestrial Flora – Charles Francis Delwiche, Endymion Dante Cooper
Excerpt: …the charophyte green algae present great opportunities for model system development, and offer a wide range of structural features potentially of use, from simple filamentous and unicellular forms in the Zygnematophyceae; to disk-like branched filaments in the Coleochaetophyceae that show developmental complexity…
Endosymbiosis and Eukaryotic Cell Evolution – John M. Archibald
Excerpt: There is value in looking back at the history of cell evolution research. There is also a lot to be gained from attempting to divorce oneself from the past while looking forward at cell biological problems with modern data. And there is clearly much about the evolution of the eukaryotic cell that still needs to be worked out. In doing so, we should enjoy the view from both perspectives.
Morphological Phylogenetics in the Genomic Age – Michael S.Y. Lee, Alessandro Palci
Conclusion: …if morphological phylogenetics is to exploit the increasingly massive genetic datasets being gathered, the current generation of morphologists will need to work in a different way to their predecessors. In some ways, they need to emulate their molecular counterparts: they need to evaluate morphology at the level of individual species and organisms (instead of higher taxa), they need to analyse all aspects of the phenotype (rather than focus on parsimony-informative traits), and they need to be mathematically and computationally adept, in order to employ appropriate models to integrate increasingly vast morphological and genomic data arrays.
Novelty and Innovation in the History of Life – Douglas H. Erwin
Excerpt: Does evolutionary biology need a new research program in evolutionary novelty distinct from the existing work on adaptation and speciation ? Some evolutionary biologists view morphological novelty as built upon the variation existing within a species. Others, particularly many evolutionary developmental biologists, view novelty as based on evolutionary changes distinct from standing variation. Considerable experimental work will be required to test the hypothesis that evolutionary novelties are underpinned by the origin of particular gene regulatory network structures [89, 90, 91, 115]. I suspect that novel individuated morphological structures will be identified that are not associated with such gene network structures, which will draw attention to the developmental mechanisms that ensure their evolutionary stability. Turning from novelty to innovation, there is great opportunity for carefully documenting the environmental and ecological circumstances under which innovations arise, how closely they are linked to morphological novelty, and whether there are particular conditions that foster increased innovation.
Life in the Aftermath of Mass Extinctions – Pincelli Hull
Conclusion: …most species that have ever existed are now dead and those losses have shaped the history of life. An integrative understanding of the role of extinction and speciation in macroevolution has yet to be achieved but is central to understanding the evolution of life.
The RNA World as a Model System to Study the Origin of Life – Abe Pressman, Celia Blanco, Irene A. Chen
Excerpt: It has been proposed that the triplet codon sequences now in the genetic code may have originally functioned in amino acid binding . Alternatively, the first codon triplets may have been small oligomers that bound to and stabilized early tRNAs, which were eventually ligated into small mRNAs that stabilized a series of tRNAs in turn (Figure 3B) . Such early mRNAs may have evolved from random sequences that happened to coordinate the synthesis of favorable small peptides using primitive tRNAs [186, 196, 197, 198] (Figure 3C). At the same time, a simple peptide synthetase ribozyme might evolve into an increasingly large and complex system of molecular alignment, leading to the modern ribosome. Indeed, the ribosome can be thought of as essentially an entropy ‘trap’ for carefully aligned substrates , and the inferred oldest core of the ribosome consists of a few surprisingly simple sequences . Perhaps ribozymes catalyzed nonspecific peptide formation initially  (Figure 3D,E), with ordering of amino acids emerging later. Alternatively, early peptides may have been aligned by aminoacyl-RNAs, but ribozyme catalysis was not initially part of the mechanism for peptide bond formation [197, 202]. Simple oligopeptides might help to stabilize folded RNAs, or even catalyze RNA replication or ligation, and therefore improved coding functions (e.g., higher fidelity, longer peptides) may have been selected. Recent work has also highlighted a dipeptide capable of stimulating vesicle growth, suggesting that some of the earliest peptides may have aided in vesicle growth and competition as well . Eventually proto-mRNAs with their protein products presumably out-competed ribozymes of similar function, erasing many, but not all, traces of the RNA World . The details of such a process are still not clear, however. A more radical hypothesis is that the earliest mRNAs may have served as templates for RNA synthesis by ligation, with the peptidyl transferase center of the ribosome having its origin as an RNA replicase ribozyme . The mystery of this major evolutionary transition remains to be solved.
The obfuscation of the idea above that “the ribosome can be thought of as essentially an entropy ‘trap’ can be placed into the context of biophysically constrained protein folding chemistry that is nutrient-dependent and controlled by the fixation of RNA-mediated amino acid substitutions, which are linked to biodiversity manifested in all morphological and behavioral phenotypes that can only arise in the context of sucessful organism-level thermoregulation and DNA repair that protects them from virus-driven entropic elasticity that links genomic entropy to extinction.
These articles linked above will all disappear behind a paywall in two weeks. After that, anyone who intends to claim that they provide evidence that “evolution is true” will need to pay to try and access supporting documentation that shows neo-Darwinian theory is, after all, nothing more than pseudoscientific nonsense. If you do not start with experimental evidence of an anti-entropic force, you cannot invent one later — when you realize it is required to make you appear to be more than just another pseudoscientist.
See for comparison: 72318Re: Transgenerational non genetic inheritance of acquired behaviors
Michael Ragland: Jay: The Bohacek article “Transgenerational non genetic inheritance of acquired behavior is too above me to really understand. However, the author(s) are very open to the idea that transgenerational non genetic inheritance of acquired behaviors is evident in mammals. You stated (as I recall) that such evidence in very weak in mammals. Have I misread/misinterpreted you (as I have sometimes done)? Or am I misinterpreting what Bohacek has stated?
Jay R. Feierman [NEW]: The evidence is strong in invertebrates, like worms. The evidence is weak in vertebrates, weaker in mammals and even weaker in humans. It does not mean it does not occur, just that the evidence is not strong especially in humans.
Michael Ragland: Do you think epigenetics (as it is construed today) is largely a political fad that will go extinct like the mental modules of evolutionary psychology . . .
Jay R. Feierman [NEW]: No, I don’t think epigenetics is a political fad. It is one of the hottest topics in neuroscience today. It is also very important. It was what was missing when I first studied genetics in the 1960s. We didn’t know what turned genes on and off. We now know how the same genes can make an arm, a leg, a kidney and a brain.
Michael Ragland: . . . or do you think it will increase in scientific discoveries/evidence but perhaps not be so politicized i.e Native Americans, Holocaust survivors, African Americans, etc.
Jay R. Feierman [NEW]: Yes. There will be an exponential increase in knowledge of what regulates genes in the next few decades. The idea that social problems present in current populations whose ancestors suffered various abuses many generations ago are due to epigenetic mechanisms is what I believe is the current fad that will fade into oblivion over the next decade or two.
For a historical perspective on what the moderator of the International Society for Human Ethology thinks, see:
7/26/13 Re: [human-ethology] Interjecting where I find others failing, at as much, even here…
James Kohl: It is now perfectly clear that this statement and any statement or inference like it is WRONG: Random mutations are the substrates upon which directional natural selection acts.
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement. Produce one such person. You can try to recruit such a person however you like. Don’t give links to articles and abstracts that don’t address that exact sentence. Your arrogance amazes me. It would be like me saying that gravity does not cause items with mass to fall to earth at 32 feet/sec/sec in a vacuum as that is how fundamental the statement that random mutations are the substrate upon which directional natural selection acts is to biology and genetics. You really want us to believe that you are the expert on this topic when 100% of university level biology textbooks for Biology 101 and all biology and genetics professors will say the exact same sentence or something almost identical.
My summary: The arrogance of biologically uninformed theorists continues to amaze me. They do not know how evolution occurs, but claim that “evolution is true” or that Random mutations are the substrates upon which directional natural selection acts, while ignoring that fact that the anti-entropic effect of the sun’s biological energy must be linked to the creation of all differences in all cell types of all individuals of all living genera via the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding and the physiology of reproduction that enables the fixation of RNA-mediated amino acid substitutions in the organized genomes via protection against virus-driven genomic entropy.