# Molecular Evolution **Domain:** Evolution / Genomics / Historical Inference **Doc Type:** Canonical Discipline Node **Maturity:** Foundational ## Definition **Molecular evolution** studies evolutionary change in DNA, RNA and proteins and uses molecular variation to infer relationships, population history, selection and divergence. ## Nexus Context [[articles/The Evolutionary Roots of Silicon Valley|The Evolutionary Roots of Silicon Valley]] treats molecular evolution as the point where the genome becomes both inherited mechanism and historical archive. The field made evolutionary reconstruction computational at a scale impossible from morphology alone. Its inference is model-dependent. Mutation rates vary, recombination complicates genealogies and different genomic regions can have different histories. The discipline's strength lies in quantifying those uncertainties rather than treating sequence as a transparent transcript of the past. ## Continuity Context Molecular descent can establish biological relatedness and provenance. It does not encode a whole person or prove conscious continuity. This separation is foundational for post-biological identity claims. ## Sources / Provenance - UC Berkeley, molecular-evolution history: https://www.berkeley.edu/about/history-discoveries/ - Joseph Felsenstein, _Inferring Phylogenies_, 2004. ## See Also [[wiki/Molecular Clock|Molecular Clock]], [[wiki/Comparative Genomics|Comparative Genomics]], [[wiki/Population Genetics|Population Genetics]], [[wiki/Proof of Descent|Proof of Descent]] ## Relationships - **Edge source route:** [[collections/Edge|Edge]] connects this topic to exact Annual Question passages promoted into the Simple Reminders archive. ## Simple Reminders, Quotations, and Thoughts > “Luckily, there are informative parallels between biological and cultural evolution. Cultural systems—like biological systems—change over time. Heritable units of culture (counterparts of genes in biology) are difficult to define, but we can observe information propagating and mutating e.g. as the packets Dawkins popularized as memes. Unlike genes, ideas or memes can be transmitted worldwide in an instant and potentially reach massive audiences, so the evolution of cultures can hurtle forth at a rate far exceeding our biological evolution. The mutation and differential survival of ideas, however, is analogous to the mutation and differential survival of genetic variants, and thus our understanding of cultural evolution can be informed by biological concepts.” > **— Kirsten Bomblies**, *2013, Edge Annual Question, “What *should* We Be Worried About?”* [[reminders/Evolution/Cultural Systems Evolve by Heritable Variation by Kirsten Bomblies|Cultural Systems Evolve by Heritable Variation by Kirsten Bomblies]] > “There's an unthinking tendency to imagine that humans will be around in 6 billion years, watching the Sun flare up and die. But the forms of life and intelligence that have by then emerged would surely be as different from us as we are from a bacterium. That conclusion would follow even if future evolution proceeded at the rate at which new species have emerged over the 3 or 4 billion years of the geological past. But post-human evolution (whether of organic species or of artefacts) will proceed far faster than the changes that led to emergence, because it will be intelligently directed rather than being—like pre-human evolution—the gradual outcome of Darwinian natural selection. Changes will drastically accelerate in the present century—through intentional genetic modifications, targeted drugs, perhaps even silicon implants in to the brain. Humanity may not persist as a single species for more than a few centuries—especially if communities have by then become established away from the earth.” > **— Martin Rees**, *2005, Edge Annual Question, “What Do You Believe Is True Even Though You Cannot Prove It?”* [[reminders/Civilization/Humanity May Not Persist as a Single Species by Martin Rees|Humanity May Not Persist as a Single Species by Martin Rees]] > “Microbial evolution, which has been going on for over 3.6 billion years, is profoundly different from what we think of as standard Darwinian evolution, where genes have to pass down generations to work slowly through the selection filter. Bacteria swap genes promiscuously within generations. They have three different mechanisms for this "horizontal gene transfer" among wildly different kinds of bacteria, and thus they evolve constantly and rapidly. Since they pass on the opportunistically acquired genes to their offspring, what they do on an hourly basis looks suspiciously Lamarckian — the inheritance of acquired characteristics.” > **— Stewart Brand**, *2011, Edge Annual Question, “What Scientific Concept Would Improve Everybody's Cognitive Toolkit?”* [[reminders/Evolution/Microbes Evolve by Sharing Genes Across Lineages by Stewart Brand|Microbes Evolve by Sharing Genes Across Lineages by Stewart Brand]] > “Like many people, I once trusted in the wisdom of Nature. I imagined that there were real boundaries between the natural and the artificial, between one species and another, and thought that, with the advent of genetic engineering, we would be tinkering with life at our peril. I now believe that this romantic view of Nature is a stultifying and dangerous mythology.” > **— Sam Harris**, *2008, Edge Annual Question, “What Have You Changed Your Mind About? Why?”* [[reminders/Civilization/Mother Nature Is Not Our Friend by Sam Harris|Mother Nature Is Not Our Friend by Sam Harris]] > “Second, as is well known, one can make consistency arguments for virtually every human behavior. Given the possibilities of kin selection (natural selection for behaviors that do no good for to their performers but are advantageous to their relatives) and reciprocal altruism, and our ignorance of the environments of our ancestors, there is no trait beyond evolutionary explanation. Indeed, there are claims for the evolutionary origin of even manifestly maladaptive behaviors, such as homosexuality, priestly celibacy, and extreme forms of altruism (e.g., self-sacrifice during wartime). But surely we cannot consider it scientifically proven that genes for homosexuality are maintained in human populations by kin selection. This remains possible but undemonstrated.” > **— Jerry A. Coyne**, *2006, Edge Annual Question, “What Is Your Dangerous Idea?”* [[reminders/Evolution/Natural Selection May Preserve Genes Through Kin Selection by Jerry A. Coyne|Natural Selection May Preserve Genes Through Kin Selection by Jerry A. Coyne]] > “Formation of new biological species usually involves isolation and independent evolution of the two populations. As one toad population evolves through natural selection, each of its novel genes is tried out in many toads and will necessarily be selected to work together with the other genes in its population. Any genes causing within-population mismatches are weeded out. But, novel genes in one toad population are never tested with novel genes in another isolated toad population. Between-population mismatches will not be weeded out and will gradually accumulate, becoming apparent only when the populations later come into contact.” > **— David C. Queller**, *2017, Edge Annual Question, “What Scientific Term Or Concept Ought To Be More Widely Known?”* [[reminders/Evolution/New Species Begin When Populations Evolve Apart by David C. Queller|New Species Begin When Populations Evolve Apart by David C. Queller]] > “Paleo-DNA sequencing has changed not only our understanding of Neanderthals, but of ourselves. Neanderthals were not modern humans: they lacked the rapid cultural progress characterizing our species, and thus presumably some of our cognitive capacities. But what precisely were these differences? Do these differences make us, the survivors, "human?" Or were Neanderthals human, but "differently abled?" Certainly, with the bodies of Olympic wrestlers and brains slightly larger than modern humans, they'd be first picks for your rugby scrum; perhaps they had unique cognitive abilities as well. Progress will be rapid in addressing these issues, because each new insight into the genetic basis of the human brain yields parallel insights into our understanding of Neanderthal brains—and of the cognitive differences between the two.” > **— W. Tecumseh Fitch**, *2016, Edge Annual Question, “What Do You Consider The Most Interesting Recent [Scientific] News? What Makes It Important?”* [[reminders/Civilization/Paleo-dna and De-extinction by W. Tecumseh Fitch|Paleo-dna and De-extinction by W. Tecumseh Fitch]] > “Cancer cells acquire a range of distinctive hallmarks—unfettered proliferation, evasion of apoptosis, motility and migratory powers, genomic rearrangements, epigenetic alterations, and changes in the mode of metabolism, chromatin architecture and elasticity (to mention a few)—that collectively confer remarkable robustness and survivability. In the standard picture, cancer, with all these attendant hallmarks, is considered to be re-invented de novo in each host organism: the result of a dream run of "lucky" genetic accidents. The gain of all these amazing fitness functions, co-located in the same neoplasm (population of new cells), over a period of as little as months or even weeks, is attributed to a sort of ultra-fast-paced Darwinian evolution going on in the body of the host organism. Unfortunately this theory, despite its simplicity and popular appeal, has only one successful prediction: that the administration of chemotherapeutic drugs is very likely to fail on account of the neoplasm's ability to rapidly evolve a resistant sub-population.” > **— Paul Davies**, *2014, Edge Annual Question, “What Scientific Idea Is Ready For Retirement?”* [[reminders/Evolution/Somatic Mutation Theory of Cancer by Paul Davies|Somatic Mutation Theory of Cancer by Paul Davies]] > “Synthetic biology is currently tightly regulated, along the same lines as GMOs. But when biosynthetic products overflow into the natural world, it will be harder to keep control. Let's look at this from the molecular level, which arguably we have more control over than the organism or ecosystem level. We can shuffle the genes and whole genomes to create something that nature did not get round to creating. But a biological unit does not exist in isolation: Genes, protein complexes, cells, all function in modules—a composite of units, finely tuned by evolution in a changeable environment to work together.” > **— Seirian Sumner**, *2013, Edge Annual Question, “What *should* We Be Worried About?”* [[reminders/Evolution/Synthetic Biology Cannot Contain What It Releases into Nature by Seirian Sumner|Synthetic Biology Cannot Contain What It Releases into Nature by Seirian Sumner]]