# Evolutionary Covariation > **Machine-Evolution Nexus:** [[articles/Digital Darwinism and the Invisible World of Machine Evolution|Digital Darwinism and the Invisible World of Machine Evolution]] places this node within the history and governance of substrate-independent evolution. **Domain:** Evolution / Structural Biology **Doc Type:** Canonical Wiki Node **Maturity:** Developed ## Definition Evolutionary covariation is correlated change among sequence positions across related lineages, often produced when interacting residues must change compatibly to preserve function. ## Nexus Context Protein-structure systems can use such statistical dependencies because descent and selection have tested combinations across deep time. ## Evidence Boundary Covariation can reflect phylogeny, sampling and indirect effects as well as direct contact. Models integrate it with other learned and structural information. ## Relationships [[wiki/Multiple Sequence Alignment|Multiple Sequence Alignment]], [[wiki/AlphaFold|AlphaFold]], [[wiki/Comparative Genomics|Comparative Genomics]], [[wiki/Scientific Inference|Scientific Inference]] - **Edge source route:** [[collections/Edge|Edge]] connects this topic to exact Annual Question passages promoted into the Simple Reminders archive. ## Sources / Provenance - Direct-coupling and protein-covariation literature; Jumper et al. (2021). ## Simple Reminders, Quotations, and Thoughts > “Bill Joy, the prominent computer scientist, argued in a Wired article last year that "the future doesn't need us" because other creatures, artificial or just post-human, are going to take over the world in the 21st century. He is worried that various technologies — particularly robotics, genetic engineering and nanotechnology — are soon going to be capable of generating either a self-conscious machine (something like the Internet "waking up") or one capable of self-replication (nanotechnologists inspired by the vision of Eric Drexler are currently attempting to create a nano-scaled "universal assembler"). If either of these events came to pass, it would surely introduce major changes in the planetary ecology, and humans would have to find a new role to play in such a world. But is Joy right? Do we have to worry about mad scientists producing some invention that inadvertently renders us second-class citizens to machines in the next couple of decades? (Joy is so distraught by this prospect he would have everyone stop working in these areas.)” > **— Robert Aunger**, *2002, Edge Annual Question, “What Is Your Question? ... Why?”* [[reminders/AI Control/Can Technology Wake up and Come Alive by Robert Aunger|Can Technology Wake up and Come Alive by Robert Aunger]] > “Natural selection favors the allocation of resources not just from parents to offspring but among genetic kin such as siblings and cousins. Just as a gene that encourages a parent to invest in offspring will be favoring a copy of itself that sits inside those offspring, so a gene that encourage an organism to invest in a brother or cousin will, some proportion of the time, be helping a copy of itself, and will be selected in proportion to the benefits conferred, the costs incurred, and the degree of genetic relatedness.” > **— Steven Pinker**, *2012, Edge Annual Question, “What Is Your Favorite Deep, Elegant, Or Beautiful Explanation?”* [[reminders/Evolution/Evolutionary Genetics Explains the Conflicts of Human Social Life by Steven Pinker|Evolutionary Genetics Explains the Conflicts of Human Social Life by Steven Pinker]] > “Our species' stroll through Design Space is picking up speed. Recreational sex, recreational eating, and recreational perception (hallucinogens, alcohol), have been popular since Roman times, but we are now on the verge of recreational self-transformations that will dwarf the modifications the Romans indulged in. When you no longer need to eat to stay alive, or procreate to have offspring, or locomote to have an adventure — packed life, when the residual instincts for these activities might be simply turned off by genetic tweaking, there may be no constants of human nature left at all. Except, maybe, our incessant curiosity.” > **— Daniel C. Dennett**, *2009, Edge Annual Question, “What Will Change Everything?”* [[reminders/Civilization/Exploring the Future Changes the Future by Daniel C. Dennett|Exploring the Future Changes the Future by Daniel C. Dennett]] > “The most difficult ideas to change are those which seem so obviously true that we can scarcely imagine otherwise until confronted with unambiguous disconfirmation. For example, even behavior geneticists had long presumed that non-genetic influences on intelligence and other human traits grow with age while genetic ones weaken. Evidence reveals the opposite for intelligence and perhaps other human traits as well: heritabilities actually increase with age. My attempt to explain the evolution of high human intelligence has also led me to question another such "obvious truth," namely, that human evolution ceased when man took control of his environment. I now suspect that precisely the opposite occurred. Here is why.” > **— Linda S. Gottfredson**, *2008, Edge Annual Question, “What Have You Changed Your Mind About? Why?”* [[reminders/Evolution/Human Evolution May Have Accelerated When We Took Control of the Environment by Linda S. Gottfredson|Human Evolution May Have Accelerated When We Took Control of the Environment by Linda S. Gottfredson]] > “Genes and their interaction networks determine the phenotype of an organism—what it looks like and how it behaves. One of the biggest problems in modern evolutionary biology is understanding the relationship between genes and phenotypes. The prevailing theory is that all animals are built from essentially the same set of regulatory genes—a genetic toolkit, and that phenotypic variation within and between species arises simply by using shared genes differently. Scientists are now generating a vast amount of genomic data from an eclectic mix of organisms. These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.” > **— Seirian Sumner**, *2014, Edge Annual Question, “What Scientific Idea Is Ready For Retirement?”* [[reminders/Evolution/Life Evolves via a Shared Genetic Toolkit by Seirian Sumner|Life Evolves via a Shared Genetic Toolkit by Seirian Sumner]] > “Consider the tedious but tenacious argument 'genes versus environment'. I'll take a well-studied case. Indigo buntings migrate annually over long distances. To solve the problem of navigation, natural selection equipped them with the ability to construct a mental compass by studying the stars in the night sky, boy-scout fashion, during their first few months of life. The fount of this spectacular adaptation is a rich source of information that natural selection, over evolutionary time, has packed into the birds' genes—in particular, information about the rotation of the stellar constellations. Thus buntings that migrate today can use the same instincts and the same environmental regularities to fashion the same precision-built instrument as did their long-dead ancestors.” > **— Helena Cronin**, *2012, Edge Annual Question, “What Is Your Favorite Deep, Elegant, Or Beautiful Explanation?”* [[reminders/Evolution/Natural Selection Packed a Star Compass into Bird Genes by Helena Cronin|Natural Selection Packed a Star Compass into Bird Genes by Helena Cronin]] > “Since this experience, I have purposely engaged other well-educated defenders of the irrational, as well as numerous students at my university, in spontaneous one-on-one debates about a host of contentious biological subjects including evolution, organic farming, homeopathy, cloned animals, "chemicals" in our food, and genetic engineering. Much to my chagrin, even after politics, ideology, economics, and other cultural issues have been put aside, there is often a refusal to accept scientific implications of rational argumentation.” > **— Lee M. Silver**, *2008, Edge Annual Question, “What Have You Changed Your Mind About? Why?”* [[reminders/Evolution/Public Understanding Does Not Guarantee Agreement on Science by Lee M. Silver|Public Understanding Does Not Guarantee Agreement on Science by Lee M. Silver]] > “2. Hunter-gatherers. Large-scale agriculture, cities, and other aspects of what we call "civilization" are recent inventions (< 10,000 years old), too young to have exerted significant evolutionary change on the human genome, and have led to cataclysmic changes in the human lifestyle. The best information about the ecological and social lifestyle to which our minds and bodies are biologically adapted lies in the few remaining foraging or hunting and gathering peoples. These peoples are now assimilating, being absorbed, being pushed off their lands, or dying of disease.” > **— Steven Pinker**, *2000, Edge Annual Question, “What Is Today's Most Important Unreported Story?”* [[reminders/Evolution/The Loss of Our Species' Biography by Steven Pinker|The Loss of Our Species' Biography by Steven Pinker]] > “Technically, evolution of the human species as a result of natural selection stopped when we became a social animal — when the strong began protecting the weak and when our scientific and technological advances allowed us to extend the lives of those individuals unfortunate enough to have genetic weaknesses that would have killed them. With humans, artificial selection (selective breeding) was never a serious replacement for natural selection possibility, and as a result there have been no significant changes to the human species since its societies began.” > **— Bruce Parker**, *2009, Edge Annual Question, “What Will Change Everything?”* [[reminders/Evolution/The Successor to Natural Selection in Humans by Bruce Parker|The Successor to Natural Selection in Humans by Bruce Parker]]