The No Preferred Level of Evolution Theory - References
Nothing in biology makes sense except in the light of evolution. This is not just a sentimental statement. Evolution is the change in replicators that occurs as the replicators become more well-suited to their surroundings. All life is made up of replicating units. All of the characteristics of living things ultimately derive from replicators becoming more and more well-suited to their environments. Genes, clusters of genes, cells, organisms, populations, and whole ecosystems are all replicators, and are all units of evolution whose characteristics are adaptations to their surroundings.
Take a look around and observe. The worms are well-suited for the environment in which they live - the dirt. The fish are well-suited for the environment in which they live - the seas. The humans are well-suited for the environment in which they live - among other humans. Darwin’s hypothesis was that organisms are well-suited for their respective environments because their characteristics are in fact adaptations to their environments. Organisms are changing over time to be better and better suited for their environments. New organisms create new ecosystems, which are new environments. And this change in organisms and their environments is responsible for all the variety of life that exists today.
The implication of Darwin’s observation is that all life comes from a common ancestor. There is a continuous spectrum of life from humans to worms. There is a continuous spectrum of life from humans to fish. And there is a continuous spectrum of life from humans to the last common ancestor of all living things. Every living thing on this continuum of life existed at some point in time, just as you exist now. Almost everything on this spectrum of life that once existed, no longer exists. Why? The vast majority of living forms on planet earth that once existed are now extinct. Why? These are not a trivial questions. Living things have the ability to repair themselves, and could keep on repairing themselves indefinitely. Sequoia trees, for example, grow stronger and hardier with each passing year for thousands and thousands of years. However, most organisms age. Aging is the increasing probability of death from internal causes with the passage of time. Aging seems to be built into most organisms. Why? Aging is one of the most important and ubiquitous characteristics of living things, and aging is no exception to Darwin’s observation. Aging is an adaptation to the environment that was selected for by evolution.
Aging does not make sense with respect to the version of evolutionary biology that has dominated the field for the last 100 years - the selfish gene theory. The selfish gene theory assumes that the only unit of evolution is the gene - the sequence of nucleic acids that codes for a protein. The selfish gene theory believes that genes are independent agents, using the organisms in which they appear merely as vehicles for their own replication. Aging does not make sense from the perspective of the selfish gene theory. If organisms are vehicles for the propagation of genes, why would the genes program those vehicles to self-destruct?
The answer is that genes are not the only unit of evolution. It is valid to view cells and organisms as survival machines built by genes. But it is just as valid to view DNA as an organelle of the cell, just like the ribosomes and the mitochondria. Some of the things we observe in biology are well-explained by competition between genes. One example is sickle-cell anemia. Other things are better explained as competition between individual organisms. Some gazelles are faster than others, and those that are better able to escape the lions survive to pass on their speed to the next generation. Still other things are best understood as competition between communities. A healthy forest is a cooperative community of many different species. It is robust and able to expand into new environments because the different species, cooperating and competing, comprise a system that is capable of adjusting to different conditions of soil and climate. In a complex, evolving biosphere, all these processes are happening at once. There is no preferred level of evolution. Genes, clusters of genes, cells, tissues, organisms, populations, and ecosystems are all replicating, are all evolving, and all possess characteristics that are adaptations to their environments. Evolution is selecting for traits that benefit all of these levels, with no preference to any particular level. In different circumstances, different levels of selection may dominate the evolutionary process, but there is no preferred level of evolution in general.
Most biologists believe that the gene is the only unit of evolution simply because that is the only level of evolution that they understand. But evolution is smarter than they are. The belief that genes are the sole unit of evolution has led to many incorrect assumptions in biology. For example, it led to the incorrect belief that the codon-amino acid translation code was universal in all organisms. For decades, it was argued that any change in the codon translation code would be lethal since evolution works to preserve the selfish gene. This objection, however, was by-passed by evolution . Even today, the vertebrate nuclear codon translation code is referred to as the 'universal code', although we now know it is far from universal. Researchers today are still making the same mistakes. Researchers still give preference to models of evolution that make sense to them regardless of the evidence. This is not science. This is hubris.
Science is the idea that we should give preference to models of the universe with powers of prediction. Consider, for example, two theories to explain the motion of the objects in the sky. Theory 1 posits that the Earth orbits the sun in a circular trajectory. Theory 2, on the other hand, posits that the Earth orbits the sun in an elliptical trajectory, with the sun at one focus of the ellipse. Theory 1 may seem more intuitive and understandable to you than Theory 2. It may seem that Theory 2 raises more questions than it answers. Why is nothing at the second focus of the ellipse? What is the cause of the asymmetry of the Earth’s trajectory? However, these questions are not valid. One could just as easily ask 'Why should something be at each focus of the ellipse?' or 'What is the cause of the symmetry of Earth's purported circular trajectory?' It matters not which theory answers what questions you deem intuitive. This is not science. Theory 2 makes better predictions about the motion of the objects in the sky than Theory 1. Therefore, Theory 2 is the more scientific theory.
Science is the idea that we should give preference to theories that have powers of prediction, even when those theories are less intuitive or believable or harder to understand. Science is a radical idea. It is very hard to give preference to scientific theories over ones we find understandable and intuitively believable. However, this is what we must do as scientists, and science has already proven itself as a good idea. Indeed, scientific thinking is responsible for the remarkable technology that exists today. The selfish gene theory predicts that every individual should be programmed to live as long as possible, and to keep reproducing through the fullness of its lifetime. Is this what we observe in nature? Science is radically empirical. Nature always gets the last word. Look around and observe.
Why do Atlantic salmon live for multiple years while Pacific salmon die right after they reproduce? Why do bats live ten times longer than mice, even though they are the same size and it is the bats that burn the candle at both ends with respect to their metabolic rate? Why do queen bees live for twenty years while worker bees, with exactly the same genome, live only a few weeks? Why do the telomeres of a cell become shorter with each division, when they could just as easily be extended to full length each time a cell divides?
The answer to all these questions is that self-destruction is built into our programming. When rodents are starved, their lifespan can be increased by up to 50%. Why does limiting resources increase longevity? Anything the body could do with limited resources, it could also do with plentiful resources. However, our bodies are not trying their best to survive. The body has the ability to repair itself indefinitely, but chooses not to.
When you place a cast on a mouse's leg, its muscle atrophies. The same pathways atrophy the cast limb as do the uncast limb during aging. These are active chemical pathways. If you knock out ATF4, muscle atrophy does not occur during aging or casting .
Your body is actively destroying itself as you age. Our bodies are programmed to self-destruct, and this is why we grow more and more prone to mortality with the passage of time. Aging is built into organisms. This is why almost everything that has ever lived is no longer alive today. All scientific evidence points to this conclusion. However, mainstream biology rejects this scientific claim simply because they find it unbelievable. They find it unbelievable because they falsely believe that the gene is the only unit of evolution.
Recently, there has been an explosion in resources devoted to defeating aging. However, almost all research programs are trying to “fix what goes wrong” by repairing the body at the cellular level. This is hard. It also may be unnecessary. If we understand that aging is a programmed process of active self-destruction, then there must be signals that instruct the body to self-destruct. The royal road to anti-aging interventions is thus to understand those signals and to reprogram the body for youthful levels of repair and even regeneration.
Just as we can intervene in the chemical pathways that cause puberty, we can intervene in the chemical pathways that cause aging. Do not be content with death. The false belief that death is inevitable was necessary for your ancestors to cope with the fact that aging would not be cured in their lifetimes. But death is not inevitable. Aging can be cured, and will be cured eventually. Society should prioritize finding interventions that stop the aging process, just as it prioritizes finding cures for cancer and vaccines for pathogens. We live in a very exciting time. With enough societal prioritization, we can be the last generation born on the clock!
 Jukes, T. H., & Osawa, S. (1993). Evolutionary changes in the genetic code. Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, 106(3), 489–494. doi:10.1016/0305-0491(93)90122-l
Relevant quote from the article:
Abstract--l. The genetic code was thought to be identical ("universal") in all biological systems until 1981, when it was discovered that the coding system in mammalian mitochondria differed from the universal code in the use of codons AUA, UGA, AGA and AGG. 2. Many other differences have since been discovered, some in mitochondria of various phyla, others in bacteria, ciliated protozoa, algae and yeasts. 3. The original thesis that the code was universal and "frozen" depended on the precept that any mutational change in the code would be lethal, because it would produce widespread alterations in the amino acid sequences of proteins. Such changes would destroy protein function, and hence would be intolerable. 4. The objection was "by-passed" by nature. It is possible for a codon to disappear from mRNA molecules, often as a result of directional mutation pressure in DNA: thus all UGA stop codons can be replaced by UAA. 5. The missing UGA codon can then reappear when some UGG tryptophan codons mutate to UGA. The new UGA codons will be translated as tryptophan, as is the case in non-plant mitochondria and Mycoplasma. Therefore, no changes have taken place in the amino acid sequences of proteins. 6. Variations of this procedure have occurred, affecting various codons, and discoveries are still being made. The findings illustrate the evolutionary interplay between tRNA, release factors and codon-anticodon pairing.
Also, you can read the tables on https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables.
 Miller, M.J., Marcotte, G.R., Basisty, N. et al. The transcription regulator ATF4 is a mediator of skeletal muscle aging. GeroScience (2023). https://doi.org/10.1007/s11357-023-00772-y