The gene’s still selfish: Dawkins’ famous idea turns 40

By Jonathan Webb, Science reporter, BBC News

As The Selfish Gene notches up 40 years in print, BBC News asked Richard Dawkins whether his most famous book is relevant today (answer: yes), whether he has any regrets about public spats over religion (no), and whether he is quitting Twitter (sort of).

“I’d so much rather talk about this than about politics.”

This, from a thinker most famous as a fearless firebrand, sounds rather incongruous. But as Prof Dawkins hunches over his laptop to dig up examples of biomorphs – the computer-generated “creatures” he conceived in the 1980s to illustrate artificial selection – it is transparently, genuinely felt.

Later, we touch on the fact that he sees public debate as a scientist’s responsibility. Right now, he wants to talk about molluscs.

Pretend molluscs.

“I don’t know whether you know the classic book by D’Arcy Thompson, On Growth and Form? He showed that all mollusc shells are a tube, which is enlarging as it coils around. You only need three numbers to specify a mollusc shell.”

Those three numbers can be plotted inside a cube, Prof Dawkins explains. “Evolution is then just a walk through this cube of all possible shells.”

In a computerised game he wrote in 1996, people could construct their own such walk by choosing for themselves which offspring would “breed” in successive generations of shells.

This game has now been resurrected online to mark the 20th anniversary of the book it arose from, Climbing Mount Improbable.

Its mollusc shells are presented alongside an ancestral explanatory exercise: the biomorphs. These were first programmed 10 years earlier, when Dawkins wrote The Blind Watchmaker. He clearly remembers getting lost in the work.

“When I discovered that I could actually start getting something that looked like an insect, I got really obsessed with the idea of breeding insects.”

diagram of biomorphs

As the biomorphs grow from simple, branching stick-shrubs into more elaborate and occasionally familiar shapes, they make an important point – and one that is better grasped by being involved than by hearing it explained.

“You get much more of an idea of what it’s like to breed dogs from wolves, or to breed cauliflower from wild cabbage,” Prof Dawkins says, clearly enjoying the sight of the spindly shapes evolving again on his screen.

Like Darwin long before him, Dawkins settled on artificial selection – selective breeding for desirable characteristics, such as speed in race horses – to explain an important point about natural selection.

For Darwin, it was the idea that variations within a population, or herd, can persist and shape future generations if they are favoured by the breeder. If we humans can coax domestic dogs into their astounding variety of breeds then nature, with vastly more time at its disposal, can produce all the variety of life on Earth through a similar, slower selection process.

For Dawkins, the focus was the notion that has underpinned so much of his work: this process has no need for an architect. Slow, subtle preferences for one form over another will gradually produce complexity.

The Blind Watchmaker, many scientists and writers agree, was Prof Dawkins at his finest. His arguments are made with infectious enthusiasm and powerful imagery.

Ten years earlier again, Dawkins’ pioneering account of the “gene-centric” view of evolution, The Selfish Gene, also won huge acclaim.

It crystallised an argument that had been brewing since Watson and Crick’s beautiful DNA structure marked a new peak in our understanding of inheritance: these sequences would tend to accumulate and propagate mutations that were beneficial to the gene itself. Any given gene “wants” to be passed on to as many future offspring as possible.

Forty years on, however, this concept faces some opposition among today’s biologists.


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31 COMMENTS

  1. @OP – As the biomorphs grow from simple, branching stick-shrubs into more elaborate and occasionally familiar shapes, they make an important point – and one that is better grasped by being involved than by hearing it explained.

    These really are a nice graphical illustration of branching evolution providing material for selective processes.

  2. Interestingly in a similar vein:-

    http://www.bbc.co.uk/news/science-environment-36344155

    US engineer Frances Arnold has won the Millennium Technology Prize for pioneering “directed evolution”.

    By driving a sped-up version of natural selection in the lab, the method has created new enzymes for industrial catalysts, household detergents, and even to make rocket fuel from sugar.

    The €1m (£0.8m) prize is awarded biennially and Prof Arnold is the first female winner in its 12-year history.

    It recognises developments that “change people’s lives for the better”.

    The Technology Academy Finland, which presents the prize, said the deliberations began in November 2015 but that “there was only one outstanding candidate”.

    Prof Arnold, from the California Institute of Technology (Caltech), spoke to the BBC before travelling to Helsinki for Tuesday’s ceremony.

    She said the “basic concept” of using evolution to create better enzymes emerged from her laboratory more than 20 years ago.

    Evolution, to me, is the best designer of all time. And I figured out that this should be the algorithm for forward design, for making new biological code that is useful to humans,” Prof Arnold said.

    With her engineering background, Prof Arnold wanted to make new, useful, problem-solving proteins. So she took her cue from the way nature does the same thing.

    “I looked at it and said, well, nature didn’t actually design enzymes… How does this happen? You make mutations randomly, you look through a large number of things for the ones that have the properties you’re interested in, then you repeat the process.

    “And you iterate, accumulating beneficial changes over multiple generations – pretty much like we’ve done for cats, dogs, cows, chickens, you name it.”

    But instead of breeding animals, the directed evolution process works directly with small stretches of DNA and the proteins they encode.

  3. Thank you Penguin team for the effort to revive Mr. Dawkins’ programs. A few months ago I read about this project. It’s nice to finally be able to see it and to use it.

    I’m curious to know, if anyone has insight, if the program’s randomness between generations is arbitrary, by chance, or is it inherited within certain reappearing designs constraints? Let’s say a parent motif (A1a) has ten children with a gene pattern that has a potential mutation with a 20% chance of being inherited and a 10% chance of being expressed. If 9 of the children (A1a1, …, A1a9) appear like their parent (A1a), and one child (A1a10) inherits both the mutation and expression of it, will all of the offspring of A1a10 (A1a10A, . . ., A1a10J) inherit the randomness, with about half of the ten kids expressing the mutation, in the motif designs of Dawkins’ program?

    Perhaps the randomness is designed to be arbitrary? At each generational iteration does the program cause a possible change in the motif, and the human (artificially) selects the design to create more children, and the kids motif is again passed through a RND subroutine to decide if a mutation occurs in a gene segment? When I used the program, I created systematic child iterations of numbering 10, 6, 5, and 4 children, at each generation from each parent, while trying to select for motif lineages with the most stable patterns. I found few “stable” patterns that didn’t begin to mutate, again, after a few generations, but there were a few.

    (A1a1B42g3) is an example of the notation system that I created to help me when I began culturing bacteria in my microbiology class, to keep track of the lineage of a colony while trying to explore a bacteria’s characteristics, to observe colony similarities/differences over generations when grown in different environments. I may have reinvented the wheel, with my system, but the pretend example is to demonstrate 3 separate plates each containing a colony with a lineage that originated from an isolated colony A, A1 (first plate/child from a selected/isolated parent colony A), A1a (plate inoculated from first plate A1), A1a1 (plate/child from plate A1a), A1a1B (second of two plates/children of plate A1a1), A1a1B42 (the forty-second plate/child of A1a1B), etc. until a plate is market A1a1B42g3 which represents the third plate grown from the plate A1a1B42g. If a plate was marked with just a C, it would be the third plate/child from the original colony used to inoculate plate A, and might have been cultured in a refrigerator, and plate B might have been cultured at room temperature, etc. Most often my plates where marked just to an A4, A3b, or D6, but I knew I needed a system to help me see branches, tests, and age, so the pendulum between numbers and letters helped my human eye. If I had a colony that grew in five days, and I had several plates growing at room temp, and I looked over and observed several plates marked A, A1, A2, . . ., A3d, and another plate marked with just a D, I knew that D was as old A, so I could look at age related margin morphology, colony appearance, or maybe try similar tests (to A2d3) on an older colony sourced from D to see if age might have changed colony characteristic reactions to certain tests, etc.

    After four/eight weeks my colonies started doing strange things, but the semester ended my experiments and my assignment was merely to id one colony from a random source that I choose (aloe juice from the plant). I repeated the experiment twice, because I found only a single slow growing colony which finally appeared after nearly 4 or 6 days, and because I thought maybe the air contaminated my petri dish. Both experiments revealed the same results after testing the colony, sourced from two separate aloe plants. Be the colony from the lab’s poorly filtered air or the aloe, I believe I identified (S. caseolyticus); otherwise, for the exception of the one colony, the aloe juice had no colony growth employing aseptic nonfastidious methods.

  4. Edit for previous message #3:

    To count test plates with a letter exceeding 26 tests (petri dishes) I would have used multiple letters, by repeating a letter (e.g. A3zg2ZZB403).

  5. A decade ago I purposed an idea to some friends, to artificially obtain eggs and sperm from polar bears to be used to impregnate land bears (grizzly bears), in mass, numbering in the several thousand plus children along the coastal polar ridge line. The premise, that when the polar ice returns, in the who-knows future of hundreds/thousand of years, the land bears will be passing forward gene segments dispersed among their children that would someday make a polar bear. When the ice returns, the land bears expressing toes with webbing, the land bears with some white fur, the land bears with other characteristics needed for the unique environment of living on the Top of The World, will eventually breed children that will hopefully yield a polar bear, when the environment selects for the genes, assuming there are still seals and other animals for a polar bear to eat, presuming we haven’t driven these creatures to extinction while looking for oil, or just being human.

    My idea has its critics, as measured by the following quote: “I hate to say it, but from a genetic perspective, it’s quite likely grizzly bears will eat polar bears up, genetically,” said Andrew Derocher, a professor of biological studies at the University of Alberta . . . .” (1) However, the way I see it, Mr. Derocher’s comment is very good and welcome news in that, even without human intervention, the natural world will possibly facilitate a means for the polar bear genome to pass forward genetic information into the far future, assuming land bears can make a living, or avoid becoming a hunter’s trophy for being an uncommon mix breed.

    Cite:
    1 DeCourcey, D. (2016) The scary reason grizzly bears and polar bears are having sex now. Available at: http://www.attn.com/stories/8561/grizzly-bears-and-polar-bears-are-mating-due-to-climate-change?utm_source=facebook&utm_medium=post&utm_campaign=internal (Accessed: 25 May 2016).

  6. As most here know, there has been a debate over what is the “unit” of natural selection. Is it the gene, the organism (genome), the “group”, the population, or the species? I believe it is a mistake to attempt to pin down what exactly is the “unit” on which selection acts. It is far more complex than most evolutionists accept as the base.

    Natural selection seems to act on the individual organism, for it is the organism that survives and reproduces. Gene frequencies in populations continue, increase, or decrease depending how well the individual organisms can reproduce more of that gene. It may very well be gene complexes that increase or decrease such as the ability of face recognition or height of the organism. In addition, gene frequency in populations are important with respect to which population with its particular adaptations survive and reproduce to changing environmental factors (biotic and abiotic).

    It seems to me that selection acts simultaneously in all levels (genes, gene complexes, individuals, population, or species), not merely one level.

  7. My daughter and I are going to the Intelligence Squared debate at Central Hall, Westminster, on July 23, and I hope to finally get Richard to sign my copy of The Extended Phenotype.

    Oh, now I feel really soppy; I’ve become a Dawkins groupie.

  8. I’ve heard Prof. Dawkins comment that perhaps the title “The Selfish Gene” was something of a mistake, because it seems to induce some people to think the book is about a “gene for selfishness” or, or suggesting that selfishness is a good idea.
    I propose that future editions of the book be called “On the Origin of Family Values by Means of Natural Selection” — because, well, that’s what the book is mostly about — that is, how natural selection produces altruistic behavior, especially toward one’s own family (those that share your genome). Also, it honors Darwin, as well as gently thumbing its nose at the religious right.

  9. Russ H. #8
    May 25, 2016 at 5:31 pm

    I’ve heard Prof. Dawkins comment that perhaps the title “The Selfish Gene” was something of a mistake, because it seems to induce some people to think the book is about a “gene for selfishness” or, or suggesting that selfishness is a good idea.

    The notion that it suggests “that selfishness is a good idea”, is nonsense which is put about by theists who have read no further than the title.

    The theme of the book IS that genes (not people) act selfishly, and may well cause considerable suffering to the organisms they inhabit.

    I propose that future editions of the book be called “On the Origin of Family Values by Means of Natural Selection” — because, well, that’s what the book is mostly about —

    That would be a mistaken view.

    that is, how natural selection produces altruistic behavior, especially toward one’s own family (those that share your genome)

    Reciprocal altruism and Kin Selection, are only covered in a minority of chapters.

  10. “Selfish”, might be a gesture of creative liberty to explain the DNA’s axioms of chemistry and physics, or what I call chemistry and physics. For folks who don’t want to study, I offer an idea I call Chemical Intelligence, that is if I can get my project off the ground. If Dawkins can say “selfish” for the random process of chemistry (inferring higher trophic effects) then I can say “chemical intelligence.”

    PBS is currently broadcasting a new show called Genius By Stephen Hawking. It’s on my teletube as I type, and I’m wondering why he doesn’t play around with his voice’s timbre, made by his machine. He could be old or young, male or female, or create a new timbre to play around with his machine.

    The show is asking the question, “why are we here?” If his show was broadcast on any other channel, I would say we are here to share 18 minutes of advertising commercials. I am utilizing my freewill to watch it, because I have many other possible channels to tune into, and I could have been born somewhere else on the planet, and in time, where censorship was the norm, where my high school records would be in an office, along with every other published paper, phone book, and little bit of info next to a copy of David Bowie’s Heroes album prior to the fall of the Berlin Wall.

  11. Jeremy #10
    May 25, 2016 at 9:49 pm

    “Selfish”, might be a gesture of creative liberty to explain the DNA’s axioms of chemistry and physics, or what I call chemistry and physics.

    If Dawkins can say “selfish” for the random process of chemistry

    “Selfish” is referring to the interests of replicating particular genes and copies of those genes – often at the the expense of the individual creatures hosting them. – This is not random.

    Examples of this would be when large numbers of related offspring are sacrificed to swamp predators (as with turtle hatchlings), so that a small number of their siblings containing identical genes, can survive to reproduce.

    Another example would be non-breeding worker ants or soldier ants, being sacrificed to promote and defend the genes they share with their queen.

    Selection acts in the “selfish” interests of the genes (or identical copies of them), not the individual organism.

  12. Alan4discussion,

    At some point in the future I will sit down to read Mr. Dawkins’ books. If I had read The Selfish Gene I would be able to more accurately reference it. Until such a time I will have to rely on what remains of my education and imagination, to say what I am trying to express. [A car accident sort of turned my brain into an etch a sketch, and shook it up shortly after I received a college degree, for drawing patterns, so to speak. Aside, two weeks after the crash I was fascinated to observe my brain’s attempt to repair itself, including what appeared to be the re-experiencing of my emotional history, beginning with my earliest adolescent memories and progressing on speed-dial to my adult self. I considered that the physical trauma may have biologically invoked strong familial emotional memories, to seek out family members for safety, protection, healing, comfort, a hug, etc. While it seems I need to relearn a great deal of academic material, I’m delightfully surprised that my imagination seems okay, and I wonder . . . am I lucky (the related part of the brain wasn’t hurt) or is the imagination’s complex located in a more stable/robust/primitive part of the brain? I may not be able to repair the structural damage from mild TBI, but I can sit down and reread books, and I can try to enhance the growth of new neurons with diet, exercise, and periodic fasting, all the while hopefully removing possible TAU proteins loitering about.]

    Alan4discussion writes, ““Selfish” is referring to the interests of replicating particular genes and copies of those genes – often at the the expense of the individual creatures hosting them. – This is not random.” My use of the word ‘random’ was to convey that the process, as a single example, of the construction of an organic molecule, such as ethanol (C2H60), did derive its parts somewhere, at sometime, using various atoms to form the molecule under the right environmental/physical conditions, which for me involves random events in the right environment, inferring multiples sources could yield the same molecule. Even on the biological level of a functioning eukaryotic gene, that has an expected/modeled behavior, I think there is still room for a random event to alter the chemical structure of the gene (not saying it will be beneficial or harmful, although mutations usually kill the organism), a change that may have downstream implications for the larger organism.

    However, I think I understand what you are trying to say regarding the nonrandom aspect of a gene, that there is modeled evidence of behavior that peer review has vetted as being ordered and predictable within a living system (animal) and its food web. Even so, the thriving spider, turtle, or other R species may have been the “gene bank” that was in a “Goldilocks zone” (of a predator, pray, resource model). The same specie that failed to reproduce enough offspring, or too many (destroying their vital resources), would not be around to pass forward their genes. I presume a trend would appear that R species in a functioning ecosystem would have familiar parent child ratios, patterns emerge as predictable outcomes, and true randomness is displaced with understood relationships that xth percentage of the eggs will grow to adulthood and continue to propagate.

    There is still room for random events in a gene. Sunburn would be an example of randomness altering a chromosome, when two nucleotides form a thymine dimer, or maybe a free radical spooks a histone tail to think its been methylated causing an epigenetic change, increasing or decreasing the expression of a gene with many potential protein pathways? Bugs eating a plant growing adjacent to a toxic source, or a radio active source, may have a normal life span that is too short for the bioaccumulation of the toxic substance to negatively alter its bodily functions, but when these bugs are eaten by a lizard, bird, or mammal (that lives many decades) the creature might have gene/reproductive problems later in life due to abnormal mutations caused by the toxic substance. Maybe, one random day of many thousands of years, the bioaccumulation of toxins causes one of these mutations to fuse two chromosomes together, or maybe it alters a heritable epigenetic pattern that causes the child to develop a slightly longer fibula or shorter hair, which inadvertently creates a beneficial attribute (without changing actual DNA), because the gene to control the bone’s/hair’s development was altered by changes in a histone boundary?

    Regarding bioaccumulation, I would think that the common hot spots would be on the bottom of the ocean, near thermal vents, where microbial life and other benthic organisms would support an ecosystem that included creatures that can swim around, animals that could get swept up to the surface during upwelling events when atmospheric weather trends are favorable? Surface creatures would likely try to feed upon these bottom dwelling creatures, accumulating possible toxins derived from an ocean vent ecosystem. This thought experiment,of animals from ocean hot spots moving toxins to a new food web, would favorably facilitate billions of iterations over time, so if a mutation has a 1 in 1,000,000,000 chance of occurring, there is the statistical situation that what may have been a random event on day one, is now a certainty and not so random after a billion cycles.

    A long time ago I read a curious comment from a person writing about the potential benefits of schizophrenia. The imagined thought experiment noted that on an island, or coastal region by the ocean, that was populated with a civilization that was the home of a schizophrenic person who was scared of dark clouds, or animals acting weird, who would react in what is considered to be an irrational paranoid manner, freaking out by running away into the hills, would be a person who might survive a hurricane, or tidal wave caused by an earth quake, when the rest of the community hunkered down along the coast only to be wiped out by a giant wave.

    Stafford Gordon is currently reading Watson’s book about DNA. There is a chapter in it (#4) that discusses a problem that nearly shut down research, regarding recombinant DNA experiments, with legislation that was based upon unscientific assumptions held by legislators and the common public. A big issue was that the public didn’t understand the scientist’s work, a vast gap existed in knowledge between a majority and a very small minority of people. My Chemical Intelligence model is an intellectual idea, for an “immune response”, to attempt to counter the Intelligent Design movement, to fix a growing gap in knowledge. Currently, in my country, a “successful” (persistent with some measure of influence) campaign has chipped away at the science curriculum of various states, where legislators/administrators seem more apt at passing laws with religious undertones. [Bathroom break anyone?] These folks are voted into office by the public. Assuming I publish someday, the wishful thinking is that the Intelligent Design network will inflame, like your jellyfish sting, using the word intelligent as a pivot point to attract readers who are repulsed by latin or titles with science terms. I’m not short of ambitious ideas, and many bounce around my brain while I wash dishes, or whatever I do for work.

    The model has been abstracted to explore systems (bound by chemistry and physics) that pass information forward, big or small, organic or inorganic, and not necessarily alive or conscious, but the organic systems should be easily audited with the same statistical stuff. Lots of folks are trying to model the same stuff, so it’s nothing too special. The passing of info forward is the “intelligence” of my model’s system, even if it happens on the nanoscale with waves. Atheists, Secularists, Naturalists, and cold Diests should be able to agree on the model as being built upon sound science, because it doesn’t purport to explain the supernatural or afterlife; although, there will be arguments . . . .

  13. I recently read a book with a somewhat pointed title:

    The Unselfish Genome- How Darwin & Dawkins Missed The 2nd Half Of The Theory Of Evolution:

    I found the arguments in this book quite compelling. His main argument is that the selfish gene misses the top down analysis because it concentrates on the bottom up approach that the gene is everything.

    An analogy might be that if one concentrated only on the actions of electrons that one might miss all the higher level emergent ideas of electrical engineering. If Einstein could ask what one would see if one were riding along side a beam of light, I wondered what an electron would think was going on when every 60th of a second it got pushed left and right inside a wire because of Tesla’s AC system.

    In the above referenced book, by Jeff T. Bowles, he maintains that certain evolutionary history cannot be explained by concentrating solely on individual genes. Aging and sexual reproduction (vs. cloning, for example) are explained as “species evolution” that can only benefit the species as a whole – which seems at odds with Dawkins Selfish Gene theory. Perhaps as the title suggests, both approaches are required for a complete understanding of evolution.

  14. rocket888 #13
    May 26, 2016 at 5:49 pm

    In the above referenced book, by Jeff T. Bowles, he maintains that certain evolutionary history cannot be explained by concentrating solely on individual genes.

    In most forms of complex science, single issues rarely explain the overall picture. Single genes are linked on chromosomes, so selection acts on groups of genes.

    Aging

    Ageing is controlled by telomeres, so is very much related to strings of genes in chromosomes.

    and sexual reproduction (vs. cloning, for example) are explained as “species evolution” that can only benefit the species as a whole – which seems at odds with Dawkins Selfish Gene theory.

    Not really! Cloning or asexual reproduction multiplies the number of individuals, so there are higher survival rates when sexual reproduction is later resumed. – Otherwise asexual reproduction becomes a dead-end heading for extinction.

  15. Alan4discussion, or anyone, please feel free to critique my ideas and writing. I was hoping weak arguments and ideas would be challenged.

  16. Jeremy #5
    May 25, 2016 at 1:21 am

    A decade ago I purposed an idea to some friends, to artificially obtain eggs and sperm from polar bears to be used to impregnate land bears (grizzly bears),

    I see there is a related news item here.

    http://www.bbc.co.uk/news/science-environment-36381785

    A possible grizzly-polar bear hybrid has been shot by a hunter in northern Canada.

    Scientists will have to wait on DNA tests to determine whether it is one of the rare crosses.

    The two bears generally inhabit different ecological niches. But some experts suggest climate change and melting Arctic ice could increasingly bring them into contact.

    The possible hybrid is said to possess physical features of both species.

    The animal was shot by 25-year-old hunter Didji Ishalook in Nunavut, the country’s biggest and northernmost territory.

    “I think it’s 99% sure that it’s going to turn out to be a hybrid,” Ian Stirling, an emeritus research scientist with Environment Canada, told the Toronto Star newspaper.

    Hybrids are known either as a grolar or a pizzly, depending on whether the father is a grizzly or polar bear.

    The finds have to be confirmed through genetic tests and are so rare that only a handful have been confirmed in the last decade.

    Prof Andrew Derocher, from the University of Alberta, said that the bear did not appear to be an albino grizzly. But its claws appear to be longer and more “grizzly-like” than other hybrids that have been caught and examined.

    “We haven’t done the genetics on this and, until we do, we won’t really be able to say anything conclusively,” he told the Toronto Star.

  17. to Alan4discussion

    “Ageing is controlled by telomeres, so is very much related to strings of genes in chromosomes.”

    I think these are now thought to be only one of many things that cause aging.

    Bowles main argument is that it is the pressure from predators that drives programmed death (aging) and led to the evolution of sexual reproduction. If one were to simply clone all the time, then any predator that evolved a new ploy against a cloning prey would likely wipe out that species. Aging is similar, and he provides examples where the longer lived species tend to have the least problem with predators. If you age long, or clone, you will not be as able to make the quick evolutionary changes needed to keep up in the evolutionary arms race.

    The book is highly interesting, and can be had for $3 as a kindle read. Obviously, I can’t summarize all this book contains in a short paragraph or two.

  18. rocket888 #19
    May 28, 2016 at 3:03 pm

    to Alan4discussion

    “Ageing is controlled by telomeres, so is very much related to strings of genes in chromosomes.”

    I think these are now thought to be only one of many things that cause aging.

    Bowles main argument is that it is the pressure from predators that drives programmed death

    Predators have the effect of removing competition from the weak and old which are past reproducing, (hence liberating more resources for more active individuals), but it is the degeneration with age which makes these individuals vulnerable to predation.

    (aging) and led to the evolution of sexual reproduction.

    Prior to sexual reproduction, variation was dependent on horizontal gene exchange – as exists in bacteria. Sexual reproduction allows greater grouping of more competitive genetic material in superior individuals, which then go on to reproduce more better adapted offspring.

    If one were to simply clone all the time, then any predator that evolved a new ploy against a cloning prey would likely wipe out that species.

    That is so, but usually cloned asexual reproduction (as with eg. budding coral polyps or offsetting plants), alternates with sexual reproduction to maintain mobility and adaptability.

  19. Regarding Telomeres, I’ve often wondered about diet and its apparent relationship with the increased longevity of a mouse – living on a reduced calorie intake. Is it feasible that a reduced calorie intake causes the cell (organ and body) expresses genes to slow down its metabolism to conserve energy expired to repair and maintain homeostasis, and in doing so causing the cell to replicate at a much slower to rate which would delay cell senescence? Microarray would illuminate an answer.

    How does a smoker – a pack of cigarettes a day who quits after a decade of smoking – get cancer twenty years later at a higher rate of occurrence? Does anyone know if daily exposure to smoke (carbon) increase the cell’s frequency rate of division in the lung alveoli, to replace damaged/diseased cells that apoptosis? If so, an otherwise healthy older adult would have lung tissue with a percentage of cells quickly approaching cell senescence, increasing the likelihood of late age telomere malfunctions, and maybe someone could package an aerosol inhaler with a substance to promote telomere repair on the existing/healthy cells?

    Dawkins asserts that evolution isn’t random. By this measure is he confining his analysis to a list of axioms (constrained by organic chemistry, probability and statistics, and favorable environmental conditions)? I have the Selfish Gene on my to read list, but I was hoping someone familiar with his ideas would try to help me to better understand his work. My current understanding of evolution is that it is, and isn’t, a random process. I guess it depends upon how a person looks at the phenomenon. For example, an organic molecule may have an affinity for another atom or molecule, but the “oxygen” atom used to fill an orbital structure could be any of many thousands available in the environment. Picking one oxygen atom apart from thousands available seems to me to be a random event because the chemical affinity isn’t thinking, “I want that atom way over there because I exclusively choose it apart from the others so I will wait for it to pass by one of these days”, but rather the molecule is going to grab the closest one (which seems random to me) at the speed of chemistry to stabilize its orbital structure; however, someone else might say, “there is nothing random about the formation of a liposome from phospholipids in water” which means we’ve skipped conversation about planet destroying phenomenon that narrowly miss the planet based upon random interstellar flight paths, or a chat about if a tide/current/weather system is necessary to advance evolutionary development, or if the Earth woke up one day and decided to move to a new spot to appear just as it is, where it is, based upon a nonrandom thought, “this is a good place to be a planet.”

    If a hundred ants are upon the ground in a pack feeding on some sugar, and a hiker with boots walks on top of the ants, a majority of ants will be crushed, but the ones that are alive will “thank God” for being alive, save the ant that read The God Delusion. Statistically it’s probable that some ants would survive due to the tread of the hiker’s boot, but the ants that survived are a random selection of their group. Is this scenario a random event or a nonrandom event, as far as which ants live?

    Chiasma, is it, or is it not, a random process of “deciding” which corn kernels get their color, when compared to another ear of corn?

  20. To Jeremy #21:

    Dawkins asserts that evolution isn’t random.

    No matter who made such a comment, it is a generalization that is only partially correct. There are two basic processes in evolutionary biology: (1) mutations that are random and (2) natural selection, a NON-random process.

    Chiasma, is it, or is it not, a random process of “deciding” which
    corn kernels get their color, when compared to another ear of corn?

    I could be wrong about this, but it appears that you confuse “nonrandom” with “purposeful behavior”, a theological concept. Natural selection is nonrandom, but there is nothing about natural selection that is teleological.

  21. cbrown @ #22,

    Thanks (Ta).

    When various scientists in various fields muse on the topic of evolution, is there an etiquette or formality that is agreed upon between the various individuals (a physicist, a geologist, a biologist, etc.), to understand where their ideas are originating based upon their field of study and the trophic level of selection (planetary, geological, atomic, chemical, organic chm, RNA, peptide, protein, cell, organ, body, intra/inter specie, etc)? For example, in film and motion picture, many decades passed before critics helped to develop a “language” to study/analyze film. Film critics critical of other critic’s critiques helped to improve the art of their craft, yet before this could occur a large body of work, over time, needed to be developed to study.

    Nothing theological about my origin of inquiry. Aside, when I work on my rough draft, in my mind, to develop a computer program to simulate an atom-to-body evolutionary scenario . . . from waves, to wind, to which atoms bind at what orbital frequency, let alone the chance of success if a cat tries to catch a mouse, in addition to creating a topological environment with soil horizon layers, etc. there are just tons of RND function calls, so I was thinking of using idle CPU time to pile onto a stack a list of RND outputs to be piped to the simulator when needed. I have some other strategies that are beyond my chat here. While there is order to the chaos, there is quite a bit of probability and statistics and nonrandom randomness involved with my project.

    I’m currently acclimating to an injury from an auto accident many months ago. In the very near future I hope to be much more involved in the pursuit of old activities, so I won’t be quite as active on the web as I have been over the last few months. Here, and elsewhere, I have spent my recovery time surfing the web, typing, reading, mousing radio buttons, cursing ads and anything that slows down my PC. I would like to thank the folks at RDF who replied and responded to my various posted comments. You helped me to pass the time, taking my mind away from my problems, during a difficult period. I had hoped for a bit more criticism of my evolutionary model. I made a small mistake with the essay, minor, but, still, I think I boiled that sap to a grade B quality, which is now called Dark with Robust Taste. It’s my favorite regardless what they call it. Note, I didn’t mention any factors/formula that affect the various radii, so you’ll have to invent your own.

  22. @jeremy #23

    You’ll probably appreciate this quote from John von Neumann:

    “Anyone who considers arithmetical methods of producing random digits is, of course, in a state of sin.”

    As for accumulating a pool of (pseudo) random values, I think /dev/random on unix/linux systems does just that. It’s a common enough technique, along with frequent background re-seeding of the PRNG (Pseudo-Random-Number-Generator) from some unpredictable source.

    In Simulations, you often need a repeatable PRNG stream (so you can debug/replay stuff), in which case your list of RND outputs could be pre-recorded once and replayed as desired. It’s not hard to store 500Mb these days, that’ll give plenty of answers to your program’s RND calls.

    Or use the same PRNG each time starting with the same predefined seed value, for repeatability without limit.

  23. oHooligan @ #24,

    Didn’t consider the debug issue, and mapping PRNG, thanks! I appreciate the info about RND info for Linux, and the quote too.

    How difficult would it be to build a tiny integrated circuit item with let’s say, a gas atom bouncing around, or groups of atoms, to close a circuit in a container with surface area (multiple potential open circuits) that will generate output in real-time to create a pool of RND seeds in buffer, and would this be random? Perhaps a dual device alternating between each per clock tic, one system opens a circuit that “reads” where the molecules are bound, while the other system is releasing the molecules which rebind before the next tic? I would think the movement of an atom would, maybe, be random?

  24. @Jeremy #25

    You’re on the right track seeking physical, non-digital, phenomena as your source of random numbers. The simplest suggestion I recall was to sample noise from an AM radio tuned between stations, capture the digitised stream to use as seed data for a reputable PRNG. A lot of real-world (analog) data has some degree of randomness (we use the term “entropy”), even if it’s not all entirely random. Scribble around with your mouse, and capture a few low-order bits from each sample, that’s another way. Log keystrokes, noting only the time interval (in milliseconds) between them, discard the high-order bits. Beware of the quantization of time caused by the system clock frequency or the underlying software libraries (that might buffer keystrokes, for example).

    I believe there are circuits that exploit the true randomness of radioactive decay.

    And one of the cheapest I’ve heard of involves a “noisy diode” before the a-to-d conversion. Unlike most electronic circuits, this time it’s the noise you want, not the signal.

    For Simulations (which is the field you described), the important aspect is that the “random” numbers appear to be random, for example having approximately 50% zero bits, and so on. There are extensive suites of software tests that can be applied to a data stream to tell you how “good” it is as a source of randomness, by detecting patterns of repetition at various scales. The godfather of all tests is a suite called “Diehard”, originally coded in FORTRAN but since ported. It does an awful lot of work that you have no need to rediscover.

    The other important use of random numbers is in cryptography, securing your data and communications. For this, the demands are higher, and “repeatability” is not a good thing. You’ll find Cryptographically Secure Pseudo Random Number Generators (CSPRNG) in various software packages, such as Java. These all, of course, need seeding from that all too precious resource, an “entropy pool”, or reservoir of True Random Data captured from some external non-digital source.

    A good, inexpensive, source of large volumes of genuinely random digits is a kind of Holy Grail for cryptography.

  25. OHooligan @ #26,

    You may get a chuckle out of the following little story. I forgot about it until I read your reply. Around 1981 my very first computer program (technically) was a step by step process to code a BASIC program, from a text conveying a lesson plan. My first original home made computer program was a little program that printed random numbers sequentially on the screen, to see if I could observe repeated patterns. The Atari text book mentioned the limitations of a computer’s ability to make a random generated number, that it would eventually repeat, so I made a tiny program to try to observe it. After a few seconds of watching numbers zip past the monitor’s screen, at a blinding speed, my eleven year old brain decided the program was not working like I wanted it too, so I went skate boarding.

    I can envision a future software label saying, “This program requires interstellar AM static to function.”

    Thanks for the thoughtful reply. I learned a few new things today.

  26. Digital “random noise” repeats eventually and identical generators clocked in step produce identical outputs. They are quasi random generators. Their principle is that of a long chain shift register multiply tapped towards its end these taps logicced together eg via an AND function and fed back to the SR input.

    There are various analogue noise generator mechanisms that are available in electronics. Thermal (Johnson) and avalanche noise these are both stochastic, and zener noise which is a quantum tunneling noise and is truly random.

    Stochastic noise is determinist noise (to link OHooligan back to free will). Each event is caused by a previous one, but in a sufficient number of instances in the “avalanche” case, two events (the release of a charge carrier) are caused by the same particle, generating a runaway cascade. Johnson noise is identical to gas in a container. Because it is thermal in origin it tells us it is phonons bumping into each other in a solid.

    Zener effect is a true quantum based effect when an electron escapes a barrier potential that in numerical terms is too high for it to cross. As the barrier is lowered when the diode is increasingly reverse biased the electrons at some point are able to probabalistically tunnel through the remaining barrier to freedom and contribute to current in the biasing circuit.

    Though called zener diodes, above a 5.1 volt diode rating these are increasingly avalanche effect diodes with a stochastic determinist mechanism creating a noisy current flow.

    Below 5.1 volts the effect is rather more a genuine zener effect and the noise is truly (officially!) random. i.e. a bigger fraction of the total bias current.

    You can tell the mechanisms are different above and below 5.1 volts. Each mechanism (avalanche and tunneling) has a different signed temperature coefficient (avalanche is positive, zener is negative.) . When the mechanisms equally contribute to the breakdown current (for nominal 5.1 and 5.6V devices) these diodes have zero temperature coefficients.

    No-one can distinguish the difference between the stochastic, avalanche breakdown noise and the true random noise of quantum tunneling.

  27. It occurred to me last night, when I should have been sleeping, that biomorphs – the computer-generated ones could also be a model for the development of religion. I could picture human thoughts as the biomorphs, with our distant ancestors having little thoughts about “Why” and sharing those thoughts. Those biomorph thoughts bounce around inside the tribe (s) and prosper or fall. The ones that prosper go through the same process again and then surviving biomorph thoughts become the prevailing wisdom.

    I think it is happening today. Religion is still evolving, branching, going extinct, renewing itself, just like the biomorphs. Maybe we are just a simulation in some kids computer in a galaxy far, far away.

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