Gene-centered view of evolution

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The gene-centered view of evolution, gene's eye view, gene selection theory, or selfish gene theory holds that adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation, with gene defined as "not just one single physical bit of DNA [but] all replicas of a particular bit of DNA distributed throughout the world". The proponents of this viewpoint argue that, since heritable information is passed from generation to generation almost exclusively by DNA, natural selection and evolution are best considered from the perspective of genes.

Proponents of the gene-centered viewpoint argue that it permits understanding of diverse phenomena such as altruism and intragenomic conflict that are otherwise difficult to explain from an organism-centered viewpoint.

The gene-centered view of evolution is a synthesis of the theory of evolution by natural selection, the particulate inheritance theory, and the non-transmission of acquired characters. It states that those alleles whose phenotypic effects successfully promote their own propagation will be favorably selected relative to their competitor alleles within the population. This process produces adaptations for the benefit of alleles that promote the reproductive success of the organism, or of other organisms containing the same allele (kin altruism and green-beard effects), or even its own propagation relative to the other genes within the same organism (selfish genes and intragenomic conflict).

The gene-centered perspective can be traced to the philosopher Henri Bergson who wrote:

Life is like a current passing from germ to germ through the medium of a developed organism. It is as if the organism itself were only an excrescence, a bud caused to sprout by the former endeavouring to continue itself in a new germ.

— Creative Evolution (1907)

Overview

John Maynard Smith

 

Richard Dawkins

The gene-centered view of evolution is a model for the evolution of social characteristics such as selfishness and altruism.

Acquired characteristics

The formulation of the central dogma of molecular biology was summarized by Maynard Smith:

If the central dogma is true, and if it is also true that nucleic acids are the only means whereby information is transmitted between generations, this has crucial implications for evolution. It would imply that all evolutionary novelty requires changes in nucleic acids, and that these changes – mutations – are essentially accidental and non-adaptive in nature. Changes elsewhere – in the egg cytoplasm, in materials transmitted through the placenta, in the mother's milk – might alter the development of the child, but, unless the changes were in nucleic acids, they would have no long-term evolutionary effects.

— Maynard Smith

The rejection of the inheritance of acquired characters, combined with Ronald Fisher the statistician, giving the subject a mathematical footing, and showing how Mendelian genetics was compatible with natural selection in his 1930 book The Genetical Theory of Natural Selection. J. B. S. Haldane, and Sewall Wright, paved the way to the formulation of the selfish-gene theory.^{[clarification needed]} For cases where environment can influence heredity, see epigenetics.

The gene as the unit of selection

The view of the gene as the unit of selection was developed mainly in the works of Richard Dawkins, W. D. Hamilton, Colin Pittendrigh and George C. Williams. It was mainly popularized and expanded by Dawkins in his book The Selfish Gene (1976).

According to Williams' 1966 book Adaptation and Natural Selection,

[t]he essence of the genetical theory of natural selection is a statistical bias in the relative rates of survival of alternatives (genes, individuals, etc.). The effectiveness of such bias in producing adaptation is contingent on the maintenance of certain quantitative relationships among the operative factors. One necessary condition is that the selected entity must have a high degree of permanence and a low rate of endogenous change, relative to the degree of bias (differences in selection coefficients).

— Williams, 1966

Williams argued that "[t]he natural selection of phenotypes cannot in itself produce cumulative change, because phenotypes are extremely temporary manifestations." Each phenotype is the unique product of the interaction between genome and environment. It does not matter how fit and fertile a phenotype is, it will eventually be destroyed and will never be duplicated. 

Since 1954, it has been known that DNA is the main physical substrate to genetic information, and it is capable of high-fidelity replication through many generations. So, a particular gene coded in a nucleobase sequence of a lineage of replicated DNA molecules can have a high permanence and a low rate of endogenous change.

In normal sexual reproduction, an entire genome is the unique combination of father's and mother's chromosomes produced at the moment of fertilization. It is generally destroyed with its organism, because "meiosis and recombination destroy genotypes as surely as death." Only half of it is transmitted to each descendant due to independent segregation. 

And the high prevalence of horizontal gene transfer in bacteria and archaea means that genomic combinations of these asexually reproducing groups are also transient in evolutionary time: "The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force."

The gene as an informational entity persists for an evolutionarily significant span of time through a lineage of many physical copies.

In his book River out of Eden, Dawkins coins the phrase God's utility function to explain his view on genes as units of selection. He uses this phrase as a synonym of the "meaning of life" or the "purpose of life". By rephrasing the word purpose in terms of what economists call a utility function, meaning "that which is maximized", Dawkins attempts to reverse-engineer the purpose in the mind of the Divine Engineer of Nature, or the utility function of god. Finally, Dawkins argues that it is a mistake to assume that an ecosystem or a species as a whole exists for a purpose. He writes that it is incorrect to suppose that individual organisms lead a meaningful life either; in nature, only genes have a utility function – to perpetuate their own existence with indifference to great sufferings inflicted upon the organisms they build, exploit and discard. 

Organisms as vehicles

Genes are usually packed together inside a genome, which is itself contained inside an organism. Genes group together into genomes because "genetic replication makes use of energy and substrates that are supplied by the metabolic economy in much greater quantities than would be possible without a genetic division of labour." They build vehicles to promote their mutual interests of jumping into the next generation of vehicles. As Dawkins puts it, organisms are the "survival machines" of genes.

The phenotypic effect of a particular gene is contingent on its environment, including the fellow genes constituting with it the total genome. A gene never has a fixed effect, so how is it possible to speak of a gene for long legs? It is because of the phenotypic differences between alleles. One may say that one allele, all other things being equal or varying within certain limits, causes greater legs than its alternative. This difference enables the scrutiny of natural selection.

"A gene can have multiple phenotypic effects, each of which may be of positive, negative or neutral value. It is the net selective value of a gene's phenotypic effect that determines the fate of the gene." For instance, a gene can cause its bearer to have greater reproductive success at a young age, but also cause a greater likelihood of death at a later age. If the benefit outweighs the harm, averaged out over the individuals and environments in which the gene happens to occur, then phenotypes containing the gene will generally be positively selected and thus the abundance of that gene in the population will increase.

Even so, it becomes necessary to model the genes in combination with their vehicle as well as in combination with the vehicle's environment.

Selfish-gene theory

The selfish-gene theory of natural selection can be restated as follows:

Genes do not present themselves naked to the scrutiny of natural selection, instead they present their phenotypic effects. [...] Differences in genes give rise to differences in these phenotypic effects. Natural selection acts on the phenotypic differences and thereby on genes. Thus genes come to be represented in successive generations in proportion to the selective value of their phenotypic effects.

— Cronin, 1991

The result is that "the prevalent genes in a sexual population must be those that, as a mean condition, through a large number of genotypes in a large number of situations, have had the most favourable phenotypic effects for their own replication." In other words, we expect selfish genes ("selfish" meaning that it promotes its own survival without necessarily promoting the survival of the organism, group or even species). This theory implies that adaptations are the phenotypic effects of genes to maximize their representation in future generations. An adaptation is maintained by selection if it promotes genetic survival directly, or else some subordinate goal that ultimately contributes to successful reproduction. 

Individual altruism and genetic egoism

The gene is a unit of hereditary information that exists in many physical copies in the world, and which particular physical copy will be replicated and originate new copies does not matter from the gene's point of view. A selfish gene could be favored by selection by producing altruism among organisms containing it. The idea is summarized as follows:

If a gene copy confers a benefit B on another vehicle at cost C to its own vehicle, its costly action is strategically beneficial if pB > C, where p is the probability that a copy of the gene is present in the vehicle that benefits. Actions with substantial costs therefore require significant values of p. Two kinds of factors ensure high values of p: relatedness (kinship) and recognition (green beards).

— Haig, 1997

A gene in a somatic cell of an individual may forego replication to promote the transmission of its copies in the germ line cells. It ensures the high value of p = 1 due to their constant contact and their common origin from the zygote.

The kin selection theory predicts that a gene may promote the recognition of kinship by historical continuity: a mammalian mother learns to identify her own offspring in the act of giving birth; a male preferentially directs resources to the offspring of mothers with whom he has copulated; the other chicks in a nest are siblings; and so on. The expected altruism between kin is calibrated by the value of p, also known as the coefficient of relatedness. For instance, an individual has a p = 1/2 in relation to his brother, and p = 1/8 to his cousin, so we would expect, ceteris paribus, greater altruism among brothers than among cousins. In this vein, geneticist J. B. S. Haldane famously joked, "Would I lay down my life to save my brother? No, but I would to save two brothers or eight cousins." However, examining the human propensity for altruism, kin selection theory seems incapable of explaining cross-familiar, cross-racial and even cross-species acts of kindness.

Green-beard effect

Green-beard effects gained their name from a thought-experiment of Richard Dawkins, who considered the possibility of a gene that caused its possessors to develop a green beard and to be nice to other green-bearded individuals. Since then, "green-beard effect" has come to refer to forms of genetic self-recognition in which a gene in one individual might direct benefits to other individuals that possess the gene. Such genes would be especially selfish, benefiting themselves regardless of the fates of their vehicles. After Dawkins predicted them, green-beard genes have been discovered in nature, such as Gp-9 in fire ants (Solenopsis invicta), csA in social amoeba (Dictyostelium discoideum), and FLO1 in budding yeast (Saccharomyces cerevisiae).

Intragenomic conflict

As genes are capable of producing individual altruism, they are capable of producing conflict among genes inside the genome of one individual. This phenomenon is called intragenomic conflict and arises when one gene promotes its own replication in detriment to other genes in the genome. The classic example is segregation distorter genes that cheat during meiosis or gametogenesis and end up in more than half of the functional gametes. These genes can persist in a population even when their transmission results in reduced fertility. Egbert Leigh compared the genome to "a parliament of genes: each acts in its own self-interest, but if its acts hurt the others, they will combine together to suppress it" to explain the relative low occurrence of intragenomic conflict.

Price equation

The Price equation is a covariance equation that is a mathematical description of evolution and natural selection. The Price equation was derived by George R. Price, working in London to rederive W. D. Hamilton's work on kin selection. 

Advocates

Besides Richard Dawkins and George C. Williams, other biologists and philosophers have expanded and refined the selfish-gene theory, such as John Maynard Smith, George R. Price, Robert Trivers, David Haig, Helena Cronin, David Hull, Philip Kitcher, and Daniel C. Dennett.

Criticisms

The gene-centric view has been opposed by Ernst Mayr, Stephen Jay Gould, David Sloan Wilson, and philosopher Elliott Sober. An alternative, multilevel selection (MLS), has been advocated by E. O. Wilson, David Sloan Wilson, Sober, Richard E. Michod, and Samir Okasha.

Writing in the New York Review of Books, Gould has characterized the gene-centered perspective as confusing book-keeping with causality. Gould views selection as working on many levels, and has called attention to a hierarchical perspective of selection. Gould also called the claims of Selfish Gene "strict adaptationism", "ultra-Darwinism", and "Darwinian fundamentalism", describing them as excessively "reductionist". He saw the theory as leading to a simplistic "algorithmic" theory of evolution, or even to the re-introduction of a teleological principle. Mayr went so far as to say "Dawkins' basic theory of the gene being the object of evolution is totally non-Darwinian."

Gould also addressed the issue of selfish genes in his essay "Caring groups and selfish genes". Gould acknowledged that Dawkins was not imputing conscious action to genes, but simply using a shorthand metaphor commonly found in evolutionary writings. To Gould, the fatal flaw was that "no matter how much power Dawkins wishes to assign to genes, there is one thing that he cannot give them – direct visibility to natural selection." Rather, the unit of selection is the phenotype, not the genotype, because it is phenotypes that interact with the environment at the natural-selection interface. So, in Kim Sterelny's summation of Gould's view, "gene differences do not cause evolutionary changes in populations, they register those changes." Richard Dawkins replied to this criticism in a later book, The Extended Phenotype, that Gould confused particulate genetics with particulate embryology, stating that genes do "blend", as far as their effects on developing phenotypes are concerned, but that they do not blend as they replicate and recombine down the generations.

Since Gould's death in 2002, Niles Eldredge has continued with counter-arguments to gene-centered natural selection. Eldredge notes that in Dawkins' book A Devil's Chaplain, which was published just before Eldredge's book, "Richard Dawkins comments on what he sees as the main difference between his position and that of the late Stephen Jay Gould. He concludes that it is his own vision that genes play a causal role in evolution," while Gould (and Eldredge) "sees genes as passive recorders of what worked better than what."

Weasel program (from Dawkins' The Blind Watchmaker

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https://en.wikipedia.org/wiki/Weasel_program

 

The software's name takes itself from dialogue in Hamlet:
Hamlet: Do you see yonder cloud that's almost in shape of a camel?
Polonius: By the mass, and 'tis like a camel, indeed.
Hamlet: Methinks it is like a weasel.

The weasel program or Dawkins' weasel is a thought experiment and a variety of computer simulations illustrating it. Their aim is to demonstrate that the process that drives evolutionary systems—random variation combined with non-random cumulative selection—is different from pure chance.

The thought experiment was formulated by Richard Dawkins, and the first simulation written by him; various other implementations of the program have been written by others. 

Overview

In chapter 3 of his book The Blind Watchmaker, Dawkins gave the following introduction to the program, referencing the well-known infinite monkey theorem:

I don't know who it was first pointed out that, given enough time, a monkey bashing away at random on a typewriter could produce all the works of Shakespeare. The operative phrase is, of course, given enough time. Let us limit the task facing our monkey somewhat. Suppose that he has to produce, not the complete works of Shakespeare but just the short sentence 'Methinks it is like a weasel', and we shall make it relatively easy by giving him a typewriter with a restricted keyboard, one with just the 26 (capital) letters, and a space bar. How long will he take to write this one little sentence?

The scenario is staged to produce a string of gibberish letters, assuming that the selection of each letter in a sequence of 28 characters will be random. The number of possible combinations in this random sequence is 27²⁸, or about 10⁴⁰, so the probability that the monkey will produce a given sequence is extremely low. Any particular sequence of 28 characters could be selected as a "target" phrase, all equally as improbable as Dawkins's chosen target, "METHINKS IT IS LIKE A WEASEL". 

A computer program could be written to carry out the actions of Dawkins's hypothetical monkey, continuously generating combinations of 26 letters and spaces at high speed. Even at the rate of millions of combinations per second, it is unlikely, even given the entire lifetime of the universe to run, that the program would ever produce the phrase "METHINKS IT IS LIKE A WEASEL".

Dawkins intends this example to illustrate a common misunderstanding of evolutionary change, i.e. that DNA sequences or organic compounds such as proteins are the result of atoms randomly combining to form more complex structures. In these types of computations, any sequence of amino acids in a protein will be extraordinarily improbable (this is known as Hoyle's fallacy). Rather, evolution proceeds by hill climbing, as in adaptive landscapes.

Dawkins then goes on to show that a process of cumulative selection can take far fewer steps to reach any given target. In Dawkins's words:

We again use our computer monkey, but with a crucial difference in its program. It again begins by choosing a random sequence of 28 letters, just as before ... it duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL.

By repeating the procedure, a randomly generated sequence of 28 letters and spaces will be gradually changed each generation. The sequences progress through each generation:

Generation 01:   WDLTMNLT DTJBKWIRZREZLMQCO P 

Generation 02:   WDLTMNLT DTJBSWIRZREZLMQCO P

Generation 10:   MDLDMNLS ITJISWHRZREZ MECS P

Generation 20:   MELDINLS IT ISWPRKE Z WECSEL

Generation 30:   METHINGS IT ISWLIKE B WECSEL

Generation 40:   METHINKS IT IS LIKE I WEASEL

Generation 43:   METHINKS IT IS LIKE A WEASEL

Dawkins continues:

The exact time taken by the computer to reach the target doesn't matter. If you want to know, it completed the whole exercise for me, the first time, while I was out to lunch. It took about half an hour. (Computer enthusiasts may think this unduly slow. The reason is that the program was written in BASIC, a sort of computer baby-talk. When I rewrote it in Pascal, it took 11 seconds.) Computers are a bit faster at this kind of thing than monkeys, but the difference really isn't significant. What matters is the difference between the time taken by cumulative selection, and the time which the same computer, working flat out at the same rate, would take to reach the target phrase if it were forced to use the other procedure of single-step selection: about a million million million million million years. This is more than a million million million times as long as the universe has so far existed.

Implications for biology

The program aims to demonstrate that the preservation of small changes in an evolving string of characters (or genes) can produce meaningful combinations in a relatively short time as long as there is some mechanism to select cumulative changes, whether it is a person identifying which traits are desirable (in the case of artificial selection) or a criterion of survival ("fitness") imposed by the environment (in the case of natural selection). Reproducing systems tend to preserve traits across generations, because the offspring inherit a copy of the parent's traits. It is the differences between offspring, the variations in copying, which become the basis for selection, allowing phrases closer to the target to survive, and the remaining variants to "die."

Dawkins discusses the issue of the mechanism of selection with respect to his "biomorphs" program:

The human eye has an active role to play in the story. It is the selecting agent. It surveys the litter of progeny and chooses one for breeding. ...Our model, in other words, is strictly a model of artificial selection, not natural selection. The criterion for 'success' is not the direct criterion of survival, as it is in true natural selection. In true natural selection, if a body has what it takes to survive, its genes automatically survive because they are inside it. So the genes that survive tend to be, automatically, those genes that confer on bodies the qualities that assist them to survive.

Regarding the example's applicability to biological evolution, he is careful to point out that it has its limitations:

Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success.

A full run of a weasel program, with 100 offspring per generation, and a 5% mutation chance per character copied. Only the "fittest" string of each generation is shown. Note that, in generation 8, the 25th character, which had been correct (A), becomes incorrect (I). The program does not "lock" correct characters, rather it measures at each iteration the closeness of the complete string to the 'target' phrase.

 

More complex models

In The Blind Watchmaker, Dawkins goes on to provide a graphical model of gene selection involving entities he calls biomorphs. These are two-dimensional sets of line segments which bear relationships to each other, drawn under the control of "genes" that determine the appearance of the biomorph. By selecting entities from sequential generations of biomorphs, an experimenter can guide the evolution of the figures toward given shapes, such as "airplane" or "octopus" biomorphs. 

As a simulation, the biomorphs are not much closer to the actual genetic behavior of biological organisms. Like the Weasel program, their development is shaped by an external factor, in this case the decisions of the experimenter who chooses which of many possible shapes will go forward into the following generation. They do however serve to illustrate the concept of "genetic space," where each possible gene is treated as a dimension, and the actual genomes of living organisms make up a tiny fraction of all possible gene combinations, most of which will not produce a viable organism. As Dawkins puts it, "however many ways there may be of being alive, it is certain that there are vastly more ways of being dead". 

In Climbing Mount Improbable, Dawkins responded to the limitations of the Weasel program by describing programs, written by other parties, that modeled the evolution of the spider web. He suggested that these programs were more realistic models of the evolutionary process, since they had no predetermined goal other than coming up with a web that caught more flies through a "trial and error" process. Spiderwebs were seen as good topics for evolutionary modeling because they were simple examples of biosystems that were easily visualized; the modeling programs successfully generated a range of spider webs similar to those found in nature. 

Example algorithm

Although Dawkins did not provide the source code for his program, a "Weasel" style algorithm could run as follows.

1. Start with a random string of 28 characters.
2. Make 100 copies of the string (reproduce).
3. For each character in each of the 100 copies, with a probability of 5%, replace (mutate) the character with a new random character.
4. Compare each new string with the target string "METHINKS IT IS LIKE A WEASEL", and give each a score (the number of letters in the string that are correct and in the correct position).
5. If any of the new strings has a perfect score (28), halt. Otherwise, take the highest scoring string, and go to step 2.

For these purposes, a "character" is any uppercase letter, or a space. The number of copies per generation, and the chance of mutation per letter are not specified in Dawkins's book; 100 copies and a 5% mutation rate are examples. Correct letters are not "locked". Each correct letter may become incorrect in subsequent generations. The terms of the program and the existence of the target phrase do however mean that such 'negative mutations' will quickly be 'corrected'.

The Blind Watchmaker

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/The_Blind_Watchmaker

 

The Blind Watchmaker

First edition cover
Author	Richard Dawkins
Country	United Kingdom
Language	English
Subject	Evolutionary biology
Publisher	Norton & Company, Inc
Publication date	1986
Media type	Print
ISBN	0-393-31570-3
OCLC	35648431
Dewey Decimal	576.8/2 21
LC Class	QH366.2 .D37 1996
Preceded by	The Extended Phenotype
Followed by	River Out of Eden

The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design is a 1986 book by Richard Dawkins, in which the author presents an explanation of, and argument for, the theory of evolution by means of natural selection. He also presents arguments to refute certain criticisms made on his first book, The Selfish Gene. (Both books espouse the gene-centric view of evolution.) An unabridged audiobook edition was released in 2011, narrated by Richard Dawkins and Lalla Ward.

Overview

In his choice of the title for this book, Dawkins refers to the watchmaker analogy made famous by William Paley in his 1802 book Natural Theology. Paley, writing long before Charles Darwin published On the Origin of Species in 1859, held that the complexity of living organisms was evidence of the existence of a divine creator by drawing a parallel with the way in which the existence of a watch compels belief in an intelligent watchmaker. Dawkins, in contrasting the differences between human design and its potential for planning with the workings of natural selection, therefore dubbed evolutionary processes as analogous to a blind watchmaker.

To dispel the idea that complexity cannot arise without the intervention of a "creator", Dawkins uses the example of the eye. Beginning with a simple organism, capable only of distinguishing between light and dark, in only the crudest fashion, he takes the reader through a series of minor modifications, which build in sophistication until we arrive at the elegant and complex mammalian eye. In making this journey, he points to several creatures whose various seeing apparatus are, whilst still useful, living examples of intermediate levels of complexity.

In developing his argument that natural selection can explain the complex adaptations of organisms, Dawkins' first concern is to illustrate the difference between the potential for the development of complexity as a result of pure randomness, as opposed to that of randomness coupled with cumulative selection. He demonstrates this by the example of the weasel program. Dawkins then describes his experiences with a more sophisticated computer model of artificial selection implemented in a program also called The Blind Watchmaker, which was sold separately as a teaching aid.

The program displayed a two-dimensional shape (a "biomorph") made up of straight black lines, the length, position, and angle of which were defined by a simple set of rules and instructions (analogous to a genome). Adding new lines (or removing them) based on these rules offered a discrete set of possible new shapes (mutations), which were displayed on screen so that the user could choose between them. The chosen mutation would then be the basis for another generation of biomorph mutants to be chosen from, and so on. Thus, the user, by selection, could steer the evolution of biomorphs. This process often produced images which were reminiscent of real organisms for instance beetles, bats, or trees. Dawkins speculated that the unnatural selection role played by the user in this program could be replaced by a more natural agent if, for example, colourful biomorphs could be selected by butterflies or other insects, via a touch-sensitive display set up in a garden.

"Biomorph" that randomly evolves following changes of several numeric "genes", determining its shape. The gene values are given as bars on the top.

 

In an appendix to a later edition of the book (1996), Dawkins explains how his experiences with computer models led him to a greater appreciation of the role of embryological constraints on natural selection. In particular, he recognised that certain patterns of embryological development could lead to the success of a related group of species in filling varied ecological niches, though he emphasised that this should not be confused with group selection. He dubbed this insight the evolution of evolvability.

After arguing that evolution is capable of explaining the origin of complexity, near the end of the book Dawkins uses this to argue against the existence of God: "a deity capable of engineering all the organized complexity in the world, either instantaneously or by guiding evolution ... must already have been vastly complex in the first place ..." He calls this "postulating organized complexity without offering an explanation."

In the preface, Dawkins states that he wrote the book "to persuade the reader, not just that the Darwinian world-view happens to be true, but that it is the only known theory that could, in principle, solve the mystery of our existence."

Reception

Tim Radford, writing in The Guardian, noted that despite Dawkins's "combative secular humanism", he had written "a patient, often beautiful book from 1986 that begins in a generous mood and sustains its generosity to the end." 30 years on, people still read the book, Radford argues, because it is "one of the best books ever to address, patiently and persuasively, the question that has baffled bishops and disconcerted dissenters alike: how did nature achieve its astonishing complexity and variety?"

The philosopher and historian of biology, Michael T. Ghiselin, writing in The New York Times, comments that Dawkins "succeeds admirably in showing how natural selection allows biologists to dispense with such notions as purpose and design". He notes that analogies with computer programs have their limitations, but are still useful. Ghiselin observes that Dawkins is "NOT content with rebutting creationists" but goes on to press home his arguments against alternative theories to neo-Darwinism. He thinks the book fills the need to know more about evolution "that others [creationists] would conceal from them." He concludes that "Readers who are not outraged will be delighted."

The American philosopher of religion Dallas Willard, reflecting on the book, denies the connection of evolution to the validity of arguments from design to God: whereas, he asserts, Dawkins seems to consider the arguments to rest entirely on that basis. Willard argues that Chapter 6, "Origins and Miracles", attempts the "hard task" of making not just a blind watchmaker but "a blind watchmaker watchmaker", which he comments would have made an "honest" title for the book. He notes that Dawkins demolishes several "weak" arguments, such as the argument from personal incredulity. He denies that Dawkins's computer "exercises" and arguments from gradual change show that complex forms of life could have evolved. Willard concludes by arguing that in writing this book, Dawkins is not functioning as a scientist "in the line of Darwin", but as "just a naturalist metaphysician".

Influence

The engineer Theo Jansen read the book in 1986 and became fascinated by evolution and natural selection. Since 1990 he has been building kinetic sculptures, the Strandbeest, capable of walking when impelled by the wind.

The journalist Dick Pountain described Sean B. Carroll's 2005 account of evolutionary developmental biology, Endless Forms Most Beautiful, as the most important popular science book since The Blind Watchmaker, "and in effect a sequel [to it]."

Phyletic gradualism

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https://en.wikipedia.org/wiki/Phyletic_gradualism

 

Phyletic gradualism, top, would consist of steady evolutionary change in small steps, in contrast to punctuated equilibrium

 

Apparently sudden changes can be explained either by macromutation or by relatively rapid episodes of gradual evolution, since 10,000 years barely registers in the fossil record.

Phyletic gradualism is a model of evolution which theorizes that most speciation is slow, uniform and gradual. When evolution occurs in this mode, it is usually by the steady transformation of a whole species into a new one (through a process called anagenesis). In this view no clear line of demarcation exists between an ancestral species and a descendant species, unless splitting occurs. The theory is contrasted with punctuated equilibrium. 

History

The word phyletic derives from the Greek φυλετικός phūletikos, which conveys the meaning of a line of descent. Phyletic gradualism contrasts with the theory of punctuated equilibrium, which proposes that most evolution occurs isolated in rare episodes of rapid evolution, when a single species splits into two distinct species, followed by a long period of stasis or non-change. These models both contrast with variable-speed evolution ("variable speedism"), which maintains that different species evolve at different rates, and that there is no reason to stress one rate of change over another.

Evolutionary biologist Richard Dawkins argues that constant-rate gradualism is not present in the professional literature, thereby the term serves only as a straw-man for punctuated-equilibrium advocates. In his book The Blind Watchmaker, Dawkins observes that Charles Darwin himself was not a constant-rate gradualist, as suggested by Niles Eldredge and Stephen Jay Gould. In the first edition of On the Origin of Species, Darwin stated that "Species of different genera and classes have not changed at the same rate, or in the same degree. In the oldest tertiary beds a few living shells may still be found in the midst of a multitude of extinct forms... The Silurian Lingula differs but little from the living species of this genus".

Lingula is among the few brachiopods surviving today but also known from fossils over 500 million years old. In the fifth edition of The Origin of Species, Darwin wrote that "the periods during which species have undergone modification, though long as measured in years, have probably been short in comparison with the periods during which they retain the same form"

Punctuated gradualism

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Punctuated gradualism is a microevolutionary hypothesis that refers to a species that has "relative stasis over a considerable part of its total duration [and] underwent periodic, relatively rapid, morphologic change that did not lead to lineage branching". It is one of the three common models of evolution.
 

Description

While the traditional model of paleontology, the phylogenetic model, posits that features evolved slowly without any direct association with speciation, the relatively newer and more controversial idea of punctuated equilibrium claims that major evolutionary changes don't happen over a gradual period but in localized, rare, rapid events of branching speciation. 

Punctuated gradualism is considered to be a variation of these models, lying somewhere in between the phyletic gradualism model and the punctuated equilibrium model. It states that speciation is not needed for a lineage to rapidly evolve from one equilibrium to another but may show rapid transitions between long-stable states. 

History

In 1983, Malmgren and colleagues published a paper called "Evidence for punctuated gradualism in the late Neogene Globorotalia tumida lineage of planktonic foraminifera." This paper studied the lineage of planktonic foraminifera, specifically the evolutionary transition from G. plesiotumida to G. tumida across the Miocene/Pliocene boundary. The study found that the G. tumida lineage, while remaining in relative stasis over a considerable part of its total duration underwent periodic, relatively rapid, morphologic change that did not lead to lineage branching. Based on these findings, Malmgren and colleagues introduced a new mode of evolution and proposed to call it "punctuated gradualism." There is strong evidence supporting both gradual evolution of a species over time and rapid events of species evolution separated by periods of little evolutionary change. Organisms have a great propensity to adapt and evolve depending on the circumstances. 

Studies

Studies use evidence to predict how organisms evolved in the past and apply this evidence to the present. Both models of evolution can not only be seen between species, but also within a species. This is shown in a study done on the body size evolution in the radiolarian Pseudocubus vema. This study presents evidence of a species exhibiting punctuated and gradual evolution, while also having periods of relative stasis. Another study also used body size and looked at both micro-evolutionary patterns and fossil records. The study uses quantitative data to make conclusions and is an example of another study using body size as an indicator of evolution.

One study focuses on how efforts to apply only one mode of evolution to a phenomenon can be inaccurate. It supports how difficult it can be to show that only one mode of evolution is at play at any given time. Another study also displays the importance of considering both models. The study supports that there can always be both models at play at any time. Another related study focuses on the extent of undefined area when trying to compare the two modes of evolution making it difficult to isolate one model.

There will always be variance in environments. Some environments present challenges that require quick adaptation for survival, while others are relatively stable. In addition, organisms differ in the amount of traits upon which selection can act. These factors along with replication time can create barriers when working to prove a single mode of evolution as being accurate. A study expresses the importance of defining the clear objectives before research is done. The study directly challenges phyletic gradualism and punctuated equilibrium. It shows how many factors can come into play when comparing the two modes of evolution.

Interactions

Other evidence for the inclusion of both styles of evolution is the consideration of how organisms relate and may interact. Two species that diverged from each other over time may both still possess a characteristic that only one still uses. The species that doesn’t use the characteristic might begin to use it for an alternate function, causing difficulty when trying to track evolution. Fossils do not always show the evolution of function. 

Research

Another avenue in which evolutionary characteristics are studied is within cancer research. There are studies on many types of cancer where similarities and differences have been identified. One study compares phenotypic characteristics to genotypic characteristics. The study concludes that genomic analysis supports both models and highlights the importance of studying the genotype, phenotype, and the relationship between the two. One study looked at pancreatic cancer. Pancreatic cancer is a rapidly progressing cancer. This study examines the punctuated genomic change that results in the rapid progression of this cancer. Cancer studies are compared to analyze modes of evolution. 

A similar study also looks at cancer to describe evolutionary change. This study challenges old conclusions and supports both models using more modern techniques providing current evidence for interpretation. A study looks at breast cancer. This study focuses on genome analysis that some of the previous studies expressed the importance of doing. The study highlights how dynamic the body can be during the progression of cancer. The changes can be seen in cancer cells as they can show patters of punctuation, gradualism, and relative stasis

Red Queen hypothesis

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Red_Queen_hypothesis

The Red Queen hypothesis (also referred to as Red Queen's, the Red Queen effect, Red Queen's race, Red Queen dynamics) is an evolutionary hypothesis which proposes that organisms must constantly adapt, evolve, and proliferate in order to survive while pitted against ever-evolving opposing organisms in a constantly changing environment, as well as to gain reproductive advantage.

The hypothesis intends to explain two different phenomena: the constant extinction rates as observed in the paleontological record caused by co-evolution between competing species, and the advantage of sexual reproduction (as opposed to asexual reproduction) at the level of individuals.

Origin

Leigh Van Valen proposed the hypothesis as an "explanatory tangent" to explain the "Law of Extinction" (known as Van Valen's law): by showing that in many populations, the probability of extinction does not depend on the lifetime of the population, instead being constant over millions of years for a given population. This could be explained by the coevolution of species, where established species have evolved cooperatively by assuming adaptive coevolutionary dependencies. These complementary relationships develop through graduated symbiosis, directing punctuated advantages specialized enough to ensure a greater survivability and fitness rate for both species. Indeed, an adaptation in a population of one species (e.g. predators, parasites) may change the natural selection pressure on a population of another species (e.g. prey, hosts), giving rise to common antagonistic coevolutions. If this positive feedback occurs reciprocally, a potential dynamic coevolution may result.

The phenomenon's name is derived from a statement that the Red Queen made to Alice in Lewis Carroll's Through the Looking-Glass in her explanation of the nature of Looking-Glass Land:

Now, here, you see, it takes all the running you can do, to keep in the same place.

Van Valen coined the hypothesis "Red Queen" because under this interpretation, populations have to "run" or evolve in order to stay in the same place, or else go extinct. 

Leigh Van Valen (1973) proposed the metaphor of an evolutionary arms race, which was appropriate for the description of biological processes with dynamics similar to arms races. In respective processes, an adaptation in a population of one species (e.g., predators, parasites) may change the selection pressure on a population of another species (e.g., prey, host), giving rise to an antagonistic coevolution.

The Red Queen at the genus level: The linear relationship between survival times and the logarithm of the number of genera suggests that the probability of extinction is constant over time. Redrawn from Leigh Van Valen (1973).

 

The Red Queen hypothesis is used independently by Hartung and Bell to explain the evolution of sex, by John Jaenike to explain the maintenance of sex and W. D. Hamilton to explain the role of sex in response to parasites. In all cases, sexual reproduction confers species variability and a faster generational response to selection by making offspring genetically unique. Sexual species are able to improve their genotype in changing conditions. Consequently, co-evolutionary interactions, between host and parasite, for example, may select for sexual reproduction in hosts in order to reduce the risk of infection. Oscillations in genotype frequencies are observed between parasites and hosts in an antagonistic coevolutionary way without necessitating changes to the phenotype. In multi-host and multi-parasite coevolution, the Red Queen dynamics could affect what host and parasite types will become dominant or rare.

Van Valen proposed the Red Queen hypothesis as an explanatory tangent to his proposed "Law of Extinction" (also 1973), which he derived from observation of constant probabilities of extinction within families of organisms across geological time. Put differently, Van Valen found that the ability of a family of organisms to survive does not improve over time, and that the lack of correlation between age and extinction is suggestive of a random process. The Red Queen hypothesis as formulated by Van Valen provides a conceptual underpinning to discussions of evolutionary arms races, even though a direct test of the hypothesis remains elusive, particularly at the macroevolutionary level. This concept remains similar to that of a system obeying a self-organized criticality.

For example, because every improvement in one species will lead to a selective advantage for that species, variation will normally continuously lead to increases in fitness in one species or another. However, since different species tend to co-evolve, an improvement in one species implies that it will get a competitive advantage over the other species, and thus be able to capture a larger share of the resources available to all. This means that the fitness increase in one evolutionary system will tend to lead to the fitness decrease in another system. The only way that a species involved in a competition for resources can maintain its fitness relative to other competing species is by improving its specific fitness. (From Heylighen, 2000) 

The most obvious example of this effect are the "arms races" between predators and prey (e.g., Vermeij, 1987), where the only way predators can compensate for a better defense by the prey (e.g., rabbits running faster than the previous generation]) is by developing a better offense (e.g. foxes running faster than their predecessors). In this case, we might consider the relative improvements (rabbits running faster than foxes or vice versa) to be also absolute improvements in fitness. (From Heylighen, 2000) 

Discussions of sex and reproduction were not part of Van Valen's Red Queen hypothesis, which addressed evolution at scales above the species level. The microevolutionary version of the Red Queen hypothesis was proposed by Bell (1982), also citing Lewis Carroll, but not citing Van Valen (see below). 

Application to human conflict

One can apply such arms races to human conflict and interpret them as a prominent cause of conflict. According to Azar Gat, the Red Queen effect arises when two competing groups find themselves in a security dilemma. The security dilemma results when a group takes defensive measures (which possess inherent offensive capabilities) to improve their security, triggering a military arms race. This arms race, much like the example previously referenced, causes each side to consume ever increasing amounts of resources in order to outpace the other and to gain an advantage. If an advantage is gained, the arms race is over and the group with more resources has won. However, typically both sides continue to match each other stride for stride, thus triggering the Red Queen effect, as no matter how many resources each side invests, neither is able to gain an advantage. The situation somewhat resembles the prisoner's dilemma. Neither side can stop the arms race, due to mutual suspicion and fears that the other group will gain a significant tactical advantage. Because of this, the Red Queen effect is a common outcome of inter-human competition and conflict.

Interspecies arms race

Predator-prey relationship between rabbits and foxes following the principle of the Red Queen hypothesis. The rabbit evolves increasing its speed to escape the attack of the fox, and the fox evolves increasing its speed to reach the rabbit. This evolution is constant, in case one of the two stops evolving, its extinction will occur.

• A number of predator/prey couple where the weapon involved is the running speed.

"The rabbit runs faster than the fox, because the rabbit is running for his life while the fox is only running for his dinner." Aesop

The predator-prey relationship can also be established in the microbial world, producing the same evolutionary phenomenon that occurs in the case of foxes and rabbits. A recently observed example has as protagonists M.xanthus (predator) and E.coli (prey) in which a parallel evolution of both species can be observed through genomic and phenotypic modifications, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, thus generating an arms race that can only be stopped by the extinction of one of the species.

• The interactions between parasitoid wasps and insect larvae, necessary for the parasitic wasp's life cycle, are also a good illustration of an arms race. Indeed, some evolutionary strategy was found by both partners to respond to the pressure generated by the mutual association of lineages. For example, the parasitoid wasp group, Campoletis sonorensis, is able to fight against the immune system of its hosts, Heliothis virescens (Lepidopteran) with the association of a polydnavirus (PDV) (Campoletis sonorensis PDV). During the oviposition process, the parasitoid transmits the virus (CsPDV) to the insect larva. The CsPDV will alter the physiology, growth and development of the infected insect larvae to the benefit of the parasitoid.

Evidence

Evidence for this explanation for the evolution of sex is provided by the comparison of the rate of molecular evolution of genes for kinases and immunoglobulins in the immune system with genes coding other proteins. The genes coding for immune system proteins evolve considerably faster.

Further evidence for the Red Queen hypothesis was provided by observing long‐term dynamics and parasite coevolution in a mixed sexual and asexual population of snails (Potamopyrgus antipodarum). The number of sexuals, the number of asexuals, and the rates of parasite infection for both were monitored. It was found that clones that were plentiful at the beginning of the study became more susceptible to parasites over time. As parasite infections increased, the once-plentiful clones dwindled dramatically in number. Some clonal types disappeared entirely. Meanwhile, sexual snail populations remained much more stable over time.

In 2011, researchers used the microscopic roundworm Caenorhabditis elegans as a host and the pathogenic bacterium Serratia marcescens to generate a host–parasite coevolutionary system in a controlled environment, allowing them to conduct more than 70 evolution experiments testing the Red Queen hypothesis. They genetically manipulated the mating system of C. elegans, causing populations to mate either sexually, by self-fertilization, or a mixture of both within the same population. Then they exposed those populations to the S. marcescens parasite. It was found that the self-fertilizing populations of C. elegans were rapidly driven extinct by the coevolving parasites, while sex allowed populations to keep pace with their parasites, a result consistent with the Red Queen hypothesis.

Currently, there is no consensus among biologists on the main selective forces maintaining sex. The competing models to explain the adaptive function of sex have been reviewed by Birdsell and Wills.

Studies

The influence of heterogeneity in species genomes has been recognized and studied since the time of Darwin (1876) in the areas of heterosis (hybrid vigor), inbreeding and genetic deterioration, operating on the theory that lessening of the choice of gene variants and of potential cooperation among different gene types limits the capabilities of the restricted organism. Resultant genetic drift or genetic isolates reduce available corresponding genetic material volumes, where variable limitations can catalyze a consequential population bottleneck.

A study published in 2013 in Science which examined the history of groups of extinct mammals illustrates the failure to adapt and evolve new species when confronted by a deteriorating environment. An interesting insight can be obtained from physical research.

The paradox of sex: The cost of males

Science writer Matt Ridley popularized the term in connection with sexual selection in his 1993 book The Red Queen, in which he discussed the debate in theoretical biology over the adaptive benefit of sexual reproduction to those species in which it appears. The connection of the Red Queen to this debate arises from the fact that the traditionally accepted Vicar of Bray hypothesis only showed adaptive benefit at the level of the species or group, not at the level of the gene (although the protean "Vicar of Bray" adaptation is very useful to some species that belong to the lower levels of the food chain). By contrast, a Red-Queen-type thesis suggesting that organisms are running cyclic arms races with their parasites can explain the utility of sexual reproduction at the level of the gene by positing that the role of sex is to preserve genes that are currently disadvantageous, but that will become advantageous against the background of a likely future population of parasites.

Further evidence of the Red Queen hypothesis was observed in allelic effects under sexual selection. The Red Queen Hypothesis leads to the understanding that allelic recombination is advantageous for populations that engage in aggressive biotic interactions, such as predator-prey or parasite-host interactions. In cases of parasite-host relations, sexual reproduction can quicken the production of new multi-locus genotypes allowing the host to escape parasites that have adapted to the prior generations of typical hosts. Mutational effects can be represented by models to describe how recombination through sexual reproduction can be advantageous. According to the mutational deterministic hypothesis, if the deleterious mutation rate is high, and if those mutations interact to cause a general decline in organismal fitness, then sexual reproduction provides an advantage over asexually reproducing organisms by allowing populations to eliminate the deleterious mutations not only more rapidly, but also most effectively. Recombination is one of the fundamental means that explain why many organisms have evolved to reproduce sexually.

Sexual organisms must spend resources to find mates. In the case of sexual dimorphism, usually one of the sexes contributes more to the survival of their offspring (usually the mother). In such cases, the only adaptive benefit of having a second sex is the possibility of sexual selection, by which organisms can improve their genotype. 

Evolution of aging

The Red Queen hypothesis has been also invoked by some authors to explain evolution of aging. The main idea is that aging is favored by natural selection since it allows faster adaptation to changing conditions, especially in order to keep pace with the evolution of pathogens, predators and prey.

Court jester hypothesis

A competing evolutionary idea is the court jester hypothesis, which indicates that an arms race is not the driving force of evolution on a large scale, but rather it is abiotic factors.

Black Queen Hypothesis

The Black Queen Hypothesis is a theory of reductive evolution that suggests natural selection can drive organisms to reduce their genome size. In other words, a gene that confers a vital biological function can become dispensable for an individual organism if its community members express that gene in a "leaky" fashion. Like the Red Queen Hypothesis, the Black Queen Hypothesis is a theory of co-evolution.