Creationism vs. ID and Other Topics, Salvador Cordova’s Interview with Stephen Meyer

By accident I discovered a file I thought was forever lost. It was my 13-minute interview of Stephen Meyer in McLean, Virginia when he was on his book tour for his book Signature In the Cell.

I asked him 4 question, the first being, what is the difference between Creationism and Intelligent Design (ID).

I characterize Meyer as a Progressive/Old Earth Creationist. Many people in the ID community are Old Earth Creationists, but there are a few who are Young Earth Creationists like Paul Nelson.

But anyway, here is Stephen Meyer in his own words:

Stephen Meyer 4Qs

NOTE1:
I somewhat adopted Meyer’s definition of Creationism and ID for several years, but after some thought, here are my definitions (which might be different from other people’s definitions).

CREATIONISM: Creationism encompasses two major lines of thought, Creation THEOLOGY and Creation SCIENCE. The two disciplines argue for miraculous special creation and a time line for those miracles. There are a variety of creationisms, mostly differentiated according to proposed time lines, such as Young Life Creationism, Young Earth Creationism, Young Age Creationism, Old Earth Creationism, Progressive Creationism, etc.

CREATION Theology: Theology regarding creation developed from sacred texts such as the Bible.

CREATION Science: Science supporting the hypothesis of miraculous special creation and time lines of the miracles. The approaches of Intelligent Design are sometimes incorporated into some aspects of creation science, but creation science encompasses larger questions than just ID.

Intelligent Design (ID): As a discipline, ID is the study of patterns in the physical world that suggest intelligent design. As a theoretical claim, ID claims that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

Intelligent Design Science: is science supporting the hypothesis of intelligent design.

At the Creation Evolution University Forum, http://creationevolutionuniversity.com/forum/

Creation Science explores things such as:

>fossil dating, flood geology, C14, K/Ar, radio metric dating, diffusion dating, racemization dating, DNA dating, stellar and planetary evolution, erosion dating, fast stratification, interpretations of the geological column, baraminology, distant starlight problem, Y-chromosomal Adam/Noah/Aaron/Abraham, mitochondrial Eve, Tower of Babel, Proton-21 laboratory, Sodom and Gomorrah, OEC,YEC, Progressive creation, white hole cosmology, Carmeli cosmology, VSL theories, alternate electrodynamics, mantle plume theories, folding rock theories, RATE work, planetary magnetism, faint young sun paradox, moon recession, ocean mineral saturation, astrometry and proper motion surveys, very long baseline interferometry, CMBR, moon evolution, cosmological vs. non-cosmological red shifts, polonium halos, Hydro Plates and Castastrophic Plates, varves, tree rings, noah’s ark, over thrusts, lithification, hydrologic sorting, canopy theory, crater theory, planetary heating, ancient civilizations, Atlantis, trophical trees in the arctic, woolly mammoths and tropical trees in Siberia, UFOs and creationism, comets and orbital mechanics, planet satellite capture problems, planetary rings, origin of folded rocks, the Grand Canyon, the Green River valley, the Three Sisters, mountain formation, seafloor formation, tectonics, etc.

Whereas, Intelligent Design explores things such as:

>design detection, design specification, irreducible complexity, origin of life, platonic forms, design matrix, population genetics, cybernetic theories, semiotic theories, Fishers’s fundamental theorem, Kimura’s neutral evolution, Darwinian evolution, modern synthesis, probability theories, fine tuning, typology, discontinuity systematics, steganography, evolutionary algorithms, published ID material, ID philosophy, front loaded evolution, omega point theory, anthropic principles, multiverses and many-worlds, panspermia, extra terrestrials, teleology in biology, redundant complexity and fault tolerance, algorithmic complexity, complexity measures, no free lunch, blindwatchmakers, bad design, evil design, junk DNA, DNA grammars, von Neumann replicators vs. autocatalysis, Quines, polyconstrained DNA, Mendel’s Accountant, DNA skittle, re-association kinetics, molecular clocks, GGU/GID models, enigma of consciousness and Quantum Mechanics, Turing machines, Lenski’s bacteria, thermodynamics, Avida, self organization, self disorganization, generalized entropy, Cambrian explosion, genetic entropy, Shannon information, proscriptive information, Programming of Life, law of large numbers, etc.

NOTE2:
There will obviously be some overlap between Creation Science and Intelligent Design Science. I’ve gone on record as saying I don’t think ID in the ultimate sense is equal to experimental science (like say electromagnetic theory), but the science supporting ID (like probability analysis and predictions from the law of large numbers) is science, hence I create a category called Intelligent Design Science.

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Cost of maintenance and construction of design, neutral theory supports ID and/or creation

Most of biological ID literature is focused on Irreducible Complexity and Specified Complexity (Specified Improbability) and information theory, no free lunch, critique of OOL, the Cambrian explosion, etc,

But there is another line of argument that is devastating to the claims of mindless evolution that has been underappreciated partly because it is highly technical, and in many cases most biologists will not even learn it in detail, namely that most molecular evolution is non-Darwinian.

Here is the simplest way to understand why evolution is mostly non-Darwinian. The ability to select for or against a trait involves the cost of sacrificing individual lives. When we spend money we have a limited budget to buy things. From our budget we can select to have maintenance done on our houses, cars, computers, our bodies (healthcare) or we can buy other thing to accumulate possessions.

What Darwin and most Darwinists do not realize is that selection for individual traits likewise comes at cost. To select to maintain one part of the genome means that there is no budget to maintain another part of the genome. To select to construct new features of the genome means one must abandon the maintenance budget of another part. This will be true even if the selection process is done by an intelligent agency like a human. The reason most computerized “proofs” of evolutionism like Dawkins Weasel and Avida are invalid is they do not model the problem of cost of maintaining and constructing mutli gigabit complex designs.

To understand things more clearly, here is a hypothetical illustration. If an asexually reproducing species could only have one offspring, selection must necessarily be neutral because there is no reproductive excess, there is zero “money” to carry out selection. If there are harmful mutations along the way, oh well, no “money” of excess reproduction to fix it. This would be an extreme case of Muller’s ratchet where the bad irreversibly just keeps accumulating.

Now if an asexually reproducing species could have two offspring, it now has a little more “money” in the form of reproductive excess to select to maintain one trait that goes bad. Let’s say one of the two offspring develops a bad mutation and the other doesn’t. We can expend him, or dare I say “spend” him to fix the genome. But our selection budget would be blown if each of the kids develop 1 bad mutation each, and it would really be blown if they develop 100 bad mutations each! And at this point we are not even considering the budget needed to build new functional traits.

When we actually do careful accounting of the costs of natural selection envisioned by Darwin and Dawkins versus the available money of reproductive excess, we realize that if evolution happens, it must be mostly free of selection as a matter of principle, and thus mostly neutral. There is simply not enough “money” in the form of reproductive excess to maintain and construct complex designs composed of billions of nucleotide and epigenetic “traits”. There is some selection obviously, because there is some “money” to do a little bit, but not enough.

The accounting of the cost of selection can be done in a number of ways. One way to demonstrate this is through the equations of population genetics, and the other way is a computer simulation that does the accounting. One of the best, if not the best computer accounting simulations is Mendel’s Accountant written by the dream team of creationist population genetics. The irony then is population geneticists, PZ Myers, Larry Moran, the YECs have had a rare moment of agreement where they have all signed the claim, “most molecular evolution is non-Darwinian.”

But if most evolution is non-Darwinian, maintenance much less construction of design cannot be explained by Darwinism, then the case for ID is strengthened.

Now if most evolution had been non-Darwinian, one would rightly argue it would have been a random walk, and thus not much better than a tornado going trough a junkyard. Creationist have seized on this and said, “well we’re not a junkyards, therefore some non-random process must have created designs in nature, hence we are designed”. In contrast, Larry Moran and friends have said “evolution is a random walk and we are obviously junkyards and you’re an IDiot if you think biological organisms are mostly functional.”

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Why fixation in gigantic but widely separated human populations doesn’t happen

If there was any time the human population was very small, fixation was likely inevitable as discussed in Neutral Evolution for Newbies, Part 2. The time for required for fixation in a population according to standard population genetics is approximately 4 Ne, where Ne is the effective population size.

For example, for an Ne of six individuals, the approximate time to fixation using this approximation is:

4 x 6 = 24 generations

In 24 generations, assuming they don’t die from inbreeding depression, everyone will be pretty much genetically identical according to standard theory. Even if their differences were huge (maybe millions of nucleotides), they should fix in 24 generations using this approximation.

In contrast consider the current human population of 7 Billion, and suppose the effective reproductively viable population is 1.5 billion. Using the approximation, the time to fixation with Ne = 1.5 billion is

4 x 1,500,000,000 = 6 billion generations
Continue reading Why fixation in gigantic but widely separated human populations doesn’t happen

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Larry almost got it right, but he just can’t turn the corner

In 2013 Larry wrote On Beating Dead Horses

I was reminded of this while reading Salvador Corova’s latest post on Uncommon Descent because he refers to beating dead horses [If not Rupe and Sanford’s presentation (8/6/13), would you believe Wiki? In this case, yes]. I’m not going to make any comments. Read it and weep for the IDiots.

Well, it turned out Larry did make comments in that very same thread. 🙂

Sal begins with …

Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian …

I’ve been trying to teach this to the IDiots for over twenty years. Yet they still insist on referring to evolution as “Darwinism” and they continue to ignore random genetic drift in their attacks on evolution. About 99% of all IDiots have no idea what Sal is talking about. (Sal Cordova doesn’t know either.)

What Sal is saying is that practically all of the mutations being fixed in humans are either neutral or slightly deleterious. That has implications. It strongly suggests that most of our genome is junk.

Not quite, but almost, let me re-write the previous paragraph with errors corrected:
Continue reading Larry almost got it right, but he just can’t turn the corner

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Specifications: detachable, not postdictive, not after-the-fact

Being able to reject chance as an explanation is critical to identifying design. The way to do this is to compare the structure of an artifact against some pattern that can help us rule out chance as an explanation.

Sometimes designers can anticipate the knowledge of observers in order to craft designs which can be recognized as designs. They can structure it according to a pre-existing pattern that the supposed observer has in their inventory or some pattern that the designer thinks can be recognized by an observer.

Here I described this exercise:

“Take the coins and dice and arrange them in a way that is evidently designed.” That was my instruction to groups of college science students who voluntarily attended my extra-curricular ID classes sponsored by Campus Crusade for Christ at James Madison University (even Jason Rosenhouse dropped in a few times). Many of the students were biology and science students hoping to learn truths that are forbidden topics in their regular classes…

They would each have two boxes, and each box contained dice and coins. They were instructed to randomly shake one box and then put designs in the other box. While they did their work, I and another volunteer would leave the room or turn our backs. After the students were done building their designs, I and the volunteer would inspect each box, and tell the students which boxes we felt contained a design, and the students would tell us if we passed or failed to recognize their designs. We never failed!

Bill Dembski worked hard to rigorously define criteria for patterns which observers can use to recognize designs constructed by designers willing to communicate evidence of design. It is worth noting, such a method will not help us find patterns to detect all possible designs, but only a small space of designs, especially those designs that designers want to be discovered as designs:

Masters of stealth intent on concealing their actions may successfully evade the explanatory filter. But masters of self-promotion intent on making sure their intellectual property gets properly attributed find in the explanatory filter a ready friend.

Bill Dembski
Mere Creation

It seems Bill is asserting the Designer of life has gone to great lengths to make his designs recognizable as designs.
Continue reading Specifications: detachable, not postdictive, not after-the-fact

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Panda’s Thumb Richard Hoppe forgot about Humpty Zombie

The fallacious results of the Avida computer simulation were used in the infamous Kitmiller vs. Dover trial to argue in favor of Darwinian evolution. Using the evidence from the Avida simulation and other testimony, Judge Jones ruled that it is illegal to contest Darwinism for all time. Prosecution witness Robert Pennock claimed in sworn testimony that Avida solved the problem of Irreducible Complexity (IC).

Unfortunately the incompetent defense team wasn’t privy to later discoveries by me and Richard Hoppe, namely, that Avida offers solutions to the OOL problem and predicts the possibility of a Zombie Apocalypse through cosmic radiation. It would have been great to have had the Zombie data entered as evidence in the trial. 🙂

Winston Ewert demonstrated that the Avida computer simulation did not refute Behe’s work on Irreducible Complexity (IC). Understandably, arch Darwinist Richard Hoppe blew a gasket over Winston’s paper. To summarize Dr. Hoppe’s arguments, I quote from Hoppe’s essay. But while blowing a gasket, Hoppe actually doesn’t disagree with Winston:

They [the Avida developers] rigged the game by using a fitness landscape that allowed the performance of EQU to evolve!!!

Well, DUH!

Once again, desperately dissing Avida.

Look at all those exclamation points by Dr. Hoppe!!!!!!!!!!!!! He admits the Avida developers rigged the simulation.

Hoppe admits irreducible complexity can be evolved by random mutation and designed selection (RMDS). But this says nothing about random mutation and natural selection (RMNS). Examples of Designed Selection (DS) to achieve desired intentional goals are Dawkins Weasel, Avida, Ev, Steiner, Geometric, Digital Ears and Cordova’s remarkable evolutionary algorithm.

But there are other things beyond Avida’s “solution” to IC. Avida has solutions to the OOL problem and predicts the possibility of a Zombie Apocalypse. Continue reading Panda’s Thumb Richard Hoppe forgot about Humpty Zombie

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Neutral theory and non-Darwinian evolution for newbies, Part 2

Part 1 laid out the claim that most nucleotides in populations cannot as a matter of principle be under strong selection, but must be neutral. MOST certainly does not mean ALL. Clearly some deleterious traits if they appear would be lethal, and conversely in certain contexts like antibiotic and pesticide resistance, some traits can be strongly selected for, but these cases do not speak for most of the rest of the molecules in various species. As one scientist said:

Most molecular evolution is neutral. Done.

PZ Myers

Part 2 will focus on how neutral or nearly neutral traits in small finite populations get “fixed” where the word “fixed” in population genetics is used to describe a trait that has practically become part of every individual and is virtually a permanent feature of the entire species.

The Darwinian view in the 1950s was that most of the genome and features of populations were the result of selection. But smart geneticists like Kimura (and unwittingly Haldane) realized that this could not be possible even in principle. This was explained in Part 1.

The present state of affairs is that both evolutionists and creationists with background in population genetics agree that IF we evolved, most of the traits became fixed without the influence of selection. Thus most evolution, if it is unguided and not front loaded, would essentially be random.

These considerations contradict Dawkins’ claim:

You often find people who say, well, evolution is a theory of chance, in the absence of a designer. If it really were a theory of chance, of course they would be right to dismiss it as nonsense. No chance process could give rise to the prodigy of organized complexity that is the living world. But it’s not random chance. Natural selection is the exact opposite of a chance process.

Dawkins proves God by mistake

The reason Dawkins is wrong is that if there was evolution and it was unguided, because most molecular evolution is neutral, Darwinian selection has almost no role, and chance would be the only mechanism left. Thus I would actually agree with Dawkins on this:

You often find people who say, well, evolution is a theory of chance, in the absence of a designer. If it really were a theory of chance, of course they would be right to dismiss it as nonsense.

Absence of selection shows unguided evolution is mostly a theory of chance. The proportion of molecular “traits” fixed by selection versus those fixed by random chance were investigated by members of the Mendel’s Accountant team. Their finding are in agreement with claims which are accepted by many scientists in relevant fields but which are not broadcast to the general public, certainly not by Dawkins.

In Using Numerical Simulation to Better Understand Fixation Rates, Rupe and Sanford show in one simulation that even with strong selection against deleterious traits, the ratio of deleterious traits that got fixed by chance versus the beneficial traits that got fixed by Darwinian selection was 6,775 to 10. This figure absolutely refuted Darwin’s fantasy of never ending evolutionary progress. This showed over time that even though some beneficial traits got fixed into the population (like maybe the color of a peppered moth), for every beneficial trait that got locked into the population, 676 bad traits got locked in as well!

So how can this possibly be? Isn’t Darwinian selection supposed to sort out the good from the bad? Well yes if that was the way nature really worked. But the only place Darwinian selection works is not in nature but in genetic algorithms that have no resemblance to biological reality — algorithms such as those implemented in Dawkins Weasel, Avida, Tierra, Ev, Steiner, Geometric and Cordova’s Remarkable Algorithm. Nature doesn’t work this way. Why?

First of all, in sexually reproducing populations, an otherwise advantageous trait can be lost just to random chance. We often observe that some children don’t inherit some of their parents traits. This is because of recombination during meiosis. For example, if Dad has one point mutational “trait” in a particular nucleotide on one chromosome, and Mom does not have that same “trait”, there is only a 25% chance that this otherwise advantageous trait will appear in any given child. And then if a child has that trait, there is no guarantee he might not die or fail to reproduce from accidents or other chance events. Thus chance has a huge role in what persists or gets lost in a population even if a trait might otherwise have a selective advantage. But since most molecular “traits” are neutral, what traits end up persisting in a population are mostly decided by chance.

On the website inbreeding and neutral evolution we see how quickly fixation happens in a small inbreeding population. The ideas for small inbreeding populations can be somewhat scaled up to larger populations provided that the individuals stir well with each other rather than stay isolated for too long. I focus on small populations to help the reader conceptualize fixation under neutral conditions:

Below is an example of drift. Imagine a rare species kept in a zoo with a population of only six diploid individuals. There are a total of 12 alleles (numbered 1-12 in generation 0). All alleles are assumed equally fit, so that evolution is neutral. The alleles may also be genetically distinguishable, or “different in state” (represented by colours).

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By generation 7, every allele has become identical by a chance processes alone.

This kind of evolution is not predictable; it is random or stochastic.

At the end of several generations, only one form exists, polymorphisms are gone, and there is monomorphism (fixation). Although the diagram shows alleles of one gene, this sort of fixation would be true of pretty much every gene locus or stretches of nucleotides. Even if the we had 1 million unfixed nucleotide loci, assuming the inbreeding didn’t kill the population, they would all fix pretty much in several generations just as this single gene got fixed to one allele from an original pool of 12.

The website cites an example where on one island all the individuals of a species were identical and probably followed this process:

in an introduced population (the island of Réunion, left), no polymorphisms are observed. This suggests that the founder population was very small, and that all variation has been lost.

In the original example, the 12 alleles came from pre-existing families, but let us suppose the 12 alleles came about from mutation. Suppose the 12 alleles came about by 1 mutation per gamete. The end result would be the same. But we can learn something from this.

First note, there is 1 mutation per each of the 12 gametes. We expect after several generations 1 mutant will get fixed and the other 11 mutant alleles lost to drift, but the bottom line is 1 mutant must necessarily be fixed in this forced illustration.

With a little imagination, we can extrapolate this forced illustration where I forced all the mutations onto the same gene locus to a more realistic situation where the mutations are spread to different loci. At each locus where a mutant allele might reside, any given mutant allele will have a 1 in 12 chance of going to fixation and an 11 in 12 chances of drifting into oblivion, but on average because there are 12 mutants each with a probability of 1/12 getting fixed, the expectation is 1 of the 12 mutants will get fixed and the other 11 go to extinction. The important point is, 1 mutant on average will get fixed because there was 1 mutation per gamete in generation 0.

And with yet a little more imagination, we can see if we increase the number of mutations per gamete in generation 0 to 100 mutation per gamete, we would on average get 100 new mutants fixed several generations down the line.

And yet with more imagination, if we were adding 100 mutations per gamete per generation, we’d be fixing 100 new mutants per generation. It just takes several generations to spool up to the point were fixation rates approach gametic mutation rates. With some math, it can be seen these ideas can be extrapolated to larger populations. But the bottom line is the fixation rate will approach the gametic mutation rate eventually for small well stirred populations. As Rupe and Sanford pointed out:

We show that neutral mutations go to fixation just as predicted by conventional theory (i.e., over deep time the fixation rate approached the gametic mutation rate).

The population sizes considered were 10,000 individuals.

But lost in all this is the quality of the mutants getting fixed. If the mutant is harmful but nearly neutral in terms of reproductive success, and if there are lots of these mutants, they will go to fixation! Thus the bad will just keep adding up, and the damage will be irreversible like a ratchet, hence we hear names like Muller’s and Haldane’s ratchets.

Part 2 describes the situation for small inbreeding well stirred populations. What happens in large non-inbreeding unstirred populations with lots of geographical isolation? That is the subject of the next post, but briefly, it doesn’t get necessarily better for large populations. I’ll cover that in part 3.

Discussion can also be pursued at CEU Forum: Neutral Evolution for Newbies.

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Neutral theory and non-Darwinian evolution for newbies, Part 1

The Darwinian view:

Natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good; silently and insensibly working, whenever and wherever opportunity offers

Charles Darwin

Software that models the Darwinian view are genetic algorithms like Avida, Tierra, Ev, Steiner, Geometric and Cordova’s remarkable algorithm. Winston Ewert discusses these here.

By way of contrast, I expressed my view as:

Evolution in the wild slowly lets go of the good, and keeps adding up the bad.

Software that models this view is Mendel’s Accountant. This view is also unwittingly modeled in most textbook population genetics — one just has to be willing to see it. Why is it that the most prominent software simulation “proofs” of Darwinian evolution are not biologically realistic, like Steiner or Avida? I pointed out the humorous fact here that evolutionists seem awfully reluctant to transform the math models of textbook population genetics into publicly available simulations of evolution in deep time, while instead they would prefer to highlight Steiner and Avida as examples of the success of Darwinism.

The most comprehensive software model of textbook population genetics for important evolutionary questions was Mendel’s Accountant. It was written by 10 or so creationists (some from top tier science institutions like Cornell, MIT and Princeton), but Darwinists refuse to acknowledge it by saying it is unrealistic, whereas they celebrate Avida and Steiner which have no basis in biological reality whatsoever! With all the nasty comments about Mendel’s Accountant, the critics seem unwilling to actually write and publish software that has the “right” parameters, and not even that, they can’t point you to an existing simulation that is in material disagreement with Mendel’s Accountant.

The claim of this essay is that real evolution of populations as modeled by textbook population genetics does not conform to the Darwinian view, but rather the non-Darwinian view. Shockingly this view is well summarized by this statement:

Most molecular evolution is neutral. Done.

PZ Myers
Former #1 Science Blog

PZ provided a succinct definition of non-Darwinian neutral theory. Done.

Neutral molecular evolution means that most molecular “traits” (a single nucleotide, a codon, a gene, etc.) are not subject to being selected for or against. Their persistence in the population is a matter of blind luck. We have to be very careful here — just because a “trait” is neutral does not mean it has no functional utility. Many organisms have had functional systems (eyes, wings, legs, stomachs, blood, etc.) selected against. So functionality isn’t necessarily correlated with selective advantage. Darwinists proudly call this Survival of the Sickest. I just have to point out that “beneficial” doesn’t necessarily mean functional, sometimes the opposite is true as described by Behe’s Rule.

What PZ may not realize is that if most molecular evolution is neutral AND most mutations erode function, then real evolution must inevitably lose functional complexity, not build it. Famed applied geneticist John Sanford of Cornell calls this principle of deterioration Genetic Entropy.

So how do we know that most molecular evolution is free of selection? First, it is helpful to understand how we mathematically model how traits are strongly or weakly selected for or against or not at all. If we say a trait is strongly selected against, we model this by saying individuals with that trait will tend to have few if any offspring. We can call such traits “deleterious” traits. Conversely if an individual has a selectively favorable trait, we model this trait by saying individuals with that trait will tend to give the individual lots of offspring. We can call this trait a “beneficial” trait. Strength of selection then is measured in terms of how a trait will TEND to increase or decrease the number of offspring an individual may have.

For example, molecular traits that make someone not want to have tons of kids are traits that are “deleterious” whereas molecular traits that make someone want to have tons of kids are traits are “beneficial”. Superficially, we might suspect Richard Dawkins (1 kid) has on balance more deleterious traits than Octomom (14 kids). Poetic justice I suppose.

Given the description of how we define strength of selection in terms of reproduction, we’re now in a position to understand the beginnings of neutral theory and how evolution as a matter of principle had to be non-Darwinian. To illustrate why without all the bewildering math, I’ll start with a simplistic model with a steady population of two individuals (one male, one female). This is purely a pedagogical model, but one than can be extend and refined to more realistic models.

Suppose further in this model that each of the first parents (call them Adam and Eve) have 3 billion nucleotides in their genome, half of which are “deleterious” and half of which are “beneficial”, and the next generation of kids will generally have about the same number on average of 1.5 billion beneficial and 1.5 billion deleterious traits as their parents for the first generational cycle. These proportions are subject to change with each generation, but this is how the model starts out.

Suppose further there will be no new mutations, all we want to do is see how we can evolve an individual that has only beneficial nucleotides and no deleterious ones from the existing gene pool. Suppose also for every generation that the 2 parents always make 8 kids, and only 2 of the kids reproduce, the other 6 are either killed or precluded from reproducing, thus the population is at a steady effective size of 2 for every generation.

If we said the selection against every “deleterious” trait was maximal, meaning any individual with such a trait would not have offspring, it is clear even if a kid somewhere down the line miraculously had only 1.2 billion deleterious nucleotides and 1.8 beneficial ones, under the assumption of maximum selection against deleterious traits, even that wonder kid would not reproduce, and hence if the best kid must die out, all the kids must die out and the species goes extinct! The only solution then is to suppose selection against deleterious traits must necessarily be weak.

Conversely if we guaranteed that individuals with “beneficial” traits had 1 extra kid for every beneficial trait they had, then each individual would have 1.5 billion offspring! Clearly this would violate the constraint that each pair of parents had only 8 kids. Thus, the only solution is to then assume “beneficial” traits are also weakly selected for in the sense that “beneficial” traits increase reproduction rates ever so slightly. The net result is we can effectively say most traits are not selected for or against, and therefore are neutral, and therefore most molecular evolution must be non-Darwinian as a matter of principle.

We can see then that reproductive capacity (number of kids per parent) and the size of the genome affect how much selection in principle can be focused on individual nucleotides in the genome in a particulate (not corporate) manner. The smaller the reproductive capacity of a species and the larger the genomes, the more dilute selection must be on each nucleotide as a matter of principle.

The bottom line is molecular evolution at the nucleotide level must in principle be mostly neutral which means it must be non-Darwinian in principle. If most molecular evolution is non-Darwinian, this strongly suggests most other kinds of evolution must be non-Darwinian! Why should other levels of evolution higher than the molecular level be exempt from the mathematical considerations just laid out? The view that almost all evolution must be non-Darwinian has been advocated by Masotoshi Nei, a fact I pointed out here.

It might be helpful at this point to draw some important distinctions since the phrase “neutral theory” can be subject to lots of equivocation. Neutral theory generally refers to the views of Kimura and Nei and other evolutionists. When I previously said many creationists were neutralists, I was merely saying many creationists argue the biological world must be free of selection as populations reproduce. This is the view of the ReMine and Sanford who are creationists but who reject Kimura/Nei’s view how complex organisms came to be.

I will try in the future to make a distinction between Kimura/Nei vs. ReMine/Sanford neutral theories. Kimura/Nei and ReMine/Sanford agree that most biological change is non-Darwinian and selectively neutral, but they disagree about what happened in the historical past. ReMine/Sanford argue neutral theory in the operational sense, but not in the historical sense. Kimura/Nei argue neutral theory in both the operational and historical sense.

Part 2 will delve into mutation accumulation, fixation, and random loss of traits by recombination or random accidents.

Hope this helps.

NOTES

1. I put “beneificial” and “deleterious” in quotes to emphasize the notions of good and bad in the evolutionary world view have gotten so twisted that sickle cell anemia, juvenile diabetes, cystic fibrosis are viewed as “beneficial” traits whereas stomachs, eyes, wings, legs, blood are occasionally “deleterious” — exactly the opposite of how we intuitively view such traits.

2. I put the word “trait” in quotes because traits are often thought of in terms of phenotypic traits, whereas for molecular evolution we are often focusing on evolution at the nucleotide level and so we have to redefine the notion of trait to include nucleotides.

3. Here is the more mathematical description of how selection is modeled.
One Gene. Anyone with better links is invited to post.

4. Any corrections to what I said are welcome. Thanks in advance.

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Reductive evolution of complexity — can we say square circle?

Walter Remine mentioned in passing about a parasite that slowly evolved to lose all its organs except for its anus. Unfortunately he didn’t recall the name of the creature or whether he got all the details right, but rather than peppered moths, if that creature really exists, it should be the poster child of Darwinism.

I’ve argued almost from the beginning that most observed evolution in real time is loss of function. Loss of function is called reductive evolution. And the fact that most selectively favored adaptations involving function is loss of function rather than acquisition of function is what I refer to as Behe’s Rule.

But far be for evolutionists to salute creationists and IDists who have pointed out evidence of Behe’s Rule. I’ll at least credit them with being brutally honest in the following papers:

Genome Reduction as the Dominant mode of Evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and
the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding.
However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by
a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.

“punctuated by episodes of complexification.” is a euphemism for POOF. I described the nature of the POOF
mechanism here.
Continue reading Reductive evolution of complexity — can we say square circle?

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Darwin’s Delusion vs. Death of the Fittest

Superficially, the phrase “survival of the fittest” seems undeniably true, but in the proximal and ultimate sense it is false. If this claim is false then Darwinism is also false. The notion of “survival of the fittest” is an illusion in the general sense though seemingly true in the Darwinian sense. Critical oversights in Darwin’s Origin of Species by Means of Natural Selection and in Dennett’s algorithm can be demonstrated. Finally, population genetics can be used to critique Dawkins Weasel, Avida and various other fallacious computer simulations that are used in promoting the falsehoods of Darwinism and Neo-Darwinism.

To demonstrate that “survival of the fittest is false” it is sufficient but not necessary to demonstrate “death of the fittest is true”. Is “death of the fittest” true? Yes, in the ultimate sense. There is the rather trivial argument from physics: the stars will burn out one day, the 2nd law will prevail, and all life will cease. The fittest along with the weakest will meet their end. QED.

But what about the history of life on Earth? Wasn’t “survival of the fittest” always true for the history of life on Earth? No. Dave Raup’s book Bad Genes or Bad Luck reveals that most extinction in the past happened through natural disasters and bad luck, not bad genes, not Darwinian selection.


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