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Thursday, June 24, 2010

God versus Darwin - When macro-evolution takes a final, it gets an "F"

We posted several articles and blogged about the articles on the subject of how reproduction actually works at the cellular level.  Facilitated Variation Theory and Genetic Redundancy Theory both falsify Neo-Darwinist hypotheses because they have shown that the cell controls reproduction, the mother sets the framework for the child and that there are built in multiple redundancies in the gene that cannot possibly be explained by natural selection.  



We have also shown that Darwinists have no explanation for the information in the cell.  Information does not arise naturally from the environment and in fact it is not material in form or substance.  Massive amounts of information that are necessary to produce irreducibly complex systems and processes are further evidence against the primitive 19th Century idea of Darwinism.   
But there is more, much more.  The concept of Darwinist evolution can be tested and has been tested in laboratories around the world as Darwinist scientists have tried to "help" macroevolution along and so far they have been a complete failure.  Speciation is all that Darwinists prove and speciation is one of the tenets of Creationism.   So thus far Darwinism has been falsified at the ground level, so to speak.

Allow me to now introduce another blow to DarwinismUsing Numerical Simulation to Test the Validity of Neo-Darwinian Theory

I will not copy down the entire paper, only excerpts.   This paper was presented at the Sixth International Conference on Creationism.   Herein are the authors and the introduction:

John Sanford, Ph. D., Department of Horticultural Science, NYSAES, Cornell University, Geneva, NY 14456
John Baumgardner, Ph. D., Institute for Creation Research, 1806 Royal Lane, Dallas, TX 75229
Wesley Brewer, Ph. D., Department of Computer Science, Handong University, Pohong, South Korea
Paul Gibson, Ph. D., Department of Plant, Soil and Agricultural Systems, Southern Illinois University,
Carbondale, IL 62901
Walter ReMine, M. S., 3003 Snelling Ave., N., St. Paul, MN 55113

"Abstract

Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to
population geneticists, but which have not been effectively communicated to other scientists or
the public. These fatal flaws have been recognized by leaders in the field for many decades—based
upon logic and mathematical formulations. However population geneticists have generally been very
reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to
surround each issue.

Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws
and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this
purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation
program. This new program is a powerful research and teaching tool. When any reasonable set of
biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal
flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively
falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.

Keywords

Mutation, Natural selection, Darwinian evolution, Genetic load, Genetic entropy

Introduction

The concept of biological evolution existed long before Charles Darwin. What Darwin added was
what seemed to be a credible naturalistic mechanism which might drive the evolutionary process. He
proposed a mechanistic force which might cause evolution to actually happen spontaneously, and
therefore “naturally”. Darwin’s mechanism was simply the idea of spontaneous variation (mutation)
plus differential reproduction (natural selection). Since the time of Darwin, evolutionary theory has
been elaborated into a very sophisticated system of thoughts, theories, and equations. However, the
simple concept of mutation/selection remains at the very heart of all these elaborate thought systems.

The book Genetic Entropy and the Mystery of the Genome (Sanford, 2005) uses logic and some simple
calculations to make it clear that there are very fundamental problems with using the mutation/
selection mechanism to explain evolution. A series of compelling arguments are used in that book to show
that in the long run mutation/selection can not produce a net gain in information. Those same arguments
are used to show that selection can not even stop the gradual but certain degradation of genetic information
(traditionally referred to as “genetic load”, but better termed “genetic entropy”). Taking all these arguments
at face value, evolutionary theory appears to be demonstrably false.

Historically, each of the arguments summarized in the book Genetic Entropy, have been
begrudgingly acknowledged within the population genetics literature. However such acknowledgement
has not been communicated to the broader scientific community or to the general public. The fact that
the textbook version of evolutionary genetic theory appears to be fundamentally dysfunctional appears to
constitute a “trade secret” among genetic theorists.


There is now an empirical method which can be used to objectively, empirically, and conclusively test
the viability of evolutionary genetic theory. This new methodology is called numerical simulation. The key
scientific operation which is needed to test evolutionary theory does not involve complex mathematical
formulations, but simply involves tracking and counting mutations within populations. It is essentially
an advanced accounting problem. Good and bad mutations are entering real populations continuously.
Some of these are adding up, while others are being subtracted away (either by selection or by random
drift). The key mathematical operations needed here are just addition and subtraction. Computeraided
numerical simulation allows a researcher to mechanistically track every single mutation within
a virtual population, from the time each mutation enters the population until its allele frequency goes to
either zero or 100%. Each mutation can be realistically processed in a biologically accurate and
explicit manner, such that its transmission to the next generation is based upon:
(a) Mendelian segregation;
(b) stochastic variation; and
(c) the mutation’s affect on its own probability of transmission to the next generation (its “fitness affect”).

Because the neo-Darwinian process is strictly mechanistic, numerical simulation can precisely and rigorously model this process. If one knows how many good and bad mutations enter a population each generation, and if one knows which individuals within that population reproduce and pass on their mutations, numerical simulation allows us to count precisely how fast the good and the bad mutations are accumulating. One can see exactly what is happening in terms of transmission and selection. It ceases being a matter of philosophy
or abstract reasoning, but simply becomes a matter of straight-forward mechanics and arithmetic.


The analysis of the mutation/selection process by numerical simulation is much like accounting. It is
concrete and objective, even as accounting is concrete and objective. In a business, one starts with certain
assets (resources) and liabilities (debts). Net worth is simply assets minus debts. Every day there are
transactions. There are incoming revenues (additions) and outgoing expenses (subtractions). Debts are paid
off and new debts are incurred. At the end of the year the accountant will tally net worth, and determine if
there was net profit or net loss. The bottom line is not so much where a given dollar went, the central issue
is always “was there a net profit or a net loss? This is neither abstract nor philosophical. It is a question
with a concrete and verifiable answer—something for which the IRS can hold us legally accountable.


In the same way, at any given point in time, a real living population has a certain “net worth.” This is
the fitness of the species, which is the total “biological functionality” of the species. Species’ fitness derives
from the total genetic information stored up in the species’ genome. Every generation, new mutations
arise within every individual’s genome. The good mutations are like income—they add to the species’
net worth or fitness. The bad mutations are like expenses—they subtract from net worth. If there are
more bad mutations than good mutations, there must obviously be a decline in net worth. This means that
there is a net loss of information in the genome, and a corresponding decline in fitness. In this case the species
has lost some of its biological functionality.Such loss of biological functionality will be physically manifested
in measurable characteristics such as shorter life span, reduced intelligence, or lower fertility. If the bad
mutations are much more numerous than the good, and they continue to accumulate faster than the good
mutations, there will a net loss of information every generation, and a continuous net reduction in fitness.
It then becomes only a matter of time until such a species’ goes extinct. This is just like a business
which every year has expenses which exceed income.


Deficit spending can only go so long before there is a serious problem. The accumulation of good and bad
mutations is a simple matter of arithmetic."

This is a ten page abstract of the study done by these scientists in which they found a way to study the actual impact of mutations on populations over time.  The assumption behind the program they created is that Darwinism is the way the world of organisms have come to be so that, if Darwinist thought is correct, the program will demonstrate success.  

"...An honest computer accounting program is all that is needed for allowing an explicit/empirical/experimental approach to understanding mutation accumulation. It was for  this reason that a team of geneticists and computer scientists developed the program Mendel’s Accountant (Sanford, Baumgardner, Gibson, Brewer, & Remine 2007a, 2007b; Baumgardner, Sanford, Brewer, Gibson, & Remine, 2008). This program has been extensively validated in terms of its fidelity in modeling the neo-Darwinian process (see Sanford, et al., 2007a). The primary underlying assumption of this program is simply the neo-Darwinian mechanism itself, as it is taught in all textbooks. Therefore, if Mendel fails to demonstrate evolution, the fault is not in the program
(which faithfully models neo-Darwinian theory), but is in the theory itself.

Mendel’s Accountant is essentially a very advanced genetic spreadsheet, useful for studying the outcome
of the mutation/selection process. The program allows us to correctly tally accumulating mutations, just as
they would accumulate in nature. Mendel’s Accountant serves as a powerful teaching tool because it can
very graphically reveal how the mutation/selection process really works. It does this in a way that any
open-minded person should be able to understand and accept. It is also a powerful research tool, which
allows us to empirically find answers to otherwise unmanageably complex genetic questions."

Some of the problems that this tool reveals are well known to population geneticists and many Darwinists are aware of them as well.  These include, and are not limited to:

"The Problem of Linkage

The problem of linkage was first described by Muller (1964). Since that time linkage has been recognized
as a serious problem for evolutionary theory, and thus many theorists have tried to make the problem “go
away”. The problem is that our genome is made up of large linkage blocks which do not recombine, and
which are on average 30,000 nucleotides long (about the size of a typical gene). So mutations accumulate
within clusters that never break apart. But one of the essential things that selection must accomplish if
forward evolution is to be feasible, is to separate the good mutations from the bad mutations. Given that
most mutations are bad, it should be obvious that any rare good mutation will always be linked to many
bad mutations within its linkage cluster."

"it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained…

it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection…

it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements."

Hermann Muller quoted by John Sanford - Appendix 1, Genetic Entropy


Or this one:

"Allele Frequency and Fixation

The mutations that can not be selected away within a population will continuously accumulate.
A small number will increase in frequency up to the point of fixation (such that every individual will
be homozygous for such mutations). However, the vast majority of mutant alleles will drift out of the
population, including most of the beneficials. Mendel’s Figure 5 (not shown here) shows allele frequencies at the end of a run, and the fraction of alleles that have become fixed. In all Mendel runs, every new mutation first enters the population as a singe copy. These extremely rare alleles will either be quickly lost, or will drift further into the population—becoming more frequent. Except in very small populations, this drifting process is
extremely slow. A disproportionate fraction of all mutant alleles will remain very rare (piling up on
the left, with frequencies of less than 1%). The more common alleles that have drifted into the population
become distributed quite uniformly—establishing an essentially level distribution across all frequencies
ranging from 5% to 99%. These “common alleles” represent what is essentially a “conveyor belt of
mutant alleles”—which gradually moves to the right. When alleles get to the far right, they become fixed
when they have an allele frequency of 100%. Mendel shows that this conveyor belt moves extremely slowly
except in very small populations. This applies equally to beneficial mutations—confirming the essence of
Haldane’s Dilemma” (Haldane, 1957)."

Or this one:

"The Problem of the “Near-Neutral Zone”

The disastrous accumulation of mutations, and the corresponding decline in fitness, is largely due to the
problem of nearly-neutral mutations. The problem of near neutral mutations has been known for a
long time. Muller first mentions it when describing Muller’s ratchet (1964), and it was extensively
developed conceptually and mathematically by Kimura (1979, 1983). Kondrashov expanded upon
this problem further (Kondrashov, 1995). Sanford (2005), describes the actual distribution of mutationeffects
in depth. It is very clear that most mutations in large genomes must be nearly-neutral (see also
Sanford et al., 2007a).

The logic behind this problem is very compelling. Since the human genome has 3 billion nucleotides, each
nucleotide contains on average, about .0000000003 of the total genomic information. The information of the
genome should most typically increase or decrease by this amount—this is the fundamental genomic unit
or mutational unit. So the loss of a typical functional nucleotide (a single deleterious point mutation) should
decrease biological fitness by about this amount. But normally we can only measure biological effects that
increase or decrease fitness by about 10% (0.1). So most mutations are a million fold more subtle than
what we can actually measure. This means there is no practical way we could detect or artificially select
against such mutations. Mother Nature (natural selection) has exactly the same problem."

We then come to the conclusion:

"Conclusion

At its most fundamental level, evolutionary genetic theory must be about tracking mutations and allele
frequencies. It boils down to a very large accounting problem. To objectively test evolutionary genetic theory
the thing that has been lacking has been a practical mechanism for tracking each mutation, through large
populations, over many generations, in a biologically realistic manner. This has now become possible
for the first time, using the numerical simulation program called Mendel’s Accountant. This program
is a powerful teaching and research tool. It reveals that all of the traditional theoretical problems that
have been raised about evolutionary genetic theory are in fact very real and are empirically verifiable in a scientifically rigorous manner. As a consequence, evolutionary genetic theory now has no theoretical
support—it is an indefensible scientific model. Rigorous analysis of evolutionary genetic theory
consistently indicates that the entire enterprise is actually bankrupt. In this light, if science is to
actually be self-correcting, geneticists must “come clean” and acknowledge the historical error, and must
now embrace honest genetic accounting procedures.

While numerical simulations can not honestly be used to support evolutionary theory, a surprisingly
wide range of very reasonable biological input parameters give rise to Mendel output compatible
the biblical account of a recent creation (not shown). Biologically reasonable Mendel input parameters
produce output consistent with:
(a) rapid local adaptation followed by phenotypic stabilization;
(b)a spike in genetic variation followed by continuously declining diversity;
(c) rapid genetic degenerationtapering into a more gradual but continuous genetic decline; and
(d) many extinction events."

Again, this link will take you to the abstract itself and you can also see the resources and references listed along with the paper. 

Serious studies are ongoing by scientists who are not limited by a predisposition to limit their studies to only naturalistic materialistic outcomes.   As a result of studies such as, for instance, the series of studies resulting from the efforts of ICR:  The Institute for Creation Research has recently launched its National Creation Science Foundation

ICR maintains laboratory facilities on its campus in Dallas, Texas.

Research Projects


ICR research projects are at the forefront of science, discovering and gathering evidences in support of biblical truth. Learn more about ICR's current research endeavors. These projects include:
  • GENE
  • RATE II
  • FAST
  • CLIMATE
  • COSMOS
  • EPIPHANY
Previously completed scientific studies include research on Mount St. Helens, Grand Canyon, and Radioisotopes and the Age of the Earth (RATE I).

~

Several other Creation or Intelligent Design institutes are found on my links list.  Some specialize in peer-reviewed periodicals and publications, some in experimentation, some in research, some in education.  If you do take the time to review some of these sites you will be able to discover that origins science comes in more than one flavor and that Creationists don't just thump their Bibles and run laps.  My contention would be that the honest scientist must abandon Darwinism now while his authenticity and integrity can still be maintained.  Mendel’s Accountant has tested Darwinism and found it wanting.  Darwin gets an "F."

12 comments:

WomanHonorThyself said...

Wow Radar...I am always in awe of the amount of research and knowledge u present...will read the comments as they pour in as always to see how they attempt to refute the irrefutable!!

Anonymous said...

You know, Woman, it's really not that hard. You know how to cut and paste, right?

Jon Woolf said...

So sad, to see such an elegant theory killed off by the ugly brutality of barbarian facts.

Of course, in this case it's the creationists' "theory" that's the victim. This lengthy exercise in armchair science fails for the simple reason that empirical evidence completely contradicts it. We can watch the evolutionary process at work in the world today, so we know that Darwin and his successors have got it basically right, and these guys got it completely wrong.

Of course, the fact that all the paper's authors are avowed creationists (with the possible exception of Gibson) doesn't exactly do wonders for its credibility either.

As for "facilitated variation," "genetic redundancy," and "information," the only thing that your posts on those topics prove is that you don't understand these subjects well enough to discuss them. All you ever do is post huge quotes from other people's work, then run away from all attempts at discussion.

The bottom line is that the evolutionary process works in the real world. We can watch it; we can predict it; we can see its evidence in the rocks and organisms around us. That should tell you that we've got the basics of the theory pretty well right ... and you don't.

Hawkeye® said...

Jon Woolf,
"We can watch the evolutionary process at work in the world today, so we know that Darwin and his successors have got it basically right..."

What you refer to as "the evolutionary process" is merely "adaptation". At best it might be called "micro-evolution". The existence of micro-evolution does not automatically confirm the existence of "macro-evolution". To claim as much is to "assume"... and you know what that means.

To say that micro-evolution validates macro-evolution is a non-sequitur. It does not follow.

Consider: A certain population of creatures is subjected to a new environment. Likewise, a mail carrier is assigned to a new postal route.

Those creatures adapt over time to that new environment and have difficulty mating with the original creatures. Likewise, the mail carrier adapts over time to the new route and has difficulty doing the old route.

This is the same process by which mankind evolved from inanimate matter. Likewise, this is the same process by which the U.S. Postal System evolved from nothing.

It does not follow.

Anonymous said...

Hawkeye, you mentioned in another comment the notion of taking an opposing viewpoint on its own merits for the purposes of argument. Would you consider applying this principle to the theory of evolution?

It seems that almost all discussion regarding the theory of evolution on this blog, from Radar and from yourself, is based on a strawman version of the actual theory, and is thus of little worth, since it relies on arguments that are not actually made by the theory of evolution.

In the theory of evolution, there is only one difference in definition between micro-evolution and macro-evolution, which is that macro-evolution is at the species level and above. When two organisms can no longer reproduce together, they are (at least) different species. This is an example of macro-evolution, by definition.

According to the theory of evolution, there is no barrier to the extent of change that a large number of small changes can bring about, and nobody has ever been able to falsify this, or to present a barrier that might prevent this.

According to creationists, all genetic information is already contained in the organism and subsequently only "lost" or regulated. Genetic information being regulated overlaps with mainstream science.

As for the genetic information already being there since, if you'll pardon the phrase, the origin of species - this is what truly differentiates the creationist model and sets it apart.

But this hypothesis - and strictly speaking that's all it is at the moment, at most - has not yet had the honor of being supported or tested.

-- creeper

Chaos Engineer said...

It seems like there's a bug somewhere in the "Mendel's Accountant" program. It claims that populations will become less fit over time, but that's not what we see in reality. (E. Coli bacteria reproduce every 15 minutes or so, and it's not terribly difficult to show that they don't become less fit even over thousands or tens-of-thousands of generations.)

I skimmed the article and found two big mistakes.

The first one is this:

If there are more bad mutations than good mutations, there must obviously be a decline in net worth. This means that there is a net loss of information in the genome, and a corresponding decline in fitness.

That will only happen if bad mutations and good mutations survive at the same rates. If good mutations survive, and bad mutations die out, then it doesn't matter that there are more bad mutations than good. One famous demonstration is Dawkins' Weasel Program, a simple genetic algorithm where less than 4% of mutations are "good".)

The second problem is here:

Therefore, if Mendel fails to demonstrate evolution, the fault is not in the program (which faithfully models neo-Darwinian theory), but is in the theory itself.

Basically the authors are a bunch of arrogant jerks. If you're writing a scientific paper, you don't waste space boasting about how great it is. You just humbly state your theory and let the readers decide if it's any good.

I mean, Einstein didn't conclude his papers on Relativity with "My calculations are flawless! Teachers of Newtonian Physics have now been exposed as the wicked liars they are!" If you approach your subject matter with that kind of hubris, then you're not going to spend enough time looking for flaws in your reasoning or asking your peers if they see anything you missed.

Anyway, if you can get the authors of the paper to provide their source code, I guess we could help them debug it.

Jon Woolf said...

To say that micro-evolution validates macro-evolution is a non-sequitur. It does not follow.

You can prove this, of course?

You can prove -- rigorously, using actual data from genetics and physiology -- that there is some Mendel's Demon at work in the genotype that says "bulldog to toy poodle is okay, but house cat to leopard is not?"

Enlighten us, please.

Hawkeye® said...

creeper,
"It seems that almost all discussion regarding the theory of evolution on this blog, from Radar and from yourself, is based on a strawman version of the actual theory, and is thus of little worth, since it relies on arguments that are not actually made by the theory of evolution.

In the theory of evolution, there is only one difference in definition between micro-evolution and macro-evolution, which is that macro-evolution is at the species level and above. When two organisms can no longer reproduce together, they are (at least) different species. This is an example of macro-evolution, by definition."


Let me start by saying that I am not an "expert" in the "theory of evolution" by any means. Therefore, it is quite possible that my understanding of the theory as it was taught to me (perhaps 100 years ago) is no longer valid. (:D)

I've read books (or excerpts) both in favor of evolution and critical of it. I've read Darwin's 'Voyage of the Beagle'. In my youth I was firmly convinced that evolution was a scientific fact. But as I matured and was presented with ever more evidence of problems with the theory of evolution, I became skeptical.

However, I must say that I find your statement that micro-evolution "is an example of macro-evolution, by definition", to be a very convenient one for you. That would be like Christians saying: "faith in God proves that God exists, by definition."

In other words, he who makes the definitions wins the argument. Because of your definition, you don't have to prove the existence of macro-evolution. You only to prove the existence of micro-evolution, because macro-evolution IS in fact micro-evolution (by definition). Rather a circular argument, wouldn't you say? Why then do you use two different terms if they are both the same thing?

You say that macro-evolution is defined as being "at the species level and above". And no doubt that is what evolutionists WANT to believe, but it cannot be so. Macro-evolution MUST be ABOVE the species level because one type of mosquito becoming a slightly different type of mosquito (even if they cannot mate) fails to address the radical differences we see between Kingdom, Phylum, Class, Order, Family, and even Genus.

Nevertheless, let's assume for a moment that such slight variations are what in fact constitutes (by definition) "macro-evolution". Then (by definition), the fossil record must be filled with millions of such small transitions from one creature to the next in an almost seamless flow of examples that irrefutably demonstrates the validity of your "theory". Correct? But this is hardly what we find, is it?

Let's even assume for a moment that you've had "billions" of years of uniform, uninterrupted fossil formation and sedimentation. Why is it that we don't find evidence of slow, continuous, seamless transitions? Why does the fossil record show rapid, widespread diversity coming in spurts (ie, punctuated equilibrium)? Why is it that many forms which exist today are completely unchanged over billions of years?

Admit it. The facts just don't support your "theory".

Hawkeye® said...

Jon Woolf,
See my comment in response to creeper.

Jon Woolf said...

You're obviously fairly new to this game of defending crank science, Hawkeye. People who have been doing it for a while are much better at concealing their attempted semantic cons.

You wrote: "However, I must say that I find your statement that micro-evolution 'is an example of macro-evolution, by definition',"

That isn't what creeper said. He said that speciation is by definition an example of macro-evolution.

To be sure, there used to be something of a controversy within evolutionary biology over whether or not macro-evolution is just accumulated micro-evolution. But not today. We know so much about the process now that the "micro vs macro" distinction just isn't defensible anymore except (as Creeper said) as a purely technical, semantic point. There is no qualitative difference between bullmastiff-to-toy-poodle and housecat-to-leopard, even though one is all within a species and the other crosses not only species but genera. It's all just evolution.

radar said...

"You're obviously fairly new to this game of defending crank science, Hawkeye. People who have been doing it for a while are much better at concealing their attempted semantic cons."

Okay, Jon Woolf! You are an old hand at defending crank science, I will give you that...I hereby declare you the best crank science defender amongst the commenters, bar none!

Hawkeye® said...

Jon Woolf,
I beg to differ. Nowhere did creeper use the word speciation. He may have implied that, but he did not say it. He said that there is only one difference between "micro-" and "macro-". That difference was so minor as to effectively make them the same thing. They are not...

Gould and Eldredge argued that macroevolution be decoupled from microevolution and proposed that a higher level process called "species selection" (a sort of natural selection of whole species) take the place of mutation and natural selection:

"Macroevolution is decoupled from microevolution, and we must envision the process governing its course as being analogous to natural selection but operating at a higher level of organization. [We would say that it is natural selection, working at a level higher than the local population.] In this higher-level process species become analogous to individuals, and speciation replaces reproduction. The random aspects of speciation take the place of mutation. Whereas, natural selection operates upon individuals within populations, a process that can be termed species selection operates upon species within higher taxa, determining statistical trends." (Gould S.J. & Eldredge N., "Punctuated equilibria: the tempo and mode of evolution reconsidered", Paleobiology, 1977, vol. 3, p140)