Darwinist Debating Device #6: “The Literature Bluff”

_{Barry Arrington

October 16, 2014

Intelligent Design}

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In this post Dr. Hunter shows us professor of English Terry Scambray completely destroying three Ph.D Darwinists on basic logic and reasoning.

Jeffrey Shallit takes to his website to rebut Professor Scambray’s arguments and falls flat on his face.

First Shallit takes Scambray to task for asserting that “Animals and plants appear in the fossil record fully formed and remain unchanged through millions of years.” Shallit dismisses the claim as “pure creationist babble.”

Eminent Darwinist Stephen Jay Gould wrote the following:

The history of most fossil species includes two features particularly inconsistent with gradualism:

(1) Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless.

(2) Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and ‘fully formed.’

Apparently the most famous Darwinist of the late 20^th century was going around spouting “pure creationist babble.” Who knew?

Next, Shallit makes a classic literature bluff.

Scambray claims, “Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies.” Really? At my university, we have access to articles that say something different. Maybe at Bizarro College, they don’t.

Notice that Shallit does not actually say what the “something different” is that refutes Scambray’s assertion. Why not? Because Scambray’s assertion is correct. Every attempt to demonstrate evolution through irradiating fruit flies has been an abject failure. What is the “something different” to which Shallit alludes? We may never know, but we do know that he is bluffing.

Note carefully the common Darwinist tactic here:

Literature bluff: There are thousands of books and articles demonstrating Darwinist proposition X.

Calling the bluff: OK, show me exactly where in just one of those books or articles this proposition is established.

Inevitable Darwinist response: [crickets]

Next, Shallit goes after Scambray over those famous Galapagos finches.

Scambray writes:

So also much the same thing happened with the famous “Galapagos finches” whose average beak size became bigger when the conditions there made it harder to find food due to bad weather. Then when food became more plentiful, the beak size of those finches that survived returned to normal. Thus the finches changed a little, adapted, while remaining fundamentally unchanged.

Shallit’s rebuttal:

Mr. Scambray, if he has ever visited the Galapagos, must have visited a parallel Galapagos, because he claims, “Thus the [Galapagos] finches changed a little, adapted, while remaining fundamentally unchanged.” He doesn’t seem to understand that there are 15 different species of finches, all descended from a common ancestor that colonized the Galapagos millions of years ago. Things must be different in Bizarro World.

First, Shallit does not actually respond to the argument that Scambray made. Scambray points to evidence that is undisputed by all researchers, whether they toe the Darwinist line or not: With respect to a particular species of finch, environmental pressures caused a change in beak size and when those pressures eased the beak sizes reverted to normal.

Shallit completely ignores this evidence and responds to an assertion that Scambray did not even make. Shallit pretends that Scambray asserted that there are never any changes within a type [this is called “erecting a strawman”] and then demolishes the argument that Scambray did not make by noting there are 15 different types of finches on the Galapagos [This is called “knocking down a strawman”].

No, Mr. Shallit. Scambray never asserted that there are never any changes within a type. He asserted that the “finch beak evidence” that Darwinists commonly assert is knock down show stopping evidence for marcroevolution is in fact no such thing. It is unsurprising that your response is to try to change the subject and demolish an argument that Scambray never made.

I HAVE SAVED THE BEST FOR LAST.

Shallit implies that the fact that there are 15 different finch species that all descended from a common ancestor over millions of years is a clincher for Darwinist macroevolution.

Now let me get this straight. Millions of years ago there was a finch. Now there are 15 kinds of finches, but they are all basically the same kind of thing. (That’s why we call all of them “finches.”)

Shallit takes evidence of minor changes within a kind that even the most fervent young earth creationist would admit and claims those minor changes are indisputable evidence for how finches came to be in the first place. Astounding.

If I didn’t have the actual citation and link to Shallit’s post I would not blame you for accusing me of making it up. But you can see for yourself that I did not make it up. This is exactly what he wrote. And this leads me to the following conclusion: The best evidence against Darwinism is often what the Darwinists themselves write.

I will concede that Shallit knows Darwinism inside out. And if anyone would know of valid Darwinist arguments to rebut Scrambray, it would be him. Yet, Shallit’s facile and childish “rebuttal” does not stand up to the slightest scrutiny.

Comments

That is not what he meant. He meant millions of generations in ‘laboratory testing’, which is absolutely correct.
I don't know what he meant, and nor do you. I only know what he said, which is absolutely incorrect. There have only been a few thousand generations in 'laboratory testing'. Do you think there have been millions of generations of humans since world war II? Roy P.S. File the rest of your post under #4 Roy

correction,, Roy,
"I’m contesting that there have been millions of generations of fruit flies in laboratory testing."
That is not what he meant. He meant millions of generations in 'laboratory testing', which is absolutely correct. Of course you know that is what he, a English professor who certainly knows how to construct sentences properly, meant.,,, You are not dumb, so why do you pretend as if we can't see thru your purposely trying to twist the meaning of what he clearly wrote? More to the point, why are you so concerned about proper English and are not concerned in the least that you, in fact, have no scientific evidence to substantiate your claims for Darwinism?? such as in the following recent large scale evolutionary experiment???
Mutation + Selection = Stasis - October 8th, 2014 Excerpt: As a trained physicist, Desai applied a statistical perspective using robots to precisely manipulate hundreds of lines of yeast to perform large scale evolutionary experiments. Scientists have long studied genetic evolution of microbes, but until now, only a few strains at a time. Robotically managing 640 lines of yeast from a single parent cell, Desai’s team was efficiently tooled to statistically analyze evolution at this level for the first time. In an interview with Singer, Joshua Plotkin, an evolutionary scientist at the University of Pennsylvania, commented, “This is the physicist’s approach to evolution, stripping down everything to the simplest possible conditions… They could partition how much of evolution is attributable to chance, how much to the starting point, and how much to measurement noise.”,,, While early mutations in the experiment initially variably influenced fitness, fitness in the final generations was the same. “Scientists,” Singer noted, “don’t know why all genetic roads in yeast seem to arrive at the same endpoint”.,,,, “I think many people think about one gene for one trait, a deterministic way of evolution solving problems,” David Reznick, a biologist at the University of California-Riverside, told Singer. “This says that’s not true.” Unexpectantly, Desai’s team discovered genetic mutations plus selection yields stasis in the microbe model– not evolution. http://www.darwinthenandnow.com/2014/10/mutation-selection-stasis/
bornagain77

Roy,
"I’m contesting that there have been millions of generations of fruit flies in laboratory testing."
That is not what he meant. He meant millions of generations in 'laboratory testing', which is absolutely correct.
Of course you know that is what he, a English professor who certainly knows how to construct sentences properly, meant.,,, You are not dumb, so why do you pretend as if we can't see thru your purposely trying to twist the meaning of what he clearly wrote? More to the point, why are you so concerned about proper English and are not concerned in the least that you, in fact, have no scientific evidence to substantiate your claims for Darwinism?? such as in the following recent large scale evolutionary experiment???
Mutation + Selection = Stasis - October 8th, 2014 Excerpt: As a trained physicist, Desai applied a statistical perspective using robots to precisely manipulate hundreds of lines of yeast to perform large scale evolutionary experiments. Scientists have long studied genetic evolution of microbes, but until now, only a few strains at a time. Robotically managing 640 lines of yeast from a single parent cell, Desai’s team was efficiently tooled to statistically analyze evolution at this level for the first time. In an interview with Singer, Joshua Plotkin, an evolutionary scientist at the University of Pennsylvania, commented, “This is the physicist’s approach to evolution, stripping down everything to the simplest possible conditions… They could partition how much of evolution is attributable to chance, how much to the starting point, and how much to measurement noise.”,,, While early mutations in the experiment initially variably influenced fitness, fitness in the final generations was the same. “Scientists,” Singer noted, “don’t know why all genetic roads in yeast seem to arrive at the same endpoint”.,,,, “I think many people think about one gene for one trait, a deterministic way of evolution solving problems,” David Reznick, a biologist at the University of California-Riverside, told Singer. “This says that’s not true.” Unexpectantly, Desai’s team discovered genetic mutations plus selection yields stasis in the microbe model– not evolution. http://www.darwinthenandnow.com/2014/10/mutation-selection-stasis/
bornagain77

I'm contesting that there have been millions of generations of fruit flies in laboratory testing. That would require about 30,000 years. Do you think there have been millions of generations of humans since world war II? Roy Roy

Roy, Are you contesting the total number of experiments done in labs trying to get some organism to evolve into 'something different'? or are you contesting the fact that no one has ever found any evidence for an organism evolving into 'something different'? In either case you would be wrong. Lenski's long term evolution experiment by itself has over 58,000 generations behind it.,,, Add all the tests done by all the thousands of graduate students, research institutes, and genetic companies, then you easily pass 'millions of generations of laboratory testing',,,
"Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment instead of regularly producing a range of new systematic species…" (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) Dr. Wolf-Ekkehard Lönnig, is (retired) Senior Scientist (Biology), Max Planck Institute for Plant Breeding Research, Emeritus, Cologne, Germany.
As to fruit flies,,
Response to John Wise – October 2010 Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies
Supplemental Quote:
Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282
bornagain77

... Scambray’s assertion is correct.
Really? You think this assertion:
Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies.”
is correct? Are you innumerate? Roy Roy

Barry, I hope you cover irrational extrapolation in your series on Darwinian debating devices. bb

Alan - “I do wonder what you mean by normal, however?” Barry - "I don’t mean anything by “normal.” You’ll need to ask the researchers who performed the study what they meant by “normal.” I assume they meant that average beak sizes reverted to the pre-famine mean." I think you are misunderstanding things from his world point of view. He views things from an Alternative Lifestyle perspective. For Alan this has never been about Science. It's always been about accountability and morality. Of course you could Google all of this, but be warned, it will make you sick to your stomach. Just sayin . . DavidD

This posting seems to have struck a chord. The darwinists are worked up in a frenzy throwing all kinds of mush at the wall hoping something will stick or serve as a distraction. Pretty entertaining reading the comments and watching any shred of an evolutionist argument effortlessly dismantled. Do these guys have anything of substance to put on the table anymore? lifepsy

Every attempt to demonstrate evolution through irradiating fruit flies has been an abject failure.
Irradiated fruit flies are a textbook example of evolution in action. The less fit don't survive. Mung

ok, so I just calculated genetic entropy. where's my nobel prize? Mung

I asked you, for simplicity, consider a sequence: CTACTAGGCTACTGGC What is its genetic entropy?
Ge = 0 Mung

This following video brings the point personally home to us about the effects of genetic entropy:
Aging Process - 80 years in 40 seconds - video http://www.youtube.com/watch?v=hSdxYmGro_Y
Verse and music:
John 8:24 I said therefore unto you, that ye shall die in your sins: for if ye believe not that I am he, ye shall die in your sins. Lecrae Live at Passion 2013 http://www.youtube.com/watch?v=gu59YLVTfV0
bornagain77

Diogenes, do you usually blatantly misrepresent what others say when you disagree with them? Unfortunately for you, anyone can check post 47 and see exactly what I claimed about that series of drawings you listed:
This following example is interesting in that the genetic entropy is not nearly as ‘in your face’ as the preceding examples Diogenes gave, but the series of fossils are still easily recognizable as being in the same ‘kind’ of species. A Pliocene Snail 10 mya to 3 mya http://www.don-lindsay-archive.org/creation/snails.html
But hey, so be it that you don't care to be exposed as so blatantly dishonest in the very thread you are commenting on, it makes my job much easier when you do as you just have done! ,,, here is another example of genetic entropy from the fossil record and genetics that hits much closer to home:
Are brains shrinking to make us smarter? - February 2011 Excerpt: Human brains have shrunk over the past 30,000 years, http://www.physorg.com/news/2011-02-brains-smarter.html If Modern Humans Are So Smart, Why Are Our Brains Shrinking? - January 20, 2011 Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.” “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,, He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.” http://discovermagazine.com/2010/sep/25-modern-humans-smart-why-brain-shrinking Study suggests humans are slowly but surely losing intellectual and emotional abilities - November 12, 2012 Excerpt: "Human intelligence and behavior require optimal functioning of a large number of genes, which requires enormous evolutionary pressures to maintain. A provocative hypothesis published in a recent set of Science and Society pieces published in the Cell Press journal Trends in Genetics suggests that we are losing our intellectual and emotional capabilities because the intricate web of genes endowing us with our brain power is particularly susceptible to mutations and that these mutations are not being selected against in our modern society." http://medicalxpress.com/news/2012-11-humans-slowly-surely-intellectual-emotional.html#jCp Is Human Intellect Degenerating? - February 19, 2013 Excerpt: A recent study of the Online Mendelian Inheritance in Man (OMIM) database, although incomplete, indicates that about half of all human genetic diseases have a neurologic component, [6], frequently including some aspect of [intellectual deficiency], consistent with the notion that many genes are required for intellectual and emotional function. The reported mutations have been severe alleles, often de novo mutations that reduce fecundity. However, each of these genes will also be subject to dozens if not hundreds of weaker mutations that lead to reduced function, but would not significantly impair fecundity, and hence could accumulate with time... https://uncommondesc.wpengine.com/intelligent-design/is-human-intellect-degenerating/
and:
Genetic Entropy in Human Genome is found to be 'recent': Human Genetic Variation Recent, Varies Among Populations - (Nov. 28, 2012) Excerpt: Nearly three-quarters of mutations in genes that code for proteins -- the workhorses of the cell -- occurred within the past 5,000 to 10,000 years,,, "One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,",,, "Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older." (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,, The report shows that "recent" events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers. The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,, http://www.sciencedaily.com/releases/2012/11/121128132259.htm Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens."
I went to the mutation database website cited by John Avise and found:
HGMD®: Now celebrating our 100,000 mutation milestone! http://www.hgmd.org/
I really question their use of the word 'celebrating'. (Of note, apparently someone with a sense of decency has now removed the word 'celebrating')
Genetic Entropy and The Mystery Of the Genome - Dr. John Sanford - video http://www.youtube.com/watch?v=GwCu4rh7kUk Notes from John Sanford's preceding video: *3 new mutations every time a cell divides in your body * Average cell of 15 year old has up to 6000 mutations *Average cell of 60 year old has 40,000 mutations Reproductive cells are 'designed' so that, early on in development, they are 'set aside' and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,, *60-175 mutations are passed on to each new generation.
bornagain77

BA77 won’t define “genetic entropy and can’t compute it because Intelligent Design is a fraud.
Those two clauses are logically unrelated, so I can only assume you said that as a rhetorical strategy. BA77 can't compute genetic entropy because there really is no such thing as genetic entropy. Yet this in no way implies that ID is a "fraud." If you must be emotional about this, at least make your clauses logically connected. Genomicus

Great- we can't say that macrevolution/ universal common ancestry exists because there isn't any equations that support it. Nice job, diogenes Joe

No. You cannot say "Genetic Entropy" exists if you can't copy and paste an equation. I asked you, for simplicity, consider a sequence: CTACTAGGCTACTGGC What is its genetic entropy? But you could not compute its genetic entropy, and you don't have the manhood to admit YOU CAN'T because YOU DON'T KNOW THE EQUATION. So I will simplify it, and cut the sequence in half. CTACTAGGC What is its genetic entropy? How simple a question do I have to ask before you either 1. answer it or 2. Be a man and admit you can't answer it! BA77 won’t define “genetic entropy and can’t compute it because Intelligent Design is a fraud. Diogenes

Diogenes, to help easily visualize how the equations of population genetics establish genetic entropy and falsify neo-Darwinism, a graph featuring 'Kimura's Distribution' is shown in the following video: Darwinian Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 bornagain77

So Diogenes I guess the 'equation(s)' that establish genetic entropy and falsify evolution (although Darwinists will not accept falsification from mathematics) are the equations of population genetics: Mathematical Methods of Population Genetics http://pespmc1.vub.ac.be/MATHMPG.html Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load: Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE http://mendelsaccount.sourceforge.net bornagain77

Diogenes (being the unbiased party he is) 'demands':
Copy and paste an equation to compute genetic entropy, or shut up.
Actually Diogenes, it is funny you would bring this up for I was just thinking about the failure of evolution to establish a mathematical basis yesterday: ,,,It interesting to note what Dr. Torley stated in his recent article exposing the 'in thin air' foundation that Darwinism rests upon:
Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013 Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? https://uncommondesc.wpengine.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/
The lack of a mathematical foundation was particularly surprising for me, because I had been assured by a evolutionary professor (whom Dr. Torley referenced in his article) here on UD, years ago, that Darwinism was 'mathematical' through and through. And yes one can say that Darwinism is 'mathematical' through and through, but what one cannot say is that Darwinism has a rigid mathematical basis from which one can make extensive predictions with) Well, after being subtly misled for years by that professor's distortion of the facts, I finally, in my slow pace, started to piece together the fact that Darwinism has no rigid mathematical foundation at all,,
Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. … http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/ Accounting for Variations – Dr. David Berlinski: – video http://www.youtube.com/watch?v=aW2GkDkimkE Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.
In fact, contrary to what the employers at Oxford would like to believe, the truth is that there is not some magical mystery equation out there waiting to be discovered to finally give Darwinism the foundation that it needs to be considered truly scientific. The fact is that Darwinists have refused to listen to what the equations of population genetics are thus far telling them. i.e. Darwinists refuse to accept the falsification of their theory from mathematics:
Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008 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. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf
This is simply unheard of in science. Both General Relativity and Quantum Mechanics subject themselves constantly to potential falsification, as well as refinement for accuracy, to see if their mathematical descriptions of reality accurately predict what is observed for reality.
"No human investigation can be called true science without passing through mathematical tests." Leonardo Da Vinci
In my unsolicited personal opinion, the main reason Darwinism cannot be formulated into any coherent mathematical model to give accurate, 'daring', predictions is because of its reliance on the 'random variable postulate' at the base of its formulation:
“In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) - Evolution and the Illusion of Randomness - Talbott - Fall 2011 Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.” In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness Murray Eden, as reported in “Heresy in the Halls of Biology: Mathematicians Question Darwinism,” Scientific Research, November 1967, p. 64. “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
Moreover, as Alvin Plantiga has shown in his Evolutionary argument against naturalism, (i.e. a refinement of "The argument from reason" from CS Lewis), this 'random variable postulate' ends up driving neo-Darwinism into epistemological failure,,,
Scientific Peer Review is in Trouble: From Medical Science to Darwinism - Mike Keas - October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga's nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: "Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not." Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. http://blogs.christianpost.com/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/
,,, the 'unrestrained randomness' at the base of Darwinism, if neo-Darwinism were actually true, results in the epistemological failure of science itself! But this really should not come as a surprise to anyone for how can a theory which denies the reality of mind in the first place be said to guarantee that our perceptions and reasoning of mind are trustworthy?
“It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”. J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.
Supplemental notes: In the following experiment, the claim that past material states determine future conscious choices (determinism) is falsified by the fact that present conscious choices effect past material states:
Quantum physics mimics spooky action into the past - April 23, 2012 Excerpt: The authors experimentally realized a "Gedankenexperiment" called "delayed-choice entanglement swapping", formulated by Asher Peres in the year 2000. Two pairs of entangled photons are produced, and one photon from each pair is sent to a party called Victor. Of the two remaining photons, one photon is sent to the party Alice and one is sent to the party Bob. Victor can now choose between two kinds of measurements. If he decides to measure his two photons in a way such that they are forced to be in an entangled state, then also Alice's and Bob's photon pair becomes entangled. If Victor chooses to measure his particles individually, Alice's and Bob's photon pair ends up in a separable state. Modern quantum optics technology allowed the team to delay Victor's choice and measurement with respect to the measurements which Alice and Bob perform on their photons. "We found that whether Alice's and Bob's photons are entangled and show quantum correlations or are separable and show classical correlations can be decided after they have been measured", explains Xiao-song Ma, lead author of the study. According to the famous words of Albert Einstein, the effects of quantum entanglement appear as "spooky action at a distance". The recent experiment has gone one remarkable step further. "Within a naïve classical world view, quantum mechanics can even mimic an influence of future actions on past events", says Anton Zeilinger. http://phys.org/news/2012-04-quantum-physics-mimics-spooky-action.html
In other words, if my conscious choices really are just the result of whatever state the material particles in my brain happen to be in in the past (determinism) how in blue blazes are my choices instantaneously effecting the state of material particles into the past?,, Here is another piece of evidence that solidly demarcates the randomness of the material particles of the universe from the randomness that would be necessarily inherent within 'conscious' creatures created by God with free will:
Quantum Zeno effect Excerpt: The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay. https://uncommondesc.wpengine.com/intelligent-design/tonights-feature-presentation-epigenetics-the-next-evolutionary-cliff/#comment-445840
Since material particles are held to 'randomly' decay, why in blue blazes is conscious observation putting a freeze on 'random' entropic decay, unless consciousness was/is more foundational to reality than 'random' entropic decay is? This point is really driven home when we realize that the initial entropy of the universe was 1 in 10^10^123, which is, by far, the most finely tuned of initial conditions of the universe.
"The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God." Charles Darwin to Doedes, N. D. - Letter - 2 Apr 1873
Music and verse:
Phillips, Craig & Dean - Great I Am - music http://www.youtube.com/watch?v=zSoz6L1vqm8 Genesis 2:7 And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.
bornagain77

Diogenes, Phillip Johnson made this astute observation: Phillip Johnson - What I saw about the fossil record again,, was that Gould and Eldridge were experts in the area where the animal fossil record is most complete. That is marine invertebrates.,, And the reason for this is that when,, a bird, or a human, or an ape, or a wolf, or whatever, dies,, normally it does not get fossilized. It decays in the open, or is eaten by scavengers. Things get fossilized when they get covered over quickly with sediments so that they are protected from this natural destructive process. So if you want to be a fossil, the way to go about it is to live in the shallow seas, where you get covered over by sediments when you die,,. Most of the animal fossils are of that kind and it is in that area where the fossil record is most complete. That there is a consistent pattern.,, I mean there is evolution in the sense of variation, just like the peppered moth example. Things do vary, but they vary within the type. The new types appear suddenly, fully formed, without an evolutionary history and then they stay fundamentally stable with (cyclical) variation after their sudden appearance, and stasis (according) to the empirical observations made by Gould and Eldridge. Well now you see, I was aware of a number of examples of where evolutionary intermediates were cited. This was brought up as soon as people began to make the connection and question the (Darwinian) profession about their theory in light of the controversy. But the examples of claimed evolutionary transitionals, oddly enough, come from the area of the fossil record where fossilization is rarest. Where it is least likely to happen. Archaeopteryx would be the prime example. Its a bird so we expect it to rarely be fossilized. Yet it has been exhibit number one in the Darwinian case. There's nothing else around it. Unlike those marine invertebrates. So you can tell a story of progressive evolution that might not work out at all if you saw through the whole body of things around it. Likewise with the ape-men. That is another area where fossilization is very rare. And where the bones of humans and apes are rather similar anyway. So (someone) can find a variant ape bone, its pretty easy to give it a story about how it is turning into a human being. If you tell the story well enough, and successfully, you get your picture on the cover of National Geographic and you become rich and famous. This could effect your judgement. One of the things that amused me is that there are so many fossil candidates for human ancestry, and so very, very, few that are candidates for ancestors of the great apes. There should be just as many (if not more) but why not? Well any economist can give you the answer to that. Human ancestors have a great American value so they are produced at a much greater rate. Now these were also grounds to be suspicious with what was going on. That there was obviously so much subjectivity. ,, The Standard explanation for why the fossil record is not more supportive of Darwinian expectations than it is, if you find that out at all (that the fossil record does not fit Darwinian expectation), is that there are so few fossils, (thus) most things aren't fossilized. That is why (we are told by Darwinists) that the fossil record has so many gaps. Not that the theory has many gaps but that the fossil record has so many gaps. Yet that is odd if the problem is the greatest where the fossil record is most complete and if the confirming examples are found where fossils are rarest. that doesn't sound like it could be the explanation. - Phillip Johnson - April 2012 - audio/video http://www.youtube.com/watch?v=FJDlBvbPSMA&feature=player_detailpage#t=903s "Fossil evidence of human evolutionary history is fragmentary and open to various interpretations. Fossil evidence of chimpanzee evolution is absent altogether". Evolutionist Henry Gee, Editor of Nature - 2001 http://www.nature.com/nature/journal/v412/n6843/full/412131a0.html And just as Phillip Johnson noted, I've found abundant evidence for extreme bias in the field of paleo-anthropology https://uncommondesc.wpengine.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/#comment-448487 'Lucy' - The Powersaw Incident - a humorous video showing how biased evolutionists can be with the supposed evidence for human evolution http://www.metacafe.com/watch/4032597 bornagain77

To reiterate: I demanded that BA77 copy and paste an equation to compute genetic entropy. He will not do so. Creationists are totally predictable. They insinuate they know science and math when they know none. Copy and paste an equation to compute genetic entropy, or shut up. Diogenes

Let's see EVEN MORE of what ID proponents and creationists have to say about the fossil record.
Creationist Todd C. Wood wrote: “The truth about evolution …Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well. I say these things not because I'm crazy or because I've "converted" to evolution. I say these things because they are true. I'm motivated this morning by reading yet another clueless, well-meaning person pompously declaring that evolution is a failure. People who say that are either unacquainted with the inner workings of science or unacquainted with the evidence for evolution… Creationist students, listen to me very carefully: There is evidence for evolution, and evolution is an extremely successful scientific theory. That doesn't make it ultimately true… It is my own faith choice to reject evolution, because I believe the Bible reveals true information… I am motivated to understand God's creation from what I believe to be a biblical, creationist perspective. Evolution itself is not flawed or without evidence. …Faith is enough. If God said it, that should settle it.” [Todd C. Wood, “The Truth About Evolution”, 2009]
Diogenes

Let's see SOME MORE of what ID proponents and creationists have to say about the fossil record.
Creationist Kurt Wise wrote: “In various macroevolutionary models, stratomorphic intermediates might be expected to be any one or more of several different forms… As an example (and to provide informal definitions), if predictions from Darwin’s theory were re-stated in these [creationist] terms, one would expect to find: – (a) numerous stratomorphic intermediates between any ancestor-descendent species pair (numerous interspecific stratomorphic intermediates); (b) species which were stratomorphic intermediates between larger groups (stratomorphic intermediate species); (c} taxonomic groups above the level of species which were stratomorphic intermediates between other pairs of groups (higher-taxon stratomorphic intermediates); and (d) a sequence of species or higher taxa in a sequence where each taxon is a stratomorphic intermediate between the taxa stratigraphically below and above it (stratomorphic series). … It is a Very Good Evolutionary Argument Of Darwinism’s four stratomorphic intermediate expectations, that of the commonness of inter-specific stratomorphic intermediates has been the most disappointing for classical Darwinists. The current lack of any certain inter-specific stratomorphic intermediates has, of course, led to the development and increased acceptance of punctuated equilibrium theory. Evidences for Darwin’s second expectation - of stratomorphic intermediate species - include such species as Baragwanathia27 (between rhyniophytes and lycopods), Pikaia28 (between echinoderms and chordates), Purgatorius29 (between the tree shrews and the primates), and Proconsul30 (between the non-hominoid primates and the hominoids). Darwin’s third expectation - of higher-taxon stratomorphic intermediates - has been confirmed by such examples as the mammal-like reptile groups31 between the reptiles and the mammals, and the phenacdontids32 between the horses and their presumed ancestors. Darwin’s fourth expectation - of stratomorphic series - has been confirmed by such examples as the early bird series,33 the tetrapod series,34,35 the whale series,36 the various mammal series of the Cenozoic37 (for example, the horse series, the camel series, the elephant series, the pig series, the titanothere series, etc.), the Cantius and Plesiadapus primate series,38 and the hominid series.39 Evidence for not just one but for all three of the species level and above types of stratomorphic intermediates expected by macroevolutionary theory is surely strong evidence for macroevolutionary theory. Creationists therefore need to accept this fact. It certainly CANNOT said that traditional creation theory expected (predicted) any of these fossil finds. ” [Kurt P. Wise (1995). “Towards a Creationist Understanding of ‘Transitional Forms.’” p.218-9. Creation Ex Nihilo Technical Journal, 9(2), 216-222. (caps original). Full article]
Diogenes

Let's see what ID proponents and creationists have to say about the fossil record.
ID promoter Jonathan Wells wrote: “Fossil evidence suggests that life on earth originated about three and a half billion years ago, starting with prokaryotes (single-celled organisms without nuclei, such as bacteria). Much later came eukaryotes (cells with nuclei), which included algae and single-celled animals (protozoa). Multicellular marine animals appeared long after that. Then came land plants, amphibians, reptiles, mammals, primates, and finally humans. Not only did living things appear in a certain order, but in some cases they also had features intermediate between organisms that preceded them and those that followed them. Kenneth R. Miller challenges critics of Darwinism to explain why we find ‘one organism after another in places and in sequences... that clearly give the appearance of evolution.’1” [Jonathan Wells. “Why Does the History of Life Give the Appearance of Evolution?”, Evolution News & Views, 21 Feb 2013.]
Diogenes

BA77, I'm not watching your YouTube videos nor clicking on your links to creationist sources. Since you blather moronically about "genetic entropy" please provide me with an equation to compute the genetic entropy of a genome before and after a process. Any process. For simplicity, consider a sequence: CTACTAGGCTACTGGC What is its genetic entropy? Oh wait, I forgot. None of you creationists can compute ANYTHING, not specified complexity and not genetic entropy. We have the fossils. We win. Diogenes

corrected link for foramen/plankton from 64.5 million years to 58 million years before present – picture http://www.don-lindsay-archive.org/creation/foram.html bornagain77

by the way ,,,your main problem is not the fossil record, Diogenes, as problematic as that is, your main problem is to demonstrate that purely material processes can generate functional information! Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 Dr. Stephen Meyer comments at the end of the preceding video,,, ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) bornagain77

Diogenes methinks thou beholdest faces in the clouds with your imagined fossil evidence for macro-evolution
“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. Polonius: It is backed like a weasel. Hamlet: Or like a whale? Polonius: Very like a whale.” ? William Shakespeare, Hamlet
The following is Diogenes' first claimed proof for 'evolution':
"Arnold shows a series of microphotographs, depicting the evolutionary change wrought on a single foram species. "This is the same organism, as it existed through 500,000 years," he says. "We've got hundreds of examples like this, complete life and evolutionary histories for dozens of species." ,,, By being so small, the fossil shells escaped nature's grinding and crushing forces, which over the eons have in fact destroyed most evidence of life on Earth. The extraordinary condition of the shells permits the paleontologists to study in detail not only how a whole species develops, but how individual animals develop from birth to adulthood. The resulting data base thus holds unprecedented power for evolutionary studies, says Arnold. Not only can he and Parker use it to describe how evolution has worked in a particular species, but they can use it as a standard for testing evolutionary theories, which are growing in number." http://web.archive.org/web/19990203140657/gly.fsu.edu/tour/article_7.html
But alas when ones looks at the image of their supposedly prime example for macro-evolution one (disappointingly?) finds what looks to me to be, for all intents and purposes, gradual deterioration (genetic entropy) of foramen/plankton from 64.5 million years to 58 million years before present - picture http://web.archive.org/web/19990203140657im_/http://gly.fsu.edu/tour/art7-foram06.jpg One sees much the same pattern of genetic entropy in this other example on the page http://www.don-lindsay-archive.org/creation/eocoelia_big.gif As well as in this example that was given: http://www.don-lindsay-archive.org/creation/orbulina_pic.html This following example is interesting in that the genetic entropy is not nearly as 'in your face' as the preceding examples Diogenes gave, but the series of fossils are still easily recognizable as being in the same 'kind' of species. A Pliocene Snail 10 mya to 3 mya http://www.don-lindsay-archive.org/creation/snails.html Diogenes, your problem is not to demonstrate the deterioration of form in the fossil record (we have that in abundance)
Dollo's law and the death and resurrection of genes: Excerpt: "As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo's law, after its propounder, and is taken as a general statement that evolution is irreversible." http://www.pnas.org/content/91/25/12283.full.pdf+html Don Patton - Entropy, Information, and The 'Deteriorating' Fossil Record - video (Notes on giant fossils in description) http://www.vimeo.com/17050184 The Cambrian's Many Forms Excerpt: "It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.""From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,"....(Yet Surprisingly)...."There's hardly any variation in the post-Cambrian," he said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites." University of Chicago paleontologist Mark Webster; article on the "surprising and unexplained" loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago. http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.html "According to a ‘law’ formulated by E. D. Cope in 1871, the body size of organisms in a peculiar evolutionary lineage tends to increase. But Cope’s rule has failed the most comprehensive test applied to it yet."(body sizes tend to get smaller rather than larger) Stephen Gould, Harvard, Nature, V.385, 1/16/97 "Also that mammalian life was richer in kinds, of larger sizes, and had a more abundant expression in the Pliocene than in later times." Von Engeln & Caster Geology, p.19 "Alexander Kaiser, Ph.D., of Midwestern University’s Department of Physiology,,, was the lead author in a recent study to help determine why insects, once dramatically larger than they are today, have seen such a remarkable reduction in size over the course of history." Science Daily, 8/8/07
Quotes:
Here is a page of quotes by leading paleontologists on the true state of the fossil record: https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg
bornagain77

The creationist Scambray pulls the 50-year-old creationist bait-and-switch: the "fully formed" bait and switch. The Bait: apparently citing Gould, who said that "species", the lowest taxonomic unit, most of the time appear "fully formed" with gaps between CLOSELY RELATED species; The Switch: therefore larger taxonomic units, which ARE NOT THE SAME "BIBLICAL KIND", appear "fully formed" with no precursors. The Bait is true; the Switch is a creationist lie floating around since the 1960's at least. This lie is 50 years old. 50 years of copying and pasting it does not make it true. Stephen Jay Gould knew the difference between major taxa and minor taxa, and he repeated many times, that 1. There are examples of gradual transitions between closely related species, that is, MINOR TAXA, in the fossil record. Here are some pictures of gradual transitions giving the lie to this 50-year-old creationist quote mine. The more complete the fossil record is, as with ocean-dwelling foraminifera, the more gradual the transitions appear. Here are some more pictures for foramen/plankton. Below, I give examples for larger animals. 2. There are examples of intermediates between structurally very different forms, that is, between MAJOR taxa, e.g. reptile to mammal, whales, seals, sirenians, bats, etc. and their precursors. Gould was clear about the distinction which creationists have obfuscated for 50 years:
Stephen Jay Gould wrote: “Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists–- whether through design or stupidity, I do not know–- as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. The evolution from reptiles to mammals...is well documented.” [Gould, 1981]. [See also: New Mexicans for Science & Reason]
Are reptiles and mammals the same "Biblical kind", "basically the same thing" as creationists say? Gould said the above back in 1981, before we had the 1980's-90's suite of land animal-to-whale intermediates, and half-bats like Onychonycteris, and pezosiren, and Puijilia, and Little Foot, the Homo erectus of Dmanisi, Ardipithecus, etc. etc.
Stephen Jay Gould wrote: “Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am-– for I have become a major target of these practices.” [See Panda's Thumb]

Arrington wrote: Now there are 15 kinds of finches, but they are all basically the same kind of thing
Real scientific there-- "basically the same kind of thing"-- OK, let me fix your quote:
Arrington should have written: Now there are 7 species of great ape, but they are all basically the same kind of thing. I am one of them.
Fixed! Some more gradual transitions, this time in a large mammal:
"From the early Ursus minimus of 5 million years ago to the late Pleistocene cave bear, there is a perfectly complete evolutionary sequence without any real gaps. The transition is slow and gradual throughout, and it is quite difficult to say where one species ends and the next begins. Where should we draw the boundary between U. minimus and U. etruscus, or between U. savini and U. spelaeus? The history of the cave bear becomes a demonstration of evolution, not as a hypothesis or theory but as a simple fact of record." [Kurten, B. 1976. The Cave Bear Story.]
Evidence like this existed in Darwin's time as well, so even then, the fossil record put the lie to creationism.
Franz Hilgendorf (1839-1904), curator at the Zoological Museum of Berlin, was the first paleontologists to publish a well-studied phylogenetic sequence at the species - and subspecies - level.13 He studied the virtually complete sections of Miocene snail-bearing lime-mud in the Steinheim Basin on the Schwäbische Alb north of Ulm. (Darwin, in the later editions of his Origins, referred to "Steinheim in Switzerland.") ...Hilgendorf found nineteen "varieties"(= subspecies) of the snail Planorbis (= Gyraulus) multiformis, which he arranged in a phylogenetic diagram. Later he admitted that the varieties might as well be regarded as individual species (Hilgendorf 1879). The gastropods in this isolated, fresh-water, crater lake evolved by transformation and by splitting of lineages. Hilgendorf was probably the first to describe what is now called the "punctuated equilibrium" (Eldredge and Gould 1972) phenomenon: "The process of transformation seems to be of short duration compared to the time span of stability of form" (Hilgendorf 1879). Hilgendorf never observed any fusion of lineages and regarded his observations as major support of Darwin's theory of descent. ...During the same excursion [Steinheim basin, 1862] Hilgendorf discovered that the various morphs of Planorbis multiformis could be combined in a phyletic tree, and he even discovered some new morphs. He submitted his results as doctoral dissertation at the University of Tübingen in April 1863 and was awarded the degree on April 28.14 Hilgendorf's thesis was never published and is not listed in any catalogue. …[Its] phylogenetic diagram; however... is much more preliminary and primitive that the published 1866 version. Comparison of this collection and a photocopy of the dissertation6 shows that Hilgendorf specifically addressed the importance to Darwin's theory of complete fossil-bearing sections. His phylogenetic tree of 1862-1863 is the oldest such tree known to date.” [The Search for a Macroevolutionary Theory in German Paleontology. Wolf-Ernst Reif. Journal of the History of Biology, Vol. 19, No. 1 (Spring, 1986), pp. 79-130.]
Again, I must repeat my repairing of Arrington's quote:
Arrington should have written: Now there are 7 species of great ape, but they are all basically the same kind of thing. I am one of them.
What creationist can argue with that? Is there evidence of any, any, ANY supernatural intelligent design going on in the ape-to-hominid transition? Arrington is right: "they are all basically the same kind of thing." Diogenes

PaV @43: Well said. Many, perhaps nearly all, of the examples of evolution of this type -- finch beaks, peppered moths, bacteria resistance, dog breeds -- teach loudly and clearly the following lesson (for those able to hear it): Minor oscillations around a norm over time, without any real directional evolutionary change. Eric Anderson

The bacteria accidentally rewire their genome...
I wonder if they said "oops" when the realized what they had done? Mung

Regarding the Galapagos Finches: All you have to do to overturn the notion of even "microevolution" is read Weiner's The Beak of the Finch. Here's what it tells us: in drought situations, the finches stop reproducing, and a larger beak size is seen due to a relative abundance of larger and harder thorn seeds. And when rain comes---and it comes in bunches---the island becomes verdant and UNEXPLICABLY (for those in Rio Lindo---they can't explain it) finches that don't normally mate, do mate, and form hybrids. The hybrids have an intermediate-sized beak, and immediately begin to flourish---i.e., they basically take over the population on a percentage basis, more than the 'smaller' and the 'larger' beak-sized finches. I guess this is called 'regression to the mean.' Alas. Given enough time, and enough variable environmental conditions, the population of finches returns to normal. What a great evolutionary story this is? Right? PaV

Innovation or Renovation? By Ann Gauger - Sept. 24, 2012 Excerpt: But how significant was this innovation? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions. After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter. Figure 2 from Blount et al. The new trait additionally required one or two pre-adaptive steps that could not be definitively identified, perhaps because of variable or weak phenotypic effects, perhaps because of epistatic interactions. Once in place though, those mutations enabled the next step, a duplication of the citrate operon that moved it next to another promoter, enabling the aerobic transport of citrate and its metabolism. The total number of mutations postulated for this adaptation is two or three, within the limits proposed for complex adaptations by Axe [2010] and Behe in Edge of Evolution. Because the enabling pre-adaptive mutations could not be identified, though, we don’t know whether this was one mutation, a simple step-wise series of adaptive mutations, or a complex adaptation requiring one or two pre-adaptations before the big event. But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised. http://www.biologicinstitute.org/post/32246480851/innovation-or-renovation?og=1 Rose-Colored Glasses: Lenski, Citrate, and BioLogos - Michael Behe - November 13, 2012 Excerpt: Readers of my posts know that I'm a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,, In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient -- that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism. http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html Moreover,, Mutations : when benefits level off - June 2011 - (Lenski's e-coli after 50,000 generations) Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually. http://www2.cnrs.fr/en/1867.htm?theme1=7 New Research on Epistatic Interactions Shows "Overwhelmingly Negative" Fitness Costs and Limits to Evolution - Casey Luskin June 8, 2011 Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn't run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does? http://www.evolutionnews.org/2011/06/new_research_on_epistatic_inte047151.html The preceding experiment was interesting, for they found, after 50,000 generations of e-coli which is equivalent to about 1,000,000 years of 'supposed' human evolution, only 5 'beneficial' mutations. Moreover, these 5 'beneficial' mutations were found to interfere with each other when they were combined in the ancestral population. Needless to say, this is far, far short of the functional complexity we find in life that neo-Darwinism is required to explain the origination of. Even more problematic for neo-Darwinism is when we realize that Michael Behe showed that the 'beneficial' mutations were actually loss or modification of function mutations. i.e. The individual 'beneficial' mutations were never shown to be in the process of building functional complexity at the molecular level in the first place! bornagain77

Carl Zimmer sed:
Chapter Two (around generation 31,500): The bacteria accidentally rewire their genome, so that a new copy of citT switches on in the presence of oxygen. Thanks to the mutations of Chapter One, this rewiring yields a modest but important improvement. Now the bacteria can feed a little on citrate, as well as on glucose.
LoL! There isn't any evidence that the cell rewired its genome accidentally, Carl. That is nothing more than your wishful thinking and your personal refusal to accept that it happened by design. Joe

sterusjon, here is a link to Alan's paper (literature bluff) if you care to dissect it: Rapid increase in viability due to new bene?cial mutations in Drosophila melanogaster Priti Azad · Mingchai Zhang · R. C. Woodruff - 2010 https://docs.google.com/file/d/0B4maSrBPNEmGNHkzZ2gtVFdkc28/edit?usp=sharing bornagain77

Sorry. Misplaced blockquote in quote of Terry Scambray in post #35. Sorry for any confusion. Stephen sterusjon

Moreover Mr. Fox, contrary to materialistic thinking, it is now found that a non-local, beyond space and time, cause must be appealed to to explain the continued existence of photons within space-time: i.e. Quantum Mechanics has now been extended to falsify local realism (reductive materialism) without even using quantum entanglement to do it:
‘Quantum Magic’ Without Any ‘Spooky Action at a Distance’ – June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically. http://www.sciencedaily.com/releases/2011/06/110624111942.htm Looking Beyond Space and Time to Cope With Quantum Theory - (Oct. 28, 2012) Excerpt: The remaining option is to accept that (quantum) influences must be infinitely fast,,, "Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them," says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,, http://www.sciencedaily.com/releases/2012/10/121028142217.htm
I have a non-local, beyond space and time, cause to appeal to, but what is your beyond space and time cause to explain the continued existence of the universe Mr. Fox and where is your evidence??? Besides several lines of empirical evidence from quantum mechanics, I even have eye witness testimony of this 'Consciousness' (with a capital "C") Cause, Mr. Fox! This following video interview of a Harvard Neurosurgeon, who had a Near Death Experience (NDE), is very interesting. His NDE was rather unique from typical NDEs in that he had completely lost brain wave function for 7 days while the rest of his body was on life support. As such he had what can be termed a ‘pure consciousness’ NDE that was dramatically different from the ‘typical’ Judeo-Christian NDEs of going through a tunnel to a higher heavenly dimension, seeing departed relatives, and having a life review. His NDE featured his ‘consciousness’ going outside the confines of space/time, matter/energy to experience ‘non-locally’ what he termed ‘the Core’, i.e to experience God. It is also interesting to note that he retained a ‘finite sense of self-identity’, as Theism would hold, and did not blend into the infinite consciousness/omniscience of God, as pantheism would hold.
A Conversation with Near Death Experiencer Neurosurgeon Eben Alexander III, M.D. with Steve Paulson (Interviewer) - video http://www.btci.org/bioethics/2012/videos2012/vid3.html Heaven Is Real: A Doctor’s Experience With the Afterlife - Dr. Eben Alexander - Oct 8, 2012 Excerpt: One of the few places I didn’t have trouble getting my story across was a place I’d seen fairly little of before my experience: church. The first time I entered a church after my coma, I saw everything with fresh eyes. The colors of the stained-glass windows recalled the luminous beauty of the landscapes I’d seen in the world above. The deep bass notes of the organ reminded me of how thoughts and emotions in that world are like waves that move through you. And, most important, a painting of Jesus breaking bread with his disciples evoked the message that lay at the very heart of my journey: that we are loved and accepted unconditionally by a God even more grand and unfathomably glorious than the one I’d learned of as a child in Sunday school. http://www.thedailybeast.com/newsweek/2012/10/07/proof-of-heaven-a-doctor-s-experience-with-the-afterlife.html
Verse and music:
Revelation 4:11 "You are worthy, our Lord and God, to receive glory and honor and power, for you created all things, and by your will they were created and have their being." Phillips, Craig & Dean - Great I Am - music http://www.youtube.com/watch?v=zSoz6L1vqm8
bornagain77

JLA, Lenski's claim of demonstrating macro evolution is a disputed one, but for the sake of argument, let's grant it. To finally get one beneficial result to the organism, it took how long? 30,500 generations was it? Is that impressive to you? This change probably involved two mutations. Wow! Lightning speed eh? When did humans and apes split apart according to evolutionists? 6-8 million years ago? How many different mutations would have been necessary for the current differences to occur? I guess that depends on what number you pick to be the difference between ape and human genomes now. I don't think anyone thinks the difference is 98-99 anymore. Even a 5% difference translates into 150 MILLION base pair differences. Do the math! At that snail's pace, it is virtually impossible. And even that "close" number was arrived at by only comparing the sections that were similar. A more recent study posits a whopping 30% difference! That equals 900 million base pair differences! See answers research journal. If this is beyond the edge of evolution as Behe would say, why believe in evolution at all? Speaking as a creationist, I don't see why we need add God to the mix to save evolution. At the very least this seriously challenges the credibility of the evolutionary doctrine of common descent. tjguy

Mr. Fox, and exactly where have I ever claimed the universe was/is only 6000 years old??? Perhaps you should check the person you are attacking position more carefully before you blurt out falsehood??? ,,, But to be fair to YEC's, their position, due to advances in quantum mechanics and relativity, actually does now have more empirical clout than the classic materialistic position has/had (the classic materialistic position of space and time being invariant and infinite)
Genesis, Quantum Physics and Reality Excerpt: Simply put, an experiment on Earth can be made in such a way that it determines if one photon comes along either on the right or the left side or if it comes (as a wave) along both sides of the gravitational lens (of the galaxy) at the same time. However, how could the photons have known billions of years ago that someday there would be an earth with inhabitants on it, making just this experiment? ,,, This is big trouble for the multi-universe theory and for the "hidden-variables" approach. http://www.asa3.org/ASA/PSCF/2000/PSCF3-00Zoeller-Greer.html.ori Time dilation Excerpt: Time dilation: special vs. general theories of relativity: In Albert Einstein's theories of relativity, time dilation in these two circumstances can be summarized: 1. --In special relativity (or, hypothetically far from all gravitational mass), clocks that are moving with respect to an inertial system of observation are measured to be running slower. (i.e. For any observer accelerating, hypothetically, to the speed of light, time, as we understand it, will come to a complete stop). 2.--In general relativity, clocks at lower potentials in a gravitational field—such as in closer proximity to a planet—are found to be running slower. http://en.wikipedia.org/wiki/Time_dilation Albert Einstein - Special Relativity - Insight Into Eternity - 'thought experiment' video http://www.metacafe.com/w/6545941/
bornagain77

Alan, I followed the link you provided in #22. I found the abstract for "Rapid increase in viability due to new beneficial mutations in Drosophila melanogaster." I had aleady read the extract when I was out on your previous wild goose chase. To save everyone else the trouble here it is:
Abstract It is usually assumed that new beneficial mutations are extremely rare. Yet, few experiments have been performed in multicellular organisms that measure the effect of new beneficial mutations on viability and other measures of fitness. In most experiments, it is difficult to clearly distinguish whether adaptations have occurred due to selection on new beneficial mutations or on preexisting genetic variation. Using a modification of a Dobzhansky and Spassky (Evolution 1:191-216, 1947) assay to study change in viability over generations, we have observed an increase in viability in lines homozygous for the second and third chromosomes of Drosophila melanogaster in 6-26 generations due to the occurrence of new beneficial mutations in population sizes of 20, 100 and 1,000. The lines with the lowest initial viability responded the fastest to new beneficial mutations. These results show that new beneficial mutations, along with selection, can quickly increase viability and fitness even in small populations. Hence, new advantageous mutations may play an important role in adaptive evolution in higher organisms.
I have a few things to say about this. How do you know they demonstrated what they say they did? Did you pay the $54.95 fee that I was asked to pay or did you get a bargain? After ponying up, did you critically assess what they wrote or did you just take their word for it? Even if you did all that, there is the issue of whether the paper actually addresses the issue. That being, Terry Scambray's statements:
Animals and plants appear in the fossil record fully formed and remain unchanged through millions of years. No knowledgeable individual denies this. Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies. So also much the same thing happened with the famous "Galapagos finches" whose average beak size became bigger when the conditions there made it harder to find food due to bad weather. Then when food became more plentiful, the beak size of those finches that survived returned to normal. Thus the finches changed a little, adapted, while remaining fundamentally unchanged. In this way, nature moves back and forth, in cycles, rather than in a permanent upward climb or downward slide. Mr. Scambray makes no denial of the existence of beneficial traits in populations nor does he express any belief they must occur slowly. What he does challenge is: "But these infinitesimal changes are not "evolution" in the way that Darwin meant the word."
Alan. You have doubled down on your bluff. I did not spend my $54.95 on your wild goose chase. If you wish to put some substance to your claims you must do work of addressing the real claim of Mr. Scambray with actual quotation from repeatable, relevant research as reported by somebody. If you cannot readily produce same, then you are still bluffing. Stephen sterusjon

Frankly Mr. Fox, if believing that God created this universe and all life in it makes me a ‘crackpot’ in your book, I’ll gladly were that mark of shame.
Phil, I did not call you a crackpot. I said you posted unadulterated Creationism. Whilst I think believing that the Earth is 6,000 years old in the face of all the evidence to the contrary is "virtuoso believing" it is your prerogative. Wear you badge of shame proudly if you wish. Alan Fox

Can someone explain to me why Lenski’s E.coli experiments produced the ability to metabolize citrate when subjected to environmental conditions and the fruit flies didn’t at all under any conditions?
As nullasalus suggested, the E.coli didn't evolve the ability to metabolize citrate - they already had it - what developed was a way to import it through the cell membrane, which did not involve the evolution of a new permease (a membrane transport protein which imports a specific substance into the cell) but a modification in the expression of an existing one, citT. Apparently E.coli can already import citrate in anaerobic conditions:
The researchers also found that all Cit+ clones sequenced had in their genomes a duplication mutation of 2933 base pairs that involved the gene for the citrate transporter protein used in anaerobic growth on citrate, citT. Wikipedia - long term evolution experiment
What seems to have occurred is that an existing permease, one which imports citrate in anaerobic conditions, became able to be used to import citrate in aerobic conditions.
The duplication is tandem, resulting in two copies that are head-to-tail with respect to each other. This duplication immediately conferred the Cit+ trait by creating a new regulatory module in which the normally silent citT gene is placed under the control of a promoter for an adjacent gene called rnk. The new promoter activates expression of the citrate transporter when oxygen is present, and thereby enabling aerobic growth on citrate. Movement of this new regulatory module (called the rnk-citT module) into the genome of a potentiated Cit- clone was shown to be sufficient to produce a Cit+ phenotype. However, the initial Cit+ phenotype conferred by the duplication was very weak, and only granted a ~1% fitness benefit. The researchers found that the number of copies of the rnk-citT module had to be increased to strengthen the Cit+ trait sufficiently to permit the bacteria to grow well on the citrate, and that further mutations after the Cit+ bacteria became dominant in the population continued to accumulate that refined and improved growth on citrate. Wikipedia - long term evolution experiment
The cooperation of proteins for the import and metabolism of specific molecules can be seen in the following video, which shows that in E.coli, lactose acts as a trigger for the expression of the lac operon, which specifies a permease and a protein which breaks down lactose. Video: The Lac Operon. We can very well imagine a point mutation might knock out the repressor protein's ability to be triggered by lactose, resulting in a strain that could no longer metabolize lactose, only glucose. If at a later time the point mutation were reversed, we would not be observing a case of E.coli evolving the ability to metabolize lactose, but rather the unlocking of a preexisting ability. Certainly the Lenski example isn't exactly this same scenario, but not entirely different either. So if my interpretation is correct, what we have is an experiment with interesting results: that existing hardware, the citT membrane transport protein, which was not subject to expression in aerobic conditions, became expressed in aerobic conditions, allowing the import and metabolism of citrate to an organism which already had the ability in anaerobic conditions. Chance Ratcliff

Mr. Fox, you make a couple of snide comments: here:
“Hmm. I realize you are a busy man but you have BA77 here posting unadulterated Creationism!”
and here:
avoids any coherent alternative to the current scientific theories of evolution
As to the first snide comment, I found this quote on a article Dr. Hunter posted yesterday:
Darwin vs. creationists is evolving debate By Terry Scambray - February 2013 Excerpt: ,,,Subsequently the tactic was to attack individuals who doubted Darwin by calling them "creationists" -- meaning "crackpots." As one historian writes, the Darwinists' attacks "have been in almost direct proportion to the shortcomings of the theory." http://www.fresnobee.com/2013/02/22/3184701/terry-scambray-darwin-vs-creationists.html
Frankly Mr. Fox, if believing that God created this universe and all life in it makes me a 'crackpot' in your book, I'll gladly were that mark of shame. I give you something else to be ashamed of me about Mr. Fox, I believe Jesus Christ was/is God incarnate and died on our behalf on the cross to deliver us from sin and death!:
The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole. Dr. Arno Penzias, Nobel Laureate in Physics - co-discoverer of the Cosmic Background Radiation - as stated to the New York Times on March 12, 1978 “Certainly there was something that set it all off,,, I can’t think of a better theory of the origin of the universe to match Genesis” Robert Wilson – Nobel laureate – co-discover Cosmic Background Radiation “There is no doubt that a parallel exists between the big bang as an event and the Christian notion of creation from nothing.” George Smoot – Nobel laureate in 2006 for his work on COBE “,,,the astronomical evidence leads to a biblical view of the origin of the world,,, the essential element in the astronomical and biblical accounts of Genesis is the same.” Robert Jastrow – Founder of NASA’s Goddard Institute – Pg.15 ‘God and the Astronomers’ ,,, 'And if you're curious about how Genesis 1, in particular, fairs. Hey, we look at the Days in Genesis as being long time periods, which is what they must be if you read the Bible consistently, and the Bible scores 4 for 4 in Initial Conditions and 10 for 10 on the Creation Events' Hugh Ross - Evidence For Intelligent Design Is Everywhere; video http://www.metacafe.com/watch/4347236 Christianity and The Birth of Science - Michael Bumbulis, Ph.D Excerpt: Furthermore, many of these founders of science lived at a time when others publicly expressed views quite contrary to Christianity - Hume, Hobbes, Darwin, etc. When Boyle argues against Hobbe's materialism or Kelvin argues against Darwin's assumptions, you don't have a case of "closet atheists." http://ldolphin.org/bumbulis/ Christianity Gave Birth To Each Scientific Discipline - Dr. Henry Fritz Schaefer - video http://vimeo.com/16523153 The Judeo-Christian Origin of Modern Science - Peter Hodgson - video http://www.youtube.com/watch?v=ZYP4dqkmXDg Also see Stanley Jaki - "The Origin Of Science"
But Mr. Fox, what is really ironic in your saying "coherent alternative to evolution" is that coherency and rationality cannot be grounded in a neo-Darwinian view of reality. Even Darwinists have conceded this point:
Evolutionists Are Now Saying Their Thinking is Flawed (But Evolution is Still a Fact) - Cornelius Hunter - May 2012 Excerpt: But the point here is that these “researchers” are making an assertion (human reasoning evolved and is flawed) which undermines their very argument. If human reasoning evolved and is flawed, then how can we know that evolution is a fact, much less any particular details of said evolutionary process that they think they understand via their “research”? http://darwins-god.blogspot.com/2012/05/evolutionists-are-now-saying-their.html
The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);
Evolutionary guru: Don't believe everything you think - October 2011 Interviewer: You could be deceiving yourself about that.(?) Evolutionary Psychologist: Absolutely. http://www.newscientist.com/article/mg21128335.300-evolutionary-guru-dont-believe-everything-you-think.html
The 'reason' reasoning cannot be grounded in naturalism is quite simple actually. It is because reasoning presupposes a objective viewpoint of conscious observation which is completely separate from whatever material object is being observed:
“If you do not assume the law of non-contradiction, you have nothing to argue about. If you do not assume the principles of sound reason, you have nothing to argue with. If you do not assume libertarian free will, you have no one to argue against. If you do not assume morality to be an objective commodity, you have no reason to argue in the first place.” - William J Murray
Verse and Music:
Isaiah 1:18 "Come now, and let us reason together, saith the Lord: though your sins be as scarlet, they shall be as white as snow; though they be red like crimson, they shall be as wool." Creed - My Own Prison http://www.youtube.com/watch?v=iBBqjGd3fHQ
bornagain77

Can someone explain to me why Lenski’s E.coli experiments produced the ability to metabolize citrate when subjected to environmental conditions ...
Because they were hungry. But that's a very non-Darwinian answer! Mung

Nope. It does not posit this. Some ID proponents believe this. Others do not.
Well, you said it! Alan Fox

Mr. Fox decides to narrow his literature bluff down from 349,000 to one :) yet when we look at it,,,
Rapid increase in viability due to new beneficial mutations in Drosophila melanogaster. Excerpt: due to the occurrence of new beneficial mutations in population sizes of 20, 100 and 1,000. The lines with the lowest initial viability responded the fastest to new beneficial mutations. http://www.ncbi.nlm.nih.gov/pubmed/19882309
the citation does not, just as with Shallit's citation, address Scambay's claim:
“Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies.”
This is a classic bait and switch on Shallit's and Mr. Fox's part. The claim is that, contrary to what neo-Darwinism posits, 'RANDOM' changes to a genome will not result in anything but "mutated, crippled fruit flies", despite millions of 'random' mutations subjected onto fruit flies. But do Mr. Fox or Shallit produce any evidence to the contrary. No, quite the opposite, they produce evidence that the sophisticated molecular machinery and programming of the cell, as well as sophisticated epigenetic feedback can 'DIRECT' mutations, out of millions of base pairs, to the appropriate spots in the genome that will be of benefit of the organism.,,, Thus Mr. Fox and Shallit dishonestly try to use evidence of 'intelligently directed' mutations to imply that random neo-Darwinism had a hand in the variations occurring. Of note:
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism. Shapiro on Random Mutation: "What I ask others interested in evolution to give up is the notion of random accidental mutation." http://www.huffingtonpost.com/james-a-shapiro/jerry-coyne-fails-to-unde_b_1411144.html -Comment section "Establishing that teleological questions are critical will itself take a considerable effort because we need to overcome the long-held but purely philosophical (and illogical) assertion that functional creativity can result from random changes." http://www.huffingtonpost.com/social/Upright_BiPed/genetic-recombination-not-random_b_1743647_175499059.html Shapiro on Cell cognition: "Recent postings have provoked numerous questions about my application of the term "cognitive" to cell regulatory processes. I base this usage on the notion that cognitive actions are knowledge-based and involve decisions appropriate to acquired information. It is common today for molecular, cell and developmental biologists to speak of cells "knowing" and "choosing" what to do under various conditions. While most scientists using these terms would insist they are just handy metaphors, I argue here that we should take these instinctive words more literally. Cell cognition may well prove itself a fruitful scientific concept." http://www.huffingtonpost.com/james-a-shapiro/cell-cognition_b_1354889.html Seeing Past Darwin II: James A. Shapiro - James Barham - May 2012 Excerpt: Much in our culture depends upon the public’s being made aware that Darwinian theory as standardly interpreted is intellectually bankrupt.(2) And little that I have encountered communicates this fact so well as the work of James A. Shapiro. http://www.thebestschools.org/bestschoolsblog/2012/05/03/darwin-ii-james-a-shapiro/
bornagain77

Good for BA77. Again, I’m sure there’s a point in there, but I am not grasping it. Perhaps you could unpack it a little.
Fair enough to have a strategy that avoids any coherent alternative to the current scientific theories of evolution but I thought you might have wanted to be a little more discreet! Barry: Still not tracking with you Alan. That's OK. I'll drop it. Alan Fox

I guess Mike Behe would have a view on this as the experiment. You could also look at Lenski's own version of the implications of his experiment. Carl Zimmer on the Lenski experiment Larry Moran on Lenski Alan Fox

JLAFan2001: "ID posits that organisms are intelligently designed to evolve to environmental cues." Nope. It does not posit this. Some ID proponents believe this. Others do not. Barry Arrington

Alan @ 20: “Hmm. I realise you are a busy man but you have BA77 here posting unadulterated Creationism!” Good for BA77. Again, I’m sure there’s a point in there, but I am not grasping it. Perhaps you could unpack it a little. Barry Arrington

Can someone explain to me why Lenski’s E.coli experiments produced the ability to metabolize citrate when subjected to environmental conditions and the fruit flies didn’t at all under any conditions?
Short answer: Lenski's E.coli didn't do that. Long answer here. In his new paper Lenski reports that, after 30,000 generations, one of his lines of cells has developed the ability to utilize citrate as a food source in the presence of oxygen. (E. coli in the wild can’t do that.) Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) nullasalus

Can someone explain to me why Lenski’s E.coli experiments produced the ability to metabolize citrate when subjected to environmental conditions and the fruit flies didn’t at all under any conditions? ID posits that organisms are intelligently designed to evolve to environmental cues. OK, why did the bacteria evolve to one condition and the fruit flies couldn’t evolve to multiple conditions? This seems like a case of random mutations. JLAfan2001

Rapid increase in viability due to new beneficial mutations in Drosophila melanogaster. Alan Fox

Alan, you are precious to us. Thank you so much for posting.
Barry, we are going to have to start talking rates. ;) Alan Fox

Barry:
Of course I accept that Alan. I don’t know anyone on either side of the Darwinism debate that disputes that.
Hmm. I realise you are a busy man but you have BA77 here posting unadulterated Creationism! And what about Joe? OK nobody takes Joe seriously but still... Alan Fox

Mapou @14
Claiming that the observation different species of finch is proof of Darwinian evolution is tantamount to saying that different species of dogs are the result of Darwinian evolution.
Actually, believe it or not, Richard Dawkins did claim different dog breeds as proof of macro-evolution!
podcast - On this episode of ID the Future, Casey Luskin talks with geneticist Dr. Wolf-Ekkehard Lönnig about his recent article on the evolution of dogs. Casey and Dr. Lönnig evaluate the claim that dogs somehow demonstrate macroevolution. http://intelligentdesign.podomatic.com/entry/2013-02-01T17_41_14-08_00 Part 2: Dog Breeds: Proof of Macroevolution? http://intelligentdesign.podomatic.com/entry/2013-02-04T16_57_07-08_00
bornagain77

Alan @ 8 and 9. Alan, you are precious to us. Thank you so much for posting. See sterusjon at 16, where he beat me to the punch. Barry Arrington

Apparently the most famous Darwinist of the late 20th century was going around spouting “pure creationist babble.” Who knew?
They all knew. They just chose to ignore it, or cover it up, or accuse the "creationists" of quote mining. Obviously Punk Eek ought not be taught in high school science classrooms. Mung

Alan, Which side are you on?
One or two article in there must be worth a glance, or am I bluffing?!
Just for kicks, I followed your link in post #8. I found 349,000 Google hits. All well and good. I found numerous hits that were irrelevant to the issue. I found that many of the top links lead to the same paper. On that account the 349,000 number is quite deceptive. In addition that often listed paper defined its "beneficial" mutation as a change that allowed subsequent generations to survive in an artificial environment of >4% NaCl in their food supply that their distant ancestors could not. Oh, the wonders of micro-evolution to bring about macro-differences is thus demonstrated. I wonder if the salt tolerance would persist if the flies where returned to "normal" feeding conditions? Just as Scambray noted about other "beneficial" mutations. But more than that, I found these two links: http://news.sciencemag.org/sciencenow/2001/10/23-05.html where I found:
The researchers turned to the fruit fly Drosophila melanogaster to test this hypothesis. By crafting synthetic chromosomes, they created flies that reproduce asexually. They then established 17 populations of these asexual flies, all with white eyes. For comparison, they also set up 17 populations of white-eyed sexual flies. The team then let the insects breed for 10 generations. They added red-eyed flies and artificially favored the red-eyed gene by adding more red-eyed flies each generation. Thus the red-eyed gene mimicked a beneficial mutation. (Emphasis added by me)
"[A]rtificially...mimicked a beneficial mutation" What's this. No real beneficial mutations? And http://harunyahya.com/en/Evrim-Sozlugu/16357/Drosophila where this was to be found:
All evolutionist efforts to establish beneficial mutations have ended in failure. In order to reverse this pattern, evolutionists have for decades been carrying out experiments on fruit flies, which reproduce very quickly and which can easily be subjected to mutations. Scientists have encouraged these insects to undergo all kinds of mutations, a great many times. However, not one single useful mutation has ever been observed. The evolutionist geneticist Gordon R. Taylor describes these evolutionists’ pointless persistence: It is a striking, but not much mentioned fact that, though geneticists have been breeding fruit flies for sixty years or more in labs all round the world—flies which produce a new generation every eleven days—they have never yet seen the emergence of a new species or even a new enzyme. Another researcher, Michael Pitman, expresses the failure of the experiments on fruit flies: . . . geneticists have subjected generations of fruit flies to extreme conditions of heat, cold, light, dark, and treatment by chemicals and radiation. All sorts of mutations, practically all trivial or positively deleterious, have been produced. Man-made evolution? Not really: Few of the geneticists’ monsters could have survived outside the bottles they were bred in. In practice mutants die, are sterile, or tend to revert to the wild type. In short, like all other living things, fruit flies possess specially created genetic information. The slightest alteration in that information only leads to harm. (Citation links removed)
If appears that more of the "evidence" is contrary to your position. Are you bluffing? Yes! If you know where the evidence is buried in your 349,000 hits, please point to it with specificity. My perusal indicates it is not so easy to find. I'm calling your bluff. Stephen sterusjon

Alan @ 1: “[It’s almost] as if you accept that environmental changes in the niche occupied by a population of finches can cause change in allele frequency and hence change in the phenotype over time.” Of course I accept that Alan. I don’t know anyone on either side of the Darwinism debate that disputes that. I assume there's a point hiding in that statement somewhere, but I can't figure out what it is. “I do wonder what you mean by normal, however?” I don’t mean anything by “normal.” You’ll need to ask the researchers who performed the study what they meant by “normal.” I assume they meant that average beak sizes reverted to the pre-famine mean. Barry Arrington

Claiming that the observation different species of finch is proof of Darwinian evolution is tantamount to saying that different species of dogs are the result of Darwinian evolution. Oh, the silliness. It's painful to watch. Darwinian evolution is a religion on the way to extinction. Then it will be forgotten. A hundred years from now, history books will just call it the era of collective stupidity, an aberration. Mapou

footnote: Genomes of similar species - Cornelius Hunter PhD. Excerpt: Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc… http://www.darwinspredictions.com/#_4.2_Genomes_of Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video http://www.youtube.com/watch?v=1Zz6vio_LhY Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf bornagain77

Mr. Fox @8, your bluffing and here's why: Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Drosophila melanogaster is a model organism for the study of genetics and some laboratory populations have been bred for different life-history traits over the course of 30 years. Professor Michael Rose, of UC Irvine, began breeding flies with accelerated development in 1991 (600 generations ago). Doctoral student Molly Burke compared the experimental flies with a control group on a genome-wide basis. This is significant because it is the first time such a study of a sexually reproducing species has been done. Burke examined specific genes and also obtained "whole-genome resequencing data from Drosophila populations that have undergone 600 generations of laboratory selection for accelerated development." The results are noteworthy on several counts: "For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do: A genetic mutation sweeps through a population and quickly becomes "fixated" on a particular portion of DNA. But the UCI work shows that when sex is involved, it's far more complicated. "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. The researchers were looking for the fixation of positive mutations within the genome and within the whole population. This is referred to using the term "selection sweep". When it occurs, the new mutation at a base pair (a novel single nucleotide polymorphism or SNP) not only experiences replication to be transmitted to the descendants of the organism, but the gene pool of variation is effectively swept clean as the new mutation becomes dominant in the whole population. However, such sweeping was conspicuous by its absence. "Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficialmutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size." The paper considers a range of possible explanations for the evidence obtained. First: "Classic sweeps may be occurring, but have had insufficient time to reach fixation." Second: "selection in these lines may generally act on standing variation, and not new mutations." Third, "selection coefficients associated with newly arising mutations are not static but in fact decrease over time." No conclusion is reached regarding these various options. "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case." This empirical work is worth noting on two counts. First, we are here considering a mechanism that is central to Darwinian evolution. Positive natural selection of hereditable variation is the key (we are informed) to understanding how descent with modification occurs. However, the first set of empirical data relating to a sexually reproducing species does not confirm that modification works this way. This is why Long's comment is worth repeating: "This research really upends the dominant paradigm about how species evolve". Many scientists have long suspected that the Darwinian mechanisms are inadequate to account for large-scale transformation - these research findings provide empirical support for such doubts. The other reason for taking an interest in this research is that the Darwinian paradigm has been widely used in the development of drugs for medical use. Whereas the classical view is that genes have specific functions, the new research supports the growing body of evidence that the norm is for genes to have pleiotropic effects. A novel SNP can then be expected to have not one, but many, effects. This has been underplayed by researchers of a darwinian persuasion. "Based on that flawed paradigm, Rose noted, drugs have been developed to treat diabetes, heart disease and other maladies, some with serious side effects. He said those side effects probably occur because researchers were targeting single genes, rather than the hundreds of possible gene groups like those Burke found in the flies. Most people don't think of flies as close relatives, but the UCI team said previous research had established that humans and other mammals share 70 percent of the same genes as the tiny, banana-eating insect known as Drosophila melanogaster." Genome-wide analysis of a long-term evolution experiment with Drosophila Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose and Anthony D. Long. Nature, 467, 587-590, (30 September 2010) | doi: 10.1038/nature09352 (preprint) Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time. See also: Scientists Decode Genomes of Precocious Fruit Flies, ScienceDaily (September 19, 2010) http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies bornagain77

50 million year old Fruit Fly fossil compared to modern Fruit Fly: http://en.harunyahya.net/fruit-fly-fossils-creation-museum/ bornagain77

Interesting story developing on Larry Moran's Blog. I challenged him to explain two issues: Self-assembly of proteins overcoming entropy barrier and Patten Baldness from evolutionary prospective: "1. Self-assembly of proteins: while I appreciate your offer to explain how proteins fold, I was looking more for the explanation as to what makes proteins self-assemble in the face of entropy barrier. To make this subject interesting to a larger audience, (I hope you appreciate that since your blog has been asleep, especially lately…) I was going to use the famous example of the bacterial flagellum motor. Most people know that it self-assembles in a perfect way within about 20 minutes. However, there are some problems there that I have issue with, such as: The number of ways that the proteins can fold to assemble the motor, which is wrong is enormous…? It is definitely greater than the number of ways that the proteins can fold together that is right… How can this happen in real time within 20 minutes? There is more to this issue, but I’m not going to bother as I would like you boring blog to revitalize a bit… I have more in store soon…Trust me Larry… 2. Regarding Pattern Baldness Larry, I didn't mean to be disrespectful just because you have this “evolutionary side-effect”... To be more specific, I was looking for a logical explanation as to how, from evolutionary point of view, you can explain this phenomenon. Not necessarily why it happens (Venter often says that we are just hairless monkeys, so what is the problem….?) While I can buy this explanation to a degree, my question earlier specifically targeted the extent of pattern baldness from evolutionary prospective, or for that matter, any prospective… Just to emphasize; If pattern baldness is part of evolutionary process, why do you, Venter and others lose hair in the hairline, top of the scalp and crown, but never, ever on the side behind the ears and the lower part of the scalp the upper neck? (There is an exception to the small part of the neck, just in case my father ever reads this…He would kill me if I omitted this ....). It does not make any sense. Just to fill you in, many of my patients complain that while they lose the hair on the scalp, they grow more and more hair everywhere else—ears, eyebrows, back and ass. This is not a joke. Why on earth would evolution eliminate the hair that is “no longer necessary” and grow the hair that is even less needed?" Larry chose two referees for this contest; Michel Behe and Michael Denton. I just need to get in touch with them to agree to this contest. Can someone help me out to contact them? This may turn out to be an interesting event and pretty high profile too... http://sandwalk.blogspot.ca/2013/02/saturday-february-28-1953.html?showComment=1362411409652#c5312255526461622950 John Witton

One or two article in there must be worth a glance, or am I bluffing?! Alan Fox

Beneficial mutations in Drosophila Alan Fox

Mr. Fox you ask
So Barry’s wrong then, Phil?
You tell me, Shallit claimed:
“Over millions of generations of laboratory testing, fruit flies, as one example, when subjected to genetic changes have not changed into anything but mutated, crippled fruit flies.” Really? At my university, we have access to articles that say something different.
That 'something different', as far as I can tell, wasn't even a mutation experiment done in a laboratory, furthermore the rapid epigenetic response in the fruit fly study he did cite, did not claim that anything appeared but fruit flies, and in fact the response was the result of 'directed' mutations. Thus it is not even an example of neo-Darwinism!,,, Mr. Arrington called it a literature bluff. I agree entirely. If you disagree, and you think Mr. Arrington was mistaken in calling it a literature bluff, please tell us exactly why Shallitt's paper supports neo-Darwinism and does not support ID!!! bornagain77

Further notes on fruit flies:
Response to John Wise – October 2010 Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 ‘No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution’ – Jonathan Wells Darwin’s Theory – Fruit Flies and Morphology – video http://www.youtube.com/watch?v=hZJTIwRY0bs Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies Gene Regulatory Networks in Embryos Depend on Pre-existing Spatial Coordinates – Jonathan Wells – July 2011 Excerpt: The development of metazoan embryos requires the precise spatial deployment of specific cellular functions. This deployment depends on gene regulatory networks (GRNs), which operate downstream of initial spatial inputs (E. H. Davidson, Nature 468 [2010]: 911). Those initial inputs depend, in turn, on pre-existing spatial coordinate systems. In Drosophila oocytes, for example, spatial localization of the earliest-acting elements of the maternal GRN depends on the prior establishment of an anteroposterior body axis by antecedent asymmetries in the ovary. Those asymmetries appear to depend on cytoskeletal and membrane patterns rather than on DNA sequences,,, http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=7751 Seeing the Natural World With a Physicist’s Lens – November 2010 Excerpt: Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them;,, the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head;,,, In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://www.nytimes.com/2010/11/02/science/02angier.html?_r=2&scp=1&sq=seeing%20the%20natural%20world%20with%20a%20physicist%27s%20lens&st=cse Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video Text from one of the Saddleback slides: 1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows. 2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring. 3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo. Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes. http://www.saddleback.com/mc/m/7ece8/ Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011 Excerpt: The problem may be summarized as follows: — There are striking differences in the early (embryonic) development in animals, even within classes and orders. — Assuming that these animals are descended from a common ancestor, these divergences suggest that early development evolves relatively easily. — Evolution by natural selection requires heritable variation. — But heritable variations in early development, in major features such as cleavage patterns, are not observed. http://www.evolutionnews.org/2011/04/understanding_ontogenetic_dept_1045581.html
bornagain77

So Barry's wrong then, Phil? Alan Fox

that ‘something different’ that Shallit places so much confidence in, is:
Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in “Evolution Canyon,” Israel – 2001 Excerpt: an analysis of microsatellites suggests a limited exchange of migrants and lack of recent population bottlenecks. We hypothesize that adaptation to the contrasting microclimates overwhelms gene flow and is responsible for the genetic and phenotypic divergence between the populations. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC60847/
Thus it is not even clear whether reproductive isolation was achieved in the 'something else' paper.
"The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared." from page 32 "Acquiring Genomes" Lynn Margulis. Selection and Speciation: Why Darwinism Is False - Jonathan Wells: Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.” http://www.evolutionnews.org/2009/05/selection_and_speciation_why_d.html
Moreover rapid response to environment pressure is a very anti-Darwinian thing to observe since, according to neo-Darwinism, the random variation is 'suppose' to be independent of the need of the organism. To find time after time that the variations to the genome are 'directed' to meet a specific stress from the environment is certainly not something Darwinists should take comfort in!
Soft Inheritance (Epigenetics): Challenging The Modern Synthesis – Lablonka, Lamb – 2008 Excerpt: We believe that rather than trying to continue to work within a framework of a Synthesis that was made in the last century, we now need a new type of evolutionary theory, one that acknowledges Darwinian, Lamarkian and saltational processes. http://www.somosbacteriasyvirus.com/soft1.pdf Epigenetics and Soft Inheritance – Challenging The Modern Synthesis – video http://www.youtube.com/watch?v=52d5jWK1vdc New Research Elucidates Directed Mutation Mechanisms – Cornelius Hunter – January 7, 2013 Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,, These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,, http://darwins-god.blogspot.com/2013/01/news-research-elucidates-directed.html (Epigenetics) Histone-modifying proteins, not histones, remain associated with DNA through replication – August 23, 2012 Excerpt: A study of Drosophila embryos,, found that parental methylated histones are not transferred to daughter DNA. Rather, after DNA replication, new nucleosomes are assembled from newly synthesized unmodified histones. “Essentially, all histones are going away during DNA replication and new histones, which are not modified, are coming in,”,, “What this paper tells us,” he continues, “is that these histone modifying proteins somehow are able to withstand the passage of the DNA replication machinery. They remained seated on their responsive binding sites, and in all likelihood they will re-establish histone modification and finalize the chromatin structure that allows either activation or repression of the target gene.” http://phys.org/news/2012-08-histone-modifying-proteins-histones-dna-replication.html
If Shallit is so impressed with that, I'm surprised Shallit didn't pull out the old Lizard cecal valve adaptation as an example of neo-Darwinism in action:
Phenotypic Plasticity - Lizard cecal valve (cyclical variation)- video http://www.youtube.com/watch?v=zEtgOApmnTA
of note on finches: Materialists/atheists never mention the fact that the variations found in nature (such as peppered moth color and finch beak size), which are often touted as solid proof of evolution, are always found to be cyclical in nature. This blatant distortion/omission of evidence led Phillip Johnson to comment in the Wall Street Journal:
"When our leading scientists have to resort to the sort of distortion that would land a stock promoter in jail, you know they are in trouble."
Here is a more detailed look at the finches
Wired Science: One Long Bluff - Refuting a recent finch speciation claim - Jonathan Wells - Nov. 2009 Excerpt: "Does the report in Wired Science mean that “biologists have witnessed that elusive moment when a single species (of Galapagos finch) splits in two?” Absolutely not." http://www.evolutionnews.org/2009/11/wired_science_one_long_bluff.html
bornagain77

Alan Fox:
That sounds almost evolutionary, Barry!
In what way?
Almost as if you accept that environmental changes in the niche occupied by a population of finches can cause change in allele frequency and hence change in the phenotype over time.
That sounds like Dr Spetner's "built-in responses to environmental cues", Alan. Evolution BY DESIGN! Joe

1- Shallit is one of many who think that anyone who argues against evolutionism, argues for the fixity of species- no change is allowed. IOW they argue against a known strawman and are proud of it. 2- And that means he also equivocates- any evidence for change is evidence for evolutionism Joe

With respect to a particular species of finch, environmental pressures caused a change in beak size and when those pressures eased the beak sizes reverted to normal.
That sounds almost evolutionary, Barry! Almost as if you accept that environmental changes in the niche occupied by a population of finches can cause change in allele frequency and hence change in the phenotype over time. I do wonder what you mean by normal, however? Alan Fox

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