Do you know how the evolutionary mechanism works at various

Comment on Gary Gilbert, Spectrum, and Pseudogenes by Sean Pitman.

Do you know how the evolutionary mechanism works at various level of functional complexity? If not (you yourself admit that you have no idea), your publications and your degrees don’t really matter when it comes to the “science” of the Darwinian mechanism or neo-Darwinism in general. Appeals to authority, without any reference to a real scientific argument, aren’t scientific. They have no explanatory value. Again, all hat and no cattle.

And yes, many mainstream scientists have been brainwashed to believe that rational scientific investigation cannot be consistent with any kind of deliberate creation when it comes to living things in particular. They do not allow challenges to be published that question the very basic fundamentals of neo-Darwinism – such as any suggestion that various features of living things are best explained by deliberate design (even on a “natural” level of design). I mean, by your definition of “science” various disciples shouldn’t be classified as true sciences – like forensic science or anthropology (certainly not SETI either). At least be consistent here. If you’re going to exclude the ability to hypothesize deliberate design from the realm of science, at least do so for all artifacts that exist in nature… which, of course, you’re not really willing to do.

Methodological naturalism is contrary to science since it isn’t based on testability with the potential of falsifiablity. It’s based entirely on a philosophical perspective. I side with Popper on this one.

Karl Popper equated naturalism with inductive theory of science. He rejected it based on his general critique of induction (see problem of induction), yet acknowledged its utility as means for inventing conjectures.

A naturalistic methodology (sometimes called an “inductive theory of science”) has its value, no doubt…. I reject the naturalistic view: It is uncritical. Its upholders fail to notice that whenever they believe to have discovered a fact, they have only proposed a convention. Hence the convention is liable to turn into a dogma. This criticism of the naturalistic view applies not only to its criterion of meaning, but also to its idea of science, and consequently to its idea of empirical method.

— Karl R. Popper, The Logic of Scientific Discovery, (Routledge, 2002), pp. 52–53, ISBN 0-415-27844-9.

Popper instead proposed that science should adopt a methodology based on falsifiability for demarcation, because no number of experiments can ever prove a theory, but a single experiment can contradict one. Popper holds that scientific theories are characterized by falsifiability.

http://en.wikipedia.org/wiki/Naturalism_(philosophy)#Karl_Popper

Again, I have to agree. Science is not based on a priori conclusions, but on testability with the potential of falsifiability. That’s science. Those who argue otherwise, that science cannot detect design by definition, have been brainwashed – however honestly.

“It is quite a shock. From my earliest training as a scientist I was very strongly brainwashed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it. I now find myself driven to this position by logic. There is no other way in which we can understand the precise ordering of the chemicals of life except to invoke the creations on a cosmic scale. . . . We were hoping as scientists that there would be a way round our conclusion, but there isn’t.

Sir Fred Hoyle and Chandra Wickramasinghe, as quoted in “There Must Be A God,” Daily Express, Aug. 14, 1981 and Hoyle on Evolution, Nature, Nov. 12, 1981, p. 105

Neo-Darwinism isn’t maintained because of the science in its favor, but because of strong philosophical passion reaching the level of fundamentalist religious fervor. I don’t think neo-Darwinists are deliberately being dishonest. I think most of them really believe what they’re promoting. However, that doesn’t mean its scientific – regardless of the popularity of the underlying philosophy. It’s simply not demonstrable or falsifiably testable. It is nothing more than just-so story telling and it always has been regardless of the lofty credentials of you and those like you who keep claiming that your stories are “science” when they’re really just fairy tales for grownups.

In short, if I’m so clearly wrong, why haven’t you even tried to argue against the published descriptions of sequence space? – at various levels? These ideas are not unique to me. They’ve been published in mainstream literature. Why are you arguing against me when you yourself admittedly have no idea why I’m wrong? Would you really understand it, all of a sudden, if I happened to win the Nobel Prize? Is that the only thing you recognize? – the degree of popularity of an idea? Can’t you consider an idea on its own merits without first knowing what anyone else thinks? Do others always have to do your thinking for you?

Sean Pitman
www.DetectingDesign.com

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Sean Pitman Also Commented

Gary Gilbert, Spectrum, and Pseudogenes

I was not clear enough in my comment. There are 14 ERV’s that are intact and able to produce virus that we share with the chimps.

This is not true. According to a study published in 2005, no human ERVs capable of replication have been identified; all appear to be defective as far as producing infective viruses is concerned due to major deletions or nonsense mutations.

Belshaw R, Dawson AL, Woolven-Allen J, Redding J, Burt A, Tristem M (Oct 2005). “Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity”. J Virol. 79 (19): 12507–14.

These occur at the same location in the genome of both humans and chimps. There is no question as to the function of these 14 ERV’s. Some of these are associated with disease states in humans.

This is also not true. While many ERVs are being found to be functional, most of these functions are beneficial to one degree or another, and some are even vital to life. Also, there have been no proven cases of human ERVs causing disease.

“HERVs have frequently been proposed as etiological cofactors in chronic diseases such as cancer, autoimmunity and neurological disease. Unfortunately, despite intense effort from many groups, there remains little direct evidence to support these claims, and moreover some studies have served only to muddy the waters for others.” – http://genomebiology.com/2001/2/6/reviews/1017

“Many still manage to generate proteins, but scientists have never found one that functions properly in humans or that could make us sick.” – http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter

It’s like arguing that regular genes cause disease. The real reason for disease is a loss of regulation of the normal function of regular genes, and perhaps ERV sequences on occasion, due to random mutations that destroy their original functionality.

If these are a product of design by God then why is reverse transcriptase part of the code in these viruses? They could have been placed directly in the genome as DNA. Did God design us to have disease? Would it not be more likely that these represent the past viral attacks on a common ancestor which were then incorporated into the germ cell and passed on the future generations of descendants? It would only require one ERV to prove common descent and we have 14. Ask yourself what is more reasonable?

Your knowledge about ERVs is very inaccurate. There are many rational reason for ERV-type sequences to be included, by design, in our genome. As already mentioned, many ERV sequences are being discovered to produced beneficial effects – some are even vital to life. Some ERVs have even been shown to fight against infection by exogenous retriviruses:

“The HERV-W env gene product has also been shown to block infection by an exogenous retrovirus, suggesting that the expressed HERV-W env gene could have a beneficial function to the host (Ponferrada et al., 2003).” – http://vir.sgmjournals.org/cgi/content/full/85/5/1203

“However, in the case of both Fv4 and Rmcf, the mode of defense is by the domesticated env gene blocking the receptor required for retrovirus entry.” – http://genetics.plosjournals.org/perlserv/?request=get-document&doi=
10.1371%2Fjournal.pgen.0010044

Beyond this, the theory that the ERV sequences within the human gene pool were derived from external viral infections is untenable given the population bottlenecks that would have been required to achieve this effect within the germline of humans or any other animal. Even modern retroviral infections never insert themselves within the germline cells of their host. Such a theory is based on something that is so extraordinarily unlikely that it hasn’t even been observed.

“No current transposition activity of HERVs or endogenization of human exogenous retroviruses has been documented so far.” – http://www.pnas.org/cgi/content/full/101/suppl_2/14572

“Most of these elements represent ancient retroviral infections, as evidenced by their wide distribution in primate species, and no infectious counterparts of human endogenous retroviruses (HERVs) are known to exist today.” – http://www.pnas.org/cgi/content/abstract/101/6/1668

In any case, for further details along these lines, please refer to these detailed discussions of ERVs:

http://www.detectingdesign.com/pseudogenes.html#Endogenous
http://www.whoisyourcreator.com/endogenous_retroviruses.html

Sean Pitman

Gary Gilbert, Spectrum, and Pseudogenes
We share far more than 14 ERVs with chimps.

Not too long ago it was thought that around 30,000 ERVs existed within the human/ape genomes, comprising between 1-8% of each. As of the 2005 Chimpanzee Sequencing and Analysis Consortium, where the entire chimpanzee genome was compared to the human genome, it is now thought that approximately 200,000 ERVs, or portions of ERVs, exist within the genomes of both humans and apes – totaling around 127 million base pairs (around 4% of the total genomic real estate). Some authors suggests a 45% ERV origin for the human genome at large (Mindell and Meyer 2001) and 50% for mammalian species in general, if all small fragments of ERV sequences are included in the estimate. In any case, of these hundreds of thousands of recognizable portions of ERVs, the vast majority of them seem to match up, at the very same loci, between humans and chimps. Less than 1% of the ERVs are lineage specific for either humans or apes. In other words, the vast majority of ERVs are shared or “orthologous” between humans and chimps (a significant increase from the seven or so that were once thought to infect both humans and chimps at identical locations).

So, doesn’t this make the case all that much stronger than humans and apes share a common ancestor? After all, what kind of intelligent designer would have put so much shared “junk” in both of our genomes?

Well, recent research is turning out some surprising discoveries on what was once thought to be junk-DNA. Much of what was thought to be junk is turning out to be functional to one degree or another – to include ERVs.

For more information on this most interesting topic, please visit:

http://www.detectingdesign.com/pseudogenes.html

Sean Pitman

Gary Gilbert, Spectrum, and Pseudogenes
Now you’re just projecting. How about putting your own ideas to the test and see where they stand? Isn’t it a bit strange that I’m willing to respond to questions and challenges regarding my position, but you are not? Are you willing to even consider that you might be wrong? What kind of evidence or demonstration would that take? – short of a conversion of most scientists?

I’ve spelled out quite clearly that my position is easily falsifiable and that I’d be more than willing to leave Adventism and even Christianity behind as convincingly falsified if reasonable evidence supporting the creative power of the Darwinian mechanism, or any other mindless naturalistic mechanism, could be produced… or that life has actually existed and evolved on this planet over hundreds of millions of years. I have no desire to believe in any falsehood – not matter how attractive it may seem to me. I really do desire to know the truth and follow where it leads as I am able to discover it.

What about you? What would make you leave agnosticism behind and consider that a personal God who thinks about you and cares for you and died for you actually exists?

Sean Pitman
www.DetectingDesign.com

P.S. By the way, science is also required to make leaps of faith. Science isn’t about absolute proof or demonstration. Science is about taking what little is known and using it to make educated leaps of faith into that which is not and cannot be known with absolute confidence.