You are absolutely right I do not want in any

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

You are absolutely right I do not want in any way to support the ID inference as it is conceived and articulated by its proponents. It was and is an argument of incredulity. That is not how science works.

It’s no more an argument of incredulity than is your argument for evident design for a highly symmetrical granite cube found on the surface of Mars. The logic is exactly the same. I see no fundamental difference…

I am sorry you cannot follow my logic.

Perhaps that’s because you haven’t even tried to present the “logic” behind your conclusion for design for a granite cube on Mars? What is the rational basis for your hypothesis of at least human-level design and creativity?

I am in responding to your bait recognizing that categorization and classification are integral to the way we function cognitively which is simply a function of the neurons in our brains.

You’re mistaken in your claim that categorization and classification are not scientifically based – i.e., are not subject to scientific methodologies or the possibility for testing and falsification.

In the Adventist tradition I am not dualist and accept that our brains are simply part of the natural world. They are not the repository of the soul or an antennae for the supernatural world but are highly complex elaborations of the invertebrates head ganglion. This was likely different to the perspective of Paley existing as he did before the development of modern biology.

The existence or non-existence of the soul or the existence or non-existence of the supernatural world is completely irrelevant to the notion that our human brains are able to detect design with the use of scientific methodologies and rational arguments to produce useful hypotheses of intelligent design. You’re bringing in completely irrelevant concepts relative to the question at hand.

Adventism has a physicalist tradition with its ideas of mind and the soul articulated by EG White. A position I happen to think was very prescient but it does have implications for a proper discussion of ID. If we accept this physicalist adventist tradition and all its implications then we must for consistency think about a world where there is only a physical substrate for intelligence, the spiritual life and our Christian ethic.

Again, I don’t see the relevance to the hypothesis of detecting design?

In the Adventist tradition of understanding mind I can understand your cube only ever based on recourse to a physicalist causation. The product of a brain since in the physical carbon based universe in which we live we only have been shown intelligence as a product of a brain. We therefore must understand artefacts as products of brains.

So? I never suggested that a brain wasn’t involved! My only question was if deliberate intelligence was involved – regardless of what produced that intelligence. That’s an entirely separate question. Who cares if a brain produced the intelligence or not? The evidence for intelligence is there regardless of the source of that intelligence.

Come on now, your only real argument against intelligent design isn’t so much against intelligent design, but against knowing where the intelligence came from? That’s it?

Paley following the common tradition of Christians of his day likely accepted Dualism and would infer there could be a divine source for a physical event. However with hjs watch he only ever considered that this indicated that intelligence as a function of a brain had been at work on this artefact.

Again, so what? At this point, the only question is if intelligence was clearly involved in the production of a given artifact – or not? Who cares where the intelligence came from at his point in the investigation? Who cares if a physical carbon-based brain was involved or not? Whatever or wherever it came from, it was intelligent. That’s it. That is the scientific question that can be investigated and empirically answered to a useful degree of predictive value.

You also seem to agree since you yourself invoked at least human-level intelligence and creativity to explain a granite cube on Mars. Does it really matter if the intelligence involved really came from a carbon-based brain or not? with regard to the scientific conclusion of intelligent design? Obviously not…

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.