Sean. As usual you are right enough to be confusing. 1]

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

Sean. As usual you are right enough to be confusing.

1] I should revise my assessment of your thought experiment of a cube at an alien location. If we break it down into its components we see what I have actually said. All experience tells us that atefacts are a product of living things and are recognized by even primitive man without recourse to science.

That’s not true. The hypothesis of artefact is a scientific hypothesis that is open to testing and potential falsification. There are many instances where anthropologists, for example, have hypothesized that a given phenomenon is a true artefact when, upon further investigation, it turned out not to be an artefact at all – nothing more than a natural “raw” formation. Fontechevade cave comes to mind as a ready example of this.

The same is true of a fragment of rock that has been interpreted to be a tool of some early hominid ancestor. Sometimes such rocks are not so clearly artefactual upon closer examination and turn out to be very very similar to naturally produced stones nearby.

So, you see, the hypothesis of artefact is a scientific hypothesis that can be tested and gain predictive value over time.

My hypothesis is that there will not in reality ever be your granite cube on mars except that products of a human brain put it there. Now test that hypothesis.

That’s not the question you originally answered. The hypothetical is important because, even if no known human ever visited a particular planet, the discovery of such a granite cube would always be interpreted as a true artefact by scientists or laymen alike – even you. Therefore, you are an IDist on at least this level.

I’m actually surprised by this particular argument. In effect you seem to be arguing against SETI as a true scientific enterprise – which is hardly mainstream. Most scientists agree that the search for non-human intelligent activity in the universe is a valid scientific endeavor. The only question is, upon what rational basis could such an endeavor be undertaken? and, does this rational scientific basis have universal application?

Clearly, the answer to both those questions is yes – even for you if you are pushed into a corner.

2] Further I do not agree with your inextricable linking of design with intelligence. This I think is a fallacious argument that appears to be based on an extrapolation, without sufficient justification, of our experience with complex artefacts. In introducing the concept of arefacts of unintelligent creatures like ants and spiders that most certainly do not have any preconceive of a design I was attempting to move the discussion beyond the simple linking of design with intelligence which is the core of the simplistic ID argument.

There is indeed very good justification for linking design with certain artefacts – as you yourself have done with the granite cube. Why did you do that? I think it’s quite obvious. It doesn’t matter if such a cube was really produced by a robot (as with robots making your car on an assembly line) or a giant space worm, because, ultimately, you know as well as I do that whatever originally produced the cube was itself intelligently designed.

3] As for living objects they may appear designed for a purpose and complex but since Darwin and Wallace the basis for this has been extensively elaborated as a process of natural selection which is not at all “intelligent” or based on cognition of planning. I know you do not recognize natural selection as anything expect an impotent curiosity but on this you differ from almost all modern biologists.

We really cannot move on to discussing the creative potential of RM/NS until we at least agree on the basis for scientifically detecting a true artefact to begin with. Once you recognize the scientific rational to detecting design in general (as with granite cubes or cars or space ships or radio signals and the like) we can discuss the possibility of detecting design in living biosystems. However, if we can’t even agree on the basic science behind detecting design in SETI, in non-living things potentially found on alien planets, we have no basis to discuss design in living biomachines.

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.