“Talk about Alice in Wonderland and the redefinition of terms

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

“Talk about Alice in Wonderland and the redefinition of terms and concepts beyond their generally understood meaning – you’ve just seen it.” – Sean Pitman

Sorry Sean it is you who disagrees with

1] The conventional understanding of science as process and repository that I have articulated on may occasions and which is what a consensus such as Wiki would describe.

You yourself have already admitted that science can be and has been done, very well, on an individual basis. Was Leonardo da Vinci not a scientist? Of course, you call such examples “exceptions to the rule”. But these “exception” prove my point.

You see, I’m not the only one who believes that scientific methodologies can and have been successfully used on an individual basis – regardless of what anyone else thinks or does and sometimes in the face of the “majority” of the intelligentsia of the day.

How then have I redefined the term “science” as being based in that which is testable and potentially falsifiable? You’re the one arguing that this isn’t enough…

2] The universally accepted definition of science as being based on methodological naturalism

Which isn’t based on testability or the potential for falsifiability as most scientists define the term. As such, some of the popular notions of methodological naturalism, such as idea that an intelligent agent cannot, by a priori definition, be detected behind any feature of living things, is a philosophical position, not true science – in the testable potentially falsifiable non-just-so-story-telling sense of the word.

3] The description of ID found in wikipedia

“Intelligent design (ID) is a form of creationism promulgated by the Discovery Institute, a politically conservative think tank based in the U.S. The Institute defines it as the proposition that “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.”[1][2] It is a contemporary adaptation of the traditional teleological argument for the existence of God, presented by its advocates as “an evidence-based scientific theory about life’s origins” rather than “a religious-based idea”.[3] All the leading proponents of intelligent design are associated with the Discovery Institute [n 1][4] and believe the designer to be the Christian deity.”

The basic conclusion of intelligent design behind a given artefact is not limited to Christians or any religious organization, but is in fact part of mainstream science – to include forensics and anthropology and even SETI. What is the fundamental difference and methodology between these sciences and any effort to detect true artefacts in various features of the universe and of living things? Absolutely nothing. The arguments and methodologies are identical.

It is simply the conclusion that the identity of the designer is the God of the Bible that is in question here. Certainly no one could conclude that God was clearly responsible for the production of some granite cube found on the surface of an alien planet like Mars. That conclusion goes well beyond what the evidence itself can support. However, the argue that it is impossible to at least detect the need for an intelligent designer of some kind behind such an artefact is just as ludicrous. Clearly intelligent design is a valid scientific hypothesis that can and is commonly used as a key part of real scientific investigations.

4] My definition of artefact is nothing extraordinary and conforms to the commonly accepted definitions at wiktionary

http://en.wiktionary.org/wiki/artifact#English

Which includes the definition of 5 which includes product of agent not human which is what I have argued for in describing examples of products of agents lacking intelligence.

I have no problem with your definition of artefact (again, mindless robots make cars). Where I have a problem is when you call a granite cube clear evidence of intelligent design on at least the human level of intelligence and design, but then claim that you aren’t promoting a hypothesis of intelligent design. What are you promoting? What would you call it? It’s like you’re trying to make English words that clearly mean one thing mean something else entirely – just like Humpty Dumpty…

5] Michael Behe who under oath at Dover gave testimony which the Judge summarized as

“Consider, to illustrate, that Professor Behe remarkably and unmistakably claims that the plausibility of the argument for ID depends upon the extent to which one believes in the existence of God.”

Its origins are in religion and not science and it is deceptive to suggest this is a view derived from any conventional science. and indeed at Dover Behe conceded

“there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred”

and

his definition of ‘theory’ as applied to intelligent design was so loose that astrology would also qualify.

http://en.wikipedia.org/wiki/Michael_Behe

I suggest you read again (since I just know you will have read bits of it already)

Humes, E. Monkey Girl: Evolution, Education, Religion, and the Battle for America’s Soul. (HarperCollins, 2008).

Oh please. Astrology would only qualify if there were actually some evidence suggesting deliberate design was necessary to explain some artefactual feature. The argument Behe was trying to get across is that one should not make a priori decisions as to what is or is not designed before testing and research is actually performed. Such a priori decisions are not based on science, but philosophy. Also, the argument that the identity of the designer must also be hypothesized is not a requirement of detecting the actions of an intelligent designer of some kind.

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.