Just to reiterate my questions for Bob Helm. Hopefully he

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

Just to reiterate my questions for Bob Helm. Hopefully he has not been spooked and left the building like Jeff Kent.

“Jeff Kent” never really leaves the building – despite all the bluster.

Bob I think you seem to have more understanding of the Science than most who comment here. I would like to ask a few specific questions to determine if Sean’s views are really mainstream Adventist.

1] Do you accept that Christianity can be supported by logic and empirical data such that any scientist will arrive at belief in Christ if he simply follows logic as seems to be Seans main premise in disparaging blind faith.

I can’t answer for Bob specifically, but it certainly stands to reason that if God exists and He is the Creator of everything, to include the empirical world in which we live as well as our own brains and rational abilities, that the works of His own hands will tell us something about their Author – and lead one to recognize His Signature in the things that have been made. The Bible itself is very clear on this.

2] Do you accept the bible is infallible in its original autograph as is one of the main premises of Fundamentalism.

It depends upon what you mean by “infallible”? Are you suggesting that those who uphold the fundamentals of Christianity in general or Adventism in particular, believe that there are no errors of any kind in the Bible? If so, you are quite mistaken. There are errors in the Bible – regarding the empirical world as well as doctrinal and philosophical errors. That is why the Bible is to be read as a whole and used as it’s own interpreter.

3] Do you accept that ID is science and is devoid of religion in its conception as Sean seems to do.

IDists, as with scientists or religious people, are not always scientific in their thinking. This does not mean, however, that the basic concept of intelligent design, or “intelligent creation” if you prefer, cannot be proposed in a scientific manner. It can be presented in an entirely scientific manner – as you yourself have effectively demonstrated.

4] Do you accept that modern science is based on both a method and a repository of knowledge. Do you think the canonical repository of scientific knowledge is the peer reviewed literature?

Science, modern or otherwise, has always been based on scientific methodologies that include the potential for testing and falsification. There has never been and is not now a requirement for the scientist to publish his/her findings in any particular journal in order for his/her theories to establish very useful predictive value for the scientist. The fact that learning can be achieved on an individual level is independent of if the scientist decides to share his/her discoveries with anyone else or if anyone else happens to agree with the personal conclusions of the scientist.

Now, this is not to say that peer reviewed literature isn’t important. It is important. The published observations and interpretations of scientists is valuable. I use published literature all the time in my own practice as a pathologist – with great success. However, this is not to say that the conclusions of scientists are always the most reasonable interpretations of their own observations. The observations themselves are most often faithfully and accurately recorded, but the interpretations of these observations can be colored by personal philosophies that are not always scientific or rational.

5] Do you think the method of science is based on methodological naturalism.

Methodological naturalism, when it defines science, a priori, as being unable to detect deliberate intelligence behind any feature of living things or of the fundamental constants of the universe, is taking on a philosophical position and is no longer a true form of science at that point.

5] Do you accept that the Divinity of Christ is a position that must be ultimately accepted through a leap of Faith after accepting there is at least a logical polemic for Christian belief.

There is no “logical polemic” for Christian belief in the empirical or historical or futuristic claims of the Bible without at least some basis in empirical evidence. Consider also that there is no science of any kind without an ability to take a leap of faith. Science is based on starting with very limited information and using that information to make an educated leap of faith beyond that which the information in hand can definitively support. That’s what science does. So, of course, any rational acceptance of the Divinity of Christ is also going to involve a leap of faith. However, this leap of faith need not be devoid of any basis in empirical evidence or rational argument. If so, what you have isn’t really a true Biblical-type faith. What you have is wishful thinking (aka: fideism).

Again, true science and true faith must walk hand-in-hand. They do not rationally exist independent of one another.

Sean Pitman
www.DetectingDesign.com

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1 Sean Pitman Also Commented
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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.