Again, true science makes no a priori assumptions about causation

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

Again, true science makes no a priori assumptions about causation before the hypothesis is tested – even if the hypothesis is that an intelligent designer produced a particular feature of biology. The assumption that the actions of an intelligent designer, especially a God-like intelligent designer, cannot be detected by science is not a scientific position. It’s a religious or philosophical position. Until you address this concept, which you have yet to do in any meaningful way, I’m really not sure of the point of continuing this conversation?

As far as creationists publishing in mainstream biomedical journals, it happens all the time – just not on the topic of origins having anything to do with deliberate design on any level. You yourself explain that this cannot happen because you define science as being unable to detect deliberate design when it comes to the origin of various features of living things. Your own argument proves my point – that those who hold to your definition of “science” will not publish papers that fundamentally challenge that notion.

The evidence is overwhelming in this regard. Pretty much nothing is published which even attempts to challenge the fundamentals of neo-Darwinism – such as the major problems that are known to exist for the evolutionary mechanism of RM/NS or how intelligent design is likely responsible for higher levels of functional complexity in living things. It’s all very hush hush… Even you don’t have a clue how the mechanism works at various levels of functional complexity. You base everything on blind faith that it must have done the job somehow based on sequence similarities and your interpretation of the fossil record.

As far as Sternberg is concerned, in particular (Link), I suppose he won his lawsuit for no good reason? Meyer’s paper wasn’t just a review of a review and it was novel when it comes to what’s been published in mainstream literature (Link). It was an interesting introduction to the concepts and basic evidences for design in living things, worthy of serious consideration. If you’ve actually read it, I seriously doubt you have any substantive response to the problems with the evolutionary mechanism that Meyers detailed in his paper – backed up by references to very good papers detailing the basis of this particular problem.

In any case, such “conversational” papers are published all the time from the evolutionary perspective – even in journals generally devoted to “systematics”. There is a clear double standard here and creationists are constantly barred from various forms of advancements and higher-level recognition in science – simply because they are known creationists.

For example, Dr. Hans Sues, Associate Director for Research and Collections, suggested in emails on August 30, 2004, and again on September 9, 2004, that Dr. Sternberg would never have been appointed as an Research Associate if Smithsonian officials had known about his anti-evolutionary views. Sues even blamed the scientist who nominated Sternberg as a Research Associate for not adequately investigating his background: “Sternberg is a well-established figure in anti-evolution circles, and a simple Google search would have exposed these connections.” The clear implication was that had a background check been conducted on Sternberg’s non-governmental activities, he would have been barred from being a Research Associate. Given the attitudes expressed in these emails, scientists who are known to be skeptical of Darwinian theory, whatever their qualifications or research record, cannot expect to receive equal treatment or consideration by NMNH officials.

As another example, consider that, “In the summer of 1985 Russell Humphreys wrote to the journal Science pointing out that openly creationist articles are suppressed by most journals. He asked if Science had a “hidden policy of suppressing creationist letters.” Christine Gilbert, the letters editor, replied and admitted, “It is true that we are not likely to publish creationist letters.” This admission is particularly significant since Science’s official letters policy is that they represent “the range of opinions received” (e.g., letters must be representative of part of the spectrum of opinions). Yet of all the opinions they receive, Science does not print the creationist ones.

On May 19, 1992 Humphreys submitted his article “Compton scattering and the cosmic microwave background bumps” to the Scientific Correspondence section of the British journal Nature. The editorial staff knew Humphreys was a creationist and didn’t want to publish it (even though the article did not contain any glaring creationist implications). The editorial staff didn’t even want to send it through official peer review. Six months later Nature published an article by someone else on the same topic, having the same conclusions. Thus, most creationist researchers realize it is simply a waste of time to send journal editors openly creationist articles. To say that a “slight bias” exists on the part of journal editors would be an understatement.”

Link

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.