1] I now appreciate why you cling so desperately to

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

1] I now appreciate why you cling so desperately to your 1000 fsaar limit as the core of your worldview and the greatest evidence for a creator. If the biological world can be explained by natural process your house of cards would fall so you cannot afford to concede this final defence against the conclusions of modern biology that there can be profound changes by the contingency of natural selection. After all you have conceded that all species are derived from the 2 of a kind by a natural process of mutation and natural selection and this is beyond what most would think very very low complexity. Having conceded variation and natural selection to this degree the gap into which you fit God is much smaller than that of our YEC spiritual ancestors within the Church who considered that everything we see about us was fixed in place by God by divine fiat.

Breeding has been going on for a long time. Not too many people who recognize the potential for variation within a particular “kind” of gene pool would buy into this absolute “fixity of the species” concept. Also, if you have some example, any example, of something evolving beyond the limit of 1000 specifically arranged amino acids, let’s have it. The fact of the matter is that you yourself admit that you have no idea how RM/NS could function at higher levels of functional complexity. You just don’t know – just as you don’t know how any mindless “raw” force of nature could produce a highly symmetrical polished granite cube. You just don’t know. Of course, raw forces of nature can produce “low level” granite cubes. It happens all the time. However, as you consider the likelihood that these same raw forces of nature will produce greater and greater degrees of symmetry within the material of granite, a threshold is eventually reached beyond which only “creative intelligence” remains as a viable hypothesis. The same is true for functional biosystems.

2] You suggest

“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.” – Sean Pitman

but I do not think I have done anything more than classify your hypothetical artifact in the way an insect would classify an object as food and non-food. It is an innate function of a brain to classify objects against their experience and memory. I have said such classification is logical not scientific.

Again, you fail to address the concept that taxonomy is a science. Classification can be and has been demonstrably wrong. You could classify an object as a true artefact, but that classification can be tested and falsified via a demonstration that some raw force of nature is capable of doing the job. That is why taxonomy is a valid science. Look it up already.

3] Unless you have a more robust definition of science such as I have articulated you most certainly are like Behe and have an idea of science that would classify astrology as science. Let me illustrate.

According to your view of science as being personal and anecdotal you simply need to construct an hypothesis and test it for the observation to be scientific.

My horoscope for yesterday http://www.psychicguild.com/Daily-Horoscope/Libra?d=-1
says.

May 16: Travel is in the stars and this could mean for pleasure or business. Don’t miss any opportunity to skip town and explore the rest of the world. When you experience different environments and cultures it can open your eyes to more possibilities then you even knew existed. Just make sure you pack your imagination and curiosity.

So if I formulate this as an hypothesis I would say if this is true then I should have made arrangement for personal and business travel yesterday. This is clearly falsifiable by my personal experience which is your criteria for science.

And indeed yesterday I made travel arrangements for 2 international flights and 3 interstate flights as well as got pricing for a ferry trip interstate. There you have it a clear experimental test, an outcome and the hypothesis is not falsified. One could logically then say that astrology has been tested and found not to be false by your science.

Let’s be a bit more specific, shall we? Let’s say your horoscope said, “The stars are so aligned that today you will win the Califoria Lottery using the following sequence of numbers…” and you do in fact win with those numbers. Then, the next day your horoscope says, “Today your mother will visit from out of town. She will show up at 9:32 am.” – and she does. Then, the next day your horoscope says, “Obama will kill a fly on national television today” and he does. After a while, if such things keep happening and your horoscope keeps being proved right, time and again, in such a specific easily falsifiable manner, it would in fact build up a greater and greater degree of credibility – of predictive value. After such a string of fantastic predictions, you might even think twice about going outside the next day if your horoscope told you that, “If you go outside today, you’ll be hit by lightening and suffer sever brain damage.”

Something similar could be said for a true prophet – if what he says, which is very specific, continues to come true, his/her claim to be a true prophet of God increases in predictive value. However, if his/her falsifiable claims, in the name of God, are in fact falsified, the predictive value of the “prophet hypothesis” declines. This is in fact a form of scientific reasoning.

So, the reason why astrology isn’t considered to be a valid science is because it’s claims are too general to be effectively tested or because whenever specific claims are made, they are, as often as not, effectively falsified. That’s why. And, the same would be true for the Bible as well if its claims could be effectively falsified as well – it would have no more rational credibility than astrology (which seems to me to be the case for certain types of “scripture” – like the Book of Mormon for example).

Of course by my criteria of science as methodological naturalism, method and repository of knowledge, this doesn’t even count as science. Science is collective public experience documented by rigorous experiments so we as practitioners do not get into this quagmire of personal annecdote and subjectivism.

It wouldn’t be a personal anecdote or subjectivism if a highly symmetrical granite cube were discovered on Mars by one of our rovers. It would hit the front page of every newspaper and science journal around the world – and you know it. Everyone, even scientists, would conclude that some intelligent agent was responsible for that cube – for very rational scientific reasons as you yourself have detailed.

Science is not good for miracles so rather than being some arbitrary definition, the cornerstone of methodological naturalism establishes both the limitations and the value of its content and process. You can of course question this but do not expect to have any credibility in the eyes of its practitioners who know the value of working by the rules.

Again, the detection of a true artefact does not require one to hypothesize a “miracle” – only that an intelligence of some kind was responsible. That’s it. That’s clearly within the realms of scientific investigation and empirically-based rationality.

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.