The logic for my analysis? 1] A polished granite cube is …

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

The logic for my analysis?

1] A polished granite cube is observed

2] by whom is it observed. To progress beyond observation there will need to be an observer who is able to compare against some comparitors. This assumes within the observer a brain and some memory of other objects with which to compare. An insect may well recognize this as different but is unlikely to have categories beyond expected and different. A full ontological analysis depends on an organism with a brain and intellect that has considerably more capacity for categorization and comparison. Such a brain would then ask;

2] is this naturally occuring?

In our (Homo sapiens) experience such an object cannot be made by natural physical forces acting on stone.
It could be a crystal but crystals are homogeneous in composition and this is a complex crystalline rock that is always naturally derived from volcanic activity and is amorphous in shape.
In our experience such an object is made by a living thing that can alter their environment
a] because it has a flat polished surface and
b] because the geometric shape is in a complex structured rock.

Very good. I’m with you so far.

3] Since living things actively modify their environment. This is likely to be an artefact of a living organisms

We know that many living organisms make nests hives tracks tunnels and webs and manifest behaviours that look intelligent such as hunting and social or community interactions. We know that birds construct quite elaborite nests and displays. There is a gradation of the ability to use tools and to have adaptive behaviour. We have to ask which of the characteristics that we know of living creatures are responsible in this instance. Among all the things we have classified what fits?

Right… (we’ll discuss the origin of complete behaviors and abilities in living things later).

4] What sort of organism?

It is a geometric shape that although it does occur naturally such as cubic zirconium or pyrite this is a cube constructed using a compound rock not found in nature in this form so the agent must have either copied a natural cubic form or possibly have had an abstraction or conception of a cube.

It has a polished surface which means there must have been some mechanisms to work a rock with hardness greater than 7.

Excellent!

5] What are the living creatures that understand geometry and have the tools to construct this object.

All that we know of with these characteristics are humans.

Yes, but we are on an alien planet where no humans are known to have visited before…

6] We conclude that the only living creatures with the tools to accomplish this are humans.

If we then postulate that this is on Mars. We then have to introduce some mechanism of how we observe it on Mars. We the observers must have the technology to get there and conclude that the constructor is equivalent in technology.

At least equivalent…

All of this process is simply comparing the object against the categories of objects we know and the living organisms and their artefacts. That may be logic and categorization but it is not science.

Yes, it is science just as anthropology is science because one’s choice of categorization is testable and potentially falsifiable. It’s called taxonomy (general) – “the practice and science (study) of classification of things or concepts, as well as the principles that underlie such a classification” (Link). To argue that taxonomy, in any of its forms, is not a valid science is certainly not mainstream…

And, as already pointed out to you, the hypothesis of a true artefact is in fact falsified all the time in anthropology and forensics. There are many published examples of this. You could be wrong about your granite cube hypothesis. There could be some as yet unknown “raw” natural mechanism that produces such cubes on certain alien planets. You don’t know for sure. You’re just hypothesizing based on limited information and making a prediction, the truth of which is not absolutely knowable. That’s science – the science of classification and prediction.

It does not involve the process of science formally defined as both method and repository of knowledge. You of course can say that science will use observation, construction of hypothesis, testing experimentally but it does not become science until it is a formal testing of a specific hypothesis by experiment and reporting that experimental data.

Testing is done all the time or else there could be no falsification of the hypothesis of design. Again, such falsifications do and have often occurred in forensics and anthropology. That is why these are in fact valid sciences and why the conclusion of intelligent design, as you’ve just explained, is backed up by scientifically valid arguments… arguments which have been tested, have established predictive value, and are open to the potential for future falsification upon further testing and examination.

My formulations assumes those of conventional science.

1] Science is methodological naturalism
2] There is a methodological naturalistic explanation for change in living organisms and the development of species; variation and natural selection

You’d be right if no creative limits to your naturalistic mechanism were ever discovered. You’d be wrong if such limits were discovered. That is why the a priori assumption that such limits cannot even be considered is not a valid scientific position.

3] There is a supernatural realm which we ascertain by faith and which cannot be ascertained by any method using methodological naturalism.

This position is not externally distinguishable from wishful thinking…

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In contrast your logic appears to be

1] observe a polished granite cube.
2] several steps or categorization probably not unlike what I have described.
3] conclude that the cube is man made or at least derived from a human like population
4] conclude it is an example of intelligent design since
a] it has evidence of design something that cannot arise by known natural means.
b] it has evidence of manipulation design that required some intelligence.
5] objects that are not constructed by physical forces are evidence of this process of intelligent design.
6] all objects showing evidence of design must therefor be derived from an intelligent designer

Good so far… and seemingly identical to your position.

7] all living things are different to objects constructed by simple physical forces (water ice and sun and physical chemistry)
8] QED all living things from the complex cell with its biomolecular structures and biomachines cannot be explained by sun water ice and physical chemistry therefore they must be the product of intelligent design
8] There must be an intelligent designer and that is the Judeo-Christian God.

No. Given the empirical evidence of a living thing, all by itself, one could not rationally conclude that the Judeo-Chrsitan God was responsible. What one could rationally conclude, given knowledge as to the low-level limits of the Darwinian mechanism (RM/NS), that a very high-level intelligence was involved that cannot readily be distinguished from what one would expect from a God or God-like intelligence of some kind.

Your formulation seems to assume certain things.

1] Science should not rely on methodological naturalism but allow for miracles as causation in generating hypothesis.

No. Science should allow for the discovery of true intelligently designed artefacts – even if these artefacts happen to be found within living things or the fundamental structure of the universe.

2] The writing of science (peer reviewed literature) are biased and skewed and little or no value

No. I use the peer reviewed literature all the time in my job as a pathologist. I also have no problem at all with the observations of mainstream scientists. I don’t think scientists are, by in large, deliberately deceptive or skewing their reporting of their observations. These reported observations can, in general, be trusted with a high degree of confidence. What cannot often be trusted are the conclusions of scientists with regard to what their observations mean – i.e., their actual hypotheses which are often not testable or potentially falsifiable (not scientific; not anything more than just-so story telling).

3] There is no adequate methodological naturalistic explanation for change in living organisms and the development of species. They are the product of divine intervention.

There is in fact no known mindless natural mechanism that can explain the functional complexity of living things beyond the level of 1000 specifically arranged amino acid residues (or codons of DNA). So, the very high degree of functional complexity that does in fact exist beyond this level within every living thing strongly suggests that an intelligent agent was involved with the production of these features. Was this intelligent agent “Divine”? That cannot be said from the study of these artefacts alone. However, the intelligence involved was certainly most magnificent indeed – not unlike something I’d expect from a Divine Designer…

4] There is a supernatural realm which is the explanation of most of what we see around us.

Yes, but this understanding is not derived from the study of living things alone…

5] we can understand the supernatural by the processes of “True science” which is an empiricism based on construction of hypothesis and testing them personally and anecdotally.

Valid science can be done on a personal level – true. And, our understanding of God can certainly be influence by studying the “works of His hands” – as the Bible itself points out again and again in both the Old and New Testaments.

Sean Pitman
www.DetectingDesign.com

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.


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