Where does one start to respond to your assertions. …

Comment on The End of “Junk DNA”? by pauluc.

Where does one start to respond to your assertions. Maybe a biologists perspective on junk DNA.

1] You seem have a very black and white view of both the bible and science. There is very limited nuancing evident in your expressed views.
“….These implications are, frankly, rather devastating to the Neo-Darwinian perspective.”
“…There is no more junk DNA and the Darwinian mechanism of random mutations combined with natural selection is untenable as a creative force beyond very low levels of functional complexity.”

2] Your essential argument is a strawman argument. You critize a caricature of the science of genetics and molecular biology and do not seem to be engaged with the basic ideas. For sure there have been profound errors and lack of understanding but that is what science is like. Increasing understanding is expected as new methods and data become available. Hypothesis testing is about detecting error and you are absolutely correct in that the “junk” DNA hypothesis as presented in the popular press has been rejected. But it was not at all rejected because some armchair scientists denied it on a priori grounds but was rejected because of new data, experiments and better models. There has been increase in understanding of genomics and the role of junk DNA but as Tim Standish breathlessly says evolutionary concepts were used both for the earlier understanding of “non-protein-coding” DNA as padding and a repository of potential reusable but unnecessary genetic information and for the newer concept of selection of functional activity found in these regions not coding for protein.

3] You seem to believe that molecular geneticists before you and fellow young earth creationists came along with vague statements in the blogoshere about function of the whole of the genome, believed that junk DNA (as Gould rightly observes a “disrespectfully” denoted shorthand predicated on the prokaryotic model of funtional genes) was completely useless. This is patently wrong. If you read even the abstract of the 1988 paper from John Bodnar “A domain model for eukaryotic DNA organization: A molecular basis for cell differentiation and chromosome evolution” J theoretical biol 1988, that is cited in the paper by William Dembski that you then cite, you will see that Bodnar was advocating consideration of the genomic organization in terms of “domains” that are much more complex than simply the promoters and coding exons assumed to be subject to evolutionary selection. This essential idea that the genome has been selected by the resultant phenotype has changed little in the last 50 years. The idea that a phenotype is the basis of selection not the genotype has gained increasing recognition as the complexity of the genome and the many levels of regulation and control has become evident. Increasing understanding of “Junk DNA” and the highly nuanced regulation of structure and function determined by regions outside conventional coding regions has enhanced neo-darwinian models premised on natural selection rather than destroyed them as you seem to hope based on your models of reality.

4] You do not seem to make any distinction between the protein coding and non-protein coding regions in terms of their contribution to phenotype. You seem to be suggesting all are essential. Do you really believe that? Are all pseudogenes functional? critical? Surely processed pseudogenes are evidence that introns are non-essential. Are alu repeats critical and essential? Is the genome uniformly critical and functional? Is there a heirarchy with protien coding at the top and supporting scaffolding and microregulatory and integrative regions below. What precisely is your model based on intelligent design? I cannot seem to find it articulated in a scientific way. Contrast your approach to a scientist such as John Mattick who recently won HUGO prize for his data on non-coding RNA. This work and the ENCODE work however raises the question that is very well articulated in this comment;

http://sandwalk.blogspot.com/2012/03/john-mattick-wins-hugo-award-for.html

What about junk RNA? Will this ongoing post ENCODE scientific debate be the source for your next blog? Would you like to articulate your view based on a YEC perspective with such specificity that we can see if you are right or wrong?

It is easy to sit at your study desk and pontificate post hoc on the errors of evolutionary biologists but to be credible as a scientist you need to propose hypotheses with some specificities and test them against the data.

pauluc Also Commented

The End of “Junk DNA”?
There is a great gulf between You and I. Where does one start in trying to find common ground and responding to your very concrete thought structure. Its as if the last 200 years have not happened. Your view of natural theology may have been accepted by William Paley but is not an approach to God thought valid by most modern theologians with any acquaintance with science. It is not the 19th century and we are called to preach the grace of God to a secular world. Your vision shows no imagination or understanding of spirituality or the reality and value of vision, myth and abstract concepts that may have no correspondence in concrete realities. Do you agree with Martin Luther in his statement about scripture trumping observation;

“People gave ear to an upstart astrologer who strove to show that the earth revolves, not the heavens or the firmament, the sun and the moon. Whoever wishes to appear clever must devise some new system, which of all systems is of course the very best. This fool [or ‘man’] wishes to reverse the entire science of astronomy; but sacred Scripture tells us that Joshua commanded the sun to stand still, and not the earth.”
– Martin Luther, Table Talk

If you truly privilege scripture over science you should really revamp this web site to be consistent with the supremacy of scripture along the lines of the site http://www.fixedearth.com/ A site that is at least absolutely consistent with biblical literalism as Luther saw it.

The reality however is that both you and I interpret the scriptures. As I have said before you appear to practice naturalistic evidence based medicine contrary to the biblical description of healing but then pretend that you are following the plain text of scripture when reject entirely naturalism when it comes to origins. You claim;

“You pick and choose what elements you will use to build your own image of “christianity”… which is quite different from the Biblical claims.”

But do not at all seem able to see that you are in fact doing exactly what you project in accepting evidence based medicine contrary to a plain reading of scripture but claiming origin by divine fiat and miracle on the basis of one particular reading of scripture.

You continue to misconstrue the point of my discussion of Santa Claus and Christmas. Children can and do grow in their understanding of reality and are able to see beyond the concrete events of Christmas to see it as a representation of a worthy abstraction that is not invalidated by rejecting a fictitious Santa Claus. You seem unable to move from the concrete to the abstract and yet again claim you will reject Christ if your biblical interpretation is found not to be consistent with a simplistic reality. As though your superior mind trumps any non-rational revelation of God. Your arrogance is unceasingly amazing.

You claim

“And, so far, the organized Adventist Church agrees with me. Of course, you can call yourself whatever you want. But, again, that doesn’t mean that the church is going to recognize your claims as actually representing the church’s view of reality. So, why would you expect anyone holding views that undermine the fundamental goals and ideals of the church, the “fundamental beliefs”, to be paid by the church?”

You are of course right if you think the church that is being rebuilt by Ted Wilson and Clifford Goldstein with their militant fundamentalism and unsavoury and ungracious political manouvering is the legitimate heir of traditional Adventism but I do not.


The End of “Junk DNA”?
@Sean Pitman:
“I’ve already explained, several times now, that I don’t know how dinosaurs were made. All the arguments I’ve heard seem like mere conjecture to me.”

So what you said on 3ABN about genetic engineering and amalgamation could be best described as just so stories? Lacking completely any evidentiary basis?


The End of “Junk DNA”?
@Sean Pitman:
“Again, just don’t expect to get paid by the Adventist Church for those efforts which fundamentally undermine the primary goals and ideals of the church.”

This statement raises serious question as to whether you understand the primary goals of the Adventist Church. At least in Australia, the vision is expressed on the web site http://adventist.org.au/about-us as;

“Our vision is to be a church that knows, experiences and shares our hope in Jesus Christ. This vision expresses the collective feelings of our church members and leaders.

The vision statement has three parts:

The head knowledge (studying the Bible)
The heart experience (unconditional commitment to Jesus Christ and to one another)
The call to action (sharing our faith) ”

It does not at all couch it in terms of being an attack vehicle against the integrity or capability of science and scientists nor of fellow believers. Nor does it suggest a primary purpose of attacking people who through a heart experience (unconditional commitment to Jesus Christ and to one another) might be labelled practitioners of blind faith. Your inability to unconditionally commit to Jesus and your completely objectionable committment to leave Adventism and Christianity if the empirical evidence for your supposed model of reality fails to reach some arbitrary misapplied criteria of “weight of evidence” stands in stark contrast to the Church’s vision of people unconditionally committed to Jesus Christ and the church and would certainly fall under the rubric of an effort to “fundamentally undermine” the Church.


Recent Comments by pauluc

Avondale College Arguing in Favor of Darwinian Evolution?

Bob Helm: With that said, I find your views to be spiritually dangerous and often scientifically weak. I detect a lot of smoke in your posts, but very little light. I hope you will continue to ponder these issues and try to have an open mind.

You are most welcome to your opinion and I know you would like nothing better than that anyone who takes Christianity and the Bible seriously but not literally to just go away. It is much better not to know of any possible problems with one current views. It very hard to get to the science when we cannot even agree on what is science. What passes as science on this site is so completely dismissive of its methodological basis and history and is entrained in a specific supernatural world view that allows arbitrary acceptance of any observation as miraculous. I think Roger’s paper may well be relevant to Adventist that believe that Christianity has and must respond to a careful study of physical reality by reconsidering its interpretations of the word of the Lord, but as Sean has indicated you are exception to that characterization. I still do not really understand why you should be interested at all in any science. It seems a bit messy to worry about facts. It really seems an unnecessary bother to argue whether the precambrian/cambrian boundary or the upper cenzoic (is that really what you meant?) as the evidence of a divine intervention.

Dont worry I do have an open mind which is why I still peruse this site to see how more knowledgable fundamentalist Adventists think. I wont worry you further.


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: So, you do see the need for a police force and a military to maintain civil society, but somehow Christians should not provide what is an otherwise necessary part of that civil society? I’m with Abraham Lincoln on this one when he noted the inconsistency of such a position – like Orthodox Jews paying others to turn their lights on for them on Sabbath

On that logic you should not have any issue with working on Sabbath in any profession serving 24/7. Be that computer support, utilities firefighters. Those giving up those jobs because of inability to have sabbath observance were all deluded. They as Christians should be prepared to “provide what is otherwise a necessary part of civil society”

You cant have it both ways. You cant because of a moral postion claim that Adventists should have exception from working on Sabbath and at the same time deny me the right to consider immoral some occupations that may be very utilitarian in a world full of selfishness and the human acts of evil that comes from that.

Lets for a moment step back from lala land. Where are we and where did we come from on this thread?

1] You posted a rehash of all your usual arguments in response to an article about the more mainstream Adventist positions that may impact the way Adventism reacts to conventional science. All very straight forward.
2] The contention was that Adventism has accepted process for the orgin and evolution of the inanimate world. The birth and death of galaxys and stars and planets in black holes supernova and impacts of spiralling planets. This is where it gets really strange.
3] You contend that Adventism has always accepted the conclusions of that process but then expand on your view of the process which involves a little bit of order and natural law but large amounts of magic. God waited a few billions years until the interstellar material generated by the big band condensed into planets onto which God created life mature and complete. This included Heaven the place of his throne-room which he populated with physical being angels which it is implied have both mass and composition and metabolism.
4] When it was suggested that the same processes and natural law resulted in life on this planet this was claimed inconceivable and would never be done by any process involving life and death. Instead the life we see now is in reality designed to live for ever and has be chemically changed because it is deprived of a particular form of nutrient from a tree that existed on the Earth some 6000 years ago.
5] The inconguity of practicing medicine by the principles of process of natural law and the technology resulting from both the processes of the innanimate and the animate world rather than accepting the much more important process of divine intervention seems to be completely obsure.
6] When someone says that the process of life and death that gave us the physical substance of our universe is also the basis of the creation of life here he must be animal hating sadistic psychopath who cannot belieive in a God of love and grace and is lying when he says that non-violence characterizes the children of the heavenly father for one must always recognize that peace and freedom are only obtained over the bodies of 1/3 of the angels of heaven and the eternal physical and violent struggle against those who would practice violence.

I really cannot understand you Sean. Your ways are way beyond me. I am just sorry that Bob seems to be drawn into your twighlight zone.

Grace


Avondale College Arguing in Favor of Darwinian Evolution?
@Sean Pitman: sorry but your curious amalgam of magic and biology is not really comprehensible to me as a biologist or as a Christian . it. is neither logical or biologically feasible


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: However, according to the Bible and Ellen White, before the Fall God specifically directed nature so that all sentient life was protected in a manner that there was no suffering or death. By eating from the “Tree of Life” God provided constant renewal and regeneration that worked against what would otherwise be inevitable entropic changes, decay, and death. It was by deliberately stepping away from the true Source of eternal life that mankind stepped away from God and into the full workings of mindless natural law alone – which does in fact inevitably lead to suffering and death.

And this interpretation is precisely why you need a theodicy. Where is the justice in killing all for the sake of the sins of one woman+man? It makes no sense logically. If they were conditionally immortal because of eating of the tree of life then did all the animals in all the world congregate around this tree like beasts around a water hole on the serengeti. how exactly do you as you are wont to do translate the account into a literal reality. And which beast had to come and eat. Or was it symbolic? Oh now that’s a thought.


Avondale College Arguing in Favor of Darwinian Evolution?

Sean Pitman: Come on now. Even I can imagine limitations to reproduction or the turnover of sentient carbon-based life. Surely you can at least imagine something similar? I know God can since such a world is described in the Bible and in the writings of Ellen White. Think about it…

Of course I have. This is not simply about reproduction. That is trivial. This is about metabolic process. Show me a carbon based life form that does not grow or metabolize anything and I will show you an organism in stasis as a spore “living” millions of year in amber. That is; effectively dead.

Real life cannot exist without metabolic process in a carbon based world and God has sanctified all this by a process of making good out of evil from the death of one comes life for others. Just as in the biological world so in the spiritual. By his death we have life. Just as God sanctified the practice of sacrifice of appeasement practiced by most cultures for thousands of years before and showed that in the Judeo-Christian tradition these same acts of sacrifice were emblematic of a monotheistic God that would become incarnate and bring life from death. So also he took the preceding accounts of creation derived as they were of the mesopotamian valley and recast it as an account of the monotheistic God who is above all but comes and dwells among us to become one of us. Participating in our life and death but showing us the importance of the transcendent life of the spirit that supercedes carbon based life and its inherent death. It is no fairy tale of 6 impossible things before breakfast. It is not pie in the sky by and by. It is rooted in a real world and it is about the transcendence of love and grace that is acted out in a real physical world by the incarnate God and us as we follow as His disciples.

That is the message I get from the images and visions of the Canon and EG White. But of course I read it for the message that it conveys not as a scientific text. That is where we fundamentally differ.


Share on Facebook0Pin on Pinterest0Share on LinkedIn0Tweet about this on TwitterDigg thisShare on Google+0Share on Tumblr0Share on StumbleUpon0Share on Reddit0Print this pageEmail this to someone