About DNA Compaction

I came across this article while reading comments to a blog entry at Uncommon Descent. There are some nice visuals to go along with brief descriptions of important biological entities. The linked article begins with this observation:

The structure of the DNA within the cell, as explained by most textbooks, is a caricature of its actual compaction and structure. In a eukaryotic cell, the DNA undergoes many levels of twisting, folding, rolling, twirling, and coiling during replication, or meiosis. Most genetics textbooks present a summary, since many of these structural discoveries are on-going. Given the dense and complex compaction DNA undergoes, only providing a summary in a textbook is understandable, but does not due the process justice.

Related Links

This blog entry at Telic Thoughts led to discussions of physics theories and concepts. A new commenter (olegt) made significant contributions. Here are some additional links that could be of interest to those who followed the TT exchanges:

What is Relativity?

Einstein Rings

Dark Matter

Potential Windfall from Nuclear Tinkering

A Science Daily article titled Location Matters, Even For Genes notes how a change in the location of a gene can affect gene expression. Specifically, moving an active gene from a cell nucleus interior to its periphery appears to inavtivate the gene. The related paper on which the story is based was published in the journal Nature. The significance to this lies in a potential to silence genes by preventing the transcription of them. This would occur when such genes are attached to the inner part of the nuclear membrane. This could become a form of treatment for medical maladies through manipulation of gene regulation. Such maladies could include cancer whose development has been, at times, associated with the malfunction of gene regulation.

Is there any significance for Intelligent design? Quite possibly. Enhanced capacities to regulate gene expression may prove useful in assessing ID concepts like irreducible complexity and front loading. Tinkering with cellular mechanisms can be a means of ascertaining the fitness value of constituent parts of a biological function. It could also indicate a hitherto unrealized hierarchical structure to biological development useful to a front loading perspective.

Introducing 'Unknown Entities'

I have frequently disagreed with a Telic Thoughts commenter who goes by the moniker of The Pixie. However, he made a comment in an active thread which I believe is noteworthy:

"No, invoking a new, unknown entity is the antithesis of parsimony!"

The key phrase is "unknown entity." Ironically it has become a routine tactic of ID critics who generally invoke such unknown entities in response to ID concepts like irreducible complexity or ID critiques of origin of life theories. The unknown entities tend to take the form of imaginary biochemical pathways. Rather then provide specifics about the pathways themselves the focus is placed on phenomenon like random mutation and natural selection with logical argument filling in for empirical data.

A Little Less Junk Found in DNA

Some 'Junk' DNA Is Important Guide For Nerve-cell Channel Production is the title of a Science News article which tells of the identification of an intron that helps insure the proper placing of BK channels. Researchers from the University of Pennsylvania School of Medicine are credited with the discovery. The intron plays a guiding role although it is not a part of the synthesized channel protein.

The location of the intron function is also of interest for it is outside the cell nucleus. Usually introns are excised in the nucleus before mRNA is routed outside the nucleus. Researchers from the same school had previously discovered that dendrites are capable of splicing mRNA.

Made in the Image of God

Chuck Colson's essay In Praise of PETA reminds us of the moral consequences of following a world view to its logical end. Quoting from the article:

What does that have to do with Darwinism? Everything. To a Darwinist, you see, there is no distinction between human beings and animals. We all came about by chance; we are made of the same "stuff," and we all end up as nothing more than dust. Instead of recognizing humans as bearers of God's image, Darwinism sees us as nothing more than competitively successful bipeds with opposable thumbs. Forget any talk of human dignity.

And that is exactly the worldview that PETA lives by. If Darwinism—which we teach in the schools—is true, then they are right: Slaughtering and eating animals is just as bad as the Holocaust. It is cannibalism. If Darwinism is true, then PETA was correct when it recently compared the American Kennel Club to the Ku Klux Klan for trying to create a "master race" of dogs. Charles Darwin and Ingrid Newkirk are so much on the same page that without Darwin, there could be no PETA. It is a perfect example of following a worldview to its logical conclusion.

If evolution is viewed as a continuum of genetic change affording no uniqueness to humans then neither is there any basis for uniqueness under the law. Treatment of human and non-human species is viewed as occurring on the same moral plane from a Darwinian perspective. Unfortunately the elevation of animals coincides with a de-emphasis on human worth. That spells trouble.

A personal universe

(Cross-posted from "More Than Words" - http://mothwo.blogspot.com/2008/01/personal-universe.html)

What is the right understanding of reality and the universe?

Introducing Naturalism

Amongst those who've made a serious effort to think through their assumptions about reality, many in the modern west hold to the system of naturalism. Naturalists seek to explain all of reality in terms of matter and the physical forces, or interactions, between matter. They treat the physical universe as a closed, self-contained and self-sufficient system. Everything must ultimately be explained in terms of physical laws. Naturalism seeks to rule out any kind of idea of a divine mind behind the universe, or a divine will active in it. Naturalism seeks to remove the category of the "transcendent" from reality - ultimately, all is matter and there is nothing beyond it.

Naturalism Expressed

In biology, naturalism is expressed in the theory of Darwinism, which seeks to explain all of life's complexity by the mechanism of natural selection working upon random mutations. In psychology, naturalism seeks to reduce all of human behaviour to the chemistry of the human brain. In theology, naturalism seeks to empty the Bible of the concepts of divine revelation, human fallenness and a gracious Saviour, and reduce it to a helpful ethical message about how to live a good life. And so on. Naturalism is a powerful, even dominant, force in many areas of study in our time.

Naturalism And Personality

One of the immense problems that naturalists have not yet approached any kind of coherent explanation for is the problem of personality.

We live in a personal universe. Beyond the molecules, cells and systems which are present in your body, there is a you which transcends them all. Almost every cell in your body is replaced within seven years - yet there is still a you which continues on throughout your whole lifetime. I am not a different being from the one I was as a little boy - even though there's hardly a molecule shared between me now and there. You are a personal, self-conscious, thinking being. You think thoughts, you weigh up moral decisions, you consider ideas - and you can do all of those things without being determined by your genes. The thoughts that go on in my childrens' heads are not pre-determined by the genes that mum and dad gave them. We might both love classical music; they will be free to decide that it's boring if they choose.

Our awareness of our own self-consciousness and of the reality of our existence as personal beings is summed up most simply, most memorably and most famously in philosopher Rene Decartes' dictum: Cogito, ergo sum. Or in English: "I think; therefore, I am".

Decartes had the aim to how much he could deduce from a position of radical skepticism. He aimed to drop every assumption and pre-conception about reality, and simply deduce what he could from the naked act of thinking. His celebrated first deduction was that since he was sure that he was partaking in the act of thinking, he must exist. There was a distinct, personal being chewing the cud.

To sum up what we've discussed here: Our awareness of the reality of the university as being personal - that we have individualities which transcend the physical - is one of the deepest, most fundamental facts about our existence.

So....

At this point, naturalism is utterly stumped. How can a lump of flesh generate self-consciousness? The concept of self-consciousness transcends the categories of naturalism - naturalism has no place for an I or a you. Naturalism has to explain how, somehow, the bone material of my skull is not self-conscious and yet the lump of brain tissue contained in that skull is!

Stories about how a physical world could develop out of nothing can be made to sound plausible. (How plausible they sound after you've thought about them a little is another matter). We can all, in our heads, at least picture the idea of fish turning into amphibians, and then into mammals, apes and then people. It strikes us as at least being worthy of discussing. It's quite another thing, however, to try to cook up a story about how there can be an I and a you.

In other words, naturalism is completely up the creek when it comes to explaining one of the most basic facts about reality. The evidence of personality as a basic and transcendent category in the universe we live in points very definitely not to an impersonal reality behind the university. It testifies clearly to a vast Personality who is behind it all.

In other words:

I think; therefore God is.