The Origin of the Ribosome

Design Inteligente is an ID blog in Portuguese. It is a visually appealing blog with substance. O Ribosomma e a Complexidade Irredutival is a blog entry which cites the irreducibly complex nature of ribosomes and links to a YouTube video. The text quotes Harvard Medical School Professor George Church, who was recently referred to in a blog piece authored by Chunkdz at Telic Thoughts. The quote:

Portanto, a questao e, como e que essa coisa apareceu? E se eu fosse um defensor do design inteligente, seria nisso que me focaria, como e que a ribosoma apareceu?

After marvelling at the complexity of the ribosome Church asks how it came to be. He adds that if he were an intelligent design advocate he would focus on that question.

Analysis of a Debunker

I posted an entry at Telic Thoughts about a book review appearing at New Scientist. The reviewer is enthusiastic about a book which is, in his view, a useful tool for debunking the concept of cosmological design. The related argument fails but the fact that it is even made, with reference to what is allegedly a scientific theory, makes one wonder about the author's real purpose.

The title of the post is Reviews. Here it is:

Review: The Universe: Order without design appears at New Scientist. The reviewer writes that NASA physicist Carlos Calle wrote a book in which he addresses the question: does the universe require a supernatural "designer" or are cosmological theories alone able explain the reality? Quoting from the review:

Physics and cosmology alone may have the answers, says Calle. Combine eternal inflation, in which the primordial false vacuum continuously grows and decays, with string theory and you end up with a multiverse - a vast collection of universes, each of which has a different amount of dark energy. We find ourselves in one where it has just the right value for stars, planets and life because... well, we couldn't find ourselves anywhere else.

That caught my attention because I recently posted Leaning on Your Own Understanding which notes Dawkins' view that the eternal existence of God does not explain anything. But is Calle's argument that a cosmological theory, encompassing eternal inflation and innumerable unobserved universes, a plausible explanation? It might be to some who see no conflict between this and Dawkins' position.

So are universes eternal or only their oscillations? This looks less like a comprehensive explanation than an attempt to dress philosophical biases in scientific garb. The last paragraph includes this:

The model doesn't require a beginning, and some theorists suspect that eternal inflation may not either.

So a physical model which incorporates eternal inflation is sufficient. No need to inquire about the origin of matter and energy. 'It just is and always was ' suffices for multi-universes.

Certainly, neither requires a designer.

That's a philosophical presumption the author is entitled to as a matter of personal preference. I suspect it explains his enthusiasm for Calle's ideas.

Eternity

I wrote an entry at Telic Thoughts (Leaning on Your Own Understanding) which I'll reproduce here. In it Richard Dawkins is quoted as referring to a question thought by atheists to be a telling criticism of theism. It's a variant of the who created God question. But atheists have their own problems with eternity, beginings and ends. So they have no alternative which avoids a causal dilemna. For believers in God his eternal existence adaquately explains creation, namely, the universe and all properties of it. But if all things need a prior existing cause then atheists have their own dilemna and need not be hiding it while asking who created God. Who created matter and energy? Do they have eternal properties? If that is the claim then Dawkins cannot avoid tarring atheism with the same charge he levels at theists.

The link for the Telic Thoughts blog is here. The TT blog entry:

I was reading a paper authored by Dembski and Marks when I came across a quote taken from Richard Dawkins' book The Blind Watchmaker. The quote:

To explain the origin of the DNA/protein machine by invoking a supernatural Designer is to explain precisely nothing, for it leaves unexplained the origin of the Designer. You have to say something like "God was always there," and if you allow yourself that kind of lazy way out, you might as well just say "DNA has always been there," or "Life was always there, and be done with it.

Dawkins' is expressing a sentiment echoed in the thread PD instead of ID by at least one commenter. But Dawkins is drawing a conclusion supported by an artificial demarcation made in a time/causal pathway depicting the origin of the universe. Specifically, he is drawing our attention to a point in time at which prebiotic earth exists and then posing questions about life's origin. In doing so Dawkins begs some very pertinent questions showing that he, like his theistic counterparts, is unable to present a comprehensive and coherent account running from A to Z. Perhaps this is because human minds are limited both in terms of their capabilities and their knowledge of what preceded them.

Dawkins does not say that God's existence precedes that of our universe. Indeed he thinks this foolishly avoids the question of God's origin. But he does not challenge another assumption inherent to Dawkins' own position namely, that matter and energy have always been there. Of course one might argue that whatever it was, that contained what is called the Big Bang and our resulting universe, was not matter and energy as we know it but that merely moves the causal goalposts back a step and illustrates a dilemna known as infinite regress. Pick your poison. Either matter and energy have always existed and no cause is attributed to this or a trail of infinite causes exists each one preceded by a prior but unidentified cause.

ID critics are fond of utilizing terms like magic to describe causal scenarios involving the action of a deity. Yet magic can be a very subjective term. It seems quite magical to me to assert that the basic components of our universe just exist and always have. Thinking that view is less "magical" than a theistic explanation, positing God at the begining of a causal series of events, is more a matter of personal preference than empirically grounded conceptions is it not? Yet for a theist, whose personal experiences indicate the presence of a deity, the choice between incomprehensible options becomes obvious.

Linking Changes in DNA to Health Problems

New tool helps researchers identify DNA patterns of cancer, genetic disorders discusses a new means of identifying minute changes in DNA patterns that lead to medical disorders. Quoting from the linked article:

David Cox, a Ph.D. student in computer science at NC State, devised the "symbolic scatter plot" tool to provide a visual representation of a DNA sequence. Cox explains, "The human visual system is more adept at identifying patterns, and differentiating between patterns, than existing computer programs such as those that try to identify repetitions of DNA sequences." In other words, the naked eye sees patterns better than computers can.

Identifying patterns in a sequence of DNA is important because it can help researchers identify the minute genetic variations between subjects that suffer from a disease, such as cancer, and subjects that do not. "Improved identification of relevant DNA sequences will hopefully expedite the development of successful treatment for a range of diseases," Cox says, "by allowing researchers to focus on the components of DNA that are related to the disease and improving our understanding of the genetic mechanisms of these diseases. For example, what turns specific genes on and off?"

Dumbing Down the American Electorate

Viewpoint has an entry that is both funny and troublesome. It is titled God Help Us and cites some anecdotal stories from the most recent presidential election as derived from a piece in First Things. Here they are:

During the campaign, a woman in her mid-twenties told me she would not vote for Gov. Sarah Palin because "Palin is so stupid she doesn't even know where Alaska is." I asked what she meant, and she explained that in a TV interview Palin had referred to Alaska as "up North," whereas everyone knows Alaska is "down there with Hawaii south of California." I surmised that her knowledge of geography is based on seeing textbooks depicting the U.S. map with an insert for Alaska and Hawaii placed in the lower left-hand corner, underneath California. When I gently explained where Alaska is, she dismissed it with, "Well, Palin's stupid anyway."

Too funny. But pathetic as well.

A second voter, a man about thirty, said he would vote for Obama rather than McCain because "Obama has young children so he probably cares more about the future than McCain does."

You cease caring about the future when your kids become adults? Brilliant.

A Catholic nun was enthusiastically supporting Obama (as was most of her order), and, when I pointed out Obama's positions on abortion issues, she refused to believe it was true on the grounds that such a wonderful man could not possibly support abortion.

The brain ceases to function and touchy feely takes over.

DNA Helicases

In prepararing to analyze a research paper I'll begin posting a series of blog entries that provide mini-tutorials about molecular biological constructs. I'll then link to them in a larger blog entry. This one is focused on DNA helicases. As this link suggests, DNA helicases play a role in the unwinding of DNA which occurs during essential cellular functions like replication, recombination, repair and transcription.

For an easy to read and informative abstract try Unwinding of Unnatural Substrates by a DNA Helicase. Its authors are Alan J. Tackett, Patrick D. Morris, Regina Dennis, Thomas E. Goodwin, and Kevin D. Raney.

Cell Cycle Arrest and DNA Repair

There is an article in the jounal Nature (Volume 459 Number 7243) titled F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage. It was authored by Manas K. Santra, Narendra Wajapeyee and Michael R. Green.

When DNA is damaged in eukaryotic cells a signaling pathway called the DNA damage response (DDR) becomes an essential part of the cellular coping response. Affected cells need to regulate their cell cycle so that DNA repair can be coordinated with the progression of the cycle. DDR coordinates adjustments in the cycle progression.

Researchers studied the function of a protein known as FBXO31. When this protein is expressed it facilitates the degradation of cyclin D1. Cyclin D1 plays a role in regulating the progression of the cell cycle from G1 to the S phase. It helps maintain the G1 phase. An increase in FBXO31 levels has been observed with the incidence of different types of DNA damaging agents.

A Book Review of Let Freedom Ring

I read a historic novel Let Freedom Ring (Thorndike Press). Al and JoAnna Lacy are the authors. The story takes place in the 19th century and centers around Russian characters struggling to maintain their Christian faith under repressive Czarist regimes. The book is packed with adventures involving conflicts between ordinary Russians and the dreaded Cossacks. Eventually a small group of Russians manage to save their lives, find their way out of the country and immigrate to the United States.

One part of the book was particularly striking to me. Chapter Nine, pages 190-191 contain the passage. The Czarist government had become callous to the needs of the people. But what was interesting was the route by which this came about. One of the main characters pointed out that in the prior century a combination of governmental promises and apathy among the populace led people to place too much trust in their government. Political leaders, acting on their greedy impulses, became increasingly powerful and abusive.

This parallels what is going on in America today. Apathy is pervasive and increasing power in the hands of greedy legislative and executive officials all too common. The trust placed in government officials is way out of proportion to what is merited. History shows that trends toward ever centralized and expanded government power erode the freedom of those governed. It may take some time before the ugliness of the power shift becomes apparent but it will. There is something pathetic about people placing too much faith and trust in the power elites of their society. It's a form of self-emasculation which burdens posterity with the consequences of the foolish choices made by their forefathers.

A Significant Finding?

New nucleotide could revolutionize epigenetics is a EurekAlert article discussing work accomplished by Nathaniel Heintz's Laboratory. Quoting from the first paragraph:

Anyone who studied a little genetics in high school has heard of adenine, thymine, guanine and cytosine – the A,T,G and C that make up the DNA code. But those are not the whole story. The rise of epigenetics in the past decade has drawn attention to a fifth nucleotide, 5-methylcytosine (5-mC), that sometimes replaces cytosine in the famous DNA double helix to regulate which genes are expressed. And now there's a sixth. In experiments to be published online Thursday by Science, researchers reveal an additional character in the mammalian DNA code, opening an entirely new front in epigenetic research.

The author notes that the DNA methylation process involves targeting sites where cytosine precedes guanine in DNA. The enzyme DNA methyltransferase attaches a methyl group to cytosine and in doing so generates a distinct nucleotide called 5-methylcytosine. The process is linked to gene silencing.

An interesting feature of methylation is the effect the environment has on methylation patterns which can be inherited.

Eroding Freedom

The commentary AMBROSE: Ugly bailout fallout appeared in The Washington Times in the wake of the passage of the bailout bill. Although published on October 19, 2008 the author's words are prophetic:

Again and again, this Wall Street package will be used as an excuse to try to take freedom out of our markets, to throttle them with excessive regulation and leave them shorn of the innovation and energy that add up to prosperity. It will be used as an excuse for something else, too — creation of a European-style welfare state.

We have not arrived at that point but are heading in that direction. Geithner and others in government have made it plain that they intend nothing less than a right to determine how business recipients of public funding go about conducting business. Not very surprising and a major concern of many critics of the bill at the time it was formulated. More:

A chief argument on behalf of a commercial police state will be that regulatory laxity gave us the moment's pandemonium when, in fact, the main instigating factor was Democratic-sponsored social engineering abetted by the Federal Reserve's easy-money policies, ultimately leading beyond a doubt to irresponsible executive behavior in private institutions.

No one is arguing that government does not have a legitimate regulatory role to play but regulating, with the purpose of inhibiting fraud and questionable business practices, is a far cry from insisting on a right to determine policies about how business is conducted.