Tag Archives: Peer-Review

News

New peer-reviewed paper endorses irreducible complexity and intelligent design

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From Evolution News.

Excerpt:

A peer-reviewed paper, “Information and Entropy — Top-Down or Bottom-Up Development in Living Systems?,” by University of Leeds professor Andy McIntosh in the International Journal of Design & Nature and Ecodynamics expressly endorses intelligent design (ID) via an exploration of a key question in ID thinking…

Notice that this journal is NOT related to the intelligent design movement in any way – this is a mainstream peer-reviewed journal.

The author of the paper has two goals:

(1) First, he defines the term “machine” (a device which locally raises the free energy) and observes that the cell is full of machines. Such machines pose a challenge to neo-Darwinian evolution due to their irreducibly complex nature.
(2) Second, he argues that the information in living systems (similar to computer software) uses such machines and in fact requires machines to operate (what good is a program without a computer to run it?). An example is the genome sitting on the DNA molecule. From a thermodynamics perspective, the only way to make sense of this situation is to understand that the information is non-material and constrains the thermodynamics so that the local matter and energy are in a non-equilibrium state.

And a bit later:

…the presence of information is the cause of lowered logical entropy in a given system, rather than the consequence.

…[T]here is a perfectly consistent view which is a top-down approach where biological information already present in the phenotypic creature (and not emergent as claimed in the traditional bottom-up approach) constrains the system of matter and energy constituting the living entity to follow intricate non-equilibrium chemical pathways. These pathways whilst obeying all the laws of thermodynamics are constantly supporting the coded software which is present within … Without the addition of outside intelligence, raw matter and energy will not produce auto organization and machinery. This latter assertion is actually repeatedly borne out by experimental observation – new machinery requires intelligence. And intelligence in biological systems is from the non-material instructions of DNA.

You can read more about the paper here.

I wonder what the fallout will be from this bold act?

Luskin writes:

I have no doubt that the editors of International Journal of Design & Nature and Ecodynamics will take much heat for publishing this paper. Even though they make it clear that “[t]he reader should not assume that the Journal or the reviewers agree with the conclusions of the paper,” they should be commended for their courage in publishing it it and calling it a “a valuable contribution that challenges the conventional vision that systems can design and organise themselves.” They write, “The Journal hopes that the paper will promote the exchange of ideas in this important topic” — showing that there is hope for true academic freedom on the debate over ID in some corners of the scientific community.

I think it’s good that some of the more honest journals are starting to post these research papers on ID without endorsing them explicitly. It’s important for people to have a free and open debate about these things. I’m sure that the other side is going to try to come back now with a published response – maybe even with some quality research. And that’s how science is supposed to march forward. We don’t want to get into the situation where there are more of these big “Climategate” scandals in biology. Let all the opposing views be heard.

News

New study shows that human and chimpanzee DNA are very different

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And this new study is from Nature, the prestigious peer-reviewed journal. (H/T Evolution News via Neil Simpson’s latest round-up)

Excerpt:

A Nature paper from January, 2010 titled, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.” Of course, the paper attributes these dramatic genetic changes to “rapid evolution during the past 6 million years.”

One of the scientists behind the study was quoted in a Nature news article stating, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” The news article states that “many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human” since “the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans.” According to the news piece, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa, whereas this is true for less than 2% of the remainder of the genome.”

I’m sure this will make it into the public school textbooks and PBS/Discovery Channel documentaries right away. Right! Away!

Polemics

Has the progress of science vindicated Mike Behe or Ken Miller?

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ECM send me a couple of articles recently from Uncommon Descent and Evolution News that I wanted to write about.

The topic is Junk DNA, which is the name given by naturalists to the portions of the DNA code that do not code for proteins. Is Junk DNA really just leftover junk from a blind, purposeless process of fully naturalistic evolution? Or does it have a function, like intelligent design theorists say? Let’s put these predictions to the test and then update our worldviews to fit with the scientific evidence.

The prediction of Ken Miller

Anti-theistic biologist Ken Miller said in 1994 that DNA is filled with junk left over from naturalistic, random evolution:

…the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

Ken Miller

One thing you have to like about Ken is that he manages to fit in some predictions along with his factually incorrect statements under oath.

The prediction of Michael Behe

Theistic biologist Michael Behe said in 2002 that DNA isn’t as junky some people think, because of the evidence:

As a public skeptic of the ability of Darwinian processes to account for complex cellular systems and a proponent of the hypothesis of intelligent design, (1) I often encounter a rebuttal that can be paraphrased as “no designer would have done it that way.” …
If at least some pseudogenes have unsuspected functions, however, might not other biological features that strike us as odd also have functions we have not yet discovered? Might even the backwards wiring of the vertebrate eye serve some useful purpose?
….
Hirotsune et al’s (3) work has forcefully shown that our intuitions about what is functionless in biology are not to be trusted.

Sincerely, Michael J. Behe
An Open Letter to Nature

Those are the two predictions.

So, what does the progress of science say to confirm one prediction or the other? Well, let’s see what Nature, the most prestigious peer-reviewed science journal, has to say.

In 1961, French biologists François Jacob and Jacques Monod proposed the idea that ‘regulator’ proteins bind to DNA to control the expression of genes. Five years later, American biochemist Walter Gilbert confirmed this model by discovering the lac repressor protein, which binds to DNA to control lactose metabolism in Escherichia colibacteria1. For the rest of the twentieth century, scientists expanded on the details of the model, but they were confident that they understood the basics. “The crux of regulation,” says the 1997 genetics textbook Genes VI (Oxford Univ. Press), “is that a regulator gene codes for a regulator protein that controls transcription by binding to particular site(s) on DNA.”

Just one decade of post-genome biology has exploded that view. Biology’s new glimpse at a universe of non-coding DNA — what used to be called ‘junk’ DNA — has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA2. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive,” says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

On the Evolution News post, pro-ID guy Rob Crowther writes:

…not that long ago, junk DNA was being defended as an important element of the Darwinian evolution paradigm… The question now seems to be whether Ayala, Dawkins, Collins, Falk and other junk DNA proponents will continue to defend junk DNA, whatever they call it?

The post by Rob Crowther has more information on this story.

If you are one of those people who thinks that naturalistic molecules-to-man evolution is as proved as is the fact that the Earth goes around the Sun, then check out the links below – ESPECIALLY the debates. Peter Atkins, Michael Shermer and Lewis Wolpert are some of the most prominent prominent proponents of naturalism and materialism out there. Watch the debates. Have an open mind. If science can be hijacked by global warmists, then it can be hijacked by evolutionists, too. We need to guard against that.

I know there is a lot of pressure on people to just believe in naturalism, especially when their degree or career depends on a public profession of faith in the power of chance and material processes. But we have to follow the evidence – science is about evidence, not ideology. Science is about testing to see what is true, not forcing the evidence to confirm what you want to believe (e.g. – materialism). There is a difference between the religious assumption of naturalism/materialism and the scientific method of predicting and testing.

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