Wintery Knight

…integrating Christian faith and knowledge in the public square

New study: fruit fly DNA reveals unexpected complexity

From Evolution News.

Excerpt:

You know about ENCODE, the project that found 80 percent or more of the human genome is transcribed and appears functional. Now, along comes modENCODE: the ENCODE project for model organisms. Results from the fruit fly are in, and Indiana University shares the surprises (for evolutionary theory, that is): “Study of complete RNA collection of fruit fly uncovers unprecedented complexity.”

The paper shows that the Drosophila genome is far more complex than previously suspected and suggests that the same will be true of the genomes of other higher organisms. The paper also reports a number of novel, particular results: that a small set of genes used in the nervous system are responsible for a disproportionate level of complexity; that long regulatory and so-called “antisense” RNAs are especially prominent during gonadal development; that “splicing factors” (proteins that control the maturation of RNAs by splicing) are themselves spliced in complex ways; and that theDrosophila transcriptome undergoes large and interesting changes in response to environmental stresses. (Emphasis added.)

Ten of the 41 researchers from 11 universities working on modENCODE came from IU. They found many genes transcribed only under stress, such as exposure to heat, cold, and toxins. “In total, 5,249 transcript models for 811 genes were revealed only under perturbed conditions,” they said. As if the “junk DNA” myth needed any more pounding, the lead author testifies:

“As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.

The post on Evolution News also talks about another study from the University of Vienna on the genome of the sea anemone.  Their genome was way more complex than expected, too.

So what is the best explanation for all this specified complexity that enables biological function?

Evolution News explains:

Intelligent design… knows how to explain the observations. Whenever we see a complex, functioning system (like a rollout of a software system), we know intelligence played a role in its origin. We also know that intelligence can explain multiple, independent instantiations of similar systems. We never see, however, complex, networked systems arising de novo by unguided natural processes.

Yes. In the company I work for, we have a release of functional code every month (at least). These explanation for the increase in specified complexity in our applications is that busy little software engineers have been carefully sequencing characters into lines of Java code, for  purpose. No rational person believes that you can get huge increases in specified complexity by random chance. Code is code is code. It all requires a coder, just like the Big Bang requires a Big Bang. 

Filed under: News, , , , , , , , , ,

Paul Davies: the hard problem of the origin of life is not “complexity” – it’s information

Check out this column on the origin of life from the radically leftist UK Guardian, written by agnostic cosmologist Paul Davies. (The same Paul Davies who is occasionally quoted by William Lane Craig)

Excerpt:

The origin of life is one of the great outstanding mysteries of science. How did a non-living mixture of molecules transform themselves into a living organism? What sort of mechanism might be responsible?

[...]Most research into life’s murky origin has been carried out by chemists. They’ve tried a variety of approaches in their attempts to recreate the first steps on the road to life, but little progress has been made. Perhaps that is no surprise, given life’s stupendous complexity. Even the simplest bacterium is incomparably more complicated than any chemical brew ever studied.

But a more fundamental obstacle stands in the way of attempts to cook up life in the chemistry lab. The language of chemistry simply does not mesh with that of biology. Chemistry is about substances and how they react, whereas biology appeals to concepts such as information and organisation. Informational narratives permeate biology. DNA is described as a genetic “database”, containing “instructions” on how to build an organism. The genetic “code” has to be “transcribed” and “translated” before it can act. And so on. If we cast the problem of life’s origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect. To explain how life began we need to understand how its unique management of information came about.

[...]Sara Walker, a Nasa astrobiologist working at Arizona State University, and I have proposed that the significant property of biological information is not its complexity, great though that may be, but the way it is organised hierarchically. In all physical systems there is a flow of information from the bottom upwards, in the sense that the components of a system serve to determine how the system as a whole behaves. Thus if a meteorologist wants to predict the weather, he may start with local information, such as temperature and air pressure, taken at various locations, and calculate how the weather system as a whole will move and change. In living organisms, this pattern of bottom-up information flow mingles with the inverse – top-down information flow – so that what happens at the local level can depend on the global environment, as well as vice versa.

[...]The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry. Therefore chemistry alone will not explain life’s origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program. Our work suggests that the answer will come from taking information seriously as a physical agency, with its own dynamics and causal relationships existing alongside those of the matter that embodies it – and that life’s origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round.

The point of me posting this is simple. The thing to be explained in the origin of life is not a cake, where you can jumble ingredients together and get something. The thing to be explained is information. The origin of life is a programming problem, not a cooking problem. Where did the software come from – the first basic program that allowed for the basic functions of life, like self-replication.

Dr. Davies is hoping for a naturalistic solution to the problem, because he is a naturalist. But at least he is clear about specifying the thing that needs to be explained. A lot more clear than the journalists who explain intelligent design as the belief that some things are too complex to have evolved. But that’s wrong. The real question is: where did the information come from?

Filed under: Polemics, , , , , , , , , , , , , , , , , ,

Prominent atheist philosopher gives mixed review of intelligent design

Consider this report on a peer-reviewed assessment of intelligent design by the prominent atheist philosopher Thomas Nagel.

Excerpt:

Prof. Thomas Nagel, a self-declared atheist who earned his PhD. in philosophy at Harvard 45 years ago, who has been a professor at U.C. Berkeley, Princeton, and the last 28 years at New York University, and who has published ten books and more than 60 articles, has published an important essay, “Public Education and Intelligent Design,” in the Wiley InterScience Journal Philosophy & Public Affairs, Vol. 36, issue 2…

[...]Prof. Nagel’s paper is a significant and substantial opening, at America’s highest intellectual level, that encourages all intelligent, educated, informed individuals — particularly those whose interest in this issue derives from intellectual curiosity, not the emotional advocacy excitement for any side — that it is legitimate as a matter of data, science, and logic, divorced from all religious texts and doctrines, to consider that intelligent design may be a valid scientific approach to understanding how DNA and the complex chemical systems of life came to attain their present form. Prof. Nagel’s article is well worth the price to put it in the library of any inquiring mind.

The actual paper is here.

Now for the summary of the paper, with supporting quotes:

Professor Nagel has read ID-supportive works such as Dr. Behe’s Edge of Evolution (p. 192). He reports that based on his examination of their work, ID “does not seem to depend on massive distortions of the evidence and hopeless incoherencies in its interpretation” (pp. 196-197). He reports that ID does not depend on any assumption that ID is “immune to empirical evidence” in the way that believers in biblical literalism believe the bible is immune to disproof by evidence (p. 197). Thus, he says “ID is very different from creation science” (p. 196).

Prof. Nagel tells us that he “has for a long time been skeptical of the claims of traditional evolutionary theory to be the whole story about the history of life” (p. 202). He reports that it is “difficult to find in the accessible literature the grounds” for these claims.

Moreover, he goes farther. He reports that the “presently available evidence” comes “nothing close” to establishing “the sufficiency of standard evolutionary mechanisms to account for the entire evolution of life” (p. 199).

He notes that his judgment is supported by two prominent scientists (Marc Kirschner and John Gerhart, writing in the Oct. 2005 book Plausibility of Life), who also recognized that (prior to offering their own theory, at least) the “available evidence” did not “decisively settle[]” whether mutations in DNA “are entirely due to chance” (p. 191). And he cites one Stuart Kauffman, a “complexity theorist who defends a naturalistic theory of emergence,” that random mutation “is not sufficient” to explain DNA (p. 192).

Prof. Nagel acknowledges that “evolutionary biologists” regularly say that they are “confiden[t]” that “random mutations in DNA” are sufficient to account for “the complex chemical systems we observe” in living things (p. 199) — but he disagrees. “Rhetoric” is the word Professor Nagel uses to rejects these statements of credentialed evolutionary biologists. He judges that the evidence is NOT sufficient to rule out ID (p. 199).

He does not, however, say that the evidence compels acceptance of ID; instead, some may consider as an alternative to ID that an “as-yet undiscovered, purely naturalistic theory” will supply the deficiency, rather than some form of intelligence (p. 203).

In light of these considerations, Prof. Nagel says that “some part of the high school curriculum” “should” include “a frank discussion of the relation of evolutionary theory to religion” but that this need not occur in biology classes if the biology teachers would find this too much of a “burden” (p. 204). Significantly, Prof. Nagel — who is a professor of law as well as a professor of philosophy — concludes that, so long as the proposal is not introduced by religiously-motivated persons “as a fallback from something stronger,” but by persons “more neutral” or “without noticeable religious beliefs,” it would be constitutional to “mention” ID in public school science classes, because doing so genuinely furthers “the secular purpose of providing a better understanding of evolutionary theory and of the evidence for and against it” (p. 203). He makes clear that the “mention” must be a “noncommittal discussion of some of the issues” (p. 205).

So Nagel does NOT think that ID is a slam dunk, just that it is worth considering in science classrooms. Teach the controversy, that’s always the right approach. Be open-minded. Look at the evidence before you decide.

Filed under: Commentary, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

Ann Gauger’s new peer-reviewed paper on Darwinian evolution

Amazing new research paper by the Biologic Institute. The PDF of the paper, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” is available here.

The MP3 file is here.

Participants

  • Jay Richards, Director of Research at the CRSC, (Discovery Institute)
  • Ann Gauger, senior research scientist at the Biologic Institute

About Ann:

Ann is a senior research scientist at Biologic Institute. Her work uses molecular genetics and genomic engineering to study the origin, organization and operation of metabolic pathways. She received a BS in biology from MIT, and a PhD in developmental biology from the University of Washington, where she studied cell adhesion molecules involved in Drosophila embryogenesis. As a post-doctoral fellow at Harvard she cloned and characterized the Drosophila kinesin light chain. Her research has been published in Nature, Development, and the Journal of Biological Chemistry.

Topics:

  • Co-authored with microbiologist Ralph Seelke at the University of Wisconsion
  • Purpose: study whether bacteria can evolve the ability to fix a broken protein (e.g. – enzyme)
  • Two areas are broken in the enzyme
  • If you fix the first one, it works a little but not fully (slight advantage)
  • If you fix the second one, it starts to work fully (huge advantage)
  • It’s a “two-step adaptive path” – a textbook case for evolution
  • should be able to hit both mutations and get back full functionality
  • At the start of the experiment, the cell is churning out broken protein
  • there is a cost to the cell for create the broken protein
  • the cell can either go through the adaptive path and repair the protein
  • OR, it can shut off production of the broken protein
  • EITHER PATH gives a selective advantage
  • So what happens? The cells NEVER followed the adaptive path
  • They almost ALWAYS turn off the production of the broken protein
  • It happens in 30-50 generations, in 14 different cultures
  • Each culture had a different way of turning off the production
  • They tested on 10^12 cells
  • Only one cell made the first repair, none made the second repair
  • It’s more advantageous to STOP PRODUCING the broken protein as soon as possible
  • The first cell that gets rid of the non-functional protein first overtakes the whole culture
  • so, even adaptive paths that provide a benefit with one mutation are unlikely to be followed
  • The point: even promising theoretical adaptive pathways MAY NOT WORK in experiments

I wrote about Doug Axe’s recent research paper here. He is the Director of the Biologic Institute.

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Doug Axe publishes a new peer-reviewed paper on protein folding

A new podcast from ID the Future is worth listening to.

Participants

  • Jay Richards, Director of Research at the CRSC, (Discovery Institute)
  • Doug Axe, Director of the Biologic Institute

The MP3 file is here.

Topics

  • the new BIO-Complexity peer-reviewed journal
  • new peer-reviewed paper challenges Darwinian account of protein folding
  • proteins are found in every living system
  • a protein is a chain of parts called amino acids
  • there are 20 amino acids used in living systems
  • it’s like a 20-letter alphabet used to make sentences (proteins)
  • if the sequence is just right, it folds up and has a function
  • the information about the functional sequences is in the genome
  • the “protein fold” is the 3D shape that a functional protein takes on
  • the folding problem is good because you can TEST Darwinian mechanisms
  • the problem is simple enough to be tested rigorously in a lab
  • Question: how easy is it to create a sequence that folds?
  • English is a good analogy to the problem of protein folding
  • you have a long string of characters (e.g. – 200 letters)
  • each “letter” can be one of 20 amino acids
  • if you assign the letters randomly, you almost always get gibberish
  • there are tons of possible sequences of different letters
  • it’s like a 200 digit slot machine with each digit having 20 possibilities!
  • the number of sequences that would actually make sense is tiny
  • protein folding is the same
  • Doug’s paper assesses how many “tries” could have been attempted
  • Doug’s paper calculates the total number of possibilities
  • cells have arrived a large number of functional sequences
  • but only a small number of the total possibilities could have been tried
  • this is called the “sampling problem”
  • there isn’t enough time to test all of the possibilities (see previous paper below)
  • how did living systems arrive at the functional sequences so quickly?
  • there are some possible naturalistic scenarios for solving the problem
  • Doug’s new paper shows that none of the naturalistic explanations work
  • the only explanation left is that an intelligence sequenced the amino acids
  • it is identical to the way that I can sequence letters to make this post

A picture is worth a thousand words

Here’s a video clip from the DVD Darwin’s Dilemma showing the process:

If you would like to know more about Darwin’s Dilemma, you can read Brian Auten’s review of Darwin’s Dilemma.

Who are these guys?

I wrote a post before on Doug Axe’s previous publications in the Journal of Molecular Biology, where he researched how many of the possible sequences of amino acids have biological function. His PhD is from Caltech, and his post-doctoral research on proteins was conducted at Cambridge University.

Jay Richards is a Senior Fellow of the Discovery Institute and a Contributing Editor of The American at the American Enterprise Institute. In recent years he has been a Visiting Fellow at the Heritage Foundation, and a Research Fellow and Director of Acton Media at the Acton Institute. His PhD is from Princeton University.

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