Tag Archives: Instructions

News

New study: fruit fly DNA reveals unexpected complexity

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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. 

Polemics

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

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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?

Podcasts

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

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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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