Tag Archives: Genome

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.

Related posts

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!

Commentary

Is the presupposition of naturalism a science stopper?

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UPDATE: Welcome readers from 4Simpsons! Thanks for the link Neil!

In cosmology, we had to wait decades for the theism-friendly big bang theory to beat out atheism-friendly theories like the eternal universe model, the steady-state model, the oscillating model, etc. Piles of taxpayer money wasted trying to prove atheistic flights of fancy. But in the end, the evidence for the big bang was too much for the atheistic theories, and we beat them out.

Junk DNA

And here is another example of how atheism is bad for scientific inquiry: “Junk DNA”.

The purpose of the genome is to contain the instructions that allow the cell to build functional sequences of smaller components. If the sequences are done right, you get a folded-up protein that can be used for all kinds of things.

But what those parts of the genome that don’t code for proteins? Well, atheists have been calling them “Junk DNA” and hailing it as proof that there is no designer to life. I can remember Christian groups like Reasons to Believe predicting that a purpose for “Junk DNA” would be found. But atheists pooh-pooh’d that idea. Gee, I wonder who was right? The same people who are always right: THEISTS.

Denyse O’Leary cites this Princeton University press release on Post-Darwinist:

Now researchers from Princeton University and Indiana University who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.

…The term “junk DNA” was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be.

She’s got a stack of other related links at the bottom of the post.

Commenter ECM also sent me this story from Cornelius Hunter’s new blog.

Excerpt:

One problem with evolution is its strong bias toward viewing everything in biology as a kludge. When a newly discovered structure is examined, evolutionists take one look and conclude it is leftover junk. After all, blind, unguided mutations and other processes just happened to produce everything we see. The evolutionist’s going in position is that biology is a fluke. We’re lucky anything works.

Hunter then cites this passage from some naturalist researchers who study “junk DNA”:

Here we have a molecule that serves an important role in how cells function and survive, but it contains these puzzling ‘junk’ sequences that don’t seem to have any apparent purpose. Our work suggests that this disorder is really a way of creating flexibility, allowing the protein to function as a molecular switch, a process that is thought to go wrong in certain diseases.

Evolution has provided researchers with convenient modular structures, areas that are repeated over and over again to make up proteins, and so we tend to dismiss the interspersed disordered sequences that don’t seem to have any definable structure. Here we show that the weak molecular interactions in a disorganized protein sequence are essential in giving this protein its unique attributes.

Know what? If you substitute “Flying Spaghetti Monster” in there for “Evolution”, it makes just as much sense! Try it! Evolution causes toothpaste to come out of the toothpaste tube when you squeeze it, and Shakespearean rhyming couplets to rhyme, and my Java code to compile. It’s all evolution!

Conclusion

Atheists, always remember this quote from agnostic NASA astronomer Robert Jastrow, regarding the progress of science:

For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.

In the 1920s, there was no theory about a universe that begins to exist out of nothing, no fine-tuning, no DNA, no Cambrian explosion, nothing. Then science progressed, reducing atheism to a kind of childish delusion, still believed by ignorant snake-handlers and people with certain persistent moral, … ah… issues. But that’s what psychiatrists are for!

Science is always for us, it’s never for you. You have faith. Blind faith. We have all the evidence. We invented science, and every new discovery makes your materialism look more silly and naive… you bravely hold out hope for some hopeful Flying Spaghetti Monster to swoop in and rescue your atheism from the big, bad mind-independent reality. When will you grow up?

There is no Flying Spaghetti Monster!