A physicist tries to understand junk DNA

Rob Sheldon has a PhD. in physics and a M.A. in religion.¹ With two strikes against him already, he attempts to understand biology by discussing evolution, junk DNA, and the Onion Test [Physicist suggests: “Onion test” for junk DNA is challenge to Darwinism, not ID]. As you might imagine, posting on Uncommon Descent in support of Intelligent Design Creationism leads directly to strike three.

The Onion Test was created by Ryan Gregory in 2007 [The Onion Test] and published in the scientific literature by Palazzo and Gregory in 2014. It goes like this. Take your favorite hypothesis suggesting that most of the DNA in the human genome is functional and use it to explain why the onion, Allium cepa, needs a genome that is five times larger than the human genome. Then explain why closely related species of onion need twenty times more DNA than humans.

Rob Sheldon has an intriguing answer that can only be created by someone with a lot of biases and very little knowledge of biology. He claims that the human genome is chock full of information and it is packaged and condensed in a way that is the best possible code. Humans have the machinery to decode this sophisticated packaging algorithm but other species are more primitive so they have much less efficient compression algorithms. Here's how he describes it ...

There may be some very good reasons for onions to have large genomes....

The DNA is software. The proteins are the video feed. The nucleus is the CPU. Humans have highly complex coding/decoding machinery in the nucleus. When mathematical analysis is performed on human DNA, it is found to have a fractal information dimension greater than 3 (papers available upon request)–indicating that at least 3 different codes are simultaneously present. This is a number bigger than chimpanzees, whose DNA is not so compressed, and if I recall correctly, come in around 2.5 or so in fractal dimensions. The paper did not analyze onions, but I think it is safe bet that the fractal dimension is < 2.0. What does this changing dimension mean for DNA size? Well the information in DNA is proportional to the volume of phase space, so if humans have dimension 3.0, then the volume ~ (3.2GBytes)^3 ==> 27 GBytes. This dwarfs the 15GBytes of the onion, but then I don’t know the fractal dimensionality of onions.

Now admittedly, the papers don’t do the entire genome, they look at little subsets, so I may be generalizing too much to say that I know the dimension of information packing. But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else.

This is categorically what is NOT found, and so even without the ENCODE results, it is manifestly obvious that human DNA is not mostly junk.

I think that's his main argument—something to do with fractal dimensionality.

But, not content with that, he enters another dimension ....

But if DNA is compressed and packed so efficiently in humans, why is it not packed that way in onions?

One paper that was published 3 years ago or so, suggested that embryonic development from ovum to embryo was driven by a clock. As the transcriptase zipped along the DNA, proteins were made successively by the cell, and the ordering and timing of the proteins were such as to drive the embryogenesis and development. In other words, the spatial location of the DNA was converted into temporal development of the organism. Then if an organism needed to prolong a stage of embryogenesis, the most direct way would involve adding more DNA. No extra machinery is needed, no added complications and regulators, just another 1GByte of DNA to transcribe and the necessary 30 minutes will be added to the development.

Most undergraduates could destroy this argument in a few seconds so I'll leave it to them in the comments.² It's a classic example of why a physicist should not try to understand biology without consulting a basic introductory textbook.

There's more ...

Crude, but why do that at such a high cost to the genome of every cell?

Well, perhaps there is a plant virus that hijacks the "clock" to crank out tumors. This onion solution would then be impervious to such a virus. It might even give it an "evolutionary advantage".

Then the "Onion Test" is not a Darwinian challenge to ID, but an ID challenge to Darwinian imagination. Why don’t they take their own medicine: if the junk isn’t functional why doesn’t it get selected out?

We are gradually making some progress in educating Intelligent Design Creationists but it is a slow and painful process. Some of them actually begin to understand modern evolutionary theory and population genetics and there's a brief glimmer of hope, from time to time, suggesting that they know the difference between Darwinism and modern evolutionary theory. Some of them even admit that natural selection isn't all there is to evolution.

All this learning seems to disappear in the junk DNA debate. They still insist that advocates of natural selection (Darwinists) are the ones who invented the idea of junk DNA. That's just dead wrong but we may never be able to convince the IDiots.

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1. Google "Sheldon physics" and look at the images. It gets you lots and lots of cool photos that I would love to incorporate into my blog.

2. Hint: how many regulatory genes would have to be regulated in this manner by inserting extra long introns and how much DNA would have to be added to delay production of the first transcript by 30 minutes?

Palazzo, A. and Gregory T.R. (2014) The Case for Junk DNA. PLoS Genetics (published May 8, 2014) [doi: 10.1371/journal.pgen.1004351]