Ever More Complex

A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called “enhancer” sequences. These are novel DNA features that were once thought to be a part of the so-called “junk DNA” regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.

Jeff Tomkins’ New Technology Reveals More Genome Complexity is one of those articles that hits you with the nonsense almost from the beginning. Deconstructing that opening paragraph we find that the first sentence is perfectly accurate. There do exist in the genome regions, called enhancers, which promote the expression of the gene(s) they are associated with. Enhancers have been known for some time – they were even taught in my biology class last year, so they must be ancient – but a new paper in Science talks about a new method for identifying these regions. To quote the abstract:

Genomic enhancers are important regulators of gene expression, but their identification is a challenge, and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, which enables screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell-type–specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantify enhancer activity in other eukaryotes, including humans.

Moving on to the second sentence the mention of ‘junk DNA’ should already have set off alarm bells. Alas, this aspect seems to have originated at least in the press release if not the original paper (which is behind paywall). It is of course perpetuating the myth that the junk DNA idea owes its origins to ignorance about the role of non-coding DNA, which is simply not true. I wouldn’t be surprised to learn that we have known about enhancers longer than the junk DNA idea has been around (they did make it into the curriculum, remember), but it wouldn’t matter if we haven’t.

It is sufficient to say of the third sentence that it is just ‘typical Tomkins’ and leave it at that. I have long grown tired of pointing out that ‘irreducible complexity’ is a claim that requires evidence – one might say extraordinary evidence – which we never seem to see. Complexity is not in itself something that could pose a problem for evolution (or other natural processes), but irreducible complexity is supposed to be strictly defined so as to only include features and structures that could not be incrementally created. However I think Tomkins recognises how hand-waving it is to point to mere complexity as something that evolution could not produce, and so adds the ‘irreducible’ part to try to make his argument more convincing.

Indeed, calling the genome irreducibly complex is particularly silly. An irreducibly complex system would not have any redundancy, because one part of a redundant system can be removed, ‘reducing’ the system while leaving its function intact. The press release for this paper, for example, even mentions redundancy as a potential explanation for why there seem to be multiple enhancers per gene. In addition, as we saw back in September, it seems to be possible to remove large sections (in the order of millions of consecutive bases) of DNA without proportionate repercussions. If the genome were truly irreducibly complex – rather than just plain old complex – we shouldn’t see such things.

Thankfully, the next couple of paragraphs are just a description of the process and don’t merit line-by-line examination. Skipping ahead, therefore:

This new technology and the increased picture of complexity described by it add even more weight to the fact that the genome is completely functional and irreducibly complex. This is a fact recently highlighted by 30 simultaneously published research papers in the 2012 ENCODE (encyclopedia of DNA elements) project reports.

Ah, ENCODE. It was inevitable, really.

In the lead ENCODE research paper, published in the journal Nature, the authors wrote, “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” For a recent review of the ENCODE discoveries and their significance to the creation-evolution debate, see the recent review of ENCODE in Acts & Facts.

So ends the important part of this article.

I didn’t go over the Acts & Facts ‘review’ because it was largely a reprint of an earlier posting, which we did look at. To be brief, even if junk DNA really doesn’t exist the evidence in the ENCODE study does not actually show that – the term “biochemical function” is quite misleading. If you have the time I recommend listening to this podcast on the issue, or start here if you prefer text.

Stripped of the irreducible complexity and junk DNA aspects, Tomkins really doesn’t have anything. Yes, we now have a tool that could potentially tell us a lot about our genome. But so far, at least, we have learnt nothing that should excite a creationist.

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3 thoughts on “Ever More Complex

  1. I certainly agree that this article from the ICR used whatever straw-man argument that they can get to support their theory.

    But I have one remark about one of your statements: Complexity could pose a problem for evolution. Evolution is just trail-and-error, and that implies probabilities. And extreme low probabilities will mean that it’s difficult that mere complexity is achieved by evolution.

    Just saying that there is a theoretical limit about how complex organisms could evolve given the time that they have to evolve within a evolutionary timescale

    • To an extent, that’s my point. Complexity in and of itself isn’t a problem – despite some claims I’ve seen to the contrary, processes that don’t involve intelligence or the supernatural are not inherently prevented from creating it. So you need to add further conditions. You can either make at quantative, like you have done, saying that there is a limit on how much complexity could have arisen. The problem with that approach is that it would be incredibly difficult to determine what that limit actually was, and if the observed complexity in life had exceeded it.

      The other option is qualatative, defining types of features that should not exist – like irreducible complexity. The problem there is finding something that really does fit that (strict) definition.

    • As a creationist I won’t say that complexity could not have arisen to some or large extent by stochastic processes, but indeed the problem is how to define that limit (But perhaps I am another kind of creationist than Tomkins).

      I know some Intelligent Design proponents have struggled (and failed, in my opinion) to elaborate what the limit is. Michael Behe leaves little room for evolution and complexity to originate by random stochastic processes (Edge of evolution).

      It also depends on how you define complexity. When I look at the interaction networks that occur within a living cell, I personally find it hard to believe that such a complexity could originate by stochastic processes. But when you say that this is just a gut-feeling, not backed by arguments that’s entirely true.

      And I certainly agree that this is the qualitative kind-of-argument.

      The problem is that with our current knowledge, we don’t know enough about the cell to make evidence-based claims about irreducibly complex systems. For example in my field of study, protein interactions are known, but even to well-researched pathways, new interactions between components are always found.

      But it’s a sure fact that scientists more and more begin to realize that the cell is more vast and more complex (in terms of interactions and different components) than they would have imagined fifty years ago.


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