Category Archives: ID

Junk DNA revisited – Implications for creation science

Junk DNA is dead. At least that is what the recent paper in Nature proposed. The press coverage was huge and responses varied. But the general reaction was that junk DNA does not exist anymore. The whole genome has a function, or at least a biochemical function.

For scientists and especially for geneticists this is a happy hour. Exciting research with exciting consequences. I was thinking about design and what implications this does have for creation science. Todd Wood said in his post about the ENCODE results that it is important that creationists do not use those results for their propaganda purposes.

And I definitively agree!

As you all know when genes are passed on through the generations, changes happen. Mutations occur. The majority of those mutations are deleterious, and could cause for example a knock-out in a gene that codes for a transporter protein that transports substances from the cytoplasm to the vacuole.

When a mutation causes malfunction of a gene, most of the times it still can be transcribed into RNA. You would expect to find biochemical activity. The functionality is gone, at least if you look to the gene product that does not work anymore. And that process happens also when you think that organisms are designed.

So you would expect DNA that does not have a real function (If you define function by having an effect on the phenotype). The number of mutations that is deleterious is huge and therefore you expect rubbish DNA that doesn’t have any impact on the growth and development of an organism. Any function does not count for real function.

And that’s why we have to look at the ENCODE results.

The ENCODE scientists have analysed 147 cell types. Each different cell type transcribes different genes and so different sorts of biochemical activity is found in different cell types. When combined they give an estimate about the amount of the genome has a biochemical activity

The authors of the article state the following:

Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).

And more:

From comparative genomic studies, at least 3–8% of bases are under purifying (negative) selection, indicating that these bases may potentially be functional. We previously found that 60% of mammalian evolutionarily constrained bases were annotated in the ENCODE pilot project, but also observed that many functional elements lacked evidence of constraint.

And:

Interestingly, even using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein-coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism.

So when I read that, I see several things:

  1. There’s a huge amount of regulatory elements discovered in all different cell types
  2. 80% of the genome has a biochemical signature, so perhaps involved with the regulation and things like that.
  3. At least 3-8% of the bases are under purifying selection (which means that those are constrained in evolution).

But does it have big consequences for creation science? No not really. It just shows that regulation is more important and width-spread in the genome than previously thought and that probably the structure of the genome is more intricate and sophisticated than we thought. 

Evolutionary scientists have longtime assumed that when something in the genome is not constrained by selection, that it is not functional. But in the past decade more and more was discovered about the genome and the concept of junk DNA was already shrinking.

For me it was not a big surprise that much of the genome has a biochemical function. It was already known that more and more of the genome had a biochemical function. This was just the confirmation.

And it also depends on the definition of junk. What do you call a function, and what’s useless?  There are probably some implications for creation science after all. But they are little ones.

  • First of all when people ask you why a designer would fill the genome up with useless stuff, you can answer that most of the genome is functional and that this does not count as an argument against design in nature. 
  • Second you could say that it is more probably that a designer would fill up the genome with functional bases, and that the little non-functionality are remnants of our short evolutionary history, but that is a counter argument against objections to design, and not an argument for worldview based on design. 

So trivial

  • Third, The ENCODE results show that regulation is more non-constrained than the biological function that genes code for. And we know that regulation is generally more species-specific. So that could have the implications for shared ancestry, but we do not know that yet.

And that’s just speculation. We need probably an ENCODE project for apes as well (Its costs will be less than $ 1,000,000) Then we can compare it. See what the differences are and what overlap can be seen.

And we have to realize that we know less than we thought we knew. So that’s humiliating. But we cannot say that this is a major victory for ID and creation science. It’s just science progressing.

See also my previous post about the ENCODE results

Please share your thoughts!

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Pseudogenes are indeed (sometimes) functional

Pseudogenes are sequences that originate from functional genes, but are not coding for proteins. Originally it was thought that pseudogenes were non-functional and that they were artifacts from the evolutionary history.

But recent developments in science propose another theory that is radically different.

The origen of pseudogenes can be explained by the retrotransposition of functional mRNA that is randomly inserted in the genome. They are similar to functional genes, but lack introns and other characteristics. A second mechanism by which pseudogenes could originate from duplicated genes that have accumulated deleterious mutations and therefore are not functional anymore.
Pseudogenes are abundant in all eukaryotic organism and in in humans 12,000 pseudogenes show evidence of being pseudogenes. A remarkable insight is that 60% of the pseudogenes in humans are also conserved.

..The high abundance and conservation of the pseudogenes in a variety of species indicate that  selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions..

Recent evidence has demonstrated that more and more of the pseudogenes are transcribed in various organisms. The authors of the article conclude that:

..that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation..

The overall conclusion of the article is that:

..The study of functional pseudogenes is just at the beginning. There remain many questions to be addressed, such as the regulatory elements controlling the cell or tissue specific expression of pseudogenes. But, definitely, the so-called pseudogenes are really functional, not to be considered any more as just “junk” or “fossil” DNA. Surely, many functional pseudogenes and novel regulatory mechanisms remain to be discovered and explored in diverse organisms…

One of the major implications of this discovery is that the portion of junk DNA in the genome is steadily shrinking. Evolutionary theory says that pseudogenes are random byproducts of evolution in action. But this demonstrates that the portion of the genome that is non-functional is less than expected.

Scientist discover over and over that most of the genome is functional,  that genomic structures are more complex than expected and that non-coding DNA has a remarkable impact on regulation of essential biological functions. To me, it seems therefore more justified to say that this gives more credibility to the concept of a designer.