Tag Archives: Encode

on ENCODE & telivision sets, apes, silence and Dawkins

It is rather an odd title for a blogpost, but I felt like it needed that. Last months were busy months and it really was not that I did not like my readers anymore, but just that it was a busy period with a lot of finishing of projects and things like that.

But in fact I think that an update is needed desperately on this blog. Do not expect new content in this blog, but it will most certainly be about what others have blogged about and about what I have thought about related to existing posts on this blog.

  1. Encode revisited: Last year I blogged about the ENCODE results which showed that presumably a large part of the genome was functional (according to their definition), and I want to point out to an paper that was published in February which tries to debunk the claims the the ENCODE project made. I don’t agree with all of the paper, but that is something which is more suitable to a stand-alone blogpost. 
  2. Similarity between chimps and humans: In the Answers Research Journal (ARJ) a study was published that genomic similarity between chimps and humans is only 70% instead of the 98% to 99% which is assumed by most of the scientific community. Dr. While (YOUNG-earth creationist) has blogged about it. But that’s also more for another blogposts, because I tend to almost agree.. (again)

That were the pieces where I did not completely agree.

  1. On the Colossian Forumreflection article was published by Daniel Camacho who wrote about the virtue of silence based on the works of St. Thomas Aquinas. This article has my recommendations.  
  2. Some time ago a debate was organised between Rowan Williams and Richard Dawkins.The subject of the evening was whether religion has a place in the 21st century. I believe it does, as does Rowan Williams.

Judging Judging

And this is for fun (at least boring fun)

In a few weeks I will have more time to blog, but those posts will still be irregular.

[edited: Dr. While is not an old-earth-creationist, but firmly in the young earth creationists camp.]

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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!

ENCODE: Exciting research but little consequences

Yesterday I saw that  huge attention was drawn towards the Encode paper in Nature which claimed that 80% of the DNA elements in the human genome has a biochemical function.

The results are indeed stunning. Scientists have longtime believed that most of the human genome was junk DNA (elements that do not have any function) but now it is shown that in contrary to that, many regions outside the protein-coding genes also have a biochemical function.

In order to determine the function to the genome they studied 147 different cell types and the biggest conclusion that they made was that junk DNA is no more. From the ID-community this was seen as a confirmation of the prediction of ID and several evolutionists responded with harsh critique of the research.

For quite some time I was thinking about the non-functional junk DNA concept, and I provided in a previous post the thought that more function of the genome gives me more credibility to the concept of a designer. Still I think that one of the major concepts from evolutionary theory slowly starts to change, although Laurence A. Moran and several others are agreeing to disagree.

No problem with that, they will come to peace with the results.

But does function really equates design? Todd Wood disagrees. He thinks that Encode is of little relevance to creation science. He provides some useful links to old  posts he wrote, which illustrate the principle in which organs have some function, but still are vestigial.

This boils down – if I am right – to the question that Nick Matzke provides at the Panda’s  Thumb. He said that the scientists that are involved in the ENCODE project use a liberal and dubious definition of functional. And that be all means it was already known that non-functional DNA would be functional when subjected to that liberal definition.

From the creationist community Todd Wood has written an excellent blogpost about it. He shows that the relevance for creation science is only limited. Furthermore he notes:

Meanwhile, yes, the press and press releases are exaggerating and distorting things as usual.  Yes, it’s annoying.  What bothers me more this time is this undercurrent I’m seeing that basically perceives this latest hyperbole as especially egregious because creationists will misunderstand the results and use them for propaganda purposes.  I hope no one is actually suggesting that scientists ought to modify the presentation of their results to prevent creationists from misusing them?  Perhaps even … dare I say it? … censor themselves to prevent creationists from taking advantage?  Because that really is starting to sound like an anticreationist conspiracy.

He is right, creationist use whatever paper they can get, and I often see claims which later have to be corrected. Let every man be swift to hear, slow to speak. Use knowledge with caution and first think before you say anything.

Especially in science, don’t ever say major things based on one paper. Major things are normally not suddenly found, and a scientific framework is built up stone by stone.