Thursday, September 6, 2012

Junk DNA Isn't So Junky After All

A massive GWAS (genome-wide association study), the ENCODE study, has just published the first draft of, basically, Google Maps for the human genome. One of the first exciting findings: it turns out that much of the 97% of so of the genome that doesn't directly code for proteins does actually have a role in determining transcription. This goes a long way to explaining many of the recently compiled evidence for how non-coding entities like copy-number variants (CNVs) can affect disease states like schizophrenia.

This is not only fascinating, it's exciting in terms of the potential for biomedical research. Unfortunately I can't help but imagine the creationists rubbing their hands with glee and getting ready to say things like "See? You secular biologists doubt the genius of the Lord's creation but there's a reason for everything." Nature does often nest function in ways that aren't immediately obvious. But hold on there Tex - before any of you creationists get too excited: why do you always have to wait for those secular biologists to make the discoveries? Why can't you seem to get your sh*t together enough to be the ones making these discoveries, instead of always spinning stories after the fact?


Unknown said...

Gee, are all those people working on the encode project atheists?

And yes, I am jumping up and down with glee.

Intelligent Designer said...

You are wrong. I am not rubbing my hands together with glee, I am jumping up and down with glee.

Also it's not like all those scientists working on ENCODE are atheists.

What you should find troubling is that some prominent atheists like Larry Moran, T. Ryan Gregory and Steven Salzberg are in denial in regard to how much DNA is functional. I am suprised PZ Myers hasn't piped up yet.

Putting all that aside, I would be happy if we dumped the space program and put all that money into ENCODE.

Michael Caton said...

Somehow you missed the point of th post which I'll ask again. Why are we always seeing a post-discovery spin effort from creationists, rather than the production of something new? Where are the creationist biotech companies? Where are the creationist discoveries? For all the hot air about how evolution doesn't work, it's sure been a lot more useful to actually MAKE things.

Intelligent Designer said...

As you probably know Francis Collins lead the Human Genome Project. He is a creationist in the broad sense of the term. I don't know the people working on ENCODE but I am sure plenty of them are creationists and there are plenty of creationists working for biotech firms.

Michael Caton said...

Collins is an evolutionist who happens to be a Christian - he's been very clear on this point and would disagree with your take on the meaning of this work. As for the biotech world, biopharma is an evolutionist enterprise to the core. I've consulted at 10 of these companies and never once met a creationist, although there could be a few around - they must be a tiny minority, and there certainly are no drug companies based on these principles, and certainly no one who wants to put their money where their mouth is and act like they believe what they're saying and invest in such a company. If evolution is wrong, it's hard to understand how the American biopharma enterprise has kept stumbing into discovery after discovery. Besides the scientists and doctors, Wall Street and the venture capitalists must all be in on the conspiracy (or just plain fools) as well. So you're not just rowing upstream against an incredibly well-supported theory, you're also calling into question the achievements of one of the most successful areas of American capitalism. Which itself, incidentally, illustrates very nicely a lot of the principles of Darwinian selection.

Intelligent Designer said...

Micheal you are thinking in black and white terms, at least in the way you use the words "creationist" and "evolutionist". One can be a creationist and evolutionist at the same time. Collins is in fact a theistic evolutionist and believes that evolution is guided by God -- and that implies design. When I was a Christian I knew many people like him.

I myself develop software for a living which is both an evolutionary and creative process. For me it is natural to combine the two.

The purpose of the ENCODE project is to understand the design of DNA. One does not have to be an atheist to participate in that research. In fact, such a narrow minded viewpoint could be a hindrance.

A few years ago we lost our most talented employee to graduate school and later a biotech firm. She was a software developer who had graduated at the top of her class from the University of Washington computer science program which is no small feat. I knew she was a Christian because she once mentioned something about church but she never brought her religion to work. A person like you could work beside her for years and still say you never once met a creationist.

Michael Caton said...

My apologies for the delay in response – I have a big test coming up (more on this later).

First, I thought it would be worth looking at what the head of the project has to say -

Based on your alias I had assumed you didn't think evolution had occurred, since intelligent design as the term is usually used refers to a non-evolutionary account of the origin of life. So, we agree that evolution occurred, but disagree on whether this was guided by a supernatural being. Your position is that finding functionality in nature where previously there was thought to be none is evidence of a designer.
Consequently our disagreement isn't about evolution at all, it's about the existence of a supernatural being.

The first question I would ask you then is - if both of us accept the same facts of evolution, then it certainly looks like it literally makes no difference whether or not we include this other variable in the discussion. So how meaningful can this point even be, at the very least, as it's relevant to this question?

Going on to theistic evolution, we can put most of the problems with it into these two categories:

1) The meaning of good fortune and the importance of context. Is all good fortune necessarily the result of a supernatural being? From the most mundane daily occurrence on up to the beneficial innovations we see in nature. This begs the question of how to make sense of bad fortune, or good fortune happening to bad-intentioned agents. A seal probably isn't too thrilled with the design of a great white shark's tooth.

2) Natural theodicy. Speaking of great whites...there are in fact lots of (without un-guided evolution) inexpicably bad aspects of biology, whose impact ranges from waste to massive suffering. Junk DNA is partly explained, but (just to keep it in the realm of obstetrics) what about Rh incompatibility, pre-eclampsia, and molar pregnancies? If there weren't so many breakdowns in the system, I wouldn't be going into medicine! As for those three examples, we've fixed those now (we=lots of un-guided evolutionists).

There's also the question of why a supernatural designer always goes stepwise using pre-existing structures instead of saying, "Wow, sharks ARE mean - so I'll just ex nihilo make them photosynthetic." That's never been observed. If it's because the supernatural being is just as bound by natural law as the rest of us, then it's hard to see how it's supernatural instead of just, say, a really smart alien.

Another answer for #2 might be, "There are only two types of designs in nature - good ones, and good ones we don't yet understand." If that's the case, are you against medicine fixing those good things we don't yet understand as good? This is an application to biology of the "God works in mysterious ways" argument. It's identical to the Hindu argument of "if something bad happened to you, it's something you did in a previous life", i.e., it seems evil but actually it's good for reasons you can't understand.

You're correct that there is no religious conviction (that there is/are or are not G/god(s)) required for the ENCODE project. Again, it seems like that
conviction makes no difference to answering these questions, which strongly suggests it doesn't really matter, at least in this context. My point in posting this was that people who want to find evidence of God's work in biology must wait until non-theistic science produces it, and then explain it after the fact.

I'm not surprised about your former colleague. I've worked with plenty of Christians at biotechs, but no creationists. We never discussed theistic guidance of evolution. Wasn't a taboo topic, just never came up, I think because it didn't matter to the theory or the outcome of experiments.

Intelligent Designer said...

Michael, thanks for letting me comment on your blog. Even though this conversation is very interesting this will be my last comment because I have a lot of work to do.

I don’t want to accidently mislead you into thinking that I think evolution occurred the way you do. Let me clarify. There are many forces of evolution. Genetic recombination together with natural and sexual selection is one of them. It allows populations to make relatively rapid changes in response to changing environments. But recombination and selection is basically a search algorithm for selecting pre-existing genetic information best suited for a given environment. The recombination algorithm itself is also information. The main difference that you and I have in our thinking is that you think random mutation plays a positive role in evolution and creating information and I don’t. My argument against random mutation playing a positive role in the creation of information is based on math not superstition. In my blog I have in some posts tried to explain this in ways that the average college education person can understand. I have left a lot unsaid because, like you, I am busy. My view point differs from other creationists in that I think this information could have been (and is still being) injected into the universe in a contemplative way over time rather than in an instantaneous, omniscient, omnipotent and omnibenevolent (you would say magical) way.

In your response you presented a problem of evil argument against God. It’s a valid argument an in my opinion effectively refutes the Christian concept of God; however, it doesn’t refute the existence of God.

Like the problem of evil, the idea of junk DNA is a favorite talking point for atheists. Prominent atheists like Richard Dawkins, PZ Myers, and Larry Moran have been fond of using it and as we learn more about DNA and epigenetics their arguments based on the ideas of junk DNA and selfish genes will look dumber and dumber.

From my perspective, the intelligent design argument is that the existence of complex information in a universe strongly affected by entropy is proof for the existence of God or some vast intelligence that exceeds ours by many orders of magnitude. Each time genetic information is discovered to be more complex than previously thought, the case for intelligent design improves.

I am aware that there is and will be a lot more argument that will surround ENCODE’s meaning of "function". While this discussion is important, from an engineering perspective it’s silly. The function of some parts of engineered systems is obvious. The function of other parts is subtle or of an abstract nature and may not be explainable to the average person or even another engineer. One could even argue about whether or not some essential parts are functional based on different definitions of the word functional.

In conclusion, it doesn’t matter to me whether a person is a Christian or an atheist or something else. I do get concerned when one’s perspective accompanied by bigotry – especially when this bigotry is accompanied by physical or psychological violence or an effort to punish someone economically. If I were to apply for a job on an ENCODE project, I wouldn’t want to be discriminated against because of my cosmological perspective. I have a tendency to live on the wild side and enjoy a conversation with someone of an opposing view point. Others are fearful that their perspective could negatively impact their reputation and employability and keep their thoughts to themselves. You most certainly have worked with other creationists. Any Christian that you have worked with is a creationist in some sense of the word.

Good luck on your test.

Michael Caton said...

Thank you for your contribution. You're referring to the information theory argument against evolution by natural selection, which I'm superficially familiar with but invite readers to Google for themselves. My understanding is that this is answered with the Earth being an open system (getting energy input from the sun) and the nonrandom selection of replicators. But I think the most important point you make is that of discrimination. If you have a publication record and output to support you, and I were in a position to do so, I would hire you! The point is that the EFFECT of our ideas is what matters. I would also decry someone else not doing so on the basis of your religion. Thanks again for visiting. Mike