They defined function as being transcribed into RNA which doesn’t seem like a reliable indicator of function with respect to fitness. At some point, there has to be a dividing line between function and “does something”. Even the trash in our trash cans does something, even if it is release odor molecules into the air. That doesn’t mean they are functional.
If your work is able to go past “does something” it will be a very interesting read.
If God can use thunderclouds to make lightning, then why not use quantum fluctuations to create universes, or chemistry to create life. Is there some sort of horizon, beyond which there can be no more natural explanations in Christian theology?
No, the key is if they are taught that science answers it all, as if God were unnecessary, or a fable, and no one has given them good reasons to believe, rational reasons, then they are likely to walk away from faith.
They defined function as being transcribed into RNA which doesn’t seem like a reliable indicator of function with respect to fitness.
Agreed. So now the hard work comes of looking for and proving function.
The mental picture I have is if a Christian is not taught one way or the other as it concerns science and faith and the come upon an atheist who says that science disproves God, why would they believe the atheist?
It could also be that I am a bit naïve, and my own experiences in the church have colored my expectations a bit. I never had a problem reconciling science and Christianity, and that included my time getting a degree in biology. Of course, it may have helped that many of my profs were Methodists. The reasons I left the church had nothing to do with the intersection of science and faith. It just turned out to be a lack of faith.
If one of the investigators happens to be an expert on metabolomics I would love to see an whole organism energy budget that includes the amount of energy spent on transcription, and how much impact junk RNA has on that budget. Of course, this will differ depending on the species (endotherms and exotherms), but I have always wondered if the cost of junk RNA is high or low.
Anyway, I look forward to seeing how you filter out junk RNA/protein and determine what has function.
Fair enough. I just know that it happens.
Listening to you, and rolling for a bit with what you’ve been saying, I wonder if one could draw a useful line between evolutionary biology and evolutionary psychology and all that comes with it. After all, it is in evolutionary psychology — explanations of psychology, sociology, morality, behavior, culture, religion, etc. through an evolutionary framework — that I see the worst examples of the “just so” stories to which you have referred. This is also where evolutionary theory steps most squarely on the toes of religion and “overlaps” on their “magisterium.” It’s the realm of things like beauty and goodness, which find such satisfying explanations in theistic thought.
To me, a line between evolutionary biology and evolutionary psychology could be a much better place to stake our battle lines — if indeed battle lines must be staked, which is not a settled question for me — than various other lines where people have dug their trenches: micro- vs. macroevolution, historical vs. observational science, irreducible vs. reducible complexity, junk vs. functional DNA, and so forth.
What do you think?
I am happy to draw a line through evolutionary psychology. It is indeed a place of many just so stories. It might be a temporary refuge though. I think we still have too many disagreements on basic views of the origins of biology—that these views while we can continue to discuss them may not be reconcilable. Not without hard evidence anyway.
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Thanks. It’s a good idea. We found a considerable cost of expression in bacteria, and others have as well. Bacteria will generate duplicates and then delete them within a few cell divisions. The turnover is remarkably rapid. So it would be interesting to see what the case is in eukaryotes. Michael Lynch’s case depends on their not being a sufficient carrying cost.
I’m sure you’re right that our views aren’t reconcilable. And even if they were reconcilable, I doubt that either of us has the time in our busy lives to get to the point where they would be. =)
I also agree that drawing the line at the break between evolutionary biology and evolutionary psychology would likely be a “temporary refuge.” The line would be fuzzy at best, and difficult to defend in debate. I just thought it would be a more defensible line than some of the others that have been proposed.
And it has been helpful for me to try and see the situation through your eyes, particular with your son’s apostasy. I suppose we could all do with a bit of humility to see that people leave the faith for all sorts of reasons — some because they see no evidence for God at all (your point) and others because they’ve been told they have to choose between science and faith (@Jay313’s point). EC solves some problems but is arguably more vulnerable to others. Praying for those who stray from faith in both directions could, theoretically, be a place where Christians from various origins camps could find common ground on our knees in intercession.
I wish you well in your pursuit of truth, and pray that you and your colleagues may have the strength to continue pursuing truth in the face of overwhelming opposition. I’m not convinced of the truth of ID (yet, anyway), but at least it’s helpful to me to have dialogued with and listened to you a bit and seen a bit of the human side of your movement. It will help me to remember this next time I am frustrated with some of the more strident ID materials I run across. =)
Your brother in Christ,
AMW
Deep RNA sequencing has led to a lot of curiosity about non-coding RNAs. I don’t think it’s entirely accurate to suggest that ID perspective is the driving force behind the renewed interest.
There are probably thousands of researchers currently deciphering the functions of various bits of noncoding DNA; an ID perspective is not necessary for conducting this line of research. Heck, even I have helped out (see here), and this is not at all my line of work.
Thank you very much, AMW. This sounds like a farewell. It has been a learning experience for me as well. I will venture to guess that in the most important things we are very much the same.
I was saddened to hear that some who hold to evolutionary creation face trouble from within the church. In fact it makes me angry. I hope it is not true for you.
I think it would be wonderful if we could join in prayer for those who struggle with faith for whatever reason. I will add it to my prayers each day.
I also wish there was some sort of vetting process for those who claim to speak for ID. I am sure I have been guilty of it myself sometimes, so I apologize. Remembering each other’s humanity is a great help, and this conversation has done that also.
an ID perspective is not necessary for conducting this line of research
No, it’s not necessary. But do you think the investigations might have begun sooner, before ENCODE, if design was the paradigm?
Yes, I really should reduce the time I’m spending here on the Forum; it’s a very busy season for me personally and I’ve been giving this a disproportionate amount of my time and energies. It’s a bad habit of mine, which is why nobody’s seen me here on the Forum in a long time. 
Thankfully, evolution has not brought me trouble from within the church. However, honestly this is because I keep my views secret to all but good and trusted friends & family. I once “liked” BioLogos on my Facebook page (which I don’t use anymore), and my senior pastor actually confronted me about it over breakfast together and said that I might not want to do that because people might get the idea that I agree with what BioLogos teaches. I didn’t set him straight, but nor did I unlike BioLogos. =)
My identity on the Forum is ever-so-thinly veiled, and this occasionally worries me, frankly. I’ve talked about my area of expertise that I’m published in here, without calling it my area of expertise as such, and I’ve been foolish enough to leak potential identifying demographic information about my children. My name barely hides my identity. But my livelihood depends in part on maintaining my Evangelical bona fides, and in some of my circles, evolution is among the vilest of heresies. Posting on here carries a very real risk for me.
Anyway, I look forward to seeing the next chapters in “gracious dialogue” between Dennis and your people. Bless you!
AMW
The investigations did begin sooner, long before ENCODE. It was because there was such a research program, and because it was recognized as being vitally important, that ENCODE happened.
You should understand that many people here, especially those who work in evangelical churches and parachurch organizations, maintain anonymity online because they would lose their jobs or be “disfellowshipped” simply for their acceptance of evolution.
What I also find interesting is that the theory of evolution doesn’t require a genome to be 100% functional or 0.1% functional. It seems that people have been arguing about this topic for a long time and have lost sight of the basics of the argument. One example that I like to bring up is the bladderwort genome which comes in at 82 million bases, more than 90% of which appears to have function. Does that challenge the theory of evolution in any way? No.
As it stands now, the positive evidence points to about 5-10% of the human genome as determined by sequence conservation. If more evidence comes in showing there is function in the other 90%, then scientists will gladly accept that evidence. However, very low level and spurious RNA transcription is certainly not that evidence, contrary to what the initial ENCODE paper tried to insinuate.
And yes, the search for function in the human genome had been ongoing since the discovery of DNA itself. The advent of new tools in molecular biology (e.g. RNA-Seq) made the ENCODE study possible, and that was why it happened when it did. The current paradigm also includes the search for non-conserved and functional sequences. All of this work is ongoing outside of a design paradigm.
I’m not disagreeing with you at all, but I would think that the cost would be directly related to expression level. One or two RNA copies wouldn’t seem to be that deleterious, especially given the existence of scavenging pathways and the total number of RNA copies at any given time. I have also studied cardiac function which uses a ton of ATP, as do all muscle contractions. I have often wondered what the nucleotide ATP budget is compared to the use of ATP for just muscle contractions.
What’s interesting to me is that the original “Darwinism” was thoroughly adaptationist. An old-school adaptationist would have the same approach to the genome (there must be functions for almost everything) as ID folks do. I find it quite ironic that ID folks (sometimes) claim that “Darwinism” predicted low levels of function in genomes. That’s just not the case. Neutral theory threw the darwinian adaptationists for a loop.
“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6
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