The Irreducible Complexity of DNA Replication
by BradfordAccurate replication of DNA is an essential component of cellular replication. There are multiple proteins which enable the DNA replication function. The process contemplated is that which occurs in unicellular organisms. I don't wish to bore the science experts who can't wait to enlighten the rest of us as to how the individual components of the DNA replication function gradually evolved. So I'll simply identify some important steps for instructional guidance purposes as well as proteins associated with them.
Replication must begin somewhere. Why not at the origin of replication with the formation of a replication fork. A prepriming complex of proteins forms. Included are DnaA proteins and single stranded binding proteins. Also involved are DNA helicases to separate the strands, DNA topoisomerases to respond to supercoils, DNA polymerase and DNA ligase.
Don't bother making semantic arguments about how to define irreducible complexity. There are multiple parts needed for function. The challenge lies in demonstrating the incremental evolution of these components. Judging by previous comments this should be a piece of cake. Identify pathways which include precursor functions and a functionally logical sequence of events supported by empirical data. Identify interpretation of data and distinguish it from the data itself.
August 12th, 2008 at 8:42 am
This is the usual, negative, “I double dare you” ID “experiment.”
I admit I probably more spoiled than most commenters, because I spend a great deal of my time in a national lab. There when someone talks about an effect they expect to find they don’t say: “I’m not doing an experiment. I will just challenge my dissenting colleagues to prove the effect doesn’t exist.” Instead, with no mumbo-jumbo, they will tell you: “Well, if we use a liquid helium target with a 6 GeV polarized electron beam with this experimental setup we should be able to see the effect in the data providing we run for x number of days.”
Arguments that evolution cannot explain DNA replication, even if they are true, is not an argument for IC. You have to:
1) Define precisely what you mean by IC, with no hemming and hawing. If it s a scientific concept, then it must have a precise definition.
2) Design an experiment that measures a prediction of IC.
3) To reiterate, double-daring a competing explanation (evolution) does not constitute an experiment.
Comment by David Heddle — August 12, 2008 @ 8:42 am
August 12th, 2008 at 9:39 am
David is correct, but in this case we specifically challenged Bradford in another thread to "put up or shut up." I suggest we use the other thread to complain about the vacuous nature of ID itself. I expected Bradford to immediately jump to the furtherest possible point in ancient history, as I said in the other thread he'd need a very large knowledge gap to surround any potential example. We are all aware of the obvious problems David has pointed out, but I suggest we ignore these obvious deficiencies in his proposed explanation and instead simply try to answer the question: what does science say about the evolution of DNA replication? I intend to poke around and see what I can find on this topic. I will respond to Bradford's claim when I have the time to investigate.
Comment by Todd Berkebile — August 12, 2008 @ 9:39 am
August 12th, 2008 at 10:43 am
David Heddle:
It's a response to arrogant assertions that mainstream theories have adaquately documented the evolution of complex biological functions.
I take it then that it is asking too much that mainstream evolutionists cite experiments that document their assertions.
It does accurately state the condition of our biological understanding.
I would define it with reference to specific functions and the components needed to sustain them. The specific proteins mentioned being required to enable function. You're right about predictions.
Comment by Bradford — August 12, 2008 @ 10:43 am
August 12th, 2008 at 10:51 am
Todd:
There is a logical reason for examining ancient events which has nothing to do with gaps. Current theories rest on the sufficiency of a replicating biological entity. DNA and its replication is central to that paradigm. It is also a key element of front loading concepts in my view. Gradual incremental changes, leading to the DNA function, are confounded by the nature of the physical components themselves. Your objection is with Nature not me.
Comment by Bradford — August 12, 2008 @ 10:51 am
August 12th, 2008 at 11:14 am
Bradford
By all means you should hold their feet to the fire. You just cannot make evolution's failings, such as they may be, the basis of support for ID as science. ID (as science) is independent of evolution's shortcomings or its successes.
Comment by David Heddle — August 12, 2008 @ 11:14 am
August 12th, 2008 at 11:52 am
Hi Bradford,
I find it interesting that successful cell division is not solely dependent on the activity of the replisome, but the interaction of various cell signaling cacades that converge to control the activity of the replisome, DNA repair, cell cycle checkpoints and programmed cell death.
Perhaps science contributed to the whole "IC mess"? Various gene knock-out studies have demonstrated that a core set of proteins are needed to control successful cell division in the various domains of life. Bacterial cell division is also a well orchestrated process. Where are the simpler variations of dividing cells? What happened to them? Can we speculate about them without proof?
Oh, you forgot to mention the sliding-clamps and clamp-loaders.
Comment by Telicmeme — August 12, 2008 @ 11:52 am
August 12th, 2008 at 3:16 pm
Hi Telicmeme. You touched on some of my favorite topics in your links. You're also giving me some ideas for future posts. That core set of proteins you speak of could be among the initial FL components needed for life as we know it. Thanks for the comment.
Comment by Bradford — August 12, 2008 @ 3:16 pm
August 12th, 2008 at 5:13 pm
Bradford,
Thanks for this interesting challenge. It seems you claim that DNA replication systems are IC. In other words, they cannot have evolved by "ordinary" means, but were front-loaded or poofed into existence by Jesus. Is that correct? If so, what's your evidence for this?
I'm not an expert at all in this field, but I found a paper that might be interesting: Forterre et al. 2007. Origin and evolution of DNA topoisomerases. Biochimie 89, 427-446.
I would suggest that early in the history of life, the DNA replication functions that are now carried out by multiple enzymes were carried out in a more crude fashion by just a single enzyme. This doesn't seem too implausible since PCR reactions are also carried out with just a single enzyme (TAQ).
Comment by Raevmo — August 12, 2008 @ 5:13 pm
August 12th, 2008 at 6:26 pm
The only part you are absolutely on target with is the point that "ordinary means" is an insufficient explanation. As I've said many times, I believe God is ultimately the source of all causation and is able to direct events as he pleases but that does not reveal details as does the study of nature. Front loading makes eminent sense.
I'll look into this.
The current variety of enzymes differ greatly from each other as do their functions. In fact, single stranded binding proteins are not even enzymes. One size fits all makes no sense when DNA is involved in the reactions.
Comment by Bradford — August 12, 2008 @ 6:26 pm
August 12th, 2008 at 9:10 pm
One logical pathway I see for irreducible complexity, is that we start off with a crap load of information and thus a crap load of complexity that goes along with it. To get irreducible complex core functions we simply fine tune that complexity into practical and usable parts. After a while, those usable parts can no longer be reduced as they have gone through extensive fine tuning that any decrease in information would lead to catastrophe. Thus, we have to have a mechanism to keep it from being reducible, maintain the status quo (ie: prevent as little changes from occurring)
Comment by computerist — August 12, 2008 @ 9:10 pm
August 12th, 2008 at 9:17 pm
BTW, I just read recently that John A. Davison now has a new blog.
here it is: http://jadavison.wordpress.com...
Comment by computerist — August 12, 2008 @ 9:17 pm
August 12th, 2008 at 11:55 pm
Of course, all we have to do is determine if all the information was there at the beginning. Once we can do that we can validate the front-loading hypothesis. If we can validate a front-loading hypothesis then we can infer a top-down approach to design rather then a bottom-up gradual and undirected process.
Comment by computerist — August 12, 2008 @ 11:55 pm
August 13th, 2008 at 1:12 am
Bradford, the very idea of a front-loading hypothesis might imply a designer. If there was or is evidence for it, I am sure that science will do a good job avoiding it.
This is part of science, to avoid any possible metaphysical implications.
Comment by computerist — August 13, 2008 @ 1:12 am
August 13th, 2008 at 4:20 pm
computerist:
Mike has pointed this out repeatedly but it merits repetition: Sufficiency of evidence is in the eye of the beholder to a great extent. I find Guillermo Gonzalez's and Jay Richard's Privilaged Planet arguments compelling. Others dismiss them. The reverse occurs with OOL arguments. There is an existing attitude that finds arguments conferring plausibility to the existence of a deity unscientific while simultaneously finding anti-deity arguments, linked to physical data, acceptable.
If it is it is doomed to failure for it is human nature to draw inferences about metaphysical issues from Nature.
Comment by Bradford — August 13, 2008 @ 4:20 pm
August 13th, 2008 at 5:01 pm
Hi Bradford,
As much as I see overwhelming evidence for design in nature, I think this whole debate is doomed to hell and for one reason alone.
The reason is simple: "people just do things"
As silly as that might sound, it has powerful implications. When I heard and read John A. Davison's prescribed evolutionary hypothesis, things made that much more sense.
Look at your threads by example, whatever evidence you point to design is simply belittled by the Darwinist's because they can't live with the idea of having to attribute design in nature to real design.
Its just that simple, there is nothing more to it.
The Darwinist might like to argue this point, but then that would only further prove my point wouldn't it.
Darwinism is as much designed or prescribed as they're biological counterparts.
Comment by computerist — August 13, 2008 @ 5:01 pm
August 13th, 2008 at 5:04 pm
So far I have found one particularly interesting study, Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases by Eugene V Koonin. This study talks about the wide variety of different mechanisms for DNA replication. It seems the three main domains of life each have very different solutions to the problem if DNA replication. Koonin actually suggests the order in which these different DNA replication systems evolved. If nothing else, in the other thread Doug and Bradford suggested the lack of variants for a system was evidence against an evolutionary explanation. So they should except the presence of variant forms of DNA replication as evidence in favor of evolution.
An earlier study, Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins had already suggested that horizontal gene transfer from viruses played a role in polymerase evolution. I found a several studies from around 2002 discussing this, and Koonin discusses this too.
If you can find it there's a whole chapter in The Genetic Code and the Origin of Life on this topic. My local college library doesn't have this book, but I intend to check whether they can get it on loan.
There's a website called Evolution of DNA that presents a "proteins first" model (most people assume a RNA first model these days). Unfortunately the website seems to be targeted for school children, the quality of the writing isn't very good, and no references are sited. The website really is little more than made-up stories. It presents a fairly detailed model, but with no research to back it up it is just a fairy tale.
There are 62,779 articles on PubMed alone related to the evolution of DNA. Its a lot of data to dig through, especially for a lay person. The hard part is that there is so much research about the evolution of specific DNA sequences and genes which hit all the same search terms. Also the origin of replication has a specific meaning which dominates search results for phrases like "origin of DNA replication". Still, I'll continue looking as time permits.
Comment by Todd Berkebile — August 13, 2008 @ 5:04 pm
August 13th, 2008 at 5:24 pm
Where did I argue this? Variation occurs when a biologically stable means of replication is in place. In fact, the blog entry itself infers variation exists. That was the point of the reference to unicellular systems.
I like reading Koonin's papers. Our views are opposite but I like his style and might use this paper as the focus of a follow-up blog entry.
Comment by Bradford — August 13, 2008 @ 5:24 pm
August 13th, 2008 at 5:26 pm
An ironic comment considering the claim entailed in the thread title.
There is, as yet, no complete theory of the origin of DNA replication, an event that occurred hundreds of millions of years ago and left scant evidence. So?
Comment by Zachriel — August 13, 2008 @ 5:26 pm
August 13th, 2008 at 5:30 pm
computerist:
I agree and have adjusted my focus. Critics have mindsets carved in stone. They are more intransigent than the extremist religious people they like to caricature. The problem with leaving open forums to them alone is that news stories get slanted to promote their perspective on things. That's the value of sites like Telic Thoughts. You get another viewpoint.
Comment by Bradford — August 13, 2008 @ 5:30 pm
August 13th, 2008 at 5:34 pm
The evolution of the DNA replication function is a clear concept. I want to avoid end runs around the topic through pedantic arguments.
Bradford: There are multiple parts needed for function. The challenge lies in demonstrating the incremental evolution of these components.
There may never be a complete theory let alone a plausible one. That is news to many.
Comment by Bradford — August 13, 2008 @ 5:34 pm
August 13th, 2008 at 5:37 pm
I, for one, have no problem with the possibility of design in nature. I do have a problem when people falsely claim to have scientific evidence to support such a claim.
Comment by Zachriel — August 13, 2008 @ 5:37 pm
August 13th, 2008 at 5:46 pm
Yes. However, you claim that DNA replication is irreducibly complex and then prohibit a discussion as to what exactly that means.
There are several plausible pathways, but no complete theory. There's just not enough data at this time, and as you point out, there may never be enough data.
So, your purpose was just to point out a particular Gap in human scientific knowledge. Keep up the good work.
Comment by Zachriel — August 13, 2008 @ 5:46 pm
August 13th, 2008 at 5:53 pm
Thanks for proving my point.
Comment by computerist — August 13, 2008 @ 5:53 pm
August 13th, 2008 at 6:04 pm
There's nothing like a plausible pathway. The glycolytic pathway is plausible because it can be repeatedly documented. The imaginative pathways to DNA replication suffer greatly by comparison.
My purpose was to point out how the data actually stacks up and leave it to others to decide for themselves whether or not the function indicates a lack of evidence for standard approaches or whether it is a signal that something more substantive is amiss.
Comment by Bradford — August 13, 2008 @ 6:04 pm
August 14th, 2008 at 10:26 am
So, the observation is that the process of DNA Replication is Irreducibly Complex as per Behe's definition of it. What would this pre/post-dict about the origin of the process from a Design Perspective?
It has been indicated that the presence of very few precursors to such systems would go against a gradualistic evolutionary scenario but could that be because of any design constraints of building such a system? Such design constraints must exist from a design view for such a central process to Life. So a prediction on consideration design constraints should be that very few precursors should be found for an irreducibly complex system like this. Is this prediction right? Does this follow? please correct me if I'm wrong. Any engineers among us would like to enlighten us on the design constraints of engineering such a DNA replication system? What are the design constraints for a CD/DVD duplication system? Is it analogical to DNA replication? If so, it could provide some clues.
Well, "very few" seems to be vague, so is there a way one can quantify the amount of precursors above which a darwinian explanation would seem more plausible? Might there be a "threshold/edge" here also? [Note that I'm not arguing that there can't be any precursors to this system and neither is Behe as far as I could tell. Doing so would be getting caught in to the Traditional Template] An analysis of the design constraints could help in estimating the 'precursor threshold' for an IC system. Then I think a definite prediction can be made from a Design Perspective.
Comment by samsen — August 14, 2008 @ 10:26 am
August 14th, 2008 at 2:03 pm
Hi samsen. I was going to respond to your very good comment with one of my own but on second thought think that it is better to devote a blog entry to your questions. It may take a few days but the issues you raise are worth the effort.
Comment by Bradford — August 14, 2008 @ 2:03 pm
August 14th, 2008 at 4:17 pm
Hi Bradford,
Thanks!
I see that I wasn't clear in my previous comment in places. I was trying to write down the thoughts and questions that arose in my mind as I read your blog entry so
let me clarify…
I meant that the scarcity of precursors could be explained by the presence of design constraints. As design constraints decrease one might expect an abundance of precursors. But to increase the plausibility of this explanation one needs to identify the design constraints. In order to do that an analogical system from human design systems could be used in analysis. Hence, my question about a CD/DVD duplication system. Btw take your time in responding to my questions…
Comment by samsen — August 14, 2008 @ 4:17 pm
August 16th, 2008 at 9:31 pm
Bradford:
I was curious whether or not Behe had anything to say about DNA replication. He does. In fact, he includes a discussion about it in the appendix section of, Darwin’s Black Box.
Primarily he focuses his discussion on the role of DNA polymerases enzymes that are critical in not only replicating DNA but also repairing it. Polymerase I’s ( or Pol I) basic function is the repair of DNA while Pol III’s main role is replication itself . There is also a Pol II whose function is not well understood.
Behe then goes on to describe Pol III in a little more detail.
Behe, unfortunately doesn’t provide any graphics. I’m imagining something like a very sophisticated zipper. Do you have you any graphics of this very amazing molecular machine? How about a movie?
Comment by JOHN_A_DESIGNER — August 16, 2008 @ 9:31 pm
August 16th, 2008 at 9:55 pm
JOHN A DESIGNER:
Try this John:
http://bioisolutions.blogspot....
Comment by Bradford — August 16, 2008 @ 9:55 pm
August 18th, 2008 at 10:09 pm
Bradford,
That’s a fascinating animation. Thankyou. Unfortunately, for me at least, it raises a lot questions than it answers– but that is science.
In DBB Behe describes the replication of prokaryotic DNA noting that the “replication of eukaryotic DNA appears to be much more complex, and therefore much less is known about it.” (p276)
Of course that brings in the inference of evolution. If eukaryotes evolve from prokaryotes, then logically eukaryote DNA evolves from prokaryote DNA. Sooner or later the critics are going to discover this and say: Aha! How can DNA replication be irreducibly complex if we can plainly see that evolution has led to a newer more complex kind of DNA replicator and replication? This appears to be the TTSS > Bact. Flagellum (or, BF > TTSS) all over again.
The problem, as exhibited over and over again on the other thread, is that the critics still haven’t grasped Behe’s argument. Behe never uses IC to argue against evolution; rather, he uses IC to argue against gradualistic evolution. Behe, BTW, is afterall, himself a evolutionist and has said so in several of his writings.
Do they have a real, empirically testable, answer to this natural riddle? Or, is it all just a lot of pretense and posturing?
When you start introducing the culture war stuff as Mr. Levine has you begin to sense that the other side is becoming more than a little desperate.
How curious, when you restrict the concept of irreducible complexity to science, and scientific answers that the self appointed defenders of science (not to mention that they also claim to be the defenders of all true rationality and western civilization) have very little to say. How curious, indeed.
Comment by JOHN_A_DESIGNER — August 18, 2008 @ 10:09 pm
August 18th, 2008 at 10:40 pm
JOHN A. DESIGNER:
That's a good site. Raising more questions is a quality inherent to virtually all disciplines. I know what you mean.
A post on eukaryotic DNA replication is coming.
I deliberately began with unicellular DNA to focus our attention at the point of DNA origin.
I think the utility of an IC perspective lies in its value as an analytical lens. If pathways are identified so be it. Functions dependent on many interacting parts are more interesting and more challenging.
There are no ready answers to some questions.
Comment by Bradford — August 18, 2008 @ 10:40 pm
August 18th, 2008 at 11:36 pm
Compare/contrast:
You have to:
1) Define precisely what you mean by [evolution], with no hemming and hawing. If it s a scientific concept, then it must have a precise definition.
2) Design an experiment that measures a prediction of [evolution].
3) To reiterate, double-daring a competing explanation does not constitute an experiment.
This is why I typically ask where the supposed singular "theory of evolution" has been specified (encoded in the language of mathematics) and verified (used to predict a general trajectory of adaptation in a group of organisms).
When it comes to those who promote Darwinian creation myths the standards with respect to "science"/knowledge always seem to be shifting. They work to control State funding and consequently research bases are developed based on their standards, yet then they often demand that dissenters meet a standard of knowledge which they haven't met even with all their funding.
The closest thing to a "precise" definition of evolution is Darwinism rooted in natural selection culling random mutation, yet apparently when the theory of natural selection is encoded in the language of mathematics very little predictive knowledge can be derived from it. It seems that what is known by the theory is what could already be known by observation and it seems the "theory" itself may be an observation. Yet to hear proponents of Darwinism tell it the theory of evolution is the epistemic equivalent of the theory of gravity. But if physics is an example then by their own comparison it's as if proponents of Darwinism believe that observing objects after they come to rest and then imagining a sequence of past events which "explains" how the object came to rest in its current position is the equivalent of having a theory with explanatory and predictive power which is open to falsification/verification. It isn't. (Note that the more people imagining things about the past based on such a theory the more overwhelming the supposed explanatory power of such a "theory" become. At any rate, it's a good thing that generally physicists tend to adhere to higher epistemic standards than biologists.)
The fight over defining irreducible complexity is a fight about a "theory of evolution" that was never specified in the first place. If anything IC is more defined and empirically verifiable than the hypothetical goo typical to evolution. Note that "double-daring a competing explanation does not constitute an experiment" but it does answer stupid attempts at explanation which weren't supported by empirical evidence in the first place. This type of notion of falsification: "If I could be shown an organism which I could not imagine coming about in a gradual series of events then my theory would absolutely break down." can indeed be answered with: "Well… I dare you to try to imagine something about this!"
If a Darwinist succeeds in falsifying IC based on empirical evidence then they have admitted that the concept is amenable to science and they have no grounds to bar it as they typically do. Yet if they have some imaginary success in reducing IC based on imagining things about the past then their success is rooted in pseudo-science even if it does seem "overwhelming" in its day as pseudo-science typically does. Either way it's doubtful that IC is going away as a scientific issue.
Comment by mynym — August 18, 2008 @ 11:36 pm
August 19th, 2008 at 7:31 am
creationism, doctrine or theory holding that matter, the various forms of life, and the world were created by God out of nothing and usually in the way described in Genesis.
Common Descent is contrary to the common meaning of creationism.
Evolution is a fact and a theory. Evolution is the observed change in allele frequencies in populations over time. The Theory of Evolution explains the mechanisms of evolution, and makes empirical predictions in a wide variety of fields, from genomics to geology. {We probably need a new thread for this discussion.}
Comment by Zachriel — August 19, 2008 @ 7:31 am
August 19th, 2008 at 8:02 am
The comment directed towards Rock in my last post belongs in the "Great Review" thread.
Comment by Zachriel — August 19, 2008 @ 8:02 am
August 19th, 2008 at 10:17 pm
mynym:
There is no point in mounting empirical efforts at falsifying a concept that does not lend itself to testing is there?
Comment by Bradford — August 19, 2008 @ 10:17 pm
August 20th, 2008 at 7:49 am
Now, Bradford. You had said that discussion of the definition of IC was off the table. How is anyone to respond to your comment without discussing the entailed equivocations? And here you are talking about the concept of IC.
Comment by Zachriel — August 20, 2008 @ 7:49 am