Yet Another Irreducible Complexity No-Brainer — Twisted Ropes

[...] Uncommon Descent | Yet Another Irreducible Complexity No …Feb 27, 2007 … 20 Responses to Yet Another Irreducible Complexity No-Brainer — Twisted Ropes. 1. shaner74February 27, 2007 at 11:03 pm. “This might … [...] Twisted descent | Bertobeyweddin

I think that the smallest genome sequenced up to now (end 2006) is of Carsonella Ruddi, a symbiotic bacterium of plants. It amounts to 160000 bp, coding for 182 proteins. But symbiotic bacteria indeed can live with reducted genomes, deriving many functions from the host cell. Probably the smallest autonomous genomes are about 400000 bp, and 300 - 400 genes. In any case, I think that even these "simple" genomes need topoisomerases, considering that "phisiological" twists around the helical axis , in a "relaxed" double-helical segment of DNA, occur once every 10.4 base pairs of sequence, and that any additional twist imposes a strain on the molecule. gpuccio

Sorry, I meant 300 genes, not base pairs. chunkdz

DaveScot, I'm thinking about the supposed evolutionary precursor. There's a lot of talk about the "minimal genome" and such - estimated at about 300 bp. Can a 300 bp DNA strand even replicate without topoisomerase? Wouldn't there be massive strain and breakage - especially in circular DNA? chunkdz

Is there a bp limit at which point topoisomerase becomes a necessity? Type IA DNA Isomerase is said to exist in all living things. Anything common to all the kingdoms of life is probably not optional to any of it. Replication of the minimal viable DNA sequence length for a free living organism found in nature doesn't appear to be physically possible without a topoisomerase. Life for an individual organism is possible without it but not reproduction so natural selection is going to come down like a hammer on any mutation which eliminates all topoisomerases. DaveScot

chunkdz: "Is there a bp limit at which point topoisomerase becomes a necessity? " A very good question. I am not sure of the answer, but from what I have read it would seem that the problem of DNA topology is rather universal, starting in bacteria, and including even the virus insertion in bacterial DNA. Besides, supercoiling is only one aspect of topological problems about DNA. So, probably, topoisomerases have a fundamental role in nature. gpuccio

gpuccio, Good point about the derived topoisomerase bearing little resemblance to the ones we find in nature. What I am curious about is the level of tolerance that DNA has to replication without topoisomerase. Supposedly short DNA's are able to replicate without topoisomerase but replicate more efficiently with topoisomerase? Is there a bp limit at which point topoisomerase becomes a necessity? chunkdz

Wonderful post, and wonderful replies. Thank you. mike1962

"There is evidence that topoisomerases can evolve from endonuclease by a single amino substitution" If I understand well, the evidence consists only in the fact that a single bacterial endonuclease (one among hundreds or thousands) can express a topoisomerase activit through an aminoacid substitution. But that molecule has no omology with other topoisomerases, nor with most other endonucleases. Really these molecules form a vast family of apparently unrelated proteins, which may share domains and functions. Regarding the molecule cited above, it seems that it may act both as a bacterial endonuclease and topoisomerase: "Nae I protein was originally isolated for its restriction endonuclease properties. Nae I was later discovered to either relax or cleave supercoiled DNA, depending upon whether Nae I position 43 contains a lysine (43K) or leucine (43L) respectively. Nae I-43K DNA relaxation activity appears to be the product of coupling separate endonuclease and ligase domains within the same polypeptide. Whereas Nae I relaxes supercoiled DNA like a topoisomerase, even forming a transient covalent intermediate with the substrate DNA, Nae I shows no obvious sequence similarity to the topoisomerases" (From: "Step-wise DNA relaxation and decatenation by NaeI-43K." by Jo K., Topal MD, 1998) As it usually happens, facts are very complex, and the evolutionary "evidence" is only a fantasy driven interpretation. gpuccio

There is evidence that topoisomerases can evolve from endonuclease by a single amino substitution, so the intermediate step from a non-topoisomerase genome to a topoisomerase genome is feasible. However, according to Cairns-Smith:

DNA topoisomerases also must date back to the time of the first circular DNA chromosomes. Topoisomerase Ia was required for releasing strain ahead of the replication fork, while topisomerase II was essential for decatenating daughter circles after the termination of replication to allow their separation into separate daughters. Since such decatenation often produces circular dimers, additional special termination enzymes able to cut and rejoin DNA probably evolved during the origin of efficient circle replication. Since circles are the simplest way of avoiding both the end replication problem caused by the origin of separate primase and replication polymerases and avoiding digestion of ends by exonucleases (whether the organism's own or those of predators or competitors: Cavalier-Smith, 2001), it is likely that both kinds of topoisomerases and the DnaG DNA primase evolved almost simultaneously during a huge bout of enzymatic innovation of many basic DNA-handling enzymes.

We are looking at three systems that needed to evolve "almost simultaneously" in order to be useful. I think any claim of IC for topoisomerase will rely on it's interdependent systems as a whole, not the enzyme itself. chunkdz

Gil: How could random variation and natural selection come up with a pair of biochemical scissors and a repair mechanism that cuts and splices the twisted DNA molecule in order to relieve torsional tension?

How a nerve comes to be sensitive to light hardly concerns us more than how life itself originated-- Charles Darwin

Which of course is also applied to scenario Gil questions. Try it. Pick any questionable scenario. How it evolved is not important because we know it did. Now all you sliders get back in line and get with the program. :) Joseph

The wonderful animation of the working of topoisomerases (especially topoisomerase II) seems to have generated a wonderful consensus of amazement, admiration, and immediate recognition of the "irreducible" nature of the problem. And I absolutely add myself to the general choir. Strange how certain things are so obvious when you see them, and yet a lot of people go on masquerading reality behind abstruse theories or false words. I really would like anybody to explain the working of topoisomerase II in terms of step by step evolution of a new protein with acquisition of phenotypic reproductive advantage at each binary step! (Obviously, some darwinist is already trying, and will end up with a new generic fairy tale of how topoisomerase was coopted from some vaguely homologous protein which served in some obscure metabolic pathway...) I have always thought that Behe (who has my complete admiration) is too conservative in his arguments. I really think that there are millions of obvious examples of irreducible complexity at the cellular level. Just think of all the informational networks working as cascades of protein interactions. Behe has correctly cited the coagulation cascade, and that's a very good example. But, in a sense, the coagulation cascade has a multiplicative function, whose final purpose is to produce the final active proteins of coagulation in significant quantities. The relation between funtion and outcome is still perceptible, although realized through consecutive steps. But think, for instance, of the protein cascades which transfer a signal from the membrane to the nucleus, where 3 or more proteins interact in cascade just to transmit and modulate information. Such a pathway is purely informational, has no other immediate function, and is interpolated between two other informational networks: the cytokine system, an extremely complex system of communication at distance between cells; and the transcription regulation network, an even more complex regulatory system, still very poorly understood, which rules DNA transcription in the nucleus, practically transforming the generic genome, common to all cells in the body, into a very specific transcriptome, unique to that cell in that moment. The irreducible complexity of these informational systems is absolutely self evident, like the irreducible complexity of any complex computer algorithm, where even a bit difference invalidates everything. gpuccio

I did 2 interviews with Steve Fuller. One on the philosophy of science, Kuhn and Popper and the ID specific one. The ID specific one wont be out for a while, it is in ID FIles 2nd Ed, but the other one should be out in about a week on the regular show feed. And i'll see what I can do about getting Angus Menuge. Any particular topic ? Just shoot me an email, thesciphishow@gmail.com rather than cluttering up the thread. Jason Rennie

Oooo, Jason, you did an interview with Steve Fuller!?! I'd love to hear that one! When will it be up? Also, if I might make a request, could you see if you could do a show with Angus Menuge? Your podcasts are great, man! Keep it up! crandaddy

GilDodgen:

I find the phenomenon of the DNA supercoiling problem and its biochemical solution even more compelling than examples like protein synthesis and the bacterial flagellum, since twisted ropes are familiar to everyone.

Gil, I absolutley feel your take on this incredible machine! When Dave posted this, I was amazed and sent straight away to my friend. It's so compelling to me. Functional intermediates? Hmm.. one that takes out a quarer twist :D haha.. ridiculous! JGuy

If I remember correctly, the early Ptolemaic model of the solar system used some extremely complicated mathematical equations to describe the motion of the planets, because they were not aware of real fact... I believe we have with the ToE a similar situation. Evolutionist are struggling to find all bunch of strange and wired explanations for the nanotechnology we are seeing now in the cells... Sladjo

I think I can explain, or at least offer an observation for why this is the case. I did an interview with Dr Steve Fuller the other day and he noted that when it comes to the "ID Controversy" have a look at the sorts of people on each side. Leaving metaphyscial commitments aside. What do you notice ? The ID side is full of engineers, mathematicians, molecular biologists, computer scientists, etc, and the Darwinist side is full of ecologists, zoologists and others like that. On the one hand you have people who deal with machines and engineering for a living and on the other side you have field naturalists (in the classic sense of the word naturalist). Is it a wonder that the engineers see the obvious engineering and the field naturalists see the broad outlines ? Jason Rennie

Well all Darwinists had to say to counter argument is: "just because we don't know how, it does not mean that we'll not find out in the future". Go figure. They are living on this supposed future scientific credit for far too long. It's time to pay out. inunison

Gil, What is amazing to me is the class II topoisomerase enzyme that allows the DNA to unwind. To cal it an "enzyme" seems like an understatement. Although it is comprised of only two proteins, it functions like a machine, performing the amazing feat of breaking a DNA double helix, passing another helix through the gap, and resealing the double helix behind it. The specified complexity of topoisomerase is mind blowing. It is truly the engineering accomplishment of a vastly superior intelligence. Jehu

shaner74 : ditto for sure I've been wondering for a long time exactly what isn't evidence of design. Just like I like to point out to atheists - there is no evidence for no God - but everything that exists can be used as evidence for a God. They say, "Can't prove a negative", then go on spreading the gospel of atheism - and it's 'science' Darwinism - as though they do have proof. IOW, the atheist fails to see that stating "there is no god" and then stating "can't prove a negative" is a blatant contradiction. Atheism thus constitutes a logical absurdity. Go figure why there are atheists huh. And consequently why there are Darwinists - they are faced with a very similar dilemma. "A scientific theory is an established and experimentally verified fact or collection of facts about the world. Unlike the everyday use of the word theory, it is not an unproved idea, or just some theoretical speculation. The latter meaning of a 'theory' in science is called a hypothesis." - http://www.whatislife.com/glossary/t.htm compared with: “The history of organic life is undemonstrable; we cannot prove a whole lot in evolutionary biology, and our findings will always be hypothesis. There is one true evolutionary history of life, and whether we will actually ever know it is not likely. Most importantly, we have to think about questioning underlying assumptions, whether we are dealing with molecules or anything else.” Jeffrey H. Schwartz, Professor of Biological Anthropology, University of Pittsburgh, February 9, 2007 Perfectly clear then that Darwinism doesn't even qualify as a theory. :D Again, go figure. Evidence for ID is everywhere. All language, codes and messages require intelligence. None of these can exist without it. DNA is a code with it's own unique language, alphabet, syntax, semantics, pragmatics, exception trapping mechanisms etc... Therefore DNA was made by an intelligence, vast and deep. Borne

"This might make for another highly persuasive ID mascot." I'm starting to wonder what *isn't* persuasive evidence for ID at the cellular level. "I’m suffering from a state of extreme cognitive dissonance. How can educated, intelligent scientists continue to defend the obviously indefensible, in light of what in now known about the nature of living systems (at all levels, not just the biochemical)?" I'm reaching the point of flat out disgust with those who cling to the notion that this kind of thing "just happened" It's insulting to expect people to believe that the inner workings of a cell are not IDed. It's so transparently obvious that Darwinism remains for philosophical reasons only . shaner74