RNA Designed to Evolve?
| March 10, 2007 | Posted by johnnyb under Intelligent Design |
I’m currently working through Robustness and Evolvability in Living Systems, and came across the following information which seems to be right in line with Denton’s evolution by natural law ideas:
A final, especially counterintuitive feature of RNA sequence space is that all frequent structures are near each other in sequence space. Consider a randomly chosen sequence that folds into a frequent structure and ask how far one has to step away from the original sequence to find a sequence that folds into this second structure…For instance, for RNAs of length n = 100 nucleotides, a sphere of r = 15 mutational steps contains with probability one a sequence for any common structure. This implies that one has to search a vanishingly small fraction of sequence space…to find all common structures.
43 Responses to RNA Designed to Evolve?
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Hi Kairosfocus,
“So, I find then excellent reason to be a design thinker.”
Me too!
I have looked for the Behe article, and here is the link:
http://www.proteinscience.org/.....04802904v1
The article has been published on Protein Science, and is very interesting. Unfortunately, only the abstract is publicly available, but I remember that in some way I got to read the whole paper.
The object of the article is perhaps not exactly the one we were discussing (functional configuration spaces), but it touches many related aspects.
By the way, and speaking of intellectual persecution, have you ever checked the site of the Department of Biological sciences at Lehigh University, where Behe works? Read Behe’s very dignified disclaimer, here:
http://www.lehigh.edu/~inbios/faculty/behe.html
and then compare the infamous “claimer” of one of his colleagues, here:
Hi Kairosfocus,
“So, I find then excellent reason to be a design thinker.”
Me too!
Here is the link to Behe’s article:
http://www.proteinscience.org/.....04802904v1
Unfortunately, only the abstract is available at this link, although I remember having read the whole article somewhere. It is very interesting and, even if it is not exactly about the subject we were discussing (functional configuration spaces), it touches many related aspects.
By the way, and speaking of intellectual persecution, have you ever checked the site of the Department of Biological Sciences, at Lehigh University, where Behe works?
Please compare Behe’s very dignified disclaimer here:
http://www.lehigh.edu/~inbios/faculty/behe.html
with the shameful “claimer” of one of his colleagues here:
http://www.lehigh.edu/~inbios/itzkowtz.html
or with the following “politically correct” citations on the pages of other members of the staff:
http://www.lehigh.edu/~inbios/.....asands.htm
http://www.lehigh.edu/~inbios/faculty/barry.htm
and, finally, with the “official” statement of the department here:
http://www.lehigh.edu/~inbios/news/evolution.htm
Evidently, a single man is creating much embarassment to a lot of “respectable” scientists, just by thinking freely in the same institution! No further comment needed…
Hi again GP:
I found the article, in full form here. Downloaded and saved for personal, non-commercial academic reasons.
Thanks.
I think you are right to highlight the issues of PC science attitudes. (I would like for Mr Behe to post somewhere his full set of research and publications . . . including difficulties with getting past “the panel of peers.” I note the apparently sharp taper-off on publications post 2004, just the time the brouhaha over Sternberg came out. Cf current discussion here in UD.)
GEM of TKI
Sorry for my delay in posting. I have injured my knee and shoulder, both my kids are sick, work is busy, and I have a midterm exam and a midterm paper due. And no, I’m not making any of that up.
Anyway, here is my discussion of front-loading and platonic forms.
JB:
Hope recovery sets in soonest!
Your remarks are a useful summary, namely that, in brief looks to me like:
1] front-loading [a la Mike Gene] is about having the quantum of information that allows later descent with modification [mostly through information loss/specialisation?], and that
2] Forms [a la Plato] define “physical” constraints that force systems to go to certain forms. [E.g. Denton on protein folding. Perhaps, too the European and Australian wolves, etc?]
3] Your own view on the relevance of the two is:
In other words, you see here agency using contingency [information] and necessity. In some part, this is in anticipation of the effects of chance causing environmental perturbations, that would otherwise be destabilising.
I add, based on the issue of feedback control, could there not also be a negative feedback system at work, in part through survival of the fittest, leading to stabilisation under stable environments, and a certain measure of adaptation under sufficiently strong environmental shifts? [This would include the founder principle and the valid part of punctuated equilibria. NB: It would also explain both the power of artificial breeding to cause emergence of diverse breeds, and the fact that there are limits to what breeding can do. This last is of course the point where IMHCO Darwin probably went too far in citing breeding as evidence for the plasticity of the species in the macroevolutionary, common descent sense.]
Interesting.
GEM of TKI
Here is my two cents. It has been said by some biologists that ecologies are the most complex systems on the planet. Because a stable ecology requires complicated adjustments to survive it is necessary for the biological part of the ecology to change when necessary or in other words to adapt.
This is a simple concept and I do not think to controversial. So if I was an intelligent designer what would I do. First, I would provide a means for each of the biological species to change somewhat as conditions change through chance or law. But second, and here is the anti-Darwinist part, the changes would be limited.
As I look out my window, I see an ecology and according to Darwin’s Malthusian view, there is a struggle for existence among its members. And this scenario is repeated billions of times over the planet. But we never see a new form of any consequence emerging from this struggle anywhere. This is the plainest refutation of Darwin I know.
So I propose there may be built in limitations on change. Otherwise why don’t we see smarter, faster, longer living, better seeing, hearing etc amongst the members of the ecology.
So while organisms have built in means to evolve in the sense that allele frequencies can change over time they must have built in limitations even for gradual adaptations. Otherwise why no faster, longer living, better seeing etc progressions. It just does not happen in nature.
So I propose there may be built in limitations on change. Otherwise why don’t we see smarter, faster, longer living, better seeing, hearing etc amongst the members of the ecology.
Ferguson Jenkin (not Jenkins), a nineteenth-century engineer, and critic of Darwin, in his criticism of Darwin pointed out a similar kind of limitation based on the idea that any form (crystalline), as it moves away from its present form, cannot vary itself without limit, but, in fact, the number of permissible permutations (or mutations) becomes more and more limited. But, of course, no one paid any attention to Jenkin apparently.
johhmyb:
first of all my best wishes for you and your kids.
Thank you for your very helpful discussion on your site. I was going to post some considerations here, but I am leaving for a few days, and time is not enough. I hope to post again on Monday.
gpuccio:
Please drop a note in my blog when you post, so I’ll know to come check.
GP & JB:
I’ll be watching out for it . . .
Jerry & PaV:
Adaptability within pre-programmed limits. Very interesting ideas. Any links on that old engineer? (Apart from a loopback to an older UD thread . . .)
GEM of TKI
Hi, johnnyb and kairosfocus:
I just want to keep my promise and give some sequel to the discussion here.
As I have already told, I found johnnyb’s summary about frontloading (on his name-linked site) very illuminating. So I would like to add some comments, completely accepting, as a starting point, his definitions and classification of the various positions. If I understand well, we could agree that, from a design point of view (we will here leave alone the darwinist points of view, assuming that we already agree they are completely unsubstantiated and self-contradictory) there are at least three great lines of thought, as follows:
1) Platonic forms. I cite from johnnyb: “Platonic forms is the idea that physics is set up so that there are only a small set of possible configurations that life could have. The reason that life keeps coming up with the same type of solutions over and over again is that these are the forms allowed by physics itselfâ€Â.
I think we have to make a distinction here. There is a weak form of this argument, which is in essence the same as the general fine tuning argument of physics: physical laws and constants are intelligently selected from an almost infinite configuration space, so that our ordered universe is possible. Any slight deviation from the specific set of values we observe would make the universe chaotic (no atoms, molecules, galaxies, and obviously no life). In this form, which I strongly support, it is evident that very important information has been selected by the designer in planning the whole universe, and that kind of design is absolutely “necessary†for life to emerge. But the point remains open about the “sufficiency†of that information for life. Life could still have emerged by completely deterministic mechanisms (once the correct premises were set before the big bang), like in the darwinian model. Or it could still need other information additions.
I think we all can agree on this weak kind of “platonic forms†in the basic physical laws, and it still remains a very strong cosmological argument for the existence of God.
But I understand that your definition of the “platonic forms†view is stronger than that. It implies that “physics only allows certain biological motifs. And thus, while there are untold numbers of protein sequences, there are only a small number of folds available to themâ€Â.
I must say that I have difficulties to accept this stronger formulation. First of all, one should demonstrate that such a “restriction†of possible motifs and protein folds is a necessary consequence of basic physical laws, and I am not aware of any argument in that sense. Second, I think that the only purpose of such a formulation seems to be that of allowing a purely “natural†mechanism for the emergence of biological information, once the basic physical laws are fixed. But all the ID arguments, CSI and IC first of all, have demonstrated that such an emergence is impossible by chance, and is best explained by design. The only other possibility is necessity, but that would require “new†physical laws, of which we have presently no knowledge, or detailed mechanisms linking known physical laws to he above said restrictions.
Besides, I can’t see how any “platonic forms†explanation could account for OOL. Not only there is no known physical law which can account for the spontaneous generation of complex organic molecules from inorganic matter, just the contrary is true: known physical laws clearly demonstrate the impossibility of such an event. Indeed, all OOL scenarios, from urey-miller ponds to rna worlds, are mere fiction, as has been well discussed elsewhere.
And even if we admitted (but I don’t!) that only few protein folds are accessible, and that for some mysterious reason they are the ones which can bear function, one should still explain the higher informational levels, like the order and control of function, the procedure code (still unknown to everyone), the error management, the general plan for multicellular organisms, etc. It seems obvious to me that all these aspects cannot be explained in terms of mere protein folding, however platonic.
So, while I perfectly agree that specific fine tuning is necessary for life to emerge, I believe that all the ID approach is evidence against a purely mechanistic explanation of biological information, even allowing for very intelligent initial choices.
2) Frontloading. I cite from johnnyb: “ Front-loading is the hypothesis that at some point in the past (usually at the origin of life), organisms were given a rather large deposit of information. The history of life from that point onward has been primarily governed by that information, specializing into the different species we have todayâ€Â.
That’s an interesting point of view, but again I have some difficulties, although of a different nature.
First of all, if I understand well, this theory assumes a specific act of “information imparting†(or creation, if we prefer), at OOL. On that I agree. I think that, however one considers what happened after, OOL can only be explained by a very unusual event. Maybe natural laws were not violated (it is possible, in principle), but it is difficult to conceive OOL as a “gradual†event, because nothing we know or can conceive of is even near to a “precursor†of the simplest living beings. So I strongly believe that the only plausible scenario for OOL is that bacteria, or archea, probably very similar or identical to those we know today, must have been “assembled†from non-organic matter according to a specific plan by a designer.
But, always if I understand well, according to the frontloading hypothesis the designer not only provided these first living beings with the information for their existence, survival and reproduction, but also with the information to “evolve†to the more complex species, up to humans. In other words, once that information was frontloaded in the first living beings, the following “evolution†can be explained by physical laws and mechanistic events, obviously exploiting the initial information. I understand also that, according to some supporters of this theory, the initial “extra†information is no more present, having exhausted its role, or as johnnyb states: “ most people who hold to this view think that there is at least some of that original deposit left hanging around in “junk DNA”â€Â. Well, that seems consistent enough, but here are my objections:
a) First of all, why? I mean, obviously one can postulate any model one likes, but usually a specific model tries to address some specific difficulty. Well, it seems to me that one of the main fights about “evolution†is that some (the darwinists) are convinced that everything must be explained in terms of known physical laws and deterministic mechanisms, while others (IDists) believe that living beings (or at least the information in them) can best be explained by the intervention of a designer. Please note that the intervention of the designer needs not (although it certainly can) violate physical laws, but it is absolutely necessary (according to ID) to explain the observable fact of the appearance of biological information. Then my problem is, what is the need for a third hypothesis which shares the difficulties of both the others? Because frontloading certainly postulates at least one intervention of the designer, at the beginning of life, and indeed such “intervention†should be “heavier†than is supposed by normal ID, having to explain not only the emergence of life, but also any future evolution of it. So, front-loading creates a problem for “naturalistic†thinkers as much as any other ID model. But, at the same time, it seems to postulate that the designer acted only once, and inside time, leaving all the rest to deterministic mechanisms. Again, I don’t understand: why? What is the advantage of thinking that way? What kind of facts are more easily explained that way? I can’t see any reason why a designer, who can impart information once, should not do that other times, or even continuously. And we know that the only “observable†facts which are brought up by darwinists are in essence omologies, either morphologic or genomic, and we know that omologies are, at best, evidence of common descent (or of reutilization of the code), and are never evidence of a specific mechanism. So again, why?
b) Second: how? It’s not enough to postulate something, you must also have a credible model for your hypothesis (unles you are a darwinist, of course…). So, what is the model? Was the extra information stored in the primordial genome of the first bacteria? How? How bigger was then that genome? How much extra information was necessary to “guide†evolution up to humans? It seems to me that here we are again in pure speculation, unsupported by any fact, but again maybe I am not aware of something.
Moreover, if many think that part of the extra information survives in non coding DNA, I see a very difficult contradiction here. I am the first to believe in the importance of non coding DNA. With Mattick and others, I am convinced that much of the “missing code†which can explain procedures and regulations must be there. But Mattick has shown that non coding DNA is the only “quantity†which constantly increases with the complexity of the species. Indeed, the ratio between non coding DNA and total DNA is the best quantitative marker of complexity in living beings, being extremely law in prokaryotes, and going up to 98-99% in humans. If non coding DNA were the repository of the initial extra information, I think we should observe the opposite.
In other words, while frontloading is a possible model, bypassing at least some of the difficulties of naturalism, still I find it unnecessarily complicated. Besides, unless a specific and credible model of this “extra information†is provided, I believe that the general ID arguments against the spontaneous generation of information by natural mechanisms still apply.
3) ID proper. This is obviously my favourite scenario. In this model, design is imparted to living beings by one or more designers, inside time, and during time, many times or continuosly. In this model, again, it is not specifically important if the imparting of information is implementing by an intelligent “manipulation†of known physical laws, like in the case of human designers, or violating them (miracle – creation acts), or by superior laws at present unknown to us. Or if it is implemented continuously or in a “punctuated†way. Personally I have always been attracted by a continuous model, mainly because I believe (not a scientific statement, this one) that God acts in the world practically always. But I must admit that the OOL problem and the cambrian explosion fossils strongly support a special intermittent implementation.
Well, enough for now. I am posting this at UD, but I will leave a note on johhnyb’s site.
Interesting
GEM of TKI
gpuccio
Read what’s been written here regarding Directed Panspermia which should answer many of your questions and objections. Basically the front loading hypothesis is consistent with Francis Crick’s postulation of directed panspermia. If you were technological species wanting to spread your kind of life to another planet in another solar system what practical ways are there of accomplishing that feat given the limitations physics imposes on traversing interstellar divides? You’d need to restrict yourself to a very small payload in order to get it moving at a significant fraction of the speed of light and you’d need a small variety of microscopic lifeforms that could “terraform” a planet into a suitable environment for the eventual expression of a rational technological species that could build a civilization and eventually continue the process of spreading life to other solar systems. Terraforming a planet takes a very long time. Laying down fossil fuel reserves to power an industrial civilization takes a very long time. But it can all be planned and executed from simple beginnings.
On the DNA information cache try reading what’s been written here about amoeba dubia. In a nutshell this is single celled organism that feeds on bacteria, is probably very very ancient, and is living proof that organisms can thrive while carrying a genome 200 times the size of a human genome. Imagine how many different phyla could be encoded in a genome 200 times the size of the human genome. And that’s just the current record holder for largest extant genome. We’ve only measure the genome size of a tiny fraction of all the different organisms that inhabit the earth today. Maybe one or several of them are there waiting for us to discover as the seed organisms we can use to continue the cycle of life by sending them to a suitable young planet around another star. We’re getting close to the point where our telescopes can locate these types of planets and we’ve already got one spacecraft (Voyager I) that has exited the solar system and is zipping through interstellar space to parts unknown even as we speak.
The beauty of this is that it follows the pattern of all life – to find fertile new places to reproduce and carry on. This is just on a grander scale in time and space. It’s also a testable hypothesis in that there should be mechanisms of preserving unexpressed genomic information for geologic timespans (you’ll find an article in the first link where evidence of such a mechanism may have discovered recently) and there should be somewhere in some extant genome a library of phylogenetic specifications or identifiable remnants of one (but I’m betting on the whole library being intact somewhere in some organism such as dubia or maybe scattered as a distributed database amongst a number of such organisms). Whole planetary ecologies reproducing on new planets like a dandelion puts its seeds into the wind seeking to expand its range is an elegant concept. It leaves the question of who and what got the ball rolling in the first place but maybe that information is awaiting discovery too as we get around to sequencing and understanding all the genomes in all the world. Our ability to sequence genomes is growing exponentially so it should be just a matter of time as we chip away at the vast store of genomic information on this planet and learn what it all means.