Yet another layer of complexity
| January 6, 2008 | Posted by idnet.com.au under Intelligent Design |
Plant study reveals a “deeply hidden” layer of transcriptome regulation.
“Cells keep a close watch over the transcriptome – all parts of the genome that are expressed in any given cell at any given time.
Before RNA transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts.
By stopping the function of the exosome, a multi-unit complex molecular machine in charge of controlled RNA degradation, researchers found evidence for widespread exosome-mediated RNA quality control in plants and a ‘deeply hidden’ layer of the transcriptome that is tightly regulated by exosome activity.
The common notion was that the exosome plays a central role in bulk RNA turnover so they expected to find the levels of all transcripts increasing when they inactivated the exosome complex. Instead the exosome mechanism seems to be very tightly regulating an already very specific group of transcripts.”
It is wonderous in the extreme to find the exosome “a multi-unit complex molecular machine” but there is also some separate information and control mechanism using the exosome to be “in charge of controlled RNA degradation”. These multiple layers of design and control engineering are clearly outside the ability of RM and NS to create.
48 Responses to Yet another layer of complexity
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xcdesignproponentsists: “An “estimate”, eh? And what rigorous methodology did Behe employ in order to demonstrate that there is a limit to what evolution can do.”
As Dr. Behe has painstakingly tried to relate on his amazon blog, he made no estimation or calculation. He has simply observed, based on actual studies, what has and what has not actually occurred. In nearly every cases where some “beneficial” mutation has occurred it is simply because it broke something already present, not because it added anything interesting or new.
Those changes RM has produced are easily quantified, and understandable, using simple statistical models and error rates.
If there is no limit to what evolution can do, then why is it that what it actually does, based upon laboratory observation, is so limited?
gpuccio says:
Perhaps, if you would like to clarify your point of view, I could understand better what you mean.
I reply:
My initial point was the the age of the universe is a matter of extreme speculation, but is often spoken of as settled fact. I think this is bad practice, however “common” a model may be. Or perhaps I should say, bad practice especially with a common but unproven model!
My secondary point was that in every case where we know how things came to be – books, paintings, musical compositions, computer programs, houses, telephones, automobiles, etc:
(1) the sudden appearance of increased complexity is common;
(2) most of the imaginable intermediate forms are missing; and
(3) any attempt to date such artifacts (without recourse to “outside data”) typically fails. For example, different parts of my car might be manufactured at different times, and a novel might be written over a period of decades.
leo,
you said,
“I’m not going to go over all the details here, but you should know where to find them, simply give them a read and understand.”
We are kind of dumb here so why don’t you select one or two examples to enlighten us. For several years we have been asking for enlightenment but no one has taken pity on us and provided it. I have read textbooks on the topic, watched evolution courses at Berkeley and they all failed to enlighten. Even evolutionary biologist such as Allen MacNeill and Darrel Falk did not help us when they were here. So be kind and help us out.
#29 xc …..
Which unfortunately ID proponents haven’t succeeded in doing. Irreducible complexity, for example, does NOT falsify evolution. In fact, it is a prediction of evolution – Behe did not coin the term.
Repeating this falsehood won’t make it true.
Ehm, are you speaking about NDE I suppose …
The so-called positive arguments for ID, i.e. CSI and IC are non-arguments.
No problem. Give a decent and proved (not just so stories please) indirect path according to which flagellum or eye or anything else have been built and you’ll have some argument about.
IC and CSI do not falsify evolution. Then again, even IF you were able to falsify evolution, that is still not positive evidence for ID. There’s always creationism or Lokism.
I understand; you are that kind of people that, going to play poker and after having lost some million $ because the opponent did have ace poker for 30 consecutive hands says to himself that there are “no positive evidence” for cheating. Congratulations
Intelligent designers can make synthetic diamonds. Does that mean that diamonds found naturally must have needed intelligence to form?
If you consider this to be positive evidence for ID, then please don’t be surprised if the scientific community doesn’t this argument very seriously. It’s merely an analogy applied (possibly) incorrectly to living organisms.
Come on sir, have you read anithing significant about specified complexity before to came here to propose this sort of (pseudo)arguments?
And all intelligent designers that we know of are all products of nature. Hence, unless humans are somehow detached from nature, it is ultimately naturalistic processes creating information.
Ehm. This is a classical logical fallacy. If the ultimate nature of reality is only naturalistic is the question, NOT the answer. Come on, correct this approach before charging Id supporters of credulity fallacy.
The evolution of the antifreeze protein in Antarctic fish (neither trivial nor insignificant, despite Behe’s handwaving).
Should here we accept your idea about? After all for diamonds you weren’t right …
Specific aspects of ID are not falsifiable. For example, even if scientists were able to provide a step-by-step breakdown of each mutational event that led to the formation of a protein complex, one could still claim that Intelligent Designer was responsible.
Sir, may I remind you Occam’s razor that NDEers use mainly where it can’t? This is acase where the use would be pretty good. Let’s wait if the fact will arise. Good luck.
After all, why must the Designer be restricted to what cannot be explained naturalistically? And the claim may very well be true -
Occam …
antifreeze protein could have evolved by a naturalistic mechanism, but that doesn’t mean it wasn’t Designed.
Occam …
kairos, don’t you know? evolutionists always fall back on the zillions of alternative universes. That way they can predict *everything*
#35
don’t you know? evolutionists always fall back on the zillions of alternative universes. That way they can predict *everything*
OK. But then they ‘ve to be coherent with themselves.
So, I repeat, going to play poker and after having lost some million $ because the opponent did have ace poker for 30 consecutive hands, they are supposed to be calm and to say that there is no reason to get angry for there are “no positive evidence” for cheating.
xcdesignwhatever is no longer with us. Anyone wanting to criticize Behe’s “Edge of Evolution” without bothering to read it first can do it elsewhere.
When I said “estimate” I only meant that although everything was based upon real observations the derived edge/limit of evolution is not a hard limit in that under certain conditions Darwinian processes “might” be capable of a bit more. This is an assumption on my part, but as we gather more evidence over the years I’m assuming we’ll derive a more accurate limit that may be slightly higher than what is currently given.
jerry,
Absolutely, I would love to. Of course this cannot be the full detailed arguments that many have set forth due to the restrictions of time and space, however, I think general outlines of the arguments presented shall suffice.
I have chosen to use two primary texts. Both are popular science books, as I have noticed that all the ID arguments are set out in popular science books and rarely/never in peer review publications. I will use Michael Shermer’s Why Darwin Matters (Owl Books, 200) and Niall Shanks’ God, the Devil, and Darwin (Oxford University Press, 2006). I chose these for the simple reason that I have read each in the last month and am therefore more familiar with their contents. I should note that while I enjoyed the writing of Shanks, I did not enjoy Shermer’s, finding it too simple (perhaps that was a goal of his, I don’t know) and in some places, petty.
I will constrain myself here to simply quoting their words as that is the task set before me. And, of course, all spelling a grammatical mistakes are mine.
On CSI…
Shanks:
What follows is a description of Benard cells, an undesigned, self-organizing process that exhibits CSI.
Dembski does not tell us which conservation laws of physics forbid self-organization. This is a vexing matter since Benard cells occur in nature – for example in the sun – as well as in the laboratory (not to mention a host of other self-organizing systems). There existence is certainly consistent with known conservation laws. Not only this. For Benard cells, forming in accord with dumb, natural mechanisms, manifest complex specified information.
…
In this regard, Dembski (in No Free Lunch) is guilty of gross oversimplification in his desire to quickly dispose of the problem posed by Benard cell patterns. The crucial difference between the Benard cell pattern and the pattern of hits by the marksman is that the Benard cell pattern does not require intelligent design for its appearance, only a dumb generating mechanism combined with the effects of dumb chance in the form of fluctuations and inhomogeneities in the dumb aqueous medium.
…
First of all, Benard cells manifest CSI and they arise from natural unintelligent causes. Moreover the central issue is not whether the system manifesting CSI is a component of a closed thermodynamical system. The central issue is whether there is usable energy to drive the formation of systems manifesting CSI. The universe we live in clearly does contain such usable energy, and is in fact teeming with such undersigned yet organized complex systems at all scales, from the molecular to the galactic.
…
In saying that information can be thought of as being inverse to entropy, Dembski is arguing that as the entropy of a system decreases, information increases, and as entropy increases, information decreases. … In these terms, entropy of an isolated or closed system will tend increase until it attains a state of thermodynamical equilibrium, at which point the entropy will tend to remain unchanged. Exceptions to these trends with respect to entropy were claimed to be due to the occurrence of random fluctuations bringing about spontaneous decreases in entropy, with large fluctuations being much more unlikely that very small fluctuations.
Blotzmann was driven to the view that the orderd, structured universe we see around us was due to an enomous, incredibly rare statistical fluctuation that had brought about a massive, spontaneous decrease in entropy. Even in its own terms, this explanation of the organized character of the universe we live in is not satisfactory. … The real problem is that neither Dembski nor Boltzmann are correct about the nature of the universe we live in. This has the consequence that Dembski’s proposed forth law of thermodynamics, the law of conservation of information, is simply not needed to explain the “highly unlikely exceptions” to the Second Law that Boltzmann had attributed to random fluctuations! … our universe is presently a nonequilibrium universe in which there is plenty of usable energy to drive the formation of organized structures on both small and large scales. But there is more. Our universe began with a Big Bang. … the entire universe (matter, energy, space, and time) was originally scrunched up into a featureless, pointlike object know as a singularity that lacked structure and organization. In the beginning, entropy was not at a minimum, instead entropy was at a maximum. …the expansion of the universe from an initial point-like singularity creates opportunities for gravity to initiate self-organizing processes the structured, feature-filled fruits of which are themselves the basis for further self-organization and emergence of additional structure and order.
…
Our universe began in a state of maximal entropy. … The universe we live in has lots of usable energy and is far from a state of thermodynamical equilibrium in which entropy and information would remain the same (barring statistical fluctuations). The resulting decreases in entropy in these islands of order, by Dembski’s own admission that entropy and information are inversely related, result in increases in information. These features of our universe point clearly to the conclusion that you can indeed get CSI through self-organization resulting from unintelligent natural causes, and that no invisible supernatural hand operating outside a system of purely natural causes is needed.
All I have time for right now. To be continued.
leo: “Benard cells, an undesigned, self-organizing process that exhibits CSI.”
(1) “Self-organizing” is a nonsense term.
D.L. Abel, J.T. Trevors, “Self-organization vs. self-ordering events in life-origin models”, Physics of Life Reviews (2006):
(2) Further, “self-ordering” phenomena are, more accurately, “order-rearranging” phenomena:
Stephen M. Barr, professor of theoretical physics, Bartol Research Institute, University of Delaware, in Modern Physics and Ancient Faith (2003), pp. 78-79:
(3) By definition, because of (1) and (2), CSI is clearly not generated by Bénard cell convection. (Besides, there is no such thing as CSI. Darwinists have proven this. Don’t you know anything?)
(4) There is no good reason to call the convenient, automatic rearrangement of order in the universe “undesigned”.
leo:
I think both you and the people you cite have not understood the meaning of CSI. I invite you to re-read Dembsi, but I’ll try to sum it up for you.
For CSI to be present, three conditions must be present:
1) The information in the system must be one of many possible “random” configurations, and the number of possible random configurations must be high enough (for instance, higher than Dembski’s UPB). That is conplexity.
2) The observed configuration must be specified in one of the possible ways (for instance, pre-specified, or functionally specified, that is it must express some function which is new, in other words which is the result of the specific configuration attained). That is specification.
3) The observed configuration must in no way be the product of necessity, that is there must be no way to attain that specific configuration because specific laws of cause and effect require that. In other words, the configuration expressing the function must be, from the point of view of physical laws, the result of pure chance, the random happening of one of the multiple possible, and equally likely, random configurations. In other words, the specified information attained must really be the result of randomness, and in no way the result of necessity. That excludes all “self-ordering” systems.
Now please, would you like to point to an example of CSI in nature, other than biological information, which is not the product of intelligent design? I am waiting…
gpuccio,
Actually, I think it is you who either don’t understand CSI or don’t understand Benard cells. Why else would Dembski, the man who co-opted the tern CSI say:
“Benard cell convection, Belousov-Zhabotinsky reactions, and a host of other self-organizing systems offer complex organized structures”
furthemore, from Shanks:
” First of all, Benard cells manifest Debski-complexity. The formation of Benard cells just by chance alone is highly improbable. In fact, they do not form just by chance. The cells result from self-organizing processes whose physical consequences are the emergence of visible patterns involving the net coherent, coordinated motions of trillions of water molecules … The patterns are thus extremely complex. The general pattern can also be specified independently of, indeed prior to, its generation. The patterns are not ad hoc. Benard cells are also contingent. They do not result from an automatic process that gives you the exact same pattern each time.
leo,
Two things:
First, we will have to discuss Bernard cells, whatever they are and find out if there is any relevance to living cells and life.
I personally find the CSI thing incomprehensible when it is attempted as a generalized approach to intelligence. There are much better definitions of CSI when aplied to life that are easy to understand and for which your self organiztion examples are irrelevant.
Second, you have provided nothing yet on evolution for us to read that would support a gradualist approach. I assume you will add to your list.
Jerry [and Leo}:
That’s why I focus on FSCI — functionally specified, complex information. Cf here on who first came up with that idea. (Hint: the spelling is O-R-G-E-L, and the year is 1973.)
Having noted that, GP is right — and IMHCO comprehensible — in his remarks in 41.
In particular, I think that we can distinguish between the order of convection cells — which form by chance plus natural regularities tracing to mechanical necessity and boundary conditions, and the aperiodic, information-bearing, functionally specified complexity of say DNA, or even the carvings on Mt Rushmore.
In particular, observe that the first step in the EF that identifies CSI is to eliminate such natural regularities.
If there is a lawlike necessity at work similar to needing heat + oxidiser + fuel to get a fire, there is not sufficient contingency to make a difference worth talking about.
Second, where there may be high contingency tracing to random distributions in appropriate parameters or boundary conditions, again we are not getting to the point, but are seeing chance at work. In the caser of Shanks’ comment, he should note that his “self-ordering” is in fact a confusion with the proper term here: naural regularites tracing to mechnaical necessity. Of course the particular initial and boundary conditions will make for differences from one case to the next, but these are either set by chance in nature or by agent action – and if we can control the agency input we could use that to store and transmit information for use.
Thus the difference should be plain.
Also, we should see that it is possible to have chance and necessity and indeed agency at worlk in a situation.
As I note in my always linked:
It is when we have complexity plus specification — especially functional specification in an informational context — that we have a proper inference to agency. In particular, what happens is that a random based search across the config space starting from an arbitrary initial point cannot credibly find the foot of a hill of functionality for hill-climbing self reinforcing optimising searches to hit on success, without exhausting the probabilistic resources of the observed cosmos.
But creative agents do that all the time, e.g the posts in this thread.
GEM of TKI
Bénard cells. Ilya Prigogine received his Nobel for his research in this area. I think he admitted they have little relevance to biology.
leo:
I insist that it is you who don’t understand CSI. I may not understand Benard cells, but I think I understand well enough the false argument you build on them.
Here is Wikipedia’s definition for Benard cells:
“Bénard cells are convection cells that appear spontaneously in a liquid layer when heat is applied from below. They can be obtained using a simple experiment first conducted by Henri Bénard, a French physicist, in 1900.”
You cite Dembski as an authority to support your arguments:
“Benard cell convection, Belousov-Zhabotinsky reactions, and a host of other self-organizing systems offer complex organized structures”
But here Dembski is not saying that they display CSI. CSI means Complex Specified Information, and not complex organized structures. So, your argument from citing Dembski is completely false, and your understanding of words is inadequate.
You cite Shanks:
“First of all, Benard cells manifest Debski-complexity. The formation of Benard cells just by chance alone is highly improbable. In fact, they do not form just by chance. The cells result from self-organizing processes whose physical consequences are the emergence of visible patterns involving the net coherent, coordinated motions of trillions of water molecules … The patterns are thus extremely complex. The general pattern can also be specified independently of, indeed prior to, its generation. The patterns are not ad hoc. Benard cells are also contingent. They do not result from an automatic process that gives you the exact same pattern each time.”
Obviously, Shanks too has not understood the concept of CSI, which he calls here “Dembski complexity”. It seems obvious that Benard cells are the product of physical laws (necessity) applied to a sistem where random variations slightly modify an outcome which is, anyway, vastly deterministic. The “self-organizing processes” are just a way to use words, unless you attribute to them the status of either a new law of nature, or a spiritual principle. Obviously, only the laws of necessity and some random variation in the conditions to which those laws are applied are the causal factors here. No CSI is present.
You should understand that CSI is completely another thing. Take, for instance, exactly the example of DNA, which is obviously relevant for our discussion. In DNA, there is no “self-organizing process” which makes specific patterns of nucleotide sequences necessary, even with slight variations due to chance. On the contrary, DNA mutations are, by definition, at least in darwinian theory, completely random. That means that, when a single nucleotide is subject to mutation, for instance a substitution, each of the possible outcomes has the same probability. In principle, each DNA sequence has the same probability to exist. There are no laws of necessity which can give specific patterns in preference to others (obviously, I am not discussing NS here, only RM).
So, if we observe complex specification in DNA, that is CSI. It is not what we observe in Benard cells or similar phenomena. The patterns of Benard cells, although they show some order, are not produced by chance. It is not chance which produces the order, chance only makes the order slightly different from time to time, and so it makes it not completely predictable. That is, after all, the role of chance. But the order in Benard cells is created by the physical laws, which are laws of necessity.
Instead, in CSI, the specified complexity arouses in systems where the laws of necessity can create no specific order, because all possible orders have the same probability to emerge, and the emergence of one configuration rather than another one is supposed to be completely random. In these systems, and only in them, if a specified and complex configuration emerges, an intelligent designer can be inferred.
By the way, I am still waiting that you point to a single example of CSI (according to its correct definition, please) in nature, apart from biological information which is at issue here, which is not caused by intelligent design.
some comments to all of you:
about not yet writing every argument:
It is true, I haven’t. I’ve barely written about one, in fact. I have not the time or the inclination to spend more than ~20min per day on here, so if you are expecting everything right away, I suppose you should look somewhere else (perhaps read the books yourselves). I have found, over the past couple months looking in, that the same arguments are recycled over and over so I feel I will have plenty of opportunities to get my ideas across.
someone said that “I thought Darwinits had already disproven the idea of CSI, so now why are they using it” in so many words.
I would say these are two different arguments. One is pointing out that, despite what Dembski says, there is CSI in natural, non-biological things. The other is saying, so what – that doesn’t mean that the term itself has any value in any discussion on the origins of biological life. For example (all pulled off Wikipedia with references therein):
And from Shanks, on an archer hitting a target (Dembski’s example of a non-random sequence of events)
thank you for the funny wikipedia comments