Intelligent Design in Universities

I have been trying to track down some information bearin on these two paragraphs of Georgi Gladyshev:http://www.endeav.org/evolut/text/pon_jour/pon_jour.htm

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Several results relating to the chemical composition variation of proteins and nucleic acids in the course of the evolution of organisms are discussed in papers [1,5,6,18]. However, there is still a lack of reliable information unambiguously confirming the thermodynamic nature of changes in the composition of these natural polymers. This is well illustrated by the growth of the melting temperature of chromatin in the course of ontogenesis. This growth is believed to indicate definitely that the evolutionary aging of chromatin in the ontogenesis has thermodynamic nature [1, p. 161-163]. New results [18] make it possible to conclude that the evolutionary optimization of the RNA structure is determined not only by the thermodynamic stability of its secondary structure, but also by that of its tertiary structure. This explains why not only the sequences containing GC pairs are selected in the course of evolution (which is most beneficial thermodynamically for the secondary structure formation). In the course of the evolution, sequences including AU pairs are also selected. We obtain (according to the theoretical predictions) that the thermodynamics of tertiary and higher supramolecular structures influences the chemical composition and structure of the RNA. Therefore, from our view point, selection of natural (AUGC) sequences is most advantageous macrothermodynamically. P.Shuster considers these sequences as the most stable ones with respect to mutations.

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http://www.endeav.org/evolut/text/ttbe/ttbe.htm

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On the other hand, there are known examples of a thermodynamic tendency in the variation of the composition and structure of nucleic acids (chromatin) in ontogenesis. It has been found that the thermodynamic stability of nucleic acids is determined by the content of G-C pairs, as well as by the ability of these biopolymers to form complexes with proteins and various low-molecular substances, and other known factors (Cantor and Schimmel, 1980; Gladyshev, 1988). Hence it is clear that efforts to accurately identify the general correlation between the degree of an animal (plant) evolution and the composition of nucleic acids have failed. For instance, the classic data (Marmur and Doty, 1962) on the relationship of the denaturation temperature (Tm) of different DNA to their content of G-C pairs gives no reason to conclude that this relationship is linked with the evolution of the organic world. It appears that only some cases contain dependable evidence of a relationship between the trend of evolution and the content of G-C pairs, whose growth (on a par with other factors) contributes to the increased thermodynamic stability of submolecular structures formed with the participation of DNA and RNA (Gladyshev, 1988).

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P. P. Gardner, B. R. Holland, V. Moulton, M. Hendy, and D. Penny. 2003. Optimal alphabets for an RNA world. Proc. R. Soc. Lond. B270, 1177—1182

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@http://awcmee.massey.ac.nz/people/dpenny/
might help as well as
http://www.sfu.ca/~eemberly/pubs/PRE_68_041904.pdf

Well, that in itself is an emotional argument.Speaking only for myself, I bear no personal hostility toward Jerry or anyone else.In the sciences, tough, even trenchant, but topical, debate on the issues is the order of the day. The first year of graduate school consists largely of getting what you think you know constantly tested and attacked, again in a topical but nonpersonal manner, by faculty, and your fellow students. This is training for the peer review process ,and it is how science, pure and applied, is done on a daily basis.

That question IS the "holy grail" of theoretical biology as I see it and the only reason I am attracted to the field. There might be probabilites or there might be a deductive structure. I for one cant choose as of yet. It seems however that I can only sense a heuristic taste for belief that such exists rather than any hard data. I like to think that some day I might try my math mind at that problem (specifically point sets) but first I would like to know if the probability space is necessary or if pure thought would yield the subject on topic(possibly rather more topology than density issues).This message has been edited by Brad McFall, 05-06-2005 07:55 PM

If ID, ahem, I mean "the controversy", is taught in the public schools, how will the students who think naturalistic evolution is a fact react?

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Los Angeles Times Reports

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Christine Caffy, 15, carefully took notes on each speaker's position. The ninth-grader from Bishop Seabury Academy in Lawrence had recently studied evolution in her biology class and came here to learn more about the debate.

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Afterward, she was curious and confused.

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"I came here thinking that I understood evolution, that I understood the facts," Christine said. "But now, I don't know what to think. Who's right? Is the science that I'm learning really true?"

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That sentiment infuriates scientists, a group of whom had gathered nearby. They insisted that though evolution should be open to criticism, the classroom was not the place for critiques based on religion.

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Glorious!In answer to your question, Christine, the "science" you are learning in class is "science falsely so called".The hearings have already borne fruit as we've enlightened one young mind. May the hearings lead to enlightenment of many more.God willing, someday we'll have ID and creationism courses in the universities to further enlighten students like Christine. This story shows that ID is ripe for the universites. Students will be seeking enlightenment. This young lady heard testimony of several scientists, and now she is beginning to see the light!

Modulous:I see you edited your post and my last post crossed your edit. Let me reply with a bit more detail because you do ask some thought provoking questions:

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Do you agree with the abstract?

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I don't know if I agree with the abstract, because I cannot get past the abstract to find the paper. Won't we have to read the paper in order to see how the abstract is derived, before we know if we agree with the abstract?What I'm saying here is an honest statement. I may actually agree with the paper, and if I do, I will openly state that, but I have to read it first before I say yes or no. The last guy did not understand this and seemed to get ticked because I refused to comment on papers I had never read.Finally on this, has it occurred to you guys that even if there are a few non-equiprobable hotspots in a genome and I do agree that this is the way it is, this will not change anything much mathematically? It might change the upper bound a bit, but we still will be viewing positive entropy showing disorganization of the genome because this does not get us by the study that showed what it did.I based those calculations statistically, but based on events that have already happened, have been observed happening and we are able to predict WILL happen.There is not a whole bunch of probability in there to begin with. And if you guys should attempt to extrapolate those hotspots to the entire genome, you would be attempting to refute a major tenet of Darwinism wherein evolution happens via random mutation and selection. Would you not then be in danger of perhaps being called pseudo-scientists by your own peers? Something to think about.

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You seemed to be implying that since someone cannot calculate a probability it must be random. Am I right? The problem of course, is that you then say that we have eggheads that can do the math, and that (as far as you know) probabilities are calcuable if we know probabilities occur.

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So either you made a slip up, which is fine, I understand, no problem. Or there isn't a probability involved in mutations, which seems odd to me. Perhaps there is another option I haven't perceived?

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To me, unknown probability seems an oxymoron. How can something be said to have a probability of happening when we don't know enough about the probability to calculate it? How then, would we even know it is probable to begin with?If we think about this, this is like an off or on relay switch that stores a bit of information when it is on and doesn't do anything when it is off. It either is or isn't. So a mutation is either stochastic or random, isn't it? What are the other choices?

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Design Dynamics

Could you please define the terms "stochatic" and "random"? Are you using colloquial english(though I don't suppose the former is colloquial) and the usual dictionaries, some other soure or your own defintions?

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Could you please define the terms "stochatic" and "random"? Are you using colloquial english(though I don't suppose the former is colloquial) and the usual dictionaries, some other soure or your own defintions?

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I probably should. Stochastic processes describe processes where at least a slightly predictable outcome can be calculated via probability. This is a type of mechanism and reflects the degree of predictability of a mechanism.I sometimes chuckle when one of my Darwinist friends uses the term mechanism to describe an evolutionary process because they do not understand that, scientifically speaking, a mechanism is a system that generates a predictable outcome every time, and if they cannot predict what will evolve out of what, they have no mechanisms.A stochastic mechanism is slightly weaker in the predictive attribute but still must point to a probable outcome. I stole this from Bill Dembski off another forum, as he was right-on in defining it.Random I am using pretty much as one of the dictionaries would define it. The first definition at dictionary.com reads: "Having no specific pattern, purpose, or objective: random movements." Without these attributes present how could we ever predict anything about it?

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Design Dynamics

So you have a "special" definition of stochastic which is not the usual definition? Is that correct?The outcome of random processes can be calculated based on a the calculation of probablities too. And what is your source for this rather "original" definition of mechanism? It seems we are having trouble talking to you because you are speaking a different English than most people.You are useing a dictionary definition of random but not for stochastic, why is that?

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It could appear that way if the system were other than a far from equilibrium, living system. Just looking at the graph above we can see that maximum entropy with the 4 coins is two heads and two tails. So technically, you are correct again.

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But the reality is, the organism will not be alive long enough to allow a genome to reach anywhere near a state of (100%)! / (50% ancestral)!(50% deleterious)! because this would mean that 50% of the proteins in our body transcribed by genes, just would not work the way they were initially designed to work.

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I'm not really concerned with the practical application, just the theoretical framework you are proposing. What is the actual relationship between functional genes and entropy according to your framework?If I take a human genome (which according to you has "devolved" from an ideal ancestral state, and therefore is higher in entropy according to the equation you used) and caused a deleterious mutation in every gene, would I therefore decrease the genomes entropy?Mathematically, using the formula W= (N1+N2)!/N1!N2!, we started with say 1000 genes that produced 1000 fully functional proteins. So originally our entropy is proportional to:W= (1000!)/(1000!)(0!)= 1Then it devolved after a couple of generations to:W1=(1000!)/(900!)(100!) > 1Entropy is increasing, as you state. Next, I cause point mutations in essential DNA triplets that decrease the function of every gene in the organism. The equation becomes:W2= (1000!)/(0!)(1000!)= 1So, as I caused more deleterious mutations, i.e., fudged up the original information, I caused the entropy to decrease.What, then, is the relationship you are trying to show between entropy and deleterious mutations? Is it that the more deleterious mutations that accumulate in a population, the entropy increases but only to a point then it begins to decrease?Also, I'm not sure, though I suspect you are right, when you say that no organism could live with 50 percent of genome having deleterious mutations. Maybe not on there own, but how about with some scaffolding? It's well known that organisms living in symbiotic relationships tend to have smaller genomes than there free living relatives. So what if we took a simple organism, an archea, mutate half their genes to a non ancestral sequence, and then supply all the limiting reagents needed for it to grow? This would be a man-made symbiotic relationship.Of course, at this time it may not be feasible to do such an experiment since our knowledge of the exact funtion of every gene in a particular genome is not known ( I think, though I could be wrong. Anybody know if we have this knowledge about any species?). But if we one day did this, what would we say about the entropy of the genome? Would we say it is then at its maximum an can only decrease from that point?This is a digression, though, since it is the hypothetical argument (above) which I am trying to put forth.And as a side question, are you using the Eyre-Walker as an argument against evolution, as an argument for ID, or both? The former could be attempted, but can the latter?The reason I ask is because the Eyre-Walker paper makes several assumptions regarding evolution (e.g., out-group comparison and age of chimp-human split) to come up with the number of delterious mutations (non-synonomous mutations, according to the study), so I don't see how this can be used in an argument for ID. Unless the argument is of the general form: not x, so y.This message has been edited by JustinC, 05-07-2005 01:47 AM

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There is not a whole bunch of probability in there to begin with. And if you guys should attempt to extrapolate those hotspots to the entire genome, you would be attempting to refute a major tenet of Darwinism wherein evolution happens via random mutation and selection. Would you not then be in danger of perhaps being called pseudo-scientists by your own peers? Something to think about.

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Random, in the evolutionary context, means irrespective of fitness. That is, mutations don't direct evolution, only create variation for natural selection to work on.

No,these are terms of science, Ned, not unique to me. A mechanism always produces something and that something is known and predictable:Mechanism: A particular technique or technology for delivering a function. Examples might be a telephone, a computer, or an electronic mail service. | University Information Services | Georgetown University Stochastic: Governed by the laws of probability.National Oceanography Centre, Liverpool – Error 404: Not FoundA mechanism is a well-defined process where each step of the process leads predictably to the next. A mechanism can be deterministic, in which case one step leads with certainty to the next. Or it can be stochastic, in which case one step leads with a given probability to the next.http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6...The difference between a mechanism and a stochastic mechanism is that the first is certain, the second is only probable.

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Design Dynamics

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Speaking only for myself, I bear no personal hostility toward Jerry or anyone else.

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Nor do I.

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Design Dynamics

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I'm not really concerned with the practical application, just the theoretical framework you are proposing. What is the actual relationship between functional genes and entropy according to your framework?

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I'm not sure I understand the question. Functional genes are those genes that continue to translate proteins that fulfill a need in the organism. I've never heard them expressed as extropy, but since extropy is the opposite of entropy, perhaps they could be if we don't take it too far.

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If I take a human genome (which according to you has "devolved" from an ideal ancestral state, and therefore is higher in entropy according to the equation you used) and caused a deleterious mutation in every gene, would I therefore decrease the genomes entropy?

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Hmmm....I'm getting rather suspicious that you are trying to set me up with something or another, Justin. What do you think would happen entropically if suddenly every protein in an organism no longer worked?

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Mathematically, using the formula W= (N1+N2)!/N1!N2!, we started with say 1000 genes that produced 1000 fully functional proteins. So originally our entropy is proportional to:

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W= (1000!)/(1000!)(0!)= 1

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Correct.

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Then it devolved after a couple of generations to:
W1=(1000!)/(900!)(100!) > 1

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Entropy is increasing, as you state. Next, I cause point mutations in essential DNA triplets that decrease the function of every gene in the organism. The equation becomes:
W2= (1000!)/(0!)(1000!)= 1

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So, as I caused more deleterious mutations, i.e., fudged up the original information, I caused the entropy to decrease.

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What, then, is the relationship you are trying to show between entropy and deleterious mutations? Is it that the more deleterious mutations that accumulate in a population, the entropy increases but only to a point then it begins to decrease?

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No, you keep saying this but I certainly never have. I know exactly what you are attempting here and I'm enjoying see you set it up.The entropy increases and the further we get to mutational meltdown, it begins to increase even more, arithmetically. The population then goes extinct. Remember the graph I posted?Additionally, You have completely left the second law of thermodynamics at this point and we are no longer on the same subject. The second law dictates that with spontaneous events, entropy will tend to increase. There is nothing spontaneous about your purposeful interference in the system by adding energy in the form of your actions (work) into it.Water heaters don't come to equilibrium either if we supply them a source of energy with intelligence in the form of a thermostat to reheat the water every time it starts cooling off.

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Also, I'm not sure, though I suspect you are right, when you say that no organism could live with 50 percent of genome having deleterious mutations. Maybe not on there own, but how about with some scaffolding? It's well known that organisms living in symbiotic relationships tend to have smaller genomes than there free living relatives. So what if we took a simple organism, an archea, mutate half their genes to a non ancestral sequence, and then supply all the limiting reagents needed for it to grow? This would be a man-made symbiotic relationship.

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Yes, but you are not stimulating natural conditions in order to show anything. And remember, The study was on people. You cannot go into organisms and start mutating genes where you want and it have any meaning as to what we are discussing.

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Of course, at this time it may not be feasible to do such an experiment since our knowledge of the exact funtion of every gene in a particular genome is not known ( I think, though I could be wrong. Anybody know if we have this knowledge about any species?).

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E. Coli, K-12 strain has been fully sequenced and may be one of the best understood. The link below is to the genes and amino acid sequences of the translated proteins. I find only three unknowns in a brief search of that document, don't know if that means anything or not.http://tula.cifn.unam.mx/.../files/data_from_fredlab/m52.seqYou can research it by starting here, because remember this is science, not religion.

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But if we one day did this, what would we say about the entropy of the genome? Would we say it is then at its maximum an can only decrease from that point?

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You totally lost me here. Entropy is at maximum, only when the organism is dead. That's why I posted Schrodinger's take on this.

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And as a side question, are you using the Eyre-Walker as an argument against evolution, as an argument for ID, or both? The former could be attempted, but can the latter?

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The reason I ask is because the Eyre-Walker paper makes several assumptions regarding evolution (e.g., out-group comparison and age of chimp-human split) to come up with the number of delterious mutations (non-synonomous mutations, according to the study), so I don't see how this can be used in an argument for ID. Unless the argument is of the general form: not x, so y.

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Well, let's clear up a few things here. I am an evolutionist as I support the tenets of evolution that are KNOWN in science. It's only when we get out of science and into the pseudo-science of whales morphing from wolf-like critters, people from monkeys and mammals from reptiloids that people in my proximity can begin to detect an audible gag emanating from my area.What this study shows is that macroevolution probably never occurred as we can now see what has been happening in the genome for the last six million years and there exists no evidence it has ever been any different.This also supports a tenet of ID in that we believe firmly in the second law (I know that sounds weird, but I have actually met Darwinists who don't believe in the laws of science that violate their religious beliefs) in that loose information will degrade as it is diffused over time. Exactly what the study shows happening.

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Design Dynamics

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I don't have a version of 2LOT, I use the same one everybody else does. So you really think that 2LOT does not apply to matter based on the logic that when I flip a quarter it is equiprobable to get heads or tails?

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Gee Paul, I kind of admire you because since 2LOT doesn't apply to your car, you never have to buy a new one. I do. Paint never gets old on your house so that is nice. And you will never grow old and die. Through this logic, you have found immortality!

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Sorry Jerry, perhaps in your mind recognising that an impossible event is indeed impossible is the secret of immortality. Sadly you are wrong. I don't beleive any of that.The simple point is that in the example you quoted 2 heads and 2 tails is the maximum entropy possible. Any change in the entropy MUST be a decrease.

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quote:There is no need to calculate any logarithms because all we need to do is observe that the entropy increases the closer the number of heads and the number of tails are to each other. Thus any change which makes the numbers closer will increase entropy and any change which makes them further apart will decrease it.

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I see. So the physics of Richard Feynman when he taught us that logical entropy is the way matter is arranged and: "The logarithm of that number of ways is the entropy." Are just not correct, in your opinion?

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I'm sorry that you are unable to think like a mathematician. My simple point is that to know the DIRECTION of the change on entropy it is unnecessary to calculate the MAGNITUDE of the change. It is the direction - increase or decrease - that concerns us, the magnitude is not relevant to the point under consideration. By the nature of the calculation the closer the number of heads is to the number of tails the greater the entropy. Therefore there is no need to calculate logarithms.

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So, I am generalising my previous example to cover all sequences - taking m as the number of heads and n as the number of tails. Thus if we randomly choose a coin the probability of it being a a head is m/(m + n) (m heads and m + n coins). The probability of it being a tail is n(m + n) (n tails and m + n coins).

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Nope. The probability of that one coin being a head is calculated via the formula:

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P(A) = f/n

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Where the probability (P) of an event (A) equals the number of actual events, (f) divided by all possible outcomes, (n).

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That works out to 1/2 = .5. That's where you're trying to go, you're just not quite sure how to get there.

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Well you are misusing the formula since we have no actual events.However if we have four coins, three of which show heads and one of which shows tails and we randomly select one of those coins (with equal probability) the chance that we will select a head is 3/4.
Using my formula with m = 3 and n = 1 we get a probability of:
3/(3 + 1) = 3/4.In your world apparently even if all 4 coins show tails there is a 0.5 probability that if we select one of them it will show a head. How does that work ?

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See, this is what happens when one chooses to get their science from a religionist atheist apologist site. They don't do science over there, they do secular humanist religion and CALL it science.

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This is what happens when people find out you're wrong. You start hurling false accusations.

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I did. Just read the study and you will know exactly what happens:

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http://homepages.ed.ac.uk/eang33/

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Which study ? There are none on that page and a whole list on the "Publications" page.

Fair enough, you just seemed overly dismissive of it in 'tone' and I wondered why. I don't know it depends on how we define our terms I suppose. I could say that there is no probability in horse racing. After all, if we can know all the information about any situation we can deduce who has to win. Unfortunately to do that we have to pull together an obscene amount of information, including the thoughts and memories of all the racers and the horses. In this case calculating who will win is done on probabilities based on what is known, but we cannot calculate the exact probabilities. Hence, our probabilities are unknown.Is the winner of a horse race random? Not really, its just so complicated as to be inherently unpredictable. When some thing is unpredictable the results might appear to be random, but just be due to incomplete information.DNA mutation surely comes under this definition of random? I'm sure quantum uncertainty will play its part to ensure true randomness, it will be insignificant compared with larger factors such as the presence of strong radioactive sources.Am I barking up the wrong tree here? I think what I am saying is that DNA mutation is unpredictable but its not arbitrarily random.Incidentally, I'm not trying to debate your central theme here, I'll leave that to others who understand (or not depending on opinion) the subject better than I. I appreciate that it might be that, on average, it is as good as totally random.