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ExYECer Posts: 36 Joined: May 2002 (Permalink) Posted: Jan. 12 2003,17:36    From Here Mike seems to have avoided addressing the real issues and instead focused on some minor issues. First of all Mike objects to me stating that his approach and Poole's approach led to the same conclusion. Mike correctly points out that I confused Poole's paper with the papers in which the link between cytosine deamination and increase hydrophobicity was made. While I thank Mike for correcting my minor error he seems to have ignored the real issue namely that he used methodological naturalism to explain the tendency of cytosine deamination to incrase hydrophobicity. In fact from the moment he defined the instance of 'front loading' his approach is indistinguishable from methodological naturalism. Neiter Mike nor others may have explained or shown how cytosine became incorporated but both work from the assumption that it was. Mike suggests that his approach allowed him to address the claim that 'an engineer would have replaced cytosine' but nothing in his approach supports this argument. All he has shown is that natural processes seem to have led to cytosome deamination and a corresponding increase in hydrophobicity. No effort was made to show that an engineer would or would not have used cytosine or would or would not have replaced cytosine. In fact Mike has made no effort to show any link between his findings and the idea of front loading. Looking back in time and then saying that it must have been front loaded because it seems to have been selected for is begging the question. Mike complains the evolutionary approach claims that it must have been chance/evolution but that is not very different from 'it must have been design'. Both are assumptions which would require some supporting evidence. The fact that cytosine deamination leads to increased hydrophobicity is no evidence of the premise that 'chance did it' nor 'an intelligent designer did it'. Mike wants to argue that different perspectives give different approaches but I'd argue that these approaches are not distinguishable from methodological naturalism. No teleology is required to explain what happened t>t_0 and no evidence of the need of teleology at t=t_0 has been provided. Mike does suggest that he provided a description with 'purpose' but that seems to be like painting the bulls eye around the arrow, to use a common metaphore. Mike suggests that his approach allowed him to pre-specify that deamination of cytosine increased hydrophobicity but that seems hard to imagine. The concept of evolution would also predict that if cytosine deamination were an important contributor to the increase of hydrophobicity and that if such increase would be increasing fitness that cytosine deamination events would be common. It has been argued that Mike's approach canm not been distinguished from methodological naturalism approach and that the findings do not help us answer the question of the presence of cytosine at instance t_0, the moment of front loading. Thus either chance/necessity or intelligent design may have been responsible for what happened at time t_0 but after time t_0 it was all methodological naturalism and not intelligent design. Mike suggests that since cytosine inclusion was not a frozen accident his premise may be preferable. But lets point out that Mike does not explain anything about the 'frozen design incident' thus leaving it for all practical purposes indistinguishable from a 'frozen accident'. Additionally Mike may have created a strawman of 'frozen accident' when the actual mechanisms may have been a combination of availability and selective advantages. That an engineer may exploit the same pathways that evolution may exploit also does not help us address the issue of front loading. Front loading/origins are separate from the evolution t>t_0. Mike however has not provided any evidence that the event at t=t_0 involved front loading. Mike did initially suggest that there was some problem with cytosine formation in prebiotic world which would have been a way to eliminate chance/regularity as a possibility and thus strengthening a design inference but as I have pointed out our knowledge has increased and potential and realistic pathways may have been identified. Mike seems to agree that from t=t0 forward evolution did play a role, so now the question is if t=t_0 requires an intelligent designer or preferably involved an intelligent designer. So far no evidence has been provided that this is the case. If Mike wants to limit his claims to just refuting Poole then his efforts may have helped towards this goal but then the issue of front loading seems irrelevant. But I would say that Mike has not shown how the engineer is in any way limited in what he/she would or would not do. Mike still seems to be confused when insisting that I claim that design has to be supernatural. I am pointing out that t>t_0 does not help resolving the intelligent design claim and that t=t_0 has not been addressed. You suggest that at t=t_0 some event took place without really defining the moment t=t_0, the circumstances of the event, the goals of the event. Mike merely claims that at t=t_0 there was an initial state namely cytosine was present as one of the four bases in DNA. Unless Mike wants to argue that at t=t_0 a supernatural design event took place, he has no reason to suggest that I am requiring a supernatural design. Mike now suggests that the existence of a 'sophisticated, universal genetic code' is positive evidence of a design event but Mike once again fails to show this to be the case. In fact no positive evidence of such a design event has been provide, merely claimed. But that sounds like a 'front loading of the gaps' explanation. Since Mike seems to agree that from this moment forward everything was fully explainable in natural terms, and no need for intelligent design was required he basically has used the data which supports common descent to argue for 'common design' without really explaining anything about this 'design'. Countless papers and hours of research have been involved in providing for and actually finding plausible pathways to explain the origins of the genetic code and none so far seem to have found any evidence of this intelligent design event, in fact what may have been a good point to place t_0 seems to have been pushed back over time from the Cambrian to the prebiotic RNA world. Mike wants to know what data would cause me to suspect that evolution was front loaded. This would require the following 1. Mike needs to define what the purpose or goal(s) are of the intelligent agent 2. Mike has to show that given the chaotic and unpredictable nature of the world around us, this goal can be reliably reached 3. it can be shown that natural processes without intelligent design could not have achieved the state at t=t_0 4. it can be shown that there was indeed an intelligent agent present at t=t_0. Mike objects to my scenarios of how cytosine may have become part of the genetic code as irrelevant but they are very relevant in understanding what happened at t=t_0. Mike does not seem to have any evidence of front loading at t=t_0 to required intelligent agent. Thus it is very relevant to show that the front loading at t=t_0 can be explained from a naturalistic perspective without the need for ID. At t>t_0 Mike and I seem to agree that it was purely natural processes at work without the need for intelligent design. As far as Nic's analogy, Mike may have responded but that may be far from having addressed Nic's observations. In fact I would argue that you did not even address Nic's claims. Edited by ExYECer on Jan. 12 2003,17:39

nanosoliton Posts: 11 Joined: Jan. 2003 (Permalink) Posted: Jan. 12 2003,19:55    Frances: First of all Mike objects to me stating that his approach and Poole's approach led to the same conclusion. Mike correctly points out that I confused Poole's paper with the papers in which the link between cytosine deamination and increase hydrophobicity was made. While I thank Mike for correcting my minor error he seems to have ignored the real issue namely that he used methodological naturalism to explain the tendency of cytosine deamination to incrase hydrophobicity. Nelson: In my opinion, this was a major error on your part. Poole's conclusion was: Quote "Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer." whereas Mike's conclusion was: Quote it's exactly this predisposition that might cause an engineer of evolution to include it. He then uses evidence from various studies that support a front-loading hypothesis concerning cytosine deamination, something Poole does not do in his paper. This shows that both hypothesis are extremely different. Frances: In fact from the moment he defined the instance of 'front loading' his approach is indistinguishable from methodological naturalism. Neiter Mike nor others may have explained or shown how cytosine became incorporated but both work from the assumption that it was. Nelson: The non-teleologist would say that it was the result of evolutionary tinkering, whereas a teleologist would say it was the deliberate result of intelligent design. This clearly seperates the teleological explanation from the non-teleological explanation. Frances: Mike suggests that his approach allowed him to address the claim that 'an engineer would have replaced cytosine' but nothing in his approach supports this argument. Nelson: Actually he has. The major points in his essay is the following: Quote Since hydrophobic interactions play a large role in protein folding and structure, the effects illustrated in figure 3 suggest C-T transitions may play a significant role in protein evolution. What's more, figures 5 and 6 suggest C-T transitions may also result in both alpha helix and beta sheet elongation/formation. This raises the intriguing possibility that the genetic code was not only designed to minimize deleterious mutations, but that this design objective was balanced against a seemingly contrary objective to evolve new proteins through what I will call the Increasing Hydrophobicity Effect (IHE). This might also explain why serine, rather than proline, is included in the amino acid pool generated by C-T transitions (figure 4 and the sole exception from figure 3). Serine is present as a consequence of losing proline. This substitution removes a strong helix breaker and replaces it with a residue that is indifferent to helix formation. And proline is not added to the mix so as to not increase the chances that an existing helix is broken. This point alone has profound implications for protein evolution. Quote proteins that played essential roles in the evolution of multicelluarity may have been spawned from the IHE. This scenario portrays at least some evolutionary events as an interaction between four dynamics: random mutation, mutation rigged by natural law, intelligent design, and natural selection. This hypothesis also makes a prediction that can be tested. For example, if the multicellular state was front-loaded with life's design, we would expect to find conserved, multicellular-specific proteins have crucial FLIYWVMCS residues that can explained by C-T transitions relative to their ancestral state. and finally: Quote Given that DNA can exist in a transient single-stranded state during transcription, this suggests that the IHE may also be targeted to genes that are actively transcribed. In fact, experimental evidence has shown there is a distinct bias for C-T transitions in the coding strand as a consequence of transcription. [11] Thus, a specified set of amino acids is being thrown at every transcribed gene. It's as if life's proteins are being forced to evolve. These ideas stem from the hypothesis that is the exact opposite of Poole's, namely, that a designer  would indeed incorporate cytosine despite it's predisposition for deamination. Frances: Looking back in time and then saying that it must have been front loaded because it seems to have been selected for is begging the question. Nelson: As evidenced from the above, Mike never said that it seems to have been front-loaded because it "seems to have been selected for". The counter-intuitive inclusion of cytosine, despite it's predisposition for deamination, lead him to study exactly what effects this phenonemon has, with an ID prediction in hand. If this is truly the result of intelligent design then he should find some utility for including cytosine. He found a working hypothesis that has implications for protein evolution, namely that cytosine's predisposition is used to almost "force" proteins to evolve. Frances: The fact that cytosine deamination leads to increased hydrophobicity is no evidence of the premise that 'chance did it' nor 'an intelligent designer did it'. Nelson: Poole used the fact that cytosine is predisposed to deamination to say that this is the result of evolutionary tinkering. And this would follow, since evolution has no foresight, it is no surprise that such inefficient design should be found in the genetic code. However, Mike shows C-T transition leads to increased hydrophobicity. This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure. Frances: The concept of evolution would also predict that if cytosine deamination were an important contributor to the increase of hydrophobicity and that if such increase would be increasing fitness that cytosine deamination events would be common. Nelson: Now this is what I call, painting the bullseye around the arrow. Before Mike wrote about this, no non-teleologist wrote that evolution indeed included cytosine because it would increase fitness. That sounds more teleological then non-teleolgical, evolution has no foresight and therefore, cannot include cytosine because of it's predisposition for deamination. However, an intelligent design can. Frances: Mike now suggests that the existence of a 'sophisticated, universal genetic code' is positive evidence of a design event but Mike once again fails to show this to be the case. Nelson: Mike has built the case for this in this essay here: http://idthink.net/biot/error/index.html Frances: As far as Nic's analogy, Mike may have responded but that may be far from having addressed Nic's observations. In fact I would argue that you did not even address Nic's claims. Nelson: I think that he did and here's why: Here are Nic's mistakes which Mike Gene pointed out in his own dialouge: 1. The arch is not irreducibly complex and therefore would not cause a intelligent design inference. Molecular machines of the cell are extremely different from the arch that anti-IDists like the point out. This is a simple and obvious point. Molecular machines are arrays of functional components that transform energy (or information) and use this transformation. .  In these machines, even the classical concept of diffusive motion still applies, and has been observed. 2. ID does not depend on religious interpreation nor does it need a religious interpretation. It simply detects design. 3. Shapiro claims that the genomes of organisms have a "system architecture", whereby gene expression is controlled by  "junk DNA" and states: "Natural selection following genome reorganization eliminates the misfits whose new genetic structures are non-functional. In this sense, natural selection plays an essentially negative role, as postulated by many early thinkers about evolution (e.g. 53). Once organisms with functional new genomes appear, however, natural selection may play a positive role in fine-tuning novel genetic systems by the kind of micro-evolutionary processes currently studied in the laboratory" 4. Co-option frequency, selection co-effiencients, and other details do not exist for any imaginary story given for the evolutionary origin of molecular machines, therefore, the accusation that ID is not science because it does not have the designer in the laboratory or lab notes to work from is just as detrimental to evolutionary theory. 5. "Well known processes that are currently observable" do not apply to molecular machines, which, like the flagellum, require the de novo appearance of over 20 parts. 6. Type III secretory systems most likely appeared after the flagellum.  Also, it seems that later gene transfer was the major mechanism by which type III systems appeared, leaving RM&NS with very little to do with it. 7. There is no reason why a designer would not re-use parts, or functions. -------------- Nelson Alonso

ExYECer Posts: 36 Joined: May 2002 (Permalink) Posted: Jan. 12 2003,20:54    Frances: First of all Mike objects to me stating that his approach and Poole's approach led to the same conclusion. Mike correctly points out that I confused Poole's paper with the papers in which the link between cytosine deamination and increase hydrophobicity was made. While I thank Mike for correcting my minor error he seems to have ignored the real issue namely that he used methodological naturalism to explain the tendency of cytosine deamination to incrase hydrophobicity. Nelson: In my opinion, this was a major error on your part. Poole's conclusion was: You are confusing two different issues. Mike complained that I had stated that Poole reached the same conclusion when it was in fact other researchers. Mike set off to address the claim that 'an engineer would have replace cytosine'. But he fails to show why an engineer would really do this. In fact he accepts that from the moment t=t_0, the moment of front loading, evolutionary pathways played their role. So the only difference between Mike and others is that he tries to explain the initial condition through appeal to design when others would explain the initial condition through appeal to chance/regularity. Since Mike has not taken any effort to try to show why the explanation through design explains the initial situation better than non-design and since science has already found likely pathways to explain the inclusion of cytosine in the genetic code, one may argue that not only has Mike failed to show that a designer were required but he has not even shown that an engineer would or would not have replaced cytosine. All Mike does is to show that evolution used the opportunity of cytosine, nothing more. Mike has not even shown that there was any predisposition to be expected which would require an engineer. None of the studies quoted by Mike support a front-loading scenario that would require an engineer. Frances: In fact from the moment he defined the instance of 'front loading' his approach is indistinguishable from methodological naturalism. Neiter Mike nor others may have explained or shown how cytosine became incorporated but both work from the assumption that it was. Nelson: The non-teleologist would say that it was the result of evolutionary tinkering, whereas a teleologist would say it was the deliberate result of intelligent design. This clearly seperates the teleological explanation from the non-teleological explanation. Nope, both the teleologist and non teleologist would have the same findings based on different presumptions. At instant t=t_0 cytosine was included in the genetic code. From there on evolution took over. Neither Mike nor others have shown how cytosine becoame incorportated both work from the assumption that it was. There is no additional benefit to the teleological presumption, clearly since both Mike and others have reached the same conclusion namely that cytosine deamination leads to primarily more hydrophobic aminoacids which may be helpful for stability. But stability may exactly be what is selected for so unless Mike can show that there is no natural pathway to Cytosine be included, Mike's argument has not explained anything that would one lead to conclude intelligent design. In fact one may argue that all Mike has shown is front loading, an initial condition without explaining if it was intelligent design or non-intelligent design which led to the initial condition. Frances: Mike suggests that his approach allowed him to address the claim that 'an engineer would have replaced cytosine' but nothing in his approach supports this argument. Nelson: Actually he has. The major points in his essay is the following: Quote Since hydrophobic interactions play a large role in protein folding and structure, the effects illustrated in figure 3 suggest C-T transitions may play a significant role in protein evolution. What's more, figures 5 and 6 suggest C-T transitions may also result in both alpha helix and beta sheet elongation/formation. This raises the intriguing possibility that the genetic code was not only designed to minimize deleterious mutations, but that this design objective was balanced against a seemingly contrary objective to evolve new proteins through what I will call the Increasing Hydrophobicity Effect (IHE). This might also explain why serine, rather than proline, is included in the amino acid pool generated by C-T transitions (figure 4 and the sole exception from figure 3). Serine is present as a consequence of losing proline. This substitution removes a strong helix breaker and replaces it with a residue that is indifferent to helix formation. And proline is not added to the mix so as to not increase the chances that an existing helix is broken. Nothing shows that an engineer would have replaced cytosine for this reason. Mike merely is painting a bulls eye around the arrow to explain why cytosine is present. Nothing is shown to indicate that the front loading requires an engineer and no effort is made to even propose the details of how or why the engineer took these steps. Nelson: This point alone has profound implications for protein evolution. So we do accept protein evolution after all? Nelson These ideas stem from the hypothesis that is the exact opposite of Poole's, namely, that a designer  would indeed incorporate cytosine despite it's predisposition for deamination. Front loading either teleological or non-teleological leads to the same facts. Mike wants to argue that an engineer would be required and in fact that this is what an engineer would do without showing much evidence to support this. Mike is in fact painting a bulls-eye around the arrow. Frances: Looking back in time and then saying that it must have been front loaded because it seems to have been selected for is begging the question. Nelson: As evidenced from the above, Mike never said that it seems to have been front-loaded because it "seems to have been selected for". The counter-intuitive inclusion of cytosine, despite it's predisposition for deamination, lead him to study exactly what effects this phenonemon has, with an ID prediction in hand. If this is truly the result of intelligent design then he should find some utility for including cytosine. He found a working hypothesis that has implications for protein evolution, namely that cytosine's predisposition is used to almost "force" proteins to evolve. Counter intuitive from a design perspective not necessarily from an evolutionary perspective. Others have taken the evolutionary perspective and reached the same conclusions that Mike has reached, cytosine deamination leads to primarily more hydrophobic 'codons'. Hydrophobic codons tend to be more stable. Nothing requires the addition of 'an engineer' Frances: The fact that cytosine deamination leads to increased hydrophobicity is no evidence of the premise that 'chance did it' nor 'an intelligent designer did it'. Nelson: Poole used the fact that cytosine is predisposed to deamination to say that this is the result of evolutionary tinkering. And this would follow, since evolution has no foresight, it is no surprise that such inefficient design should be found in the genetic code. However, Mike shows C-T transition leads to increased hydrophobicity. This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure. Could you show where pool made this claim? Showing utility is hardly sufficient to show evidence against evolution and for design. Frances: The concept of evolution would also predict that if cytosine deamination were an important contributor to the increase of hydrophobicity and that if such increase would be increasing fitness that cytosine deamination events would be common. Nelson: Now this is what I call, painting the bullseye around the arrow. Before Mike wrote about this, no non-teleologist wrote that evolution indeed included cytosine because it would increase fitness. That sounds more teleological then non-teleolgical, evolution has no foresight and therefore, cannot include cytosine because of it's predisposition for deamination. However, an intelligent design can. It should be helpful if nelson were to familiarize himself with the arguments and available research before making such strawmen claims. I am not saying that cytosine was included because it had foresight I stated that if cytosine were included that evolution explains the rest of the story, as does Mike. The only difference is the reason for inclusion of cytosine. Mike argues that it was done by an intelligent designer, I argue that it was because it has been shown that cytosine, while not optimal, may have been the only available chemical. As Joyce has shown cytosine does seem to increase the fitness despite the impact of cytosine deamination. Frances: Mike now suggests that the existence of a 'sophisticated, universal genetic code' is positive evidence of a design event but Mike once again fails to show this to be the case. Nelson: Mike has built the case for this in this essay here: http://idthink.net/biot/error/index.html Not really. He merely paints a bullseye around a target while ignoring the available evidence. Mike makes no effort to explain why the front loading has to be intelligent At most Mike argues that Quote One way to distinguish an intelligent designer over natural selection is that the former has foresight, while the latter is myopic, working only on immediate benefits. While the argument is fuzzy, it would seem that the error correction capabilities, inherent in the DNA chemistry (and perhaps the genetic code) appear to reflect foresight, when such capabilities would become essential in the high-information state life forms that would exist hundreds of millions of years after the putative simple replicators. But appearance is not evidence. But I find his parting comment to be ironic since he also argues that early in the origins of life, cytosine was added to help increase the mutation rate of DNA. Quote One thing seems clear. Very early on, life became obsessed with error correction. The chemistry of DNA/RNA, the Genetic Code, and the proof-reading mechanisms behind information transfer are all biological universals. Apparently, one of the first "objectives" of evolution was to put a layer of constraints on evolution. What is it? Does a designer place restrictions on evolution or actually losens restrictions on evolution. Or are we perhaps talking about two uninformed designers? Or perhaps more? Edited by ExYECer on Jan. 12 2003,20:58

JxD Posts: 16 Joined: Dec. 2002 (Permalink) Posted: Jan. 12 2003,22:05    I am confused by the nature of this dialogue.  Why is Nelson here in place of Mike Gene to defend, uh, Mike Gene's thesis?  I am extremely disappointed by Nelson's sweeping claims in his essays, which come often without much support except for arguments from authority (i.e. Mike Gene).  Let us consider a few of them: 1. Quote The non-teleologist would say that it was the result of evolutionary tinkering, whereas a teleologist would say it was the deliberate result of intelligent design. This clearly seperates the teleological explanation from the non-teleological explanation.  Who is a "non-teleologist?"  Nelson has not even been established that modern biology is devoid of teleological notions.  For instance, is "natural selection" a non-teleological concept?  Perhaps one of the philosophers here can enlighten me on the demarcation that is so clear to Nelson.  I had a quick read of this link, and found this quote: Quote Other forms of teleonaturalism regard the teleological aspects of biology as unique and ineliminable. One class of such views maintains that teleological claims in biology depend on natural values that apply to biological entities (such as what is good for an organism or species). A different approach, that avoids normative notions, is to define biological teleology explicitly in terms of natural selection and the theory of evolution. Several theorists have argued for the pluralistic idea that biology may incorporate two notions of function, one to explain the presence of traits and the other to explain how those traits contribute to the complex capacities of organisms. Others have argued that these two apparently distinct notions of function can be unified by regarding the target of explanation as the biological fitness of a whole organism. Nonetheless, the mainstream view among philosophers of biology is that natural selection accounts best explain the majority of uses of teleological notions in biology.  It seems to me that there is more to such a simple categorization of 'teleological/non-teleological' than is suggested here. 2. Quote This point alone has profound implications for protein evolution. Between quoting verbatim some source that Nelson is purporting to elucidate and writing down substanceless replies, the point, in my opinion, is lost.  He claims that there are "profound implications" but then follows that with speculative arguments that deal vaguely with the possibility of "multicelluarity" being evolved with "IHE." I find this particular conclusion to be rather nebulous: "It's as if life's proteins are being forced to evolve."  How is that conclusion any different empirically from, "It's as if life's proteins are evolving"?  I agree with Frances here, in that the counter-argument to a notion that "any engineer" would have replaced cytosine has been fairly weak.  I will explain below. 3. Quote And this would follow, since evolution has no foresight, it is no surprise that such inefficient design should be found in the genetic code. However, Mike shows C-T transition leads to increased hydrophobicity. This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure.  This is an unsubstantiated claim, and more than likely false without further qualifications or support.  In point of fact, in the other thread, I have pointed to various other factors that are also significant determinants of protein folding. 4. Quote Now this is what I call, painting the bullseye around the arrow. Before Mike wrote about this, no non-teleologist wrote that evolution indeed included cytosine because it would increase fitness. That sounds more teleological then non-teleolgical, evolution has no foresight and therefore, cannot include cytosine because of it's predisposition for deamination. However, an intelligent design can. [...] There is no reason why a designer would not re-use parts, or functions. Why is "tinkering" (to use Poole's words) non-teleological?  Again, this seems to me to be a false demarcation.  But, I agree with your very last sentence that an IDer can "include cytosine because of it's predisposition for deamination."  Of course, the point is that ID, as you have presented it, can explain anything.  Notice that Poole made his assertion from his experience with engineers -- presumably human engineers.  It is arguably true that no human engineer would have incorporate such an unstable element in their designs.  But, let's count what else the IDer would have to know beforehand, if Mike Gene's hypothesis is true.  i) He would've had to know that merely increasing hydrophobicity would be sufficient to evolve prepackaged states.  Otherwise, the utility of cytosine seems to be diminished significantly.  ii) He would've had to forecast which key cytosine deaminations would lead with near certainty to the desired end states.  Otherwise, gambling on the right C->U transitions from all possible ones seems to me rather "non-teleological."  iii) He would've had to include sufficient feedback (either by front-loading the cell, or by evolving just in time) to prevent some kind of hydrophobic catastrophe.  But, then after we have addressed all these additional knowledge/foresight that the designer required, it becomes clear that Poole was right after all.  No human engineer would design with such uncertainty and abandon.  Of course, one can always posit that the IDer put in place the necessary subsystems to address these concerns... Frances is right again.  As more ad hoc reasoning is employed in the scenario above, it seems to me that you are the one that is painting bullseyes around the arrow.

ExYECer Posts: 36 Joined: May 2002 (Permalink) Posted: Jan. 12 2003,23:59    JxD: I am confused by the nature of this dialogue.  Why is Nelson here in place of Mike Gene to defend, uh, Mike Gene's thesis?  I am extremely disappointed by Nelson's sweeping claims in his essays, which come often without much support except for arguments from authority (i.e. Mike Gene).  Let us consider a few of them: I am also disappointed with Nelson's sweeping claims, this is not the only thread in which Nelson makes sweeping claims and rejects evidence for evolution out of hand. The reason I posted the thread here is as an archive for material posted at ISCID since the moderator has been known to delete my postings.

ExYECer Posts: 36 Joined: May 2002 (Permalink) Posted: Jan. 13 2003,11:33    Moderator, You seem to be confusing me pointing out that Mike's approach is nothing different from what science would do namely methodological naturalism to show that for instance cytosine deamination leads to preferentially hydrophobic coding codons. I am not 'defending. methodological naturalism, since it quite obviously needs no defending. If Mike wants to argue that his argument of 'front loading' gives some utility then I agree but in the end both the presumption of a utility preloading or a natural preloading leads to the same finding about cytosine deamination. But Mike went beyond the claim of utility to state that he set out to show why an engineer would use cytosine. His argument however seems to amount to painting the bullseye around the arrow. I am more than happy to accept that there was a different starting point between Mike and scientific researchers into cytosine deamination but I am merely pointing out that the starting point does not seem to make much difference to the final conclusion. His framework is indeed completely naturalistic for t>t_0 with one minor variation. At a certain instance t=t_0 there is an initial condition which Mike considers to be designed and science considers to be due to regularity/chance. But the impact of this assumption on the scientific method to determine the impact of the initial conditions uses purely methodological naturalistic approaches. In fact Mike himself has stated that at t>t_0 all the processes are natural. I am sorry to hear that you believe that these are pre-canned arguments since I have not really dealt with front loading in this detail before other than pointing out Murray's compelling arguments. One may not like the direction the conclusions of this thread seem to have taken but is that not the intention of this forum? Btw I find your statements to be hovering on argument ad hominem, moderator or not. And since you raised them in public rather than in private I feel compelled to defend myself. Unless you want to open up a discussion which seems to be contrary to the spirit of this forum I suggest that you contact me in the future via private messaging. Edited by ExYECer on Jan. 13 2003,11:35

nanosoliton Posts: 11 Joined: Jan. 2003 (Permalink) Posted: Jan. 13 2003,20:55    JXD: I am confused by the nature of this dialogue.  Why is Nelson here in place of Mike Gene to defend, uh, Mike Gene's thesis?  I am extremely disappointed by Nelson's sweeping claims in his essays, which come often without much support except for arguments from authority (i.e. Mike Gene). Nelson: Actually I usually defend most ID theorists and their thesis in many forums. I don't see a problem with this, do you? Secondly, I do not use Mike Gene's statements as "authority", I discuss the data and go through great pains to put it in my own words so that I can defend them. In fact, I do this with Dembski's, Behe's, and sometimes even Wells' arguments as well. JXD: Who is a "non-teleologist?"  Nelson has not even been established that modern biology is devoid of teleological notions.  For instance, is "natural selection" a non-teleological concept?  Perhaps one of the philosophers here can enlighten me on the demarcation that is so clear to Nelson. Nelson: Eh? JXD must have not read my posts in this thread. What I was referring to here was Poole's statement: Quote "Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer." This is indeed a non-teleological statement countered by Mike Gene's hypothesis, which is clearly the exact opposite, that an engineer would in fact use cytosine because of it's predisposition for deanimation. What that article you linked it states: Quote Opinions divide over whether Darwin's theory of evolution provides a means of eliminating teleology from biology, or whether it provides a naturalistic account of the role of teleological notions in the science. Many contemporary biologists and philosophers of biology believe that teleological notions are a distinctive and ineliminable feature of biological explanations but that it is possible to provide a naturalistic account of their role that avoids the concerns above. Terminological issues sometimes serve to obscure some widely-accepted distinctions. I contend that Darwinian evolution fails to eliminate teleological notions because I think there is design in biology, not apparent. JXD: Between quoting verbatim some source that Nelson is purporting to elucidate and writing down substanceless replies, the point, in my opinion, is lost.   Nelson: Please be specific. What source am I quoting verbatim? Which reply is substanceless? I'll be waiting. JXD: He claims that there are "profound implications" but then follows that with speculative arguments that deal vaguely with the possibility of "multicelluarity" being evolved with "IHE." I find this particular conclusion to be rather nebulous: "It's as if life's proteins are being forced to evolve."  How is that conclusion any different empirically from, "It's as if life's proteins are evolving"?  I agree with Frances here, in that the counter-argument to a notion that "any engineer" would have replaced cytosine has been fairly weak.  I will explain below. Nelson: JXD writes this and then accuses me of writing substanceless replies. I find that almost laughable. How is it vague? The evidence that was discussed at ISCID that lead to the observation that it seems as though proteins are being posed to evolve is based on this paper: A. Beletskii and Ashok S. Bhagwat. 1996. Transcription-induced mutations: Increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. PNAS. 93: 13919-13924 Deamination of cytosines in DNA is caused by DNA transactions that also cause single stranded DNA. I wrote: And this would follow, since evolution has no foresight, it is no surprise that such inefficient design should be found in the genetic code. However, Mike shows C-T transition leads to increased hydrophobicity. This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure.   JXD replied: This is an unsubstantiated claim, and more than likely false without further qualifications or support.  In point of fact, in the other thread, I have pointed to various other factors that are also significant determinants of protein folding. Nelson: I find this quite telling. Actually, hydrophobicity is the key element in protein design. This has been shown experimentally and was expressed 40 years ago by chemist Walter Kauzmann. W. Kauzmann, Adv. Protein Chem. 14, 1 (1959). Secondly, that other factors are also signifcant determinants of protein folding is irrelevant.  The fact remains that a key element for protein folding and structure is hydrophobocity. JXD: Why is "tinkering" (to use Poole's words) non-teleological?  Again, this seems to me to be a false demarcation.   Nelson: Non-teleological inferences are mechanistic. Whereas teleological inferences express that intelligence is not reducible to mechanism. External teleology is very different from Darwinian thinking. telology. For example, teleology would hold that a car was consciously intended by some agent. JXD: But, I agree with your very last sentence that an IDer can "include cytosine because of it's predisposition for deamination."  Of course, the point is that ID, as you have presented it, can explain anything. Nelson: This is contradicted by Poole's very own statement, that an intelligent engineer would not have used cytosine because it can lead very easily to errors. Intelligent design cannot "explain anything", at least not empirically. I do not say that hemoglobin was designed, just as I would not say that an amorphous cloud in the sky was designed by an air plane, as opposed to the one that says "Happy Birthday".   JXD: Notice that Poole made his assertion from his experience with engineers -- presumably human engineers.  It is arguably true that no human engineer would have incorporate such an unstable element in their designs.   Nelson: There is no mention of "human" engineers. Poole was obviously referring to a rational agent. JXD: But, let's count what else the IDer would have to know beforehand, if Mike Gene's hypothesis is true.  i) He would've had to know that merely increasing hydrophobicity would be sufficient to evolve prepackaged states.  Otherwise, the utility of cytosine seems to be diminished significantly. Nelson: I don't see how the first sentence in (i) follows to the next sentence. The hypothesis states that C-T transitions increase hydrophobicity, removes proline, and  replaces it with helix and beta-strand formers. I would say that the utility for protein evolution was quite known by the designer JXD: ii) He would've had to forecast which key cytosine deaminations would lead with near certainty to the desired end states.  Otherwise, gambling on the right C->U transitions from all possible ones seems to me rather "non-teleological." Nelson: It's C->T transitions, not C->U. As the author of the genetic code, and error corrections within it, it is logical to infer that the designer knew what he was doing. JXD: iii) He would've had to include sufficient feedback (either by front-loading the cell, or by evolving just in time) to prevent some kind of hydrophobic catastrophe. Nelson: What is a "hydrophobic catastrophe"? JXD: But, then after we have addressed all these additional knowledge/foresight that the designer required, it becomes clear that Poole was right after all.  No human engineer would design with such uncertainty and abandon.   Nelson: I don't see how this is established, if including cytosine turns out to be efficient and effective for protein evolution then a good hypothesis is that an engineer would include it. JXD: Of course, one can always posit that the IDer put in place the necessary subsystems to address these concerns... Frances is right again.  As more ad hoc reasoning is employed in the scenario above, it seems to me that you are the one that is painting bullseyes around the arrow. Nelson: Poole states that an engineer would not have used cytosine because it leads to errors. If what you say above is valid, then your criticisms apply to Poole's hypothesis as well. Sorry, you can't have your cake and eat it too. -------------- Nelson Alonso

JxD Posts: 16 Joined: Dec. 2002 (Permalink) Posted: Jan. 13 2003,22:02    Quote Actually I usually defend most ID theorists and their thesis in many forums. I don't see a problem with this, do you? Secondly, I do not use Mike Gene's statements as "authority", I discuss the data and go through great pains to put it in my own words so that I can defend them. In fact, I do this with Dembski's, Behe's, and sometimes even Wells' arguments as well.  Any reader can judge for themselves the amount of parrotting that is done by you.  The problem, imo, is not so much defending concepts put forth by other authors.  Rather, you have gone so far as to use the same arguments, the same primary sources, and the same phraseology as Mike Gene, that I wonder why I should not be debating him instead.  In my view, your effort demonstrates how stale ID is in producing research, and how unoriginal and uncreative its proponents are, that arguments have to be thus recycled.  But, no, I honestly do not see a problem with this conclusion. Quote "Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer." This is indeed a non-teleological statement countered by Mike Gene's hypothesis, which is clearly the exact opposite, that an engineer would in fact use cytosine because of it's predisposition for deanimation.  No, Nelson.  This is an unsubstantiated claim.  You have failed to make your case that a tinkerer is an inherently nonteleological conception.  In fact, engineers do plenty of tinkering too.  The only distinction that Poole draws is between a "tinkerer" and "an engineer."  The fact that C->U events are stochastic suggests that  evolution is making of use "tinkering" strategies.   Quote "Opinions divide over whether Darwin's theory of evolution provides a means of eliminating teleology from biology, or whether it provides a naturalistic account of the role of teleological notions in the science. Many contemporary biologists and philosophers of biology believe that teleological notions are a distinctive and ineliminable feature of biological explanations but that it is possible to provide a naturalistic account of their role that avoids the concerns above. Terminological issues sometimes serve to obscure some widely-accepted distinctions." I contend that Darwinian evolution fails to eliminate teleological notions because I think there is design in biology, not apparent.  LOL.  Nelson, re-read the quote above: "Many contemporary biologist and philsophers ... believe that teleological notions are ... ineliminable feature of biological explanations.  Thank you for reiterating my point, that Darwinian evolution is perfectly compatible with teleological notions. Quote Deamination of cytosines in DNA is caused by DNA transactions that also cause single stranded DNA.  DNA transactions?? causing single stranded DNA?? Quote And this would follow, since evolution has no foresight, it is no surprise that such inefficient design should be found in the genetic code. However, Mike shows C-T transition leads to increased hydrophobicity. This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure.  [...] I find this quite telling. Actually, hydrophobicity is the key element in protein design. This has been shown experimentally and was expressed 40 years ago by chemist Walter Kauzmann. W. Kauzmann, Adv. Protein Chem. 14, 1 (1959). Secondly, that other factors are also signifcant determinants of protein folding is irrelevant.  The fact remains that a key element for protein folding and structure is hydrophobocity.  Moving the goal post from "the dominant force" to "a key element."  Actually, it is interesting that you quote-mined from this site: http://www.aps.org/BAPSMAR98/vpr/layg10-1.html ... because it goes on to say: Quote Forty years ago, Princeton chemist Walter Kauzmann identified hydrophobic interactions as a primary source of protein stability [2].  [...] In subsequent years, with more and more x-ray-determined structures solved, it sometimes appears that other factors are at work besides the hydrophobic interaction as imagined by Kauzman. There seems to be little doubt that hydrophobic effects play an important role in protein structure, and in related phenomena. Basic theory for understanding such effects, and the extent to which they affect protein structure, however, has proved elusive. In his paper delivered at the March Meeting of the American Physical Society, David Chandler argues that at least part of the problem is an issue of length scales. In work carried out with Ka Lum, his student at the University of California, Berkeley, Chandler shows that under the right conditions, hydrophobicity of the traditional Kauzmann sort can appear, but only for extended oily surfaces in water. When surfaces are too small (or the concentration of oil too low), the energetic cost is insufficient to cause segregation. Instead, a different hydrophobic interaction occurs, one that acts only weakly and on only small length scales. Weak short-ranged hydrophobic effects have been understood for about twenty years, on the basis of a theory developed by Lawrence Pratt and David Chandler [3]. That theory, and its contemporary variant [4] are based on the idea that because mutual attractions between water are so favorable, water-water attractions will persist even in the presence of oily species. The bonding will simply go around the oily groups. For this picture to be geometrically plausible, the concentration or size of oily species must be small. Hydrogen bonds cannot go around a sufficiently extended oily surface. The nature of hydrophobicity changes when the spatial extent of oily surfaces leads to a depletion of hydrogen bonds. It is this energetic effect, the loss of hydrogen bonding, that leads to the segregation of oil from water. This consequence of depletion was anticipated long ago by Lucent Technologies theorist Frank Stillinger [5]. The quantitative analysis put forward by Chandler and Lum exploits a statistical mechanical theory of non-uniform fluids recently developed by John Weeks and his students at the University of Maryland. Weeks' theory compactly describes drying transitions in terms of an unbalancing force [6]. Chandler and Lum view the depletion of hydrogen bonding near extended oily surfaces in terms of this force. The principal conclusions of their analysis: A cluster of oily groups 0.8 nm in radius is sufficiently large to induce depletion and drying, or the expulsion of water molecules. The depletion will induce effective attractions between oily surfaces that are relatively far apart, distances as large as nanometers or more. Many of the effects that are explained by this analysis have been observed experimentally with studies of forces between macroscopic surfaces in water [7]. Quantitative implications for the folding of proteins remain to be explored. Chandler notes, however, that current theoretical models for protein folding [8] have not yet accounted for the multifaceted nature of hydrophobicity. [References included in website] Quote Non-teleological inferences are mechanistic. Whereas teleological inferences express that intelligence is not reducible to mechanism. External teleology is very different from Darwinian thinking. telology. For example, teleology would hold that a car was consciously intended by some agent. So then you admit that the distinction is not non-teleology v. teleology, but "external" teleology and "intrinsic" teleology?  This imo seems to be the key difference.  Your version of ID explicity requires a particular type of agency: one that is unexplainable by naturalistic mechanisms.  First, this qualification by itself seems to suggest supernaturalist agency.  After all, you are describing an "intelligence ... not reducible to mechanism."  Second, it seems to me that it is this extra-biotic agency that is doing all of the "designing."  But, then, given these two observations, it follows that the utility of ID, at least your version of it, is heavily dependent on demonstrating the actual existence of such an agency.  To date, I have seen none. Quote Intelligent design cannot "explain anything", at least not empirically. I do not say that hemoglobin was designed, just as I would not say that an amorphous cloud in the sky was designed by an air plane, as opposed to the one that says "Happy Birthday". That you do not explain something as designed means nothing logically.  Consistent with intelligent design, you are making an argument by inducing from a negative experiment. Quote There is no mention of "human" engineers. Poole was obviously referring to a rational agent.  Tell me, Nelson.  What other types of "engineers" do you think the good Dr. Poole is aware of, besides human ones? Quote The hypothesis states that C-T transitions increase hydrophobicity, removes proline, and  replaces it with helix and beta-strand formers. I would say that the utility for protein evolution was quite known by the designer. [...] As the author of the genetic code, and error corrections within it, it is logical to infer that the designer knew what he was doing.  These statement of yours prove my point, that the designer can do just about anything.  Your faith in its abilities is rather profound. Quote I don't see how this is established, if including cytosine turns out to be efficient and effective for protein evolution then a good hypothesis is that an engineer would include it. That "cytosine turns out to be efficient and effective for protein evolution" is your unproven hypothesis.  But your hypothesis depends on your premise that "a good engineer" exists and did use it.  But that depends on cytosine being "efficient and effective for protein evolution."  But that depends on ...  etc. ad nauseam.

JxD Posts: 16 Joined: Dec. 2002 (Permalink) Posted: Jan. 13 2003,22:05    [double post]

nanosoliton Posts: 11 Joined: Jan. 2003 (Permalink) Posted: Jan. 13 2003,22:38    Quote-mined , oh geez. I'm going to offer a full response to this post a little later but I wanted to point out that  notion that I am "moving the goal post" is laughable. My use of "key-element" and important role, and dominant force are equivalent. By the way, your bolded quote doesn't contradict the notion that hydrophobocity is important in protein folding and structure. I didn't "quote mine" from that site, but I noticed that you have no idea what it says anyway, since the site reiterates my point: Quote There seems to be little doubt that hydrophobic effects play an important role in protein structure, and in related phenomena. I wonder why JXD didn't bold this part? Could it be that it actually supports my post? That other factors are included is irrelevant. More later. -------------- Nelson Alonso

JxD Posts: 16 Joined: Dec. 2002 (Permalink) Posted: Jan. 13 2003,23:06    Quote "There seems to be little doubt that hydrophobic effects play an important role in protein structure, and in related phenomena." I wonder why JXD didn't bold this part?  Just for you Nelson: Quote There seems to be little doubt that hydrophobic effects play an important role in protein structure, and in related phenomena. But, let's consider what Nelson is really claiming: Quote This has utility, since the hydrophobicity is the dominant force in stabilizing a folded structure. Now, let's look at the meaning of dominant, from m-w.com: Quote 1 : commanding, controlling, or prevailing over all others 2 : overlooking and commanding from a superior position  I ask the readers: has Nelson demonstrated to you that hydrophobic effects are "commanding, controlling, or prevailing over all [other]" protein interactions that are also "important" and "key" determinants of protein structure?  But, semantic games aside, I do not want to distract from the main challenge that I issued in the other thread: Quote Nelson: So C-T transitions are used to evolve new proteins.   OK.  But so are all other types of mutations.  A major assumption made in your argument is that, of the changing properties in amino acids resulting from C-T transitions, the differences in hydrophobicity dominate over, say, steric effects and other structural characteristics with regards to overall protein structure.  Otherwise, it does not seem to me that you can say C-T transitions affect evolutionary pathways through a particular mechanism (i.e. changes in hydrophobicity), especially in a manner that suggests intelligent foresight.  However, consider for instance Arg (CG_) -> Cys (UG_) changes.  Is the potential of the new Cys in forming new disulfide bonds with other Cys residues necessarily a negligible effect when compared to the changes in hydrophobicity?  The problem here is that you have greatly oversimplified the mechanisms underlying the propensities for alpha and beta chain formation.  A single residue and its specific properties do not by themselves determine peptide folding. This challenge seems to go straight to the issue here.  In fact, I repeated pretty much the same concerns here: Quote i) He would've had to know that merely increasing hydrophobicity would be sufficient to evolve prepackaged states.  Otherwise, the utility of cytosine seems to be diminished significantly.  ii) He would've had to forecast which key cytosine deaminations would lead with near certainty to the desired end states.  Otherwise, gambling on the right C->U mutations from all possible ones seems to me rather "non-teleological."  iii) He would've had to include sufficient feedback (either by front-loading the cell, or by evolving just in time) to prevent some kind of hydrophobic catastrophe.    In other words, so what that hydrophobicity increases?  If there are in fact other determinants of protein structure, then it is short-sighted of a designer to consider only the IHE at the expense of all the other possible effects that may affect protein structure.  I issued another challenge that was also not answered.  If hydrophobicity had to be "evolved" from some front-loaded state, then did the initial cell have no membrane-bound proteins?  no ion channels?  no receptors?  So many unaswered questions.  But to quote Nelson: Quote it is logical to infer that the designer knew what he was doing.  All of the sudden, the questions are answered! On the other hand, I'd love to give Nelson the benefit of the doubt that he did not quote mine from the source above.  Let's consider the coincidences: Quote Nelson: Actually, hydrophobicity is the key element in protein design. This has been shown experimentally and was expressed 40 years ago by chemist Walter Kauzmann. W. Kauzmann, Adv. Protein Chem. 14, 1 (1959).  And then let's look at the site. Quote Forty years ago, Princeton chemist Walter Kauzmann identified hydrophobic interactions as a primary source of protein stability [2].   Quote W. Kauzmann, Adv. Protein Chem. 14, 1 (1959).  Gee.  Even the punctuations and spaces in the citations match exactly... as well as the missing article title.  I wonder what Dembski's explanatory filter would say about the coincidences here.

ExYECer Posts: 36 Joined: May 2002 (Permalink) Posted: Jan. 15 2003,22:39    Nelson on ARN claims that Quote Nelson: I don't see how this is irrelevant. A reverse transcriptase is a special form of polymerase enzyme that uses an RNA template to make a DNA strand, whereas telomerase is an enzyme which functions to recognize the tip of a G-rich strand of an existing telomere DNA repeat sequence and elongates it in the 5'-to-3' direction, and is unique in that it carries it's own RNA template at all times. Source This sounded a bit too non-Nelson to me and I checked and guess what? See This link " reverse transcriptase is a special form of polymerase enzyme that uses an RNA template to make a DNA strand" Chapter 5, page 264 Figure 5-42 "A reverse transcriptase is a special form of polymerase enzyme that uses an RNA template to make a DNA strand;" and "Telomerase recognizes the tip of a G-rich strand of an existing telomere DNA repeat sequence and elongates it in the 5¢-to-3¢ direction. " and "The telomerase is protein–RNA complex that carries RNA template for synthesizing a repeating, G-rich telomere DNA sequence. Only the part of the telomerase protein homologous to reverse" Maybe someone may want to calculate the likelihood of coincidence

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