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Everything posted by cypress

  1. cypress

    Gene Limit

    In other words there is indeed a relationship as I said but that relationship is not one to one at any particular time or for any particular cell. Yes, I am also aware of that reality. Again I appreciate your desire to be precise and to ensure that I understand.
  2. I don't understand what you are asking for then. In the Lenski research the ecoli which is able to metabolize citrate in anaerobic conditions underwent a two or three step mutation and was able to metabolize free citrate in an oxygen rich environment. It was a modification of existing function due to a change in expression controls. Is this not a substantive change that was selectable? If it was then my definition seems to be consistent.
  3. Then you don't believe chance alone was involved and you would be hard pressed to make a case that the argument is fallacious because you reject the premise of chance alone. I don't see any reason to argue a point you don't accept in the first place. Hoyle's analysis applies to those who falsely stipulate chance alone. No you reject the chance only hypothesis. my statement on an appeal to ignorance applies to those who pitch the chance only hypothesis. I find this argument to be very weak. One can use almost anyheavy solid that is denser than water for a boat anchor. Molecular biology confirms that the great majority of functional proteins are components of five or more multiprotein systems. Cherry picking exceptions does not impress me. I appreciate that you seem to be retracting your earlier implied argument about chance systems (where you took exception to Hoyle's indictment against chance alone) and have made clear you are with the rest of us who, like Hoyle reject that chance alone might have generated life from non-life.
  4. Skeptic asked the same question and I answered it several posts ago. Substantive changes are function and form modifications and new function or form subcompontents that were incorporated into the entire population. this disposes of ChardonY's 2nd point. I am also speaking of population effects which disposes of the first point. The third point does not explain or demonstrate how natural processes actually derive digitaly encoded functional information faster than a blind search so it is irrelevant either way. Marat's argument is interesting but it is a just so narrative without a causally adequate process and is as meaninless as pure speculation. Could haves and would haves, ifs and ands.
  5. Sure but the analysis already accounted for that. My previous description skipped past the math and took shortcuts and simplified and estimated to avoid what I considered too much detail to make the post more brief. Perhaps we will need to go into the details. If so I will start a new thread on this too. As I have previously acknowledged, we do not lack examples of mutation generating function in one to three steps which is in the realm of what a blind search can accomplish, what we lack are actual examples of the multistep evolutionary pathways the theory predicts exist. Whether I object or not is not the issue. Nor does it matter what I agree. The issue is that when experiments are conducted and numbers are run, known and observed natural processes including evolutionary processes simply do not generate this kind of information at a rate consistent with observed diversity and estimated geologic time. This is a fact that cannot be hidden in back of side issues.
  6. This is a different issue I think. You suggest that Hoyle's analysis is faulty simply because it uses analogous biological structures instead of actual ones because we lack the data required to use the structures that actually were involved in generation of the first biologically active self-generating system. Scientists use analogies all the time. Should we dismiss them because some people don't care for the analogies? It illustrates the point and it addresses one proposed mechanism directly. If you have a better set of components to illustrate the issue than the minimal set of proteins, lets have them. While we are at it, let's make sure you are actually arguing a counter point rather than making an appeal to ignorance. Do you claim that there is a reasonable probability that life arose from non-life by random chemic processes alone?
  7. The vacuole membrane is also denatured by methanol and this makes sense since the vacuole holds waste products and thus the mechanisms across the two membranes should be similar and affected by the same chemicals.
  8. I don't know of any informed individual who makes the suggestion that life as we know it appeared suddenly by chance. I do know of many who suggest that random processes generated the first biologically active system we would describe as life-like and it is this suggestion I and the names I provided dismiss. An interesting aspect of proteins is that generally the primary sequence does not determine function, what generally does determine function is the shape and chemical and spacial affinities of key active areas (binding sites) of the protein.
  9. They survived along with the other variations and became diluted in the population unless purposely isolated. Hardly the model that is described by the theory. But even if I were to accept all 20 as examples of selective advantage the 5+ order of magnitude gap has closed by less than two orders of magnitude so we are arguing over an insignificant difference. I don't discount the variation, since any change in mutation rate in the lab experiments figure into the results, that factor has been included. Your hypothesis is far more than "mutation rates change though, yours is that higher mutation rates in the past account for the observed gap. Significantly greater mutation rates (the several orders of magnitude needed) won't help anyway. By Genetic population models, as you significantly increase the mutation rate the number of catastrophic mutations overlap with any neutral and beneficial mutations so that any pathway that otherwise would emerge is cut off. Besides if significant changes in mutation rates were observed and were advantageous then Lenski's research would not be the one we used as an example as that research would show better results. Your claim that mutation rates in the past could account for the gap not only seems theoretically incorrect, it does not seem to be testable. My hypothesis is testable. It is that we observe that biological systems contain large amounts of digitally encoded functional information. We also observe that mind/intelligence is the only causal entity that generates large amounts of this kind of information. Therefore an agent with a mind/intelligence likely generated life. We test this by conducting experiments to see if natural processes do generate this kind of information and we observe genetic engineers closing in on the task of generating new life forms by design. My hypothesis does not make any appeal to an omniscient god. However this is evidence that suggests. No it's not the key. Regardless of how we define terms, observed evolutionary processes simply do not generate large amounts of digitally encoded functional information any faster than a blind search. Artificial selection (captive breeding) does however, but even it seems to have limits. Only genetic engineering is known to bridge the gap. We can sit here and quibble about the finer points but none of it will change the outcome.
  10. cypress

    Gene Limit

    There is a relationship between gene count contained in an organisms genome and the quantity of genes expressed, and I understand the distinction. Thanks for your concern.
  11. Good in the sense that alternative estimates are not clearly better. P.T. Mora a Research Biologist at the National Institute of Health provided a critique of the chance hypothesis for life from non-life back in the early sixties in published in Nature. That assessment was very similar to Hoyle's. In addition Robert Shapiro and Francis Crick accepted the probability of life by chance was effectively nill also. I find that those who suggest that life arose from non-life by chance are simply concealing an appeal to ignorance in a chance wrapper. If you believe I am wrong about this, by all means suggest a different number a we can discuss the relative merits. Given the relative rarity of functional proteins, I would expect that very few of the genes in artificial life will be unique. I would expect that most will be reused from the pool of known and functional proteins.
  12. They were under selection pressure with oversupply of citrate in an oxygenated environment and limiting supplies of nutrients readily metabolized. Speculation. Ifs and ands, but hardly scientific. Estimates are fine but only one is documented by the normal measure what the theory of natural selection predicts, and that is the ability to outperform and out-reproduce relative to the others. The model for evolutionary algorithms is always to kill off the weakest for a reason. Only the one alteration significantly outperformed the others. The rest of these changes did not outperform the rest of the population. Sorry, it is not proper to move the goal post. I repeat, just one significant alteration. Science requires citation to processes currently in operation. We observe a narrow range of mutation rates today, anything different than that is speculation. If speculation is allowed in this debate then let's also allow the creationists their speculations. There are several estimates based on extensive study of differences between modern humans and modern primates. There are hundreds of millions of point level differences and even a few thousand unique gene sequences. Is it hard to believe the estimate? It may take me a few hours to find this the source material and confirm my estimate, so can you indicate what number you believe is correct? If we are close I prefer not to quibble over a side issue since this will not change the substance of the primary point which is encoded functional information and the inability to demonstrate if natural processes do generate it. How many substantive alterations would you accept as reasonable? What about from say the first mammal to modern humans? Lenski's definition of beneficial seems loose as does your definition of substantive. Neutral mutations don't eliminate options and thus do not change information content. Have a look at the lab notes regarding the change in mutation rates it appears to be isolated cultures where mutation caused damage to critical replication components. Note what happens when these strains are made to compete with slower mutating lines. We don't know if human ancestors had different mutation rates, we can only go by the processes and rates we observe today plus what we know about the mechanisms that lead to faster rates and it does not seem encouraging for your position. I find it even more naive to use speculation to prop up a untenable position. That's just it, I seem to be quite informed about what Lenski's research shows and what it doesn't show. We only seem to get into contention when either Lenski or you want to go off and speculate about what things might mean or might have been. Returning to the primary point, experimental results (and Lenski's seems to be among the most optimistic available) we have documented evolutionary pathways where selection is actually selecting an advantageous mutation only once and then the pathway is just three steps long with one neutral or detrimental step. This pathway fits within the range of what one would predict from a random walk so we have no example of known evolutionary processes deriving functional information beyond what little is predicted by information entropy. With this, it seems clear to me that naturalism is in need of a new and improved process in order to explain life and the diversity we observe. Sounds hypothetical. Is this a real event or a just so story? Not so. It fits the definition of encoded functional digital information in every sense. It has both semantics and syntax. It is translated and transcribed. It is independent of the material it is encoded on. The messages are independent of the carrier. The ratio of functional to non-functional messages is very small 1 in 10^74 by our best estimate. I addressed most of this already, but I add that none of your objections substantially change the result. We can quibble over the numbers and still fall many orders of magnitude off the mark. The evolutionary tale fits the historical record because it has been carefully molded over 150 years to fit it. Now with modern experimental techniques its ability to morph is falling on hard times. If we apply scientific rules to the predictions by requiring citation to observable processes it falls way short of accomplishing what is prescribed to it in the timeframe assigned. We simply do not observe evolution generating functional change at the required speed. It does not generate new information any faster than a random walk. In other words the fitness function does not appear to contain smooth pathways from one functional advantage to the next. It appears that there are discontinuities that limit the traverse. That being the case we should be looking for alternative processes. You have offered a number of hypothetical examples of how evolutionary processes might generate this kind of information but it is all presupposed or imagined. We know that a mind generates this information. My point in going down this path was to demonstrate that those who claim that known evolutionary processes do generate new function and form are unable to offer known examples, instead they show that diversity happen by comparative analysis and they presume that it happened a particular way without knowing if it did or not. You have taken this same tact. Of course it has. Life had a beginning and diversity happened. The question is how? Information has increased over time, but how? You presuppose the answer is by natural processes but I have shown that thus far only mind is known to be capable of generating the quantity of information required to begin life and allow for its diversity. You have offered only hypothetical imaginations of how known natural processes might do so. Personally I suspect there is some group of undiscovered processes that account for generation of functional information at a rate sufficient to account for diversity of life but at this time, mind is the best explanation for life and the universe and perhaps even diversification. Unless there is some real example of natural processes in operation today that can be demonstrated actually generating large amounts of information quickly, I don't see much point in continuing this discussion. We have gone down many rabbit holes and chased many a goose and we have come away empty. You are suggesting that every mutation is functional but Douglas Axe and several others have already shown that this is false. The ratio of functional to non-functional expressed sequences seems to be less than 1 in 10^74
  13. I can only conclude you don’t understand my position. Like many things, information takes on several forms. We are focused on a particular kind of information as I have defined. I am being specific about the kind so we avoid confusion. These sentences also contain and convey information by virtue of the fact they eliminate vast quantities of alternate possibilities, however in this conversation I am being more specific. Functional information is information that when processed results in a functional system. Data is different from information because data requires analysis and interpretation in order to derive meaning and thus eliminate alternatives. I understand your definition of information and I accept it for what it is. It is a very broad definition that is useful in data and information transmission especially in that the compressed instruction set is information since when it is processed, the original sequence, or a representation of it, is regenerated and thus alternative configurations are eliminated. I don’t find this kind of information applicable to biological systems and thus making a comparison to it makes little sense. However, the compressed instruction set is information and I do not know of any example where random processes are able to generate the compressed representation of a particular sequence, irrespective of the source of that sequence. Is it? You can describe the stepwise evolutionary pathway that derived the components, expression controls and developmental controls for glucose metabolism from a system that lacked it? Nonsense. Let’s test your claim with what the theory predicts about human evolution and compare it to the lab. Human history is estimated at 6 million years. The human genome contains at least 10,000 substantive differences from the predicted primate like ancestor. In 6 million years that is about 200,000 generations, and thus about 20 substantive alterations per generation amongst fewer than a trillion cumulative population . In the lab Lenski’s ecoli work alone has covered nearly 35,000 generations with over a million, trillion cumulative population and he got a total of 1 substantive alteration. The prediction would have Lenski getting several orders of magnitude more and this is only one of the thousands and thousands of relevant lab experiments being conducted to observe evolutionary processes. By this example it should take just a few years to confirm the presence of evolutionary pathways by noting and comparing the rate that these pathways precede as compared to the rates required by evidence from the fossil record. By Lenski’s example and others including several focused on applying observed rates with population genetic models, it is clear that the rates are orders of magnitude too slow. Your claim falls flat. Please don’t exaggerate. My request is far more reasonable as I demonstrated above and furthermore unlike yours, it allows you to cite observations of process known to exist and in operation today. Nonsense, historical and DNA evidence cannot tell us how the similarities and differences came to be the way they are, a prediction that cannot be verified is of no use. I am asking for just a handful of observable modifications. Protein-protein binding sites are generally made up of 5-10 amino acid loci. Likewise for expression and developmental controls. Protein shape is determined by folds, which are also based on binding sites. All of these are the lowest level functional precursors to novel form and function. I am not asking for development of an entire system I am only asking for evidence that random error and selection generates these lowest level subunits. Based on population genetic models these would need to occur every few hundred generations, but even after over 35,000 generations of observations in ecoli and 50 years of observing malaria with countless tens of thousands of generations and trillions of trillions of organisms (10^15 times as many as the total number of mammals that have ever lived) still no example of a new binding site The bible is not a science manual. Are you suggesting that science is similar to religion? If not, perhaps you should use a better example. For the record I have not once suggested that the Bible provides an accurate representation of how life diversified. Turns out neither are accurate. I would not expect the Bible to be accurate on these issues but I would expect a valid theory to be accurate. The number of exceptions to this model are staggering. Take the gene that codes for histone IV for example. It is highly conserved with fewer than 6 of its hundreds of nucleotides showing variation between a very diverse group of species. Your model predicts there should be strong functional constraints (vital as you call it) but lab experimentation in yeast cells confirms that the constraints are mild. Several mutations do not alter fitness by any measurable amount. Even more astounding are the thousands of ultra-conserved elements (UCE’s), these DNA segments, hundreds of base pairs long are found across a wide range of species. Perhaps you misinterpreted what I said. Duplication and then modification can increase information but this in direct observations, this is rare relative to the losses occurring by other mechanisms. Since historical analysis can only provide measures of similarity and differences but don’t provide objective measures of the various mechanisms nor any information about processes we can’t use it to derive meaningful measures of information gain or loss. Experimental analysis indicates that on average information does not accumulate. This is as we would expect from information entropy laws. If you are putting context to the data then it is your mind that is deriving information based on the data string. I am quite aware that human minds are capable of deriving data and don’t see any value in this demonstration. I will stipulate now that your mind can generate information in the process of analyzing any data stream I was to provide. However this is quite different than encoded digital information that is translated, transcribed and then processed by chemic processes (without a mind) to derive a functional system.
  14. cypress

    Gene Limit

    As you and skeptic suggest, arbitrary was a poor word choice. Variable might have been better since it depends on many of the factors mentioned by other posters. As far as where this limit lies for any particular organism given the environmental conditions, I don't have enough data to say.
  15. Most origin of life researchers reject the notion that life arose by chance and for good reason too. The probability of deriving biologically relevant systems by chance processes is estimated in excess of 1 in 10^41,000 even by the more favorable chemic processes by numerous calculation methods, one of the more rigorous was by Sir Fred Hoyle. Current research is focused on self-assembly processes but thus far these are not faring any better. Perhaps you meant to use the word "assuming" rather than "considering".
  16. cypress

    Gene Limit

    Biological processes in general are functionally efficient. Controls that regulate gene expression tend to switch of expression of non-functional genes and this imposes an artificial and somewhat arbitrary upper limit on the quantity of expressed genes in organisms.
  17. No I don't think so. Your use of the term "value of information" seems altogether different than "coherent digitally encoded information that when processed generates functional systems". Did you intend to change the meaning? I recognize that you were attempting to make analogies, but I consider them to be misapplied. I am also somewhat disappointed in your lack of trust. Unfortunately we will likely not face this issue because there are no such examples. The neo-Darwinian narrative of gradual change over time predicts millions upon millions of these pathways and yet we can identify none. How odd. It makes a great deal of sense because we don't know of any evolutionary process in operation today that is observed to have generated any significant quantity of new information required for new form or function beyond what little can be shown to be derived by a blind search plus the probabilistic resources available to search shape and chemical affinity space using population genetics modeling. It is a tautology for you to presuppose that there exists such a process. If observations of known processes existed then you would be able to provide an example of one of these multistep evolutionary pathways we discussed. Again let me remind you that research has not yet identified any pathway greater than three steps but we need pathways in the millions of steps. Once again I must correct you. We have a metaphysical belief but we do not know if natural process produce new organisms. We do know that evolution can generate adaptations of pre-existing function but these adaptations on average destroy as much or more information as they generate. Adaptations tweak the dials within the range minimal range of survival but they must be in that range to begin with for adaptation to work. Yes we should, but first we need to adjust the criteria for what constitutes the kind of information we are talking about. If we relax the criteria enough we can describe nearly anything as information.
  18. If you look at the research more closely what you will find is that by some percentage estimated between 10% and up to 90% of the expressed sequences that generate proteins share a degree of similarity to protein sequences in microbes depending of course on how you account for unique protein sequences. similarity to other species display a range of values for the same reason. If you don't include unique proteins with no corresponding function between the two species being compared then the percentage is high, but if you do include them the percentage can be much lower. The degree of similarity is also somewhat vaguely defined in that the cutoff for what constitutes similar is somewhat arbitrary. It is this similarity that leads to a conclusion by induction that gene sequences in humans have microbes as the original source.
  19. Good point. So what would we have then? It would depend again on how the designer used the random numbers. Would we have the computer making unconstrained free choices? No, it would react in accordance with the rules prescribed by the designer and the results would be random with constraints. The computer and code is passively delegated the constrained range of outcomes to a random generator. We now have an example of a designed system that generates outcomes based on design, necessity and chance.
  20. Computer programers sometimes choose to use pseudo-random number generators that are deterministic in their code to add a degree of variation and complexity because the range of inputs is great so the range of output can be as well. However, there is no contingency in the outcome of these functions. They are as deterministic as every other computer function.
  21. From the beginning I have been speaking of evidence as opposed to proof and if you read my posts you would note that I am not assuming this is proved. The questions I asked were rhetorical to help illustrate how I believe your complaints were misplaced. Uniform experience and observation confirms that intelligent agents generate coherent encoded information but there are no confirmed cases of natural processes accomplishing the same. This is evidence but since alternatives are still in play, it is not proof. If you believe that my statement is incorrect and that natural processes do generate coherent information then let’s discuss it. Otherwise the minor complaints you raise are side issues that I don’t think need to be discussed any further. Random strings of data is .... well.... data so there is no reason to redefine it as information. If random strings “had value” in the sense that it could be processed to produce functional systems, then it indeed would be information in the sense I mean. Do you have any example of random data containing large amounts of this kind of information capable of being processed to produce functional systems? I am speaking specifically of encoded digital information such that when processed generates functional systems. Computer code is an example. Instruction manuals are another. The information encoded into DNA is a third example. Would I? Do you read minds? I have asked for this example because the inability to produce one is confirmation of the claim I have made. If you produce an example then I will have to retract my claim that random error and selection does not produce novel function and body plans within the available geologic timeframe. Perhaps not, but unless the claim cites a causally adequate process currently in operation and known to be capable of generating the claimed effects it is not a scientific claim, it is metaphysical. Are you making an appeal to the unknown? Demand what you like but I don’t make these claims. For someone who objects to logical fallacies you seem awfully fond of them. So what we have at this point is the fact that the physical constants in this universe are fine-tuned and we know that mind is capable of fine-tuning while we are unaware of any natural process capable of fine-tuning. We also have coherent encoded digital information as fundamental and necessary component of biological systems and we know that mind is capable of generating encoded digital information while once again we are unaware of any natural process capable of generating this specific kind of information. These are two pieces of evidence that suggests this universe and life in it was created. Furthermore since there is no causally adequate natural explanation for attributes of the universe or life in it, creation is currently the best explanation for both. This may change with new data but it is silly to deny the current reality.
  22. Coherent Information trims away alternatives. When I say "It will rain", I have conveyed very little information but when I say "It will rain between 6 and 7 this morning in New Orleans" I have eliminated a great deal of alternative scenarios and have conveyed a great deal of information. In information theory the quantity of information is measured by the quantity of alternatives it eliminates. So when I said that the designer eliminated a huge number of alternative configurations that person inserted large amounts of information into the simulation. I find your claim vacuous. Something is functional if it has a configuration that can be employed for any useful task. I am surprised you would deny this reality since these parts can and are used for multiple purposes with the same configuration. Likewise protein components have configurations that are functional and a great deal more that are disorganized blobs with no shape conformance, no stability and therefore no function because we know that protein components require shape stability, shape conformance and matched binding sites to be functional. Sequence conformance is generally not required. How can you demonstrate this to be true. I don't see any way for you to say they are arbitrary. If anything could have been used then the simulation would require these anythings to be included. They were not included because the simulation would have failed. I don't know if there are or not, but the designer of the simulator programmed it with a definition of best as opposed to "survive". Only those that run closest to the same speed as time survive. This is artificial, it is active information and it guarantees the simulation will suceed. Do you actually believe this simulation demonstrates that natural processes are capable of generating the information required to generate functional systems?
  23. Hmm, I reread my post and find it quite informative regarding the reasons the example is not relevant to this discussion. Was there something I said that requires elaboration? The designer only included functional parts. This amounts to an incredible amount of active information since the algorithm is guaranteed to apply only functional components. The designer also rigged an oracle to guarantee that correct fits are better than incorrect fits, more information. Survive in the wild is not a target as there are countless ways to survive in the wild, they are overlapping, codependent and no configuration is clearly "best". No, importing information is a more subtle way to help out. Incorrect. The information added by the designer accomplished this task by eliminating innumerable unworkable combinations and the designer coded in an artificial fitness function that guaranteed success. Are you defending this person's simulation because you actually believe it demonstrates that natural processes without aid and without importing any information (we can quibble about how much information was imported into this simulation but nobody can deny that some was imported and that information was critical to success of the simulation) can and does generate coherent information? If so can you provide a demonstration? If you don't believe this or you can't demonstrate it then why are we discussing this? First off unless I am mistaken, you quite clearly claimed that genetic algorithms only need the same attributes that evolution has to function. Perhaps you are claiming that evolutionary processes contain active information imported by a designer, but if not, then I have not mischaracterized your claim, I have not moved the goalpost, and you have claimed by induction that information can be made without information. Have I misunderstood your position? If it did take several more steps in fewer generations then it would be the example I was looking for. Speculation is nice but it is not evidence.
  24. Show me a genetic algorithm that does not import active information and I might agree with your claim. The reality is that they do not function without the designer artificially adding information to the search. In other words they function because the designer designed them to function. Likewise natural selection can only derive the diverse organisms we observe if there exists contiguous advantageous stepwise evolutionary pathways from one organism to another. I have asked for an example of a pathway just four steps long and I am certain that nobody will be able to provide even one. Yet if natural selection generated diversity then there would have to exist hundreds of millions of them each one of them hundreds of thousands long. Actually I conclude that some things are natural because natural processes in operation today are observed to generate them. It is because life has the appearance of and contents that we observe only design processes construct and never natural processes that I conclude that design is a possible explanation for life. I personally believe there may be other processes yet to be discovered so I have not "concluded" that life was designed, however I note that currently design is the better explanation since there is no coherent natural explanation at this time that is causally adequate in that it cites known processes in operation today that have been shown to be capable of generating the effects ascribed to it. Genetic algorithms are all designed and purposely import active information. Are you sure you want to place evolution into that category? I am speaking of your prior commitment (and certainty) to natural processes that have not been shown capable of generating the effects you have assigned to them. I know of no other prior commitments you hold and they don't seem relevant to this discussion. What prior commitment have you noticed I subscribe to because I don't think I have offered any. Sure I don't see that I implied that the experiment previously contained the derived mutations, but the mutations were an alteration of a pre-existing capability to metabolize citrate in deoxygenated conditions. This is clearly an adaptation. Furthermore the mutations involved fewer than four steps and was well within the reach of a blind random search. I don't find the slide show or the code particularly informative to this subject. The simulation quite obviously imports substantial information and also has a target defined by the designer. It is interesting in that it illustrates the narrative regarding selection very well but it does not in any way demonstrate that natural selection is actually capable of generating what it purports to generate. A better description of it is documentary/propaganda.
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