jerrywickey

DrDNA I am going to address your objections the most important first. 1) "Replication is only one activity of ribozyme." While this is true, it is immaterial. Any RNA sequence which does not replicate, will never be plentiful enough to have any lasting effect. It could be a wonderful sequence that does everything including the dishes. But if it can't replicate or be replicated by association with a sequence which can replicate, it is ultimately doomed. My model assumes this replicating sequence as its starting point. 2) We already know that the sequence my model uses would do nothing. In fact using the designations U C A G are simply familiar decorations. The assumption is that the model arbitrarily assigns meaning to some sequences. We do not know what the sequence was. We cant even find a self replicating sequence. But if life started with out some sort of extra natural "stirring of the pot," then there must have been one. My mathematical model simply arbitrarily assigns a sequence as the one which accomplishes this. It then arbitrarily assigns other sequences with functionality which augments or reduces the effectiveness of the replication sequence. I do not intend to model chemical activity at all. That would be impossible on that scale with today's desktop computing power. The effects of the mutations will be judged not by a model of their chemical activity but by the arbitrary assignment of function to sequences. I covered this in the post. I hope that clears up your objections to the arbitrary designation and to the possible chemical environment. Simply put, if the chemical environment made it impossible for RNA to replicate, we are suggesting extra natural involvement to facilitate the activity. My model assumes condusive chemistry with out specifying it. 3) I will be using four nucleotides. But this is only decorative. It is a mathematical model and the use of A G U C is just a familiarity. 4) RNA may not have been the first replicator. Amino adenosine triacid ester was a candidate which MIT proposed. Ultimately it proved unsuitable. But since the world we see today is exclusively DNA, what ever the first replicator was, it must have made a transition to DNA and the only doorway is RNA. Unless we theorize some sort of extreme complex step directly to DNA. This software models that point at which RNA would catalyze its own replication. To quote MIT regarding a the first instance of an RNA replicator. "If emergence of the first RNA replicase ribozyme coincided with the origin of life, it would have had to arise in a single step from prebiotically synthesized RNA, without the benefit of Darwinian evolution. " MIT suggests that if it was RNA, the nucleotides would have had to be assembled randomly. The more difficult questions is getting nucleotides to assemble. There is research which suggests that nucleotides can spontaneously assemble in the presence of proflavin. An organic environment, containing a compound which could act as a "midwife" facilitating prebiotic nucleotide assembly would yield many RNA sequence permutations. We have to start somewhere, unless you are suggesting some sort of extra natural "stirring of the pot." Any replicator must have become DNA based at some point to provide for the current total domination of DNA. There is not another more plausible pathway to DNA than enzymatic RNA. 5) "dependant output variables. Maybe it is the difference in chemistry/biology and programming" this is simply semantics. The software doesn't really care what it is called. It will produce the output all the same. Do you have any suggestions as to unsuitability of: Assume a replicating RNA sequence whose environment is particularly conducive to random mutation which acquires other sequences which alter its functionality, sometimes advantageously, sometimes disadvantageously. Is this an accurate model in your opinion? And would the results of this model lend helpful insight into the possible patterns of earliest life? Jerry

Thank you foodchain, That is an excellent question. You are really thinking about it. Keep them coming people. There is no provision for proteins at all in my software. Proteins require ribosome or some sort of ribozyme. A RNA transcriptase system of some sort is also required. Even the simplest of these systems would be ridiculously complex to have arisen in a single random step of the very first minutes of life. Earliest replicators would have to have utilized the enzymatic properties of nucleotide chains to effect the functionality of reproduction. Other advantageous or dis advantageous sequences might have effected protection from the "hot" environment by sacrificially binding to corrosive compounds which threatened the replicator sequence. There are other ideas. My software does not propose any particular functionality for the additional advantageous or dis advantageous sequences, only that some are good and some bad. These additional sequences are the closest thing to a set of proteome which may have been present. Thanks so much! KEEP THEM COMING. And remember I am new here, so please if you feel I am worthy, don't hesitate click the button to add to my reputation Jerry

At some point in the far distant past, when earth was devoid of all life, somewhere on the planet, the first short assembly of nucleotides became the first RNA replicator. In the seconds and minutes after that event, this randomly assembled sequence replicated itself over and over again, as fast as it could. This was its only purpose in the universe, to replicate itself. The conditions at that exact point in time and at that exact location were very conducive to the random assembly of nucleotides. Conditions were "hot." So this sequence, perhaps for a short period of time or perhaps extended period, not only replicated itself, but because of the conducive conditions responsible for its spontaneous assembly, it also easily acquired other sequences. Some were advantageous and augmented the original or its daughter's ability to replicate. While others disrupted or stopped completely this ability. If replication ceased, the sequence would quickly be reassimilated in this "hot soup." But none the less, in only minutes or hours, there would be thousands or millions or billions of copies of this first successful replicator RNA sequence. It is this period of time, that I want to see from a front and center seat. I am writing software to simulate just that, the first few seconds of evolution. It will puke out a simplified "RNA genome" of every daughter of the first replicator, while simulating the mutations which must have taken place. I need to double check my parameters. There are program parameters for: base replication rate frame shift mutation rate large frame shift mutation rate (i.e. inclusion of a large chunks of RNA) single nt exchange mutation rate rate of advantageous RNA sequences rate of dis-advantageous RNA sequence rate of fatal RNA sequence We don't need to know the correct values for these variable. The values of these variable can be manipulated to find the set of values which must have represented the first primordial pond, "the fountain of life," But I need some input. I need people's ideas and comments on my model's consistency with observations. I need to know if these are the right variables. Of if I need to replace some with others. Please read Software model of early evolution that really works -- http://www.scienceforums.net/forum/showthread.php?t=31212 I describe the model in detail there. Post your thoughts. Even an idea that seems nonsense might shake loose another idea which will really help. After all variable mutation and natural selection of ideas works too. Help me out. When I am finished with the software I will post an executable, so everyone can enjoy the show. And I will post the source code, so anyone can play. I am soliciting help with this in this forum and on several other fora. Even fora compete for success. Jerry

I am hoping for input from people just as your self. Thank you This software will model only the very first few hours after the introduction of an RNA self replicator. No way yet to model all the way to a cell, which would require proteins, ribosome, polymerase functionality. My model could be taken a step further in complication even with desktop computers. But by keeping it simple and attempting to adhere closely to the limiting parameters, I hope to see the action as it were. I am beginning debugging now. I am tired but so excited I can't sleep. I am working on it right now. taking a break to write this. The core computing engine is done. But there are countless typos that express themselves as gibberish output. This is common for coding. I will plug away at it. Please lend a hand. And carefully overview the parameters and expected results. Comment on what you see as might be inconsistencies with observations and the parameters interpretation of them. ON the other hand, if you see no discrepancies, comment. Thanks so much Jerry I like the Max Headroom avitar. That is correct? isnt it?

The creationists were right. Darwin was reaching into a black box to answer the questions that he could not with the observations of his day. But now with our new found genetic understanding, we should finally be able to piece together the missing pieces. I am writing, almost ready for first debug, software that will allow anyone to actually see a plausible evolution of the very first RNA creatures which must have existed in some primordial pond, just moments after the first replicator arose. Anyone will be able to track the lineage of any single organism by comparing genomes of each new organism on the map the first few seconds of evolution. I need your help though. Read on to find out how. Below you will find the complete parameters of my model and the first replicator's genome is assumed to have arisen in a single step. It will be arbitrarily assigned as GACUCUUCUCAGGGCC The sequence which allows an organism to reproduce, in my model, is CUCUUCUC. If that sequence is present in an organism's genome, that organism is very very likely to replicate its entire genome, in my world model. When complete I will place the source code in the public domain and I will post a running version for any one to download for free and use. It will be called First Colony. If you read the parameters of my model, and find that they do in fact agree with empirical observations, PLEASE POST THAT. If you find a discrepancy, post that. The encouragement will mean a lot to me while I am up in the middle of the night coding this software. I puzzle over the first replicator. A molecular creature which gave rise to all life but for some reason, has now mysteriously disappeared. Very smart people have tried to "engineer" a plausible example of what it might have been, but with out luck. God Damn it! if that doesn't sound exactly like any other creation mythology. "Long ago a creature birthed all of life but it is now gone forever. We will never see him again." I looked at amino adenosine triacid ester. I looked at MIT's 195 nucleotide first RNA replicator candidate. But MIT concedes as well, neither fit the bill. So instead of looking harder, I have switched tracks a little. I am trying now to find a plausible immediate precursor protein to myoglobin. There is a reason I chose that protein. It is explained in that post. But the point here is, I ran into a road block finding a plausible incremental step between proteins. I looked at gene splicing regulatory mechanisms of intestinal micro flora. I looked at single base pair mutations of coding regions which were not functional. I looked at frame shift mutations. None answer it. So I have a solution. I want to see it work for my self. I heard of several pieces of software which model evolutionary development in an analogous, reduced complexity simulated sample. In software like this, I could watch the things work and perhaps get a clue as to the process. The exact biochemical process would of course still need elucidation, but I might be able to see patterns that could be applied to the more complex reality. I only found more road blocks. The software models organisms with predetermined variability. i.e. They move from mutation to mutation along single steps which are provided by the software. Now who needs software to tell you that any set with variability and where undesirable variability is deselected will gravitate toward desired variability? I certainly didn't need software to tell me that. I was shocked at the simplistic approach, and the time that must have been wasted writing this sort of software. The software itself was subjected to intelligent evolutionary pressure by the author. It is useless to model what really could have happened. SO, I am writing my own software. This is where I need you guys help. I have most of the code written last night and this morning. I have not made the first run yet. But I want to detail the parameters and ask for any ones help pointing out inconsistencies with my model's analogy to observations. The model starts with a self replicator, as the RNA sequence CUCUUCUC. I am simply going to assume one. We already know that this sequence will not replicate itself and it is far too short to have functionality at all. But throw me a bone. Lets make this assumption and see how our first colony will develop. This organism is an RNA self replicator If the sequence CUCUUCUC is found in the genome of any organism in my world, that organism will self replicate its whole genome. So my first self replicator has an initial genome GACUCUUCUCAGGGCC. This genome size is not fixed by the model. As you will see, it may grow, shrink or mutate. You will find the proper sequence which provides for reproduction in there, and accordingly every software generation pass will give this organism a chance to duplicate itself. However, every pass may not produce a duplicate. I will list the factors for reproduction in a second. I am assuming that this random assembly of 16 nucleotides might have arisen in a single step of chance. In my model, all organisms in the colony are periodically and randomly subject to mutation of their genome . There are three ways a mutation may occur. 1) A single nt in the organism's genome my be changed. 2) A single nt may be added at any point in the middle or at either end. This will lengthen the genome of that particular organism. 3) Any of the nt in the organism's genome may be randomly removed. This will shorten its genome. There are other functional sequences besides the reproductive sequence as well. The reproductive success of any organism depends on more than just a replicating sequence, It also depends upon the organism acquiring advantageous genetic material and on it not acquiring dis advantageous genetic material. Some of these genetic traits speak to predator evasion, acquisition of nutrients, etc. My model will not try to sort out or simulate all these activities. It will simply make up a number of genetic sequences which provide advantage and make up a number of sequences which incur disadvantage. Reproduction will be augmented or retarded simply according to the number of each type of sequences found in each organism of the colony. The system variables are FERTILITY RATE -- the base likelihood that any organism containing the reproductive gene sequence will reproduce in any given generation pass of the software MUTATION RATE FRAME SHIFT PLUS-- The rate at which frame shift mutations which add a random nt take place MUTATION RATE FRAME SHIFT MINUS-- The rate at which frame shift mutations which remove a random nt take place MUTATION RATE EXCHANGE -- The rate at which mutations which alter a random nt which is already in it's genome take place ADVANTAGEOUS SEQUENCES RATE-- rate of occurrence of arbitrarily assigned sequences which are interpreted by my model to increase the base reproductive rate. DIS ADVANTAGEOUS sequences RATE -- rate of occurance arbitrarily assigned sequences which are interpreted by my model software to decrease the base reproductive rate. FATAL SEQUENCES RATE. rate of occurance of arbitrarily assigned sequences which if found by my model software, immediately extinguish the organism. Before each run, a number of these meaningful sequences will be generated. They will be generated according to the proportions dictated by the sequence rates. These arbitrary sequences will remain the benchmark for all organisms while they undergo random mutations which will work to deselect disadvantaged organisms. All sequences found in an organism which are not one of these are ignored. They are "junk DNA." They are left over evolutionary baggage and do nothing, no harm nor good. When I am done, I intend to make the source code available with out charge. I intend to post the working software so that anyone can download it and actually see a plausible evolution of the very first RNA creatures which must have existed in some primordial pond, just moments after the first replicator arose. Anyone will be able to track the lineage of any single organism by comparing genomes of each new organism on a map the first few seconds of evolution. Now for the, "your help" part: I need creation proponents and evolution proponents alike to input their comments. Here is what I need. Look carefully at the parameters to see anything that is not consistent with observations. Here are some of the things I expect to see in the results of software runs: The single most important goal for me will be tracing the ancestry of one of the advantageous sequences from nothing to the sequence. I want to see it happen. I want to see how often successful organisms retain nearly but not yet the whole sequence and how they pass it along until finally one of the offspring pops and thereby becomes more successful at reproduction. Another thing which will be very interesting to me is how two sequences may overlap. A successful organism may survive to carry two genetic sequences in fewer nt than intuitively imagined. How prevalent will this be? Will the two sequences diverge in some organisms? Is this one protein turning into another? Other things 1) sometimes the very first replicator will mutate fatally. in which case there will be no life 2) there will be a lot of mutation which do nothing and genomes will grow, including and carrying many nonsense sequences. 3) among all the organisms the most successful will predominate in large numbers 4) there will be several groups of successful organisms arising from a few good starts 5) each group of similar organisms will share very similar genomes but neutral mutations will cause diversity 6) This diversity while neutral by itself may contribute to building advantageous or disadvantageous sequences in later mutations Can anyone see anything else? I would also greatly appreciate any positive comments for my efforts. Any one think this is a good idea? Anyone interested in the software? Please let me know. Post a warm thanks. Thanks from me in advance. Jerry

I understand your comments. But the flaws to the software are still glaring. Help me fix this. Look at my thread Software model of early evolution. Dont be so quick to decide which side I am on. I could really use your help in pinning down the criteria Jerry

I have looked over several "evolution" simulations programs. Unfortunately every one I looked at is flawed. The most common flaw is that all permutations of all possible organisms are limited by the design of the software. This isn't representative of observations. The organisms cant grow in any way the program didn't already anticipate. i.e. every organism is made of eight bits. only eight bits. always eight bits. The results from these programs are exactly what the author expects because, the author has unwittingly evolved the program to be successful. ================== So I am writing new software, which solves this and the other flaws. But my software is no black box. In this thread I will list the parameters and ask anyone to comment on them. I want to make the parameters closely representative of observations. I will then post the software for anyone to run on their computer. I am the most curious about how many generations will be required between a colony of similar organisms and a consistent and advantageous change in the colony. each organism will have a "genome" made up of two nucleotides instead of four. These "genes" will be greatly simplified also. The "genome" can evolve to include any number of "genes." organisms in my world, may grow and adapt, by collecting as many advantageous genes as their evolution gives them. They may grow to any size. the larger they grow and the greater number of them will increase the length of time to process one generation. since in the real world the average length of a protein coding sequence is about 200 codons. This provides for a possible number of genes somewhere in excess of 20^200 I don't have the computing power to simulate that. In my simplified world a gene is always eight "nucleotides". In my world there are 256 possible gene sequence. I will refer to these "genes" as sequences I will start with a single self replicator. The first replicator has only one "gene" sequence of 0101 1010. these eight "nt" are its entire genome. when this "nucleotide" sequence appears in the genome of any organism it will cause one organism to be added to the colony with an identical genome to its own. Of course mutation may occur during duplication as well as other times in real life but mutations in my world can occur at any time and the mutation routine may be called to act on the new organism immediately after its creation. So I think that adequately covers that possibility. from time to time during an organisms life a random mutation might occur. =R= will be the rate at which these mutations occur. 1 is one mutation per generation. 10 is 10 per generation. 0.1 is once per 10 generations. The mutations can do one of six things change a 1 to 0 or change 0 to 1 or add one "1" nucleotide at any random point in the genome this makes the genome longer or add one "0" nucleotide at any random point in the genome this makes the genome longer or subtract one nucleotide from any random point in the genome. this makes the genome shorter or it could do nothing A random set of sequences xxxx xxxx will be assumed to be advantageous by any means such as making it easier for the organism to acquire nutrients or making it easier to elude predators or any other advantageous characteristic. all these advantageous mutation really add up to only one thing anyway increased reproduction. So each generation pass will compare the list of advantageous sequences with the sequences found in the genome of each organism. If an advantageous sequence is found the likelihood of multiple reproductions of this particular organism grows. i.e. if three advantageous sequences are found, this generation pass generates three copies of this organism instead of just the one for the reproduction sequence. =A= will represent the number of advantageous sequences. A random set of sequences xxxx xxxx will be assumed to be disadvantageous by any means such as making it more difficult for the organism to acquire nutrients or making it more difficult to elude predators or any other disadvantageous characteristic. all these disadvantageous mutation really add up to only one thing anyway decreased reproduction. So each generation pass will compare the list of disadvantageous sequences with the sequences found in the genome of each organism. If a disadvantageous sequence is found the likelihood of multiple reproductions of this particular organism is diminished. if three disadvantageous sequences are found, there is only a one third chance that this particular organism will reproduce in this generation pass. This is a different way of dealing with limited resources. In a new world full of the chemicals which spawned the new life, limited resources might or might not play a significant role in early evolution. But by including disadvantageous sequences we answer the possibility. There is no difference between the effect of an disadvantageous sequence in my world then the effect of a real life gene mutation which makes an organism less successful at competing with more successful organisms for a limited resource. The effect is the same, reduced reproduction. =D= will represent the number of disadvantageous sequences. A random set of sequences xxxx xxxx will be assumed to be fatal. So each generation pass will compare the list of fatal sequences with the sequences found in the genome of each organism. If a fatal sequence is found the organism is extinguished =X= will represent the number of fatal sequences. all other sequences are neutral, neither causing harm or an advantage. In my model of the early world there is no death except by fatal mutation. A single cell replicator continues to replicate with no arbitrary life expectancy. Death of old age, life span, must have presented some evolutionary advantage at some point to be introduced into the genome of the world as we see it today. In my early world model, death has not yet been introduced. R is the rate of mutation A is the percentage of sequences which are advantageous (note this is not the rate of advantageous mutations. This is important because, a mutation could cause a disadvantageous sequence to arise but the organism survive anyway. Later this same mutation augmented by another mutation might give rise to a very advantageous mutation.) D is the percentage of sequences which are disadvantageous X is the percentage of sequences which are fatal. Does anyone have any ideas? Any corrections? I will check back in the forum as I am writing this software. What I expect to happen is 1) sometimes the very first replicator will mutate fatally. in which case there will be no life 2) there will be a lot of mutation which do nothing and genomes will grow, including and carrying many nonsense sequences. 3) among all the organisms the most successful will predominate in large numbers 4) there will be several groups of successful organisms arising from a few good starts 5) each group of similar organisms will share very similar genomes but neutral mutations will cause diversity 6) This diversity while neutral by itself may contribute to building advantageous or disadvantageous sequences in later mutations that looks like about it to me. Can anyone see anything else? I am very curious to see the software results. I am starting to write it tonight, right this minute. I would also greatly appreciate any positive comments for my efforts. Any one think this is a good idea? Anyone interested in the software? Please let me know. Post a warm thanks. Thanks from me in advance. Jerry

Evolution proponents have a nice video that is bouncing around FrostCloud.Com right now. It does very good job of proving that when random mutations are introduced into an organism and adverse mutations are selected out, the advantageous mutations alter the organism advantageously. Did we need software to prove that? Now, just to be a little sciencey here, You know, ask questions and all. The software makes assumptions about the ratio of advantageous mutations to disadvantageous mutations. Are these assumptions empirically derived? Simple math tells us that if fatal mutations occur at even a slightly higher rate than advantageous mutations then even organisms which gain advantage will eventually fall prey to a fatal mutation and ultimately any life based on this mutation, natural selection model will cease after some time. It seems that recent genetic studies show that the likelihood of an advantageous random mutation is ridiculously low. A single base pair random mutation in the sixth codon of hemoglobin causes Sickle-cell anemia. Can anyone demonstrate a single base pair mutation that was advantageous? The video says that advantageous mutations have been observed. Are these single base pair mutations or are they relatively large chunks of genetic material that were spliced by some yet unknown RNA polymerase regulatory mechanisms? I suspect the author of the video is unable to answer that question. But the answer tells us if the assumption of advantageous mutation made by the software in the video is justified or not. I do know the answer to this question. What I do know is that an RNA polymerase splicing regulatory mechanism is responsible for observed advantageous mutations in intestinal microflora. But this solves nothing. It only serves to open the evolution question again. Is such a complex regulatory system irreducibly complex or can it be constructed by random mutation and natural selection? I observe just as much if not slightly more irrationality in evolution proponents as I do in creation proponents. The author of the video is also quick to point out the difference between abiogenesis and evolution. Which raises the important question: Why can't evolution proponents demonstrate a plausible first replicator? What is so difficult? If evolution had an organism to begin with, then a first replicator must not have been too difficult to arise. The notion of some creature which existed long ago and which gave birth to all life but is now long gone and impossible to replicate, smacks very strongly of a creation mythology. Are evolution proponents suggesting a negative proof? "Since no other explanation is possible, a first replicator must have arisen by chance." If anyone responds to this post, please try to address the three questions instead of just puking derogatory remarks. I understand the questions. I know they are essential questions required to prove the theory of evolution. It is still a theory for an important reason. It remains unproven scientifically. Q1: Why does a first replicator prove so elusive? Q2: Can anyone demonstrate an adventitious single base pair mutation? Q3: Is the RNA polymerase spliceosome mechanism irreducibly complex? If so, we have an answer, ToE is dead as a theory. If not then while we still have a working theory, we continue with out positive proof. Negative proof is not acceptable for scientific justification. i.e. "There is no other explanation, so a first replicator must have arise and it must have mutated." Is simply not acceptable from an empirically scientific point of view. Jerry