Software model of early evolution that really works

[jerrywickey]

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

[Realitycheck]

Can't you make it figure out how it makes the jump from chemical compound to divisible protocell?

 

Sounds better than all of the competition. Hope you get somewhere with it.

[jerrywickey]

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?

[foodchain]

 

 

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

 

Creationists were not right about much anything I can think of. On your program which sounds very nice btw, do you account really for the proteome and how do you go about such?

[jerrywickey]

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

[DrDNA]

What is your background Jerry?

 

1. Are you attempting to discredit evolution theory with a computer program Jerry?

 

2. If you are, then why are you talking about biogenesis? They are 2 completely different things. Neither of which go against the existence of God or the truths in the Bible in any way shape or form. The Bible doesn't go into the mechanism of bird flight either, but no one ever has a problem with it. The theologians don't, the physicists don't and the bird certainly doesn't.

 

I happen to be a born again Christian and a scientist and know for certain that faith and science are reinforcing; absolutely not opposed.

 

This is not the way, Jerry. This will only lead to an ugly mess.

[jerrywickey]

Like I said in the sister thread to this one. I am not pulling any punches.

 

I want to see what the values for the parameters I identified must be such that a viable colony could have arise from a single first replicator.

 

I understand the difference between abiogenesis and evolution. I understand it very well. This simulation is the crux of that change over, the advent of an abiotic first replicator taking on the characteristics we define as evolving life. The problematic definition of life not withstanding.

 

The reason for the post is to engage help in identifying any inconsistencies between the parameters my simulations engines will use to model these few generations and the actual parameters which might have actually applied. The values of the parameters are not important. Fiddling with the values and evaluating the results of each simulation run will yield the greatest gain.

 

I am not attempting to prove anything or change anyone's mind of anything.

 

I claim that I am guided only by empirical evidence and the logical evaluation of it.

 

Positions I hold relevant to this discussion and germane to your question regarding your query about my objective follow. The following might flesh out an image of me for you. But my goal is as stated above.

 

Abiogenesis is crucial to a valid theory of evolution. If no naturalistic means can be demonstrated to provide a plausible first replicator, we might assume an extra natural means. IF that IS the case, we have some very new and very powerful new information directly relevant to the forces which apply to evolution. Namely if an extra natural force was involved, is it still involved? What might be its motive? And what effect might it still have on the forces which guide evolution?

 

I have tried very hard, but am still unable to find a plausible first replicator of any kind. RNA, RNP, prebiotic, Clay theory, Crystal theory. None.

 

I do not subscribe to negative proofs. i.e. "A naturalistic process must have given rise to the first replicator because it could not have been an extra naturalistic process." Just show me the evidence and a plausible step by step process. Then we can talk.

 

However, I have no interest in discussing the possible nature of any such extra natural force in this thread.

 

This software and this discussion, are not concerned with the origin of the first replicator. I would entertain any discussion regarding it. But in another thread. And I have no interest in supposing the possible nature of any such force.

 

This thread and its sister is confined to the assumption of the first replicator. My software begins with the assumption the first replicator has already assembled itself with out regard for the means of its assembly.

 

I don't know if you are asking about my education. I am an electronics engineer, with a strong pension for molecular biology. But I made my living in real estate. I also hold credentials in finance and equities trading.

 

That all makes me sound way more educated than I am. You can find my most successful electronics product at http://www.satellitemagnet.com The picture on the site is of me.

 

I peddle this product myself. Of course, I designed the satellite tracking system electronics myself. This product is actually one of my simpler designs. But it is the most marketable. I enjoy designing esoteric electronics which really have no market. Hence my living in real estate.

 

I find the logic required to design electronic devises from scratch helps me immensely in separating the relevant from the irrelevant in other disciplines including molecular biology.

 

Oh,... and I am a bit verbose.

 

Jerry

 

To keep this thread on track, Please let me know what parameters might be relevant in the first generation after the advent of a first replicator. And if the parameters I chose are consistent.

[iNow]

Abiogenesis is crucial to a valid theory of evolution. If no naturalistic means can be demonstrated to provide a plausible first replicator, we might assume an extra natural means.

Frankly, your statement is completely off. Evolution is the process of change, and abiogenesis is only tangentially related to it. It is not crucial to a valid theory of evolution any more than a solid knowledge of the internal combustion engine is required to successfully drive a motorized vehicle.

 

Further, inputing something outside of nature (or super natural or "extra" natural as you put it) into your model or system adds zero value. All it does is place an arbitrary and unsupported value into a gap which you're not clever enough to fill accurately.

 

Putting a purple unicorn as a variable in your equation for what started life doesn't make it better, it makes it less accurate and less representative of the very reality you're trying to understand.

[jerrywickey]

Please, people if you believe that I am a kook, don't bother reading the post and surely do not post reply.

 

But if you would like to see a model of the first generations of the first replicator, after its emergence, post any ideas you have regarding the consistency of the model's parameters to the parameters which must have governed those first generations of replication.

 

 

INow,

 

You need to read the post before you comment again.

 

INow wrote:

"abiogenesis ... is not crucial to a valid theory of evolution any more than a solid knowledge of the internal combustion engine is required to successfully drive a motorized vehicle. "

 

Dude,

 

1) If there is no internal combustion motor to put in vehicle, driving it successfully should prove difficult. On what did evolution act, if abiogenesis, (advent of a first replicator by an entirely naturalistic means,) couldn't have occurred? We study evolution with the certain assumption that abiogenesis did take place with out extra nature involvement. Should this be discovered to be in error, we have a great deal of rethinking to do.

 

If you take each of my 4 sentences above and evaluate it, no reasonable person could disagree with even one of them. Try it! And if you feel I am in error, post the sentence and explain how it is in error.

 

2) If you read the post, you would have realized, I am not dealing with abiogenesis in the modal at all. The model assumes that has already taken place with out posing any source for it.

 

I am not studying abiogenesis.

 

This model does not address abiogenesis.

 

Abiogenesis or any of the variables associated with it, purple unicorns not with standing, are not addressed in the model.

 

INow;s post illustrates exactly my point regarding evolutionists similar affinity to irrationality as we are used to associating with creationists. INow has clearly not read the description of the simulations engines. If he has, he did not understand it.

 

When he read the word abiogenesis, his thought process became completely derailed. He clearly did not understand any thing he read after that word abiogenesis.

 

INow, please, Lets leave this level of irrationality up to people of faith. After all faith is defined as the belief in something which has no proof. Faith is by definition, irrational. I am not knocking faith. Love is also irrational. And who wants to be with out love. But don't let irrationality derail, a study of the first generations of an assumed abiogenic first replicator. Shall we?

 

 

 

Please, people if you believe that I am a kook, don't bother reading the post and surely do not post reply.

 

But if you would like to see a model of the first generations of the first replicator, after its emergence, post any ideas you have regarding the consistency of the model's parameters to the parameters which must have governed those first generations of replication.

 

Jerry

[iNow]

Wow... I don't recall calling you a kook. Also, that's a lot of personal comments about me, as opposed to the content of my objections.

 

I responded to a direct quote of yours. I stated that abiogenesis is NOT crucial to a valid theory of evolution. I also stated that "extra natural" variables only hurt your model.

 

That's all, mate.

[Realitycheck]

The question coming up in my mind is this. Do we have any idea how big of a sequence is necessary to eventually spawn some form of life? CUCUUCUC and GACUCUUCUCAGGGCC sound trivially small compared to what we work with today, though I am quite unversed on the subject. And in order to keep adding "mutations" to the chain, the "soup" that everything is mingling with must be full of these component nucleotides and/or nucleosides, correct? I don't see any major obstacle to this occurring in certain places in nature, given the grand scale of the world, though the chances of everything happening in one place must be few and far between. I'm just brainstorming to see how it all would work. That's what the software is for, right? Of course, the final workable product would somehow have to find its way into a lipid encapsulation of cytoplasm or something like that, but if we made it this far, why not, right?

[jerrywickey]

Thank you INow.

 

I don't hold any grudge against you. And your pointed comments do show you thought about the distinction between abiogenesis and evolution. If you can help, please know that I value your suggestions.

 

 

 

agentchange

 

Excellent comments I need more of these

 

1) yes the arbitrary sequence I chose to endow reproductive characteristics is ridiculously small. But the software does not model chemical activity. It models the effects of small mutations on sequences which ultimately endow relatively complex functionality.

 

To do this with out addressing the chemistry allows the software to replace chemistry with logical math. Similar to popular complex war games where two army fight based on the role of a die by weighting the die's outcome with considerations for the opposing army's strengths and weaknesses.

 

2) If evolution of the first abiogenic replicator actually took place, then this perfect chemical soup must have exists at some place and in some time. My model assumes this very soup as its starting point.

 

3) My software will go no where near anything that approaches a cell. It will only model the first several hundred, thousand or ten of thousands of generations after the first replicator.

 

I expect to see patterns that are similar to what millions of years later will become protein evolution.

 

I expect to see patterns of development which show overlapping function of sequences. This is one of the most exciting processes I hope to observe.

 

Else where in these posts I comment on other things I hope to elucidate.

 

 

 

 

 

 

 

First Colony software development progress update 2/16/08

 

I have neglected other work to do this. I am going on 19 hours total work on the software now.

 

The choice of programming language was tough. I am very sure that experienced programmers will bitch about my final choice. The language I chose is archaic. But I wanted to use a language that intuitive to novice programmers.

 

I was not interested in writing the software for programmers. Many people whose primary interest is biology not programming will find this software interesting. So I certainly did not want to use a programming language which was intuitive for people not up to date on the latest fun new programming language.

 

So if you are a programmer, you will surely have no problem fiddling with the source code.

 

If you have little programming experience, the language I chose was originally designed with novice programmers in mind.

 

It has intuitive instructions and structure. It shuns any contrived programming structure which is attractive to professional programmers but usually difficult for novices to understand with out experience

 

The speed of the executable does not suffer at all compared to the more advanced programming languages. So there is no down side.

 

There are four math engines in the software

 

1 mutation of sequences

2 disadvantageous effects of some sequences

3 advantageous effects of some sequences

4 reproductive effects all successful sequences

 

There are also housekeeping routines

 

1 generating the arrays that keep the organism data and the sequence assignments

2 keeping track of each organism and shuttling it through the engines at the appropriate time.

 

I have finished both housekeeping routines and tested them

I have written all 4 of the simulation engines

1, 2 and 3 are written but not tested

4 the repo engine is proving challenging.

 

I have not begun the generate report routine yet

 

Jerry

 

I forgot to mention that if you are not interested in fiddling with the programming, you can use the executable alone.

 

It will give the user the opportunity to alter the values for all of the parameters, run any number of simulations, and review the complete "genome" of every organism of every generation of as many generations as you chose.

 

And do this with out ever looking at a single programming instruction.

 

Jerry

 

Here is the ini file for the software. It makes the parameters much more understandable. I hope that anyone interested will better understand the purpose and scope of the software by a quick review of this information.

 

FCINI001.TXT

 

First Colony Initialization file.

 

no ,< has this ini file already run?

1 ,< total number of initialization files

FCOUT001.TXT ,< file name for output. 8 characters or less

1 ,< replication rate

1000 ,< limit of resources

10 ,< frequency of frame shift plus mutations

10 ,< frequency of frame shift minus mutations

10 ,< frequency of single point nucleotide mutations

5 ,< ratio of advantageous RNA sequences

50 ,< ratio of disadvantageous RNA sequences

5 ,< ratio of fatal RNA sequences

0.2 ,< percentage of RNA sequences expressing activity

 

 

Explanations below.

 

First Colony

 

Software simulation of very early evolution.

 

Software written by Jerry Wickey, 800 353 0056, Key West, FL jerrywickey@comcast.net

 

Version 1.0 Feb. 16, 2008

 

This is a simulation of the first generations after the occurrence of a prebiotic RNA first replicator sequence. This simulation assumes a chemical environment conducive to random nucleotide assembly, and which catalyzes such random assemblies. Prebioticaly synthesized RNA nucleotides and enzymatic activity of some RNA sequences is assumed.

 

Characteristics of nucleotide assembly and activity are alterable by the following parameters.

 

Do not change the order of the values. Change only the number. If the program yields wildly unexpected results and you suspect ini file corruption, simply delete all ini files and run the software again. A default ini file will be written by the software.

 

 

 

no ,< has this ini file already run?

if this value is yes, First Colony will not run this ini and will instead look for the next ini file in the sequence up to the total number of ini files.

 

1 ,< of total number of initialization files

Leaving this value one, will cause the software to run once, using the values found in fcini001.txt

You may use a value as high as 999. The software will make consecutive runs for each ini file labeled fcini001.txt fcini002.txt fcini003.txt etc. Each may contain related parameter values or completely different unrelated values.

 

 

FCOUT001.TXT ,< file name for output 8 characters or less

This will be the file name of the output file. If running successive ini files, 001 002 003 will be appended to the output file name.

 

 

1 ,< replication rate

Zero or a negative number will always result in no replication at all. It is a base probability. Positive values are augmented or reduced by other factors, including random factors and the number of advantageous and the number of disadvantageous sequences each organism Acquired by random mutation of single or multiple nucleotides in its RNA "'genome'.

 

 

1000 ,< limit of resources

this is the number of organisms our assumed pond can sustain. The number of organisms can not exceed this number. If replication causes this number to be exceeded, an organism chosen at random will be extinguished to make room. The weaker the member the more likely to be chosen the stronger the less likely. This is representative of a competition for limited resource. The maximum value out theoretical pond can support is 1000 organisms.

 

 

1 ,< frequency of frame shift plus mutations

All three mutation ratio values are comparative. So that if one desires to model evolution such that frame shift plus mutations occur three times as often as frame shift minus and two times as often as exchange mutations then one would enter 3, 2, 1 respectively

 

Frame shift plus mutations are mutations which add random nucleotides at random points along an organisms RNA 'genome.' Only one nucleotide is added most often, but multiple nucleotides may be added. The number of nucleotides added is randomly calculated on a logarithmic scale favoring fewer nucleotides.

 

 

1 ,< frequency of frame shift minus mutations

frame shift minus are mutations which remove a random nucleotide. One only is always removed.

 

 

1 ,< frequency of single point nucleotide mutations

exchange mutations are the random change of a single nucleotide to anther random along the RNA 'genome'

 

 

1 ,< frequency of advantageous RNA sequences

All three sequence generator ratio values are comparative. So that if one desires to model evolution such that advantageous sequences occur three times as often as disadvantageous sequences and two times as often as deadly sequences then one would enter 3, 2, 1 respectively

 

Advantageous sequences are assigned arbitrarily. The software generates random sequences and assigns its activity as advantageous to an organism in some unspecified manner. This same sequence will be advantageous to any organism which acquires it by random mutation.

 

 

10 ,< ratio of disadvantageous RNA sequences

Disadvantageous sequences are assigned arbitrarily. The software generates random sequences and assigns its activity as disadvantageous to an organism in some unspecified manner. This same sequence will be disadvantageous to any organism which acquires it by random mutation.

 

 

1 ,< ratio of fatal RNA sequences

Fatal sequences are assigned arbitrarily. The software generates random sequences and assigns its activity as fatal to an organism in some unspecified manner. This same sequence will be fatal to any organism which acquires it by random mutation.

 

 

0.2 ,< percentage of sequences expressing activity

This value is the percentage (per 100) of sequences which express activity of any kind. Not all RNA sequences do anything. In fact perhaps very few permutations express activity at all of any kind. They simply are inactive. If one desires to model very early evolution where 2 RNA sequences of any given reasonable length per thousand express activity of some kind, one would enter this value as 0.2

 

-end-

[foodchain]

I think the software sounds nice but its I think outside of something a typical computer could really calculate at least. Also I think it would be pretty evidence that science does not posses some mathematical quantization of evolution that certainly satisfies for what has occurred, but to me that does not say much. I mean you could plug in some population genetics stuff really on a giving selection of genotypes of genomes, but without a way to actually see just that part of life in action with the rest, like the proteome for instance I also doubt would really be useful for solving evolution. I also don’t understand how you are equating the environmental relationships really. I guess some form of a probability might be able to generate results, but I doubt that it would represent really evolution past just showing a Darwinian mechanism.

 

I am not thinking that you are trying to make some software that will automatically show various ways in which you might become a penguin, just that I don’t think you can really model evolution if you don’t have all the parameters in the first place. I mean tomorrow or next month some new discovery will come along that seriously hinders such computer based modeling if the modeling itself is not really scalable constantly. I was at a database site not to long ago on the web which listed just human biological processes and the current number of such was astounding to say the least.

[Realitycheck]

I think I would arrange it in terms of nucleotide density within the pond. Say you have 4 types of nucleotides and, for the sake of ease, equal amounts of nucleotides within the pond. One of the variables can then be "How dense is the nucleotide content within the pond?" This will then have an effect on how often additions to the chain occur and you can keep a running total of free-floating nucleotides within the pond, gradually decreasing as they get scooped up by valid ends of the sequences. It looks like it wouldn't be too hard to make it "chemistry legal", as certain nucleotides will only pair with certain others. Since we're only talking about 4 nucleotides, it shouldn't be that hard to enforce. Again, I am a bit out of my league here, but this is what I have read so far. It sounds a little more complicated, but I don't see how it would overwhelm the computer mathematically unless you start factoring in other processes such as tRNA, mRNA, DNA, and so forth. Even then, computers are pretty powerful and isn't it just a matter of time before it adds it up? Again, I really wouldn't know for sure.

[foodchain]

I think I would arrange it in terms of nucleotide density within the pond. Say you have 4 types of nucleotides and, for the sake of ease, equal amounts of nucleotides within the pond. One of the variables can then be "How dense is the nucleotide content within the pond?" This will then have an effect on how often additions to the chain occur and you can keep a running total of free-floating nucleotides within the pond, gradually decreasing as they get scooped up by valid ends of the sequences. It looks like it wouldn't be too hard to make it "chemistry legal", as certain nucleotides will only pair with certain others. Since we're only talking about 4 nucleotides, it shouldn't be that hard to enforce. Again, I am a bit out of my league here, but this is what I have read so far. It sounds a little more complicated, but I don't see how it would overwhelm the computer mathematically unless you start factoring in other processes such as tRNA, mRNA, DNA, and so forth. Even then, computers are pretty powerful and isn't it just a matter of time before it adds it up? Again, I really wouldn't know for sure.

 

I don’t know a whole lot also on the subject but really I don’t think its valid to just use dna. We have no idea what early life was or is or could be past microbes:D We can say protobionts but really what is that, a precursor to a possible prokaryote? What about RNA world and all that stuff.

 

Its like the thermodynamic argument. Who knows exactly what all can occur in a giving amount of energy. I mean a simple point is just to flick a coin with the same amount of energy on a surface, to trying to digest what all can occur on the earth in time within the constraints of that system whatever it may be concerning the fact the earth is not isolated in any sense. Its also I think hard to program in the reality of time. Billions of years is something I doubt any person can come close to realistically considering. More so within say "biological" time. The mutation some individuals carry in Europe that makes them immune to aids is a perfect example of that.

 

Lastly biology as studied by physical science is weird really. For instance electron density as related to photosynthesis is found to have easy properties to study by quantum mechanics, or papers exist on the topic. To me along with vision, the nervous system, chemistry and so on implies that such a theory can be applied to the theory of evolution. How hard do you think it will be to discovery all of what evolution and QM have in common alone?

[Realitycheck]

Well, the way I look at it is that it all had to start somehow. I am using the assumption that it all started with a do-it-all type of nucleic acid, something that is no longer present because it is long obsolete. RNA/DNA works better. Maybe the first replicator died out when the earth became oxygenated. Maybe the type of prokaryote that this first replicator helped form died out for whatever reason soon after it mutated and formed the prokaryotes that we know of today. There's a lot of maybes, but it had to happen somehow and there has been a lot of research into how it may have happened, how we can maybe make it happen today in the lab. If we can make it happen in the lab, then given the vast scale of the raw undeveloped earth, why couldn't have it happened there? The logistics are the only limiting factor, but there had to be a way, period.

 

All Mr. Wickey is doing is demonstrating how the primary building blocks may have formed, and it had to have happened in a hot spring. Ocean vents would have had water that was much too diluted for it to occur there.

[foodchain]

Well, the way I look at it is that it all had to start somehow. I am using the assumption that it all started with a do-it-all type of nucleic acid, something that is no longer present because it is long obsolete. RNA/DNA works better. Maybe the first replicator died out when the earth became oxygenated. Maybe the type of prokaryote that this first replicator helped form died out for whatever reason soon after it mutated and formed the prokaryotes that we know of today. There's a lot of maybes, but it had to happen somehow and there has been a lot of research into how it may have happened, how we can maybe make it happen today in the lab. If we can make it happen in the lab, then given the vast scale of the raw undeveloped earth, why couldn't have it happened there? The logistics are the only limiting factor, but there had to be a way, period.

 

All Mr. Wickey is doing is demonstrating how the primary building blocks may have formed, and it had to have happened in a hot spring. Ocean vents would have had water that was much too diluted for it to occur there.

 

Primary building blocks of what? That is also an assumption. You cant say past life on earth what chemistry is required in what environment really, but that’s mildly beyond the point.

 

The environment as you point out with the vents is entire subject of its own, the abotic conditions. Whatever clocks geologic functions run on, which are usually forever to abrupt on up to the atmosphere are surely of massive impact. Your are then faced with the very real possibility at least in my opinion that geologic environments like the lithosphere or heck the asthenosphere or who knows may have been the breeding grounds to life on this planet. I agree fully with a historical approach giving the reality of organic evolution but I don’t know if I would look at it from any kind of a classical perspective really.

[Realitycheck]

Yeah, I hear what you're saying. I've been trying to think up some other way, some thing that a prokaryote could have evolved out of, but no luck so far. Maybe I should read some of these MIT articles. The abstracts seem fairly straightforward and most of it seems built around the classical model, but maybe there are some alternative ideas nestled in there.

[foodchain]

Yeah, I hear what you're saying. I've been trying to think up some other way, some thing that a prokaryote could have evolved out of, but no luck so far. Maybe I should read some of these MIT articles. The abstracts seem fairly straightforward and most of it seems built around the classical model, but maybe there are some alternative ideas nestled in there.

 

Well here is a weird question. Say you have a trophic system. The bottom of that is microbes. So is the microbe sort of like the plug in for a power socket which in turn powers genetics for instance? I know its a weird way of wording it but if autotrophs simply died out the rest of evolved life on earth would follow simply because of evolution. So thermodynamics would seem important but that all implies energy/matter stuff over time, not that in some instant the organic soup was just right out of the blue with no past.

[Realitycheck]

I thought that autotrophs were alive and well. What I was referring to as maybe having died out were pre-prokaryotes that did not utilize the complex interactions of DNA and RNA, but rather one nucleic acid that somehow does it all, seeing how the chances of two nucleic acids working in conjunction in a first working cell is a lot less likely to happen than one nucleic acid. Of course, that is pretty hard to fathom anyway. But even when you get into the area of protobionts, we are still looking at nucleic acids driving everything from inside, so really protobionts are what I was essentially referring to. I need to do more reading on it.

 

Also, I forgot all about the prions, proteinaceous "cells" that don't have DNA. It could have all started from something like this, but somewhere it had to form or acquire a nucleic acid, among other things, in this case.

[foodchain]

I thought that autotrophs were alive and well. What I was referring to as maybe having died out were pre-prokaryotes that did not utilize the complex interactions of DNA and RNA, but rather one nucleic acid that somehow does it all, seeing how the chances of two nucleic acids working in conjunction in a first working cell is a lot less likely to happen than one nucleic acid. Of course, that is pretty hard to fathom anyway. But even when you get into the area of protobionts, we are still looking at nucleic acids driving everything from inside, so really protobionts are what I was essentially referring to. I need to do more reading on it.

 

Also, I forgot all about the prions, proteinaceous "cells" that don't have DNA. It could have all started from something like this, but somewhere it had to form or acquire a nucleic acid, among other things, in this case.

 

 

 

Right, I can understand the DNA/RNA bit. I think you could easily just say it was simply a proteome like mass that did not react to natural selection until inheritance of some form became established, the reality though is using inheritance for the only definition of life via DNA/RNA is why such statements fall to the wayside. Everything is gene centric in view, its crappy I think if you happen to hold theoretical ideas. I guess it sounds like a logical goal really, but I just don’t understand giving evolution in the first place why to make the view so narrow, even just using carbon-hydrogen bonding its hardly like we know all the possibilities.

[jerrywickey]

agentchange wrote:

 

"...but rather one nucleic acid that somehow does it all, seeing how the chances of two nucleic acids working in conjunction in a first working cell is a lot less likely to happen than one nucleic acid."

 

 

You are correct that DNA and its necessary polymerase complex of proteins could not plausibly be the first occurrence of life. DNA must have come much later.

 

At the first occurrence of DNA, there was no ribosome, but there must have been some form of functional ribozyme. The polymerase protein system must also have been present, for DNA and the polyerase system to have tried many combinations before two complimentary RNA sequences could have been utilized as a storage media.

 

Earliest life must have been RNA. The only alternative is to assume that some prebiotic replicator made an implausible jump directly to DNA. RNA has to be the answer. This fact alone, however does not prove RNA world theory. However, for a plausible pathway to DNA, which of course is not only dominate but all self contained RNA systems have been eliminated.

 

 

 

agent change

 

Yes I agree the probability of additional single nucleotides and segments of sequences are essential parameters. But, happily there is no mRNA, tRNA or DNA to deal with in this changeover from the prebiotic to evolution. All those things are still millions of years in the future for the First Colony.

 

foodchain,

 

Your point shows you appreciate the challenges.

 

Remember that I am not even attempting to model the actual chemistry. The computing power is simply not yet available. Should this level of computing power currently be available, we would already have the exact RNA sequence of the first replicator. But of course we do not.

 

Think of it this way. Many popular games simulate battles between opposing armies by throwing a die and weighting its outcome in accordance with the opposing armies strengths and weaknesses.

 

For instance I assume an RNA replicating sequence. We all know it is not the one. We all know that it is too short. But we all know that one did exists. My model simply makes the assumption that we do know it was this one. And instead of modeling the chemistry that makes it work. It simply applies the net result of a RNA replicase sequence. That is it replicates the entire sequence including junk sequences, advantageous sequences and disadvantageous sequences that are attached to the replicase sequence.

 

So I don't need to model the chemistry to see what would happen if we did know the exact sequence and could model its chemical activity.

 

Jerry