It's ready! You can download -First Colony- early evolution simulation

[jerrywickey]

It's ready! You can download -First Colony- early evolution simulation software at www.satellitemagnet.com/fcolony.exe

 

Download it and double click it. If it fails to start the first time, It just ran into a little problem writing an ini file for itself. Opening that file with note pad will allow you to adjust all of the parameters. Just double click Fcolony again to see it run.

 

Press enter to get through the welcome screen and both parameters screens. It will begin the simulation by displaying the detail of every nucleotide of every random sequence in a theoretical primordial pool where we assume that the chemical environment was conducive to catalyzation of random nucleotide assembly. Then press the zero key to see a panoramic view of early evolution.

 

After you press 0, you will see a white X for each random sequence that can not replicate. A red O for any that can.

 

You will see white X, random RNA sequences, slowly give way to red O, simple replicators. Then you will see the red O give way to more advantaged green repicators with longer genomes. As you can see in the (len) indicator, the average genome length is getting larger and larger, contrary to what random mutations can cause.

 

The O and X will turn green if a random mutation has resulted in a nucleotide sequence which the sim engine has identified as advantageous and blue if disadvantageous.

 

As the simulation continues in front of you, you will see that the red replicators will slowly take hold. Sometimes random mutations will kill all of them before they get the chance. Just press Q on your keyboard to end the simulation and double click Fcolony.exe again.

 

As the replicators begin to consume all of the resources, you will notice that the info bar at the top, (explained below) shows expected number of advantageous and disadvantageous mutations in all of the random sequences including the sequences capable of replication. You also see that the average length of all sequences is about 15 as one would expect by random activity.

 

But as the replicators take over and natural selection begins to select out disadvantaged sequences, the numbers of each shown on the info bar at the top start to be very distorted compared to the values which random mutations caused before replicators took over.

 

After about a thousand generations you will find nearly no resources available to random sequences and advantaged organisms have actually grown the average length of their genomes, having packed them with advantageous sequences.

 

Jerry

 

 

What you see is an info bar at the top.

Across the top from left to right.

 

Displaying the current generation / total generations to model.

 

Total number of random sequences which the simulation is tracking. They are not organisms yet. But they will be when they assume replicate capability.

 

Total number of sequences which can replicate themselves

 

Total number of sequences which have acquired advantageous RNA sequences by random mutation.

 

Total number of sequences which have acquired disadvantageous sequences by random mutation.

 

Last the average number of nucleotides among all the sequences being tracked.

 

I will guide you through the first run and show you what is most interesting. After the first run is done, you will find two additional files in the same directory as the First Colony file. FCINI.TXT and FCOUT.TXT.

 

FCOUT will be replaced every run. So if you saw something interesting in a run, rename this file before executing another run. This file contains the entire sequence of every critter in every generation complete with a serial number that references its parent sequence. So that you can follow the genealogy of any interesting evolved "bug" back to the first replicate and see each of the intermediate steps.

 

FCINI.TXT must be opened with note pad. Because its exact DOS file name is important. You can change any or all of the parameters in that file. Save it and run Fcolony.exe again to see what changes occur.

 

When you run it for the first time, press enter to get past the welcome screen then read the default run parameters. The important things to read are that advantageous nucleotide sequences are set to be three times more likely than advantageous sequences. You will find that life is tenacious. This apparent disadvantage is meaningless to life taking a foot hold.

 

The other values you can play with on other runs.

 

Press enter again, This screen simply shows you a sample of the nucleotide sequences which have been arbitrarily assigned functionality. This screen's purpose is merely to allow the user to verify by random sample.

 

Now the simulation begins. press the space bar to begin the simulation one frame at a time. That way you will be able to follow along reading the description while it is running.

 

You now see the first 40 random sequences in a pool of 1300 random sequences. You can read the nucleotide sequence for each one, if you want. I selected an average of 15 nucleotides because researchers at MIT suggested that current understanding of prebiotic chemistry suggests this to be the upper limit of random prebiotically assembled nucleotides.

 

The very first two sequences contain within them a sequence which the simulation engines have been told endows replication functionality. These two were seeded by the ini file. In later runs you don't have to seed any first replicators, if you want to see it happen randomly.

 

The info bar at the top of the window shows the generation number of the total generations which will be simulated, the number of sequences that the sim engines are keeping track of. Imagine a pond or ice sheet or deep ocean environment where conditions are catalytic for the random assembly of nucleotides. Imagine that this "pool" has the materials to support 1300 sequences of about 15 nucleotides each. All these conditions can be altered by accessing FCINI.TXT for later runs.

 

Now imagine that the law of chance continually assemble and disassemble these sequences. That as soon as more than 15 to 20 nucleotides come to gether that the same chance chemistry that brought them together takes them apart and the average sequence length is about 15 nucleotides. This is what you are about to see, but first take note of the other four numbers

 

They are the number of sequences being monitored that contain the replication sequence, the number of sequences which contain more than one advantageous sequence, the number of sequence being monitors that contain disadvantageous sequences and finally the average length of the sequences being monitored.

 

press the space bar a few times to see the details of the first 40 sequences effected by random mutations. The ini file tells the sim engines that random mutations will occur at a rate of 5 sequence per 100 per generation. So as you can imagine only about two of the sequences on the screen right now will be effected by each press of the space bar. You also notice that the first number labeled repl. shows 2 and the top two have turned red. This is because the sim engine has identified them as containing the replication sequence CUCGGCUC Look for it.

 

Actually current science believes that a nucleotide sequence of this length is far too small to express any functionality at all. But also we never actually observed nucleotide sequences do any thing at all that was not in support or close association with a ribosomally translated protein. But we know that nucleotide sequences alone can exhibit functionality and have demonstrated such in the lab. We have no catalog of sequences which might exhibit functionality. So my sim engine simply arbitrarily assigns functionality to some sequences. You can change the frequency and assignment ratios of this in the ini file.

 

That second number will always show the total number of the 1300 sequences being tracked that contain the sequence which endows replication functionality. The second and third numbers show the number of sequences which contain sequences the sim engines have assigned as advantageous and disadvantageous. The advantage of any sequence is to reproduction. This is very early evolution. No organism is capable of expressing predatory characteristics or camouflage. A plausible advantageous sequence might be one that binds to chemicals present in the environment which prohibits the functionality of the reproductive sequence.

 

A plausible example of a disadvantageous sequence might be one which causes the sequence to bend around itself, obscuring the reproducing sequence making replication less likely.

 

These hypothetical but very plausible sequence have been randomly generated and randomly assigned functionality according to the parameters found in the FCINI file. The numbers will be about 1 2 or 3 replicators, less than 10 advantageous sequences found in the 1300 sequences being tracked and perhaps as many as 20 or so disadvantageous sequences as well as an average sequence length of 15 or so. The numbers on your screen may differ. This is a real time random simulation. But come close. The organisms containing disadvantageous sequences number nearly three time the number of organisms which contain advantageous sequences. And the average length of all organisms is about 15 nucleotides.

 

Keep pressing the space bar. The simulation engines will process each generations. Keep pressing it until there are about 10 replicators.

 

The generations will pass and you will notice that the number of replicators will increase. On occasion the first replicators will succumb to random mutations which interrupts their functional replication nucleotide sequence. If this happens you can end the simulation by pressing q or wait to see if another replicator arises randomly.

 

Once the replicator have taken hold nothing will stop them. You will see their numbers increase.

 

Now press 0 (the zero key) this will take you to a broad view of the entire pond. random sequences will be represented by whites X repliators by red O . The sequences will often turn green or blue briefly. Green if they contain advantageous sequences acquired by mutation and blue if disadvantageous sequences.

 

By the hundredth or two hundredth generation, replicators may number nearly a thousand already. Nearly taking over the entire primordial ponds resources.

 

Take notice that the random sequences, which are now organisms because they are daughters of a replicator and can replicate themselves, look at the ratio of advantageous and disadvantageous sequences which are contained inside these organisms. They still remain at the original ratio which was dictated by random chemical activity. As does the length of the average sequence. It remains at near 15.

 

But soon this will change as the replicators take over.

 

you can press space bar to proceed a generation at a time. You can press any of the number keys except zero to return to a detailed view of about forty random organisms Or 0 will take you to a panoramic representation. pressing enter will cause the simulation to proceed as fast as possible.

 

Watch the magic of life. As the replicators which now steal all resources from organism which retain a lower rate of replication and nucleotide acquisition start to alter conditions. As the generations proceed you find that the random distribution of advantageous and disadvantageous sequences gets skewed wildly toward the advantageous. And watch the average length grow as replicators which are endowed with advantageous sequences push out weaker competitors and the replication of their longer genomes outweighs the random manipulation of the original sequences.

 

If you let the simulation go on for its 5000 generations you will find that not only have replicators taken over but that they have evolved genomes ten times their original size and have adopted strongly advantaged sequences. It is remarkable to watch the red take over and then more slowly green creep across the screen.

 

Life has begun. The default parameters demonstrate activity exactly as predicted

 

by evolution.

 

I hope you enjoy and have as much opportunity to learn from using First Colony as I had writing the software.

 

Please comment negative or positive. Especially positively.

 

Jerry

[timo]

Perhaps you should think about a different distribution form than a (windows-only?) executable. Many people will refrain from downloading and running an executable provided by some anonymous person from an internet forum. Perhaps add a download for the source, even if just as an additional option.

[insane_alien]

it would appear to be clean. clam av, avg and avast detect no viruses and i'm not noticing any unusual activity on the virtual machine it is installed on.

 

did result in some hefty amounts of errors though. had to restart to get rid of all the 'this program has performed an illegal operation' errors.

[jerrywickey]

I have the good fortune of living on the sunny sub-tropical island of Key West, FL. A town I share with Dr. Alex Aller, molecular biologist whose work, among other things, involved developing the process of tagging cancer cell genomes with the bio-luminescent protein coding gene of fireflies.

 

I am very happy to report that First Colony was informally validated in its ability to accurately model nucleotide sequence replication behavior by Dr. Aller.

 

The new ini parameter file which the Dr. and I optimized this afternoon is available for download. I have also improved the visualization option to make each wave of advantageous mutation more obvious from the panorama view. Simply erase the current ini file, FCINI.TXT and the fcolony.exe file and download the program again.

 

http://www.satellitemagnet.com/fcolony.exe

 

Also the source code is also available http://www.satellitemagnet.com/fcolony.sor

 

I called him this morning to discuss my new early evolution software. And I would not be writing this had our lunch not have gone well.

 

Dr. Aller had a hundred questions about the assumptions and the parameters of the simulation software. As he agreed one by one with logic of the parameters, we also discussed the many values which might be used in these parameters and the various possible results.

 

By the end of the lunch, he invited me back to his home to attempt some simulation runs that we had discussed over lunch. We ran several simulations values for the parameters with which Dr. Aller had empirical lab experience. We wanted to see if my simulations software, actually reported accurately when posed with values for the parameters which the Dr., had actually observed in the lab.

 

Every single one returned results well with in the statistical variation of the results observed in the lab.

 

Please everyone, be encouraged to play with the values for the parameters. Please post interesting results. There is always the chance that you will make an observation which directs new discoveries. And... even if none of us make a new break through discovery, no one ever went wrong taking the time to learn.

 

Jerry

[jerrywickey]

I understand your concern. And I give you my word I put nothing harmful in the code.

 

Of course, I wrote every line in fcolony.exe

 

When you download the exe it will create one or two files in the directory in which you downloaded it. The fcout.txt file will get very large 50 megabytes sometimes. But simply deleting the name fcout.txt from its place in the fcini.txt file will stop its creations and you can delete fcout.txt as often as you like.

 

enjoy,

 

Jerry

[swansont]

It's not necessary to start a new thread every time you want to post on this topic.

[jerrywickey]

That post does fit well with this one.

 

I am just not used to forum members actually following a thread. I am new here. I hope this is the case.

 

Thanks swansont

 

Jerry

[Sayonara]

Most people use the "new posts" link when they revisit SFN, so if you add posts to one of your existing threads you can be sure that the people who have been following it will check back, and the people who have not read it yet will see it in their list.

The problem with scattering the same topic across several threads is that you increase the chances of interested parties missing one of the threads. Quel horreur!

[jerrywickey]

Thanks

 

Jerry