What is currently known from a paper about the epigenetic circuit for bird beak morphology is here best represented by a screen form that allows setting of the gene expression levels which control depth, width and length proportions.


https://sites.google.com/site/intellige ... enFull.bmp

Zip file with a RAM resident compiled .exe that does not need to install anything in the disk system or was given Internet or other outside connectivity. Code and compile is as safe and trouble free running and closing the program as possible.

https://sites.google.com/site/intellige ... ignLab.zip

Shown below is the math code to calculate final PmxDepth, PmxWidth and PmxLength development from setting of 7 scroll bars (controlling 5 gene expression levels) named TGFB, Bcat, Dkk3, EarlyBmp4/LaterBmp4 and EarlyCaM/LaterCaM.



Here is the same code without the comments:



All variables are shown in the Truth Table in the lower right corner of the screen. It can be switched from the illustration found in the science paper, or filled with numbers from the above calculations. The corresponding variables are:



The paper boils all this down to a simple truth table, where I made the math easy to check in case anyone wants to argue that it is not an accurate representation of what the researchers described happening.

http://www.pnas.org/content/108/10/4057.full

It’s now kept simple. Is possible to tweak it so that it does not become totally flat when a proportion is 0% and I can maybe refine a few of the numbers. With it being easy to change the math all that is needed is the new equation.

The truth table fills using computer/electronic format where don’t care is shown with “x” not the conditional “0” that is the result of a gene being off, which does care to calculations.

What this form is connected into can even include the GA technique but with there not much excitement over what is then a most simple feedback circuit controlling 7 scroll bars. Need to include what else exists in its circuit that does the higher level thinking that moves all the genes it has from place, as well as the slower lower level molecular thinking that controls what is produced in future generations. We then have a system that even includes multilevel intelligence where there is a circuit that has a place for everything that will in time be discovered about how it works. Not end up with a simple feedback loop with lifeless entities controlled by timers instead of their own intelligence. So where the next step is to make this a Design form for an Intelligence Design Lab it’s because that’s how it’s possible to get past the limitations of the now popular GA that leaves out more detail than it may seem. Raising the bar to having to account for multilevel intelligence produces the most complete models possible.

I have good reasons for not using a GA to bring beaks to life in a simulation even though some might find a way to make an issue out of it. Not requiring the reducing down to a “natural selection” variable eliminates from the model a world of problems trying to quantify something that is at times subjective and debatable. Here have place to hook in muscles and sensors and on its own figures out how to control what it has. We know that a genome is another self-learning system so is not scientifically unusual to represent that with a self-learning circuit as well. The result is an easy to use model that keeps itself going through time without needing to quantify “selection” or “fitness” whatever happens just happens. Where some get carried off by bananas to another island then they end up far away, so program then needs a way to track them all but that’s easy to add.

I can later adapt an Intelligence Design Lab to work with a beak and this time include cellular and molecular levels that this epigenetic system is most a part of. Where I left off with that software there is an unused visual subsystem just right for mouth touch/taste sensors to feel around with inside of tube feeders where the easy to eat seeds are usually harder to get at. Only have to connect the muscles and beak sensory into the brain level system for it to on its own figure out how to get at something with its new beak, which makes it easier to model the other self-learning processes that are at work in the system.

If no real problem can be found in this forum (and another) with the new screen form that introduces the chemistry of Darwin’s Finches then I’ll ask the authors of the paper whether it all looks right to them. The software then right away belongs at Planet Source Code as a tutorial for coding the epigenetics into 3D programs. Might then make an easy paper to write for biologists, but with the best peer review imaginable from the authors of the paper because of their having most experience with that part of it. First wanted to show it here to see what you think, or could maybe add to make it easier to figure out.

It is hopefully no big deal to make operational a truth table explained in a science paper. And in this case it’s not an Intelligence Design Lab it is a Beak Design form that would get added into one. This Lab does not need to include the latest intelligence theory that’s for something else. To keep things as uncomplicated as possible I am purposely keeping everything fully concentrated on what is in that one science paper, and that is it. There is no Intelligence Algorithm or any control of the settings other than your changing them to make the mouth move or turn. It is to have exactly what they describe, and no more which is why it just sits there waiting for you to change one of the scroll bar controls, for it.

As simple as this part of it is, the simple epigenetics is all it needs to model, what’s in the one paper and no more, with what it’s used in up to whoever can use it in their code. Discussion about what it can ultimately be included with is here irrelevant, only thing that matters is the simple math of the problem that the researchers explained. What do you think?

I have to update with a paper that adds detail, and shows the upper beak morphology working somewhat independently of the lower beak:

http://www.pnas.org/content/107/8/3356.full

The authors will be publishing their latest efforts on beak developmental evolution modeling in the near future. I’ll do what I can to get that here when the paper is out.

In the meanwhile I’ll follow up on new leads that suggest it's connected to a mechanism similar to what I have seen before that allows cells to set up a spatial communication grid for feedback to orient themselves to each other such that cilia are aligned in the same proper direction, and later keep proper timing.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720100/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747024/


http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed

I'm not sure whether my hunch is correct, but something similar to this would be a cellular (whole cell not one molecule) communicative response to conditions that very much complicates a gene based model, but simplifies the model I’m working towards that already has and expects a cellular level of interaction in addition to the molecular gene level. Virtual cells have to form the beak shape. But after development it’s just a 3D solid that stays the same which simplifies modeling a number of virtual birds in the same world at the same time.

And one more paper to help with some of the embryology this gets into.

http://www-hsc.usc.edu/~widelitz/2007_wu1.pdf