Kansas Citizens for Science

[Gary S. Gaulin]

There is a whole new science coming of age called "Systems Biology" that is more or less trying to go from genes to what the theory predicts will be a "system" like shown by this circuit:

From: http://theoryofid.blogspot.com/


Here is an introduction to the science:
http://www.systemsbiology.org/Systems_Biology_in_Depth/Premise_of_Systems_Biology

This directly relates to what I show in bold below. It's part of the sensory feedback and memory addressing:

[wffarrell]

It seems to me that the vision part would have been written in Visual Basic, and the part that "wakes up and smells the coffee" would be written in Java.

Perhaps French organisms were written in Pascal.

Fish were probably written in C.

[Gary S. Gaulin]

Shhhhhh! We're busy studying, you troll you!

At least I finished scanning the BioTapestry Quick Start Tutorial.

http://www.biotapestry.org/quickStart/QuickStart.html

I also downloaded the source code. What a collection of files that is! Not a beginners project, that's for sure. But I get the idea of drawing with arrows and repressors with the foot at the end of the line that connects to the gene. That gets me on the same page with scientists as how to connect into genetic regulatory network schematics.

Now I need to try getting Cytoscape running. How did it work for thine all knowing teacherlyness?

http://www.cytoscape.org/features2.php
_________________
http://gaulintracksite.blogspot.com/

[wffarrell]

It took me all night to think of this so pay attention.

What was the Garden of Eden written in?



Python!

[Jack Krebs]

And clams are written in ....?

[Gary S. Gaulin]

Clams are written in a shell!!!!

As in "Shell program" where you just write in the vital code so do not have to write the whole thing. That's what right away came to my mind as an obvious one.

But I did not spend all night thinking up an answer like wffarrell probably did (not that I would want to) so maybe there's a better possibility. That would sure prove their scientific superiority!

Good news is that I managed to get Cytoscape running then took a look at the source code download, which included an interesting test data file called ontologySession that has metabolic pathway clusters with recognizable names to help figure out what is going on. With gene number "3015" it connected straight to NCBI then I soon had 500+ nodes showing human "Signaling in immune system" on the screen, all different ways.

Now I need a model organism but there does not look like much is there to work from. All that science does not know yet is so darn annoying! Wffarrell needs to do something about that!!

[Jack Krebs]

Nice try, but no. Clams are written in Perl.

[wffarrell]

Yeah, Jack, but Perl stands not alone.

It must be in a shell. Furthermore, I predict that the California (Berkley) shell would be morphologically different from the African (gnu) shell, both, of course, descended from the common marine shell, C-shell.

[Jack Krebs]

Ah yes, perl in a shell that came from the C. I get it now.

[Gary S. Gaulin]

But pearls come from oysters! Then again the shell is made of "mother of pearl" so I guess it works. kinda.

Pearl is also used in bioinformatics, a little. I would much rather program in that than Java. So I'll try to make like a clam and (where possible) use pearl. Problem seems to be in a good easily available visual editor. Without that writing a program can take forever. The Microsoft Visual Studio - Visual Basic editor system set the standard and might still be the fastest way to develop a program. I noticed a Perl add-in for Visual Studio so maybe I'll try it.

And I found a MUST SEE video on nucleosome self-assembly and the replication mechanism. First time I saw it. This is incredible!

http://www.ecolicommunity.org/?option=com_content&task=view&id=2263

There is no doubt that molecular biology is running right straight into robotics and all else. It's the only way I see of explaining how all of that is possible. Science just keeps making everything more complicated all the time. What ever happened hey to the good old days that wffarrall knows where DNA just unzipped then there are two and that was all there was to it? These days science just keeps on making things harder to explain, all the time.

Thankfully I made progress in finding a model organism. There are videos here showing how the BioCyc database works and what it shows. Very educational.

http://www.ecocyc.org/webinar.shtml

From what I can see the most studied "E.Coli K-12" is perfect. It has a simple genome with nothing fancy. The "K-12" strain easy to remember and sounds like it was supposed to be the critter for K-12 education.

Yeast has a good deal of experimental metabolic data but it's kinda boring. E.Coli have flagella!


http://www.aip.org/pt/jan00/berg.htm

[Gary S. Gaulin]

After watching the video on how EcoCyc works I found an "Escherichia coli transcriptional regulatory network for sensing the extracellular and intracellular environment" database and cell sensing info!

http://regulondb.ccg.unam.mx/html/CellSensing.jsp

And notice how drawing it all out by function is such a mass of lines it's hard to tell what is going on:

http://www.ccg.unam.mx/Computational_Genomics/regulondb/CellSensing/sup-fig2.pdf

You can't see what switches the flagellum in response to environment. Probably not much there to explain that yet, anyway. So here there is a "system" to explain. If it is the "random behavior" mechanism in control of the flagella then there is no "cellular intelligence" present. If there is associative memory in control of flagella then there is cellular intelligence present. It does not matter to the theory which it is, the theory provides a way to determine that.

The theory predicts molecular intelligence is present to account for the ability to come up with such brilliant design, so there is the genome itself to explain the same way (already know it's a memory) but that has the same kind of visualization problem in addition to it having to replicate. A computer model could then be environmentally stressed with a resulting lineage within range produced by experimentally stressing real E.Coli to the same conditions. Epigenetics should be relatively predictable. Code changes lesser so, but a computer model should find possibilities.

I'm not sure how much I can sort out from all the data, but at least there is now something available to start drawing a model E.Coli from. Learn how it works by putting an E.Coli together sort of thing.

The following are vital basics worth noting: