Glazed fountain spouts

My friends John and Chris Gray at Clayworks glazed and fired the spouts I built last week. They look very nice. Next step is to mortar them in to place -- which is going to be a pain because it is now 103 degrees outside!

Edge Detector Paper

The genetic edge detector paper just came out in Cell! Congratulations to Jeff and everyone else who worked on this paper. This is a project that we hatched about 3 or 4 years ago and it is finally out after a lot of hard work by everyone involved except me :-).

The project engineered bacteria to act as a communal signal processor implementing an "edge detector". You can think of the engineered bacteria as being like very simple computers, each running the following program: "Am I in the light? If so, shout to my neighbors. Otherwise, if I'm in the dark and I hear my neighbors shouting then raise my hand." Those that are in the dark and hear a neighbor must be near an edge. The "shout" is implemented by having the cells produce a small molecule which diffuses to their neighbors to be "heard" (actually, "smelled" is a better description). The "raise my hand" is implemented by having the cells produce a dark sugar which is visible to the naked eye when you look at the plate.

Interestingly, natural cells implement this edge-detection algorithm: the retina -- the first stages of image processing in the eye is to extract edges by a similar algorithm. The Nobel prize was awarded in 1967 to Hartline for this discovery in the retinas of the horseshoe crab.

Fountain spouts

Today I sculpted the spouts for the fountain on my back porch. The white boards under each are scaffolds supporting them until the dry at which time I will remove, glaze, and fire them. The firing should cause them to shrink so then I will be able to mortar them back into position.

Bed stain

Stained the bed today (not what you're thinking!). Almost done with this project! It's taken way too long.

Bed

I haven't been posting house progress for a while. My night-time project for the last week has been construction of a bed with a little bit of a floating cloud theme. I laminated four 4x8 sheets of maple plywood together and then cut out circles of various radii.


After Alex's sanding for many hours...


Here's the rough-cut end table before I cut out the circles...

Molecular model transfer function

Today I got around to trying out a simplified molecular version of the gate model that will replace my hyperbolic function.



The kinetics are all arbitrary for the model, but the shape of the transfer function looks even better than the made-up model from before. There's an almost perfectly linear section in the middle -- it looks more made-up than my made-up model! This is assuming that all three reactions have the same strength. Next, I need reasonable terms for the three reaction rates.

More parameter space of "standing" circuit

Using the parameter space maps made last time, I've set the "standing" circuit into a place where it has a nearly symmetric bi-stable steady-state at p1 =0.25 and p2=0.50.



The following is the derivative at a given concentration of standing. This dy/dt vs y plot (I don't know if there is a correct name for this find of plot) shows that there are two stable steady states at the zero crossings -5, and +5. There's also the unstable point near zero. It is not exactly at zero because the gate model functions do not cross at zero as seen below.






Now I continue the analysis with the "tired" half of the circuit. I'm interested in the response of "tired" when the "standing" input reaches 0, the point at which the tired circuit will charge fully.



Charging of the tired circuit when standing is 0 and tired starts at its steady-state value of -5


So, "tired" reaches 0 (the point at which the gate 5 is going to be fully on) within about 20 time units when standing = 0.

The following is a sampling of the parameter space for p1 and p2 given "standing" = 0. The steady-state value of tired changes as a function of p1, so for each graph I've started "tired" off at the appropriate steady-state and then watch the evolution when "standing" = 0. This demonstrates that I can delay both the onset of tired (when it hits zero) and how high tired gets at steady-state by adjusting these two parameters.


Next up, I put the circuit back together again...