Second Set of Review Questions for Second Exam


Posted February 23, 2016

A) In the particular version of Turing's mechanism that I asked you to memorize,
? How many diffusible chemicals are used?
?? These chemicals are increased in concentration in proportion to what?
??? These chemicals are destroyed or otherwise decreased in concentration in proportion to what?
???? Which of these chemicals either diffuses faster than the other, or in some other way produces its effects at longer range?

B) Describe the spatial patterns produced by this combination of rules in a one-dimensional graph of the concentrations of the diffusible chemicals. C) Is Brownian motion sufficient to initiate pattern formation by this set of rules?

D) Is the resulting pattern more irregular when initiated by random variations than when initiated by regularly-spaced stimuli?
(Actually, the exact opposite is true; but how can computers be used to answer this question?)

E) What are some embryological phenomena that could possibly be produced by this kind of "reaction-diffusion system", like the ones invented by Alan Turing?
Somite formation, color spots and stripes. & please think of some others.

F) Imagine that some cells obey the following sets of rules:
Tension stimulates its own increase, and also stimulates increased osmotic pressure
Osmotic pressure stimulates decreased tension, and also stimulates a decrease in pressure.
Tension spreads faster than osmotic pressure can diffuse.
Predict the net effects.

G) Imagine cells that obey the following rules:
Cell type A stimulates its own growth and division, and also causes more B cells to form.
Cell type B stimulates death of both A and B cells.
Cell type B crawls faster than cell type A.

H) Why can't Turing's and other reaction-diffusion systems explain embryonic regulation (what Driesch discovered)?
Hint: What if the diffusion rate of substance B increased in proportion to the total size of the space within which the chemical reactions are ocurring? What then?

*I) Why are computer simulations useful (or necessary?) to answer such questions as whether the patterns generated can be regular, whether their wave-lengths can vary with diffusion rates or sizes of tissues where the reaction is going on? (I realize you probably have not yet experimented with such computer programs, but you have observed them in class and on web sites.)

J) Consider and compare which is more useful for understanding how genes cause embryos to form spatial patterns:
one) An actual combination of chemicals whose reactions produce regular spatial patterns?
two) Computer programs that test the effects of any combination of rules that you choose?
three) Mathematical equations?

K) How could a computer program be useful for testing whether hypotheses actually predict the phenomena that they were invented to explain. (Don't the inventors of hypotheses know what they predict? Why not just ask the author of a theory?)

*L) Did you ever notice that zebra stripes are narrower around the legs, as compared with the broader stripes that encircle the main body like belts?
Does this contradict the possibility that these patterns are generated by reaction-diffusion systems?
Might the cause help understand what Driesch discovered (when separating embryonic cells)?

*M) Notice that animals with spotted color patterns tend to have rings around their tails, instead of spots. Is that a confirmation of reaction diffusion systems; or does it confirm what they predict.
How could you use a computer to find out?

*N) If developing embryos really do use reaction-diffusion systems (like those invented by Turing) to generate anatomical patterns (like pigmentation patterns), does that mean that they can only have a limited range of geometrically different patterns? In contrast, if development uses Lewis Wolpert's "positional information" type of mechanism would any such limitation be expected? hint: why not?

Maybe we have 5 fingers for reasons related to the reason echinoderms have 5 planes of reflection symmetry. Argue pro or con.

O) Did Driesch discover what amounts to dilation symmetry?

P) If so, do echinoderm embryos have this dilation symmetry? Or is dilation symmetry possessed by the mechanisms that echinoderm embryos use to break reflection and displacement symmetry?

Q) Do tensor variables have more or less symmetry than scalar variables.
(usually less; sometimes the same, examples when the same symmetry?)
(Remember Weyl's system for defining different kinds of symmetry?)

R) In terms of historical dates, could Curie have met Driesch? What could they have learned from each other? (By coincidence, both got interested in occult seances)

S) Argue pro or con: Gastrulation in mammals breaks reflection symmetry? Or maybe primitive streak formation? Or formation of Henson's node?

T) Argue pro or con: Somite formation breaks displacement symmetry?

*U) Alternatively, are such embryological processes controlled by mechanisms that break symmetry?
Or are the physical processes (the various cell reorientations and rearrangements) themselves what break symmetry?

V) What symmetries do Dictyostelium slugs and fruiting bodies have at their sequential development from chemotactic aggregation to fruiting body?

W) If small particles of plastic or carbon become stuck to the outside surfaces of crawling cells, contrast the observed directions and amounts of transport of such particles attached to the plasma membranes of the following:
Amoeba proteus
Rolling amoebae
Shelled amoebae
Tissue culture cells from humans or other animals
When such particles are embedded among extracellular collagen fibers near mesenchymal cells

X) Describe the directions of actin movement in tissue culture cells as compared with Amoeba proteus.

Y) Argue pro or con (while demonstrating knowledge and creative imagination)
* The key difference between mosaic versus regulative development is whether or not the control mechanisms have dilation symmetry.
* These key differences (between mosaic versus regulative development) is whether cell fates are irreversibly decided early or late in development? ...Decided at the times of cleavage?
* Something else you can think of...?

Z) How is the crawling locomotion of tissue culture cells related to the invasiveness of cancer cells?








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