Monday, April 7, 2014

A nice quote

"It is not birth, marriage, or death, but gastrulation, which is truly the most important time in your life." - Lewis Wolpert, pioneering developmental biologist
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Wednesday, April 2, 2014

To what extent to the assumptions we make, collectively and independently influence the models we construct in the world? In other words, how strong are our assumptions? Also, what are they?

This is something I ask generally, about all scientific fields. Most interestingly, what are the assumptions made by physicists which might be hindering the achievement of things like teleportation of matter and faster than light travel (if these are even possible).

If the assumptions are too great, how could we break out of them? What would we find?
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Thursday, March 20, 2014

I have this idea about life systems. It's that at least part of their function is to take states in the present, past, and future and map to states in other time frames. How can I make this notion falsifiable/testable?
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Thursday, March 13, 2014

As far as TagFS goes (and all of the projects in a similar vein -- dhtfs, TaggedFS, all of the other "TagFS"), the fundamental problem is and always has been interface. I effectively use tagging on my Firefox bookmarks to annotate and retrieve data that interests me. The great advantage provided by this interface is that it makes tagging like second nature, so it's unobtrusive and helpful. My approach with TagFS would never have worked because it's cumbersome to set up and use the tags in a heterogeneous system and more importantly, there was no way to declare tags at file creation points: those critical moments in time when you still give a damn about the files, but haven't yet lost them. Harnessing the motivation surrounding the initial data entry and aligning annotations with the thoughts that first compelled the user to save the data -- what I think of as the "retrieval memory" -- must be the key concern for a successful interface and that's what Firefox bookmark tagging gets right.

How can we bring such an interface to the desktop? My first suggestion would be a modification of the file/save dialog in most applications. This is usually tied into the interface toolkit (e.g., GTK) in a way that it should be possible to modify it directly and have that modification spread to all applications that use it. There are, however, other ways to create and save files, such as through the command line or through applications that do not use the standard interface toolkit. One other suggestion is to create a virtual file system layer that presents a secondary prompt for tagging on file creation. This, of course, has its own problems in that not every file created in the user's name needs tagging (e.g., applications frequently create cache and config files). We can get around that limitation by demanding that the user selects directories to be managed. There are still no guarantees that a third-party program won't attempt creation of files in this directory, but adding to the prompt an option to never tag a certain kind of file may solve this problem.
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Wednesday, March 12, 2014

A useful site!

I often have trouble with pronouncing words I've read.

I've found this wonderful site (and bookmarked it this time!) to help me out: HowJSay is a site which has a list of words spoken by (apparently) 2 or 3 British men. I've found a few pronunciations that have differing pronunciations in America from Britain, which the recordings speak also.
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Thursday, March 6, 2014

Why, if cortical areas were largely the same in their organization, would there be visual differences in the various regions of the cerebral cortex?
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Monday, March 3, 2014

LTP and learning

How could we test the relationship between long term potentiation and learning?

That's hard. Anyway. How could we test if increasing the surface area of a
terminal bouton results in increasing post-synaptic response? I guess first
it's necessary to affirm that it isn't a foregone conclusion that this
mechanism already operates. According to Dr P, the increase in the area of
a terminal bouton results in increase in the number of docking sites (mediated
by the presence of precursors for the creation of synaptotagimin and SNARE
molecules I suppose). We also know that under low-Ca++ concentrations, the
primary means of exocytosis into the synapse is through complete fusion and
collapse of the vesicles. However, the reason that under these conditions
(which are typical for at least some of the neurons) the result isn't to have
the boutons grow unbounded is that the membranes are also recycled into new
vesicles through the process of endocytosis
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2343565/ and others].

So anyway, first stop endocytosis at the axon terminal without hindering the
process of exocytosis or creation of new docking sites, or anything really
having to do with the movement of vesicles (if possible...maybe some virus?).
Second, monitor the extracellular concentration of neurotransmitter following
either the introduction of Ca++ into the terminal (this might be achieved also
with an AP, but that may have additional consequences not considered).
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