Computer Science and Biology 361
Submitted by SunnySingh on Wed, 2006-02-15 03:44
I should preface this post with some warnings. First and foremost, it’ll probably be rather verbose. Second, I anticipate catching much flak for this; I have discussed these opinions with many others in the past and have always received strange looks. Finally, it's 2:30 am and though this is all clear in my head, it may come out as pure incoherent blabber. Last night I watched the movie
Pi for probably the 108th
time. Yeah, I know it’s just a Hollywood movie sprinkled with inaccuracies…but my love for math, physics, and computer science was born when I saw this movie. It opened up my mind to ideas I would never have fathomed in my wildest dreams. There are redeeming qualities in this movie-—many of which are related to our study of emergence. For those who have not seen it, I highly recommend doing so. Keep in mind that it IS a movie and not completely factual. Anyway, I’d like to post and comment on some of the more illuminating quotes/scenes which pertain to emergence.
Submitted by Flora Shepherd on Tue, 2006-02-14 01:15
Slime Mold Controls ROBOT!!!
I just thought this was pretty pertinent given today's discussion about slime mold/sand and emergent properties.
Submitted by Kathy Maffei on Mon, 2006-02-13 21:20
With Doug's help, I posted my tree growing model
with some documentation that may be useful. There's a link on the page to download the nlogo file, in case it's of interest.
Doug wanted me to document how to post netlogo aps. For BMC students:
1) make sure you have an html folder in your root directory called "public_html" and make sure it and your root directory both have read and execute permissions for everyone. You can also use a subdirectory within public_html - just be sure it has the appropriate permissions.
2) place a copy of your nlogo file in the public_html folder (or whatever subdirectory you want to use within public_html)and open it in Netlogo. You may want to edit the Information tab for your model because Netlogo will place this information in the html it creates when you ask it to save as an applet. Go to File -> Save As Applet... and save the html file it creates with the nlogo file in your public_html folder (or the subdirectory you're using). You can edit the html according to its directions.
Submitted by Flora Shepherd on Mon, 2006-02-13 19:31
”Machines take me by surprise with great frequency.”
Alan Turing, found
When thinking about emergence, my mind ping pongs between three different issues. The first two, my overwhelming distrust of Wolfram and explorations of the top down dichotomy, I will save for another post. Since we are still discussing agent based modeling, I will stick to my third fury.
From the first day of class
, I have been troubled by the idea that in making computer models, our objective “is to be ‘surprised’, to ‘surprise’ others, to establish that some pattern/phenomenon that is presumed to depend on complexity/planning/a directive element can be produced without that. To show what might be, rather than what is.” This has been a recurring theme in lecture and it just does not sit well with me. Why is it that models cannot be used to solve problems? Why don’t they portray what is? This rankles me. If the modeling method has no utility beyond surprise, then it is little more than an intellectual jack in the box: entertaining and beautiful but not appropriate for solving problems in a science class (see my icon? ).
Submitted by Leslie McTavish on Thu, 2006-02-09 18:16
I've found something that I found interesting with the ant.
Given 2 ants and enough time, more times than not (I think I've tried it 4 or 5 times and it's only failed once) the two ants will eventually retrace their steps back to the beginning, erasing everything they have done, and then start all over again. Curious, no?
Perhaps I never ran Langton's ant long enough to see of this would happen with his one ant..
Submitted by Kathy Maffei on Wed, 2006-02-08 13:45
Ok, I’m no philosophy major, but I’m going to try to better explain my feelings about the concept of purpose:
To start, I find only 1 definition of the word purpose
that appears to relate to our discussions: what something is used for. Sure, it’s also affected by context (i.e. “What’s your purpose for being in this building right now?” vs. “What is the program’s purpose?” vs. “the purpose of my existence”), but either way, it boils down to pretty much the same thing: function / use / reason.
Now, I think it’s safe to say that anything and everything can have more than one use. Take for example something as straightforward as the Hello World program, which simply prints the statement “Hello, World” onto the screen. It can be said to have the purpose of printing “Hello, World” onto the screen, or its purpose could be to serve as a basic example for beginning programmers, or it might be used to quickly test your success at installing C libraries on your machine, etc.
Submitted by LindsayGold on Wed, 2006-02-08 11:19
So I know that there have been a lot of new theories about the beginning of the Universe since I learned about the Big Bang
, but that's the oh-so-ancient premise I'll start my post on. Paul said in class on Monday that at some point the universe was computable - there were few enough particles and little enough space, I suppose, that you could follow what happened from microsecond to microsecond. My question is this: when did it stop being computable? Where was the breaking point?
Submitted by Laura Cyckowski on Tue, 2006-02-07 23:10
I've been thinking more about the concept of "purpose" and think that it could be said that an agent has a purpose in that it's activity is necessary (/sufficient) to a system/thing/property (still meaningless w/out an observer), in which way it seems intent is not necessarily implied by purpose and the agent need not be aware of a similar "bigger picture"/"goal" like the observer.
Also, wanted to post a link to an interesting set of rules for The Game of Life called Brian's Brain/Brain Rules
(I think I saw a module for this in NetLogo as well). The spin on this set of rules is that there are intermediate stages to "life" and most everything reasonably winds up as a glider. I was looking through the modules from the Game of Life again last week and although the ones that start out as already configured patterns are neat the ones that are still most fascinating are the ones that start out very simple and lead to complexity/organization that rivals the former, since these second type are able to account for both a (likely/random/simple) origin and from there a progressive development of the "system" to higher complexity/organization.
Submitted by SarahMalayaSniezek on Mon, 2006-02-06 17:53
This might seem quiet apparent to others, but after class I was thinking about Langton's ant and how it relates to CA and emergence. It seems to me that Langton's ant just clarifies and supports our understanding of emergence. As I see it, Langton's ant is a CA inside of a CA. Does this seem like this to anyone else? This mainly became clearer with the examples on NetLogo, but I have not tried it out myself yet. I feel that Langton's Ant example, and the many more we will come up with using NetLogo will help support Wolfram's theory that everything is computable. I do not necessarily believe in what he says, but what is leading me to believe otherwise now? I have been trying to think of things that do not fall under being computable, but maybe they are computable, but not in the way we think. That is not too clear, but what I mean to say is maybe we cannot compute the answer to the halting problem, but that does not mean it is not computable at this time. I absolutely this whole time have been thinking that everything is interconnected and builds on each other, that it was maybe started with just simple rules and a simple state and evolved to be something bigger. It is possible; I do not see anything proving against it...so where do we go from here? It just seems there is not a right answer and we all see it somewhat differently, but for purposes of this class, I can see the relationship that Wolfram is trying to make, but that does not mean i believe in it. I really think that Wolfram has opened something up for the rest of us, and that is something to question and really think about so that we can find an answer that is less wrong. I do see that Wolfram does not account for free will and other things, but then how can we make it clearer and incorporate free will and the other things he does not account for into Emergence? I honestly think that everything is connected and makes up a bigger picture, I am still though unsure of how we got where we are. Is it because we just evolved from some little agent and rules, or just from something like CA?
Submitted by PeterOMalley on Sun, 2006-02-05 20:57
This isn't directly related to the recent discussions of purpose and determinism, but I stumbled upon
this on the web and I thought it was too good to pass up:
and the gallery thereof
I don't know how simple the algorithms are, or how emergent the phenomena are, but I think it definitely deserves a link.