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Topics - shvarz

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151
Biology / Enzyme regulation
« on: March 18, 2005, 10:56:58 AM »
Working on metabolism, it occured to me that there is a big problem we face and we don't have means to address it.  Imagine a metabolic chain:

A>B>C>D (releases energy)

and corresponding

A<B<C<D (consumes energy)

These need to be regulated somehow, otherwise they both run at the same time and just waste precious energy.  How do cells do it?

One simple way is "mass action".  PY (being a chemist) might explain it better.  But basically it is like a gradient and diffusion.  If you have a lot of A and little D, then reaction goes from left to right.  If you have a lot of D and little A, it goes from right to left.  The problem is that D and A are not compared in 1:1 ratio (this has something to do with free energy of reactions).  So for a cell 1000 A may be less than 1 D and reaction will still go from right to left.  And we will need to define these ratios of what is bigger than what and by how much.  Or bots will need to.  And these ratios are parts of cell's life strategy.  They come up with a lot of crazy ways to adjust that.  

For example, imagine that step B>C is actually B+X>C+Y.  The cell can make huge amounts of X and throw away Y.  Now because X is so much bigger than Y, the reaction will go from left to right, even if C is bigger than B.

This may sound complicated, but this is the meat and essense of any metabolism system.  I don't see any way around this crazy thing at the moment.  Especially if we have multistep reactions.  If all reactions are one-step it is a bit easier.  Bots can say

20
eatfat

and it would convirt fat to energy, or

20
makefat

and it would convert energy to fat.  

But having multistep reactions requires control, so we'll need all these commands like

eatpyruvate
make AcCoA
etc

Which means that idea of having metabolism run behind the scene goes to hell.  

Any ideas?

152
OK, here is a very brief metabolism that we can already start using.  I decided to go with the barest minimum for two reasons:
1. Don't want to intimidate people
2. We can always add stuff later as a way to introduce balance/diversity.

As a result, what you'll see below is only about 0.1% of all reactions that are happening in our bodies.  I assume that we'll have carbs/protein/fat system.  These turn up in bot's stomach, and then are digested.  What follows below is description of how bots can use them to extract energy.  Theoretically all these reactions are reversible, meaning that they can be used to create carbs/protein/fat, but the energy required to make stuff is always more than you get when you destroy stuff.  It is especially true for proteins, which require 10 times more energy to make them, than energy that is released when you destroy them.

Another note:  I'll use ATP to keep track of how much energy is generated.  Simply assume that ATPs will be converted to nrg with some coefficient.

So here it goes:

CARBS
' Note: carb degradation is the major route of energy production.  Fats and proteins join in as small streams join big river.

carb+7 H20=8 glucose
glucose = 2 pyruvate + 2 H2O + 8 ATP
pyruvate + 1.5 O2 = AcCoA + CO2 + 3H20 +6 ATP
AcCoA + 2 O2 = 2 CO2 +12 ATP

FAT

fat + ATP = fatCoA
fatCoA +7 O2=8 AcCoA + 42 H2O + 35 ATP
(see above for fate of AcCoA)

PROTEIN

protein = 8 am.acids
am.acid = pyruvate + NH4
(see above for fate of pyruvate, see below for fate of NH4)

NH4
'Note: This is very-very toxic.  If bot does not get rid of it, it gets really messed up.  It cannot be directly thrown out, it has to be converted to urea.

2 NH4 + CO2 + 3 ATP + H2O = urea
(urea is basically "waste", it can be discarded as such).

Final summary of how much energy you get from each type of food:

1 fat = -1+35+8x12=130
1 protein = 8x6+8x12-4x3=116
1 carb = 8x36=288

P.S: As I said, this is only the barest possible basics.  We can add more steps everywhere.  Two possible reasons to do that: a) make sim more complicated, leading to bigger diversity and b) balancing issues - adding more steps means that it takes longer to digest and requires more enzymes.

153
Biology / God doesn't play dice
« on: March 15, 2005, 11:49:10 PM »
I found this absolutely AMAZING article about...  well, about life as a bacteria.  You ALL must read it, it will change your world!  It is written in very easy-going and plain style, so it is acceptable to everyone.  There are some cool facts about inertia in bacterial life in the beginning of the article and some cool ideas about movement and diffusion near the end.  Read it!

Here is the link: http://brodylab.eng.uci.edu/~jpbrody/reyno...lowpurcell.html

154
Biology / Sharks and grass
« on: March 10, 2005, 12:09:33 PM »
In discussions about specialization it has often been mentioned that certain species spcialize in eating certain types of food and can't switch to others.  One of the examples was shark, which cannot suddenly learn to eat grass if meat becomes unavailable.

Cows eat only grass, wolves eat only meat, some bacteria survive only on certain and very rare chemical compounds, which can be found next to active volcanoes.  But ability to digest and extract energy from different things cannot be likened to distributing some "points" between different categories.  It cannot be stated that cows gave all their "feeding points" to grass and there was nothing left to give to meat.  In fact, cows could have meat-digesting enzymes.  But why bother?  They don't hunt anyway.  Take a bear - it can eat almost anything - meat, fish, berries, mushrooms, eggs, garbage.  Is bear worse in digesting meat than a wolf?  No.  Is it worse in digesting mushrooms than a squirrel?  No.

The real specialization does not come in form of enzymes - it comes in form of different behaviours and different strategies to find food.  If you can find food in abundance - the enzymes will come.  Here is an example with humans.  Originally the enzymes that digest milk were only present in babies - to digest mother's milk.  Adult humans could not digest milk.  Then they learned to grow cows and obtain milk from them.  As a result, a mutation appeared that allowed adults to digest milk.  Now it is present in majority of population and only some unfortunate people don't have it.  Availability of food lead to appearance of enzymes.

155
Biology / Volvox
« on: March 10, 2005, 11:35:41 AM »
So, you want to make a multicellular bot?  Here is the simplest known multicellular organism with complete division of labor: Volvox!  
- It is a ball of cells consisting of two cell types.  
- It does not have a pre-determined body plan.
- Cells in volvox act together to achieve common goal.
- It protects offspring until it is big enough to duke it out on its own.
- It is a veggie.

Can we make Volvox in DBs?

Just some links for you to get more sense of what volvox is:

Some pictures and basic info

Some movies of Volvox in action

Finally, just some copy-paste for your reading and enjoyment:

What is Volvox? The name comes from the Latin volvere, to roll, and -ox, as in atrox, fierce. Volvox is a spherical multicellular green alga, which contains many small biflagellate somatic cells and a few large, non-motile reproductive cells called gonidia, and swims with a characteristic rolling motion.

Ever since van Leeuwenhoek first viewed these algal ‘fierce rollers’ with utter fascination in 1700, one biologist after another has pointed to Volvox as a model organism that could be used to support or refute some important biological concept of the day, such as spontaneous generation, preformation, epigenesis, the continuity of the germ plasm, and so on. All attempts to exploit Volvox as a laboratory model system failed, however, until the 1960s, when Richard Starr's group finally discovered a medium in which the organism would thrive and reproduce in captivity. Starr then circled the globe, bringing into culture all 18 known (and several previously unknown) Volvox species. By 1970, he concluded that a mating pair of isolates of V. carteri from Japan had the best combination of properties to serve as a genetic model system. Most studies of Volvox reported in the last 30 years have used those strains of V. carteri or their descendants, and so this guide will be similarly restricted in scope.

How does Volvox reproduce? Although V. carteri has a sexual cycle that can be induced and exploited for Mendelian analysis, the sexual cycle is not used for reproduction in nature; it is used to produce dormant, diploid zygotes that are able to survive adverse conditions. During all active phases, Volvox (like other green algae) is haploid and reproduces asexually.

In V. carteri, an asexual cycle begins when each mature gonidium initiates a rapid series of cleavage divisions, certain of which are visibly asymmetric and produce large gonidial initials and small somatic initials. The fully cleaved embryo contains all of the cells of both types that will be present in an adult, but it is inside out, and to achieve the adult configuration it must turn right-side-out in a gastrulation-like process called inversion. Cleavage and inversion together take about 8 hours, and the complete asexual cycle takes precisely two days when it is synchronized by a suitable light–dark cycle.

Following inversion, both the adult spheroid and the juvenile spheroids within it increase in size (without further cell division) by depositing large quantities of a glycoprotein-based extracellular matrix. Part way through the expansion phase, the juveniles digest their way out of the parental matrix and become free-swimming. By that time, the somatic cells of the parental spheroids, having fulfilled their function, are already moribund, and will soon be history.

Thus, whereas the gonidia are non-motile and potentially immortal, the somatic cells are specialized for motility, but destined to die when they are only about four days old. This difference raises with particular clarity a central question of developmental biology: how are cells with entirely different phenotypes produced from the descendants of a single cell?

What is the genetic program for germ–soma differentiation in Volvox? In most close relatives of Volvox, all cells first execute motility and other vegetative functions, and then they redifferentiate and engage in asexual reproduction. Mutational analysis has defined three types of gene that play the major roles in converting this ancestral program for biphasic development into a germ–soma dichotomy in V. carteri: first, the gls (ImageonidiaImageesImage) genes act during cleavage to permit asymmetric division and formation of large–small sister-cell pairs; then the regA (Imageenerator Image) gene acts in the small cells to prevent all aspects of reproductive development, while the lag (Imagete Imageonidia) genes act in the large cells to prevent formation of somatic features such as flagella and eyespots. Genetic and experimental analysis indicates that it is the difference in cell size at the end of cleavage that determines whether regA or the lag genes will be activated.

156
Off Topic / Specialization again
« on: March 08, 2005, 12:03:06 PM »
OK, just for the fun of it, I am going to play devil's advocate and argue that we don't need a specific "specialization system" at all in DBs.  Throw your arguments at me for the contrary.  But please be specific.  I dont want any general pylosophical questions, I want direct things that don't work in DBs and how specialization system will fix them.  Let's see where it leads us :)

So far, I've seen one very specific comment (from PY?): Bots don't specialize in feeding.  There is no way for a bot to specialize in eating only a particular type of bot (say a veggie).  So we need a system to force it to specialize.

My answer:  Bots don't specialize, because there is no need for it.  Energy is energy in DBs, regardless of where it came from - from veggie or from competitior bot, or from your own species.  If we make bots to consist of different types of energy (protein/carb/fat system discussed), then specialization will appear on its own, without any artificial "specialization system".

157
Off Topic / Hmmm
« on: February 22, 2005, 01:14:35 AM »
Yesterday I was told that the guy with whom we were drinking vodka last summer near Mt. Rainer was Alexei Pazhitnov.  THE Alexei Pazhitnov (link for dumb people: http://absolutist.com/tetris/tetris.html

I feel like Forrest Gump :)

BTW, don't bother to reply - I am off to Hawaii for 10 days.  Talk to you later, guys!

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