BioSec: Artificial Life

= Note #1

Date the note was created was: 
2012-01-05T20:20:30
The contents of the note were: 
examples of genotypes that exploit others?? (in a program?) memory hogging / cpu time hogging 

Note #2 
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Date the note was created was: 
2012-01-05T20:23:46
The contents of the note were: 
The context of evolutionary biology is phylogeny, the connections between all groups of organisms as understood by ancestor/descendant relationships.

/ref{http://www.ucmp.berkeley.edu/exhibit/introphylo.html} retrieved January 5, 2012 at 20:24 EST4

Note #3 
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Date the note was created was: 
2012-01-05T20:27:38
The contents of the note were: 
punctuated equilibrium: 

Punctuated equilibrium predicts that a lot of evolutionary change takes place in short periods of time tied to speciation events.

example: mollusks that got separated from the main group evolved faster to deal with new surroundings, when reintroduced back into the general population - beat out the competition, and the static group died out.

ref: {http://evolution.berkeley.edu/evosite/evo101/VIIA1bPunctuated.shtml} Retrieved January 5, 2012 at 20:28 EST

Note #4 
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Date the note was created was: 
2012-01-05T20:32:19
The contents of the note were: 
basic compiler optimization is known as 'loop unrolling'.

The goal, then, is to limit the amount of loop overhead as a proportion of the commands, to decrease the number of control hazards in the total run of the loop, and to fill the unavoidable stall spots with independent instructions. The first two can be done somewhat through loop unrolling, and the last through rescheduling.

/ref1{http://www.cs.umd.edu/~meesh/cmsc411/website/proj01/proja/why.html}

Simple Example:

While much of the time, the entity that performs the loop-unrolling will be an optimizing compiler, you the programmer can also do the task in your high-level language. Taking the loop

for(int i=0;i<1000;i++) a[i] = b[i] + c[i];

You can quickly and simply halve the number of iterations by changing it to this, instead:

for(int i=0;i<1000;i+=2) { a[i] = b[i] + c[i]; a[i+1] = b[i+1] + c[i+1]; }

/ref2{http://www.cs.umd.edu/~meesh/cmsc411/website/proj01/proja/soft.html} Retrieved January 5, 2011 at 20:35 EST

Note #5 
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Date the note was created was: 
2012-01-05T20:38:56
The contents of the note were: 

/ref{http://www.wired.com/wiredscience/2010/05/scientists-create-first-self-replicating-synthetic-life/} Retrieved: 20:38 EST

the first life form to be entirely controlled by synthetic DNA. But they show that making a living cell with a synthetic chromosome is possible. Dr Craig Venter and his colleagues hope to use this technology to design new bacteria from scratch - cells that could carry out useful functions.

/ref{http://www.bbc.co.uk/news/10134341} Retrieved: 20:42 EST

The creation of synthetic life is a goal of scientists working in the fields of synthetic biology or exploring the origin of life. The term has also been used to describe recent experiments [1] that transferred the chemically synthesized copy of a bacterial genome into a different (but closely related) bacterial host cell. However, the term Synthetic Life is usually associated to the creation of a living system "from scratch", that is from isolated building blocks. This has not yet been achieved. Synthetic life is artificial life created in vitro from biochemicals and their component materials as opposed to the normally implied in silico when using the broader term "alife".

/ref{en.wikipedia.org/wiki/Synthetic_life} Retrieved Jan 5, 2012 at 20:53 EST

Note #6 
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Date the note was created was: 
2012-01-05T20:56:40
The contents of the note were: 
examine how objects and patterns can arise from simple interactions in ways that are surprising and counter-intuitive. We will present examples with simple squares that turn on and off, but the underlying ideas will provide you with a new perspective for thinking about many phenomena in the everyday world.

(The Game of Life)

/ref{http://www.playfulinvention.com/emergence/} Retrieved Jan 5, 2012 at 20:56 EST

Annotations for page 1 were: 

Note #1 
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Date the note was created was: 
2012-01-05T21:04:04
The contents of the note were: 
Pantograph: "Pantograph" is a drawing instrument to magnify figures.

Tracing the original figure by moving the red point, we can automatically obtain the magnified figure with the pen at the blue point.

/ref{http://www.ies.co.jp/math/java/geo/panta/panta.html} Retrieved January 5, 2012 at 21:04 EST

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Note #1 
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Date the note was created was: 
2012-01-05T21:08:40
The contents of the note were: 
Cambrian explosion: Most major animal groups appear for the first time in the fossil record some 545 million years ago on the geological time scale in a relatively short period of time known as the Cambrian explosion. Of great worry to Darwin, the explanation of this sudden, apparent explosion persists as a source of numerous major debates in paleobiology. While some scientists believe there was indeed an explosion of diversity, others believe that such rapid acceleration of evolution is not possible; they posit that there was an extended period of evolutionary progression of all the animal groups, the evidence for which is lost in the all but nonexistent precambrian fossil record.
The theory of the Cambrian Explosion holds that, beginning some 545 million years ago, an explosion of diversity led to the appearance over a relatively short period of 5 million to 10 million years of a huge number of complex, multi-celled organisms. Moreover, this burst of animal forms led to most of the major animal groups we know today, that is, every extant Phylum. It is also postulated that many forms that would rightfully deserve the rank of Phylum bothCambrian Fossils appeared in the Cambrian only to rapidly disappear. Natural selection is generally believed to have favored larger size, and consequently the need for hard skeletons to provide structural support - hence, the Cambrian gave rise to the first shelled animals and animals with exoskeletons (e.g., the trilobites). With the innovation of structural support, the early Cambrian period also saw the start of an explosion in the size of many animals.

The Cambrian Explosion is the outcome of changes in environmental factors leading to changes in selective pressures, in turn leading to adaptive diversification on a vast scale.

/ref{http://www.fossilmuseum.net/Paleobiology/CambrianExplosion.htm}

Note #2 
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Date the note was created was: 
2012-01-05T21:12:40
The contents of the note were: 
Notes on above note:

Phylum: the primary subdivision of a taxonomic kingdom, grouping together all classes of organisms that have the same body plan.

/ref{http://dictionary.reference.com/browse/phylum}

Retrieved January 5, 2012 at 21:14 EST

speciation: The evolutionary formation of new biological species, usually by the division of a single species into two or more genetically distinct ones.

speciate: (Life Sciences & Allied Applications / Biology) to form or develop into a new biological species

/ref{http://www.thefreedictionary.com/speciate}

Note #3 
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Date the note was created was: 
2012-01-05T21:25:34
The contents of the note were: 
Fitness functions: 

The genetic algorithm is a highly parallel mathematical algorithm that transforms a set (population) of individual mathematical objects (typically fixed-length character strings patterned after chromosome strings), each with an associated fitness value, into a new population (i.e., the next generation) using operations patterned after the Darwinian principle of reproduction and survival of teh fittest and after naturally occurring genetic operations (notably sexual recombination).

/ref{"Genetic Programming" -on the programming of computers by means of natural selection - John. R. Koza, 1992, MIT press "a Bradford Book"}

Note #4 
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Date the note was created was: 
2012-01-05T22:59:54
The contents of the note were: 
the conditions of our pre-biotic earth. It all started about five billion years ago. Our solar system was filled with hot gases and dust, which swirled and revolved around a white hot core. When the core approached one million degrees Fahrenheit, our sun was born. The gaseous dust clouds gradually condensed and formed asteroids. It is estimated that over 100 trillion planetesimals, or large asteroids, existed when our solar system was formed. As these huge pieces of matter were revolving around the sun, many of them collided with one another. While some of these collisions destroyed the planetesimals, others caused them to combine. As their mass increased, gravity pulled in more particles and debris, and the planetesimals grew larger. This process, called accretion, is how the earth and the other planets were formed.

Over hundreds of millions of years, the earth continued to change due to the bombardment of asteroids.

For a long time it was thought that the early Earth had a reducing atmosphere. A reducing atmosphere contains reductants, or molecules saturated with hydrogen atoms, which are able to reduce other molecules. Many scientists believed that the atmosphere consisted of CH4, NH3, and H2. This is the mixture of gases Miller and Urey used in 1953 to mimic the conditions of the early earth. Their experiment showed that abiotic molecules could be used to create important biotic compounds thought to be necessary for the origin of life.

/ref{http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/PBearth.html}

Annotations for page 3 were: 

Note #1 
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Date the note was created was: 
2012-01-05T23:04:00
The contents of the note were: 
Ribo nucleic acid - RNA

Annotations for page 5 were: 

Note #1 
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Date the note was created was: 
2012-01-05T23:11:47
The contents of the note were: 
Von Neumann

A von Neumann language is any of those programming languages that are high-level abstract isomorphic copies of von Neumann architectures[citation needed]. As of 2009, most current programming languages fit into this description, likely as a consequence of the extensive domination of the von Neumann computer architecture during the past 50 years

/ref{http://en.wikipedia.org/wiki/Von_Neumann_programming_languages} Retrieved January , 2012 at 23:13 EST

The term Von Neumann architecture, aka the Von Neumann model, derives from a computer architecture proposal by the mathematician and early computer scientist John von Neumann and others, dated June 30, 1945, entitled First Draft of a Report on the EDVAC. This describes a design architecture for an electronic digital computer with subdivisions of a processing unit consisting of an arithmetic logic unit and processor registers, a control unit containing an instruction register and program counter, a memory to store both data and instructions, external mass storage, and input and output mechanisms.[1][2] The meaning of the term has evolved to mean a stored-program computer in which an instruction fetch and a data operation cannot occur at the same time because they share a common bus. This is referred to as the Von Neumann bottleneck and often limits the performance of the system.[3]

/ref{http://en.wikipedia.org/wiki/Von_Neumann_architecture} Retrieved January 5, 2012 23:14 EST

Annotations for page 6 were: 

Note #1 
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Date the note was created was: 
2012-01-05T23:20:27
The contents of the note were: 
cytoplasm:

Cytoplasm is basically the substance that fills the cell. It is a jelly-like material that is eighty percent water and usually clear in color. It is more like a viscous (thick) gel than a watery substance, but it liquefies when shaken or stirred. Cytoplasm, which can also be referred to as cytosol, means cell substance. This name is very fitting because cytoplasm is the substance of life that serves as a molecular soup in which all of the cell's organelles are suspended and held together by a fatty membrane. The cytoplasm is found inside the cell membrane, surrounding the nuclear envelope and the cytoplasmic organelles.

/ref{http://sln.fi.edu/qa97/biology/cells/cell3.html} Retrieved January 5, 2012 at 23:21 EST

Note #2 
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Date the note was created was: 
2012-01-05T23:22:29
The contents of the note were: 
Diffusion: 

the process by which molecules spread from areas of high concentratiion, to areas of low concentration. When the molecules are even throughout a space - it is called EQUILIBRIUM Concentration gradient - a difference between concentrations in a space.

Molecules will always move down the concentration gradient, toward areas of lesser concentration. Think of food coloring that spreads out in a glass of water, or air freshener sprayed in a room.

/ref{http://www.biologycorner.com/bio1/diffusion.html} Retrieved January 5, 2012 at 23:23 EST

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Note #1 
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Date the note was created was: 
2012-01-05T23:26:26
The contents of the note were: 
Cellular automata:

A cellular automaton is a collection of "colored" cells on a grid of specified shape that evolves through a number of discrete time steps according to a set of rules based on the states of neighboring cells. The rules are then applied iteratively for as many time steps as desired. von Neumann was one of the first people to consider such a model, and incorporated a cellular model into his "universal constructor." Cellular automata were studied in the early 1950s as a possible model for biological systems (Wolfram 2002, p. 48).

/ref{http://mathworld.wolfram.com/CellularAutomaton.html} Retrieved January 5, 2012 at 11:26 EST

Annotations for page 16 were: 

Note #1 
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Date the note was created was: 
2012-01-06T07:31:37
The contents of the note were: 
Look up keystone parasite effect 

Annotations for page 17 were: 

Note #1 
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Date the note was created was: 
2012-01-06T07:33:56
The contents of the note were: 
look up 'optima' 

Annotations for page 18 were: 

Note #1 
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Date the note was created was: 
2012-01-06T07:35:29
The contents of the note were: 
look up fecundity 

Note #2 
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Date the note was created was: 
2012-01-06T07:36:06
The contents of the note were: 
look up obligate commensal parasites

Annotations for page 22 were: 

Note #1 
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Date the note was created was: 
2012-01-06T08:00:17
The contents of the note were: 
look up diploidy