H.2 The Evolution of Life

Question 1

Systems, definition and hierarchy

Answer 1

A system: A whole consisting of connected components. These are in turn systems as well.
Hierarchy:
-Supersystem…to
-Systems…to
-Subsystems…

…From universe to aatoms

Question 2

Input, Output, Environment and Coupling of Systems
The importance of interaction

Answer 2

-Input: Matter, energy, or info from the environment4 that enters AND alters a system.

-Output: Idem, it exits the system and affects the environment.

-Environment: Other systems, in interaction with each other and initial system
-Coupling: A system’s output being used as another’s input. This points o a certain degree of interdependency.

-To be observed and to exist in an environment, a system must undergo coupling with its environment. Without this interaction, it doesn’t leave an observable trace?

Question 3

Systems in the context of Evolution

Answer 3

Systems are processes through which energy is transformed from intput to output. This interaction has a ripple effect on environment, which makes the universe as a whole intrinsically dynamic.

Question 4

Variation in the context of Evolution

Answer 4

Change under influence of external or internal processes

Question 5

Natural Selection in the context of Evolution

Answer 5

A selective retention of systems that are stable in the face of change, and an elimination of those that fall apart when confronted to change, internal or external.

Question 6

Darwinian Evolution

Answer 6

Mechanism that through variation and selection, generates a never-stopping variety of living species

Question 7

What makes a system survive selection? Fitness, adaptation, flexibility, complexity and intelligente

Answer 7

-Fitness: The grade to which a stable system is able to survive change AND reproduce (Fitter: more around. Humans everywhere is a testament to our fitness as species. Such as rats or cockroaches).

–Adaptation: Efficient exploitation of environment to subsist and grow stronger. Ability to evade danger. The degree to which a system is capable of finding a niche/way of life that provides balance in the approach of challenges: both opportunities and dangers.

Question 8

Development of a “successful” system in the evolutionary process

Answer 8

Ongoing variation and selection—–Increasing fitness and resilience towards challenges—Increasing internal complexity (more components and processes and interconnections)—–A growing intelligence (ability to put the growing complexity to good use)

Question 9

Dissipative structures: Intermediate state between living and non-living.

Answer 9

-Dissipative structures: Ever-active physical structures/systems with an organized flow of matter and energy that keeps it going for as long as there is input (Rivers, the Ocean, the Sun, hurracains).
-The input energy dissipates in the process into the environment, therefore it needs constant replenishment to subsist as a dynamic entity (ejemplo: Corriente del Golfo).

-Have no autonomous action towards challenges in the environment
Have no boundaries/skin
-Have no goal directedness

Question 10

Stable systems

Answer 10

Two types:

-Rigid-static: The moon, crystals, other rocks

-Constantly dynamic: Earth, the Sun

Question 11

Life: Autopoiesis and metabolism

Answer 11

-Autopoiesis: The hability of a system to produce all of its own components and copies of itself (reproduction)

-Metabolism: The constant flow of matter and energy to keep a system going. This constant consumption and production serves to repair damages (regeneration, healing) or growing new tissues.

Question 12

Boundary and Body

Answer 12

-Boundary: A protection of the metabolic cycle from outside interference or inside loss- Provides stability and autonomy that dissipative systems lack: In living systems, the existence of a membrane to protect the metabolic process and keep it running within and for itself, is a key component to the development of life.
-Body: A separate, physical object (thanks to a boundary).

Question 13

Genome

Answer 13

-A list of procedures or
instructions that specify how to keep the
metabolic cycle going and how to build
the different components. These instructions must be stored in a stable “memory”,
so that they can be consulted whenever
needed, and passed on safely to offspring.

-That memory is what we call the genome.
It consists of individual genes representing specific instructions.

Question 14

Genes

Answer 14

Specific instructions in how to keep a metabolic cycle going and how to build the different components. As a whole this list of instructions is called genome.

Question 15

DNA

Answer 15

-Molecule of which genes are made, with a characteristic double-helix shape.

Question 16

A DNA string

Answer 16

-A DNA string forms a “text” that can be read, decoded, and carried
out by the machinery of the cell. It contains instructions for producing the molecules (proteins) that are needed to perform the right chemical reactions.
-

Question 17

How the DNA string works: DNA string as a text to create proteins

Answer 17

-A string contains a sequence of bases, where each base is conventionally represented by
one of the letters {A, C, G, T}.

-Each triplet of three letters, e.g. ATG, constitutes a “word”
in the text. A “word” codes for a particular amino acid, in this case methionine. A “sentence” consists of a sequence of “words”. It is separated from other “sentences” by “stop” signs.
- A “sentence” represents a chain of amino acids. These amino acids are chained
together in the right order by the ribosome, a specialized part of the cell, so as to form a
complex protein molecule.

-Thus, a “sentence” or individual gene consists of the instructions for building one particular type of protein.

Question 18

Proteins and tool-proteins: Enzymes

Answer 18

-Proteins can function either as building blocks of the cell or as tools to work with other
molecules.

-When a protein is used as a tool, it is called an enzyme. An enzyme “catalyzes” (i.e. facilitates or enables) certain chemical reactions.

-An enzyme has a complex three-dimensional shape where specific other molecules
can fit in.

-When two molecules are thus brought into contact, they may “stick” together, forming a new molecule. In this way, enzymes can assemble the molecules needed by the
cell.

• Similarly, enzymes can break molecules apart, separating their components (e.g: digestion of food).

Question 19

DNA behavior

Answer 19

-Different enzymes are needed in different circumstances.

-In different conditions different segments (genes, “sentences”) of the DNA must be read or “expressed” to form enzymes.

-A gene can be active (being read off
to produce a particular protein) or non-active (when that protein is not needed).

-The pattern of activation or expression of genes (and therefore of enzyme production) can change
from moment to moment. This depends on which reactions are necessary

-Thepattern of activation can also change over the longer term, so as to adapt to the environment. Such a more stable activation pattern can even be passed on from parent to child.
This allows the child to “inherit” metabolic functions that are not part of the DNA itself.

-The information that specifies the activation patterns is called “epigenetic”, while the
information inherent in the DNA itself is “genetic”.

Question 20

The role of DNA: Both memory and real-time reactor. A library of potentially useful procedures and not so much a determinist programme.

Answer 20

-On the one hand, the overall instructions on how to run the metabolism of a living organism are passed on via the inheritance of DNA or genes.

-On the other hand, DNA actively regulates the activity of the metabolic network, by making sure that the right enzymes are produced at the right time. But DNA alone cannot intervene in the metabolism. The metabolic cycle itself needs to “activate” and read the right stretch of DNA whenever it needs the corresponding enzyme

-Thus, DNA and metabolism are mutually dependent, and the one cannot function without the other. The traditional idea that genes determine or control the organism is misleading. Depending on the state of the metabolism, which itself depends on external conditions, instructions stored in the DNA may be carried out or ignored. Nature AND nurture, both relevant.

Question 21

Agents

Answer 21

-An agent is an autonomous system that acts, i.e. that performs specific actions that
change its situation.

Question 22

Actions

Answer 22

-These actions are intended to achieve the
agent’s goals. A goal is a situation that the agent prefers over other situations. Having enough to eat is a goal and hunger is a deviation from that goal. The most fundamental goal for evolved systems is fitness.

Question 23

Needs

Answer 23

Needs: The conditions that must be fulfilled for the organism to survive, develop and reproduce (achieve fitness).

Question 24

Challenge

Answer 24

A situation that invites action from the agent, so as to exploit an opportunity and/or solve a
problem. Thus, challenges stimulate the agent to act—or at least consider whether action
is worthwhile. Not all opportunities need to be exploited, and not all problems are serious
enough to require action.

Question 25

Feedback

Answer 25

-Cybernetics, the science of goal-directed systems, describes that interaction as a feedback loop (Heylighen, 2014b).

-Feedback means that the output of a system (in this case the effects of the agent’s actions) is led back to become the input of that same system (in this case, these effects are perceived by the agent and affect the agent’s functioning).

Question 26

Negative Feedback

Answer 26

It reduces any deviation between your goal

Question 27

Goal-Directedness/Purposiveness/Agency

Answer 27

-A characteristic of living systems, built-in drive for survival.

-A feedback mechanism that counteracts any deviation from the goal.

-If the agent systematically manages to reach its goals, in spite of a variety of disturbances, problems or challenges put up by the environment, then we say that the agent is in control of its situation.

Question 28

Components of goal-directed action:
-Perception
-Mental interpretation
-Sense-making and evaluation
Knowledge
-Intelligence

Answer 28

-Perception through sensors that indicate -de forma sensorial- challenges/disturbances in the environment
- Mental Interpretation through the recognition of patterns in the aforementioned sensation.
–Sense-making and evaluation: Processing the percieved phenomena in terms of goals or values.
-Deciding which action to undergo requires knowledge about which actions are appropriate for which situations.

Question 29

Condition-Action rules

Answer 29

Most rudimentary form of goal directedness, present even in bacteria:

-If the perceived condition is A, then perform action B.
We can express this more simply as:
if A, then B,
The simplest notation is the following:
A → B.
For example,
danger → run away;
too hot → cool down;
food → eat.

ANEMONE RETRACTION EXAMPLE

Question 30

Effectors and the role of feedback

Answer 30

-Organs, such as hands, muscles, or vocal cords, that convert decisions
into physical movements.

-The actions performed by the effectors will change your situation. But the world is not just passive, waiting to be manipulated in any
way you conceive. Effects and new challenges might derive from one’s actions, urging us to go into goal-directed action again.

-Agents are engaged in a feedback-driven interaction that constantly cycles through body, mind and world, making these components in practice
impossible to separate.

Question 31

Nervous systems

Answer 31

-They distinguish animals from other living beings. Initially just carried signals from sensors to effectors.

-As the network of interconnections between nerves becomes more complex, it takes the
shape of a “central nervous system”, i.e. a brain (through neurones).
-This can now deal with more complicated situations by integrating the signals from many different sensors while simultaneously
activating different effectors.

Question 32

Learning

Answer 32

-Learning happens through a process of differential reinforcement of the connections between nerve cells or neurons.

-Connections that led to positive results, in the sense that the eventual action did bring the
agent closer to its goals, will become stronger.

-Connections that led to negative results, in the sense that the resulting action brought the agent farther from its goals, will be weakened.

Question 33

Reinforcement learning

Answer 33

See Skinner Box, operant conditioning, behaviorism

Even very simple animals with few neurons, such as snails, can be trained in this way to
respond in particular ways to particular sensed conditions (“stimuli”).
-This flexibility in their neural organization, and thus knowledge, is what allows animals to adapt to a wide range of conditions for which their genetic programs have not prepared them.

Question 34

Hebbian learning

Answer 34

-Animals can learn not only to associate conditions with actions, but conditions with
associated conditions.

-Neurons that are activated simultaneously (or with a brief interval in
between) develop stronger connections

Question 35

Prediction

Answer 35

-The more often a condition A is followed by (or presented simultaneously with) a condition B, the stronger the connection between A and B will become in the mind of an animal
(or human).

-This allows an animal to predict or anticipate the appearance of B just by
perceiving (or conceiving) A. This creates a useful shortcut, so that the animal can already
prepare the action appropriate to B even before B has occurred.