Unity: pattern & process in biology [Biology 150 U.M.]

To date there is no single agreed upon definition of life, even though there
are some 123 published definitions of Life (E. Trifonov, 2011).

Chemistry may provide a foundation for defining Life: All Living Things
are complex, organized molecular systems that undergo complex chemical
reactions (metabolism and genetics), coordination, and self-preservation,
which can unambiguously distinguish the living from the non-living.

           NASA's Exobiology Division has a statement of life as...

        Life is a self-sustaining chemical system
               capable of Darwinian evolution.

Life has an Evolutionary Origin - "all living things have evolved from a common ancestral cell "
    thru processes including natural selection & genetic drift acting on heritable genetic variation.

   ► LUCA - Last Universal Common Ancestor* is the most recent population of organisms
                                   from which all organisms now living on Earth have a common descent.

    SUPPORTING EVIDENCE ...
    the hypothesis that all cells are derived from a primordial cell is mostly based upon the
           circumstantial evidence, due to the commonality that occurs in all known living cells:

    commonalities as...
       1. all living things (cells) are composed of very similar organic molecules:
               the same proteins, lipids, carbohydrates, & nucleic acids (DNA & RNA), etc...

       2. all proteins, the biological catalysts responsible for life's chemical reactions,
               are made from one set of 20 standard amino acids... amino acids

       3. all contemporary organisms carry their genetic information in nucleic acids [DNA/RNA]
               and use the same genetic CODE.





The Tree of Life...    biologists study living things organized from the simplest to the
                                   most complex in levels of organization known as the Tree of Life.

Biological taxonomists organize living things into Kingdoms* traditionally by structural morphology.

        but, newer molecular approaches have added to our taxonomic patterns...
        today we recognize a HIGHER TAXON* taxon (above Kingdom) -->   3 DOMAINS*
   EUBACTERIA - true bacteria
   ARCHAEA -   ancient microbes
   EUKARYA -   modern eukaryotes
These Domains are based upon analyses of ribosomal RNA sequence*
         i.e., nucleotide sequence homologies of the small ribosome subunit rRNA molecules.

By comparing the rRNA sequences of many cells Carl Woese (U. Illinois) over a 10 year period observed
unique and different rRNA sequences, suggesting there were 3 distinct groups that he described as
"Eukingdoms" - Eubacteria, Archaeabacteria, and Eukaryotes, now widely accepted as the 3 Domains of Life*

In 2015 from a depth of 2,300 m in the Arctic Ocean Asgard archaea microbes were discovered that have
genome segments that make characteristic ESP's (eukaryotic signature proteins), such as actins and
ubiquitins, which suggests the origin of eukaryotes may have arisen from archaea, thus only 2 domains?

To answer the question... What is Life, we will divided the course into (3) segments:

                    3.   HEREDITY...             (Gene Theory - Information Flow)

                      4.   BIOENERGETICS    (Energy Transformations within Cells
                                                                   and Equilibrium Thermodynamics)

         Some important facts about cells
            - their diversity : - many sizes, shapes, & types* [200+ cell types in humans]^NAS-6
            - their similarity: - have same basic structural plan*
                                        - surrounded by cell membrane
                                        - contain nuclei     (bacteria = nucleoid/genophore* = area of DNA)
                                        - many contain similar sub-cell parts (ORGANELLES)

What are some of the UNIVERSAL PROPERTIES-Processes of all cells*

2. EVOLUTION..."Descent with modification"
"Nothing in biology makes sense except in the light of evolution"
Theodor Dobzhansky (1973) in Amer. Bio. Teacher 35:1125-129.

     simply... Evolution is a change in natural/physical characteristics of a population over time.
                             Evolution proposes that organisms living on Earth today
                   are the modified descendents of common ancestors.

    1858 Charles Darwin & Alfred Russell Wallace presented papers to Linnaean Society
        with 2 important new hypotheses about biological PATTERNS observed in the natural world.

   Hypotheses:
        1... all species (past & present) are related by descent from common ancestor
        2... all species come from preexisting species that have changed through time
               - individuals in a population vary in hereditable traits...(look around class)
                 - this accounts for the diversity one sees in biological organisms...
                 - living things change gradually over time and become new forms...

What is the PROCESS (mechanism?) Darwin proposed for (PATTERN) of descent & change...

   Can we observe examples of SELECTION acting on Populations?

    Artificial Selection... examples
      in wild cabbage plants*... horticultural selection of morphological traits results in
              a number of cultivars: broccoli, cauliflower, Brussels sprouts, cabbage, kale,
              and collard greens have all been derived by selection from wild mustard plants.
      Horticulturalists SELECT* wild cabbage with large buds to produce Brussels sprouts



Natural Selection... examples:
       case study 1* - Peter & Rosemary Grant & medium ground finch evolutionary adaptation.

          The GENE THEORY is a foundational theory of Biology which states...

                Morphological traits are passed from parents to offspring thru gene transmission.

                Genes are located on chromosomes (the Chromosomal Theory of Inheritance) and
                chromosomes are composed of deoxyribonucleic acid (DNA) complexed with proteins.

                The Laws of Heredity transmission were described by Gregor Mendel in 1860's
                 and include the Law of Segregation and Law of Independent Assortment.

                 The structure of DNA was deciphered by Watson & Crick in 1953

4. BIOENERGETICS   -    (aka... EQUILIBRIUM THERMODYNAMICS)...
             science of energy flow and transformation
                                       within, through, and between cells and organisms...

      "cells do not produce energy...
                 - they consume & transform energy to stay far away from equilibrium"

Unity... is chemical reactions of life being the same in bacteria, plants, animals

       case study 2  - feeding preferences of different predators can cause changes in guppy
                              populations favoring long-term evolutionary changes via natural selection
                               David Reznick (UCR) & John Endler (UCSB) - Trinidadian guppies (1982)
                                experimental design and results*     and    30 years later

       case study 3 - camouflage coat color in NM dessert mice & selection HHMI video^{10 min View@home}