Our Search for Life is a Journey thru "Cosmos" of the Cell
Biological Domains & Classifications* 

human sperm

fertilized egg cell

egg cell

Hela cells
spirogyramushrooms

Darwin finch

T-even bacteriophage Polar bear

     Unifying Concepts of Biology...  CELL DOCTRINE, EVOLUTION,  &   BIOENERGETICS
                                  Modern Biology  is often looked upon as... Biochemistry of the Cell
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Properties of Life...                                          
  
                       Top Ten things that characterize a Cell as Living.

    1.  Cells obey Laws of Energetics -  i.e., they transform energy
NAS-2
    2.  Cells are Highly Structured
NAS-3 with emergent properties
    3.  Cells have an Evolutionary Origin  (from a single primordial cell)
NAS-1
    4.  Cells Metabolize
                possess metabolic pathways, process nutrients, 
                self adjust to environment via metabolic regulation
    5.  Cells Self-Replicate (divide)   
µ
    6.  Cells Osmoregulate
    7.  Cells Communicate
    8.  Cells show Animation (cyclosis)
    9.  Cells Grow, Divide, & Differentiate
   10.  Cells Die
 
 
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Top 10 Properties of Life...                
the basic unit of life is the CELL...
               
µ  "inanimate mix of biomolecules - selected for their fitness 
                      to perform certain (cell) biochemical functions characteristic of life
".
  

1.    Life & Cells OBEY physical/chemical LAWS of Universe
NAS-2
                                all living things are parts of larger systems of matter & energy, and
                                matter continually recycles through systems as energy flows thru the systems

              No unique laws defining the Living State separate different from natural/physical laws.
              Cells transform energy via:  1. capturing light energy2. redox rxs, & 3. e-flow 
                          a) extract energy from surroundings --> autotrophs (light) & heterotrophs (food)
                          b) transform energy --> to do 'work': osmotic, mechanical, electrical
                          c) cells constantly expend energy to maintain a non-equilibrium ordered state

 
2.    Cells are Highly Structured
NAS-3
                                all living things maintain a high degree of order & complexity
              Diverse, yet similar... (all have membranes, nuclei, & organelles)
                            uniqueness is structural organization brought about by 
                            interaction of elemental molecules selected for by living systems

 
next panel  table - elements of body*       mix --KAM-->         Emergent Properties  [Table 1.1]  JMM
 

 

 

 

 

 

 

 

 

  

 3. All cells are derived from a single PRIMORDIAL cell* NAS-1
                                    all living things are descended from a common ancestor
 

    a Fundamental Question of Human Inquiry has been... Where did we come from
                       
µ  What chemical conditions may have lead to origins of life?
                             How did the first cells form?
                             What were the first living entities like?
                            Are there living cells elsewhere in the Universe?

     There are 3 major hypotheses of ORIGIN of LIFE...
     

             1.  Special Creation... benevolent supreme being suspends
                                                laws of physics & chemistry to create life.
                                                                                   
[not treatable by scientific method]
  

             2.  Extraterrestrial... life was formed or evolved elsewhere in Universe
                                                 and was seeded on the newly formed planet Earth,
                                                
this idea includes such concepts as..."Panspermia".
   next panel                                                                                      (more later)
 

 

 

 

 

 

 

 

 
 
3.  Chemical Evolution - complexity arose from an assembly of large molecules
     
in the beginning
... origin of the Universe = BIG BANG (Explained*)
                Beginning of the Universe approximately  13.7  billion yr ago + 10%
                                   (Hubble Constant = 70 km/sec/MPc  + 10% and using White Dwarfs)
                                    (
MPc = megaparsec... one megaparsec equals 3.26 million light years*)

 Formation of Earth
        Earth coalesced from space dust 
 4.5 billion yr ago
 bombarded by interplanetary dust & comets
        water source for oceans 
 4.5 to 4.0 bya
 Heavy comet bombardment stops > life begins   3.9 bya
 Oldest fossil rocks  3.8 bya 
 Life (anaerobes  3.5 bya 
 advent of oxygen* (evolution of aerobes)  2.0 bya
 eucaryotes  1.0 bya 
 multi-cellularity 0.7 bya 
 early animals 0.6 bya 
                                                             john kyrk's evolution webpage 

                                                                                                            
 

 

 

 

 

 a closer look Chemical Evolution Origin ideas which are based upon...
   chemical evolution is... simple chemical rx's that form complex molecular systems favoring life
  
        1) today's known molecules of "living cells" are made from small number of
                          chemical functional groups [ OH,  NH3C=O,  COOH, etc. ]
        2) these chemical functional groups easily form into simple monomers...
                          molecules such as - amino acids, fatty acids, nucleotides, sugars  
.
        3) these monomers easily make polymers or macromolecules...
                         which favored the energy transforming & self-replicating features,
                         so called - emergent properties that help define today's living cells...

      

   
* the concept of chemical evolution of life conforms to scientific method, 
       for it is
EXPERIMENATLLY TESTABLE...   
          1st experiments by geochemistsMiller & Urey* 
(U Chicago 1953) --> made organics
                 
[ including HCN and H2CO (formaldehyde) --precursors to --> amino acids & sugars ]
            today, cryochemists (NASA) study such molecular activity @ absolute 00
 
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Experimental Approaches to
Origins of Life Research
                                                                       Origins Institute (McMaster University) & Origins of Life Initiative (Harvard)       
       

        
 Ultimate Goal may be  "creation of an artificial cell, as a model of a life system"

  4 experimental approaches are active in today's origins research
                 ...mostly searchs for sources of early precursor organic molecules of Life ???

     I)  classical chemical evolution approach...  [life began when chemistry begat biology]
            i.e., life formed from a chemically reactive soup... in the early oceans of Earth
                
1922 - Oparin & Haldane:  suggest early Earth had a reducing atmosphere
                         
                                one rich in gases as NH3, CH4, H2, & H2O vapor
                 1953
* Miller & Urey ---> make organics in the lab
                                    >  abiotic origin
of organic molecules from simple inorganics
                                    > 
H2O, NH3, CH4, & H2  from a reducing atmosphere
                                    >
produce HCN and formaldehyde which leads to...
next panel                       > organics* as amino acids and sugars.            
 

 

 

 

 

 

 


       CRITICISM of research:  it was not really a reducing atmosphere, so chemically unlikely

            but,  experiments recently redone by J.L. Bada & S.L. Miller using a weakly reducing
                    atmosphere (irradiated with protons)... have obtained bioorganic compounds
                    in amounts comparable to those of original Miller/Urey type experiments.
                              
                    March 2007 ACS Annual Meeting Bada Presentation*

     II Deep dwelling (ocean) hydrothermal vents*  
                
 discovered in 1979 by researchers @ Oregon State U. - hot vents on Pacific seafloor
                  
with minerals spewing up from pressurized, hot springs; source of chemical evolution?...
                            these vent areas (660oF) are full of organically rich molecules --->

                            even with life* (tube worms @ vents)  &  bacteria living in hydrothermal vents.

            speculation is that life's molecules may have originated in the hydrothermal vents regions.

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    A role for the hydrothermal vents in ?...   Origin of Metabolism  

            Gunter Wachterschauser (German biochemist) has speculated that origins of
                    bioorganic chemical reactivity may have originated near hydrothermal vents
                    before genetics - a cycle of chemical reactions that produce energy.
                             > earliest primordial biochemical cycles may have functioned there...
                              > metabolic cycles likely predate cells...
                                                      took place on mineral surfaces that acted
                                                      as catalysts & surfaces for early reactions
                            
  key reaction may have been a reductive reaction like citric acid cycle...

            Researchers including M.J. Russell, M.M. Hanczyc, D. Deamer, C. Huber, and G. Cody
                    have synthesized amino acids and assembled/disassembled polypeptides
                            under vent like conditions,
                    all crucial metabolic processes that might have arisen at hydrothermal vents 
                            so maybe the bioorganic molecules evolved at hydrothermal vents.

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What is source of bioorganic molecules
 ?  (chemical evolutionary precursors to life)
            a) Miller & Urey - abiotic synthesis in tidal pools of Earth's early oceans
            b) hydrothermal vents (spewed up from "middle Earth")
 
  
            C) 
SPACE DEBRIS: 
                  
       chemical evolution   vs.   meteorites         
               
                early bombardment with dust, meteorites, asteroids, &  comets
                                may have deposited organics
on newly forming planet Earth.

    

                  Asteroids  rocky objects, that hit Earth & contain molecules such as kerogen...
                                   [an organic material known as - PAH* - polycyclic aromatic hydrocarbons*],  
                                   nucleobases,  quinones,  carboxylic acids, and
                                   amines & amides =  some 70 amino acids,  including 8 of common 20 aa's. 

                                                                                                                              
               
  Comets are mostly ice crystals on cores of silicates & carbon 
                                contain about 10%  COCO2CH4CH3OH, and  NH3     NASA-Stardust

                                
  
 next panel                        Campbell - Concept Activities - chapter 2.1 - How space rocks are analyzed for the signs of life*   

 

 

 

 

 

  some more   Astrobiology & Extraterrestrial    experimental models:
                            

    SETI - Universe some 10
20 stars with properties similar to our sun's [?]
                 
     if 10% have planetary systems & if 1/10,000 has a planet equal in size &
                      properties to earth then life as we known it (carbon based life forms) may still
                      occur on as many as 1015 planets           (Carl Sagan & Fred Hoyle)
                
Extra-Solar planetary systems - 220 to-date   &   Gliese581c   &   When ET Phones Home
  

    PANSPERMIA - idea that living microbes drifted in from space & colonized Earth
  
                                     Svante Arrhenius (1908) radiation emitted by stars carried 
                                         microbes thru space;   (also supported by Francis Crick)

           

   "Life Happens* bumper stickers now have more meaning in terms of chemical evolution.
                           
 Life may have originated when the mix of different molecules in the primordial
                             soup passed a certain level of complexity and self-organized into living entities;
                             (if so, then life is not a highly improbable chance event, but almost
inevitable).
      
                                 (optional:  Some quotations & historical perspectives :  On the origins of Life.)   next     maybe it even happened on Earth "More than Once*"?

 

 

 

 

 

 

 

  Evenspace debris ICE may have been the cradle of Life...
                                                                         all ice contains some water...
    Max Berstein
(NASA - 1999) has modeled cryochemistry reactions in the lab,
            to look at molecular events within comets... he has observed... 

                   
...chemical reactions can occur even in very low temps [25K (-400oF)], 
                    ...UV light can break chemical bonds 
                                  - forming ketones, esters, alcohols, and quinones (for e- transport). 
                    ...some molecules formed spherical, capsule-like droplets when
                                  - exposed to water, with properties akin to cell membranes.
    some experiments have shown that units of RNA can spontaneously string themselves in ice.
    

         so besides abiotic or hydrothermal origins    a new speculation ???

                          maybe
extraterrestrial  aa's   built 1st proteins ?

  
    but wait,   there's still a possible Role for Minerals* in Earth's chemical evolution...

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3rd experimental approach of Origins of Life research  
        
       III) study of the Origins of Self-Replicating Chemical Systems...
                            
i.e.,  Evolution of an RNA world... 
 (which came 1st DNA or RNA)
    
        
   a key characteristic of life is self-replication...   Can molecules self-replicate???

               in 1989 Sidney Altman and Thomas Cech - received Nobel Prize
                  for demonstrating that RNA molecules may have CATALYTIC ACTIVITY* (RIBOZYMES)
                  i.e., these RNA's catalyze hydrolysis & condensation rxs of phosphodiester bonds.

               If RNA can catalyze polymerization of like molecules maybe it can be a template also,
               akin to DNA --> figure*   i.e., replicate itself, then RNA molecules may have been the
                                                                                    1st SELF-REPLICATING living entity
.

        No self-replicating RNA molecules exists naturally today, but lab experimentation may
                  establish that it was feasible, and that RNA molecules can be selected for via
                  Darwinian evolutionary mechanisms (natural selection).       
next panel                                                                            tba      a metabolism first - thermodynamic alternative

 

 

 

 

 

 

 

 4th experimental approach of Origins of Life research
  

     IV)  Knock-out Cells...                                           
 News Release - new funding
   
        By modifying a simple microbe, scientists hope to create a new form of single cell life.

        >  J. Craig Venter, a principle investigator (P.I.) of the Human Genome Project is attempting
                to make a new type of bacterium using DNA manufactured in the lab;
        > using the sequenced the genes of a bacterium called Mycoplasma genitalium, a gram-positive
                parasitic bacterium, whose primary infection site may be the human urogenital tract.
                        (it probably causes non-gonococcal urethritis and it is also one of the simplest
                         known microbes with only one chromosome and 517 genes).
        > researchers began systematically removing genes to determine how many genes
                are essential for life.  In 1999, they published a paper that narrowed the needs
                of M. genitalium to between 265 and 350 genes using  knockout genes concept*.
        > a genomic goal will be to learn on a molecular level the minimum genes a cell needs
                to thrive and reproduce and how to artificially make those and other genes.
        > Venter plans to
construct a synthetic chromosome that is 381 genes (580,000 bp) long
          
using lab-made chemicals, & transplant it into bacterial cell = new synthetic life form.
 next panel                                                                                                                          Mycoplasma laboratorium.

                                                                                                                                               

 

 

 

 

 

    

current paradigm: "simple chemical self-assembly has lead to complex self-replicating systems"

5 Steps in Chemical Evolution of Life- "It was a Dark and Stormy Night"

                                     


"Life Happens"

 
     1Abiotic synthesis of small organics  hydrogen cyanide & formaldehyde -->
 makes sugars, aa's, nucleotides, etc...
  figure*
     2Autocatalytic assembly of polymers*
                      self-assembly leads to complexity*
 CONDENSATION REACTION*        
 HYDROLYSIS*                CD - Activity 5A - polymers
     3Origin of Heredity...
                       
most probably RNA (?)
 abiotic synthesis RNA strands        BASE PAIRING
 figure* -->  unique polymer sequences of RNA(?) 
                   RNAs become polymeric catalysts   
                & show errors in replicating process   
     4Translation of RNA sequence  into amino acid sequence? [no experimental evidence]
  5 Membranes probably define First Cell   Proto*bionts*               Origin of Life Prize   NY cartoon

 

 

 


 

 

 

 

 

 

 

 
      
 (?)Some imProbable Steps  in Chemical Evolution of Eukaryotes...
              it's a long way from a protobiont to a typical eukaryotic cell of today
                         the evolution of the eukarya was single most important step in evolution 
                         of multi-cellular life forms & was a key step that lead to plant & animal life. 

        1. cell membrane encapsulates genetic DNA...  
development of nucleus
                    greatest evolutionary invention - it internalized the genome

        2. loss of a rigid cell wall...
                  
 cells developed ability of phagocytosis - allowed engulfing of foods
                         also allowed cells to clump together -->   multi-cellularity  -->   tissues

        3. evolve a selectively permeable membrane...
                  
 protects cell, allows uptake gases & nutrients & exchange with environment
        4. evolve a cytoskeleton...
                  
 provides framework- allowed cell to grow larger, move, & permitted
                           metabolism;    eukarya are 10x larger that bacteria

        5. evolve aerobic respiration...  
more efficient energy transformation
        6. develop various organelles
(maybe by endosymbiosis)...
                
   a sub-cell part that catalyzes a specific metabolic function
        7. development of sexual cell cycles
(transposons - moveable genes)...
               
a method to shuffle genes along chromosomes favored cellular evolution
           end 4                                                                                 a possible Script for Life*read?

 

 

 

 

 

 

 

 

Top 10 Characteristics of life... cont'
  

    4. All cells METABOLIZE
                              
all life depends on chemical reactions that take place within cells
           metabolism is chemical processes & reactivity in living cells, where molecules are broken  down
                    
to yield energy for vital processes & other molecules are made.
  
 
       When classifying organisms, biology often looks at the mode of Nutrition
                i.e., how cells obtain energy & carbon from their environment [metabolism]
 
  

       
µ   AUTOTROPHS - capable of synthesizing all their organic molecules 
                                            using CO2 as sole C source 
                1) photosynthetic autotrophs... use solar light energy

                               ...capture light by chlorophyll,    transfer e- from hydrogen donor  
                                  to CO 2 to reduce it to CH 2O              (first reductant H2S, now...H2O

                2) chemotrophic = use simple inorganic molecules as their energy source

  

       
µ   HETEROTROPHS - obtain energy from chemical fuels (as sugars) by oxidation
                    
unable to synthesize all needed molecules - i.e., obtain nutrients by dietary means
 
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Cells possess Metabolic Pathways (linked sequences of individual chemical reactions)... 
     

        ANABOLIC - synthetic reactions...  making larger from smaller molecules
                                                                     CO 2  +  H 20    <---->    C 6H 12O 6 
        CATABOLIC - degradatory reactions..  breakdown of larger into smaller
  
    Metabolic Pathways exhibit: 
     

                            A   ------>   B   ------>   C   ------>   D   ------>   E
                                     e1               e2               e3               e4 
                    economy & efficiency...
                    dynamic steady state...  equal in/out rates of intermediates
                                                            rate of synthesis = rate of degradation
                                          living things regulate use of energy and respond to their environment  
                    control is... by ENZYMES...
i.e., they are Self-Regulating...
                             an ex: negative feedback (feedback inhibition*) --> can lead to human diseases*
                                                                     Concept Activities - Chapter 1.2 - Positive-Negative Feedback*
                    integration...  work in a coordinated fashion...  everything at the right time
 

next panel   One definition of Life is:   carefully orchestrated chemical reactions.

 

 

 

 

 

 

 

 

 

 

    5.  Self-replication (reproduction is single most definitive property of life) 
                  
all living things share same genetic code, which is passed from parent to offspring
  

               genetic info is in DNA      - asexual
* cell division   =   MITOSIS  &
                                                         - sexual
* cell divsion     =   MEIOSIS 

               some inanimate counterparts (or model systems) for experimental study...    
                                growth of crystals in chemistry
                                computer simulation models of evolution...

  

                
Tierra - is a computer simulations of evolution
                 
       by Thomas Ray @ U. Delaware - TIERRA         
                       
small computer programs of assembly code with directions on how to copy self...
                        like a computer virus, competes for cpu time & memory space,
                        but is designed to be able to mutate & evolve
   
 
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 Tierra -                                                                       [Avida - Digital Life Laboratory]
  
    a simple computer program with instructions allowing code changes (mutation & evolution)
   
Primordial program had some 80 instructions and....       [some anthropomorphic analogies
            it was stored in cpu (lived),   it consumed cpu cycles (metabolized), 
            copied itself (reproduced),   it moved up in que (animation),   &   it was removed (died)
   

   
New programs (code changed) emerged (mutated & evolved)... first variant had 79 instructions,
                one variant had 22 instructions, but replicated 6x faster,
                some variants had only 45 lines, but lost the ability to replicate 
                        however, it borrowed instructions from others = acted like a parasite
                some programs became defensive, ie, immunized itself against parasites

 

   
    
Are the Tierrans alive       What about  "Star Trek's® Cloud"    Is It Alive ?
    Are we to be "Borg"?  - term borrowed from StarTrek® used by me
                                        for the premise by some cosmologists that artificial intelligence 
                                        may be the evolutionary consequence for human-kind

 
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  SKIP this Material
"Life is too improbable to be due to chance"
- Creationists & Intelligent Design Theorists
      just as watch needs a watchmaker, an eye, a biochemical pathways is too improbable
      to be due to chance... it must be due to intelligent design.

  

Richard Dawkins -
"the Blind Watchmaker"
        Natural selection, is the unconscious, automatic, blind, yet essentially non-random process that Darwin discovered, and has no purpose in mind. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker. The only watchmaker in nature is the blind forces of physics, albeit deployed in a very special way. A true watchmaker has foresight: he designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye. Natural selection is a blind, automatic process, which scientists now know is the best explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind's eye. It does not plan for the future. It has no vision, no foresight, no sight at all.
    By gradual, step- by-step transformations from simple beginnings, and with each successive change in the gradual evolutionary process, relative to its predecessor, leads a whole sequence of cumulative steps leads to complexity of a final end-product relative to the original starting point. The cumulative process is directed by nonrandom survival. Cumulative selection is a fundamentally nonrandom process and evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection.

 

Is it Experimentally Testable ?  
   Weasel Applet -
a computer "breeding" program = possible solutions to match a supplied phrase; exhaustive search -- systematically trying all possible guesses -- that would virtually never complete, but artificial selection via random chance can lead to a solution and seeming great complexity.
   
Biomorph Applet - plausibly lifelike forms - a variety of tree-like shapes... coded by 8 genes, with change allowed.  Result: wide variety of forms from a  limited genome - total of 1,071,794,405 different biomorphs! The accumulation of changes turns one form into quite different forms.
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    6. Osmoregulate...
  all life requires liquid water (water's properties will be covered later)
                    regulate exchange material across cell membrane
                    with the environment - solvents & solutes in/out of cell
                    helps maintain differences between in/out
    7. Communicate...  
                    intra (within) & inter (between) individual cells
                    ex: hormones/neurons
    8. show Animation (cells reveal significant motion,
                          especially @ molecular level:   vesicles moving along MT's,
                          flagella, and molecules across membranes;   
                          also  cyclosis  or  cytoplasmic streaming  
    9. cells...
   all living organisms change form & function at different statges of their life cycles
                   Grow... (increase in mass),  Divide... (increase in cell number),  Develop..., &
                   Differentiate... become structurally, functionally & biochemically different
                                from a fertilized egg ---> to adult cells
   10. Die... absence of properties of life

     

 
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Conclusions about  Life,  Cells, &  Living Systems
           
    Life is manifest in the structure we call the
CELL
  

            all cells are presumed to derive from a single primordial cell
NAS-1
  

            born some 4 billion years ago,
                 
   it out reproduced its contemporary competitors,
                 
   and had a family resemblance to today's cells...
                            ...all use DNA
                            ...all have same genetic code 
                            ...all possess same basic molecules
                            ...all have similar properties & metabolic functions 
                            ...all use same metabolic pathways that define properties of life
                            ...all are very
dynamic entities

                                   has a number of unique intra-cellular parts common among all cells,

                
   universal properties of all cells*
  next panel      Campbell animal cell 7.7*  [animal cell]  &   Campbell plant cell 7.8*    [plant cell]  

 

 

 

 

 

 

 

 

 
      A living  CELL  is a .....              a paradigm *     

            self contained,
            self assembling,
            self adjusting,
            self perpetuating,
            isothermal mix of biomolecules,
            held in a specific 3-D conformation by weak non-covalent forces,
            which can extract raw materials (precursors) & free energy from its surroundings,
            and can catalyze reactions with specific biocatalysts (enzymes), that it makes,
            which shows great efficiency & economy of metabolic regulation,
            and maintains a dynamic steady state far from equilibrium,  and
            that can self-replicate, using the linear information molecule DNA.

  
    
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