What is the
ORIGIN of LIFE...   a paradigm question for Cell & Molecular Biology...
            the origins of the Primordial Cell...                                                           
                  Was it a  chemical evolution 
 or an   astrobiological event   or   what was it?  
                            Life Happens (a Panspermic event)   or   Chemical Evolution & Emergence?        a text decscription of the origins of the first cells.*read this

   CURRENT PARADIGM...                                                                           
     most experimental evidence favors a
chemical evolutionary origin of life...
          "simple chemical self-assembly has lead to complex self-replicating chemical systems"

     timeline:   Earth
forms 4.5 billion years ago,
4.5 to 4.0 bya -
asteroids bombard & sterilize planet's surface
                     then by           
4.0 bya - first fossil evidence of microscopic life is present

                  Initial chemical events may have been evolution of CARBON BASED MOLECULES
                            ancient atmosphere (
was it reducing ?) with simple reduced carbon gases...
                                                               carbon monoxide,    carbon dioxide,    methane

        Let's look at experimental approaches & research done to study Origins of Life*




4 experimental approaches are used in today's  Origin of Life  research:
1st) experimental search for bioorganic precursor molecules of life...
[J. Lucentini, "Darkness before Dawn", The Scientist 17:(23) 28-29, 2003]
   A)  they were formed from a chemically reactive soup... in early "
oceans" of primitive Earth.
         1953 -
Miller & Urey* ---> abiotic making of organics in lab experiments @ U. Chicago.
                        > H2O, NH3, CH4, & H2 make HCN & formaldehyde: then
amino acids
*, nucleotides,& sugars
 timeline of experimental organic syntheses
B)   1979 - Deep dwelling (ocean) hydrothermal vents...  (deep sea volcanic plumes) 
                         >  vents* are full of organically rich molecules --> life 
[ tube worms* & bacteria ]
                                  Speculation: chemosynthesis may have helped life originat in vents regions...

C)   1990's - astrobiological origins for biomolecules...                 Great 20th Century Discoveries ?
> SPACE DEBRIS... space dust, meteorites, asteroids
                                        may have deposited organics on newly formed planet Earth.
                         > Comets are mostly ice crystals on cores of silicates & carbon  
NASA Stardust
                                 contain about 10%  CO,  CO2,  CH4,  CH3OH, and  NH         methylamine  &  ethylamine
> Asteroids  contain molecules as... kerogen [a PAH], nucleobases, quinones,
                                    COOH's, amines & amides = some 70 amino acids, with 8 of common 20
 D)  2007   > repeat of Miller-Urey famous experiments*







2nd) experimental approach: built a MODEL  MOLECULAR  REPLICATIVE  SYSTEM
     Evolution of an RNA world...   (consequence of "which came 1st DNA or RNA"?)

in 1989  Sidney Altman  &  
Tom Cech  - received Nobel Prize
          for demonstrating that RNA molecules (RIBOZYMES) have CATALYTIC ACTIVITY
          i.e., these
RNA's catalyze hydrolysis & condensation rxs of phosphodiester bonds,
       RNA molecules able to catalyze polymeric cleavage in a sequence-specific way.                                                                                ribozymes*   
maybe, if RNA can be a template and also catalyze polymerization of like molecules,
          then RNA molecules may have been the
1st SELF-REPLICATING living entity.
                             complementary templating*
No self-replicating RNA molecules exists naturally today, but lab experimentation may
                           establish that it is feasible, and that RNA molecules can be selected for
via Darwinian evolutionary mechanisms (Natural Selection).
Robert Shapiro from NYU suggests life began within a mixture of simple organic molecules,
          multiplied through catalyzed reaction cycles and an external source of available energ
          a bunch of molecules that replicated each other...a thermodynamic theory for origin of life.

                                                  Origins of Life Prize - Abiogenesis        









3rd Experimental approach) PROTOBIONTS... chemically made artificial vesicle systems...
                              aggregates of prebiotic macromolecules that acquire a boundary to maintain
                              an interior chemical environment distinct from "primordial soup"...

Sidney W. Fox   Univ of Miami (1912 - 1998) - Director of NASA supported Institute for Molecular Evolution at UM.
                                                                            his laboratory conducted analyses of the
first moon rock samples...
                   he produced proteinoidsg from amino acid solutions... dropped on hot lava rock,sand or clay.


        Experimental Protobiontsg include:  coacervates,  proteinoid microspheres,  and  liposomes.
  • coacervates droplets form from polypeptides, polysaccharides & nucleic acids
    •  tough skin water molecules held by hydrophobicity, possess osmotic capability
    •  maybe with enzymatically active interior  =   figure*
  • poteinoids form microspheres* or water filled vesicles (1-2um dia), which     (above)
    • are osmotically active with selective permeability
    • have membrane potentials 
  • liposomesg form from phopspholipids,     figure-1*   &    figure2*,   which
    • are microscopic spherical vesicles that form when phospholipids are hydrated
    • can engulf smaller proteinoids making more active ones
    • in 2003 M. Hanczyc, S.Fujikawa, & J.Szostak made liposomes that grow & divide via clays
             (reproduce?) & if RNA present it was encapsulated [
      a plausible route to 1st cells ?] 






4th experimental approach)    Synthetic Biology  &  Protocell Research...

       A) a bottom-up approach: assumes one can't truly understand what one can't build from scratch. 

goals: to assemble all the molecular components to be able to synthetically form life
                      to understand why & how matter can self-organize... and become living.

Synthetic Biology... is the construction of fully functional cells (or parts) from scratch.
                      the engineering of new genetic circuits, entire genomes, or organisms
                                           to make complex biological machines,
                      taking genetic elements to the level of
engineering a cell, and
                      altering gene content & arrangements to make novel designer genes.

      i.e., the artificial creation of DNA, genes, viri, & cells that mimic, or surpass, natural systems.







some bottom-up experimental examples:
   1. Synthetic Polio Virus - July 12 ,2002 : Molecular Origin of Life Research or Bioterrorism?  
E. Wimmer from the University of New York at Stony Brook used the poliovirus' widely known genetic
to synthesize the virus from shelf chemicals.
They followed a recipe they downloaded from
         the internet
and used gene sequences from a mail-order supplier. The artificially constructed virus
         appears identical to its natural counterpart; when injected it into mice the animals were paralyzed and died.

                                                                                                                                                                  Science 297, 1016-1018 (2002)
   2. Phi X-174 virus synthesized - November 2003 :  Craig Venter and colleagues created an artificial
         version of
Phi X-174 by piecing together synthetic DNA ordered from a biotechnology company.
         They used a technique called polymerase cycle assembly (PCA) to link the strands of DNA together.
                (Phi X-174 was 1st sequenced in 1978, has 5,386 bp, 11 genes).
   3. The 1918 Spanish Flu Virus is Reconstructed - October 2005 : Jeffery K. Taubenberger, a molecular
         pathologist at the Armed Forces Institute of Pathology and his colleagues were able to piece together the
         virus's genes from two unusual sources: 1) lung tissue removed at autopsy from  a 21-year-old soldier &
 2) the frozen body of an Inuit woman who died of influenza in November 1918 & was buried in the Alaskan
         permafrost. These sources provided intact pieces of viral RNA
* that could be analysed and sequenced. The
         virus has eight "RNA gene segments" & by gene sequencing & PCR, they reassembled the virus.
         of the 8 genes:
Hemagglutinin-A type 5 [H5] and Neuraminidase type 1 [N1] are
surface coat proteins.
         There are at least 16 different HA antigens, which binds the virus to the host cell. Hemagglutinin-A is a
         surface glycoprotein that bind virus to host cell.  Neuraminidase is an surface antigenic glycoprotein enzyme
         Nine neuraminidase subtypes are known, which aid in the efficiency of virus release from infected cells.
         H5-N1 make up a subtype of human influenza virus A and the avian influenza virus type A




B) synthetic biology... a top-down-up approach:      
KNOCK-OUT Cells...   looking for the minimalist essential genome required to make a cell...

J. Craig Venter, a principle investigator (P.I.) of the Human Genome Project is trying to make
  a new type of synthetic bacterium using DNA made in the lab from the sequenced genes of
  a bacterium
Mycoplasma genitalium, a gram-positive parasitic bacterium, whose primary infection
  site may be the human urogenital tract that causes
non-gonococcal urethritis
It's circular
  chromosome has 
582,970 base pairs, the smallest known genome of any independently replicating
M.g. has a total of only
525 genes (482 protein encoding genes & 43 RNA genes).

     > How many genes does it take to make an organism? What is the minimum genes a cell needs?
The scientists at The Institute for Genomic Research (TIGR -Venter's group) who sequenced
Mycoplasma genitalium genome followed this work by systematically destroying its genes
[so called knock-out cells* - done by mutating them with microRNAs to see which ones are
        essential to life & which are dispensable]. Of the 482 protein-encoding genes, they concluded
        that only
265–350 of them are essential to life.
     > The next step is to artificially assemble these 300+ genes to create a synthetic cell
                                                             Mycoplasma laboratorium* - life from scratch?












So what did it take to evolve a Eukaryotic Cell as we know it today ?
                                                                                these experiments are not yet done..

               the evolution of the eucarya was single most important step in evolution 
mutlicellular 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
                              eucarya 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





 Replicative Systems are an experimental bridge between molecules & living organisms...
            the derivation of stable self-replicating molecules represents a fundamental obstacle
            to our understanding of the events in the origin of life.
Some Molecular Evolution  Artificial Life...   EXPERIMENTAL SYSTEMS...
          the goal is to find molecular structures, simple enough to have formed spontaneously 
molecular self-assembly, but complex enough to have evolved into life as we know it.

    some examples include:
         1.   Molecular Replication Systems
    Jack Szostak (Mass. General Hosp.) - REPLICASE System...
a replicase is a molecular complex that has the ability
to make a copy of itself and direct other molecules to replicate themselves…
              looking for or new functional RNA, DNA, and protein sequences...
               "aptamers", which bind a wide range of small biomolecules (nucleotides, aa's, cofactors).
                      using in vitro selection and directed evolution
they generate stable, covalent
                      RNA-protein fusions in vitro
novel ribozymes and deoxyzymes (ssDNA's)
                      with catalytic activity, especially, RNA's that can make other RNA's...
               which may represent the origins of biological catalysis. 
    2.  Ribozymes - Gerald Joyce & Martin Wright, et al  (@ Scripps)  

     Joyce & Wright used a test tube of ribozymes that can reproduce indefinitely,  
some even with mutations, which improved rate of replication...
   Scripps Report
     using RNA's with distinct structural domains, using in vitro selection they formed
     RNA's with alternate structural conformations & different functionality:
          "…with a starting ribozyme molecule, with barely detectable DNA-cleavage
activity, after 63 "generations" of in vitro selection for catalysis, 
showed a number variants of ribozymes, that cleave single-stranded DNA with
high efficiency and specificity. These ribozymes had accumulated an 
      average of
27 mutations relative to the wild type ribozymes and had
            improved their ability to cleave DNA by

                  i.e., the ribozymes evolved (???)    

some additional top-down research... continued

   >  E. coli, a favorite bacterial chassis, is being re-engineered to improve its properties
              1st by removing prophage, transposon, & other unnecessary genetics elements,
              & then by re-coding many genes to enhance their rates & efficiency of protein synthesis.
                       akin to building a 'hot-rod' dragster.

     > Mesoplasma florum, a Biosafety level I organism, that doesn't infect humans is being used
              by Tom Knight to rebuild its genome synthetically


     > Dusko Ehrlich has inactivated some 4,000 genes of B. subtilis, and narrowed its minimum
             set genome to some 271 genes, of which some 80% are commonly present in all bacteria.

                     It's a long way from these 1st synthetic steps in the lab to a eukaryotic cell.