Evolution: more details

    1.    Non-living synthesis of organic molecules,  from inorganic compounds available in the early Earth
    2.    Assembly of molecules into more complex and organized polymers, 
    3.    Origin of self replicating molecules that made inheritance possible, such as RNA
    4.    Packaging of these molecules into membranes with an internal chemistry different than their surroundings - which would otherwise tend to disorganize them

Dr. Stanley Miller, 1999
(Source: http://www.nytimes.com/2007/05/23/us/23miller.html?_r=1&oref=slogin)

Dr. Harold C. Urey
(Source: http://diogenesii.wordpress.com/page/9/?tag=history-of-science)

The Wiki page on this topic is very good; check it out:  http://en.wikipedia.org/wiki/Miller-Urey_experiment

Another fun page, with downloadable movie is : http://www.ucsd.tv/miller-urey/

Comets contain a variety of organic compounds.

Heavy bombardment about 4,000 million years ago may have delivered both organic compounds and water to the early Earth...

Researchers have also wondered if COMETS added to the formation of organic by providing the energy enabling polymerization, or by themselves carrying amino acids to the surface of the Earth from outer space, or perhaps even bringing the first bacteria on the planet.

An interesting read on this topic can be found at: http://www.anl.gov/Media_Center/Frontiers/2002/b8excell.html

"...More than 70 varieties of amino acids have been found in meteorites — many the suspected cores of comets that smashed to earth — and are presumed to exist in interstellar dust clouds.
"Comets are all frozen, so amino acids could be preserved within them," Winans said. "Assuming that the comets did not directly hit the Earth, but glanced the surface, they could have survived the fall."
Not only did a good fraction of the amino acids survive the simulated comet collision, but many polymerized into chains of two, three and four amino acids, so-called peptides. Peptides with longer chains are called polypeptides, while even longer ones are called proteins.
After the experiment, Winans and Ahrens analyzed the materials at Argonne, taking advantage of the laboratory’s liquid chromatography and mass spectroscopy expertise, to determine the species and concentrations of molecules present.
The experimental results suggest that some ice from the comet would remain intact as a liquid puddle concentrated with organic molecules ideal for the development of life. This impact scenario provides the three ingredients believed necessary for life: water, energy and organic material.

Possible locations where conditions would have allowed the synthesis of organic compounds 
include communities around deep-sea hydrothermal ventsvolcanoes and extraterrestrial locations.

"A hydrothermal vent is a fissure in a planet's surface from which geothermally heated water issues. Hydrothermal vents are commonly found near volcanically active places, areas where tectonic plates are moving apart, ocean basins, and hotspots. " (Wiki)

"Hydrothermal vents have given us many things, including new autotrophic paradigms, new species, a new appreciation for seafloor spreading centers, some cool websites and a best-ever IMAX movie ."
(Source: http://www.windows.ucar.edu/tour/link=/comets/comet_il.html)

"Shifting Volcanoes Made Early Complex Life Possible"

"Primitive" extraterrestrial life

"An alternative to Earthly abiogenesis is the hypothesis that primitive life may have originally formed extraterrestrially, either in space or on a nearby planet (Mars). (Note that exogenesis is related to, but not the same as, the notion of panspermia). A supporter of this theory was Francis Crick.
Organic compounds are relatively common in space, especially in the outer solar system where volatiles are not evaporated by solar heating. Comets are encrusted by outer layers of dark material, thought to be a tar-like substance composed of complex organic material formed from simple carbon compounds after reactions initiated mostly by irradiation by ultraviolet light. It is supposed that a rain of material from comets could have brought significant quantities of such complex organic molecules to Earth." (Source: http://en.wikipedia.org/wiki/Origin_of_life#.22Primitive.22_extraterrestrial_life)

Two properties of
RNA that would have allowed it to play a role in the origin of life i
    the self-replicating and
    the catalytic activities of RNA

DNA replication requires enzymes, which are made by DNA, therefore it does not seem plausible that DNA arose as a self-replicating molecule on its own

1.    Certain types of RNA can exist as single strand, and appears to be potentially self-replicable, which could suggest that these could be pre-cursors of the more complex DNA and     RNA realm.

2.    Another type or RNA acts as enzymes - it is called RIBOZYMES, it works both as an enzyme as as RNA.  It is found in nature, and can also easily be synthesized in the lab.

Please read on this topic on wiki at: http://en.wikipedia.org/wiki/RNA_world_hypothesis


The phrase "RNA World" was first used by Nobel laureate Walter Gilbert in 1986, in a commentary on recent observations of the catalytic properties of various forms of RNA.[1] However, the idea of independent RNA life is older and can be found in Carl Woese's The Genetic Code[2]. In 1963, the molecular biologist Alexander Rich, of the Massachusetts Institute of Technology, had posited much the same idea in an article he contributed to a volume issued in honor of Nobel-laureate physiologist Albert Szent-Györgyi.

[edit]Properties of RNA

The properties of RNA make the idea of the RNA world hypothesis conceptually possible, although its plausibility as an explanation for the origin of life is debated. RNA is known to form efficient catalysts and its similarity to DNA makes its ability to store information clear.

A slightly different version of the hypothesis is that a different type of nucleic acid, termed pre-RNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. Such nucleic acids are sometimes more easily produced and/or polymerized under pre-biotic conditions. Suggestions for such nucleic acids include PNATNA or GNA [3] [4].

[edit]RNA as an enzyme

Further information: ribozyme"

First cell-like organised molecules:  

NOTE: A web-link in WIKI seem to summarize this in a sensible manner:
    • Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles
      • Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacervates



From Dr. Hoback at UNK, Bebraska, pers. communication Jan 5th 2009:
Protobionts: Chemicals trapped within membrane of proteins.  May have metabolic activity, but not replication ability.  May generate voltage (like a neuron does)
Liposomes: These are like protobionts, but they include lipids in thier membranes.  These are dynamic, may capture other liposomes, and split apart.
Coacervates: These are liposomes with functional enzymes inside them, and their membranes ARE lipid bi-layer.


Polymer-rich colloidal droplets, have been studied in the Moscow laboratory of A. I. Oparin because of their conjectural resemblance to prebiological entities. These coacervates are droplets formed in an aqueous solution of protamine and polyadenylic acid. Oparin has found that droplets survive longer if they can carry out polymerization reactions. "
(Source: http://www.biog1105-1106.org/demos/106/unit04/3a.protobionts.html)

"Scientists think that the protobionts are the evolutionary precursors of prokaryotic cells. Protobionts may be originated as an array of microspheres of diverse organic and inorganic compounds enclosed by lipidic membranes. Proteins, carbohydrates, lipids, and other organic substances were the most important autocatalytic organic compounds. Water was a very important factor in the assembly of the protobionts' endoplasm. After this event, several microspheres could self-organize into organelles that were able to perform specific functions; for example, lysosomes, peroxysomes, vacuoles, etc."

Prokaryotes (bacteria and archea) existed on the energy rich Earth for millions or years.  Over time, some of these evolved the capability of storing the sun's energy (light) into carbohydrates through photosynthesis.  These early cyanobacteria generated oxygen as a bi-product of this process.  

Over a long period of time, this contributed to a significant change in the Earth's atmosphere.

"The Cyanobacteria (blue-green algae) are a group of prokaryotes that are extremely important both ecologically (especially in global carbon and nitrogen cycles) and evolutionary terms. Stromatolites, which are formed by cyanobacteria, provide living and fossil evidence of cyanobacteria going back 2700 million years. Today stromatolites grow only in shallow, salty pools in hot, dry climates (e.g. Shark Bay in Western Australia), and their abundance in ancient rocks implies similar environmental conditions in those times. Stromatolites and other cyanobacteria were the main contributors to the marked increase in atmospheric oxygen concentrations that began around 2000 million years ago. Today, cyanobacteria are found everywhere - in marine, freshwater and terrestrial environments and as symbionts e.g. lichen - and contribute up to 50% of the atmosphere's oxygen."

"DNA evidence suggests that the first eukaryotes (green plants) evolved from prokaryotes (through endosymbiotic events) between 2500 and 1000 million years ago. Fossils of eukaryotes that resemble living brown algae have been found in sedimentary rocks from China that are 1700 million years old, while possibly the oldest photosynthetic eukaryote,Grypania, comes from rocks 2100 million years old. Note that the diversity of modern algal groups, and particularly of their chloroplasts, suggests that these endosymbiotic events were not unusual. Modern algae comprise a range of organisms with very different structures but identical photosynthetic pigments. This suggests that very different host organisms have formed a symbiosis with the same photosynthetic cells. That is, the algal groups must have evolved through separate endosymbiotic events, and the group as a whole is identified on the basis of a similar level of structure, rather than on its evolutionary origins. Such groups, where the members have several different evolutionary origins, are described as polyphyletic."

From the fossil record, we now have enough evidence to see that:
(Source: http://ircamera.as.arizona.edu/NatSci102/text/extfirstlife.htm)  


The endosymbiotic theory for the origin of eukaryotes.

This is such an interesting idea and concept.  Little bacteria with diverse functions getting together into a larger cell, and the eukaryote cell begins to exist.  

(Source: http://io.uwinnipeg.ca/~simmons/16cm05/1116/16protis.htm)

But how, and why?

There are several pieces of evidence that support this theory, and until recently, these types of events were never observed in naturally occurring living setting.  I found this read on this topic to be very well done:

Can Secondary Symbiosis Still Occur?

Probably so.

Two Japanese scientists have discovered a heterotrophic flagellate that engulfs a unicellular green alga that lives freely in the surrounding water. Once inside,
  • the alga loses its flagella and cytoskeleton;
  • the host loses its feeding apparatus;
  • the host switches from heterotrophic to autotrophic nutrition (photosynthesis);
  • the host becomes capable of phototaxis.

When the host divides by mitosis, only one daughter cell gets the plastid. The other cell regrows the feeding apparatus and is ready to engulf another alga.

You can read the details in Okamoto, N. & Inouye, I., Science310:287, 14 October 2005.


 Species and speciation


Allele Frequency:  For a specific trait if more than one allele is possible, then the total of each possible allele frequency = 100%.
In theory, unless there is an external factor affecting the allele frequency, the fruency of alleles in apopulation will remain constant from generation to generation.

Example:  (this is totally made up example, not based on any facts) 
In rhinoceros the horn can be either long (L) or short (l). Long is dominant over short.  In a population of 456 rhinos in a National Park in Ivory Coast, the frequency of the short horn allele is 25 %, then the frequency of the long horn allele is 75%.

Why is this significant?

1.    Knowing the frequency of alleles can help predict the number of individual with a characteristics, or the number of individuals that are heterozygous for the alleles.
2.    If the allele frequency is NOT the same from generation to generation, then evolution has occured.

Genetic Drift - Result of chance events, usually within a small population, may cause the allele frequency to change.  
Founder Effect - When small sub-group of a population get displaced into a new area, as it colonizes this new area, its allele frequency will likely be different than that of the original population.
Bottle-neck effect - When only a small portion of a population survives a major change event, its allele frequency might be different than that of the original population.
Gene flow - If new individuals from another population migrate into a population, or away from the population, then new alleles, or a change in the allele frequency might occur.

- Selective mating (certain traits more favored than others)
- Differential reproductive success
- DIfferential survival success
- Mutation

We will discuss this using numerical example in a few minutes.

Microevolution:  a change in allele frequency in a population’s gene pool over a number of generations

What is a SPECIES????  How do we define the word species???

This always more complex than it seems....  It seems easy when comes the time to differentiate between a giraffe and an elephant, but much more tricky in some groups of plants, in insects, in protists, in bacteria.

.................  try it   ............

From Wiki: "In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are often used, such as based on similarity of DNA or morphology. Presence of specific locally adapted traits may further subdivide species into subspecies."

The entire article on this issue is well worth a read...  http://en.wikipedia.org/wiki/Species#Difficulty_of_defining_.22species.22_and_identifying_particular_species

There are so many things to consider, that nowadays biologist have many different TYPES for the concept of species... each with its advantages, and with its problems:

Typological species - Based on fixed physical properties of individuals. (Problems here as members of the same within a population may have different traits)

Morphological species  - Based on average physical  properties of population.  (Problems here when closely related populations have very different traits, or vice-versa)

Biological / Isolation species - Based on morphology, and on the distinct ability to interbreed.  (Problem here for species that do not reproduce sexually,, or that could have a potential to interbreed that has not been recorded).  This is often the msot pratcial and commonly used concepts, especially for macroscopic life-froms.

Recognition species

Mate-recognition species 

Phylogenetic (Cladistic)/ Evolutionary / Darwinian species[verification needed] 
A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. 

Ecological species
A set of organisms adapted to a particular set of resources, called a niche, in the environment. 
Genetic species 
based on similarity of DNA of individuals or populations. Techniques to compare similarity of DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding).
Phenetic species
based on phenotypes.
Species that reproduce without meiosis or fertilization so that each generation is genetically identical to the previous generation. See also apomixis.
Cohesion species 

Evolutionarily Significant Unit (ESU) 
An evolutionarily significant unit is a population of organisms that is considered distinct for purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several possible definitions, which coincide with definitions of species.

In practice, these definitions often coincide, and the differences between them are more a matter of emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective, or can be applied in all cases without resorting to judgment. Given the complexity of life, some have argued that such an objective definition is in all likelihood impossible, and biologists should settle for the most practical definition."

Barriers between gene pools: events which lead to speciation:


(Source: http://evolution.berkeley.edu/evolibrary/article/_0/history_21)


The mule is an example of hybrid infertility; it is a hybrid between a male ass (Equus africanus) and a female horse (Equus caballus).  Mules are sterile.

(Source: http://www.theage.com.au/news/arts-reviews/mule/2006/10/03/1159641300317.html)


Some closely related species may co-exist in the same habitat, but become fertile during different seasons, or at different times of the day.  Examples of this includes flowering plants, insects, birds.


Behaviours such as physical courtship (dances, building of nests, decorations, antler wrestling matches), vocalization, displays of colours, or even chemical signals in the forms of hormones and scents may lead to successful or unsuccessful breading.  Birds songs are such a classical example of this... the incorrect song, and some birds won't even come close to the potential mate.

(Source: http://lhs2.lps.org/staff/sputnam/Biology/U6Evolution/U6Notes.htm)


In some species, during meiosis an error can occur where the chromosomes are not divided ("meiotic non-disjunction").  The result are gametes containing 2n chromosomes (instead of n).  If such gametes successfully merge and form an offspring, the new offspring may end up with 3n or with 4n chromosomes:

(source: http://en.wikipedia.org/wiki/Polyploidy#Amphidiploidy)

One consequence of polyploidy is that the resulting organism cannot breed with others - are there are no others like it! However, this is not always a problem: many plants are both male and female, so they can simply fertilize themselves. Some earthworms can do this too.  In garden plants, this process is often used in order to get showy varieties.  Horticulturist can induce polyploidy by exposing a plant to a hormone called colchicine.

Is this a common method of speciation?

About half of angiosperm (flowering plant) species seem to have originated this way. Relatively few animal species are thought to have originated this way, because not all animals can self-fertilize or reproduce asexually. However, brine shrimp, weevils, bagworm moths and flies seem to have arisen this way. 

(Source: http://www.don-lindsay-archive.org/creation/polyploidy.html)

SYMPATRIC SPECIATIONthe formation of a new species by splitting of an existing species in the same geographical area.

(source: http://www.geo.arizona.edu/Antevs/nats104/SymptrcSpctnSml.jpg)

ALLOPATRIC SPECIATIONthe formation of a new species by splitting of an existing species in different geographical areas.

Our example of geographical isolation earlier on WAS actually an example of ALLOPATRIC speciation, where speciation occurs when individuals that originally were part of the smae population become separated by some physical barrier.  Here is another example:
(Source: http://www.brooklyn.cuny.edu/bc/ahp/LAD/C21/graphics/C21_Isolation_1.GIF)


This is when a more ancient population of a species undergoes speciation over thousands of generations, such that several changes occur at the same time, but in different directions.

This is something Darwin realized after observing finches on the Galapagos Islands:

"Previously, the finches occupied the South American mainland, but somehow managed to occupy the Galapagos islands, over 600 miles away. They occupied an ecological niche with little competition.

As the population began to flourish in these advantageous conditions, intraspecific competition became a factor, and resources on the islands were squeezed and could not sustain the population of the finches for long.

Due to the mechanisms of natural selection, and changes in the gene pool, the finches became more adapted to the environment, illustrated by the diagram below.

(Source: http://www.biology-online.org/2/15_adaptive_radiation.htm)

Convergent and divergent evolution.

CONVERGENT EVOLUTION: When two different species undergo the same kinds of environmental pressures, natural selection may enhance in each features that become over time progressively similar.  An good example of this are the swimming structures on fish, and on marine mammals.  They appear superficially alike, and they do serve the same purpose (to aid in swimming), but upon investigation, they happen to be very different.  


DIVERGENT EVOLUTION: When within a single population, two groups arise from different and separate environmental pressure and selection.  If sufficient amount of such differences accumulate, this can give rise to two different species.
(Source: http://www.wvup.edu/ecrisp/parallel.gif)

Modes of selection

(Source: http://www.evoled.org/images/modes.gif)

The Pace of Evolution:

 is the slow change from one form to another. Punctuated equilibrium implies long periods without appreciable change and short periods of rapid evolution.


Punctuated equilibrium
(Source:  http://anthro.palomar.edu/synthetic/glossary.htm#phyletic_gradualism)

"Volcanic eruptions and meteor impacts affecting evolution on Earth"....
Large cataclysm may have caused serious and sudden changes in the earth's biosphere resulting in what is know as the GREAT MASS EXTINCTIONS.

The greatest of them all appears to have occured 250 millions years.  Follow the link from NOVA to learn about more about this 'mother of all extinctions: 

TRANSIENT POLYMORPHISM: The presence in a population, at a particular gene locus, of alternative alleles in which one is progressively replaced by another. (Encyclopedia.com)

The classical example of this as observed in nature is the case of INDUSTRIAL MELANISM, or the variation of allele frequency in the peppered moth.  In the picture below, please note how well the pale moth is camouflaged on the lichen covered trees (left picture), while the darker variant is better camouflaged on the naked bark (pic on the right).

(Source: http://home.comcast.net/~mkent595/Microevolution.html)

And be prepared to answer Q. on a quiz or EXAM on this!

BALANCED POLYMORPHISM: A genetic polymorphism that is stable, and is maintained in a population by natural selection, because the presence of the different alleles (heterozygotes) for the particular alleles have a higher fitness (survival rate and reproductive success) than either homozygote. (Encyclopedia.com)

The example we have already discussed in class about this is the maintenance of SICKLE-CELL ANEMIA in human populations, in areas where the heterozygotes are better survivors of MALARIA than non-carriers.  

(Source: http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html)

Read on at: http://www.bio.davidson.edu/people/midorcas/animalphysiology/websites/2005/Eppolito/other.htm