Endogenous Development of evolution

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BIOSCIENCE
OPEN ELECTIVE
JULY – DEC 2020

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8:30 am 9:30 am 10:30 am 11:30 am Recess 1:30 pm 2:30 pm 3:30 pm 4:30 pm
MONDAY OE0202
TUESDAY
WEDNESDAY OE0202
THURSDAY OE0202
FRIDAY
BIOSCIENCE SCHEDULE FOR OPEN ELECTIVE, 2020-21

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How engineer play important role?
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Combining engineering with Biology – Biotechnology
The origins of biotechnology and humans using biological material as a commodity to
improve lifestyle, increase longevity and create convenience, we need to go back to the
dawn of human civilization itself.
THE NEOLITHIC REVOLUTION – First Agricultural Revolution: Humans started living in
settlements and growing their crops.
FERMENTATION - Mixing wheat with yeast to create bread is one of the oldest and
simplest applications for biotechnology. Yeast occurs naturally, and its use creates
irreversible chemical and nutritional changes when heat is applied.
IRRIGATION – A very important subject under Environment Engineering involving water
systems and cultivation
PASTEURIZATION – A method to destroy harmful bacteria and prolong life of dairy
products.

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Standing at the Modern Age:
THE SECOND AGRICULTURAL REVOLUTION - Use of crossbreed crops that led to surplus food
production. Use of pesticides and fertilizers.
ANTIBIOTICS - Development of preventives in livestocks and humans.
GENETICS – Genetically modified crops to increase yield, pest resistance, hardiness and
safety with additional ability to cope with our food demands for tomorrow.
BIOFUELS – As alternative fuel, crops are grown and converted to diesel. The organic
material used in biofuels such as Miscanthus (Elephant Grass) and Prairie Switchgrass are high
yield and low maintenance. The ability to convert organic material to fuel is a recent
development.
BIOROBOTICS - Engineers work to develop robots whose applied methods, mechanics, and
theory are inspired by living systems. In theory, they should present advantages over and
above traditional robotics systems. By examining evolution of biological systems, we can
design better robots, prosthetics and automation in industry.
BIOLOGICAL COMPUTERS - Cellular machines that can perform simple computational
operations and store, then recall, memory. The DNA helps in storing and processing the

6. Year 2020 – The Pandemic year
Frequently heard terms:
1. Virus
2. Ventilator
3. RT-PCR
4. Antigen test
5. Droplet transmission
6. Vaccine
7. Drugs
8. Test kits
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Meaning, functioning, significance –
Not very clearly understood by most
Other Applications
1. Pacemaker for heart
2. Glucometer
3. Sorting of blood for preservation in Blood banks.
4. Development of surgical instruments
5. Brain imaging studies
6. Developing programs for genome study.

7. Unit -1
Evolution and Biochemical Evolution

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EVOLUTION – environmental, molecular, species
Creation of earth and changes in the environment through billions of years. The picture shows
a description of the primitive world.

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THEN NOW

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 Earth was created – 4.54 billion years ago
 Conditions of primitive earth – high temperatures, water in the form of vapor
 Gradually temperatures cooled down below 100 oC.
 Volcanic eruptions resulted in non-oxygenous gases including – carbon dioxide, ammonia,
hydrogen, methane.
 Meteorologists suspect that lightning, torrential rains, and ultraviolet radiation combined
with the intense volcanic activity and constant meteorite bombardment to make early
Earth an interesting but inhospitable environment.
 Under the sunlight and UV, hydrogen cyanide was formed which later participated in
creation of amino acids and nitrogen bases.
Stages of the earth’s evolution

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Creation and Progression of life on earth
 Life created – 3.5 billion years ago
 Fossilized cyanobacteria in stromatolites
is the oldest form of life aging 3.45
billion years.
 The earliest forms of life were unicellular
organisms respiring anerobically.
 These years have been divided into
different ages and eras that give
chronological order of appearance of the
various species.
 Evolution is the gradual changes in the
characteristics of a population of
animals or plants over successive
generations which accounts for the
origin of existing species from their
ancestors.

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Alongwith the change of the earth’s environment, the types and complexity of the molecules
In different spheres changed. These changes eventually gave birth to life – the first cell.
Before going in depth about the formation of the first cell, it must be first understood what
cells are. All life is formed by cells. What makes organisms different, is how many cells
there are, what type of cells there are, and how these cells are organized.
Many micro-organisms consist of only one cell, which carries out all functions needed to
survive. Other organisms consist of more cells, such as humans, who contain over a trillion
cells, most of which are specialized for a certain function.
Every cell is made up of many smaller parts. There is the nucleus present in most cells,
which contains DNA which stores the blueprint of the cell.
There are many other parts in a cell, each of which has a specific function. These parts of
the cell are made up of proteins, which are made up of long strands of amino acids. Amino
acids are made up of different combinations of the base elements of carbon (C), hydrogen
(H), nitrogen (N), and oxygen (O).

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The origin of life: Origin of life is a continuous process
• Origin of life is NOT an event:
 19th Century Ideas: life created supernaturally, cannot be proven scientifically.
 20th Century: life generated spontaneously and evolved through different steps
• First cells may have originated by chemical evolution involving 4 steps:
1. Abiotic (Non-biological) synthesis of small organic molecules
(monomers)  C+H = organic molecule
2. Monomers joined together to form polymers (proteins, nucleic acids)
3. Development of a genetic code of self-replicating molecules (RNA, DNA, protein).
4. Production of the first cell by separation of these codes from the outer world by a
membrane.

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Evidence that supports the four-stage hypothesis for the origin of life
Oparin and Haldane theory:
Oparin and Haldane in the 1920s  Abiotic synthesis of
organic molecules is testable in the laboratory
Hypothesis: Conditions on primitive earth favored chemical
reactions that synthesized organic compounds from
inorganic precursors. These conditions were different from
what is now present and include:
- Reducing environment (no oxygen, but instead H2O, CH4,
NH4, and H2) = lots of free electrons that could be used to
reduce carbon and produce organic molecules.
- Energy from lots of lightning, UV radiation (no O2 to block
UV rays from the sun) and volcanic activity (heat).

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Miller and Urey in 1953
In the early 1950s, Professor Harold Urey and one of his students, Stanley Miller, began
experimenting to prove Oparin's theory.
Miller built an closed apparatus which circulated gasses likely to
be present in the early atmosphere (Methane (CH4), Ammonia
(NH3), Water (H2O), and hydrogen (H2) ) past an electrical
discharge, simulating the UV Rays at 8000C and violent electrical
storms present in the early atmosphere.
The experiment was continued for one week and the results
were startling.
 The previously colorless solution inside the apparatus had turned red.
 Many organic were molecules present, some of which couldn't be readily identified.
 The most important of created compounds, however, where amino acids.
 Further studies showed that some amino acids would have combined with hydrogen cyanide
(HCN) to form purines and pyrinidines, used to create DNA and RNA (nucleic acids)

17. RNA as The Primitive Genetic Material – RNA World
• RNA or a similar molecule may have been the first gene and the first catalyst.
• One of the earliest stages of biological evolution was the chance formation, in the primordial
soup, of an RNA molecule that could catalyze the formation of other RNA molecules of the
same sequence—a self-replicating, self-perpetuating RNA.
• The fidelity of self-replication was presumably less than perfect, so the process would
generate variants of the RNA, some of which might be even better able to self-replicate. In the
competition for nucleotides, the most efficient of the self-replicating sequences would win,
and less efficient replicators would fade from the population.
• New variants of self-replicating RNA molecules developed, with the additional ability to
catalyze the condensation of amino acids into peptides.
• Occasionally, the peptide(s) thus formed would reinforce the self-replicating ability of the
RNA, and the pair—RNA molecule and helping peptide—could undergo further modifications
in sequence, generating even more efficient self-replicating systems.
• Its been recently discovered that in the protein-synthesizing ribosomes, RNA molecules, not
proteins, catalyze the formation of peptide bonds.

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The First Cell
A critical moment in chemical evolution was the transition from systems of
randomly generated molecules to systems in which molecules were organized
and specifically replicated.
Once RNAs gained the ability to self-perpetuate, the primordial environment would have
become enriched in molecules that were best able to survive and multiply.
Formation of fluid filled vesicles provided protection from the surroundings and hence gave
birth to first cell.
With passage of time, the molecules evolved and became complex which eventually changed
the structure and function of cells.

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From Biochemical to Biological Evolution
There are 3 major phylogenetic classes which show the variation in organisms

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Phylogentic relationships are best deduced by comparing polymeric molecules—RNA, DNA, or
protein—from different organisms.
The archaea include some unusual organisms: the methanogens (which produce CH4), the
halobacteria (which thrive in concentrated brine solutions), and certain thermophiles
(which inhabit hot springs).
The three-domain scheme also shows that animals, plants, and fungi constitute only a small
portion of all life-forms.
It is unlikely that eukaryotes are descended from a single prokaryote, because the
differences among eubacteria, archaea, and eukaryotes are so profound. Instead,
eukaryotes probably evolved from the association of archaebacterial and eubacterial cells.
The eukaryotic genetic material includes features that suggest an archaebacterial origin.

22. Darwin’s Theory of Evolution
What is a genotype?
A set of genes inherited by an organism from the parents. But this may vary due to
environmental factors. Not all organisms with the same genotype look or behave similarly.
What is a phenotype?
It is the observable characteristics of a particular organism i.e. the morphology,
development and behaviour.
Genotype + Environment + genotype-environment interactions = phenotype.

23. Correlation between Molecular Evolution and Species Evolution
Hemoglobin contains the protein “globin” and is a constituent of blood. If we compare the
structure of globin and analyze the peptide sequence, it is explicit that the protein is not
identical although the function if the protein is broadly similar – oxygen transport
Species No. of AAs difference with
respect to humans
Gorilla 1
Rhesus monkey 8
Mouse 27
Chicken 45
Frog 67

24. Darwin’s Finches
“Seeing this gradation and diversity of structure in one small, intimately related group of birds,
one might really fancy that from an original paucity of birds in this archipelago, one species
had been taken and modified for different ends."
Darwin killed and preserved 14 different Finch
birds from Galapagos island which he later handed
over to Gould, an English ornithologist. Darwin was
already interested in the variety of species that he
saw on the island and their similarity with some
species in South America. The analysis of Gould
regarding the bird beak type and its type of food
was included by Darwin in his book:

25. Theory of Natural Selection
The theory suggests a course of NATURAL SELECTION that prefers one species to the other.
Thus comes the theory of SURVIVAL OF THE FITTEST.
Amongst the various phenotypes arising in a species, the ones best suited for a particular
geographical and environmental feature have survived.
The theory also suggests that all organisms originated from a common ancestor who
gradually underwent modifications following natural selection.
However, the last observation of Darwin has been rejected as branching in phylogeny has
been proved using fossil studies.
This was written in the book “ON THE ORIGIN OF SPECIES”

26. 1. Sheep in cold region have more wool as compared to plain lands as a protection against
cold temperatures.
2. Humans in mountain region have higher level of haemoglobin for efficient oxygen
supply in the body for a low atmospheric oxygen area.
3. Tropical zone humans have higher content of melanin (dark skin) due to stronger
exposure to sun rays.
Can We See Natural Selection?

27. 1. Evolution is not directed toward a particular goal. It proceeds by random changes that may affect the
ability of an organism to reproduce under the prevailing conditions. An organism that is well adapted
to its environment may fare better or worse when conditions change.
2. Variation among individuals allows organisms to adapt to unexpected changes. This is one reason that
genetically homogeneous populations (e.g., a corn crop) are so susceptible to a single challenge (e.g.,
a fungal blight). A more heterogeneous population is more likely to include individuals that can resist
the adversity and recover.
3. The past determines the future. New structures and metabolic functions emerge from pre-existing
elements. For example, insect wings did not erupt spontaneously but appear to have developed
gradually from small heat-exchange structures.
4. Evolution is ongoing although it does not proceed exclusively toward complexity. An anthropocentric
view places human beings at the pinnacle of an evolutionary scheme, but a quick survey of life’s
diversity reveals that simpler species have not died out or stopped evolving.
Principles of Evolution

28. Examples
From whales to terrestrial animals Evolution of sharks in 400 million years

29. Evolution of humans