one note using one note? alan ward. molecular microbiology resources and communication lecture email...
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One Note
Using One Note?
Alan Ward
Molecular Microbiology
Resources and Communication
• Lecture • Email• Web• One Note
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Another way of looking at it
Multiple pagesViewing page 2
They give another example of why you need Data driven discovery as well as hypothesis driven research
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Some thing to do
Slide 1
Some commentary
Evolution
What is the structure of life?
Alan Ward
EvolutionDepth first or breadth first
Two different strategies for computer search algorithmsWhich is best?
That heavily depends on the structure of the search tree and the number and location of solutions.If you know a solution is not far from the root of the tree, a breadth first search (BFS) might be better. If the tree is very deep and solutions are rare, depth first search (DFS) might rootle around forever, but BFS could be faster. If the tree is very wide, a BFS might need too much memory, so it might be completely impractical. If solutions are frequent but located deep in the tree, BFS could be impractical. If the search tree is very deep you will need to restrict the search depth for depth first search (DFS), anyway.
Evolution
So what is the structure of living things that we are exploring?
The structure of life is dictated by evolution:
“Nothing in biology makes sense except in the light of evolution”
(Dobzhansky)
• How did life arise?
• How did it evolve?
• How is it evolving now?
Why did it evolve?
Evolution
Why did it evolve?
1st Law of thermodynamicsEnergy is neither created nor destroyed
but reactions, in which energy changes, still occur
Evolution
ΔG = ΔH - TΔS
2nd Law of thermodynamicsSystems change from ordered to disorderedbut living things are highly ordered
EvolutionWhy did life evolve?
1st Law of thermodynamicsEnergy is neither created nor destroyed
but reactions, in which energy changes, still occur
Processes proceed from High energy to Low energyBut the 1st Law of ThermodynamicsEnergy is neither created nor destroyed
Direction of chemical change
often corresponds to -ΔE
but not always
(NH4)2SO4
ΔG = ΔGo + RT loge [A][B][C][D]_____
A + B C + D
Glyceraldehyde-3-P = dihydroxyacetone-PΔGo = +1.8 kcal
[G3P] = 3 x 10-6M [diOHAcP] = 2 x 10-4MΔG = 1.8 + 1.98x10-3x298xloge(3x10-6/2x10-4)
= - 0.7 kcal/mol
Why did life evolve?
ΔG = ΔH - TΔS
2nd Law of thermodynamicsSystems change from ordered to disordered
Early EarthHot (>100oC) Meteorite bombardment Volcanic
Gases – H2O CH4 CO2 N2 H2S/FeS HCN CO H2
virtually no O2Energy sources
UV light
Pre-biotic synthesis of bio-molecules
Primitive atmosphere + energy (heat, UV, electric discharge)
Amino acids, purines, pyrimidines, sugars ..
Polypeptides, polynucleotides
Energy and life
Spontaneous direction of change
Times’ arrow
H2O
CO2
High energy Low energy
Organic inorganicOrdered Disordered
It doesn’t go backwards
SimpleComplexMore ordered
Kept warm but no net energy in
Vitalism
Living organisms possess a vital force that enables them to defy the laws of physics and chemistry.
In 1809 Berzelius stated the theory as that organic compounds could not be synthesized in a laboratory.
In 1828 Wöhler, whose mentor was Berzelius, synthesized urea, previously only obtained from biological sources, from inorganic reactants disproving the theory.
The second law may be expressed in many specific ways, but the first formulation is credited to the French scientist Carnot in 1824.
The first explicit statement of the first and second laws of thermodynamics was probably by Clausius in 1850.
Evolution
Evolution
CO2
+ H2O
Simple mixture of proteins
ΔSegg = moderateΔSchick = low
ΔSenergy = high
Net ΔE = 0 Net ΔS = positive ΔG = -ve
Living organisms are highly complex and ordered = low entropy but create disorder = high entropy
Evolution
CO2
+ H2O
Simple mixture of proteins
ΔSegg = moderateΔSchick = low
ΔSenergy = high
Net ΔE = 0 Net ΔS = positive ΔG = -ve
Living organisms are highly complex and ordered = low entropy but create disorder = high entropy
more disorder – higher ΔS
= low E high S
= higher E lower S
Evolution
ΔG is negative
but it doesn’t say how fast!
Evolution
EvolutionEvolution of the Universe Entropy increases
Life catalyses the rate of increase in entropy in the Universe!