The Common Vein Copyright 2012
In the beginning of time there was 0…
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And Then There was 1…
And then 0 and 1 started linking organizing
…. sometimes in the presence of a facilitator and the two equations (1+1=2, and 1+1= 1 were born)
The poem was written following a discussion between 3 school friends inspired by the concept of the whole being greater than the sum of its parts.
1+1 = 1
Davidoff Abelson and Leveen
In the Beginning
There was 0
Then there was 1
Then 0+1 = 1
1 to the power 0 = 1
1 to the power 1 = 1
1 to any power = 1
Any number to the power 0 = 1
Though 0 to the power 0 is indeterminate
And finally 1 + 1 = 1
Big Bang and the Formation of the Hydrogen Atom … and the beginning of the build up
In the beginning – about 13.7 billion years ago after a big bang, the universe was so hot and then as it began to cool protons neutrons and electrons were born and then the simplest atom – the hydrogen atom was born first, and remains the most abundant atom in the universe contributing to 90% of the atoms in the universe. After about 300 million years the hydrogen atoms started to clump together under the force of gravity generating pressure as they clumped and then heat resulting in nuclear fusion. As a result of nuclear fusion of two hydrogen atoms helium , then lithium was formed and then the rest of the elements up to iron (26 hydrogen atoms) were formed (http://www.physicscentral.com/explore/poster-stardust.cfm) Therefore matter formed creating the stars and then galaxies in the heavens and the table of elements on the earth up to iron. After iron nuclear fusion requires more energy than it produces. The inner core of the earth has a large amount of iron.
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The Birth of the Forces of the Universe and the Beginning of Biology
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There were two basic forces in nature … positive and negative, and a neutral force, called the neutron.
In the atomic world, the positive is encapsulated in the proton and the negative in the electron while the neutron resides with the proton in the nucleus.
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When positive and negative interact – it is not a simple interaction. It is not a 1+1 =2 , and is closer to 1+1=1. It is like marriage. Firstly by their union they still retain their individuality, go their separate ways with the electron in orbit and the nucleus staying central, but remain bonded and together they form a new unit.
When a new unit is formed from its component parts, an interaction has taken place in a given space, in a given moment in time, in a given environment. The new unit has unique characteristics that is not manifest in either of the component parts.
At the time of big bang the electron, proton, and neutron were formed.
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The hydrogen atom is the building block of all else to come.
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Some Universal Principles
The marriage between the electron and the proton is not a simple one. It is not as black and white as it seems since as a result of the marriage the electron is bound to the nucleus and the proton is bound to the electron. The motion of the electron in an orbit allows it to keep its distance from the proton and prevents the two from crashing and falling head over heels into each other, or nulling each other. The hydrogen atom is set in motion and as a result of the electrical force in motion an electromagnetic field is set up. The spinning of the hydrogen atom forces the atom to be in a certain position in space at a given time as it moves – Voila – the elements of space, time and motion, are manifest in the units. The units have mass and elements of electromagnetic and mechanical forces. The interactions, allow bonding, and new units are established. Uniqueness, dependence and independence of each of the units follows. These are elemental and foundational principles common to all matter- organic and inorganic, biological or otherwise and will be repeated ad nauseum in the following texts.
With the birth of the universe, an infinitismal number of hydrogen atoms were born and let loose to build bigger and better units with their new found expression through mass, time, space, electromagnetic force, and motion.
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The electromagnetic forces and the fact that the hydrogen atoms are moving, forced the atoms to come into contact with other hydrogen atoms and random reactions took place in the presence of the given environment in which temperature, mass, motion, space, time, electromagnetic forces, and facilitators were relevant to the reaction and the result was the creation of other atoms and elements.
The Building of New atoms and Elements
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And as we double the units of force we find that there is a relatively weak electric force and another force called a strong force
Fission and Fusion – Strong forces and Electrical forces – (http://www.youtube.com/watch?v=yTkojROg-t8
And as we build up the negative and positive charges and we add neutrons in the mix the units get linked and organized in different ways to create new units with completely different characteristics
As we add units things start to change to a point where electrical forces start to dominate
|The Atom – The Powerful and Indivisible
This atom has 56 electrons in 6 orbits It is called barium
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The remarkable similarity between the structure of the atom, and the structure of the solar system, leads one to ponder the recurring organizational pattern of things in between. If one considers the atom as a unit and the solar system as a unit then the technique of combining units to build bigger units more powerful than the individual parts allows us to understand in some measure the unifying units to units concept or 1+1= 1
Atoms are the smallest parts of matter that possess the distinctive chemical characteristics of chemicals that we can recognize in our surroundings
If for example split a piece of charcoal, which consists of pure carbon, and break it up into its component parts, it will end up as an atom of carbon that will have the same chemical characteristics as the original charcoal If you were to do the same thing of chopping up an iron molecule till it ends up with characteristic component parts, you would end up with iron atoms that behave in similar fashion as the original iron bar If the chopping continues then the iron particles will be broken up into protons, neutrons and electrons.
If on the other hand we took water and started breaking it up into its component parts then we would arrive at the molecules of water wth 2 hydrogen atoms and one oxygen atom. Individually these would not behave like the water molecule but rather like hydrogen and oxygen individually. Then as they get broken up further into electrons protons and neutrons, they will not behave like oxygen or hydrogen but like protons electrons and neutrons.
When a substance consists of a single type of atom it is called an element. There are 92 different elements found naturally on the earth .
A substance that is made up of more than one atom is called a compound.
And atoms of same type link and organize and they form an element
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and then there are now only 118 of them. The elements are categorized into the groups of alakali metals, alkali earths, halogens, noble gases.
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The atoms also link to different atoms to form molecules
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So what about biology
The Units of Biology
Fundamentals of life:
atomic particles —>molecules—> macromolecules (DNA, RNA)—> self assembling macromolecules—> lipid bilayer formation—> lipid bilayer encapsulating self assembling macromolecules—>compartmentalization—> evolution of those compartments with respect to environment—> replicating cells—>formation of basic bacteria in hot springs—> formation of eukaryotes—> evolution of the cells to organize into tissues—> into organs—>then into living creatures
Carbohydrates fats and proteins
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Carbohydrates (hydrates of carbon) are organic compounds that usually contain carbon hydrogen and oxygen in the ratios: 1 Carbon: 2 Hydrogens: 1 Oxygen.
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The type of carbohydrates include monosaccharides disacharrides
A monosacharride such as glucose is linking and organization to create something bigger and more powerful than the individual parts
Molecules molecules and then macromolecules
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Lipids triglycerides eg fat and oils
Sterols – Choletserol Vit D and Sex hormones
Phospholipids eg lecithin
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95% of the lipids that we eat and 99% of the lipids in our body are triglycerides
Three fatty acids and a glycerol
All fats are derivatives of fatty acids and glycerol. They, like the carbohydrates are created from a combination of carbon hydrogen and oxygen which link and organize to form a fat soluble compound. The triglycerides consist of one unit of glycerol and three units of fatty acids
The fatty acid is a usually a long chain of even number of carbons (usually between 4 to 28 each carbon allowing for 4 bonds. When there are fewer than 6 carbons it is called a short chain fatty acid. When there are 6-12 carbons it is called a medium chain and when there more than 12 carbons it is called a long chain fatty acids.
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When the carbons are linked to each other by single bonds then ther are two hydrogens per carbon and the fatty acid is said to be saturated with hydrogen atoms. When there is a double bond between two carbons then each carbon in the double bond only has room for 1 hydrogen each and the fatty acid is unsaturated with hydrogen atoms
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Enter another molecule called glycerol – a type of alcohol with a hydroxyl group on each of its three carbons
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When glycerol links and organizes with with 3 fatty acids a new product is born called triglyceride
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Proteins are polymers constructed from a series of 20 different amino acids. This is the linking part.
An amino acid is composed of an amine linked to an acid
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The organizing part is the a specific sequence specified by the gene resulting in the primary structure.
As a result of the specific linking and organizing a secondary structure results which is a specific coiling of the structure in a unique 3D manner There are two basic types of secondary structure The alpha helix and the beta pleated sheet based on the hydrogen bonds that occur at regular intervals
The tertiary structure is a result of linking of side chains of various amino acids
When other proteins join a quaternary structure results
Amines N HH
Amino acids carbon
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The 20 amino acids form polypeptides and polypeptides form proteins
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Making Biological Materials from Proteins
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Hydrogen bonds between the amino acids determine whether the secondary proteins particpate in almost every aspect of the cell structure and function
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A base is a a substance that can accept hydrogen ions (protons) or more generally, donate electron pairs.
The base in the nucleotide is a nitrogen containing base = nitrogenous base
3 parts Phosphate group sugar (deoxyribose)and one of four bases adenine guanine cytosine thymine
sugar phosphate = hand rails together thy form a nucleotide
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the basic pairs never change the order of the pairs varies from one species to the next
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Made of nucleotides
Ribose as a pentose sugar
Uses Uracil and not Thymine
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A U or T
G to C
Self Assembling Macromolecules
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The Making of Membranes Lipid Bilayer Formation
All cells and organelles are bound by a cell mebrane
Cell mebranes are made of fats and proteins
The fats (phospholipids) form a double layer and the proteins which are contained within the membrane
Phospholipids consist of a head and a tail
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The head universally contains an alcohol phosphate and glycerol and the tail two fatty acids
The backbone of the head is glycerol
An example is lecitihin
The head which is hydrophilic is made of
a- choline component
b- phosphate component
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Linking and organizing with hydrophillic head facing outside environment, two fat soluble hydrophobic layers facing each other, and the other layer of hydrophilic heads facing the inside environment of the cell.
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The cell membrane has to add more units to reach full functionality
are needed identify the cell – a tag if you will to say who the cell is
enable interaction with external and internal environment
allowing products to enter and products to leave the cell
Movement is by
Types of functionality demanded of the cell membrane and how proteins assist
surface protein markers – identifies the cell
receptor proteins bind to messengers or hormones that change permeability of a cell
ion channels Charged pores allow molecules to pass through the cell membrane as long as they are the correct size and charge
membrane pumps uses energy (ATP) to open and close gates – Classical is the Sodium potassium pump
carrier proteins Bind to a solute and carry it into the cell
trigger the formation of another messenger and then activate enzymes in the cell to accelerate chemical reactions
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Lipid BilayertEncapsulating Self Assembling Macromolecules
Evolution of the Compartments with Respect to Environment
Cytoplasm soup of proteins fats carbohydrates nucleic acids ions waterbody
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The mitochondrion 3D video Harvard – All Visual http://www.youtube.com/watch?v=4OgCMzvjaws
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Connects cells to each other and form tissues
In the world of language the single and the simple is the letter, while in the world of music and painting it is the note, and the brushstroke respectively. The letter moves on to the word, the note to the bar, and the brush stroke to an object in the painting. In biology the cell is the basis of the organ and organism. The Mozarts, van Goghs, Einsteins and Shakespeare’s of the world, organized connected and integrated the units in such a way so as to create a genius result – certainly one that is more powerful than the individual parts. In biology, years of evolution have slowly crafted the human body into a miraculous machine which we have the good fortune to own, honor , learn about, and opportunity to unravel and understand its mysteries in the context of the medical world.
The yearning to be “one” drives us, whether we conciously know it or not. The atom thinks it is indivisible (and probably invincible) but it also has smaller parts. The atom by itself is powerless unless it combines with similar atoms to make up molecule. This same feeling of power and individuality comes to the cell, which for practical purposes, is the smallest living individual and independent unit in biology. It is made up of smaller parts of macromolecules that combine to form microstructures such as the ribosome, endoplasmic reticulum, and the nucleus. All parts in combination make up the cell, giving it singularity and oneness. The cell is powerless without the tissue, and so it combines with similar cells to humble itself before the tissue. Although the tissue claims individuality, it too seeks combination with other tissue as it searches for oneness in the organ. The seeming accomplishment of unity continues through the body to the individual, the family, the community of the village, the community of the nation and the community of the world – and even the solar system, which bears uncanny structural similarity to the atom. The solar system probably thinks it is the end of the world, but the universe has a surprise in store. At this writing, the universe resides at on the one end and the atom on the other – both claiming singularity – but we have to suspect there may be something beyond both of them.
size of structure
coffee bean = 12 X 8mm
grain of rice = 8 X 2.5mm
sesame seed = 3 X 2mm
grain of salt = .5mm
ameba = 500 microns
paramecium = 210 X 60 microns
human ovum =130 microns
photoreceptor =100 X 2.5 microns
sperm = 60 X 5 microns
skin cell = 30 microns
red cell = 8 microns
X chromosome = 7 microns
baker’s yeast = 3 X 4 microns
E Coli bacterium = 3 X .6 microns
mitochondrion = 4 X .8 microns
lysosyme = .1 micron
measles virus = 220 nanometers
influenza virus = 130 nm
hiv virus = 130 nm
coated vesicle = 90 nm
hepatitis virus = 45nm
rhinovirus = 30nm
ribosome = 30nm
antibody = 12 nm
tRNA = 7nm
phospholipid = .9 X 3.4nm
methionine = 1100 X 700pm
adenine = 1300 X 760pm
glucose = 900pm
water molecule = 275pm
carbon atom = 340pm
Carl Sgan Explores the Cell http://www.youtube.com/watch?v=UT_HQ6l72Og
So our bodies contain 7X1027 atoms and of those approximately 4.2X1027 hydrogen atoms. Hydrogen is big bang dust.
How do the atoms get from the big bang to the body?
Miller Urey Experiment http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html
Botany More Complex than the Cosmos
The construction of the universe is certainly very much easier to explain than is that of the plant.
Georg Christoph Lichtenberg
Aphorisms, trans. R. J. Hollingdale (1990), 119.
Atoms and Sparrows
Who sees with equal eye, as God of all,
A hero perish or a sparrow fall,
Atoms or systems into ruin hurl’d,
And now a bubble burst, and now a world.
‘An Essay on Man’ (1733-4), Epistle I. In John Butt (ed.), The Poems of Alexander Pope (1965), 507.
Understanding Physics and Biology Together – The Goal (a)
Yet is it possible in terms of the motion of atoms to explain how men can invent an electric motor, or design and build a great cathedral? If such achievements represent anything more than the requirements of physical law, it means that science must investigate the additional controlling factors, whatever they may be, in order that the world of nature may be adequately understood. For a science which describes only the motions of inanimate things but fails to include the actions of living organisms cannot claim universality.
Arthur Holly Compton
The Human Meaning of Science (1940), 31.
Understanding Physics and Biology Together – The Goal (b)
[Certain students] suppose that because science has penetrated the structure of the atom it can solve all the problems of the universe. … They are known in every … college as the most insufferable, cocksure know-it-alls. If you want to talk to them about poetry, they are likely to reply that the “emotive response” to poetry is only a conditioned reflex …. If they go on to be professional scientists, their sharp corners are rubbed down, but they undergo no fundamental change. They most decidedly are not set apart from the others by their intellectual integrity and faith, and their patient humility in front of the facts of nature…. They are uneducated, in the fullest sense of the word, and they certainly are no advertisement for the claims of science teachers.
In Science is a Sacred Cow (1950), 18-19
Hubble’s observations suggested that there was a time, called the big bang, when the universe was infinitesimally small and infinitely dense. Under such conditions all the laws of science, and therefore all ability to predict the future, would break down. If there were events earlier than this time, then they could not affect what happens at the present time. Their existence can be ignored because it would have no observational consequences. One may say that time had a beginning at the big bang, in the sense that earlier times simply would not be defined. It should be emphasized that this beginning in time is very different from those that had been considered previously. In an unchanging universe a beginning in time is something that has to be imposed by some being outside the universe; there is no physical necessity for a beginning. One can imagine that God created the universe at literally any time in the past. On the other hand, if the universe is expanding, there may be physical reasons why there had to be a beginning. One could still imagine that God created the universe at the instant of the big bang, or even afterwards in just such a way as to make it look as though there had been a big bang, but it would be meaningless to suppose that it was created before the big bang. An expanding universe does not preclude a creator, but it does place limits on when he might have carried out his job! — Stephen W. Hawking A Brief History of Time: From the Big Bang to Black Holes (1988), 8-9.