I am filled with
wonder that we live in an era when we can consider the world in which
we live and the physical nature of our solar system with the added ability
to verify what we see.
Human beings on
our earth have enormous capacity to see, hear, feel, smell and taste,
as well as the ability to store information internally in our memories.
They then invented
other storage forms such as drawings, painting and symbols, as writing,
leading to the making of books and libraries.
They then invented
photographic recording, auditory recording and computers, so that all
of the above constitute records of our knowledge.
We now have access
to the most amazing repertoire of human records and observations as
well as the many interpretations human beings of different eras and
epistemologies have placed before us.
Science refers to
the area of human endeavour where rigorous observations can lead to
possible hypotheses and ongoing efforts to verify or refute these hypotheses.
This is a never-ending
process, as long as there are sentient creatures working to explore
every aspect of everything!
PHYSIOS BEFORE
BIOS
I am filled with
wonder that we live in an era when we can consider the world in which
we live and the physical nature of our solar system with the added ability
to verify what we see.
The territories
of human learning are named and categorized.
Astronomy is now
a major human science. (Astron=star and nomos = law)
We know that the
earth has a diameter of 12,756 kilometres, and that it is rotating around
the sun, which is about 150 million kilometres away from us.
Since the earth’s
orbit is elliptical, this distance must vary.
The sun itself has
a diameter about 1,392,000 kilometres.
But we also know
that the whole solar system is about 30,000 light years from the centre
of a spiral galaxy that we call the Milky Way.
(Light travels at
about 300,000 km per second in a vacuum, which comes to about 9.5 trillion
km in one year)
This galaxy contains
about 300 billion stars, but is only one of billions of galaxies in
the Universe.
In the Monty Python
comedy film “The Meaning of Life” the song about the universe
tells us that we go around this centre, taking 250 million years to
do so!
In our small part
of this universe life has appeared, and advanced into complexity.
The most plentiful
element in the known universe is hydrogen.
Vast masses of hydrogen
are present in every star.
When a cloud of
hydrogen reaches a size of some 10 billion kilometres across, sufficient
gravity exists to form stars over a period of time of 1-10 million years.
The compression
leads to generation of high temperatures, so that the interior of stars
reaches temperatures of 15,000,000 degrees Celsius.
This results in
a kind of burning called fusion where hydrogen nuclei combine to make
a new element called helium.
There is a balance
between of gases expanding outwards, and gravity pulling inwards to
lead to stars being stable over very long periods of time (about 10
billion years for the average star.)
The energy inside
the star moves some 700,000 km to the outside of the star where the
surface temperature is about 6,000 degrees Celsius (white hot)
It was astronomer
and physicist Fred Hoyle who discovered that there are specific temperatures
inside stars to allow more complex elements to emerge.
For hydrogen to
convert to helium the temperature (T) is around 10 million degrees
Celsius. (See references and note personal conversations with Dr P
Tillett)
For helium to
carbon it is around 200 million degrees Celsius.
For carbon to
magnesium and sodium, it is around 500-600 million degrees.
For oxygen to
silicon it is about 1.2 billion degrees.
For silicon to
the iron group it is 2-3 billion degrees
When stars are burning
up most of their hydrogen, gravity increases and the interior temperature
can rise as high as > 100,000,000 degrees Celsius.
Our sun has probably
never reached these temperatures in its core, but it is only 5 billion
years old, and arose in regions where other stars with hotter cores
or explosions (Supernovae) allowed the complex elements to develop.
The orbiting material
became the planets of our solar system.
Helium eventually
reaches the temperatures that allow formation of lithium, boron, carbon,
nitrogen, oxygen, fluorine, and neon and so on until the entire periodic
table of the elements emerges.
Thus stars are the
mass and energy of the production of their orbiting planets and their
building blocks.
This is why it is
true for us to say that we are all made from “stardust”.
If the sun appears
to be about 5 billion years old, the earth is about 4.6 billion years
in its present location.
Evidence suggests
that the earth began as a large asteroid, which attracted and accreted
other asteroidal material.
It became hotter
and close to being molten (say 1000 degrees at its surface and 3,500
degrees at its core.
Then about 45,000
years after the formation of the solar system, the earth seems to have
been hit by a planet, which was about the size of Mars.
This planet has
been called Theia.
Theia’s metallic
core entered the core of the earth and a rocky part spun off and became
the moon.
The present Earth’s
core is thus composed of 2 separate origin molten masses.
This is confirmed
by dating techniques.
The earth acquired
a tilt in its axis from the impact of the collision.
A bonus for the
earth is that the large satellite, which we call the moon, has stabilized
the planetary wobble.
Earth was set on
course for the situation which we find today!
THE COMING OF
BIOS
All living things
are composed of elements and those that connect together in living things
make up the many building blocks of carbohydrates, fats (lipids) and
proteins, together with essential compounds called vitamins.
Scientists have
found it convenient to have specific names for the molecules of life.
I want to introduce
some of these concepts to the non-biologist, particularly because science
is increasingly able to explain more and more about the inherent properties
of molecules, which make the march of evolution into more complex life
possible.
As I write I am
conscious that what I am doing is one of many ways of representing our
structures and functions to our selves and to others.
Hundreds of volumes
of writing are required to even describe what is known so far.
It is usual rather
than unusual for specific biological scientists to know their own areas
but have major gaps in their knowledge of other molecular biological
territories.
A return to basics
is a required step when we are to integrate what is being uncovered
with the texts of the recent past.
Those of you who
have studied chemistry will have some exposure to these concepts or
representations.
In some rather mysterious
way, when we look again and again at certain forms or representations,
they become familiar to us.
Someone has said,
”Whatever we do a lot of, we become good at”
How important can
it be to recognize our own patterns?
We now address both
parts and wholes, and the patterns that enable them to connect.
This is the mystery
of life.
Everything that
has unfolded in the history of the Kosmos is grounded or founded upon
the capacity of atoms and molecules to be arranged with emergent properties.
It is a dynamic
happening, which is difficult to capture in prose.
Hydrogen
This simplest of
all elements is the most plentiful atom in the Kosmos.
It consists of one
proton as the nucleus and one electron in orbit around the proton.
Water
Water itself is
an amazing substance, with electrons changing more that 1 billion times
per second in the bonds between the 2 hydrogen atoms and the oxygen
atom. (H20)
It is described
as a very polar molecule. The oxygen has a strong negative charge, and
the hydrogens have positive charges
Molecules that dissolve
in water are able to do so by being able to dissociate into positive
and negative ions (e.g. Salt is sodium chlorideàNa+ and Cl-)
Hydroxyl (OH) groups
on glucose are polar, and make glucose almost infinitely soluble in
water.
Science maps the
possible and can confirm whether molecules can interact and if so, in
which ways.
There are also ways
to number the atoms and designate where a group is located.
Carbohydrates
These have the formula
Cx (H20) y, sometimes with attached other pieces.
The smallest carbohydrate
units are called monosaccharides (sugars) with longer groupings (two=
disaccharides, 3-11= oligosaccharides and longer chains being called
polysaccharides)
The general terms
are 1= monomer, 2= dimer, 3= trimer, increasing to oligomers and polymers)
Plants use the process
we call photosynthesis to combine carbon dioxide and water into carbohydrates
and giving off oxygen.
Sugars may contain
amino groups (e.g. glucosamine and galactosamine)
The amino groups
are often acetylated.
Inside cells monosaccharides
usually contains phosphate groups. This results in the phosphorylated
sugar being unable to cross membranes.
Phosphate groups
may join sugars to nucleosides.
Sulphated sugars
are found in connective tissue.
Glycosides are formed
when the hydroxyl group on the anomeric carbon of a monosaccharide react
with the –OH or –NH of another compound.
These bonds are
called glycosidic or glycosyl groups.
N-glycosidic groups
are found in nucleotides. (e.g. In adenosine triphosphate (ATP), the
base adenine is linked to the sugar ribose via an N-glycosidic bond.)
The reader can note
the forms of substances that are vital to certain life happenings.
In this example,
ATP is storage energy for cell activities
Fats
Fats (oils and lipids)
are made up of fatty acids, esterified fatty acids (e.g. glycerol),
and interesting acyl glycerols (here fatty acids react with alcohol
(hydroxyl groups). Triacylglycerols are called triglycerides.
They are called
hydrophobic in that they are not very soluble in water.
The fatty acids
are chains of carbon atoms with a carboxyl (COOH) group at one end and
a methyl group (CH3) at the other end. (This latter is called the N
or omega (w) end)
Short fatty acid
have chain lengths of 1-4 carbon atoms, medium chains are of 4-12 carbon
lengths and long chain 14-20. (There are longer chain fatty acids sometimes
called very long chain fatty acids>20 carbons.
If there are no
double bonds in the molecules they are called saturated fatty acids.
If there is a single
double bond(C=C) in the molecule the fatty acid is called a monounsaturated
fatty acid, and if more than one(C=C—C=C), a polyunsaturated fatty
acid.
Most fatty acids
in human beings are even numbered and are usually 16-20 carbon lengths.
It is now known
that in all biological membranes, the basic permeability barrier is
a lipid bilayer (double layer)
It was discovered
that the lipid molecules and the protein components of these membranes
are free to exhibit a variety of motional modes, such as translation,
vibration and rotation which endow these membranes with dynamics such
as are needed for the crossing of the membranes by crucial molecules
of life.
In biological membranes
there are three classes of lipids, namely
Glycero-phospholipids,
sphingolipids, and sterols.
The arrangement
in certain cell locations exhibits considerable diversity.
Transport of fatty
acids into cell membranes can be important, as for example long chain
fatty acids (C 20 and higher) need acetyl carnitine to transport them
into mitochondrial membranes.
With the existence
of this lipid layer membrane, there is a barrier that nature has used
to evolve localized structures to enable cells to sense and respond
to changes outside themselves.
Cells may respond
to an amazing array of stimuli, including amino acids and peptide structures,
products of cell metabolism, ions, and even photons.
In the writing ahead
I will refer to these recognition units or receptors, along with coupling
structures and gene responses to these signals.
Gene products are
made and chemically changed by other gene products in order to carry
out crucial functions.
These responses
are often specific, but result in other intracellular events.
It would be a scintillating
sight if we could see what is happening in cells in every second of
their lives!
For readers who
want to study the basic structures and functions of lipids, I direct
them to any recent biochemistry textbook, and I will mention the optimal
dietary requirements in the section on therapy.
Medical biochemists
may be tempted to study only human biochemistry, but in truth we need
to grasp the chemistry of all living things and the domains of their
existence.
Proteins.
Aminoacids are the
monomeric units from which proteins are assembled.
Two amino acids
combined= dipeptide, 3-5= oligopeptide, and longer chains are called
polypeptides.
Depending on the
chemical groups on the amino acids (great diversity here), the amino
acid may be nonpolar, polar uncharged, or polar charged.
The side chains
are crucial to specific amino acid functions.
Amino acids that
our bodies cannot make are called “essential amino acids”.
Fascinating new
molecules with diverse functions emerge when carbohydrates are combined
with proteins (glyco-proteins), as well as when lipids are combined
with proteins (Lipo-proteins)
Enzymes are proteins
which increase the rate of chemical reactions.
We call the chemicals
acted upon by enzymes "substrates", and the resulting compounds
from these actions are "products".
The balance of these
reactions in living systems can be measured.
Isoenzymes are variants
of an enzyme with different aminoacid sequences and different properties.
Protein shapes.
The 3 dimensional
shapes of proteins are crucial for their functions.
If you can imagine
a chain of amino acids, some are on the inside and some on the outside
of the chain.
The chain can have
variations in terms of folding, and misfoldings can result in dysfunction.
Cells have genetically
determined molecular helpers called “chaperone” proteins,
which can counter” molecular mess” inside cells.
If the chaperones
do not work properly, diseases can result.
Examples are an
inherited form of cataracts, and desmin related myopathy.
Major protein misfolding
diseases include Alzheimer’s Disease, Creutszfeldt-Jacob disease,
Huntington’s disease, Parkinson’s disease and Type 2 Diabetes.
Something more is
needed for us to begin to understand about how all of these building
blocks come together and operate as a living system.
The next chapter
is about this.
medicine