Dirk Bertels

The greatest malfunction of spirit
is to believe things (Louis Pasteur)

The Life Sciences - a compilation

Last updated 25 November 2016

A collection of notes on the life sciences compiled from various sources. See also philosophy of science.

Index

the brain, neurons and synapses
anesthetics
microtubules
tubulin
fertility and sex
evolution
DNA and genetics
biology and cells
the Mole and Avogadro's number
the red dye phenomenon
amino acids and proteins
enzymes
molecules
proteins
archaea, bacteria and viruses
water
the Bose-Einstein condensate
glucose

the brain, neurons and synapses

A human brain has around 1011 neurons and 1015 synapses.


Transference of learned skills: i.e. we can write words with our left elbow.


nerve regrowth

The following is an excerpt from an interview with the Chief Scientist of Western Australia and Professor of Zoology, Lyn Beazley. The text, which is a selection from an hour long interview, has been slightly adapted to maintain the narrative.

The retina provides the easiest access for doing research on the brain. Doing a little bit of damage to a nerve at the back of the eye of a frog, we observed how nerve fibers track back to the brain, choose the part of the brain concerned with vision and even within that find exactly the right spot to connect with.

The way the brain does this is to have a molecule in high concentration at the top of the eye and low concentration at the bottom, and similar gradient accross the nerve cells in the visual part of the brain. And then a second molecule at right angles to it of high density at one side of the eye and low density at the other.

These gradient molecules magically appear when nerve damage is done.

When the brain cell is first born they look like any other cell, spherical with a nucleus in the middle. Very soon after that they start getting very specific in their morphology - they grow a lot of dendrites which extend for about 1/2 to 1 mm from where they pick up information from other cells. Then they have a very fine, long nerve fiber that connects to the next cell in the line. This fiber has a growth cone in the end that connects to even finer fibers which just senses the environment, feeling their way, picking up chemical signals. Some of these nerve fibers can be very long, spanning all the way from our brain to the base of our spinal chord.

The brain over-produces cells, almost wice as many as you're going to end up with. Eventually, the ones that die are those that end up in the wrong place.

When a nerve fiber is severed in a human, it seals off and makes another one of these growth cones and for about a week or so we see that these nerve fibers are trying to regrow but then it reaches a chemically inhibitory environment.

In frogs however, this inhibition does not exist and the nerve fiber fully regrows. We are trying to find out what are the chemicals that appeared in our evolution that stopped this regrowth and how can we switch them off again.

Nerve fibers are often surrounded by an insulating layer (the myelin) which ensures contact points are happening at the right points and it also speeds up the conduction. One of the by-products of the breakdown of that insulating layer (as happens in MS) is one of these nasty chemicals.

Lyn Beazley: interview in 'Conversations' on Australian ABC Radio National


hallucination

Konorski conceived of a dynamical system which, he wrote, "can generate perceptions, images and hallucinations ... the mechanism producing hallucinations is built into our brains, but it can be thrown into operation only in some exceptional conditions." Konorski brought together evidence - weak in the 1960s, but overwhelming now - that there are not only afferent connections going from the sense organs to the brain, but 'retro' connections going in the other direction. They provide, Konorski felt, the essential anatomical and physiological means by which hallicunations can be generated.
What then normally prevents this from happening? The crucial factor, Konorski suggested, is the sensory input from the eyes, ears and other sense organs, which normally inhibits any backflow of activity from the highest parts of the cortex to the periphery. But if there is a critical deficiency of input from the sense organs, this will facilitate a backflow, producing hallicunations physiologically and subjectively indistinguishable from perceptions. (There is normally no such reduction of input in conditions of silence or darkness because "off-units" fire up and produce continuous activity).

Oliver Sacks: Musicophelia, pp77


brain cell loss

Most estimates say we have about 100 billion brain cells (neurons), and about ten times that many, or one trillion, support cells (glia) that help the neurons. We'll just concentrate on the neurons themselves.

The brain weighs about 3 pounds, and after age 20, you lose about a gram of brain mass per year. So if the brain weighs 1400 grams and there are about 100 billion neurons, that comes to about 70 million neurons per gram. Now we could stop here and say that we lose 70 million neurons a year, or about 190,000 per day, but that wouldn't really be right. That's because most of that gram isn't really neurons dying. Some of that loss is glia (support cells) dying, some of it is because the neurons are shrinking but not dying, and some of it is that the neurons lose some of their insulation (myelin), which makes them slower, but doesn't cause them to die.

Even if we say that only 5% of the gram is neurons actually dying, we get neuron loss of about 9,000 neurons a day!

A side note: This is all assuming you're a person who takes care of yourself. But there are lots of things people do that cause much higher rates of brain cell death. The big one is using certain drugs. Not all drugs cause brain cells to die, but the ones that do are very damaging. Ketamine, nitrous oxide (laughing gas) and volatile inhalants (glue, gasoline, paint thinner) can cause brain cell death at THIRTY TIMES normal rates - that's almost 300,000 neurons a day! And alcohol also increases the rate of brain cell death, but less than the others.


Nerve cell discharge

In their study of nerves, the biologists have come to the conclusion that nerves are very fine tubes with a complex wall which is very thin; through this wall the cell pumps ions, so that there are positive ions on the outside and negative ions on the inside, like a capacitor. Now this membrane has an interesting property; if it "discharges" in one place, i.e., if some of the ions were able to move through one place, so that the electrical voltage is reduced there, that electrical influence makes itself felt on the ions in the neighborhood, and it affects the membrane in such a way that it lets the ions through at neighboring points also. This in turn affects it farther along, etc., and so there is a wave of *penetrability* of the membrane which runs down the fibers when it is "excited" at one end by stepping on the sharp stone. This wave is somewhat analogous to a long sequence of vertical dominoes; if the end one is pushed over, that one pushes the next, etc. Of course, this will transmit only one message unless the dominoes are set up again, and similarly in the nerve cell, there are processes which pump the ions slowly out again, to get the nerve ready for the next impulse.

... when the impulse reaches the end of the nerve, little packets of a chemical called acetylcholine are shot off (5 or 10 molecules at a time) and they affect the muscle fiber and make it contract ...

R.Feynman: Six easy pieces, pp50


It was known that the electrical communications that take place between the brain's nerve cells, or neurons, do not occur alone. Neurons possess branches like little trees, and when an electrical message reaches the end of one of these branches it radiates outward as does the ripple in a pond.

M. Talbot: The Holographic Universe, pp20


Left and Right side of the brain

Patients that suffer from epilepsy sometimes have their L/R Brain connection surgically 'split' in order to prevent seizures. Testing some of these patients suggests a kind of independent 'consciousness' for each half of the brain:

  • L side of the brain regulates the R side of the senses (R eye, ...)
  • R side regulates the L side of the senses.

An object was shown to the R eye only and the patient remarked that he could see it. But when it was shown to the L eye only, he remarked he couldn't see it, though nevertheless he could grab the said object from a multitude of other objects.

The right brain saw the object but couldn't interpret it. This is done by the L Brain which is the interpreter. The Left brain doesn't know why the Left hand (eye) is doing something - but tries to explain it in its ongoing narative.

This often leads to the curious situation where the interpreting is done after the fact - so it reverts forwards in time.

This suggests 2 separate systems of consciousness. The Left hemisphere's job is to tell the story → origin of false beliefs. the Right hemisphere has language but no syntax, e.g. it doesn't know the difference between a venetian blind and a blind venetian. It is very good at say, detecting a peeler in a draw of cutlery.

Dr Jill Bolte Taylor gives a most intriguing insight into the brain by describing her experiences after suffering a stroke in her left hemisphere in one of her video talks. She compares the 2 hemispheres with computer processors:

  • The left side is the serial processor that takes care of past, future, language. The I am separation.
  • The right side is the parallel processor that handles the here and now.

Plasticity

When we think and learn, we change the connection between the nerve cells. Freud, who really was a neurologist rather than a psychiatrist, called this "the law of association by simultaneity". Neurons that fire together, wire together. And neurons that fire apart, wire apart.


Synapses

Well it has been said that the number of synapses in the human brain is about a million billion. But something we've discovered about the molecular composition of the synapses is that they have over 1,000 different proteins within this.

Seth Grant - 'All in the Mind' ABC radio - 3 December 2011


If you were looking at a synapse and imagining yourself down inside the synapse amongst all of the molecules you would see what you might call molecular machines, large sets of proteins the sort of components which assembled together make these large molecular machines. But what is the extraordinary thing about these molecular machines which would look like large sort of blobs of molecules is that they're actually like computers, they're information processors, they handle all of the information that comes from the animal's environment, they convert it into chemical signals and they process that information in very complex and specialised ways. Everything we hear, see, taste, touch and smell is converted into these kinds of digital electrical codes and the synapse will pass that information from one nerve cell to the next, which then passes it to another nerve cell and the next and in that way the information is transported around the nervous system. But the specialised thing about the synapses is they don't just transmit the information, they listen to the information sort of like the spy agency that listens to your phone calls, it listens to that information as it goes past. And then responds and does things with it and one of the most extraordinary and important things it does it allows that information to be written down and stored in the form of memories. And this is really a key function which synapses do.

Seth Grant - 'All in the Mind' ABC radio - 3 December 2011


Well that's right, in fact the brain is all about the chemistry and it is, as far as electrical transmission and chemical transmission of information is concerned, it's at synapses where the electrical information is turned into chemical information, the chemicals are squirted across the synaptic cleft. These are called neuro transmitters and those neuro transmitters then stimulate and activate the electrical activity in the next nerve cell.

Seth Grant - 'All in the Mind' ABC radio - 3 December 2011

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anesthetics

Gas anesthetics work by very weak, purely physical, quantum-mechanical interactions. they don't form chemical or ionic bonds of any kind, they're not polar molecules, they don't bind to receptors and they can be inert. For example, the inert gas xenon is an anesthetic.


Within proteins are specific tiny pockets that are lipid-like and the anesthetic gas molecules get sucked into these little pockets. Once there, the anesthetic molecules don't form chemical bonds like other drugs, they bind only by very weak Van Der Waals London forces. One or two gas molecules per protein do the trick.


Proteins normally dance back and forth between different forms and shapes to perform their functions. And what controls the dancing are quantum-mechanical forces in these pockets. The pockets are like the tiny brain within each protein.


What choreographs them all together is quantum coherence. The 'brain' proteins dance synchronously due to coherence among quantum actions in the pockets throughout wide regions of the brains. So by forming their own quantum interactions in the pockets, anesthetics inhibit normally occurring quantum-mechanical forces necessary for consciousness.

Stewart Hameroff: Could Life And Consciousness Be Related To The Fundamental Quantum Nature Of The Universe?

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microtubules

Microtubules are one of the components of the cytoskeleton, the cell's framework. They have a diameter of 25 nm and length varying from 200 nanometers to 25 micrometers. Microtubules serve as structural components within cells. They are essential for a variety of biological functions including cell movement, cell division (mitosis) and establishment and maintenance of cell form and function.


In neurons, microtubules self-assemble to extend axons and dendrites and form synaptic connections.


Microtubules interact with membrane structures and activities by linking proteins and 'second messenger' chemicals.


Biological cells typically contain approximately 10^7 tubulins. Nanosecond swithcing in microtubule automata predicts roughly 10^16 operations per second, per neuron. As the human brain contains about 10^11 neurons, nonosecond microtubule automata offer about 10^27 brain operations per second.


Unlike chemical synapses which separate neural processes by 3050 nanometers, gap junction separations are 3.5 nanometers, whithin range for quantum tunneling.

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tubulin

A Tubulin is one of several members of a small family of globular proteins. The most common members of the tubulin family are a-tubulin and -tubulin, the proteins that make up microtubules.


The tubulin protein turns out to be a dimer consisting of two monomers that are almost identical in structure. Each monomer is formed by a core of two beta sheets surrounded by helices, and each binds to a guanine nucleotide. In addition to a nucleotide binding site, each monomer also has two other binding sites, one for proteins, and one for the anti-cancer drug taxol.


Interest in tubulin structure heated up intensely in recent years when taxol, a natural substance found in the bark of the Pacific yew tree, was shown in clinical tests to be an effective treatment for a number of cancers including ovarian, breast, and lung. Cancer occurs when cell division runs amok.


By binding to tubulin and causing the protein to lose its flexibility, taxol prevents a cell from dividing.

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fertility and sex

Oestrogen in the vagina wards off invasion of harmful organisms. Oestrogen smeared on the foresking reduces risk of AIDS.

If the contraceptive pil is taken continuously, menstruation will be avoided with no drawbacks (Roger Short). Breast-feeding serves as contraceptive, naturally a woman gets pregnant every 4 years or so. It's only since people started feeding cow's milk instead of breastmilk that the probability of pregnancy occuring yearly (or less) became high.

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evolution

Today it is understood that 99% of all the species that have lived on the earth have since died out.

T. Ferris: Coming of age in the Milky Way, pp222


... Because the world is constantly in a state of change, nature favours the varied - a community of predominantly white moths is better off if it contains a few dark moths, against a smoggy day - and the geographically dispersed, those who do not keep all their eggs in one basket.

T. Ferris: Coming of age in the Milky Way pp238


Humans have been around 2 million years. The dinosaurs were wiped out 65 million years ago. The recently discovered multi cell organism Charnia lived about 560 million years ago. Microscopic single cell organisms first appeared about 3.5 billion years ago.

Just before complex life appeared, the world was in the grip of the biggest ice age in known history, called Snowball Earth. In places the ice was more than a kilometer thick. Microscopic bacteria managed to live in this environment. These organisms are referred to as Extremophiles. They can be burried a kilometer down in ice and still survive.

After some million years, Snowball Earth began to warm due to a global surge in volcanic activity. The released gasses created a greenhouse. Cyanobacteria and other oxygen producing microbes began to bloom accross the globe.

This increase in oxygen was the key to the rise of the animal kingdom. It enabled some cells to stick together. Sponges are just collections of simple cells. Sponge cells are bound together by collagen, a glue-like substance. It is the commonest protein in our body and present in animals only. You need oxygen to be able to manufacture collagen.

Looking at the genes, the sponge is clearly an animal. Little pieces of sponge can be squeezed through a filter. After about 3 weeks, the cells will recombine and form a sponge again.

Gradually more complex creatures appeared. Some of the first animals to live on this planet lived on the bottom of the ocean. They were Proto Animals, living on dissolved carbon and other nutrients from the deep ocean. They were simple animals which were built using fractal geometry requiring only 6 or 8 genetic commands. Compare this with the 25 thousand or so commands needed to build a mammal. Fractal animals enabled the early creatures to absorb nutrients over a very large area. However after just a few million years of evolution, they vanished.

The first animals to appear with the same basic body plan as today's animals appeared 550 million years ago. Simple molluscs that were able to move. The modern animal body uses bilateral symmetry. A head at one end and a tail at the other points to the fact that sensory capacity had evolved. Animals started to reproduce sexually, exchanging genes with each other. Sexual reproduction is one of the fundamental steps in evolution.

The uniformity of size of a group of animals is an indication that sexual reproduction has taken place because animals breed around the same time to maximize success. Now over many generations, species were able to adapt to their environment. Mobile animals now needed to consume vast quantities of food and hence developed internal organs to help digestion.

Compiled from D. Attenborough: First Life Documentary


The term Evolution can confuse some people thinking it implies purposeful change, but the better term is Natural Selection.


Most educated people are aware that we are the outcome of nearly 4 billion years of Darwinian selection. But many tend to think that humans are somehow the combination of all of that. Our sun, however, is less than halfway through its lifespan. It will not be humans who watch that sun's demise, 6 billion years from now. Any creatures that then do exist will be as different from us as we are from bacteria or amoeba.

Sumatian Reece: Dark Materials (speech)


The brain didn't evolve to see the world the way it is, instead, the brain evolved to see the world the way it has been useful to him in the past.

Beau Lotto on TED Talks

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DNA and genetics

Our DNA consists of about 3 billion bases (nucleotides). Sequences of these nucleotides that are responsible for creating protein molecules are called genes. The human genome contains about 22,000 of these genes. This amounts to only 2-3% of the total amount of nucleotides.

Contrary to popular believe, the DNA doesn't look like the textbook double helix. It has a double helix structure but folded in a very complex manner. It is a complex world buzzing with activity, as complex as we are.


The DNA in each of our cell nuclei is 2 meters long. To visualise some of the complexity regarding synthesizing this DNA (making copies), it helps to size the DNA up to scale:

  • Pack 2000 kilometers of diameter 2 mm string to fill an ordinary size room (diameter 6 m) in such a way that every single bit of it is available for synthesis (copying).
  • This string is synthesized from 100,000 different starting sites, which needs coordination.
  • A certain protein is distributed at each of these sites. Before synthesis, excess protein is removed. As the DNA is synthesized, the protein is also gradually removed. This protein is a 'ticket' that you give up as you pass along the string to synthesize, but can't go back over the same bit of DNA until a new ticket (license) is issued.
  • There are 6 of these protein which come as a hexameric ring.
  • Since this protein is a good antigen and remains within the nucleus even though it travels in and out the DNA, we can use an antibody to look for cells that contain this marker for cancer diagnosis. Cells such as our hair, urine or flem should not contain this protein.

Reworked from a talk by Paul Davis on the Australian Science Show


The ENCyclopedia Of Dna Elements (ENCODE) Project

The Human Genome project which decoded all 3 billion base pairs of the human DNA completed in 2003. The aim of the ENCODE project since then has been to determine functionality.

One part of the DNA, called exomes consist of the 20,000 genes that code for protein, about 1.5% of the total DNA. Another part, the regulomes modulate the expression of the exomes. It is the central aim of ENCODE to map out this regulome.

On 5 September 2012, initial results of the Encode project were released in a set of 30 papers, published in various journals, such as Nature. So far it has determined that over 80% of the genome has biochemical functionality, much of it involved in controlling expression levels of coding DNA.


Professor John Mattick, director of the Garvan institute in Sydney - Australia, elaborates on this:

Humans have about 20,000 protein coding genes. So do all other mammals and vertebrates and even sponges. And most of those genes code for proteins that have the same sort of functions

...at least 20% of the human genome shows evidence of being biologically functional. And about 80% is biochemically functional. That is, they produce protein or an RNA or they have some structure in the chromatin that's specific.

The evidence is now pretty compelling that these RNAs are controlling the site specificity of the proteins that organise the genome, and organize it in different ways in cheek cells and knee cells.

John Mattick - Australian Science Show, 20 October 2012


Gene Expression

A simplified view on gene expression, taken from a You tube animation:

  • Receptors on the cell's surface trigger signalling mechanisms involving other proteins in the cell's cytoplasm.
  • In the cytoplasm, the signalling elements are involved in a cascade of events.
  • The final components interact with the DNA in the nucleus at very specific sites to begin the expression of the desired gene.
  • To start transcription, several proteins are often required to bind the regulatory elements on the DNA. This step in the process is were DNA is read and a complementary strand of RNA is produced.
  • The RNA undergoes many changes, and is cut into sections. One of these sections codes for the required protein.
  • RNA then takes the information encoded in the DNA out of the nucleus.
  • In a process called translation, ribosomes interact with the messenger RNA and transfer RNAs to create the chain of amino acids coded for on the DNA.
  • This amino acid chain undergoes changes in configuration including specific folding. Each protein takes on a 3D shape required for a functional end product.
  • The new protein then leaves the cell.

Genes are at the mercy of experience - behaviour causes changes in the expression of genes. The means is still Darwinian - culture sets up the selection pressure. Following are some examples given at a talk in Melbourne, Australia 2011:

  • when in stress you are more likely to get ill. Nervous system tells endocrine system to release hormones such as cortisol which surpresses the immune system by means of switching off genes (blocking gene expression).
  • Cultures that domesticate cattle have a LCT gene (on chromosome 2) which enables them to digest lactose.
  • Blue eyes and pale skin occured around the Baltic sea about 6000 years ago when agriculture was starting off. The grain diet is devoid of Vitamin D. Vitamin D needs UV. Since the area was devoid of sunlight, the paler skin and blue eyes enabled more UV absorption.

Matt Ridley, Genes, Technology and the Evolution of Culture


Chromosomes form only when cells are dividing


Mitochondrial DNA

Mitochondrial DNA was discovered in the 1960s by Margit M. K. Nass and Sylvan Nass

Mitochondria are structures that convert food into energy using Adenosine Triphosphate. Since its DNA can be determined from a large number of species, it is used in anthropology and field biology.

The vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.

The DNA present in these structures are solely inherited from the mother. An egg contains 100,000 to 1,000,000 mtDNA molecules, whereas a sperm contains only 100 to 1000. The mitochondria in mammalian sperm are usually destroyed by the egg cell after fertilization.

Unlike nuclear DNA, which is inherited from both parents and in which genes are rearranged in the process of recombination, there is usually no change in mtDNA from parent to offspring.


Epi-genetics

The process by which the marking on the genomes gets changed instead of the genomes themselves. The study of changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. The binding of 'epigenetic factors' to histone (long chains of amino acids) 'tails' alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated...DNA associates with histone proteins to form chromatin.

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biology and cells

All life forms are build from 4 types of large molecules:

  • Carbohydrates, consisting of sugars
  • Lipids and membranes consisting of fats
  • Nucleic acids consisting of nucleotides
  • Proteins consisting of amino acids

The simplest cell contains 1011 atoms in very complex structures.


Each chromosome contains a long coil of DNA. If all the chromosomes were unwound, the DNA in just one of our cells would stretch 2 m long.


The finest cells in the retina measure about 2 microns accross. Current (2009) household digital cameras have about 7 to 8 microns resolution.


T cells

T cells are a progeny from the same stem cells that give rise to all your other blood cell types, so they are distant cousins of red blood cells, of the macrophages which are major infection fighting cells.

But the T cell precursors don't grow up in the same environment as these other cell types, they migrate out of the bone marrow where the other kinds of blood cells are generated to the thymus which is a school for T cells, it's kind of an academy for T cells. The cells that first come into the thymus are not committed to become T cells, and there is a fantastic analogy with a real human education; it's like taking a young student and enrolling them in a religious seminary before they are actually certain whether they have a religious vocation not.

And over the next little while they have to decide whether they really have this vocation, and they are certainly influenced by the environment. Finally they become committed to it, and then they still have to undergo training. So the commitment process is really what we study in my lab. They do this through a very error-prone and random receptor-generating process that has the potential for creating a great deal of trouble for the body unless it is very well filtered.

And so the cells go through an extraordinary selection process, and the thymus is a really relentless purifier of the population, selecting only those cells that have happened to get receptors that are potentially useful and not harmful for the body. And that's a remarkable process. Also it's coupled with making professional subspecialty choices on the parts of these developing T cells. They finally come out from this process maybe after a month, and they then go out into the body and they then begin their function.

Ellen Rothenberg - ABC Science Show, Australia 21 May 2011

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the Mole and Avogadro's number

It is surprising how so many text books seem to mystify this concept. It is easy to understand once you know the basic constituents of the atom: the protons, neutrons and electrons.

Avogadro's number relates the mass of a substance to the number of particles (atoms, molecules, etc) it has. It is a huge number: 6.022 x 1023, also referred to as a Mole. A Mole of rice grains would cover the land area of the world to a depth of 75 meters.

  1. All protons have the same mass, so do all the neutrons. The electron's mass is negligable. Since both protons and neutrons are located in the nucleus, all the mass of an atom resides in its nucleus.
    • Mass of proton : 1,6726 x 10-24 g
    • Mass of neutron: 1,6749 x 10-24 g
    • Mass of electron: 0,00091 x 10-24 g
    • So the ratio of electron to proton is 1/1840, roughly the difference between a paperclip and a 2 ton truck.
  2. It is the number of protons that determine the type of element. The atomic mass of an element is given in the periodic table. It is the total number of protons and neutrons in that atom. It is also called the Mass Number.
    • Not to be confused with the Atomic Number, which only gives the number of protons.
    • It is not a round number since it gives a medium (means) to allow for the isotopes (isotopes have the same number of protons but different number of neutrons).
  3. Each proton or neutron constitutes 1 Atomic Mass Unit (AMU)
  4. Avogadro determined that 1 gram of any substance contains Avogadro's number of AMU. That is, a gram of any substance contains Avogadro's number protons and neutrons.
  5. When a substance contains Avogadro's number of anything (not just protons or neutrons, as we shall later see), we say that it contains 1 Mole of that substance.

Examples

  1. From the Periodic table we can see that Iron (Fe) has an atomic mass of 56, meaning that each atom of Fe contains 56 Protons and Neutrons in its nucleus. From the reasoning above it should be clear that if we had Avogadro's number (1 Mole) of these Fe atoms, we would have a mass of 56 grams. This locic requires some reverse reasoning - but if you think about it a little, it makes sense: 56 amus in 1 atom. 1 gram has Avogadro's number of amus, i.e. 1 gram has Avogadro's number / 56 atoms. Therefore 56 grams will have Avogadro's number of atoms.
  2. From the periodic table we can determine that iron oxide, Fe2O3, has 160 AMU. This means that 1 Mole of Fe2O3 has a mass of 160g

General Rule

Determine how many AMU a substance has. 1 Mole of that substance will have a mass of that AMU in grams.


See also Red Dye Example.

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Red Dye Example

I've always been fascinated by the Red Dye example:

One bottle of red dye is emptied and mixed in all
the oceans. One bottle of water from these oceans
still contains 5000 molecules of this red dye.
This is because there are many more molecules of red
dye in a bottle than there are bottles in the oceans.

This also relates to Avogadro's number, 6.022*1023. This number corresponds to the number of atoms or molecules needed to make up a mass equal to the substance's atomic or molecular mass, in grams.

For example, Hydrogen has an atomic mass of 1. Therefore one gram of Hydrogen has 6.022*1023 atoms. Oxygen has an atomic mass of 16. From this we can calculate that one molecule of water (H2O) has a total atomic mass of 18. So we can conclude that 18 grams of water contains 6.022*1023 molecules.

The atomic mass of a chemical element is the mass of an atom at rest, most often expressed in unified atomic mass units (AMU). 1 AMU is defined to be 1/12 of the mass of one atom of carbon-12.
For example, the atomic mass of iron is 55.847 amu, so Avogadro's number of iron atoms (i.e. one mole of iron atoms) have a mass of 55.847 g. Conversely, 55.847 g of iron contains Avogadro's number of iron atoms. This number is approximately 6.022*1023.

Another common sense application shows that without determining the actual weight of a substance, a good rule of thumb to use is that a cubic centimeter of solid matter contains about 1024 atoms

This means that, assuming the ocean's waters are properly mixed, a glass of sea water contains a sample of virtually any solveable substance that exists in the oceans! That this complexity could give birth to living organisms makes the understanding as regards the origin of life a little less mind-boggling.

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amino acids and proteins

All proteins are various compositions of twenty specific naturally occurring amino acids.


The twenty naturally occurring amino acids that comprise proteins are (almost) ALL of the L- form. Only ONE of the twenty amino acids is not in the L- form, and that is glycine. The reason for this is that the side chain group is a hydrogen atom.


Aside from the twenty standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins.


Amino acids form short polymer chains called peptides or longer chains called either polypeptides or proteins.


Proteins are versatile macromolecules which perform a variety of functions by changing their conformational shape. Life is organised by changes in protein shape.


The main driving force in protein folding occurs as uncharged non-polar groups of particular amino acids join together and avoid water (hydrophobic).


Each protein begins as a polypeptide, translated from a sequence of mRNA as a linear chain of amino acids. However each amino acid in the chain can be thought of having certain 'gross' chemical features. These may be hydrophobic, hydrophilic, or electrically charged, for example. These interact with each other and their surroundings in the cell to produce a well-defined, three dimensional shape. The resulting three-dimensional structure is determined by the sequence of the amino acids.

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enzymes

Thus most chemical reactions do not occur, because there is what is called an *activation energy* in the way. In order to add an extra atom to our chemical requires that we get it close enough that some rearrangement can occur; then it will stick. But if we can not give it enough energy to get it close enough, it will not go to completion, it will just go partway up the "hill" and back down again. However if we could literally take the molecules in our hands and push and pull the atoms around in such a way as to open a hole to let the new atom in, and then let it snap back, we would have found another way, "around the hill", which would not require extra energy, and the reaction would go easily. Now there actually *are*, in the cells, *very* large molecules, much larger than the ones whose changes we have been describing, which in some complicated way hold the smaller molecules just right, so that the reaction can occur easily. These are very large and complicated things we call *enzymes*...

R.Feynman: Six easy pieces, pp52

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molecules

Avogadro's law: Equal volumes of all gases contain equal numbers of molecules.
E.g when it takes 0.1 gram of Hydrogen to fill a balloon, it would take about 1.6 grams of oxygen to inflate the balloon to an equal size, but both balloons will contain the same amount of molecules.

Isaac Asimov: Atom


See also Red Dye Example


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proteins

Next comes the question, precisely how does the order of the A,B,C,D units determine the arrangement of the amino acids in the protein? This is the central unsolved problem in biology today. The first clues, or pieces of information, however, are these: there are in the cell tiny particles called microsomes, and it is now known that that is the place where proteins are made. But the microsomes are not in the nucleus, where the DNA and its instructions are ... the RNA, which is a kind of copy of the DNA ... The RNA, which somehow carries the message as to what kind of protein to make goes over to the microsome, that is known. When it gets there, protein is synthesized at the microsome. That is also known. However, the details of how the amino acids come in and are arranged in accordance with a code that is on the RNA are, as yet, still unknown.

R.Feynman: Six easy pieces, pp57

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archaea, bacteria and viruses

Current view on early history of life

The earliest forms of life, the archaea, appeared around 4 billion years ago. They are similar to the bacteria which appeared a little later and for a long time co-existed alongside the archaea. About 2 billion years ago, bacteria and archaea merged to create more complex cells. Our mitochondria is believed to have originated from bacteria which our cell uses as a 'power station'. Because of this the cell now has the means to get bigger and thus maintain bigger genomes. Evidence of this can be read in the DNA. We share about 200 genes with archae DNA. Our mitochondira houses short stretches of DNA, very similar to bacteria's DNA.

Vaious facts

Some 10 to 100 trillion cells make up our body. For every cell in our body, there are 20 bacterial cells. 10 percent of our dry weight are bacteria


Viruses can alter the DNA of its host cells; 5 to 8 percent of the human genome is from ancient retroviruses.


Viruses can change RNA to DNA and transport DNA from one organism to another.


In 2002, Dr Eckard Wimmer and his team first managed to synthesize the Polio virus, which contains 7500 nucleotides. To construct the virus, the researchers say they followed a recipe they downloaded from the internet and used gene sequences from a mail-order supplier.

Having constructed the virus, which appears to be identical to its natural counterpart, the researchers, from the University of New York at Stony Brook, injected it into mice to demonstrate that it was active. See this BBC article


Bacteria have been found in nuclear power plants, were spent rods are kept in a pool of water. They feed off the stainless steel container.


Bacteria have been found in the camera on the moon where it had been left for several months.


The majority of the planet's bacteria live underground


Microbes make up half of the earth's bio-mass. Animals make up 1/1000th of the earth's bio-mass. There are an estimated 6*10^30 microbes.


Each ml of seawater has 1 million bacteria and 10 million viruses


Viruses affecting our brain in real time?

Professor John Mattick, director of the Garvan institute in Sydney - Australia, dares to speculate on virus sequences dynamically affecting our brain in real time.

Viruses are packets of genetic information that jump around.

[previously it was thought that much of the DNA was a graveyard of viruses and retratransposons] ... there is a possibility that ... these retroviruses are not just agents of change in evolutionary time but they may have been domesticated and be agents of change in real time. And in fact a paper in Nature ... showed that this is actually happening in the brain. These virus sequences are actually waking up in our brain and moving around, probably, this is just early days, but probably to create the extraordinary diversity that we need to have a functioning brain.

... a much more mature and sophisticated way of thinking about viruses is as sequences that are mobile but where our system has made use of them and where they've contributed to our dynamics...

John Mattick - Australian Science Show, 20 October 2012

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water

When magnifying a water drop until it is 24 km accross ... we see a kind of teeming, something which no longer has a smooth appearance - it looks something like a crowd at a football game as seen from a very great distance. In order to see what this teeming is about, we will magnify it another 250 times ... the water is now magnified a billion times and we can see the individual molecules.

Adapted from R.Feynman: Six easy pieces, pp4

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the Bose-Einstein condensate

A state of matter of a dilute gas of weakly interacting bosons confined in an external potential. Under such conditions, a large fraction of the bosons collapse into the lowest quantum state of the external potential, and all wave functions overlap each other, at which point quantum effects become apparent on a macroscopic scale.


"Condensates" are extremely low-temperature fluids which contain properties and exhibit behaviors that are currently not completely understood, such as spontaneously flowing out of their containers. The effect is the consequence of quantum mechanics, which states that since continuous spectral regions can typically be neglected, systems can almost always acquire energy only in discrete steps. If a system is at such a low temperature that it is in the lowest energy state, it is no longer possible for it to reduce its energy, not even by friction. Without friction, the fluid will easily overcome gravity because of adhesion between the fluid and the container wall, and it will take up the most favorable position (all around the container).


Bose-Einstein condensation is an exotic quantum phenomenon that was observed in dilute atomic gases for the first time in 1995, and is now the subject of intense theoretical and experimental study.


If the physics of condensed phases (coherent phases) is to prove relevant to consciousness, then there would have to be such mechanism that functions at normal body temperature. And, in fact, there is one. The 'pumped system' first described by professor Herbert Frohlich some 20 years ago, and known to exist in biological tissue, seems to satisfy all the necessary criteria. Frohlich's 'pumped system' is simply a system of vibrating electrically charged molecules (dipoles) into which energy is pumped. The vibrating dipoles (molecules in the cell walls of living tissue) emit electromagnetic vibrations (photons), just like so many miniature radio transmitters, as they jiggle. Frohlich demonstrated that beyond a certain threshold, any additional energy pumped into the system causes the molecules of that kind to vibrate in unison. They do so increasingly until they pull themselves into the most ordered form of condensed phase possible - a 'Bose-Einstein condensate'.

Danah Zohar: The Quantum Self (pp61)


Evidence for coherent states (Bose-Einstein condensates) in biological tissue is now abundant, and the interpretation of its meaning lies at the cutting edge of exciting breakthroughs in our understanding of what distinguishes life form non-life. I think that the same Bose-Einstein condensation amongst neurone constituents is what distinguishes the conscious from the non-conscious. I think it is the physical basis of consciousness.

Danah Zohar: The Quantum Self (pp67)


The Bose-Einstein condensate which gives us the physical basis of consciousness arises from the correlated jiggling of molecules in the neurone cell walls. The exent to which these molecules are correlated, and hence the extent to which the Bose-Einstein condensate is coherent depends upon the amount of energy pumped into the brain's quantum system at any given moment. If there is less energy available to the system, then the unity of consciousness will be less marked; if here is more energy, there will be greater unity. The range of unity possible in both directions is enormous.

Danah Zohar: The Quantum Self (pp98)


The difference between a living system and a non-living system is the radical increase (an order of magnitude 20 times greater) in the occupation number of the electronic levels. That is, in living systems photons are very much more (exponentially more) bunched together, literally squashed into a coherent Bose-Einstein condensate, whereas in the non-living they are less tightly packed. But this difference is one of degree, not of principle.

Fritz Popp

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glucose

TODO: Check Facts

The pancreas produces hormones that regulates blood glucose levels.

Insuline, produced by beta cells is a hormone that lowers blood sugar levels.

After a meal, glucose is released in the bloodstream. This triggers release of insuline. Insuline travels to muscle, fat and liver and helps these tissues to store the glucose as an energy source.

The amount of glucose in a non-diabetic person is about 1 teaspoon (in about 5 liters of blood). The amount of glucose rises when digesting a meal, after which it slowly declines until it settles back to 1 tspoon.

In diabetics, the decline is much slower

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