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A Little Background

The land between the Jordan river and the Mediterranean Sea, known as Palestine, is one of the most fought over in human history.  Anthropologists believe that the first humans to leave Africa lived in and around this region and that all non-African humans are related to these common ancestors who lived perhaps 70,000 years ago.  At first glance this interest seems odd, because as bits of territory go it's nothing special.  These days it's mostly desert and semi-desert.  Somewhere back-o-Bourke might look similar, if a bit redder. 

Yet since humans have kept written records, Egyptians, Canaanites, Philistines, Ancient Israelites, Assyrians, Babylonians, Persians, Greeks, Romans, Byzantines, early Muslims, Christian Crusaders, Ottomans (and other later Muslims), British and Zionists, have all fought to control this land.  This has sometimes been for strategic reasons alone but often partly for affairs of the heart, because this land is steeped in history and myth. 

Perhaps the most enduring cause for this conflict is that about four thousand years ago this was the land of a semi-nomadic war lord who came to be called Abraham and who's god Yahweh became the 'One God' of Moses then, in due course, the single, universal, all-encompassing, deity shared by all three 'Abrahamic' religions: Judaism, Christianity and Islam.

Once-upon-a-time this land was far more attractive to human habitation, lush and welcoming. Along with adjoining Lebanon, Jordan and Syria, the eastern shore of the Mediterranean was said to be a land of milk and honey. But climates change and expanding populations over-graze and cut down trees, as we have seen in desertified and deserted Petra, nearby in Jordan, that was a populous city in a green and pleasant landscape in the time of Herod.  Now much of the Palestinian countryside varies in appearance from cultivated farmland, dependent on irrigation, to absolute desert. 

In many ways this is vast improvement since the end of the nineteenth century, when it was most frequently described by visitors from more verdant Europe as desolate, poor, backward and diseased.  Malaria and malnutrition were endemic and Western aid focussed on the provision of hospitals.

 

Israel Israel2
Israel3 Israel4

Israel

 

Today modern parts of Israel are a like resort areas of southern Europe or perhaps California. Many private houses are large and well appointed. There are many new high rise apartment blocks and more under construction. The use of a more or less standard colour scheme with light sandstone walls, and even raw concrete, gives the cities and towns a uniform clean or sandy look. The roads and other public infrastructure are of a high standard and prices are similar to those in southern France or Spain.

 

Jerusalem - A Modern City
Israeli Jerusalem - A Modern City

 

Some parts of Jerusalem, Israel's largest city, remind me of Amman in Jordan or Damascus in Syria, before the recent destruction.

Although not nearly as rundown as those in neighbouring Egypt, Arab areas are not nearly so wealthy in appearance as the up-market, mostly European, Jewish areas.  But not all Jews are rich or live the high-life either.  Around half of the Jewish population is ethnically middle eastern, from poorer backgrounds.  The late model cars of the wealthy mix with the not so grand.  If you are interested Google Street-view is worth a look. Try clicking this link to see a not so wealthy area.

Physical appearance is where the similarity to Europe or California ends. This is a Jewish homeland, in many ways a theocracy.

Very orthodox groups abound and we were told by a cab driver when driving us on Saturday that some areas are out of bounds as cars moving on the street are stoned.  Almost all official public signage is in Hebrew.  English is widely understood which is good as otherwise it would be a difficult place to visit.  This is complemented of replaced by Arabic in the Arab areas. Comprehensible to us, English/Latin signage is reserved for commerce, like shop and restaurant names and advertising displays.

About 20% of Israeli citizens are Arab, both Muslim and Christian, and they are in a strange coalition with each other in contrast to the Jewish majority.  We found the Muslim Arabs almost universally friendly, but not necessarily adverse to ripping-off tourists.  People of unknown religion we interacted with on public transport and and in street cafés particularly outside the old city were usually polite and helpful and might have been in a major city anywhere in the world.  But Jews who were self-identifying by their mode of dress were frequently aloof to rude to us tourists, except when they seeking contributions to various causes like the Synagogue or the defence of Israel.  One exception was an elderly German man who went out of his way to talk to us and had, he told us, come to Israel as a young adult.

 

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Travel

Egypt, Syria and Jordan

 

 

 

In October 2010 we travelled to three countries in the Middle East: Egypt; Syria and Jordan. While in Egypt we took a Nile cruise, effectively an organised tour package complete with guide, but otherwise we travelled independently: by cab; rental car (in Jordan); bus; train and plane.

On the way there we had stopovers in London and Budapest to visit friends.

The impact on me was to reassert the depth, complexity and colour of this seminal part of our history and civilisation. In particular this is the cauldron in which Judaism, Christianity and Islam were created, together with much of our science, language and mathematics.

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Fiction, Recollections & News

Remembering 1967

 

 

 

 

 

 

 

1967 is in the news this week as it is 50 years since one of the few referendums, since the Federation of Australia in 1901, to successfully lead to an amendment to our Constitution.  In this case it was to remove references to 'aboriginal natives' and 'aboriginal people'.

It has been widely claimed that these changes enabled Aboriginal Australians to vote for the first time but this is nonsense. 

Yet it was ground breaking in other ways.

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Opinions and Philosophy

The Chemistry of Life

 

 

What everyone should know

Most of us already know that an atom is the smallest division of matter that can take part in a chemical reaction; that a molecule is a structure of two or more atoms; and that life on Earth is based on organic molecules: defined as those molecules that contain carbon, often in combination with hydrogen, oxygen and nitrogen as well as other elements like sodium, calcium, phosphorous and iron.  

Organic molecules can be very large indeed and come in all shapes and sizes. Like pieces in a jigsaw puzzle molecular shape is often important to an organic molecule's ability to bond to another to form elaborate and sometimes unique molecular structures.

All living things on Earth are comprised of cells and all cells are comprised of numerous molecular structures.

Unlike the 'ancients', most 'moderns' also know that each of us, like almost all animals and all mamals, originated from a single unique cell, an ova, that was contributed by our mother.  This was fertilised by a single unique sperm from our father.

This 'fertilisation' triggered the first cell division. These two cells divided; and divided again and again; through gestation and on to birth childhood. So that by the time we are adults we've become a huge colony of approximately thirty seven thousand billion, variously specialised, cells of which between sixty and a hundred billion die and are replaced every day. Thus the principal function of a cell, over and above its other specialised purposes, is replication. 

As a result, the mass of cells we lose each year, through normal cell division and death, is close to our entire body weight. Some cells last much longer than a year but few last longer than twenty years. So each of us is like a corporation in which every employee and even the general manager has changed, yet the institution goes on largely as before, thanks to a comprehensive list of job descriptions carried by every cell - our genome.

Cell replication is what we call 'life'.  The replicating DNA molecule can therefore be regarded as the 'engine of life' or the 'life force' on Earth.  So it is quite a good thing to understand. 

 


What makes us human?

Different animals and plants have different numbers of genes and chromosomes that together make up their genome.  Many are far more complex than humans.  The 32 thousand  human genes are organised into 23 pairs of chromosomes within each of our cells.  But the protein-coding genes, that differentiate us, form only a fraction (about 1.5%) of the instruction and memory data that is stored in DNA. The remainder, coding for other aspects of cell chemistry, seems to be administrative overhead.

When human girls are born, they have about a million eggs in each of their two ovaries, nestled in fluid-filled cavities called follicles. But this number declines quite rapidly so that it is depleted by the time of menopause (usually before 50 years of age). Unless fertility treatment is in use, just one or sometimes two of these (apparently randomly selected) ova descends from the ovaries each menstrual period - down the woman's fallopian tubes where it (or they) may become fertilised if the woman has recently engaged in coitus (had 'sex').

As in vitro fertilization (IVF) demonstrates every day; we now understand that a unique version of your father's genome was injected into your mother's egg by just one of his millions of spermatozoa. So that when the two genomes merged a doubly unique cell, that became you, was the result.

Our genes, that are encoded in their DNA, come in equal proportion from both parents.  Unless we have an identical twin, resulting from division of the zygote (see below) after fertilisation, each of us is genetically unique; our genetic identity determined by that successful fertilisation. 

 

 


Human Reproduction - Click here to Expand

 

Within our species we are said to be of Caucasian or Asian or African appearance, to have dark or fair complexion and so on, and possibly to bear a ‘family resemblance’.  These traits are due to the particular gene variants we have inherited from our parents.

These have been passed down to us, with regular variations, from parent to child, and through many ancestor species, since life began on the planet. And all plants and animals on Earth belong to a single family because we all inherit the same system of reproduction from one original replicating cell, our last universal common ancestor (LUCA) 3.5 to 3.8 billion years ago.

 


Replication

The DNA molecular structure resembles a zip fastener, where each tooth can be any of four molecular bases.  The bases G-C and A-T are each small organic molecules that at one point are covalently bound to a triphosphate (containing three phosphorous atoms) and a sugar group that binds them in a ribbon.  At their free end Guanine is attracted to Cytosine, with triple hydrogen bonds, and Adenine is attracted to Thymine, with double hydrogen bonds. 

In the following notation: black = Carbon;  blue = Nitrogen;  red = Oxygen; white = Hydrogen.   Bars joining them indicate a covalent bond, an electron shared between the atoms.  A double bar indicates two shared electrons.   

 

  Cytosine (C4H5N3O) has a shape that attracts (fits)   Guanine (C5H5N5O) 


but not  Thymine (C5H6N2O2)  or   Adenine (C5H5N5), that attract (fit) each other.

 

Each of these bases is bound to a ribbon of  sugar molecules and at its other end lightly bonds to a matching base on the other half of the 'zipper' such that when it is 'unzipped' each attracts its opposite number (like magnets attracting the opposite pole) thus recreating a new matching half in the same sequence.

 


DNA replication. 

 

This unzipping and reforming is called self-replication. It is going on continuously in all living things as new cells are created to replace those that die. In an adult human around three quarters of a million of our cells divide every second.  This cell division is the process we call organic life and may continue (usually briefly) after we are legally (brain) dead.

Other chemical mechanisms within the cell translate the genetic information stored in the DNA sequence to manufacture the proteins from which new cells are built and differentiate themselves, organising to become our various organs and to thus arrange themselves to form a human; and not a gorilla or a crocodile or a kola or a rose or a cabbage. The human genome project had now identified 32,185 human genes.

Accurate reproduction is very important to the viability of an organism.  Just as: 'WOLF' does not have the same meaning as 'FOWL' the location and order of sequence G-A-T-C within a particular DNA string (chromosome) will result in a different outcome to the sequence C-A-G-T .   And this difference will influence cell structure and purpose:   'The wolf eats the fowl' has a totally different meaning to: 'The fowl eats the wolf'.

This method of storing and reproducing instructions and data is twice as efficient as the binary method we presently use in electronic devices.  For example the binary processor in your computer or reading device requires each character in in each word in this sentence to be encoded in two bytes (each of 8 characters or bits).  In other words 16 ones and zeros are required for every character on this page (eg 'a' = 0000000001100001) and a similar number for each pixel in a simple colour image.  But DNA can encode the same information (sufficient for every unique character and symbol in every language in the world) in just eight characters.

There are a fraction over 3 billion characters in the human genome (3,079,843,747 base pairs).  In computer terms this is equivalent to about three quarters of a gigabyte of information storage. The same data is stored in the nucleus of each of our cells.  This is in nuclear DNA, before taking into account separate, but smaller, storage in each of the mitochondria (see below). 

A 'gig' isn't much you might say (less than $1's worth) but the actual data storage density is in excess of anything offered by our present electronic technology.  Cells are a lot smaller than the chip in a memory stick - there around a billion cells per cubic centimetre in hard tissue.

This also points to another reality.  Had not this replication chemistry been available, and the conditions for the reactions been just right, life could not have occurred in its earthly form. 

Life relying on another replication method that was say binary would be at a disadvantage and would have to use different replication mechanisms.  If there was a chemistry, at different temperatures and chemical concentrations, allowing say six base pairs it would be different again.  We and our cousins (the other animals, plants and other organisms) that are all descended from the original replicating cell (LUCA - see above) are here because the conditions on Earth were and are just right for our kind of life to prosper.

Elsewhere in the universe it may be different.

 


Gene Mapping

Genes are just patterns of chemical molecules that are held within the replicating DNA mechanism.  The way they are encoded onto DNA can be likened to any other mechanism for copying and recording data: a DVD or even a vinyl record or the memory in this computer.  As a result they can be altered or damaged from time to time and some of these variations are successfully copied into subsequent offspring.  If they are particularly advantageous to survival and reproduction these changes, or mutations, rapidly spread throughout the species, so that over tens of thousands of years, individuals successful in one environmental niche are so different from those successful in another that a new species has formed (followed by a new genus, family, order, and so on). 

This process of periodic differentiation has been likened to the branching of a tree but because of the activity of bacteria and viruses and residual DNA that may be reactivated as well as limited cross-species reproduction  (for example later Humans and Neanderthal) it is no longer believed to be quite that simple.

DNA encodes the instructions for creating each cellular colony, defining each species, and each individual within a species. DNA changes over time in such away that each change is a development on previous generations. So it is possible to trace DNA ancestry back through generations of a particular species over time.  For example, DNA studies are increasingly shedding light on the questions around human origins. 

Most animals, including humans, carry two types of DNA.  Our main genome is carried by the chromosomes in the nucleus of each of our cells. This comes from both our parents. The secondary genome, mtDNA, is carried by bacteria-like organelles within each of our cells, that convert sugars for cell energy, called mitochondria. These are all cloned (reproduced by asexual division) from the mitochondria that were within the original egg cell provided by our mother.

Cells may contain from one mitochondrion to several thousand mitochondria depending on species and cell differentiation.  As a result this is the predominant DNA found in a cellular sample.

So our mtDNA comes only from our mother; in turn from her mother; and so on and mtDNA allows us to map the female ancestral line.  This original egg cell was fertilised by a sperm from our father (sperm do not contribute their mitochondria). Once fertilised, the egg cell then divided repeatedly, differentiating in accordance with the coding instructions in our DNA, into the many cells that form the cellular colony that became 'us'.

Males are differentiated from females by a Y chromosome in place of one X. So sons can only inherit this from their father (like their family name in our culture) and periodic mutations in the DNA of the Y chromosome allow the (actual) male ancestral line to be traced back.

As a result of this work we now know that humans on the planet are all descended from a single group that left Africa less than 70 thousand years ago. 

Recent DNA analysis shows that early humans sometimes interbred with the Neanderthal; a separate hominid subspecies that left Africa much earlier and settled in the Middle East and Europe over quarter of a million years ago.

It's amazing to think that we have only understood it within my lifetime. Now the ancient view that people grow from a seed, provided by their father, and gain the spark of life at 'conception' from a god is totally debunked. So throw away all those ancient texts.

 


Viruses

Viruses have been around since life began but they are 'of life', they are not technically 'alive' because they cannot themselves reproduce. They are extremely small - about 70 microns in diametre - and until the invention of electron microscopes in the 1930's their existance had only been inferred. 

To create copies of themselves they need a host cell with the necessary reproductive mechanisms. Over the millennia viruses have evolved the necessary mechanisms to penetrate cells, much like spermatozoa, and inject their DNA or RNA and capture the host's replication mechanisms so that the infected cell begins manufacturing thousands of virion (virus particle) clones of the invader. These then capture other nearby cells in the host animal or plant; or in similar bacteria.  Huge numbers of infected cells are usually destroyed in the process, sometimes killing the plant or animal.

 

Coronavirus particles (yellow) on the surface of a dying cell (that produced them)
Niaid/National Institutes of Health/Science Photo Library (from 
https://www.newscientist.com)

 

But animals plants and bacteria have become familiar with this threat and have in turn evolved means of dealing with or living with viruses to the extent that some are exploited for the benefit of the host.

In turn viruses evolve new strategies to perpetuate their reproduction. Thus new viruses arise from time to time, sometimes jumping from one species to another when an opportunity arises.

Many animals, including humans, have an immune system that has a memory of harmful viruses and means of neutralising them. Thus, once the animal has been infected and survived, the chances of reinfection are reduced.  Vaccines work by presenting our immune system with a harmless sample that allows it to recognise a particular harmful virus.

Since I first wrote this article the World has suffered a new viral pandemic.  It is a novel corona virus for which we have no established immunity and there is no vaccine.  At the end of June 2020 the Covi-19 virus has already killed half a million people.

It is estimated that this virus will no longer find sufficient vulnerable hosts to spread further after infecting around 70% of the populations in which it is spreading.  It has a case fatality rate of just under 1%, that is, of those who catch it just under one in a hundred die.  

Quarantine restrictions are in place in many countries to protect relatively uninfected areas, with local measures to eliminate 'hot spots'.  But the majority of the world's population, in excess of five billion, are in countries in which it is presently spreading.

Unless a vaccine is available soon it seems inevitable that many millions more will be killed.  The economic consequences are also dire.

 

 

 

 


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