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Regular readers will know that I have an artificial heart valve.  Indeed many people have implanted prosthesis, from metal joints or tooth fillings to heart pacemakers and implanted cochlear hearing aides, or just eye glasses or dentures.   Some are kept alive by drugs.  All of these are ways in which our individual survival has become progressively more dependent on technology.  So that should it fail many would suffer.  Indeed some today feel bereft without their mobile phone that now substitutes for skills, like simple mathematics, that people once had to have themselves.  But while we may be increasingly transformed by tools and implants, the underlying genes, conferred by reproduction, remain human.

The possibility of accelerated genetic evolution through technology was brought nearer last week when, on 28 November 2018, a young scientist, He Jiankui, announced, at the Second International Summit on Human Genome Editing in Hong Kong, that he had successfully used the powerful gene-editing tool CRISPR to edit a gene in several children.

Two girls, twins, have been born and are thriving and another gene-edited baby is on the way.

The reaction was outrage. Dr He has been condemned by most of his peers - and by ethicists in general - for undertaking this ground-breaking work outside of a suitably structured and safe environment and for the ethical and ongoing implications concerning these children and their possible future off-spring, who may also carry and spread this genetic modification throughout the human population. 

The putative justification for the work was to confer HIV (human immune-deficiency virus) immunity on these children who may otherwise have contracted the disease from infected parents. The successful parents were chosen from among seven couples at risk who had volunteered. 

CRISPR was used to modify a number of IVF (in vitro fertilised) human embryos to prevent the expression of a CCR5 protein, that is exploited by HIV. People who, naturally, have a variant of the CCR5 gene that fails to express the protein, that is required by the virus for replication, had been found to be immune to HIV.

But there is at least one additional implication of editing this gene. Experimental mice that were similarly made immune to HIV also demonstrated cognitive improvement.  So the gene may be important in brain development.  As a result these children may exhibit, as yet unknowable cognitive, or other developmental changes that will only be evident as they grow and learn.  This is a matter of serious concern, particularly if the impact is negative in humans.  Among the many criticisms of Dr He is that he may have opened the flood-gates to increasingly dangerous genetic 'improvements' with similar long-term implications.

CRISPR technology can be used to: edit; remove; add; or replace genes and is already used to create 'improved' plants and animals. It's easy to imagine transgenic 'super' sportsmen and women.  Failures would undoubtedly result in Frankenstein-like scenarios. Yet successes might result in people with a range of new, unnatural, abilities or attributes.  Might such more-able people be more desirable partners for their ability to hand on their more desirable genomes?  Might human evolution thus accelerate? 

Upon Dr He's announcement the World Health Organisation (WHO) warned that gene-editing may be dangerous, and announced it would establish a panel of experts to set clear guidelines and standards after studying ethical and safety issues.

When considering Dr He's motivation, in the face of possible punishment, he is no doubt aware that the first IVF baby, Louise Brown, was similarly the outcome of a rogue experiment, that was similarly announced after she was born in 1978.  At that time moral outrage resulted from 'scientists playing god' and when it was revealed that almost all the fertilised human embryos failed to thrive.  Even today, when the technology is well advanced, over two thirds of the transplanted embryos are unsuccessful and are aborted.

At the time it was a commonly held myth that new life is conferred by a god or gods at the instance of fertilisation.  It followed that these abortions were actual human babies being slaughtered en mass.  As Monty Python told us soon afterwards: 'every sperm is sacred'.  Then in 1996 there was the case of Dolly the sheep - a complex mammal, like us, cloned from a single stem-cell taken from her mother.  This technology too has become commonplace.

The ancient belief that life begins anew at each conception was thus reduced to the point of absurdity. Is God in the lab standing by to create life anew each time a technician brings ova and sperm together on a glass slide or when she multiplies a single living cell to create a new independent animal?   Where is the 'new' life in this when there is no point of conception at all?  Clearly the laboratory process is simply perpetuating the pre-existing life of the cells involved.  As it is in nature, living cells reproduce by division and life is not created anew at each division. Thus all life on Earth today is inherited from our last universal common ancestor (LUCA), around 3.5 to 3.8 billion years ago.  Sooner or later after coming into being - sometimes very quickly - all cells then die.   

Humans are colonies of billions of such continuously dividing and dying cells. At birth we have around 26 billion cells, all originating from that single original cell. By adulthood that number will grow by over a hundredfold of which total some 60 billion cells die and are replaced every day.  See: Are we the same person we once were? 

Thus in nature there is but one life but trillions upon trillions of deaths every day.

In the light of modern technology and knowledge the point at which a cluster of cells can be said to be a new person has become much less obvious than it was just two centuries ago. Many doctors and ethicists now agree it's at the point when he or she is potentially capable of successful independence from their mother.  Yet some Roman Catholics and others persist in the ancient and obviously erroneous idea that a new life (and soul) begins at conception. Thus the debate over abortion and morning-after pills persists.

Despite potential jail time Dr He no doubt takes solace in the history of IVF.  After initial moral outrage in just four decades IVF technology has become very widely used, including by many Roman Catholic parents. 

According to the European Society of Human Reproduction and Embryology by mid 2018 more than 8 million people owed their creation to IVF.  And 68 years after their breakthrough one of the 'rogue' researchers: Robert G. Edwards was finally awarded the Nobel Prize, in Physiology or Medicine, his two controversial IVF co-developers, Patrick Steptoe and Jean Purdy, being dead and thus ineligible, yet for their friends and decedents, posthumously vindicated.

 

 

 

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Travel

Burma (Myanmar)

 

 

This is a fascinating country in all sorts of ways and seems to be most popular with European and Japanese tourists, some Australians of course, but they are everywhere.

Since childhood Burma has been a romantic and exotic place for me.  It was impossible to grow up in the Australia of the 1950’s and not be familiar with that great Australian bass-baritone Peter Dawson’s rendition of Rudyard Kipling’s 'On the Road to Mandalay' recorded two decades or so earlier:  

Come you back to Mandalay
Where the old flotilla lay
Can't you hear their paddles chunking
From Rangoon to Mandalay

On the road to Mandalay
Where the flying fishes play
And the Dawn comes up like thunder
out of China 'cross the bay

The song went Worldwide in 1958 when Frank Sinatra covered it with a jazz orchestration, and ‘a Burma girl’ got changed to ‘a Burma broad’; ‘a man’ to ‘a cat’; and ‘temple bells’ to ‘crazy bells’.  

Read more ...

Fiction, Recollections & News

Reminiscing about the 50’s

 

 

Elsewhere on this site, in the article Cars, Radios, TV and other Pastimes,   I've talked about aspects of my childhood in semi-rural Thornleigh on the outskirts of Sydney, Australia. I've mentioned various aspects of school and things we did as kids.

A great many things have changed.  I’ve already described how the population grew exponentially. Motor vehicles finally replaced the horse in everyday life.  We moved from imperial measurements and currency to decimal currency and metric measures.  The nation gained its self-confidence particularly in the arts and culture.  I’ve talked about the later war in Vietnam and Australia embracing of Asia in place of Europe.

Here are some more reminiscences about that world that has gone forever.

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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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