#6.Carbon: infrastructure for life

Hydrogen (H; #1) and Helium (He; #2) atoms form from the Big Bang.  The He atom is also the He molecule, as it has a complete shell.  H atom needs to pair to become the hydrogen molecule (H2): two electrons shared and the first orbital level is filled.

Gravity brings these atoms and molecules together until a critical mass is reached, nuclear fusion starts mostly converting #1 to #2. A star is born. As its nuclear fuel ( #1) runs out, the star dies. Its dying flames leads to more fusion: #2 into #6 (through #4, but Be has no role in this story, nor #3, Li).  Heavier elements will form in the next star; many are essential to life.

Carbon (#6) is created in each generation star, so this is perhaps why it is the most common element in the universe after #1 and #2. Our sun is a third generation sun, and the Earth formed from the ashes of a second generation sun that exploded some 5 billion years ago.

Why is life carbon based? With 6 electrons it pairs with 4 atoms to complete  its electronic shell (2 in first orbit, 8 in second) for stability. Four bonds is the most that elements with two orbits can have. Is it a coincidence that silicon (Si, #14), below C in the Periodic Table, also needs four bonds and is the base for digital life (computer chips)?

The versatility of carbon can be seen in coal and diamond. Very different materials because the carbon atoms are organised in different ways.  Let’s  look at life through the lens of food, which itself it just life or formerly living cells of plant, animal, or fungal origin.

There are three types of major nutrient in food: protein, fat, and carbohydrate (carb).  Although only the last has carbon in its name, carbon provides the structure for each of these elements, but aided by Nitrogen (#7) in the case of proteins.  Carbon also provides the scaffolding for the DNA molecule, through ribose a 5-carbon ring; but that also needs nitrogen.  (And phosphorous for the spiral)

Protein

Proteins are made from amino acids:  a central carbon atom (C) connected to an amine group (H:N:H, NH2) and a carboxyl (O::C:O:H, COOH) group.  The proton (H) of the carboxyl group can be attached to the N, creating a hydrogen bond between the two groups. This chaining mechanism allows creation of some very complex molecular structures and machines. Other elements, for example iron for haemoglobin, may be needed for protein function.  This is why certain minerals are essential in our diet.

Every amino acid also has a unique side chain that provides the fourth bond to the central C atom.  The side chain also has a C backbone that determines how it behaves when linked with other amino acids.

Proteins are molecular machines that provide structure, enzymes, hormones, and more. These functions derive from their shape, the specific linear list of amino acids  and its unfolding into a 3-D shape that enables its function. The 20 amino acids create the amazing range of molecules needed for life.

Fat

Dietary fat are the fatty acids, chains of 4 to 28 C atoms with a carboxyl (O::C:O:H, COOH) end that makes it acid (a proton donor). The proton of the carboxyl is ‘loosely held’ as COO with a negative charge is relatively stable.

If there is one or more double bond (share two electrons) between the carbon atoms, the fat is unsaturated. A monounsaturated has a single double bond, a polyunsaturated fatty acid has several. If the carbon chain has no double bonds, it is called saturated as it cannot take on any more hydrogen atoms.

A saturated fatty acid is straight, while the unsaturated bend at the double bond.  So, both the position and number of carbon double bonds change the shape of the fatty acid.  And shape leads to function. A key function of fatty acids is to make the cell wall. We can also store excess energy as fat, and can convert glucose to fat.

Carbohydrate

Unlike fat and protein, carbohydrates have no structural function apart from energy storage. Plants convert sunlight, carbon dioxide and water into glucose, the ‘model’ carbohydrate unit, a 6-Carbon ring, with one C atom replaced by an oxygen atom in the hexagon, and the C atom outside the ring providing the link from one glucose molecule to the next to form a disaccharide or polysaccharide – multiple of these hexagonal units of the glucose molecule.

So, I could not use #6 for Carbon, but could use C its standard abbreviation. And I don’t want this biochemistry to get too complex. But I hope you got the message, the chemistry of life happens on the scaffold  of C atoms, because of its position in the periodic table which reflects the number of electrons in a carbon atom: 6.

#1. Hydrogen

Democritus over 2000 years ago proposed the idea of atoms as the fundamental constituent of all matter. The Greek word means no ‘cut’; the indivisible smallest unit of matter. In the 19th century, Dalton (1766-1844) used atom in the modern sense that continues to day, even though we know the atom can be split, and the real ‘atoms’ are the sub-atomic particles with the quaintly wonderful names of quarks and leptons.

If you want to briefly go into this strange world, then let me start with the origin; if not skip two paras! A quark was created in  fiction by Joyce, a lepton is derived from greek  ‘small’, even though they are larger than quarks! The six types of quarks combine in various ways; here we are just concerned with two combinations:  two ‘up’ and one ‘down’ quarks make a  protons with a positive charge (2/3+2/3-13/); while One ‘up’ and two ‘down’ quarks make a neutrons with no charge (2/3-1/3-1/3). that form the core or nucleus of the atom. Electrons, are the  only one of six types of leptons that we are interested in for this exercise.

Quarks and leptons are called Fermions, named for Fermi. The universe is composed of Fermions and Bosons, named for Bose-Einstein equation. The Bosons are the ‘force carrier particles’. The photon is the only one that is commonly known, and this is the particle of electromagnetic radiation. Remember light is both wave and particle, and the particle is the photon. There are also Bosons for other fundamental nuclear forces (weak and strong force), but the particle for gravity (graviton) has yet to be found, even though we now have shown that gravity travels in waves.

An atom has a nucleus with neutrons and protons; the neutrons maintain the nucleus, despite the positive charge of the protons against each other.  Each element has a unique atom with an equal number of protons and electrons: its atomic number. (The number of protons + neutrons is atomic weight.) Neutrons also generally balance protons, but these can vary a little to create isotopes. The one exception is Hydrogen, #1 as it has a single proton at its core.

The Big Bang describes the expansion of the Universe from a tiny point, smaller than an atom. It expands faster than the speed of light. Cools as it expands. High energy plasma form into sub-atomic particles and then Hydrogen atoms.

Hydrogen is the first element formed, and remains 75% of the known universe. Initially, as Deuterium (with a neutron), but hydrogen does not need this neutron. Electrons spin in pairs, so two hydrogen atoms make a molecule, with each proton sharing.

The dance of electrons and protons (hydrogen atom without its electron) follows strict rules. In addition to the fact that a single electron will always search for a partner, electrons can only occupy specific ‘orbital level’. This means that when an orbital level is full, the atom is more stable – the noble gases on the periodic table, with atomic numbers 2 (Helium),  10 (Neon) and 18 (Argon) have complete first, second and third levels.

Similarly, two H atoms are relatively stable (H2), but can easily oxidise or burn to become water if enough energy is provided to disrupt the relative stability.  Hydrogen is indeed so called because that is how it was first identified in the 18th century: a gas that turns into water upon.  Instead of pairing with each other, each proton shares its electron with an oxygen atom: H2O.

Hydrogen is unique – a word derived from the Latin for ‘one – in many ways.  The dance between the proton and electron in the hydrogen atom is the basis of the chemical dance that gives us life.

In the 19th century, we thought that chemistry would not be able to fully explain life.  Yet, we no longer need to seek divine factors to explain life, including its simple yet magnificent genetic code.  Science provides a coherent and compelling account of how the Universe becomes self-aware. To my mind it is far more awe-inspiring account of our origins than any Divine myth. And yet still leaves space for God, without needing that factor to explain anything.

And it all starts with hydrogen, the deficient atom!

A fresh start: atoms

I was trying to recall the periodic table to help me visualise molecules. Initially for the biochemistry of ketosis, then the structure of a transporter protein used by bugs causing Cholera and Typhoid to enter our intestinal cells. The protein is defective in Cystic Fibrosis. Perhaps the heterozygote protects against these diseases; and it dose seem that gene causing it arose during the Bronze Age in Europe, when the size of settlements would have increased enough to allow the spread of infections between people.

And it led me to the idea of the dance of life, proton and electrons moving between the atoms of our molecules.  And how that could be explained with numbers. I’m not sure if it works, as I’m still struggling with #1, Hydrogen.

Before the dance can be explained, first we need to learn about the partners and the setting for the dance.  Why is life Carbon (#6) based? DNA, the molecule that codes for all life on earth (if we include its sibling RNA and viruses). is composed of only three more elements: Nitrogen (#7), Oxygen (#8) and Phosphorous (#15), in addition to the Carbon skeleton of all organic molecules.

Two. Start 2 x 2

develop_zygote_cleavage_stages_blastula_etc.pngOnce the first sperm enters the egg, the egg closes off its outer wall so that no other sperm can enter.  The winner takes all (with the odd failure!).  This is the start of you;  and you are who you are, because of the specific egg and sperm that won the race.  Your unique genetic code resulted from the unique combination of sperm and egg that became you.

(I used to wonder,  who would I would have been if my mum had married someone else; what would I have been like.  But, that would not have been me.)

It doesn’t take long before that one cell splits into two almost identical cells, and that doubling keeps going until you become hundreds of trillions, a newborn baby that emerges from your mother’s womb about nine months later.  But let’s go back to the start of you.

When the sperm and egg combine combine, each comes with a single set of  23 chromosomes.  When they combine to create a new human, it starts with a single  cell, now called a zygote, with the full set of 23 pairs of chromosomes.

Doesn’t that word sound full of colour and meaning?  Chromosomes contain the ‘instructions’ that create each cell, coded in the 4-letter alphabet of DNA (molecules of De-oxy-ribo Nucleic Acid).  All life is made of cells, and DNA and its precursor RNA (Ribo Nucleic Acid) is central to making and controlling each cell.  Each one of our trillions of human cells has nearly exactly the same genetic code.

That genetic code is created form the unique pairing of sperm and egg.  And here we learn that 1+ 1 = 1 since 1 sperm and 1 egg make a single zygote that then becomes a baby in mothers’ womb.  For humans, as for all other mammals.  One could also argue that  1 + 1 = 3, for mummy and daddy create out of themselves a new baby.

It seems obvious here, but may be hidden: arithmetic demands you use numbers that refer to the same thing.  You cannot add up or do any other operations on number and expect a meaningful answer.  The arithmetic of reproduction is meaningful, but it is not useful for an arithmetic where the answer to 1 + 1 is not reliable. So, whenever you see two or number used or compared; ask yourself, what’s the unit in each case.  Is it the same; and a quick way to see that is to imagine what does single unit look like.

When you are a single cell and divide into two cells, are the two the same? They seem to be, yet one is destined to become embryo, the other the placenta. Each cell divides by first creating two sets of 23 paired chromosomes; so your cells enter the Noah’s ark of life two by two.  And the power of multiplication of just keeing dividing by two to create the trillions of cells that you became as a new baby.

This is the power of compound interest, the exponential factor that is behind biology as well as human society.  This is the power of mathematics.  When my father taught me chess, he told me of the story of the ruler who was so pleased to play the game that we wished to reward the person who taught him. He just asked for a single grain of rice to start, but to be doubled on every square of the chess board, which has 64 squares.  The ruler was happy to agree. A single grain multiplied a few times did not seem so much.  But before covering half the board, the number is over 4 trillion, more rice grains than the ruler had.

You grew from one cell that kept dividing. It takes a while to start after fertilisation, the moment that the sperm enters the egg, and the two cells to become one, the zygote.  It takes a little more than a day for zygote your to start dividing, first into two equal cells.  These two cells divide into four, the four into eight, then by the time you have become 16 cells, you are called a morula. As your cells keep dividing, you become a blastula that enters the lining of your mother’s womb, and into a gastrula, with three layers of cells that will make your inside, outside and middle (respectively), though not in exactly the way you might think.

Somehow equal cells have become different, and that difference continues to develop as your cells develop into at least 200 different types of cells that a human is made of.  All of them from one single cell, who at this stage in your story is a few hundred cells of each of these three types: endo-,  ecto-, and mesoderm.   Can you relate to yourself, when you were just a single cell or the three layers of cells?

 

 

 

 

One. Odd Odds

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Here, I found this pretty picture: a tiny fraction of the hundreds of millions spermatozoa (sperm cells) swimming as fast as they can, to be the first to enter the egg cell.  Guess who won?

This is how you started: you won the race against incredible odds.  Odds is an odd word, but then so is odd; why does it need two ‘d’s: od would look odd, but sounds the same.  It is derived from a peak of land, then became a triangle, then for not-paired, being the third point. Odd being left on its own, somehow became probability, for the odds is just another way of saying what’s the probability.  The minor difference is that odds is stated as 1 in some number; and odds against when that number is less than 1; and probability is generally stated as a decimal or percentage.  In history, all probabilities have become 0 or 1; until we know whether the event happened or not, its chance of happening, or probability will be a number between 0 and 1, like 0.5 which is exactly in the middle.  Here the odds are even; like whether you get heads or tails when you toss a coin.  But let’s get back to your story.

If another sperm had won, it would not have been you.  Strange thought, but well done for winning that race with bigger odds against you than winning the lottery:  one sperm in 100 to 500 million just for that race; but you might not even been able to enter that race, if your mother had become pregnant with the egg she released the previous month.  So, what is the probability that YOU are here, instead of the brother or sister that could have been here instead?  And if your parents had not met; and so on.

You need to be careful not to mis-use probabilities.  They have no bearing on history; it already happened; it’s either 0 or 1; and even though the prior probability was so close to 0 that the one that you call you should be here; the probability is actually 1, because you are here.

Want to do some arithmetic? If not, skip the square brackets.

[Let’s round out to saying there are 16 sperm in the picture, and there were  128 million (128,000,000) sperms competing for that egg.  Now if you happen to know that 16 = 2^4 and 128 = 2^7, then you know that 128 divided by 16 is the same as subtracting the exponents of the common base.  The ^ symbol means ‘to the power of, or ‘exponent’.  It’s the number of times the number is multiplied by itself. So, 128/16 =2^7 -2^4 = 2^(7-4) = 2^3 = 8.  And there  was a 1 in 8 million chance that ‘your’ sperm won. What’s that probability? But now that you’re here, its odds are 1 in 1 – it already happened.]

[[{Ever heard of log tables?  Before we had calculators, they were used to simplify complex calculations by converting a number (x) to its ‘exponent’ (y) or logarithm: [x = 10^y].  Adding the logs is the same as multiplying the numbers; subtraction division.  The result is found in the anti-log table where the resulting exponent(y) is converted back to a number (x). }]]

In epidemiology, the science of disease distribution and determinants, careful use of data is vital.  The Texas sharp-shooter fallacy: shoots first in the wall, then draws the target around the bullet hole.  To state that you have beaten the odds to be here is kind of like that.  Can you see the analogy?

Once something has happened, what does it mean to calculate the odds of it happening.  The lady who just won the lottery did not beat the odds, she just won.  Even though winning was incredibly unlikely, and very much against the odds to the tune of one in close to a billion; those odds no longer carry any information once she won; and somebody had to win!

Knowledge is very slippery, so is logic.  Words are the problem.  They aren’t real; and they can never fully describe reality.  We can just get close. Shall we try?

 

Pre-amble

We, the People, seek to order: a more perfect union of peoples, Justice, peace and prosperity; a secure life and liberty to pursue our individual goals, including happiness.

This paraphrase of the 1787 US Constitution explains what we want from government.  Democracy demands active citizens, knowledge is a pre-requisite.  Numbers count.

Vaccines are designed to prevent infection by preparing the immune system to ward off the specific bug each vaccine targets.  There are different types of bugs that cause serious illnesses and so, different types of vaccines to protect against these.

I am trying to develop a story to explain how vaccines work and why these marvels of science are considered so dangerous by a small fringe.  And to tell this story properly, we will need to understand the cognitive illusions created by our minds, and the biases that can make us certain of our view, even after we see evidence against it.

In the process we need to learn about numbers; the first lesson is that numbers can lie.

 

Smallpox the First: a human triumph!

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Lady Mary Wortley Montague (1689–1762)

Source: Reidel 2005, Photo courtesy of the National Library of Medicine.

Smallpox the First

Did you hear the good news? Smallpox is dead!  The smallpox virus was murderous.  It killed more people than war.  In the 20th century alone, smallpox killed between 300 million (300,000,000 or 3*10^8) and half a billion (500,000,000 or 5*10^8) people.  The first disease conquered by humans: How did we vanquish this angel of death?

Continue reading →

What’s a vaccine to you?

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A vaccine against ignorance?  “Humanity certainly needs to be immunized with a vaccine for ignorance, and we propose that that vaccine is education. But education would have to be coupled to restrictions on people, agencies, and corporations determined to follow the profit motive, and in so doing, undermine the intelligence of the populace.”

Vaccines have been so good at preventing disease, that the above article uses ‘vaccine’ metaphorically to describe prevention of ignorance.  And has been used to describe other preventive interventions: what would you like a vaccine for?  Something to stop what you don’t want.  I would like a vaccine to be more kind and less mean; to love.  Sadly, we have not yet discovered that.  But education and changing the economic system could help.

The picture above uses shapes, sizes, and colours to show different bugs; and the hand as defence that stops them. Vaccines stop harmful bugs by preparing our defences. A vaccine does not protect against bugs in general, only the specific bug that it targets. It does this by ‘looking like’ the bug to our immune system.

Continue reading →

Recap & Plan

Vaccines and numbers  introduces a new child to the world.  One more.  Addition. A  starting point for maths.  We introduced big numbers like the  over 7 billion (7*10^9 or 7,000,000,000) people who live on our planet.  All of us members of a family that emerged some two hundred thousand (200,000 or 2*10^6) years ago from the Rift Valley in East Africa.

A child born today benefits from life-saving tools. Vaccines, antibiotics, clean water protect children from infection caused by bugs. We now have vaccines against more and more bugs. In New Zealand, children are given vaccines against at least 12 families of bugs.  But what are bugs?

The germ theory of disease introduces you to the idea of bugs.  These are microscopic (tiny) creatures that are too small to be seen by the naked eye.  Some are too small to be seen in normal microscopes.  These many kinds of life forms include  viruses and bacteria, the two  main kins of bugs that  vaccines protect against.

Surprising fact:  some people do not believe or understand germ theory.  Surprisingly many are not even exposed to the idea; their only teaching being religious.  Surprising, because the evidence has been so strong since Pasteur developed the theory  in the late 19th century (1880s).  Today, the evidence is even stronger as we learn about new kinds of bugs, including the Archaea that did not even exist as a separate kingdom of life when I was at school.  And we now have anti-cancer vaccines as we have found  the viruses responsible for liver, cervical, and other cancers.

For me, the idea for Vaccine Logic came from decades dealing with anti-vaccine arguments, prompted by  doing a logic course. A lot of science is needed to understand vaccines.  To learn about vaccines requires understanding many disciplines of the science of our human bodies: medicine, physiology, immunology.

Our   cells of immunity protect us from  bugs.  But our relation with bugs is more complex than a simple war, and may be better thought of as an interplay of another level of our existence; in the same way as we can think of the interplay between the

  • subatomic quarks and electrons that make up all matter
  • molecule machinery of our cells
  • different organs and systems that create our existence and consciousness.
  • individuals who make up a family
  • communities of households and families
  • corporations and nations; religions
  • Gaia, the planetary entity; an almost closed environmental system that has been brewing life for at least 3.8 of its 4.5 billion year life.

Each level can provide some insight to the level above it or below it. For example, the electron dance from the orbit of one atom to that of another, as they seek to find a new partner.  Electrons always want to spin in pairs.

Chemical reactions involve bumping an electron off  to break up and then create a new molecule by shifting the bonds, the shared electrons between the atoms.  This idea helped me understand chemical reactions – but not how to learn about the specific biochemical reactions. Different domains behave by distinct laws.  The social is more plastic.

We do not have the mental machinery to be able to model the quantum world. Why do think we can understand the increasingly complex social one?

Can electron behaviour provide insight into social dynamics?  Humans too seem to need to pair; and to be in society. So, while we don’t need to traverse all the sciences to explain vaccines, perhaps the journey will be more satisfying.

From simple atomic processes, the chemistry of life and the shapes of immunology. To the behaviour of human individuals and populations. It does not matter how effective a vaccine is, unless it is taken up by enough of the population to prevent spread in the community. The impact of vaccines demands population coverage.

With the exception of tetanus, vaccines prevent diseases that are spread person-to-person.  While the protection from a vaccine is to the individual, the impact depends on community coverage.  For some vaccines, when coverage is high enough, the bug will become unable to pass form person-to-person.  This is the ‘herd immunity’ threshold.

The concept of herd immunity is another one that seems to challenge people.  It can be described as derived from a number, that we call R0 (R zero).  The herd immunity threshold is 1 – 1/R0 (one minus the inverse of R zero).  R0 is the average number of people an infected person will pass the disease onto.  Measles has one of the highest know R0, estimated to be between 12-18 in most settings, so the herd immunity threshold is 92-94% immunity.  As no vaccine is 100%, but two doses of measles vaccine give about 99% protection, immunisation coverage needs to be about 95% to prevent spread.

We will then take a diversion to reflect on what is happening with measles in New Zealand as we get close to this level of immunity, before starting to address the various anti-vax arguments, and from this to learn about the different types of logical flaws.  Here we need to be very careful, as it is surprisingly easy to be trapped by faulty logic.

With that caution, we can then look further at the individual versus population view of the risks and benefits of immunisation.  Through this to see if we can test and strengthen the logical proof that vaccination is an act of love for others, in addition to ours.

Please let me know if you have some other suggestions.