Atoms & Molecules - Tiny Factories

Rumi lived in the 1200s and knew nothing of modern atomic physics.

In the past, people thought that matter was made up of four elements - earth, air, fire and water - even though some Greeks and Indians had proposed that the world was made out of small indivisible parts - atoms. 

atomssiliconcrystalAtomic resolution Au100

To the left is an image of Gold [Au] atoms made with a scanning tunneling microscope - STM. 

To the right is an STM image of silicon atoms in a crystal lattice.

But as information was gathered over the centuries through the work of alchemists, more experimental  methods gave a new picture and alchemy became chemistry. Here is a link to a great timeline of this change.

Many high school students puzzled over this picture in the form of the periodic table of elements arranged by the structure of their atoms. :


Click for a full size image in a new window.

NOW here is the Periodic Table colored by the origins of elements. The universe started out with only Hydrogen - H and Helium - He. All the other elements were made later by stars !!:


Click for a full size image in a new window.

Even though the Greek word atom - atomos - ατομος -  means not cuttable, It turns out that atoms are divisible and have parts. The number and arrangement of the internal parts is what gives the periodic table its form.


In fact, if we drill down further inside atoms, we find electrons around a nucleus consisting of protons and neutrons. A proton weighs as much as 1836 electrons, although their charges are equal. It is estimated that there are 1080 protons in the visible universe. Here is a diagram of the simplest atom, hydrogen, with just one proton and one electron.


It is still beyond our technical ability to see inside individual atoms because they are smaller than the wavelength of visible light. But we can represent the way electrons hover around a nucleus in a probablistic electron cloud: 

Investigating further, inside these particles, we find that they are not elementary either, but also have parts.  We discover yet another periodic table within, consisting of even more elementary particles. This one is obviously unfinished thus far. Maybe you can work on it. We call it the standard model. [click for larger image in a new window.]:


An aside: Although starting out in physics and elementary particles, I later departed their study for information / computer science. As for elementary particles, even though we have built the LHC and powered down to the Higgs boson I think there is no bottom and that particles come from the nature of space-time itself.

Now on about particles, atoms and structure:


One of my parishioners in St. James' Episcopal  Church in Cedartown, Georgia - raised thoroughbred horses. In NW Georgia the grass there, like in Kentucky, made strong bones. He used to say to me:
"Some horses are faster than others." - a truth to which every fan of fast horses will attest. 

Well, some atoms are faster than others as well. In turns out that at the temperature on the surface of the planet Earth where we live, hydrogen, oxygen, carbon and nitrogen are very active. They have structures that support assembly into larger combinations, somewhat like

Children's Tinkertoys:                                                                  or Legos:


Only a few volts, like the output of a small battery, or a few degrees difference in temperature, are necessary to push these tiny atomic building blocks around, hooking and unhooking them up into larger structures - molecules - giving:

Alkanes like natural gas - methane - CH4, ethane - CH6, etc. - hydrocarbons, like those we burn in our cars and bodies, are assembled around carbon :


While Amines like these are assembled around nitrogen , sometimes making proteins, etc.:



Longer chains of these parts lead to amino acids and proteins - basic building blocks of life in our cells. and ultimately to the most important molecule to us and all life on Earth - Deoxyribonucleic acid (DNA) - the double helix. >>>>>

Each living cell has many, sometime thousands, of ribosomes - tiny molecular factories or  assemblers that can each put together many proteins per second. 



Now consider this. This picture of atoms assembled into letters was done in 1989 by IBM’s Don Eigler placing Xenon atoms in a special electron microscope. There are 35 atoms. Even after everything was set up and working, it took hours to assemble these letters.

Remember Avogadro's number from your high school chemistry? Well, it is the number of atoms in a mole - a molecular weight of some element - for carbon that's about 12 grams.
Like the term dozen always means  a specific number - 12,
Avogadro's number always means 10^24, a trillion trillions

If you could count the atoms in one mole of carbon - 10^24 atoms - at one per heartbeat,
it would take a million times the age of this universe.

                               [10^24 atoms divided by  10^18 seconds leaves 10^6 - a million.]

Now look at this period, this dot at the end of this sentence . In it there are many trillions of atoms banging into each other every second. SImilarly, in each of the trillions of cells in your body, there are billions of ribosome molecules, each churning out tens of proteins every second. Trillions of trilliions and billions of billions means very large scale operations. We call mechanisms operating on this scale nanotechnology.

Now you can understand the push to make everything smaller:
 the smaller things are, the more there are, and - the faster they go. 

Nature is churning out assemblies on a scale we can hardly imagine. One of our factories might make a few hundred cars or computers at a time or even a few thousand screws per hour, but
nature is making  assemblies by the trillions in every dot of matter every second. 

We are just now learning how to do this. In the near future, computers will be thousands even millions of times smaller - and faster. And with that speed we can begin to make molecules like nature does. 

This century we will make assemblies like nature does - we will grow them.

Now that we have a little feeling for the scale of the engines of creation, let's go on to one of Nature's most amazing products, the structure called the cell - an amazing organic mechanism.

Next >>> Cells & Life - Emergence

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