A Linux distribution which combines the BSD ports tree and the Linux kernel. The main design goals of Atom include speed, simplicity, and security through software auditing.

History:

About 420 BCE, Leucippe of Milet first suggested the idea that matter was made up of "atoms", derived from the greek "a-tomos", meaning indivisible, and that the atoms were in constant motion. His disciple, Democrite of Abdere, took this idea and expanded on it. That they were invisible because of their small size, were solid, were surronded by empty space (to explain movement and density changes), had an infinite number of shapes, and were eternal, because they were perfect. The theory was not accepted by more notable philosophers of the time, including Aristotle, and the theory was ignored, left off to the side. In the meantime, the idea of the four elements - air, fire, earth, and water reigned.

The Greeks were not the only ones with this idea - there was also a philosophy in India, "Vaiseshika", which taught that matter was formed from indestructible particles, and that their assembly into visible, tangible objects were temporary, and that the assemblies would degrade. Eventually, their bonds would dissolve, the particles would need to rest, and then could reassemble into a new world. From the Bhagavad Gita:

"The phenomenal world or material world is also complete in itself because the twenty-four elements of which this material universe is a temporary manifestation are completely adjusted to produce complete resources which are necessary for the maintenance and subsistence of this universe. There is nothing extraneous, nor is there anything needed. This manifestation has its own time fixed by the energy of the supreme whole, and when its time is complete, these temporary manifestations will be annihilated by the complete arrangement of the complete. There is complete facility for the small complete units, namely the living entities, to realize the complete, and all sorts of incompleteness are experienced due incomplete knowledge of the complete."

Eventually, the theory came back into view, this time with experimental evidence to support the idea. In 1808, a book published by John Dalton, "A New System of Chemical Philosophy", revealed experimental conclusions that all atoms of an element had the exact same size and weight, and that all molecules were formed by simple ratios of atoms.

In 1869, russian scientist Dimitri Mendeleïev first constructed a table which classified elements according to their chemical properties. Eventually, this table would become the Periodic Table.

In 1897, Sir Joseph John Thomson made the first discovery that atoms were not indivisible, but also made up of sub-atomic particles, by discovering the electron. This was done using a cathode-ray tube, showing that the cathode ray was actually negatively charged particles smaller than an atom. His first proposed model of the atom was known as "Thomson's Pudding", or more commonly, the "plum pudding model" - as the model suggested that there was a sphere of positively-charged material, and that negatively-charged electrons were mixed into the sphere.

In 1911, Ernest Rutherford discovered the existence of the nucleus of the atom, due to an experiment that found that alpha particles sent into matter would sometimes reflect, and sometimes pass right through. He first explained the internal structure of the atom as a positively charged nucleus, surrounded by negatively charged electrons, which orbited the nucleus like planets orbiting a star, with an attractive electric force representing the role of gravity. The model was also called the "atomic planetary model". (See: Rutherford model of the atom)

In 1913, Niels Bohr expanded on this, as the previous theory hadn't been able to properly handle cases where electrons absorb and emit light. Bohr proposed the theory that electrons could only exist in certain orbital energy states around the atom, and that by jumping between orbits, they could absorb and/or release photons. (See: Bohr model of the atom)

In 1919, Rutherford refined the concept of the nucleus. He discovered the existence of the proton, and that the nucleus contained those protons. In 1932, Sir James Chadwick discovered the existence of the neutron as also existing in the atomic nucleus, which helped a lot with the theories of the atom - as up to that point, scientists couldn't explain the weight differences between different elements. The two particles were known as "nucleons".

Properties:

The atom is the smallest piece of an element that still contains all the properties of that element. All normal matter is made up of these elements. Currently, about 90 different atoms have been found to exist in nature, and about 118 (at last count) elements have been defined, with the difference being due to ones created in the lab in particle accelerators.

Atoms are very small - the smallest, the hydrogen atom, is about 10-8 cm in size - and most of the atom is empty space, between the nucleus, and the electrons.

Atoms are identified mainly by their "atomic number", or the number of protons in the nucleus. This determines the chemical properties of the element. The number of neutrons in the nucleus may also vary - the number of neutrons determines the isotope. The isotope may alter the stability of the atom, and different isotopes may react differently in nuclear reactions, but they don't affect the chemical properties. For example, there are three known isotopes of Hydrogen. The most common form, simply known as Hydrogen, has no neutrons. Deuterium, or heavy hydrogen, has 1 neutron. Adding a second neutron created Tritium, or ultra heavy hydrogen. Atoms have an "atomic weight", which is approximated by the number of nucleous in the nucleus.

Atoms have a number of electrons "orbiting" the nucleus. (Technically, they are more accurately described as a charged "cloud" around the nucleus, representing the most probable locations for the electron, but that's not truly important for basic understanding.) A neutrally charged atom has exactly the same number of electrons in orbit as it does protons in the nucleus, as the two have the same charge. If their is a difference between the number of protons and electrons, an atom is said to have a charge. If there are fewer electrons, the atom has a positive charge - known as a cation. If there are more electrons, the atom has a negative charge - known as an anion.

Two recent types of microscope, the Microscope Electronique à Transmission (or MET) and the tunnel effect microscope have allowed scientists to actually view individual atoms, making them no longer completely invisible. A special version of the tunnel effect microscope, the atomic force microscope, even allows scientists to deposit and move individual atoms - IBM recently used this to spell out their company name with individual Xenon atoms.

A technology on the horizon, molecular nanotechnology, offers the possibility of actually building machines directly out of individual atoms, instead of carving large pieces of matter to small size.

Sources:
History of the atom, http://www.neutron.anl.gov/hyper-physics/histatom.html
Atom History, http://perso.club-internet.fr/molaire1/e_histoire.html
Atom Development, http://members.tripod.com/~mrbeens/atom.html

Major General Panic's definition below still doesn't seem to match any Lisp (or Scheme) I've ever seen in use, in various subtle ways, so I prefer to keep this writeup. While it is shorter -- a fact that earns it downvotes -- I believe it to be correct.

Drawing on the Greek tradition, in Lisp, Prolog, most functional programming languages (and Scheme and Emacs Lisp and YAPL...), an atom is any ``indivisible'' entity, such as a symbol, number, character, ...

Contrast various "containers", such as lists, arrays and structures, which hold subobjects — they're divisible.

The question of whether NIL is atomic or not is great fun for the budding undergraduate philosopher/troll set.

In the k programming language, atom is the monadic case of @.

@x returns 1 if x is an atom, 0 otherwise; atoms are single characters, integers, floats (floating point numbers), symbols, dictionaries, null, and lambdas.

Non-atoms are vectors, arrays, and lists of all types.

Illustrated at the k command prompt (user input indented 2 spaces, results flush left):

  atomlist:(1;-1;0.0;.();_n;;`a;"a")
  atomlist
(1;-1;0.0;.();;;`a;"a")
  @atomlist
0
  @:'atomlist
1 1 1 1 1 1 1 1
  @1 2 3
0
  @"cat"
0
  a:3 2#!3*2
  a
(0 1
 2 3
 4 5)
  @a
0
  @:'a
0 0 0
  @:''a
(1 1
 1 1
 1 1)

The Atom syndication format is similar to Rich Site Summary (RSS). RSS and Atom are both formats designed to syndicate headlines or articles from websites or information systems, in a kind of format where you see (headline) (date) (author) (content). These are interpreted by either plugins to blogging systems, RSS aggregators, or RSS readers. They allow a kind of thin client model to browsing lots of sources of information quickly, without having to go through all of the stylistic decisions and heavier content of the main website. Atom is oriented more towards weblog syndication and its model of categories, authors, and integrated metadata, whereas RSS is more oriented towards web site headlines. You can think of Atom as the progeny of RSS, although Dave Winer, the author of RSS, would not agree. Atom was primarily engineered in order to provide more of a standards-based development process to the syndication format arena, providing a more open model than Dave Winer's single stewardship of RSS. They both are fundamentally similar in functionality.

Technically, Atom is attempting to bring some rigidity to the "everything's optional" world of RSS. It adds some structure and definitions to the content allowed in specific elements, whereas RSS aims to be as "undefined" as a specification can be, allowing more flexibility for the developer but less for the user in interpreting the data. It also simplifies the technical aspects of accessing an RSS feed, essentially saying HTTP is the protocol instead of the hodgepodge that makes up RSS (HTTP, XML-RPC, all the different RSS versions, the different blog APIs, etc).

Atom intends to provide specifications for, among other things,

  • Encoding content (how the data is interpreted by a program)
  • Internationalization (I18N, Unicode) - currently RSS is technically focused around ASCII only
  • Clear "plugins" and extensions, offering more features to the Atom format. Rather than RSS's attitude of "allow everything", Atom says, "Allow the base model, and if the user has these plugins loaded, do x with the data.
  • Simplifying the data model (same APIs for both syndication and blog updating), making Atom more focused around the data itself rather than XML-RPC/RSS's model of focusing around the delivery.

Atom's development is led by Sam Ruby and is/was also called by the names Echo and Pie.

Examples of RSS (as well as Atom) readers and systems include:

In LISP (and Scheme, and all of the other variants) an atom is one of the two major categories into which all S-expressions fall - the other being the dotted pair. This is the first thing that you'll learn upon picking up a copy of The Little LISPer or Schemer. At its simplest, an atom is an alphanumeric string which doesn't contain a parenthesis or the comment operator (usually the semicolon ( ; ) or double solidus ( // )). Consider the following examples:

n
is an atom, because it's a character.
42
is an atom, because it's a number.
abc
is an atom, because it's a string.
ATOMNUMBER75
is an atom, because it's a string of letters and numbers.
(+ 3 5)
is not an atom, because it's a list.
(chemical . compound)
is not an atom, because it's a dotted pair.

(atom? S)
This operator tests whether or not its input is an atom, although it is not standard in some interpreters. It's functionally the same as
(not (pair? S))
so it can easily be synthesized if you don't have it.

Atoms, being absolutely fundamental to the language, have been with us since the first LISP interpreter was made in 1959.

Thinking about atoms in biology

This is not an introduction to chemistry or even to atomic theories. It's an introduction to what atoms are with the aim of providing enough background to be useful for understanding molecular biology.

Introduction

"Nothing exists except atoms and empty space; everything else is opinion." (Democritus c. 400 BCE)

Atoms are the building blocks of the world. There are different atoms, which differ in their weights and the way they can interact with each other. So for example lead atoms are heavier than oxygen atoms. Different atoms can join with each other. For example, hydrogen atoms can attach to oxygen atoms to make dihyrodgen oxide - H2O.

Biologists don't normally need to think about individual atomic structures, and we don't need to know what they atoms made of. Instead, biologists normally think about atoms which join with each: molecules. In the example above three atoms (two hydrogens and one oxygen) combined to form a single molecule (H2O).

Biological chemicals you've heard of are molecules: proteins, vitamins, fats and cholesterols, DNA etc. These are all molecules that have been classified into types based on something peculiar to them. So proteins are made by cells and composed of amino acids (see below), but by contrast, vitamins have nothing in common on an atomic level and are classified as vitamins due to their dietary role.

It's worth getting some perspective on the scale we're talking about here. DNA is a huge molecule, and back of the envelope calculations ([link]) says that the amount of atoms in the DNA in a single human cell is 204 billion. That's just in one cell, and the human body is made of trillion of cells, and those cells are composed of heaps and heaps of molecules, not just DNA.

From atoms to molecules

Atoms that connect to each other form molecules. Most of the time, biologists don't need to know much about the molecules they work with. They just need to know what they do. It might be important to know whether a molecule is big or small, and whether it attaches itself to water or fats, and any other special properties it has.

An important type of molecule are proteins. Proteins are big molecules built out of small module molecules called amino acids. The important thing to know about amino acids is that because they're ubiquitous biologists are often quite familiar with them and their properties. But even though biologists are familiar with amino acids, most of the time it's not important to know what amino acids a protein is actually made out of. Instead it's important to know how the protein behaves. In cases when it's not known how the protein behaves then it might be helpful to know how it is expected to behave, based on its shape and the amino acids it's made of.

From atoms to proteins

You might know that two different proteins, for example Erk and Mek, interact with each other. The names of proteins often don't mean very much. What's more important is to think about Erk and Mek as two unique shapes and that their shapes are determined by their amino acids. You might also think about what actually happens when Erk and Mek interact, whether they exchange any atoms or whether they force each other to change shape.

Molecules are sometimes atoms connected in chains, sometimes as webs, and most of the time as a mixture of the two: long lines of linked atoms with other atoms coming off in various directions. But that's just their structure on paper. Their shape is far more complicated. Molecules can be envisioned as atoms (small balls) connected to each other by forces (sticks). But the connections aren't rigid and so molecules often fold in on themselves or wrap around themselves to form complicated shapes.

Amino acids are small molecules that connect to each other in a line. But once that line is made they squiggle around themselves to form a unique structure that is very important to their function. Their structure determines which atoms are facing outwards and can touch other molecules, and also determines their shape, allowing them to do things like latch onto other proteins.

Final notes

Atoms like hydrogen, carbon, nitrogen, oxygen, and others are important building blocks of the world. When atoms join one another they form molecules, and there is a special list of molecules called amino acids that join together to make up proteins.

What I've written above is sufficient for a basic biological understanding. But of course the more you know the better. A background in organic chemistry might help you predict what a change in conditions (e.g. pH or redox potential) might have or how different molecules may interact. A familiarity with amino acid chemistry helps understand the shapes and activities of proteins. Some amino acids are known to act as disruptors of beta-sheets while other offer potential for forming reducible bonds. And of course, not everything is organic chemistry, and an understanding of ions and inorganic compounds can be valuable.

 

Caveat: References: Myself and some google.

At"om (#), n. [L. atomus, Gr. , uncut, indivisible; priv. + , verbal adj. of to cut: cf. F. atome. See Tome.]

1. Physics (a)

An ultimate indivisible particle of matter.

(b)

An ultimate particle of matter not necessarily indivisible; a molecule.

(c)

A constituent particle of matter, or a molecule supposed to be made up of subordinate particles.

⇒ These three definitions correspond to different views of the nature of the ultimate particles of matter. In the case of the last two, the particles are more correctly called molecules.

Dana.

2. Chem.

The smallest particle of matter that can enter into combination; one of the elementary constituents of a molecule.

3.

Anything extremely small; a particle; a whit.

There was not an atom of water. Sir J. Ross.

 

© Webster 1913.


At"om, v. t.

To reduce to atoms.

[Obs.]

Feltham.

 

© Webster 1913.

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