My very basic understanding is that it is something to do with the speed the atoms vibrate, but like a static-filled tv screen, it’s all very fuzzy.
If you can do it without referencing The Holy Ghost, all the better. 
The only difference between them is the molecules that they’re part of. Carbon, in particular, forms chains; if the chains are long enough, they can form loops, rings, branches, and more complex structures. Most important, there is room on the carbons in a chain to hold other atoms – hydrogen, oxygen, nitrogen, phosphorous, sulfur, and more – all of which create subtle variations on the basic structure, generating a vast variety of massive molecules which take part in a staggering array of chemical and physical interactions, including energy transfer, construction and destruction, replication, and all the rest of life’s processes.
In my understanding, there is no difference. But according to an insufferable hippy I once knew, atoms and molecules in inorganic matter “don’t have a soul”.
OK, having read the absurd and very nearly ptolemaic screed in your link, I can answer more succinctly.
The difference is in the arrangement of molecules, the maintenance of that arrangement, and the orderly propagation of certain changes in that arrangement.
There is no difference in the atoms in organic and inorganic matter. A carbon atom inside you is exactly the same as a carbon atom inside your pencil.
The reason why you are animate and your pencil is not is because you atoms are arranged in the correct way to be animate. Pretty much like the difference between a functioning car and a lump of iron smeared with petrol.
There are two meanings of “organic” in common use that are relevant to this question. One meaning is that life is involved. For example if somebody says a crop was organically fertilized they would be implying that the fertilizer came from animals or silage or compost, not from a chemical plant. The other is that carbon is part of the chemical compound. For example if you sign up for a course in “organic chemistry” you will be studying compounds of carbon.
The atoms don’t behave any differently by either of these meanings, except that in the second meaning some of the atoms by definition have to be carbon atoms.
Actually, not all carbon compounds count as organic (in the chemical sense). For instance, carbon dioxide gas, and carbonates, such as bicarbonate of soda and carbonate rocks such as limestone and chalk (both mainly calcium carbonate) are considered inorganic. Generally speaking, tor something to count as an organic molecule, it needs to contain carbon atoms linked to other carbon atoms in a chain or ring. (An exception to this rule is methane, CH4, whose molecule has has only one carbon atom. It generally counts as organic because it is closely related in its structure and properties to other hydrocarbon molecules that do have chains of multiple carbons. Formic acid is also a molecule with one carbon atom that counts as organic for similar reasons. There may be a few others.)
Anyway, the answer to the original question, as others have already pointed out, is that there is no difference in the atoms themselves whatever.
This is like assuming that the Legos used to build a space ship are different from the Legos when they’re still loose pieces in the box. Or like assuming that bricks used to build a church are different from bricks used to build a wall.
It’s not the atoms (or the Legos or bricks) that change. The function of the overall structure changes based on the structure itself without any changes in the building blocks. Build a protein, you get protein. Build a rock and you get a rock.
Just to make the point clear, there’s no inherent difference in vibration speed of the atoms in living vs. inanimate matter. Where did that idea come from?
Good luck building a rock out the atoms from protein. You could get a little bit of rock, but you are are going to have a lot of hydrogen and carbon left over. (Well, I guess the spare carbon could be graphite or diamond, which are sort of rock.)
Obviously you’d have to buy the right Lego kit for the structure you intended to build.
Okay, first: the matter of the Universe is predominantly hydrogen and helium, with traces of the other elements present. The terrestrial planets, asteroids, etc., are aberrances from the Universe at large, where enough of the heavier elements have coalesced to form a macroscopic entity but with insufficient gravitation to retain much of the Big Two.
Matter can exist in the form of metals, ionic crystals, glasses, ores, etc. Each of them has a specialized physical chemistry distinct from that of organic matter. In addition, some inorganic compounds bond covalently, in a manner similar to that of organic matter.
Carbon is unique among the elements in its ability to bond covalently to itself and other elements, with the carbon-carbon bonds forming the ‘backbone’ for a wide array of organic chemicals. Almost all of every living thing is made up of these carbon-chain organic chemicals. (Some protists, plants, and animals have formed the ability to absorb, and then secrete a protective covering or support structure of, some inorganic compounds – human bones are hydroxyapatite, calcium phosphate hydrate, for example, and some shells are composed mainly of calcite, calcium carbonate. Also, organisms with internal fluid flow (blood, sap, etc., are likely to have ionic electrolytes such as sodium chloride present in those fluids. But with these specialized exceptions to one side, the generic statement about carbon-chain-based chemicals is true.)
All organic chemicals, the building blocks of life, are composed of this carbon-chain ‘backbone’ with hydrogen and in most cases oxygen attached to it. Proteins also have nitrogen and sulfur present, and some compounds essential to life as we know it, such as DNA, RNA, ADP, and ATP, also include a phosphorus atom. These six elements are the key to the chemistry of living things. Other elements will be present in some compounds – chlorine, iron in hemoglobin, and cobalt in Vitamin B-12 come quickly to mind – but they are incidental to the majority of bioogical functions. Because carbon is able to produce these long chains, which have differing characteristics according to their length and what is bonded to them, there is an amazing array of organic compounds: methane, natural gas; ethyl mercaptan, eau de skunk; chlorophyll, C[sub]55[/sub]H[sub]72[/sub]O[sub]5[/sub]N[sub]4[/sub]Mg; stearic acid, the basis for soaps; trinitrotoluene, TNT; phthalocyanine, a blue pigment; hemoglobin; and quite literally over a million other compounds, most of them closely related to living things.
If you were to compile a list of ‘chemicals’ in the broad sense, ranging from helium atoms to the protein present in beef stock, well over half of them would be organic chemicals – covalent carbon chains with ‘other stuff’. mostly hydrogen and oxygen, attached. Things such as thorium oxide, dysprosium suplhate, and calcium potassium silicate, would be in the minority, even though they constitute the majority of the list of elements.
I love this place.
Understatement of the decade. The inorganic chemicals would only come anywhere remotely close to half if you first considered only those compounds which have been named and studied, and then further lumped together huge classes of different but closely related organic compounds and called them all by the same name. Heck, there are probably more distinct compounds called “paraffin” than all inorganic compounds combined, not even to mention the incredibly vast number of compounds we lump together under, say, the name “DNA”.
Please get one with a red 2-by-8 hinge piece.
I lost one of mine, and now I can’t build the planet Mars.
This isn’t so unique - silicon, for instance, does exactly the same thing - most every non-carbonate rock is built of a staggering array of silicate minerals of various forms. Unfortunately, the energy/timescales required for Si chemistry to duplicate those aspects of C chemistry that we think of as “life” is much greater, which is why life (here, at any rate) is C-based.
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Not true - Silicon does this too.
I think you’re both grossly underestimating the number and variety of silicate minerals out there, especially with all the possibilities that solid solution allows. While conventional classification lists some 4-5000 minerals, these are better thought of as groups.
Yeah, I was overlooking silicon. Let’s say instead, then, that the number of paraffins is greater than the number of compounds without carbon or silicon: I think I’m on pretty safe ground there, unless there’s some other chain-forming atom I’m overlooking.
For the record, I’m considering two hydrocarbons with the same number of C and H but with different branching structures to be different. You can come up with a heck of a lot of different branching structures with, say, 40 carbons.
Point taken about Silicon. Though to nitpick, my understanding is that the carbon chain:
…-CH[sub]2[/sub]-CH[sub]2[/sub]-CH[sub]2[/sub]-CH[sub]2[/sub]-CH[sub]2[/sub]-…
is not paralleled by a silicon sequence:
…-SiH[sub]2[/sub]-SiH[sub]2[/sub]-SiH[sub]2[/sub]-SiH[sub]2[/sub]-SiH[sub]2[/sub]-…
but rather by a silicate sequence:
…-SiH[sub]2[/sub]-O-SiH[sub]2[/sub]-O-SiH[sub]2[/sub]-O-SiH[sub]2[/sub]-O-…
However, your point about energy/timescale considerations helps explain why one can make the organic/inorganic distinction.
I don’t think overlooking silicon is such a big deal in Chronos’ statements. Just look at the enormous variations possible with just two carbons. Ethane, ethene, ethanol, thioethanol, ethanoic acid (acetic acid), ethanoyl, chloroethane, dichloroethane (which of course has 1,1 and 1,2 variations), trichloroethane (which has 1,1,1 and 1,1,2 variations), bromoethane (which also has dibromo and tribromo variations), chlorobromoethane, nitroethane… I’m not even scratching the surface here.
When you get up to something like 40 carbon molecules, I’m not sure that our best computers could calculate every single possibility.
And then there’s DNA… which, just in humans, has 6 billion living possibilities.