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At the simplest level, we're all just atoms, animals, plants and humans alike. But what I don't understand, is how a particular arrangement of atoms such as us can become self aware, and be able to not only understand our environment, but manipulate it to our will? How is that even possible?

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closed as too broad by WYSIWYG, Cornelius, daniel, Bez, The Last Word Jun 8 '14 at 14:11

There are either too many possible answers, or good answers would be too long for this format. Please add details to narrow the answer set or to isolate an issue that can be answered in a few paragraphs.If this question can be reworded to fit the rules in the help center, please edit the question.

well, we have to not think of the atoms themselves. It's the macrostructure that is more important, the cells themselves. It is the interaction of cells that make us self-aware, as they are able to communicate via Cell Signalling. It is like thinking of a computer, it is just a bunch of transistors really, and on their own they are not capable of calculating, but together they form a computer. You have to think of an object/organism as the sum of it's parts – J_mie6 Jun 8 '14 at 11:00
this belongs in a philosophy forum :P – WYSIWYG Jun 8 '14 at 12:46

You are skipping too many steps.

$Atom \rightarrow \color{red}{molecule \rightarrow structure \rightarrow cell} \rightarrow organ \rightarrow organism$

The following is a proposed speculation regarding the steps in red on the above:

How life originated and how the first cell came into being are matters of speculation, since these events cannot be reproduced in the laboratory. It was first suggested in the 1920s that simple organic molecules could form and spontaneously polymerize into macromolecules under the conditions thought to exist in primitive Earth's atmosphere. At the time life arose, the atmosphere of Earth is thought to have contained little or no free oxygen, instead consisting principally of $CO_2$ and $N_2$ in addition to smaller amounts of gases such as $H_2$, $H_2S$, and $CO$. Such an atmosphere provides reducing conditions in which organic molecules, given a source of energy such as sunlight or electrical discharge, can form spontaneously. The spontaneous formation of organic molecules was first demonstrated experimentally in the 1950s, when Stanley Miller (then a graduate student) showed that the discharge of electric sparks into a mixture of $H_2$, $CH_4$, and $NH_3$, in the presence of water, led to the formation of a variety of organic molecules, including several amino acids.

enter image description here

Although Miller's experiments did not precisely reproduce the conditions of primitive Earth, they clearly demonstrated the plausibility of the spontaneous synthesis of organic molecules, providing the basic materials from which the first living organisms arose.

The next step in evolution was the formation of macromolecules. The monomeric building blocks of macromolecules have been demonstrated to polymerize spontaneously under plausible prebiotic conditions. Heating dry mixtures of amino acids, for example, results in their polymerization to form polypeptides. But the critical characteristic of the macromolecule from which life evolved must have been the ability to replicate itself. Only a macromolecule capable of directing the synthesis of new copies of itself would have been capable of reproduction and further evolution.

Of the two major classes of informational macromolecules in present-day cells (nucleic acids and proteins), only the nucleic acids are capable of directing their own self-replication. Nucleic acids can serve as templates for their own synthesis as a result of specific base pairing between complementary nucleotides. A critical step in understanding molecular evolution was thus reached in the early 1980s, when it was discovered in the laboratories of Sid Altman and Tom Cech that RNA is capable of catalyzing a number of chemical reactions, including the polymerization of nucleotides. RNA is thus uniquely able both to serve as a template for and to catalyze its own replication. Consequently, RNA is generally believed to have been the initial genetic system, and an early stage of chemical evolution is thought to have been based on self-replicating RNA molecules—a period of evolution known as the RNA world. Ordered interactions between RNA and amino acids then evolved into the present-day genetic code, and DNA eventually replaced RNA as the genetic material.

The first cell is presumed to have arisen by the enclosure of self-replicating RNA in a membrane composed of phospholipids.

enter image description here

Phospholipids are the basic components of all present-day biological membranes, including the plasma membranes of both prokaryotic and eukaryotic cells. The key characteristic of the phospholipids that form membranes is that they are amphipathic molecules, meaning that one portion of the molecule is soluble in water and another portion is not. Phospholipids have long, water-insoluble (hydrophobic) hydrocarbon chains joined to water-soluble (hydrophilic) head groups that contain phosphate. When placed in water, phospholipids spontaneously aggregate into a bilayer with their phosphate-containing head groups on the outside in contact with water and their hydrocarbon tails in the interior in contact with each other. Such a phospholipid bilayer forms a stable barrier between two aqueous compartments—for example, separating the interior of the cell from its external environment.

The enclosure of self-replicating RNA and associated molecules in a phospholipid membrane would thus have maintained them as a unit, capable of self-reproduction and further evolution. RNA-directed protein synthesis may already have evolved by this time, in which case the first cell would have consisted of self-replicating RNA and its encoded proteins.

Source: Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. The Origin and Evolution of Cells. Available from:

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