Let's continue our exploration into the obstacles the first living cell faced, according to the Theory of Evolution. We already know that there's not really much of a place to get the right chemicals to react in the first place. But let's give the Theory of Evolution's origin-of-life story the benefit of the doubt for now. What are the next steps?
Two types of molecules are necessary for a cell to survive: DNA (made up of nucleotides) and proteins (made up of amino acids). To make DNA, you can't just have any old line up of nucleotides. DNA contains information. The order must code for the features of the cell, and even for proteins that (when translated) must work somehow in maintaining or regulating the cell.
Making a protein is tricky too. There are actually several "levels" to protein structure. Primary structure is the line-up of amino acids, their order. Secondary structure includes a little bit of folding with what are called hydrogen bonds (hydrogens on one part of the protein will be attracted to and form a weak bond with nitrogen or oxygen atoms on other parts of the protein). If the amino acids aren't ordered right, the hydrogen bonding will cause the folding to come out all wrong. Then there's tertiary structure, in which a protein is folded again into a three-dimensional shape. (To make things even more complicated, other proteins are involved in folding new proteins to their tertiary structure). Some proteins even have a quaternary structure - two or more tertiary-folded proteins are linked together to form a single giant protein.
Once again, if anything is off in the amino acid chain (primary) or folding from hydrogen bonding (secondary) the tertiary (and quaternary) structure will be out of whack, and the protein will be useless.
But it can be hard to get amino acids to react properly to get just the right order and shape to the protein. First of all, each of the twenty different amino acids in life's proteins has a different reactivity.
Reactivity: how quickly a molecule reacts. In this case, how quickly an amino acid links up in a growing protein chain.
If you mix a bunch of amino acids up and have them start randomly reacting together, the most reactive amino acids will link up first. The last amino acids on the chain will always be the least reactive. In other words, you'd end up with a chain of amino acids following a nice little gradient of fastest-reactors to slowest-reactors. And guess what? Real-life proteins are not ordered in any way by their amino acid's reactivity.
(What about in a cell that's already 'been made?' How can amino acids there get linked together in specific orders that counteract how fast each one wants to react? Well, there are lots of other things in the cell - ribosomes, RNA, and still more proteins - that regulate this process of making a new protein).
Another problem is that there are actually more than one places where you can add the next amino acid. You can add it to one end, or the other end. Plus, there are two corners on each end to choose from. Only one of those places will get you the wanted protein, mind you. Add it on the wrong place and you've got the wrong protein.
Other organic molecules behave in much the same way. We call such molecules isomers.
Isomers: molecules with the same chemical formula but different shapes.
Consider glucose and fructose. Both have six carbon atoms, six oxygen atoms, and twelve hydrogen atoms. But they are totally different sugar molecules simply because they arrange their atoms in different ways.
The same can be said for proteins. Proteins can have isomers. Two proteins might have the very same amino acids in their chains, but if added in the different places, you'll end up with an entirely different protein. If amino acids are randomly reacting, there is no telling where they will add to the newly forming chain, and the chances are even smaller that they'll line up in just the right way (again, living cells can generate proteins the right way here because they regulate their formation with other proteins).
Finally, many organic compounds (including amino acids and nucleotides) are chiral.
Chirality: the "handedness" or mirror-image nature of two separate molecules.
In other words, you can have two amino acids that are alike in every possible way. It's just, they're totally distinct types from each other because they're actually mirror-images. Compounds in living cells are chiral. In fact, taking the wrong chiral mirror-image of an organic compound (like Tylenol) can be harmful, since the mirror-image molecules are actually toxic to life. If you have a chain of amino acids randomly reacting, and just one amino acid hops on with the wrong chirality, the entire protein chain is toxic to life.
Also - you know that lovely double-helix shape of DNA? It only works because each nucleotide in the DNA chain is the right chirality. Add a nucleotide of the mirror-image, "evil twin" chirality, and the DNA chain is ruined. No life. At all.
So, can amino acids and nucleotides react randomly such that the evil twin chiral compounds aren't in the picture? Actually, no! Natural chemical reactions generate half-and-half mixtures of each "twin." The only way to get around that is to work in a lab. A scientist can provide a special chiral surface that selects for only one type of chiral product in a reaction. But guess what? That has never been observed in nature.
So random, natural processes - the exact kind of processes the Theory of Evolution relies upon, as a naturalistic theory - can't provide a single organic protein or DNA strand for it's first living cell. Random processes determine a set order that's useless for life. Randomness allows amino acids to be added to the chain in any which-a-way, making it harder to get the right protein. And natural reactions always result in a 50/50 mixture of good and bad chiral twins, making it downright impossible to get a protein (or DNA strand) that's nontoxic to life.
Once again, living cells get around all these processes because of the regulation of pre-existing proteins and genetic material (i.e. DNA) in the cell. Life - even a tiny, "primitive," bacteria-like cell - is extraordinarily complicated. To try and get one from non-living things is to through yourself into a cul-de-sac of irreducibly complex, interconnected proteins, DNA, and ribosomes. And tRNA, mRNA, a mitochondrion somewhere to provide the energy to let it happen in the first place . . .
Life can come only from life. Naturalistic, observational science we can study in a laboratory does not provide the circumstances necessary to get a living cell. The Theory of Evolution fails abysmally in explaining this first crucial step.
References (for all three):
McCombs, C. 2004. Evolution Hopes You Don’t Know Chemistry: The Problem of Control. Acts & Facts. 33 (8).
McCombs, C. 2004. Evolution Hopes You Don’t Know Chemistry: The Problem with Chirality. Acts & Facts. 33 (5).