second, before i start, i want to give a disclaimer: i am NOT a molecular biologist, nor have i spent any particular amount of time studying evolution. therefore, my answers aren't going to be perfect by a long shot. but i still know a lot of the thought behind this stuff (and have at least the backbone of an education in these fields), so i can give a shot at explaining where these authors went wrong.

i guess i'll start with answers to your questions, then discuss some excerpts from the linked website to apply some of the general ideas discussed in my answers.

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"Are amino acids required to produce proteins?"

Definitionally, yes. A protein is a molecule comprised of a large number of amino acids joined by peptide bonds.

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"How high are the probabilities (or improbabilities) for amino acids to combine to produce proteins spontaneously? I assume that proteins are necessary for cell structure, therefore, how high are the probabilities for proteins to spontaneously combine to form a simple cell?"

I can't give you a number, but I can tell you that the numbers reported on that website are woefully inaccurate for two big reasons: 1) they assume a singular end-product must be reached, which distorts their calculation beyond repair, 2) they grossly exaggerate the importance of exactitude within the order/type/etc of each amino acid. i'm going to discuss each of these in detail, separately, below, because both concepts are so important to where their calculations became inapplicable.

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Examining the first point, there is a huge irony in their calculation, which is that it revolves around an assumption that only someone who believed in intelligent design would make: the proper calculation to make for "whether evolution could have occurred" is to calculate the odds of the spontaneous generation of the proteins that actually DO exist.

What am i getting at?

The idea of evolution is that those iterations of chemicals which reproduce themselves best will, definitionally, be the ones that continue on. Intuitively, the environment will "decide" which chemicals/compounds/cells/organisms/etc whether a certain iteration is "fit" to "survive."

These authors make an implicit assumption about what is needed to "survive" -- namely, the specific proteins that we are made of are the ONLY proteins that allow survival. But this is false at many, many levels. Let's look at a few of the ways in which this assumption is indefensible.

First, we can look at our own species. Somehow, the authors don't realize a fact about that the human population, as it currently lives, breathes and reproduces, that absolutely everybody knows: There is great diversity in proteins across the species. Surely, you're aware of this already -- it's the basis of inheritance (getting green eyes from your mom, balding from your grandfather, etc, etc).

Why is this important? Well, if you're going to claim we "need" specific proteins -- rather than a RANGE of potential proteins -- to survive, then it doesn't make much sense for there to be five or six types of proteins coding for specific types of dopamine receptors or calcium channels or hair pigments or nearly everything else. The fact that we are actually allowed a range of proteins loosens up the calculations significantly.

But let's not stop at humans -- what about all other species? Simply put, there are many, many ways of solving some of the environment's obstacles. Giving an example at the organ level (because speaking in proteins is too abstracted from what I'm talking about, though those examples abound as well), examine the problem of vision. for any organism capable of movement, visuo-sensory information is hugely important to survival, so the development of some photon-detecting device is critical. Interestingly, the types of eyes that exist in nature vary tremendously across species, from the "human" eye, to the compound eyes of arthropods, to the omatidia of horseshoe crabs, to the ocelli of snails, to the stemmata of caterpillars.

The point? A simple yet complex problem -- light detection -- can be solved in multiple ways. Similarly, the supposed "solutions" the human proteome has offered to "surviving the environment" is far from the lone solution to the problem.

The important takehome point from all of this is the abstraction to be gained from it, because that's where their numbers REALLY fall apart. The real message is that the species could have evolved in millions of ways. Indeed, the "construction" of humans is deeply flawed (which is why many scientists get paid -- to "fix" some of the flaws in the body!) , but it is the result of random events, constrained by biochemical mechanisms and evolutionary forces, built over billions of years so that certain "paths not taken" became forever closed off to the entry of life.

Theoretically, however, there are MANY other possible paths by which "living organisms" (defined however you want to define it, but, to leave open the broadest number of "potential pathways," we can say merely defined by the ability to reproduce, meaning this "life" needn't even be carbon-based) could survive to create similarly constructed progeny (the basis of evolution).

Once we realize that the "chances of evolution" require only that SOME path was taken that created life, and not a SINGULAR path that describes precisely what DID HAPPEN, you realize the probabilities given in this paper are meaningless. They do indeed describe SOMETHING: the probability that, for example, any particular protein that does exist WILL exist. But that doesn't describe what is needed for evolution.

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On to the second point: The authors exaggerate the degree to which exactitude in amino acid sequence is necessary for proteins.

Let's look at these two quotes from the author:

"The crucial point is this. The absence, addition, or replacement of a single amino acid in the structure of a protein causes the protein to become a useless molecular heap."

"Of all of these possible sequences, only one forms the desired protein molecule. The rest of them are amino-acid chains that are either totally useless, or else potentially harmful to living things. "

These two statements are simply false.

First of all, in most proteins, there are only a few "key" cites where the action takes place. The rest of the amino acids provide stucture for the protein. Though the same basic number of amino acids must be present, and there are many places within the structure that changes would render the protein useless (or else EVOLUTIONARILY ADAPTIVE in rare examples, something which the authors don't mention as an alternative in the second quote, for obvious reasons), it is also true that major section of a protein are literally irrelevant, other than that they be filled in with SOME amino acid, so as to provide length in the creation ultimate creation of the protein's tertiary structure.

Second, EVEN WITHIN CRITICAL SITES, it is often true that amino acids with similar properties (similar polarity, similar sterics, similar functional groups that can create similar bonds, etc.) can be substituted with the "normal" amino acid.

Often, these substitutions occur without any noticeable effect to performance of the protein whatsoever. Other times, these differences account for the variation across a species, as discussed above (for instance, the difference in D4 dopamine receptors that is correlated with varying levels of "risk-seeking" behavior, a pop-culturally famous example).

In fact, scientists manipulate amino acid sequences in laboratory settings as a living: transgenic animals are based on the fact that we can interchange critical region of a protein with a new series of amino acids, and the animal will live at least long enough to observe the differences in behavior.

Basically, as stated in my first bulletpoint, the attempt to calculate a probability here for "the chances of life" is probably hopeless and pointless. BUT, even if you were, the number these authors calculated is monumentally exaggerated by a false assertion about the specificity by which each protein needs to be created. If we allow for greater freedom in the calculation, that probability increases tremendously.

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"Have any of these two conditions between artificially produced in a lab or have they been observed in a lab?"

Spontaneous production of life? Hell no.

Then again, it took billions of years of random trials before multi-celled organisms emerged, so I think you're a little impatient if you think 40 years of research should have produced results already.

The creation of a cell is not as complicated as these authors make it sound. We have created many elements of a cell on our own, and used machinery already in a cell to do the rest of the work. We have synthesized individual pieces on our own all the time.

As best I can tell, the authors are saying, "Unless we recreate evolution in a single experiment, it can't have happened," but this makes no sense.

As the authors discuss at LENGTH while DISCOUNTING experiments WHICH HAVE created the beginnings of "spontaneous" proteins, the environment under which "life" began was drastically different than the one today. Though we're making rough attempts to mimic it in the laboratory, surely we're missing tons of critical elements of the conditions on Earth 4 billion years ago. If the authors discount the CREATION of amino acids under inexact conditions, surely they too realize that it would be futile to EXPECT the creation of amino acids UNLESS we DO create the correct conditions.

Furthermore, as stated above, the authors are trying to convince you that our inability to mimic several billion years of evolution over a 40-year period (a period during which, mind you, we are STILL in what could be considered an infancy) is PROOF that we will never be able to create these conditions. This is utterly absurd.

Actually, the authors are guilty of this line of reasoning throughout. Take the headlines to one of their pages: "DNA Cannot be Explained by Non-design." On this page, they give SCIENTIST'S complaints about the failures of current theory to give a fully satisfactory picture of how DNA evolved. The authors want to use this as evidence that, since we currently have no explanation of all the fine points in DNA evolution, we must, by default resort to non-design.

The first error in this logic is, of course, that it assumes "design" a default, without giving any evidence whatsoever that "design" DOES explain DNA.

More importantly, it assumes we will NEVER have an explanation of these current puzzles. After 40 years of research. Really?????

There are so, so many things we have studied for much longer than 40 years -- even really simple questions. Surely these authors don't propose we stop research on all open issues today and proclaim that "science has no answer to the cause of autism, or the cure for cancer, or how it is Prozac cures depression -- henceforth, all answers should be attributed to the unattributable."

More generally, I found the article quite odd for quoting so many so-called "evolutionists." The authors used this as a sort of "caught you guys slipping up!" technique, quoting them for things they've said about improbabalistic events, or pointing out discrepancy between competing theories, etc.

However, all of those quite-intelligent and extremely-well-versed-in-their-fields people is STILL a proponent of evolution. Isn't this ODD? That THEY would point out that something is improbable, yet STILL stick with the theory.

To me, this makes two points:

1. Many of these quotes are taken out of context. Or, I would guess, many times right BEFORE the context where the scientist goes on to make a hypothesis about how some of these improbabilities and/or contradictions might be resolved. Obviously, the authors didn't like the answers these scientists gave, but it's pretty disingenuous to quote them in this manner as if they're SUPPORTING your assertion that the problems are intractable when, in fact, these individuals DO NOT believe that.
2. Far from being intractable, these are the very problems scientists are currently working on. Unlike the slightly-conspiracy-theory-ish tone of this article, scientists actually LOVE to figure out what hasn't been figured out already. That's how you get famous as a scientist. Making a ground-breaking discovery to "disprove" evolution would be ENORMOUS for a scientist's career. But such "disproof" doesn't exist.

Actually, I'm still baffled by how the authors resolve their theories about what the evolutionists they quote are motivated by. These evolutionists: 1) really know what they're talking about within their fields, 2) have every incentive to find the truth, evidenced by their even-handed criticism, and 3) still believe in evolution. Yet the authors believe, what???? That these evolutionists have an agenda, yet let slip "the truth" in moments of weakness, then try to "cover up" their slip-ups by proposing more flawed theories, that someone these authors (and not well-trained scientists) are able to see through? Doesn't make much sense to me.

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Now to examine a few points the authors make, just to discuss a few more points on the subject, and also to show a little application of these ideas.

"Thus, the first cell on earth was necessarily a complete cell possessing all the required organelles and functions, and this definitely means that this cell had to have been created."

This just isn't true. "Irreducible complexity" has no teeth. There is no reason smaller pieces of a cell couldn't have been adaptive separately. The combination of these pieces to CREATE a cell was simply a superiorly-reproducing machine, and thus it spread more quickly.

Further, we can only hypothesize what the first cells did actually contain (f.y.i., they were NOT complete, according to an evolutionary account). The number of changes that have occurred within cells over time are doubtlessly tremendous. And they CERTAINLY adapted dramatically right around the time when they were first formed -- the creation of a cell from all its component parts quite obviously provided an environment where all kinds of new and different proteins would be more or less adaptive.

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"Evolutionists claim that molecular evolution took place over a very long period of time and that this made the impossible possible."

True. But these authors also ignore the other point about early evolution, which is that it occurred in extremely rapidly reproducing single-celled organisms. The number of "trials," and thus, the chances for potentially positive mutations, is immense.

Of course, this refers to a point past the formation of the first cell. BEFORE the creation of a cell, we're talking about the time it takes for certain chemical reactions to take place. Again, I think we're talking about a LOT of permutations.

And, yes, there is a trial-and-error mechanism, which the authors deny. There is certainly NOT "irreducible complexity" in an amino acid chain, right?

Well, only chains that create other adaptive chains will survive.

When a random reaction occurs that allows for a better chain to exist, then that one reproduces more.

The next step will only occur when an even better chain comes along.

The point at which chains can start connecting is when some fortuitous combination of chains creates a more fit combination of chemicals.

The authors again assume that what these chemicals had to create was "us." Instead, "we" are created within the framework of how chemicals came together. Quite obviously, combinations of structure that were able to survive/reproduce are the only ones that DID survive/reproduce. But our bodies are quite limited by how these chains DID decide to randomly link up, and the limited options those chains had for what step was feasible to take next and still survive.

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"If even a single right-handed amino acid gets attached to the structure of a protein, the protein is rendered useless....The question of how proteins can pick out only the left-handed ones from among all amino acids, and how not even a single right-handed amino acid gets involved in the life process, is a problem that still baffles evolutionists. Such a specific and conscious selection constitutes one of the greatest impasses facing the theory of evolution."

This is drivel. It's entirely irrelevant. Here's why:

IF, at the time we evolved, there WERE right-handed amino acids creating the protein backbone, they would NOT be "rendered useless."

There is nothing "magical" about left-handed AAs. They are simply the type of AA that we evolved with. GIVEN that we evolved around protein structurally based upon left-handed AAs, it is unsurprising that their inclusion in a protein would be deleterious to function. This point is merely a reiteration of the earlier exaggeration that substitution of amino acids leads to protein malfunction.

Let's pretend, now, that right-handed AAs WERE involved in our evolutionary process. Would this create any intractable problems? None that I know of. Structure of proteins would simply have to be made from different sequences of amino acids in order to create the same result. We could also create NEW structures, having new options for which amino acids we can use.

An analogy to see what I'm getting at: Pretend earth had no oxygen but instead was covered in carbon monoxide gas. Would life survive? Not as we know it: Our bodies are built to run on oxygen. But what if we'd EVOLVED with carbon monoxide? Here, we might have an entirely different circulatory system, and a different means for energy production, that could use CO as fuel. There's no reason a machine couldn't be built to operate that way; it's just the one we've already built can't do it. Similarly, it's not surprising you can't substitute RH AAs for LH AAs and not expect it to be catastrophic (you ARE changing the tertiary structure of a protein much, much more than you would be with any other LH AA substitution).

These authors want to ask HOW DO WE select just LH AAs, but that question of how is unnecessary, since we'd be fine if there were RH AAs. An interesting question is how did it happen originally, of which their are many relatively unestablished theories (some positing that this selection was entirely random, others taking guesses as to why). Of course, how it CONTINUES to happen isn't a question for anybody: Our DNA specifies it.

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"Yet there is no natural selection mechanism which can identify that a right-handed amino acid has been added to the sequence and recognize that it must therefore be removed from the chain."

This is: 1) misleading, and 2) untrue even if it weren't.

It's misleading, because it discusses "natural selection mechanisms" when I think it actually means to be discussing "mechanisms within the body." Namely, are there enzymes that would tell you if there were a RH AA within the protein? The answer is, yes, and they will stop production/make corrections/etc if there is one.

Second, RH AAs should never be randomly added to a protein chain, since our body doesn't specify for them. That's like saying, "Our body could randomly add a fluorine atom when it means to add an amino acid." RH AAs are not "the same but a little bit different" from LH AAs. They are completely different chemicals. Furthermore, they aren't naturally produced by our bodies. So how would an RH AA end up in a protein chain any more than every other chemical on the planet capable of bonding with amino acids?

Then we examine the second point: that there's no evolutionary mechanism. Well, of course there is -- these authors have totally contradicted themselves.

One minute ago, they said having RH AAs causes instant death. Now they're saying that evolutionary forces wouldn't create mechanisms to AVOID the incorporation of RH AAs?????? These guys clearly don't know the first thing about evolution.

If something kills an organism instantly (namely, before reproductive age), there is TREMENDOUS evolutionary pressure that preserves only those species which DON'T do that thing.

To be specific, if accidental incorporation of RH AAs into 10% of proteins causes an animal to only make it to reproductive age 50% of the time, a mutation in an enzyme of that animal which better prevents against these accidents will have a HUGE "fitness" advantage.

If these authors wanted to claim that "no evolutionary mechanism existed," they would have to show that it had ABSOLUTELY ZERO EFFECT for an RH AA to be incorporated into a protein. At this point, it would be mere coincidence that chains were entirely made of LH AAs, and we would question how such a bizarre event occurred, given that it would be completely by chance and unregulated. But the authors argue, quite to the contrary, that this regulation is necessary for survival. They completely shot themselves in the foot, here.

(Alternatively, the authors could have argued that no mechanism exists by which the body actively avoids incorporation of RH AAs, and thus evolution couldn't be acting on anything. But this is untrue.)

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"That is, when we consider a protein made up of 400 amino acids, the probability of all amino acids combining among themselves with only peptide bonds is 1 in 2399."

The thing is, this isn't random. Machinery exists that ENSURES peptide bonding inside cells, meaning this shouldn't be a probability calculation at all.

Of course, I assume they're mainly discussing bonding in the pre-cellular environment. The thing is, we have only slight clues the chemical structure of proteins back then was, or how long these protein had to be before forming the basic organelles of a cell which would allow for cooperative enzymes/etc to ensure proper bonding.

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Anyway, this post is already way too long, and I'm pretty exhausted. But let me know if you have any questions, responses, etc, or if there's anything you'd specifically like me to address.