Open Rebuttal to Cross Examined

This is an open response to this article, featured on the crossexamined.org website.

Let's start with breaking this down, line by line, as necessary.

As a homicide detective, I understand the power of alibis.  When a potential suspect can prove he or she wasn’t available to commit a crime because they were occupied elsewhere, they are eliminated as a candidate for the murder.

So, this is our establishing shot.  The first sentence, fine.  I'll let it stand for now.  It might prove useful later.  That second line is particularly useful.  It uses proof, and since he's a homicide detective, I'll presume he understands the meaning of proof in the scientific sense.  That's to say, it's synonymous with 'evidence.'  Not just in the legal sense, but in the full-fledged, evidence is literally proof in science sense.  This is what any scientist means when they use that word, evidence supporting a hypothesis.  In this case, the suspect can clearly show the alibi, which gives fairly solid evidence they were where they claim to be.  Perhaps it's a photo from a grocery store camera.  Maybe it's corroborating evidence from trustworthy witnesses.  Maybe it's the lack of DNA evidence at the crime scene.  For our purposes, the fact is demonstrated.  This is proof, evidence.

Alibis create conundrums: conditions difficult to explain based on the impossibility of simultaneous appearances.

 I want to break this down momentarily.  Alibis don't create conundrums.  Alibis which are reasonably sound merely eliminate the possibility of another solution.  Jim was seen on grocery store surveillance at the time of the murder, in a grocery store over two hours away.  The evidence creates no conundrum. The evidence merely means we need to ask more questions.  Jim being in two places at once is not the only solution to this problem, ergo there is not a conundrum here.  If it were the only solution, then we'd have to re-evaluate the evidence more closely.

In a similar way, the relationships between DNA, proteins, enzymes, and the cell’s membrane present a biological conundrum.

I'm not sure what this conundrum is.  The mechanisms by which DNA (more specifically RNA) synthesize proteins and enzymes are pretty well understood.  I'm not sure exactly what the cell wall has to do with it at this point, but I'm sure we'll come back to it.

Those who believe life can originate in our universe without supernatural interaction (and guidance) must overcome this conundrum if they hope to account for the presence of life “inside the room” of the natural universe by staying “inside the room” for an explanation.

 Actually, this is called a fallacy.  Specifically, it's the false burden of proof fallacy.  This fallacy involves someone making an assertion, then claiming that the negative must be proven.  In this case, the positive assertion is that life could not arise without a supernatural force.  It is therefore the burden of proof of the person making that claim to substantiate it.  We have evidence (read:proof) that relatively simple chemical reactions can cause relatively simple chemical reactions to reproduce.  We have evidence that abiogenesis can indeed happen independently.  We do not have evidence (again, read that word as proof) that anything outside of nature is required to explain phenomenon that happen within nature.  Using his 'alibi' metaphor, poorly tied in as it is, this means that we've actually got an alibi for the natural processes existing here, but we haven't any alibi that can be substantiated of a supernatural force ever being here.  Don't blame me, I said it was a poor analogy.

Specially formed functional proteins “unzip” a specific portion of the DNA by separating the helix at the middle of its rungs. Additional specialized proteins then act as molecular machines, helping to assemble nucleotide bases along one of the unzipped DNA segments.

 I'm actually going to just go ahead and let that one stand.  It's a reasonable enough approximation for the layman to understand what is indeed going on.  It's also in direct contradiction to the point of creationism he's trying to posit, but we'll get there soon enough.  Just remember, he's using science that supports the ability of this process to happen naturally to presume without an alibi (evidence/proof) that this very process can't happen naturally.  More on that later if he comes back to it.

 This new assemblage of nucleotides is called a messenger RNA (mRNA). Once formed, the shorter mRNA molecule detaches from the DNA and is carried off into the cell by additional protein “helpers.” The mRNA is carrying instructions needed to build a protein. It is helped by another RNA molecule known as transfer RNA (tRNA). The mRNA and tRNA meet in a molecular machine called a ribosome. This important mini-factory is constructed from proteins and RNA complexes. Here, the tRNA transfers the message carried in the mRNA so amino acids can form each protein:

Again, pretty much how it happens, simplified into a high-school textbook explanation.  Not bad!  Still, the point remains, he's using a process that happens in nature to say that this process can't just happen in nature.

His picture is basically the same as this one.
This one is from Wikipedia, on the article about protein synthesis.

 So, the picture above basically shows exactly the same thing as the picture on his blog.  It's correct.  This wonderful natural process does indeed happen, and it's essentially what DNA did before DNA became DNA.  More on that later if we really need.  If he can use simplified arguments, so can I.  I realize this paragraph isn't perfect, but it doesn't need to be for this purpose.  If I were a molecular biologist, I'd be glad to go more in-depth.

Once the sequence of amino acids has been established, something amazing happens. Rather than remain in a long chain, the amino acids begin to roll up and fold onto one another, forming the specific finished shape of the protein required to accomplish its job. This may take a few seconds and scientists are still mystified as to how amino acids accomplish this task.

 Actually, scientists aren't mystified because you aren't a scientist. Just because you want to cherry-pick what you put in your articles doesn't mean I will.  Amino acids and protein folding are reasonably-well understood at this point.  It's not mystifying as to how it works.  Seriously, google is your friend. 

Moving on.

None of this can happen without the aid of enzymes and the protection of the cell membrane. Enzymes are large molecules constructed primarily with proteins. These important molecules activate and accelerate the reactions related to everything from food digestion to DNA formation. Nearly every chemical response in the cell requires an enzyme to help it happen fast enough for life to result.

 Again, bravo.  Good science.  Practically correct for our purposes.  This guy ain't half bad, if it weren't for the completely illogical and unfounded premise he is trying to sew in, without much subtlety.

 Finally, all of this activity must be protected. That’s where the cell membrane becomes critical. The membrane separates the interior of the cell from hostile exterior forces. It is constructed with fatty molecules (lipids) and proteins (along with carbohydrates). Some cells also have an additional cell wall surrounding the membrane. Cell walls are tough but flexible, and offer an additional layer of filtering and protection.

The main problem here is that he's saying that, because most of it happens within a cell today, it must have fundamentally always happened in a cell for all of time.  This is the part he hasn't supported, where he says it must be protected.  Simple proteins constructed by simple amino acids a long time ago would not have had the same sort of environmental pressures they do today, like viruses and stuff.  There's a time before lipids and cytoplasm would have existed, but the proto-RNA would have still functioned.  This is evidenced by the fact that some cells do indeed lack walls even today.  This is the alibi (proof) by which the 'must' in his assertion fails.  Cells don't need cell walls.  Cell wall are mostly required for multicellular things like you and I, plants and mushrooms, fish and wallabies.  There are indeed unwalled cells living in you and I, in the form of protozoa for example. These aren't necessarily good for you. 

Now, had he said that some cells do require cell walls to function, then he'd be correct.  However, his implication is that DNA/RNA/all cellular things can't exist without a cell wall, which is wrong.  Just wanted to clarify that.

Now that we’ve reviewed the inner activities of the cell, you’ve probably already recognized the “chicken and egg” problem. Enzymes are necessary for the timely formation of proteins, but these enzymes are built, in part, with proteins. Worse yet, this “chicken and egg” problem is also present in the larger relationships between the DNA, RNA, proteins, ribosomes and cell membrane.

 Indeed, he got most of that first sentence right.  He did indeed talk about the inner workings of a large group of types of cells.  However, there's no chicken and egg conundrum.  This has been addressed by others in one way or another, but there was no first chicken.  Neither came first because they developed convergent in the same animal.  For example, the group of things typically called 'birds' that lays eggs were probably all related at a time in the very ancient past.  Also, none of them would have resembled a bird like you probably think of today, most likely.  There was initially a very simple organism that somehow gave birth, probably to a single cell, incubating it.  A chicken egg is still indeed a single cell, until it starts incubating and dividing.  It's not difficult to imagine that chickens were at one time much smaller, perhaps the size of finches or wrens, laying tiny eggs.  Go back further, even tinier birds laying minuscule eggs, with progressively softer shells.  Eventually, there would have been an even more primitive bird-like creature (probably also lizard-like and a lot of other animal-like, being an ancestor to lots of things) which gave an even more primitive birth.  Take it back further and you start to see close to the beginnings of life, the original multicellular organisms, which split in various ways to reproduce, resembling nothing like egg-laying at all, but nonetheless still using a single cell perhaps to start it's child lines.

Wheh, that was a big paragraph.  Let's see what else he has to say.

Paul Davies describes the conundrum: “Take DNA… It has a grand agenda, but to implement this, DNA must enlist the help of proteins… proteins are made by complicated machines called ribosomes, according to coded instruction received from DNA via mRNA. The problem is, how could proteins get made without the DNA code for them, the mRNA to transcribe the instructions, and the ribosomes to assemble them? But if the proteins are not already there, how can DNA, ribosomes and all the rest of the paraphernalia get made in the first place? It’s Catch-22.”

Again, this implies that proteins haven't changed in 4 billion years or so.  The simplest proto-RNA wouldn't have looked much like RNA at all, probably.  The simplest proto-amines or proto-protiens probably wouldn't have looked much like their modern counterparts, either.  It's entirely possible that some different chemical reaction, that happened naturally as a result of the strikingly different earth that would have existed, would have produced a proto-builder molecule of some sort, which would eventually have given rise to RNA.  Remember, this natural process would also be catalyzing something, meaning it would have been creating a byproduct.  Both can happen at the same time, and if they happen to have been opposite sides of a chemical reaction, we'd expect exactly that.

But I'm no chemist.  You can look this stuff up yourself if you prefer.  There's plenty of great resources on this kind of thing.  And it can happen in exactly the same way that dropping a bit of potassium in a bit of water creates a completely natural exothermic reaction, without need for any supernatural explanation.  In exactly the same way baking soda and vinegar create a completely natural chemical reaction.

All these important machines, transportation vehicles and tools must arrive at the cellular factory simultaneously and function in unison if life is to be possible.

 Again, an assertion without basis.  Apart from him feeling it should be (appeal to emotion fallacy), what reason is there these things could not have developed in response to natural factors, at roughly the same time?  In fact, the evidence supports just such a hypothesis.

The cell membrane and enzymes cannot be constructed without proteins, but the protein formation must be accelerated by enzymes and protected by the membrane.

And as I've pointed out already, this false dichotomy simply doesn't exist.  There's other options.  They can develop somewhat simultaneously, or independently.  Or it could be that a cell wall will only happen if the stuff in the cytoplasm happens to have code to make it.  Or it could be something else, but the evidence supports that.

  Proteins can’t be formed without DNA information and RNA activity, but machines formed from proteins (like ribosomes), are a critically necessary part of this process.

 In fact, this is actually falsifiable.  Here's one scholarly article on the subject.  The point is, cell membranes are not a requirement for protein synthesis.  Yes, it typically happens in nature that way, but it doesn't have to, as the blog post would have you believe.  This is unethical, and is called begging the question, a type of fallacy.

And we'll leave it there.  The last paragraph from his article is the merest posturing, and has no actual bearing on the rest of this article.  As always, this falls under fair use, especially since it is dealing with scientific inquiry.

Peace!