Friday, October 2, 2015

Open Rebuttal to Cross Examined

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


Gun Control

This is going to be a bit more on the editorial side, so please bear with me.

Gun control and regulation is a topic that is at the forefront again, as I suspect it shall be for a long time.  This is not an easy topic to digest, mainly because it's got so many factors working into it.  Specifically, this is in reference to the latest mass shooting (and it's a sad indicator when I don't even have to mention which one because in two days there will be another, statistically).  People will naturally want to discuss gun control, because guns are used quite a bit in these events.  However, I think it's necessary that we look at factors other than simply regulating guns, and here's some reasons why.  Please feel free to discuss them in the comments, remembering to keep it civil.  This is the internet, and you're probably going to disagree with some of the points I make.

This post is spurred by a conversation I was engaged in recently on twitter, but its components are basically the same in most debates of this nature.  Specifically, let me address the issue of safe firearm storage first.

This seems like a logical thought, locking up a firearm makes it safer.  I would argue that anything less than a bolted-down safe (or a very heavy one) is probably not going to deter the average thief.  Locking up ammunition and guns to protect children, and to prevent accidental discharge, is one thing.  Trigger locks aren't nearly as effective in the hands of people who steal your guns.  If someone is determined enough to enter your locked house, I'm fairly certain same person could easily disable a locking mechanism on your gun.  There are technologies coming up to make it harder to use guns, like smart lock tech, however it's going to be nearly impossible to make enough of those locks at a reasonable enough price to safeguard every gun.  This also assumes that people would want such a thing, and I'm fairly certain that people who already have illegally obtained firearms aren't going to get much use out of them.

Which leads to my second observation.  Yes, locks can help.  Any deterrent is useful, and even locking half the guns currently in existence, and mandating all new guns have these sort of safety features, would indeed cut down on some gun crime.  However, I think it safe to presume that it's still not going to greatly deter people who want to find unlocked guns.  This also brings up another point, that a gun is not a difficult thing to fabricate.  A firearms registry might help a bit, and it's clear that most mass shootings are happening with automatic rifles.  This reduces the number of guns we would need to identify and lock/register.  However, as we've also seen, several of these incidents happen with the use of more traditional rifles, handguns, and shotguns. 

Moving back to the lock argument, I think there's another facet that's typically overlooked.  Lots of people, including many who advocate for less restriction on gun control, claim it is for a purpose loosely defined as 'self-defense.'  This can include anything from protecting your home from armed invaders, to protecting yourself in public from the selfsame individuals perpetrating mass shootings and armed robberies, et cetera.  Locking a gun in a cabinet defeats this purpose pretty directly.  A trigger lock makes the gun fairly useless for home defense.  Smart lock technology would certainly negate most of this effect, but for now, most guns don't have fingerprint scanners built into grips. 

Another argument that was brought up was that the owner of the gun should be held responsible.  I think this is, at least in part, a good idea. I also think it would be difficult to enforce, for various reasons.  Some people compare it to licensing cars.  Make every gun registered and criminals will be more quickly apprehended.  I'm completely for a gun register, and I think it's a good idea.  I think there's several hurdles to overcome first.  For example, in no particular order:

  • Unlike a car, you can't see the gun's license/serial number easily when it's used in a crime.  
    • Car tags work because we can see them, and car styles are fairly unique
    • Most handguns are black, and it's difficult to tell one caliber from another when it's pointed at you, let alone get its license number.
  • There are lots of unregistered guns
    • Taking a near-complete census of every gun in circulation today would be impossible.
    • Guns aren't nearly as easy to find as cars after a crime.  
  • Stolen guns would take a lot of paperwork to track.
    • Even if your gun was reported stolen, it's trivially simple to remove most serial numbers.
    • This means it would be hard to prove which stolen gun is yours.  
    • We could have a ballistics sample of every gun on file as well, but that would be incredibly costly, especially considering most guns aren't used in crimes, and lots of times guns used in crimes aren't fired.
  • What, exactly, constitutes a gun?
    • A paintball gun can be just as lethal as a regular firearm if you use appropriate-caliber shot.
    • Air rifles, crossbows, slingshots, and a plethora of other types of weaponry can potentially be as dangerous as firearms, and are largely unregulated.  If traditional firearms suddenly became much more heavily regulated, one could argue that these sort of weapons would overtake traditional firearms in these roles.   
      • Granted, this doesn't appear to be a concern at present, but some people do indeed use air rifles, airsoft guns, and other non-firearms to commit crimes.  Similarly, it provides a good exercise in demonstrating just how hard it is to regulate something that is not very well regulated at present.
Again, I'm not arguing against registration.  Although, in my state, a background check is required, and the serial numbers of most of the guns I own should already be in a database somewhere in some governmental office in my state anyway.  Registration isn't really even the hard part.  There are numbers out there demonstrating that there are perhaps 320 million guns in America, that we know about.  I'm willing to guess that this number is considerably lower than the actual.  I would guess that there are potentially twice that number.  There are around 240-260 million registered vehicles in America, by comparison.  Registering and tracking 320 million guns, plus the approximately 5.5 million new ones per year (we don't do this with cars, but we'd almost certainly have to do it with guns) would require a massive undertaking.  Not to mention the number of guns imported, that's a lot of guns.

However, all this aside, I think there's bigger issues to deal with.  Mental health is definitely one of them.  America doesn't do very well at the healthcare thing, for several reasons which I won't get into here.  We have the Affordable Care Act now, and we could certainly stand to spend a bit more of the VA, Medicare, Medicaid, Welfare and other social service money on making sure people are healthy mentally, as part of routine services.  Granted, this might require something of an overhaul of our taxation/spending scheme, but I think it's far from impossible to guarantee every American access to affordable or free healthcare, without hurting working individuals.  I'll touch on this idea, as well as others, in another post. 

Gun law reform, and gun control legislation is definitely necessary.  The proposition is not to remove guns from the hands of everyone (although Switzerland does pretty well with there scheme), but to regulate the firearms industry.  I think the above points I've made are valid, and I think we could easily overcome some of the problems up there if we were willing to tweak other areas of our policy.  However, that might come across as a bit socialist, and for whatever reason, we are quite hesitant to approach that.  I will leave my socioeconomic ramblings to another post, but suffice to say, a more socialist governance policy is not necessarily a bad thing, and is perhaps necessary to the next stage of fixing this problem.  Access to better healthcare, attempting to eliminate poverty, increasing standards of living and enabling people to get help they need before this kind of thing happens, is perhaps not the worst possible outcome.  We can't do it with our current structure, but I don't think that means we shouldn't be open to changing the current structure, including more regulation on guns.  I'm saying this as a gun owner, no less. 

If you have any points, feel free to post them in the comments below.  Again, let's try to keep it civil, and have a good debate.  I'm not sure there's an easy solution, or even a 'right' solution, but I'm sure there's a way to improve things if we can work together.  Just because we may disagree on some things doesn't mean we can't work together.  I'm willing to compromise if it means a better future for the next generation.  Are you?