The Problem with Christians

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Maybe I'm misunderstanding you, but I think you must be lying if you say that the very complex proteins begin to appear any time we have close to the right conditions. If you're talking about naturally occurring amino acids, then that isn't the same a proteins. That's like saying we see lightning in nature, therefore computers may form if the electricity strikes the right thing in the right sequence. 

And it is reasonable to say we see a feature that is created all the time by intelligence. If we are trying to explain that same feature (irregular sequential information), then there is no reason that intelligence should not be considered as a possible cause. 

I like the cathedral example. It would be completely illogical to assume that the bricks were ordered that way on their own. They needed a designer. I realize that this wasn't the point of the example though. We can invoke unobserved scaffolding as well, but if it is not empirical to invoke unobserved processes/enzymes in order to explain how it arose. It is just as speculative as saying it all came into existence at once because we see parts that depend on each other. 

There are videos where Behe counters the mousetrap response. But I'm not overly concerned with that. Obviously there is a lot more combined brain power trying to debunk ID than to support it. But I recommend that you read Signature in the Cell. It is an excellent book about the scientific credibility of ID. 


And I've already completed genetics, and I understand how allele frequencies change in a population, but that is hardly an explanation of intricate mechanisms arising. For example I have a test monday in Biochemistry, and one of the topics is how glycogen breakdown and synthesis are inversely regulated. Simple version: Glucagon leads to cAMP which causes protein kinase A to phosphorylate both phosphoryl kinase (now active) and glycogen synthase (now inactiv). Phosphoryl kinase then phosphorylates glycogen phosphorylase (now active), which then becomes active and binds protein phosphatase 1 and degrades glycogen. When there is plenty of glucose, then glycogen phosphorylase switches to its inactive conformation which causes protein phosphatase 1(PP1) to unbind. PP1 then dephosphorylates both glycogen phosphorylase (now inactive ) and glycogen synthase (now active). This elegant mechanism ensures that glycogen breakdown and glycogen synthesis are not occurring at the same time. Failure of these mechanisms lead to pathologies, some of which are lethal. How did they reproduce before they had these mechanisms and how could it evolve without them surviving to reproduce? 

As you can see, evolving this is not the same as evolving a larger beak size (which can probably be explained just be a mutation in the consensus sequence to increase the expression of the protein that leads to beak formation). I'm not too concerned with the ID people, I was doubting all out evolution long before I discovered their arguments.

The "intricate mechanisms", such as the biosynthetic pathways you're describing, do evolve by the scaffolding example I gave, where parts function differently in their original form, but add different bits from related systems over time, often due to a duplicate gene, as I previously explained. It's neither a linear process, nor is it one that preserves the full process once bits that formed the scaffolding fall away with successive generations of that population. You're looking at a completed bridge and saying it could not be built except intact, because it only supports its own weight that way. We HAVE found the scaffolding traces, in several of Behe's early ID/IC "mousetrap" arguments, which is what I was talking about in the Kitzmiller v. Dover case... Behe tried to present the argument you're making, and they presented the papers that showed the very scaffolding you guys claim cannot/doesn't exist.

Your way of tearing down my metaphor, in order to try to imply that only intelligence can cause these chemical reactions to happen, ignores that chemical reactions do happen naturally (even though we can duplicate those reactions artificially by duplicating the conditions under which they happen-- something you've done a hundred times in your chemistry labs, by now), while brick-stacking does not. The same applies to Paley's watchmaker analogy (which ID seems to be a modern variant of), since there is no known natural pathway by which metal would even possibly form into such shapes, but we know that humans do it all the time. On the contrary, we know that naturally-occurring reactions cause organic molecules, including ones that are component materials of our cells/DNA, and have managed to duplicate the conditions under which some of those reactions occur. It's a false equivalency, and I'm a little embarrassed for people who make that argument without seeing it for what it is.

And yes, it is the same thing as evolving a larger beak size. It's still just genes, which make amino acids/proteins and direct the function of other DNA, being mutated and selected/deselected.

I mean, really, are you seriously arguing that the biosynthetic pathways you're highlighting were always as they are, today, and that there's no other possible pre-functional form? I get sick of that same argument when people try to point to the complexity of the eye, since we know the process by which eyes developed and then evolved into their modern versions. But it you take one piece out of the modern version, a result of many many many generations of changes and scaffolding, it does look like the mousetrap problem. Except it's only an illusion. Irony!

I know how they theorized it happens, but just assuming the scaffolding that you're talking about ever existed is highly speculative. How did the enzymes get there? 'well other enzymes that were less developed morphed into them over time'. How did it survive before it had a mechanism to accomplish the regulation? 'well these other enzymes could regulate it too, but they were simpler and less intricate'. I read an article a few weeks ago about how catalytic promiscuity may aid enzymes in their evolution. One of the many speculations that they made were that enzymes with < 10% amino acid similarity were closely related because they shared the sequence for an active site. 


And I genuinely have no idea what you are talking about with the chemical reactions done hundreds of times to show polypeptide formation. Forming nucleotides or amino acids is NOT the same or equivalent to forming a functional sequence of them. And nobody is saying that you couldn't simplify the biochemical pathway a little, but you would really have to do some mental gymnastics to try to get it reasonably simple for the mechanisms of evolution to be sufficient.