Intelligent Design

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I wasn't trying to oversimplify it to make it seem unrealistic. I'll call it neo-Darwinian evolution if that's better.

We just get this stuff a lot, these sorts of rhetorical tricks designed to make evolution look silly before the conversation has even begun. Happily, you seem like you're actually taking this seriously, which is a nice change from the usual creationist dreck.

Information: what is conveyed or represented by a particular arrangement or sequence of things. This is exactly what the genetic code is. It is relevant to evolution. Evolution must account for the particular arrangement of the nucleotides that leads to functional proteins. 1000 nucleotide long sequence that leads to a protein has more information than a 100 nucleotide long sequence. Evolution would have to have a mechanism to increase the number of nucleotides while maintaining functional proteins.

Proteins are hardly magic, we're already learning how to manipulate their expression via gene therapy, specifically through the introduction of specific nucleotide sequences that have been linked to protein expression. In fact it was early last year that, via some RNA injections, scientists were able to produce up to a threefold increase in protein expression in Zebrafish embryos. This mechanism is not only evidently extant- given that the scientists were able to locate and manipulate the nucleotide sequences that could increase protein expression- but we're also able to toy with it and ramp it up.

Frameshift mutations are a subclass of point mutations. I already talked about these (maybe not to you), but they destroy the function of the protein. The protein is made of amino acids. Amino acids are coded by a specific set of 3 nucleotides. When you insert a nucleotide, you shift each following nucleotide over a space. This disrupts each following codon, which changes each amino acid in the protein.

Granted, I should have done more to familiarize myself with that phenomena. However, not all frameshift mutations do this, as I'll explain further down.

As for duplication events, if the duplicated genes are expressed, you get too much protein product which disrupts the cell's functions. This organism would get selected against. If it isn't expressed it can't be selected for.

If it isn't expressed it's still present in the organism and passed on when it breeds, whereupon further mutations could alter it such that it is expressed or used for a different function. Evolution most commonly deals with successive mutations, not singular events.

The nylonase enzyme is about 1500 nucleotides long, which shows that it is a derivative of a preexisting protein. I haven't looked into it that much, but my guess would be that nylon's chemical structure closely resembles the chemical structure of the original substrate. It wouldn't take much change in the existing protein to break down the similar molecule.

What's interesting about nylonase is that originally, it was pegged as a gene duplication followed by a frameshift mutation, which just goes to show, successive mutations are a real thing in evolution. Eventually this hypothesis was dismissed, but the point remains that a frameshift mutation isn't an automatic negative.

Moreover though, the nylonase enzyme isn't a single thing, but three different enzymes that are completely different from the normal enzymes that strain of flavobacteria uses. Nylonase enzymes- of a completely different sort- have also been evolved into different strains of bacteria by means of adjusting selection pressures; you're not just looking at an alteration to a single protein to deal with a chemically similar substance, but at a cross-species tendency to develop new, differing enzymes to deal with an imposed selection pressure, which is the textbook definition of an evolved trait.

But I'm curious, too: why do you think that evolution isn't a change in existing proteins and structures?

I read a quick article on the lizards. It says that they still don't understand the genetic basis for the change, and that they will look into it. I will predict right now that the genes that led to the valves were present (but not expressed) in the original lizards. These sequences were then selected for in the new environment. Something like this would require very high mutation rates with extremely fortunate nucleotide sequences to happen that quickly.

Apparently the isolated population is genetically identical to its parent population, in the sense that they're the same species still. But natural selection working to select and intensify new traits based on environmental pressures is still evolution. Seriously, could you define what you think evolution is? Every contention you've made fits neatly within evolution, though you're using them to argue that evolution didn't happen. It's weird.

You say evolution doesn't need to make new information because it can modify existing information. This just asks the question of where the old information came from.

Earlier species. And that information came from earlier generations still. We can keep going like this, right up until the point where you'll have to falsely conflate evolution and abiogenesis to continue having a problem with this, at which time I'll just point out that you're falsely conflating two separate theories and at that point you'll have a problem with abiogenesis and not evolution... which kinda means I was right.

I didn't say that proteins are magic. Just because we are beginning to understand how DNA, RNA, and proteins interact doesn't mean that they aren't the product of design. Understanding how something works is different than understanding how it originated. The way that enzymes function within the cell looks like design to me. You have a specific sequence of nucleotides. An enzyme (which itself must be produced through the following mechanisms) will attach to the code based on chemical specificity (which is decided by its structure, which is determined by the DNA sequence). It then runs along the code and incorporates molecules into an mRNA strand at a rapid pace. Different enzymes then look at this sequence and add amino acids in order, which, based on their chemical properties, fold into certain shapes which allow them to interact with the desired molecules. Other enzymes then attach to these enzymes and take them where they need to go in the cell (again dependent upon chemical specificity). It is just so complicated and intricate. The enzymes interact with each other and would all have to mutate together and change with each other in order to develop. Intuitively this seems like design to me. I realize that intuition is not always correct, but I don't think evolution does a good job of explaining change in proteins on the genetic level. Further evidence may arise, but until then I think it is more rational to think it was designed.

I accept that changes do occur in existing proteins. I just think that there is too much genetic material required to enter the evolutionary pathway that would not arise in an abiotic world. I realize this is different than evolution, but it still is necessary. Protein sequences are highly specific, and mutations give them problems which is the cause of almost all diseases. I think that the sequences we see are more consistent with the idea that they started off good and are slowly getting worse.

What I accept from evolution is that organisms can change. The consensus sequences and promoter regions are read in such a way that allows for variation. However, I think that altering protein coding sequences will degrade their function. I don't know where exactly I draw the line yet, but evolution doesn't explain the origin of all of these genes and the interaction between them. The fossil record seems to indicate that almost all the major body plans came into existence in a relatively short period of time.

You talk about how evolution of new information could have come from pre-existing organisms until we go back to the first life. But that is almost entirely speculation, and there is no way to test it. There never will be. We have to use historical science at this point, which favors the intelligent design argument for the origin of genetic information. I'm not talking about the origin of life, but the origin of all the gene sequences we see.