So you say that you buy into the idea of speciation, but you seem to balk at the idea of common ancestors.
Can you please tell me what you think speciation is if it is not the divergence of species from a common ancestor?
Have you read the previous posts regarding this? The “dog-like” reference was used probably due to general size and morphology. It was used as an example because you can visualize the general size and shape of a dog. The common ancestor proposed is no more a prehistoric dog than it is a prehistoric whale. Being a common ancestor, it was the predecessor of both.
The concept of common ancestry is key to Evolutionary theory. It is very different from your linear banana to human and dog to whale misconceptions.
No, but Evolution does propose (and support) that plants and animals and all (currently or previously) living things…shared a common ancestor at some point in the (very distant) past.
He can’t imagine that it’s possible. Therefore, it isn’t possible. He doesn’t need a reason – given enough time, he’ll find some way to discard the idea.
You obviously haven’t been paying attention because no one is trying to tell you any such thing. A mere nine posts above yours, I wrote
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And who the heck is telling you organisms evolved “from an entirely unrelated organism”?! The whole point is that organisms descend from related organisms. You know, that whole “descent with modification” thing?
Assertions like this one seem to be part of a larger pattern… I’m sure many of you have noticed that many who refuse to accept evolution will give common misconceptions about evolution to back up their reasoning.
Thus the “ridiculous” idea of dog one day suddenly turning into a whale. I’ve even heard a Creationist say that since evolution implies “survival of the fittest” species should be going extinct all the time (This was phrased to me as “Shouldn’t species be going extinct?” - As if they weren’t). Another one that has thrown me is “if the world is so old, how come there aren’t more fossils?” He seriously believed that since there weren’t enough bones and graves to account for “millions of years” worth of life, evolution had a fatal flaw.
Now I realize that in the case of the young-earth Creationists, this is very much a result of the strawmen they have been fed at church. It is those who dismiss evolution not on the basis of religious programming but rather because they never studied enough about the subject to resolve percieved contradictions that truly worry me. There is also that fascinating bit of human psychology that anyone who has come across a 1=.999… thread should be entirely familiar with. People will outright rationalize their beliefs in the face of a shocking degree of proof to the contrary.
If there is one thing I do have faith in with regards to science, it is the fact that it abhors a contradiction. It may be enough for interacting with reality, but it will never be enough for interacting with other humans.
Tertius01, let me say that I haven’t read your article. The reason is that when you tell me that the article says the genetic code is near-optimal, then I wonder whether it’s worth wasting my time on. (Let me say that I will, however, shamelessly rip off its bibliography, and go to the original literature- I’ve been reading up on the origin of the genetic code for a while now, and have been planning to incorporate it into the abiogenesis FAQ.)
The fact is that there’s plenty of evidence that the genetic code is evolved. For example:
biochemically early amino acids are coded for with biochemically early nucleotides, suggesting that as new amino acids evolved, organisms had to evolve new nucleotides to code for them.
While we’re at it, uracil is a biochemical precursor to thymine, precisely as you’d expect from the RNA world hypothesis.
In general, redundancy in the genetic code involves the third position. Why not the first or second, if God can do it however he likes? Third-base redundancy suggests that an early code used two bases per codon, with the third serving as a placeholder, like the space between words in written text.
Thus when new amino acids evolved, the third position was placed into service as a coding region. This is exactly what you see: biochemically early amino acids tend to be distinguished by the first two codons, while biochemically late ones are distinguished by changes in the third position.
One last thing to bear in mind is that if you know anything at all about information theory, you know that the genetic code is far from optimal. A sort of “quote mining” (albeit probably unintentional) is going on if any IDist tells you otherwise.
If you work from the idea that evolution is true, then yes, the genetic code has a lot of error-resistance. But it’s being measured against the standard of, “what kind of genetic code could have evolved?” If you’re an IDist, you’re not constrained by that. You could, for example, imagine a genetic code based on Hufmann coding, which would be resistant to frameshift mutations and would encode more information per nucleotide. For that matter, this all begs the question of why God would even need to create an optimal genetic code. If God is going to let things evolve over billions of years on their own, sure, it’s good that the genetic code has some error-resistance. If God is going to keep tinkering and introducing IC systems, or is going to create new species entirely, then He can just keep correcting mutations. If you can’t answer those questions, then you’re just making a “gee-whiz” argument: the genetic code is so cool, God must have done it.
Now, all that being said, does you article really address the evidence for the evolution of the genetic code?
Incidentally, I forgot to mention that the “optimization” of the genetic code is a natural consequence of the fact that it was evolved. When an enzyme evolves to change one amino acid into another, similar amino acid, naturally you’re going to end up using a similar codon for each. (For example, the old AA might originally have a redundant third position, and when the new AA evolves, the two AA’s are distinguished by differences in the third position as the old codon “splits” into two.) This is the kind of thing you see over and over again when you read the kinds of papers your site had in their bibliography. Did they even mention it, or did they just handwavingly (and falsely) declare that the code’s optimization is just plain inconsistent with evolution?
For one thing, as TVAA mentioned, the genetic code was only optimized for the particular size of the codon (three nucleotides, the minimum necessary to handle start, stop and twenty amino acids). Certainly a codons made up of more nucleotides would be more error resistant, but in a sense, less efficient.
The article’s claim is that, of all the possible pairings of codon with amino acid, our particular code of pairing minimizes the amount of mutation errors, especially when you factor in the likelihood of different substitution errors. In fact, our particular code appears to be head and shoulders above the one million randomly generated possible codings in the experiment.
If the code is indeed optimal (or very near optimal), I think it is up to those who attribute the optimality to natural selection to provide a force driving the optimality and the time for the optimization to occur. The obvious problem is that a change in codon assignment leads to changes in amino acids and defective proteins.
Mutations happen; error-resisance seems like it is always a good thing. Saying an intelligent designer could tinker anytime it liked is missing the point I think.
As I first said, I am not a biologist, so I really can’t offer any more information than is contained in the article. It isn’t very long, especially if you skip over the basic genetics at the beginning.
This was written before your second post Ben. No it wasn’t mentioned, and that is exactly why I brought this here.
But there’s the question: Why should God be concerned with making trade-offs between accuracy and efficiency? Why wouldn’t he take the trouble to make a virtually-perfect system?
(We can imagine a coding scheme that makes each amino-acid sequence unique, so that any change to the code itself would make it non-functional. This would prevent ALL mutations. Why didn’t God do this?)
If God were willing to constantly fix errors that would pop up, why would He care about accuracy at all?
Logic and religion don’t mix. In religion, you always get to say “Well, God is mysterious and we are incapable of understanding his ways”. How conVENient.
I don’t think any advocate of an intelligent designer has said that the designer would be willing to constantly fix errors.
I can’t imagine a coding scheme that would prevent all mutations. Even if you had codons with more than three nucleotides, the possibility for a double or triple nucleotide substitution is always there.
Lets say for a moment that we have four nucleotides in a codon. Now lets say there is a “standard codon” related to a certain amino acid. You would have to include 12 additional “one substitution” codons (each nucleotide of the four nucleotides has three substitution options). Thus a 13 codon block, where the standard codon was always used, would be insensitive to single substitutions. For the 22 required actions, you would need 286 codons, but a four nucleotide codon only has 256 options. You would have to have a five nucleotide codon to be insensitive to single substitutions (352 codons required, 1024 available). Insensativity to double subsitutions would require an even longer codon.
I’m not sure what you mean, TVAA, about making each amino-acid sequence unique. It seems you trade off between codon length and error resistance. You brought this up to begin with.
It’s not just a matter of length. If each amino acid had its own unique chemical “symbol”, then it would take a sequence of massively improbable events for a mutation to occur that wouldn’t just make the sequence non-functional.
