rlogan

Hi Principia. Acknowledged.

There is value to me in knowing their arguments, and yes - it isn't a positive presentation of creation.

Thus far, the assertion that all radiometric dating has huge flaws is falling on its face. I see CD accepts the age of the earth is > 4 billion years anyway, so it's on to the assertion that there are not gradual evolutionary fossil forms in successive layers of strata.

From a layman's view it seems obvious to me the simple organisms are on the bottom, eh? I find the horse literature pretty convincing so far...

Albion

All through this thread you've been saying that people who accept evolution are doing so for metaphysical or theological rather than scientific reasons. Ken has every reason to interpret your posts the way he did. There's now over 30 pages of posts from people ranging from interested laymen to researchersin evolutionary biology, with a variety of different metaphysical positions, that are describing the scientific basis for accepting evolution, and the best you seem to have been able to come up with in opposition is nitpicking followed by statements that none of the evidence is compelling and that the people who think it is compelling aren't being motivated scientifically. Not that we seem to be any nearer a definition of "compelling," since most people here do consider the current theory of evolution compelling as an explanatory and predictive scientific tool.

Charles Darwin

No, I've been pointing out metaphysics as they arise.

Sorry, I was trying to engage the scientific claims you are making. Can you give me an example of nitpicking in response to a scientific claim (and I'll try to fix it)?

Charles Darwin

No, the convergent mutations involve the gorilla, the orangutan, the gibbon, the chimp, and the human. The authors explore alternative explanations but find the mutations to be most likely independent.

Several problems here. First '323823762662400 possible topologies' is irrelevant. The authors computed phylogeny had extremely little to do the with the convergent mutations. Their phylogeny was based on the entire gene. The fact that their phylogeny is similar to the accepted species phylogeny is no surprise at all.

What is interesting, as we discussed, is the erroneous grouping of the chimp and gorilla; and especially the fact that it is supported by 100% bootstrap probability. They had no choice but to resort to the just-so polymorphism story with random sorting. What is the probability of that is giving you 100% bootstrap probability?

But this sort of thing is common even under evolution. For instance, in the paper the nonsynonymous substitutions show different rates in the hominoids versus the Old World and New World monkeys. Likewise, mutation frequencies in the promoter region as compared to intron 4 must be different in the hominoids versus the non hominoids:

So we can ask the same question of evolution. Why should mutation trends and rates differ between hominoids and the monkeys? I realize I am not answering your question, and I agree with you that I do not have an explanation for why the convergent mutations occur at all. But they do. They are empirically observed, and under evolution we infer them historically. Therefore it is perfectly reasonable for creationism to appeal to them as well. The fact that they are more predominant in more similar species is what would be expected since this is what is emprically observed.

monkenstick

the convergent mutations occur in those species, but any one of the convergent mutations is only shared by two species at a time

the computed phylogeny took ALL positions into consideration - including the convergent ones and the inactivating ones, and more positions supported the phylogeny than didn't (including the inactivating ones)

i.e. the amount of mutations in favour of the phylogeny far outweighed those that weren't (the convergent ones) even so much as to have 100 percent bootstrap probability

this is how phylogeny works CD - you don't select the positions you want to construct whatever phylogeny you want - you sum over all of them - because the random nature of mutations demands that phylogenies are supported in a statistical rather than absolute sense

if it is due to lineage sorting thats exactly what you'd expect - i.e. the allelic inheritance is supported 100 percent, but the allelic inheritance doesn't reflect the species tree because of lineage sorting

haha
CD, its not the mutation rate that is different. Its the rate of fixation of mutations

Oda et al found exactly what they were expecting

the reason that the nonsynonymous mutations have accumulated as rapidly as the synonymous mutations in the hominids is because their sequences are neutral - nonsynonymous mutations make no difference to fitness, and so are fixed at the same rate as synonymous mutations

the reason that the same isn't the case in the old world monkeys and the new world monkey is that their urate oxidase still functions -> so the nonsynonymous sites are under selective constraint -> changes in nonsynonymous sites are not fixed at the same rate as synonymous sites, because they have phenotypic consequences

so the difference is in the selection on the sequences - not the mutation rates of the sequences - this is confirmation of the fact that the urate oxidase pseudogene in hominids is useless, and its why they looked at nonsynonymous/synonymous rates of substition

Jack the Bodiless

Charles:
Which part isn't ludicrous? I've already explained the problems with "multiple abiogenesis events". As for "rapid rates of change that occurred in the past": these would have to be VERY extreme to erase all traces of the hirearchy (e.g. a cat giving birth to a winged kitten: the creationist caricature of evolution). As evolution is constrained to operate in small incremental steps, and to work with modifications of existing structures rather than suddenly adding new organs with no pre-existing template, it follows that the hirearchy cannot be quickly erased.

Evolution is a scientific theory which accounts for the fact of common descent. If there was no visible evidence of common descent, there wouldn't be any theory to account for it: just as there wouldn't be a theory of gravity if we were all floating about weightlessly in a hollowed-out asteroid with all memory of our planetary origin erased by mischievous aliens. Why bother to speculate about a parallel Universe in which the evidence for common descent doesn't exist? That isn't the Universe we inhabit.
Well, I've struggled to understand what you're getting at here by substituting each of your various usages of the term "evolution", but I'm stumped. What sort of "evolution" do you NOT have evidence for?

And why do you still resort to such obfuscation?
Who says that "evolution" is a fact? What are you talking about, man?

See my earlier post on this.
No, the REAL issue is that vestigial structures undoubtedly DO exist. Again, you want to draw us into your parallel Universe in which they do NOT exist.

There's also a very curious use of tenses here: "whether evolution can sustain the failure to find...". You should be using the conditional tense when discussing your fantasy Universe: "whether evolution COULD sustain a failure to find...". There is no ACTUAL "failure to find any vestigial structures". You seem to be having difficulty keeping reality and fantasy separate.
Where are you getting this from?

A vestigial organ is one whose ORIGINAL function is obvious from its structure, and from comparisons with otherwise similar organisms. The organ is no longer adequate for its ORIGINAL function, and any additional function is plainly incidental, because (in most cases) the organ is poorly "designed" for its new function also. The human appendix is a classic example of a vestigial organ: there is no reason at all why a dead-end section of intestine should be "designed in" as a site for a concentration of immune-system defenses (but, conversely, a good reason for extra defenses at a site that represents a dangerous avenue of infection).

Are you seriously admitting that you do not know how complexity can arise through evolution?

That is a rather startling admission of ignorance from one who otherwise claims to know more about evolution than professional biologists!

I could explain it for you, but first I want to check that this isn't another bizarre "let's pretend to be stupid" ploy. My apologies in advance if you are genuinely unaware of this.
Please explain how there is more evidence for either of those theories than for common descent. If it is fact that the Norman Conquest occurred in the 11th century, based only on a handful of old documents: there is FAR more evidence for common descent from the fossil record (MILLIONS of fossils) and from the Linnaean "Tree of Life" hirearchy visible in living organisms today.

...But, if you're using another meaning for "evolution" here, please explain this.
It is pointless to pretend that there are only "one or two" individual pieces of evidence. Going back to my earlier analogy of wave-sorted pebbles on a beach: this would be like being asked to point to one or two pebbles as evidence that sorting had occured.

It is the staggering totality of the fossil record, and the "Tree of Life" of cladistics, that makes the evidence so overwhelming. Thousands upon thousands of species forming a nested hirearchy, supported by millions of fossils confirming the pattern of development of that same hirearchy. And genetics is providing new support of the same hirearchy: again, it is the totality of the genome similarity that matters. Individual genes can be tweaked by mutation in unpredictable ways, but the overall pattern of relationships (based on the percentage difference between the genome of one species and that of another) correlates with the same "Tree of Life" derived from other sources.

I am not aware of anything else in science that is better supported (other than obvious observations such as "the Sun emits light"). The odds against this correlation being "accidental" are truly astronomical: the number of possible permutations involved dwarfs such numbers as the number of atoms in the Universe, for instance.
Again, what aspect of "evolution" are you talking about? There is far more evidence for common descent than for the age of the Earth. Also, more evidence for mutation and natural selection.

pz

This thread is going to be closed later today.

At this point, it is just going around and around in circles, and lacks any kind of focus. The issues being discussed now were also discussed 20 pages ago.

I recommend that if anyone still wants to persist in this, that they start a new and much more specifically titled thread.

Oolon Colluphid

Aw, spoilsport! This hasn't yet reached the length of the good ol' E/C Ed Thread!

(Seriously: good move. It has long since been imitating the fabled Oozlum Bird.)

Oolon

Charles Darwin

No, this is not true either:

The bottom line is there are several instances of independent, yet identical mutations.






You keep talking about mutations driving the phylogeny; sorry, but the majority of the loci show no substitutions whatever. They are driving the phylogeny, not the relatively few mutations.





Good point, I wasn't reading carefully. Bad example, but my point still stands; namely, that convergent mutations occur. Therefore it is perfectly reasonable for creationism to appeal to them as well. The fact that they are more predominant in more similar species is what would be expected since this is what is emprically observed.

Let me say something else that, from reading your posts, I gather needs saying. You keep on referring to the inactivating mutations common to the gibbons, and to the human, chimp, gorilla, and orangutan; as though they are great coincidences explainable only via common descent. You seem to be missing the fact that they have been carefully culled from a larger set of mutations, which are all over the map. Most of them do not explain the gene inactivation, but if you look hard enough you find one that is common to the human, chimp, gorilla, and orangutan; and you find two that are common to the gibbons. So these are identified by evolutionists as the probable inactivating mutations. OK, fine. But from a non common descent view, if you have a set of mutations and if there are mutational hotspots (an empirical fact), then it is not surprising that (a) they generally will agree with the consensus phylogeny, and (b) amongst all those mutations you will find some that occur in all sequences in a group. The mutational hotspots would be species specific most often; but sometimes specific at higher levels.

This is a perfectly reasonable explanation and not, as you have been saying, incredibly unlikely.

Charles Darwin

But what you present to us is a false dichotomy. Our choices are not between evolution and accident. Yes, the odds against this correlation being "accidental" *are* truly astronomical; so what? Hierarchies are also a characteristic of created things; and long before there were paleontologists or microscopes creationists predicted an orderly progression to creation. They had no idea the fossil record would reveal, guess what, an orderly progression.

Furthermore, your theory of evolution does not require such a hierarchy, so it is hardly so compelling as you suggest.