Charles Darwin

Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. And even if they are found to have greater functional constraint, so what? One does not need evolution to explain such a finding. You are contriving evidence where there is none.

Here are some samples.

"Genomes are evolving in a completely nonuniform way" Science 296:1601

"The phylogenetic position of the platyhelminths within the metazoan tree is examined using two independent sets of molecular characters, the evolution of 18S ribosomal RNA sequences and the diversity of the genes belonging to the HOX cluster. Among the various hypotheses that have been considered by zoologists, a position of the platyhelminths within the protostomes, related to the phyla with typical spiral cleavage, appears to be favoured when taking into account all separate lines of evidence. It is in conflict with the traditional hypothesis of an early emergence at the base of the bilaterally symmetrical animals. This relatively late emergence is compatible with the old idea that flatworms are derived from a coelomate ancestor. New evidence from the sequences of Hox genes suggests that the duplicated genes Ultrabithorax/abdominal-A constitute a genetic synapomorphy of the whole protostome clade." C R Acad Sci III., 320:83

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other." Nature, 387:489

"Sequence data can sometimes mislead or even give an entirely wrong answer." Science, 276:1032

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought." Science, 279:505

You also have distant species with similarities and allied species with similarities that derive from different development paths.

Charles Darwin

[QUOTE]Originally posted by Doubting Didymus
QUOTE]

What do you think the separate creation hypothesis predicts the tree to look like?

I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.

When an area produces no polypeptide, or a polypeptide is degraded before being put to use, or a finished polypeptide results that does not have a function. You think when geneticists say 'this stretch of nucleotide sequence has no function' they're just making shit up?

Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

Yes, dolphins are different from sharks. However, dolphins have very nearly got the exact genes of a placental mammal. Why should this be? Evolution explains it nicely: dolphins have mammilian genes because they are descended from mammals. How do you explain this with a separate creation model of biodiversity?

"Evolution explains it nicely"? You've got to be kidding? Evolution has no idea (beyond hand waving) how all this change and complexity is supposed to have come about. You see some similarities between the dolphin and other mammals, and say evolution explains this nicely?! There's got to be something behind this, for science doesn't work this way.

You ask about a separate creation model. It is an interesting question. I don't have anything to add beyond the obvious, such as dolphins share genetic similarities because they share many traits with those mammals that evolutionists think they are descended from. But what's that got to do with evolution being a scientific fact?

lpetrich

Charles Darwin:
(endosymbiosis -- most successful is naturally selected...)
I'm not doubting that we can contrive explanations, where we are free to imagine.

Let's imagine that we could go back about 1.5-2 billion years ago to where some early protist was eating last year's crop of cyanobacterium colony.

The endosymbiosis hypothesis states that one of those protists swallowed, but did not digest, some alpha-proteobacterium. That bacterium multiplied inside, living off of the protist's waste products, like acetic acid. One day, due to some membrane-synthesis defect, the bacterium's outer membranes became a bit leaky, allowing some synthesized ATP to escape and AMP, ADP, and inorganic phosphate to return for assembly. This ATP supplied extra energy, helping its host eat more cyanobacterium and grow more and reproduce more, assisting the reproduction of that bacterium.

And that's what I would expect to see -- that or something similar. As opposed to this:

One day, some protists popped into existence with a big *POOF!*. They looked like some existing protist inhabited by an alpha-proteobacterium, however.

"Charles Darwin", is this what you believe?

I was referring to membrane-bound organelles, independent of the plasma membrane, such as things like acidocalcisomes which are found in both some prokaryotes and eukaryotes.

That ONLY means that some organelles have not originated by endosymbiosis; I've yet to see anyone claim that they have that origin.

Doubting Didymus

Which is exactly why my first statement read with the following sentiment: "There is no particular reason for any two phylogenetic tree creation methods to produce the same results, if species were are not in fact related."

You do not appear to understand what I am talking about. Humans and mice are closely related. I should expect functionless DNA from those two species to be similar. I should also expect functionless DNA from a species closer to humans than mice to be more similar still to humans. Why shouldn't human and mouse junk DNA be similar?

Now it's my turn to not understand what you are talking about. Lets stay on this one specific topic: If an organisms genome is created without adapting it from ancestral genomes, we should see genome similarity correspond to similarities in environmental needs. It doesn't. Instead, genomes are more similar when organisms share more recent hypothesised ancestors. We should not be able to build ancestor trees if there were no ancestors, but we can. These ancestor trees should not be borne out by the hypothetical history in the fossil record, but they do (e.g. we should not find transitional forms in the right places. I do hope we can finish with this topic before discussing those, however, as I am no paleontologist, and the topic deserves its own thread. Deal?). This is the same for every phylogentic tree, of which there are many. Every time a new tree agrees with an old tree it is a confirmation of the common descent hypothesis. This particular argument has nothing to do with explaining 'how all this change and complexity is supposed to have come about', so your motivation for mentioning that escapes me.

First, the idea that genomes are more similar because the genes are catering to similar functions does not work, as I mentioned earlier, because we can get the same phylogenetic tree results with genetic segments that do not do anything to the organism. The similarity we see is therefore not linked to functional similarity.

As for what this has to do with 'fact' status: If a theory makes a prediction, and the prediction is correct, then it helps the theories standing. If a theory makes many many many predictions, and they all turn out right without any falsifying evidence showing up, then eventually the theory is considered a fact. So, what I'm doing is showing you some occasions where evidence confirms evolutionary predictions. As I have demonstrated several times now, evolution expects there to be one true phylogenetic tree of life that shows which species diverged at what times in relation to each other. There is no reason to expect any such thing if species are not related. Therefore, every time a phylogenetic tree based on one thing agrees with the phylogenetic trees based on another method, it is a strong confirmation of evolutionary prediction. Phylogenetics is a very precise science with well established guidelines. I don't see how you can call it handwaving.

If you insist, you can still call the theory of common descent just a 'well evidenced theory' and forget about calling it a fact. The distinction there is purely semantic.

Can I help you with anything else?

lpetrich

Charles Darwin:
Again, all you are doing here is parroting the standard evolution line. Segments that share greater similarity are assumed to have evolved more slowly, and are therefore assumed to have more functional constraint. ...

Why don't you look at discussions of protein structure and function some time? Real discussions, not creationist literature.

"Genomes are evolving in a completely nonuniform way" Science 296:1601

So freaking what?

And how is that supposed to mean that new species come into existence by poof-poof-poof?

"The phylogenetic position of the platyhelminths within the metazoan tree is examined using two independent sets of molecular characters, the evolution of 18S ribosomal RNA sequences and the diversity of the genes belonging to the HOX cluster. Among the various hypotheses that have been considered by zoologists, a position of the platyhelminths within the protostomes, related to the phyla with typical spiral cleavage, appears to be favoured when taking into account all separate lines of evidence. It is in conflict with the traditional hypothesis of an early emergence at the base of the bilaterally symmetrical animals. This relatively late emergence is compatible with the old idea that flatworms are derived from a coelomate ancestor. New evidence from the sequences of Hox genes suggests that the duplicated genes Ultrabithorax/abdominal-A constitute a genetic synapomorphy of the whole protostome clade." C R Acad Sci III., 320:83

No real difficulty. That's because there has not been much to work from when working out the relationships between the animal phyla. So if you choose some character that's been affected by multiple evolution, you will get false results.

However, molecular characters are more detailed, and the authors of that paper used two different sets of them -- 16S/SSU rRNA sequences and HOX-gene sequences.

Furthermore, some old ideas about animal-kingdom relationships have survived. Bilateria, Protostomia, and Deuterostomia. And a relatively close relationship between mollusks and annelids, previously suggested from their very similar larvae.

"The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other." Nature, 387:489

So what? And how is that supposed to imply poof-poof-poof?

"Sequence data can sometimes mislead or even give an entirely wrong answer." Science, 276:1032

However, biologists have learned how to be careful, and to apply various significance tests.

"Animal relationships derived from these new molecular data sometimes are very different from those implied by older, classical evaluations of morphology. Reconciling these differences is a central challenge for evolutionary biologists at present. Growing evidence suggests that phylogenies of animal phyla constructed by the analysis of 18S rRNA sequences may not be as accurate as originally thought." Science, 279:505

Again, so what? Is that the end of the world or something like that?

lpetrich

Doubting Didymus:
What do you think the separate creation hypothesis predicts the tree to look like?

Charles Darwin:
I don't think the separate creation hypothesis supplies sufficient detail to say how the species comparisons would play out.

Thank you for being so honest about the gross deficiencies of your pet hypothesis.

Then if evolution is true, why do segments in the human and mouse genome, which evolutionists say are functionless, show near identity?

These are noncoding sequences, which can be involved in gene regulation and production of functional bits of RNA, like ribosomal and transfer RNA.

Urvogel Reverie

These quotes are all fascinating, and they all confirm for any skeptic, that you completely misunderstand phylogenetic reconstruction. You have regurgitated excellent examples of the conflict between phenetic, geological, phylogenetic, and other methods of systematics, and the fact that restoring phylogney is in fact not easy. What you have utterly failed to do, is display why this should be a fatal flaw which undermines systematics, or on a greater scale, evolutionary biology as a whole.

Urvogel Reverie

Jack the Bodiless

CD:

Why did you claim to be a "physicist" if you reject the entire basis of the scientific method? Will you now retract your claim to be a physicist, or any other sort of scientist?

And why do you accept that evolution is a fact, while repeatedly questioning this? It seems that you just won't let go of your erroneous (creationist) definition of the word "evolution", despite being corrected many times.

Mutations happen, and you accept this.

Natural selection happens, and you accept this.

Changes in the frequency of alleles in a population happen, and you accept this.

Therefore evolution happens, and you accept this.

Why, then, are you questioning the "fact" of evolution, which you accept?

Ape31

This has been a most amusing thread and I, like most here it seems, thought CD was a genuine (mustn't say creationist) anti-evolutionist.

However, he has shown a reasonable understanding of most of the arguments and has shown the ability to read and reference primary literature so the only conclusion I can draw is that we are dealing with a most excellent sock-puppet!

I must offer my most sincere congratulations on such a wonderful creation. :notworthy

Or did he evolve perhaps?

r.

Charles Darwin

I don't think we need to be overly concerned about how to define "scientific fact." I would agree with arguments evolutionists make about how scientific facts are different from empirical facts.

I think you are raising an interesting question, but I don't think it is highly relevant here for the simple reason that evolution isn't anywhere close. Pick you favorite definition of "scientific fact." I'd probably agree with it.