Freethought & Rationalism Archive

Charles Darwin · 10-04-2003, 10:02 PM

Quote:

Originally posted by monkenstick
there is convergent evolution in the hominidae and in the gibbons, except that the mutations which are "convergent" are different for both of these monophyletic groups

so a C->T transition in codon 33 just happened to occur in all the members of hominidae, but no C->T transition in codon 18

and a C-> T transition occured in codon 18 in all the gibbons, but not a C->T transition in codon 33

take a look at the tree in the link. All the convergent mutations you're asking me to accept support the current tree - its a co-inincidence that is so ridiculous as to be preposterous

I'm afraid you missed my point. Convergent mutations are observed in the same species, or in highly related species. They are not observed otherwise. So it is not "preposterous" to hypothesize that the same mutation observed in similar species could be the result of convergent mutations rather than common descent; and that a different mutation observed in a farther species is not convergent (and therefore likely to be at a different location) because the species are not so closely related. It is an independent mutation. So, you had independent mutations in these four species, but three species, the most similar, had convergent mutations.

I'm not saying I know that this is what happened. I'm merely saying that it need not be viewed as some great coincidence. We observe empirically that convergent mutations occur, and that they occur in highly similar species. Now we observe a pseudogene that has the same apparent mutation in the most similar species, and a different mutation in the more distant species. This fits.

Also, you ignored my question about the gibbon sequences. You say "all the gibbons" but I aware of only a single gibbon sequence. Are there more? If so, can you specify them?

Quote:

Originally posted by monkenstick
A more recent paper posits the explanation that the pseudogene took two hits - a reduction in promoter function in the common ancestor of gibbons and hominidae followed by different nonsense mutations in those lineages

I wonder what the citation is? Thanks.

Charles Darwin · 10-04-2003, 10:25 PM

Quote:

Originally posted by Jack the Bodiless
Let me ask you a variation of caravelair's question:

just out of curiosity, exactly what type of evidence would you need to see to be convinced of common descent? would you be convinced by ANY evidence, or have you closed your mind completely to the possibility? give me an example of something you think would be convincing evidence of common descent, if such evidence existed.

Let me give you some examples. Two related species of frogs, Rana fusca and Rana esculents have, as you would expect, very similar eyes. Yet they form differently. As Gavin de Beer put it, "This is no isolated example." It is not unusual that structures thought to be homologous, in fact, develop from different genes and/or different development pathways. Homologies that develop differently conflict with common descent.

There are similar pseudogenes in an endosymbiotic bacteria (Buchnera, as discussed in a recent post) from different hosts, which, even if one is an evolutionist, look independent. It would be very strange if they share a common ancestral pseudogene. But if we admit that these pseudogenes, with identical mutations, formed independently, then why not other pseudogenes as well? So we don't require common descent for pseudogenes.

There are HERVs that conflict with, and are not easily explained by, common descent.

There are fossils that appear planted there and have no obvious precursor. The general pattern of the fossil record is one of an upside down evolutionary tree. That is, you get a myriad of diversity all at once followed by a winnowing. This pattern occurs repeatedly.

Would I be convinced by ANY evidence. Sure I would. I'd be happy to jump on-board, but I need scientific evidence. Right now we have a lot of evidence against common descent. What evidence would suffice to accept common descent? Well, a great solution would be to provide the mechanism that accounts for all these anomalies and negative evidences. But then we're going beyond mere common descent, and we're talking about evolution. And that means we're going to hit the probability problem head-on. Now you've got even bigger problems.

Charles Darwin · 10-05-2003, 12:04 AM

Quote:

Originally posted by Ken
You've shared with us a couple hairs of the camel of negative evidence for common descent (e.g., missing HERV). Do you have others in mind?

Two related species of frogs, Rana fusca and Rana esculents have, as you would expect, very similar eyes. Yet they form differently. As Gavin de Beer put it, "This is no isolated example." It is not unusual that structures thought to be homologous, in fact, develop from different genes and/or different development pathways. Homologies that develop differently conflict with common descent.

There are a great many cases of convergent evolution. Similar designs which must have arisen separately. This conflicts with common descent.

There are similar pseudogenes in an endosymbiotic bacteria (Buchnera, as discussed in a recent post) from different hosts, which, even if one is an evolutionist, look independent. It would be very strange if they share a common ancestral pseudogene. But if we admit that these pseudogenes, with identical mutations, formed independently, then why not other pseudogenes as well? So we don't require common descent for pseudogenes.

There are HERVs that conflict with, and are not easily explained by, common descent.

There are fossils that appear planted there and have no obvious precursor. The general pattern of the fossil record is one of an upside down evolutionary tree. That is, you get a myriad of diversity all at once followed by a winnowing. This pattern occurs repeatedly. This is not common descent.

Quote:

Originally posted by Ken
I have not read the detailed journal description, but I have enough faith in the researchers to know that they would not have published anything about dormant teeth genes if it were possible to add certain mouse genes to any old chicken gene to make teeth. Furthermore, I assume they knew which chicken gene(s) to choose based on its placement in the genome relative to genes responsible for teeth formation in other species. You can't just dismiss this so easily. How simple a matter it would have been for the Intelligent Designer to make the chicken gene(s) unreceptive to tooth formation, and then our poor gullible minds would not have been led astray! It would have been much easier to make these genes unable to contribute to tooth formation than not, since it requires a specific set of functions to make teeth, even with the help of the mouse genes. If this were not so, the researchers could have simply used mouse genes to instruct our appendix gene(s), for example, to make teeth! Ken

First, you need to understand that results are routinely cast in the light of evolution, even if the connection is only remote. I'm not dismissing the Science paper so easily. The results simply do not support the claim that there is a dormant set of "teeth" genes in the bird.

Second, you say "How simple a matter it would have been for the Intelligent Designer to make the chicken gene(s) unreceptive to tooth formation." But would it really be so simple? You see we know not enough to make such a statement; not nearly enough. Also, it is not as though God has allowed for such an ambiguous situation to arise as you make it out to be. What more do you want? There are all kinds of problem with common descent; yet you would require for it to be impossible for common descent theories to be constructed. But how can such a thing be done when we are so adamant that it must be true. I suspect it really doesn't matter how much evidence one stacks up against common descent, we'll still find a way to argue for it. And then people come along and ask why the Creator didn't short-circuit that argument too. This is testing God.

Charles Darwin · 10-05-2003, 12:30 AM

Quote:

Originally posted by Ken
You've given us one case where HERVs argue against common descent.

Two.

Quote:

Originally posted by Ken
Rather than assuming this has no explanation, let's wait to find out whether in fact there may exist traces of the HERV in question, or whether this may be a different kind of HERV (or not an HERV altogether) that is more prone to disappearing from the genome than other HERVs. If indeed there is no possible explanation for the disappearance of this HERV, then that would indeed be good evidence against common descent, and I would be willing to reconsider my position. But there are so many instances that do testify to common descent that I would be surprised if a good explanation for the missing human HERV is not forthcoming. I will go further out on a limb and make this prediction: A reasonable explantion for the missing HERV will come to light. If it does, then will you be willing to accept it as a argument against your position?

Certainly.

Quote:

Originally posted by Ken
Yes, assuming the sub-populations (i.e., races) have interbred. But once you have isolated populations (e.g., Australian Aboriginees), this is no longer feasible. But the main point, as others have expressed, is that given this data:

1) Chimps, the animals most closely allied to humans genetically, have 24 sets of chromosomes, and

2) Humans have 23 sets of chromosomes,

then, not knowing anything about the actual structure of the chromosomes, the only reasonable way to account for the difference, from the perspective of common descent, is to posit a fusion event sometime after the split of the chimp-human lineage. Why? Because it highly unlikely for a creature to lose a whole chromosome and survive. So when evidence of fusion was discovered (i.e., telomeres in chromosome 2), this was a fulfillment of evolutionary prediction.

Now, you can say "Big deal! This doesn't preclude special creation, nor is it surprising in the light of special creation." But here's the point, a point which can be made for hundreds of other like phenomena (e.g., nested hierarchies): While special creation could accommodate either outcome (e.g., fusion or no fusion, nested hierarchies or no nested hierarchies), evolution could not be true (or would suffer a great setback) if it were any other way (e.g., evidence that fusion had not occurred).

More later,

Ken

You are operating under a great misconception. Common descent would not be disproved if the human genome chromsome 2 was not fused. I don't know where you got that from. There are all kinds of genotype changes from species to species that common descent has no problem with. Was there a dilemma with common descent and evolution before the fusion hypothesis was posited?

The same for your nested hierarchies. Anomalies and difficulties are routinely explained by evolutionists using such devices as extraordinarily and temporarily high rates of mutation. Such events would erase the hierarchical pattern. And if you are willing to swallow the origin of life once, why not twice? And thrice? Who knows, life may have been popping up like corn. Maybe cladogenesis is rare, but anagenesis is prolific. With life originating so often, you could get many species, but no hierarchy. You greatly underestimate our ability to contrive the desired result.

lpetrich · 10-05-2003, 02:48 AM

"Charles Darwin":
I'm afraid you missed my point. Convergent mutations are observed in the same species, or in highly related species. They are not observed otherwise.

Convergent mutations? What are those supposed to be???

That mutation happening in some ancestor and being faithfully preserved by descendants is a MUCH more reasonable hypothesis.

Imagine that CD was a lawyer defending someone charged with plagiarism. The prosecution thinks it has an open-and-shut case. But CD has a comeback. "You see, my client can easily have come up with the exact same writing as the one he copied off of, grammatical and vocabulary quirks, typos, and all. So that is why one cannot determine whether anyone had committed plagiarism from their writing alone."

But if one can conclude plagiarism from comparison of writing alone, then one can infer evolution from patterns of similarity and difference.

Let me give you some examples. Two related species of frogs, Rana fusca and Rana esculents have, as you would expect, very similar eyes. Yet they form differently. As Gavin de Beer put it, "This is no isolated example."

I'd like to see CD explain what he means by "form differently", and why this is not an "isolated example". I also note that Gavin de Beer had wrote 32 years ago, and a lot can happen in that amount of time. Finally, is this his only example?

It is not unusual that structures thought to be homologous, in fact, develop from different genes and/or different development pathways. Homologies that develop differently conflict with common descent.

I notice that CD has not listed any specific genes that this is allegedly true of.

There are similar pseudogenes in an endosymbiotic bacteria (Buchnera, as discussed in a recent post) from different hosts, which, even if one is an evolutionist, look independent. ...

However, the hosts could easily have diversified with ancestral Buchnera bacteria living inside of them. Aphids could well have had these bacteria for as long as their ancestors had been sucking plant sap, which is around 200 million years according to some estimates.

There are HERVs that conflict with, and are not easily explained by, common descent.

Yawn. HERV's can become lost.

There are fossils that appear planted there and have no obvious precursor.

Which oens.

The general pattern of the fossil record is one of an upside down evolutionary tree. That is, you get a myriad of diversity all at once followed by a winnowing. This pattern occurs repeatedly.

Except that this diversification typically has a treelike structure; all that's happened is repeated pruning.

Right now we have a lot of evidence against common descent.

Like video of new species being poofed into existence?

There are a great many cases of convergent evolution. Similar designs which must have arisen separately. This conflicts with common descent.

Except that convergent evolution can often be recognized by differences in detail. Consider all these examples:

Wings:
Birds
Bats
Pterosaurs
Insects

Anteating:
Echidna (spiny anteater)
Pangolin
Aardvark
South American anteater

Camera Eyes:
Vertebrates
Cephalopods (squid, octopuses)

Antishness:
Ants
Termites

Prickly Coats:
Porcupines
Sea Urchins
Thorny Plants
Etc.

Venom:
Arachnids
Hymenopterans (wasps, bees, ants)
Snakes
Etc.

Armor:
Tree bark
Seed/nut shells
Aquatic-invertebrate shells
Arthropod outer skin
Fish, lizard/snake scales
Turtle shells
Armadillo skin plates
Etc.

Fins:
Squid
Fish
Ichthyosaurs
Plesiosaurs
Cetaceans

Hopping limbs:
Orthopterans (grasshoppers, locusts, crickets, katydids)
Frogs
Kangaroos
Rabbits

Grasping limbs:
Scorpions
Mantids
Lobsters/crabs
Perching birds (can grab a branch with their feet)
Primates

In many cases, the convergent feature's details are different enough to clearly indicate convergence. Bird wings closely resemble each other, and bat wings closely resemble each other, but bird and bat wings are very different-looking. Likewise, porcupine and sea-urchin spines are made in very different ways. Rabbit hind legs do not look much like grasshopper hind legs. And human hands do not look much like songbird feet or lobster claws.

In some cases, the convergent features are very similar-looking, but the rest of the organism gives it away. The various anteaters have long, thin snouts and tongues, but the rest of the animal is different enough to indicate convergent evolution -- the closest relatives of each one are non-anteaters.

monkenstick · 10-05-2003, 04:42 AM

Quote:

I'm afraid you missed my point. Convergent mutations are observed in the same species, or in highly related species. They are not observed otherwise. So it is not "preposterous" to hypothesize that the same mutation observed in similar species could be the result of convergent mutations rather than common descent; and that a different mutation observed in a farther species is not convergent (and therefore likely to be at a different location) because the species are not so closely related. It is an independent mutation. So, you had independent mutations in these four species, but three species, the most similar, had convergent mutations.

I'm not saying I know that this is what happened. I'm merely saying that it need not be viewed as some great coincidence. We observe empirically that convergent mutations occur, and that they occur in highly similar species. Now we observe a pseudogene that has the same apparent mutation in the most similar species, and a different mutation in the more distant species. This fits.

Also, you ignored my question about the gibbon sequences. You say "all the gibbons" but I aware of only a single gibbon sequence. Are there more? If so, can you specify them?

*sigh*
Maybe i'd better list it

Members of family hominidae:

H. Sapiens - nonsense mutation in codon 33
P. Troglodytes - nonsense mutation in codon 33
P.Pygmaeus - nonsense mutation in codon 33
G.Gorilla - nonsense mutation in codon 33

Members of the family Hylobatidae:
H.lar - nonsense mutation in codon 18
H.agilis - nonsense mutation in codon 18
H.muelleri - nonsense mutation in codon 18
H.concolor - nonsense mutation in codon 18
H.syndactylus - nonsense mutation in codon 18

Now, look at the tree again, click on hominidae, and then click on hylobatidae
http://tolweb.org/tree?group=Catarrh...group=Primates

putting these mutations down to convergence rather than descent is clutching at straws trying to avoid a conclusion you don't like. Parsimony, maximum likelihood and bloody common sense indicate that these mutations are a shared derived characters

The amount of fortuitous convergent mutations you're proposing would make paternity tests useless, and forensic DNA analysis inadmissible

REF:http://www.ncbi.nlm.nih.gov/entrez/q...&dopt=Citation

Ken · 10-05-2003, 08:11 PM

This site (whose accuracy I cannot necessarily vouch for) suggests that the GLO mutation affects the entire sub-order Anthropoidea, including the family Hominidae, the gibbons and others, but not the prosimians. If this is accurate, CD, would you suggest that these dozens of species all acquired the same mutation independently, while the urate oxidase mutation affected only the species of the family Hominidae and not the gibbons (in keeping with the expectations of common descent)? If the mutations arose independently, should there not be an anthropoid species here and there that does not suffer from the GLO mutation? I don't think all the species have been surveyed, but the theory of common descent predicts that when the data is all in, all the anthropoid species will be shown to suffer from the same mutation. If not, then your theory would begin to look more promising. Otherwise, common descent appears to have more explanatory power.

markfiend · 10-06-2003, 03:27 AM

Quote:

Originally posted by Charles Darwin
So it is not "preposterous" to hypothesize that the same mutation observed in similar species could be the result of convergent mutations rather than common descent; and that a different mutation observed in a farther species is not convergent (and therefore likely to be at a different location) because the species are not so closely related.

and in a different post...

Two related species of frogs, Rana fusca and Rana esculents have, as you would expect, very similar eyes.

CD, do you not realise that by accepting "related species", and species that are "similar" or "not so closely related", you are implicitly accepting common descent?

If common descent is false, then how can you say that species are related to each other at all?

Oolon Colluphid · 10-06-2003, 03:31 AM

Quote:

Originally posted by markfiend
CD, do you not realise that by accepting "related species", and species that are "similar" or "not so closely related", you are implicitly accepting common descent?

If common descent is false, then how can you say that species are related to each other at all?

But you see, they're still the same 'kind'.

Has CD defined 'kind' yet? If not, it's about time he did, since it is crucial.

Oolon

Jack the Bodiless · 10-06-2003, 05:32 AM

Quote:

There are fossils that appear planted there and have no obvious precursor.

You keep saying this, but we're no closer to finding out which fossils you're referring to.

This is a dangerous argument for creationists to use, because we keep finding the "missing" fossils. The history of this argument is one of uninterrupted retreat by the creationists.

Quote:

The general pattern of the fossil record is one of an upside down evolutionary tree. That is, you get a myriad of diversity all at once followed by a winnowing. This pattern occurs repeatedly. This is not common descent.

...Yes, it is. Why are mass-extinctions, and subseqent rapid diversification to fill vacant niches, supposedly "not common descent"?

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10-05-2003, 02:48 AM	#615
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	"Charles Darwin": I'm afraid you missed my point. Convergent mutations are observed in the same species, or in highly related species. They are not observed otherwise. Convergent mutations? What are those supposed to be??? That mutation happening in some ancestor and being faithfully preserved by descendants is a MUCH more reasonable hypothesis. Imagine that CD was a lawyer defending someone charged with plagiarism. The prosecution thinks it has an open-and-shut case. But CD has a comeback. "You see, my client can easily have come up with the exact same writing as the one he copied off of, grammatical and vocabulary quirks, typos, and all. So that is why one cannot determine whether anyone had committed plagiarism from their writing alone." But if one can conclude plagiarism from comparison of writing alone, then one can infer evolution from patterns of similarity and difference. Let me give you some examples. Two related species of frogs, Rana fusca and Rana esculents have, as you would expect, very similar eyes. Yet they form differently. As Gavin de Beer put it, "This is no isolated example." I'd like to see CD explain what he means by "form differently", and why this is not an "isolated example". I also note that Gavin de Beer had wrote 32 years ago, and a lot can happen in that amount of time. Finally, is this his only example? It is not unusual that structures thought to be homologous, in fact, develop from different genes and/or different development pathways. Homologies that develop differently conflict with common descent. I notice that CD has not listed any specific genes that this is allegedly true of. There are similar pseudogenes in an endosymbiotic bacteria (Buchnera, as discussed in a recent post) from different hosts, which, even if one is an evolutionist, look independent. ... However, the hosts could easily have diversified with ancestral Buchnera bacteria living inside of them. Aphids could well have had these bacteria for as long as their ancestors had been sucking plant sap, which is around 200 million years according to some estimates. There are HERVs that conflict with, and are not easily explained by, common descent. Yawn. HERV's can become lost. There are fossils that appear planted there and have no obvious precursor. Which oens. The general pattern of the fossil record is one of an upside down evolutionary tree. That is, you get a myriad of diversity all at once followed by a winnowing. This pattern occurs repeatedly. Except that this diversification typically has a treelike structure; all that's happened is repeated pruning. Right now we have a lot of evidence against common descent. Like video of new species being poofed into existence? There are a great many cases of convergent evolution. Similar designs which must have arisen separately. This conflicts with common descent. Except that convergent evolution can often be recognized by differences in detail. Consider all these examples: Wings: Birds Bats Pterosaurs Insects Anteating: Echidna (spiny anteater) Pangolin Aardvark South American anteater Camera Eyes: Vertebrates Cephalopods (squid, octopuses) Antishness: Ants Termites Prickly Coats: Porcupines Sea Urchins Thorny Plants Etc. Venom: Arachnids Hymenopterans (wasps, bees, ants) Snakes Etc. Armor: Tree bark Seed/nut shells Aquatic-invertebrate shells Arthropod outer skin Fish, lizard/snake scales Turtle shells Armadillo skin plates Etc. Fins: Squid Fish Ichthyosaurs Plesiosaurs Cetaceans Hopping limbs: Orthopterans (grasshoppers, locusts, crickets, katydids) Frogs Kangaroos Rabbits Grasping limbs: Scorpions Mantids Lobsters/crabs Perching birds (can grab a branch with their feet) Primates In many cases, the convergent feature's details are different enough to clearly indicate convergence. Bird wings closely resemble each other, and bat wings closely resemble each other, but bird and bat wings are very different-looking. Likewise, porcupine and sea-urchin spines are made in very different ways. Rabbit hind legs do not look much like grasshopper hind legs. And human hands do not look much like songbird feet or lobster claws. In some cases, the convergent features are very similar-looking, but the rest of the organism gives it away. The various anteaters have long, thin snouts and tongues, but the rest of the animal is different enough to indicate convergent evolution -- the closest relatives of each one are non-anteaters.

10-05-2003, 08:11 PM	#617
Ken Junior Member Join Date: Feb 2003 Location: Duncanville, TX USA Posts: 64	This site (whose accuracy I cannot necessarily vouch for) suggests that the GLO mutation affects the entire sub-order Anthropoidea, including the family Hominidae, the gibbons and others, but not the prosimians. If this is accurate, CD, would you suggest that these dozens of species all acquired the same mutation independently, while the urate oxidase mutation affected only the species of the family Hominidae and not the gibbons (in keeping with the expectations of common descent)? If the mutations arose independently, should there not be an anthropoid species here and there that does not suffer from the GLO mutation? I don't think all the species have been surveyed, but the theory of common descent predicts that when the data is all in, all the anthropoid species will be shown to suffer from the same mutation. If not, then your theory would begin to look more promising. Otherwise, common descent appears to have more explanatory power.

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