when it comes to the truth of evolution, many Christians feel compelled to look the other way … While Genesis contains wonderful insights into the relationship between God and the creation, it simply does not contain scientific ideas about the origin of the universe, the age of the earth or the development of life.
So religious beliefs should not inform our views on origins, got it.
And all life forms are related to each other though evolution. These are important truths that science has discovered through careful research.
Scientific research has revealed on such thing. Not even close.
Anyone who values truth must take these ideas seriously, for they have been established as true beyond any reasonable doubt.
This is the universal claim of evolutionists, but it has never been even remotely demonstrated scientifically.
There is much evidence for evolution.
There is much evidence for geocentrism.
The most compelling comes from the study of genes, especially now that the Human Genome Project has been completed and the genomes of many other species being constantly mapped.
In particular, humans share an unfortunate “broken gene” with many other primates, including chimpanzees, orangutans, and macaques. This gene, which works fine in most mammals, enables the production of Vitamin C. Species with broken versions of the gene can’t make Vitamin C and must get it from foods like oranges and lemons.
These similar broken genes (the so-called pseudogenes) are found with broken parts that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that the breaks are not due to common descent. It is therefore the fallacy of special pleading to claim that when such breaks fit the expected evolutionary pattern they serve as proof texts for evolution.
Of course none of this matters because the argument was never scientific to begin with.
Thousands of hapless sailors died painful deaths scurvy during the age of exploration because their “Vitamin C” gene was broken.
How can different species have identical broken genes? The only reasonable explanation is that they inherited it from a common ancestor.
The only reasonable explanation is common descent? It is the umpteenth time evolutionists have proclaimed their metaphysics in the guise of science. And it is the umpteenth time they have done this right after insisting religion must have nothing to do with origins science. You can read more about this here, here, here, here and here. Simply put, this claim that the only reasonable explanation for pseudogenes is common descent does not come from science—it can’t.
Such evidence proves common ancestry with a level of certainty comparable to the evidence that the earth goes around the sun.
True, given the evolutionist’s religious mandates, evolution is highly certain. But from a scientific perspective the idea has substantial problems.
This is but one of many, many evidences that support the truth of evolution
True, evolution’s religious view converts a great many unlikely evidences into proof texts. Religion drives science, and it matters.
Not sure if it's worth repeating that "Is not" doesn't constitute much of an argument.
ReplyDeleteAnd all life forms are related to each other though evolution.
Yes, that has been well-established by science.
These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.
ReplyDeleteAny references to the primary literature on that point?
In these cases even evolutionists admit that they are not due to common descent.
Primary literature references?
Pedant said...
ReplyDeleteThese similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.
Any references to the primary literature on that point?
In these cases even evolutionists admit that they are not due to common descent.
Primary literature references?
Cornelius doesn't 'do' the primary scientific literature. It's too much trouble. Since this blog is written as propaganda for his scientifically illiterate IDC sycophants, there's no need for him to be technically accurate, or back up his bombastic rhetoric.
"Making it up as you go" has always been a key component of every Creationist argument. Cornelius has embraced the style with open arms.
Zachriel said, "And all life forms are related to each other though evolution.
ReplyDeleteYes, that has been well-established by science"
---
It's those kind of exaggerated statements inform me of just how ridiculous and sloppy this whole sordid field of evolutionary study is.
Matter of fact words like, "ALL", "WELL-ESTABLISHED" is nothing but over the top hogwash. This is not careful and methodical science, it is akin to reading tea leaves.
Cornelius: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern."
ReplyDeleteCornelius, I think we're approaching the one year anniversary of the first time I asked you this question: Can you give examples of pseudogenes that don't fit the expected evolutionary pattern? (my guess is 'no')
Cornelius: "The only reasonable explanation is common descent? It is the umpteenth time evolutionists have proclaimed their metaphysics in the guise of science."
Say we found a series of two dozen animal tracks by a riverbed in Africa. they are consistent in size, shape, and stride with elephant tracks, and inconsistent in size, shape, and stride with any other known animal. Am I then off my rocker if I say: "The only reasonable explanation is that an elephant made these tracks?" Am I introducing metaphysics into the conversation because I haven't considered an unspecified, undocumented, unverified animal made the tracks as a likely possibility?
Neal, three questions for you, one at a time:
ReplyDelete1. Do you think paternity tests are reliable? If someone wrongly accused you of fathering an illegitimate child, and a paternity test confirmed that you were not the father, would you consider yourself vindicated by the test?
Derick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?
ReplyDeleteOut of time for now. More to follow for you and Scott
CH: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent."
ReplyDeleteWhaa? Can I buy a link?
Derick:
ReplyDelete===
Say we found a series of two dozen animal tracks by a riverbed in Africa. they are consistent in size, shape, and stride with elephant tracks, and inconsistent in size, shape, and stride with any other known animal. Am I then off my rocker if I say: "The only reasonable explanation is that an elephant made these tracks?" Am I introducing metaphysics into the conversation because I haven't considered an unspecified, undocumented, unverified animal made the tracks as a likely possibility?
===
If you're going to make this argument, then (i) briefly mention the alternatives and why they were ruled out and (ii) briefly mention the status of the explanation you are proposing.
Evolutionists do the former but not the latter. In the former, they explain that no designer would have created pseudogenes. In the latter, they sometimes fail to explain that evolution has substantial scientific problems, they in fact misrepresent the science, saying there are no substantial scientific problems.
Tedford the idiot said...
ReplyDeleteDerick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?
Seriously Tedford, you are a clueless idiot.
DNA comparisons are used all the time for establishing ancestral relationships.
They can be used to establish direct paternity as described above.
They can be used to establish more distant relationships, as the descendants of slave Sally Hemings were linked to Thomas Jefferson.
They can be used to establish the relationships between large groups of even more distantly related people, as Canadian and Alaskan Inuits have been genetically identified as closely related to indigenous Siberian and Mongolian populations.
The exact same techniques are also used to establish the relationships between species, such as humans and chimps sharing a common ancestor approx. 6 MYA.
Why don't you tell us why the techniques work and are accepted in the first three cases, but suddenly become invalid in the fourth case.
"They sometimes fail to explain that evolution has substantial scientific problems"
ReplyDeleteMaybe you should define the 'substantial scientific problems'. Controversies,yes. Works in progress, yes. But substantial problems? I've yet to see one here, that you've actually interpreted the evidence for correctly, that presents a falsification of common descent.
Cornelius Hunter said...
ReplyDeleteEvolutionists do the former but not the latter. In the former, they explain that no designer would have created pseudogenes. In the latter, they sometimes fail to explain that evolution has substantial scientific problems, they in fact misrepresent the science, saying there are no substantial scientific problems.
Sorry Cornelius, but only in your little fantasy Creationist world does your bellyaching "ToE can't explain everything to my personal satisfaction!!" count as substantial scientific problems.
Guess you'll just have to live with the disappointment.
Neal: Derick, try running paternity tests on all species and see if they all come back as positive! Your analogy is flawed. Seriously?
ReplyDeleteNeal, you seem to have a pathological aversion to answering simple, direct yes or no questions. My question had nothing to do with other species. I'm taking about human paternity tests. And apparently, you can't distinguish between an analogy and a question. I made no analogy in my question to you.
I'll rephrase for simplicity and clarity:
1. Do you think that paternity tests are a reliable means of determining human paternity? Yes, or no.
(typing either a two or three word response shouldn't demand much of your time)
Cornelius: "If you're going to make this argument, then (i) briefly mention the alternatives and why they were ruled out and (ii) briefly mention the status of the explanation you are proposing."
ReplyDeleteI believe I did already.
(i) the footprints are not consistent in size, shape, or stride with any other known animal; rhinos, hippos, lions, hyenas, pandas, kangaroos, polar bears, turtles, antelopes, geese, etc. We of course cannot rule out chupacabras, yetis, dragons, pixies, or centaurs, but that is of no consequence.
(ii) With a reasonable degree of certainty, one can say that upon finding elephant tracks, it is a fact that elephants were in the area at one point in the past. With more corroborating evidence, such as elephant stool or elephant blood (from an attack) the fact of the elephant's presence can be asserted with a higher and higher degree of certainty.
How can different species have identical broken genes? The only reasonable explanation is that they inherited it from a common ancestor.
ReplyDeleteThe only reasonable explanation is common descent?
It would be nice if you could sketch some alternative explanations so we can discuss the empirical basis of these ideas.
RobertC:
ReplyDelete===
Maybe you should define the 'substantial scientific problems'. Controversies,yes. Works in progress, yes. But substantial problems? I've yet to see one here, that you've actually interpreted the evidence for correctly, that presents a falsification of common descent.
===
Falsification?
It is amazing how consistent is this evolutionary fallacy. Darwin used it and ever since it has key to evolutionary arguments. It shifts the burden away from the evolutionist who is making the claim, and then trades on a false dichotomy between falsification and fact.
"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, then my theory would absolutely break down. But I can find out no such case." --C. Darwin.
I think these posts prove CH's point. If all the intelligence that goes into these posts can not come up with a reasonable interpretation of the biological facts, then how unlikely is it that chance by itself can account for the diversity of life. Probability = 0. Therefore all the evidence is against evolution. Evolutionists are just religious science stoppers.
ReplyDelete.
Zachriel"
ReplyDelete===
"And all life forms are related to each other though evolution."
Yes, that has been well-established by science.
===
Actually that has *never* been established. Not once. Even giving evolution all the breaks, and allowing for the uncertainties of a historical process, it has absolutely failed to prove its claims. We can argue about the details of just how badly evolution does on the evidence, but there is no question that evolution is not a scientific fact, or even anywhere remotely close to such a status. Evolutionists universally claim this, but never back it up. Read Jerry Coyne's latest book, as one recent example.
RobertC:
ReplyDelete===
CH: "These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent."
Whaa? Can I buy a link?
===
Uh, what do you mean?
Derick Childress:
ReplyDelete===
I believe I did already.
(i) the footprints are not consistent in size, shape, or stride with any other known animal; rhinos, hippos, lions, hyenas, pandas, kangaroos, polar bears, turtles, antelopes, geese, etc. We of course cannot rule out chupacabras, yetis, dragons, pixies, or centaurs, but that is of no consequence.
(ii) With a reasonable degree of certainty, one can say that upon finding elephant tracks, it is a fact that elephants were in the area at one point in the past. With more corroborating evidence, such as elephant stool or elephant blood (from an attack) the fact of the elephant's presence can be asserted with a higher and higher degree of certainty.
===
So now let's bring it back to Giberson's claims. Can you provide these two for his case of the pseudogene?
Pedant:
ReplyDelete===
These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern.
Any references to the primary literature on that point?
===
Inferred fitness-reducing mutations in pseudogenes that do not align with common descent are not hard to find. I'd be glad to assist you, but I wonder what difference it would make for you? It has never changed anyone's mind before. Such mutations are simply chalked up to convergence.
Hunter:
ReplyDeleteInferred fitness-reducing mutations in pseudogenes that do not align with common descent are not hard to find. I'd be glad to assist you, but I wonder what difference it would make for you?
Try. Take a chance. Why the diffidence?
I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent."
ReplyDeleteI really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.
RobertC and Pedant:
ReplyDelete===
RobertC:
I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent."
I really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.
===
Rationalism is theory-driven, not data-driven. Data that do not align are explained by the appropriate epicycle, filed away and forgotten. This isn't about science. Biologists are not puzzled, evolutionists are puzzled.
===
Pedant:
Hunter: What difference it would make for you?
Try. Take a chance.
===
It's all about "chance" with evolutionists. Who knows, says the evolutionist, perhaps those random nerve firings in my head with just happen to enlighten me. Sorry, not going to happen.
Pseudogene examples:
1. Wu XW, Muzny DM, Lee CC, Caskey CT., “Two independent mutational events in the loss of urate oxidase during hominoid evolution,” J Mol Evol. 1992 Jan;34(1):78-84.
Quote: The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.
2. Inai Y, Ohta Y, Nishikimi M., The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon, J Nutr Sci Vitaminol (Tokyo). 2003 Oct;49(5):315-9.
Quote: Assuming an equal chance of substitution throughout the sequences, the probability of the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences.
Cornelius Hunter said...
ReplyDeletePseudogene examples:
1. Wu XW, Muzny DM, Lee CC, Caskey CT., “Two independent mutational events in the loss of urate oxidase during hominoid evolution,” J Mol Evol. 1992 Jan;34(1):78-84.
Quote: The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.
Oh dear oh dear oh dear..
Cornelius caught passing on another quote-mined quote from a paper to paint a dishonest and misleading picture of the results:
"Abstract: Urate oxidase was lost in hominoids during primate evolution. The mechanism and biological reason for this loss remain unknown. In an attempt to address these questions, we analyzed the sequence of urate oxidase genes from four species of hominoids: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and gibbon (Hylobates). Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. Because the disruption of a functional gene by independent events in two different evolutionary lineages is unlikely to occur on a chance basis, our data favor the hypothesis that the loss of urate oxidase may have evolutionary advantages."
Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.
Thorton:
ReplyDelete===
Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.
===
Never heard of it. If they figured it out, then good for them.
Cornelius Hunter said...
ReplyDeleteThorton:
===
Interesting that Cornelius "I'm not a Creationist, honest!!" Hunter pulled his two examples from a piece of BS by John Woodmorappe (Jan Peczkis) at AnswersInGenesis here.
===
Never heard of it.
Sure you didn't. It was pure luck that the two quotes from two different papers you posted above are the exact verbatim ones provided in the 2004 crappy AIG Woodmorappe article on pseudogenes.
What an amazing coincidence.
I invite the readers of this thread to view the AIG article here and see this remarkable coincidence for themselves.
Look on the bright side Cornelius. Only two more miracles like the "identical quotes" one above and you'll qualify for sainthood!
ReplyDeleteYeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent," but they are horribly dishonest quotemines.
ReplyDeleteCornelius, I know you have the computer skills to do a GULO gene phylogenetic tree. Why don't you show us how it conflicts with common ancestry?
Here's some:
http://pandasthumb.org/archives/2008/05/23/images/GULO_PHYLIP_Tree_Common_names.png
http://pandasthumb.org/archives/2008/05/24/images/GULO_CLUSTAL_ALIGN_V2.jpg
ps-I'll give you a hint-Rats were the outlier in that paper, the ones with the mutational hotspots, skewing the results. With more genome sequences, this is clear.
These data are public, and you could repeat these experiments yourself.
Or you could keep pulling from AIG. Guess it is a matter of what literature matters to you.
Cornelius Hunter: Actually that has *never* been established.
ReplyDeleteOf course common ancestry has been established. The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.
We've attempted to have this discussion before, but even basic discussions of the basic patterns, or the meaning of correlation, have been fruitless. It's like being stuck on the same chapter of the same Bio 101 textbook forever.
NATIONAL ACADEMY of SCIENCES: "The theory of evolution has become the central unifying concept of biology and is a critical component of many related scientific disciplines. In contrast, the claims of creation science lack empirical support and cannot be meaningfully tested."
RobertC:
ReplyDelete===
Yeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent,"
===
You would think the evolutionist, when challenged, would at least defer to the facts. Particularly when the facts were explained beforehand, he expressed disbelief, and then the facts were presented. You can imagine evolutionists making their silly claims when the facts are not readily apparent. But when the facts are right here in plain sight? Incredibly, this is a typical example of evolutionary thought. Even in such a case the evolutionist continues with the bluster. Rather than read what is presented, acknowledge the facts, and deal with them, evolutionists simply look the other way, in convenient denial, and claim the one who points out evolutionist's silliness has failed. Let's review the facts for all to see:
===
CH: These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent.
RobertC: I think we'd all like a reference to an example where biologists "admit that they are not due to common descent" or find "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent." I really think the biologists here are puzzled at these claims, particularly at the not aligning with common descent part.
CH quoting paper: "The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation."
RobertC: Yeesh. Not only did the articles Hunter went for fail to demonstrate evolutionists "admit that they are not due to common descent" or finding "Inferred fitness-reducing mutations in pseudogenes that do not align with common descent," ...
===
The non scientific bluster is really surprising. What is it about "requires multiple origins" that the evolution fails to understand? Or in the other quote provided, what is it about "the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences" that the evolution fails to understand?
===
but they are horribly dishonest quotemines.
===
Horribly dishonest? Now the evolution skeptic is the one who is dishonest? Exactly how does that work? What is dishonest about this interchange on my part?
===
Or you could keep pulling from AIG.
===
But I already stated that I didn't pull from AIG. Oh, that's right, I'm dishonest. This is evolutionary thinking in action.
Cornelius Hunter said...
ReplyDelete===
Or you could keep pulling from AIG.
===
But I already stated that I didn't pull from AIG. Oh, that's right, I'm dishonest. This is evolutionary thinking in action.
If not from AIG, then where exactly did you get this quote CH?
"The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation."
CH: "Or in the other quote provided, what is it about "the same substitutions in both humans and guinea pigs occurring at the observed number of positions and more was calculated to be 1.84 x 10-12. This extremely small probability indicates the presence of many mutational hot spots in the sequences" that the evolution fails to understand?"
ReplyDeleteUmm, the evolutionist has provided you links on why the paper is wrong. Rats, guinea pigs, and humans were compared in the paper. With more genes from other organisms sequenced, it is abundantly clear rats are the outlier. It is the rat that has evolved significantly from the ancestral sequence, not the Guinea Pig and primate that have converged. The calculation does not apply because the human and guinea pig conserved changes are conserved across other species. The authors had the small probability of human and guinea pig sequences converging right, but came up with the wrong explanation-they came up with mutational hotspots, when the answer was that the sequences were ancestral, and not converged!
This is clearly explained here, with primary data:
http://pandasthumb.org/archives/2008/05/the-revenge-of-1.html
This is the danger of approaching the literature non-critically, picking tidbits found by AIG and trumpeting them as falsifications.
By the way, genome sequences are publicly available. You could do these analyses yourself. Try it, and tell me what you find so compelling about this pseudogene.
And all life forms are related to each other though evolution. These are important truths that science has discovered through careful research.
ReplyDeleteSometimes I envy the BLIND FAITH of evolutionists.
"Sometimes I envy the BLIND FAITH of evolutionists."
ReplyDeleteIronic, considering the evolutionists are the onces advancing the empirical data over the "Answers in Genesis" based misinterpretation thereof.
RobertC:
ReplyDelete===
picking tidbits found by AIG and trumpeting them as falsifications.
===
Why do you say "picking tidbits found by AIG" this when I already corrected you?
===
This is the danger of approaching the literature non-critically
===
I did not approach the literature non-critically.
===
trumpeting them as falsifications.
===
Now you're back to the "falsification" fallacy again. Where did I say this falsified evolution?
===
The authors had the small probability of human and guinea pig sequences converging right, but came up with the wrong explanation-they came up with mutational hotspots, when the answer was that the sequences were ancestral, and not converged!
This is clearly explained here, with primary data:
http://pandasthumb.org/archives/2008/05/the-revenge-of-1.html
===
That's fair. My notes predate this blog post by Musgrave (as well as that AIG link). But of course the so-called "hotspots" are not controversial, except I guess with evolutionists.
===
By the way, genome sequences are publicly available. You could do these analyses yourself.
===
I did a fair amount of sequence aligning and analysis of both the GULO and urate oxidate pseudogenes. The comparisons are not nearly as simple and straightforward as you suggest.
===
Try it, and tell me what you find so compelling about this pseudogene.
===
I didn't find anything compelling about it (another strawman of yours?). These pseudogenes do not tell a real obvious story. I have no problem with Musgrave's post about the hotspots. That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about.
Zachriel:
ReplyDelete===
Cornelius Hunter: Actually that has *never* been established.
Of course common ancestry has been established.
===
No it has not.
===
The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.
===
That is (i) affirming the consequent and (ii) confirmation bias. For (i), successful predictions do not confirm the theory, except is you are an evolutionist I guess. For (ii), the data are riddled with prediction failures which are not mere "noise." So if you really believed in your method, you would have dropped evolution already.
===
We've attempted to have this discussion before, but even basic discussions of the basic patterns, or the meaning of correlation, have been fruitless. It's like being stuck on the same chapter of the same Bio 101 textbook forever.
===
Your ideas on why the trees prove evolution were like arguments about why epicycles prove geocentrism. On the other hand, if there is a textbook, journal paper, etc, that makes your point, then let's have a look.
===
NATIONAL ACADEMY of SCIENCES: "The theory of evolution has become the central unifying concept of biology and is a critical component of many related scientific disciplines. In contrast, the claims of creation science lack empirical support and cannot be meaningfully tested."
===
There is no doubt that evolutionists make this claim that evolution and common descent are established facts. That is not in question here. The problem is they don't support this rather remarkable claim. So these high claims are nothing more than arguments from authority. In science, we need to evidence, not the bluster.
Cornelius Hunter said...
ReplyDeleteRobertC:
===
picking tidbits found by AIG and trumpeting them as falsifications.
===
Why do you say "picking tidbits found by AIG" this when I already corrected you?
You say a lot of things that turn out not to be true CH.
My notes predate this blog post by Musgrave (as well as that AIG link)
Do tell. The AIG article by Woodie dates from Dec 2004. When did you read the papers and make your notes?
"That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about."
ReplyDelete"Not according to the expected pattern."
We've come a long way from:
"In these cases even evolutionists admit that they are not due to common descent."
But regardless, you can't present a single example of a significant unexpected pattern that we'd have to admit is not due to common descent, and I'm supposed to admit my denial, and abandon evolution?
You present data, and tell me I'm wrong. I show the data is false/misinterpreted, I'm still wrong? Is this moderate empiricism, or are you trying to rationalize your beliefs?
RobertC:
ReplyDelete===
"That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern. A fact that you still seem to be in denial about."
"Not according to the expected pattern."
We've come a long way from:
"In these cases even evolutionists admit that they are not due to common descent."
===
A long way? Robert these are synonymous. If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear.
This denial is just bizarre, but this isn't Robert. This is typical for evolutionists.
===
But regardless, you can't present a single example of a significant unexpected pattern that we'd have to admit is not due to common descent,
===
What happened to the urate oxidase example? Doesn't count?
===
and I'm supposed to admit my denial, and abandon evolution?
===
For the umpteenth time, no one is asking you to abandon evolution, as if that were even remotely possible. The question at hand is Giberson's, and evolution's continual, assertion that common descent is the only explanation for pseudogenes. Rationalists are so wedded to their false dichotomy between the certainty of their theory or its absolute falsification, they are unable to work through the evidence.
===
You present data, and tell me I'm wrong. I show the data is false/misinterpreted, I'm still wrong?
===
You did not show that mutational hotspots are false. You showed that in a *particular* case, there was a personal communication from an author taking back one particular conclusion of hotspots. No problem, that's fine. But that doesn't mean hotspots are a fiction.
CH,
ReplyDelete"What happened to the urate oxidase example? Doesn't count?"
Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).
Zachriel: The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.
ReplyDeleteHunter: That is (i) affirming the consequent and (ii) confirmation bias. For (i), successful predictions do not confirm the theory, except is you are an evolutionist I guess.
Successful predictions don't confirm a theory? Tell that to Einstein.
Zach:”The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data."
ReplyDeleteThe problem is that word “constructed”, the trees are not observed, you have actual morphological, embriological and molecular data. You do not see the the branches and the junctions, you see only the supposed tree from the top. In the top you draw the nested hierarchies and imagine a tree behind.
And also the darwinist admits that at the base you do not have the supposed log of the tree but a net where genes jump from one side to other of that net by LGT.
4afb9302-32ec-11e0-becb-000bcdcb471e said...
ReplyDeleteCH,
"What happened to the urate oxidase example? Doesn't count?"
Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).
Awww, you spoiled my punch line!
As you note, that quote does not appear in the paper that CH claims. The one he supposedly read and took notes on. It actually came from this paper.
Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications
Masako Oda, Yoko Satta, Osamu Takenaka, Naoyuki Takahata
Mol Biol Evol (2002) 19 (5): 640-653.
"Another nonsense mutation at codon 187 is shared by the human, the chimpanzee and the gorilla, so that it is most likely to have occurred in their ancestral species. The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation. Overall, it is remarkable that, except one CGA codon in exon 6, all the other four CGA codons are converted to the TGA termination codon in all or some of the hominoids."
Cornelius was in such a hurry to sling any mud he could find at evolution that he C&Ped the wrong reference.
Also as noted, the paper was egregiously quote-mined by Woodmorappe and doesn't come close to supporting Cornelius' original claim.
Oopsie!
4afb9302-32ec-11e0-becb-000bcdcb471e: Hard to say, since the quotation you provided ("The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.") doesn't appear anywhere in the cited paper (Wu et al.1992).
ReplyDeleteOda et al., Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications, Molecular Biology and Evolution 2002.
Here's the abstract:
http://mbe.oxfordjournals.org/content/19/5/640.short
Hunter:
ReplyDeleteWhat is it about "requires multiple origins" that the evolution fails to understand?
Is this an equivocation about the word "origins"?
The authors could have said "requires multiple occurrences" just as well.
Cornelius Hunter: That doesn't change the fact that pseudogenes, like the rest of biology, reveal similarities that are not according to the expected pattern.
ReplyDeleteYou say that, but you provide examples that are consistent with common descent.
Zachriel: The strongest evidence is in the phylogenetic trees constructed from morphological, embryological and molecular data. But there is also substantial fossil data.
Cornelius Hunter: That is (i) affirming the consequent and ...
Confusion on the very basics of the scientific method is why discussions of the particulars of biology are so often unfruitful.
Affirming the consequent
if p then q, q, therefore p.
Hypothesis-testing
if p then q, q supports p
The more unexpected the result, the more types of tests, the wider the divergence in methodologies, the stronger that support.
Cornelius Hunter: For (ii), the data are riddled with prediction failures which are not mere "noise."
Sorry, but there is a very significant nested hierarchy pattern. It exists, and it won't go away because of any supposed anomalies or misunderstandings on your part.
Cornelius Hunter: Your ideas on why the trees prove evolution were like arguments about why epicycles prove geocentrism.
Again, that is incorrect. Geocentrism doesn't make *entailed* predictions about planetary movements. Any point in space can be treated as the center and yield the same results. Compare to the entailed predictions concerning Newtonian Mechanics, such as the retardation of the pendulum.
Cornelius Hunter: But that doesn't mean hotspots are a fiction.
Mutations are thought to be random with respect to fitness, but they are not purely random by any means. There may be mutational biases, mutational hotspots, or different rates in different species. None of this calls into question common descent, or evolution generally.
Cornelius Hunter: If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear.
ReplyDeleteThere are only four bases. Across a large genome, it is quite easy to find random substitutions that are identical due to chance alone. If there are mutational biases, then the chances are even greater.
Zach"Hypothesis-testing
ReplyDeleteif p then q, q supports p"
That is wrong. AT least in my world.
Blas said...
ReplyDeleteZach"Hypothesis-testing
if p then q, q supports p"
That is wrong. AT least in my world.
That says more about your world than it does about hypothesis testing.
Blas said...
ReplyDeleteZach"Hypothesis-testing
if p then q, q supports p"
That is wrong. AT least in my world.
And yet we all use inductive reasoning every day, usually without realizing it.
Science 101- Lesson #1
ReplyDeleteHow evolution differs from other sciences (C02 climate predictions excluded).
Rather than critically look at exceptions and flukes in their findings as problems with their theory, they are quick to answer these problems with almost willy-nilly answers. They are in a constant search to cherry pick evidence that could, may, possibly lend support to their theory. Whatever could, may, possibly lend support is hyped and milked for every ounce they can imagine its worth (i.e. missing link fiasco's, etc).
Next, let's look at how real science is performed.
CH in quotes:
ReplyDelete"If identical mutations occur independently then they are (A) Not according to the expected pattern and (B) Not due to common descent. I don't know how I can make this any more clear. This denial is just bizarre, but this isn't Robert. This is typical for evolutionists."
LOL. You kill me. Of course if mutations occur independently (after the last common ancestor) they are not due to common ancestry! This is absurd! But you pile on the rhetoric, and we're suddenly to:
"These similar broken genes (the so-called pseudogenes) are found in patterns that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that they are not due to common descent. "
So the evolutionists admission is the changes that occur after divergence from a common ancestor aren't due to common ancestry? Rhetorical gymnastics, designed to appear as if you are saying evolutionary biologists are admitting something is wrong with common descent.
But my main objection here is to "expected pattern." What is the expected pattern? I'd say substitutions that neatly align to understood phylogeny, with some changes after divergence from a common ancestor. I'd also say there is NO example you've provided that violated the expected pattern in any substantial way.
"What happened to the urate oxidase example? Doesn't count?"
Well, until this morning there was no REAL reference. At any rate, the paper shows really nice patterns of substitution across the primate UOX pseudogene. Almost all (of many changes) align with known primate phylogeny. One substitution appears in gibbons, orangutans and gorillas, but not humans and chimps (if you believe the sequence data-it is quite old, and BLAST shows some gorilla sequences without the substitution). Regardless, this suggests two events, like the change being present in an ancestor, and reverted in the human/chimp lineage. 1 of 4 bases, unconstrained, long times. Not that improbable. Does a .1% minor mystery falsify the other 99.9%?
"You did not show that mutational hotspots are false. You showed that in a *particular* case, there was a personal communication from an author taking back one particular conclusion of hotspots. No problem, that's fine. But that doesn't mean hotspots are a fiction."
When did I argue for or against mutational hotspots? I merely pointed out the authors were wrong to claim mutational hotspots in humans and guinea pigs, when additional sequences clearly show rats were an outlier. This renders the big number calculation for the convergence of human and guinea pig meaningless. That is all. Not trying to disprove hotspots.
Pedant:
ReplyDelete===
Hunter: What is it about "requires multiple origins" that the evolution fails to understand?
Is this an equivocation about the word "origins"?
===
No.
===
The authors could have said "requires multiple occurrences" just as well.
===
Makes no difference. "Origins", "occurrences", pick your favorite word.
One more note:
ReplyDeleteBecause there are only 4 bases, and DNA sequencing makes mistakes, molecular phylogeny is not based on eyeballing single bases. It is a statistical science.
You will always win the "violates a pattern" argument if you scour the literature for single bases in 20 year old sequences.
Now, do a phylogeny for me with say, good bootstrap values that breaks the mold, and we'll talk.
Data and methodology is publicly available:
http://www.soe.ucsc.edu/classes/bme110/Winter09/Lectures/BME110-Lect8.Feb17.print.pdf
Blas: The problem is that word “constructed”, the trees are not observed, you have actual morphological, embriological and molecular data.
ReplyDeleteSo are elliptical orbits. So?
Blas: And also the darwinist admits that at the base you do not have the supposed log of the tree but a net where genes jump from one side to other of that net by LGT.
Indeed, there is substantial horizontal gene flow even in modern organisms. Again, so?
Zachriel: Hypothesis-testing
if p then q, q supports p
Blas: That is wrong. AT least in my world.
It's the basis of the scientific method, hypothetico-deduction. Let's take an example. Newton proposed laws of gravity and motion. Halley took those laws and applied them to cometary data. He determined that certain of those comets were actually the same body, and he predicted when and where that comet would reappear. The comet was observed in the predicted quadrant on Christmas night, 1758. The observation provided dramatic support, something the entire world could see, but it didn't "prove" Newton's Laws.
Teford:
ReplyDeleteScience 101- Lesson #1
How evolution differs from other sciences (C02 climate predictions excluded).
How about that? A science-ignorant pastor is lecturing us on science.
Chalk one up for hubris on Tedford's list of deadly sins. Looks like you're gonna be holding hands with your colleague Ted Haggard in the lake of fire.
And why am I not surprised you're a AGW-denialist?
Neal,
ReplyDelete1) Are paternity tests a reliable indicator of relatedness? If a paternity test returns a positive result, is that a reliable indicator that the two people tested are closely related?
Lest you think I'm trying to 'trick' you in some way, feel free to ask me any number of yes/no questions yourself.
What exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?
ReplyDeleteRobertC:
ReplyDeleteFair point about the OP. More explanation is needed.
===
But my main objection here is to "expected pattern." What is the expected pattern? I'd say substitutions that neatly align to understood phylogeny, with some changes after divergence from a common ancestor. I'd also say there is NO example you've provided that violated the expected pattern in any substantial way.
Not that improbable. Does a .1% minor mystery falsify the other 99.9%?
===
That's not the issue. That is, the question is not whether or not there are similarities, genetic and otherwise, between species. The evolutionary argument is that there are similarities that don't make sense which myteriously are identical between cousin species. An obvious and compelling sign of common descent.
The pseudogenes provided a great example of this, and are commonly used, such as by Giberson. But inferred mutation events sometimes are not homologous. In those cases even evolutionists agree they are not due to common descent. And these cases show up on pseudogenes. Urate oxidase has several. And sometimes they are debilitating. So the evolutionary argument amounts to special pleading.
In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. This is special pleading. If a mutation (that doesn't align with CD) can be explained by common mechanism, then mutations that do align with CD can also be explained by common mechanism.
===
That is all. Not trying to disprove hotspots.
===
OK, good.
Nat, look here for starters. Is it really so hard to do a little research on your own? What do you tell your students if they ask where to find information on a certain subject?
ReplyDeletenatschuster: What exactly is the mechanism for HGT in modern multicellular organisms?
ReplyDeleteHorizontal gene flow is most prevalent in single-celled organisms, such as through conjugation. Bacteria will even pick up stray pieces of DNA from the environment.
As for multicellular organisms, hybridization is not uncommon, especially in plants. Retroviruses are another mechanism, whereby a virus becomes incorporated into a cell's genome. If this occurs in a germ cell, then it can be transmitted to new generations.
I know hybridization has been observed. But usually works only in closely related species. And would retroviruses be able to, for example, get dog DNA into a cat, or do they only get virus DNA into the host species.
ReplyDeleteTroy:
ReplyDeleteI looked at the article you linked. It talked a lot about bacteria and articifial gene transfer. What I'm asking about is how do we get dog DNA into a cat by natural means.
The evidence indicates that genetic transfer is rare between distantly related animals, though may be more common in aquatic organisms. Plants are more prone to distant hybrids.
ReplyDeleteNat, what makes you think there's dog DNA in cats?
ReplyDeleteZach:"So are elliptical orbits. So?"
ReplyDeleteYou can measure the position of the planets for each day during a rotation around the sun, you do not have the animals or plant to fill the branches of the tree.
"Indeed, there is substantial horizontal gene flow even in modern organisms. Again, so?"
Then you do not ahve a tree of life you have net, then you can prove the unique common ancestor.
"The observation provided dramatic support, something the entire world could see, but it didn't "prove" Newton's Laws."
Exactly, q do not support p. p stands because q.
There is no number of q will prove p.
CH,
ReplyDelete"In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. "
you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?
"But inferred mutation events sometimes are not homologous."
ReplyDeleteRight
"In those cases even evolutionists agree they are not due to common descent."
Because they can't be by definition (post-common ancestor). Naively, someone might misconstrue your statement implies a failure of evolutionary biology.
"And these cases show up on pseudogenes. Urate oxidase has several."
And sometimes they are debilitating."
Debilitating? This is a pseudogene, and "..... the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2..." This is not position 107 in exon 3, which you quoted, where a difference was seen, so I'm at a loss at to where fitness would come into this.
"So the evolutionary argument amounts to special pleading."
Special pleading would be arguing one substitution matters where another does not, all things being equal. Sort of like harping on position 107 as some sort of problem for evolution-it is choosing the 0.1% exception vs. the rest of the data, with no justification.
Drawing a statistics-based conclusion based on the patterns of substitutions across this and other genes is not. Again, with only 4 bases, reversions can occur. Sequencing errors can occur, or polymorphism in the ancestral species. Thus, the statistical science of molecular phylogeny.
So, concluding all great apes share a broken gene (apparently broken at the same position), is not special pleading. And as you say, these pseudogenes are "myteriously are identical between cousin species. An obvious and compelling sign of common descent."
Blas: You can measure the position of the planets for each day during a rotation around the sun, ...
ReplyDeleteThe ellipse is a construction, just like the nested hierarchy.
Blas: ... you do not have the animals or plant to fill the branches of the tree.
You're confusing the nested hierarchy (observed) with the phylogenetic tree (inferred). We can discuss the latter, but not when you deny the former.
Blas: Exactly, q do not support p. p stands because q. There is no number of q will prove p.
Q never "proves" p. It supports it or falsifies it. If you prefer, q shows the consistency of p with the evidence. However, strong predictions can offer significant support — unless you are saying that the sighting of Halley's comet didn't support his hypothesis. Lucky guess, that.
Zach:"Blas: You can measure the position of the planets for each day during a rotation around the sun, ...
ReplyDeleteThe ellipse is a construction, just like the nested hierarchy.
Blas: ... you do not have the animals or plant to fill the branches of the tree.
You're confusing the nested hierarchy (observed) with the phylogenetic tree (inferred). We can discuss the latter, but not when you deny the former."
I always was talking about the tree, why are you bringing the nested hierarchy now? I said you observe it looking the tree from the top.
"unless you are saying that the sighting of Halley's comet didn't support his hypothesis. Lucky guess, that."
Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth? at least a scientific truth?
natschuster said...
ReplyDeleteWhat exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?
Seems to me you asked this same question about a month ago, and it was answered a month ago.
I guess you were too busy cutting pages out of textbooks so your students wouldn't be exposed to scientific ideas that contradict your religious beliefs.
What will be the next topic you deny your students knowledge of? Radiometric dating? Hominid fossils? I'm sure your list must be long.
Blas: I always was talking about the tree, why are you bringing the nested hierarchy now?
ReplyDeleteThat's fine.
In any case, you have to start with the observed pattern, the nested hierarchy. You would still need to understand hypothesis-testing, though.
Blas: Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth?
It means that you can get on a plane and reliably fly across oceans.
Blas: at least a scientific truth?
Eppur si muove.
4afb9302-32ec-11e0-becb-000bcdcb471e said...
ReplyDeleteCH,
"In other words, when such mutations are found in pseudogenes that align with common descent, then they are declared to be compelling proof texts for common descent. But when they do not align with CD, then such mutations are simply explained by common mechanism. "
you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?
Cornelius is just following the standard Creationist playbook:
1. Examine a large collection of data, find a few outliers.
2. Ignore the explanation for the outliers.
3. Scream bloody murder that all the data must be wrong because of the outliers.
Cornelius doesn't seem to be savvy enough to freelance his own anti-science attacks. It's standard Creto Rhetoric 101 the whole way.
Troy and Thorton:
ReplyDeleteThe article posted did say that there was fungus DNA in a plant. I'm asking how it got there. I couldn't find any mention of a plausible mechanism. Dogs and cats was just an example.
And I taught radiometric dating. I even came up with an effective way to teach the concept to leanring disabled kids. (I used jelly beans.) The problem I had with Haeckel's drawing was the fact that they were, at best, wildly inaccurate, if not actually fraudulent. I didn't skip the pages in the textbooks that had photographs instead of the drawings. Though I did mention that the embryos are different at the blastula stage, and at gastrulization, just for the sake of accuracy and balance.
Correction:
ReplyDeleteThe fungus DNA is actually in an aphid. Sorry, my bad.
Zach:"Blas: Maybe the problem is the meaning of the word "support". A hypotesis well supported is a truth?
ReplyDeleteIt means that you can get on a plane and reliably fly across oceans."
That is not truth, what make me get a plane to reliably fly is not the Newton´s theory, but the tested aplication of it. If we never get the dark matter, the plane will fly again and the Newton´s theory will be wrong.
Blas: at least a scientific truth?
Eppur si muove.
That is not an answer.
Blas: That is not truth, what make me get a plane to reliably fly is not the Newton´s theory, but the tested aplication of it.
ReplyDeleteNewton's Theory isn't judged by some measure of philosophical truth, but its fit to the evidence, its reliability at making empirical predictions.
Blas: at least a scientific truth?
Galileo thought the scientific evidence supported the motion of the Earth, so he was speaking the truth as he knew it when he uttered "Eppur si muove", but falsely when he abjured to the Inquisition.
These similar broken genes (the so-called pseudogenes) are found with broken parts that do not fit the expected evolutionary pattern. In these cases even evolutionists admit that the breaks are not due to common descent. It is therefore the fallacy of special pleading to claim that when such breaks fit the expected evolutionary pattern they serve as proof texts for evolution.
ReplyDeleteSo, in support of the above, Hunter came up with two classic creationist arguments with literature references from AIG. And those arguments have now been roundly discredited.
Surely there must be many, many more examples of sequences not fitting common descent in the vast and growing genomic databases available online and elsewhere. That represents a challenge and an opportunity for Hunter (or one of his acolytes) to storm those peer-reviewed publication ramparts and BLAST evolution to the dustbin of history.
Isn't that what a motivated empiricist would do?
nano:
ReplyDelete===
you are ignoring Robert's point that you have to look at the total data. when 99% of the data fit the predicted pattern (as is true for pseudogenes and other data), you say your hypothesis is supported. the 1% is certainly interesting, and should be explored further, but a 100% fit is not even expected, esp. in biology. or does the fact that 1 out of 10 dentists doesn't recommend sugar-free gum convince you to chew Bubblicious?
===
No, I'm not ignoring that point. I'm not pointing to a couple of homoplasies and claiming the CD model therefore fails.
The evolutionary argument is that there are similarities that don't make sense (ie, shared errors) which myteriously are identical between cousin species. An obvious and compelling sign of common descent.
What I am pointing out is that this argument amounts to special pleading. Why? Because there are shared errors that are not homologous. They are homoplasies. Evolutionists say they were produced by identical, indendent events (common mechanism). It is special pleading to turn around and explain the ones that are homologous as such powerful evidence. Without first presupposing evolution, one could just as easily explain those also by common mechanism.
Pendant-
ReplyDeleteI'm sure we'll be hearing about the "problems" of evolution for years to come, despite the huge amount of data and excellent statistics in papers like:
A molecular phylogeny of living primates.
PLoS Genet. 2011 Mar;7(3):e1001342. Epub 2011 Mar 17.
http://www.ncbi.nlm.nih.gov/pubmed/21436896
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.
This comment has been removed by the author.
ReplyDeleteCH,
ReplyDelete"What I am pointing out is that this argument amounts to special pleading. Why? Because there are shared errors that are not homologous. They are homoplasies."
Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.
"It is special pleading to turn around and explain the ones that are homologous as such powerful evidence. Without first presupposing evolution, one could just as easily explain those also by common mechanism. "
no. convergence is mathematically much less likely to occur than inheritance through common descent.
RobertC, it would kill Hunter to even consider the possibility that humans share a common ancestor with all those other primates.
ReplyDeleteWhere would that leave Adam and Eve?
I'm puzzled by the use of 'common mechanism.'
ReplyDeleteThere are many causes of gene mutation. The cause of an A->T conversion in one organism need not be the same in another organism. Nor is it the same as a T->A reversion that might give the appearance of misgrouping by species at a single position.
Further, the numbers are relevant. A reversion, for example, capable of causing the same base (1/4) to appear at a single position seems not at all improbable.
However, If multiple positions follow such a pattern, things become less probable-here the guinea pig math you cited above actually would apply! By the time we reach the 99.9% of bases that follow a pattern-the odds are exceedingly low of all of them independently aligning without common ancestry. So, if you can dismiss common descent, and have a "common mechanism" to explain such low probabilities, then please, describe this mechanism and how it overcomes insurmountable odds.
Until then, can we take common descent as the only reasonable model that fits the phylogenetic data like in the paper I've presented above?
RobertC:
ReplyDelete===
"But inferred mutation events sometimes are not homologous."
Right
"In those cases even evolutionists agree they are not due to common descent."
Because they can't be by definition (post-common ancestor). Naively, someone might misconstrue your statement implies a failure of evolutionary biology.
===
Right. I agree more explanation is needed.
===
Debilitating? This is a pseudogene, and "..... the inactivation of the gene in the clade of the human and the great apes results from a single CGA to TGA nonsense mutation in exon 2..." This is not position 107 in exon 3, which you quoted, where a difference was seen, so I'm at a loss at to where fitness would come into this.
===
That quote illustrates the similarities that are non homologous, that's all. There are several such examples in urate oxidase across the primates. In fact some must have occurred more than merely twice. An identical 8 residue segment is inferred to have inserted independently. An exon 2 nonsense mutations is thought to have occurred independently multiple times. An exon 3 nonsense mutation is inferred to have occurred independently, multiple times. These are low probability events that call for common mechanism.
===
"So the evolutionary argument amounts to special pleading."
Special pleading would be arguing one substitution matters where another does not, all things being equal. Sort of like harping on position 107 as some sort of problem for evolution-it is choosing the 0.1% exception vs. the rest of the data, with no justification.
Drawing a statistics-based conclusion based on the patterns of substitutions across this and other genes is not. Again, with only 4 bases, reversions can occur. Sequencing errors can occur, or polymorphism in the ancestral species. Thus, the statistical science of molecular phylogeny.
So, concluding all great apes share a broken gene (apparently broken at the same position), is not special pleading. And as you say, these pseudogenes are "myteriously are identical between cousin species. An obvious and compelling sign of common descent."
===
Right, but there are breaks that are not homologous.You can argue the multiple, identical mutations constitute low probability events that just happened anyway. Or (more plausibly) you can look for common mechanism. But either way, you are explaining them without CD. So to then pick out other such breaks as evidence of the so-called "shared error" proof, is special pleading.
nano:
ReplyDelete===
Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.
===
No, common mechanism (CM) can explain a prevalence of homologous mutations (though pseudogenes are not as clean as you make it sound). Indeed, the hypothetical you describe (homoplasies vastly outnumbered homologies) I think would be difficult to explain.
CH,
ReplyDelete"common mechanism (CM)" is this the long-awaited glimmer of an alternative hypothesis? please do tell more.
Cornelius Hunter said...
ReplyDeletenano:
===
Of course. but the vast majority are homologous. if the the situation was reversed and homoplasies vastly outnumbered homologies (or even if they were more evenly distributed) you would have a point. but they don't and you don't.
===
No, common mechanism (CM) can explain a prevalence of homologous mutations (though pseudogenes are not as clean as you make it sound). Indeed, the hypothetical you describe (homoplasies vastly outnumbered homologies) I think would be difficult to explain.
LOL! Ain't Cornelius cute?
He took the Intelligent Design Creationist argument "common design can explain it" and changed it to "common mechanism can explain it"
Maybe "CM" will be his big contribution to the ICD movement, like Behe's "IC" and Dembski's "CSI".
Tell us Cornelius, what observations couldn't be explained by "common mechanism"?
This comment has been removed by the author.
ReplyDeleteQuotes from natschuster
ReplyDeleteThe problem I had with Haeckel's drawing was the fact that they were, at best, wildly inaccurate, if not actually fraudulent.
No need to skip them. Explain them in their historical context, informed by real scholars.
For "balance" on this, check Gould and Richardson's works on the subject:
http://ncseweb.net/creationism/analysis/icon-4-haeckels-embryos (NCSE review)
http://home.uchicago.edu/~rjr6/articles/Haeckel--fraud%20not%20proven.pdf (paper by Richardson citing many papers by Gould)
I didn't skip the pages in the textbooks that had photographs instead of the drawings.
Good.
Though I did mention that the embryos are different at the blastula stage, and at gastrulization, just for the sake of accuracy and balance.
That's not "balance". It doesn't contradict evolutionary theory. There's nothing to balance against. I once gave you a link to an article about the hourglass model of animal development. You should really check that out.
"You can argue the multiple, identical mutations constitute low probability events that just happened anyway."
ReplyDeleteAnd depending on how 'multiple' these events are, I don't think the probability is so low.
"Or (more plausibly) you can look for common mechanism."
I'm not sure what this 'common mechanism' you are referencing is. Especially in the context or explaining away multiple homologous mutations. Could you elaborate? Is common mechanism an alternative to common descent? Can you give an example of a common mechanism.
"But either way, you are explaining them without CD."
No, actually all my explanations have referenced common descent. A common ancestor could contain a change which a sub-lineage reverts back, giving the appearance of mis-grouping species on that gene tree.
Is this without common descent?
A ancestral population might not be fixed at a certain position (insertion of 6 bases). Some descendent species (gorilla, orangutan) fix the insertion, which others fix the non-inserted allele. Is this without common descent?
What explanation for an unusual substitution patterns has been made outside the framework of common descent?
"So to then pick out other such breaks as evidence of the so-called "shared error" proof, is special pleading."
Statistics. See above. It isn't cherry-picking, it is observation of the bulk of the data that supports the hypothesis.
Quotes from natschuster
ReplyDeleteAnd would retroviruses be able to, for example, get dog DNA into a cat... [?]
Yes.
What exactly is the mechanism for HGT in modern multicellular organisms? Has it been observed or just inferred?
Other mechanisms involve parasitic or endosymbiotic bacteria, like Wolbachia... actually, better check the introduction of this paper, it's well-referenced .
http://vsites.unb.br/ib/cel/microbiologia/tebm/wol4.pdf
Robert C said:
ReplyDeleteIronic, considering the evolutionists are the onces advancing the empirical data over the "Answers in Genesis" based misinterpretation thereof.
What 'empirical' data....biased assumptions and smoke and mirrors???
Geoxus:
ReplyDeleteThat article explains bacteria genes in fruit flies. What about fungus genes in aphids?
natschuster: What about fungus genes in aphids?
ReplyDeleteWhat about them? Fungi will invade animal cells in order to ingest nutrients. This close proximity can lead to lateral transfer. Many transfers are probably neutral, and just become genomic detritus, but others may provide an advantage. Such transfers will show as an anomaly against the background nested hierarchy pattern.
Science 101. Lesson #2
ReplyDeleteEvolution differs from other fields of science (excepting C02 based climate predictions) in its lack of self-disciple to consistently follow a true scientific methodology. The willy nilly evolutionist posts on this article that are presented as matter-of-fact dogma are a case in point.
Compare the willy nilly posts here explain the myriad of exceptions with this piece of recent news from the field of physics...
TITLE: New subatomic particle: real or anomaly?
http://www.msnbc.msn.com/id/42497555/ns/technology_and_science-science/
"The catch is, the pattern could represent a real physical phenomenon, or it could be a statistical anomaly. Scientists say there's a 1 in 1,000 chance the finding is just a fluke. To get a better idea of whether the signal is real, researchers need to sort through more data.
Inside the Tevatron, protons and their antimatter partners, antiprotons, are accelerated in a giant ring until they crash into each other at near the speed of light. In the ensuing explosions, many different combinations of exotic particles are created.
The new result, found at the Tevatron's Collider Detector at Fermilab (CDF), hinges on detecting a couple of hundred extra, unexpected instances of a particular combination of products. Such a finding could indicate that an unknown particle is being created in these collisions."
Compare this to the uber-hype that was presumptuously generated by the most recent "missing link" or Tiktaalik roseae five years ago. Science appears to be a self policing endeavor, but in the case of evolution and C02 climate predictions the fox is guarding the hen house.
Here's a link from Discovery.org (which evolutionists hate), but it is an interesting review of Evolutionist Lynn Margulis skepticism of neo-Darwinism. Margulis is calling a spade and spade, which is what science is all about.
ReplyDeleteWhile the evolutionists on this blog are repeating the party line sound bites as if they were "well-established" settled science, behold all is not well in Darwin's house. Even the foxes are revolting!
The various mechanisms of evolution that you guys proclaim as well established by science, are being challenged by Margulis. Not just the minor points, but the very foundation of neo-Darwinism. Some of the points I have been asking you guys to seriously think through.
Margulis quoted: "This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create.... [N]eo-Darwinists say that new species emerge when mutations occur and modify and organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence."
Here's the link:
http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html
Margulis should give you guys something to chew on for a long time.
"What 'empirical' data....biased assumptions and smoke and mirrors???"
ReplyDeleteThe empirical data I presented here is 8 megabases of new sequence, on top of the completed primate genomes, aligned into a robust phylogeny with excellent statistics.
A molecular phylogeny of living primates.
PLoS Genet. 2011 Mar;7(3):e1001342. Epub 2011 Mar 17.
http://www.ncbi.nlm.nih.gov/pubmed/21436896
"Compare the willy nilly posts here explain the myriad of exceptions with this piece of recent news from the field of physics..."
Odd choice. This is a three-sigma finding, which fails to cross the threshold of five sigma that the field sets. That's this line: "Scientists say there's a 1 in 1,000 chance the finding is just a fluke."
Contrast this to the paper I presented, with very robust statistics (bootstrap and others).
"Tiktaalik roseae five years ago"
What's your problem with Tiktaalik?
Neal Tedford: Margulis quoted: "I was taught over and over again that the accumulation of random mutations led to evolutionary change-led to new species. I believed it until I looked for evidence."
ReplyDeleteMargulis earned her PhD in 1963 (UC Berkeley), and was in college when the discovery of DNA was still a novelty. She is still fighting the battles of her youth. Science has moved on from simplistic models of mutation and selection.
... the discovery of {the structure of} DNA ...
ReplyDeleteZachriel, Margulis also said in the same article that "evolutionary biologists believe the evolutionary pattern is a tree. It's not."
ReplyDelete---
Zachriel, That's certainly a mighty blow to your starboard bow.
Your argument against her is because she is too old!!!
Someone could not make this stuff up.
She maybe old, but she obviously struck a nerve!
Tedford the shameless charlatan:
ReplyDeleteCompare this to the uber-hype that was presumptuously generated by the most recent "missing link" or Tiktaalik roseae five years ago.
A bigger hype than the search for the Higgs boson, aka the "God particle"? I get twice as many Google hits for "god particle" than for "tiktaalik", and 6 times as many for "higgs boson".
Don't you ever get tired of lying for Jebus?
Neal,
ReplyDeleteMargulis was right on endosymbiont theory. This earned her acclaim. She also believes HIV doesn't cause AIDS, is a 9/11 truther, and pushed such lousy articles into PNAS that the journal banned communicated submissions by PNAS members.
So she's entitled to her opinions, but I'd take them with a grain of salt.
RobertC said...
ReplyDeleteNeal,
Margulis was right on endosymbiont theory. This earned her acclaim. She also believes HIV doesn't cause AIDS, is a 9/11 truther, and pushed such lousy articles into PNAS that the journal banned communicated submissions by PNAS members.
So she's entitled to her opinions, but I'd take them with a grain of salt.
What RobertC said. Margulis made some very important contributions to science early in her career, but since then has gone farther and farther off the track. Some of the stuff he espouses now is just plain nutty, like the HIV/AIDS denier stuff.
Tara Smith has a good write up of Margulis' going off the deep end here:
Margulis does it again
Being right in one area (symbiogenesis) doesn't make her correct in all areas.
Neal Tedford: Margulis also said in the same article that "evolutionary biologists believe the evolutionary pattern is a tree. It's not."
ReplyDeleteEvolutionary biologists are quite aware of the many exceptions to the nested hierarchy. Again, she is fighting old battles. Science has moved on.
Thorton: Being right in one area (symbiogenesis) doesn't make her correct in all areas.
ReplyDeleteQuite so. Darwin made huge contributions to biology, and was a very careful observer and researcher. But Pangenesis, his 'provisional hypothesis' of inheritance, was more a bad guess than a theory based on evidence.
Anyone else waiting to hear what "common mechanism" is?
ReplyDeleteRobertC said...
ReplyDeleteAnyone else waiting to hear what "common mechanism" is?
Cornelius is probably madly searching AIG even as we type.
Robert C: Anyone else waiting to hear what "common mechanism" is?
ReplyDeleteSure are!
natschuster,
ReplyDeleteSorry, I liked to the wrong paper. This is the right one:
http://www.pnas.org/content/105/44/17023.full
It doesn't say much, but cites many references with different examples for different mechanisms.
What about fungus genes in aphids?
Thorton explained it.
In cases of parthenogenetic reproduction, Buchnera cells are transferred into the parthenogenetic blastoderm-stage embryos; Buchnera are localized proximal to the host germ cells during early development of the host. Moreover, in cases of sexual reproduction, Buchnera enter sexual eggs at the pre-cellularization stage; at this stage, there are no membranous barriers between Buchnera and the germ lines [14,15]. Such localization of Buchnera cells proximal to host germ lines might provide opportunities for the LGT from Buchnera into the germ lines.
From the paper:
http://www.biomedcentral.com/1741-7007/7/12
I didn't know about that. I just did a Google Scholar search.
Anyone else waiting to hear what "common mechanism" is?
ReplyDeleteI bet it involves an intelligently designed algorithm for simulating common ancestry.
Jerry Coyne has a nice post on horizontal gene transfer, including a link to a free recent Current Biology "primer" on the subject.
ReplyDeletehere
Margulis is a crackpot, apparently more interested in boosting her own ego than science.
ReplyDeleteAmong her most crazy claims: her "theory" that sperm tails derive from spirochete bacteria was rejected - not because of lack of evidence, no siree - but because men (the male variety of humans) don't like the idea that part of their sperm is bacterial in origin.
Yeah, an orgasm (I hope this word is not on the black list) just isn't the same knowing that.
Zachriel,
ReplyDeleteMargulis is member of the National Academy of Sciences. The same organization you quoted in a post on April 11 to argue your position from authority.
So, only those members who are under a particular age can be used for your arguments from authority?
Do you have something against old people?
---
Also, its good to see that your moving in the right direction concerning nested hierarchies. Yes, there are, as you say, "many exceptions" to the nested hierarchy. Are you ready to embrace the web pattern of life and leave behind your "old battles"?
Neal Tedford: Margulis is member of the National Academy of Sciences. The same organization you quoted in a post on April 11 to argue your position from authority.
ReplyDeleteAn appeal to authority is valid when
* The cited authority has sufficient expertise.
* The authority is making a statement within their area of expertise.
* The area of expertise is a valid field of study.
* There is adequate agreement among authorities in the field.
* The authority is stating the consensus of those authorities.
* There is no evidence of undue bias.
The proper argument against a valid appeal to authority is to the evidence.
In any case, Margulis is a Darwinist.
Neal Tedford: So, only those members who are under a particular age can be used for your arguments from authority?
ReplyDeleteMargulis isn't wrong because she is old. She's wrong on the evidence. As for her fighting old battles, that's quite obvious in her reference to what she was taught (c. 1960).
Neal Tedford: Yes, there are, as you say, "many exceptions" to the nested hierarchy. Are you ready to embrace the web pattern of life and leave behind your "old battles"?
The nested hierarchy is strongly supported for eukaryotes. Even for prokaryotes, there is still a discernable phylogeny.
Zachriel said, "In any case, Margulis is a Darwinist. "
ReplyDeleteIf you mean she is an evolutionists, then yes, I would agree. But, she is quite plain about neo-Darwinism being a failure, so technically I doubt she would like to be lumped into the Darwinist or neo-Darwinist group.
It is apparent that anyone who disagrees with a neo-Darwinist becomes a target of distain and personal insults.
It shows the poverty of your theories.
Neal Tedford: But, she is quite plain about neo-Darwinism being a failure, so technically I doubt she would like to be lumped into the Darwinist or neo-Darwinist group.
ReplyDeleteMargulis says she is "definitely a Darwinist". That means she accepts the importance of natural selection for determining which variations propagate in nature. However, she is not a neo-Darwinist, meaning she rejects what she considers simplistic and reductionist mutation and selection models. Of course, very few biologists today still adhere to such simplistic models, so it's clear she is still fighting old battles.
In any case, she considers Intelligent Design to be vacuous, and that evolution is a natural process.
Tedford:
ReplyDeleteIt shows the poverty of your theories.
What's your theory, Neal?
Zachriel said, "Of course, very few biologists today still adhere to such simplistic models"
ReplyDeleteSo she is fighting a make believe strawman that "few" accept anyways?
So you acknowledge that she is right in what she says is wrong with neo-Darwinian mechanisms, but her problem is that hardly anyone believes in neo-Darwinism anymore?
Are you trying to have it both ways again?
This comment has been removed by the author.
ReplyDeleteNeal,
ReplyDeleteLet me illustrate the difference between Margulis and yourself.
You have still yet to answer my question, which I'll repeat here for your convenience…
At a minimum, evolutionary processes played a significant role in speciation.
Would you agree with this statement or or disagree?
You've continued to dodge this simple question, dispute the conclusion being based on observations we both appear to agree on.
You're NOT approaching the issue seriously. Instead, you're simply throwing anything you can find at a theory which you personally find objectionable and hoping it sticks.
While you might not realize this, or may even attempt to deny it, we can piece this together based on the arguments you present, the observations you accept and your refusal to accept their combined implications. We don't need to guess. You're made this quite obvious.
Neal,
ReplyDeleteOn further reflection, the same apparent blindness to our ability to piece together the disingenuous nature of your own objections would also explain your apparent blindness to the significance of evolutionary processes in speciation dispute observations you supposedly accept.
If you deny or fail to recognize the former, it would come to no surprise that you'd deny or fail to recognize the latter.
Of course, given the above, you're likely deny or fail to recognize the relevance of this observation as well.
Scott said, "At a minimum, evolutionary processes played a significant role in speciation. "
ReplyDeleteSpecifically, which evolutionary processes are you referring to and what speciation event that has been observed are you referring to?
Neal,
ReplyDelete1) Is a positive result from a paternity test a reliable indicator of relatedness? Yes, or no.