Darwinian Debating Device #5: The False Quote Mining Charge

_{Barry Arrington

October 16, 2014

Intelligent Design}

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One of the Darwinists’ favorite tactics is the “False Quote Mining Charge.” For those who do not know what “quote mining” is:

Quote mining is the deceitful tactic of taking quotes out of context in order to make them seemingly agree with the quote miner’s viewpoint or to make the comments of an opponent seem more extreme or hold positions they don’t in order to make their positions easier to refute or demonize. It’s a way of lying.

In summary, to accuse someone of quote mining is to accuse them of lying. It is a serious charge. Let us examine a recent example of the charge to illustrate.

In Origin of Species Darwin wrote this about the lack of transitional fossils in the fossil record:

But just in proportion as this process of extermination has acted on an enormous scale, so must the number of intermediate varieties, which have formerly existed, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.

In a prior thread I asked Alan Fox the following question:

Are you suggesting that the fossil record now reveals the “finely graduated organic chain” that in Origin Charles Darwin predicted would be ultimately revealed as the fossil record was explored further?

He replied:

As far as it reveals anything, yes. The current record is certainly not incompatible with gradual evolution over vast periods of time.

I replied:

Again, leading Darwinists disagree:

Darwin’s prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record.

Niles Eldredge and Ian Tattersall, The Myth of Human Evolution (New York: Columbia University Press, 1982), 45-46.

In response, in three separate comments, Mr. Fox charged me with quote mining:

Nice selection from the Bumper Book of Quote-mines, Barry

The quote-mine lifted (and I bet not by Barry) from a book implies that Eldredge has a problem with evolutionary theory.

Returning to the thread topic and Barry’s quote mine of Eldredge:

Let us summarize:

1. I quoted Darwin for the proposition that the fossil record should show a “finely graduated organic chain” and the fact that is does not show any such chain is the strongest objection to his theory.

2. I asked Alan Fox whether he believed the fossil record does show such a chain, and he said yes and that the record was not incompatible with gradual evolution.

3. I quoted Eldredge for the proposition that “Change in the manner Darwin expected is just not found in the fossil record.” VERY IMPORTANT: When I quoted Eldredge I called him a “leading Darwinist.”

4. Alan begins screaming “Quote mine”!

Now let’s go back to the beginning. To accuse someone of quote mining is to accuse them of quoting a source out of context to make it appear as though they agree with you when they don’t. It is a form of lying.

The proposition that I was advancing was that the fossil record has not turned out as Darwin expected. Alan disagreed. I quoted Eldredge to support my claim. Alan accused me of quoting Eldredge out of context to support my claim. This means Alan was accusing me of taking Eldredge’s words out of context to support my claim when in context they do not. He then said that I implied Eldredge has a problem with evolutionary theory. Bottom line: He accused me of lying and gross deceit.

But the truth is that I did not quote Eldredge out of context. Eldredge wrote that change in the manner Darwin expected is just not found in the fossil record, and that is exactly what he meant. Nothing in the context of the quotation changes that. He has never changed his views.

I never implied that Eldredge had a problem with evolutionary theory. Indeed, the whole point of quoting him is that his is an admission against interest. I called him a “leading Darwinist.” Alan’s charge is not only false it is imbecilic. He said I implied that a leading proponent of a theory has a problem with the theory, and that is absurd on its face.

In summary, Alan Fox should be ashamed of himself. He came onto these pages and falsely accused me of lies and deceit.

Comments

Here's Prothero on rhino/horse evolution: http://books.google.com/books?id=QeKWpRX77JgC&lpg=PA377&dq=evolution%20Hyrachyus%20Hyracotherium&pg=PA305#v=onepage&q=evolution%20Hyrachyus%20Hyracotherium&f=falseNickMatzke_UD_{December 7, 2013
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I would think this would make a fantastic dissertation, examining the genomes of these two species. How long ago did they part? What changes to the genome took place between the two? What proteins/control processes differ between the two species?
That's not one dissertation, but several! You could do divergence times with just a few genes, in fact I bet this has been done. I don't think they've done whole-genome sequences for either yet. Even having the whole genome sequence wouldn't answer all your questions yet, since just having the genome doesn't tell you the details of how it works to produce development. Minimally, you'd want transcriptomes throughout development as well. It's imaginable but it's a large project!
One could even speculate on an unicorn which if a rhino is close to a horse, has the tusk or horn sticking out of the middle of the head. Why couldn’t a horse develop the same trait?
What? Unicorn horns are supposed to come out of the forehead and be super long and skinny. I believe they are actually derived from narwhal whales, and in narwhals those are actually teeth/tusks, not horns. In Cambridge they actually have a narwhal with two tusks, one from each side of the jaw. Rhino horns come out of the nose and are basically made of keratin I think.
I am not being facetious but it seems to me that this would be an extremely useful analysis to bolster one sides point of view versus the other. As I said there must be the origin of new proteins in each and then one could speculate on how these proteins arose and if there are any intermediaries in other species. I am a big supporter of ID but am far from one who believes each species was created and that natural processes are probably at work to modify species. But the question is just how much can these natural processes do? So I am fascinated by how much is known. I would think the rhino/horse ancestry would be a good place to start as well as some others that may have live examples of each. Rhinos and horses do not come together in the classification scheme till the class level which is pretty high up the ladder.
Actually, horses and rhinos are both in the order perissodactyls, within class mammals, on the Linnaean system. I think the earliest rhino relative is Hyrachyus, and the earliest horse is Hyracotherium, so googling those would provide an entry to the literature.NickMatzke_UD_{December 7, 2013
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Matzke, you erect a strawman because no one here has claimed that there are no transitional fossils at all. What is being said is that there are far too little transitional fossils to meet Darwinian expectations. ‘Some known transitional fossils’ is not enough by a longshot within this context.
You mean "too few transitional fossils."
The quotes below by G.G.Simpson are addressing this problem and I don’t understand how presenting them qualifies as quote mining.
They are quote-mining because Simpson was writing in the 1950s, and the record of transitional fossils has improved dramatically since then. Most of the transitional fossils for the origin of most of these:
birds, mammals, hominids, whales, Cambrian arthropods, tetrapods, angiosperms, dugongs, giraffes, horses, canids, turtles,
...were discovered after the 1950s. (Of this group, the only good ones back then were really mammals and horses, I believe.) Anyway, unless you develop some fair statistical argument about how many transitional fossils are expected, and how many we have, the claim about having "too few" is just a dodge to avoid admitting the fact that we have lots of transitional fossils covering lots of major transitions.NickMatzke_UD_{December 7, 2013
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Mr. Matzke, I have a question for you that if answered should help settle a lot of misunderstandings. The answer may not be currently available but it is certainly within current technology to answer. You said that horses and rhinos were essentially the same species at one time in the past.
he points out that the earliest rhinos and the earliest horses are almost indistinguishable from each other, i.e. no different than two closely-related species in the same genus.
I would think this would make a fantastic dissertation, examining the genomes of these two species. How long ago did they part? What changes to the genome took place between the two? What proteins/control processes differ between the two species? One could even speculate on an unicorn which if a rhino is close to a horse, has the tusk or horn sticking out of the middle of the head. Why couldn't a horse develop the same trait? I am not being facetious but it seems to me that this would be an extremely useful analysis to bolster one sides point of view versus the other. As I said there must be the origin of new proteins in each and then one could speculate on how these proteins arose and if there are any intermediaries in other species. I am a big supporter of ID but am far from one who believes each species was created and that natural processes are probably at work to modify species. But the question is just how much can these natural processes do? So I am fascinated by how much is known. I would think the rhino/horse ancestry would be a good place to start as well as some others that may have live examples of each. Rhinos and horses do not come together in the classification scheme till the class level which is pretty high up the ladder. Some of the others you mentioned have long since disappeared. I would think the various carnivore would also be a good place to look or just how variation exist within ungulate which is also pretty high on the classification scheme. There must have been a sequence in the history of life to lead to all these distinctions. They must be written in the genome.jerry_{December 7, 2013
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As long as you keep refusing to admit the context of the Eldredge quote, you will be guilty of quote-mining when you use it to argue that the fossil record doesn't support evolution. It wasn't deliberately deceptive when you first did it, since presumably you were just unaware of the context and the different aspects of the fossil record (transitional fossils covering tiny transitions between sister species versus transitional fossils covering major transitions between major groups). But, the more you refuse to acknowledge this distinction, after you've been informed of it, the more you look like you are deliberately ignoring relevant information and context, just to avoid admitting having made an error. It's not lying, I don't think, just an emotional reaction to being shown up. Side note: we've already been over what Darwin said he expected from the fossil record, and Eldredge got that bit wrong. Eldredge's "admission" wasn't really "an admission against interest." Eldredge's interest was in promoting the punctuated equilibria idea. Very often, scientists will set up their new idea as being a correction to some previous authority. The more famous the better, because the more famous the authority is, the more famous your proposed correction is. Sometimes scientists get a little carried away and a little less than careful when they do think, particularly with Darwin, when they think they know what he said on a particular topic, but didn't research it carefully.NickMatzke_UD_{December 7, 2013
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Matzke @ 96:
You need to admit that transitions between closely-related species and transitions between major groups are different things, and that Eldredge was talking about the former.
No, you need to admit that your accusation that I engaged in deceitful quote mining was boorish and morally inexcusable. Nick, I know you are a moral relativist, but even relatively speaking wouldn’t you admit that accusing someone of lying when they did not is wrong? Again, the only right thing for you to do is to man up, admit you were wrong and apologize. I won’t be holding my breath. Your statement above would have some force if I had ever argued that transitions between closely-related species and transitions between major groups are different things. I did not. I argued only that change in the manner Darwin expected did not occur, and that is what Eldredge said. Again, your refusal to admit the obvious is helpful. When you burn your credibility on obvious things – as you are doing here – it ramifies when you discuss more subtle things. The thousands of people who read these pages each day are right now watching you bob, weave, evade and dissemble, and they know that is exactly what you are doing. Your cred it toast. Do you think your cred will magically rematerialize next time you engage on a more substantive matter? As the Brits say, “not bloody likely.”Barry Arrington_{December 7, 2013
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Matzke #91: But, even in the 1950s, there were a number of significant transitional fossils and series, which Simpson knew about, acknowledged, and described, although you don’t get that when you quote-mine him like this. Even mined quotes posted here don’t say there are no transitional fossils, if you read carefully. There were some known transitional fossils back then, there are more now.
Matzke, you erect a strawman because no one here has claimed that there are no transitional fossils at all. What is being said is that there are far too little transitional fossils to meet Darwinian expectations. ‘Some known transitional fossils’ is not enough by a longshot within this context. The quotes below by G.G.Simpson are addressing this problem and I don’t understand how presenting them qualifies as quote mining.
“Gaps among known orders, classes and phyla are systematic and almost always large.”G.G.Simpson. “Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.” G.G.Simpson.
I believe that the Elderidge quote, “Change in the manner Darwin expected is just not found in the fossil record”, is to be understood in that very same context: indeed there are some known transitional fossils, but there are far too little to meet Darwinian expectations. And, like I argued in posts #85 and #87, even if Eldridge’s context was confined to the rank of species, it would not matter, because in ‘the era before the game changing discoveries’ his statements would also be accurate with regard to higher groups.Box_{December 7, 2013
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Emphasis added. This is not going where the evidence leads. It’s cherry picking. You get to line up the things that support your theory, and reject the data that doesn’t agree. This is pathetic.
Oh noes! Minor differences in results between two analyses! Therefore common ancestry is wrong! These are all closely-related salamanders on any analysis. They are all on the same little branch of the tree of life, and there is no particular guarantee that one random old-fashioned dataset (allozymes) and old-fashioned techniques (UPGMA and distance methods) will perfectly resolve every last detail. You might as well be arguing that the Earth is flat because maps from the 1800s aren't quite perfect. Call me when some analyses put some salamanders inside frogs and other salamanders inside mammals. That would be a really significant disagreement.NickMatzke_UD_{December 7, 2013
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You need to admit that transitions between closely-related species and transitions between major groups are different things, and that Eldredge was talking about the former.NickMatzke_UD_{December 7, 2013
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NickMatzke @ 78: In my essay I advance a proposition, to wit, that change in the manner Darwin expected – whatever that is – is just not found in the fossil record. I quote world-renowned Darwinists Niles Eldredge and Ian Tattersall to support my thesis. They wrote: “Change in the manner Darwin expected is just not found in the fossil record.” Quote mining is the deceitful tactic of taking quotes out of context in order to make them seemingly agree with the quote miner’s viewpoint. It is a form of lying. You accuse me of lying through quote mining for using the Eldredge/Tattersall quotation. In order for your accusation to be true, it must be true that I took the Eldredge/Tattersall quotation out of context to make it seem like they supported the proposition I was advancing – i.e., that change in the manner Darwin expected is just not found in the fossil record – when they did not. But the fact of the matter is that Eldredge and Tattersall meant exactly that. I did not quote them out of context. I did not make it seem as though they agreed with my viewpoint when they did not. I asked you of you agreed with what they said. After evading the question for a couple of days, you finally admitted you believe the statement: “was only partially true, then and now. So, it turns out that your problem with Eldredge and Tattersall. You just don’t think they are right. Your “quote mine” attack was not based on the fact that I misrepresented Eldredge and Tatersall. It was based entirely on your personal opinion that the view that they (and I) was advancing is wrong. It follows that your accusation that I engaged in lying by quote mining is false. Now it is time for you to do the right thing and admit you were wrong and apologize.Barry Arrington_{December 6, 2013
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NickMatzke_UD retaliated with
You were misunderstanding him. Are you trying to say that proteins are not a good way to tell apart closely related species? If so, you should say that, it’s sort of correct, although not completely.
No, I wasn't misunderstanding him. Our discussion was specifically about the taxonomy of some kangaroo rats that he collected and released---if I had meant phylogenetics, I would have said so.
Really? You’re using an article entitled “Proteins help solve taxonomy riddle” to argue that proteins aren’t used on taxonomy issues?
Yes. The authors thought this was unusual.
All the article is saying is that collagen isn’t good for closely related species. Collagen is just one protein. There are thousands of different proteins.
And some are sensitive to heat, such as mentioned in your paper. But of course you know that collagen is not "just" another protein.
Some evolve slowly, some evolve quickly. You use the quicker ones for more recent divergences and the slower ones for more ancient divergences. If you are studying both at once, you include some of both in the analysis.
The cool thing is that Darwinists get to arrange them in any convenient order, discarding the results as needed. So where are the intermediate stages between any two proteins? How do they change in small increments? What came before collagen? One of your search links stated:
Salamanders (Aneides) The relationships of species in the plethodontid salamander genus Aneides (and the outgroup Plethodon neomexicanus) are supported by parsimony analysis of morphological data and by Fitch-Margoliash analysis of albumin immunological data (Larson et al.,1981). The only disagreement between these two data sets concerns the relationships among the species A. ferreus, A. flavipunctatus, and A. lugubris (Fig. 1A). There are two well-supported clades among the six species for testing the performance of methods on the allozyme data of Larson et al.(1981). None of the parsimony methods recover the two well-supported clades. The majority, missing, and unordered parsimony methods all give unresolved consensus trees for Aneides relationships. The frequency, polymorphic, and scaled parsimony methods all resolve the same, incorrect tree (P. neomexicanus, lugubris (hardii (ferreus (aeneus+flavipunctatus)))). This tree is not only rejected by the morphological and immunological data, but also makes little sense biogeographically (i.e. ferreus, lugubris,and flavipunctatus all occur in the extreme western U.S., whereas aeneus occurs in the Appalachians). UPGMA (both distances) recovers the two well-supported clades correctly, whereas CONTML, neighbor-joining, and FM group the West Coast species (ferreus, lugubris, flavipunctatus) together but incorrectly place A. aeneus as the sister taxon to this clade rather than A. hardii.
Emphasis added. This is not going where the evidence leads. It's cherry picking. You get to line up the things that support your theory, and reject the data that doesn't agree. This is pathetic. As I said, Darwinism artificially lines up similarities in selected features of animals in a some non-unique sequence, and claims ancestry. Not only is this technique non-scientific, it prevents you from making some really cool discoveries as to how and why certain proteins have come to differ. -QQuerius_{December 6, 2013
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micro-RNAs and Non-Falsifiable Phylogenetic Trees - (Excellent Research) video http://www.youtube.com/watch?v=qv-i4pY6_MU Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885 pdf: http://www.nature.com/polopoly_fs/1.10885!/menu/main/topColumns/topLeftColumn/pdf/486460a.pdf Nature Article Finds MicroRNAs are "Tearing Apart Traditional Ideas about the Animal Family Tree" - Casey Luskin June 29, 2012 Excerpt: When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn't cooperate. If the traditional tree was correct, then an unprecedented number of microRNA genes would have to have been lost, and Peterson considers that highly unlikely. "The microRNAs are totally unambiguous," he says, "but they give a totally different tree from what everyone else wants.",,, Maybe the reason that different genes yield different evolutionary trees is because there isn't a single unified tree of life to be found. In other words, perhaps universal common ancestry is simply wrong. http://www.evolutionnews.org/2012/06/nature_article061471.htmlbornagain77_{December 6, 2013
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Archaeopteryx was discovered in the 1860s,
"The first and most complete fossil of archaeopteryx, found in 1855, was misidentified as a flying pterodacylus for 115 years. The newest finding, though, demonstrates that our understanding of even well-studied fossils like archaeopteryx -- scrutinized, measured, modeled for 150 years -- can still be upended." Bye Bye Birdie: Famed Fossil Loses Avian Perch - Oct. 2009 Richard Dawkins Dumps the Fossil Record - May 18th, 2013 Excerpt: The dumping of the Archaeopteryx as a missing link between birds and reptiles by palaeontologists during the late twentieth century, however, was gaining solid support. According to Larry Martin, an American vertebrate paleontologist and curator of the Natural History Museum and Biodiversity Research Center at the University of Kansas, the “Archaeopteryx is not ancestral of any group of modern birds.” Missing link status of the Archaeopteryx is only an illusion; a “once upon a time” story according to Henry Gee a British paleontologist and evolutionary biologist and senior editor of the prestigious journal Nature. Abandoning the Archaeopteryx as a transitional link was actually only a tip-of-the-iceberg of the larger fossil record problem for evolution. Geneticist Wolf-Ekkehard Lönnig of the Max-Planck Institute in Germany in the book entitled The Evolution of the Long-Necked Giraffe, like Dawkins, candidly points to the fact that a “gradual series of intermediates in Darwin’s sense has never existed and hence will never exist.”,, http://www.darwinthenandnow.com/2013/05/richard-dawkins-dumps-the-fossil-record/
etc.. etc.. etc.. Seems someone needs to update their notes!bornagain77_{December 6, 2013
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Nick, are you saying that discoveries since the 1980s dramatically changed the general perspective on the incomplete state of the fossil record; above the rank of species? So, are you saying in effect that before the 1980s Simpson’s observations were supported by the evidence at that time?
I would say that we have been accumulating transitional fossils since the mid-1800s. Archaeopteryx was discovered in the 1860s, the transitional fossil horses and rhinos in the late 1800s, the "mammal-like reptiles" and some proto-tetrapods in the first half of the 1900s, and various hominids were available by 1950. So there were various transitional fossils known to Simpson, and he discusses them quite well, if you bother to go read his work. E.g. he points out that the earliest rhinos and the earliest horses are almost indistinguishable from each other, i.e. no different than two closely-related species in the same genus. But, major fossil discoveries kept coming, and at an increasing pace. Olduvai gorge and Homo habilis, african Homo erectus, etc. were described in the 1960s, and hundreds of more specimens have followed. The whale stuff started in a big way in the 1980s. The feathered dinosaurs were mostly the 1990s. The Chengjiang arthropods were discovered in the 1990s but are only just now getting thoroughly described and analyzed. And all of the other cases I mentioned (tetrapods, mammals, etc.) have gotten much more filled in in recent decades. So, quoting ancient quotes on the fossil record is just bad practice, since we have much more data now. But, even in the 1950s, there were a number of significant transitional fossils and series, which Simpson knew about, acknowledged, and described, although you don't get that when you quote-mine him like this. Even mined quotes posted here don't say there are no transitional fossils, if you read carefully. There were some known transitional fossils back then, there are more now. There are still some big gaps left. Bats are one where we have almost nothing in the way of transitional forms. But birds, mammals, hominids, whales, Cambrian arthropods, tetrapods, angiosperms, dugongs, giraffes, horses, canids, turtles, have all been conquered, with a series of fossils available for each. Back in the 1950s the coverage was much more spotty, or there would just be one spectacular fossil for a particular transition, like Archaeopteryx. Really, this whole thread would just melt away if people just got up off their tushes and went and read Prothero's book Evolution: What the fossils say and why it matters. If you want to know why the youth are melting away from fundamentalism/conservative evangelicalism, it's shenanigans like the ones people are pulling here. Transparently crude quote-mining is only convincing to people who don't bother to google these topics.NickMatzke_UD_{December 6, 2013
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Of note: A New Model for Evolution: A Rhizome - Didier Raoult - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html Didier Raoult, who authored the preceding paper, has been referred to as 'Most Productive and Influential Microbiologist in France'. Here is what he had to say about Darwinism: The "Most Productive and Influential Microbiologist in France" Is a Furious Darwin Doubter - March 2012 Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin's theory of evolution is wrong. http://www.evolutionnews.org/2012/03/the_most_produc057081.htmlbornagain77_{December 6, 2013
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Nick to Q's statement here:
No, it was made clear to me that unless you cherry pick the data, proteins are not a good way to resolve taxonomic issues.
States in reply:
You use (i.e. choose) the quicker ones for more recent divergences and the slower ones for more ancient divergences. If you are studying both at once, you include some of both in the analysis.
That sure sounds like you are saying that you are allowed to cherry pick whatever sequences you need to make your tree work to me! Isn't that special! Reminds me of this recent yeast study:
Here Are Those Incongruent Trees From the Yeast Genome - Case Study - Cornelius Hunter - June 2013 Excerpt: We recently reported on a study of 1,070 genes and how they contradicted each other in a couple dozen yeast species. Specifically, evolutionists computed the evolutionary tree, using all 1,070 genes, showing how the different yeast species are related. This tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches.,,, http://darwins-god.blogspot.com/2013/06/here-are-those-incongruent-trees-from.html That Yeast Study is a Good Example of How Evolutionary Theory Works - Cornelius Hunter - June 2013 Excerpt:,,, The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene. These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.” And how do we know that these genes have strong phylogenetic signal. Because they give the right answer. This is an example of a classic tendency in science known as confirmation bias.,,, http://darwins-god.blogspot.com/2013/06/that-yeast-study-is-good-example-of-how.html
Well all I can say is,,,
Must have hurt http://www.youtube.com/watch?v=OnifY5WiASQ
But is there any real empirical evidence demonstrating that proteins can evolve (quick or slow), as Nick presupposes, so as to allow Darwinists such unfettered latitude in the reconstruction of their hypothetical trees? None that I am aware of!
Science & Human Origins: Interview With Dr. Douglas Axe (podcast on the strict limits found for changing proteins to other very similar proteins) - July 2012 http://intelligentdesign.podomatic.com/entry/2012-07-24T21_33_53-07_00 Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.html When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide
Where Here is a note on the severe dissimilarities that are being found. Dissimilarities that Nick will most likely never ever admit to, and will most likely deny to his dying day until he meets the Lord:
Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php
Verse and Music:
Revelation 22:14 Blessed are they that wash their robes, that they may have the right to come to the tree of life, and may enter in by the gates into the city. Kari Jobe - Revelation Song - Passion 2013 http://www.youtube.com/watch?v=3dZMBrGGmeE
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In a non-nested tree, a design still inherits functionality from parent designs. Besides, why even claim, as Darwinists do, that the Darwinian tree of life is purely nested if the converse is not possible?
The converse is theoretically possible, but it wouldn't be a tree, it would be a network or web or some such. Hierarchies have groups within groups. Simple inheritance doesn't necessarily mean you have hierarchy/trees, e.g. inheritance within sexual populations isn't treelike, since everyone has two parents. You could make a tree of just the father relationships, or a tree of just the mother relationships, but when you stick them together you'd have a network. (Which, BTW, shows that a non-tree pattern does not particularly indicate intelligence was involved.)NickMatzke_UD_{December 6, 2013
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Follow up on #85 It is important to this discussion about ‘quote mining’ whether the evidence supports Simpson’s observations. Because if this is indeed the case, it doesn’t really matter what the context was when Eldridge wrote “change in the manner Darwin expected is just not found in the fossil record.” My point is that Eldridge wrote this before the discovery of Matzke’s game changing transitional fossils. So Eldridge would also be right if the context was not confined to ‘transitions between very similar species’, as Matzke claims, but included higher groups - it would be on par with the consensus view at that time. This renders the allegation of quote mining invalid or inappropriate at best.Box_{December 6, 2013
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NickMatzke_UD:
Funny the entire ID movement never decided to use it, then.
A monumental mistake on the part of the ID movement, in my opinion. But I understand why they chose to distance themselves from this. It's because the fundamentalist undercurrent within the ID movement has blinded them. I am a Christian but certainly not a fundamentalist.
If it’s non-nested, it’s not a hierarchy or a tree. But you said it was both hierarchical and a tree. Methinks you need to work on your description a bit.
You don't understand hierarchies then. Multiple class inheritance is used in object-oriented software design all the time. Why is it not hierarchical? In a non-nested tree, a design still inherits functionality from parent designs. Besides, why even claim, as Darwinists do, that the Darwinian tree of life is purely nested if the converse is not possible? You're losing it, Matzke. These truths are more than you can bear. :-DMapou_{December 6, 2013
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Nick Matzke,
“Gaps among known orders, classes and phyla are systematic and almost always large.”G.G.Simpson. “Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.” G G Simpson

Nick Matzke #41: “These are 60-year old quotes!! Dinobirds, whales with legs, many new transitional-proto-tetrapods, transitional-proto-arthropods, etc. were all discovered since the 1980s!”
Nick, are you saying that discoveries since the 1980s dramatically changed the general perspective on the incomplete state of the fossil record; above the rank of species? So, are you saying in effect that before the 1980s Simpson’s observations were supported by the evidence at that time?Box_{December 6, 2013
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It’s a term I’ve been using for over two decades. It’s a common term among human designers, especially in fashion design, interior design, architectural design, automobile design, software and video game design, smart phone design, etc.
Funny the entire ID movement never decided to use it, then.
What we observe among designers is that, over time, designs evolve and can be classified hierarchically, as in a tree. The difference between the Darwinian tree of life and the Intelligent Design tree of life is that the former is purely nested by the necessity imposed by common descent whereas the latter is non-nested.
If it's non-nested, it's not a hierarchy or a tree. But you said it was both hierarchical and a tree. Methinks you need to work on your description a bit.NickMatzke_UD_{December 6, 2013
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80 QueriusDecember 6, 2013 at 6:46 pm NickMatzke_UD claimed
This part is bizarre and indicates you don’t know what you’re talking about.
Apparently then, neither did the (evolutionary) Biology professor with whom I discussed this with. No, it was made clear to me that unless you cherry pick the data, proteins are not a good way to resolve taxonomic issues. I’m surprised that you seem to think so.
You were misunderstanding him. Are you trying to say that proteins are not a good way to tell apart closely related species? If so, you should say that, it's sort of correct, although not completely. "Taxonomic issues" involves everything from species distinctions to large-scale phylogeny. Proteins are particularly useful for the latter.
Allozyme research was very important in the early days of molecular systematics, although these days it has mostly been replaced by DNA sequencing. Protein sequences, though, are routinely used in phylogenetics. I have published several such papers myself.
Routinely used in phylogenetics? Really? Please provide the links?
Here's one I just did: http://www.pnas.org/content/early/2013/06/12/1305813110.short It's not hard to check that protein phylogenetics is a thing: http://lmgtfy.com/?q=%22protein+phylogenetics%22 Heck, even allozyme data: https://www.google.com/search?btnG=1&pws=0&q=%22protein+phylogenetics%22#pws=0&q=allozyme+phylogeny
Early efforts by Ostrom, Collins and others focused on individual proteins that are abundant in bone remains, such as collagen. “We call it the barcode of death,” says Collins, who uses collagen sequencing to quickly and cheaply identify species found at archaeological sites, such as the animals used to make parchment or the horns on Viking helmets. Collagen is also remarkably stable: it has been sequenced from a 3.5-million-year-old fossil of a giant camel from the Arctic2. But collagen differs very little between closely related animal species, making it useless as a marker for evolutionary change. “You cannot tell an ibex from a domestic goat; you cannot tell a human from a Neanderthal,” Collins says.
-From an article in Nature titled “Proteins help solve taxonomy riddle” from November 2013. Sorry, looks like you’re busted. -Q
Really? You're using an article entitled "Proteins help solve taxonomy riddle" to argue that proteins aren't used on taxonomy issues? All the article is saying is that collagen isn't good for closely related species. Collagen is just one protein. There are thousands of different proteins. Some evolve slowly, some evolve quickly. You use the quicker ones for more recent divergences and the slower ones for more ancient divergences. If you are studying both at once, you include some of both in the analysis. Like I said, you don't know what you're talking about. Why do creationists feel they can make confident pronouncements about evolution when they get absolutely basic, introductory, obvious-if-you-bothered-to-think-about-it-for-even-a-second things wrong?NickMatzke_UD_{December 6, 2013
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NickMatzke_UD @79:
“Design evolution” is a term you invented just now. I’ve never seen it before. Please tell us what you think happened in evolutionary history, under “design evolution”.
It's a term I've been using for over two decades. It's a common term among human designers, especially in fashion design, interior design, architectural design, automobile design, software and video game design, smart phone design, etc. What we observe among designers is that, over time, designs evolve and can be classified hierarchically, as in a tree. The difference between the Darwinian tree of life and the Intelligent Design tree of life is that the former is purely nested by the necessity imposed by common descent whereas the latter is non-nested. This is means that ID predicts that (distant lifeforms very high in the tree of life) will be found to have horizontal gene sharing. We already knew this by observing distantly related species but this is what the genetic records of various species are also beginning to reveal. The future looks very bleak for Darwinism. Y'all got it coming, though.Mapou_{December 6, 2013
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NickMatzke_UD you ask:
Do you think Prothero thinks there are lots of transitional fossils, and that transitional fossils support evolution?
I have no doubt that Prothero thinks, i.e. believes/imagines, there are lots of transitional fossils, and I have no doubt that he would be a true Darwinist (i.e. an atheist) no matter what the evidence said to the contrary. But the fact of the matter is that his very own research has left him, and every one he has given his presentation to, without, quote/unquote, "a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate." For me this is rock solid proof that Darwinism is first and foremost, as Dr Hunter would say, metaphysically-driven and is not driven by what the evidence actually says as should rightly be done in science. Moreover, I remember Prothero got fairly well embarrassed in his debate with Stephen Meyer in 2009, in which, among other things, the fossil record around the Cambrian era was touched upon:
D. Prothero & M. Shermer vs S. Meyer & R. Sternberg - debate http://www.youtube.com/watch?v=8WN5wcbCtjg
I would also like to point out the extreme stasis observed for bacteria going back as far as we can in the fossil record:
Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13 Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages. http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1 Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637
Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made through him; and without him was not anything made that hath been made. In him was life; and the life was the light of men. O Come, Emmanuel - (Piano/Cello) - ThePianoGuys http://www.youtube.com/watch?v=iO7ySn-Swwc
Supplemental note as to the complete lack of empirical evidence for neo-Darwinian claims:
Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information - September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski's research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution'," Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html
here is a short note as to the informational complexity Darwinism is trying to explain with the unguided 'random' process that Dr. Behe highlighted:
Learning from Bacteria about Social Networking (Information Processing) - video Excerpt: I will show illuminating movies of swarming intelligence of live bacteria in which they solve optimization problems for collective decision making that are beyond what we, human beings, can solve with our most powerful computers. http://www.youtube.com/watch?v=yJpi8SnFXHs How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. - Paul Davies http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk
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NickMatzke_UD claimed
This part is bizarre and indicates you don’t know what you’re talking about.
Apparently then, neither did the (evolutionary) Biology professor with whom I discussed this with. No, it was made clear to me that unless you cherry pick the data, proteins are not a good way to resolve taxonomic issues. I'm surprised that you seem to think so.
Allozyme research was very important in the early days of molecular systematics, although these days it has mostly been replaced by DNA sequencing. Protein sequences, though, are routinely used in phylogenetics. I have published several such papers myself.
Routinely used in phylogenetics? Really? Please provide the links?
Early efforts by Ostrom, Collins and others focused on individual proteins that are abundant in bone remains, such as collagen. “We call it the barcode of death,” says Collins, who uses collagen sequencing to quickly and cheaply identify species found at archaeological sites, such as the animals used to make parchment or the horns on Viking helmets. Collagen is also remarkably stable: it has been sequenced from a 3.5-million-year-old fossil of a giant camel from the Arctic2. But collagen differs very little between closely related animal species, making it useless as a marker for evolutionary change. “You cannot tell an ibex from a domestic goat; you cannot tell a human from a Neanderthal,” Collins says. -From an article in Nature titled "Proteins help solve taxonomy riddle" from November 2013.
Sorry, looks like you're busted. -QQuerius_{December 6, 2013
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By the way, transitional fossils do support evolution but which one, Darwinian evolution or Design evolution? I choose the latter. What does not support Darwinian evolution is the lack of a fine graduation in the fossil record between major taxa. This finding is actually very strong evidence for design evolution.
"Design evolution" is a term you invented just now. I've never seen it before. Please tell us what you think happened in evolutionary history, under "design evolution".NickMatzke_UD_{December 6, 2013
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And I explained very carefully that I am asking you whether you agreed with Eldredge, not with me. I am pretty sure you are not too stupid to understand that that means I am asking you whether you agree with Eldredge’s statement as Eldredge meant it to be understood in the context in which he made it.
This is the first time that you've specified "in the context which which [Eldredge] made it". In that context, Eldredge's statement was only partially true, then and now. The evidence for the punctuated equilibrium pattern in the fossil record of those small species-to-species transitions is mixed. Some groups show it, some groups don't, and in some groups (like hominids), for parts of their record we don't have enough fossil specimens to really do the relevant statistical tests properly. In Homo erectus and Homo sapiens, there are several cases of traits (like brain size and tooth size) where you have hundreds of dated fossils within species through time, and you can see the change in those traits happening quite gradually, i.e. not in a punctuated pattern. For earlier parts of the hominid record, we probably don't have a continuous-enough fossil record to tell the difference. The case is often similar with other mammals. Terrestrial vertebrates in general have spottier fossil records than marine invertebrates. People like Prothero are advocates of punk-eek patterns in mammal fossils, but other fossil mammologists like Gingerich are not. The pattern seems to be more common in marine invertebrates, but here too there are exceptions. In any case, the question of whether or not there are smooth transitions between closely related, extremely similar fossil species is distinct from the question of whether or not there are transitional fossils writ large, between major extant groups. There are lots of such fossils, and they are strong evidence for evolution. Prothero would say so (he wrote a book specifically saying this, specifically to creationists!), Eldredge would say so, Gould would say so, even Kurt Wise says so! So: would you agree it would be a mis-use of the Eldredge quote to imply that there are no transitional fossils?NickMatzke_UD_{December 6, 2013
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NickMatzke_UD @73:
Hey bornagain, Do you think Prothero thinks there are lots of transitional fossils, and that transitional fossils support evolution? Check his 2007 book Evolution: What the Fossils Say and Why it Matters.
Well, since you love to play the date game, anybody else can play it too. bornagain77 posted a quote @67 by Prothero dated February 2012 that supersedes your 2007 date (strange that you don't provide a quote) by five years. So which one should we accept as Prothero's current view on the matter, eh? By the way, transitional fossils do support evolution but which one, Darwinian evolution or Design evolution? I choose the latter. What does not support Darwinian evolution is the lack of a fine graduation in the fossil record between major taxa. This finding is actually very strong evidence for design evolution.Mapou_{December 6, 2013
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By the way Nick, you probably noticed I have not put you in mod for refusing to answer. The reason? Because your refusal to answer a simple question makes you look like the fool that you are, and that is, in some ways, better than having you answer the question, because it serves further to discredit all the nonsense you spew on these pages. Thanks!Barry Arrington_{December 6, 2013
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Nick Matzke,
“Gaps among known orders, classes and phyla are systematic and almost always large.”G.G.Simpson. “Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.” G G Simpson

Nick Matzke #41: “These are 60-year old quotes!! Dinobirds, whales with legs, many new transitional-proto-tetrapods, transitional-proto-arthropods, etc. were all discovered since the 1980s! Act like a scholar if you want to be treated like one.”
Are you saying that discoveries since the 1980s dramatically changed the general perspective on the incomplete state of the fossil record; above the rank of species? So, are you saying in effect that before the 1980s Simpson’s observations were supported by the evidence at that time?Box_{December 6, 2013
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