From the Biologic Institute, “A Facebook Dialogue”

_{Denyse O'Leary

November 12, 2012

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Ann Gauger posted an amusing facebook dialogue on the blog of the Biologic Institute: “Sometimes it might be a good idea to actually read what ID proponents write before critiquing it.” Click here to read the rest.

Comments

Nick: Thanks, that is helpful. Ultimately, though, everything is supposed to converge back on a smaller and smaller population and, eventually, a single organism, under the traditional evolutionary story. I guess there is no way to know at what point the widening cone stops widening and starts converging, so we can only guess as to that aspect . . .Eric Anderson_{November 27, 2012
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Nick Matzke:
Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.
No, I don't.Mung_{November 20, 2012
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Nick Matzke:
In both cases [paternity testing and common ancestry between species], similarity in DNA is the observation, inheritance of DNA through copying is the mechanism causing similarity, and common ancestry is the inferred, not observed, conclusion. Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.
While the cause of similarity is the same, the cause of the differences is different -- for paternity testing, it's mixing with alleles from other ancestors, while the differences used to infer ancestry between species are due to mutation (with selection etc complicating things). I'd argue that this is a pretty significant difference. (However, at least as I understand it, tracking both HIV ancestry and human chromosome chunks do depend on mutations for their differences, and so are legitimate parallels for inferring common ancestry between species.) But both methods have been tested. Checking paternity tests is easy: check them on people with known parents, and you find that DNA testing generally agrees. Common ancestry is similar: we'd inferred a lot about the ancestral tree of different organisms before we even knew DNA existed, and we find that the tree inferred from DNA similarities generally agrees. There are two complications here: first, all those "generally"s, and second the fact that some of those here think the inferred common ancestry is wrong. I'll deal with the second one first. Why should the agreement between the ancestral tree inferred by DNA similarities and that inferred by older phylogenetic techniques be significant if you don't think either one works? It's because of the principle of consilience -- basically, if you get the same answer from several different methods, it's a good indication that they're all working. There have been attempts to explain the agreement in some other way, but I haven't seen any that actually worked. For example, the obvious option is that DNA similarity is is measuring functional similarity, which is essentially the same thing older methods are based on. This doesn't work for two reasons: first, a disproportionally large number of the DNA differences (at least within genes) are changes that don't affect function -- silent substitutions that don't change the protein at all, or that change the amino acid sequence of the protein in ways that don't change the protein's function. Second, the pattern of DNA similarities doesn't really match the pattern of functional similarities. In a recent comment, Robert Byers pointed out the functional similaries between certain marsupials and placental mammals:
The marsupial wolf is just another wolf with a pouch. A marsupial lion likewise was a lion. There is no reason to classify them as a unrelated other group of animals. This is why they are unique to areas and not in other areas. tHey simply are the same creatures who upon migration had a general change in these details for good reasons back then. One can see moving or still pictures of the marsupial wolf and be convinced its just another dog. All the points of anatomy surely trump the few points of difference.
So if the DNA similarities are due to functional similarities, we should expect the marsupial wolf's DNA to be very similar to that of the placental wolf, and the marsupial lion's DNA to be similar to the placental lion's, right? While if the DNA similarities are due to common ancestry we'd expect for example the marsupial wolf's DNA to be more similar to other marsupials than to any placentals, and not be significantly more similar to placental wolves than any other placental. Anyone want to bet which prediction is correct? And if you don't want to bet against the common ancestry prediction, wny not? Joe mentioned another possibility: that DNA similarity might be due to common design. But how does this explain that some organisms have more similar DNA than others? Were the placentals designed by one designer, while the marsupials were designed by another? Now, the other point: that there are cases where both paternity testing and DNA-based inference of common ancestry sometimes disagree with what we "know" by other methods. This happens in both cases, and in both cases the interesting thing is that the DNA methods are thought to be more accurate than the methods they were tested against. Measurement methods in general have uncertainties and are subject to errors. The figures I've seen say that around 10% of the time, someone's socially accepted father isn't actually their biological father. So we expect DNA paternity testing to disagree with the "known" father about 10% of the time. I don't know of a good way to quantify the agreement between DNA-inferred common ancestry and other methods (Nick might), but it seems to me that where there's a disagreement, there's usually some ambiguity in at least one of the methods, and the inferred trees are usually only slightly different.Gordon Davisson_{November 20, 2012
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Nick Matzke:
In both cases, similarity in DNA is the observation...
Different sequences of DNA. One of which is explained by common descent and the other is easily explained by a common design.
inheritance of DNA through copying is the mechanism causing similarity,
Common design is another mechanism causing similarity.
Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable “common design” in the second case, but not the first.
So IEEE design standards are magical? Building codes are magical and miraculous? Cars are very similar to to common descent or common design? PC clones are very similar due to common descent or a common design? So do tell Nick, without the DNA similarities, what else do you have to supprt common descent? Ya see, Nick, inheriting SIMILAR DNA is NOT going to explain the physical DIFFERENCES required to get an upright biped from a knuckle-walker/ quadraped. Lactase persistence is not going to get an upright biped from a knuckle-walker/ quadraped. You have NOTHING to explain/ account for all the transformations required- you need to invoke magical, miraculous, mytery mutations. So shut up about non-testable positions already. Yours has been exposed as a big fraud.Joe_{November 19, 2012
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The current debate with Nick is over the sequences, tools, methods and reasoning used. From the fact that we can do a DNA test on blood found at a crime scene it does not follow that humans and chimps share a common ancestor. From the fact that we can do a paternity test it does not follow that humans and chimps share a common ancestor.
In both cases, similarity in DNA is the observation, inheritance of DNA through copying is the mechanism causing similarity, and common ancestry is the inferred, not observed, conclusion. Yet you arbitrarily invoke magical, miraculous, non-explanatory, non-testable "common design" in the second case, but not the first.NickMatzke_UD_{November 19, 2012
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wd400,
Why do you think ”are all descended from a common African ancestor who lived only 140,000 years ago” is evidence against the most recent common ancestor of some of our genes was found in ape?
I don't.
You don’t seem to have grasped the point that different genes have different histories (each of which can tell us about the population-level history of our species).
I don't think I have any problem with that point at all. The current debate with Nick is over the sequences, tools, methods and reasoning used. From the fact that we can do a DNA test on blood found at a crime scene it does not follow that humans and chimps share a common ancestor. From the fact that we can do a paternity test it does not follow that humans and chimps share a common ancestor. Nick claimed it's all the same:
The real point is that no matter how you slice it, chimps are the closest living relatives of humans, and the evidence for this is exactly the same sort of DNA evidence that we use to determine paternity, identify the source of blood samples at crime scenes, track who gave HIV to whom, determine what portion of the world various chunks of some American’s chromosomes came from, etc.
Mung_{November 19, 2012
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Mung, Why do you think " are all descended from a common African ancestor who lived only 140,000 years ago" is evidence against the most recent common ancestor of some of our genes was found in ape? You don't seem to have grasped the point that different genes have different histories (each of which can tell us about the population-level history of our species).wd400_{November 19, 2012
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Nick Matzke:
Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are “totally different” from human-chimp DNA tests:
Nick doesn't cite anything to support his desperate attempt to establish that paternity and forensic DNA tests are “like, totally the same” as human-chimp DNA tests.Joe_{November 19, 2012
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nick:
well, except that the “person” might be an ape that was part of the species ancestral to humans/chimps/gorillas, or in some cases might even be a rodentlike animal tens of millions of years ago.
Or not.
Such questions are even more remarkable in light of genetic evidence that we are all descended from a common African ancestor who lived only 140,000 years ago.
https://genographic.nationalgeographic.com/science-behind/Mung_{November 19, 2012
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National Geographic Explorer-in-Residence Dr. Spencer Wells and team designed Geno 2.0 based on the new technologies and insights that emerged since the launch of the Genographic Project in 2005. Using an exclusive, custom-built genotyping chip, we test nearly 150,000 DNA markers that have been specifically selected to provide unprecedented ancestry-related information.
https://genographic.nationalgeographic.com/science-behind/ Maybe those are the same markers they use to test human-chimp ancestry, but I doubt it.Mung_{November 19, 2012
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Nick:
Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are “totally different” from human-chimp DNA tests:
Well Nick, I see you have to resort to a straw man and have tried to float a brick. Is this human-chimp DNA test available over the counter yet? I'd like to take that test.Mung_{November 19, 2012
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Nick @70: I’m familiar with the cone idea, and also understand the idea that each DNA locus has its own “ancestor” (which may or may not be different from any other ancestor). I referred specifically to mitochondrial DNA, which presumably does not go through recombination and presumably is why we see statements like this (I know, I know, it’s Wikipedia, but you get the idea): “In the field of human genetics, Mitochondrial Eve refers to the matrilineal most recent common ancestor (MRCA) of modern humans. In other words, she was the most recent woman from whom all living humans today descend, on their mother’s side, and through the mothers of those mothers and so on, back until all lines converge on one person.” This statement would seem to suggest that the human lineage converges on a single person, no?
It suggests it, sorta, but if so it's a misinterpretation of the science. The "human lineage" does not converge to one person, just the human mitochondrial lineage. Every other locus converges to a different person -- well, except that the "person" might be an ape that was part of the species ancestral to humans/chimps/gorillas, or in some cases might even be a rodentlike animal tens of millions of years ago. The human lineage converges back on an ancestral population, the rough charactersitics of which can be inferred from the histories of the individual loci in our genomes.NickMatzke_UD_{November 19, 2012
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Mung cites a random page from the US Immigration Service in some kind of desperate attempt... Arbitrary maybe, but not random. A random search would not likely have turned up a document relevant to the subject matter from the US government. Yet one more case of design in action.Mung_{November 19, 2012
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Mung cites a random page from the US Immigration Service in some kind of desperate attempt to establish that paternity and forensic DNA tests are "totally different" from human-chimp DNA tests:
If a relationship is in question, and you have suggested DNA testing for additional evidence, you must identify the specific genetic relationship to be tested. It is not sufficiently specific for you to ask whether two people are “related;” rather, you must indicate how you think they may be related – parent/child, grandparent/grandchild, siblings, etc.
This requirement is here just for legal purposes. I.e., if you are someone's child, perhaps that makes you eligible for citizenship, but not if you are someone's brother.NickMatzke_UD_{November 19, 2012
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You're misunderstanding the magic. You don't count a number of generations to determine relatedness. First you assume that the two organisms are related by descent. Then you count the DNA differences to calculate the number of generations.Eric Anderson_{November 19, 2012
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Unless I am mistaken, we will of course reach a point beyond where we can’t determine the number of generations between two people.
That's my belief as well. And Nick, if he doesn't know it, ought to know it. It would also mean that not only are his facts wrong, but so is his reasoning.Mung_{November 19, 2012
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I trust you spot where the last part of my comment got nested into the "I know ..." quoteCabal_{November 19, 2012
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Nick, tell us, how many generations does it take before you can no longer tell how closely related any two people are?
Unless I am mistaken, we will of course reach a point bgeyond where we can't determine the number of generations between two people. But the subject of determining genetic differences began already about 100 years ago with Cambridge professor Nuttall. Followed by Professor Goodman at Wayne State University School. Later, in the 1960's Vincent Sarich, who said:
I know my molecules had ancestors, the paleontologist can only hope that his fossils had descendants.
That was long before the discovery of the double helix... Yet it was possible to determine to a certin degree relationships between species. It's all in the DNA, but sequencing is of course the more accurate of any methods. Evolutionary trees had been growing for a long time before sequencing was invented... Scientists actually are smart, they make theories, perform testing, invent methods, do experiments, draw conclusions, make inferences - and repeat it all, again and again never at rest as long as new frontiers are coming into sight. How much evolution of ID during, say, the last decade?
Cabal_{November 19, 2012
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Nick @70: I'm familiar with the cone idea, and also understand the idea that each DNA locus has its own "ancestor" (which may or may not be different from any other ancestor). I referred specifically to mitochondrial DNA, which presumably does not go through recombination and presumably is why we see statements like this (I know, I know, it's Wikipedia, but you get the idea): "In the field of human genetics, Mitochondrial Eve refers to the matrilineal most recent common ancestor (MRCA) of modern humans. In other words, she was the most recent woman from whom all living humans today descend, on their mother's side, and through the mothers of those mothers and so on, back until all lines converge on one person." This statement would seem to suggest that the human lineage converges on a single person, no?Eric Anderson_{November 17, 2012
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Nick @ 69 Thank you for taking the time to respond to my comment, though I am a bit disappointed in your lack of substance. It's hard to see how aliens or God are relevant to what I posted previously. Perhaps I should be gratified, though, as off-topic replies generally indicate an inability to seriously engage a cogent argument. I was simply pointing out what seems to be obvious, namely that using genetic similarities to establish phylogenetic relationships requires the prior assumption that such relationships are in fact possible. If that assumption is invalid, then the inferences based on comparative analysis are likewise invalidated. And given what we know from direct observation, that assumption is hardly established. But perhaps your seemingly off-topic tirade conceals a genuine worry. Since you did not state it clearly, I shall endeavor to guess at it... Perhaps your concern is that a design inference could be used as a sort of explanatory panacea, invoked with reckless abandon to explain anything and everything. I think that fear is vastly overblown. Like any other inference, the inference to design should only be invoked when there is reason to. If you want an example of an idea that is absurdly over-applied, look no farther than Neo-Darwinism.Optimus_{November 17, 2012
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Nick Matzke:
Please prove that aliens or God did not magically intervene in each fertilization event.
Please prove that you are not an infant. Or better yet please step up and demonstrate that unguided evolution can account for fertilization events and people may listen to you.
Maybe the DNA similarity between you and your parents is due to common design, not common descent.
ALL humans owe their similarities to a common design. And all observations say common design with common descent lead to more of the same- humans give rise to humans, chimps give rise to chimps. What you need to do Nick, is focus on the observed differences- the anatomical and physiological DIFFERENCES and link those to the genomes.
Or did someone watch your egg get fertilized?
Mung has/ had an egg? "I am the eggman I am the eggman I am the Mung(er) coo-coo-ca-chu" "Has anyone sen the egg? Where is that confounded egg?"Joe_{November 17, 2012
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Nick Matzke:
This is one of the (many) ways that genetic data disproves a literal Adam & Eve…
So you are saying that YEC can indeed be tested. However to test it you need to know more about the MECHANISM. Sure under unguided evolution's framework, a literal Adam & Eve doesn't work in the timeframe of 6,000-12,000 years. But given a design scenario in which real GAs are free to manipulate the genome virtually at will in order to achieve the goal, your equations do not apply and neither does your "refutation".Joe_{November 17, 2012
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Or did someone watch your egg get fertilized?
Not beyond the realm of possibility.Mung_{November 17, 2012
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Nick @45: Nick, you indirectly raise a question I’ve been contemplating recently. I’m sincerely interested in your thoughts on this issue. The concept of a “mitochondrial Eve” has received a lot of press over the years. Do you think there is in fact a single female individual from whom all humans descended? That individual would presumably have come from two parents, who also each came from two parents, etc., in a broadening cone of ancestors, if you will. So this would suggest that there is a kind of “hourglass” shape to our descent: broad now, but converging in the past to a single mitochondrial Eve, and then broadening again after mitochondrial Eve. Does that make any sense, or am I not describing this clearly?
It makes a little bit of sense but it's mostly wrong. You need an intro popgen course or textbook. I'll give you some buzzwords to look up. The "cone of ancestors" indeed increases as you go back in time (you, your 2 parents, your 4 grandparents, etc.) but pretty soon you start having relatives mating, so it doesn't expand forever. With genetic data for a population you can calculate an "inbreeding coefficient" that measures this. This is closely related to how you can calculate an effective population size given data about genetic diversity. Basically, small population size = more inbreeding = less genetic diversity. As for mitochondrial Eve, there is an "Eve", i.e. a last common ancestor, for every locus in the genome -- the mathematics of inbreeding mean that this must eventually happen. But essentially every one of these loci will have a different common ancestor at a different time. This is one of the (many) ways that genetic data disproves a literal Adam & Eve...NickMatzke_UD_{November 17, 2012
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Nick @ 35,43 What distinguishes using DNA in forensics or paternity testing from using it to infer phylogenetic relationships is that the former cases possess sufficient empirical warrant whereas the latter does not. We have abundant, incontrovertible evidence that gives us good reason to use DNA similarities WITHIN a species to infer relationships. Descent with modification is an observed fact in that limited context.
Oh really? Please prove that aliens or God did not magically intervene in each fertilization event. Maybe the DNA similarity between you and your parents is due to common design, not common descent. Or did someone watch your egg get fertilized?NickMatzke_UD_{November 17, 2012
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Optimus:
We have abundant, incontrovertible evidence that gives us good reason to use DNA similarities WITHIN a species to infer relationships.
And the efficacy is even limited WITHIN species. And they do not use the same tools as those used in phylogenetic analysis. Joe Felsenstein:
A quibble: within species, the molecular and morphological evidence does not show that the differentiation of individuals is treelike. My genealogy is not treelike because (shock! horror!) I actually had not one ancestor, but two: my mother and my father. Samples of individual gene loci have trees of ancestry — coalescent trees — but they differ from locus to locus. Above the species level the pattern rapidly becomes treelike, and that is where the dispute between PaV and Alan is mostly occurring, but within species the pattern is not a single tree.
Mung_{November 17, 2012
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Alan Fox:
Methods might differ...
You think? Why would the methods need to differ? Maybe it's because they are not asking the same question.Mung_{November 17, 2012
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They use DNA, therefore they are the same, is a huge non sequitur.Mung_{November 17, 2012
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Alan Fox:
Comparing DNA sequences is the same process.
But they use DIFFERENT DNA sequences, so it is NOT the same. Evos just have to use deception in order to "win"- pathetic, really.Joe_{November 17, 2012
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What distinguishes using DNA in forensics or paternity testing from using it to infer phylogenetic relationships is that the former cases possess sufficient empirical warrant whereas the latter does not.
Comparing DNA sequences is the same process. Methods might differ and evolve (pun intended!). 40 years ago, I recall as an undergraduate performing crude experiments involving passing samples through an electrophoresis column and measuring the radioactive tritium levels of labelled samples. One could then extrapolate an approximate measure of the percentage similarity of samples. I remember our prof. claiming that from this simple test it was possible to infer that yeast samples and moth samples shared a common ancestor about a billion years ago. At the time I was skeptical. Research continues.Alan Fox_{November 17, 2012
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