Moderator’s remark: this post is long enough to need a “more” tag. But the wordpress editor will only allow me to add that at the very beginning or the very end. So here it is at the very beginning.
Do you want to be my cousin?
Sure. If not me, then who?
- “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
- No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
- Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
- The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
- The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
- The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
- A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”
John Harshman,
What is your objective test for ancestry in crocodilians or any other species?
If they aren’t interested in learning anything, sure. But that’s not what this site is supposed to be about.
I am perfectly capable of having ongoing non-acrimonious conversations with a number of members here. It should be obvious that I am a voracious reader and that I can be reasonable. Who knows what might happen if you adjusted your attitude.
Why does it have to be objective, why does that matter?
I don’t think it is the same and I’ve never seen anyone actually defend the claim that it is. They merely assert it to be true without ever backing it up.
It’s one of those fantastic evidences for evolution that upon closer examination doesn’t even exist.
Sorry Joe 🙂
Well, which is it? Is it an inference or an assumption? Because you appear to be saying it’s both.
I explained it, but you have apparently snipped it out without reading it. Or you could just read the paper. It’s a strong signal from multiple sets of data all supporting the same tree.
It seems to me that your attitude is more in need of adjustment. It’s impossible to tell when you’re making a serious argument and when you’re trolling, and you switch between modes constantly. If you want to have a real discussion, you need to permanently exit trolling mode. And you should probably respond seriously to serious attempts at discussion. Instead, whenever I try to engage you, you drop back into trolling. Here, you have dropped into sincere mode, but I expect you will go back to trolling mode if you respond to this.
Yes. You were personally selected by The Intelligent Designer. Don’t you feel special?
Your reasoning is circular. 😉
Bill’s incoherent, but it is in fact possible to be both. One can make assumptions and then test those assumptions. You mentioned models. Every model contains assumptions, and the fit of the model to data can be used to test whether the assumptions are valid for the data. A chi square test is a simple example. And an inference made in one study can then be used as an assumption in another; thus science builds on previous work.
This is “reasonable” in Mung’s world, considering he claims to believe in common descent. Heh
That may be true. Yet you just accused Neil Rickert of all people of being a creationist. And you’ve been accusing me of being a troll. Neither of these is conducive to actually attempting to discover what we agree on and what we disagree on and why. They raise hackles and impede discussion.
Perhaps at some point we could have a reasonable discussion about what is trollish behavior and what isn’t, and when it’s acceptable and when it isn’t. In my direct interactions with you, you could try telling me when I do something specific that annoys you and ask me to not do that.
You do understand though, that to ignore is not the same as to overlook. Right? One is intentional, the other is not. It’s not word games. So accusing me of playing word games is, in my opinion, inappropriate and signals to me that you are not actually interested in honest discussion.
Perhaps my response was not appropriate either. But hopefully I’ve expressed myself a bit more fully.
I don’t see any conflict. Your actual DNA can be compared to the actual DNA of your known mother and father and brothers and sisters and cousins. We have far stronger grounds for accepting the results of a paternity test.
We don’t have the actual DNA of the common ancestor of humans and chimps, other than by inference.
I am not convinced that creationist ideas of what “correctly” means are completely divorced from the way I use that term. Doesn’t everybody get upset if our explanations fail to comport with this or that observation? Creationist undoubtedly have some additional purpose for an explanation of biodiversity, but they still like their account of how events have transpired in the past to be supported by established scientific insights. Just browse the Adam & Eve thread to see what I mean.
No worries. I know. 😉
T H E C I R C U L A R C H A I N O F R E A S O N I N G
Satisfied?
What did I win?
John Harshman,
I have no idea why one pair of species would pass and one would fail. What does a “strong signal” mean? If you think the tree is really evidence of decent you are talking to the wrong guy. The tree to me is nothing more then evidence of similar features.
The discussion is about what common descent predicts, not about what evolution predicts. But I don’t believe either evolution or common descent predict that.
And don’t know why it matters.
Yes. These things often come down to something more fundamental that isn’t stated which is utterly philosophical in nature and cannot be adjudicated by the methods of science. Including Neil’s preference for pragmatism.
In this case it is probably the correspondence theory of truth. You probably think that science provides us with truth. Neil would probably dispute that.
LOL, so if you don’t have the DNA of your ancestors, there’s nothing you can do to determine how closely related you are to someone else, or even if you’re siblings, right?
You won an audience with Bill and I. Aren’t you thrilled!?
I do believe you missed the point. 🙂
There is a reason DNA evidence is accepted in court, and it’s not because of evolutionary theory.
Mung,
Maybe the wrong word. John’s claim that there is a strong signal from multiple lines of evidence. What does “strong signal” mean. There is no null hypothesis and no pass or fail criteria. What he feels is a pass maybe a fail to you.
What does that have to do with anything? The question is, if the same tests used to determine relatedness among humans also work interspecies, doesn’t that count as evidence for common descent?
He would? The correspondence theory of truth? Does that exist?
I will settle for science that provides us with a little less doubt, if that helps.
Haha. So this is the Good News, is it?
Mung,
OK, that was a serious reply. If you try that approach in the on-topic discussion, we could actually go back and forth.
Lamb: The Gospel According to Biff, Christ’s Childhood Pal
Can’t believe they misspelled Bill’s name though.
I don’t know what sense of truth you think you are claiming.
As best I can tell, we evaluate truth by applying standards. And colewd was, in effect, asking about the basis for the standards.
Yes, IF.
But they are not the same tests. And there is probably a very good reason they are not used to determine relatedness among species.
Thus, my objection to Joe’s post.
You quoted my reply to John.
If you are going to massively switch context like that, then you are going to look like a quote miner.
No, the earth is definitely not flat. There’s a pot hole just down the street.
I fully acknowledge that talking to you is futile. A “strong signal” refers to consistency — agreement on a single tree — within a data set. This is often assessed using the phylogenetic bootstrap (Joe’s innovation, incidentally), in which the data are resampled with replacement many times. If a high proportion of the resampled data sets agree on the same tree, that means that the data are consistent in their support. Now, why should the data be consistent? One hypothesis is that they all evolved on the same branching tree. Do you have another?
Of course this isn’t about pairs of species. A pair of species don’t make a tree. You need at least four species for that. The more species, the more unlikely it would be for different data to support the same tree, absent an evolutionary explanation. But I despair of ever getting you to see any of this. One reason is that you refuse to look. If you will just actually read the croc paper and try to understand its argument, that might help. But you won’t.
This seems absurd.
Reductio ad absurdum amounts to testing by using.
“The proof of the pudding is in the eating” amounts to testing by using.
The entire basis for Christianity is to accept it on faith and then test it by using it.
You don’t? You appear to have been arguing against it. How could you if you don’t know what it is? The sense I’m talking about is the ordinary one: there is such a thing as reality, and a statement is true if it matches reality. Whales really are mammals because whales actually are descended from the most recent common ancestor of all mammals. I don’t consider that true because it’s convenient or useful. I consider it true because it reflects the actual history of species.
Sure. However, the means by which we evaluate truth are not the definition of truth. How does your claim connect to Bill’s?
I don’t think that I implied they were “completely divorced”.
Sure — if they agree about what is an observation. But often they disagree.
When we have agreed standards for correctness, then most people will usually agree. The argument is over whether the standards themselves are correct. And often, there are no standards by which we can evaluate that.
I am skeptical of the correspondence theory. It seems empty.
I want to put that as a two step procedure.
Step 1: Science provides us with something that works well.
Step 2: We then choose to adopt the operating rules of that science as standards by which to evaluate the truth of statements arising from that science.
What’s wrong with inference? Pretty much all science consists of inference. Now, in your analogy between human paternity testing and primate phylogeny, you have conveniently made the father’s DNA available. But what if it weren’t? Could you not use siblings, in the complete absence of parental DNA, to determine whether they were in fact siblings and even to derive information about the otherwise unknown parents? Similarly, you could use a great many relatives from a single generation to determine a great deal about their common ancestor(s), as far back as their shared ancestry goes. And you could do the same even if the relatives didn’t all belong to one species too.
There are methods of analysis that only work with close relatives within populations; just counting shared SNPs, for example. But have you ever seen a mitochondrial haplotype tree of a human population? That’s employing exactly the same methods that are used among species. Those are also the methods that are used to track down “patient zero” in viral epidemics.
No, that’s wrong.
I was arguing about a specific use of truth by you. But now that you have broadened that to “sense of truth”, I need to know what that is before I can comment further.
Okay, fair enough. Now all we need is an acceptable definition of “actual history”.
I hope you have plenty of time, because this is an infinite recursion. It’s turtles all the way down. Or it’s making up stuff all the way down.
As best I can tell, there is no satisfactory definition of truth.
Is there simply no room for literary license at this site? It was an allusion to an earlier comment by Joe about “defenders of Nonlin” (or some such). It wasn’t an attempt to say that you were ACTUALLY a defender of Nonlin. FFS.
I can’t help you, because I don’t now what the difference is between “specific use of truth” and “sense of truth” is.
Is there a satisfactory definition of anything, by that standard? Words are defined in terms of other words, which are themselves defined in terms of other words. At some point we have to find some words whose meaning we can agree on if the infinite regress is ever to end, not just for “truth”, but for “apple” or “green”, or for anything at all. So can we agree that there is such a thing as reality, existing whether or not we understand it?
I should probably also ask what you mean by “works”. How do you know if something works?
John Harshman,
The other is that they were independently created. I looked over the paper again and don’t think your methods test the hypothesis. You have asked me to take a firm position and so this is it.
Absolutely nothing. We make inferences all the time, both within science and apart from science.
My objection is to the claim that the methods are the same. We don’t create trees of species relationships by using paternity tests, or the methods of paternity testing.
The question is, are they the same methods used for paternity testing.
The question is, would we trust paternity tests and use them in our courts of law if we did not have actual known ancestors and relationships that could be used to validate the methods.
The other elephant in the room about this method of determining “relatedness” is just how far back it can be trusted. It’s my belief that the “signal” gets lost after not that many generations. That’s just a hunch, I have no evidence for it. But to date no one has been able to disabuse me of it by showing me I’m wrong.
Take any two random people of the street and tell me how closely they are related using the methods of paternity testing. Take 100 people and tell me how many and which ones shared a great-great-great-grandfather.
Something works if it is not broken. 😉
How does independent creation predict that the data will support a single tree? How would any method test that hypothesis? It seems to me that the expectation of independent creation would be that there would be no treelike pattern in the data. Of course independent creation could follow any pattern or no pattern at all, at a creator’s whim. But a tree would not be our expectation, so independent creation should not be our go-to explanation for a tree pattern in the data. That hypothesis just doesn’t survive any scrutiny.
How would we test that hypothesis?
ETA: Ninja’d!
And saying that the above statement is actually true is pointless. And since there is no reason to believe that what you have said is true, we have no reason to believe it. Which is why I wonder what it is that you are arguing about, and why.
Good. So you weren’t using “inference” as a pejorative when you said “We don’t have the actual DNA of the common ancestor of humans and chimps, other than by inference.” You meant that it’s perfectly valid to use inference to discover the nature of that common ancestor. Right?
True, but you made a stronger claim. There actually are similarities in the methods, and we do use phylogenetic methods within the human population, once the question gets much beyond simple paternity testing.
I think you were addressing quite a bit more than that. But the answer to that particular question is indeed “no”.
We probably wouldn’t. But once the methods were validated, we would not require re-validation in every case, right? Because that would render the tests redundant and useless. Now, it happens that phylogenetic methods have frequently been validated by known pedigrees, in human populations, viral populations, and bacterial populations. Given that, should you not accept their validity also in cases where you can’t check directly? If the answer to that question is “no”, wouldn’t paternity tests collapse too?
I would add that there is another way to validate results: if independent tests using different data, and different sorts of data, all converge on the same answer, that also validates each of the methods used. Consider radiometric dating: if K-Ar, U-Pb, and U-U dates for a rock all agree, is that not a reason to believe that all three methods have correctly dated the rock? If we reject that validation, don’t we have to reject radiometric dating methods in general? What else supports them? We certainly don’t have direct observation of the age of a rock that’s hundreds of millions of years old on which to validate the methods.
How did you come by this belief? How could anyone show you that you’re wrong? Now, if we’re talking about phylogenetics, the mere existence of a signal, i.e. lots of data that separately agree on one tree rather than others, is evidence that signal wasn’t lost. Thus the fact that just about any DNA sequences you pick, even at random, will support the same tree of primates seems to me to be quite good evidence that the signal wasn’t lost, and incidentally that primates are related by common descent.
I think you actually could do the second bit. Though you might not be able to tell a great^3 grandfather from a great^3 grandmother. The first is too vague. But you’re right that the signal does fuzz out over time. It isn’t lost, but it becomes harder to tell, for example, a 6th generation connection from a 7th generation connection than it is to tell a 2nd generation connection from a 3rd generation connection. But this particular problem doesn’t affect phylogenetic methods, which as you say are different.
No, I wasn’t using inference as a pejorative. 🙂
I accept common descent John. And I don’t try to limit it to “within kinds.”
I don’t think I would put it in those words, I don’t think we discover the nature of the common ancestor. But I accept that we can make inferences about relationships between species. All the way back to a LUCA. Yes.
I am not of the opinion that over time God has “poofed” new species into existence from nothing, either recently, or over long ages.
I am interested in understanding better why I accept common descent. Beyond accepting it as current science. If I came across someone who did not accept common descent, how would I convince them of my position.
So I actually appreciate all the work you guys do in that regard in these threads.
I bet that comes as a shock!
So have I convinced you that phylogenetic methods have been adequately validated and that we should in fact accept their results (with the appropriate tests of data concordance) as evidence of common descent?
I accept that. I do not think common descent is false, or misguided, or without evidence, or any of that nonsense. Whether you personally convinced me though, can I take the fifth on that? 🙂