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 […].”
Is there anyone here among the ID supporters who agrees with nonlin.org’s criticisms of evolutionary biology? If so, could they explain the logic?
I don’t usually pay much attention to nonlin. But for you I’ll take a look. 🙂
Nonlin’s beef doesn’t seem to be against evolutionary biologists, but rather with gardeners.
Mung,
Some are valid, some are questionable, and some I don’t understand. He takes very hard positions on subjects that are not necessarily black and white.
He accepts “selection” and “common descent.” Human breeders even take advantage of those evolutionary elements.
I don’t agree with yours…
Would you like me to tell you why? Or should I quote your own statements in your own book?
Please tell all the readers for the record how many times you have gone outside of your, no doubt comfortable office, and observed, documented and tested, the speculation you have been making all your life? You do have at least one… don’t you?
So you are one more ID supporter who isn’t able to explain and support nonlin.org’s statements. Still looking for one who can.
Are you talking about the OP or a specific post?
I don’t like to use the language some do to describe your work… Nonling?
Don’t be a child! Your work stinks as it is… why would I need someone else to expose it?
You have never been outside of your theoretical lab, so if I were you, I’d never question anyone who has…
At least the OP. That would do, one need not defend every comment. Even defending and explaining individual points in the list in the OP would help.
How long have you been speculating, Joe?
Please be truthful! At least once…
Better to just let those things stand without comment, Entropy.
OK, point out one valid item in the list of points in the OP and we can discuss it.
… and to laugh your socks off at J-Mac being unable to react in any other way than by making childish taunts like a 6-year old would.
I know, I know. Still, J-Mac’s reaction was something to be treasured.
ok, let’s start with the last one from the OP.
A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure
That seems trivially obvious to me. Except for the part about cladistics giving us a hierarchy. Cladistics gives us trees.
But every rooted tree is isomorphic to a nested hierarchy. So what’s the difference?
You tell me John. I’m willing to learn. I grant cladistics gives us trees. I don’t know what you mean when you say a tree is isomorphic to a nested hierarchy if it is rooted.
As far as I know cladistics doesn’t give us classes and phyla, so what “hierarchy” are you referring to, to which a rooted tree is isomorphic?
ETA: Do you disagree that these trees that are presented to us as hypotheses by the cladists are in fact artificial human constructs?
I already dealt with that crap.
You’ve been on Ignore, so I missed it. I felt like I needed to cut down on my pointless and whiny responses to the moderators and you were right near the top of my list.
Is there a reason you cannot post here and remain within the rules?
I mean that there’s a one-to-one-correspondence between the nodes of a cladogram and the nested sets of a nested hierarchy.
Classes and phyla aren’t what a nested hierarchy is. A nested hierarchy is simply a collection of sets in which every pair of sets A and B has one of three relationships: A is a subset of B, B is a subset of A, or the two sets are disjunct. Or, to choose a less pedantic definition, groups within groups. Whether you give those groups names, ranks, both, or neither is not relevant.
I’m not sure what connotations you are attaching to that statement. They are artificial human constructs in that they are derived by analysis of the data. The tree diagrams are constructed. Then again, if you do it right those diagrams reflect an underlying reality of relationships among taxa. So what does that make them?
I ask you to check out the book The Origin of Higher Taxa
Those diagrams represent a hypothesis of relationships among taxa. There is no “doing it right” involved. There is merely “doing it according to a model using certain assumptions.”
Which is what is pointed out in the OP.
I’m not sure what to make of this comment. Are you saying that the Linnaean taxonomy is not a nested hierarchy? Is the Linnaean taxonomy isomorphic to a nested hierarchy?
The Linnaean taxonomy is a nested hierarchy. However, it isn’t the only nested hierarcny. It has features, i.e. names and ranks, that are not necessary to a nested hierarchy. Does that make it clear?
Why? What specifically in that book?
I don’t understand this objection. Are you denying that there is an underlying reality? Are you denying that hypotheses can be more or less strongly supported by observation and test, such that we can approach reliable inference of truth? And “doing it right” would involve wisely chosen models and assumptions. Some models and assumptions are better than others. Some hypotheses turn out to be better founded than others. That, in fact, is how science works.
I don’t believe that the OP pointed out anything. It made a number of claims, most of them dubious. Now if you would care to pick one or more of those claims and defend them, I would be willing to listen.
Yes, thank you.
You say that the Linnean taxonomy is a nested hierarchy, yet of cladistic trees you only say only that they are isomorphic to a nested hierarchy, if they are rooted.
This indicates to me that you know the difference.
Have you not answered your own question?
I have chosen the seventh claim and I am defending it. I simply don’t know how that has escaped your attention.
He delineates the models used in classification. Yours, in particular, fails to conform with reality. 🙂
You may enjoy empty wordplay, but I don’t.
Could you explain in greater detail? What models does he delineate, and what in particular is my model? Is there a model that does conform to reality, and if so what is it?
Now, why is a surprise that “multiple different parts of the genome come up with more-or-less the same tree”?!?
How is point 5 not making any sense and what about 6 is “wrong”?
Point 7 is exactly what you admit: “phylogeny programs will always come up with a tree”. Do you disagree trees are human constructs? That organisms do not come labeled with their position in a tree?
You have to demonstrate misrepresentation. Just stating your displeasure doesn’t do anything for anyone.
Not “quarrelsome”, but open about minded that which I don’t know for sure to be otherwise.
“Descent with modification” and “(universal) common descent” have the very specific meaning given by Darwinistas and that meaning excludes Intelligent Design. Get your buddies to change that definition and you have a deal. Remember this:
“11. Intelligent Selection should replace Natural Selection but only if we ever transmutate organisms”
?
No, you did not answer. I said: “Venter claims to have done that (more or less)“. You know full well why you avoid an honest answer. I give you credit for intelligence, but not for honesty and courage.
No matter how you look at it, LUCA is not compatible with the neo-Darwinist story. Either life started Once and Only Once making abiogenesis a singularity that screams for an explanation, or abiogenesis is trivial under the right condition in which case your tree gardeners are clueless and we’re looking at multiple trees if not independent creation events. The other two “explanations”: Darwin’s “four or five” or “they all died except LUCA that miraculously survived to fill the earth” are downright retard. Now, which one is it?
The definition shows that “ancestor” – if you chose to use that word – needs not be tied to biologic reproduction (mitosis, meiosis).
Let me enlighten you, Corneel: because neo-Darwinist evolution utterly fails.
And here comes someone or somebot like Entropy saying:
“common ancestry can be established for a group before starting a phylogenetic analysis” as if this is a proven fact… and not accepting:
http://www.ucmp.berkeley.edu/clad/clad1.html assumptions
http://www.ucmp.berkeley.edu/clad/clad2.html method
…as if I wrote that instead of your own Darwinosaur buddies.
When will you Darwinstas learn that science is not a democracy?
Why don’t you simply ask if you disagree with specific statements?
You understand nothing. Since when is “selection” owned by the Darwinistas? And why can’t “common descent” be simply a reference to you and your
first order cousins?
Because you have so far been shown incapable of coherently explaining yourself, Joe searches for someone else who can make sense of you. He probably searches in vain, but there’s always hope.
First, I don’t know what a first order cousin is. But to the larger question, when you start using it that way. You’re definition of “common descent” is so loosey-goosey as to be pointless arguing over.
I’ll stipulate that when you use the term neither one of us knows what you mean by it and neither should anyone else. Fair enough?
So far in vain, though a couple of ID advocates who comment here have said that they’d take a look at it. But alas, they never returned. Search parties are out looking for them …
Ah, you associate common descent with natural selection? Rejoice, for they are distinct concepts. Quoting myself from one of the many times this has come up:
You have accused me multiple times of putting words in your mouth, so now I have learned my lesson. I will not answer your question until you have carefully explained to me what the connection is between making a synthetic bacterial genome and “dogs giving birth to cats”, ’cause I sure as hell don’t see one.
Don’t know how many times life got started, sorry.
Why do you mention abiogenesis? Did you miss the point that LUCA has ancestors as well? You did, didn’t you? 😉
An argument ad lexicon? That’s a new one.
Are your ancestors prototypes of you? Did you get an upgrade lately? What nonsense! You cannot use the meaning of prototype for biological organisms. I note that this appears to be a quirk of the English language. In Dutch for example, “voorouder” doesn’t have that additional meaning for machines. Are we discussing linguistics or biology?
Corneel, I agree, nonlin.org just hasn’t understood what LUCA is. LUCA is not the first organism but is the Last Universal Common Ancestor, so LUCA could have ancestors, who would be Universal Common Ancestors but just not Last ones. Think of a tree which is Y-shaped. LUCA is at the fork, not at the bottom of the stem.
Look Nonlin, you’re just showing astounding, truly astounding, incompetence. Had you read carefully what I wrote, besides everything others have tried to explain to you, you’d avoid some embarrassment, but to you, the embarrassment is inconsequential, right? You think that if you say so it is so.
In science, we can talk about assumptions in the sense of justified assumptions, and unjustified ones. You shall not mistake your poor language skills for everything there is to know about the contexts under which things are discussed.
You’re having another context-related problem. You link to a site about cladistics. Again, cladistics doesn’t establish common ancestry, it just tries and establish the order of lineage separation (this is perhaps the third or fourth time I mention this, how hard is this to understand for you Nonlin?). So, it’s not too surprising that you would not find procedures for establishing common ancestry in a procedure that assumes that you already know, or expect, that.
(To drive the message home, check point one in the methods section. It tells you that the taxa must be clades. In other words, the method assumes that you already checked for common ancestry. Maybe you should take a few remedial courses on reading for comprehension, and a few more on logic.)
Now, of course there’s ways to establish common ancestry independent of cladistics. I gave an example, of several, in the vitamin-C pseudogene being broken in the very same way in different primate species, like humans, chimps, gorillas. The probability of breaking a gene in the very same way in three independent lineages is so small, that the best explanation is that the gene broke once, in a common ancestor, and we all inherited that version of the broken gene from that ancestor.
See how that doesn’t use cladistics at all? Now, if we took all the organisms for which we have pretty strong evidence for common ancestry, we can now test their order of separation using phylogenetic analyses. If different pieces of data give very similar trees, then that’s further support for the common ancestry, but that’s not what the analysis is for. Again, the analysis is for establishing the order of separation.
Well, there’s more. I’d help you better, but I’m sure as hell that you’ll conveniently miss the whole thing yet again. You’re not here to understand. you’re here to establish your mental superiority by making grandiose, yet extremely ignorant, claims, because you think you know everything, and that your poor googling and linguistic skills are enough to shut up those scientists who think they know better just because they have seriously studied all of that stuff that you don’t believe to be true in the first place. You think you already know what’s true, and you google for excuses to support your a priori beliefs, rather than to actually check if your beliefs have any support in reality.
I know that won’t help you out. I know you’ll show yourself to be nothing but the same arrogant-yet-ignorant Nonlin we know you to be. Yet I hope someone else who might have been fooled by your misleading know-it-all tone will be less of a fool after reading some answers.
Not for Nonlin.
Nonlin here is mistaking phenomena with the history of life. Evolution proceeds regardless of how many ancestors there might have been for current life forms.
Oooooh How scary! Screaming for an explanation! Must be that fi we didn’t know then god-did-it! Magical-being-in-the-sky for the win!
Interesting dichotomy, either a “singularity” or trivial, nothing in-between. Isn’t Nonlin clever? She saved us a lot of time figuring things out. If it’s not trivial it must be a “singularity.” So simple and obvious. How come we never thought of that!?
If “trivial” were the case, there would be indications of it. So far none.
Ah! Right! Let’s not forget to include fantasies as potential explanations!
It’s interesting that Nonlin would be so fond of absolutist false dichotomies. I’d mention coalescence to Nonlin, or the possibility of life being a mosaic of several ancestral life forms, or ask Nonlin if he understands that Darwin was just speculating about alternatives he could think of at a time when data was much more scarce, etc. etc. But what for? It’s not as if Nonlin would start reading for comprehension, or even cared.
I think you just overlooked my posts somehow.
I didn’t. But you seem to have overlooked mine.
And that proves evolution? Do matryoshka dolls prove evolution? https://www.vermontcountrystore.com/ccstore/v1/images/?source=/file/v1572392947014410569/products/70072.main.png
Can you make a distinction between what a thing looks like versus what it behaves like? Such as a stuffed toy cat and a real cat? The distinction seems important to me because one of these would not be an object of biology.
No. I saw yours. I just chose not to respond. Perhaps another time in a different thread. Giving you some time to read the book.