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,
Exactly, you are depending on the assumption of common descent for parsimony.
As you make modules of the genes that are not following the tree and group them into a dependency graph the fit is quite good.
Are you claiming common descent is a tree or that common descent is the only process that generates a tree?
This is why it’s hard to talk to you. You have no idea what you’re saying. Parsimony is a criterion by which we compare hypotheses. That the tree hypothesis is parsimonious is an argument in its favor. If you want to call that tree an assumption, then the parsimony criterion tests that assumption. In this particular case, the test is positive: the assumption is warranted.
Obviously, as the “modules” are characterized only by their fit to the data, adding them must improve fit. This is evidence of nothing.
Not sure what you mean to convey by either of those alternatives. As usual, your inability to clearly state a claim gets in your way. Common descent is certainly the only process we know of that results in the sort of trees we observe in analyses. None of this seems relevant to the current discussion.
John Harshman,
Tests that assumption against what?
What I claimed was an assumption is common descent not a tree.
They are not arbitrarily added. The modules exist because some gene families only partner outside taxonomic relationships, which is no longer a perfect tree. This is evidence against an ancestral tree and for a dependency graph.
Against a different tree or no tree.
Distinction without a difference. Testing the existence of a tree is a test of the main model of common descent. One could of course have common descent without a tree, but one can’t have a tree without common descent.
That’s an admission that the “modules” are arbitrary: they are just sets of genes selected because they have the same pattern of distribution. That is, the pattern of distribution produces the modules which are then used to explain the pattern of distribution. And you complain about circular reasoning!
Further, most of the “modules” do not partner outside of taxonomic relationships. Either they are synonymous with taxa or they represent single losses. “Modules” with different patterns are much smaller sets.
I wasn’t talking about that philosophical problem. I wasn’t even talking about any design argument. I was talking about natural phenomena and the limits of our conceptual frameworks. Again, I’d rather not go there because it’s useless for the discussion, and it would take forever to discuss.
You want to attach some proof to your wish list?
You’re as helpless as Bill Cole, Nonlin.
Yes, assume true only to make predictions that can verified by the hypothesis BUT NOT BY the alternative hypothesis. This is NOT happening with UCD as it makes no predictions whatsoever and alternative hypothesis is eliminated before analysis.
Even if it were the case (IT IS NOT), this would only say “hypothesis 1 fits better than hypothesis 2”, but NOT “hypothesis 1 is thus proven true”.
Furthermore, “Tree of life” is curve fitting and not hypothesis testing as shown.
John Harshman,
Not a very difficult test.
Ewert showed that a tree formed with modular software designs.
True they are selected because they have the same pattern of distribution. This is a criteria and by definition is not arbitrary. Do you think this method will automatically generate a dependency graph that is preferred to a tree with any set of data?
1. A false inference and assumed in cladistics as shown – stop lying.
2. False. “Very similar lineage” doesn’t make it “further evidence” – it is to be expected from curve fitting.
3. False and stupid – read again:” Cladistic analysis is not really hypothesis testing since statistics are not essential to the methodology, “
At one point you have to stop lying.
John Harshman,
Per the Ewert paper:
While I don’t know what gene losses you’re talking about, the example I was about to offer, where common ancestry can be established before attempting to build a tree is our small group of great apes. Among many other things that support common ancestry of the great apes there’s shared pseudogenes. A typical example is vitamin C. The gene is normally intact in many species. However, the versions we see in the great apes are broken. The interesting thing is that the broken genes (pseudogenes), share the disabling mutations. The best explanation for that would be the most parsimonious, namely, that the gene was inactivated only once, in a common ancestor. Why? Well, that requires only one inactivation event, rather than independent inactivation by identical mutations (which is highly, but really highly unlikely), in different species.
So, if John is talking about something like this, then he’s not depending on the assumption of common descent for parsimony, he’s inferring common ancestry because that’s what makes sense of the data.
Entropy,
Yes, this is a good example of positive evidence for common descent.
We are on a more challenging adventure right now which includes genes that are not following the branching pattern.
1. UCD is NOT LOGICAL from “man births man” and “duck births duck”, etc.
2. False. “Ape births man” and “fish births reptile” was never observed
3. Has nothing to do with anything
4. False. Curve fitting ASSURES patterns fit assumption. It DOES NOT PROVE assumption
5. 1 and 2 are not the subject of this OP, but 4 is. “Tree of life” fails to prove UCD in any way as shown repeatedly.
Stop fooling yourself and others!
I was about to praise you again and then I read this. First off, “evolve” is not a fact as you know from our debates. Second, what’s with the squishy “likely”, “unlikely” and “substantially”? Next you’ll tell me about your feelings 😂
I don’t know that variations are strictly genetical. Do you? Can you prove? Who cares anyway?
What’s “an originally created group”?
Point the “contradiction” if any.
Your problem is that you are stuck in the wrong frame of mind and can’t get out therefore keep asking senseless questions. How about you start communicating YOUR counterargument instead?
And let me ASK YOU a question this time: Say one of these days humans get a cat born from a dog. Would that be proof of Intelligent Design? Darwinian evolution? Both? Neither?
There is no such thing as “fitness”: http://nonlin.org/natural-selection/
But you tell me what your ‘fitness’ is and I will reconsider.
To be expected from Common Design aka ID aka ONE Creator, but not from “evolution”. Why ONE SINGLE LUCA and not more? Darwin said it: “…the littlest creature (or “four or five” of them)…”. But why not 1 million “littlest creatures”?!? 10 million?!? 1 trillion?!?
Try again!
You don’t need 5,000 comments, you need one good experimental evidence. ONE! But there’s NONE!
No, it isn’t very difficult. Why is that a bad thing?
All that shows is that you don’t understand Ewert. He was contrasting trees with “dependency graphs”.
It’s arbitrary because it isn’t based on anything other than fit to the data. You can always make a dependency graph by this process that’s a perfect fit to the data. But the cost is the addition of all those ad hoc parameters.
Note that a tree is a subclass of dependency graph, so it’s impossible for a tree to be preferred to a dependency graph. Given any losses or homoplasy of any sort, a dependency graph that includes “modules” that don’t represent tree nodes should be preferred to a tree. Adding parameters can always improve fit. They claim that some simulated data preferred the tree to the dependency graph, but I admit that I don’t see how that’s possible. Absent details, there’s no way to examine this claim.
Will you ever stop lying? Or misunderstanding? The tree is not “inferred from DNA”. it is curve-fitted to the DNA.
And I was pointing out a weakness(!) – namely that a supposed historical tree must rely on current DNA. And don’t forget that we see no DNA “evolution” in these 700K years. Ouch!
Yes, this is the claim that simulated data didn’t fit a dependency graph. For reasons I have mentioned, that doesn’t make sense. But at least they allude to a penalty for extra parameters. How this penalty was applied, and whether it was sufficient, is unclear at present. Perhaps Joe will look at it. I’m also unclear on just how that simulation worked. Did it match the expectations of real data at all? No way to tell.
For those open to it, the 4-billion-year history of life, regarded altogether, is ONE good experiment. Do you need another?
In much the same way that we don’t infer the moon’s orbit by observation, we “curve fit it” to the axiomatic presumption of an orbit. It’s clearly faked.
John Harshman,
Thank you. Have you looked at his description of the algorithms in the methods section?
Hard to say. Darwinism IS a religion and it is embedded in the state structure, so it might take a long time. Look at the communist retarded-ness – it just won’t die no matter how many people it kills and oppresses.
It’s always amusing how religious people try and ridicule whatever they reject in science by calling it a religion.
Start taking your meds.
1. There is no possibility of “no designer” – your “theory” is impossible. “Design without a designer” is a full retard assertion as are
1. “Design by multiple choice”
2. “Multiple choice from ALL random answers”
3. “Designing without trying”
4. “Self design”
5. “Design by incremental optimization”
2. I compared ‘vehicles’ to organisms. Are you saying they are NOT different? Or more likely that you can’t read?
Only glanced. It’s a hard slog. Have you?
This is what I said: “Cladistic analysis is not really hypothesis testing since statistics are not essential to the methodology“. Too bad your reading comprehension sucks.
Truly you are a Savant. My goodness.
So tell us about the parameters you measured throughout that 4-billion-year experiment. Presumably you or your buddies have WITNESSED that experiment. Yes or No?
Are you saying there are no observations of the moon’s orbit? Ridiculous.
Perhaps I should take your meds. What exactly are you smoking?
False, you didn’t show anything, you just made a lot of astoundingly ignorant claims, as shown. Stop lying yourself.
It’s not “very simiar lineage,” it’s “very similar order of lineage separation.” That you’d miss the important bits of my explanation come only to confirm that you have no idea what you’re talking about.
Similar order of lineage separation isn’t to be expected from “curve fitting.” If that were the case there would be no need to do the fitting in the first place. Curve fitting would not even exist. When curve fitting is done, two things are tested: (a) if the data fit some curve, and, if so, (b) what the shape reveals about the data. In the case of phylogenies, (b) would reveal the order of lineage separation. There’s nothing in the “curve fitting” procedure that would force a single order of separation into the data.
Your claim is akin to saying that any data fit to a straight line would show the same slope.
It would be a good idea if you took a course in statistics, but not before taking a very comprehensive one in reading for comprehension. You have to finish elementary school first.
Cladistic analysis is a statistical procedure you poor ignorant and arrogant fool. Curve fitting is a statistical procedure you poor ignorant and arrogant fool. The amount of arrogance you put into your claims does not determine what’s statistical and what’s not. Thus, quoting your ignorant claims time and again won’t change the facts.
The procedures include testing whether the data fit one order of separation or another, or none. There’s all kinds of [statistical] testing done during the procedure and after the procedure is finished.
At one point you have to stop lying to yourself. You have to learn that your desires and beliefs, no matter how strongly held, don’t determine reality. Your level of arrogance won’t allow it to happen any time soon though.
My last answer to you. You’re full of shit, and full of yourself, which, in your case, are one and the same. You come back repeating your ignorant claims after being corrected on precisely those ignorant claims. As if that wasn’t enough, you come back insulting people who clearly know much better than you. What you imagine to be accomplishing with your attitude only you can know. What you’re actually accomplishing is confirming that you’re just too ignorant, and mentally immature, for the conversation.
Your stupidity shall become legendary. I was agreeing that vehicles and organisms are different. You have thus demonstrated that it’s you who can’t read. Talk about shooting yourself in the foot … multiple times!
John Harshman,
Yes, but I need to spend more time with it.
6/7
Again, not for Nonlin, since she does not care for, or is incapable of, reading comprehension.
This could be the one and only part where Nonlin could be making an actual point. However, she missed the opportunity and made some pretty ignorant and confusing claims instead.
There’s plenty of biochemistry shared by loads and loads and loads of anatomically different life forms. From bacteria to humans even. I’d think that alone invalidates this poor attempt at a conclusion. Do we need to look any further?
(Emphasis mine)
Well, it was worth looking further. I hereby learn that, according to Nonlin, whose words are divine decrees for reality to follow, biochemistry and the age of DNA are one and the same. There’s also the contradiction of terms. Here Nonlin is saying that the trees are independent, but she said above that they weren’t. Which is it? Rather, which of Nonlin’s decrees will reality follow?
What? A far as I know, anatomy and biochemical-based trees are not done with fossils. I’ve never heard of people checking the biochemistry of a fossilized life form.
Also, of course fossils can be linked to one another and extant life forms without presupposing UCD. It’s enough if we can infer common ancestry among the organisms in question, rather than among all of life, to justify checking if they fit well into a tree.
So this magical being in the sky is a biological reason? Woa! Nonlin’s decrees must be very hard for reality to follow.
Entropy,
I notice that you use “she” and “her” to refer to Nonlin. Has Nonlin actually self-identified as female?
I’d like to use the correct pronouns when referring to him/her.
Nonlin:
Here’s what you said:
That’s why we’re laughing at you.
Predicted Nonlin response:
Joe:
Nonlin:
It’s a curvy, helical tree.
Flint:
Nonlin:
Were you there, Flint?
Nope. Not that I know. I was trying to be neutral using a generic “she her.” Any suggestion? Maybe “they / them” like some poet, whose name escapes me, used to do?
I wrote the standard reference/text book on inferring phylogenies, entitled, amazingly enough “Inferring Phylogenies”. I must admit, though, that on page 577 I do show how you can draw curvy trees.
Certainty, thy name is nonlin.org !
Joe:
Then whatever you do, don’t show that page to Denyse O’Leary, who had this to say about one “curvy” tree of life:
petrushka’s incredulous reaction:
On page 577 of my 2004 book I also draw one of those circular trees. They were invented by David Swofford and David Maddison, and are often a quite useful way to draw phylogenies.