Nested Hierarchies (Tree of life)

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?

  1. “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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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 […].”

 

1,059 Replies to “Nested Hierarchies (Tree of life)”

  1. Rumraket Rumraket
    Ignored
    says:

    Nonlin.org: 1. Joe Falsenstein thinks that parts of the genome are independent but this is ILLOGICAL as parts of the genome are NOT separately inherited (acquired) and can NEVER be found separate from the genome (decomposition and lab experiments aside).

    Their independence is in nucleotide sequence. They do not mutually constrain each other to follow a particular tree topology if subjected to phylogenetic analysis. There isn’t an influence that is making them functionally (or in some other way) be dependent on having a sequence that would yield similar trees. THAT is the way they are said to be independent.

    That is not to say they are not causally influenced by the same factors or forces in other ways, they clearly are as they are both part of the same genome of the organism, sit in the same gravitational field, are both replicated by DNA polymerases at cell division and so on and so forth.

    2. Furthermore, an organism genome INCLUDING its genes is 100% (not 99.9…%) correlated with that organism’s morphology.

    This is just confused nonsense. Yes an organism’s morphology is in some sense determined by it’s genes and their sequences, but that relationship does not hinge on what kind of tree will result if similar versions of that gene from different species are subjected to a phylogenetic algorithm. Why would it be? That’s ridiculous.

    But even if we suppose, just for the sake of argument (and contrary to all available evidence), that there are some genes that are somehow mysteriously constrained through their function to also corroborate the same branching topology as that implied by morphology, there are still many other genes that are obviously completely independent of morphology.

    To pick an example, salivary or pancreatic Alpha-amylase is an enzyme, secreted in spit and by the pancreas, which breaks down starch in the food you eat. This enzyme is encoded by a gene in your genome that has a particular nucleotide sequence (and results in a particular amino acid at sequence at the protein level).

    You have it, all other primates have it, rats and mice have it, dogs and cats have it, horses, pigs, cows, and birds have it, countless other animals (and even fungi) have it. But it only does one thing: it breaks down polysaccharides such as starch.

    Clearly this enzyme does not cause you to have the human body morphology. It’s deactivation, or mutations in it, does not cause you to become a pig, or a bird, or a fruit fly, or a fish, or a fungus. Humans who have defective or mutated versions of the gene, either can’t make it, or have less active versions of it (and might have various metabolic disorders, but they remain morphologically clearly human). They don’t grow bat wings, or trunks, or lion manes, or a segmented body, or feathers, or lay eggs. It is independent of morphology because it’s function is to digest carbohydrates, not to affect how your tissues grow and shape themselves.

    Nevertheless, we can look at the nucleotide sequence of the gene encoding Alpha-amylase and see that it is slightly different in each species that has it. But the nucleotide sequence of this gene encoding the Alpha-amylase enzyme does not cause these organisms to have a particular body morphology. It’s function is independent of morphology. Mutations in Alpha-amylase do not cause a mouse to look more like a dog, or a dog to look more like a cat, or a horse to look more like a bat. That’s because the gene only encodes the amino acid sequence of an enzyme that breaks down chains of carbohydrates in food.

    But if we subject the nucleotide sequence of the Alpha-amylase gene to a phylogenetic inference, we get a tree that is very similar to the one we get from morphology. Why would that be the case? The only answer that makes logical sense is that the nucleotide and amino acid sequence of the gene is constrainted by it’s history, as in the genealogy of the organism, just as the morphology is.

  2. Rumraket Rumraket
    Ignored
    says:

    Nonlin.org: 3. Finally, cladistics based on different genes is SAME AS cladistics based on parts of the organism’s morphology like limbs, digestive, reproductive system, etc and is 100% RETARD as anyone knows there are no functional limbs, etc. independent of the organism with its morphology, genome and COMMON genealogy.

    This is just incoherent. But I see you wrote “100% RETARD” in all caps. How ironic.

  3. Nonlin.org
    Ignored
    says:

    Nonlin.org: 3. Finally, cladistics based on different genes is SAME AS cladistics based on parts of the organism’s morphology like limbs, digestive, reproductive system, etc and is 100% RETARD as anyone knows there are no functional limbs, etc. independent of the organism with its morphology, genome and COMMON genealogy.

    In this context, ‘RETARD’ is not an attribute of any particular person.

  4. Nonlin.org
    Ignored
    says:

    Rumraket: This is just incoherent. But I see you wrote “100% RETARD” in all caps. How ironic.

    How so? For any organism, its genome comes in ONE PIECE same as its morphology. Mentally breaking up one and pretending its parts are independent is the same as mentally breaking up the other and pretending its parts are independent. Is this hard for you?

  5. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Nonlin.org: anyone knows there are no functional limbs, etc. independent of the organism with its morphology, genome and COMMON genealogy.

    Same unaddressed problems, same inability to show that any nonindependence is enough to keep trees from different sets of characters from reinforcing each other.

  6. Nonlin.org
    Ignored
    says:

    Rumraket:
    1. Their independence is in nucleotide sequence. They do not mutually constrain each other to follow a particular tree topology if subjected to phylogenetic analysis. There isn’t an influence that is making them functionally (or in some other way) be dependent on having a sequence that would yield similar trees. THAT is the way they are said to be independent.

    That is not to say they are not causally influenced by the same factors or forces in other ways, they clearly are as they are both part of the same genome of the organism, sit in the same gravitational field, are both replicated by DNA polymerases at cell division and so on and so forth.

    2. This is just confused nonsense. Yes an organism’s morphology is in some sense determined by it’s genes and their sequences, but that relationship does not hinge on what kind of tree will result if similar versions of that gene from different species are subjected to a phylogenetic algorithm. Why would it be? That’s ridiculous.

    1. Can you summarize? You don’t seem to address anything I said.
    2. This is not addressing the point either. My comment was about the entire genome and the entire morphology, not about genes. It is only saying that whatever classification done on the basis of the genome is bound to match another classification done on the basis of morphology because the two are 100% correlated. For instance, a human gene, can only be found in humans with human genes and human morphology. Causation or not, it doesn’t matter.

  7. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: Same unaddressed problems, same inability to show that any nonindependence is enough to keep trees from different sets of characters from reinforcing each other.

    Very funny. I take it you’re speechless. It’s OK. Go think about it, ask your coreigionists, and see if you can come up with something remotely plausible and logical.

  8. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Not expecting nonlin.org to be convinced, of course. I’m happy to let any lurkers who have seen our exchanges, and the very cogent comments of others, draw their own conclusions.

  9. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: Not expecting nonlin.org to be convinced, of course. I’m happy to let any lurkers who have seen our exchanges, and the very cogent comments of others, draw their own conclusions.

    Seems you’re not getting any support here, Joe Felsenstein.

    One more thing: Common descent is the ultimate redundant assumption.

    Think about it, we’re still using the basic Linnaean taxonomy complete with his hierarchy because it worked in 1758 as well as today. Yet we all know he had no need – as we don’t – for the “common descent” hypothesis that came 100 years later anyway. Furthermore, taxonomy is based on OBSERVABLE ‘shared characteristics’, not on the imagined but NEVER OBSERVED “common descent”.

    This brings back Carl Sagan’s funny definition of life: “a system capable of evolution by natural selection”:
    Astronaut: “Houston, we found something that looks like life”
    Houston: “Well, is it capable of evolution by natural selection”
    Astronaut: “How would I check that? Let me ask it.”

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