I promised John Harshman for several months that I would start a discussion about common design vs. common descent, and I’d like to keep my word to him as best as possible.
Strictly the speaking common design and common descent aren’t mutually exclusive, but if one invokes the possibility of recent special creation of all life, the two being mutually exclusive would be inevitable.
If one believes in a young fossil record (YFR) and thus likely believes life is young and therefore recently created, then one is a Young Life Creationist (YLC). YEC (young earth creationists) are automatically YLCs but there are a few YLCs who believe the Earth is old. So evidence in favor of YFR is evidence in favor of common design over common descent.
One can assume for the sake of argument the mainstream geological timelines of billions of years on planet Earth. If that is the case, special creation would have to happen likely in a progressive manner. I believe Stephen Meyer and many of the original ID proponents like Walter Bradley were progressive creationists.
Since I think there is promising evidence for YFR, I don’t think too much about common design vs. common descent. If the Earth is old, but the fossil record is young, as far as I’m concerned the nested hierarchical patterns of similarity are due to common design.
That said, for the sake of this discussion I will assume the fossil record is old. But even under that assumption, I don’t see how phylogenetics solves the problem of orphan features found distributed in the nested hierarchical patterns of similarity. I should point out, there is an important distinction between taxonomic nested hierarchies and phylogenetic nested hierarchies. The nested hierarchies I refer to are taxonomic, not phylogenetic. Phylogeneticsits insist the phylogenetic trees are good explanations for the taxonomic “trees”, but it doesn’t look that way to me at all. I find it revolting to think giraffes, apes, birds and turtles are under the Sarcopterygii clade (which looks more like a coelacanth).
Phylogeny is a nice superficial explanation for the pattern of taxonomic nested hierarchy in sets of proteins, DNA, whatever so long as a feature is actually shared among the creatures. That all breaks down however when we have orphan features that are not shared by sets of creatures.
The orphan features most evident to me are those associated with Eukaryotes. Phylogeny doesn’t do a good job of accounting for those. In fact, to assume common ancestry in that case, “poof” or some unknown mechanism is indicated. If the mechanism is unknown, then why claim universal common ancestry is a fact? Wouldn’t “we don’t know for sure, but we believe” be a more accurate statement of the state of affairs rather than saying “universal common ancestry is fact.”
So whenever orphan features sort of poof into existence, that suggests to me the patterns of nested hierarchy are explained better by common design. In fact there are lots of orphan features that define major groups of creatures. Off the top of my head, eukaryotes are divided into unicellular and multicellular creatures. There are vetebrates and a variety of invertebrates. Mammals have the orphan feature of mammary glands. The list could go on and on for orphan features and the groups they define. Now I use the phrase “orphan features” because I’m not comfortable using formal terms like autapomorphy or whatever. I actually don’t know what would be a good phrase.
So whenever I see an orphan feature that isn’t readily evolvable (like say a nervous system), I presume God did it, and therefore the similarities among creatures that have different orphan features is a the result of miraculous common design not ordinary common descent.
None of that answers the question, which was “How is it [groups within groups] explicable under your creationist paradigm?” Please try again.
God did it because evolution can’t.
stcordova,
Do you have any gene tree that places mammals outside of the clade to which they are conventionally ascribed? I am doubtful. I think at that taxonomic level, the gene trees agree very well with the taxonomic and morphological hierarchies (one still wonders why they would agree at all, but we’ve easily cleared that bar). The branch order with lungfish and coelacanths may be less certain; that hardly makes us ‘not fish’.
That’s cute.
Evolution predicts the pattern. It would inexorably follow from a branching genealogical process.
But God must have done it because the mechanism that intrinsically yields nesting hiearchical groupings(common descent through branching evolution), can’t have yielded nesting hiearchical groupings.
stcordova,
That looks like a white flag!
We are still left with a question: where lies the restriction on what evolution ‘can do’? Can it, in fact, do anything in contribution to taxonomic divergence?
Even you should realize that’s not an explanation. Further, you have once again confused the nested hierarchy with the origin of innovation. Let me suggest an alternative position that’s more intellectually respectable: the nested hierarchy is strong evidence for common descent, but nevertheless you believe in separate creation because Genesis says so.
It’s a better explanation than “evolution did it.” You only pretend you have a mechanistic explanation when you don’t.
Rumraket showed random mutation on a pre-existing gene can create a phylogenetic hierarchy provided evolution doesn’t happen so quickly it erases the signal. Bill Cole saw that.
But, slight random mutation on a pre-existing gene isn’t the same as sets of new coordinated genes with no homolog. These changes are POOFs. You only pretend one kind of transformation (slight changes to pre-existing genes) is the same as radical transformation (Taxonomically Restricted Genes). They are not. It is an equivocation, therefore an illegitimate argument, to represent them as such.
Both kinds of changes will create nested-hierarchies, but evolution doesn’t give a mechanistic explanation of the latter kind of nested-hierarchy.
So for all your complaints that I don’t have an explanation, you have even less of an excuse to say you’ve explained anything of substance at all since “evolution did it” is not a mechanistic explanation.
Furthermore, quantum mechanics, as described in an article by Richard Conn Henry in the prestigious scientific journal Nature 2005, argued an intelligent MIND, namely God, is a necessary implication of quantum mechanics.
Intelligence doesn’t have to be mechanistically described to count as an explanation. That is, I can assert Mount Rushmore was created by an intelligence. I don’t have to provide mechanistic reasons why Washington, Jefferson, Rosevelt, and Lincoln were chosen instead of Bozo the Clown or Charles Darwin.
Ironically, if you claim you won’t believe in a theory without mechanistic detail, you should be one to be talk! “Evolution did it” is even less of theory than “God did it.”
“God did it” at least has quantum mechanics backing it as a possibility. Further, as I’ve shown on many levels, “evolution did it” doesn’t even work as a theory with it’s contradictory gene trees and flimsily concepts like “fitness” and last but not least, the inability to demonstrate from first principles of physics and chemistry that a giraffe is within the expected outcomes of what will descend from a fish. Evidence is on my side that, barring a miracle, the descendant of a fish will be a fish, not a giraffe.
So on many levels, the arguments I’ve presented in this discussion highlight so much of your claims are based on non-sequiturs and equivocations and only the veneer of real mechanism. In contrast, I provided examples of miraculous transformations that were required. Hence, relative to your inept defense of common descent, I’ve defended the notion of common design to my satisfaction.
The pattern your simulation made only predicts SOME gene tree patterns from pre-existing, it doesn’t predict patterns of sets of novel Taxonomically Restricted Genes with no ancestors. Evolution doesn’t predict nested hierarchies of the latter pattern even though in some limited cases it will predict the former nested hierarchy. You are equivocating and conflating concepts, and further I demonstrated, when we talk real genes, the nested hiearchies from gene trees are only congruent because of cherry picking and fudging.
Regarding my non-acceptance of the prevailing interpretation of the fossil record being old.
Nuclear chemist Jay Wile points out:
This agrees with a term paper I wrote in Physics Grad school 5 years ago which actually referenced a lighting strike experiment that observed neutrons in 1984. God is giving us more and more reasons to doubt the fossil record is old. The first doubts for me were things like the Faint Young Sun Paradox. But anyway, here is stuff on chemical and electrical alchemy:
Once again you mistake the explanation of mutations or innovations for the explanation of nested hierarchy. Are you truly incapable of recognizing that these are different things? Nothing you say is about the nested hierarchy and never has been.
The explanation for the nested hierarchy of life isn’t “evolution did it”. It’s a branching tree of descent. Can you see that common descent would be expected to produce a nested hierarchy? It should produce a nested hierarchy even if genes are poofed into existence, as long as they’re poofed at particular times into particular species, rather than being sprinkled randomly across species. And that’s what we see, even for the genes you think are poofed. (Of course you think all genes were poofed, despite evidence to the contrary, but forget that for the moment. Even if we accept your ideas, the nested hierarchy is explained by common descent, nothing else.)
Not the kind of nested hierarchy defined by features with no ancestors. Common descent implies features with mechanistically feasible descendants from ancestors, it doesn’t imply features with mechanistically IN-feasible descendants from such ancestors. Mammals are mechanistically IN-feasible descendants from fish. Ergo, God did it because evolution can’t.
Rumraket’s example shows evolution of mechanistically feasible descendants from an ancestor using random mutation. I already affirmed the accuracy of his claims, heck I even built phylogeny trees independently confirming the branching and hierarchical pattern.
However, if we had sets of coordinated orphan genes in each extant “species” in his example, common descent by random mutation would only explain the genes he listed, it wouldn’t explain the others, especially if they are mechanistically coordinated.
What do I mean by mechanistically coordinated? Many systems in biology have well-match interacting parts. Their coordination doesn’t look like the product of random mutation and natural selection. Insulin-regulated metabolisms are generally associated with vertebrates. We can put the insulin exons together so as to make a gene even bacteria like E. Coli can express. It doesn’t do much good for E. Coli to have such a man-made insulin in it because the change isn’t coordinated to create something functional in E. coli.
Evolution by random mutation doesn’t predict branching patterns defined by coordinated changes like say a mammalian placenta or a mammalian immune system or a mammalian mammary gland for feeding.
Rumraket’s example was nested hierarchy via random mutation. That is not a legitimate representation of branching defined by coordinated systems like a mammary gland. It’s an equivocation to represent such illustrations of random mutation as the same thing as coordinated change. Yes they both generate nested hierarchies, and I’ve shown there is reason to doubt there is substantive congruence between the hierarchies.
Case in point: some molecular phylogenies nest mammals within Sarcopterygiian fish, I’ve said this is strongly incongruent with the fact morphology makes mammals not nest within Sarcopterygiian fish, not to mention, if we included genes unique to each group we could make a good argument mammals don’t nest within Sarcopterygiian fish — they are sister groups that nest under some unspecified Vertebrate which creationists like Owen believe are purely conceptual and archetypal, not actual physical ancestors.
Incidentally, phosphorylation creates different folds. This means that evolutionists need pause a little bit before they model the gene tree phylogenies as the result of random rather than coordinated changes.
The phospho proteome should give advocates of random mutation as an explantion for the branching pattern in biology some pause:
https://www.nature.com/articles/nature13999
When all else fails, just brainlessly decare as fact what you have persistently failed to prove.
Please try to grasp this elementary concept: There wouldn’t BE a nesting hiearchy (whether defined by nesting groups of clade-defining characters, like mammary glands, or by divergent orthologous genes) if common descent did not take place.
The very thing you are trying to claim couldn’t have evolved, is objectively sortable into nesting hiearchies exactly because common descent took place.
Your objection literally couldn’t be more false. Which is astonishing.
You have absolutely zero reason to expect that there should be hiearchical structure in the data (groups within groups) from any of your ridiculous “design-plan” rationalizations. As has been demonstrated in this thread. And the same applies to the unfathomable level of congruence between independently derived phylogenetic trees. Which you are completely unable to explain.
Sal, why would there be ANY congruent trees? All Bill Cole’s rationalizations about how this would follow from some sort of “design plan” completely failed.
So what now? What do you have left other than to brainlessly repeat the same silly phrase over and over again? “God did it because evolution can’t”. Who but yourself are you even trying to convince with this mindless regurgitation?
At this stage I’m inclined to conclude that even you don’t actually believe that, deep down.
Whoosh. You still are incapable of understanding that the nature of the features, including what caused them to appear, is irrelevant. Common descent doesn’t explain those. Common descent explains the nested hierarchy in which the features are arranged. That includes the features “with no ancestors” if there are any, which I doubt.
Still confusing the pattern with the origin of its elements. Common descent doesn’t imply “mechanically feasible” anything. It’s not an explanation for the origins of features. Why can’t you learn that simple fact?
Note that you had to put in “by random mutation” in order to make that sentence meaningful? That’s you confusing the causes of features with the cause of nested hierarchy yet again.
Actually, morphology does nest mammals within sarcopterygian fish. This was known long before there was any DNA sequencing. Of course it’s necessary to go beyond kindergarten ideas of taxonomy (“doggie! fishie!”) in order to decide that. And fossils help a lot.
stcordova,
Could I repeat my request for an exception? You say ‘some’ as if there are others that don’t (ie they nest them elsewhere). I’m not aware of any.
I’d be even more interested in a misplaced mammal genus. As in, a mammal (like a primate, or a rodent) that is placed with.. sponges, or bacteria, or fungi, or birds, or [pick a non-mammalian clade] instead of with other mammals?
Maybe an example will help Sal.
Imagine an empty backpack.
It replicates, magically.
Every so often, a sorcerer poofs a novel item into a backpack.
When backpacks replicate, they also replicate their contents. It’s magic.
Taxonomists come along at a later date, and examine the contents of the 1% of backpacks that are extant. They are able to determine the ancestry of the extant backpacks, based on their contents.
If (on rare occasions) the sorcerer’s apprentice, Mickey, moves an item from one backpack to a distantly related backpack, this will show up as an taxonomic anomaly, and be noted as such. If, OTOH, the sorcerer routinely poofs the same item into multiple unrelated backpacks [the way that human designers do], or Mickey is as busy as the sorcerer [early life], then the ONH will not be discernable.
The nested hierarchy that we observe is evidence of primarily vertical descent, with low levels of HGT (which are spotted as anomalies).
It’s got absolutely nothing to do with the poofing mechanism, rather it is a consequence of the poofing rules.
Interferon Lambda (Primates), Cox1.
And all those genes in that hated Pan-Genome diagram where mammals share genes that they don’t share with fish, and vice versa. At that point this is perhaps in the thousands of genes that were cherry picked away from consideration based on ad hoc rationalizations.
Sure you can say, “well the genes were added and deleted in the process of evolution.” That’s well and fine, but then that’s a tacit admission that there are incongruities that exist between nested hierarchies created by wholistic comparisons and nested hierarchies constrcuted via cherry picking.
A wholistic comparison is comparisons of total gene sets and morphological features. Focusing on a few hundred genes shared between all species is a bit ridiculous when one should also be focusing on genes existing in one group that are non-existent in another when trying to aggregate groups of creatures by total similarity, not cherry picked similarities.
Case in point: the immune system of a mouse is much more similar to a human immune system than the primitive system in fish. I cited one gene in the human/primate immune system. Interferon Lambda (Infl3). Not surprisingly, there are no orthologs in fish of the gene. It’s not exactly honest to say the typological/taxonomic hierarchies are congruent with the phylogenetic hierarchies when they aren’t.
You want to insist we still evolved from fish and the pattern missing and present genes is by addition and deletion along the way, that’s fine. But let’s not pretend the nested hierarchies of taxonomy/typology are congruent with the nested hierarchies of cherry picked genes. They aren’t. The fact you have to invoke addition and deletion of genes along the way is tacit admission the tress are not congruent with each other.
Nope. COX I was your bad taxon sample and analysis. And you haven’t even analyzed interferon lambda; you haven’t even been able to find orthologs, even though they clearly exist.
Are you assuming that gene duplication and other events that make new genes don’t exist? Are you assuming that gene loss doesn’t exist? On what basis? Anyway, how is that diagram in any way incompatible with a nested hierarchy? It’s in fact good evidence for that nested hierarchy. We’ve been over this before, but maybe you had me on ignore.
No, it isn’t, because gene additions and losses happen in a nested hierarchical way. Even your favorite diagram shows that.
Nobody tries to aggregate groups by total similarity, because that requires an assumption of exactly equal rates of evolution in all lineages. Now if you want to compare whole genomes, that will require a complex analysis. We could talk about how to do it, but you certainly aren’t capable of it. In essence, you treat missing genes as missing data and you add a set of binary presence/absence characters to account for the information in gene additions and losses.
Those aren’t the same thing. Interferon Lambda is a gene family, of which Infl3 is a single member. Note that zebrafish has at least one interferon lambda ortholog. You just can’t find things very well.
Not surprisingly, you are wrong about this. Just a little literature search would show you your error.
Of course they’re congruent. The nested hierarchy of morphology fits the standard tree (in fact, that’s where the tree has historically come from), the nested hierarchy of gene presence/absence fits that tree, and gene/protein sequences fit that tree too. You tend to ignore corrections of this sort, and you certainly don’t look at the literature on your own.
stcordova,
Neither of those analyses place mammals outside of Sarcopterygii. I’m doubtful that there are no orthologs of interferon lambda, but you must realise that, even if it were true, this does not place mammals anywhere else. With a branching process of descent with modification, it must be the case that a given modification appears ‘out of the blue’ when comparing sister taxa. So if interferon lambda arose on land, this in no way invalidates the tree based upon shared genes. It’s just not a synapomorphy in the entire clade.
Sigh. No-one hates your diagram Sal. Your analysis of it is flawed, however. Imagine, as an exercise, removing one taxon in its entirety. You’d have to redistribute all its genes with the circles in which they nest – ie, simply by changing your taxon sample, you have apparently magicked up a whole bunch more ‘poof’ differences. Since you haven’t done anything more than change granularity, there’s clearly something fishy about the analysis you are trying to do on this diagram.
OK, instead of removing taxa, consider adding them. Add more and more, and your differences are split up among finer and finer gradations of the taxonomic whole. That is, we get closer and closer to recovering an apparent phylogenetic series.
Note that, at no point, are you doing anything other than changing the granularity of your analysis. You are not adding anything to underlying reality, just changing your sampling of it. A 2,000-gene ‘poof’ becomes halved, then halved again …
How is it even possible to ‘cherry pick’? Why are there so many genes held in common?
Do genes not held in common between Common and Spotted Sandpipers invalidate the assumption of their common descent? You can ‘cherry pick’ almost the entire genome there. With increasing taxonomic distance, the amount available to ‘cherry pick’ goes down in quite a neatly consistent manner. I have an excellent explanation of that curious fact.
You don’t say. I have an excellent explanation of that curious fact.
See above. A gene present in a clade but not in a sister group is not actually an incongruity, any more than a morphological feature present in a clade but not a sister group. The absence of vertebrae in flies is not incongruent with the tree linking flies and chordates.
Differences between branches do not make trees incongruent. Indeed, if there were no changes, you could not build a tree. The differences are data, and they are not ignored. Any difference with a sister group is still an apparent synapomorphy within that clade. Why is that?
Nope. You just don’t like the fact Humans and Lungfish were very dis-similar from each other compared to how similar Lungfish were to Coelecanths. In fact, human vs. lungfish was the most divergent pair within the vertebrates. Adding more taxon won’t change that fact.
It is well known mammalian immune systems are different than fish immune systems. Interferon Lambda is but one gene among many parts of the primate, therefore mammalian system that isn’t the same as the fish immune system.
Adult mammals don’t breathe with gills. The circulatory system of adult mammals doesn’t include gills connected to arteries connected to the heart. In contrast Coelecanths and Lungfish have gills and circulatory systems.
Mammals have sweat glands and mammary glands. The means of locomotion is different in mammals than Sarcopterygiian fish. Mammals are heomeothermic and thus optimizing the enzymatic efficiency of enzymes that are optimal at a specific temperature.
Though marine mammals have fins, they are not like fish fins. So mammals don’t have fish fins. With one exception, and it’s not a Sarcopyterygiian, fish lack a pelvic girdle. Tetrapods also have digits. Fish lack a sacrum (pictured below).
To insist mammals “nest” within Sarcopterygiian fish is a force fit. It is not a straightforward nesting according to major characters. To force the mammals to nest within Sarcopterygiian fish, one most ignore major differences, and thus cherry pick data.
Sure the Sarcoptyrygiian fish and mammals share characteristics, like all those shared by vertebrates.
Adult mammals don’t breathe with gills. The nested hierarchies of supposed phylogeny and taxonomy/typology are not congruent. I just highlighted some of those incongruities from a morphological standpoint.
Just like lungfish and coelacanths. They don’t have fish fins either. This of course proves that lungfish and coelacanths are not fish, just like girafes.
That a fact huh?
Yes, mammal fins derive from terrestrial limbs. Unlike shark fins.
Evolution has no choice in this context but to modify terrestrial limbs into fins. A designer could have modified shark fins (or anything else, for that matter) to make mammal fins.
Somehow, the Designer reliably derives organs from ancestral material, never quite managing to think across separate lineages. A very curious sort of “intelligence.”
Glen Davidson
Actually, it might. Adding more taxa might split long branches, which sometimes has the seemingly paradoxical effect of showing they were longer than you thought. That is, denser sampling gives better estimates of true branch length. More importantly, simple dissimilarity is not the proper guide to phylogeny. What you need to see is tree topology. The relationships among the three living sarcopterygian groups are contentious, but that isn’t what’s wrong with your COX I tree. What’s wrong is that your tree shows the sole actinopterygian, the tuna, as sister to the coelacanth/lungfish clade, closer (topologically) than the mammals were. A better taxon sample would be almost certain to change that.
Do you even read what I write? Interferon lambda isn’t a gene, it’s a gene family. It’s not just a mammalian family, but is widely distributed in tetrapods and there’s even at least one homolog in zebrafish. Even more importantly, we don’t expect all species to be the same, and “X is different from Y” is not a reason to suppose that X is unrelated to Y. Differences have a nested hierarchical organization. Why?
Yes, tetrapods have a number of derived characters compared to coelacanths and lungfish, and coelacanths and lungfish have a number of derived characters compared to tetrapods. So?
“Cherry pick” seems to be your new mantra. All these differences between mammals and other sarcopterygians are derived characters of various groups within Tetrapoda. They all evolved (or even poofed, if you prefer) after the split between tetrapods and other sarcopterygians. They don’t say that we aren’t sarcopterygians; they just say that we’re really odd sarcopterygians.
Ah, but here’s the point: they also share characters not shared by other vertebrates, and those are the characters that tell us mammals are sarcopterygians.
You appear not to know what “congruent” means or what makes hierarchies incongruent. Again I remind you that tetrapod relationships to other sarcopterygians were well known, on the basis of morphoogical data, long before there were any DNA or protein sequences. The morphological hierarchy and the molecular hierarchy are the same. Better reread Joe’s book, or perhaps something on a more elementary level, to learn how we detect nested hierarchies.
My book is too technical. Baum and Smith’s Tree Thinking: An Introduction to Phylogenetic Biology would be at a more accessible level.
It would be helpful to describe what “nest within” means, and what nested hierarchy means in terms of taxonomy/typology, NOT what nested hierarchy means in terms of phylogeny. I’ve argued the two approaches to constructing nested hierarchies result in incongruent trees, and this is contrary to the false claim the trees agree.
We can start at the very top. There are living things and non-living things, maybe viruses that are ill defined in the classification. For living things we have prokaryotes and eukaryotes. Within eukaryotes there are animals and non-animals. Within animals there are the vertebrates and non-vertebrates. Within vertebrates there are mammals. Within mammals, there are placental mammals. Within placental mammals there are primates, and within primates there are humans.
So humans nest within primates, primates nest within placental mammals, placental mammals nest within mammals, mammals nest within vertebrates, vertebrates nest within animals, animals nest within eukaryotes, eukaryotes nest within living things. We thus have a conceptual branching pattern and nested hierarchy. There are a few levels I skipped in this hierarchy like chordates, but the nesting is quite evident nevertheless.
The hierarchy can be demarcated by morphological features. Additionally, a few diagnostic markers are congruent with other diagnostic markers.
At the genetic level, there are orphan gene associated with mammals, and primates.
https://www.researchgate.net/profile/Jose_Villanueva-Canas/publication/319260839_New_Genes_and_Functional_Innovation_in_Mammals/links/599ea07a0f7e9b892bb8f789/New-Genes-and-Functional-Innovation-in-Mammals.pdf
Thus if we built gene trees with that recognized orphan genes like:
SCGB Secretoglobin, PRM3 Protamine 3, CSN1S1 Casein alpha s1, Interleukin 2, MUC7 Mucin 7, NNAT Neuronatin, IGIP IgA-inducing protein, SMCP Sperm mitochondrial-associated cysteine-rich protein, HMHB1 Histocompatibility (minor) HB-1
one would conclude mammals aren’t fish, giraffes aren’t fish, primates aren’t fish in terms of taxonomy/typology and gene lists. This is in contrast to the contortions and Phylogenetic Phudging and cherry picking required to argue “mammals nest within Sarcopterygian fish”.
So, this demonstrates the incongruence of taxnomic/typological trees conceptualized using PRESENT extant characters vs. phylogenetic trees conceptualized using a narrative about the PAST which may or may not even be accurate. It’s inaccurate to represent them as being congruent with each other because they simply aren’t. The only congruence is that phylogenetic trees that are cherry picked and fudged to agree with other phylogenetic trees result in congruent trees, but that’s not really the question at hand.
It is worth mentioning about 10% of human and mouse genes are overlapping, this again puts a wrinkle on modeling gene evolution with random mutation.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335118/
Before I forget, there is one peculiar transition I find interesting. The evolution of temperature dependent sex determination. How does chromosomal sex determination poof into temperature dependent sex determination? This is one feature that doesn’t seem to follow exact hierarchical pattern in terms of their distribution in the vertebrates.
The late John Davison pointed out male birds have ZZ chromosomes whereas human males have the Y chromosome. In other animals, emergence of the male form is driven by temperature.
https://en.wikipedia.org/wiki/ZW_sex-determination_system
It is worth pointing out in humans, one of the X chromosomes in females has to be partially shut down by the XIST lncRNA to create proper dosage compensation. There has to be a lot of coordinated change to go from one sex determining mechanism to another.
Now regarding temperature:
https://en.wikipedia.org/wiki/Temperature-dependent_sex_determination
So even though creatures may share many characteristics in common, they have differences that are significant enough that suggest one creature could not evolve into another without a miracle. If they can’t evolve one from another, then there is no common descent, and the patterns of similarity are due to common design by act of miraculous special creation based on the additional evidence the fossil record is likely not millions of years old.
stcordova,
Yes! Yes, let’s start at the very top! Oh, hang on, you mean bottom … OK, but my interest is in determining where one thinks Common Descent shades into Common Design. Starting from very close taxonomic relationship and broadening out to pairs of increasing divergence or (possibly) separate origin.
So: Common and Spotted Sandpipers – or any other close species pair of your choosing. Is there any reasonable inference that can be made as to their relationship, based upon gene trees and/or morphology? Genetically connected, or no?
stcordova,
And lo, God said, let the sex of snakes, most lizards, birds and mammals be determined by a binary code in the diploid. But – and this is very important, for reasons I am not at liberty to disclose at this point – let the sex determination of all crocodilians and ‘most turtles’ be temperature dependent. For I am a whimisical God, and I like introducing differences for a laff. It’s a test.
If you don’t know what it means, you really need to read something simpler than Joe’s book. I agree with his recommendation of Tree Thinking. A nested hierarchy consists of sets, in which either each pair of sets isdisjunct or one is a subset of the other. Groups within groups. Or if you think of trees, X is nested within Y if the common ancestral node of all Y is also an ancestral node of X. Mammals are nested within Sarcopterygii because The common ancestor of all Sarcopterygii (not just the living ones) is also an ancestor of mammals. Now of course molecular data doesn’t necessarily show this, because the topology might be (tetrapods,(coelacanths, lungfish), and thus mammals might not nest within a tree of extant sarcopterygians. Still, a tree of vertebrates would show those three taxa more closely related to each other than to actinopterygians or chondrichthyans.
No, you have claimed that, which is different from arguing that. Your claim is incorrect, because there is no such thing as “the taxonomic nested hierarchy” separate from a phylogenetic hierarchy. There used to be, because until around the middle of the last century paraphyletic groups were in fashion. But that’s all.
So why should that nesting exist?
Yes. Why should that be so?
Are you not redefining the term “orphan gene”? Isn’t is pretty clear where these genes came from? I thought orphan genes were supposed to have no apparent ancestry and appear out of nowhere.
No, you would instead conclude that mammals aren’t non-mammals, nothing more. You would conclude that primates aren’t non-primates. And so on. You really need to understand how phylogenetics works and what trees look like.
Nonsense. Present extant characters, even PRESENT ones, give you the same nested hierarchy as you are talking about here. You just don’t understand how to use data. Nothing is cherry-picked or fudged, and I will point out that you have just accused scientists of fraud. Did you intend to?
stcordova,
Equally remarkable, there is a virus or phage (can’t be bothered finding it now) whose sense and antisense sequences both produce functional product. I actually think this kind of thing is a bit of an own goal for the ‘islands of function’ proponents, but there you go.
I mentioned thermal regulation in birds and mammals. This is yet another large scale policy difference in the physiology of birds and mammals vs. fish.
http://www.bioone.org/doi/abs/10.1554/0014-3820%282000%29054%5B1768%3AAETOTT%5D2.0.CO%3B2?journalCode=evol&
Btw, the experiment reported in the paper falsified one evolutionary speculation about the evolution of thermo regulation.
There are just a few problems with your syllogism. First, the evolution of sex determination is pretty well studied and doesn’t require miracles. Second, note how you have elided from “not without a miracle” to “not at all”, which is once more you confusing the origin of character states with common descent. Try not to do that again. Third, there is no additional evidence that the fossil record is not millions of years old. Perhaps you could start a new thread to discuss the age of things. Fourth, you still have no explanation for the nested hierarchy. Why?
Which one? Nobody has ever proposed that endothermy in various fish is homologous to that in birds and mammals, and in fact endothermy isn’t homologous between birds and mammals either. It’s evolved in various ways many times.
Ok, so how do you argue a mammal is a fish if adult mammals don’t respirate using gills. And how do you account for lungfish and coelecanths not having sacrums like mammals? I know, you just disregard this and cherry pick out the differences in the way you conceptualize morphological comparisons.
Seems pretty clear that there is a distinct morphological difference between one group that uses gill respiration and another that doesn’t, and one group with sacrums and the other without. Of course you’ll say, the mammal lineage lost gills, wherease lungfish and coelecanths didn’t acquire sacrums but mammals did.
Ok, so you want to believe it, that’s fine, it is still a tacit admission extant mammals don’t nest within extant Sarcopterygiian fish morphologically speaking. The only way they nest morphologically is to redefine morphology in terms of phylogeny — which is bass-ackward. I already pointed to papers where botanist grew tired of using phylogeny to define morphological characters, and instead they went back to old school structure-based Linnean-type taxonomic approaches.
Phylogeny is simply too unstable and subject to cherry picking and fudging as I’ve demonstrated (i.e. look at the list of mammalian orphan genes for starters, and try to build gene trees that account for them).
The one described in the paper I linked to. 🙄
John Harshman,
What type of nested hierarchy? Phylogenetic?
stcordova,
I think you are being very silly here. I don’t argue that mammals are fish in the sense of swimming and having gills. I argue that the mammalian clade nests, with a very high degree of support, in a clade which – at the time of the original split – we would both have been perfectly happy to agree were definitively ‘fish’.
[eta: I now realise that the quote was wrongly attributed to me. But, point still stands.]
Yes I did. God did it because evolution can’t. I’ve given several examples why one should seriously doubt one creature can evolve by common descent from another without miracles. You haven’t shown evolution can explain mechanistically how one creature can evolve from another in terms of major features, starting with spliceosomal introns ….. sacrum, thermo regulation, orphan genes, etc. etc.
If one creature can’t evolve from another, then God did it. We don’t need to answer “why” to demonstrate God did it.
You only pretend evolution gives a mechanistic explanation. The absence of your responses shows rather poignantly evolutionary theory is no better than “evolution did it”. In that respect my speculation are no worse than yours, you only pretend your explanation are mechanistically superior, when in fact they are totally vacuous.
By “Why” do you mean “what were God’s intenetions” or “why” as in “why common design is a better explanation.” I’ve covered both.
“Why” in terms of God’s intentions are moot if “why” in terms of “common design being a better explanation than common descent because of POOFs” is answered.
You framed the “why” question incorrectly. I corrected you numerous times, but I guess if you don’t have a case, all you can do is go into robot mode rather than actually deal with the numerous mechanistic problems with random mutation and “natural” selection I keep listing.
All you’ve demonstrated is the phylogenetic nested hierarchy (which uses the word “clade”) agrees with the phylogenetic nested hierarchy. It doesn’t agree with the taxonomic/typological nested hierarchy based on structure.
Evolutionists have claimed the conceptual branching pattern seen in taxonomy/typology is explained by the branching pattern of phylogeny. But phylogeny gives a branching pattern that doesn’t agree with a branching pattern given by taxonomy/typology/structure.
So the “best” evidence for common descent, the supposed agreement of branching patterns of phylogeny and taxnomomy/typology is a total myth. I’ve demonstrated it in modest detail in this discussion, and you know, if any one really really tried, the disagreement between the trees (phylogeny vs. taxnomy)would even be more brutally evident.
A giraffe isn’t a fish. I learned that like in Kindergarden. Nothing a PhD evolutionary biologists have done with the fudging and systematic cherry picking has changed that fact which was so evident to me when I was a lad.
A giraffe isn’t a fish. A kangaroo isn’t a fish. A parrot isn’t a fish. This isn’t just labeling, it proceeds patterns of similarity based on morphology and genetics when considered with representative samples of characters and genes, not cherry-picked data.
Pretty simple, really. Both absence of gills and presence of sacral vertebrae are synapomorphies of tetrapods, a group that’s within Sarcopterygii. Of course Sarcopterygii is diagnosed using other characters. What you call cherry-picking is just attaching each innovation to a particular branch on the tree. Together, it all makes a nested hierarchy.
Yes, and the differences make a nested hierarchy. Why? You can point to differences all you want, but why do those differences form a nested hierarchy?
The evidence using only extant species isn’t all that strong for any resolution of the trichotomy, but the characters you mention are not relevant either way, since they’re synapomorphies of Tetrapoda. Evidence that living tetrapods don’t nest within living sarcopterygian fish would take a different form: some derived character shared by coelacanth and lungfish but not tetrapods. Can you name any?
Anyway, if you add fossils, tetrapods are clearly sarcopterygians. You like to ignore Eusthenopteron and Panderichthys and for unknown reasons you discount Tiktaalik, but they and other fossils make a very clear case.
You pointed to one paper by one fringe botanist. I should be impressed? And the first sentence can’t be interpreted.
Phylogeny isn’t as unstable as you suppose. There are a few nodes that are so far not clearly resolvable. But this improves with more data. You need to stop accusing biologists of fraud without evidence. And you have presented no case that any mammalian genes poofed into existence from nowhere.
I mean “How do you explain the nested hierarchy of life?”, which you have never attempted. Nor do I recall you saying anything about God’s intentions, and your arguments for common design consist entirely of attacks on natural evolution of characters, which has nothing to do with separate creation of species.
I am unable to parse that sentence.
Random mutation and natural selection have nothing to do with explaining nested hierarchy. You still consistently confuse the origin of novelty with the explanation of nested hierarchy. When I point this out, you always ignore me. Common design does not explain nested hierarchy and you have never attempted an explanation. At times you have even admitted that you have none. You reject common descent entirely because your reading of Genesis demands separate creation. Admit it.
There’s your problem in a nutshell. You’re stuck in a kindergarten view of classification and can’t be affected by evidence.
And again you accuse biologists of fraud. That’s a serious charge that you need to back up. At least realize what you’re doing and admit it.
That isn’t an explanation, and it also relies on confusion between the origin of novelty and common descent, which you have always ignored when I bring it up.
All irrelevant to the question of common descent. You seem to realize this at some level when you find it necessary to insert “without miracles” to qualify “common descent”. For the sake of argument, let’s grant miracles. So why are those miracles organized into a nested hierarchy?
If. And why isn’t “God did it” compatible with common descent? What explains the nested hierarchy?
Mechanistic explanation for what? Common descent explains nested hierarchy. It doesn’t explain the origin of characters. Since the origin of characters is irrelevant to the subject of this thread, mechanistic (or otherwise) explanations of those origins are irrelevant too. You never get this or even respond to it.
stcordova,
You are simply wrong. Of course it does not agree in every last respect – how could it, when we are talking ‘descent with modification‘? – but nonetheless, a great number of structural commonalities exist between fish and mammals. Which is why they were placed where they were, taxonomically.
Anyway, Common and Spotted Sandpipers. Commonly descended or not? If so, why; if not, why not.
Allan Miller,
If this is true how can you make the claim that the pattern is irrefutable evidence that common descent is the cause of life’s diversity? If there were no exceptions you guys might have a point.