There are statistical methods for evaluating a phylogeny. It is an objective measure.
Thousands of biologists are laughing at the idea that apomorphies are not a part of cladistics or phylogenetics.
Where are these genes shared by zebrafish and humans, but no other vertebrates?
Already done, long ago. Surely you remember. Perhaps you can find that analysis and re-read it.
You are not capable of evaluating what Scd says (well, he isn’t either). He has shown no evidence that vehicles form a nested hierarchy. All he does is make a cartoon tree based on somewhere from zero to one character, chosen because it gives him what he wants.
Once again you confuse the origin of new features with the pattern formed by features.
It looks that way because there are only four species being considered, and those genes don’t “appear” and “re-appear”. They’re just lost twice.
@scd @Rumraket @T_aquaticus @John_Harshman
This paper might be useful with regards to the discussion about the differences between nested hierarchies in biology vs designed objects. The 2 links are to the same paper, but the first is just a scan of a paper copy, so text can’t be highlighted, copied, or pasted. I put the second link in there for this purpose for those who feel they can overcome the terrible ethical quandary of avoiding a paywall.
https://sci-hub.tw/10.1662/0002-7685(2005)067[0283:bonbpe]2.0.co;2
The paper is published in “The American Biology Teacher”, a journal for (you guessed it) Biology teachers, presumably mostly those of the American persuasion. It discusses the pros and cons of the common classroom exercise used to teach students the basic principles of phylogenetics: constructing a phylogenetic tree by coding characters of (gasp) designed objects like nuts and bolts, screws and nails, etc. I myself experienced this exercise years ago, and I remember that the teacher made the point to emphasise both the utility of the exercise, but also the clear differences it had with actual biological phylogenetics. These differences are well-described in the paper, and it’s a fairly quick read.
The basic point has already been described in this thread already: producing phylogenies of designed objects will always be problematic because there are just so many different ways of producing the tree - different characters will give very different tree topologies. In contrast, actual biological organisms produce much more congruent trees because their sets of characters aren’t arbitrary, they’ve been shaped by a branching pattern of common descent.
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I have found playing cards to be a good analogy as well. You will find that there are numerous ways to organize playing cards into different clades, just as with nuts and bolts. Thanks for the reference!
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Exactly. @colewd show me those *73 genes absent in more basal teleosts like salmon, trout, etc, basal actinopts like gar, polypterus, etc, sarcopt fish like coelacanth and lungfish, a few amphibians and reptiles, a few other birds, platypus, some marsupials, and then just a few more representatives from several clades of mammals and then you’d have a good case for those *73 genes “appearing in zebrafish and not reappearing until humans”. Not before.
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No, you found a picture that had lines going between different mac computers.
At no point did you do the work that would show that when sorting by characters is actually done, that the “tree” of macs depicted in the picture you found would actually emerge from the data. You haven’t done the actual work, and merely finding some picture with lines and computers at the ends of the lines isn’t how that work is done.
Here’s a linkthat shows how a simple character matrix looks, which should give you some idea of what kind of work is required(all these organisms of course have many more characters than are shown here):
You need to do that for mac computers (make columns for number of keyboard buttons, hard drive space, cache size, color, monitor screen size, monochrome vs color display, maximum resolution, memory size, chip manufacturers, connectors/plugs, etc. etc.) and then from this show that you get a neat nesting hiearchy with groups nesting within groups. What group does laptops nest in? Will they even sort into a group that does not include any workstations, desktops, or tablets?
You continue to ignore arguments on this subject so I am not going to repeat myself as I made the same argument here.
No I’m trying to explain why you (and scd) aren’t doing what you think you’re doing just by drawing trees and putting stuff at the ends of branches.
What you continue to ignore is that nested hierarch is just an abstract description of the data.
So is a sinusoidal curve that depicts the seasonal variations in average temperature over a year. But that’s a real pattern, with a real explanation. The fact that it can be depicted in some abstract form in a coordinate system doesn’t mean the data’s ease of depiction in that form is not something worthy of explanation.
What matters is the real data and common descent does not explain it because new features are part of the data.
Bill, any single nucleotide difference between two sequences will be a “new feature” not found in the other. It is that very thing that is used to infer the nesting hiearchy from. If there were no genetic and morphological differences no tree could be inferred at all. There would not be any character to use to infer what goes into what group.
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Just off the cuff here, I’m pretty sure there doesn’t have to be any mutation. Many developmental abnormalities are not genetic, but environmental.
The chart shows what it shows so does Ewert’s dependency graph so does the paper Scd just cited. Over time we will see how problematic this really is however the data appears to be building against evolution being a real description of what caused the diversity of life.
Thanks for the paper. Look forward to a more detailed review to understand this conclusion. This data may be an interesting add to the dependency chart.
I
n this systematic analysis of the sponge gene repertoire, we show that the genomic complexity, at least in terms of gene content, was already present at the very beginning of animal evolution, before the appearance of tissue-grade animals or any other complex morphological feature found in all present day Metazoa. Striking similarities between sponge and human protein-coding genes indicate a short distance from both sponge and human genomes to the genome of the metazoan ancestor. Next, according to gene content, sponges are more similar to the sea anemone, human, and sea urchin than to the sea squirt, fruit fly, or nematode. Regarding the latter three, divergence from the sponge/human repertoire seems to serve as a reliable signature of accelerated evolutionary rate in distinct metazoan lineages. This also corroborates the findings that many genes were eliminated from the genomes of analyzed lineages (especially from two invertebrates) and further emphasizes the importance of gene loss in evolutionary processes. Our findings also raise many questions about the roles of numerous genes/proteins in the life of such a simple animal. Finally, the implication that sponges have unusually complex genomes, especially in contrast to unicellular eukaryotes, leads to a conclusion that the ancestor of all metazoans (Urmetazoa) also had a complex genome and strengthens a theory toward a Precambrian “gene explosion” view on metazoan evolution.
Neither of those show that humans and zebrafish share 70 some genes that are not shared by any other vertebrate, as you were claiming. Perhaps you could give us the name of one of those genes and we could see how it is distributed among species.
Also, Ewert’s dependency graph does not predict the same tree we see for life. It groups bats and whales together which isn’t what we see in real biology.
If you understood how biology works you wouldn’t be coming to this conclusion.
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Thank you for the tautology that the chart shows what it shows. The point is that what it shows is not what you said it shows.
Which paper from scd are you referring to? I believe Ewert’s work has been discussed here before.
Saying “the data is building” in your favour isn’t particularly convincing, given that creationists/IDers have been saying that since Darwin’s day without effect.
What is “real biology” 
It’s a subject in which we seek out all the relevant evidence.
The biology that exists in the outside world instead of in the heads of ID/creationists.
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Exactly. The gene data is not matching the morphological and sequence data.
You will have to be more specific than that. Ewert’s paper doesn’t deal with sequence data at all.
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Should say not matching. I agree with your comment.
What is or isn’t matching, and what is it being matched to? This is confusing.
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