Discussion of Phylogenetic Methods

I think you're over-selling this nested hierarchy concept.This nested hierarchy is as changeable as any common ancestry narrative will allow.For example, an animal group with an even mix of bird and mammal traits would not necessarily violate a nested hierarchy, it would only require modeling the branches of the tree of life accordingly. Mammals and birds would now be placed much closer. Their relationship to dinosaurs would also likely be changed.So yes, animals must fall into "a" nested hierarchy, but this is a very soft criteria to meet. Nothing like a law of physics that would be shattered if a parameter was slightly out of place.

But you can't do that and still have a tree. But you couldn't change the genetic distance between birds and crocodiles.---You over-estimate your capacity for ignoring and fudging the data. It might win you the admiration of creationists, but this sort of sloppy nonsense wouldn't fly in scientific circles.

Once more you are raising an objection which if taken seriously would destroy the whole of science and the scientific method.

Nested hierarchies are an artifact of design. Human designers create nested hierarchies constantly without even thinking about it.You may not like that because it undermines your entire argument, but it doesn't change the fact.Your argument is only convincing if you assume the "random-creature-generator" absent of evolution, whereby you then invoke the "infinite possibilities" aspect, no one more likely then the other. Only against this contrived backdrop does common ancestry seem more likely.

IIRC, you have given only one example of this, which turned out to be bollocks. Would you like to try again?Cos if you can't think of a single valid example of this happening then you should probably stop pretending that it happens "constantly". Leaving aside for now the moral issue that it's wrong to tell lies, there's also the consideration that you're not fooling anyone.

Can you show us the nested hierarchy for Fords, Nissans, Volvos, etc.?

Interesting claim. Let's see your evidence that you can do that and maintain a nested hierarchy.(Hint: youy can't. E.g. Birds don't have hair. Mammals don't have flow-through lungs. There are many more such characteristics.) On the contrary, it's a very difficult criterion to meet.So, demonstrate.

No, human designers do not create nested hierarchies (of any significant numbers of items) because they are free to "cross-pollinate" characteristics from one item to an unrelated item.A nested hierarchy such as life's has absolutely no duplication of labels. All labels are unique.I challenge you to produce a nested hierarchy of, say two dozen man-made objects of your choice with at least four levels that does not duplicate labels or cannot be easily shown to require duplicate labels to be extended.Many have tried.All have failed.Here's an example. It does not duplicate labels, but it does require duplicating labels to extend it significantly. Can you see why? Nobody has claimed a random uniformly distributed "creature generator". But we have observed a fact; there are many possibilities of how life could be organized that are not a single nested hierarchy. That fact screams for explanation. Got one? Why do we see what we see?

So what.. for argument's sake let's say you find "cross-pollinated" violations, it's still true that designed traits tend to fall into nested hierarchies, especially models that are based off small variations of a basic design.Maybe only 90% of the traits can be arranged in this hierarchy. That's still a dominant pattern of nested groupings.Thus, nested hierarchies are a proven signal of design, whether you want to accept it or not.This completely undermines your argument that non-evolutionary life should be a chaotic mish-mash with no decipherable phylogenetic signal.

So, still no examples?If we needed any confirmation that you're bullshitting, this would be it.

Let's see them. With, of course, significant variation between the items. But not a nested hierarchy.

While we're waiting for vaporwave to think of a single example of the thing he says happens "constantly", let's look at a counterexample.A quick look round on google shows me that there are cars having any of the following traits independently:* 2 door / 4 door
* Gas / diesel
* Front-wheel drive / rear-wheel drive
* Manual / automaticThat gives us sixteen possibilities, every single one of which has been realized. And I would bet a reasonable sum that the same range of options exists in the UK and suchlike countries, meaning that having the steering wheel on the left or on the right is another independent trait.(What's more, it often happens that many of these options are available in the same range of cars. If I liked, I could have two Mercedes, one with manual transmission and a diesel engine, the other with automatic transmission and a regular engine, and otherwise absolutely identical down to the last button on the dashboard and stitch on the seat upholstery. As though you saw what looked like two identical twins, but when you X-rayed them only one was human on the inside and the other had the lungs and heart of a reptile.)Designed things do not form an nested hierarchy.And the same, of course, can be said of any kind of consumer good that comes in varieties. Do you want your cigarettes full-strength or light, mentholated or plain, king-size or 100s? Pick any of those options independently, and someone makes what you want. Would you like your wine sweet or dry, red, white, or ros , sparkling or still? Those options are independent, so that's twelve kinds of wine. You're thinking of buying software to store your commercial information? Were you thinking of a spreadsheet or a database? For PC or Mac? Using the Roman or Cyrillic alphabet? You got it. Would you like your sandwich on white bread, wheat bread, rye? With or without mustard? With or without mayo? American cheese or Swiss? Pickle or no pickle? Let's build a house. How many stories would you like? Brick, wood, concrete, stone? How about the roof? Gable, hip, gambrel, mansard? How do you feel about dormers? Would you like pilasters with that? Should your windows be bay, bow, casement, picture, awning, double-hung? If you have no sense of aesthetic taste, why not one of each?That's design for you. And it precludes the sorting of designed objects into nested hierarchies, because traits can freely vary independently of one another.And now by contrast let's pick an animal. You want it to lactate? Right then. In that case --- no arguing, I'm telling you how it's going to be --- it will be endothermic, endoskeletal and featherless, it will have three bones in its inner ear and one in its lower jaw; it will have no sclerotic rings and no gastralia; it will have a four-chambered heart; its red blood cells will lack nuclei; it will have no renal portal system; its teeth will have prismatic enamel ...Etc, etc. You don't get to mix and match. That's evolution for you. 'Cos it produces nested hierarchies.

Good post, Dr. A Another way to put this is that evolution put constraints on future evolutionary processes. In other words, once on a particular lineage or branch, future generations are constrained to be part of that lineage - they cannot jump lineages. This was really the big insight provided by the Lenski long-term experiment - that each evolutionary step determines the range of possibilities for future evolutionary processes - ie. constraints. Design has no such constraints. Sure, a designer could have designed life in such a way (in fact, personally I believe the "designer" did design life to evolve; ie. used evolution to design life) but there are no constraints on the process and designed objects can "jump lineages." And as you have aptly demonstrated, the evidence from human designs does not support the design hypothesis ("nested templates"?) in biological systems.HBDEdited by herebedragons, : typo

Your initial premise was that phylogenetics is not a test of common ancestry, yet you continue to discuss how phylogenetics supports design and how problems with phylogenetics point away from common ancestry.It is important that we test our hypotheses against competing hypotheses. At this point, common ancestry is a well established and widely accepted part of evolutionary theory. When we test hypotheses about descent, we test opposing theories that all involve common descent. However, on this thread, you wish to argue that design is a better hypothesis than common descent. What we need to do is compare the design hypothesis to the hypothesis of common descent.Since you are claiming that phylogenetics is not an adequate test to compare these hypotheses because they would give the same results regardless of the process, how would you propose to test these competing theories? Just claiming that common descent has some problem areas where the relationships are uncertain or ambiguous is not sufficient to support your design hypothesis - design is NOT the null hypothesis.The test needs to be designed so that we can compare which hypothesis or model explains the data better. Remember that a theory is a framework that explains why we observe a particular pattern or phenomenon. Evolutionary theory is the best explanation of why we observe nested hierarchies in biological systems. Your claim is that "nested templates" provides a better framework for understanding this pattern/phenomenon. Provide us a test that can be used to directly compare these two models.HBD

You haven't shown that limbs show up after footprints. Tiktaalik does not establish the earliest limbed fish. Tiktaalik only establishes that there were limbed fish at a precise time in history.Your argument boils down to the old "if men evolved from apes, where are there still apes?" fallacy. Are chimps out of order because they exist after H. erectus? No. Is the platypus out of order because it exists after the extinction of many placental mammal species? No. Is the frog out of order because it exists after the extinction and evolution of more derived amniotes? No.Guess what? Sister taxa branch off of other lineages and preserve less derived characteristics. That is what Tiktaalik is. It is a side branch on the tetrapod lineage. You haven't produced a counter-example.