Let’s have a serious discussion about phylogenetic systematics.
What are the assumptions, the methods, and the inferences that can be drawn from phylogenetic analysis.
For example, is there anything to the creationist claim that phylogenetic systematics assumes common ancestry and does it even matter?
I’ll be using a number of different references such as Molecular Evolution: A Phylogenetic Approach and Molecular Evolution and Phylogenetics.
This thread will not be password protected, but it will be protected by angels.
What is the claim here? Is it that the greater the similarity the higher our confidence is of their evolutionary relationship, or is it that the greater the similarity the closer the evolutionary relationship?
In one sense you could say that phylogenetic analysis assumes common ancestry, as most analyses only look at trees, not disconnected species. Of course there are exceptions, e.g. the proverbial Theobald 2010. More importantly, analyses test common descent, because a significantly supported nested hierarchy can’t be explained any other way.
Now, to test common descent vs. separate creation, you need a model of separate creation. Do you know of any? Theobald’s model is mutually randomized sequences. If you don’t like that, you need to consider something else. I could imagine what’s called a star tree, because it looks like an asterisk. In such a case we would expect no resolved tree to have better support than any other.
I’d be interested in molecular evolution of alternative splicing, dual coding genes and duons… unfortunately evolution didn’t predict duons but since 2013, when they were discovered, Darwinists act as if it did…
John Harshman,
You don’t need to test that in utricularia… most species have many different trap mechanisms that prove separate creations… Theobald didn’t even bother to check…. the trap door closes with speed close to the speed of light and only recently developed technology prove this very fact….
Are systematists the same as the molecular phylogeneticists (the guys who build gene trees)? Does it depend on whom you ask?
Molecular phylogeneticists are a subset of systematists. I suppose everything depends on whom you ask, and this is no exception.
AMEN. Yes they are saying the greater the similarity the higher the confidence!!
Yes Common descent is assumed as the ONLY OPTION for likeness in traits/characters.
Another intellectual false boundary that undermines it as a scientific subject. Unless they repent.
yES they can’t even imagine cOMMON DESIGN. so they have elinated other options AND SO only common descent remains.
Just dumb research and thinking. Especially when they make a gong about defeating a creator or the genesis story.
i think YEC and iD should pounce on this error more.
folks here do not answer it. they can’t.
If they were confident CD was true they could humour critics by checking it all IF Cdesign was true WHAT WOULD IT LOOK LIKE.
I think creationism has hit a intellectual nerve.
The common design tree should be decorated along with the christmas tree or in NYC the holiday likeness to a christmas tree but not the same thing. Convergent trees indeed!!
No. its not only assuming trees as opposed to unconnected species.
oh no. it assumes as only the option for traits/characters that alike in any biology close or far.
It assumes there is no other option.
No COMMON DESIGN.
its a intellectual scientific failure of investigation.
Unless they just admit NO WE WON’T have a option for design by a creator.
Well how can critics of evolutionism and evolutionists communicate then?
how can evolutionists persuade same critics that biology shows common descent by similarity if critics must already accept only a common descent option?
No more thinking please. no more imagination. no more errors!
it seems, it does, to be breaking the rules for science.
In fact falsifying as part of science methodology is threatened here. Evolutionists are saying you can’t falsify common descent trees.
Are creationists wrong here?
Yes, inference of phylogenies does assume a tree, as John said. Applied to any set of characters it will come up with a tree or trees. But the really interesting question is whether trees inferred from different sets of characters, particularly different parts of the genome, are similar. That’s what Theobald’s 2010 test is about (it follows in the footsteps of the work on Penny, Hendy and Poole in 1982 and in 2003, and is followed in turn by a paper by Penny in 2011).
This more formally validates the insights of biologists from Linnaeus on, that underlying systematic data a common tree seemed to be shining through. In effect, the coming of molecular sequence data largely validated the trees made from morphology in the previous 200 years.
All this has been hashed over ad nauseam in the Common Descent thread here, with much diversionary dancing around by the creationist / ID side.
Joe Felsenstein,
Instead of accusing the other side of dancing, while you pirouette, wouldn’t it have been much easier to just answer Mung, does more molecular similarity infer closer relationship? Always, sometimes, whatever?
Mung,
To have a discussion you have to discuss. What is your opinion on that?
My opinion on your opinion is that you obviously think there is something to that creationist claim, otherwise why even reference it?
I find that hard to believe. Do you have some supporting evidence for that claim?
What % of the speed of light is achieved?
Does it not bother you that you can’t answer either of those questions?
The plant accelerates a piece of it’s anatomy close to the speed of light? Yeah, that’s bullshit. Surely he must have meant close to the speed of sound, that’d be believable.
Well, the action of a bladderwort trap has been video’d here and presumably light had to travel fast enough for the camera to capture the event!
This is something you would have to ask Rod Page.
Did a quick and dirty calculation. Trap is a little more than 1mm. Closing speed is a bit less than 1ms. With a lot of rounding off the trap closes at 0.0000012 % the speed of light…………so JMac is right!!
That fast huh? I wasn’t being literal but I knew it was very fast…
I think I’m gonna have to ask dumb luck to design a raccoon trap with the door closing that fast… as current human intelligence has failed to accomplish anything even remotely fast and effective in comparison to the achievements of dumbness…
Dumb luck doesn’t design raccoon traps but natural selection already has …..its called a wolf
This is what dumb luck has been able to accomplish via randomness:
“Referring to Rutishauser34, the authors favour saltational evolution for the origin of suction: “Possible key innovations (e.g., suction) may have resulted in novel phenotypes facilitating the establishment of new habitats and thus amplified the morphological diversity in Utricularia. Such saltational evolutionary innovations have been proposed to play a crucial role regarding the vegetative morphology in Lentibulariaceae” (Westermeier et al. p. 19). Well, could such saltational innovations mean that simultaneously in a passive trap (as assumed for U. multifida), for instance: (1) The door rather suddenly became watertight? (2) The door quickly obtained fully functional antennae (or other trigger mechanisms)? (3) The middle cells of the digestive-absorptive hairs of passive traps all at once produced a “highly developed wall labyrinth”, which is “associated with rapid water transport during removal of water from the Utricularia bladders”35? (4) The different glands (inside and outside) the trap abruptly produced the necessary negative hydrostatic pressure? (5) The trap walls swiftly obtained the indispensable flexibility to accurately function correspondingly? Hardly probable, neither by just one ‘macromutation’ nor by several simultaneously occurring mutations with smaller but additive effects on the phenotype36. Hence, the synorganization (coadaptation) problem for the origin of active suction traps most probably cannot be solved by saltational evolution, not even on the basis of an already rather complex but passive bladderlike trap. “,
What would an engineer say if I asked him to design a trap like that by random, undirected events?
I don’t have to answer that… anybody in the right frame of mind knows the right answer… Unfortunately, when one is married to materialism, combined with Darwinism, that bond is unmovable…. No evidence can break that bond because:
“Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism.
It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.”-Richard Lewontin
Why would anybody lie to himself? Beats me…
Or… maybe… this can explain it:
“If you repeat a lie often enough, people will believe it, and you will even come to believe it yourself”-Joseph Goebbles Hitler’s propaganda man
Is someone here babbling about the evolution of Utricularia?
If that’s a smart one, she would tell you that pure randomness would not work, that she might need a method for selection, reproduction after selection sweeps, preferably with recombination, and then another round of random variation, etc. She might even explain to you that there’s such a thing as genetic algorithms, which are based on precisely those things: random variation, selection, recombination, reproduction.
You don’t seem to understand how evolution works. You have your mind fixed on the process that produces variation, and forget everything else for no reason but your preference for rhetorical effects over understanding.
Would it hurt you to understand J? Is it that much better for you to pretend that your brain doesn’t work that well?
This reminds me of a propagandist who keeps referring to natural phenomena as “dumb luck”? The propagandist has repeated the lie so many times that (s)he has come to believe it himself (or herself).
I imagine the utility of such a position will be obviously after a couple of years.
Hey, J-Mac, how many biologists have you turned to your side with your erudite expositions regarding “dumb luck”.
The funny thing J-Mac is that’s you. The lies that someone like Salvador has taught you you’ve repeated a sufficient number of times so that it seems you even believe them yourself.
For example, you forgot a critical bit of your quote there:
You’ve lied to yourself for so long about what the part you quoted was meant to mean you’ve never considered it’s a quote mine.
J-Mac believes in god. J-Mac believes plants accelerate parts of themselves to close to the speed of light. J-Mac believes any old BS. That’s because in a world where miracles can happen who is to say that plants won’t be granted the ability to move at lightspeed?
The world has been laughing at you and yours for a very very long time J-Mac.
OMagain,
The most gullible think that they’re immune to gullibility.
Or, you know, they wouldn’t be so gullible.
Glen Davidson
‘Recorded speeds reach around 1 m/s, with accelerations of a few hundreds of g. To understand what is at the root of such a fast suction, physicists and biologists recently studied traps of different aquatic species of Utricularia with a fast camera up to 15.000 frames per second.”
Carnivorous Utricularia – NCBI – NIH
Impressive, but unlikely to distort spacetime.
Mung,
According to Berkeley common descent of all life is a working assumption.
If however we look at two of John’s papers (add 2008 on flightless birds) we see a wide variation in the DNA sequence between two species that are claimed to share a common ancestor yet very little variation in his 2003 paper based on two species MYC genes. Why would this not be problematic for the inference of common descent for flightless birds?
John claims every time a DNA phylogenetic analysis is done common descent is tested. I wonder on what objective standard it would be determined that common descent is no longer the correct inference.
Having a better inference!
You can think of it that way, but it’s an assumption that is tested by phylogenetic analysis.
I truly do not understand your objection. Are you claiming that any two sets of related species must differ by the same amount? If so, why? If not, what are you claiming?
It’s not clear what “no longer the correct inference” means to you. At some point of divergence the data would no longer be capable of affirming common descent because they would have been randomized. But it would not be possible by that means to distinguish separate creation from lots of divergence. Still, that’s the point at which the data would provide no evidence for common descent. As long as one tree is significantly better than other trees, we have evidence.
1 mps vs 299792458 mps?
Yep 😛
I reckon that’s an error of only 0.13 Dembski’s, so yeah that’s “close to” the speed of light in ID(tm) math.
John Harshman,
Can you clearly describe the test method and on what basis you would reject the common descent hypothesis.
John Harshman,
So I think you agree with Berkeley that common descent is the working hypothesis. Your conclusions in your 2008 paper was based on common descent as a working hypothesis. This is an excellent paper as is your 2003 paper but there was no examination of a possible special creation event which would obviously have been very problematic for the paper.
We are discussing common design an as an alternative in these threads so I think it is fair game to point out that special creation has less assumptions then multiple losses of flight which was a necessary conclusion based on common descent as a working hypothesis.
For everyones reference.
Go to PNAS Homepage > Current Issue > vol. 105 no. 36 > John Harshman, 13462–13467, doi: 10.1073/pnas.0803242105
Phylogenomic evidence for multiple losses of flight in ratite birds
John Harshmana,b,c, Edward L. Braund,e,c, Michael J. Braunf,g,c, Christopher J. Huddlestonf, Rauri C. K. Bowiea,h,i, Jena L. Chojnowskid, Shannon J. Hacketta, Kin-Lan Hand,f,g, Rebecca T. Kimballd, Ben D. Marksj, Kathleen J. Migliak, William S. Moorek, Sushma Reddya, Frederick H. Sheldonj, David W. Steadmanl, Scott J. Steppanm, Christopher C. Wittj,n, and Tamaki Yurid,f
John Harshman,
When there are differences of 10x variation I would think it deserves examination.
You can’t actually reject the common descent hypothesis. What you can do is fail to reject the separate creation hypothesis, since separate creation can’t be distinguished from enough divergence to reduce sequence similarity to random expectation. You test common descent by rejecting separate creation, i.e. having nested hierarchical structure significantly greater than expected from separate creation. There are a number of methods to do this, including bootstrapping, jackknifing, likelihood ratio tests, testing consilience of independent data sets, etc.
Still don’t know what you mean by this. How are differences of 10x variation a problem for common descent? What if some taxa have been separated for 10x the time as others? What sort of examination are you proposing?
Yes, and it also tested that hypothesis, which turned out to be correct.
There was no explicit consideration of special creation, but the paper certainly shows that the data are incompatible with special creation.
Special creation has huge assumptions. It requires entities and processes for which we have no evidence. Nor can special creation explain the nested hierarchy in the sequence data. Can you think of an explanation other than common descent? Be the first.
What makes one inference better or worse than another?
According to the text this is “the most important principle in molecular evolution.” Do you disagree about that then?
I mean, my thinking is that anyone touting molecular evolution ought to be familiar with it and what it means, if it is in fact.the most important principle in molecular evolution.
Anyone else care to tackle this?
If two genes share identical sequences we can be certain they shared a common ancestor? If two genes share identical sequences we can be certain they share a close relationship?
I’ve asked repeatedly just what it is that can be inferred from similarity (or lack thereof). It seems somewhat important to the subject matter.
I’m unwilling to respond to Rod Page filtered through Mung. Let me look up the context and see what I think he meant.
I’d say so, since molecular evolution doesn’t stand still. Even highly conserved protein-coding genes should evolve at some reasonable rate at third positions.
The problem is that you try to parse any answers to make them confusing or contradictory. Perhaps you shouldn’t do that. Now of course identical genes could have been created separately by a god who just likes to re-use parts. And completely different genes could be created by a god who doesn’t. That’s why I keep talking about the nested hierarchy , not identical sequences, as evidence for common descent.
If you read the rest of the book, you will find that Page doesn’t actually do phylogenetics this way. Ranking by simple similarity works just fine under certain conditions: evolutionary rates have to be precisely equal among lineages and not too fast. These conditions seldom obtain closely enough to support a good analysis, so the methods Page actually uses do not make those assumptions. In other words, all things being equal, it’s true, but things are seldom equal.
Mung,
And you’ve been told repeatedly too. One can infer common descent from a high degree of molecular similarity, as the hypothesis to be preferred given that there is no other apparent cause of it beyond the fidelity of genetic copying processes.
Well, first there has to be an inference. Then you can examine how well it fits with evidence and how well predictions fit observation.
John Harshman,
While I would agree common descent best explains the limited sequence data in your 2003 paper it fails to explain the data in your 2008 paper especially significant sequence variation and loss of flight.
Special creation assumes a creator which is a single assumption that is shared by the majority of our population. It is impossible to know the process so the explanation is limited but at this point your 2008 paper points directly in the common design direction as common descent is not a fit for the data.
As I think about your papers, it appears that common descent and common design are required to explain all the data in both papers.
You aren’t being clear. How does common descent fail to explain significant sequence variation? And of course it doesn’t explain loss of flight. Don’t you remember that common descent doesn’t explain the changes themselves?
Why is “shared by the majority of the population” relevant? The explanation isn’t just limited; it’s nonexistent. Again, you will have to explain why common descent is not a fit.
What is common design required for? Please try to be coherent and clear.
John Harshman,
There is simply too much sequence variation between nested species in your 2008 paper. 60x more then in your 2003 paper. This discussion is interesting because you have one paper that is signaling common descent and one that is not.
These birds being specially created in their current location is by far the explanation with the least assumptions.
Please explain your reasoning here. I simply don’t understand it. How is the amount of sequence variation relevant? How can special creation explain nested hierarchy?
John Harshman,
You are assuming loss of flight because common descent is you’re working hypothesis.
We don’t have any evidence that inheritance can result in significant sequence variation.
Thats why you are getting agreement on your 2003 paper which has significant similarity. Mutations in nuclear proteins (MYC is a nuclear protein) are often fatal so a random walk through a nuclear protein sequence is problematic. The gene you selected is an onco gene (cancer causing) that is mission critical for the cell cycle. The sequence similarity does look like common descent at this point yet the data set is limited.
Other people have data that you do not. There is significant data supporting a created universe which you have not studied. I am not asking you to suddenly believe it, I am asking that you do not dismiss it out of hand and follow the data where it leads.
It is required for novel sequences that result in new genetic function. Flight and sight are examples of new genetic function. DNA lives in almost infinite sequential space. Design is required to create new functional sequences in that vast space. In your 2003 paper it is mentioned that the sequence variation for the MYC gene between birds and crocks is 14%. How is a random walk through the sequence of an onco (cancer causing) gene going to account for this change? A group of hikers have a better chance taking a 3 week trip through a mine field.
John Harshman,
As I showed by the Mac laptop example some nesting will occur due to designers leveraging component designs. In the case of computers it is memory chips and logic chips and other components. In life it is genes and other biological components which a designer would want to leverage. As in life the components and systems over time become more complex.
I also believe the nested hierarchy may be due to the combination of both common design and common descent as your papers show. Common descent alone does not explain the extreme difference in sequence variation between nested flightless birds and nested crocks.
This is a very interesting exploration to find the line of common descent demarkation if there is one.