Taking a new tack with the common descent/common design theme, I’d like to sneak up on it. As Sal Cordova likes to do, I offer a hypothesis for critique. Here’s an old phyogenetic analysis of mine. Does it show common descent? If not, what’s wrong with it?
This one is about crocodiles. Are crocodiles all the same kind? How do you know? If they aren’t how many kinds are there within the group and how do you know? If they are, are they a whole kind or just part of a larger kind? And if the latter, what is the larger kind?
Well, since you put it like that … Yeah. Is there a problem?
My, you are the glass half-empty type.
Try to focus on the species that are not in Gavialis. What do you see?
John, has anybody already told you that this is excellent work?
This thing with the trees not matching each other exactly every time is like having multiple ultra-sensitive thermometers to measure a temperature, and because they disagree at the 38th decimal place, well then it’s all “they agree except when they don’t”.
That is directly analogous to what Mung is saying here. Potentially Hundreds of thermometer agree that the temperature is 20.00000000000000000000000000000000000000X degrees C. The disagreement is at X.
“They agree except when they don’t”. “There isn’t just one nested hiearchy/there isn’t just one temperature”.
Channeling Mung:
Oh yeah, you think there’s a real temperature huh? Well, is it the 20.000000000000000000000000000000000000004 or the 20.000000000000000000000000000000000000007 degrees C? They agree except when they don’t.
Rumraket,
Yep – an analogy that came fleetingly into my mind is that I’m at home except when I’m not. Does this mean i have no fixed abode – that there is no ‘attractor’ in the pattern? 🙂
The paper contains no identifiable hypothesis, at least none that could be related to common descent. It proposes the following:
Okay, topology of Crocodylia, placement of the root, and molecular and morphological data for that.
Where is the common descent in this picture? Why and how would the molecular and morphological data be relatable to a hypothesis about a common ancestors of the species studied?
The hypothesis is unstated. “Common descent” does not occur in the paper. Instead, the paper begins,
i.e. molecular and morphological trees are often known to be in conflict. Does the paper solve this in principle or at least with regard to Crocodylia? A bunch of data is presented, which is cool, but I see no clear indication what the data is about. Certainly no indication if any of this has to do with common descent (as distinguished from drawing trees, which you can do on any abstract data on any kinds of objects).
Of course, there is no especial need to hold the morphological and the molecular as a simplistic dichotomy. Molecular sequences and structures are simply character states, albeit with more of a ‘digital’ quality.
Morphology came first, so retrospectively we could see that molecular states mapped onto those trees pretty well. But it must go further – because of the underlying mechanics, they are more reliable than morphology, with caveats. In order for that to be the case, there must be occasions when they do not agree precisely, otherwise there would be no need for the one to trump the other – there would be nothing to adjudicate.
What are the caveats?
stcordova,
Sal, I don’t think it was needed for crocodiles and the likes to enter the ark…
From what I have read all “kinds” of crocodiles and similar to them “kinds”, are able to float in the water for very log periods of time, so there was no need for them to be taken into the ark…
Bottleneck according to you or speculative population genetics?
I can speculate too…
Let’s just speculated that none of the crocs were taken into the ark, as they shouldn’t, and each was created separately…
With which option (crocs taken or not taken on to the ark) will John’s paper agree with more?
Oddly enough, Sal has.
Erik,
I can’t really do anything for you. You seem unable to interpret ordinary language. How odd for a linguist.
Bottleneck according to the Noah’s Ark fable. Obviously.
It seems you are very selective in your choice of fables… It must be because you are unbiasedly searching for the truth with metaphysical naturalism as the only game in town…
How many species of crocodiles do you know can float nonstop for a year in freezing and turbulocean water?
I’m perfectly able to spot hidden assumptions, conflations and equivocations. It’s just that there can be no rational discussion on such terms.
I clearly spelled out the issue. Your silly answer is that it’s a language problem. So fine, talk to the others.
He’s just being kind. He cant possibly believe that since you neglected to mention that the evidence points to separate creation for all of these species within the last million years or so
Nature is right here around me. The mythological beings of all religions I know about are only in my imagination. Which one looks worth checking? This is not about unbiasedly searching for the truth, this is about searching where it makes sense to search.
Do you search for the truth in Harry Potter? In Pinocchio? In Snow White? In the Lord of the Rings? In fantasy literature? No? Then you’re not unbiasedly searching for truth either.
Interesting question. Ok, so during The Flood was the ocean salt water, fresh water or brackish water? From the depth of the ocean and additional depth from rain I’d say it was mostly salt water: instead of 35 ppt it might have been 28-30 ppt. I would think that would mean that alligators and crocodiles couldn’t survive in it for long ( salt water crocodiles would be an exception.) So now we’re back to the ‘kinds’ question and the question Harshman posed. A creationist paper claimed that the 2 gharial species came from a single kind on the ark – no doubt they just read the paper by biologists based on morphological comparisons. But molecular comparisons now say they’re not closely related. Who to believe??
Other way around, which is what makes this story unusual: morphologists say convergence, molecular systematists say homology. Creationists say whatever comes into their heads today.
Crap, I should have read the abstract again today. Well then creationists probably decided they were kinds based on their names and superficial appearance
How do you know the water was freezing? You must have been there… It’s understandable….
Yeah.. yeah… It’s a miracle they didn’t die through excessive submersion…
I agree completely. Thus it makes sense to ask which tree or which hierarchy someone is referring to. I tried to explain this to Rumraket but I am sure it must sound more reasonable coming from you.
Didn’t you read John’s paper? They are close relatives of the Mississippi crocodile.
Entropy,
I like the metaphysical nature that was more intelligent than Nobel Prize winners like Szostak and created the first cell by using dumb luck… I don’t need to watch Harry Potter to be entertained… I read origin of life papers with all the experimental evidence pointing to several poofs at the same time… Comedy clubs will never make me laugh as hard as speculations of Nobel Prize winners about how dumb luck achieved the poofs and continues to outsmart human intelligence ….You should try reading it 😉
Isn’t the Mississippi River cold and turbulocean like for half of the year or so?
One would think they could freeze or drown…
Why couldn’t there be more then one type of water? You’ve never heard of strong water currents? Even today the animals that live in salty water do not enter into the fresh water river beds and the other way around… O lot of them can survive in both…
Scientists have been able to part the water with electromagnetic field, just like Moses did in the Red Sea…
You don’t say…another miracle of covetous evolution! Praise dumb luck!
I don’t know what you’re talking about, but you ignored my point altogether. So I’ll just repeat, I look for answers where it’s sensible to look. Fantasies, however you might to call them “metaphysical,” just won’t work. Mischaracterizing natural phenomena as mere dumb luck doesn’t help your case either. Your fantasies will remain fantasies regardless of how strongly and funny your rhetorical comebacks might be.
I wasn’t talking about entertainment, I was talking about unbiasedly searching for truth. If you don’t find fantasy tests competing in search for truth, then you understand why I don’t take religions that seriously.
Again, mischaracterizing natural phenomena as dab luck doesn’t help your fantasies become anything better than the fantasies they are.
Why shouldn’t nature “outsmart” human intelligence? Human intelligence comes from nature, not the other way around. So it’s to be expected that nature should “outsmart” any human.
Entropy,
Could we keep the origin of life out of this thread? I’m trying for a narrower focus here.
J-Mac,
One can readily analyse the genetics and determine the minimum size of population required to carry that amount of variation. Ann Gauger has elsewhere attempted to do just that for Adam and Eve. Are you going to tell her she’s barking up totally the wrong tree, or shall I?
Why would anyone who is not a moron give any credence to the Ark story?
Mung,
I don’t think we do agree completely actually. I am saying that the distinction between molecular and morphological character states is, to some degree, artificial. You can build trees on the one, the other, or both; there is no real ‘which’, you are just told what states go into the analysis for any particular case.
What we do have is the situation in which an analysis on one set of character states (be they morphological, molecular or a combination) maps pretty well on the analysis on another, otherwise uncorrelated set (be they etc etc etc). That’s very well explained by common descent – their descent, with linkage of states in genomes, provides the reason for that ‘meta-correlation’.
Just to make this clear. In the current case, the argument is over the position on the tree of a single species, Gavialis gangeticus. Doug Theobald has a web page that discusses exactly this case and shows how unlikely that little disagreement is by chance.
John Harshman,
OK; I was talking more generally. There’s an endless thread-hopping argument about what ‘twin / multiple nested hierarchy’ signifies.
ok, so we’ve eliminated the chance hypothesis. God does not play dice. 🙂
Not from me. I say it’s BS. Isn’t that what you’re saying as well?
No, really. I agree completely. The “twin-nested hierarchy” is a myth. I’m sure it sounded great when it was first proposed, but it doesn’t really exist. It’s mythical. Yet otherwise reasonable people continue to believe in it.
Do you have an alternative hypothesis to common descent? If so, what?
So, what is the genetic analysis based on? The famous, speculative population genetics? lol
I don’t know what Gauger attempted to explain. I didn’t read her piece…
But If I were to guess, she could have attempted to try to explain that within the acceptable framework of say population genetics, it is still possible that Adam and Eve could have been at the root of humankind tree… It doesn’t mean she believes that Adam and Eve lived 2 millions years ago… It could very well mean that it is still possible theoretically… especially if one is familiar with the law of recurrent variation…
IF you want details, ask her…I don’t know what she was thinking and what she believes…
Why would anyone who is not a moron buy Harshman story that now has more than 1 option? Can both be right? If you want to believe it…lol
I have a feeling that this OP has a great potential to become the flop of 2017…
Anybody with me? 😉
Too bad Sal is busy today… he could have help to explore this now interesting OP…
Mung,
No. I understand what people mean when they say ‘twin nested hierarchy’, though I prefer ‘multiple’ – trees built on sets of character states map pretty well onto those built on other sets of character states, and there is more than one other such set. I don’t think that’s BS, it’s true, however one chooses to apportion the data between the molecular and the morphological.
One can, if one wishes, dichotomise character states into molecular and morphological ones. Doing that, one has two nested hierarchies. That’s not a myth, it’s a thing. Do these hierarchies disagree completely? Or do they generally concur to a statistically significant degree?
J-Mac,
Population genetics is a perfectly respectable mathematical analysis of the behaviour of collections given particular assumptions. If you think the entire endeavour flawed, perhaps you could pen an OP; this is not the place to discuss it. It’s certainly easy to just stick ‘speculative’ or ‘evolution fairy tale’ in front of anything you say and make it appear as if you are engaging an argument, but you clearly ain’t.
As to your apparent belief in an actual Ark, I can only point and laugh.
Assumptions huh? Such as there has to be the minimum size of population required to carry that amount of variation? Or else what?
Or that there is no element of randomness in natural selection?
How about dual coding genes? Has population genetics predicted how many douons will be shared between chimps and humans? I can go on and on…
Come to think of it, you may be right. However, I think the YECs at AiG would still agree with John Harshman about the two creatures being commonly descended from an ancestor as they believe the ancestor was a created kind (Baramin) whether or not they were on the ark.
So, unfortunately I don’t think John is always wrong. Occasionally what he says agrees with the way God did it.
I don’t care if I’m right or wrong… I’m wrong a lot… (my wife keeps reminding me about that lol). What I’m trying to figure out is if crocks didn’t have to go to the ark, John’s conclusions must be wrong because they are based on the premise that they did…
There can’t be 2 or 3 truths based on his paper…
BTW: I was just lectured by Alan Miller how population genetics is so mathematically reliable and all…
How about multiple, miraculous insertions of multiple genes into the tree of life? Have you ever even considered them? I believe you have …
So, what’s the problem?
J-Mac,
Bottlenecks pretty obviously cause a reduction in variation. One would only have to imagine the present human population being reduced to 2 to see the effect this would have on the variation the future population can carry. If you think that’s speculative, then that’s what you think.
I know you can; that’s not really in dispute.
Sigh of relief… I was almost terrified that John could have been wrong all his life all the time producing so many papers and performing so many experiments… What a waste that would have been…
So, what you are saying there is hope… even for stubborn Darwinist like him…
Will see about that… 😉
Thanks Sal!
It’s always a pleasure…
What variations exactly are you talking about here?
I took offense because I went to great lengths to commend your work and highlight sections I was impressed with.
You’re getting to be in such a reflexive mode to disagree with me, that even when I post a section from your work and say, “excellent work” you’ll complain that I posted it. Those sequences posted bear you name as lead author from the associated publication does it not?
In any case, I was simply trying to learn aspects of the sequences in question and then learn about the phylogeny methods. I have pointed out the YECs at AiG don’t have issues with your conclusion, maybe even God approves. You asked “what is wrong with your paper?” As far as your conclusion that false gharials are likely true gharials, I think you could be right, and in that respect “NOTHING” is fundamentally wrong with your paper’s conclusion at this time.
I was however bothered as I read it that I couldn’t get any sense of the sequence divergence in the c-myc gene. You discussed introns, so I showed the picture of where I think the intron/exon regions are, and I wanted to know how you identify the UTRs.
I wasn’t trying to disagree with your paper. For a change the criticism was on the friendly side.