Barry seems to have noticed TSZ again, and so I will take this opportunity of inviting him over here, where he can post freely, and will not be banned unless he posts porn or malware or outs someone, which I expect he can manage not to do.
And he responds to my post, Lawyers and Scientists. He does so in two parts, so I will devote two posts to them. Here is my response to his first part. Barry writes:
PART 1
First Liddle writes that I have
. . . confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none.
Where did I do such a thing? Boiling that paragraph down I made the following claims:
- Common descent is not necessarily false.
- But Cladistics does not establish common descent one way or the other.
- Instead, cladograms are constructed ASSUMING common descent.
- It is circular reasoning to conclude that a technique establishes that which it assumes in the first place.
- Therefore, anyone who says that cladistics establishes the fact of common descent has used faulty reasoning and is mistaken.
- There are in fact people who make that mistake.
To establish beyond doubt point 6, Glen Davidson kindly jumps into Liddle’s own combox with this:
Barry: “This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.”
Glen: “Of course it does. What a ridiculously ignorant dweeb.”
All six assertions seem to me to be on solid ground. Not only are they true, they are not even controversial. But for Liddle’s charge to be correct, at least one of the points I made must be false. OK Liddle, which of the six totally non-controversial points I have made do you disagree with? If the answer is “none,” then the only gracious thing to do is to withdraw your claim.
The short answer is that I disagree with 2-6, for the reasons I gave in my first post: the answer lies in null hypothesis testing. Far from “assuming a tree”, both linear correlations and tree distributions are tested by FITTING a slope/tree, and testing whether the best fit is a better fit than would be expected under the NULL of no linear relationship/no underlying tree structure. If, having fitted the slope/tree, the fit is no better than would be expected under the null of no linear relationship/no underlying nested hierarchy, then you RETAIN THE NULL. If it is better, i.e. if a fit as good as that observed is UNLIKELY under the null, you reject the null and consider your hypothesis (linear fit; common descent pattern) supported. Of course there could reasons other than common descent that could explain the tree – but the tree can be established as an OBSERVATION to be EXPLAINED. Which Linnaeus did before Darwin. And it was that clear tree that Darwin sought to explain by, firstly, Common Descent, and, secondly, by a mechanism that would explain adaptive change-over-time.
If Barry cannot understand that testing a NULL HYPOTHESIS is the OPPOSITE of assuming that your model is true, then perhaps he could shoot an email to the former owner of his site.
It is of course true that null hypothesis testing is counter-intuitive and doesn’t do what many of its practitioners think it does, but it’s still an excellent workhorse, and what’s more, is the beating heart of ID’s very own eleP(T|H)ant.
[My response to the second part will have to wait – I have some null hypotheses to test first….]
ETA: Looks like this response deals with Pt II at as well.
It’s used in courtrooms to establish paternity and maternity. Used medically to determine risk of heritable diseases, and by people as hobbyists, to determine ancestry.
Basically the methods used by biologists to determine relationships between species and the descent of genes are universal solvents, solving all kinds of problems that aren’t evolution.
William J. Murray,
Are you asking specifically about usage in human medicine? If so, why do you suppose that human medicine is the only interesting or useful thing to be studying? You seem to be saying that if it doesn’t help us invent new drugs, we have no reason to do it. I wouldn’t agree at all.
Phylogenetics (and let’s drop that faulty “cladistics” label) has indeed been used in medicine, but I don’t think there is a reason to ignore other uses. But if you insist, it’s been used to trace the origins of diseases, both within the human population and to their non-human reservoirs. It’s also been used to examine the evolution of pathogens, which can be quite useful in designing drugs and vaccines.
Perhaps if you would just come out and state what you really want to know or what your point is, that would make for better communication.
That’s the kind of example I’m talking about. Thank you.
John Harshman said:
No, I’m just talking about a practical application, like Robin gave me.
Those also are the kinds of practical applications I was looking for. I was just trying to understand how phylogenetics is put to practical use in biology/medicine outside of simply creating databases of inferred relationships.
I appreciate these answers, they have helped me better understand, to some very small degree, phylogenetics and how it is applied in a practical sense.
An obvious example is PhastCons, which is an explicitly phylogenetic framework for measuring the degree to which a sequences are conserved over evolutionary time. PhastCons scores are key way in which the likely effects of mutations are predicted, so a big part of modern clinical genetics.
Similarly, phylogeny is often key to understanding the origin and dynamics of disease outbreaks. The recent Ebola outbreak being an example. Indeed, it’s through phylogenetic analyses that we now the most recent outbreak was the result of a new transmission of the virus from bat to human.
There are countless other examples, as google scholar will show you.
GlenDavidson,
That is one of the best pieces of content I’ve seen on this site. Thank you.
I think I would agree. Any pattern at all is subject to the same subjectivity, Did you ever see the movie A Beautiful Mind?
I hope you know I would disagree. I don’t want to derail this thread but there is a much better option. Perhaps we can discuss sometime.
Again I disagree that this is the way to get past epistemic nihilism.
Given materialism It seems to be an unjustified assumption that some inferences are valid since that itself is an inference. It’s viciously circular
I’m not sure I would be the first to provide an explanation for supposed patterns in nature . Surely you know there were explanations before Darwin. We humans are explanation machines.
I can think of some explanations off the top of my head for almost any pattern I come across. You might not find them to be convincing but that’s the point when it comes to subjectivity
I’m not sure what you mean by the tree does not have to be imposed could you elaborate. Doesn’t data have to be interpreted?
It might just be that we humans are imposing a pattern that is not there at all.
peace
I can support the claim that common descent does not produce a nested hierarchy- transitional forms have characteristics of more than one set group. That means the nest is broken. Darwin went over that in “On the Origins of Species”. Wagner went over that in “Arrival of the Fittest”. See also Denton “Evolution: A Theory in Crisis”
And that you didn’t know that proves your ignorance of it.
The problem is you guys think that a branching pattern is a nested hierarchy just because nested hierarchies can be depicted as branching patterns. However a nested hierarchy has specific entailments that mere branching patterns do not have to have.
A SUMMARY OF THE PRINCIPLES OF HIERARCHY THEORY :
For example the Animal Kingdom consists of and contains all of the organisms that have the defined characteristics of an animal. And a reptile-like mammal and a mammal-like reptile would have the characteristics of BOTH nested groups- mammals and reptiles. They wouldn’t belong to either set and because of that containment is lost and a nested hierarchy is also lost.
Evolution is too complex a process to produce the pristine order required of nested hierarchies:
and
fifthmonarchyman,
I note that you provide no answers at all. You just deny that I’m right. Even when I ask for an alternative explanation of the data you merely state that you are sure you could come up with one, but you don’t actually do so. And you deny epistemic nihilism while defending epistemic nihilism. Very confusing.
fifthmonarchyman,
The tree doesn’t have to be imposed because the methods we use discover it rather than forcing it into a preconceived pattern. Phylogenetic methods do begin by assuming there is a tree, but they don’t assume any particular tree. If different data end up giving the same tree (and they generally do), that’s good evidence that the tree is correct and that the data do have that structure inherent in them. I’ve mentioned bootstrapping: that’s way of making resampling the original data to test for consistency and agreement among different bits of it. A high bootstrap number means the conclusion is not imposed on the data. Sure, data has to be interpreted, but some interpretations are warranted while others are not. It isn’t just pareidolia, and imagining so is indeed nihilism.
I am doing my best not to bog down this interesting thread. Experience here has shown me that if I provide specific answers this thread will immediately degenerate into a culture war swamp.
I apologize but that is the hand we are dealt.
There is nothing to be confused about
Epistemic nihilism is only warranted if we don’t have a secure objective foundation for knowledge that exists outside ourselves. I believe such a foundation is available.
So an overall pattern is imposed on the data and specific details are added in later but overall rough original pattern is never called into question? Is that a fair characterization?
Is it possible that humans are subject to confirmation bias noticing stuff that conforms to our preconceived notions and missing data that does not ?
peace
No, it is not.
Thankfully, the statistical programs that run on computers don’t have preconceived notions. Humans, on the other hand, do suffer from confirmation bias, as you have so helpfully demonstrated yet again.
fifthmonarchyman,
I admit to curiosity about this secure foundation, given your prior claims that biologists are just making up shit.
As for the rest, DNA_jock had a decent reply. It’s possible to distinguish a tree that’s just imposed on the data from one that the data actually support using various statistical tests, of which I have mentioned bootstrapping, and these tests are commonly performed. This is not subjective opinion.
Makes me want to ask, what is the essence of a tree?
Humans decide which statistical programs to run they choose the features to be evaluated and assign relative weights to the results presented,
There are lies dammed lies and statistics. When it comes to patterns there is no getting past the observer that I can see.
peace
exactly
Who is to say a particulate pattern is a tree and not a lattice or a starburst?
When exactly does a vine or bush become a tree?
A tree pattern is in the eye of the beholder it seems.
peace
fifthmonarchyman,
Do you in fact know anything whatsoever about phylogenetic analysis? You seem to be imagining a scenario to fit your fantasies.
I never said that.
I think that biologists (and other folks) have genuine knowledge
It’s just that I don’t think knowledge comes inference from patterns of data.
peace
I think so but mostly I’m just responding to your comments here.
It’s possible there is something solid behind it all but you would not know that from what you have posted so far IMO.
Please feel free to elaborate and clarify if you need to.
peace
Yes, dismiss what you don’t understand. Everyone gets it.
You had me at “I don’t think”.
Ask Joe G.
fifthmonarchyman,
“Please feel free to elaborate and clarify if you need to.”
If “you” need to? Why would John “need to”?
Would or could a free science education from John or anyone else convince you to stop believing in religious gibberish?
I don’t know, perhaps he feels that he has not expressed himself adequately. If he meant to convey that the tree pattern was more than just subjective convention
Do you have more than opinion to support your case? If so it would be nice to hear your argument for a tree.
No I tentatively dismiss what can’t be independently and objectively verified. It’s called being a skeptic. You might want to give it a try.
peace
PS Do you see what I mean by a culture war swamp?
OMagain,
Speaking of patterns and essences
Any progress on the tool/Game?
It’s whole point is to investigate whether patterns we see are actual or just imposed on the data in an ad-hock manner. It or something like it might work with the data we are talking about here.
peace
Not. Even. Wrong.
It would be like scratching marks on a rock and thinking you have created David. The level of sophistication in the tools used is evidently very far outside of your experience.
But I’ll have something for you in a week or so now.
Yet you hold that there is an archetypical species for every example of extant biology. I’d like to hear how you independently and objectively verified that.
No, I see people who make claims that cannot be verified in any imaginable way, then dismiss others work because they don’t have the knowledge or experience to understand it.
An entire branch of science dismissed by you.
Oh? To be skeptical you need to understand something about the subject first. You should try it some time.
Perhaps you should do some reading up on phylogenetic analysis before you start claiming the patterns are inventions designed to support Darwinism (or whatever)? As any toy tool I might create will have zero relation to the tools used in that field.
Perhaps.
But I would say the problem is not the relative sophistication of the tools but the subjective nature of the choices made in their use. John Harshman has conceded that a tree pattern is assumed from the outset. Sophisticated tools can’t change that fact.
The validity of that choice is what I’m interested in.
peace
My point is not about this particular pattern but the subjective nature of patterns in general. It’s especially not about “Darwinism”.
You can relax.
peace
If you are genuinely interested, go crack a book, don’t wait to be spoon fed.
Was it really a concession?
Tell me fmm, do you believe that life had a single common ancestor? If so, what sort of shape does that create?
Well, luckily for you the patterns emerge on their own. There is nothing subjective about it. But you will no doubt see this as you do your own research.
Patronise much?
And this will no doubt be your excuse later on when things don’t go your way too.
Then you know nothing about science works, since everything we know comes from inference from patterns of data. Where do you think that genuine knowledge comes from?
John Harshman,
Revelation? And what’s revelation? Well, scientists discovering the truth is also revelation.
Trust me, don’t go there! 😛
From what I’m reading, if one thinks Divine Revelation is the ONLY avenue to knowledge, then clearly we are all drowning in a sea of incorrigible subjectivity, seeing only what we wish to see and completely unable to construct true reality without the help of Divine Insight.
This being the case, the answer can never be more knowledge, more observations, better analytical tools, more accurate predictions, etc. These serve only to obscure the underlying delusion that we are approaching Truth, which can be approached only by revelation directly from the correct god.
Fortunately, the technology behind the internet was revealed, so that Truth can be communicated more broadly. It lets us tell scientists that science itself is nothing more than pure substance-free confirmation bias, while completely missing the irony embedded in the tools we use to preach this message.
It’s clear that either you didn’t read the OP or it went way over your head. Remember all that about null models and such? The tree is assumed for the sake of testing it. If the data didn’t fit a particular tree we would be able to tell from those tests.
As for explanations, I put up a link to a very simple case a while ago. Did you read it? I expect not. Here is it again.
I can’t spoon-feed you unless you open your mouth. And I draw the line at an IV drip.
I would not be so bold to say all life has a single common ancestor but I’m open to that idea. .
With HGT and convergent evolution and hybridization, I would expect to see a tree like lattice or tree/web combination.
I would not rule out a sort of winding river system pattern with channels that diverge and converge depending on the terrain.
I see no reason to limit ourselves to a tree.
peace
I have no problem testing a null model but I think the test should be pattern verses no pattern rather than tree pattern “A” verses not tree pattern “A”.
At least initially
Do you see the difference?
Peace
Then what idea do you hold as most likely? And does it really make much difference once you get past the first parts of the base of the tree?
Nobody is stopping you from doing anything and seeing what happens. Who knows, you might actually stumble on something useful.
Go on.
Again, your lack of knowledge is leading you astray. Tests are not of tree pattern A vs. not tree pattern A; they’re of whatever tree patterns is the best fit vs. all other tree patterns; if the data don’t fit any tree pattern, we see that too. One could of course go further if one finds no tree pattern and test for other sorts of patterns, but that isn’t relevant to most data.
We can, incidentally, test for reticulation, and there are many cases of hybrid species discovered through such analysis, almost entirely in plants and sometimes in the quite distant past.
Did you look at the article I linked yet?
Got a pencil? Get drawing, it’ll make a fascinating OP I’m sure. You could call it “guy who’s just heard about a thing 10 minutes ago thinks he has something to contribute”.
I’m agnostic. It depends on who is making the best argument at any given time
Why should we limit ourselves to the first parts of the base? HGT and convergent evolution and hybridization and epigenetic changes can happen at any point along the “tree”.
Like I said I think the concept of a tree is pretty limiting. Other patterns or no pattern at all would seem to be just as likely
peace
How exactly? Be specific as to how science can prove a negative
peace
I personally know of two recent animal hybrid “species”.
But this begs yet another question, What counts as a species if hybridization is a real factor in the data?
How do you know it is reticulation without assuming divergence in the first place?
peace
And right now, who is making the best argument? Don’t be coy.
I’m not saying we should. But the point is that the root is likely to be more of a “bush” which turns into more of a “tree” later on. But you know this already.
And therefore….
Demonstrate a better way then. Or do you only point out things you think are wrong without suggesting alternatives?
Why? On what basis do you make that claim?
You’ve somehow forgotten to demonstrate how you know that species are a distinct concept in the mind of god.
The signal is there. You just don’t like what it’s telling you.