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Author Topic:   Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Tanypteryx
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Posts: 1593
From: Oregon, USA
Joined: 08-27-2006
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(1)
Message 1 of 16 (777683)
02-05-2016 6:44 PM


The editorial in the February issue of the scientific journal Cladistics reads “Phylogenetic data sets submitted to this journal should be analysed using parsimony.”

Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud

quote:
“If alternative methods give different results and the author prefers an unparsimonious topology, he or she is welcome to present that result, but should be prepared to defend it on philosophical grounds.”

That did not go over well.

quote:
“They said if you want to use another method, you have to show that it’s philosophically better, not scientifically better,” says Jonathan Eisen, an evolutionary biologist at UC Davis. “That’s why I said it seems like they’re dropping science for dogma.”

What if Eleanor Roosevelt had wings? -- Monty Python

One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie

If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy


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AZPaul3
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Posts: 3428
From: Phoenix
Joined: 11-06-2006


Message 2 of 16 (777689)
02-05-2016 9:33 PM
Reply to: Message 1 by Tanypteryx
02-05-2016 6:44 PM


Calling all Bayesian Phylogeneticists
This will be a good one for herebedragons. He's one of them Bayesians.

Maybe we can watch his head explode.


This message is a reply to:
 Message 1 by Tanypteryx, posted 02-05-2016 6:44 PM Tanypteryx has not yet responded

Replies to this message:
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Modulous
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Posts: 7537
From: Manchester, UK
Joined: 05-01-2005
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Message 3 of 16 (777699)
02-06-2016 6:16 AM
Reply to: Message 1 by Tanypteryx
02-05-2016 6:44 PM


“They said if you want to use another method, you have to show that it’s philosophically better, not scientifically better,” says Jonathan Eisen, an evolutionary biologist at UC Davis. “That’s why I said it seems like they’re dropping science for dogma.”

Well actually they said that you'll need to defend it on philosophical grounds. Not that it has to philosophically better rather than scientifically so. And that's not why it seems they are dropping science for dogma. They seem to be doing this by make a 'dogmatic' declaration that certain methods have yet to prove themselves able to stand alone in their journal {That's my best attempt to spin this as dogmatic in any sense}.

While Elsen may dislike their position it doesn't sound dogmatic, more pragmatic:

quote:
The epistemological paradigm of this journal is parsimony. There are strong philosophical arguments in support of parsimony versus other methods of phylogenetic inference (e.g. Farris, 1983).

The high citation index of Cladistics shows that the journal is publishing some of the most ground-breaking empirical and theoretical research on the history of life, and we remain committed to the publication of outstanding systematics research. As a community of scientists, the Willi Hennig Society is always open to new methods and ideas, and to well-reasoned criticisms of old ones. However, we do not hold in special esteem any method solely because it is novel or purportedly sophisticated.

Phylogenetic data sets submitted to this journal should be analysed using parsimony. If alternative methods are also used and there is no difference among the results, the author should defer to the principles of the Society and present the tree obtained by parsimony. Unless there is a pertinent reason to include multiple trees from alternative methods, a tree based on parsimony is sufficient as an intelligible, informative and repeatable hypothesis of relationships, and articles should not be cluttered with multiple, often redundant, trees produced from other methods. If alternative methods give different results and the author prefers an unparsimonious topology, he or she is welcome to present that result, but should be prepared to defend it on philosophical grounds.

In keeping with numerous theoretical and empirical discussions of methodology published in this journal, we do not consider the hypothetical problem of statistical inconsistency to constitute a philosophical argument for the rejection of parsimony. All phylogenetic methods, including parsimony, may produce inconsistent or otherwise inaccurate results for a given data set. The absence of certain truth represents a philosophical limit of empirical science.

Cladistics will publish research based on methods that are repeatable, clearly articulated and philosophically sound. We believe these guidelines implement the vision of Willi Hennig (1965, p. 97), who said, “(i)nvestigation of the phylogenetic relationship between all existing species and the expression of the results of this research in a form which cannot be misunderstood, is the task of phylogenetic systematics.”


I mean, good luck trying to argue that something is 'scientifically better' without resorting to philosophy. Given your first step must surely be to define 'scientifically better', you plunge into philosophy from the outset.

Edited by Modulous, : No reason given.


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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 4 of 16 (777734)
02-06-2016 10:45 PM
Reply to: Message 3 by Modulous
02-06-2016 6:16 AM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Well actually they said that you'll need to defend it on philosophical grounds. Not that it has to philosophically better rather than scientifically so. And that's not why it seems they are dropping science for dogma. They seem to be doing this by make a 'dogmatic' declaration that certain methods have yet to prove themselves able to stand alone in their journal {That's my best attempt to spin this as dogmatic in any sense}.

Yeah, but the point is that they want authors to defend their use of non-parsimony methods on philosophical grounds, rather than scientific grounds. Which, you know, is kinda odd. I mean, like, do they expect researchers to dig up philosophy papers arguing the merits of Occam's razor? It's just weird. Why don't they want authors to defend their use of, say, Bayesian methods on scientific grounds? Why did Cladistics turn into a philosophy journal?

And they're adherence to parsimony comes across as kind of dogmatic. Anyone who's worked in molecular phylogenetics or bioinformatics knows that the most appropriate method depends on the data set. Plus, there are good lines of evidence that Bayesian and maximum-likelihood methods are generally superior to parsimony.

And we know that parsimony is often an incorrect map of biological reality. According to parsimony based on molecular structure, the type III secretion system and bacterial flagella should be monophyletic. But molecular phylogenetic evidence strongly indicates that type III secretion systems nest within flagellar sequences, violating the notion of parsimony.

So for a journal like Cladistics to ask for uniform acceptance of parsimony as the default phylogenetic method is dogmatic and a little creepy.

Edited by Genomicus, : No reason given.


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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 5 of 16 (777735)
02-06-2016 10:54 PM
Reply to: Message 2 by AZPaul3
02-05-2016 9:33 PM


Re: Calling all Bayesian Phylogeneticists
This will be a good one for herebedragons. He's one of them Bayesians.

Maybe we can watch his head explode.

To be honest, my head is coming close to exploding. I am presently weirded out by the editorial board of Cladistics. Just a bunch of fervent cladists.

Edited by Genomicus, : No reason given.


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 Message 2 by AZPaul3, posted 02-05-2016 9:33 PM AZPaul3 has acknowledged this reply

  
Modulous
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Posts: 7537
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 1.7


Message 6 of 16 (777744)
02-07-2016 7:36 AM
Reply to: Message 4 by Genomicus
02-06-2016 10:45 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Yeah, but the point is that they want authors to defend their use of non-parsimony methods on philosophical grounds, rather than scientific grounds.

And the question I asked in response was 'How are you going to defend the epistemic superiority of a method without resorting to philosophy?'

And they're adherence to parsimony comes across as kind of dogmatic.

Saying your journal prefers parsimony and if authors want to use others they have to preset a defence of this is not dogmatic. It's a policy:

quote:
dogma: a belief or set of beliefs that is accepted by the members of a group without being questioned or doubted

quote:
what they said: All phylogenetic methods, including parsimony, may produce inconsistent or otherwise inaccurate results for a given data set. The absence of certain truth represents a philosophical limit of empirical science.

Why did Cladistics turn into a philosophy journal?

hrm, yes when did a journal that focussed on gaining knowledge about the relationships between groups of entities suddenly get philosophical?

Oh wait, that IS philosophy. It's a philosophy of nature. A natural philosophy - if you will. Quick let's shroud the whole think with the Latin word for knowledge 'scientia' rather than the Greek one (epistēmē ) so nobody will suspect we're doing dirty philosophy.

OK so that was tongue in cheek, but there are groups of scientists who both hate philosophy and reject that they do it for a living. I would have thought, even if they couldn't be persuaded, they would have made the empirical observation that there other scientists who regard their activities as sort of a subset of philosophy and that therefore they would have learned to NOT meltdown whenever the word philosophy gets raised by said scientists. They should replace it mentally with 'methodology' or something and try going from there.

Plus, there are good lines of evidence that Bayesian and maximum-likelihood methods are generally superior to parsimony.

If you think that's reason to publish them, your argument for so doing would be a philosophical one.

So for a journal like Cladistics to ask for uniform acceptance of parsimony as the default phylogenetic method is dogmatic and a little creepy.

They aren't.

They say they will uniformly accept results from parsimony methods in their journal and that the use of other methods, if the author believes them better, will need to be defended.

It's not dogmatic and creepy for them to reject papers on the atmospheric conditions of TransNeptunian objects. They have a focus, a scope for their journal. They have reasons for adopting this scope. They are free to reject every paper that comes to them. They are free adopt policies.

If it's a terrible idea, maybe they'll lose their impact.

if it's not, then people who don't want to defend alternate methods may go elsewhere to get published or they may just publish the parsimony tree and their preferred one along with a brief defense as to why they prefer theirs. Or something.


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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 7 of 16 (777753)
02-07-2016 5:24 PM
Reply to: Message 6 by Modulous
02-07-2016 7:36 AM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
And the question I asked in response was 'How are you going to defend the epistemic superiority of a method without resorting to philosophy?'

There are two approaches to defending the superiority of a given phylogenetic method: philosophical and scientific. As an example of how these are fundamentally different: one can debate the merits of Neo-Darwinian evolution vs. creationism on epistemological grounds, but that belongs in a philosophy journal, not a technical scientific journal.

So the real question is this: why did Cladistics, a technical journal, decide that authors needed to articulate a philosophical defense of their phylogenetic approach instead of outlining the scientific rationale for their method of choice?

Saying your journal prefers parsimony and if authors want to use others they have to preset a defence of this is not dogmatic. It's a policy:

Yeah, but:

1. A policy can be grounded in dogmatism.

2. Their preference for parsimony -- asking all phylogenetic research submitted to their journal to always use parsimony as a method of tree construction ("Phylogenetic data sets submitted to this journal should be analysed using parsimony") -- indicates a dogmatic, parochial bias towards a particular technical method. And it's dogmatic because they don't actually give very good reasons for this preference for parsimony.

OK so that was tongue in cheek, but there are groups of scientists who both hate philosophy and reject that they do it for a living.

Science is, of course, based on philosophy. It's unfortunate that many scientists don't have a solid grounding in the philosophy of science. But Cladistics isn't a philosophy journal in the colloquial sense; it's a technical scientific journal. They're essentially asking scientists to become expert philosophers who can appropriately analyze the epistemic merits of Occam's razor vs. probabilistic approaches.

If you think that's reason to publish them, your argument for so doing would be a philosophical one.

Sure, because everything ultimately traces down to philosophy. But you can use this argument for just about everything: "If you reject creationism, you'll be doing so based on philosophical grounds."

"If you think vaccines are safe, it's because of philosophical reasons."

"Oh, you think the anthropogenic global warming has merit? Well, that's just your philosophical perspective."

See how easy it becomes to make anything philosophical? So let me rephrase my original comment:

There are good lines of scientific (that is, falsifiable) evidence that Bayesian and maximum-likelihood methods are pragmatically superior to parsimony.


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Pressie
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Posts: 1858
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 2.1


Message 8 of 16 (777770)
02-08-2016 5:52 AM
Reply to: Message 7 by Genomicus
02-07-2016 5:24 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Genomicus writes:

There are two approaches to defending the superiority of a given phylogenetic method: philosophical and scientific.

Nope. Philosophy doesn't work on predicting what's going to be found underground. Science does.
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Modulous
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Posts: 7537
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 1.7


Message 9 of 16 (777771)
02-08-2016 8:40 AM
Reply to: Message 7 by Genomicus
02-07-2016 5:24 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
There are two approaches to defending the superiority of a given phylogenetic method: philosophical and scientific.

And I challenged this position in my first post:

quote:
I mean, good luck trying to argue that something is 'scientifically better' without resorting to philosophy. Given your first step must surely be to define 'scientifically better', you plunge into philosophy from the outset.

And in my second

quote:

'How are you going to defend the epistemic superiority of a method without resorting to philosophy?'

Show me the difference using the subject at hand, Cladistics.

As an example of how these are fundamentally different: one can debate the merits of Neo-Darwinian evolution vs. creationism on epistemological grounds, but that belongs in a philosophy journal, not a technical scientific journal.

It depends when you are doing it. In 1869, this is probably still a discussion one might find in scientific journals.

So the real question is this: why did Cladistics, a technical journal, decide that authors needed to articulate a philosophical defense of their phylogenetic approach instead of outlining the scientific rationale for their method of choice?

The real question is, what's the difference?

Their preference for parsimony -- asking all phylogenetic research submitted to their journal to always use parsimony as a method of tree construction ("Phylogenetic data sets submitted to this journal should be analysed using parsimony") -- indicates a dogmatic, parochial bias towards a particular technical method.

You can keep repeating it, but it's going to take more than repetition to persuade me that someone who says
'We prefer method x. Please use method x if you want us to publish your work. If you want to use another method instead, you may do so, but you must defend your decision' is being dogmatic.

And it's dogmatic because they don't actually give very good reasons for this preference for parsimony.

Your opinion on their reasons (which I disagree with), is not a factor in determining dogmatism.
Dogmatism is ruthlessly inflexible and would assert that Parsimony is the only true method. Which is exactly the opposite of what they did.

Science is, of course, based on philosophy.

Science is, of course, a branch of philosophy.

But Cladistics isn't a philosophy journal in the colloquial sense

No it isn't. And that's my point. We are talking 'philosophy in the colloquial sense'. We are talking in a technical sense. In a technical sense Cladistics is a philosophy journal in that it is a scientific one.

They're essentially asking scientists to become expert philosophers who can appropriately analyze the epistemic merits of Occam's razor vs. probabilistic approaches.

Scientists are meant to be expert philosophers. They are after all, professional philosophers. But they don't have to be, its just that Cladistics has standards. If some scientists can't meet those standards, they can try to publish elsewhere.

I wouldn't expect sentences such as 'epistemic merits' or 'Occam's razor'. I'd find phrases such as 'in this case Parsimony methods are so inaccurate as to be deceptive, for completeness we include those results in Appendix II'.

Sure, because everything ultimately traces down to philosophy.

So why the complaint?

There are good lines of scientific (that is, falsifiable) evidence that Bayesian and maximum-likelihood methods are pragmatically superior to parsimony.

I agree. But let's break this apart. First, science is a branch of philosophy. So it would be correct to say there are goods lines of philosophical evidence. Whether something is 'Good' as a line of evidence is an epistemological concern and is thus philosophy. 'Falsifiability' is philosophy concept and so is 'Pragmatism' and 'Superiority'. So merely by stating your position and using only 4 words in its defence (good, falsifiable, pragmatically superior) you have created a a philosophical defence.

Which takes me right back to the start

quote:
I mean, good luck trying to argue that something is 'scientifically better' without resorting to philosophy. Given your first step must surely be to define 'scientifically better', you plunge into philosophy from the outset.

quote:

'How are you going to defend the epistemic superiority of a method without resorting to philosophy?'

This message is a reply to:
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Replies to this message:
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Taq
Member
Posts: 7282
Joined: 03-06-2009
Member Rating: 4.0


Message 10 of 16 (777803)
02-08-2016 5:49 PM
Reply to: Message 4 by Genomicus
02-06-2016 10:45 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Yeah, but the point is that they want authors to defend their use of non-parsimony methods on philosophical grounds, rather than scientific grounds. Which, you know, is kinda odd.

What type of scientific grounds would there be for non-parsimony method being better?

And they're adherence to parsimony comes across as kind of dogmatic.

Would it be fair to say that parsimony is the traditional gold standard? If so, I don't see why it would be dogmatic. It simply requires one test that all papers can have in common, in order to compare one data set with another.

As a comparison, I deal a lot with proteins. There are multiple ways of measuring protein concentrations, and different methods can produce significantly different for the same protein solution. It would actually be helpful if all publications required that at least a single method be used in all papers, while still allowing authors to report different values using different methods. I can understand why they would do it.


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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 11 of 16 (777804)
02-08-2016 6:57 PM
Reply to: Message 8 by Pressie
02-08-2016 5:52 AM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Philosophy doesn't work on predicting what's going to be found underground. Science does.

You do realize that the statement "There are two approaches to defending the superiority of a given phylogenetic method: philosophical and scientific" is not incompatible with your statement that science is better at generating hard predictions? You're not really disagreeing with me with your above comment.


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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 12 of 16 (777805)
02-08-2016 7:23 PM
Reply to: Message 10 by Taq
02-08-2016 5:49 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
What type of scientific grounds would there be for non-parsimony method being better?

See Gadagkar and Kumar (2005) for an example of datasets where maximum likelihood is more appropriate than maximum parsimony.

Would it be fair to say that parsimony is the traditional gold standard?

For phylogenetics as an overarching field? Yes, parsimony has long dominated phylogenetic constructions based on, e.g, morphological characters. But the application of parsimony to molecular sequences occurred at about the same time as maximum likelihood methods and distance matrices were use for constructions of molecular phylogenies (in the 60s and 70s). So parsimony as a method for molecular phylogenetics has never been a gold standard per se, with the caveat that sophisticated statistical methods took longer to develop than parsimony methods.

It simply requires one test that all papers can have in common, in order to compare one data set with another.

Well, different phylogenetic methods are more appropriate depending on the data set. I hear you, Taq, but when it comes to molecular phylogenetics it's pretty hard to have an absolute standard given the diversity of sequences involved. So, for example, I've published molecular phylogenies of certain gram-positive protein systems, but opted to use more than one phylogenetic method (ML and Bayesian analysis) to see the extent to which the phylogenies were congruent.

It'd be inappropriate, IMHO, to always adopt a given phylogenetic method as a standard -- particularly given that molecular phylogenetic analysis is based on either a method that is philosophically grounded or statistically grounded.

Reference

Gadagkar, S., Kumar, S., 2005. Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous. Mol Bio Evo, 22(11): 2139-2141.


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 Message 10 by Taq, posted 02-08-2016 5:49 PM Taq has responded

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Taq
Member
Posts: 7282
Joined: 03-06-2009
Member Rating: 4.0


Message 13 of 16 (777849)
02-10-2016 1:36 PM
Reply to: Message 12 by Genomicus
02-08-2016 7:23 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
See Gadagkar and Kumar (2005) for an example of datasets where maximum likelihood is more appropriate than maximum parsimony.

Thanks for the example. Using computer simulations is something that should have donned on me from the start.

In the paper, they show that ML outperforms MP when there is a certain amount of heterotachy. Is there a way of determining the amount of heterotachy in a data set independent of the phylogenetic method?

Well, different phylogenetic methods are more appropriate depending on the data set. I hear you, Taq, but when it comes to molecular phylogenetics it's pretty hard to have an absolute standard given the diversity of sequences involved. So, for example, I've published molecular phylogenies of certain gram-positive protein systems, but opted to use more than one phylogenetic method (ML and Bayesian analysis) to see the extent to which the phylogenies were congruent.

I totally get what you are saying. Going back to my protein assay analogy, the appropriate method can also depend on the protein mixture. If you have an nearly pure sample with just one protein in it, then you can very precisely and reliably measure the concentration of the protein by using UV absorbance since specific amino acids have specific absorbances. If you have an unknown mix of proteins you can't say how many UV absorbing amino acids there are per protein molecule, so the UV method may not be as appropriate.

So, for example, I've published molecular phylogenies of certain gram-positive protein systems, but opted to use more than one phylogenetic method (ML and Bayesian analysis) to see the extent to which the phylogenies were congruent.

By congruence, do you mean congruence to the accepted species tree? If so, are you assuming a lack of horizontal transfer?


This message is a reply to:
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Genomicus
Member (Idle past 36 days)
Posts: 846
Joined: 02-15-2012


Message 14 of 16 (777870)
02-10-2016 11:39 PM
Reply to: Message 9 by Modulous
02-08-2016 8:40 AM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
Show me the difference using the subject at hand, Cladistics.

You can defend the scientific superiority of ML vs. parsimony through the use of, e.g., statistical evidence. As an example of this, see Gadagkar and Kumar (2005), referenced in a prior post.

Now, you could respond that the choice to use statistical evidence reveals a prior philosophical commitment. And you would be right. However, statistical evidence based on simulations of sequence evolution is falsifiable (that is, scientific). The philosophical perspective is not falsifiable. So why would Cladistics, a technical journal, ask for authors to philosophically defend their choices instead of asking them to defend their method of choice through falsifiable evidence? Think about it.

The actual reason Cladistics made that decision -- for authors to articulate a philosophical defense -- is because that journal has an ideological commitment to parsimony-based phylogenetics (as revealed by their history). Parsimony-based phylogenetics doesn't fare so well when it comes to falsifiable evidence; it does better when philosophy a la William of Ockham is invoked.

The real question is, what's the difference?

What's the difference between a philosophical defense of Neo-Darwinian evolution vs. a scientific defense? I'm genuinely curious how you approach this demarcation.

You can keep repeating it, but it's going to take more than repetition to persuade me that someone who says
'We prefer method x. Please use method x if you want us to publish your work. If you want to use another method instead, you may do so, but you must defend your decision' is being dogmatic.

Are you familiar with the history of the cladistics vs. frequentists debate, and the role that the Willi Hennig Society played in this? An examination of this history will reveal that the Willi Hennig Society has long had a dogmatic commitment to parsimony over statistical approaches to phylogenetics.

Dogmatism is ruthlessly inflexible and would assert that Parsimony is the only true method.

You have a rather dogmatic definition of dogmatism. I think "positiveness in assertion of opinion especially when unwarranted or arrogant" suffices in this case as an adequate definition of "dogmatism." Cladistics made no mention of why exactly they consider parsimony to be so much superior to other methods that it should be adopted as the default method by authors.


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Modulous
Member
Posts: 7537
From: Manchester, UK
Joined: 05-01-2005
Member Rating: 1.7


Message 15 of 16 (777907)
02-11-2016 9:58 PM
Reply to: Message 14 by Genomicus
02-10-2016 11:39 PM


Re: Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud
However, statistical evidence based on simulations of sequence evolution is falsifiable (that is, scientific). The philosophical perspective is not falsifiable.

Science decided to adopt the philosophy of strict falsificationism at or around the time of Popper. One can do science that is unfalsifiable, by some reckoning of the term, but otherwise science has more or less decided that a minimal entry requirement to be worthy of the label 'science' is falsifiability. This, of course, is a blatant philosophical position, which makes sense if science is a subset of philosophy, which until a couple of centuries ago everyone basically agreed on.

Falsifiability is a quality a philosophical argument might possess or lack. Being falsifiable does not make something scientific. For simple example: All cats are bright purple. This is falsifiable, but it is not scientific. It is not scientific because the hypothesis was not based on observation and a hypothetico-deductive process (or whatever), I just pulled it out of a random concept generator in my head. If I turn around, I see a black and white cat. The philosophical view on universal purple cats is falsified.

To repeat, to a reasonable approximation a philosophical position has to be falsifiable to qualify as science, but possessing those qualities isn't sufficient for science, and even if it were - it doesn't exclude it being philosophy.

So why would Cladistics, a technical journal, ask for authors to philosophically defend their choices instead of asking them to defend their method of choice through falsifiable evidence? Think about it.

It gives the authors more scope. Think about it.

The actual reason Cladistics made that decision -- for authors to articulate a philosophical defense -- is because that journal has an ideological commitment to parsimony-based phylogenetics (as revealed by their history).

How does this actual reason differ from their stated reason?

quote:
The epistemological paradigm of this journal is parsimony.

What's the difference between a philosophical defense of Neo-Darwinian evolution vs. a scientific defense? I'm genuinely curious how you approach this demarcation.

I'm arguing there isn't a demarcation as such. Science is a subset of philosophy. Dawkins
wrote some excellent philosophic works on neo-Darwinian evolution (eg., The Blind Watchmaker) and Dan Dennett has done so while explicitly and openly being a philosopher (eg., Darwin's Dangerous Idea: Evolution and the Meanings of Life). Also Stephen Gould's On The Structure of Evolutionary Theory may serve as an example of a philosophical work on the subject.

Are you familiar with the history of the cladistics vs. frequentists debate, and the role that the Willi Hennig Society played in this?

I wouldn't commit to familiar. I am aware of the broad strokes.

An examination of this history will reveal that the Willi Hennig Society has long had a dogmatic commitment to parsimony over statistical approaches to phylogenetics.

So why is Cladistics' announcement vaguely interesting to anyone? It's just making explicit what would be obvious with an examination of the history.

Cladistics made no mention of why exactly they consider parsimony to be so much superior to other methods that it should be adopted as the default method by authors.

Depends on your meaning of 'exactly'. They cite

Farris, J.S., 1983. The logical basis of phylogenetic analysis. In: Platnick, N.I., Funk, V.A. (Eds.), Advances in Cladistics. Columbia University Press, New York, Vol. 2, pp. 7–36.
Hennig, W., 1965. Phylogenetic systematics. Annu. Rev. Entomol. 10, 97–116.
CrossRef,Web of Science® Times Cited: 334


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 Message 14 by Genomicus, posted 02-10-2016 11:39 PM Genomicus has not yet responded

    
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