Alexei Drummond is visiting Canberra this week and today he has given a BEAST workshop hosted by our ANU/CSIRO Centre for Biodiversity Analysis. I have participated in the workshop and as one might expect I am most interested in the species tree analyses one can do with *BEAST. It was very rewarding and great fun. A few learnings I am taking from this, mostly as a kind of supplement to my species tree post from April, and a few thoughts:
The official position is that one can run an analysis with only one sample per species but it is not advisable because at least two samples are needed to estimate population sizes. From what people who have run their own analyses tell me, two samples are generally not enough for good results either.
That has an interesting consequence: because one should preferably have several samples per species but computing time explodes with larger sample numbers, these analyses are then only realistic for limited numbers of species. Unless, that is, you are prepared to assemble a ridiculously large dataset even for small studies and run your analysis on a supercomputer for a few weeks.
There are methodological alternatives (see my post linked above) but of course they have their own weaknesses. And as one of the course instructors pointed out, the parsimony based methods I like so much may come without such warnings and happily give me a species tree for every data set I throw at them, but they may give me a false sense of security where *BEAST would honestly show me how uncertain the result is.
There is a way around the problem of *BEAST not accepting missing data (i.e. one locus missing for a species): one can make a dummy sample of the species for that locus and fill the whole sequence with Ns. The analysis will then run without an error but it may take longer to mix.
It was confirmed that *BEAST will run with only one locus. This and the previous point are really important because it means that the program is even more flexible than I had assumed so far, apart from being reasonably fast and user friendly for a Bayesian phylogenetics tool.
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It is funny to observe how different scientists see different methodological issues, and how everybody is convinced that the one they have experienced is the most important one. The same instructor mentioned above was really concerned about the problem of non-Bayesian methods giving me one best tree even if there might be two more or less two equally good tree islands in the landscape. A parsimony method, for example, would pick one of them but a properly done (!) Bayesian analysis would sample over both and then show the uncertainty.
Apart from the fact that one can implement measures of certainty also for non-Bayesian methods (and of course that has been done), Bayesian approaches come with their own host of issues. They are slow, there are all the controversies around prior selection, and they demand an enormous up front investment on part of the end user. What is gamma? What is theta? What chain heat should I chose? How do I know what is a realistic prior for any of these dozens of items? What substitution model to chose? How to evaluate whether the run has been sufficiently long? Why do I have to learn how to use at least four different programs for one measly analysis?
Of course, some would argue that one should not do an analysis if one is not willing to do it right, but that steep learning curve is definitely also reducing the accessibility of science and sometimes borders on Herrschaftswissen (a term for which there might not be a good English translation). Not everybody interested in the phylogenetic relationships of one genus can be expected to become one of the world experts in Bayesian phylogenetics.
And again, sometimes I find it good to know where the computer has its hands... Bayesian analyses come with a huge and ever increasing number of variables and, importantly, assumptions that one has to accept. Parsimony analyses, on the other hand, have one simple assumption: of two possible explanations, the simpler one is to be preferred. It is very clear what actually happens inside the computer when you use them. So, sometimes you need a Sojus to get somewhere, but in other situations you would be better served just taking your bicycle.
Still, if you have the right data and can defend your assumptions, then BEAST is the most flexible and most sophisticated tool one may find.
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Finally, do not try to conduct any significant MCMC run on an ASUS Eee PC Seashell series. Good for conferences and field trips, not so good for doing science.
The blog of a systematic botanist of German origin, now working in Australia. It covers botany, phylogenetics, cladistics, science in general, freethought, and occasionally sillier issues.
Thursday, July 18, 2013
Botany picture #86: Parentucellia latifolia
Parentucellia latifolia (Orobanchaceae), Australia, 2010. This may well be the prettiest of several introduced Orobanchaceae in this country. I particularly like the dark margin around the bracts. No idea what the specific epithet refers to though; the leaves aren't particularly wide, quite the opposite.
Tuesday, July 16, 2013
Botany picture #85: Equisetum sylvaticum
Equisetum sylvaticum (Equisetaceae), Germany, 2012. Another genus that I miss a bit on this continent are the horsetails. I always liked them since I became interested in plants in general, and this may be the prettiest of all species due to its lacy, gracile appearance. It is widespread but not frequent in the northern hemisphere. As a member of the summer green subgenus Equisetum, it is unfortunately hard to propagate because one would have to dig up a good part of the easily fragmenting rhizome with storage tubers to establish it in the garden. Subgenus Hippochaete is much easier, often capable of growing a new plant out of a branch fragment, but (at least in my opinion) not as attractive.
Monday, July 15, 2013
Why bother about cladism?
A topic that I return to again and again is the sadly never-ending controversy around phylogenetic systematics, or cladism. There are, I would say, perhaps three major positions in the debate:
The thing is, I am actually quite sympathetic to the post-cladist stance. As long as it is understood that one cannot make sense of the evolution of Banksia without considering Dryandra to be part of it, I don't care if somebody speaks of Dryandra and Banksia despite the former genus formally having been sunk into the latter. As long as it is understood that examining the historical biogeography of Primula does not make sense without including Dodecatheon, it really does not matter if somebody still says Dodecatheon despite that genus formally having been made a synonym of Primula. So why do I care?
There are two reasons. The first is that, pace the post-cladist dismissal of their importance, formally named taxa do matter because they have the potential to mislead people. Not everybody will refer back to the phylogenetic trees when they want to conduct a biological study or just understand the diversity of the natural world. If all taxonomists and systematists accept a formal taxon Banksia that does not include the species of Dryandra then some end-users of taxonomic research will be mislead into thinking that Banksia is a natural group. And that means that they remain unaware of the fact that some Banksias are more closely related to Dryandra than they are to other Banksias, and depending on what they do in their ignorance it may have adverse consequences. Taxonomy potentially does have an impact beyond ivory tower squabbles.
The second reason why I care, and why I promote the cladist position, is of course the existence of its opponents, the continued attempts of "evolutionary" systematists to reverse the conceptual progress of biological classification in the 20th century. It would be one thing if there were only cladists and post-cladists, if it were understood how important it is to base decisions and study design on a knowledge of the correct phylogenetic relationships. In that situation, the cladist's constant harping on the importance of rejecting all non-monophyletic taxa might arguably appear a tad obsessive, and "we get it already, but who cares about the formal circumscription of that small genus that nobody knows anyway" might arguably be an understandable reaction.
It is quite another thing, however, if there is still a dozen or so professional botanists out there who actively want to destroy phylogenetic systematics and return the practice of the field to where it was ca. 1930 while, to add insult to injury, using arguments that have repeatedly been shown to be completely misguided. It is the same as with all too many other issues, be it something political such as women's rights or something scientific such as the acceptance of evolution: It is naive to assume that progress cannot be undone. If one side rests on its laurels while the other is constantly pushing back then it can and will be undone. I at least intend to do my bit to not let that happen if it can be avoided, and while the other two issues I just mentioned are clearly more important, phylogenetic systematics is relevant for my chosen profession.
- The cladist one, according to which all formally named supraspecific taxa should be monophyletic.
- That of "evolutionary" systematists, according to which formally named taxa should be allowed to be paraphyletic (they generally don't understand the part about "supraspecific" and why it is important).
- One that we could perhaps call post-cladist, held by people who would say something like this: "Who cares about formally named taxa? As long as we have a phylogenetic tree, we know what the relationships of species are, and that gives us all the information we need right here, e.g. for plant breeding or designing biological pest controls. And we can use the phylogenies for studies in historical biogeography, evolutionary biology, and many other areas. So will you stop shouting at each other? Nobody gives a damn."
The thing is, I am actually quite sympathetic to the post-cladist stance. As long as it is understood that one cannot make sense of the evolution of Banksia without considering Dryandra to be part of it, I don't care if somebody speaks of Dryandra and Banksia despite the former genus formally having been sunk into the latter. As long as it is understood that examining the historical biogeography of Primula does not make sense without including Dodecatheon, it really does not matter if somebody still says Dodecatheon despite that genus formally having been made a synonym of Primula. So why do I care?
There are two reasons. The first is that, pace the post-cladist dismissal of their importance, formally named taxa do matter because they have the potential to mislead people. Not everybody will refer back to the phylogenetic trees when they want to conduct a biological study or just understand the diversity of the natural world. If all taxonomists and systematists accept a formal taxon Banksia that does not include the species of Dryandra then some end-users of taxonomic research will be mislead into thinking that Banksia is a natural group. And that means that they remain unaware of the fact that some Banksias are more closely related to Dryandra than they are to other Banksias, and depending on what they do in their ignorance it may have adverse consequences. Taxonomy potentially does have an impact beyond ivory tower squabbles.
The second reason why I care, and why I promote the cladist position, is of course the existence of its opponents, the continued attempts of "evolutionary" systematists to reverse the conceptual progress of biological classification in the 20th century. It would be one thing if there were only cladists and post-cladists, if it were understood how important it is to base decisions and study design on a knowledge of the correct phylogenetic relationships. In that situation, the cladist's constant harping on the importance of rejecting all non-monophyletic taxa might arguably appear a tad obsessive, and "we get it already, but who cares about the formal circumscription of that small genus that nobody knows anyway" might arguably be an understandable reaction.
It is quite another thing, however, if there is still a dozen or so professional botanists out there who actively want to destroy phylogenetic systematics and return the practice of the field to where it was ca. 1930 while, to add insult to injury, using arguments that have repeatedly been shown to be completely misguided. It is the same as with all too many other issues, be it something political such as women's rights or something scientific such as the acceptance of evolution: It is naive to assume that progress cannot be undone. If one side rests on its laurels while the other is constantly pushing back then it can and will be undone. I at least intend to do my bit to not let that happen if it can be avoided, and while the other two issues I just mentioned are clearly more important, phylogenetic systematics is relevant for my chosen profession.
Saturday, July 13, 2013
Murrumbidgee River
We have a visitor this weekend and have made a trip to Kambah Pool Reserve and Red Rocks Gorge on Murrumbidgee River today. This is SSE of Canberra, near Tuggeranong.
Red Rocks Gorge in the light of the setting sun.
Rapids in Red Rocks Gorge. Signage at the lookout indicated that the entire river is popular with kayakers.
Near Kambah Pool and along the way there were quite a few weeds, especially Verbascum (mullein), Hypericum perforatum (St. John's wort) and Echium (Patterson's curse). This is the capsule of Datura stramonium (thorn apple).
One of the few native plants flowering now, in the middle of winter, was Melichrus urceolatus, a heath.
Finally, a bizarre lichen growing on dead branches.
Friday, July 12, 2013
Botany picture #84: Pityrogramma ochracea
Pityrogramma ochracea, Pteridaceae, Bolivia, 2007. Not much that I can tell you about this particular species except that it is an attractive, reasonably large terrestrial fern that I photographed in the Andean foothill region, but I thought this blog could feature a few more ferns. Pityrogramma is currently in the Pteridaceae family but the familial classification of the polypod ferns is still in flux. Since my studies in the late 90ies I have not seen any sense in learning the circumscription of fern families in the polypod lineage, and the situation is still the same. The ones further out - Schizaeaceae, Gesneriaceae, Lygodiaceae, tree ferns, etc. - appear to be clear-defined and easily recognized, but in the polypod lineage the dust hasn't settled to a sufficient degree to make sense of relationships. "More work is needed."
Thursday, July 11, 2013
When the charitable assumption of honest ignorance must be dropped
There appear to be basically only three reasons for the long persistence of an intellectual controversy.
The first is that the difference between the two sides is one of values and not one of demonstrable fact. If, for example, I think marzipan tastes best and you would say the same about chocolate, then there is simply no rational way to resolve our difference. The same is true for many controversies in politics, especially those that have to do with the more or less equal distribution of money and other resources, although perhaps not as many as one would think; there are many cases where at least one side builds its case on demonstrable falsehoods or on an intellectual framework that contains internal contradictions.
The second is that the two sides are continually talking past each other. Either they do not realize that the other side isn't actually saying what they think it is saying and thus attack a straw man of the other side's position, or some relevant terms are undefined or ill-defined. I believe that the continually resurfacing discussion about free will in the atheist blogosphere is one such issue: the participants virtually all agree on the wrongness of Cartesian dualism, they virtually all agree on some form of determinism (plus perhaps randomness bubbling up from quantum or whatnot, but definitely a complete absence of libertarian or supernatural free will), and they appear to all agree on the emphasis on rehabilitation and prevention in dealing with crime, as opposed to revenge. The entire controversy revolves around whether, all that being agreed on, the word "free will" can still be used in a compatibilist sense: does the word still have a use given determinism? In other words, it is an entirely semantic issue, only some people don't grasp that because they are using different definitions of the term "free will".
Finally, the third possible reason why a controversy never ends is because at least one of the sides is not operating in good faith, does not listen to counter-arguments, is overly prone to confirmation bias, and exhibits willful ignorance. Note that for a long-lasting controversy it cannot merely be honest, innocent ignorance because that would at some point be cleared up, and then the controversy would by definition not be long-lasting. A good example is creationism, where the following has been observed: a creationist argues that evolution is demonstrably wrong because nobody has seen a crocodile give birth to a duck; somebody carefully explains that that is a caricature of evolutionary theory, expounds on the gradual changes in allele frequencies and the long times involved in such a process, etc; and half a year later the very same creationist is again seen arguing that evolution is demonstrably wrong because nobody has seen a crocodile give birth to a duck.
There are of course two stages here: at first one can charitably assume that the creationist is innocently ignorant, although they should perhaps not have entered the discussion in the first place before making an effort at understanding what they are arguing against. But after it has carefully been explained to them why their argument did not make any sense whatsoever, we must drop the charitable assumption of innocent ignorance and must assume that they do not want to listen to what the other side has to say, that they simply do not want to understand the topic at hand, in other words that they are willfully ignorant of it.
I am thinking about this because I recently had to mentally move some "evolutionary" systematists from the potentially innocently ignorant folder into the willfully ignorant folder. Using creationism as an example might appear unnecessarily inflammatory in this context, but the situation is quite the same (and an example from another area such as economics would have been too obscure). Yes, some might argue that the preference for this or that approach to classification is ultimately a question of personal taste akin to marzipan vs chocolate, but even if we grant that - and I don't because systematics should be a science - there would still be valid arguments and demonstrably nonsensical arguments for one of those approaches, and somebody arguing in good faith would not continue to use a nonsensical argument once they know that it is nonsensical. Also, to paraphrase what I recently read elsewhere, the continual use of bad arguments by one side is indirect evidence that their position is not all that defensible.
So in this case I previously charitably assumed that the colleagues in question were honestly ignorant when they published papers promoting the acceptance of paraphyletic taxa and those papers made it abundantly clear that they did not understand (1) what a synapomorphy is, (2) essentially any of the relevant terminology, including even terms like "grade" or "sister group", (3) how parsimony analysis works, (4) that there is a difference between tokogenetic and phylogenetic structures, and (5) that phylogenetic language and phylogenetic systematics only ever apply to the latter, or in other words basically anything they simply need to understand before being qualified to participate in a professional discussion on the merits of phylogenetic systematics.
Don't get me wrong: everybody can have an opinion, but it is another thing to publish scientific papers on a topic without understanding even the very basics of it. Privately I have an opinion on economic policy and I may voice it among family, friends and colleagues, but I would not dream of submitting papers to The American Economic Review. But I digress; the important thing is that until recently I could assume that the "evolutionary" systematists in question simply did not do their homework and honestly believed to have found flaws in the school of systematics that they are campaigning against.
Now, however, I know for a fact that these specific colleagues have read refutations of several utterly fallacious and misguided arguments that they have used before, and they still continue to use them without so much as a blink. They still argue that long branches are a good criterion for the recognition of paraphyletic taxa after they have demonstrably read a clear explanation of why that doesn't work (gradual nature of evolutionary change, intermediate fossils breaking those long branches, lack of an objective and universal quantitative cut-off for "long enough", etc). They still claim that phylogenetic systematics "ignores" evolutionary divergence in lineages after they have demonstrably read an explanation of how information on divergence is found in lists of synapomorphies and how the very recognition of a nested taxon in phylogenetic systematics is necessarily based on the observation that it has diverged from the other members of the containing clade. And they still base their promotion of paraphyletic taxa on circular reasoning after they have demonstrably read a paper pointing out the fallacious nature of the relevant arguments. Part of the problem may be that they appear to also be ignorant about what the word fallacy means - they seem to believe it means "something somebody disagrees with" - and thus presumably ignorant about why it would be problematic to use fallacious reasoning.
Obviously I am not expecting people to quickly change their mind about the paraphyly issue as a whole merely because they have seen some of their arguments blown out of the water, just like I would not expect a creationist to stop being a creationist merely because it has been shown that evolutionary biologists do not actually believe that ducks evolved by a crocodile giving birth to a fully formed duck. Also, no matter how convinced that my own position is the correct one, I should nevertheless still entertain the possibility that proponents of paraphyletic taxa might ultimately be right, perhaps because of some argument that I have not yet fully considered.
But at a minimum I would expect them to make some attempt at at least somehow dealing with very clear refutations of their individual arguments. They could try to show that their arguments are actually not wrong (although admittedly in the case of their straw man version of phylogenetic systematics that would be quite difficult) or they could switch tactics and use another line of argument. But instead they blithely repeat the same talking points, never even so much as acknowledging that those might possibly just have been addressed in some way or another.
So they now knowingly continue to mischaracterize the school of systematics that they are attacking, and they knowingly repeat arguments that are demonstrably fallacious and/or based on faulty assumptions, and that is seriously not a question of values or taste. At some point, they have to dimly register that the other side always replies "actually, no, that's not how it works" when they describe how phylogenetic systematics supposedly operates. At some point, they have to realize that an argument does not become less unfounded merely by repeating it over and over again while going "lalala I can't hear you" whenever somebody answers.
And that is where the charitable assumption must be dropped. We all should, ourselves, whether it is a topic of professional relevance or only of private interest to us, whether it is about science, religion, politics, economics or whatever, listen to opposing arguments, evaluate them honestly, put our own ideas to the test, and assume until the opposite is proven that others are doing the same. But at some point one has to observe the behavior of the other side in a controversy and decide whether they can still be assumed to argue in good faith. If they are visibly ignoring even the clearest refutation of one of their arguments, if they appear continually disinterested in learning about and understanding even so much as the basics of what they reject, then one has to conclude that a rational discussion is not possible.
That does not mean one should stop arguing, of course. It is still important to try to convince the people sitting on the fence. But that realization has consequences for the way one has to argue as well as for what degree of intellectual honesty one might potentially expect from the other side.
The first is that the difference between the two sides is one of values and not one of demonstrable fact. If, for example, I think marzipan tastes best and you would say the same about chocolate, then there is simply no rational way to resolve our difference. The same is true for many controversies in politics, especially those that have to do with the more or less equal distribution of money and other resources, although perhaps not as many as one would think; there are many cases where at least one side builds its case on demonstrable falsehoods or on an intellectual framework that contains internal contradictions.
The second is that the two sides are continually talking past each other. Either they do not realize that the other side isn't actually saying what they think it is saying and thus attack a straw man of the other side's position, or some relevant terms are undefined or ill-defined. I believe that the continually resurfacing discussion about free will in the atheist blogosphere is one such issue: the participants virtually all agree on the wrongness of Cartesian dualism, they virtually all agree on some form of determinism (plus perhaps randomness bubbling up from quantum or whatnot, but definitely a complete absence of libertarian or supernatural free will), and they appear to all agree on the emphasis on rehabilitation and prevention in dealing with crime, as opposed to revenge. The entire controversy revolves around whether, all that being agreed on, the word "free will" can still be used in a compatibilist sense: does the word still have a use given determinism? In other words, it is an entirely semantic issue, only some people don't grasp that because they are using different definitions of the term "free will".
Finally, the third possible reason why a controversy never ends is because at least one of the sides is not operating in good faith, does not listen to counter-arguments, is overly prone to confirmation bias, and exhibits willful ignorance. Note that for a long-lasting controversy it cannot merely be honest, innocent ignorance because that would at some point be cleared up, and then the controversy would by definition not be long-lasting. A good example is creationism, where the following has been observed: a creationist argues that evolution is demonstrably wrong because nobody has seen a crocodile give birth to a duck; somebody carefully explains that that is a caricature of evolutionary theory, expounds on the gradual changes in allele frequencies and the long times involved in such a process, etc; and half a year later the very same creationist is again seen arguing that evolution is demonstrably wrong because nobody has seen a crocodile give birth to a duck.
There are of course two stages here: at first one can charitably assume that the creationist is innocently ignorant, although they should perhaps not have entered the discussion in the first place before making an effort at understanding what they are arguing against. But after it has carefully been explained to them why their argument did not make any sense whatsoever, we must drop the charitable assumption of innocent ignorance and must assume that they do not want to listen to what the other side has to say, that they simply do not want to understand the topic at hand, in other words that they are willfully ignorant of it.
I am thinking about this because I recently had to mentally move some "evolutionary" systematists from the potentially innocently ignorant folder into the willfully ignorant folder. Using creationism as an example might appear unnecessarily inflammatory in this context, but the situation is quite the same (and an example from another area such as economics would have been too obscure). Yes, some might argue that the preference for this or that approach to classification is ultimately a question of personal taste akin to marzipan vs chocolate, but even if we grant that - and I don't because systematics should be a science - there would still be valid arguments and demonstrably nonsensical arguments for one of those approaches, and somebody arguing in good faith would not continue to use a nonsensical argument once they know that it is nonsensical. Also, to paraphrase what I recently read elsewhere, the continual use of bad arguments by one side is indirect evidence that their position is not all that defensible.
So in this case I previously charitably assumed that the colleagues in question were honestly ignorant when they published papers promoting the acceptance of paraphyletic taxa and those papers made it abundantly clear that they did not understand (1) what a synapomorphy is, (2) essentially any of the relevant terminology, including even terms like "grade" or "sister group", (3) how parsimony analysis works, (4) that there is a difference between tokogenetic and phylogenetic structures, and (5) that phylogenetic language and phylogenetic systematics only ever apply to the latter, or in other words basically anything they simply need to understand before being qualified to participate in a professional discussion on the merits of phylogenetic systematics.
Don't get me wrong: everybody can have an opinion, but it is another thing to publish scientific papers on a topic without understanding even the very basics of it. Privately I have an opinion on economic policy and I may voice it among family, friends and colleagues, but I would not dream of submitting papers to The American Economic Review. But I digress; the important thing is that until recently I could assume that the "evolutionary" systematists in question simply did not do their homework and honestly believed to have found flaws in the school of systematics that they are campaigning against.
Now, however, I know for a fact that these specific colleagues have read refutations of several utterly fallacious and misguided arguments that they have used before, and they still continue to use them without so much as a blink. They still argue that long branches are a good criterion for the recognition of paraphyletic taxa after they have demonstrably read a clear explanation of why that doesn't work (gradual nature of evolutionary change, intermediate fossils breaking those long branches, lack of an objective and universal quantitative cut-off for "long enough", etc). They still claim that phylogenetic systematics "ignores" evolutionary divergence in lineages after they have demonstrably read an explanation of how information on divergence is found in lists of synapomorphies and how the very recognition of a nested taxon in phylogenetic systematics is necessarily based on the observation that it has diverged from the other members of the containing clade. And they still base their promotion of paraphyletic taxa on circular reasoning after they have demonstrably read a paper pointing out the fallacious nature of the relevant arguments. Part of the problem may be that they appear to also be ignorant about what the word fallacy means - they seem to believe it means "something somebody disagrees with" - and thus presumably ignorant about why it would be problematic to use fallacious reasoning.
Obviously I am not expecting people to quickly change their mind about the paraphyly issue as a whole merely because they have seen some of their arguments blown out of the water, just like I would not expect a creationist to stop being a creationist merely because it has been shown that evolutionary biologists do not actually believe that ducks evolved by a crocodile giving birth to a fully formed duck. Also, no matter how convinced that my own position is the correct one, I should nevertheless still entertain the possibility that proponents of paraphyletic taxa might ultimately be right, perhaps because of some argument that I have not yet fully considered.
But at a minimum I would expect them to make some attempt at at least somehow dealing with very clear refutations of their individual arguments. They could try to show that their arguments are actually not wrong (although admittedly in the case of their straw man version of phylogenetic systematics that would be quite difficult) or they could switch tactics and use another line of argument. But instead they blithely repeat the same talking points, never even so much as acknowledging that those might possibly just have been addressed in some way or another.
So they now knowingly continue to mischaracterize the school of systematics that they are attacking, and they knowingly repeat arguments that are demonstrably fallacious and/or based on faulty assumptions, and that is seriously not a question of values or taste. At some point, they have to dimly register that the other side always replies "actually, no, that's not how it works" when they describe how phylogenetic systematics supposedly operates. At some point, they have to realize that an argument does not become less unfounded merely by repeating it over and over again while going "lalala I can't hear you" whenever somebody answers.
And that is where the charitable assumption must be dropped. We all should, ourselves, whether it is a topic of professional relevance or only of private interest to us, whether it is about science, religion, politics, economics or whatever, listen to opposing arguments, evaluate them honestly, put our own ideas to the test, and assume until the opposite is proven that others are doing the same. But at some point one has to observe the behavior of the other side in a controversy and decide whether they can still be assumed to argue in good faith. If they are visibly ignoring even the clearest refutation of one of their arguments, if they appear continually disinterested in learning about and understanding even so much as the basics of what they reject, then one has to conclude that a rational discussion is not possible.
That does not mean one should stop arguing, of course. It is still important to try to convince the people sitting on the fence. But that realization has consequences for the way one has to argue as well as for what degree of intellectual honesty one might potentially expect from the other side.
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