Tuesday, December 31, 2013


Some time ago, deep in the understorey of the internet, I argued that somebody was advancing an intellectually inconsistent position, and was rewarded with the witty reply "consistency is the hobgoblin of little minds".

I was then puzzled about two things. First, how one could be so cavalier about not contradicting oneself; I had rather assumed that that was a necessary precondition for making sense. Second, where that quotation came from, for I assumed that it had not originated with the blogger who was hurling it at me.

Thanks to Ana Mardoll I have now found out where it came from. Wikiquote (accessed 31 Dec 2013) has a large collection of quotes on the topic of intellectual consistency, and they must have been assembled by someboy who is very much of one mind with the guy mentioned above because they pretty much all ridicule the concept:
A foolish consistency is the hobgoblin of little minds, adored by little statesmen and philosophers and divines. With consistency a great soul has simply nothing to do. He may as well concern himself with his shadow on the wall. Speak what you think now in hard words, and to-morrow speak what to-morrow thinks in hard words again, though it contradict every thing you said to-day. — 'Ah, so you shall be sure to be misunderstood.' — Is it so bad, then, to be misunderstood? Pythagoras was misunderstood, and Socrates, and Jesus, and Luther, and Copernicus, and Galileo, and Newton, and every pure and wise spirit that ever took flesh. To be great is to be misunderstood. --- Ralph Waldo Emerson
Well, so it appears at first sight. Of course it would not matter anyway what a bunch of famous people thought on a topic because it is quite possible that they were all idiots honestly mistaken. But if we look closer, we notice that there are actually two sets of quotes here. There are those that proudly declare that you do not have to make any sense if you are just awesome enough (apparently without wondering how we are supposed to recognize awesome people as awesome if they contradict themselves all the time). In addition to the hobgoblin one, for example:
Consistency is a virtue for trains: what we want from a philosopher is insights, whether he comes by them consistently or not. --- Stephen Vizinczey

Consistency is the last refuge of the unimaginative. --- Oscar Wilde

Consistency is the enemy of enterprise, just as symmetry is the enemy of art. --- George Bernard Shaw

The test of a first-rate intelligence is the ability to hold two opposed ideas in the mind at the same time, and still retain the ability to function. --- F. Scott Fitzgerald
No idea who Vizinczey is, by the way. And then there are a few that have a completely different thrust:
If a person never contradicts himself, it must be that he says nothing. --- Miguel de Unamuno

Consistency requires you to be as ignorant today as you were a year ago. --- Bernard Berenson

A silly ass ... wrote a paper to prove me inconsistent. ... Inconsistency is the bugbear of fools! I wouldn't give a damn for a fellow who couldn't change his mind with a change of conditions. --- John Arbuthnot "Jacky" Fisher

The facts changed. Since the facts changed, I changed my position. What do you do, sir? --- John Maynard Keynes
These are quotes in which people defend themselves for having been inconstent not in the same argument, but inconsistent over time. In other words, they argue that being able to change one's mind is a virtue. And it is; it is the opposite of being unreasonable and dogmatic. I do hope that whoever organized that Wikiquote entry is aware that there are two completely unrelated issues.

But even given that being able to change one's mind in the face of new evidence or better arguments is good, I have to stay by my original position in this case. Intellectual consistency in one and the same discussion is not a goblinoid of whatever species (whether hobgoblin or bugbear). It is not an unworthy obsession of those who have run out of arguments. It is the first, lowest hurdle you have to clear for your position to make any sense whatsoever. Only after it is clear that you aren't obviously contradicting yourself is it even worth the effort to check whether your position is also supported by evidence.

For example, those who use 'faith' and 'religion' as insults when discussing other people's beliefs and criticize them for not having an evidence based worldview but then turn around and promote their own religious faith should be laughed out of the conversation. And somebody who manages to write in two consecutive sentences that (1) there is no clear line between the birds and the non-avian dinosaurs that were their ancestors and (2) there is such a strong divergence between birds and non-avian dinosaurs that we should accept the latter as a paraphyletic taxon without realizing what they have just done does not deserve to be taken seriously.

People who contradict themselves within the same line of argumentation may be confused, they may be dishonest, or they may be insane, and at least in the first case pointing the problem out to them may be helpful. But those who are downright proud of making incoherent arguments simply do not have anything to offer to rational discourse. They aren't misunderstood geniuses surrounded by nagging little minds, they are charlatans.

Tuesday, December 24, 2013

Botany picture #129: The Victorian Christmas Bush

Prostanthera lasianthos (Lamiaceae), the beautiful 'Victorian Christmas Bush', Victoria, 2012. Several states of Australia have their so-called Christmas bushes, perennial plants that flower impressively around the time of Christmas. I hear the New South Walesian one is a Cunoniaceae, and the Western Australian one is hemiparasitic Nuytsia floribunda. The others I don't know yet. Being a great fan of the mint family Lamiaceae, this one will probably always be my favorite. The flowers surely do not have to hide behind even pretty orchids.

Happy holidays and a great new year!

Monday, December 23, 2013

In the case of collections, the humanities seem to have the edge

From colleagues in plant taxonomy I have repeatedly heard anecdotes and rumors indicating that some managers and politicians appear to have a remarkably myopic attitude towards natural history collections such as herbaria or insect collections and towards the research being done within them. Indeed at the conference in Sydney three weeks ago somebody who would know it mentioned that at least one unnamed Australian State Herbarium (!) was in real danger of being shut down.

Apparently there are actually people in governments or science administrations who think that once most of the specimen data from a herbarium are placed into a searchable database the herbarium can be closed down, and that once a flora of a given region has been published all taxonomists studying the local plants have become redundant. Those ideas leave me very puzzled.

Don't get me wrong. I am not at all puzzled by the prospect that people would cut or close down valuable institutions in general. That happens all the time and is, no matter how shortsighted, entirely unsurprising.

No, what puzzles me is why some people come up with these ideas for closing down taxonomic research and natural history collections when they would never in their wildest dreams suggest the same for other, comparable research and institutions outside of biology. Or would you consider it plausible to see the following suggestion from a politician?
Did you hear? All the works of art in our National Gallery have been entered into a searchable image database. That means we can save a lot of money by closing it down. Maybe some other museum elsewhere will take those superfluous paintings and statues?
Or perhaps this out of the mouth of a science manager?
Hey, I only just realized that a book exists that discusses the history of the Roman empire. Great! Now we can fire all historians and archaeologists dealing with that period of history because obviously they will never be needed again.
Of course not. When applied to any other type of museum or research, these suggestions would immediately be recognized as bizarre. Yet from what I hear, they are made in all seriousness for natural history collections, our priceless repositories of preserved specimens from which information can be extracted on biodiversity, evolutionary relationships, morphology, anatomy, DNA, and historical changes in phenology, species distributions, land use, vegetation cover, and weather patterns. Why would somebody consider this type of museum redundant who would laugh at the same suggestion were it made about, say, the National Coin and Stamp Collection? That is what I don't understand.

It is a common assumption that the natural sciences get all the money and that the humanities are not taken seriously. But in the case of collections and collections based research, the humanities actually appear to have more support. Weird.

Friday, December 20, 2013

How not to decrease the confusion about monophyly

Today this year's last issue of Australian Systematic Botany has come out, and the first paper in it is 'Defining and redefining monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of definitions' by Vanderlaan, Ebach, Williams and Wilkins.

It provides a historical overview of the various ways in which the term 'monophyletic' has been used over the years. A perhaps overly simplistic take is this:
  1. Haeckel introduced the term to describe a group with a common ancestor.
  2. Hennig found it important to distinguish two types of groups that have a common ancestor. Monopyletic ones include all descendants of that ancestor, paraphyletic ones only some of the descendants.
  3. Ashlock was unhappy with the redefinition of monophyletic and wanted to return to what he saw as the original definition by Haeckel. He thus used monophyletic to refer to both Hennig's monophyletic and paraphyletic and created the new term holophyletic for Hennig's monophyletic only. Because they have a vested interest in blurring the line between mono- and paraphyly, so-called Evolutionary Systematists prefer Ashlock's definitions.
Confused yet? In reality, as the authors of the present paper point out, it is even more complicated because there is some disagreement about whether a monophyletic group includes the descendants and everything back in time to the ancestor or only the descendants existing in one time-slice.

Vanderlaan et al now propose two new terms: diamonophyletic for a clade that is seen through time to include the ancestor and all, and synmonophyletic for a group of contemporaneous species that are more closely related to each other than to anything else.

Yes, definitions are important. But I still have a few issues with this paper. First, I do not have the foggiest idea why we really need to distinguish these cases. Assuming that evolution is true (and I do hope the four authors of the present paper agree), is there really any imaginable group where an extant species would be assigned to a diamonophyletic but not to a synmonophyletic group or vice versa? I cannot imagine how that would be possible.

And that means that a monophyletic group is a monophyletic group is a monophyletic group, as long as we ignore Ashlock's re-redefinition. In a phylogeny, being each others closest relatives means being descended from the same ancestor. So maybe I miss something, but I cannot imagine a situation in which I am talking about a plant group, let us say the genus Senecio, and somebody would ask back, 'do you mean including the ancestor or only the species that exist today?' That is just not a thing that happens.

The second issue here is that as recent as 2010 Podani had already suggested new terms for what (at first glance at least) appears to be precisely the same distinction: monophyly/paraphyly for phylogenies seen through time, i.e. including ancestors, and monoclady/paraclady for contemporaneous species only. The strange thing is, I vaguely remember one of the authors of today's paper (or his blog partner?) lambasting Podani over this for somewhat unclear reasons, and now he goes and does what sure looks like the same, only ignoring the previous contribution (yes, they don't even cite it).

And that is then another problem. We now have even more terms floating around than before because Vanderlaan et al have created new ones where Podani's would have been available. How that is meant to decrease the conceptual confusion instead of increasing it exponentially is not immediately clear.

Thursday, December 19, 2013

Botany picture #128: Actites megalocarpa

Actites megalocarpa (Asteraceae), Tasmania, 2013. Although it looks like an introduced weed in this country more dominated by paper daisies, this unassuming plant is a native. It is found on dunes along many of the Australian coasts, not only in Tasmania. Strange then that so many invasive weeds have been introduced to stabilize dunes when Australia already had an array of species for that purpose. I have read hints that Actites might merely be an unnecessary segregate of the sow thistle genus Sonchus, and with the spiny leaves there is surely some striking affinity here.

Wednesday, December 18, 2013

More editorial blindness please

Apart from phylogenetic systematics, another topic that I seem to be writing a lot about is scientific publishing, and there especially about peer review and the trade-offs between the system we have now and the potential problems of open access.

Just today I had a short conversation at work that made me think about what I would change if I were made the dictator of science publishing. Really there are two answers, one dealing with the commercial publishing versus open access issue and one dealing with the gate-keeping and peer review issue.

The first one is simple. If I could reorganize scientific publishing, I would run it all through non-profit public utilities. There would be no publication fees for authors and no access fees for the reader. Everything would be open access and financed directly from taxes. Note that scientific publishing is, with the exception of a few advertisements in the journals, also entirely financed from taxes now, only it happens indirectly, through tax-funded libraries and tax-funded scientists paying publication costs. So the only difference would be that we would stop wasting taxpayer money to provide profits for commercial publishers. (Sad, I know.) As an added bonus from the open access perspective, with no author fees there would also be no incentive to accept crappy papers.

That would still leave the second issue, which is essentially one of quality control. If everybody could get published for free, how do you know what research is sound? As mentioned before, I do not think much of post-publication review because it is not clear how an author would be motivated to correct a manuscript that has already been published. It would also make it harder for newcomers to get their work noticed. Under the current system, they can get a good manuscript into an influential journal and people will read it. In a system relying on post-publication review, anybody without a famous name is likely to get lost in the flood of useless papers using the same key words.

So I would, if I were asked to reorganize things, probably try to keep our current peer review practices pretty much in place: Have a few colleagues assess the manuscript and make an editorial decision whether it (a) is sound science and (b) has been submitted to the right journal or archive. It isn't perfect but it allows me to put more trust into a publication in a high ranking journal than, say, into what somebody wrote on their blog.

However, one thing that bugs me mightily about the procedures in my area of science is that while the authors of a manuscript generally do not know who the peer reviewers are, the peer reviewers and editors can see who the authors are. Some people even call for the abolition of anonymous peer review but that would make it harder for young researchers to critically evaluate the manuscripts of influential older colleagues, especially those having a say in funding decisions.

I would go exactly the other way: peer review should be double-blind. If the peer reviewers and the editors don't know who the authors are, many possible sources of bias disappear. They will not as easily be able to wave through a sub-par manuscript from a big name in the field. They will not be able to be negatively predisposed towards articles coming from specific countries or specific universities. They will not be able to see whether an author has got a female or foreign sounding name. And so on.

But is that not technically difficult? It should not be, anymore. Most journals these days have online submission systems for manuscripts. Of course the manuscript management software needs to know the contact details of the authors to communicate with them, but there is no reason why even the chief editor of a journal should know it before they have decided whether to accept the manuscript. The following set of rules would appear workable:
  • The manuscript management software hides the names and affiliations of the authors from the editor(s) in charge of deciding whether the manuscript ultimately gets accepted. It organizes all communication between editor(s), reviewers and authors anonymously.
  • To ensure that the manuscript is not sent out for review to the authors themselves or to their close collaborators, a different editor or editorial assistant, in other words somebody who does not decide on ultimate acceptance, chooses the peer reviewers.
  • Authors may not disclose their name on the manuscript. If they do so, it is rejected outright. They can be invited to resubmit the manuscript without their names on it, but then a different editor is assigned to it who has not yet seen their names.
None of that is all that hard to achieve; it would merely be a matter of changing journal policies.

Tuesday, December 17, 2013

Botany picture #127: Kunzea ambigua

Kunzea ambigua (Myrtaceae), Tasmania, 2013. Or at least so I hope; I am not exactly a Myrtaceae expert and find them much harder to determine than Proteaceae, for example.

Monday, December 16, 2013

So what's the deal with ResearchGate?

Some time ago I became a member of ResearchGate, a social network site that appears to want to be something like Facebook for scientists, but I still have very mixed feelings about it.

The site is actually quite complex. There is, obviously, your profile. You can add your list of publications ('contributions'), a link to your departmental website, information on previous and current projects and positions, and a list of sometimes rather ill-defined skills that you consider yourself to have.

Where Facebook has 'friends', ResearchGate has 'followers'. You can 'follow' other scientists, the idea presumably being that you get updates on what they are publishing or otherwise doing, but I have to say that I am notified of little of any use (see below). As could be expected, you might feel some implicit pressure to 'follow' somebody back if they 'follow' you even if what they do does not interest you. On Facebook, one can simply ignore a friend request and pretend to have been too distracted to notice it (lalala) but there appears to be no way of keeping somebody from following you here.

The last major aspect of ResearchGate is the Q&A section where people can ask questions, hoping to get helpful advice on some scientific problem or methodological challenge.

Thursday, December 12, 2013

Botany picture #126: Bedfordia salicina

Bedordia salicina (Asteraceae), Tasmania, 2013. The few species of Australian Bedfordia are shrubs and treelets and can be of a rather impressive size for members of the daisy family. This species and its mainland relative B. arborescens are known as blanket leaves because of the nicely soft and dense cover of hairs on the lower leaf sides. The genus is probably not really distinct from mostly New Zealand Brachyglottis; at the least from my experience they look pretty much like hairier Brachyglottis brunonis.

Wednesday, December 11, 2013

Botany picture #125: Rubus gunnianus

Rubus gunnianus (Rosaceae), Tasmania, 2013. If you saw this plant for the first time, would you guess that it is a member of the raspberry or blackberry genus Rubus? Probably not. Its congeners are generally large, prickly shrubs, and this is a herb, and a really tiny one at that. See it in fruit on this page if you are interested.

Monday, December 9, 2013

Is punctuated equilibrium an argument against phylogenetic systematics?

I have mentioned before on this blog that one of my interests is the continuing opposition of a minority of systematists against the requirement that formally accepted supraspecific taxa have to be monophyletic.

I was originally trained under the paradigm of phylogenetic systematics and considered the issue to be settled. Sometime around 2010/2011 I grew sufficiently puzzled about the flood of opposing articles being published especially in the botanical journal Taxon to wonder whether I had overlooked something. Maybe the opposition was right? Maybe I had overlooked something, and cladism was really incoherent or at least undesirable as a scientific practice?

So I systematically read through a large number of publications promoting the acceptance of paraphyletic taxa to examine their arguments - only to find very nearly all of them severely wanting, and the one that at least made some sense to be based on a number of assumptions that can certainly be questioned, such as that we can ever positively know that a fossil species is ancestral to extant species instead of a side branch of the tree of life close to the real ancestor.

What is more, except for that last one, which was advanced somewhat more convincingly by the late Richard Brummitt, the papers advocating the acceptance of paraphyletic taxa can mostly be assigned to one of three styles of argumentation:
  1. The Gish Gallop, i.e. the attempt to throw as many PRATTs out there as possible, clearly in the hope that the reader is too overwhelmed by their number to ask if any of them make sense and that a cladist will find it impossible to address all of them in the limited space of a rebuttal. Many of the aforementioned publications in Taxon fall into this category.
  2. Mere assertion, in other words short opinion pieces or letters that simply proclaim organisms should be grouped by overall similarity instead of relatedness and/or that nomenclatural stability is more important than scientific accuracy. They generally do not present any arguments whatsoever with the possible exception of an argumentum ad populum, presumably because the author considers their position to be too self-evident to stoop to actual reasoning.
  3. Utterly incoherent gibberish.
If you find that a position is consistently promoted as badly as this, the likelihood is great that there are no good arguments to be found because if there were they would probably have been used in the first twenty papers you read. This observation has, of course, sometimes been made in the context of the creationism manufacturoversy but it applies equally to the proponents of paraphyly.

Nonetheless, or perhaps precisely because of the wry amusement that can be derived from seeing catastrophic errors of reasoning presented either as deep insights or as common sense, I remain interested in papers that promote paraphyletic taxa. (And who knows, maybe I am wrong, maybe one of them will finally present a new argument that will sway me?)

Google Scholar appears to understand me better than I expected because it recently suggested I might want to read an opinion piece published in the journal Zootaxa: Why Drosophila is not Drosophila any more, why it will be worse and what can be done about it?, by one Jaroslav Flegr. And indeed this paper does not disappoint because it presents a line of argumentation that I have not come across before.

Sadly, that does not mean that it is any more convincing than the others. If you are here for the plant pictures, you may want to look away now because this is not going to be pretty. Also, it is going to be long. I apologize in advance.

Friday, December 6, 2013

Botany picture #124: Amperea xiphoclada

Surely one of the oddest plants we found in Tasmania, Amperea xiphoclada (Euphorbiaceae) has reduced its leaves and photosynthesizes with its flattened stems. We were very unsure what it was at first - in the above picture you can see it in full bloom, what would you have guessed it is? - but once more the aforementioned fabulous online key helped us out.

Thursday, December 5, 2013

Back from conference

I spent Tuesday and Wednesday at Systematics without Borders in Sydney, a joint conference of the Australasian Systematic Botany Society, Invertebrate Biodiversity & Conservation, and the Society of Australian Systematic Biologists. Although I sadly had to miss the first of its three days I enjoyed the meeting immensely. It is always good to see all the science that is being done in the field and to catch up with people.

A few highlights for me:

Phil Garnock-Jones received the ASBS' Nancy Burbidge medal for his work in plant systematics. From his prize lecture I learned many astonishing facts about plant sexuality, especially about that of mosses. When we talked a bit in one of the coffee breaks I also learned that he runs a very interesting botany blog, Theobrominated. Check it out!

Quite a few of the talks most relevant to my work were from New Zealand, actually, such as Rob Smissen presenting work on gene flow between different species of southern beeches and Ilse Breitwieser talking about the difficulties of circumscribing species in their native clade of Craspedia.

Having done my PhD on a Lamiaceae and being somewhat interested in pollination ecology, I also particularly enjoyed hearing about Trevor Wilson's work on the awesome Australian mint bushes (Prostanthera, Westringia and relatives). It turned out that quite a few generic limits will have to be redrawn because the stamen characters used for the traditional definition of groups have evolved several times in parallel. I guess I should post more botany pictures of these attractive plants in the future.

In addition there were many others, for example on biogeography and plant-insect interactions, too many to do them justice.

Just a pity they decided to have the conference in the first week of December, just when our summer students start...

Sunday, December 1, 2013

The new Red Centre Garden at the ANBG

Today we spent the afternoon in the Australian National Botanic Gardens. Among other things we also had a first chance to see the newly inaugurated Red Centre Garden.

This nicely designed section of the ANBG showcases the unique flora and landscape features of the arid centre of the Australian continent. There are several elements visible in this picture: red sand areas, a desert river (to drain the water from the slopes in the background), and rock outcrops. There is also an area of saltbush outside of the picture to the left.

Obviously the section is still young and will look much more natural in a few years when the ephemerals have had time to find their niches and the shrubs have grown a bit. But there are already some nice carpets of daisies and chenopods. In this case you can see the stunning 'Swan River daisy' Brachyscome iberidifolia in the foreground.

Beyond the Red Centre Garden, at the moment also appears to be a good time to see several impressive monocots in flower. Many of the grass trees are in full bloom, here Xanthorhoea glauca near the parking lots.

And this is the massive 'Gymea Lily' Doryanthes excelsa from the Sydney region. The budding stalk on the left shows that it will still continue to flower for some more time.

Finally, we were delighted to see a male Gang-gang Cockatoo closer than we ever have so far (the picture would have been better if there had been more light but this was in the understorey). They are very attractive and likeable birds that constitute the faunal emblem of the Australian Capital Territory, but unfortunately they are not exactly common.