Wednesday, July 31, 2013

The taxonomic impediment and DNA barcoding

Further to yesterday's conference, there was also a talk about DNA barcoding. First, what is that?

Some time ago I did a post on the taxonomic impediment, the problem that the number of taxonomists worldwide is too small (and, due to short-sighted funding policies, shrinking) to deal with the massive amount of biodiversity still to be described and classified, a situation that impedes downstream studies in ecology, evolutionary biology, conservation management etc relying on an accurate description and classification of life.

The idea behind DNA barcoding is to allow an easier determination of species by sequencing a few carefully chosen gene regions for as many species as possible and depositing that information in a searchable database. So if you found, for example, a plant in a rainforest plot and you needed to know what it is, you don't collect a specimen any more and send it to a botanist for determination, but instead you extract DNA, sequence the right gene regions, and then use the database to find out, say, that there is an 98.9% likelihood that the plant you are dealing with is Ruellia brevifolia.

Optimists could say that this is a good solution to take superfluous work off the shoulders of overtaxed taxonomists so that they can get on with describing new species. Cynics might think that the idea is ultimately to de-fund taxonomic research and to replace taxonomists with shiny DNA sequencers.

There are good reasons to believe that barcoding cannot work in principle, at least not at the species level. (Hint: the most important one starts with "i" and ends with "ncomplete lineage sorting".) But the talk I heard yesterday raised a different issue.

You see, the colleague who presented it had earlier been at a different conference dedicated specifically to barcoding, and one of the things she learned there was that the vast majority of barcode reference sequences in Genbank are what is called "level 0", meaning that nobody knows what species they are from because the people who produced them were unable to find a taxonomist who could confidently determine the specimen they got the DNA out of.

Is that not just awesome? Of course barcoding, even discounting other technical problems, can only work if there is a high quality, reliable reference database. Maybe at a minimum one should have waited with starving taxonomic expertise to death until such a high quality database was in place.

Tuesday, July 30, 2013

Bush Blitz Symposium 2013

All day today I was participating in the Bush Blitz Symposium 2013, a one day meeting here in Canberra at Old Parliament House.

What is Bush Blitz? In the words of the eponymous website:
Bush Blitz is Australia’s largest nature discovery project - a three-year multimillion dollar partnership to document the plants and animals in hundreds of properties across Australia’s National Reserve System. Since the program began in 2010 Bush Blitz has discovered about 600 new and undescribed species and has added thousands of species to what is already known - providing baseline scientific data that will help us protect our biodiversity for generations to come.
Perhaps most importantly, the initiative organizes targeted surveys to document all species of certain focus groups (one of them being vascular plants) in defined areas, often properties that are being transformed into nature reserves. In every case, botanists and zoologists with different specialties are brought together for one or two weeks to inventory the biodiversity of the place, with all the logistics provided by the Bush Blitz team. The scientists collect samples, process them in the base camp, determine them to species and ultimately compose species lists. The Bush Blitz team then writes a report on the survey summarizing the results.

I was lucky enough to participate in two Bush Blitz surveys, one in New South Wales and one in central Tasmania. While I did my part to document the local plant diversity, both field trips also allowed me to obtain samples for my research and to learn more about the Australian flora. One of the most interesting aspects of those surveys is the close interaction with biologists studying other groups of organisms.

In addition to the surveys, the initiative also provides grant money for taxonomic research resulting from the survey work. The symposium today presented results from the activities conducted so far and additional talks on topics relevant to the Bush Blitz project. Topics of the talks were extremely diverse, including teaching and outreach, collaboration with the traditional custodians of the land, hard scientific analyses as well examples of species discovered as new to science, and conservation planning. (I presented a talk on collecting biases - field botanists collect mostly close to where they are and along roads, and they under-sample spiny, very small, ugly and non-native plants. Bush Blitz addresses all these issues by targeting neglected areas and by inventorying all species of a group, not only the conspicuous ones.) The talks were very interesting and the speakers were really enthusiastic about biodiversity. All in all a great meeting.

In summary, the Bush Blitz is a fantastic and globally unique institution; if you want to learn more, you could do worse than reading through their website.

Monday, July 29, 2013

Moral philosophy and personal maturity

A few more remarks on morality. Often when people disagree they ask themselves whether the other side is stupid or evil (or, if you want to be more charitable, uninformed or dishonest). But that clearly does not exhaust the possibilities. Many controversies, especially in economics and politics, simply do not allow for a rational resolution because they are questions of values instead of questions of fact. In those cases, the two sides might merely have different economic interests and/or different value systems, and the solution cannot be a clear decision on who is right but only a compromise.

Another option might be insanity of one side in a controversy although that will not be a problem so terribly often, one would hope. Finally, one possibility that I think is under-appreciated is different levels of maturity. For example, it is a sign of immaturity to prefer immediate gratification over greater deferred gains, so a conflict over two possible courses of action could be simply based on one person being more mature than the other.

Although I do believe that there is no objectively, universally deducible system of morals, I also think that we humans share many of the same instincts and interests and could potentially agree on more ethical questions than we generally manage to do, and that the problem has its roots at least partly in different levels of maturity. It seems fairly clear that there are different stages of moral development that a person can go through as they mature:
  1. They are completely self-interested and lack empathy. Rules are only followed because of the fear of some form of punishment (ranging from the mild disapproval of authority figures to severer penalties). It is perhaps an oversimplification to assign this state to babies and very young toddlers but not by much. It is certainly also the stage at which most house cats appear to be stuck: once you turn your back, they do what they see fit.
  2. They know that there are rules and that one should follow the rules, and that is it. In hindsight it was fairly clear when my daughter had reached that stage of her personal development.
  3. They understand that rules exist for a reason, and that what really counts is whether the intention behind the rules is being achieved. Some rules may be in conflict with each other, and knowing what they were written to achieve allows you to figure out which of them to break in such a case. In fact some rules are silly and can be ignored while others are crucial. A clear example would be rules whose real purpose is to minimize harm to people; if you can minimize that harm better by exceptionally breaking one of the rules, so be it.
  4. Finally, they start to question how the intention behind the rules can actually be justified. Who says that achieving accident-free traffic flow, minimizing harm or suchlike are actually the things we should care about? Can we justify them from first principles? Some people might fear the collapse into nihilism here but really this stage of moral development is both necessary and liberating. Leave nothing unexamined. (And yes, ultimately we make our own rules, but that is how it has to be because they are for us and about us and by us. Pretending that the rules came from the gods, for example, is merely a self-serving lie because they were really created by humans. If we all acknowledge that we have a better basis to improve them.)
The point is now that different people have gotten stuck on different of these developmental stages. A small minority even of adults never makes it past the first, and they are often called psychopaths.

Many more are stuck at the second stage, the one of blindly following rules. This is behaviour often associated with bureaucrats although that is perhaps unfair as administrations are built precisely to foster it. More importantly, it is obviously what we might generously call the moral philosophy of religious fundamentalists: X is bad because God says so, look it's here in my holy book. Ah, but X does not actually hurt anybody, so who cares? Doesn't matter, God says X is bad, that settles it. The same is true for many very conservative people who value stability over all and fear that not following the traditional mores of society will result in whole-scale societal collapse (instead of merely a similarly stable and healthy society with different mores).

It is because large numbers of people are stuck at stage 2 in their moral development and many others have advanced to stage 3 that moral controversies (the "culture wars" in American terminology) are so intractable. If one side thinks that rules are rules are rules, and that is it, and the other side thinks that rules are only tools that need to be changed if they don't achieve some more transcendental goal, then it is hard to ever reach an agreement.

Friday, July 26, 2013

Botany picture #89: Hydrocotyle laxiflora

Hydrocotyle laxiflora (Apiaceae), Australian Capital Territory, 2010. In central Europe, nearly all members of the carrot family Apiaceae look very similar: medium sized herbs with double umbels of small usually white or rarely yellow flowers and deeply divided leaves. Easy to recognize as a family but hard to determine to species or even only genus, especially for a beginner and especially if you have a specimen without fruits. Towards the Mediterranean, it gets morphologically more diverse with increasing representation of interesting genera such as Bupleurum or Eryngium. Here in Australia, there are also quite a few unique looking Apiaceae, and it is sometimes even harder to figure out that you are dealing with an Apiaceae than to determine the species once you have done so. Admittedly the genus Hydrocotyle is fairly easily recognizable as a member of its family but it is still interesting to somebody who is used to the Apiaceae of northern Germany. It is well represented in the flora with both native and introduced species.

Thursday, July 25, 2013

Objective versus arbitrary morality, and aliens

Jerry Coyne recently wrote a post on his website expressing his conviction that there is no objectively deducible and universally valid morality or ethics comparable with the objectivity and universality that one would find in empirical science, abstract logic or mathematics.

I would argue the same. There simply does not appear to be a way to bridge the famous is-ought gap. Claims such as the one that morality is ultimately about the well-being of sentient creatures are really just begging the question. Why should (mostly) human welfare be the yardstick of moral decisions? Ultimately only because we humans say so. And really, that is okay - who else except humans should decide what human morality has to look like? But let us not pretend that such a decision is universally and rationally justifiable.

And let's not get started on other proposed solutions such as divine command theory, which collapsed under the weight of its intellectual incoherence more than two thousand years ago. Even if there were a cosmic tyrant, why should it be moral to follow their arbitrary orders?

No, a more interesting set of questions than whether we can rationally deduce a single set of objectively and universally true norms would be where our actual norms in fact do come from, and how much of them is contingent versus a necessary development. As we will see, the second of these questions is somewhat related to that of arbitrary versus objective morals, only  without the claim of a rational derivation.

Wednesday, July 24, 2013

Botany picture #88: Wahlenbergia graniticola

Wahlenbergia graniticola (Campanulaceae), Australian Capital Territory, 2010. Well, I am not entirely sure I got the species right, I find Wahlenbergias rather hard to determine to species. This genus of bellflowers is nearly cosmopolitan but could be seen as the southern hemisphere counterpart to northern hemisphere Campanula. The major difference between the two is apparently the opening of the capsule, but apart from that they are fairly similar. The state flower of the ACT is also a Wahlenbergia but not this particular species.

Tuesday, July 23, 2013

An analogy that might help to clarify some issues with cladism

An extended discussion I am currently having with a colleague and tangentially related observations on a discussion over at Larry Moran's Sandwalk blog have made it clearer to me why some people reject phylogenetic systematics, or cladism. Because there are events of lateral gene transfer, introgression, endosymbiosis, chloroplast capture and suchlike, all processes that transfer genetic information between different species or lineages, they see life as having a fundamentally net-like or tokogenetic instead of a tree-like or phylogenetic structure. They consequently reject phylogenetic systematics because you cannot have clades in a non-phylogenetic structure.

That conclusion follows from the premises, but unfortunately one of the premises of the argument is seriously flawed, and it is the premise that life does not show a phylogenetic structure. There are different levels at which evolutionary processes take place, and to really understand what is going on we need to ask ourselves two questions: What are the items that need to form a phylogenetic structure? And what do I see if I zoom in or out while looking at evolutionary history?

As for the fist of these, let us be clear that there are, at a minimum, the following items to be considered: Individual gene copies evolving within organisms and forming gene families which may be mostly tree-like but also potentially net-like through recombination; mitochondria and chloroplasts, both of which are endosymbiontic bacteria inside of Eukaryote cells, and which fairly clearly evolve in a tree-like relationship; individual organisms which stand in a net-like relationships with conspecific organisms if they are sexually reproducing and in a tree-like relationship if they are asexually reproducing; and finally lineages or biological species of organisms.

The claim here is now that evolutionary relationships of species are net-like because the relationships of individual organisms are often net-like. That, however, would mean succumbing to the fallacy of composition, assuming that what is true of the parts must also be true of the whole. A more familiar example would be to claim that an airplane cannot possibly fly because any single part it is constructed from cannot fly, and that claim is obviously wrong. Similarly, biological species can be in a tree-like relationship with each other although there are net-like relationships of individuals within the species.

However, the problems people see with cladism are not all as easily addressed as this. As pointed out in the first paragraph, there are also processes that transfer genes between species. Does that turn everything into a big net, making cladism impossible because we do not have a phylogenetic tree any more?

And this is where I would like to introduce an analogy that might help to visualize a few concepts and clarify why that argument does not really show all that it is supposed to show. That analogy is a river system. Rivers are familiar and they also have generally tree-shaped structure, with the major difference that the directionality is exactly opposite: where life diversifies into more and more branches, a river system starts out as many small branches that ultimately unite into one river and flow into the ocean. Still, the similarities are instructive.

Monday, July 22, 2013

Botany picture #87: Orobanche minor

Orobanche minor (Orobanchaceae), Australian Capital Territory, 2010. Another introduced Orobanchaceae, this is species if holoparasitic, meaning that in contrast to the Parentucellia featured recently on this blog it does not even do its own photosynthesis any more but obtains all it needs from other plants.

Friday, July 19, 2013

Two news items: scientific literacy and stolen art

So apparently there is this thing called the report on Science Literacy in Australia, and the latest results are making the rounds. Lots of wailing and gnashing of teeth is involved because too many people didn't know the answers to all the questions they were asked. Having looked at the questions, I find them to be a fairly odd mixture, and accordingly I would judge the results.

The first (how long does it take for the earth to go around the sun?) is not really a question of science literacy but more one of not being a complete and utter dimbulb literacy. This is not science but everyday orientation knowledge, on par with "what are clouds made of" or "into what bodily orifice goes the food". That more than 40% of the people asked got that one wrong is indeed cause for concern, to put it mildly. Really any percentage above perhaps 2% is frankly unacceptable.

That more than a quarter (and even more than a fifth of university graduates!) apparently believes that dinosaurs and human existed contemporaneously is a bummer but already less surprising. Although as a biologist I would wish for everybody to have a good overview of natural history this is hardly as crucial a piece of orientation knowledge as understanding the basic dynamics of the solar system.

9% of those asked do not believe in evolution; that is actually less than I would have feared. Another 10% believe that it is a thing of the past but does not happen any more, another mistake that I would have expected to be considerably more common. So this surprises me pleasantly.

Utterly bizarre is, on the other hand, the question about what percentage of the water on the planet is freshwater. It appears as if the people surveyed were asked to give the percentage, and now the media report "only 9% gave the right answer" (which is 3% of the water). That is just idiotic. The right answer is "very little, who cares about the exact value", and thus quite sensibly a quarter of those surveyed answered with "not sure". Surely getting the precise number wrong cannot be compared to getting questions with simple yes or no answers in the same survey wrong. If we count everybody who answered anything above 10% as significantly overestimating freshwater reserves we find that only a third of the people surveyed did so. Not that terribly dramatic, is it?

Really what I would find more important is for people to get a feeling for statistics, burdens of evidence and just plain plausibility. It seems more useful to teach somebody about the big picture (which would of course include dinosaurs living before the evolution of humans) and critical thinking than to have them remember dates and values like that freshwater one.

In entirely unrelated news from Europe, several irreplaceable and valuable paintings that were stolen from an art museum a few months ago appear to have resurfaced as a heap of ash in the oven of the suspected burglar's mother. While the world of art lovers is understandably shocked, I am pondering the following questions:

Why are artworks like these worth tens of millions of dollars? Now don't get me wrong, I am not saying they are worthless. Of course they are rightly considered to be priceless historical artifacts. But that means "priceless", not "having a price tag of millions of dollars". Why anybody would pay millions to own one of them is what is beyond me; if there was any significant amount of sanity in the world of art lovers their actual monetary value would be something to the tune of $120 or so apiece. Nobody should wish to own them privately anyway because of the responsibility that would come with it. Artifacts like these should belong to the public, and they should never be auctioned. As an added bonus, if everybody were that sensible about them then there would be no incentive to steal them.

Why do art museums hosting items that are (bizarrely) valued at millions of dollars so rarely seem to have even half way decent security? Why do they appear to have enough money to buy a painting for $10M but not enough to pay for a few guards?

Now I know that the kind of person who tries to earn their bread with burglaries and theft is not actually Nobel prize material, but seriously, what are art thieves thinking? "Hey, let's steal this painting that everybody who might ever be interested in paying to own it will immediately recognize as recently stolen! We'll be rich!" Calling a thought process like that idiotic would be an insult to idiots everywhere, and yet this happens again and again and again.

Finally, once those criminal masterminds realize that there is no way they will ever even get a hundred bucks for the stolen artwork, why do they so regularly destroy it? Why not at least leave it somewhere to be found? Admittedly, I personally consider the extinction of a single species of plants or animals that nobody has ever heard of to be a greater tragedy than the potential destruction of all paintings humanity has every produced. Sorry, but ultimately they are only things and we can paint new ones while the extinction of a species of living organisms is forever. Yet I still find it hard to fathom the mind of a person who would pointlessly destroy items that others find valuable enough to exhibit in a museum and write books about. Apparently there are simply people on this planet who are civilized and others for whom the description "boorish unthinking vandal who should never be allowed to step outside without supervision" would be flattering.

Thursday, July 18, 2013

*BEAST, species trees in general, and Bayesian versus parsimony

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.


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.


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.

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:
  1. The cladist one, according to which all formally named supraspecific taxa should be monophyletic.
  2. 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).
  3. 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."
Readers of this blog may well take the third of these positions and wonder whether I am not a bit weird for investing so much energy into promoting the first.

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.

Wednesday, July 10, 2013

Botany picture #83: Primula florindae

Primula florindae (Primulaceae), Botanic Garden of Zürich, Switzerland, 2009. The botanic garden has a great research collection of this attractive genus, thanks to the work of the professor who hired me as a postdoc there. Other groups that were well-represented were the orchid genus Ophrys and the Restionaceae family of grass-like monocots, reflecting the research interests of two other professors.

Monday, July 8, 2013

Botany picture #82: Scutellaria orientalis

Scutellaria orientalis (Lamiaceae), Botanic Garden of Halle, Germany, 2008. An Asian species of this large, distinctive and cosmopolitan genus. Unfortunately, I hear that the city of Halle and also its botanical institute have suffered significantly from the recent floods in central Europe.

Friday, July 5, 2013

Crumbling foundations

In biodiversity science there is something known as the taxonomic impediment. It describes the situation of lack of taxonomic expertise, resulting from decreasing funding of taxonomic positions and research, impeding downstream biodiversity studies, e.g. those of a phylogenetic, ecological or conservationist nature.

The underlying problem is clear enough and can be observed in staffing decisions of universities and the policy of funding bodies worldwide. While there is a lot of lip service to the idea that taxonomy is critical to understanding the diversity of life, in daily practice taxonomists have to compete for jobs and funding against colleagues who can publish in higher impact journals and/or who conduct research that is much more easily sold as innovative (say, genomics).

Part of the problem is the same as faced by all scientists doing fundamental, basic, non-applied research, but the problem is exacerbated by the fact that taxonomic papers are much less cited than they are used:
  1. First, somebody who consults a state flora or a monograph to identify the samples used in their phylogenetic study or vegetation analysis is generally not required to cite those works.
  2. Even if they did so, floras and monograph series are not included in impact factor statistics because they have too few issues per year (or are one-off books). Impact factors and related stats such as the h index favor areas of research that publish lots of small papers instead of few large ones.
  3. Every time somebody uses a plant name (such as Xerochrysum collierianum A.M.Buchanan) in, say, a phylogenetic or ecological study, they are essentially citing a scientific hypothesis advanced by a taxonomist called A.M. Buchanan in a publication in 2004 when the species was described. However, in contrast to a reference to the publication of some analysis software used in the study, that "A.M. Buchanan" after the plant name is not formally counted as a citation, and thus the use of the hypothesis is not scored anywhere.
Indeed the entire system looks very much as one would expect it to look if it were deliberately designed to minimize the perceived importance of taxonomic work.

It is thus no surprise that scientists working on plant morphology, identification and taxonomy are getting rarer and rarer, and I assume the same would be true in zoology. Why hire a new taxonomist, or replace the last one your university had and who has just retired, when the same money could be used to hire a sixth or tenth "omics" researcher? That is where things are happening these days!

Well, perhaps it is understandable that morphological or taxonomic research is not seen as cutting-edge, but what I don't get is why it is considered acceptable to not even have somebody in the institution who can teach it. Sure, you can have 30 experimental ecologists, molecular phylogeneticists and conservation genomics people (genomicists? Is that a word?) but hey, at some point maybe the students need to be taught how to use an identification key? Maybe they need to learn how figure out what species they have on their experimental native grassland plot in their honours project? Maybe one of them goes on to start a career assessing the conservation value of an area that is considered for inclusion in a national park, or that is scheduled to be turned into an open cut mine?

Of course you can do omics and ecology if you are only ever working on one species, but if you are interested in landscape ecology, phylogenetics, conservation planning or whatnot, you need to understand plant identification, and for that you need to understand plant morphology and plant taxonomy (swap "plant" for "animal" or "fungal" if that is what interests you more). Therefore it would appear reasonable that every university that has a biology program at all should also have at least one part-time lecturer who teaches those things.

But perhaps I approach the issue from the wrong direction. If the taxonomic impediment becomes too big, it will disappear all by itself!

Think about it: when there is nobody left who knows how to properly identify or recognize plant species, then there will be nobody to criticize the ecologist for scoring two different species on their plot as one. There will be nobody to point out that the molecular phylogeneticist has misinterpreted their results because half the herbarium specimens they extracted their DNA from were misidentified. There will be nobody to realize that the open cut mine was once the last population worldwide of this particular species of endangered plant. And everybody will be unconcerned; ignorance is bliss. [/cynicism]

What I wonder though is whether other areas of science and scholarship are as short-sighted as biology. Do contemporary chemistry departments also say, "Ah, we don't need anybody to teach the students about the periodic table or about titration - that is sooo 20th century. Let's hire five more nanotechnology researchers instead!" Or would contemporary geologists find the following convincing? "Who cares whether our graduates know about sedimentation and metamorphism, or know how to recognize different types of rock, let's just limit ourselves to training them in the use of instruments for seismic, gravitic and magnetic surveys, that's where the money is at!"

Perhaps that is also how it works outside of biology, but I would be surprised to hear that.

Thursday, July 4, 2013

Slowing down a bit

The next few weeks will be rather crowded: five weeks of teaching, a small conference and a phylogenomics workshop are all coming up, and seminars and committee meetings are looming. Things will become mellower the last week of August, but until then I will be hard pressed to write a lot of long blog posts. Expect the continued regular posting of botany pictures and a few shorter posts but nothing profound.

And because it is my daughter's birthday today, here's a nice picture from her namesake plant genus:

Presumably Viola hederacea (Violaceae), New South Wales, 2012.

Wednesday, July 3, 2013

Botany picture #81: Ribes punctatum

Ribes punctatum (Glossulariaceae), Argentina, 2009. The genus Ribes is of course best known for the cultivated currants and gooseberries but it comprises more than a hundred species. Quite a few of them occur in southern South America, where this picture was taken during a conference trip.

Tuesday, July 2, 2013

My own take of the species problem

This is the final post in my short series on species concepts. After discussing a selection of synchronous species concepts, with particular focus on the biological one and the Genotypic Cluster Species Concept, and a rather short summary of asynchronous concepts, I will now sketch out my own current thinking on species. Note again that I am not a specialist on speciation or suchlike, and that my conclusions are obviously tentative. But well, as a systematist and taxonomist I cannot avoid dealing with the issue every day, and that includes sometimes problematic controversies even with collaborators, so I have to have an opinion.

Monday, July 1, 2013

Botany picture #80: Fothergilla major

Fothergilla major (Hamamelidaceae), Botanic Garden of Zürich, 2009. I know little about Hamalelids except that they are woody, tend to flower very early in the year and can be very pretty, such as this one.