Wednesday, February 27, 2013

Botany picture #41: foam

On Sunday we were caught in a heavy downpour while walking through one of the small nature parks dotting Canberra. I noticed that the rain running down the bark of a eucalyptus carried a lot of foam - this just a small detail, it was the same all around the base of the tree. Yesterday I asked a few colleagues, one of them a eucalyptus expert, and while they agreed that the phenomenon was well known and occurred regularly with many different species of the genus none of them had any idea why. Perhaps it is because of some waxy substance that is being washed out of the bark?

Tuesday, February 26, 2013

Cycling in Canberra

Unless exceptional circumstances apply, I cycle to work and back every day. I am still unsure whether this increases or decreases my life expectancy. On the one hand there is the beneficial effect of the exercise I get, on the other hand there are the Canberra car drivers.

There are some, usually young couples or groups of friends, who sneak up to you with their car and then the person in the passenger seat loudly shouts at you, apparently hoping to startle you so that you amusingly crash from your bike and get run over by the car behind them. There are some, from my experience usually middle aged women, who scream abuse at you because they have to stop for you at a traffic light when you cross their road. There are friendly looking grandmothers standing in a traffic jam who see you coming and deliberately roll another half a meter forward to block your way across the pedestrian crossing. There are some who throw beer bottles or cups at cyclists when overtaking them (luckily, only a paper cup full of coke for me so far).

Although in contrast to all the rest I cannot vouch for the stories in this specific sentence personally, colleagues also told me of bus drivers knocking cyclists off the road and then blithely driving on despite passengers making them aware of the accident, of bus drivers overtaking a cyclist and then immediately turning left, and of judges deciding that the resulting injuries were the cyclist's own fault because... well yes, that is where it gets puzzling. Finally, there are pedestrians who try to bully you off a wide shared pedestrian/cyclist sidewalk next to a fast and dangerous road, and there are car drivers on extremely wide roads screaming abuse at you for being on the road instead of the sidewalk. From all that, I can only assume that the average Canberra car driver does not consider cyclists to be legitimate traffic participants - they should quite simply not exist. Certainly I have never seen the same level of abuse directed at cyclists in any city in Central or Western Europe.

It is probably also in this context that a peculiar piece of local terminology has to be seen. You see, here in Australia they do not call a bicycle a bicycle (as I learned it at school) but a "push-bike". At first I wondered where the pushing comes in because one generally, what was it?, "rides" a bicycle. But upon further consideration it is well possible that the term describes what Canberra car drivers would prefer cyclists to do: push the bike along the sidewalk and stay off the road. Of course, if they got their wish and everybody stopped cycling, the most likely consequence would be even larger traffic jams than we already have.

Admittedly, the lack of respect is mutual: Similar to how so many Canberra car drivers appear to believe that cyclists do not have a right to even exist, I do not consider most of the car drivers here to have a legitimate reason to be car drivers. Each day when I am cycling to work, masses of cars stream from places like Belconnen, Watson or Gungahlin into the inner city, forming tremendous traffic jams and stinking everything up. The first two are within cycling distance (as my own example shows) and the last has an excellent express bus connection to the city. I will cut some slack for those who car-pool, have children to drop off elsewhere or are disabled, but the vast majority of the cars I see appear to contain only one apparently healthy person.

Since about the end of the 19th century it is clear that the greenhouse effect is at a minimum a possibility to be taken into consideration, and everybody who is not hopelessly dedicated to wishful thinking will have to realize that the amount of oil humanity can burn is sharply limited. What is more, cars and petrol are expensive while my current bicycle cost $300. So why are so many people driving when they don't have to? And a good number of them probably spend a lot of time and money on a gym membership that they would simply not need if they cycled to work every day.

To end on a lighter note, this morning I saw something that was puzzling in a different way. For some time a young lady, presumably an undergrad judging from her age and the fact that she was heading towards the ANU, was cycling a bit ahead of me, and she was constantly taking off and putting on her helmet. Street ahead, on it goes, stretch of park ahead, back to her left hand. I assume she does not like wearing it but fears being seen by the police when crossing a street in between following the bicycle path across the parks (helmets are mandatory for cyclists in this country), but seriously, is this procedure not considerably more tiresome than just keeping it on your head? People can be odd sometimes.

Monday, February 25, 2013

Botany picture #40: Dipodium variegatum

Something Australian for a change. As mentioned sometime when I started the blog, Australian plants will not feature that strongly among the botany picture because while I obviously take many photographs of them they are mostly for work. On the other hand, I have tons of plant pictures from Europe and South America that I would like to present here...

Still, there are a few nice plant pictures that I take in Australia without collecting a voucher and without using them for work, and this is one of them. Dipodium variegatum (Orchidaceae), New South Wales, 2011. One of the colleagues at my institute is an orchid expert and he is kind enough to sometimes put names onto my pictures when I am unsure.

Sunday, February 24, 2013

Science and the supernatural

Before I can have an opinion on whether science can address claims about the supernatural, I have to have a definition of supernatural. Unfortunately, it is not really clear to me what it is supposed to be. People seem to have very different ideas of what they mean with it. Or perhaps the definition is mutable, to be changed however it currently suits those who want to argue that science should keep its muddy paws off their cherished beliefs? Let's try to nail it down by looking at possible definitions on offer, see what sense each of them makes, and whether the definition really implies an inability of science to address related claims.

Saturday, February 23, 2013

Botany picture #39: Clematis flammula

Fruiting Clematis flammula (Ranunculaceae), France, 2008. I assume the name is derived from the reddish fruits because the flowers are white. In fact in flower it is a bit similar to better known Clematis vitalba except for being smaller and having more slender leaflets.

Thursday, February 21, 2013

Botany picture #38: Carduus nutans

Carduus nutans (Asteraceae, Carduoideae) in Germany, 2005. It appears to have a bumblebee for lunch. Note the nice "arachnoid" hairs on the phyllaries.

There will probably be no large posts until after the weekend because I am doing a lot of manuscript writing at the moment.

Wednesday, February 20, 2013

Botany picture #37: Pyrola asarifolia

Pyrola asarifolia (Ericaceae), Canada, 2012. When comparing it with the previous botany picture, it is not immediately clear to me why it is called the Asarum-leafed Pyrola. Apparently the flowers are pink, but this plant may already be past flowering and developing fruits.

Tuesday, February 19, 2013

What is science?

One of the discussions that regularly fires up again in one part of the blogosphere that I am reading is about the demarcation problem. There are several angles to the issue. One is simply how to differentiate science from non-science, which may be legitimate rational inquiry that simply is not science at one end and pseudo-science at the other. Another angle is concerned with the concept of "scientism", the charge that there are many scientists who think that science is the only way that knowledge can be generated and that all the humanities are basically worthless. Thus defined and directed at the majority of scientists, scientism is probably a strawman, but not entirely; I have surely come across people who think that way. The final angle worth mentioning here is that of whether science can address supernatural claims, in particular whether science can take a stance on topics such as the existence of gods or souls.

It should be obvious that one's stance on the whole complex of issues depends at least in part on one's definition of the term "science", and consequently I want to develop my thoughts on that matter, always aware that I am certainly not a philosopher of science. (I am, however, a professional scientist and thus perhaps not completely unqualified to write about science.) Note that defining the term science is not entirely the same question as the demarcation problem as such: first you need a useful definition of the concept, then you can apply it to various things to see whether they do, under that definition, fall under the concept or not.

Monday, February 18, 2013

Botany picture #36: Asarum europaeum

Asarum europaeum (Aristolochiaceae), Germany, 2008. A small creeping plant on the forest floor, with small dull brown flowers hidden between the leaves. As in the case of the orchid featured in the previous botany picture, fungus gnats are tricked into pollinating the flowers.

Sunday, February 17, 2013

Some interesting links

A blogger called Armondikov at RationalWiki takes apart the wishful thinking of Singularitarians about Nanotechnology. Complete agreement - both with the real promises of Nanotech properly understood and their criticism of Singularitarians who perennially fail to realize that we have nanobots already, and we have had them for the last three billion plus years. (They are called enzymes.) The idea that you can build something like a robot at the micrometer scale and still expect it to work as it would on the macro scale is ludicrous. There are simply constraints on and tradeoffs with "machines" that small that are very counter-intuitive to somebody used to thinking in terms of centimeters and more. The comment stream under the post is a bit depressing though, as they often are.

Just like probably everybody else, I sometimes have these "if only people would" thoughts. You know, the hope that there is some simple solution that would, if adopted, make a big positive difference in many fields at the same time. Others may think "if only people were nicer to each other", but in my case it is generally something on the lines of "if only people would receive a better education in science and formal logic". Another one that I would immediately second is discussed by blogger Mathbabe: If only people would consider it a sign of honesty when somebody admits that they don't know something, as opposed to a sign of incompetence. As a third option I would add: if only it would be considered courageous and reasonable when politicians publicly change their mind in the face of new evidence, as opposed to flip-flopping and a sign of weakness.

Finally, a very funny exchange between creationists and a real scientist.

Why are botanists more opposed to cladism than zoologists?

One interesting thing a colleague once said when we were discussing continuing opposition to phylogenetic systematics was that that opposition is stronger among botanists than among zoologists - if there is any left in zoology at all. Now obviously I have much more contact with other botanists on a daily basis than with zoologists, but that observation rings true. But why would it be so?

One might suggest that Willi Hennig himself having been a zoologist could have something to do with it, but that seems a bit spurious. I favor a different explanation, and it has to do with the way ranks are treated in the two fields.

Friday, February 15, 2013

Botany picture #35: Listera cordata

Look, another orchid! Listera cordata (Orchidaceae), 2004. This fairly tiny and easily overlooked species, here growing in Sphagnum cushions in a wet mountain forest in the European Alps, is distributed around the northern hemisphere. According to a book I consulted, the brownish little flowers are pollinated by fungus gnats and small beetles but seed set is low.

Thursday, February 14, 2013

Botany picture #34: Trientalis europaea

Trientalis europaea (Primulaceae) from Germany, 2012. This often overlooked, delicate plant is found on acidic soils especially in moist forests across much of the northern hemisphere. In Germany it is known as Siebenstern (seven-star) because of its unusual number of petals.

Wednesday, February 13, 2013

How to give a good scientific talk

Recently I got drawn into a short discussion on how best to give scientific talks. As a reaction to that discussion, the following is in part a note to myself and in part a piece of advice in case an early career scientist happens on this blog via a search engine and finds this useful. As always, while the following is based on my own experience as a career scientist speaking at various conferences from ca. 25 to more than 2,000 participants, please note that I am not a professional instructor for public speaking courses. In addition, the culture of speaking will vary from one area of research to the next, and what is appropriate in mine may or may not be appropriate in yours.

What we are talking about here are the typical self-submitted, non-keynote talks at scientific conferences. They generally last 12 min plus 3 min for questions or 15 min plus 5 min for questions, and the resources at your disposal are generally PowerPoint slides projected at the wall behind you, a laser pointer and a microphone. You may have a remote to advance the slides or you stand behind a lectern with a keyboard and press the arrow keys to change slides. So here is my advice.

Tuesday, February 12, 2013

Botany picture #33: Prunella hyssopifolia

Finally, the last species of the genus, Prunella hyssopifolia (Lamiaceae). Its area of distribution is limited to SW France and NE Spain, and I had been trying to get my hands on seeds for several years before I finally found it fruiting in southern France. Of course, a year later I donated everything to the Botanic Garden of Zurich, where this photograph was taken, in preparation for my move to Australia.

The most interesting thing about trying to find this plant was that several German botanic gardens thought they had it in their collection, but the plants invariably turned out to be another species, usually simply P. grandiflora. I hope that this accession now makes its way around so that the real P. hyssopifolia can be found in more gardens in the future. It is similar to both P. grandiflora and P. vulgaris but differs from the former in its smaller flowers, from the latter in the absence of stolons, and from both in its narrow, sessile leaves.

Monday, February 11, 2013

Ranunculus, part 7: Information content of classifications

This is the final part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous installments here: part 1, part 2, part 3, part 4, part 5, part 6.

The internal logic of the paper so far suggested that the major arguments for paraphyletic taxa would be (1) the existence of polyploidy, reticulate evolution and anagesis, as mentioned in the introduction, (2) the lack of five morphological synapomorphies to circumscribe monophyletic taxa, as mentioned in the materials and methods section (because only four clearly aren't enough!), and (3) the paraphyly of phenetic clusters, as mentioned in an earlier part of the discussion section. As seen previously, the first justification is pretty fuzzy to start with, all issues it raises except reticulate evolution are entirely irrelevant, and rampant reticulate evolution would result in the absence of any phylogenetic structure so that there could be no paraphyletic taxa either. The second is arbitrary and unscientific, and the third is an example of circular reasoning.

However, in the last paragraphs of the paper's discussion, under the heading "conclusion for classification", the authors advance two more arguments for paraphyletic taxa that are in part clarifications of what they had only hinted at earlier in the paper. Instead of going through the text sentence by sentence, I will try to synthesize the arguments very concisely and then point out what is problematic about them.

Saturday, February 9, 2013

Botany picture #32: Prunella 'Summer Daze'

The interesting thing about the small genus Prunella (Lamiaceae) is that all the species can be crossed, and their crosses are even fairly fertile. This cultivar, here seen on our balcony when we were in Switzerland in 2009 and before I had to give all my plants away (sigh), is the result of a plant breeder's work on a hybrid swarm. As can be seem from the dissected leaves, genes from P. laciniata feature strongly in the mixture. The cultivar is very popular because of its robustness and the profusion of pink flowers it produces.

An obvious question arising from the interfertility of the various species is how they are able to maintain their identity and distinctness. A possible explanation can be found in this interesting study published in 2000. The authors examined neighboring populations of P. vulgaris and P. grandifolia and found that hybrids are maladapted to the two types of habitats inhabited by the two parental species; they can't grab either of the two available chairs and are left standing, so to say. That means that while they don't show any prezygotic isolation, the two species may be ecologically isolated through selection against hybrid plants.

Friday, February 8, 2013

How to acknowledge your peer reviewers

I have recently received reviewers' comments on a manuscript and am now revising it for resubmission. In my field the peer reviewers are usually mentioned in the acknowledgement section of a paper to thank them for their efforts, anonymous or not. Or so I like to think...

In this case, I looked at the relevant section and wondered how to phrase the thanks; don't want to use the same words over and over again. And so I decided to look through the articles in individual issues of three very different journals, chosen simply for residing in my office at the right time, to get some inspiration.

Note that I have not counted thanks for feedback on the manuscript that sounded as if it came from colleagues approached by the authors themselves - this is about the peer review organized by the journals. The results:

Thursday, February 7, 2013

Botany picture #31: Prunella grandiflora

Prunella grandiflora, Germany, 2004. It is fairly similar to P. vulgaris but, as the name implies, much larger in all parts including the flowers. Another difference is its clumped as opposed to long-creeping growth form, and its uppermost leaves are not directly under the inflorescence as in P. vulgaris. This is the species from which a splitter would segregate another species restricted to the Pyrenees. Prunella hastifolia, as the segregate was once called, is a bit larger-flowered even than the typical P. grandiflora and prefers different soils, but it currently only has the status of a subspecies. I don't have a picture of it, sadly.

I had grown very fond of this genus already when I was lucky enough to co-supervise a German Diplom thesis (~honours/M.Sc.) on gynodioecy in P. grandiflora. Gynodioecy means the occurrence of hermaphroditic and female individuals in the same species. See below:
The left flower is from a hermaphroditic plant and has fertile stamens, the right one is from a female plant where the flower is smaller and the stamens are underdeveloped. The puzzle is of course why a plant would do that, as it loses 50% of its reproductive potential (plus it might be less attractive to pollinators because the flower is significantly smaller and, well, it offers no pollen.) If there were a simple gene coding for male sterility, one would expect it to be heavily selected against, so that gynodioecy would die out rather quickly. Instead, there are many Lamiaceae plus a few other plant groups showing this phenomenon, so the explanation must be more complex.

Wednesday, February 6, 2013

Scholarly Journals of Professional Science Publishing No Really I Swear

Ever so often I get scientific spam. It falls into three categories:
  • advertisements for bogus or predatory conferences,
  • invitations to submit articles to bogus or predatory open access journals, or
  • requests to lend such journals a veneer of legitimacy by participating in a sham review process.
Today's e-mail appears to fall into the second category. As explained here before, and discussed in much greater detail at this blog by another researcher, these "journals" are websites (often run by somebody in Nigeria, India or Pakistan) that will "publish", online only, manuscripts submitted to them in exchange for a fee. It may be a match made in heaven for those who produce such poor quality manuscripts that they cannot publish in real journals, but any competent scientist would only be wasting their time and money.

In this case, the contact information leads to Nigeria. The "publisher" hosts a small fleet of "journals" on their website:
  • Scholarly Journal of Biological Science
  • Scholarly Journal of Agricultural Science
  • Scholarly Journal of Biotechnology
  • Scholarly Journal of Medicine
  • Scholarly Journal of Business Administration
  • Scholarly Journal of Mathematics and Computer Science
  • Scholarly Journal of Engineering Research
  • Scholarly Journal of Physical and Applied Chemistry
  • Scholarly Journal of Education
  • Scholarly Journal of Science Research and Essay
Such creativity in the naming department - sounds legit, doesn't it? I especially like Science Research and Essay. But it gets better.

Tuesday, February 5, 2013

Some interesting stuff in TREE

Just received an alert for the latest issue of Trends in Ecology and Evolution, and I find there is an usually high number of interesting articles in it. Two of them I want to draw particular attention to.

The first article  is essentially an advertisement for crowdfunding of scientific research. Because of the ever-decreasing availability of public funds, researchers should think about more intensive public outreach followed by begging the public to throw some spare change their way, Kickstarter style. Or so the authors argue. While there are surely opportunities, especially if one has a flashy and charismatic idea, there are several problems that are avoided or barely alluded to in the article:
  • Is it really a good idea to have research funding distributed not based on scientific merit as judged by peer reviewers, but based on what the public finds interesting? Don't get me wrong, scientists always have to do something that is considered useful, be it by the taxpayer or by a private sponsor; my idea is not to let me do whatever takes my fancy without regard for the needs of society. But at least the taxpayer can be fairly sure that they have a layer of critical review between a scientist's project idea and the public money they want to use for it. In a crowdfunding world, how much money do you think will be wasted on "alternative medicine" frauds? Would the public be able to judge how promising or how ridiculous a particular scheme for the generation of renewable energy is? Peer review of grant proposals exists for a reason. Of course, one might argue that it is the sponsor's own decision if they want to waste their money, but...
  • ...this is also about the entire culture of funding and what it does to science. What would it mean for the job of a scientist if, instead of fighting for better public funding, science managers take the easier path of animating their staff to start crowdfunding initiatives? Should a scientist spend half their time in public relations, making YouTube videos and designing t-shirts as rewards for the sponsors instead of doing, you know, science? And ultimately, this is just another form of privatization. Instead of using taxes paid by all of society to fund projects of value to all of society, one would be using donations to fund projects of value to whoever happens to have enough money to afford a donation. As always in those cases, what about those who don't have that money?
  • Crowdfunding will also face the same problem as any other charity: in a time of crisis, the funds will quickly dry up as the public needs to reduce its expenses. A government does not have that problem to the same degree and can instead take a longer view, continuing to strategically fund services that are of long-term value.
  • Once large numbers of scientists try their hands at crowdfunding, as the authors apparently hope, competition will get fierce. It can reasonably be assumed that under those circumstances, uncharismatic research will not stand a chance, and the other problems listed above will only be compounded.
The other one is an opinion piece that argues against the Intermediate Disturbance Hypothesis (IDH). I am not an ecologist myself, but this is an idea that I learned during university and that always made intuitive sense to me: If a habitat experiences very frequent disturbances (fire, flood, etc.), all species that aren't adapted specifically to dealing with these disturbances, especially climax species with long generation times, will die out. If the disturbances are too rare, fast-growing and quickly reproducing but uncompetitive pioneer species will be driven to extinction by the more competitive climax species. Species richness of a habitat or area is then maximized at intermediate levels of disturbance because both sets of species can persist.

The paper makes two arguments, that there is little empirical evidence for IDH and that its theoretical foundations are wrong. Again, I am not an ecologist and find the second argument hard to follow, but the first one is of course already problematic enough.

Botany picture #30: Prunella laciniata

The greatest possible contrast to the first Prunella provides its congener P. laciniata. This picture was taken in 2008, in the Botanic Garden of Halle University, Germany, if memory serves. The species is quite rare in Germany and restricted to specific dry grassland habitats but more abundant in the Mediterranean area. It is the most distinctive species in the genus due to its usually white (rarely pink) flowers and dissected leaves.

Monday, February 4, 2013

Ranunculus, part 6: Guess the fallacy

This is part of a series on a paper by Hörandl & Emadzade (subsequently H&E) suggesting an "evolutionary", i.e. pre-cladistic, classification of Ranunculus. See the previous installments here: part 1, part 2, part 3, part 4, part 5.

After the previous part, one could arguably already move on. I was curious if the paper would contain a suggestion for a scientific criterion to accept paraphyletic taxa but as always it reduces to the personal feeling that X morphological differences are sufficient dissimilarity to replace, in that particular case, classification by descent with classification by, if we are honest about it, phenetics. Because it mixes two incompatible criteria - phenetic and cladistic - such a system is incoherent. Because it is arbitrary to demand X morphological differences instead of X+1 or X-1, the system is subjective instead of objective. Finally, a system like this will always be less natural and less accurate a description of biological reality than a classification of nested clades simply because said biological reality has a nested structure shaped by common descent.

Nonetheless, I have two more parts to this series in me because there is another aspect in this paper that I would like to discuss, and there are more arguments for paraphyletic taxa in the last part of the discussion that it would be interesting to examine.

Saturday, February 2, 2013

Botany picture #29: Prunella vulgaris

Prunella vulgaris, the common self-heal, Switzerland, 2009. Now you will perhaps be thinking, what is so special about that? I can see that in my front lawn. Or, if you are for example from Australia or Argentina, you just need to find the right kind of disturbed forest habitat in your country. Yes, this thing is all over the place, and it is small and unspectacular to boot.

But this is merely the start of a small series on the genus Prunella of the beautiful and aromatic mint family (Lamiaceae), and as such this least interesting species represents the warm-up for nicer plants to come.

Opinions vary on how many species Prunella has. The most lumping opinion is four, with one restricted to SW France and NE Spain, two mostly European, and one cosmopolitan. This is the cosmopolitan one, obviously. Splitters would recognize a segregate of another species in the Pyrenees and perhaps a few segregates of P. vulgaris especially in China, but for present purposes I will assume the lumper's stance. The four species accepted on that stance are then fairly easy to recognize; P. vulgaris is unique with its stoloniferous (long-creeping) growth form.

Friday, February 1, 2013

The secret sauce of science is the culture of criticism

During breakfast I read Jerry Coyne's latest post about E.O. Wilson, a celebrated biologist who unfortunately promotes group selection in the face of overwhelming evidence against it. My thoughts next went to other highly qualified and otherwise rational scientists who believe in very silly things. There are colleagues who reject long distance dispersal despite being aware of the existence of Hawaii, those believing in immortal, immaterial souls despite being aware of Alzheimer's and the effects other organic and physical traumata have on memory and personality, those believing in the efficacy of homeopathy despite, well, everything humanity has learned about chemistry, physics, biology and medicine in the last few hundred years...

Closer to home, those few colleagues still arguing for the acceptance of paraphyletic taxa are also very unlikely to ever change their mind no matter how many fallacies and misconceptions are pointed out in their thinking. Oh, and have you heard the term Nobel disease? Many weird examples at that link. Of course, I may well also believe something really stupid but will, by definition, not be aware of that, otherwise I would stop believing it.

So sometimes one may start to wonder why science works at all if the individual scientists can be so irrational and unable to accept the evidence. You could mention all manner of technical details, but to me it boils down to the culture of criticism. Every thought and idea is dissected, criticized and tested. Every piece of writing is reviewed and may invite rebuttals.

That is what makes the difference. For every relevant question, the cranks will likely be in a minority, and no matter how influential or famous they individually are, their colleagues will crankily and publicly tear into them when they publish something that is wrong. And so science as a whole is very likely to accept only what is correct. Although it can of course be unpleasant for the individual who is on the receiving end of such criticism, the net effect is beneficial for all of humanity.