Thursday, October 31, 2013

Botany picture #119: Hibbertia riparia

Hibbertia riparia (Dilleniaceae), Australian Capital Territory, 2013. The genus Hibbertia has many species in Australia. It is one of those weird cases (another one would be Calceolaria) where a large group is extremely diverse vegetatively, to the point of including vines, shrubs and small herbs, while being extremely uniform in flower morphology. One can immediately recognize Hibbertia flowers because they basically all look the same.

Wednesday, October 30, 2013

Sience spam number the infinity

There is so much science spam these days that I comment only on the most atrocious eMails I get. Today is one of those occasions.

My inbox recently featured a message from an organization called "RRP" with a call for articles. The text was a charming all bold ca 14-16 pt (?) font in dark red on a bright blue background. I will keep that combination in mind for future PowerPoint presentations just in case I ever have the need to deliberately cause headaches and vomiting in my audience. The text ran as follows:
Dear Colleague [ my work eMail address ],
That is an interesting start. Not only are those square brackets in the original, making abundantly clear that this is a field into which an anonymous algorithm has pasted a list entry, they do not even use a name. They don't say, dear Joe Average, they say, dear [ ]. Is that supposed to impress anybody?
Call for Articles:
RRP ( ) is a well-known publisher and has Journals whose scopes and policies fit with yours.
The first half of that sentence is a blatant lie, and the second half is gibberish. I am not aware of having scopes. Can I get mediation against them somewhere?
We have done some WWW searches and came across one or more of your articles.
Gosh. Do you want a cookie for that? And again, you could at least make a half-hearted attempt at concealing that this is a spam message and that you have not actually looked into my research. "One or more" indeed.
So we believe you may be interested in publishing you valuable work in one/some of our journals.
Your are sadly mistaken. Please feel free to take that R and see if you might need it somewhere.
I briefly summarize what makes RRP Journals unique and desirable in the following sentences. Why our journals are unique and desirable:
1.) "RRP Journals" offers detailed feedback on all submitted manuscript. We do not just publish good research and review papers, we help authors grow.
You could increase the desirability of your journals, albeit probably at the cost of their uniqueness, by learning a bit more about English grammar. Also: randomly placing quotation marks around names? Always a nice touch. Sorry, do continue.
2.) "RRP Journals" has online manuscript tracking system. This allows authors to keep track of the status of/progress on their manuscripts any day any time.
3.) "RRP Journals" has article tracking system through which authors can keep track of their published articles, and know who read their articles. 
Is it time to say gosh again? I think you are confusing two things here: "unique" and "standard practice of most scientific journals". Look up what those terms mean.
4.) "RRP Journals" is currently bilingual in that we publish abstract s of all articles in both English and French. We hope to add two more languages in 2014.
Admittedly that is not a bad idea from the reader's perspective; not sure why it is supposed to be a selling point to prospective authors here.
5.) "RRP Journals" offers various forms of assistances to authors. If you require any form of help at any time, you can easily contact us through the form available here ( ).
How pleasantly vague. It is, unfortunately, to be assumed that they are mostly interested in helping the author if they are unsure about where to pay the article processing fee or however else RRP call their publication charges.
We hope you will:
[A] submit ( ) your valuable manuscript to us for possible publication in any of RRP Journals, and/or
[B] join our editorial board/become a peer-reviewer ( ) for one/some of our Journals.
Yep, that's a sure sign we are dealing with a serious and professional publisher: mass-spamming random people with requests to join whatever editorial board they fancy. Isn't that how all the good journals do it?

I think we are done here.

Tuesday, October 29, 2013

Botany picture #118: Scribblygum

I am really not very good at knowing eucalyptuses, which are here commonly called 'gum trees'. The various important groups are then distinguished with some terms that refer to their bark or wood qualities, their ecology or colours. Examples are ironbark, yellowbox, or river red gum. One group that even I can easily recognize are the scribblygums, such as this one. Their name derives from the tunnels that mining insect larvae eat into the bark.

Monday, October 28, 2013

Free will once more, with a growing realization

Round and round it goes, perhaps forever. One may be forgiven for wondering whether one side is so sure that it is right that it is not actually listening to what the other says.

It could be either side. Note, however, that the discussion, at least as conducted over at the linked comment threads, is quite asymmetrical: Incompatibilists say quite openly that they consider compatibilism to be merely a crutch manufactured to soften the blow of determinism, that compatibilists are deluded or even outright dishonest, and that everybody should stop using the term "free will" and, depending on their mood, sometimes also the term "choice", because they supposedly mean something supernatural. Compatibilists, on the other side, merely reply that these terms do not necessarily mean something supernatural, and would you please stop talking about us in this aggressive and demeaning way when the discussion is only about terminology anyway?

Or in other words: Incompatibilists condescend towards compatibilists but the compatibilists do not condescend back. That might explain something about the dynamics of this discussion.

To recap: When discussing free will vis a vis determinism, it is generally assumed that there are three different positions, or groups of people:
  1. Those who hold that we have a form of free will that allows us to make decisions independently from the laws of physics, our genetic makeup, the environmental influences that shaped us, our current state of brain chemistry, whatever, either because our body is steered by a supernatural soul (contra-causal/dualist free will) or without any attempt at explanation because it is a necessary premise for libertarian ideology (libertarian free will).
  2. Those who hold that everything is determined by cause-and-effect, with perhaps a bit of (quantum) randomness thrown in, and thus our decisions are also predetermined with a bit of random, and thus it does not make sense to speak of free will and choice because those terms are commonly understood in the sense that the first group is advocating* (incompatibilism).
  3. Those who hold that everything is determined by cause-and-effect, with perhaps a bit of (quantum) randomness thrown in, and thus our decisions are also predetermined with a bit of random, but it still makes sense to speak of free will and choice because those words do not necessarily imply anything contra-causal and supernatural*, and even given determinism we still need some terms to describe the difference between somebody acting out of their own free will and being forced to do something, or between a kleptomaniac and somebody stealing for profit (compatibilism).
For me, at least one thing came out of the discussions linked to above: I am increasingly coming to the realization that the first two positions are not actually, really, in practice, held by any significant number of people, or at least not by anybody who is sound of mind. And yes, I realize that this can be seen as at least as condescending as the idea that compatibilism is nothing but motivated reasoning because it may be taken to mean that the incompatibilists are either deluded or dishonest; but I would prefer to stress that the difference between the second and third position boils down to semantics anyway.

So why would I think that the first two positions do not really exist? Aren't there a lot of people advancing them?

Sunday, October 27, 2013


I had long decided to read more classics when I came upon Mary Shelley's Frankenstein at the last Book Fair. I have recently finished it and must sadly admit to some disappointment, although it is probably mostly an issue of wrong prior expectations.

Obviously: Spoilers ahead.

Thursday, October 24, 2013

Botany picture #117: Leucopogon microphyllus

Leucopogon microphyllus (Ericaceae), Australian Capital Territory, 2013. Does this heath not simply have awesome flowers? They are tiny, yes, but how cute when you look at them more closely...

Wednesday, October 23, 2013

What makes reviewing a paper enjoyable?

One more about peer review. To get our papers published, we all have to go through it, and the pleasantness of that experience can vary depending on the reviewers you run into.

But the same goes for the other side. In my role as peer reviewer, I find myself sometimes enjoying it very much and sometimes hating it. Apart from the obvious fact that it is no fun to do it if you have too much work already, what makes the process enjoyable?

Well, papers that are fun to review are the ones that inspire, that present new methods or insights, that make one think "I wish I had come up with that", while bad papers are often formulaic and uninspiring. As for quality, it is a pleasure to review a well written, concise and coherent, high quality paper because it is just a good read and you do not have a lot to criticize.

But interestingly, at least to me there is another peak on the fun/quality graph at the bad end of the spectrum. In a perverse way, reviewing becomes enjoyable again when the manuscript is sufficiently atrocious.

So really the papers that I enjoy reviewing least are somewhere around the middle. The ones that contain reasonably competent but completely uninteresting research, the ones that could actually be good if the authors knew how to write a coherent sentence and develop a clear line of thought, and, crucially, the ones containing overall sound science but a suffocating number of individually minor mistakes. In other words, those that have potential merit but force you to write pages and pages of suggestions on how to make them publishable.

The really hopeless manuscripts make for short reviewer's reports, just like the really good ones. If the science is completely bonkers, it is easy to decide what to recommend. If the entire text is beyond repair, you don't need to bother with making suggestions for individual sentences any more. But most importantly, if a paper is sufficiently bad, reading it can be a very invigorating experience. You may laugh, you may pull your hair, but at least you emote instead of getting bogged down in drudgery.

Tuesday, October 22, 2013

Botany picture #116: Rhytidosporum procumbens

Rhytidosporum procumbens (Pittosporaceae), Australian Capital Territory, 2013. I really have no prior connection to the family Pittosporaceae because they do not appear to occur in Germany. All the more important to learn more about them now that I am here. Many of them are shrubs but this is a rather weak, scraggly one.

Monday, October 21, 2013

Cycling in Canberra (cont.), oil

If you want any proof that a good number of car drivers here in Canberra simply despises cyclists, you do not have to look any further than their reaction to cyclists riding across zebra crossings.

A few days ago (I waited with writing this to get some distance, so it is less of a rant), I rolled down a hill towards a zebra crossing. There was one car that had already driven over it and several that were lined up in front of it, and none of them moved because this was a T-crossing and dense traffic was flowing along the bar of the T. So I rolled down the hill, across the crossing, and then stopped right behind it to wait for the lights to get green so that I could get across the bar of the T myself, if you get the picture.

Now the guy standing with his car right in front of the zebra crossing grew visibly upset when he saw me approaching. At first he made a half-hearted attempt to roll forward to block the zebra crossing so that I could not pass, but then he probably realized that that would be too irresponsible or prickish a thing to do and resigned himself to merely shouting at me.

Is that really necessary? Consider the situation.
  • I did not slow him down by riding across because he was stuck in a traffic jam anyway.
  • I did not endanger him, anybody else, and not even myself, which is generally the reason why cyclists are supposed to dismount before crossing, by riding across because he was stuck in a traffic jam anyway.
  • I did not inconvenience him in any way whatsoever because he was stuck in a traffic jam anyway.
Although, perhaps the last one is not entirely correct. Let me try again: I would not have inconvenienced him in any way whatsoever if he had not been an unpleasant character who is viscerally offended by the sight of cyclists riding their bikes. Yes, that looks better. (If you are a kind person, you might submit that he is perhaps just a stickler for traffic rules. But sorry, no he can't be, because then he would not have tried to block the zebra crossing first.)

In this case his behavior was particularly stupid because he could not move anyway. The problem is a more general one though. What do you do when you come towards a zebra crossing when there is no traffic jam, when the cars stopping to let you cross could in principle be moving? Do you always dismount?

From my perspective, it is like this. I come towards the crossing, slow down and prepare to stop, and some car driver sees me. Because they know that somebody crossing the zebra crossing has right of way, they also slow down and stop (unless they are real pricks). Now I have two options: I can (1) stop entirely, laboriously dismount from my bike, and push it across, or (2) wave a thank you to the car driver and quickly ride across. The thing is, which option makes the car driver angry will depend on their personality.

Somebody like Mr I-Hate-Cyclists from above will want me to dismount, so if I don't do so, he will shout abuse at me. If I do so, experience shows he will most likely use the time I need to dismount to run the crossing and deny me my right of way.

Nice and sensible car drivers, on the other hand, will not mind me riding across because that allows them to continue their own journey as quickly as possible. If instead I dismount, they will most likely think to themselves, "what an idiot, why doesn't he just ride across instead of walking across, taking five times as long? There is no danger, I already stopped for him!"

In other words, I could facilitate the flow of traffic while antagonizing unreasonable people, or I could slow myself and everybody else down while antagonizing reasonable people. That is not really a conundrum, is it?


Also a few days ago, I had a chat with two reps of a producer of lab consumables. It turns out that oil is so expensive now that companies (not them of course, that was their pitch) are producing shoddier plastic consumables, trying to use less high quality oil and to replace it with cheap substitutes. And some of these substitutes leach into the tube and interfere with scientific measurements and molecular reactions.

Quite apart from the question of how we will manage food production for several billion people, transport, electricity, and heating when the fossil fuels are gone, just consider this small issue, materials science. Look around your living room, around a supermarket, around a scientific lab. What the heck will we do once we cannot produce plastic anymore? Can you even imagine that?

Please remind me again why the use of petrol-powered private cars has not been outlawed worldwide ca in the early 1980ies, because sorry, somehow I don't get it. We are all sawing off the branch on which we are sitting, and we cannot even pretend we don't know.

Friday, October 18, 2013

Botany picture #115: Triptilodiscus pygmaeus

Triptilodiscus pygmaeus (Asteraceae), Australian Capital Territory, 2013. As one can see from my finger tip, this daisy species well deserves its specific epithet.

Thursday, October 17, 2013

New South Walesian geography

The following may be considered quite impolite but some time I just have to say it: The Australians here in this area are just weird with their approach to geography. We are in Canberra and thus, although the city has its own territory, essentially embedded in New South Wales (NSW). And talking about localities in NSW with Australian colleagues is a constant struggle.

You see, when they tell you that a species of plants occurs at the "south coast", they do not, in contrast to what anybody outside of Australia would reasonably surmise, mean a coast that does anything so base as actually being situated on the southern edge of any land mass you might be thinking of. You would thus waste your time if you were attempting to locate this plant species on the coasts of Victoria or South Australia.

No, here in NSW, Sydney is the navel, the pole, the hub of the world, the focus of all thought. So obviously (?) to a local, the "south coast" is the coast of NSW south of Sydney, and the "north coast" is the coast of NSW north of Sydney. The fact that both are really the east coast relative to land and ocean is apparently a minor detail, and people can get quite exasperated if you are unkind enough to point it out. Of course this makes it much harder to communicate when you really do need to say that something occurs on the southern coast (for reals) of the continent, but I have by now gotten used to dealing with this particular weirdness.

Recently I had an even more bizarre exchange. A colleague came back to work and told me that she had spent the extended weekend visiting relatives in a town in "western NSW". After she mentioned the nice wildflowers there I asked her to show me the town on the map because the interior of the state has many interesting species of the group I am working on. So when we stood in front of the map, my finger and eyes quickly focused on the western half of NSW but I could not find the town.

The joke was on me! As it turns out, the town is literally in the easternmost fifth of the state. But of course, as I learned from the aforementioned colleague, that is still western NSW. Presumably because it is just slightly west of the ridge of the Great Dividing Range or something. Again, the fact that this place is nearly as far east as you can get in NSW without falling into the Tasman Sea is a minor detail, and she was quite surprised at the misunderstanding.

Admittedly, when I was a child everything south of the Elbe river felt to me as if it weren't really northern Germany any more. But well, when I thought like that I was what, 10 years? And even then I would not actually have called Lower Saxony "southern Germany"...

Wednesday, October 16, 2013

Botany picture #114: Diuris

Diuris (Orchidaceae), Australian Capital Territory, 2013. This genus is known as donkey orchids although individual species may also be tiger, leopard or whatever other animal orchids. Sadly they look too similar for me to determine them to species just from this picture.

Tuesday, October 15, 2013

In practice, people are determinists anyway

Jerry Coyne once more raises the issue of free will, about which I have also written before, so I do not want to repeat myself. Instead, let us look at some of the premises of the discussion. It appears as if the motivation of incompatibilists is founded on the following assumptions:
  1. If left to their own devices, people are naturally leaning towards a black/white dichotomy of dualism versus incompatibilism, i.e. they believe that the only possible meaning of "free will" is some kind of supernatural or libertarian free will that allows people to do whatever they want independent of their genes, upbringing, personality, current state of brain chemistry, and whatever other influence of the natural environment you may want to add. In other words, when you say "free will" everybody will assume you believe in supernatural stuff.
  2. If one could only convince people of the truth of determinism and incompatibilism, if they could only be convinced that there is no free will, they would become better people. For example, revenge would not make sense any more if it were understood that a criminal is the sum of their genes and experiences and thus never had any really free choice in committing their crime.
  3. If one could only convince people of the truth of determinism and incompatibilism, that would be a mighty blow to religion, at least partly because religious apologists use free will as a standard defense for the so-called problem of evil.
The thing is, there seems to be some good evidence that all three of these assumptions might be wrong.

Monday, October 14, 2013

Botany picture #113: Glossodia major

Glossodia major (Orchidaceae), Australian Capital Territory, 2013. One of the most spectacular orchids here but also one of the most frequent. The entire plant above ground consists of only one leaf and one flower.

Saturday, October 12, 2013

Job, career, calling

My short blogging break this week was due to my participation in a work-related workshop (forum?). It was in many ways very useful and inspiring, although one aspect that I have mixed feelings about is the coaching aspect. The coaches at these kinds of events really LOVE personality tests, the kind where you answer a few dozen questions and then end up in one of four or more rarely three overly simplistic boxes. It does not help that this is at least the third workshop at which I was subjected to this kind of test, making my experience a bit repetitive.

On the other hand, one thing mentioned by the coach we had on Friday was very interesting because I had not previously considered it from that angle. He pointed out that there are different stances people can take towards their work:

Job - they do it because they need to bring money home.
Career - they do it because they want to rise through a hierarchy.
Calling - they do it because they are really passionate about this kind of work.

It is clear that sadly most people will be unable to do professionally what they see as their calling and thus a great part of the workforce will see their work merely as a job. That does not mean, however, that they will be under-performing, quite the opposite. What the coach wanted to drive home is that a supervisor who sees their work as a calling or a career and who happily works many hours of unpaid overtime cannot expect everybody else to do the same. They can only expect them to do the work that they are paid for, and to do it well, and expecting everybody to be like yourself is atrocious leadership.

The funny thing is, I consider the aspect he stressed to be a no-brainer. I know that many people perform superbly and, if you give them the right environment, identify very much with their workplace even if they see their work only as a job. What I would be more concerned about are overly career-oriented people!

You may ask reasonably why that would be so. Should they not be very productive due to their great ambition?

Well yes, but productive in what sense, and to whose benefit? A job oriented person will aim to satisfactorily complete the task at hand because that is their job. A person who feels a calling will aim to complete the task well because they are enthusiastic about that type of task. But career oriented people may only see the task at hand as a minor stepping-stone on the way to where they really want to be, and it may forever be so because there is nearly always an even higher management level above them. Can I be focused enough on what I am currently working on to do it well if my real interest is not having to do something like that any more? Will I really work to the benefit of my current organization if my eyes are already on a more prestigious job elsewhere?

Perhaps that is a nasty way of thinking about it. Nor do I begrudge anybody their aspirations. What I mean to show is that, from my personal perspective, it might be a much harder to learn leadership skill to understand the personal needs and motivations of very career oriented people around oneself, and to balance the fulfillment of their ambitions and the needs of the organization as a whole, than it is to understand and deal with job-oriented people, although the latter seemed to be the major concern of the coach.

Wednesday, October 9, 2013

Botany picture #112: Trifolium subterraneum

Trifolium subterraneum (Fabaceae), Australian Capital Territory, 2013. It is an introduced weed here in Australia but mostly, as far as I can tell, in urban areas (?). Forming quite pretty carpets at the moment.

Tuesday, October 8, 2013

Botany picture #111: Cryptandra amara

Cryptandra amara, Australian Capital Territory, 2013. Among the early spring flowers in nearby Mount Majura Nature Reserve is this white-flowered dwarf shrub. It looks superficially like a heath but the spinose branches and a closer look at the flowers betray its affiliation with the Rhamnaceae. When in bloom, it exudes a strong sweet smell that is very noticeable even from a distance.

Monday, October 7, 2013

Failures and virtues of peer review

For a few days now, scientists have been discussing a small experiment conducted by a Science correspondent. He invented several variations on a bogus study in cancer research that contained several fundamental flaws and sent them out to 304 open access journals. 255 of them made a decision, and of those, 157 (or slightly more than 60%) accepted them.

Predictably, this experiment is being discussed along what we might call partisan lines. Those skeptical of the OA model see this as one more illustration of the problems of a system in which journals earn their money based on the number of accepted papers, pretty much regardless of their quality. Those advocating the OA model consider the affair a piece of propaganda for the traditional commercial publishing industry and stress that the experiment did not feature a control group of subscription based journals to see if they would have a lower acceptance rate.

I have already written about my concerns about the OA model so I will not repeat myself here. Note simply that I would very much prefer a system in which the rainbow press of science would be seen for what it is, in which all major journals are run as non-profit public utilities, and in which the results of scientific research are as available to the public as access to publishing venues is available to those who cannot afford $1,300 in article processing fees. I am merely worried about the incentives publishers operate under when using the OA model.

Instead, I wonder about the general issue of peer review. To express his opinion that the problem is not with OA but with peer review in general, Michael Eisen uses his linked blog post to call peer review a "joke", and similar sentiments are being expressed elsewhere. Others stress that this process is the gold standard that allows us to distinguish real scholarship from crankery. What gives?

Friday, October 4, 2013

Botany picture #110: Heracleum mantegazzianum

Heracleum mantegazzianum (Apiaceae), Botanic Garden of Zürich, 2009. When I was a child there was quite a scare about this species in Germany. It had been introduced from the Caucasus as an ornamental and nectar source for beekeepers but had started invading natural habitats, and the problem is that the plants produce a substance that burns the skin when exposed to intense sunlight. Parents were worried that their children might play with it in summer, and many people were concerned whether it would outcompete native plants. The scare seems to have fizzled out over the years, or at least I did not hear much about it any more as I got older.

Thursday, October 3, 2013

Speciation in plants

On his Sandwalk blog, biochemist Larry Moran recently posted about the many different definitions of the term evolution. Very interesting topic but I see no reason to duplicate his efforts on this much less frequently visited blog. What got me thinking instead was a somewhat incoherent creationist who immediately jumped into the comment thread to declare
Evolution is not a fact or a theory in explaining changes in populations beyond reproducing types at any one point in history. Show where a population changed so that it could no longer reproduce with its parent population??
So he denies the possibility of speciation. Would be laughable in face of all the evidence we have, but the problem is of course that somebody like that will never be satisfied with the kind of evidence a biologist can actually produce. Speciation rarely happens over a human lifespan (although sometimes it can, see below), and so the retort will always be, "were you there?", or to let the creationist speak,
Of coarse extrapolating from these is not scientific evidence for a history of biology. Even if true history.
That is a fairly myopic stance, entirely comparable to doubting that the Roman Empire existed because nobody who is currently alive has seen it and historical documents and archeological artifacts do not constitute direct evidence. I think Richard Dawkins used the same analogy in a recent book, actually.

No, the standard of evidence for processes that take hundreds of thousands of years to happen cannot possibly be "have you seen it with your own eyes?" But just as with the Roman empire or with a murder trial lacking direct witnesses, we can infer events beyond reasonable doubt. The nested structure of biological diversity is our friend here - we can produce phylogenetic trees to find out which species are most closely related, and sometimes we find two species that are genetically so extremely close together that we can infer what may have happened to make them different species, perhaps as little time ago as before the last ice age. In other cases, we find groups in the incipient stages of speciation, somewhere uncomfortably between being able to interbreed and not being able to interbreed.

Anyway, this got me thinking. The evolution/creationism controversy is usually fought over animals, whereas plants are usually cruelly neglected. So what is the state of evidence in plants? I am not talking about a formal review here, but merely a short list of spectacular cases, well understood mechanisms of speciation, and some well researched examples. Here goes.

Tuesday, October 1, 2013

Botany picture #109: Olearia pimeleoides

Olearia pimeleoides (Asteraceae), New South Wales, 2013. As currently circumscribed, Olearia is the largest genus of daisies on the continent, accounting for a bit more than 10% of the known native species of the family. They are simply known as daisy bushes, and several of them are grown as ornamentals.