Sunday, December 30, 2012

Family trip to Wee Jasper

Today we went on a day trip to Wee Jasper to visit Carey's Cave, one of the largest accessible cave systems on the continent. Photos below the fold.

Saturday, December 29, 2012

People saying interesting things about creationism

Rejecting evolution expresses more than an inability to think critically; it relies on a fundamentally paranoid worldview. Think what the world would have to be like for evolution to be false. Almost every scientist on earth would have to be engaged in a fraud so complex and extensive it involved every field from archaeology, paleontology, geology and genetics to biology, chemistry and physics. And yet this massive concatenation of lies and delusion is so full of obvious holes that a pastor with a Bible-college degree or a homeschooling parent with no degree at all can see right through it.
    Katha Pollitt

(The same goes for many other conspiracy theories and denialisms, by the way.)

The fact remains that the human body is pretty much of a disaster from the standpoint of basic engineering. We'd better hope we're the result of a long, haphazard evolutionary process, because any designer responsible for human anatomy has an awful lot of explaining to do.
    Jason Rosenhouse

Creationists like terms like "different view" or "alternate view", because those sound much nicer than "wrong". I would love to be able to present my bank with a book entitled "Five Minus Three: A Different View", in which, through rhetorical wordplay, ad hominem attacks, and general ramblings, convince them that five minus three is in fact FOUR, and that my checking account should be retroactively adjusted accordingly.
    Bryan Lambert

Thursday, December 27, 2012

Boxing Day trip to Deua National Park

Yesterday we made a family trip to the Marble Arch Walk in Deua National Park in New South Wales; pictures below the fold.

Monday, December 24, 2012

Happy holidays!

Got this from another blog, but unfortunately I don't remember where and when. Blogging is going to be sporadic until the new year.

Saturday, December 22, 2012

Botany picture #17: Silene otites

Silene otites (Caryophyllaceae) from Eastern Germany, 2006. Not the most impressive carnation you will ever see, but that is just the point. Species like these are under-appreciated, and it pays to have an eye for the less obvious ones.

Thursday, December 20, 2012

Botany picture #16: Monotropa uniflora

Monotropa uniflora, Canada, 2012. These plants are entirely without chlorophyll and so, in contrast to most plants, they cannot get their energy from photosynthesis. Instead, they parasitize on mycorrhizal fungi in the forest floor. Due to this aberrant lifestyle and its herbaceous habit, Monotropa was traditionally placed in a separate family, but it is now considered part of the heath family Ericaceae.


Wednesday, December 19, 2012

Open access publishing

I am still not entirely sure what I should think of open access publishing of scientific research. Don't get me wrong, I am not at all fond of the traditional system which, in case a non-scientist reads this, works like this:
  1. Jane and Joe Taxpayer fund a researcher's salary and their research costs.
  2. The researcher submits a manuscript presenting their results to a journal, where it is peer reviewed by qualified colleagues. This quality control is done for free, as a service to the scientific community, with the understanding that other colleagues will in turn referee the referees' own manuscripts sometime.
  3. If the manuscript is accepted by the journal, it is handed over to a commercial publisher. That publisher sends it to some underpaid chaps usually in India who typeset it into the journal format.
  4. The final paper is then printed and placed behind a paywall on the internet. If your (taxpayer funded) university library wants to provide access to the published results of the (taxpayer funded) research, it has to fork over a hefty fee to the commercial publisher. If a (taxpayer funded) research institute wants its staff to be able to access the results of the (taxpayer funded) study online, it has to fork over a hefty fee to the commercial publisher. Note also that Jane and Joe Taxpayer cannot read the research papers they funded unless they happen to be staff members at an institution that is forking over aforementioned fees.
  5. At the end of the year, the shareholders of the publishing company buy themselves a second yacht or another villa at the coast. Seriously, this is not about paying a reasonable price for good quality, this business is so obscenely profitable that the term "market failure" springs to mind.

The problems are obvious, and the last few years have seen a strong movement in science trying to make scientific publishing more open and to pry it from the hands of a small number of publishing houses. This movement reaches from a grassroots campaign to boycott the publishing company Elsevier to the government of the United Kingdom, and accordingly diverse are the reforms that are suggested:

Tuesday, December 18, 2012

Botany picture #15: Allium farreri


Allium farreri in the Botanic Garden of Zürich University, 2009. The genus Allium is of course familiar to us all from garlic, onion, leek and chives. It contains many more edible species that are used locally in various parts of the world but also a great number of very attractive plants with ornamental potential. I like the group very much although I never had particular research interest in monocots so far.

The short half-life of suprageneric classifications of petaloid monocots has become something of a running joke in botany, and I am not sure whether and why the genus should now be considered to be a member of the Liliaceae, the Amaryllidaceae or the Alliaceae.

Monday, December 17, 2012

Readability scores

As a scientist, I am writing a lot, especially manuscripts and grant proposals. Next to content and structure, one of the aspects that has the greatest impact on whether somebody else will appreciate or even be able to make sense of what we write is the complexity of the language we use. Long and convoluted sentences are off-putting and confusing, and the use of unnecessarily technical terms can come across as pretentious. In the worst case, we may write a text that most of the intended audience cannot understand, especially if we are a specialist addressing non-specialists.

Now obviously we can have a hunch about this, but if in doubt we can use various metrics that have been developed to provide quantitative tests of readability: the automated readability index, the Flesch reading ease score, the Flesch-Kincaid grade level, the Coleman-Liau index, the Gunning fog index and the SMOG index.

Friday, December 14, 2012

Botany picture #14: Minthostachys acris

Minthostachys acris (Lamiaceae) from the highlands of southern Peru as a second example. It is the dominant species in the area around Cuzco and used by the local population although not as intensively as its congener in Argentina. For decades it was mistakenly called Minthostachys glabrescens but that scientific name actually belongs to a rarely collected local endemic from northernmost Peru, while this species was left without a formal name despite being much better known.

Thursday, December 13, 2012

Minthostachys literature (repost from old website)

I have retired my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Update June 2014: I am in the process of making this list more useful by adding links to the papers in the cases where they are available on the internet. Of course, if you are not at a university or other research institute they may still be behind a paywall.

This page provides a list of references to studies on the genus Minthostachys, organized into four areas: one for ethnobotany, pharmacology, biochemistry and domestication, another for taxonomy, systematics, morphology, anatomy and cytology, a third for (mostly very old) papers only containing descriptions of new species, and the last for theses submitted at Latin American universities. The section is mostly meant to serve as a source of information for other researchers. Note that many of the publications use an outdated taxonomy; just because it says Minthostachys mollis in the title does not mean that the paper in question actually examined that particular species.

If you know of any articles that should be added, please comment below so that I can add them.

Wednesday, December 12, 2012

Botany picture #13: Minthostachys verticillata


With all the reposts of information on Minthostachys it seems fitting to show a representative of this genus of aromatic plants: Minthostachys verticillata (Lamiaceae) from Argentina, where it is commonly known as peperina. It is harvested for oil extraction and consumption as tea, especially around Cordoba. Overuse of wild populations is a major issue, and Argentinian colleagues are attempting to address the issue by working to educate the collectors about sustainable management practices and by domesticating the species.

Tuesday, December 11, 2012

Algunas notas sobre las especies de Minthostachys y sus nombres (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Some notes on the species of Minthostachys and their names (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Monday, December 10, 2012

Botany picture #12: Genista pulchella

Genista pulchella (Fabaceae) from France, 2006. A creeping dwarf shrub that I saw on a very exposed, rocky slope in the Corbieres.


Sunday, December 9, 2012

Aceites esenciales, usos tradicionales y cultivación de Minthostachys (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Essential oils, traditional uses and cultivation of Minthostachys (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Friday, December 7, 2012

Botany picture #11: Elytraria


Believe it or not, this little beauty is also an Acanthaceae, an Elytraria from Mexico, 2007. Unfortunately I do not know the species name.

¿Qué es Minthostachys? (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

What is Minthostachys? (repost from old website)

I am considering to retire my Minthostachys website, but it would be good to have some of the information still available on the internet. The genus is, after all, of some cultural and economic significance to the people of the Andes. This is therefore one of a series of posts transferring previously written texts from the aforementioned website. Please disregard unless you are interested in this particular genus.

Thursday, December 6, 2012

Botany picture #10: Justicia comata

To show the diversity of the genus, another Justicia, in this case J. comata, Bolivia, 2007. This one is more of a weed, very frequently found in lowland South America in disturbed moist places. The flowers are tiny but the typical fishbone pattern on the lower lip is clearly visible.

A few words on Hennig's Internodal Species Concept

I recently discussed this over lunch with a colleague who has the strong conviction that this species concept is "wrong".

Tuesday, December 4, 2012

Botany picture #9: Justicia mirandae

Justicia mirandae (Acanthaceae), Mexico, 2007. The Acanthaceae are a pantropical family of flowering plants. Despite its large size of several thousand species, the family is usually easily recognizable by its unique fruit: few-seeded capsules with explosive seed dispersal (ballistochory). The seeds are often flattened, and their funiculi, the stalks that supplies them with nutrients while they are ripening, harden and build up tension to flick the seeds away.

Surprisingly for such a large family, relatively few species of Acanthaceae are of practical use. However, the family contains many stunning ornamentals because they often have extremely showy and colourful flowers or bracts, like this species. Part of the reason is that they have many bird-pollinated species, again like this one.

Justicia is the largest genus in the family but appears to be polyphyletic in its current circumscription. Spotting characters for the genus are strongly zygomorphic flowers, often with a fishbone pattern on the lower lip, only two fertile stamens, and often very asymmetric anthers. The latter two characters are clearly visible here but the fishbone pattern is lacking.

As you can probably tell, I had dealings with these plants once.

The Google alternatives to ResearcherID and Journal Citation Reports

In a previous post, I explained how to use ResearcherID. In my post on assessing publication records, I explained what an h-index is and mentioned how many people judge journals by their impact factors. ResearcherID, which you can use to automatically calculate your h-index and other metrics, and the Journal Citation Reports (JCR) are run by Thompson Reuters, the first as a free service, the latter as a subscription service. However, Google has recently introduced its own variants of these services, and both are free. This post examines how they differ from the Thompson Reuters products and explores their advantages and disadvantages.

Sunday, December 2, 2012

Botany picture #8: Eranthis hyemalis


Eranthis hyemalis (Ranunculaceae) is one of the earliest plants to flower in Germany; it is not strictly native to that country but the genus is Eurasian, so it may just not have made it back after the last ice age. It is perennial but the above ground parts are very short-lived. Note also the funnel-shaped, modified petals in the lower picture; they contain the nectar.

How to use ResearcherID

ResearcherID is a free service offered by Thomson Reuters that is very useful to scientists for two reasons: First, it allows you to select all your publications and connect them to the eponymous ID. This is especially important if you have a relatively common name, because in that case some potential employer who wants to look you up in a publication database will find a confusing number of entries from many different people. With ResearcherID, you can put the ID onto your website or CV, and people searching for your ID will find your and only your publication record.

Second, you may need to calculate your citation metrics - most frequently lifetime citations and h-index - for an internal report or for the CV that goes with a job or grant application. It is annoying to have to calculate these metrics from scratch every time you need them. With ResearcherID, you merely have to tell the system once which publications are yours and then add any new publication when it appears. If you keep the list updated in that way, ResearcherID will automatically calculate these and other metrics every time you look up your own profile (simply click on "Citation Metrics" under "My Publications" on the left and wait a few seconds).

Friday, November 30, 2012

Botany picture #7: Parnassia palustris

Parnassia palustris (Celastraceae) from the European Alps, 2004. It is trivially easy to recognize in the Alps by the beautiful glands on the flowers.

How to assess publication records

Publish or perish has become such a well-known expression that it should be nothing new even to those who have never played with the thought of pursuing an academic career (see Wikipedia, or, more cynically, SMBC). The idea is that there is ever increasing pressure on academics not necessarily to produce work of high utility and quality but simply to produce lots of publications in renowned journals.

Academics are evaluated on the basis of their publication record in nearly all professionally relevant situations: when applying for a job, when considered for a promotion, when applying for a research grant. By extension, research groups within an institute, institutes within a university, and universities among universities are evaluated based on the publication record of their researchers. So, how does one assess publication records?

There are different ways people do this, and they are listed below in order of decreasing stupidity.

Wednesday, November 28, 2012

Botany picture #6: Pinus sylvestris

Pinus sylvestris (Pinaceae) seedling in Germany, 2012. A seed plant embryo consists of the primary root (radicle), the embryonic leaves (cotyledons) and a small stem connecting the two (hypocotyl). While flowering plants have only one or two cotyledons, conifers like this one have several.

Continuing opposition to Phylogenetic Systematics in botany

I will write more about other stuff, but as mentioned before, I would like to write this all out for once in case I ever want to refer to it. Warning: long and technical, although perhaps even a non-biologist may find the last part amusing.

As indicated in my introductory post on the topic, Phylogenetic Systematics (PS) is today the dominant paradigm in biological classification. Perusing the pages of the major journals of systematic botany, such as Taxon, the Botanical Journal of the Linnaean Society, Plant Systematics and Evolution or appropriately named Systematic Botany, we will always find numerous publications either suggesting that a plant group be recircumscribed to make it monophyletic or expressing satisfaction at having confirmed the monophyly of a group in its traditional circumscription. And the latter happens more often than many people assume, by the way.

Still, a vocal minority of botanists remains opposed to the requirement to accept only monophyletic supra-specific groups. This might appear surprising: should scientists not be able to figure out amongst themselves what is the best approach and then be reasonable enough to all follow it? Well, most of us think we have done so.

Monday, November 26, 2012

Botany picture #5: Baccharis rhomboidalis

Baccharis rhomboidalis (Asteraceae) from the vicinity of Bariloche, Argentina, 2009. Baccharis is a large genus of shrubby daisies in the Americas. It is considered to be taxonomically very difficult, i.e. many species are hard to identify or tell apart (not this one though). The English Wikipedia, as of this writing, calls it the largest genus of the daisy family with 500 species despite also writing that the genus Senecio has 1250 species. Ah, the joys of crowd-sourcing.

Scientists' CVs

After comparing the application procedures in different countries, maybe I could write a bit about scientists' curricula vitae*, again with the idea that a young scientist at the beginning of their career might consider this useful and find it with some applied Google-fu. But it could also be interesting, as a kind of ethnological excurse, to curious non-scientists. Again, this is not professional career advice, so take it just as my personal opinion.

Sunday, November 25, 2012

Botany picture #4: Aragoa abietina


Aragoa abietina (Plantaginaceae), at the Páramo de Chingaza, Colombia, 2007. This species was still in the Scrophulariaceae when I went to university, but phylogenetic studies found the family in its old circumscription to be polyphyletic. Essentially, the Scropulariaceae used to be a wastebasket where many genera went that did not fit into better defined families around it.

Addressing a common misconception about Phylogenetic Systematics: Species do not have to be monophyletic

In my previous post introducing Phylogenetic Systematics (PS), I explained that its criterion for the recognition of supra-specific taxa (groups of species in the formal, scientific classification of life) is monophyly. A monophyletic group is one that includes all descendant species of its common ancestral species, as opposed to only some of them.

Unfortunately, the way many people memorize this, and the way they are even sometimes taught it as students, is as follows: "All taxa have to be monophyletic". This makes no mention of grouping species into supra-specific taxa, and so they may come to assume that PS demands that species also be monophyletic.

Friday, November 23, 2012

Botany picture #3: Melittis melissophyllum

Melittis melissophyllum (Lamiaceae) from south-western France. This is one of the most spectacular representatives of the mint family in Europe, but from what a botanical garden curator once told me it is a bit demanding in cultivation. Another interesting aspect is that the distribution of colours on the corolla is extremely variable in this species, even within the same population.

Introduction to Phylogenetic Systematics

As indicated in my first post, one of my professional interests is Phylogenetic Systematics (subsequently PS). As a reference for future discussion, this and perhaps a few follow-ups will provide a concise introduction. However, there is a limit to how concise one can be and still make sense, so this post will necessarily be quite long.

First, what is PS? 

Tuesday, November 20, 2012

Botany picture #2: Equisetum giganteum


Thicket of Equisetum giganteum (Equisetaceae) in the Bolivian lowlands, 2007. While of course the extant species are not the same as the ones that existed during the Mesozoicum, there is supposedly not a lot of difference in appearance between this and the fossil genus Equisetites, meaning that dinosaurs would already have stomped through very similar vegetation.

Job applications and selection procedures in three different scientific communities

In the course of my career, young as it still is, I have nonetheless already had some experiences with job applications and selection procedures in three different scientific communities: (1) Central Europe, especially Germany and the German-speaking part of Switzerland; (2) the United States; and (3) the United Kingdom and Australia. (I lump the latter two for present purposes because of similar procedures, but of course they are really two communities.) Because this might be of interest to young scientists who are willing to look beyond their home country in search for new challenges, be it permanent employment or a postdoc, and who might happen upon this from a search engine, I thought it would be a good topic to write about.

Monday, November 19, 2012

Botany picture of the unspecified time unit #1

Cynanchum diemii (Apocynaceae: Asclepiads). In 2009, I was on a conference trip in Argentina with a German colleague, and we stayed a few days longer to explore the area around Bariloche. We were walking through a forest where nothing much seemed to be in flower - it was essentially very late winter - when we suddenly walked through a cloud of intense, sickly sweet scent. Searching around us, we finally located this delightful vine with small yellow flowers as the source.

Welcome

Hello, in case you have just found this. I do not expect this blog to become very popular or well-noted, but start it merely to have a place to write about some of my thoughts and experiences, and who knows? Maybe it will in due course contain something that somebody will find interesting or useful.

I am a systematic botanist of German origin who is now working outside of his home country. What you can find to expect here are posts of varying length and quality on the (non-personal) topics that are of greatest interest to me. In order of decreasing narrowness:
  • Botany. This aspect will be covered with regular postings of photographs of nice or interesting plants, especially from the time before I took up duties at my current institution (the photographs from my current work ultimately end up on a searchable database anyway), and discussions of relevant work or publications that I find interesting. At some point in the future I may also life-blog from a conference if I get the feeling that somebody has started to follow the blog who might be interested in that.
  • Cladistics and phylogenetic systematics. I am fairly sure I will, at some point, feel inclined to grumble about what is known as "evolutionary" systematics.
  • Science in general, especially our habits and work culture as a scientific community.
  • Freethought and the importance of using evidence and reason to inform our view of the world.
It should go without saying, but the views and opinions I express on this blog are mine and mine only, and not necessarily the ones of my employer, colleagues, or family members.

Enjoy - or feel free to search for greener pastures elsewhere!