Friday, May 31, 2013

Botany picture #70: Thlaspi arvense

Thlaspi arvense (Brassicaceae), Germany, 2012. This I found one of the easiest Brassicaceae that I had to learn in the first year botany course in university. The fruits are very characteristic, and it is a fairly common weed of building sites and agricultural fields.

Wednesday, May 29, 2013

Mopping up the remaining synchronous species concepts

It is time to pick up writing about species concepts again (other posts in this series can be found under the eponymous tag). I have dealt at some length with Biological Species, Genotypic Cluster Species, Morphospecies / "typological" / autapomorphic species, and the idea that species must be monophyletic. There are numerous synchronous species concepts left before I can tackle the asynchronous ones, but unfortunately I do not feel that I can treat all of them in the same depth. Some of them are simply variants of others, some apply only to very special cases, and some I simply don't really understand. I will therefore deal with all of them together in this post.

Tuesday, May 28, 2013

Botany picture #69: Callistemon pollandii

Callistemon pollandii (Myrtaceae), Australian National Botanic Garden, 2013. This pretty treelet is known as the gold-tipped bottlebrush because of the striking contrast between the yellow anthers and the red filaments.

Monday, May 27, 2013

My two cents on academic freedom

Some parts of the science blogosphere that I am following have been discussing the case of a professor called Eric Hedin over the past few weeks. From what has been reported, he has been offering an elective course at his US American public university that awards science credit but consists mostly of Christian apologetics and proselytizing, with a liberal sprinkling of creationist pamphlets but no real science included in the reading list.

The interesting thing is that rationalist and atheist scientists divided into two camps over the issue: evolutionary biologist Jerry Coyne and now physicist Victor Stenger argue that the university should scrap the course while developmental biologist PZ Myers and biochemist Larry Moran defend Hedin's right to teach unscientific nonsense with reference to academic freedom.

Part of this seems to be based on a misunderstanding; Myers, for example, claims that Coyne and Stenger are calling for Hedin to be fired but they did no such thing. The most forceful position taken by Coyne appears to be that such a course violates the US constitution.

Now I don't really have a horse in this particular race. Not being a US American or in the USA, I really have no opinion on their constitution. (Except perhaps that they should consider doing what every other country does and adopt a new one one of these days, perhaps one that was not written for the era of slavery, horse-drawn carriages and front loaded muskets. But I digress.) What interests me here is the concept of academic freedom.

As a German, I have learned about academic freedom in the historical context of the Goettingen Seven, and thus assumed that it was about being able to publicly hold a controversial opinion without being fired for it. But surely academic freedom cannot entail a professor not doing their job?

Thought experiments are always enlightening when faced with discussions like these, and of course Coyne and Stenger have already offered them. What if a physicist used one of their classes to promote a political party, or if a chemist awarded science credit for a course whose reading list consisted entirely of objectivist "philosophical" tracts? Would that also be acceptable under the banner of academic freedom? What if all tenured professors of a university decided, hey, we don't want to teach the students science anymore, we will all just award science credit to whoever reads the entire bible?

Perhaps even more interesting would be the following scenario: What if Hedin were promoting not Christianity but instead filled the reading list of his course with works of Wahhabi theology? Would his Christian supporters still be defending his "academic freedom" in that case? Let's just say I have my doubts.

Yes, academic freedom is important. Hedin should have the right to believe and publicly say controversial things, even to try and convert people to his sect. But in his science courses at a public university, I would argue he is supposed to teach science. That is not a question of academic freedom, it is a question of doing the job one is being paid to do by the taxpayer.

From that perspective, the slippery slope arguments invoked by Myers and Moran also don't apply because there is no slippery slope to be had between saying that a professor should not proselytize or teach theology in their science class on the one side and a professor being forbidden to teach good science in their science class on the other side.

Saturday, May 25, 2013

Botany picture #68: Maianthemum bifolium

Maianthemum bifolium (Asparagaceae), Germany, 2012. A rather unassuming liliaceous monocot forming part of the rich spring flower carpets in European temperate forests. It is apparently related to the more impressive genus Polygonatum.

Friday, May 24, 2013

Carbon dioxide milestone

This is old news, of course, but we recently passed 400 ppm carbon dioxide in our atmosphere. The following cartoon seems to say it all (click here for full version):

Mind you, that cartoon is on an American leftie website, so among the currently 82 comments on it you will not find the usual climate change denialism that descends on every other place daring to mention the topic. But what you do find is an also fairly typical pair of defensive reactions:
  1. Yeah, I needlessly waste a lot of petrol, but it is not really my fault because industry is worse.
  2. Yes, our industry is a bad polluter, but it is not really our fault because China is worse.
It can be assumed that a Chinese commenter would be inclined to argue that others are still worse on a per-capita basis and that China has the right to develop.

One of the greatest impediments to solving our global problems is that people consider this type of argument to be clever: "Yes, I am doing something suicidally stupid but that guy over there does the same, so stop bugging me."

Thursday, May 23, 2013

Botany picture #67: Aseroe rubra

I have never had the opportunity to learn much about fungi beyond the classification into Ascoymcota and Basidiomycota and a few theoretical details about their life cycle. The point is, I never had a course on the systematics or identification of fungi, so I really do not have a good overview. This truly bizarre species, however, is really easy to recognize. Aseroe rubra, the "starfish fungus", Australia, 2011.

Tuesday, May 21, 2013

Botany picture #66: Banksia heliantha

Banksia heliantha (Proteaceae), Australian National Botanic Garden, 2013. This species used to be known as Dryandra quercifolia but was transferred to Banksia in 2007. As in the case of the Epacridaceae being nested within the Ericaceae, it was discovered that Dryandra was nested within Banksia, and thus the former genus was sunk into the latter. And as in the case of the epacrids, in my eyes this should never really have been controversial. Epacrids look just like Ericaceae s.str. except they have lost one ring of stamens. Dryandras look just like Banksias s.str. except they have short head-like inflorescences instead of longer spike-like ones - the difference is merely how long a number of internodes in the inflorescence are.

A staff member of the ANBG once brought me a pot of a Dryandra as demonstration material for a talk and when he put it down, he said "I have never seen this species before, is it a Banksia?" No further comment needed.

Saturday, May 18, 2013

Botany picture #65: Epacris impressa

Epacris impressa (Ericaceae), Australian National Botanic Garden, 2013. Here in Australia every state has an official state flower, and this is the one of Victoria. Not sure if German states have any; if so, it is at least not common knowledge. I guess if Germany as a whole has a national plant it is the oak. Here in Australia the national floral emblem is a wattle (Acacia, Fabaceae).

Friday, May 17, 2013

Where to submit a manuscript

In the past few weeks I have repeatedly poked fun at science spam advertising poor quality for-profit "journals", and I have cited an article that claimed it would become difficult for some universities to evaluate scientists' resumes due to the meteoric rise of legit-sounding pretend-journals. I really do not "get" any of this.

That is to say, I do not get why a significant number of people would be willing or foolish enough to submit their manuscripts to pretend-journals, by extension how these pretend-journals can be profitable enough to the spammers for them to continue spamming (many of these "journals" have few to no articles and sometimes the few articles they have are plagiarized from elsewhere so presumably they cannot earn a lot of fees), and finally why anybody would find it hard to know the good journals in their field.

When you start out as a scientist (or scholar) you generally obtain a decent university education and write your thesis under a hopefully competent supervisor. The supervisor will be able to teach you not only how to write a decent paper but also to what journal to submit it. By extension, they will teach you what the good journals in the field are and what kind of "publication strategy" is expected of you if you want to become a career scientist/scholar in the field. In addition to your supervisor, can talk with other colleagues and learn from them. Finally, the papers you needed to read to prepare for your thesis as well as the reference list of said thesis will also give you a clear idea of where the relevant literature in your field is published.

Thursday, May 16, 2013

Botany picture #64: Epacris purpurascens

Epacris purpurascens (Ericaceae), Australian National Botanic Garden, 2013. The epacrids are a southern hemisphere clade of the Ericaceae that was once treated as its own family. However, although there are a few freakishly aberrant genera that look more like monocots than like Ericaceae, the differences between epacrids as a whole and the other Ericaceae are actually very small: the loss of one ring of stamens and, in most but not all cases, parallel leaf venation. This particular species has the fairly typical ericaceous habit: a smallish shrub with small, hard leaves and small, radiate flowers.

Wednesday, May 15, 2013

Reference managers

So far I have lived in the grey zone where the investment that would have been necessary to start using a reference manager appeared just a wee bit larger than the hassle of not using one. But after this Monday I am coming round to it.

The problem that reference managers solve is not so much having to add references to a manuscript per se - one still has to remember which was which to selected the right one, after all - but rather constantly having to format and reformat reference lists at the end of manuscripts. Every journal has its own idea of how a reference should look like. A few examples:

Smith A, Miller B, Ngyuen C, Kim D, 2009. Some paper title. Journal of Research 15: 42-48.

Smith A, Miller B, Ngyuen C, Kim D (2009) Some paper title. Journal of Research 15: 42-48.

Smith A, Miller B, Ngyuen C, Kim D (2009) Some paper title. J. Res. 15:42-48.

Smith, A., Miller, B., Ngyuen, C., Kim, D. (2009). Some paper title. Journal of Research 15: 42-48.

Smith, A., Miller, B., Ngyuen, C., Kim, D. (2009). Some paper title. Journal of Research, 15, 42-48.

Smith, A., B. Miller, C. Ngyuen & D. Kim (2009). Some paper title. Journal of Research 15: 42-48.

Smith A et al., 2009. J. Res. 15: 42-48.

And all possible combinations of the above and more! You can imagine that having to manually format all this for dozens of references gets tedious at some point. A reference manager does all that automatically for you, but of course you first have to import into it all the references you need and you have to provide it with the correct style information for the journal you want to submit a given manuscript to. And because I hopped so much from one study group to the next and from one methodology to the next during my career it never seemed profitable to import references and double check them to use them only in one, two or perhaps three manuscripts.

Because I now expect to work on the same plant family for a long time, and after having gone through a particularly annoying bit of reformatting, I have decided to start using the freeware reference manager Zotero with which I had already dabbled a bit a few years ago. Still, the trouble is the same as what put me off then:

If you don't want to enter all references manually, the easiest way is to import them from a website. Now Zotero is actually really clever at this: if your browser displays search results from Web of Knowledge or Google Scholar, it can open a list of boxes for you to tick and import several references at the same time. Unfortunately, Web of Knowledge finds only a ridiculously small percentage of the references I need and Google Scholar is stupid. I spend a distressing amount of time correcting what is imported from GS because it may provide first names as part of the family name, cities as publishers, paper titles or author names in ALL CAPS, and so on. Still, if I use the same references often enough it will hopefully be worth the effort.

The second problem is styles. Here it would probably pay off if I just invested the money to get EndNote instead, but I want to give Zotero a chance, and the Zotero style repository is simply missing most systematic botany and plant taxonomy journals. I assume I will in time have to figure out how to edit styles for my own purposes.

Tuesday, May 14, 2013

xkcd: birds and dinosaurs

Just about the most concise explanation of why phylogenetic systematics makes more sense than the alternatives:

From the webcomic xkcd, with thanks to Jerry Coyne for drawing my attention to it with a recent post on his website.

Monday, May 13, 2013

Settling controversies in science, philosophy and economics

Recently I came across a post by blogger Chris Hallquist in which he described his frustration with philosophy. His major points:
one of the biggest things that stands out is how I realized even big-name philosophers often produce arguments so awful that it’s hard to even say anything interesting about why they’re bad. [...]
A big part of the problem is that nobody seems to know how to resolve any of the major disputes in philosophy. This is closely related to the fact that, as philosopher Peter van Inwagen once said, “philosophers do not agree about anything to speak of.” [...]
The total lack of agreement among philosophers on just about anything is problematic for a couple of reasons. For one, many people would like to be able to settle philosophical disputes by looking at what the experts say, an approach that can make perfect sense on issues where the experts genuinely are agreed. But for any given philosophical dispute, while there may be many philosophers who take a certain position, there will pretty much always be many other philosophers who disagree. It’s safe to assume that anyone who tells you otherwise is trying to pull a fast one.
Another problem, which I detailed in retrospective part 1, is that the lack of agreement on what good philosophy is makes it hard to filter the good philosophy and reward the philosophers who produce it.
Another area comes immediately to mind in which similar problems appear to exist is economics, also known as "the dismal science". In contrast, physicists, chemists, climate scientists, astronomers and geologists agree virtually unanimously on virtually anything of importance in their disciplines. It becomes a bit fuzzier in ecology, evolutionary biology and biogeography but the fact of evolution, for example, is in no doubt whatsoever, something that cannot be said, as Hallquist points out, for any of the major issues in philosophy, nor for a question as fundamental as how to deal with a financial crisis in economics.

So what is the difference? Is philosophy simply fuzzy nonsense, or is it dealing with problems that are simply harder to solve? What about other areas where it seems no agreement is being achieved? I must admit I am not writing this post with a great deal of preparation, but it seems to me that there are, as often, various factors to be taken into account.

Sunday, May 12, 2013

Mother's Day in the Australian National Botanic Garden

People having a Mother's Day pick-nick in the Australian National Botanic Garden.

The canopy of the Rainforest Gully.

A species of Syzyngium (Myrtaceae) in the Rainforest Gully. This must be one of the oddest-looking genus names in the family.

Rulingia magniflora (Sterculiaceae). The flower is really quite small, it is only "magni" for a Rulingia. But pretty.

The spectacular Lechenaultia formosa (Goodeniaceae) growing in a pot directly next to the Visitors' Centre at the entrance. Although Goodeniaceae flowers are usually the other way around I think this is right. Maybe this species has resupinate flowers.

Thursday, May 9, 2013

Botany picture #63: Sinningia brasiliensis

Sinningia brasiliensis (Gesneriaceae), Botanic Garden of Zürich, 2009. The Gesneriaceae are a large pantropical family of mostly herbaceous plants. Like the related Acanthaceae, they are comparatively irrelevant for us humans except as ornamentals. What makes these families, and not least the genus Sinningia, particularly interesting are their diverse pollination syndromes. With its greenish color, short, wide opening and the placement of the anthers and stigma, this species is clearly adapted to bat pollination but others are hummingbird- or insect pollinated.

Wednesday, May 8, 2013

More funny science spam

Ye gods, I wonder when we will pass peak ridiculous.

An editorial "manger" advises me to "always publish work in journals not on webpages as publication in journal have value in carrier". Next time I want to have something of value in a carrier I will consider these wise words. Also, by my count, the message uses nine different font colors, including three shades of green, and four different fonts. Stay classy, Earth Journal Publishing Group!

About a month ago the New York Times ran an article on predatory open access publishers that gives a good overview of the situation. A few remarks:
But some researchers are now raising the alarm about what they see as the proliferation of online journals that will print seemingly anything for a fee. They warn that nonexperts doing online research will have trouble distinguishing credible research from junk. “Most people don’t know the journal universe,” Dr. Goodman said. “They will not know from a journal’s title if it is for real or not."

Researchers also say that universities are facing new challenges in assessing the résumés of academics. Are the publications they list in highly competitive journals or ones masquerading as such?
It is easy to believe the first part - surely one cannot expect somebody from outside the field to know the good journals. But in my own area I know nearly all the relevant journals, and I surely know how to judge a scientist's output by looking at the names of the journals in their publication list. Are they getting into the ones that publish high-quality research? Are they taking the path of least resistance, always submitting to the same two or three journals, one of them published by their own employer? And the names of predatory open access journals have a kind of method to them that makes them relatively easy to spot in most cases. If it is the Journal of XYZ, it is most likely legitimate. If the name is something convoluted like International Research Journal of XYZ your alarm bells should be going off. So if you let resumes be evaluated by a competent peer of the scientists in question you should have no problems there.

At the time of my reading, the first reader's comment to the article is this:
This article gives the false impression that charging academic authors to publish is unusual, or limited to dubious upstart journals. In fact, the vast majority of academic journals, including the most respected ones in many fields, have long charged authors to publish, and reaped substantial profit from enforcing such charges. This is the bread and butter profit of many respected publishing houses. Publishing academic papers costs money, but since they are read by almost nobody, a charge the reader approach (even with libraries as the main 'readers') does not work. Thus, academics pay to publish their research, just like bad novelists do. Of course this payment is generally covered by their government grants, so in fact it is the taxpayer that pays in the end.
That is a fairly odd view of things. I have no great love for the profit-making of certain science publishers, and yes, ultimately the taxpayer finances all non-profit research. Well, duh. Perhaps it would indeed be better to have scientific journals treated as utilities, financed directly from taxes and run as non-profits.

But at least in my area traditional, non-open-access publishing is predominantly financed by journal subscription fees paid by the libraries and not through fees paid by the authors. There are some caveats: Some society journals offer free publication to members but demand page charges from non-members. Some journals demand page charges above a certain page count of your article. And generally all journals will publish greyscale figures for free but demand an additional charge for color figures. But these fees are usually quite reasonable and/or easily avoided: become a member of the society or chose a different journal, write more concisely, use greyscale figures. The real cost is on the side of the reader.

That is just the point of the movement towards open access publishing, after all, with its advantage of allowing the public to access all the science it has financed. But, it will have to be admitted, this move also comes with the attendant problem of shifting the commercial publishers' incentives towards publishing as many articles as possible instead of only the best, a problem that reaches its epitome in the predatory publishers discussed in the linked article.

Well, maybe the reader who made this comment comes from an area where traditional publishing works very differently than in biology.

Tuesday, May 7, 2013

Botany picture #62: Epipactis atrorubens

Epipactis atrorubens (Orchidaceae), Germany, 2012. For some reason I had never seen so many orchids in such a short time as during our visit in Europe last year, and that despite having participated in many field courses in my home country. One problem is clearly that one does not really learn much about orchids as a student. All orchids in Germany are rare and protected, and consequently it is not possible to simply collect a big bundle of them as course material for biology students to dissect.

Monday, May 6, 2013

What to avoid when writing the resume for a job application in science

Not enough time to continue the series on species at the moment. But apropos of nothing in particular, it might be helpful for somebody who searches the web for advice on job applications in science to read what irritates me when going through resumes. Just my own opinion, of course, but it can reasonably be assumed that I am not alone.

So when somebody writes their application for a job as a scientist and compose their CV or resume, they may want to consider the following:

Do not mix your publication list with conference posters or talks. A poster at a conference is not a peer-reviewed journal publication. At best, the recipient of your application will resent having to figure out what is what, at worst they will assume that you are trying to inflate your perceived publication record by deliberately confusing the reader. Keep the two in separate sections.

Do not include submitted manuscripts or manuscripts in preparation as part of your publication list. The word publication kind of implies that the manuscript in question has actually, you know, been published. If it is still in preparation, it may never be. One can have six papers in preparation and then never finish three of them because there is just no time for it at the new job or now that the baby is born, and even submitted manuscripts may be rejected by three journals in a row and then the authors give up on them. That happens. The same applies as in the above item: Make separate lists titled "publications", "submitted manuscripts" and "manuscripts in preparation".

List your publications in a logical sequence, preferably from youngest to oldest, alternatively the other way round; "in press" obviously counts as youngest. Jumbling them up randomly in a non-chronological order makes it harder to see what you have done the last few years and will only annoy the reader.

If you do not quite fulfill one of the criteria or do not have one of the skills for the job, the best strategy is to honestly admit it. It may not be a fatal weakness of your application because there is a chance that no other candidate has all the skills that would make them perfect either. It is not a good strategy to write nothing whatsoever on the topic. Instead you should try to make the case that it would be easy for you to obtain those skills because you are good at learning, that you always wanted to do it anyway but never had the resources to try it, that it is sufficiently similar to something else you have done, something like that. The worst strategy is to write a long and rambling but completely unrelated text block that patently tries to confuse the reader and distract from the fact that you do not have that skill, especially by deliberately misunderstanding the question. People will see through it and they will not necessarily interpret it in your favor.

Apart from that, a reader who found this helpful might also want to check out my old post on job applications in three different scientific communities.

Saturday, May 4, 2013

Botany picture #61: Suessenguthia barthleniana

Suessenguthia barthleniana (Acanthaceae), Bolivia, 2007. Named after a German professor, Suessenguthia is a small genus of only six species found in southern Peru, Bolivia and Acre, although it will perhaps have to be united with the larger genus Sanchezia at some point in the future. They are shrubs with large pink to red flowers, and one species is used as an ornamental.

Friday, May 3, 2013

Science is not just a method, it is also a community of professionals and a body of knowledge

Although I have written about my view of what science is twice before, I feel that there is at least one angle that I have not covered yet. It has to do with different views of whether science is merely a method or more than that, and how these views collide in discussions about the demarcation problem and the accommodation of religious belief. "Science" is at least three things:
  1. A toolbox of methods for generating objective knowledge (i.e. justified true beliefs) about the universe around us.
  2. The community of professionals using this toolbox of methods, and their workplaces, journals, organizations and institutions.
  3. The ever increasing edifice of documented facts, observations, hypotheses that have survived testing, models that outperformed all other models, theories that haven't yet been superseded, and probably more besides, commonly called the body of current scientific knowledge.
Following the way disambiguation is handled in Wikipedia, we could call the first science (method), the second science (community) and the third science (worldview). I find it very hard to separate the three: the community exists as soon as the method is used, the method does not exist unless there is a community that actually uses it, the community would not know what best to use the method for if it would not first consult the worldview to find unanswered questions, and the entire purpose of using the method and paying salaries to the community is to build the worldview. You cannot reasonably view any of these in isolation.

Thursday, May 2, 2013

Botany picture #60: Porophyllum ruderale

Porophyllum ruderale (Asteraceae), Bolivia, 2007. Since I saw this species for the first time during field work in 2000 I only ever thought of it as an unusually ugly roadside weed. But it turns out that this unassuming daisy is actually a culinary herb! It is also known as quillquiña.

Wednesday, May 1, 2013

Ridiculous sophistry that nobody actually believes if they are honest

The actual, historical sophists were a school of ancient Greek philosophers. Their teachings may or may not have had merit, I really would not know, but today they are mostly known from the term sophistry, which means to make spurious or dishonest arguments to win a discussion. This is because supposedly the actual sophists were also more interested in teaching how to win a discussion than in finding the truth. Be that as it may, sophistry in the modern sense can be pretty exasperating.

One of my "favorites" is the argument that nobody can really know anything, perhaps due to the problem of induction, perhaps because science cannot prove that the scientific method works, or because every belief is just arbitrary opinion or ideology anyway, even science. This is obviously what comes out of the south end of a north facing bull because the people who argue like that still leave their houses through the door instead of attempting to walk through walls, they still board airplanes, and they still trust that their jacket will not spontaneously turn into a tree while they are wearing it. In other words, they do believe that one can tentatively gain knowledge through observation and the use of reason and rely on this knowledge, they only pretend not to do so when shown that another of their beliefs (e.g. in some supernatural process or entity, or in the efficacy of some "alternative" medicine) is ludicrous.

Here is another one that I have recently come across:
Absence of evidence is not evidence of absence.
Sounds reasonable, right? At least at first sight, and from the perspective of an armchair philosopher. But do you actually reason like that, as we say these days, in real life? What would you say if you met a well-educated adult who argued, well, I have no evidence that smurfs exist, but I cannot disprove their existence either, so they may well exist? Would you consider that reasonable? No, you would rightly consider that person to be an idiot, or at a minimum to be somewhat unsound of mind.

Of course where I did encounter the argument was once more in the context of discussing certain supernatural entities, where for some bizarre reason people seem to consider it legitimate. But it could just as well be used to defend claims for the existence of alien visitors, Bigfoot, unicorns, the continent of Lemuria, reptilian shape-shifters from the hollow center of the planet, and other spurious nonsense. And that is just the point.

So what this sentence should look like is this:
Absence of evidence where we would reasonably expect to find evidence is tentative evidence of absence.
Does not roll off the tongue quite so easily but it has the advantage of not being as stupid.