Maths and Biology Students: My take on EO Wilson’s essay

12 04 2013

Last week, E. O. Wilson wrote this controversial Wall Street Journal essay that has set the biology blogosphere on fire, a fire that’s mostly headed towards Wilson. I don’t want to be left out of the fun and games, so I want to add my own opinion into the cauldron. Before doing so, I will stress that while I consider Wilson one of my personal idols as one of the last remaining old-skool field naturalists, I am setting aside this bias here.

In a nutshell, the essay’s premise is that to be a great biologist, you don’t necessarily need to be good at maths. My take on the essay is that it’s split right down the middle: half of it is good and I agree with, half of it I consider invalid or at least badly argued.

In Wilson’s general defence, I read it as a semi-autobiographical take on the issue. From this point of view, I will have to disagree with the many commentaries that say he was trying to advise students in a particular direction. No. Wilson merely took his own experiences and extrapolated from them in order to give a pep talk to those students who have trouble with maths.

His experience, as described in the essay, is that you don’t necessarily need to be even an adequate mathematician in order to be a biologist, because in biology, you get new hypotheses and ideas by creative thinking, writing down notes and observations from the field, and putting these all together.

I have a lot of empathy for this. In fact, I encourage my students to do exactly this: write down all your ideas, no matter how crazy. Mull them over, talk them through with colleagues. Come up with hypotheses, and test them. It’s how the scientific method works. To me, the students that impress me the most are the ones that ask odball question, that will come to me after class and share a wacky idea they thought of, or that will run impromptu experiments out in the field because they noticed something weird. It’s also how I work as a biologist: most of my knowledge and research ideas came about as the results of thought experiments I conducted by myself and had fact-checked by professors and colleagues.

But the flipside that Wilson seems to have ignored is that instead of writing your notes in English, you can write them in maths. He considers maths as just a toolkit, when in fact it’s a language. It’s just as creative to write down a mathematical equation as it is to write down an idea in English, and putting together a mathematical model is exactly analogous to combining a series of related ideas into a general theory.

The main difference, as I see it, is your own bias. As primarily a strictly empirical field biologist, I tend to jot down ideas in a strange variant of written English only I can understand (a security measure or lazy writing? You decide). But in some cases, maths was superior: when I was wrapping my head around the concepts of genetic drift, natural selection, or group selection, maths was my thinking language of choice, because it allowed me to focus on the relevant factors and their relative importances, rather than trying to concoct an intuitive story based on wild ideas in my head. I draw my personal line at evolutionary theory and some ecology, but I know people who can break down every part of an organism into equations, and others who can’t even stand the idea of putting together a model of energy transfer from Sun to top predator (something you learn in middle school biology).

Mathematical modelling isn’t for everyone, nor should it be for everyone. This is where I agree with Wilson. But there is a very important caveat: not all biologists should have to build models, but all should be equipped to understand models. This isn’t a contradiction: my genetic and developmental labwork skills are nothing short of pathetic, but that doesn’t prevent me from successfully working on microevolutionary problems that need insights from genetics and developmental biology. Similarly, even if you can’t build a fancy Lotka-Volterra competition model from scratch, that shouldn’t prevent you from reading one in an ecology paper or even downloading the R script and playing around with it.

This is the point I feel Wilson canvassed over. He seems content to leave well enough alone. Can’t understand these differential equations because you don’t know maths? That’s okay, here’s a paragraph explaining what they mean. Such a perspective is fine if you want to popularise the science, but as a working scientist, you must be able to get down and dirty not only with results and conclusions, but with the data-generating methods, which may be mathematical models. Just like you might criticise a phylogenetic paper for not having a large enough taxon sampling, you ought to be able to take a model and criticise it. If you can’t, then you risk intellectual dishonesty that may potentially be grave: if you can’t understand how the results came to be, then you’re in no position to judge the validity of those results, and by extension, you can’t in any honesty use that data for your own research purposes.

I can’t stress this point enough. You must realise that much of the critical basics of evolution and ecology, as two of the most important fields of biology, are based on mathematical models. Fisher, Haldane, Price, Maynard Smith. Household names in evolutionary theory; their foundational work is mostly centered around mathematical models they built. If you can’t understand them and aren’t willing to make the effort to do so, then quite frankly you can just give up on truly understanding evolutionary theory. (Sidenote: I’m torn on whether it’s okay to cite papers you don’t understand completely. Ideally not, but then again we do have a trust among us, reinforced by peer review, that the conclusions are tentatively reliable. But it’s iffy, I personally wouldn’t recommend it.)

All this time, I’ve been talking about mathematical models, because I see absolutely no excuse for any biologist to not be well-versed in statistical methods. You can be forgiven for not knowing the mathematical backgrounds for them (I confess ignorance for most), but considering the myriad books available specifically for biologists, and the ubiquitous need for statistics, they’re a required part of your basic toolset.

Wilson’s solution to not knowing maths is one I mostly agree with: collaborate and cooperate (hooray consilience!). As stressed above, I don’t agree in the case of statistics, but for mathematical models, do go ahead. Wilson has done this many, many times. He comes up with the ideas, goes to a trusted mathematician colleague, and they whip up a combo mathematical model and naturalistic explanation. This was how Wilson revolutionised biogeography and community ecology. His own ideas alone were great, but what really elevated them to biological mainstay status were the accompanying models by MacArthur. The firestorm he started over kin selection is very similar: he’s had these ideas in his head, and used the help of Nowak and Tarnita to develop the mathematical models to back them up. (About that: I think there was a lot of smoke in the negative reaction towards it, as I’m pretty certain kin selection has deficiencies, which was Wilson’s point).

Finally, I need to go back to my roots and stress that I, personally, will take data gathered from observation over mathematical models anytime, because while models offer incredible precision, that precision may well be illusory. Biology is an intrinsically messy discipline that doesn’t take too well to too much reductionism. Even when I have the skill to build a model for a phenomenon, I will always prefer getting empirical, experimental, field data from the real world.

That’s all I wanted to say about this. As a teacher, I’ve often observed the same thing that Wilson did: talented students turning away from biology because suddenly they come across maths. I had the very same problem, and my mathematical abilities are very specifically self-taught (I am completely helpless with any physics maths) and are merely an extension of my intuitive biological daydreams. For the gifted students who think they’ve hit a wall, here are my two tips.

  • Befriend some mathematicians, or take some basics maths courses, or buy a “maths for dummies” book. Maths is basically a very logical language, and you just have to learn how to read it. Don’t be daunted by the apparent complexity of it (I personally find the writing of maths the most tedious aspect).
  • Find mathematical models, break them down, reconstruct them. The letters there all stand for something. Follow the thought pattern through the equation, and you will be able to piece together a paragraph explaining the meaning of every single equation you come across. I did this as a student for all the models I came across, and also tried to reconstruct the classic models of evolutionary theory. This is how I learned maths.

And whatever you do, don’t give up. If all else fails (which I understand, as even after 4 years, I still couldn’t properly calculate how fast a stupid egg will drop from an airplane), you can always collaborate, or get into a field where you need not build any mathematical models.

Basically, where I agree with Wilson is when he says that creative thinking is the most important quality of a scientist. Where I disagree with him is when he says that expressing oneself mathematically is somehow not creative.





Resource For Schools

1 03 2013

Amid calls from several readers for me to write and compile basic-level biology articles into a nifty coursebook (calls that I will address below), I would like to share an alternative I discovered: Shmoop. Their free biology learning guide covers everything that middle- and high-school biology courses cover. Each topic has an in-depth look at each relevant section, along with glossaries, problem questions, great links, and outlooks to real-world applications (to answer the “why should we learn this?” questions). After skimming through the whole thing, I can heartily recommend it for any teenager, or if you yourself want a refresher in the fundamentals of biology.

There are also teacher’s resources, but I haven’t checked them out (paywall). The website also offers guides for other courses, which seem to be of the same general quality. As a Shakespeare fanboy, I checked out their Shakespeare guide and was satisfied.


Now, about a biology/evolution/palaeontology coursebook, and even a full-blown online course. First, I must say I’m flattered by the idea, and that several of you independently converged on it. While I will not rule out revising and compiling the meaty posts from the blog into a self-published book, I don’t see why I should bother to make a complete coursebook or online course. Two reasons for my blindness, one practical and one philosophical.

The practical reason is simple: I’m unemployed, only taking on projects that I feel will eventually provide a return on my investment. Unless someone offers me a financial incentive, I will not waste my time doing something that I see as useless, such as a coursebook or online course.

The reason I see it as useless is because a coursebook/online course is nothing more than an information delivery system. Raw information is not understanding, and delivery of that information is not education. That underlines the critical difference between an online course and a real life course, at least in any subject I would be qualified in teaching.

I already do information deliveries through the blog. But while someone who has read my entire blog archive will know a lot of trivia and be able to spout off an impeccable literature list for any relevant subject, they wouldn’t have learned much about a topic. To me, a course is emphatically not about gathering information, but about understanding and learning. Both of these require feedbacks, they require the teacher and students to constantly exchange ideas. This is why teaching using a good old blackboard will generally be superior to a Powerpoint lecture or the numerous webcam lectures I do to help out lazy colleagues – a blackboard is interactive. An online course doesn’t have this element, which I see as critical. It’s fundamentally the same reason why problem essay questions are always superior to simple or multiple choice questions.

A coursebook I would prepare would be identical to any already-existing textbook, except with worse graphics. One could argue that it’s cheaper, but with free resources like Shmoop around, that argument also falls apart. There simply is no reason why I should be wasting my time doing something with minimal profit – the little amount of money I would make from it would certainly not pay off for the long time spent doing something completely derivative.

So, to summarise: learning, to me, is all about stimulating thought, not about sponging up information. And I don’t see how an online course, written or video-based, can achieve this goal, at least not yet.





My Work: External Advisor With Schools

11 10 2012

One of my current projects is working with various private schools in Cyprus (not public because I can’t teach biology in Greek), giving students various extracurricular opportunities that give them more insight into nature and how to think like a biologist, things that for various reasons aren’t/can’t be done within a regular school year and curriculum. Since I don’t have the qualifications to be a proper school teacher (EU law states that one has to have a proper education degree), these are all one-off activities or long-term projects in which I act as an advisor or guest lecturer.

The activities I propose all come from my own areas – evolution, zoology, palaeontology, geology, and basic ecology. Luckily, these are fields that are left woefully untouched by most European curricula. Based on a short (and probably inaccurate) survey I did, worldwide ones are sorely lacking as well, except the Japanese curriculum which is heavily steeped in natural history. The standard EU curriculum is actually pretty boring, with most of the material concerning cell biology, biochemistry, and genetics, with the actual cool parts of biology nowhere to be seen. Cool may be relative, but I know from my own experience as a museum guide that the best way to inspire kids and teens to become biologists isn’t to bore them with biochemical cycles like photosynthesis and the Calvin Cycle, but by showing them weird stuff and using those as a jumping point into biology proper. I became a biologist not because I learned the word phosphorylation, but because I saw a picture of a trilobite in my textbook and thought it was freakin’ awesome.

Note that these are strictly extracurricular. They can be tied in many ways to the set curriculum, but they can’t replace it. For example, the zoology fieldtrips can be done as an addendum to the ecology or evolution sections of the course. I may later do a post on what ideal elementary and high school biology curricula should look like (because current ones certainly don’t fit my vision!).

Note that these activities aren’t necessarily only for schools – if you’re a parent, you can do these with your kids (note: this is not an endorsement for home schooling!). These are general things I’m suggesting, with infinite customisations possible to suit individual classrooms, age ranges, and situations. Teachers, I strongly encourage cooperating with a local environmental institution or university – you’d be surprised by how much cooperation is possible if both sides just bother to get in touch with each other. The way I’m getting these done is by going to the reception desks of schools and asking for meetings with biology teachers – at least in Cyprus, going through a personal approach is the best way; don’t try to meddle with school affairs, and be sure to be fully accommodating to the teachers. After all, you’re providing a service with the teachers as customers, and unlike other service industries, in this case the customer knows what’s best.

Activities for Kids (= elementary school age)

Kids need visual and experiential stimulation, if only because the average attention span of a child isn’t really conducive to lecturing and textbook reading. You need to get them excited about a subject by telling them random cool trivia about it, and then you let them experience it hands-on. This is the thinking behind these activities. Note that for fieldtrips, it’s not a good idea to take them for more than a couple of hours – they tire easily.

  • Fossil fieldtrip (2 hours): Take the kids on a short fieldtrip to a single fossil locality, as near as possible (to let them feel that fossils really are accessible). The best would be a place where fossils can be picked right off the ground or can be seen clearly in the outcrop, to avoid them having to use hammers. Let them see everything, but keep collecting limited so they learn the value of geoconservation. Make sure you prepare an illustrated checklist of the common fossils so they have an incentive to look for everything. Combine this with a visual explanation of the locality’s palaeoenvironment – make everything into a story.
  • Zoology fieldtrip (2 hours): Take the kids on a short fieldtrip to a nature trail/nature spot nearby. Have them dig around under stones to try and collect any invertebrates. Have them check tree trunks and flowers for insects. It’s best if there is a stream or lake or other water body nearby for the opportunity to get aquatic organisms too. Make sure that anything they do collect gets released in the same spot. The kids will be happy just being out in nature, but this can also be a powerful long-term project – take them to the same spot once a month for them to get a feel for how the environment changes with the seasons. Combine all of this with classroom looks at select organisms, and they’ll be hooked.
  • Urban ecology (2 hours): This is exactly the same as the zoology fieldtrip, except the nature spot is within the city. This can be a park or a cemetary, or a tree-lined pathway or even street. This will teach them that biodiversity isn’t something that one has to travel far to see, and that the city itself isn’t some desolate place, but an ecosystem also teeming with life. It’s a powerful realisation for kids, and will make them more considerate of the environment.
  • Stereoscope sessions (1 hour); only if equipment is available (can be substituted with large magnifying lenses): Magnified things are infinitely cooler than when they’re regular-sized, and this is doubly true (yes, double of infinity!) for organisms. Just get some insects (perhaps from one of the field trips), earthworms, and whatever other small organisms are available in your vincinity, and have the kids look at them under a stereoscope or large magnifying lens. They’ll be hooked, and it wills erve as a good precursor to basic anatomy lessons.
  • Terrarium (long-term project): Simply build a terrarium and have them raise an animal in there. Ant farms are the classics, scorpions are also pretty cool to keep, as are beetles and caterpillars. Other animals may require more maintance (e.g. praying mantises), so I advise against them. Contact me if you want rearing information, or just do some googling. They can observe their behaviour first-hand and even do basic experiments.
  • Aquarium (long-term project): As with terrarium, but using brine shrimp or vernal pond sediment.
  • Anatomy (1 hour): Prepare sets of body parts out of card, from all over the animal kingdom (tentacles, proboscises, arms, legs, antennae, fingers, etc.). Have them combine them to form real animals (provided with simple diagrams/pictures to guide them). They’ll learn the true diversity of animal life, beyond the charismatic animals they see all the time on TV. Feel free to contact me for assistance with this.

Activities for Teens (= secondary school age)

The typical teenager will just be glad to do something other than the usual school stuff, so use that to your advantage by sneaking in as much raw information as you can without making your activities boring. Teenagers are my second favourite age group to teach (first is undergrads), and that’s because when you get them inspired, they work harder than anyone else. So if you’re dealing with a classroom full of them, you may face an ocean of apathy, but you may also uncover some gems and talent, so it’s worth it. They’re also fun because you can be a bit risqué with them. I once took a class of teens on a trip to a forest, and euthanised and dissected a squirrel to show them parasites (the squirrel was almost dead anyway, there were no ethical quandaries). They loved it, because it was cool and gory, and yet they still learned a lot of information about parasitology. You should use such spontaneous opportunities when teaching teenagers – think of it like doing improv comedy.

The activities here follow pretty much on from the ones for kids, so read above for the full descriptions. Here I will only write the modifications to make the activities more advanced.

  • Fossil fieldtrips (3 hours): Instead of taking them to a single, spectacular fossil locality, take them to a less spectacular one where they may have to look harder for fossils. Maybe even have them simulate a fossil dig. Alternatively, take them to multiple close fossil localities so they can see the basics of stratigraphical correlation, in which case they can learn how to draw and describe profiles too.
  • Geology fieldtrips (3 hours): This is mostly aimed specifically at Cyprus due to its iconic geology, but other countries must have places to visit some great geology too (best to ask at your local university’s geological or geographical department). The advantage in Cyprus is that the localities here can very easily be used to teach basic geological principles; these may be lacking in other countries. In such cases, a classroom introduction would be a good idea, and then taking them to the field so they can see the rocks and geology first-hand.
  • Zoology fieldtrips (3 hours): As in the Kids section, except with a more rigorous identification lesson, and an introduction to field ecological methods – maybe do a transect walk, have them take notes on where and how they collected their insects, and other such practicalities, so they get to know how a proper work method is like.
  • Urban ecology fieldtrips (3 hours): Same rigorousness from above.
  • Stereoscope sessions (one hour); only if equipment is available at school: As with the Kids section, but combined with a proper anatomy lesson. Contact me if you want help with this.
  • Dissections (2 hours): Dissections of already-dead specimens – you want to take this chance to teach them about basic bioethics as well as anatomy. Get vertebrate parts from the butcher’s, fish and cephalopods from a fishery, and invertebrates captured as part of a fieldtrip or a sampling station (see later). If you want help with how to carry out the dissections, or explanatory diagrams, contact me.
  • Standardised sampling (long-term project): Set up an insect trap somewhere on school grounds, a nearby field, or other convenient area that will not be vandalised. Have the class maintain the trap. This was originally conceived as a free data collecting mechanism for my research, but it can be easily be used for educational purposes. Just the data-logging is enough to teach them statistics, especially when combined with weather data. Work with a local entomologist or zoologist, and you will have a reliable source of Ids, and you can use your trapped specimens for your dissections, stereoscope sessions, or anatomy lessons. Or, you can start a classroom insect collection, and give each student a research project to find out about the insect and do a presentation about it. The possibilities are endless – but as I said, this is my attempt at setting up a citizen science network, and I haven’t really thought of the educational potential.
  • Terrarium, Aquarium (long-term projects): As with the Kids section, except have the kids run experiments. If you cooperate with a zoologist/ecologist, you can even do novel work, as with the Blackawton Bees project that got published in Biology Letters. You can have these experiments replace the usual dead-boring chromatography experiments or whatever is now done in high school biology. Remember: working with living organisms is always cooler than working with molecules, unless your students want to become chemists (which means they’re a lost cause anyway).
  • Scientist interview (30 mins): This is aimed more at those in the last 2 years of school. Invite a scientist (from the local university, or internationally by Skype), have them introduce themselves and their research, and have the students quizz them on their study and career path, why they went into science, and other such questions that will both inspire the students and give them a realistic perspective. For best effect, do this multiple times, with scientists of different genders and rank (a professor, a grad, an assistant prof.), and even scientists from outside academia.
  • Animal Biodiversity (2 hours): This is a presentation on animal biodiversity and phylogeny (can be done for plants and microcritters, but that’s not something I can do), preferably with a couple of specimens to check out in addition to the powerpoint/video. If you don’t have access to a zoologist, go here and prepare a lecture yourself. The basic point of this is to let them know that the charismatic animals they see on TV are a tiny percentage of even phylogenetic diversity (too often, I encounter kids and students who think that vertebrates form the bulk of biodiversity, which is too flawed to even compute in my head). Show them meiofauna, parasitic organisms, and the enormous diversity of “worms”. That is quite a lot of work if you’re not familiar with the stuff though (contact me for help if you need it!), so an alternative would be a presentation on the local biodiversity – but please try to avoid the charismatics. Show them interesting animals, not the ones they’ve already seen hundreds of times (take them to a zoo if they’re really itching to see charismatic fauna).

Activities I wish I could offer:

  • Biology in science fiction, fantasy, and mythology: No school would accept this, but I think this is a great way to get kids and teenagers interested in biology. From the biology of great mythical and fantastical creatures (dragons, orcs, griffins, etc.) to the heredity of midichlorians to the population biology of humans in Tengen Toppa Gurren Lagann, there’s a lot of offball questions that can stimulate students to think biologically. With the examples pulled from fiction, it adds a refreshing and fun touch, they’ll definitely enjoy the course because they get to watch awesome movies and, if I’m running the course, they’ll get an additional education in cinematography, filmmaking, and scriptwriting (personal factoid: my decision to study biology at university was last-minute; I was on track to getting signed up in film school). I think these three reasons are why no school would ever accept such a proposal.
  • Biodiversity showcase: This is only hard to do because getting enough samples would be very hard without a sponsoring natural history museum; it’s also logistically difficult. This is basically an addendum to the animal biodiversity presentation, with a thorough showcase of specimens. Each phylum gets one or two cabinets, and the students go around and draw the organisms. Pick one and do a small research project and presentation on it.
  • Rock and mineral ID: Same as above (incl. problems), except with rock and mineral types.
  • Geological exercises: Show them how geological features form in the lab. Very easy to do for sedimentological features, all you need is a deep tray with sand, water, and a paddle. Igneous and volcanic ones can also be simulated.
  • Roleplaying exercises: This is something that you can do to encourage them to think practically in environmental terms. Take them to an ecosystem, give them a tour of it (zoology fieldtrip!), then pretend you’re a developer who wants to build a hotel on that ecosystem. Have them come up with arguments to dissuade you. There is a small risk of turning them into eco-terrorists, but most will simply come away with all the good arguments for conservation.




Imaginary Ramblings: My Perfect Natural History Museum

4 07 2012

I’m a huge fan of natural history museums, especially zoological museums (see this post on their origin). Every time I go to a new city, the first thing I visit is its NHM. On a recent fieldtrip (token postcard picture up there), my partner suggested that I should open a natural history museum for Cyprus with all the samples that I’ve collected. This is, of course, pure fantasy – such an endeavour would never get funded locally, and a finished museum would never be visited by Cypriots anyway (a cynical view, but one that will be corroborated by any Cypriot you speak to). But hey, if any reader happens to be acquainted with a millionaire with money to spare for science education for a country sorely lacking in science knowledge, feel free to hook us up (alternatively, link them to my Petridish project!). And make no mistake, the only reason I’m not opening such a museum is because it costs too much money in just sample preparation costs, just to buy the materials and chemicals necessary (I haven’t even considered things like electricity or building space or poster printing costs).

Anyway, it is an interesting thought experiment, and as someone who’s worked in museum-related activities (museum guide, small-time curatorial work, a lot of sample preparation), I’ll admit I’ve often thought about what the “perfect” NHM would be like (note that I’m referring only to the public side of the museum in this post; the research side that makes up the bulk of any NHM but that the public barely sees functions like any academic institution).

Perfection is subjective of course, so before starting off, I’ll define what, to me, the goal of an NHM is, because my opinion might differ from others’. To me, the goal of an NHM is primarily to inspire, with education being a secondary goal. Of course, up to a certain age, any exhibit will necessarily be educational, but a museum that dedicates itself to a purely educational cause is bound to restrict its audience to schoolchildren.

Allow me to give you an example. The most awesome museum exhibit I’ve been to is the Darwin exhibit of the Zoological Museum in Copenhagen. If you haven’t been there, definitely pay it a visit. The exhibit had two rough parts: one on Darwin, with a recreation of Darwin’s workplace on the Beagle and at home. But the majority of the floor was devoted to exhibiting the diversity of animal life. Vertebrates dominated due to their sheer size, but at the far end of the room, the entire wall was dedicated to displaying a tree of animal life, with specimens instead of names. So you had a giant wall with all sorts of animals pinned on it. Of course, I learned nothing new while looking at this. But I was so inspired that when I got back home, I thumbed through some of the lesser explored parts of my invertebrate zoology textbook (a plump 980-page hardback) just because the exhibit awakened this desire in me to learn more. This, to me, is the goal of an NHM: to stimulate people of all types, from experts to laymen to children, to learn more. Go to an exhibit, come back home with a sense of wonder, and hop on Wikipedia or buy a science book.

Also, an NHM shouldn’t be a place you visit once. The exhibits have to be engrossing enough to really take people in so that they don’t have time to visit the other exhibits. This isn’t a money-making ploy (I would sell tickets that are valid multiple times to make up for this effect). It’s to ensure that the visitors really get a sense of how treasurable what they’re seeing is. If they just breeze through a museum, nothing will stay in.

With all that in mind, I will describe what my NHM would be like, if I were given an infinite budget and no restrictions. To me, “natural history” encompasses three areas: geology, biology, and palaeontology. And the NHM has to have two aspects: the general aspect with the basics of a subject, as well as a focus on the local natural history, because the latter will allow visitors to really connect with the stuff on display, and encourage them to do some exploring on their own (or with organised field trips with the museum experts).

Biology: General

“Biology” is an enormous discipline. In the general section, I would include exhibits on evolution, ecology, and biodiversity.

The evolution exhibit is probably the toughest to do, since evolutionary biology is such a broad subject consisting of many disparate fields. For a basic display, what must be included are:

  • History: poster going from Darwin to Modern Synthesis to evolution nowadays;
  • Genetics: poster about DNA and mutations;
  • Natural selection: poster, and an exhibited example that changes every month;
  • Speciation: poster, and an exhibited example that changes every month;
  • Evolution and society: examples of evolution in action from medicine and agriculture; I’m torn about including creationism and countering accomodationist dreck since it would count as intellectual pollution, but at least in Cyprus, a thorough smackdown is necessary (also, it carries a security risk around these parts).

The ecology exhibit is a tough one. What I would include is idealised models of local ecosystems – a pine forest, an arid grassland contrasted with a rainy-season grassland, typical Mediterranean garrigue and chaparral, a salt lake, a dry vs. wet vernal pond, and various marine depths. Animals will be included as prepared specimens on a painted background, and (holographic!) panels explain the major life cycle points (e.g. the life cycle of anostracans in the vernal ponds). As for other ecosystems (Arctic tundra, alpine, tropical rainforest, etc.), these can be featured one by one, on rotation every couple of months.

All the exhibits, even from the opther sections, will pale in comparison with the biodiversity exhibit. I imagine this taking up the space of an entire warehouse (including a bathroom and some benches for people to rest). My concept is taking the Goldfuß Museum from my old university and hyping it up on steroids. It’s the old-skool style of NHM, with rows of systematised cabinets showing off individual specimens, highlighted only with a taxonomic name plate. I love this style, but you won’t find it in many NHMs anymore because it’s not flashy. So I will modify it to include another old-skool favourite of mine, cabinets of curiosities, those frames and cabinets with random animals pinned together for purely aesthetic value. They look amazing and I have no idea how they went out of fashion. So the following paragraph describes how my perfect biodiversity exhibit would be like.

One side of the warehouse is devoted to animals, with 25 cabinets laid out in rows along the length of the warehouse. Each cabinet contains several things. Specimens of constituent animals placed together in a cabinet-of-curiosities-style display will make up the center of the display case, with individual specimens representing each major grouping making up the rest of the case. Each cabinet will have two drawers. One will contain texts explaining the phylogeny and anatomy of the animals. The second will be the true pièce de resistance, containing specimens for individual study. Whole organisms and dissected one, studiable under a magnifying glass, stereoscope, microscope, whatever is most appropriate, with a guide to help of course. This is the true tour de force that my museum will have. Few experiences are cooler and more awe-inspiring than the first glimpse of an insect at very high magnification, and seeing all the tiny hairs and details. My museum would provide this exclusively taxonomical experience to everyone. The cabinets are as follows: Porifera, Cnidaria, Ctenophora, Plathelminthes, Gnathifera, Nemertini, Kamptozoa, Mollusca (x3), Sipuncula, Annelida (x2), Arthropoda (x4), Nemathelminthes, Tentaculata, Hemichordata, Echinodermata (x2), Chordata (x2), Misc. (Placozoa, Myxozoa, Chaetognatha, Xenoturbellida, Mesozoa).

The other side of the warehouse is similarly devoted to plants, and is laid out similar to the animal one (done after consultation with a botanist to ensure similarly complete taxonomic coverage). The style will be similar to a herbarium with pressed plants, but if a gardening team can be hired, I see no reason why this section can’t be covered as a greenhouse and turned into a mini-botanical garden in order to properly cover trees.

Two major sections of biodiversity are left: unicellular eukaryotes and fungi, and bacteria. In an allusion to history, a cabinet devoted to fungi can be placed between the plant and animal rows, next to the entrance to the geological section of the museum (with a panel describing why they’re placed like this). As for the micro-stuff, I know of no way to observe the majority of them at any time, so leaving microscopes with pond scum samples isn’t too useful. My idea would be to have the walls plastered with a wallpaper depicting each baterial and unicellular eukaryote lineage (each “tile” is a different lineage, with a giant labelled drawing of the creature). Algae, cyanobacteria, and other photosynthetics can be used to cover the walls on the plant side; the rest on the other walls, making sure that the opisthokonts are concentrated on the animal side.

Viruses can be crammed in somewhere too, it is a warehouse after all.

Every month, a taxon will be chosen by visitor polling, and will be highlighted with its own prominent cabinet. Taxon can be anything between family and order level (only exceptional species, genera, or subfamilies deserve such special treatment).

Biology: Local

As I said, each museum section also has to have exhibits about the local natural history, so what I am writing here applies only for Cyprus. The exhibits are: biogeography; endemics; island ecology.

The biogeography exhibit places Cyprus in its context in the Eastern Mediterranean. Besides posters with distances, bird migration routes (Cyprus is a major stopover point for all kinds of worldwide migrations), and ocean currents (important for marine biogeography), there will also be exhibits showcasing the similarities and differences between Cypriot ecosystems and those of North Africa, the Middle East, Turkey, and Greece (the closest neighbours).

The endemics exhibit is obvious: specimens of endemics presented as in the biodiversity cabinets (complete with examinable portions), with very generalised ecological information. The lack of precision is purposeful, to prevent people from needlessly collecting from these often-endangered populations. Endemic plants and animals only; sorry, microbiologists.

The island ecology exhibit is one that’s shared with the palaeontological section. It describes the peculiarities of evolution on islands, with examples from Cyprus. For example, dwarf hippo and elephant fossils can be showcased to show island dwarfism.

Palaeontology: General

This would have three exhibits (including another mammoth one, pun not intended): fossilisation, history of life on Earth, and the fossil record.

The fossilisation exhibit is a simple outline of the processes underlying fossilisation and taphonomy, from initial death and burial to diagenesis and actual fossilisation. The first parts can have practical demonstrations showing how fossils can get buried in different positions, how trace fossils are formed, etc.

I envision the history of life on Earth exhibit as taking up one room, with visitors walking through a snaking trail going from the origin of life all the way to the Quaternary. Each 50 Ma can be one regular step (number can be changed), Important fossil localities and first appearance of taxa can be highlighted at the appropriate times with specimens, and key events can have a panel dedicated to them (the mass extinctions, Cambrian Radiation, terrestrialisation, etc.).

Finally, the fossil record exhibit uses the same principles as the biodiversity exhibit, with some key differences due to the nature of the fossil record. The room is split into three longitudinal sections: one for palaeobotany, one for invertebrates, one for vertebrates. The major taxa are gone through, with a focus on extinct biodiversity. The texts describe the evolutionary history of the taxa, and fossil specimens can be examined as far as possible (you can’t stuff a T-Rex skull in a drawer). The two walls of the room are devoted to micropalaeontology. One for the taxonomic scope, and one for applied micropalaeontology (oil, stratigraphy).

Palaeontology: Local

Cyprus has quite a rich fossil record, practically uninterrupted for 70 Ma. Unfortunately, most of the older stuff is microfossil material, exhibitable only with magnifying glasses and stereoscopes. Witht hat in mind, I would have three exhibits: the fossil record of Cyprus, the Messinian Salinity Crisis, and the mammals of Cyprus.

The fossil record of Cyprus exhibit is just that: sedimentary rocks placed side by side in their temporal sequence, with explanations of what they tell us about the palaeoenvironment – painting a picture of hydrothermal vents (yes, there are hydrothermal vent fossils from Cyprus), followed by deep marine microfossils, and very gradual shallowing until we get to typical shallow marine stuff from the post-Messinian, eventually tocomplete terrestrialisation. The latter two are the focus of their own exhibits.

The Messinian Salinity Crisis (MSC) occurred 6-5 Ma when the Mediterranean dried out completely due to its connection to the Atlantic getting cut off. Cyprus preserves the state of the East Mediterranean before, during, and after the MSC (one of the things I would be researching if I had funding and weren’t an umemployed bum). The deposits from the post-Messinian Nicosia Formation are especially spectacular, with large, unbroken oysters, snails, barnacles, even crabs being common (the latter not so much). They not only make very nice show pieces, but combined with the information they tell us about the recovery and recolonisation process after the MSC, this exhibit would be quite informative.

The mammals of Cyprus exhibit refers to the dwarf elephants, hippos, and the first human colonisers of Cyprus (who also were pretty damn small). This exhibit is combined with the island ecology exhibit. The animals can be compared in size to regular African elephants and hippos, with the evolutionary, ecological, and physiological reasons behind their dwarfism explained.

Geology: General

There are two parts to this. The first is a lot of typical basic exhibits crammed together logically, not worth describing in detail: the composition of the Earth (shown with a typical dissected globe and labels); the rock cycle (poster); plate tectonics (poster with world map and evidence); volcanism (poster, with demonstration using Coke and Mentos, vinegar and bicarbonate of soda, whatever); earthquakes; sedimentology (with practical demonstration using an aquarium simulating a beach, visitors can create waves with a paddle and observe how ripples form as an example of sedimentological structures).

The second part is the mineralogical and petrological part, with exhibits showing the major minerals and rock types, complete with thin sections observeable with stereoscopes (with polarised light too, since there’s no budgetary limit in this fantasy land). This will also have a strong interactive element, with mineral and rock identification tests. One potential pitfall is the difficulty of getting proper lighting fixtures that highlight the minerals properly in the display cases, especially when it comes to rocks, but that can be surpassed (rotating platforms?).

Geology: Local

Cyprus played a pivotal role in the correct interpretation of what ophiolites are – pieces of uplifted oceanic crust. The Troodos mountains preserve the prototypical ophiloitic sequence impeccably and completely. So this makes it an ideal special exhibit.

A stratigraphical column made up of actual rock types can be prepared from Troodos rocks, demonstrating the composition of the oceanic crust from its bottom, through the Moho, to the top of the mantle, to the volcanic sequences from when uplift began, to the deep-water sediments. The column can have a map next to it showing the provenance of the rocks, highlighting how the entire sequence is inverted, with the peak of Troodos being the deepest part of the crust and the beginnings of the mountain being the umbers.

This can be supplemented by panels about each individual rock type and its formation, and what that tells about the the conditions under which it formed in Troodos.

A poster showing Cyprus’s role in the unlocking of the ophiolite mystery may help in getting people to wake up to the wonders of geology on this island – it’s amazing how this place is a must-visit for any geologist worth their salt, but Cypriots don’t know a thing about geology, which is openly spectacular (it’s no Grand Canyon admittedly, but some locations are truly jaw-dropping from a geological perspective).

Conclusion

So yeah, this would be my ideal NHM. Some parts are usual, others are unrealistic and way too idealistic, and the overall thing is unthinkable – it takes up way too much space. As a pragmatic person, I realise this would be impossible to achieve on this island of apathy; heck, it would be difficult enough anywhere else, unless I somehow end up running the Smithsonian or the Senckenberg or one of the other major museums. But hey, it’s nice to dream about it ^^





The Scientific Method, Exemplified By Palaeontology

30 06 2012

Note: You can read this post over on Cyprus FreeThinkers.

This talk is aimed at the basic, general public level, and is about how science is done through the scientific method, and how to differentiate ideas that belong in the yellow circle downwards from the ideas that are in the nebulous circles outside. To save it from being a very dry, boring, philosophical talk, all introduced concepts will be exemplified using my own science, that of palaeontology.

The talk was organised by the two organisations I’m affiliated with, Cyprus FreeThinkers and Enalia Physis Environmental Research Center, and took place in an impossible-to-find building at the University of Cyprus. Here is the original announcement.

The talk is very simple with only four parts. First is a definition of what science’s aims are. Then we will look at what makes an idea a proper scientific hypothesis, then we’ll see how hypotheses are tested to confirm or reject them. Finally, all we’ve seen will be summarised in order to demonstrate why science has been so successful since its inception.

I took this definition of science’s goals from Carl Hempel‘s excellent 1965 book, Aspects of Scientific Explanation. Science has two goals: to describe and to understand. In other words, the scientist gathers observations (description) and tries to find hypotheses (theoretical understanding) to explain those observations.

Basically, all of science can then be boiled down to why questions. “Why do I observe this, and not that? Because of this hypothesis.” For example: Why do we observe humans alive today, and not Neandertals? Because humans managed to survive the climate changes; or humans killed all the Neandertals; or whatever other hypothesis comes to mind.

As an example of the interplay between observation and hypothesis, consider cetaceans. If you dissect any cetaceans from any species, any gender, and any life cycle stage, you will notice that they all have these tiny bones in their abdomen that don’t have any conceivable function. So as a scientist, you have to ask yourself why they’re there.

So you start hypothesising. Maybe the first hypothesis that comes to your mind is that these bones are just pieces that, for some reason, break off from the spine or the rib. But additional observations don’t match up with that hypothesis: the bones don’t look like spine or rib bones, and they don’t develop that way anyway.

Then you notice the position of the bones and think to yourself that they’re in precisely the spot that hindlimbs would be. So you hypothesise that they’re pubic and femoral bones. The problem with that hypothesis is that they don’t have the proper attachments: they’re not attached to themselves or to the rest of the skeleton, as pubic and femoral bones should be.

But then you notice the size of the bones, and another hypothesis pops into your mind. However, biology using modern organisms will only take you this far. To test your new hypothesis, you need to look at palaeontology.

This hypothesis is that they’re vestigial pubic and femoral bones, i.e. that they got reduced through evolution because they no longer had any use (think of cave fish and how they become blind over evolutionary time). In order to test this hypothesis though, you need to look at the evolutionary history of your taxon, and the only line of evidence that directly preserves the evolutionary history of any taxon is, of course, the fossil record.

The slide summarises the major points of the fossil record; look at this post for some more information. At the beginning, 52 Ma, cetaceans were completely terrestrial dog-like animals. Gradually, they became more and more amphibious and eventually became fully aquatic, as demonstrated by the last common ancestor of the whales, Basilosaurus.

If you look at the hindlimbs, you’ll also notice their evolution: as soon as the animal became aquatic and no longer used the hindlimbs for locomotion, they immediately became small (no doubt because having useless legs flopping around would also be an impediment to the aerodynamics of the animal).

In summary, your hypothesis is now supported by your observations of the fossil record.

Diagram Source: Uhen MD. 2010. The Origin(s) of Whales. Annual Review of Earth and Planetary Sciences 38, 189-219.

Hypotheses can’t just be any idea that plop into your head. They have to fulfil certain criteria. The four most essential ones will be introduced here.

The first criterion is rationality. Your hypothesis has to make sense. I couldn’t think up of an example from real palaeontology that was irrational (creationist poppycock doesn’t count), so I made one up: the hypothesis that trilobites are made of cheese.

This hypothesis makes no sense at all. Cheese is mostly-edible rotten milk. Trilobites are now-extinct arthropods that, when alive, had a calcitic exoskeleton, and are now known only as rocks. Rock that are not made of cheese. The hypothesis simply does not compute. And even if you had to test it, a quick geochemical analysis shows you the chemical composition of your fossilised trilobites. Heck, a taste test could confirm that they’re not made of cheese.

Picture and Analysis Source: Klug C, Schulz H & de Baets K. 2009. Red Devonian Trilobites with Green Eyes from Morocco and the Silicification of the Trilobite Exoskeleton. APP 54, 117-123.

The next criterion for a hypothesis is truth. I don’t want to get into any philosophical wankery about truth is and what truth means; what’s meant here is that your hypothesis has to conform to the most basic factual standards that we have. As an example, I chose a monumental screw-up from Cyprus’s own Ministry of Education.

The pictured page is taken from the new school year’s 7th grade (12-13 year olds) biology textbooks for the public schools, and it brings forward a hypothesis for the origin of modern biodiversity: some dude called Noah built a big boat and brought all organisms on it, to save them from a global flood that lasted 40 days. He then released them. This is, of course, the myth of Noah’s Ark from the Book of Genesis, part of the Christian mythological canon.

This does not conform to the truth criterion for way too many reasons to list. We know that this is nothing more than a fable, plagiarised from earlier fables from the Babylonians and Sumerians (see here). We know that the story is logistically impossible. Building the boat is one story, gathering up all biodiversity is another, and both are as impossible as each other (how did he plan on making sure he got every single bacterium without a microscope?). We know that there was no global flood at any relevant time (there was one large local flood, which was probably the original inspirations for the story). And, most importantly, we have the entire fossil record telling us that the origin of modern biodiversity did not involve a boat, either literal or metaphorical (there was no single center of origin for modern biodiversity).

In other words, the story is complete bunkum and fails as a hypothesis because it completely ignores established fact. If, like any reasonable person, you feel a sense of outrage at such bullshit being taught to 12-13 year olds, feel free to send an e-mail to our ministry of education. Here is my own letter, with personal intro and without personal intro. You can also sign this petition (Greek) that we at Cyprus FreeThinkers set up.

The next criterion is objectivity. What’s meant here is that your hypothesis has to be based on lines of evidence that don’t just come from the subjective melting pot that is your brain. It’s a big problem in palaeontology, given the nature of fossils.

The example shown is that of the Apex Chert “microfossils”. The validity or not of their interpretation is not what’s underscrutiny here, just the strength of this one piece of evidence, taken from one of the original papers where they were presented. See this post for more about them; basically, the Apex Chert comes from a 3.465 Ga locality in Australia with these strange structures preserved in it, and these have been postulated as being the earliest body fossils of microorganisms (they have a mention in every relevant textbook or popular book).

Consider this one piece of evidence for this hypothesis presented up there: pictures (objective evidence) and drawings (subjective). The pictures are fine, even if not very informative. The drawings, however, are not very solid – they are too subjective and show only what Professor Schopf saw in these structures. If I were to draw them, I probably wouldn’t see the same things. As I said, this is a problem in a lot of palaeontology, especially when dealing with such old and enigmatic stuff. The surefire way of supporting your drawings is finding intruments that support your interpretations – pictures, 3D models, geochemicals analyses. But drawings alone are not sufficient, at least not without copious amounts of justification.

Paper: Schopf JW. 1993. Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life. Science 260, 640-646.

The last criterion is realism. A hypothesis has to be realistic. I couldn’t think of a real palaeontological hypothesis that’s not realistic, so I turned to a notorious lunatic from the internet, Wretch Fossil. I knew him from lurking around Usenet, and he also has a website (the one on the slide is his old domain, doesn’t work anymore).

His MO is rather simple. He looks at thin sections of meteorites and moon rocks, and misinterprets what are basic mineralogical and petrological structures as animal parts (look at the captions in the screenshot up there: neurons, brain tissue, blood vessels, meat).

If Wretch Fossil was smart – a rather difficult thought experiment to go with, but bear with me – then he would have misinterpreted these structures as “microorganisms”, or something similarly vague. That would have fulfilled the minimal standard of realism, since it is not entirely unplausible for biology at a microscopic scale to have happened somewhere else in the universe (I would still call him a crackpot, but someone with an investment in astrobiology might give him some benefit of the doubt).

However, his critical error is saying these structures are animalian – and brain tissue, blood vessels, neurons, and meat are distinctly, autapomorphically animalian structures, not found in any other taxon. The reason is that animals, the Metazoa, are just a single branch of evolution, one of over 50, and it undoubtably originated right here on Earth, as all sources of evidence tell us. Heck, we even have good glimpses of their early fossil record (with major gaps, of course). In other words, postulating that this one single branch of evolution can be found in space is quite simply insane, even if convergent evolution is brought into play.

One thing that you will never see is any sort of minimal boundary for how realistic a hypothesis has to be to be acceptable. The reason is that in science, you never deal with absolutes of certainty, just levels of certainty. This is in contrast to maths, where you do have a concept of proof; in science, all you have are probabilities and likelihoods.

To demonstrate this, look at the four fossils on the slide. The ones on the left and in the middle are very obviously snails, as you can tell from the coiled calcitic shell. In colloquial terms, anyone would say these are “definitely” snails. In purely scientific semantic terms, one would say these are 99.999999% snails, leaving a 0.000001% opening in case future systematic changes disrupt what we currently characterise as “snails” (it happens to even the most iconic groups; think “Reptilia“).

Now look at the two on the right. Above is Acaenoplax from the Silurian Herefordshire locality, described by Sutton et al. (2004) as a relative of the Aplacophora, wormish molluscs without a shell. However, it’s not so hard to reinterpret it as a polychaete worm (Steiner & Salwini-Plawen, 2001). What this means is that you can only say that this is “probably” a mollusc, but not with any higher level of certainty; if you’re confident in your analsis, you would say it’s “likely to be” a mollusc.

The fossil below is pretty much the same story: the Ediacaran Kimberella. Current concensus places it as a bilaterian animal due to the bilateral symmetry of the body fossil. Trace fossils associated with it have allowed a further consensus to form that Kimberella is a stem-group mollusc. However, nobody will say that “Kimberella is definitely a mollusc”, because that wouldn’t be intellectually honest.

Pictures:

Platyceras: Sutton MD, Briggs DEG, Siveter DJ & Siveter DJ. 2006. Fossilized soft tissues in a Silurian platyceratid gastropod. Proc. R. Soc. B 273, 1039-1044.

Acaenoplax: Sutton MD, Briggs DEG, Siveter DJ & Siveter DJ. 2004. Computer reconstruction and analysis of the vermiform mollusc Acaenoplax hayae from the Herefordshire Lagerstätte (Silurian, England), and implications for molluscan phylogeny. Palaeontology 47, 293-318.

Kimberella: Xiao S & Laflamme M. 2009. On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota. TrEE 24, 31-40.

The fact that science only deals with levels of certainty and not in absolute proof underlies what is one of the most powerful concepts of the scientific method: that of falsifiability. For a hypothesis to be considered scientific, it has to be falsifiable, i.e. you must be able to show it to be wrong. By definition, every single hypothesis fulfils this criterion.

To demonstrate it, we’ll look at the anomalocarids, stem-group arthropods characterised by their large eyes, pineapple mouths, and great appendages. They were the very first apex predators back in the Cambrian, and reached a reasonable diversity – we know of three complete body fossils and a dozen or so isolated appendages.

Anyway, up until five years ago, anomalocarids were known only from the usual Cambrian Lagerstätten – Burges, Chengjiang, Sirius Passet. In addition to the fact that a small mass extinction apparently occurred at the end of the Cambrian, it was most reasonable to hypothesise that anomalocarids died out at the end of the Cambrian.

But then this fossil was discovered from the Hunsrück Slates: Schinderhannes bartelsi. The Hunsrück Slates are Devonian in age, having been dopsited 405 Ma – that’s 100 million years after the last anomalocarids of the Burgess Shale. And Schinderhannes is a clear-cut anomalocarid.

Therefore, the hypothesis that anomalocarids died out at the end of the Cambrian has been falsified.

Schinderhannes paper: Kühl G, Briggs DEG & Rust J. 2009. A Great-Appendage Arthropod with a Radial Mouth from the Lower Devonian Hunsrück Slate, Germany. Science 323, 771-773.

The key to falsifying a hypothesis is to always test it. Hypothesis testing is just about what a scientist does all day when working. As an example, imagine you’re digging around in Carboniferous sediments and you find this spectacular insect fossil, which you immediately recognise as a protodonate.

You measure it and notice it’s 70 cm big – the largest insect to have ever lived,a s far as we know. This is a far cry from the largest insects nowadays, which are 16 cm big beetles. So as a scientist, you have to hypothesise about what made these insects grow so large. You know from geochemistry that that the oxygen levels back in the Carboniferous were much higher than today, so you hypothesise that the oxygen levels had something to do with the large size, knowing full well that insects breathe mostly through diffusion because of their tracheal system.

You then have to test this hypothesis, and there are two ways. The first is to look at the fossil record of insects and see if their general size changes correlate with oxygen level changes (they do, roughly). The other way is to apply the uniformitarian principle, that processes happening today are also happening in the past (the laws of physics haven’t changed, etc.). In this case, you can raise insects in artificially oxygen-enhanced atmospheres in the lab (and you notice that theydo get bigger).

From there, you can then hypothesise about how these enormous animals lived. They have strongly-supported veins, so you hypothesise that they were agile predators. Testing this hypothesis can be through modeling (CFD on your computer, scale model, a robot), or by looking for modern analogues and comparing (dragonflies).

For more on gigantism in insects: This post.

Once your hypothesis is tested with positive results, you can the go to a conclusion by inference. There are three types of inference used in science, all of them known since Aristotle and probably from before: deducation, induction, and abduction.

Deduction is when you have a set of statements, and your inference is a logical follow-up to those statements. “Humans are mortals. I’m a human. Therefore I’m mortal,” is the classic example. As long as your statements are true, your deduction will also always be true.

Phacopid source: Fortey RA. 2001. TRILOBITE SYSTEMATICS: THE LAST 75 YEARS. Journal of Paleontology 75, 1141-1151.

Induction is basically prediction based on previously-known facts. The classic example is from the periodic table in chemistry: if you know the properties of calcium and magnesium, you can derive the properties of barium or strontium, for example. Palaeontological examples come a dime a dozen. For example, all known sauropods are enormous (with the exception of island sauropods), so by induction, you can predict that any sauropod you find in the future will also be enormous, and you then infer that gigantism is therefore a sauropod trait.

Size diagram: Sander PM, Christian A, Clauss M, Fechner R, Gee CT, Griebler E-M, Gunga H-C, Hummel J, Mallison H, Perry SF, Preuschoft H, Rauhut OWM, Remes K, Tütken T, Wings O & Witzel U. 2011. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews 86, 117-155.

Abduction, while also known for a long time, was formalised only at the start of the 20th century by Charles Sanders Peirce. The way it works is if you have an observation that can only be explained by a certain hypothesis, then that hypothesis must be valid by virtue of that observation existing.

The classic example comes from the discovery of the cause of the K-T mass extinction, the one that killed off the non-avian dinosaurs. The picture shows a picture of the Fish Clay layer from Stevns Klint, Denmark. Stevns Klint is a cliff that preserves Cretaceous layers at the bottom and Tertiary layers at the top, with the Fish Clay in between. If you were to do a geochemical analysis of this Fish Clay layer, you’d notice an enormous spike in iridium. Iridium is an element not produced on Earth, only found in space.

The Alvarez father and son team, back in the 1980s, discovered this iridium anomaly in Italian rocks from the K-T boundary and, by abduction, came to the only logical conclusion: that the iridium must have gotten there from space, probably by asteroid impact. A huge controversy ensued, but the abductive inference was solid – and later vindicated with the discovery of the Chicxulub Crater.

While nobody can generalise how science is done with every person and in every lab, what can be done is tracing the ideal way a research project would go through, from the inference standpoint. The first step is to look at what it is you’re researching and, by abduction, think up of all the hypotheses that could possibly explain your observations. You then distill your research observations to the most basic facts and, by deduction, think of what logical conclusions those facts lead you to. This will tell you how to test your hypotheses. Finally, you do the science and test your hypotheses, which will allow you to come to conclusions about whether your hypotheses are right or wrong, by induction.

For example, imagine you’re digging around the Messel pit, and you find a fossil of two turtles arranged in this peculiar position.

You have to think of hypotheses to explain this position, by abduction. Your null hypothesis would be that this is coincidental – they happened to be like this and they died. But then you notice the size difference, and you can hypothesise that maybe this is some kind of social clue: maybe parent-offspring or maybe sexual dimorphism.

By deduction, you distil everything down to statistics, in this case measurements. You find more similar fossils and measure them all. You notice a consistent dimorphism in the tails.

Such dimorphism is a classic, tell-tale sign of sexual dimorphism. And so, by induction, you come to the conclusion that your turtles are representatives of male-female pairs; the one pictured first was probably in the act of copulation, given the position.

Paper: Joyce WG, Micklich N, Schaal SFK & Scheyer TM. in press. Caught in the act: the first record of copulating fossil vertebrates. Biology Letters.

The final point about inferences that one must keep in mind is the nature of the evidence on which inferences are based. The evidence must be relevant. This may be an obvious statement, but it’s an important aspect to keep in mind at all time, especially in palaeontology, where every single fossil has many stories to tell. I don’t mean to be poetic, but it’s true that any palaeontologist worth his salt will be able to tell you amazing narratives based only on a single fossil.

Consider that random ammonite I pulled off the internet, and think of just how much disparate evidence there is in that single shell.

Here’s a small selection. One can get stratigraphical evidence from it – where it was found, and use it to date other layers where it’s present. One can stick it in a synchrotron or µCT and get the detailed structure of the mouthparts. One can place it in the grand scheme of ammonite evolution, or use it to reconstruct the life cycle of its species (in combination with other conspecific fossils), or it can be used to place more detail in the phylogeny of the ammonoids. Finally, its ecological position can be inferred.

But consider what evidence is used to get each of that information. The structure of the mouthparts will inform you about the ecology. The ecology will give you information to enable you to better interpret the stratigraphy. But the stratigraphy will not help you at all with reconstructing the life cycle (stratigraphy deals with geological time, life cycles with biological time). Many life cycles might inform you about evolutionary trends, but the evolutionary trends would never, ever be able to be reconstructed without a solid phylogenetic framework. This framework might use mouthpart information, but it will not help you in interpreting your stratigraphy.

In other words, there is an entire web of evidence, and while there are tentative strings connecting them all, some of these strings are nearly invisible and way too fragile to be used. The very best scientists are the ones who can combine disparate types of evidence in novel ways to come up with innovative concepts.

Diagram sources:

Stratigraphy: Ifrim C & Stinnesbeck W. 2007. Early Turonian ammonites from Vallecillo, north-eastern Mexico: taxonomy, biostratigraphy and palaeobiogeographical significance. Cretaceous Research 28, 642-664.

Ecology: Klug C, Kröger B, Kiessling W, Mullins GL, Servais T, Frýda J, Korn D & Turner S. 2010. The Devonian nekton revolution. Lethaia 43, 465-477.

Mouthparts: Kruta I, Landman N, Rouget I, Cecca F & Tafforeau P. 2011. The role of ammonites in the Mesozoic marine food web revealed by jaw preservation. Science 331, 70-72.

Evolutionary trends: Monnet C, de Baets K & Klug C. 2011. Parallel evolution controlled by adaptation and covariation in ammonoid cephalopods. BMC Evolutionary Biology 11, 115.

Life cycle: Klug C. 2001. Life-cycles of some Devonian ammonoids. Lethaia 34, 215-233.

Phylogeny: Bilotta M. 2010. Aequiloboidea: A new Early Jurassic ammonite superfamily of the Mediterranean Tethys. Geobios 43, 581-604.

What has been said so far are the basic generalities of how the scientific method works in practice. We will now see why those generalities have combined to make such a powerful tool.

The first reason, harkening back to the slide about the goal of science, is that science doesn’t allow for miracles. Everything in science can be explained – that’s the goal of science. Consider this painting of the Baltic Amber forest up there. Nothing there is made up by the artist. The mantophasmatodean in the foreground is known to have lived in the Baltic Amber forest. We know that praying mantises could have been caught in amber resin. We have a fairly good idea that those painted trees could have produced this resin. We know that the Baltic Amber forest was this kind of environment. That lemur whatever animal on the tree, and the emu-like animal in the background, both are known to have existed there.

The existence of these freaky animals in the Baltic Amber forest wasn’t miraculously divined by Richard Bizley, nor did he make them up. We know they were there, due to the application of the scientific method.

Painting: Richard Bizley; to be released in David Penney’s 2013 book, Fossil Insects.

The second reason why science is so successful is because science is self-correcting. Hypotheses and inferences have to be, by definition, falsifiable, so anything in science can potentially be wrong. But the only process that will uncover and correct these “mistakes” is more science.

Consider the stylophorans, a bunch of extinct echinoderms. For a logn time, three hypotheses for their functional morphology and systematic position have been around. The first one (C and b in the diagrams) is that it’s some form of stem-group echnoderm. The second one (B and d) is that it’s a relative of the crinoids. The third (A and c) is that they’re calcichordates, a hypothesised grouping of the Chordata and Echinodermata as sister clades, with the stylophorans being the last common ancestor. This obviously would have an enormous impact on how we view deuterostomian evolution.

The view was tenable and supportable – a notochord in the stalk, and area at the front was occupied by a brain and organs. However, recent fossil finds and associated trace fossils have shown that the proposed morphology and behaviour of the stylophorans isn’t compatible with the fossil record, and so the calcichordate is discarded. Science has corrected itself.

Diagram sources:

Behaviour: Sutcliffe OE, Südkamp WH & Jefferies RPS. 2000. Ichnological evidence on the behaviour of mitrates: two trails associated with the Devonian mitrate Rhenocystis. Lethaia 33, 1-12.

Anatomy: Clausen S & Smith AB. 2005. Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora). Nature 438, 351-354.

Stylophoran: Smith AB. 2005. The pre-radial history of echinoderms. Geological Journal 40, 255-280.

A natural consequence of the self-correcting property of science is that science is always evolving by discovering new things or reworking old knowledge. Science will never, ever be static, by definition.

For example, consider the origin of birds. It’s something that biology with extant organisms could never, ever throw light on. But the discovery of Archaeopteryx (and other theropods) and its correct interpretation provided a huge revolution in the study of both birds and dinosaurs.

In the past couple of decades, China has proven itself to be the most exciting place for palaeontology, in no small part due to the amazingly-preserved feathered dinosaurs found there (many more unpublished fossils still lie in archives or undiscovered).

Zhongjianornis source: Zhou Z & Li FZZ. 2010. A new Lower Cretaceous bird from China and tooth reduction in early avian evolution. Proc. R. Soc. B 277, 219-227.

Eoconfuciusornis source: Zhang F, Zhou Z & Benton MJ. 2008. A primitive confuciusornithid bird from China and its implications for early avian flight. Science in China D 51, 625-639.

Confuciusornis source: Benton MJ, Zhongzhe Z, Orr PJ, Fucheng Z & Kearns SL. 2008. The remarkable fossils from the Early Cretaceous Jehol Biota of China and how they have changed our knowledge of Mesozoic life: Presidential Address, delivered 2nd May 2008. Proceedings of the Geologists’ Association 119, 209-228.

These new, spectacular fossils give us unprecendented insights into the early evolution of birds, not only among themselves (as in the phylogeny above), but also their evolution from their theropodan ancestors. This is how science always advances – the individual steps are incremental (individual fossil finds), but gathered together, you get an ever-shifting landscape of discoveries.

Phylogeny source: Padian K & de Ricqlès A. 2009. L’origine et l’évolution des oiseaux: 35 années de progrès. Comptes Rendus Palévol 8, 257-280.

And finally, the final reason why science has been so successful is precisely because it’s been successful. A tautology, but it’s true. Think of every single advancement in the history of human culture. Now I challenge you to name one that wasn’t the result of science (even before the scientific method was formalised, science existed on the intuitive scale).

That’s right. You can’t name one. The agriculture revolution, from the Middle Ages to today – all the work of science. The medical revolutions, all the work of science (and the wrong ones, all corrected by science). The technological revolutions, again, all brought forward by science. The fact that you can read this post is purely because of science, nothing else.

And I’ll take this one step further. Any modern scientific revolutions would not have been possible without the application of the scientific method in palaeontology. The reason is oil. No matter what your stance on environmentalism is, the there’s no use denying that our entire world runs on oil. If you want to deny that, shun the use of plastics (including medicinal products and apparatus). Don’t live in a building, since buildings are all built with oil-run machines. Just go into a cave and live as a hermit.

Oil is all micropalaeontology, not just in its composition, but in prospecting for oil. Long gone are the days when you can dig an oil well with a shovel – we’ve exhausted all of those. Now, all the oil is wither buried deep, or well-hidden. And the only way to get to it is by trusting a micropalaeontologist to use the inferential methods outlined earlier to properly get the layout of the underground, and guide the drill straight into the oil reservoir. Otherwise, he’s cost the oil company millions of dollars, and is doomed to a future of selling hot dogs.

Foraminifera: Husinec A & Sokač B. 2006. Early Cretaceous benthic associations (foraminifera and calcareous algae) of a shallow tropical-water platform environment (Mljet Island, southern Croatia). Cretaceous Research 27, 418-441.

That does it for the talk. Just a bit of advertising for me – you can help me in applying the scientific method, by helping support my research project on Petridish.org. Share it around your social networks, and consider donating if you can! See here for more scientific background info.





Creationism in Schools: An Example from the Government of Cyprus

18 05 2012

Hi, Pharyngulites! This topic is something we at Cyprus Freethinkers are greatly concerned about, as the only freethinking and skeptic group of the island. Our website is over here: http://www.cyprusfreethinkers.org/. This is only my personal blog, stick around if you enjoy biology, you’ve already single-handedly broken my site visit records! :)

The persistence of creationism is one of the greatest examples of human stupidity. And I mean the entire spectrum of creationism, from the Young Earth crazies to the moderate theistic evolution permutations. When we live in an age where scientific information is available to anyone with an internet connection, there is simply no excuse for such an outdated religious concept to still be considered valid by a notable segment of the population.

Of course, a lot of creationists aren’t creationists by choice, but by virtue of their environment. If someone grows up having been taught no critical thinking skills, false evolutionary biology, and with little access to information, that person will not be able to challenge the ideas taught to them. This is how creationism largely gets propagated: under the guise of religious freedom and using the power of false equivalence, creationists push their drivel into biology curricula, claiming religious discrimination if challenged.

I’m an ardent opponent of all pseudoscience, and especially of creationism. The opposition to creationism comes not only from my duty as a biologist and my pedagogical instincts, but also from personal experiences. I met many creationists in my time in Germany, because of my courageous trolling of the strong evangelical community of the city I was in (Bonn). But encounters with deluded individuals are only nice as party stories.

I became entrenched in the manufactured debate when I encountered schoolchildren being taught creationism by their schoolteachers. Reasons vary, from the teacher not feeling comfortable with evolution due to religious beliefs, to the students demanding not to be taught evolution due to it contradicting their religion. Such stories represent clear failures on the part of teachers, an incredible sense of privilege among students, and an unacceptable lack of control in educational systems.

But nonetheless, these were isolated incidents – single teachers and students going their own rogue way. I have never personally encountered any official endorsement of creationism (in any of its forms) in school biology textbooks, besides the occasional stories one hears from that great paradox of a country, the USA.

Until now. The Ministry of Education of Cyprus has issued new biology textbooks for schoolchildren, and one of the pages there is devoted to retelling the story of Noah’s Ark, placing him as the saviour of Earth’s biodiversity. The offending page and my letter to the Ministry are below. Please, if you care at all about this issue, share the letter (or this whole post), sign the petition linked at the end, and spread the word around. A clean copy of the letter without my lengthy introduction can be found at Cyprus Freethinkers.

A school serves many purposes, but the two primary ones are to teach a sense of critical thinking, and to teach about our current knowledge of the world. This is especially true for the science classes. This is why we view the addition of a section on Noah’s Ark in school biology textbooks, pictured above, as a travesty and an embarrassment to the Cypriot educational system.

There are several reasons for this. First and foremost, the story of Noah’s Ark is nothing more than that: a story. It’s a fable with no basis in reality, and has been conclusively shown to be an impossibility by all relevant branches of science, from biology to palaeontology to geology.

The offending page in the textbook brings it up in the context of the development and evolution of Earth’s biodiversity, citing the Book of Genesis from the Bible, a book written long before modern science, let alone biology as we know it, emerged. It claims that Noah continued Adam’s work by gathering up the organisms of Earth (as a biologist, I must presume this includes bacteria and all sorts of unicellular eukaryotes) to save them from a cataclysmic flood. This ridiculousness is then couched in a positive environmental message encouraging the student to also do their part in preserving Earth’s biodiversity.

It must be stressed that this story of a global flood leaving a blank slate for humanity and life is quite a common one in world religions, with over 40 creation myths from around the world having developed a nearly-identical version of the story (the Abrahamic version was probably plagiarised from the preexisting Babylonian and Sumerian Gilgamesh Epic). This independent recurrence of the theme serves to highlight how much of a tribal concept this is – it’s a universally understood plot mechanism.

It could be argued that its inclusion in the book is not meant to be taken as a literal endorsement, that it’s merely a carrier for the environmental message. But this is nothing more than a pathetic excuse. Why should students be told a blatant lie, when we know the real history of biodiversity? That’s a story that is much more inspiring, and would put the environmental message in the proper context. Most importantly however, it can be backed up by scientific evidence – as befits a science class.

The scientific inaccuracy of this page is the main area of contention, but there are other troublesome aspects. One is the implicit assumption that the reader is familiar with the cast and outline of this story; in other words, it discriminates against any child who is not from a Jewish, Christian, or Muslim household. This is an unacceptable favouring of religions that treat the Bible as a holy book. Considering that these textbooks are official government documents, this represents an undeniable breach of the right to freedom of religion by forcing the myth of one set of religions onto all students, regardless of their personal faith and cultural background.

One might wonder why such an idiotic change in the textbook was approved. The answer lies in the person responsible for setting biology curricula, Demetrios Mappouras, a Christian priest and biologist whose judgement is clearly being impaired by his religious beliefs. The current page is nothing more than Christian propaganda, and would be more fit for a creationist magazine than a school biology textbook.

Our demand is simple: replace the content of this page with a scientifically accurate depiction of the evolution of biodiversity. The current page is highly misleading, contradicting all known science; especially worrisome is the anti-evolutionary undertone. There is a lot of research available from which to provide an appropriate overview; resorting to an irrelevant ancient holy book is a resounding failure on the part of the writers. If allowed to persist, this will not only damage the credibility of Cyprus’s schools and Ministry of Education, but will more importantly have a negative effect on the academic potential of the students.

Marc Srour
Research Associate, Enalia Physis Environmental Research Center (entomology, palaeontology)
On behalf of Cyprus Freethinkers

Further Reading:

A thorough debunking of the plausibility of Noah’s Ark can be found here (Greek).

Sign this petition to help get rid of this page from the textbook (Greek).





So you want to be a zoologist…

15 03 2012

I often get asked about what a student should concentrate on if they want to become a zoologist. I find this a very tricky question, because zoology is a very wide discipline, with subfields of it often not having much to do with each other. The lists here reflect my own bias as someone interested only in systematics and evolution, and ecology (the latter unrelated to the previous two).

Note that I’m not including typical obligatory courses – evolution, ecology, biochem, genetics, etc. Just courses that are usually (in my experience) offered as optional or specialisation modules, or that you might not consider as essential. It’s aimed at first-year bio students, but I see no reason why high-school students can’t begin their studies early (as I did, but mostly because I hated school, not out of ambition).

The list is not comprehensive; if you have any other ideas, comment/e-mail and I’ll consider.

All Zoology

Physics: I cannot stress this enough. A knowledge of classical physics goes a long way towards making the various contrivances that animals have more understandable. Optics for the more complex visual systems; mechanics for locomotion types and biomechanics; waves for audio systems. You don’t have to go the mathematical route (I don’t), just an intuitive understanding of such things.

Organismic Biology: Take as many as you can. Even if it’s not your taxon of interest, you should endeavour to have as wide a grasp of the animal kingdom as possible. Usually, an invertebrate zoology course is more than enough for this (vertebrate zoology is limited by the fact that they have no diversity, but it also doesn’t harm to take one); but if you find specialised ones (biology of mammals, of insects, of Crustacea, etc.), all the better. Also take as many courses on individual systems (there will often be one on nervous systems, for example).

Cladistics: You must learn about cladistics. You will definitely learn about molecular phylogenetics since it’s in vogue, but a knowledge of classical methods will be much more useful to you. I guarantee it. *bias alert*

Palaeozoology: Don’t even think you can study modern animals without knowing their evolutionary history. For general zoology, a simple evolution of animals series of lectures is enough, or evolution of mammals, insects, whatever your taxon of interest is.

Ecology

Neuroethology: A specialised course in this is critical; while it may be touched on in a general ethology or ecology course, neuroethology is, in my opinion, a field that anyone interested in animal ecology should have a grasp of – how animals perceive their environment and react to it.

Zoogeography: These are specialised courses in animal biogeography and dispersal. Take them.

Ecology of xyz: Where xyz is a geographical area. Take as many as you can; similar to the organismic biology, you should strive to know as many different ecosystems as possible, to get different insights into a system you will study in the future (I know that my experiences from Germany are pretty useful to me here in Cyprus, even though the ecosystems are very different).

Statistics: Goes without saying. Don’t just take the typical “stats for biologists” courses. Dig deeper, the effort is worth it.

Conservation: Even if conservation isn’t your interest, conservation biologists often have some good ideas and are the most well-versed people in the specific ecology of their animal groups/ecosystems. So I recommend conservation biology courses, because the amount of knowledge you get is really quite valuable.

Systematics

Programming: Learn some programming languages. R, Python, Perl, and/or C are my choices. They will make your life easier. Even if you can’t learn a new language, at least know how to work a command line.

Maths: Many systematists fall into the trap of making a checklist and copying the methods from papers, without thinking of what they’re doing. This is the primary reason for a paper being full of shit. You have to understand the algorithms, why you’re doing this analysis instead of that, what a bootstrap really is, etc. Or else you can never ever hope to properly interpret your trees.

History: While the history of biology is interesting, thats not what I’m talking about. It’s more the methods historians of biology use. This is so you avoid synonymies and can identify when a hypothesis you propose was actually proposed by Herpaderp in 1947 and you just brought it back from the dead. Related with this is a good knowledge of libraries and archives, and the ability to conduct searches in ancient documents written on paper (how quaint!). The ability to understand written Western European languages is also useful. Many ancient texts were written in Latin, French, Italian, even Spanish. You don’t have to be fluent in the language, just be able to parse the sentences.

Taxonomy: Some will scold me for mixing these two together, but I must recommend a course in taxonomic principles and rules. At the very least, it will teach you how to get a proper taxon sampling and how to properly describe any new species your systematic analyses might bring up.

Morphology: Just to counteract the molecular phylogenetics you will most likely have shovelled down your throat. Morphological phylogenetics is regaining ground nowadays, and we need to push for it to become commonplace again. Morphometrics is also recommended.

Palaeontology: Confucius say, “Systematist who ignore fossil record is a moron.” True story. As a systematist, your job is to figure out the evolutionary history of your taxon, and the only tangible evidence of it is the fossil record. Take a palaeontology course to find out all the pitfalls and dangers of palaeontological data (biases, etc.) and you will be much better equipped to do your job; make sure basic geology is included (often the first 2 lectures are basic geology and sedimentology). Historical Geology would be a natural companion, to know in what kind of environment the animals were living in.

Palaeobiology: This is a subdiscipline of palaeontology, the one that investigates evolutionary patterns in the fossil record (e.g. those species curves through time). I recommend it so that you can integrate palaeobiological methods with your analysis; the potential is then there to not only uncover the history and relationships of your taxa, but also to say something about evolution in general.





5 Twitter Accounts Every Biology Student Should Follow

11 02 2012

This is a guest post by Jemima Lopez from Zen College Life.

Twitter — while most will argue that the social media website is a distraction and can hinder a student’s productivity, in actuality it can be a very informative and useful learning tool if the student chooses to “follow” the right accounts. Filling one’s timeline with Biology-related material can not only keep students informed with the most up-to-date industry news, but it can also give students great ideas for project proposals and serve as study guides. To see the top five Twitter accounts that we’ve hand-selected for aspiring biologists, continue reading below. Read the rest of this entry »








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