Final fieldtrip for the 2008 Biophilia programme

Here's a little summary from the final fieldtrip to sentosa for the biophilia programme (24th May 2008). The students have been great to work with thanks to their initiative and level of enthusiasm. (hmmm but why haven't they contributed to this blog?!?). Fellow colleagues that came for the fieldtrips made the programme successful in its own way.

We've been lucky with the tides this year and all the saturdays low tides were around 9 am so we could schedule those saturday fieldtrips.

For me again, there were new things to see (as with every fieldtrip to this spot) and this school of catfish was one. It was a tight ball and they were swimming around each other and moving as a school.


[youtube=http://www.youtube.com/v/haKV3YYZ89s]

I chanced upon another school of smaller catfish later and demonstrated to the students the fountain effect of how a school of fish move away from an incoming predator. See embedded video. Here, I wade towards the school of fish and through the school. Note how the school doesn't swim away but split into 2 and swim around me by first swimming away and doing a flanking turn to the outside and around me and regrouping behind me. That's apparently optimal evasion tactics from a predator... cool. I got the chance to gather the students to demonstrate this in situ, something I had learnt from Prof Munroe in Animal Behaviour class when I was in year 2 or 3 when I was an undergraduate. Those are just some of the biodiversity lessons that I never forgot. It was nice to demonstrate this to a bunch of students who may not take any Biodiversity modules as undergraduates. In fact its hard to imagine that with the ever changing syllabus to molecular biology that students will ever learn this.



Here's a mermaid's purse or more informatively, the egg that is laid by a shark, stingray and attached to seawead. The eggcase is usually washed to shore after the baby shark emerges. There are plenty of this around at the sentosa beach.



And finally, a picture of students working at the site. Its nice to see that they have learnt much from this experience. It has been a fulfilling programme and one that the teachers and I have found exciting, refreshing and something we looked forward to. Its definitely a different pedagogy, the open classroom. Some students have remarked that they enjoyed the freedom to explore and craft their own projects. Will post some reflections below as they are nice (I have omitted some parts)

~"The most memorable part of Biophilia will definitely be the day on the beach when for the first time in my life I watched 2 ‘blue-blooded’ horseshoe crabs mate. I was really surprised to be able to find such amazing creatures in Singapore, because all along I saw Singapore as a place with minimal biodiversity. This programme has thus taught me not to underestimate the biodiversity of creatures in Singapore."~

~I really enjoyed every single session of the Biophilia programme as I was working with what I enjoy and am interested in most. The fieldtrips really heightened my interest towards marine organisms and I really learnt a lot about Singapore’s shores during the trips. I have also started to fully appreciate Singapore’s biodiversity after seeing such a huge variety of organisms living on such a small stretch of beach. I used to think that Singapore does not have any sea anemones or coral reefs but I realized was very much mistaken after seeing the beautiful sea anemones on the Sentosa beach. I’m glad to know that there are such programmes to let me learn more about Singapore’s biodiversity as I feel that our biodiversity is just as important as the developments in our country. Our biodiversity is part of our environment as well as our heritage so we should treasure it as well and not cast it aside as something less important. If I have a chance I would want to go for this programme again and I hope that it will be for a longer period of time as I feel that the time period this time is too short.~

~From the fieldtrip I attended, the experience and new discoveries I made gave me a great sense of achievement. I think it is wonderful that I have had this opportunity to observe and even touch some of the organisms we found. Wading in the water and sometimes mud in search of fish, crab and whatever else we could find was truly a great experience. I am glad to have been selected to participate in this program. I never realized that the area behind underwater world had so many cool organisms despite all the times I have been to Sentosa. The thought that that little ecosystem will most likely be destroyed in the future with the ongoing construction around that area is rather depressing. As unlikely as it is, I hope that the short video that my group has produced throughout this program will achieve its purpose in increasing the awareness about the ecological value of that area, and perhaps more might learn to value this more than the monetary profits it could bring. ~

The Biophilia Programme

One fieldtrip left and a seminar series at the science centre before the Biophilia programme draws to a close for the year. Hopefully we can run it again next year. The idea is to arouse biophilia in students, who otherwise would not have an authentic experience of nature here in Urban Singapore. But its more than that. Besides the place-based learning, the students come up with their projects here and all we do as part of that process is socratic questioning. Its a bit frustrating for students and its not easy to come up with a scientific question. But we've been to the fieldsite for about 5 times already and each time we spend about 3 hours there (what a blessing to have enthusiastic and supportive colleagues taking turns or even coming regular for this). We've seen some "ecological literacy" developing so that's a nice development.



Here's a pair of anemone shrimps. We found 2 pairs on two different anemones. They are delightful creatures to watch and they are, as we found out through the weeks on the Biophilia programme, almost always there when there is a submerged carpet anemone. They are known to wait out in a nearby pool if the anemone is totally exposed during the low tide, and return again.

This is the second time I have seen it in the flesh/carapace, and they provide a nice source of distraction from the world. The seem to potter about busily around the tentacles of the anemone and its been recorded that they fend off any outsider (be it a fish) that comes close to the anemone. So the pair's highly territorial. Their almost transparent body makes them hard to spot but once you know there's a high chance of spotting them beside the nice obvious bloom of the anemone, their movements give them away. The smaller one of the pair is the guy.

For much better pictures and a sciency account go to the Annotated Budak post



Nat Low and I were debating over this row of eggs. I had roughly remembered it to be some mollusc that would lay such eggs. She, being more cephalopod-biased, suggested it was too big for small snails... well not too big for the spiral melongena I guess.

Here's a nice picture of the spiral melongena from Dai Jiao's photostream in Flickr.

Because the tide was low, we decided to hope over to another stretch of rocky beach on the southern most point of Singapore and saw this pair of horseshoe crab doing their thing. What an interesting sight for students who have not even seen the creature before, seeing the mating ritual of the horseshoe crab. I am sure they, like me before, find it interesting to know that the horseshoe crab has blue blood, as unlike us, they have copper instead of iron as the prosthetic group to carry oxygen. The blue blood is very valuable as it has anti-bacterial properties that scientists have been studying. See the youtube video here.

Darwin's first draft goes online

Darwin's first draft of his theory of evolution now goes online, now joining the 20,000 archive items in the online archive run by Cambridge University 'The Complete Work of Charles Darwin Online'.

This will definitely be a valuable resource for educators and scientists alike.

For more read:
Darwin's first draft goes online

Biophilia and a Demon-haunted world

Sometime in 2006, I was looking for a seashore environment to bring students to study the intertidal zone. The Changi coast near the Tanah Merah Ferry Terminal was a nice choice but there were too many sandflies. So one day, I decided to go to Sentosa with my family. The reclaimed beaches just didn't make it cos it was void of life... almost except for pesky sunbathers. I was there for about half an hour when Joshua needed to pee, so I brought him to the toilet in one of the areas in Sentosa. It happened to overlook a sandy/rocky seashore beach which happened to be exposed as the tide was low. That was the beginning of many visits to the area.

Beautiful Life




The tide was low and the waters just reached ankle height even when we waded far from shore... I was instantly brought back to my childhood days of beach exploration when my parents used to bring me to the beach and I would explore the rocky areas and look at the rock pools, fascinated by the creatures like hermit crabs and little fish that got trapped with the outgoing tide. Josh, Matt and I waded in the waters for about an hour or more. We met a carpet anemone, sea cucumbers, an octopus (would you imagine that!), a leaf porter crab. Every now and then Josh and Matt would be amazed at the little crab who would hide under a leaf... how curious it was.. and I was there to show it to them. We spent the remainder of the time chasing crabs, fast swimming flower crabs that darted about in the surprisingly clear waters... The kids' amazement and wonderment were enough to make me satisfied. It was an enrichment class, or place-based learning experience, well call it what you will but we totally were in the flow (see "Flow: The Psychology of Optimal Experience, Csíkszentmihályi")

Just some of the beauties at the beach area.






Naturally I was excited about this and decided that this would be the place to bring some students to experience it as a fieldtrip. After assessing the safety and planning and making sure that the students wouldn't affect the environment, we went there and had our fieldtrip. We caught several creatures, displayed them in tanks and released them back to their habitats. The feedback was good and generally, most would not have experience that kind of environment here. A year later we brought another batch of students there and the same "magic" was felt. I had hoped to instil some kind of love for the environment and creatures in this students. This year, I have expanded the fieldtrip to an enrichment programme called the Biophilia Programme where students will propose and study the ecology of the site to assess biodiversity and ecology there with minimal impact.

However, the last field trip there last week left me with a heavy heart. Just a few hundred metres away, there was a big barge and major construction works. I guess for the resort world. Was this place going to be affected, will it totally go? Can the programme still continue... will Joshua and Matt see Mr Octopus? My heart sank further when I realised that the patch of halophila (or sea grass) that was verdant the year before had now been razed to the muddy substrate.. all the sea grass and sea weed was gone. Those seaweeds and seagrass were home to the octopus, the carpet anemone and the many leaf porter crabs my sons and I had discovered by flipping the the floating leaves. They were now gone. Naturally I am upset... depressed if you will. Even more so when I read this post by Rambling Leaf monkey... here.

This rich patch of halophila and seaweeds is now gone...


I can't reconcile with the fact that the rocky shore habitats at Sentosa may be gone along with its denizens, the octopus, the curious leaf porter crabs, the many scurrying crabs, baby squids, the file fishes, the carpet anemone, the sea cucumbers will be gone... Will there be an Oceanarium there? Will it be part of the habitat destruction? Already underwaterworld puts me off with the lonely dugong and a gazillion fish swimming in what seems to be overcrowded tanks. Honestly, I think picking up some hermit crab along a rocky shore is more authentic. I can't help but feel the greed of society impinging on God's creation or mother nature, whatever floats your boat. Will Sentosa become more artificial again. I had hopes that all the rocky shores might be left unharmed and I hope that they will be, but the razed patch of seagrass has me thinking deep.

In this age of science, I would think that as Carl Sagan, puts it albeit a little righteously, that Science will be a candle in the dark. Its a demon-haunted world in a different sense today where biodiversity is concerned. Look at over-fishing, pollution, animal slaughter in the abbatoirs. No longer are people ignorant, they just turn a blind eye. I hope that this isn't the case for the Sentosa management and that the people at Sentosa realise that the rocky shores are precious and hopefully, hopefully, any biodiversity surveys of the rocky shores there will be a candle in the dark for them...

Darwin, coming to 150

2009 will be the 150th anniversary of Darwin's theory of natural selection. After all these years, the unifying principle of biology still face resistance amongst certain groups. Irrationality still clouds good science.

To ensure the success of the 150th anniversary celebration of the theory of natural selection, the British Research Council has launched a website to support and debate the importance of Darwin's legacy.

Human Genome Project

I am relooking at some notes and slides I prepared for this topic. Its an interesting topic not only because of the science behind it but also the ethical, social and legal implications (that makes the acronym "ELSI") which blur the lines between right and wrong. Here are two very good resources

The first is the NOVA programs. The videos capture authentic situations that individuals face with regards to genetic diseases and also feature the scientists, science behind the project. Its more information packed in multimedia than I can summarize in a set of lecture notes. More information meaning the drama of the video that will contribute to affective learning and hence motivate students to learn more about the subject.



The 2nd is this free,... yes free, online book you can download. Its easy to read and the examples giving illustrate clearly the perplexing "ELSI" issues about genetic testing, abortions, genetic determinism... that will surface once genetic tests become more accessible..



Think ELSI and genetic testing are still far off... well read this groundbreaking and probably as "Brave New World" as it can get article in the New York Times on how you can pay just under USD$1000 for the company 23andMe to scan your genome for 580,000 SNPs (Single Nucleotide Polymorphisms). You actually can order the kit.. not sure how it works but I guess you can do it at home for yourself and children. There are at least 3 companies who will do that for around that price.


Just spit..




This NYT journalist got her own genome scanned by just spitting saliva into a little test tube . Here's a snippet of the article titled "My Genome, Myself: Seeking Clues in DNA"

"I don't like brussels sprouts. Who knew it was genetic? But I have the snippet of DNA that gives me the ability to taste a compound that makes many vegetables taste bitter. I differ from people who are blind to bitter taste -- who actually like brussels sprouts -- by a single spelling change in our four-letter genetic alphabet: somewhere on human chromosome 7, I have a G where they have a C."

But that's just information.... trivia about your genes. It gets more serious when people actually use that information to determine the genetics of their progeny. This couple actually had their daughter "genetically determined" so that she wouldn't inherit forms of genes that would make her highly susceptible to a certain form of colon cancer. This testing is termed preimplantation genetic diagnosis, or P.G.D., which means you need to cull embryos to get the right one. An eight-cell embryo has gone through fertilization.

For this couple, 4 were culled leaving 10 good ones that didn't have those forms of genes that cause cancer, 2 more were culled when a Down's syndrome test was done. Think that is unethical? Well there are people who actually remove their large intestines or breasts as a prophylactic measure against such cancers once they find they harbour just the forms of genes that make them susceptible. They may have siblings who have died because of that disease. Watch the 3rd video called One Wrong Letter in the set of videos on Nova and you will know why it becomes so grey.

(thanks to Kevin Lam who pointed out the genome scan link).

What our Biology students are learning

I understand that some of the readers of and contributors to this blog are involved in biology education in Singapore, so I thought it might be interesting to share what biology students are learning now in schools at the A level, in light of the 'life sciences' focus that biology has taken in Singapore. What I'm describing is derived primarily from the biology H2 syllabus as available for download from the MOE website. The following are some key points about the new syllabus that are different from the former one:

1. Biology education from primary school to JC has been reorganised on the following lines: 'How life works at the systems level' for Pri 3-6, the 'physiological level' in secondary school, and 'at the cellular and molecular level' for JC students. The 'systems' level presumably refers to the highest levels of organisation (i.e. from the ecosystem to the population). Quite clearly this scheme seems founded on the premise that fields like ecology and studies of the whole organism are less complex and more easily understood and so are suitable for study by children, but not quite worth the attention of older students.

2. "The H2 syllabus is moving away from the current syllabus model that was based on a 'survey' of topics.' I.e. it is moving away from breadth of coverage to depth of coverage, and the fields that have been picked for in-depth coverage are primarily cellular and molecular.

3. The syllabus is divided into two parts: the Core and Applications syllabuses. The core topics are: (1) Cellular functions, (2) DNA and genomics, (3) Genetics of viruses and bacteria, (4) Organisation and control of prokaryotic and eukaryotic genomes, (5) Genetic basis for Variation, (6) Cellular physiology and Biochemistry, and (7) Diversity and Evolution. The applications are (1) Isolating, cloning, and sequencing DNA, and (2) applications of molecular and cell biology. Furthermore, there is the H3 paper offered by advanced students, possibly the equivalent of the former 'S' paper. However, this paper is devoted entirely to Proteomics, and comprises a mixture of structured and essay questions, where the former S paper was entirely essay-based.

4. The so-called 'cellular physiology and biochemistry' topic actually contains some non-cellular physiology subjects, viz. homeostasis, and nervous and hormonal control. The other subjects are entirely cellular, though, viz. cell signalling, signal transduction, the fluid mosaic model of membrane structure, and the like.

5. 'Diversity' is being taught with three learning outcomes: (i) to explain the binomial nomenclature and hierarchical classification, (ii) to describe the classification of species into taxonomic groups (genus, family... kingdom), and appreciate various species concepts, (iii) to explain the relationship between classification and phylogeny. In short, learning about the theory of classification without reference to any content. On the other hand, the learning outcomes for evolution are fairly conventional.

6. What is not being taught any more: plant transport and animal transport, liver and kidney, all of ecology and environment, the former option topics -- growth, development, and reproduction (imagine a whole generation of male bio students with no knowledge of the menstrual cycle...), biotechnology (much of it is subsumed into the new applications syllabus, however), biodiversity (which was a lost cause from quite a while before; few junior colleges actually taught it).

7. Practical skills are assessed using a system called SPA, which is a form of continual assessment, rather than one practical exam at the A levels. The skills are divided into four phases, A. planning, B. implementation, C. analysis, and D. evaluation. However, savvy students with a knack for seeing through learning objectives and the like can probably figure out what examiners are looking for, to give 'model answers' fairly easily. On the other hand, microscopy is no longer deemed necessary as a skill for biologists (either that or they haven't found a way to assess it yet within the SPA framework) so school microscopes in JCs all over the island are sitting unused and loveless.

The above are my observations. The following are my grouses:

1. Breadth is underrated. My vice principal (I am presently relief-teaching at my former junior college) had an anecdote to share about how breadth of education is important. Readers might remember the Asian Tsunami and how a little girl on holiday saved the life of the people at her hotel because she remembered what were the warning signs of a tsunami from her geography class. She didn't have to know this, it was just introduced for interest's sake but because of this, not only her life but that of everyone else there was saved. Now biology may not be so dramatically life-saving, but certainly breadth of knowledge adds flavour to life and may come in handy. It would certainly be embarassing to call oneself a biology student and yet have little idea about what differentiates a squid from a fish, but just try asking our A level students today. I haven't dared try myself, for fear of what I might hear.

2. If the aim of the syllabus is to prepare A level students for the modern life science economy, then the polytechnics will probably do a better job. I'm not trying to be elitist, nor am I saying that the polys are inferior to junior colleges. My hunch is based on the following points: (i) the poly courses in life sciences cover pretty much the same ground as this bio syllabus, (ii) the poly students have more hands on lab experience with the modern apparatus, while JC students are still stuck doing cucumber strip osmosis and food tests with iodine and Benedict's reagent, (iii) the JC students are not learning a concept of biology broad enough to distinguish them from the poly students. By and large the polys will probably prepare a life science student better than the JCs can.

3. The A levels should be the basis of a general education. The structure of the new A level system as a whole reflects this belief, in that students are required to have one 'contrasting' subject to their other subjects, i.e. a student taking arts subjects must offer one science subject, and vice versa. The biology syllabus in particular, though, is hardly in this spirit. By focussing intently on one area of biology, the new syllabus (i) turns off students who took up biology because of an interest in plants and animals, (ii) prevents them from gaining a broad vision of biology as a unified subject, in which they can put whatever they subsequently learn in university into context, (iii) privileges certain kinds of biology over others. With regards the last point I know that the money is in life sciences, but the privilege I refer to is intellectual privilege. All aspects of biology are equal contributors to our integrative knowledge of it.

4. Overspecialisation in the molecular (or in any subfield of biology for that matter) is ultimately self-defeating. I say this because new discoveries are most frequently made on the basis of integrating knowledge from various disciplines. What is the use of knowing so much detail about plant hormones and signalling in plant cells if one doesn't have any knowledge of plant anatomy and physiology to apply it in? Research questions in molecular biology are also generated from observations at the higher levels of organisation, an important example being the study of genetic diseases, which are physiological and phenotypical manifestations of malfunctions at the genetic level. A biologist with little appreciation for whole-animal physiology, for instance, would have difficulty appreciating pleiotropy and associated concepts.

4. Teachers are told that they should 'relate information on the cellular and molecular level to the systems level.' It is a difficult thing to do. It is an imaginative and courageous teacher who can dredge up a student's long-lost knowledge of the water cycle and pond ecosystem from his primary school days and make a link from there to the molecular and cell biology that he is learning at the moment. It is so much easier not to bother because does the teacher really think it will come out in the exam?

5. Another learning aim of the syllabus is to 'stimulate interest in and care for the local and global environment, and understand the need for conservation.' I don't quite see how the syllabus achieves this.

6. The sciences are treated unfairly in curricular reform, vis-a-vis the arts and humanities. I say this because science education is overhauled with an economic imperative in mind, while the same is not done for arts and humanities subjects like Literature, Music, and Art. We don't see topics like 'Music for the Popular Market' and 'Art of Manga and Anime' being introduced to keep up with new and upcoming trends which seem quite profitable. The reason why Literature isn't discarded as being entirely unimportant to keeping our country's economy purring is because if the syllabus-makers did so, they would be branded as philistines and made a laughing stock. But they are doing something analogous to the sciences and nothing is being said about it. Biology has suffered the most because its coverage, out of all the sciences, is the most broad and modular in nature, so it seems easy to pick and choose only what is the flavour of the day and ignore the rest. In this I think the philosophical biologists have not put enough effort into making a sufficiently persuasive and public case for the integrative unity of biology.

What can be done about this:

1. Partition. Acknowledge that biology is too broad and vast to cover in one syllabus, and petition the MOE to offer two biology syllabuses: one cellular and molecular, the other organismal and integrative.

2. Send indignant letters to the MOE.

3. Continue grassroots efforts to get students interested in biodiversity, ecology, and the like, so that they might consider continuing biology in the university and taking these modules up.

4. Take over the geography syllabus and use physical geography as an avenue to get more coverage of ecology and environmental science in schools.

More suggestions are welcome.

People in the universities need to take the lead in making biology more balanced. Bear this in mind: the students coming out of our junior colleges with their new A levels will be the students going to the universities. Imagine trying to explain something as basic as plant transport, xylem and phloem to a lecture hall of clueless undergrads. Imagine setting an elegant demonstration of fungi growth in the presence of antibiotics only to have students ask if fungi are plants or bacteria. Imagine students who can handle micropipettes but not microscopes (and who blow out all the lamps and crash their 100X lenses into coverslips). Imagine having to explain the four-chambered heart and double circulation to clueless medical undergrads (who would have taken biology to find out it was of little immediate use). Just imagine...