Where is the Toddycat!?

The evolutionary relationships among Asian palm civets were recently reconstructed using DNA sequences of four genes.

Patou, M.L., Debruyne, R., Jennings, A.P., Zubaid, A., Rovie-Ryan, J.J., Veron, G., 2008. Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora). Molecular Phylogenetics and Evolution 47, 883-892.

Here is the trimmed down tree to show where the palm civet that inhabits Singapore and the logo of RMBR stands phylogenetically.

It is in fact most closely related (in this sampling) to the brown palm civet that is endemic to Western Ghats... And has the binturong and masked palm civet (implicated in SARS) at the base of the lineage.

The study also shows some interesting stuff:

(i) the Asian palm civets (Hemigalinae + Paradoxurinae) have a single origin, in other words monophyletic, the gold standard in systematics
(ii) Paradoxurinae, containing the Toddycat, is also monophyletic
(iii) the Asian palm civets (Hemigalinae + Paradoxurinae) apparently diverged from the rest of the Viverridae family in the Late Oligocene/Early Miocene (~20-25 million years ago)
(iv) the Toddycat, as a species, is probably between 5-10 million years old, one of the younger ones in this group of mammals.

David Attenborough's 1973 Royal Institution Christmas Lectures

"The Royal Institution Christmas Lectures have been held in London annually since 1825." [see Wikipedia] Michael Faraday (who is quite the man) is the star of the series which continues to this day. He lectured a record of 19 times between 1827 - 1860! The scene of one of his lectures is depicted on a UK 20-pound note and is a depiction I remember from my childhood.

In 1973, Sir David Attenborough, who has inspired many a naturalists' career in Singapore and elsewhere, participated in this grand event by giving a series of five lectures over five days, on "The Language of Animals":

1. "Beware" (Wed 26 Dec 1973)
2. "Be mine" (Thu 27 Dec 1973)
3. "Parents and children" (Fri 28 Dec 1973)
4. "Foreign languages" (Sat 29 Dec 1973)
5. "Animal language, human language" (Sun 30 Dec 1973).

The videos are available at the Royal Institution of Great Britain's webcast archive (you have to “shop” and “checkout” but can watch the webcast for free).

This excellent series of videos (and a dashing David) are available on YouTube courtesy of threespeed. Due to YouTube's 10 minute limitation, the series of five hour-long lectures are in 30 parts!

Besides highlighting these clips to the biodiversity and animal behaviour students, they serve as appropriate inspiration just before my module-heavy semester begins. I'll soak in ol'David to stoke those flames of passion and hope some fire is evident during the 8am ecology lecture!

Revisiting Lamarck

Now epigenetic inheritance pertaining to DNA methylation influence phenotypic expression. That implies that traits can be inherited without changing the gene sequence at all.

Lamarck might be right in some sense.

After so many years of dismissing Lamarck's theory, AND telling students that no, a giraffe's neck does not grow long because of all the stretching its parents did, I never thought the day will come where one has to look at his theory closely again.

For more read this fascinating article by New Scientist

Some interesting excerpts:

but over the past decade it has become increasingly clear that environmental factors, such as diet or stress, can have biological consequences that are transmitted to offspring without a single change to gene sequences taking place.

Epigenetics deals with how gene activity is regulated within a cell - which genes are switched on or off, which are dimmed and how, and when all this happens. For instance, while the cells in the liver and skin of an individual contain exactly the same DNA, their specific epigenetic settings mean the tissues look very different and do a totally different job. Likewise, different genes may be expressed in the same tissue at different stages of development and throughout life. Researchers are a long way from knowing exactly what mechanisms control all this, but they have made some headway.

Inside the nucleus, DNA is packaged around bundles of proteins called histones, which have tails that stick out from the core. One factor that affects gene expression is the pattern of chemical modifications to these tails, such as the presence or absence of acetyl and methyl groups. Genes can also be silenced directly via enzymes that bind methyl groups onto the DNA. The so-called RNA interference (RNAi) system can direct this activity, via small RNA strands. As well as controlling DNA methylation and modifying histones, these RNAi molecules target messenger RNA - much longer strands that act as intermediaries between DNA sequences and the proteins they code for. By breaking mRNA down into small segments, the RNAi molecules ensure that a certain gene cannot be translated into its protein. In short, RNAi creates the epigenetic "marks" that control the activity of genes.

We know that genes - and possibly also non-coding DNA - control RNAi and so are involved in determining an individual's epigenetic settings. It is becoming increasingly apparent, though, that environmental factors can have a direct impact too, with potentially life-changing implications.

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 Programme - Finding Nemo

The morning started out with a nice view of the seashore exposed by the low tide (0.3m). The sky was clear and the sound of the ebbing waves beckoned.


The students were to carry out their transect study. I was with a group of them when they set up a 40 m long line transect across the intertidal zone. It must have been one of those fulfilling days as a bio teacher. The sun, the sand and the ebbing waves washing at our ankles as we looked for yet one more creature to surprise us with its existence in its strange form. The day's new creature of the day started off with the slender seamoth.

Its not uncommon on these fieldtrips to the shore to hear students go "wow" in amazement at an entirely new creature they have seen.... Come to think of it.. how many times in our lives do we come across anything really new in the flesh.



The slender seamoth was really calm as we comtemplated it... see the shadows of our heads hovering over it as we trained camera lenses on it. We pondered over whether it was a stargazer or seawasp.

That's the 40m transect which took a group an hour plus to complete documenting the creatures they saw.


And here's a makeshift square transect that the group who had done were particularly proud of.


The low tide really exposed a lot of creatures and lots of carpet anemones were exposed in those pools. It was with Mr Nah's patience and keen eye that we spotted the prawn that was swimming within those tentacles of one. And soon enough what must have been quite the highlight of the day was to spot a clownfish, at home within the tentacle of the carpet anemone. Now, we have seen Nemo in aquarium and the movies, but to come across on in situ was a different thing all together... we all beamed at such a discovery.



It must have been on of the most fulfilling visits to that fieldsite. I think partly it could be attributed to the fact that we set up transects and had a more considered approach to our survey.



We work to the ominous backdrop of mega construction and each time I go there, I half expect the place to be cleared and cordoned off for some pointless attraction. The day that happens, I will be cynical, for I have come to know of creatures who await discovery by students.

Parasite makes ant mimic fruit

Parasites frequently modify the behavior of their hosts to encourage the infection of new hosts. For example, see this video (taken from the Planet Earth documentary) of the fungus Cordyceps that makes insects climb to the top of grass stems, and then erupts its fruiting body from the host's body, and disperses its spores over more hapless hosts from this elevated position. Yanoviak et al. (Am Nat 2008. Vol. 171, pp. 536–544; DOI: 10.1086/528968) describe a case of parasite-induced mimicry in the ant Cephalotes atratus. A nematode infection causes the gasters (rear portion of the abdomen) to become bright red and swollen, resembling a berry fruit, where normally it is black and inconspicuous. The infected gasters are also full of parasite eggs. Birds that feed on berries would then pop off these packets of parasite propagules, and pass out the eggs in their faeces. Ants congregate around bird faeces, which represent food resources to them, and collect them to feed to their brood, completing the cycle.

Here's the lesson from all this, kids: don't eat dung.