There is always one more thing…

With three concurrent modules, it would be best to leave some lecture slides alone, that was the plan. If they are good enough, surely they can survive without tweaks?

But most things can be improved, and science is hardly stagnant. Well, even my public talks get edited each time, no matter how many times I have done some topics.

Mr Bats is mostly resigned about these ovenight sessions

This inevitably means going hungry in front of the mac. And the cats will have to remind me about mealtimes – theirs.

For an explanation during lectures can be clearer, a better delivery attempted, a conversation with a student prompts an idea or clarification, there is recent research to add to mix, an idea has been enhanced or weakened, a better image avails itself, recent news can be incorporated…

And then suddenly, its 4am.

Mr Bats is sitting on Yoda (arrowed) and with Xylo stalk me
in demand of dinner. Slide says predator deterrence.

After the edits, what to chuck out since an early finish is desired for some students to get to U Town. But the socratic method is time-costly. But third year students deserve encouragement to think.

This morning, there was no relaxing cup of coffee but more edits. Then I jumped into a cab because I had lost track of time. By this time, I had inserted a photo of Mr Kinky Tail the Civet from Weiting honours year study, to show his masked face, suggested to be “sunglasses” typical of crepuscular and riparian animals who deal with a harsh glare.

In the taxi, I thought of the banded-leaf monkey we saw in the forest. It was difficult to get a clear photo of its face, as it dodged behind branches and trunks, just enough to break the line of sight with me.

Very much like the anti-predator behaviour I describe on one slide.

So hunt, hunt, hunt for the slide on my Mac Book Pro, while advising the taxi driver of the best route to take. “Not that lane, most cars will turn into NUH”, and then get him to slow down at Lower Kent Ridge Road. “Don’t run down my students!”

I got to the LT at 9:57am. Thankfully, everything worked.

Then in the afternoon, amidst a meeting, I realised I had approached the earlier two lectures all wrong! So immediately, I made plans to reorganise next year’s lectures. And I’ve just about figured out how.

For NUS Students and Staff: An Invitation to NUSSU SAVE, Save3s’ Plant-A-Tree

On the 30th of October, Tuesday, NUSSU SAVE will be conducting another tree planting event and Save3s cordially invites you to join us in this upcoming event! In this coming tree planting event, trees grown from our very own NUS Native Plant Nursery would be planted at both Arts and Business faculty!

A total of 10 trees, following the same theme, would be planted at the respective sites: Rambutan saplings @ Arts and Malang-malang @ Biz. See the poster below for details and to join in, please fill in the form here: http://tinyurl.com/nussusave-pat2012

www.facebook.com/nusfightsclimatechange

Accessing NUS Digital Library subscriptions within Google Scholar

Open Sesame!

To access a subscription-only pdf of paper in a journal which NUS has access to, staff and students simply have to insert the NUS Digital Library proxy (.libproxy1.nus.edu.sg) into the root URL of the paper or site and type enter.

An NUS Digital Library access window appears once per session, requiring your NUS userid and password (which your browser can insert automatically). You are then redirected to the now accessible pdf and this is immediate thereafter.

I share this with the first and second year undergrads, who mostly seem to skip the library services briefing. Big mistake since their academic digital literacy skills are poor. Well, assignments provide motivation to learn, and first years have to cite literature appropriately in their first assignment in the first week of university life.

For its important for them to see how this “Open Sesame!” proxy leads to a treasure trove, and I shared with NUS librarians just how well all this helps me prepare and update lectures.

Enhancing the Google Scholar environment

One night over twitter, NUS Librarian Aaron Tay told me that NUS Digital Library can be accessed from within Google Scholar. Users with a google account can edit settings such that a “Find It! @ NUS Libraries” link appears next to individual papers in search results – then all you have to do is click to read the pdf.

So, like he says, in Google Scholar, go to Settings > Library Links, search for NUS, add, and save!

Subsequently after a Google Scholar search, a link appears to the right of search results indicating access to the pdf, here available.

Pretty neat, huh?

Adding NUS Digital Library access to Google Scholar

“Find It! @ NUS Libraries” appears in Google Scholar search results;
click for access within NUS Digital Library

In the absence of results, you may need to flex some muscles – click “More” > “Check Library Holdings” to see if NUS Libraries can reveal more.

Isn’t this wonderful – especially if you’re the sort to hunker down in Google Scholar.

I’m a Visitor, not a Permanent Resident in Google Scholar

Since I use a lot of keyboard shortcuts, I’m not going to be a permanent resident in Google Scholar just yet. I venture there about 10-20% of the time when a topic is hopelessly littered with noise in Google (e.g. when researching cats) or for the odd stubborn paper.

To search with Google, I simply type my search term into the URL bar (which I access with a ctrl-L), so its fast.

Do I find what I need? Well, in the short time of Google Scholar’s existence (2004), most publishers, institutions and authors have realised the need for their material to appear clearly in Google as much as it does in Google Scholar. So results variability has narrowed. Noise within Google has lessened as well, and my searches usually use biological terms, which narrows down results further.

I also rather read abstracts before downloading a paper which takes time (even with fibre). When I’m finally ready to acquire a pdf though, its not tough as I summon the NUS Digital Library proxy using Typinator which converts a shortcut at the root of the URL.

During new topic searches, I find the cross-referencing offered by the mega-publishing sites (which I proxy into) very useful. And then citations within the papers I’ve downloaded leads me to even more useful material.

This new feature is now part of Google Scholar, as it is in my account settings. Its automatically happening wherever I am logged into google, which is wonderful. And this probably fits my students’ search methods very well.

Having time to read

The most important part in all of this, though, is uninterrupted time to read the acquired material. I tell research students that the literature review phase of the project is a meant to be a heavenly period of uninterrupted reading. They will experience a grasp of details, an appreciation of context and eventually, the joy of true understanding.

—-
See comments below by Aaron about an update!

Google Scholar now provides reference citation in search results!

Google has introduced a new feature which has reduced citing from search results to a mere copy and paste!

In the information line which appears below search results, click “More” to reveal and select “Cite”. A window appears with the reference organised in three formats – click once to select the desired format and copy!

The APA style is close enough to what I prefer and is going to save a LOT of time during lecture preparations. It has required great determination on my part in the past to extract information to configure the citation in slides.

Oddly enough many journals do not promote citation of their articles and extracting relevant information clumsily tucked away involves a struggle with the mouse just to select relevant text!

And when rushing a presentation, which is every time, this is an agonising part of the process!

Stopping to smell the roses

Mindless copying promotes mimicry, and not scrutiny, in undergraduates.

So I will still require the first and second year students to fit their citations to the style I prefer, which is based on the The Raffles Bulletin of Zoology style which I managed in the 90’s. This forces students to examine and reorder citations, help them acquire a familiarity with the details in the process by having to scrutinise the authors, journals and dates.

For example, students often cite a popular landscape change paper about Singapore because it is well ranked in a typical search they conduct. However, they fail to realise its from the early 90’s and after two decades of changes in Singapore, that paper alone isn’t enough.

Organising the citation could have alerted them to this.

Thanks to Aaron Tay of NUS Libraries who retweeted this alert on twitter.

Reducing file size of pdfs – Jerome Colas’ Standard Compression quartz filter

[Apr 2019 update –  I use wecompress.com or NXPowerLite Desktop 8 for 90% compressions now: link]

[Update: if you just dropped in for the filters, here you go: link]

Apple’s Keynote has been very helpful for creating my image intensive lectures slides since it was unveiled in 2003. Each presentation I make is a very large file which is fine, but the pdf of the lecture slides are also large, which can be a problem for my students.

I do two things when creating lecture pdfs – first, I change the slide background (or theme) to white, to save on printer ink and speed when printing out slides [20180925 update – I print slides without background these days].

Then I reduce the file size of the pdf as much as possible to save students the grief of a lengthy download.

This used to be difficult, for with too much reduction, some images would get pixelated. I struggled with this until 2007 when I discovered Jerome Colas’ quartz filters. Colas provided eight filters which he developed after experimentation, but I really only use his “Standard Compression” filter.

He tweaked that for a balance of image quality and file size and it is much better than Apple’s “reduce file size” filter.

His original public folders are offline now but you can download them here.

Once downloaded, move the unzipped file to Root > Library > PDF Services. If you cannot find the folder, simply create one – which is safe to do, no worries!

When you are next viewing that large pdf, select “File > Export…”, and in the window that opens, select the standard compression filter in the Quartz Filter drop down menu.

That often reduces a 90MB file to 9MB – yes, a 90% reduction is the norm! All my slide lecture pdfs are thus below 10MB. The pdfs look fine on screen and when I peek at my student’s printed notes, they look clear.

This filter is one of the first files I copy back onto my hardisk after a clean reinstall, and is working fine on Mountain Lion. It should be every educator’s arsenal – thanks Jerome!

For other apps I use, see macapps.sivasothi.com.

Adrian Loo called me when he was preparing the SIBiol newsletter on Pages and needed to reduce the newsletter size. So I decided to post this for a reference. Hope it helps.

“Wild Singapore” the book – a very special sale for NUS students/staff – this Fri and Tue only

Update – the story of the book is this: Geoff Davidson, who led the red data book revision, approached Ria about contributing to this book. The title is part of the Wild series which includes Wild Malaysia and Wild China, and which John Beaufoy obtained the rights to.

Ria says, “I’m glad when they decided to do Wild Singapore that they asked me to help out. And astonished that they chose a reef shot for the cover.”

In fact, that’s precisely the kind of photo Ria has highlighted many times in her talks and blog posts, a reef with the city skyline in the distance.

The person slaving sway to coordinate this has been Geoffrey Davidson and I’m glad to see veteran Benjamin Lee involved too.

Well, I was prompted to secure the discount for my students after seeing the reef shot and Ria’s name, as she runs the WildSingapore webpage, which is quite a different thing altogether.

The Wild Singapore webpage by Ria Tan is a standard reference for NUS students in LSM1103 Biodiversity, LSM2251 Ecology and the Environment and other biodiversity modules since 2007 as Ria feed the site with well curated images, species information sheets, a list of related events and news compilations from mainstream and social media relevant to Singapore and this region.

I particularly love the images tagged with taxonomic categories which are a useful resource when first years are discovering life out there and at our doorstep!

For some time now, Ria has been agonising over the production “Wild Singapore” the book! I am glad it seems to have come to fruition by a different path!

Photo by Ria Tan

Super-Special Sale for NUS students and staff

The hard cover book will be launched in November and the price will be $69.90. Prompted for a discount or our biodiversity students, the publisher, Pansing Distribution Pte Ltd, agreed to extend a limited and super special offer of $40.00 to ALL students and staff of NUS at the first book sale for this publication!

How nice is that and how very appropriate too!

So all NUS staff and students are welcome to come down and purchase the Wild Singapore book at these locations and times. Just turn up with cash and show your matric/staff card to enjoy the super-special price!

Fri 19 Oct 2012: 1.00pm-3.00pm
Outside Life Science Lab 7 (S2-03)
(Before the LSM1103 Animal Diversity Practical)

Tue 23 Oct 2012: 3.00pm – 5.00pm
NUS LT32 lobby (S1A-01)
(Before the LSM1103 Ecydysozoa II & Deuterostomes I Lecture)

Map: http://map.sivasothi.com

“The Elephant Ivory Trade: To ban or not to ban?” Roadshow and Seminar by Project Wild-NUS PEACE, 31 Oct 2012 @ NUS

Register at tinyurl.com/peaceivory

Click for pdf

For more information, see the NUS PEACE blog.

Unravelling the Protists!

Decades ago in university, we used interesting names for many microscopic organisms and hadn’t names for many. Relationships were guessed at but mostly we were unsure of it all.

Well, biologists started out putting anything that wasn’t an animal, plant into a cabinet of curiosities called the Protists. By the time I was was an undergrad, we had settled for a five kingdom arrangement which included Kingdom Protista – it held anything which was not an animal, plant, fungi or bacteria.

A revolution of molecular information and imaging technology over the past decade or so led to an explosion in the tree of life which has better placed these microbial entities.

Just a couple of weeks ago, I used these supergroups to describe the lot – Unikonts (includes animals and fungi), Archaeplastids (plants, red/green algae), Rhizarians, Chromalveolates and Excavates (see Tree of Life).

Changes were promised and last week (28 Sep 2012), the International Society of Protistologists published “The Revised Classification of Eukaryotes” (free download) and the tree looks like this now:

We were chatting about all this recently during a Lee Kong Chian Natural History Museum gallery design meeting and this morning, Rudolf Meier alerted me about this paper.

The authors reduced several paraphyletic and polyphyletic groups and say (amongst other things):

• “Chromalveolates are probably polyphyletic”, so that show was blown.
• Stramenopiles, Alveolates, and Rhizaria are clustered into SAR (apparently common usage).
• Since “Unikonta” is misleading, it’s dropped but the grouping of Amoebozoa with Opisthokonta is recognised and a new taxon is coined for the super-duper group, the Amorphea.
• The other super-duper group is Diaphoretickes. Yes, we’ll enjoy saying that.
• An “Incertae sedis” bin holds uncertain groups.

So now eukaryotes are represented by these supergroups:

• Sar
• Archaeplastida
• Excavata
• Amoebozoa
• Opisthokonta

The protistologists really took pains to communicate this news to ensure it is better reflected in new textbooks: the paper is free, it has a pretty, coloured tree and they say “Unlike a phylogenetic tree that tries to reflect correctly the relatedness of lineages, a classification has a utilitarian purpose of categorizing diversity in a practical manner. Thus, we have resisted in this classification creating ranks that were not necessary.”

Woo-hoo!

And the best part, they agree to disagree – “While these individuals [the 25 authors] share authorship of this work, this does not mean that all the authors endorse every aspect of the proposed classification.”

Nice going, people! Until next time.

Ernst Haeckel would’ve loved this!

Metazoan connections are stable.

Fav Apps

This is why I finally bought an iPhone – it is really cheap for a mobile computer. I will complete this list in time. For now, some critical ones I use in the field. I am unfamiliar with the Android but imagine there are the same or equivalent apps there.

Battery life need not be limiting even with energy-expensive GPS apps. I use a Choiix Power Fort 5600mAh external battery charger which keeps the iPhone going for two additional charge cycles.

Field notes

• Twitter – because photos and comments can be shared on twitter immediately. My tweets are imported to Facebook immediately and friends are more comfortable to comment there, which helps raise awareness or source for information.
• Twitter in combination with BackUpMyTweets, provides for a virtual field notebook, recording critical information such as location details of a roadkill.

Maps and GPS

• Google Maps – detects current location, route suggestions to a known point (use postal codes where possible), distance of route, approximate arrival time, traffic conditions (use to divert past bad traffic)
• Pocket OneMap, uses the Singapore government’s map, which may be critical with iOS6 removing the Google Map app. OneMap keeps improving and agencies all use this.
• Runkeeper – easiest interface with which plot route on foot or bicycle, has live tracking for other to monitor, tag photos to points along route, keep a archive of routes online. More sophisticated tools exists for greater needs like Motion-X GPS
• Digital Compass Free – in case you prefer a digital interface instead of your analog iPhone’s compass. I find a compass useful for reorientation in a dense patch of forest to help me get out using short cuts, and even in unfamiliar urban environments if I am unfamiliar with landmarks. Still, always keep a proper compass in your field pack for when your battery runs out. The iTunes Store has some interesting variations like Free HD Compass

Weather

• WeatherLah – taps NEA data to project sound of crackling thunder loud enough to alert me on a field trip. The early warnings about the possibility of an oncoming storm with attendant dangers of lightning strike and falling branches is helpful and prevents me from being caught unawares, especially when focus is elsewhere.
• SG Weather – this projects NEA’s rain cloud radar map which I used to determine the size of the thundercloud, its speed and angle of approach. A decision to clear a beach of undergrads often rests on careful use of this app!

Environment

• CleanLah for photo-reports of trash and other problems direct to NEA
• Dengue Lah – early warning if there is a dengue cluster in an area I might venture into. If there are two cases in a 150m radius within 14 days, I alert students and volunteers to avoid being bitten by mosquitoes. Most times it is the densely populated urban areas with enough of trash catching rain water which pose a bigger threat.

First Aid

• St. John’s Ambulance First Aid for quick information on First Aid, it’s a good way to get or stay familiar with procedures.

Transport

• ComfortDelGro Taxi Booking – summons a taxi to odd places with clear instructions – I use Google Maps or One Map to determine the specific location and try to get a postal code. The app’s location suggestion is usually inaccurate. There is also SMRT Book a Taxi.

If you have suggestions, drop me a note or tweet to @sivasothi!

Self-healing Mac

The Mac Book Pro never fails to surprise me, and did so this time not through its OS but in an entirely different area.

A few weeks ago after an ICCS meeting, it tumbled off a table in LS Lab 7 at NUS. It landed on its edge and despite the encasement of the messenger bag it was in, appeared dented.

Back home, a blue sheen greeted me, which I ignored to carry on working. Eventually the screen gave up its ghost and was dark. I borrowed Civetgirl’s MacBookAir to run Keynote at my ecology lecture. At work, I used an external monitor since the hard disk and CPU were still whirring

By the second ecology lecture after the mishap, the MacBook Pro had somehow revived. Leaving it plugged in and alone had worked!

Or maybe the cat fixed it.

Oddly enough, the external monitor at work has blacked out. It seems while it was a primary display, the MacBook Pro sucked out all its mojo, like a Dementor. I know how that feels.

“I fix external monitors too”