The swiftlets nest

The nest of some swiftlets species are made from their saliva and are farmed and commercialised as food. The farmer builds a large building for the swiftlets to make their nest. Then, they would call the swiftlets using a playback sound of the switlets to attract them to make their nest in the building. After the swiftlets makes their nest, the farmer would collect only the nest without harming the swiftlets.

Figure: Swiftlets nest cleaned (left) and before cleaning (right)

The nest would be put into the refrigerator to kill bacteria before proceeding with the cleaning process. Once cleaned, the nest will be graded A.B or C according to the level of cleanliness and weight. An estimated price for 10g of cleaned nest is about RM50.

Principal Component Analysis (PCA)

Principal component analysis is used to determine many variables and determine which variables that fit best for the subject. PCA is used for the subject when there is linear correlation between the variables.

The PCA investigates the multiple variables in more than two axis, so you can choose the best axis that represent your variables with indication on the % for the Axis selected. This plot shows Axis 1 (65%) and Axis 2 (20%) with a total of 85% from the variables used.

Candidature Defense Presentation

I had my candidature defense (CD) on 27th Jan 2015 (1140-1210) at SA2 seminar room at ISB, UM.

The aim of the CD was to overview the research progress that the student had done already. The advantage of it is that if we make mistake, the appointed examiners would pinpoint it, by asking questions and correcting the mistakes so that we proceed our research smoothly. This should give us more ideas as we proceed with our research.

Field of specialization: Behavioural ecology

Area of expertise: Arachnology

There are three disciplines in my work (taxonomy, behavioural ecology, phylogenetic), and my main goal is to master the discipline in behavioural ecology in wild animals.

Poster Flora & Fauna

Cara membuat poster flora & fauna.

Langkah 1: Mengumpul foto-foto yang sesuai
Langkah 2: Membuat pengecaman spesies (rujuk kepada pakar masing-masing)
Langkah 3: Hantar kepada susunan & reka bentuk poster (bayaran dalam RM200-700)
Langkah 4: Cetak dalam 500-1000 unit poster
Langkah 5: Edarkan kepada orang awam

P/S: Senang kan? Kenapa tak buat? Masih mengharapkan orang luar untuk buatkan?

Kursus Biologi bersama pelajar Kazakhstan

Seramai 80 pelajar Kazakhstan berusia antara 14-16 tahun membuat lawatan sambil belajar selama 2 minggu di Malaysia. Mereka ini terdiri daripada kalangan pelajar terbaik di sekolah mereka.

Dalam kategori Biologi, Thary, Benjamin, Gary, Dr Sugumaran dan saya telah menyediakan 2 hari modul untuk berkongsi ilmu mengenai flora & fauna.

Dr Sugumaran sedang menerangkan mengenai tumbuhan yang boleh digunakan untuk perubatan

Pelajar diberi peluang untuk melihat struktur tumbuhan dengan menggunakan mikroskop

Selain itu, modul fauna yang disediakan adalah mengenai mikroorganisma kecil dalam air, amfibia & reptilia dan labah-labah. Diharapkan dengan sedikit ilmu yang dikongsi ini dapat memberi dorongan kepada pelajar Kazakhstan untuk berjaya di masa akan datang.

Penyelia VS Pelajar

Semenjak kebelakangan ini, saya seringkali mendengar rintihan daripada pelajar pascasiswazah mengenai penyelia yang hanya tahu MENGARAH dan bukan MENDIDIK. Antara perkara yang saya halusi ialah PENYELIA sebenarnya tidak memahami beberapa perkara asas berikut:

1. Bidang tugas Penyelia
    - Penyelia perlu mendidik disiplin ilmu penyelidikan tersebut dan bukan hanya memberi arahan seperti 'saya nak kamu tulis satu artikel mengenai sekian dan sekian'.

2. Disiplin penyelidikan
     - Penyelia tidak tahu atau kurang memahami disiplin ilmu penyelidikan yang pelajar sedang buat dengan baik

3. Tahu mengambil pelajar sahaja
     - Ada juga penyelia yang hanya tahu mengambil pelajar sahaja untuk tujuan tertentu dan bukan kerana fikir mengenai tanggungjawab yang akan dipikul di kemudian hari

Namun, saya juga mendapati di pihak pelajar pascasiswazah pula, terdapat SIKAP berikut:

1. Spoon-feed atau tukul dengan paku
      - Setiap satu benda perlu beri arahan, seolah-olah tidak boleh berfikir, mencuba atau mencari inisiatif sendiri.

2. Kurang memahami hala-tuju pascasiswazah
      - Pelajar perlu memahami bahawa di peringkat Pascasiswazah, setiap pelajar perlu MENGUASAI DISIPLIN ILMU yang diceburinya supaya dia boleh berdikari selepas tamat pengajiannya

3. Malas atau putus asa
      - Terdapat juga pelajar yang malas, tiada keazaman yang tinggi untuk menghabiskan pengajiannya dalam tempoh yang diberikan sehingga mencecah sehingga 5-7 tahun untuk menamatkan pengajiannya.

Phylogenetic Analysis

There are several software that are needed to be downloaded.

1. BioEdit Sequence Alignment Editor was used to align forward and reverse sequences for sequence clean-up. The reverse sequences was set to reverse complement, grouped together with the forward sequences, align together using the pairwise alignment (optimal GLOBAL alignment), delete sequence where appropriate based on chromatogram and saved as FASTA files. Then, all the cleaned sequences for tetragnathid species with the downloaded selected tetragnathid species and two out-group sequences from genbank were saved as into one file as FASTA. 

2. Clustal X program was used for multiple sequences alignment and saved as NEXUS. Phylogenetic Analysis Using Parsimony (PAUP) software was used to elucidate the phylogenetic relationships between the tetragnathid species.

3. The PAUP software was keyed as follows:

a.       Neighbor-joining (NJ):

begin paup; log start file=NJ.log; outgroup 50;  set criterion=distance increase=auto;  dset distance=K2P; NJ treefile=NJ.tre; set autoclose=yes; bootstrap nreps=1000 search=NJ treefile=NJBt.tre; log stop; end

b.      Maximum Parsimony (MP):

begin paup; log start file=MP.log;  set criterion=parsimony; set autoclose=yes; set root=outgroup;  outgroup 50; set increase=auto; hsearch swap=tbr start=stepwise addseq=random nreps=100 hold=1; contree; set storebrlens=yes; bootstrap nreps=1000 treefile=COI/18S.tree search=heuristic / swap=tbr start=stepwise addseq=random nreps=1 hold=1; savetrees from=1 to=1 file=COI/18S.cb.pa.tree.nex format=altnex brlens=yes savebootp=nodelabels maxdecimals=0; pscores / tl ci ri rc hi; log stop; end;

c.       Maximum Likelihood (ML):

For COI: begin paup; log start file=ML.log; set autoclose=yes; set criterion=likelihood; set root = outgroup; outgroup 50; set storebrlens=yes; set increase=auto; Lset  Base=(value)  Nst=value  Rmat=(value)  Rates=type Shape=value  Pinvar=value; bootstrap nreps=100 search=heuristic/ addseq=random swap=tbr hold=1; contree; savetrees from=1 to=1 file=COI/ML.cb.mlb.tree.nex format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0; log stop; end;

d.      d. Genetic distance

Begin paup; dset distance=p; showdist; savedist format=nexus file=P_dist.nex; dset distance=p; showdist; savedist format=onecolumn file=P_dist1.txt; end;