Publications list and short hands (will be updated regularly)

1: Berg, C. C. and J. T. Wiebes. 1992. African fig trees and fig wasps. North-Holland, Amsterdam/Oxford/New York/Tokyo. Series: Verhandelingen Afdeling Natuurkunde. Tweede reeks / Koninklijke Nederlandse Akademie van Wetenschappen ; d. 89

2: Berg, C. C. and E. J. H. Corner. 2005. Moraceae (Ficus). Flora Malesiana. Series I - Seed Plants. Volume 17. Part 2. Nationaal Herbarium Nederland.

I'm currently searching for the email addresses of Ficus experts so we could check with them the status of many un-accesses species.

Holding onto the files of monographs, revisions and floras, I have a sense of loss and wonder.

Loss because some of these experts have passed away. Some go without saying, because the manuscripts are ancient, others require a few google clicks. Yet, I stare at disbelief when I see the obvious. I'm starting to think a cross symbol next to a name signals a passing away. Is it so?

K.M. Matthew †

Late of the Rapinat Herbarium, St. Joseph’s College, Tiruchirapalli, India, obit. 16th March 2004. Prepared for publication and edited by H.J. Noltie, Royal Botanic Garden, EH3 5LR Edinburgh, United Kingdom

I think the older generation of systematists/ecologists are not so active online as traces of them on the internet are hard to find.

Excel is my new best friend

Actually more like "Paste Special" is my new best friend.

And google as well and all those who pose questions about excel functions and those who reply them with the answers...

Wow, couldn't do you, without you guys.

Thank you!

Excel

My statistical analysis has led me to use R, SPSS and also Excel to a new level.

It's so important for a dataminer to be familiar with statistical tools and also data management programmes like Excel.

Because if one knows the tricks, it saves SO MUCH time.

I'm very grateful for all who have given me input on how I can cut down the amount of time I spend dealing with all the nitty gritties.

Excel functions are cool!

It's out of my personality to manage such things, but through this project, I believe it's one area I've grown in.

To be given a task, and to work out how to do it, instead of just lingering at the idea level and having no idea how to churn it out into something practical.

Now, I question myself if there are simpler and more cost-effective ways of doing things and I seek the easier and smarter ways.

"Models arise from questions about biology and the manner in which biological systems function." p. 16

"We recommend developing a set of candidate models prior to intensive data analysis, selecting one that is "best", and estimating the parameters of that model and their precision (using maximum likelihood or least square methods)." p. 22

"AIC is useful in selecting the best model in the set; however, if all the models are very poor, the AIC will still select the one estimated to be best, but even that relatively best model might be poor in an absolute sense." p. 62

"It is not the absolute size of the AIC value, it is the relative values over the set of models considered, and particularly the differences between AIC values, that are important." p.63

"AICc merely has an additional bias-correction term." "Unless the sample size is large with respect to the number of estimated parameters, use of AICc is recommended." p. 66

"change in AIC = AICi - AICmin"
"The model estimated to be best has change in AIC ~ 0" p. 71

"We can order teh change in AIC from smallest to largest, and the same ordering of the models indicates how good they are as an approximation to teh actual, expected K-L best model." p. 72

Burnham and Anderson, as below

Modeling, Model Selection and Multimodel Inference

"A model is a representation of the world, but it is rarely a perfect representation. There will always be some differences between the model and the world, that is some error. If we could build a perfect copy, it would not be a model, it would be a duplicate."

"DATA = MODEL + ERROR"

From "Applying Regression and Correlation" by Miles, J. and Shevlin, M. (2001)

"This book is about making valid inferences from scientific data when a meaningful analysis depends on a model of the information in the data."

"There are many studies to understand our world; models are important because of the parameters in them and relationships expressed between and among variables. These parameters have relevant, useful interpretations, even when they relate to quantities that are not directly observable. Science would be very limited without such unobservables as constructs in models."

"We do not believe that model selection should be treated as an activity that precedes the analysis; rather, model selection is a critical and integral aspect of scientific data analysis that leads to valid inference."

"Often, one first develops a global model (or set of models) and then derives several other plausible candidate (sub)models postulated to represent good approximations to information at hand. This forms the set of candidate models."

"... selection of an estimated "best approximating model" from the a priori set of candidate models."

"Modeling is an art as well as a science and is directed toward finding a good approximating model of the information in empirical data as the basis for statistical inference from those data."

From "Model Selection and Multimodel Inference" by Burnham, K. P. and Anderson, D. R. (2002)

I've come to such a stage that I cringe at seeing Chinese taxonomic description more than Latin or Spanish.

It's time to start with the thesis, with or without results.

It's time to prioritize and work smartly.

Proverbs 27:12
A prudent person foresees the danger ahead and takes precautions. The simpleton goes blindly on and suffers the consequences.

My researching has reach the stage where I start to dig out papers written in Chinese, Japanese, Spanish, Portuguese, the language of Iran...

Yes.

And actually. It's fun. To try reading the paper in Chinese. To use language tools on Google to translate Spanish...

Library Books

One thing I love about doing research is going to the library and finding old materials. When I get my hands on bounded journals from 1914, from 1925, from 1948, my heart oozes joy and I get all sentimental, imagining who used these before. :)

I realized the collection we have in the NUS library is really good! :) Nice oldies in the closed stack. And they help us find documents we don't have too.

The Botanical Gardens Library has some goodies too.

:)

I love books and old stuff and libraries! :)

I am reading this book called "Rheophytes of the World" by C.G.G.J. Van Steenis. It is such a fascinating book. I really like the author's writing style. These older writers write like they're talking to you.

Check this out on page 7 when he tells of the difficulty in identifying rheophytes because herbarium collection descriptions are vague.

"Field notes should contain all information which can be observed on the spot, that is: precise locality and habitat, frequency, and altitude, and furthermore a record of the life structure of flower, fruit and seed that will be obscured or lost in the drying process (scent, fleshyness, etc.). Many labels fall short of this information. Not long ago (1977) I made an urgent plea to collectors to improve their field data. The time is past that plant collecting consisted of two actions: grab and dry. What we need is scientific collecting, with full notes on structure, habit and habitat, enabling the taxonomist to make use of field data not otherwise available to him. I want to emphasize this strongly here."

Wow! This is writing at its best. Can you feel he is trying to educate his potential readers? Surely many collectors, botanists, students would read this book and they're be educated by him, though the topic of the book is not really "how to be a good collector"! Can feel how strongly he believes in this!

Name Changes

Plant names are changed for three basic reasons.

1. Nomenclatural (to conform with the rules of the Botanical Code)
A change results in a new correct name while the former name becomes known as a 'synonym' and should no longer be used.

2. Taxonomic (as a result of a revised view of plant relationships)
"Taxonomy is the study of the principles and procedures of classification. A plant taxonomist reconsidering the classification of a particular group of plants has certain aims: to clearly delimit the taxa; to discern natural relationships; to produce a practical classification; and to ensure that plant names are correctly applied in relation to the type specimens." (Oh, so this is what Berg's been doing! :))

3. to correct a misidentification or misapplied name
"Plant identification is the act of determining the name of a plant (botanists actually refer to the is formal process as 'determination').
Misidentification-the act of giving an incorrect name to a plant.
Misapplication- the perpetuation of names resulting from an original misidentification. The name did not change, but the application of the name has.

From source of previous post. :)

infraspecific

"Infra" means "below" so when we talk about subspecies, varieties and forms, we are talking about infraspecific ranks.

Principles of the Botanical Code

(Spencer, R., Cross, R. & Lumley, P. 2007. plant names - A guide to botanical nomenclature.  Third edition. Melbourne: Csiro Publishing)

Principle 1: plant nomenclature, animal nomenclature and bacteriological nomenclature are independent.

Principle 2: the names of plants or plant groups are based on TYPES which, with rare exceptions, are actual dried specimens of plants.

Principle 3: nomenclature is based on priority of publication. This principle stresses the overriding importance of the first published name and, together with Principle 4, provides a means of determining which of several published names for the same plant is correct.

Principle 4: each plant or group of plants within a particular system of classification can bear only one correct name: the earliest one following the rules.

Principle 5: scientific names are to be treated as Latin.

Principle 6: rules of the Botanical Code are retrospective.

What I learn from ST 2137

What is Data?

"Data" is defined as

-things known (the attributes of Ficus species worldwide)

-assumed facts or figures

for which conclusions can be inferred. (which attributes are related to invasiveness, threatenedness)

What are the uses of data?

-To draw conclusions and make decisions (So which species are potential invasives and which species might we potentially lose forever? So we know which not to be cultivated and which to protect)

-To confirm statements (Is it true that smaller fig size mean more animals can eat and more well dispersed thus more weedy?)

-To make predictions on events to come (This species might go weedy, this might be threatened)

What is data analysis?

-The art of examining, summarizing, and drawing conclusions from data

-Transforming the data into knowledge.

Questions (hypothesis)-->Collecting data (which I don't do physically, unlike my other Honours friends)-->Analyzing data-->Answers/More questions/Any patterns/relationships (we all must do this and write it in our thesis)--> either conclude or collect more data

So technically all research students who work with data collection are doing data analysis.

Also Prof. Chan Yiu Man mentioned "we must get evidence to support what we believe in". This is my weakness. I must believe in Science. I must trust that the data and analysis method I use and produce evidence that creates knowledge and I must be able to stand by my work.

I work hard and I believe in what I do.

Fascination with Ficus

Sometimes I get a little disappointed. I am not still not good at doing research. I still don't quite get it. I might feel a little inferior to others actually.

But let me not do research to prove to others I can do it, rather, let me do it out of love, a passion for knowledge, to know and be known.

Sitting down here, looking at papers and websites, can get dry at times. I'm not very explorative (what an irony right?) but just now I was exploring Fig Web and I found faces, faces of Ficus lovers, Ficus researchers. Check out George Wieblen. He looks very extroverted and a fun person. And I see the smiles on their faces, the many many publications they have come up with... It's crazy, I mean they really love Figs, to do all these things. And they're people like my Professor, like my lab mates and possible people like me. 

Let this passion drive me to do work, not obligation.

I feel like I'm living in a world of Science.

taxonomic revisions

I am slightly stunned. 

I am reading a paper by C. C. Berg called "Proposals for treating four species complexes in Ficus Subgenus Urostigma Section Americanae (Moraceae)" [Blumea 52:295-312].

The problem with the Neotropical taxa of Ficus is that "The species complexes in Urostigma section Americana comprise a number of partly allopatric entities ('forms') that are morphologically so close that recognition is often very difficult or sometimes even impossible. Moreover, the pollinators of entities within within the complexes can be different, possibly implying genetic isolation" [Experientia 45:605-611].

Hmmm... I think basically what it means is that it is hard to classify these species because they are similar, yet different. So should we treat them as distinct species, or should we see them in a broader sense, as complexes or a common species/subspecies.

What Berg did was to propose a treatment for the four species complexes (F. americana, F. aurea, F. citrifolia & F. pertusa).

What stunned me was that many of the species known to be threatened are now being grouped together with others under one name. What that possibly could mean is that I might have less threatened species than previously thought...

It took me a long time to get used to this shifting and moulding, this plasticity of taxonomic groups. How one day, this species is here, another day, it's there when someone realizes it's been identified or evaluated wrongly. It's so flexible and changing. There are rules, but with new discoveries and knowledge, species are shifted around and sometimes ceased to exist when I suppose identified wrongly.

I feel very raw and new to this. A actually you probably can tell from the way I tried to explain what I know. I still can't grasp it proficiently at the moment. But I am in awed at the complexity and have started loosening up.

I used to think these things were fixed and do not change. But they do, they do!

*sigh*

It's true isn't it. The more you find out, the more you realize you have not found not. The more you know, the less you really know. 

The more you try to dig deeper, the bigger the mess you realize it really is.

But... There should come a point when it all makes sense, despite the mess.

I can't wait to arrive there.

I think too because Man gives plants their name and their classification, these things changes and there's not clear cut answer to a classification scheme.

Prof. Tan told me today that a data-miner must be resourceful. I must be about to plough through all the information and find what I need...

I hope to have a good reference section that I can be proud of. Being a perfectionist, if that can be something I am proud of, it must be very good.

Okay!

I really pray I can get my act together and do my best for this project.

I want to be a good data-miner and a Ficus expert by the end of the project.

And every step of the way, I will get better.

Some Hands On

Biologists are known to get their hands dirty and all. And being an "arm chair" biologist, brings its fair share of mocking. I feel that a lot of the data miners, the Plant Systematics Lab denizens, are not well looked upon by the people in the other labs.

Just moments ago, I brought out my Flora Malesiana and my Fig book and my camera and went to have a look at Ficus glossularoides on the ridge (I forgot we have it in our native plant garden). I read the description, I looked at the plant to understand, and took some photos. (I am so blessed. A cute little black bird with a red cap and a red patch on its back was chirping happily away and picking on some red fruits near me. I took a photo of it, shall put it up here once I can.) 

Ficus grossularioides (White - leafed fig)

"This shrub is very common along secondary forest edges, in wooded undeveloped land and along disturbed hedges. It may grow to a small tree, up to 9m... distinguished by its characteristic white leaf undersides. This fig is also called Ficus alba in older references..."

"Figs usually below the leaves on previous season's growth, in pairs, sessile or with a peduncle up to 0.2cm long."

"Leaves spirally arranged; lamina elliptic to oblong to ovate or (when juvenile) (sub)palmately 3-5(-7)-lobed to -fid, 3-15 by 1.5-7.5 cm (when juvenile up to 35 by 30 cm)"

Dicaeum cruentatum (Scarlet-backed Flowerpecker)

"A tiny bird of the tree tops constantly on the move feeding on flower nectar, buds and small insects and fairly common where these occur but due to its very small size may be easily missed..."

In a way, I really like my project. I actually much prefer this kind of "field work". (Actually there's no field work involved, but I hope to on my own initiative, do my own. But I look forward to any herbarium kinda visit.) I like to identify, I like to appreciate the structure and take some photos. I actually don't quite like doing experiments, even the outdoor kind, like we did in Tioman. I don't like to repeat experiments, being a perfectionists, I cannot stand it that there are factors we cannot control (but that's life isn't it. We face that in life all the time), I prefer collecting and making lists. 

I only realized it now, but this project actually quite suits me. Plus the fact that it allows me the flexibility that I need, with my external commitments.

By the end of this project, I'm supposed to become a Ficus expert (wouldn't that be cool? Work hard if you want that, dear girl!). I will know the geography of the pan tropical region (excellent for Missions). 

I really need to work hard if I want that effect. So, this  really must be my priority. I don't know where this will lead me, but if it were to lead me anywhere at all, I must do a good job. 

Currently the list is getting longer. I've yet to get rid of the synonyms or find a way to do that. But hope to have a chat with Prof. soon and get that going. 

I took a long one month break to focus on this Special Semester module called LSM4263 Field Studies in Biodiversity. I was rushing to complete the oral presentation and report.

Now, I'm back to figging.

I have visited the Botanic Gardens library twice to check out their Floras. They have a wider collection than our lab.

I'm currently trying to complete my list. I'm searching for the 730-755 species of Ficus. Currently I have about 700. But it's an incomplete and imperfect list with probably quite some mistakes, so the numbers could be lower.

I'm also finding out the cultivation status. Could it be that cultivated figs are more prone to becoming weedy??

Soon, I would need to find these figs corresponding wasps.

It looks like things are picking up speed.