It’s the first Monday after the course here at XTBG and life is back to ‘normal’.  I hope that everyone had a safe and comfortable trip home.

Hey, Bhakta and Peter, check the dates on your visa and airplane tickets when you get them, not the day you leave!!!  It’ll save you and everyone else a lot of worry and extra work.

As I said at the last symposium, let’s not let this be the end.  Stay in touch and I am going to work through the essays over the next couple of weeks.  I hope you are interested in revising them!  The only way to improve your writing is to practise and revise.

All the best,

Chuck

Your next assignment is to write a short essay (800-1500 words) about one of the assigned readings.  Please do a bit of research as well and find a couple of related papers as references.  Properly cite your references, using the bibliographic style of the paper you are writing about.

Just post these on your own blog by the evening of Aug 1.

DOH!

I have spent almost an hour this morning trying to fix my internal DVD player in Windows, which mysteriously quit working.  And I am going nowhere fast.

The only reason I am in Windohs as the moment is because SONY is forcing me to (so much for the free market model).  First, we bought their videocamera because it was supposed to have a GPS unit installed.  Well, at least in China, the HandyCam HDR-XR500 does not have a GPS unit.  Fine, we can synch up an external GPS unit.

Next, SONY now has its own exclusive video file format *.MTS and none of the free editting software can deal with it.  Converting the files loses quality.  Great.  At least the trial version of the “Vegas” software (what a name!) is good for 30 days but it is horribly complex and it’ll take that long to master it.

So, all I am trying to do is install the viewing software that came with the camera and now, the DVD drive decided to not work.  One of the very few times that I have ever asked it to work in Windohs.

The thing I hate about Windohs is that you have NO control.  You use the little “wizard” but nothing changes, so your only option is to reboot and try the dumb little “wizard” again, which assumes the extent of my ability to use a computer involves choosing between “Next” “Back” and “Cancel”…

Anyway, I have now been using Ubuntu for two years and I have spent far less time fixing things than I have on Windohs this morning.  And the amount of information out there about how to fix things in Ubuntu is amazing.  Numerous times, I have encountered a problem and I search it on the internet, bingo, an entire thread of discussion pops up with a variety of options about fixes.  Usually one of them works and I actually learned something about my computer, instead of simply punching “next” “next” “finish” no change <reboot> <repeat>

DOH!

Okay, now it is time to gain a little bit of experience with accepting constructive criticism from our peers.  This can be a difficult thing for some of us.  Giving ‘constructive’ criticism, instead of just criticizing, can be a difficult thing for some people as well.

Peer review is one of the most important aspects of scientific research and it is one aspect which people mostly learn without any formal training.  The quality of peer review often varies considerably, both in quality and ‘constructiveness’.

So, I have assigned each of you to review one proposal.  You will do this anonymously, which is how the peer review process typically works.  In other words, the people who wrote the proposal will not know your identity, when you contribute your comments.  I want you to take this responsibility seriously. I realize you might not be an expert on the particular topic.  It may be worth doing a bit of exploration on your own.  One quick way would be to return to their original proposal and look at some of the references that are cited in the first proposal.

When you finish, please submit your comments via email to me <chuck@xtbg.ac.cn>.

Comment on three things:

1. Overall quality and strength of the idea or hypothesis in the proposal

2. Quality and power of the methods

3. Are the proposed analyses and outputs adequate?

We’re having a bit of trouble communicating with everyone over the past few days, so I am putting a white board next to the entrance of the office/lab building that you pass through on the way to the third floor lecture room.  I realize that not everyone has easy access to the internet and this blog.  For that reason, if you read this, please spread the word about the board.  Please pay attention to the announcement board each day.  Thanks!

test

I always believe things should be natural and fluid and adaptable.  This means that I have never seen a schedule that I could not modify at the last minute, because things always change.  So, here’s the latest concept for the schedule for that last week or so of our time together.

Jul 28 Revision of project proposals due in the evening
Jul 29 Peer Review of proposals due in the evening

19:30 Miller – Spider evolution and phylogenetics

Jul 30 19:30 Cannon – Phylogenetics
Jul 31 19:30 Helmus – Ecological Phylogenetics
Aug 01 19:30 Harrison – getting published
Aug 02 16:00 Roundtable- Data Analysis

18:00 Frisbee!

20:15 Meet at Basketball Court- BBQ in town

Aug 03 19:30 Roundtable – Species co-existence revisited
Aug 04 Free
Aug 05 Student presentations – informal
Aug 06 Final symposium

09:00 Presentations Begin

12:00 Lunch at Hotel

14:00 Resume Presentations

18:00 Dinner at Hotel

20:00 Party and Awards Ceremony at Tropical Rainforest

Aug 07 To Kunming

I am having fun, I hope that everyone else is.  I’ve had quite a nice day so far.  On the way out with the videotaping team, we saw about four other teams already doing their work, watching birds, measuring trees, or at least, we saw their bicycles parked next to the road.  This afternoon, I’ve had interesting discussions with several other groups about how to make consistent decisions, how to quantify things which are very difficult to quantify, and on and on.  I find it quite exciting.

Another good thing about this course, that has been especially good for me, personally, is that it has managed to drag me away from my computer.  Despite having been here for two years now, I have not actually explored the local environment around the garden much at all.  Instead, I have been struggling with the next-gen sequence data for months now and a great deal of my work, either reviewing or writing manuscripts, is done on computers, so I have had very little excuse to go out into the woods.

This course has given me the excuse and I have realized something.  I like to sweat.  I like to be out there, getting scratched by thorny plants, scrambling up slopes, etc.  It feels good.  I have had fewer aches and pains in the past few weeks than I have had when I spend a month, nicely air-conditioned and sedentary, in front of my computer.

I hope to not fall completely back into that rut once the course is over.  While I think we are all doomed a bit to stare at these little glowing rectangles in wonder at the marvelous things they can do, there is still a very marvelous world out there, to go get dirty in and come home with a tangible feeling of accomplishment – “I measured that” or “I got those samples” — it’s a very rewarding feeling.

No lecture tonight.  We will postpone Matt’s talk about using phylogenies in ecology for a few days because of a conflict with one group’s night time activities (no, it is not just a BBQ).  So, you are ‘free’ tonight.

HA!  But, I do have an assignment.  You shall revise your proposals, given the comments that you have received both online and in personal, and upload them as a new topic.  Let’s not try and continue the old ones.

There revised proposals are due by July 28 in the evening.

I will then assign you each to give a peer review of at least one proposal.

Chuck

Spatial Autocorrelation and Experimental Design

I felt that I learned a good lesson the other day from Dr. Prasit about doing experimental work.  I normally study variation in natural populations and in this situation, it is best to minimize the spatial autocorrelation between samples.  In this way, you can be sure that each sample is independent.  The easiest way to do this is to simply distribute the plots as far apart as possible across the sample area.

But, this is a bad idea for setting up experiments in which you want to compare the effect of different treatments.  Because you want the treatment to be the ONLY difference between your different treatment plots.  Let’s say, if you have one control and two treatments, these need to be set up in groups of three, in close proximity.  In this situation, you actually want to maximize spatial autocorrelation between treatments.  Now, of course, you should then separate the replicates of the experiment across the range of natural environmental factors.  So, depending on your objectives, you may want to maximize spatial autocorrelation within each replicate of your experiment but then minimize spatial autocorrelation between replicates.

I know I talked about this in the field but I thought this was an interesting topic and I wanted to make it clear.  Is it clear to you?

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