Kai's research thread/caddisfly geekout

[Cain]

Is there any particular reason you are hijacking Kai's thread to talk about your personal issues?

[Honey]

Do you think that you could write a thesis on the discovery of a new species?  I honestly don't know how much work that would require.

I don't know about anybody else here, but I happen like reading about your research, even if it does turn into a livejournal type thing.

Ditto this!

& Holy Shit Kai!  This is NOT the kinda thing (discovering a new species! no less!) that 1 does everyday!

Salut!

[Kai]

There are too many "Proffessionals" that have their parents pay for their education for them to have a name nailed to their door to give us a name as to what's wrong with us.  If you asked me ( and you probably wouldn't)  most people that have a mental illness have just had a really bad time in life over the last few years and they respond with the the only way that they know how ... primordial instincts.  Don't push me and I won't push you.  This hasn't worked for so long ... but why shouldn't it work.  This planet has been evolving for over 150,000,000 years and the rest, and is still evolving... Can't we connect on a spiritual level and feel the vibe without all the shit that is happening in front of us so that we feel that we are malformed or we have something wrong with us.  WE ARE THE FUTURE but we have to be very careful as to what we do to to create this new world.

I'm not sure what that has to do with anything....Also, planets age = 4.5 billion years, first life = 4-3.5 billion years, "cambrian explosion = 500 mya, K-T boundary = 65 million years ago, humans = 1 mya. 150 million years doesn't even take us to the cambrian, it barely takes us out of the mesozoic and the age of reptiles. Just pointing that out.....


Anyway, been trying to work on my research proposal. I have had little or no energy for the past week and I am trying to find ways to remedy that. Every time I sit down to write, or even think about writing, I get an overwhelming feeling of fatigue. I feel fatigued right now, and I haven't been thinking about it. Its not sleep, I just got up after 9 hours of it. It could be diet.

I can't think about this right now, its making me tired.

[Cain]

You might need to mentally switch off for a while.

Are you still regularly doing T'ai Chi?  It might be worth taking a day off, if you can afford to or not, and giving over a few hours to some mindless, graceful violence.

[Kai]

You might need to mentally switch off for a while.

Are you still regularly doing T'ai Chi?  It might be worth taking a day off, if you can afford to or not, and giving over a few hours to some mindless, graceful violence.

I just started again yesterday. Its been a long time but I fall back into the patterns so easily. I need to rememorize the third section of the form, but once I do thats a whole hour of defensive dance. I also just recently started doing Chi Gung. Whether or not chi actually exist, the visualization of inner chi movements downward from "energy gates" out through the feet relaxes the muscles in that area. I don't know how the psychosomatic response really works, but it does seem to work.

I've also taken to running a ten minute timer on the computer again, to make sure I get up and do things instead of just sitting here all day.

[Kai]

so, after some thought tonight, I have decided that I want to change my thesis. There has not been a good key to the african trichoptera genera published since the 1960s, and its about time that one was. I don't know if I could pull it off for both adults and larvae, but if it is feasable I would try.

Just did a search on the trichoptera world checklist. In the Afrotropical region:

24 Families

87 genera

1043 species


The last number is unimportant to my potential project, as I would only be looking at families and genera.

I have to talk to my adviser tomorrow, see what he has to say. He might say no. I might then tell him I don't have a project then, because every time I think about the Cheumatopsyche project I feel exausted.

[Mesozoic Mister Nigel]

Wow, cool! Good luck!

[Kai]

Wow, cool! Good luck!

If he says no, I'm gonna need it, because I'm gonna pull the "are you paying me then?" arguement.

You know, the one where I say "I'm paying to be here, you aren't paying me, the Cheumatopsyche project was my choice, and unless you have a project you want to pay me on, I am doing something different."

Edit: Actually, what will likely happen is that he will somehow convince me to go for this cheumatopsyche project and I will once again completely loose faith in it at some point, possibly crucial.

[Mesozoic Mister Nigel]

Hold your ground! You have a project right here that you are actively engaged in, that excites you... stick to your guns and make it your thesis, rather than killing yourself trying to complete a project that doesn't excite you.

[Kai]

Hold your ground! You have a project right here that you are actively engaged in, that excites you... stick to your guns and make it your thesis, rather than killing yourself trying to complete a project that doesn't excite you.

Oh, it all excites me. Till I actually start working on it. Then it feels dull and tiring. I'm already starting to feel a lack of energy about this project and I haven't even talked to him about it yet.

Or maybe I just need to sleep.

[Mesozoic Mister Nigel]

Sleeping is definitely a GOOD idea.

[Kai]

Edit: Actually, what will likely happen is that he will somehow convince me to go for this cheumatopsyche project and I will once again completely loose faith in it at some point, possibly crucial.

Prophesy fulfilled! Well, the first part. Lets hope that the second part doesn't occur as well.

Actually, I convinced myself with some help. Sorry, new species, you will have to wait for someone with more time than me (or me with more time!).

Full story later. Right now, I have to go to a seminar.

[Kai]

Okay, talked with the Dr. this morning. First thing I said "I have lost all faith in my project". We sat down and talked. I told him about my concerns. I think I don't give him enough credit. He wants to see me do something excellent. I told him about the difficulty I saw with doing all this molecular work I knew nothing about. He said that, although it was a large portion of the other grad student's project who left, it doesn't have to be for mine. I can just send material off to be sequenced and focus on morphology. Furthermore, he said there was nothing keeping me from going into the specimens already associated by other people and looking at those. I felt better about it after he told me that a high school student found morphotypes to separate larvae, a high school student, not even in college, in a six week project. I also felt better when he told me that the reason this hasn't been looked into before has nothing to do with it being impossible. HH Ross never looked into this because he had other higher level taxonomic projects to work on. The same is true for GB Wiggins. Schefter and Wiggins produced some information on setal characters in the past but they never looked into it deeply because like Ross they had other higher level work to do. Wiggins actually had a graduate student working on Cheumatopsyche for a time but he apparently disappeared, never to work in Trichoptera again. Schefter never did more because she has trouble with research due to illness.

So, curiously, the reason that no work has been done on this is not because it is impossible, it is because people have been very interested in higher level taxonomy, and now that most of those issues have been resolved (what with the molecular and morphological phylogenetic analysis by Kjer in 2002 of the whole order, and the same for the family Hydropsychidae in 2005 by Geraci), the focus has come back down to the genus and species level, and its time for someone to resolve the diagnosis of North American Cheumatopsyche. So its not that it hasn't been done because it can't be, its that it hasn't been done simply because people haven't devoted the time to do it. And you can see the interest that biomonitoring professionals have in this resolution, because every time there is any information presented on the genus in North America, many people come to see.  It is very telling. Just a poster or a student presentation gets people interested, it is such an important genus.

So I'm going to do it. I need encouragement, but I am going to do it.

[Kai]

Annnnnd, now its time for me to talk about adult/larval associations. Due to the fact that taxonomy, original species naming and diagnosis, are done using the adult life stage, you have to find some way to associate the larval stage with the adult stage before you can start separating larvae to the species level. In the case of Trichoptera, there are 2 classical pathways:

The morphotype approach

The pharate pupa approach

The morphotype approach is the most simple. Say you have a bunch of caddisfly larvae you collected from a stream. First you separate these out by what looks similar, if two things have the same characters, then they are the same morphotype. You preserve a portion of the larvae of each morphotype, and then rear the rest of each morphotype separatly to adult. If, when the adults emerge, each morphotype turns out to be a single species, congradulations! You have successfully discovered the larval diagnostic characters. If a morphotype turns out to be several species, you go back to the larvae and look for further characters to create further morphotypes, and rear more larvae. Its trial and error, mostly.

Pros: When you get it right, you know it, because you have a single species of adults raised from a morphotype that happened to be a single species of larvae. It is very easy to tell if you are wrong for the sample you have.

Cons: This requires equiptment. And work. And time. And more time. And more work. SRsly, rearing is a process that is time consuming and heavy on the work. It also may just happen that there is a species elsewhere, away from your sample area, that shares the characters but is of a different species. The characters have to be tested across a species' distribution to be deemed reliable.

The pharate pupa approach is like sticking characters of the larva, pupa and adult all in one sack, a three for one deal. Essentially, you go out to a stream at the right time of year and look for pupae that are nearly ready to emerge. The pupa, at this point called a pharate pupa, will have the genetalia of the adult stage and characters of the pupa at the same time. In addition, most Trichoptera schluff off their larval cuticle and sclerites inside the pupal chamber, and these pieces remain there throughout the development.

Pros: Three for the price of one, what more could you ask for?! You can diagnose all three life stages with the material at hand.

Cons: Try wandering through a river in the cold parts of the year, searching underwater for a male (because the males are the ones that determine species in insects) pharate pupa. They are hard to find, and you have to find it at just the right time in the development. At the same time, you have to hope to god that the larval cuticle is in good condition, and even then all the membranous parts tend to be destroyed, so you are left trying to figure out what sclerite goes where (pin the sclerite on the larva, if you will). If you have the perserverence, this works sometimes, like when the only characters you need are on the sclerites, or when the pupa actually KEEPS the larval parts inside the pupal chamber instead of voiding them out the case. Yeah..... and then you have the same pitfalls as the morphotype method when it comes to distribution.



There is one other more current method for adult/larval association: the barcode approach.

The barcode approach uses mitochondrial COI DNA, a rapidly evolving sequence of DNA that codes for a metabolic enzyme. Since COI genes tend to be the same throughout a species, you can compare the sequence for adult insects to a sequence for a larva, and figure out what species it is.

Pros: Holy shit is this less time consuming than the other methods. My GOD. It just blows my socks off what we can do with technology these days. In fact, biologists are trying now to create a complete database for the COI gene for every species of organism on the planet. Its relatively cheap to sequence too, and once you draw up the techniques for a group of organisms, the rest comes easy. If you collect adults and larvae from the same location, the association is rather unambiguous, most of the time. You don't even have to destroy the specimens to sequence, all you need is a leg. Furthermore, you can sequence some pinned material that has been dead for more than 25 years.

Cons: its the times where it is ambiguous that it causes a problem. COI can vary across the range of species, so you have to barcode from across the range. You also have to have the sequencing equipment, and even if it is cheap, its still around 3 bucks a specimen.  It also is a problem if your material is stored in alcohol. Wet specimens have to be rather fresh, within a year or so.


So, thats how associations work, in a nutshell. I'm going to take the third approach for this project, and not do the sequencing myself; I'm going to send it off to be done, and concentrate on diagnosis.

[Vene]

I'm the first to admit I am biased in favor of molecular techniques (especially with regards to DNA), but I think that the gene based analysis is just awesome.