I haven't had a chance to talk it over with the PI yet, but I've convinced myself that AI (see previous posts) says what the lit says it means. I'm still not totally convinced on the direct, biological applicability of it, but I accept that you can draw the ecosystem level conclusions from it that you are supposed to (polluted environments, proxy for dissolved oxygen, etc).
I also still haven't been able to get my hands on the original citation. The original citation is from a paper presented as a meeting in 1969. Not an article, or a book chapter, or even a thesis/dissertation. A paper at a meeting. I was always under the impression that it was not kosher to cite presentations until they had become published. And perhaps it did....but that doesn't change the fact that the oldest citation for AI is a paper at a conference. (I imagine that olden days scientific meetings were a lot like humanities meetings today; where your "presentation" consists of some one standing at a podium reading a paper they wrote, with maybe a few projected slides for graphs and such. How close am I?)
In other news, I have spent the last week working in Rhode Island on a new project! It's weird coming back from a trip like this. Even though I was working (field and lab work), I was in a new place and there was quite a bit of eating out, so part of my brain is trying to tell me I was on vacation, even though my body and the rest of my brain knows I was working. Now that I'm back in my own lab, I have that usual pile-up of work that happens when you go on vacation, but the mental conflict of knowing I wasn't.
It feels so weird....
Oh, and a memorial here to my sunglasses that I lost yesterday at the beach. I seem to do this every year; I go to the beach, fully intending to take off my shades before getting in the water, and then I get so excited to play in the waves I forget, and splash! they're gone.... C'est la vive.....
Monday, August 27, 2012
Friday, August 17, 2012
Autotrophic Index Update
To hash out my frustrations with this topic of Autotrophic Index, I wrote a blog post just a few minutes ago. I had concluded that I had all this information about the definition of the AI, but just didn't know what exactly it meant.
Now I have a better idea, PI to the rescue! I really don't know why papers can't just SAY what they mean, why it's got to be so circular...but here's the biological definition we came up with.
Now I have a better idea, PI to the rescue! I really don't know why papers can't just SAY what they mean, why it's got to be so circular...but here's the biological definition we came up with.
Autotrophic Index is the proportion of the organic matrix which is viable algae.
I'm still not a huge fan of this definition, because "proportion" implies some sort of percentage or ratio or other <1 number; the values for AI are usually in the 100's or 1000's. But at least it's a way of restating what all these other papers have said in a way that conveys something about the biological implications of what these numbers mean, rather than just saying that various number classes lead you to conclude a specific result.
So, I'll give you that AI is a valid metric.
However, I still think that the way we want to do it (Chl/AFDM) is also a valid and implies a different, biologically meaningful, result. I say that Autotrophic Potential (AP) means the amount of potential photosynthesis occuring per unit of organic matter.
And here's what I think the functional difference between these 2 values is: AI is more of a statement on who's in the community whereas AP can look at what that portion of the community is doing. The amount of chlorophyll present in a community has been strongly linked to the photosynthetic activity of that community. By putting chl in the numerator you can make the assertion that this is potential photosynthetic activity. By having it in the numerator you take that away.
Both of these are useful metrics, but give different information...all with just the same numbers.
Or I'm stupid and crazy and should hand in my lab coat...What do you think?
Coulda been a Contenda'
Yesterday I was so happy. I thought I was going to be on the vanguard of over-turning a metric in use for the last 50 years which doesn't seem to make a whole lot of sense. Now, I'm not so sure...And after I go over all this with you, I'll probably look like an idiot...but whatevs, that's what the internet is for, right? I also want to think about this outloud. Science isn't conducted in a vacuum.
The metric in question is the Autotrophic Index (AI). This is defined as AFDM (mg/m2) / Chl a (mg/m2). So far, the best definitions I can find of this say that this is "...indicative of the proportion of the community composed of heterotrophic and autotrophic organisms" (Biggs & Kilroy NIWA manual 2000) or "...as an indicator of organic enrichment...[heterotrophic] biomass can increase more than pigments in algae when nutrients are enriched with organics" (Stevenson & Lowe 1986).
What the literature has to say, so far, about this measurement is that it assesses how autotrophic a community is. Generally a value of <200 means that it's an algae dominated, more autotrophic; 200-400 is kind of equally (but not really) autotrophic and heterotrophic; and >400 is less algae dominated, more heterotrophic. And what this means, biologically, is....I don't know what...I don't quite understand what it really means to say that a community has a higher proportion of biomass per unit chlorophyll.
However, we are pushing for a different measurement. One we think is more biologically meaningful. We would like to use Autotrophic Potential (AP) defined as Chl a (mg/m2) / AFDM (mg/m2). Here, a higher number would mean a more autotrophic community, and a lower number would mean a less autotrophic community. Biologically, this says that communities with a higher value (more chl/AFDM) have more autotrophic potential, and are more autotrophic, than communities with a lower number.
Now, one of my committee members has thrown a big monkey wrench into my thought process, because it all seemed fairly straight forward to me until I talked to him. He says that having lots of biomass per chl says that the chl present is supporting a lot of biomass and is therefore highly productive/photosynthetic/efficient/whatev. And now I can't reconcile his definition with what the literature says. If less chl can support more biomass (a high number) then wouldn't that be more autotrophic than a community where more chl is needed to support comparatively less biomass (a low number)?
I'm so confused....
The metric in question is the Autotrophic Index (AI). This is defined as AFDM (mg/m2) / Chl a (mg/m2). So far, the best definitions I can find of this say that this is "...indicative of the proportion of the community composed of heterotrophic and autotrophic organisms" (Biggs & Kilroy NIWA manual 2000) or "...as an indicator of organic enrichment...[heterotrophic] biomass can increase more than pigments in algae when nutrients are enriched with organics" (Stevenson & Lowe 1986).
What the literature has to say, so far, about this measurement is that it assesses how autotrophic a community is. Generally a value of <200 means that it's an algae dominated, more autotrophic; 200-400 is kind of equally (but not really) autotrophic and heterotrophic; and >400 is less algae dominated, more heterotrophic. And what this means, biologically, is....I don't know what...I don't quite understand what it really means to say that a community has a higher proportion of biomass per unit chlorophyll.
However, we are pushing for a different measurement. One we think is more biologically meaningful. We would like to use Autotrophic Potential (AP) defined as Chl a (mg/m2) / AFDM (mg/m2). Here, a higher number would mean a more autotrophic community, and a lower number would mean a less autotrophic community. Biologically, this says that communities with a higher value (more chl/AFDM) have more autotrophic potential, and are more autotrophic, than communities with a lower number.
Now, one of my committee members has thrown a big monkey wrench into my thought process, because it all seemed fairly straight forward to me until I talked to him. He says that having lots of biomass per chl says that the chl present is supporting a lot of biomass and is therefore highly productive/photosynthetic/efficient/whatev. And now I can't reconcile his definition with what the literature says. If less chl can support more biomass (a high number) then wouldn't that be more autotrophic than a community where more chl is needed to support comparatively less biomass (a low number)?
I'm so confused....
Thursday, August 16, 2012
50 Shades of Ivory Tower
This is a post I've been meaning to write for a while. I'm that desperate to procrastinate reading.
Back in July, I was asked to chaperone the bio-station's undergrad summer students to a regional UER/URO/whatever conference/lecture series. It was a whole day about communicating science from different people's perspectives. There was a science reporter who talked about what it's like to interview scientists, a private consultation scientist, government scientist, and a couple of professional/academic scientists talking about their various experiences.
One of the later people who spoke was a new prof at a big university. I don't even remember what her "communicating science" perspective is because I was so (I don't want this to come across in a bad way, but it will) shocked at something fairly unrelated she said...During her Q&A, some one asked something along the lines of "how did you get to where you are?", a pretty standard question. And she gave the usual "BS here, MS there, etc" answer. And then she said (paraphrased) 'if you know you want to go into academia, skip the MS and go straight for the PhD'...and then my brain began spinning.
Skip the MS?? My MS is the whole reason why I'm going into academia! Everyone I know who is doing a PhD is going into academia because of their MS. Those people I know who are doing a PhD w/o an MS are miserable, sometimes floundering (more than usual), and have serious doubts about what the hell they're going to do with this doctorate once they've got it.
As she went down this road of "skipping the MS", she began talking about how everyone who goes into science as a profession (be it private sector, government, academic, or just teaching at a CC) has scaled their own version of the Ivory Tower, different shades if you will. Some Ivory Towers end at a university, others at the government.
As for skipping an MS for going into academia, I generally think that's a bad idea. I'm not saying everyone should do an MS or needs to do an MS, but it seems to be very helpful. My MS taught me how to be a grad student, how to do research, how to play the game of academia. By learning all these things then, I could jump right in to the middle depth of the pool and start going for it. Sure I get kicked a lot, I've swallowed my fair share of water, but my head's up and we're going towards the deep end. I couldn't do it without my MS.
Over half the faculty list themselves as following the BS/MS/PhD path. The other half don't say, though anecdotally probably half of them also have an MS and just didn't list it. So Internet, what do you think? Thumbs up or down on the MS?
Back in July, I was asked to chaperone the bio-station's undergrad summer students to a regional UER/URO/whatever conference/lecture series. It was a whole day about communicating science from different people's perspectives. There was a science reporter who talked about what it's like to interview scientists, a private consultation scientist, government scientist, and a couple of professional/academic scientists talking about their various experiences.
One of the later people who spoke was a new prof at a big university. I don't even remember what her "communicating science" perspective is because I was so (I don't want this to come across in a bad way, but it will) shocked at something fairly unrelated she said...During her Q&A, some one asked something along the lines of "how did you get to where you are?", a pretty standard question. And she gave the usual "BS here, MS there, etc" answer. And then she said (paraphrased) 'if you know you want to go into academia, skip the MS and go straight for the PhD'...and then my brain began spinning.
Skip the MS?? My MS is the whole reason why I'm going into academia! Everyone I know who is doing a PhD is going into academia because of their MS. Those people I know who are doing a PhD w/o an MS are miserable, sometimes floundering (more than usual), and have serious doubts about what the hell they're going to do with this doctorate once they've got it.
As she went down this road of "skipping the MS", she began talking about how everyone who goes into science as a profession (be it private sector, government, academic, or just teaching at a CC) has scaled their own version of the Ivory Tower, different shades if you will. Some Ivory Towers end at a university, others at the government.
As for skipping an MS for going into academia, I generally think that's a bad idea. I'm not saying everyone should do an MS or needs to do an MS, but it seems to be very helpful. My MS taught me how to be a grad student, how to do research, how to play the game of academia. By learning all these things then, I could jump right in to the middle depth of the pool and start going for it. Sure I get kicked a lot, I've swallowed my fair share of water, but my head's up and we're going towards the deep end. I couldn't do it without my MS.
Over half the faculty list themselves as following the BS/MS/PhD path. The other half don't say, though anecdotally probably half of them also have an MS and just didn't list it. So Internet, what do you think? Thumbs up or down on the MS?
Tuesday, August 14, 2012
Where have I been?
I've been trying really hard to make this blog not just the place where I kvetch in paragraph form and where I publicize my to-do list. But I also realize that it's been almost a month since my last post, so I wanted to make just a quick update on what's going on. And I promise that, from now on, this blog will be less bitching and listing and actually focus on some grad school/science stuff.
Really, baby! I've even got some post titles saved already!
So, at the end of July we had the Bar exam. It went...ok I guess. He won't really talk about it. It's just like it's these two days that didn't happen. But since then, I've been trying to help the Hubby catch up on all the summer he's missed, so I've been slacking.
But now, all that time off has come home to roost! I am dealing with several spinning plates:
Really, baby! I've even got some post titles saved already!
So, at the end of July we had the Bar exam. It went...ok I guess. He won't really talk about it. It's just like it's these two days that didn't happen. But since then, I've been trying to help the Hubby catch up on all the summer he's missed, so I've been slacking.
But now, all that time off has come home to roost! I am dealing with several spinning plates:
- The EPA project I've been recruited for is getting under way. I'm headed out there for a week of field work next week!
- I am working on making the stats all pretty for the publication I'm trying to get out.
- Over the course of the semester I'm going to be applying for an EPA, NSF, and NOAA grant. That's a shit-ton of writing (don't worry, shit-ton is a metric unit)
- I am going to try to schedule my defense for the middle-ish of December. I don't wanna...this is like scheduling dental work...
- MS manuscript is going off for it's final review THIS WEEK! Come hell or high water, I need that shit done.
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