Friday, September 27, 2013

Parrotfish and sand production (part 2)

Stoplight Parrotfish (Sparisoma virde)
The sight is common on the reef: a parrotfish swims by and a thin stream of coral dust and sand particles is ejected from underneath.  Coral sand is made here in the belly of the beast.   

Here’s a picture I took last week in Bonaire.  You can see the stream of sand coming from below.  

(BTW - do you know how hard it was to get this shot?  I took a LOT of photos, trying to capture this magical moment.)  
Parrotfish caught in the act of creating more sand.

Our question is simple:  How much sand is created by an average parrotfish in the course of a year.  One set of sources says it’s 200 pounds, another says it’s 2000.  One of those can’t be right. 

This kind of discrepancy comes up all the time, and it’s the reason you don’t want to single-source anything, even simple facts like this.  (In an earlier SearchResearch episode wefound widely varying numbers for how far a specific bird flies.)  

So where do these numbers come from?

200 pounds / fish / year?  The source for most searcher’s “200 pounds” claim seems to be from the Wikipedia article on Parrotfish which points to the article by Thurman (see below for reference list).   The Wikipedia entry looks like this: 

Unfortunately, the link to the Thurman article specified in Wikipedia is dead (it was last checked in 2009) and the target site no longer supports this reference.  I spent some time searching for this chapter, and while I can find lots of references to it, I can’t find the book chapter itself. 

Even worse, many of the references to this chapter I found are clearly copies of the citation and link from Wikipedia.  (Even at such well-respected sites as the Encyclopedia of Life whose parrotfish page--—would be considered authoritative—merely quote the Thurman reference and give the same link to a dead page.) Sigh.  

So went to my local library’s website and inter-library loaned the darn thing.  Amazingly enough, I got the book after only 3 days!  And there, on page 310 is the assertion:  “By eating coral (and corraline red algae) a single parrot fish may produce up to 90 kg  (190 lbs) of sand per year.” 

Case closed?  Not yet.  Unfortunately, THEY don’t give any reference for that bit of data.  Where did THEY get that information from??   

2,000 pounds / fish / year?  The other data SearchResearchers found was the "1 ton / year" number.  The source for most searchers’ “2,000 pounds” seems to originate from the Ichthyology department’s page about parrotfish at the Florida Museum of Natural History (FMNH). 

On that page they say “Parrotfish may produce as much as one ton of coral sand per acre of reef each year.” 

But read that carefully:  This means “all of the parrotfish on the reef in 1 acre” are producing around 2,000 pounds of sand over the entire acre.  That’s the contribution by all of the parrotfish working (so to speak) together. 

Sadly, they don’t give a reference for their source material either.  And when I search for the exact phrase as seen on the FMNH site,

     [“Parrotfish may produce as much as one ton of coral sand per acre of reef each year”]

it’s clear that all of the references are using the FMNH page as their source.  (Typically, much of the text in the article is quoted directly, including that phrase. This kind of not-thought-out copying always makes me suspicious.  )

However, by being diligent and following various sources, I also found the 2,000 pound reference as coming from the book “Fishes of the Bahamas” by (Bšhlke & Chaplin, 1993).  The citations would look like this:  
Bšhlke, J.E., and C.G. Chaplin 1993. Fishes of the Bahamas and Adjacent Tropical Waters. University of Texas Press, Austin, 464-482. 
So I go to Google Books and find…  this citation is slightly wrong.  The first author’s surname is Böhlke, not Bšhlke.  (Some character encoding failed and people weren't careful about their cites.)

And, once again, this book falls into the “scanned on Google Books, but snippet-view only” (which doesn’t help).  It’s not scanned on or any of the other sources.  So…

… back to the library.  I ordered this book and got it along with the Thurman book.  Thing is, “Fishes of the Bahamas” is a giant tome:  771 pages of fish data.  Not much plot, but still pretty interesting to read (if you’re a diver). 

In this book I found the sentence:  “On a Bermuda study reef it was recently estimated that one ton per acre per year of this material [“calcareous material,” i.e., coral sand] passes through the intestinal tracts of reef fishes and is redeposited as fine sand, and that the scarids [ parrotfish ] are primarily responsible.” [pg 465]

And the reference given here is…   (finally, a real reference!)
Bardach, John E. "Transport of calcareous fragments by reef fishes." Science 133.3446 (1961): 98-99.

By going to Google Scholar and searching for that author + title I was able to get to the original article:

Now we’re getting somewhere.  In that paper (published originally in the well-respected journal, Science) the author writes:   It was found that browsing omnivorous reef fishes which rely, in part, on a plant diet ingested and redeposited at least 2300 kg of such material on a 1-hectare study reef near Bermuda.  

Let’s do some Google conversions to check this number. 


     [ 2000 pounds per acre in kg per ha ] 

means  2241.7 kg per ha (a hectare is 10,000 square meters) 


     [ 2300 kg per ha in pounds per acre ] 

means  2052.0 lbs per acre (an acre is pretty close to 1 football field).  

I wanted to get the full text of the paper, but that’s $20 for a “short-term use” (1-day) license.  As you can imagine, I’m not about to pay for that. 

But we still don’t know how much sand/fish/year that represents.  To figure this out we need to know How many parrotfish live in on an acre of reef?  

Hoping to figure out this sub-puzzle, I started doing searches like this, using the scientific name of the Stoplight parrotfish: 

     ["Sparisoma viride" sand OR sediment production ]

This is reasonably productive (esp. when done in Google Scholar) and leads to several papers on the topic.  The most cited paper is:
Bruggemann, J. H., et al. "Bioerosion and sediment ingestion by the Caribbean parrotfish Scarus vetula and Sparisoma viride: implications of fish size, feeding mode and habitat use." Marine ecology progress series. Oldendorf 134.1 (1996): 59-71.
I got a PDF of the paper by doing this search:

[ filetype:pdf  “Bioerosion and sediment ingestion by the Caribbean parrotfish Scarus vetula and Sparisoma viride" ]
That led me to the PDF file, which I printed out and carefully read. 

This is when I realized that this is a much more complex problem than just looking up the number of parrotfish / square meter on the reef. 

By reading this (and a few other papers) I learned that the density of parrotfish on the reef varies hugely by depth.  (Shallow water has a lot; water deeper than 50 feet has fewer.)  They also sleep at night, and feed only between 7AM and 6PM (and, btw, they mate daily, between 7AM and 9AM… but I digress).  I also found out that the quantity of coral ingested when they bite varies a good deal by the size of the fish, but it varies even MORE depending on the kind of parrotfish.

Among other things, we HAVE to be careful not to mix up our parrotfish species (e.g, Hawaiian parrotfish with Caribbean parrotfish, or even parrotfish that live side-by-side in the waters of Bonaire—as the paper points out “…the erosion rates per bite by Sparisoma viride is more than an order of magnitude higher than in Scarius vetula.”  That is, the Stoplight parrotfish (Sparisoma viride) has a bite size that’s ten times larger than that of Scarius vetula (Queen parrotfish). 

But we’re getting somewhere. 

If you read this paper carefully, you’ll eventually find Figure 5 “Scarus vetula and Sparisoma viride Erosion rates per bite (upper graphs) and per day (lower graphs) as a function of fish size.” 

Figure 5 from Bruggemann, et al. (Yellow highlighting mine)

If you look at the graph in the lower right corner, that’s a chart of “mean daily erosion rate (g ind -1 d -1)” – that is, “grams per individual fish per day.”  Although the “grams / day” vary greatly by fish size, the average is right around 300 grams / fish / day.   Basic math shows us:

300 grams * 365 days = 109,500 grams / year

Or, 109.5 kg / year (204 pounds), which is close enough (given all of our averaging) to our earlier estimate of 95 kg / year.  (And, incidentally, nothing close to 2,000 pounds / fish / year.) 

If this is correct, then to get 2000 lbs of sand contributed per acre by all of the parrotfish, we’re going to need around 10 Stoplight parrotfish / acre.  By my direct observation on the reefs of Bonaire, that seems low, but let’s see if we can’t find some numbers in the literature. 

Another paper I found from my previous query is

Choat, J. Howard, et al. "An age-based demographic analysis of the Caribbean stoplight parrotfish Sparisoma viride." Marine Ecology Progress Series 246 (2003): 265-277.

He “conservatively estimates” 4 individuals / 300 square meter plot.

     [ 1 acre in square meters ]

is 4046.86 square meters in an acre.  If we divide 4046.86 / 300, we should get an estimate of the number of Stoplight parrotfish / acre (according to Choat).  This number is 13.5, a little higher than we estimated before, but not a crazy number. 

Search Lessons:  First, this one took me a long time.  I’m guessing I spent about 10 hours researching this, and I learned a huge amount along the way.  (Not just about the sex life of parrotfishes, but also about why it’s so difficult to estimate the total number of fish on the reef.) 

But I figured out that 1 Stoplight parrotfish generates around 0.6 pounds of sand / day (on average, mid-depth of the reef). 

I did this by going back to the original papers (using Scholar and Google Books) to dig out the charts and original data. 

In some cases, it’s hard to get to the original source document.  As you saw, I had to use my local library to get to the original paper by Thurman.  But once I had it, the rest of the story unfolded easily.  (Although slowly—I had to look up a lot of words.  Acanthurids and scarids and fork length were all new terms for me). 

This is a nice example of sensemaking: Pulling together information from multiple resources and cross-checking them against each other. 

In truth, I read much more than I’ve reported on here.  I didn’t want to tell you that I actually read about 10 papers, some of which were duds.  They seemed good from the abstract, but the reality was that the paper encoded the data in an unhelpful way or that it was about parrotfish on some other continent, or the wrong kind of fish. 

AND... a beautiful 2 minute video of parrotfish feeding from the "Blue Planet" BBC series (discovered by regular reader Ramón... thanks!).   Note the part at  56 seconds in--a lovely shot of sand being delivered to the reef.

Reference List

Bruggerman JH, van Kessel AM, van Rooij JM, Breeman AM (1996) Bioerosion and
sediment ingestion by the Caribbean parrotfish Scarus vetula and Sparisoma viridae: implications of fish size, feeding mode and habitat use. Mar Ecol Prog Ser 134:59-71.

Choat, J. Howard, et al. "An age-based demographic analysis of the Caribbean stoplight parrotfish Sparisoma viride." Marine Ecology Progress Series 246 (2003): 265-277.

Gygi RA (1975) Sparisoma viridae(Bonnaterre), the stoplight parrotfish, a major
sediment producer on coral reefs of Bermuda. Ecol Geol Helv 68:327-359

Thurman, H.V; Webber, H.H. (1984). "Chapter 12, Benthos on the Continental Shelf". Marine Biology. Charles E. Merrill Publishing. pp. 303–313. 

van Rooij, Jules M., et al. "Resource and habitat sharing by the stoplightparrotfish, Sparisoma viride, a Caribbean reef herbivore." Environmental Biology of Fishes 47.1 (1996): 81-91.


For comparison purposes of parrotfish feeding and sediment production on the Great Barrier Reef:

Bellwood D.R. (1995a) Direct estimate of bioerosion by two parrotfish species,
Chlorurus gibbus and C. sordidus, on the Great Barrier Reef, Australia. Mar Biol 121:419-429
Bellwood D.R. (1995b) Carbonate transport and within reef patterns of bioerosion and
sediment release in parrotfishes (family Scaridae) on the Great Barrier Reef. Mar Ecol Prog Ser 117:127-136.
Bellwood D.R. (1996) Production and reworking of sediment by parrtofishes (family

Scaridae) on the Great Barrier Reef, Australia. Mar Biol 125:795-800.

Thursday, September 26, 2013

Answer: What IS that thing? Another undersea mystery.

Yesterday's challenge wasn't all that hard.  There were a number of good clues here. 
I'd said "In around 30 feet of water (10 m), I found several instances of this... " 
General world knowledge tells you that this is something in a tropical reef, and it occurs not too deeply.  
I also gave you a few clue words:  "spheres" and calling them "pearly."  I wanted to say that because the opalescence doesn't quite come across in the photos.  

When I started this search, I really didn't have any clue what they were.  I figured they were some kind of algae, but that was a pure guess.  The ocean has all KINDS of mysterious creatures in it, ones that defy your normal terrestrial boundaries.  
So I started this search as several others did.  I used "plant" rather than "algae" since I really wasn't very sure: 
     [ spherical reef plant ] 
And that was enough to get me to a page on "Coral reef plants" which mentions "...Grape algae (Valonia ventricosa) - this odd algae grows in a spherical form with peg-like attachments that fasten it to a hard surface..."  
In this case, it was the text, rather than the image that caught my attention.  I'd described it as "spherical" because it (and the pearly quality) were the most striking characteristics.  I figured that anyone writing about it would comment on that.  
So I next looked up the scientific name, Valonia ventricosa, and I knew I had the answer.  The Knowledge Panel (see below) had an image that was striking. 

Valonia ventricosa, also known as "bubble algae" and "sailors’ eyeballs" (a remarkably vivid common name) is a species of oceanic algae around the world in tropical and subtropical regions.
Even more amazing: These things are single cells, one of (perhaps THE) largest single cell organism around.  
 Clicking on the Wikipedia entry, I read a bit about them, and then, as I often do, I clicked through the links on the article.   
The first link was broken.  It was a link to:
I thought this might be an interesting article, so I did a query to see if that article was still on that website: 
     [  Gazing_Balls_in_the_Sea ] 
Sure enough, it's still there (I should go fix up the Wikipedia entry to reflect this).  And it IS an interesting article.  These things are also called "sea pearls" (makes sense), AND the article mentioned "...Ventricaria ventricosa, or Valonia ventricosa..."
Well.. that's interesting.  Two names for the same plant?  
I kept following up the other links (and found other problems), but was impressed when I followed the last link on the Wikipedia article, a reference to the AlgaeBase site.  The link is to the AlgaeBase description of the "sailor's eyeballs." 
This is pretty clearly the definitive site for questions about algae.  And here you can see the story.  
The original publication describing this plant was published in: 
Agardh, J.G. (1887). Till algernes systematik. Nya bidrag. (Femte afdelningen.). Acta Universitatis Lundensis 23(2): 1-174, 5 plates.  
If you're curious, you can see the original publication.  (PDF)  This is the way science used to operate--it's in Latin.  It's long text passages.  There are a few lovely sketches at the end. 
But what's with the two names? 
The original name was given by J. Agardh in the late 19th century.  But as AlgaeBase points out: “This name, Ventricaria ventricosais,  currently regarded as a taxonomic synonym of Valonia ventricosa."  
Renaming and reclassification happens all the time.  What USED to be called a brontosaurus is now called an apatosaurus. A similar thing happened here.  A newer publication came out put Valonia into a new category, Ventricaria.  

In that paper, Olsen and West point out that our favorite algae actually belongs to a newly described genus that they call Ventricaria.  If you look at publications since 1988, they all (well, nearly all) use the new name. -- tells that it’s a problem
1.  What IS that thing?  Answer:  Ventricaria ventricosa, previously known as Valonia ventricosa.  Common names:  bubble algae, sailor's eyeballs, sea pearls.  

The second question asked how to control it.  To answer this, I thought I'd try asking an easy query: 
     [ bubble algae aquarium problem ] 
That took me to which has a long, really interesting article with more information about Valonia / Ventricaria (including great photos of other forms of the algae).  
It ALSO has a long section about controls, including the use of snails and crabs to eat them.  In particular, the article mentions the crab Mithrax sculptus (aka "green" or "emerald" crab) as a way to control the spread of bubble algae in your tank.  
2.  What biological agent might you use to control them in your salt water aquarium?   Answer:  You might try using a crab in your tank to eat up the bubble algae. 

However, not everything is perfect. 
3.  (Extra credit)  Why does it now seem that the use of this biological agent might be a really bad idea? 
The article also mentions that the crabs, as they dine, might well end up spreading spores from the interior of the bubble, and end up making matters worse.  You start with one algal cell, but end up with them infesting the tank.  
I also checked on Google Scholar for: 
     [ emerald crab control bubble algae ] 
And found this interesting article that confirms what we read at ReefKeeping: Efficiency of using emerald crabs Mithraculus sculptus to control bubble alga Ventricaria ventricosa (syn. Valonia ventricosa) in aquaria habitats  (see (2) below).  " the crab tears the algal cell apart, the cell liquid that contains juvenile cytoplasmatic spheres is released into the water; this behaviour might contribute to algal dispersal and consequently algal infestation. These results seem to indicate that M. sculptus might not be such an efficient bio-controller of the pest V. ventricosa as previously thought..." 

Search lessons:  There are a couple of things to note here. 

1.  Keyword choice:  Try to use terms that you think someone else would use.  If it's not working for you, ask someone else for the words they would use to describe it.  

2.  Wikipedia as a starting point: As we've discussed, Wikipedia is a great place to start your research on a topic, but don't think of it as the ending point.  In this article, Wikipedia has dead links (easily fixable), and uses outdated names in the article.  

3.  Triangulate what you find:  Look for multiple sources to get the same data in different ways.  I used Scholar to find that article about emerald crabs, and I found AlgaeBase as a great authoritative source for the latest on algae from a botanical perspective.  

Hope you enjoyed this as much as I did! 

Tomorrow, the resolution of the parrotfish problem! 

Search on!

(1) Olsen, J.L. & West, J.A. (1988)."Ventricaria (Siphonocladales-Cladophorales complex, Chlorophyta), a new genus for Valonia ventricosa."  Phycologia 27: 103-108.  

(2) Figueiredo, Joana, et al. "Efficiency of using emerald crabs Mithraculus sculptus to control bubble alga Ventricaria ventricosa (syn. Valonia ventricosa) in aquaria habitats." Journal of the Marine Biological Association of the UK88.01 (2008): 95-101.  

Wednesday, September 25, 2013

Wednesday search challenge (9/25/13): What IS that thing? Another undersea mystery.

Diving in Bonaire was immensely satisfying, it also led to multiple mysteries, each perfect for a search challenge.  I'm trying hard to not turn SearchResearch into a long series of "Mysteries of the Deep!"   

While there I took several hundred underwater photos, and when I was going through them this past week for the parrotfish problem (more on that later), I ran across a few snapshots of something I couldn't identify.  

In around 30 feet of water (10 m), I found several instances of this... 
These spheres are a remarkable sight.  They're not pearls, although they definitely have that kind of pearly, opalescent quality to them.  They're about 2 inches (5 cm) across, slightly bendable when you press on one, but firm too.  They're strongly attached to their substrate, in this case, sponges, but I saw them attached to other things as well.  

When I finally figured out what they were, I learned they're kind of a pest in saltwater aquariums, and aquarists look for ways to control them.  (Although they are fairly remarkable in appearance.)  They're certainly not a pest in Bonarian waters; I'd always see a few per hour while swimming over the reef.  

These wonderful things lead to today's challenge: 

1.  What IS that thing?  (I'm looking for the genus/species scientific name, although the popular names are interesting too.) 
2.  What biological agent might you use to control them in your salt water aquarium?  
3.  (Extra credit)  Why does it now seem that the use of this biological agent might be a really bad idea?   

Let us know HOW you found the answer.  For SearchResearchers, the search method to get to the right answer is as important as the answer itself!  It's how the rest of us learn to be better searchers.

Search on! 

Parrotfish update:  I hope to finish my update to the "parrotfish poop" problem from two weeks ago.  

It turns out that (much to my surprise) figuring out a credible answer to "how much sand does a parrotfish make in 1 year?" is pretty tricky.  I've been on the job, though, reading lots of scholarly papers on fish, and yes, how parrotfish process what they eat.  Fascinating stuff.  (But it's also really busy at work these days, so I haven't had nearly the amount of time I'd like. Ah, the irregular, but joyous life of a researcher!  I'm enjoying having a reason to read through ichthyology papers.) 

Thursday, September 19, 2013

Yesterday's Challenge:  

Who is my (meaning me, Dan Russell's) great-great-great-great-great-great-great advisor?   (And why is that an incredibly cool thing to know?) 
That is, who was my advisor's-advisor-advisor-advisor-advisor-advisor-advisor was (back 7 PhD generations).

Answer:  Simeon Denis Poisson (one of the greatest mathematicians of the early 19th century).  

Simeon Denis Poissonmy advisor's-advisor-advisor-advisor-advisor-advisor-advisor
Image from Wikimedia)

How to find out:  Well, by now you know who my advisor is--Jerome Feldman.  (He was my advisor at the University of Rochester, although he is now at UC Berkeley.)  He's been the advisor for a LOT of students.  (As someone pointed out, I work with 4 other Feldman students at Google.)  

But probably the simplest way to figure out my great (* 7) advisor is to use The Mathematics Genealogy Project advisor tool.  If you start with my name and work backwards - Daniel Russell  - you'll find that I'm a descendent of S. D. Poisson.  

And the simplest way to discover the Genealogy Project advisor tool is to search for my name and the title of my thesis.  Like this: 

     [ Daniel Martin Russell "Schema based problem solving" ] 

The Genealogy Project tool shows up pretty high in that list. As several readers pointed out, once you do the search and notice that there's a tool labeled "genealogy," the rest is simple.  

Why use my full name in the search?  

Lesson 1: Because different kinds of sites use different conventions for naming individuals. For genealogies, typically you want to use the full name.  (But be careful; you still might have to hunt around on name variations.  Geoffry vs. Jeffry vs. Jeffery, etc.)  I used my full name here because I know that this is the convention for official documents (and the PhD degrees are very, very formalized).  

And then, you just work backwards from me: 
Daniel Martin Russell (1985)  
Jerome Arthur Feldman (1964)  - advisor 
Alan Jay Perlis (1950) - grandadvisor *1 
Phillip Franklin (1921) - * 2 
Oswald Veblen (1903) - * 3 
E. H. (Eliakim Hastings) Moore (1885) - * 4 
H. A. (Hubert Anson) Newton (1850) - * 5 
Michel Chasles (1814) - * 6 
Simeon Denis Poisson (1800) - * 7  
And of course Poisson's advisors were the even more famous mathematicians / physicists Joseph Louis Lagrange (1754) and Pierre-Simon Laplace (~1760).  

Still, I like Poisson as one of my great-advisors because his Poisson distribution is used so often in statistics and computer science. (1)   When I first learned about a Poisson distribution and figured out how it works, I felt... empowered.  It sounds silly, I know, but for the first time in my undergraduate career, I felt as though I'd learned something that I would never have figured out on my own.  It was my first moment of mathematical awe and surprise. 

I never imagined that I was intellectually related to the man himself.  That was a second great surprise.  

But perhaps the best / coolest thing is that his name is one of 72 French geniuses inscribed on the Eiffel Tower.  (As both Sarah and Ramón pointed out.)  

Lesson 2: Be sure to look for a tool that can do the computation for you.  Sometimes (especially for repeated information links, like we see in this kind of a problem), you'll find a tool that will do the heavy lifting for you.  

More on parrotfish tomorrow. 

Search on! 

(1) Background: In the context of queueing theory the Poisson distribution is a pretty good model for how items arrive into a queue that needs to be managed.  Queues are pretty fundamental to the way all computers work, so everyone in CS needs to learn this at one point or another.