Tag Archives: non-photo

Report of snakes

Below is a working list of snakes I’ve  found and identified (with help from various others, including Juan and Cristian) during NAPIRE programs.

Species Date Location
Cope’s Coffee snake Ninia psephota 5 July 2015 Road leading to Las Alturas
Shiny whipsnake Chironius grandisquamis 16 July 2015 In the Rio Java at Las Cruces
Plain wormsnake Geophis hoffmanni 10 July 2015 Drive-way of Wilson Botanical Garden
Sock-headed snake Enuliophis slateri 27 June 2015 Drive-way of Wilson Botanical Garden
Black-banded Cat-eye Snake Leptodeira nigrofasciata 18 July 2015 Rio Java Trail near Quebrada Culvert
Blunt-headed tree snake Imantodes cenchoa 18 July 2015 Rio Java trail near Quebrada Culvert
Green  Parrot Snake Leptophis ahaetulla 25 July 2015 Near researcher cabins
Bird snake juvenile Pseustes poecilonotus 25 July 2015 Rio Java trail
Snail-eating Snake Sibon argus 6 July 2016 In bromeliad bed outside of Casa Wilson
Blunt-headed tree snake Imantodes cenchoa 29 June 2016 Outside of Reception
Red-tailed boa Boa constrictor 8 July 2016 At entrance to Rio Java trail

Cope's Coffee snake - Ninia psephota - 07.05.2015 - 08.54.06


AFS: Some other days


I saw a number of contributed talks on Tuesday, including one on an endangered snail, Assiminea pecos, given by Beth Roesler at Texas Tech. A. pecos is a small, ~2 mm, freshwater snail found in a handful of counties in Southwester United States.   Its status and major threats are unclear, so Beth set out to characterize preferred habitat for the snail and consider methods in quantifying snail densities. One characteristic important to snail presence-absence was related to moisture. The snails seemed to occur in a fairly narrow band of soil saturation/moisture levels, and in arid environments, like the South West, these bands can be pretty sparse and easily impacted. She also suggested that common reed Phragmitis australalis invasion may add to the threats facing A. pecos.

One interesting thing I noticed in her talk, and a number of other talks here, is that regression tree analyses seems to be increasing in popularity.  I recall my first experience with it in a paper by Usio et al. on native and invasive crayfish presence in Japan. It seemed like an unusual and powerful analysis at the time.

Some food, beer and ska

In the evening, I enjoyed my first gastropod meal at Le Moine Enchanson, and a beer at Barbarie.  The beer was a coffee stout, and, while not quite as caffeinated as the Southbound Brewery + Perc coffee stout sold in Savannah, it was creamy and delicious. On my way back to the hotel, I saw a few posters for an upcoming ska show with the Planet Smashers in the line up – would love to see them again.



I started today with a 5k run – the Spawning Run – which is held during each AFS meeting. The course took us through Battlefields Park, and it was quite hilly. I finished in 26:01, which is, to the best of my knowledge, nearly a two minute PR. Certainly a good start to the day.


From the run, I began sitting in on the Larval Fish conference and saw a talk by Michael Miller. Miller discussed some hypotheses regarding movement of pelagic leptocephali from off-shore to near-shore habitats. Leptocephali are slimy, snot-like, larval forms of some marine fish, including Angullid eels. There’s not much to these little fish, so it’s expected that after adults spawn off shore (often hundreds of miles), the leptocephali larvae are at the mercy of the ocean currents, with little active movement on their own. Miller, however, proposed that the “leptos” may actively swim back to their near-shore habitats. While he didn’t really present any data to support this directly, surveys of adult and larval locations suggest that the larvae are crossing large ocean currents – something that is unlikely if they are riding the currents. The lack of support was actually the most interesting thing to me. It says that we don’t know what some large, ecologically and sometimes economically, groups of fishes are doing as larvae. Most importantly, with dramatic changes in ocean currents predicted under climate change, leptocephali fishes have some big challenges ahead.

Tonight ends with the big networking event. Traditionally, this event has been open bar… I guess I’ll go ahead an post this one a little early.

The Final Countdown: An Overall Score Cut-off

CrossFit Games Open workout 14.5 will be released in about 24 hours, and there are many athletes still on edge about qualifying for Regionals.

The Question

My overall score is 466, is it too late? Is this likely to disqualify me from Regional qualification?

Remember, the overall score is calculated by summing each of the placings for each Open workout. So if you place 1st, 2nd, 11th, and 1st in the past four workouts within your region, your score is 15 (and your awesome and likely named Emily Bridgers). The score can quickly get jump though, given the huge number of competitors there are… something like 5,000 women in just the South East region.

Let’s look at a simple plot to see what has happened in 2012 and 2013.

Fig. 1: Women’s overall score plotted against overall place in Open competitions 2012 and 2013 within five CrossFit Regions. The red line is drawn to illustrate the top 60.

Figure 1 shows overall scores against overall placings for women after completion of the Open competition in five Regions across two years. If I were to draw a trend line or linear regression, you’d see a positively sloped line following the center of that cloud of points.

However, there is variation – not all of those points would fall along the trend line.  And to make my point clearer, let’s zoom in:

Fig. 2: A magnified portion of Figure 1 illustrating ‘edge-qualifiers’. The red line indicates top 60, and the green line indicates top 48.

Look at the red line: Any points that lie on the line are individuals who placed 60th overall. Their overall scores ranged from 390 to 508. Similarly, any points on the green line are individuals who placed 48th (the Regionals cut-off for 2014). Their scores ranged from 302 to 435. The minimum score in the Top 60 was 7 attained by Lindsay Bourdon and Julie Foucher of the South East and Central East, respectively.

Big Picture

So there is some overlap in the ranges (years and regions can vary), but the point is that 500 points is a rough cut-off for ‘edge’ athletes. At 466 points after four workouts, there is a lot of pressure to keep the score low in 14.5. Low as in top 50.

I also want to emphasize something. Variation: This is NOT all of it. The data I have is a tiny sub-sample of all the Open data on http://games.crossfit.com. This means that my 500 point cut-off is conservative. With more data, the cut-off will probably increase. Additionally, because no one has made the Top 60 with a score above 508 in my data set, does not mean it can’t or won’t happen this year. The Open is more competitive this year; there are more athletes registered that can cause more dramatic swings in scores… which will only lead to increased variation, and a higher score cut-off for 2014.

Lastly, if it wasn’t obvious, Allison Brager, my wife, is my imaginary CrossFit competitor inquiring about her score and chances of Regional qualification in this year’s Open. I’m a scientist: I’m trying to be objective and realistic. This is not a fluffy, “you can do it”, feel-good, post to encourage her to perform well in 14.5. I sincerely believe she can make it – I would have written this with much more cynicism if I didn’t (she knows that I’ll call her out if chances, acts, or statements are bullshit…).

Are muscle-ups that important, Castro?

In previous posts, I’ve presented on the range of Open workout placings athletes have and its impact on CrossFit Games Regional qualification. These results were posted in a series entitled “Predicting regional competitors from single open workouts” and can be found here:

I believe these results partially counter Dave Castro’s statement during the introduction to Open workout 14.4 (around minute 37:00 here):

We wanted the best of the best to be able to finish it and get back to the rower. … You should not go to Regionals, you should not go to Regionals if you don’t have a basic move like the muscle-up. Period.

The Open is changing year-to-year, becoming more competitive and more challenging to qualify for Regionals, but one thing my posts have illustrated: there is a lot of variation and a single Open workout is a poor predictor of regional qualification.

So how can Castro make this claim? Have muscle-ups been a deciding factor in Regional qualification in the past?


In fact, muscle-ups have been featured in the past two Open competitions during the Karen-esque, miserably painful 12.4 and 13.3, and there were plenty of Regionally qualifying women who didn’t perform a single muscle-up during these workouts. Indeed, 39 in 2012, and 5 in 2013 just from my sub-sampled data set (described in my first post).

The range in scores for 12.4 and 13.3 for Regional qualifiers (overall place is less than 60) in my data set: 240-270, and 240-273, respectively. This means that an athlete needed to complete double-unders, (the workout was 150 wall balls, 90 double unders, then muscle ups), but muscle-ups were optional…

But… the Open is becoming more competitive. It was much harder to get to Regionals last year than in 2012 without muscle-ups (i.e., 39 athletes in 2012 versus 5 in 2013 in the sub-set I’m working with).

So Castro might be right this year: Perhaps no one will qualify for Regionals this year that doesn’t compete a muscle-up in 14.4. We can only, anxiously wait. But the way I see it: CrossFit is more than a muscle-up, and the Open generally does a good job of demonstrating it.

Tadpoles of Parque Nacional Palo Verde

Mahmood Sasa-Marin, the station director at OET Palo Verde, requested that I photograph tadpoles and metamorphs of the anurans of Palo Verde that he has collected.  He has been attempting to rear most of the species here with the intention of learning rearing techniques for experimental purposes.  The posts included here are a series of photographs I’ve taken of these tadpoles and metamorphs.  In most cases, I’ve photographed the mouth of each species as they are important in identification.

The links below provide access to pages for each species presented.  This is not a comprehensive list – it’s a work in progress.  The included species are those that have been more or less separated and are being reared.  Other anuran species present and breeding in Palo Verde are Leptodactylus poecilochilus, Leptodactylus fragilis (formerly labialis), Hypopachus variolosus, Incilius coccifer, Chaunus marinus and Lithobates forreri.

The post for each included tadpole are below, and this post is available in the above link as a more permanently visible page.

Tadpole posts:

Rhinophrynus dorsalis
Engystomops pustulosus
Incilius luetkenii
Smilisca baudinii
Hyla microcephala
Leptodactylus melanonotus


This is my 500th post!  Although that number isn’t that substantial compared to some others (i.e., over 10,000 here or 5000 here), I think that nearly all of my posts include original work (photographs) and rarely have I essentially reposted about a topic with a brief, original comment, as is what ‘big’ blogs sometimes do.  Sure, those ‘big’ blogs require tons of work and time, but I contend that the content per post is low or the physical effort needed per post is low (i.e., reading and commenting on the latest news item from a computer screen).  Regardless if that’s the truth, I’m excited.

My first post was on 31 January 2009, which was about 513 days ago (0.97 posts/d), so, basically, for the last 500 days I have made one post a day.  To that end, I will have one Imperial today.  Cheers.


A tentative herp count from my four months in Costa Rica: 62 species.  It may increase (or decrease) slightly as I add and update photographs with uncertain identification and scientific names from Savage and Bolanos (Zootaxa 2009).  The majority of the herps discovered were reptiles, which makes sense, given my extended stay in the dry forest.  I missed out on much of the phenomenal diversity of anurans and didn’t see a single salamander because they tend to be more diverse in wetter parts of the country.  When I was in those areas (i.e., the Osa Penninsula), it was the dry season, so many of the herps were hiding out.

herps of CR