Snippet of the review from the Amazon ....
See Peru's Amazon Basin and the diverse wildlife of South America's magnificent lowland rainforests from comfortable lodges. Let REI get you there!
Pros: Once in a Lifetime Experience, Guides, Exceeded Expectations, Flexible itinerary, Activity Level
Describe Yourself: First-Time Adventurer
Why Did You Choose to Travel with REI Adventures?: I Liked the Itinerary, Active Adventures, Destination, Commitment to Sustainability
I can't think of a single bad thing about this trip. Despite the high floodwaters (12m higher than normal), the folks at A&E Expeditions were fantastic and kept up the food and the high trip quality. Our guide, Jonathan, knew huge numbers of species in the area and simply made the whole trip a fantastic experience.
Welcome to Scientia Pro Publica, 32th edition!
This round, it seems that the name of the game is biology. Submissions really ran the gamut in biology, including some delightfully from-left-field posts. Bryan Perkins having some fun with embryological development, and Amanda Morti shows us why we have actinomycete bacteria to thank for that fresh rain smell (and for throwing off Latinate intuition - anyone else read "actinomycete" and think muscley whale?). Speaking of whales, David "WhySharksMatter" Shiffman does a great bit of ResearchBlogging and reminds us why not all fish (fine, non-sarcopterygian gnathostome) stock are created equal - sandbar sharks (Carcharhinus plumbeus) are closer in population dymanics to bowhead whales and other balaenids than cod.
That wasn't the only bit of ResearchBlogging this time around (Hey! ResearchBlogging! Stop hating my feeds!). Kelsey has a great post about the intraspecific male competition among red-eyed treefrogs. Sure, they amplex for dear life, but what about before that? Turns out that ... they shake their butt (Does that mean that the frog Sir Mix-a-Lot is a lady?). Madhu R-Blogs over at Reconciliation Ecology takes the opportunity to do a great smackdown on a pet peeve of mine — evolution is not a "ladder" or any such silliness. It is blind and targetless. It was a statement from a Stanfurd professor, though, so what can you expect (Go Bears!)? But before we get ranty, Luigi diverts our attention from critterland and the rivalries of my alma mater to teach us about why Kibale's Wild Coffee Project didn't get off the ground, concluding that scientists, once again, just can't do "messaging".
Illustration: Peter Trusler for Wildlife of Gondwana/NOVA (PBS). From Grrlscientist's post.
Thonoir continues to take us down our diversion away from Critterland, showcasing two sets of endangered non-metazoans, and my total ignorance of plant/photosynthizing phylogenies. We don't stray from Critterland for long, though, as John at Kind of Curious details a very interesting ponderous borer. Emily talks about sensationalism, mountain lions, and that Fox, even as they get extirpated from areas densely populated by a certain primate. Which, as Amanda points out, is no good thing, and there are difficulties restoring predators to ecosystems that they have been extirpated from (trust me, a one sentence synposis does not do that entry justice). The great Grrlscientist brings us some aborignal rock art possibly depicting Genyornis newtoni (Dromornithidae, incomplete phylogeny link (Anseriformes)). This is both the oldest paintings in Australia at 40,000 years (predating the earliest European cave paintings) and is of something that can be loosely imagined as an ostrich-sized duck, which simply can't be awesome.
Now, we don't end here. Oh no. That was just organismal biology and evolution. How about a dose of medicine? Michelle Dawson is better than Mary Poppins, because her post about circadian rythyms certainly doesn't need any sugar for you to take it down (and introduces you to an interesting side effect of autism-spectrum disorder). Scientific Chick writes about cell phones improving mental performance in Alzheimered mice. Meanwhile, Wendy at Bioloser gives us the physiological background of shock, and a shocking description of shock in a man nearly severed in half.
The larger constructs of medicine were not neglected, either. Bradley Kreit discusses the fact that we need to accept our intellectual limits, while Luke examines the crazy in large groups, looking at HIV denialism and Ryan looks at child mortality.
Bisected men and child mortality? Lets get a bit more lighthearted. Jessica Drake at Soilduck ponders what makes a scientist a scientist, and Romeo Vitelli tells us how subliminal messaging was an advertising gimmick (how many levels of fake-out is that?). Adam Park redeems some sci-fi stories with various predictions made therein that have come true today. Of course, Asimov gets a mention for the mention of pocket calculators in Foundation, but Asimov also nailed our reliance on them as time went on in The Feeling of Power (psh, arithmetic).
BP, the Gulf, and the utter dismaying farce of the spill have been in the news, and oil makes its showing in Scientia this time around. Scienceguy238 gives us a history leading up to the spill, and Grrlscientist looks at the ethics involved with oiled seabirds. Jeremy at The Voltage Gate writes about how the Saudi coast has recovered, 20 years later, from the 11-million-barrel (1.2 GL, or 1.2e6 m3) spill. A decade afterwards, 1 million cubic meters still persisted. Every spill is different, though, so hopefully ours won't be as bad.
You know you love it.
Finally, we round out with the physical sciences, which didn't get much love this time around. Lab Rat talks about bacteria and climate change, while Matt Wills talks about the more metaphorical breathing Earth, Charles Lyell, and mollusk damage in Greek columns. Finally, Sarah Kavassalis gives a great article on one of my favorite subjects: special relativity, astronomical distances, and the meaning of "now". After all, if a star (super)nova's in the distance, but you don't see (E&M) or feel (gravity) it, has it gone? She even does it without the inevitable jargoning I'd go into!
That does it for this round of Scientia Pro Publica! This was my first blog carnival, so I more than welcome suggestions. Hope you all enjoyed it!
If you want to learn more about this carnival, head over to the carnival's website. Be sure to check out the next round hosted by Andrew over at Southern Fried Science, on June 21st. And remember — this is a blog carnival! Submissions and hosts are wanted! If you're interested in hosting, check out the current schedule on the official schedule thread and drop Grrlscientist a line (or leave a note in the comments). If you find a cool article, submit it! Send a link via this submission form. Thanks again all!
Just a quick update, before I head to Indiana to visit Purdue and my friend Jessica. I realize I missed yesterday's tetrapod, but I prefer to postpone a week and post a better update rather than a very breif post every week (look forward to sea snakes next week).
In this week's science, there is a paper describing unidirectional airflow in alligator lungs, strongly suggesting that this formerly "avian-style lung" is in fact an archosaurian synapomorphy. That is to say, this paper gets as close as a single paper can get to outright saying that this is a mechanism that helped nonavian dinosaurs get so large. Archosaurs just keep being awesome.
On somewhat related news, I think I'll try to put up a few evolutionary YouTube videos. Rather than a pure bash-on-creationist style, though, it'll be focused on describing particular evolutionary lineages and evidence. We'll see how that works out, though I need to become much more familiar with movie editing software.
2010 is the International Year of Biodiversity according to the UN — the IUCN will highlight a different endangered animal each day of the year, apparently. Today's animal is apparently the polar bear (remember last week's Tuesday Tetrapod? Ursus maritimus), but I can't find the list yet. I'll update this post when I do, but it looks like events and press releases and such will kick off on the 11th of January.
Yes, I know I failed on the Tuesday Tet. I know what it will be (and will be a double-feature next week), but I couldn't bring myself to do a short entry without some research first.
Also, the entry on the basal theropod (DOI 10.1126/science.1180350) will be coming. More importantly though, I wanted to note that my good friend Sara Weinstein had her first paper published in Copeia today. You can view the abstract at asihcopeiaonline.org ("An Aquatic Disease on a Terrestrial Salamander: Individual and Population Level Effects of the Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis, on Batrachoseps attenuatus (Plethodontidae)" DOI: 10.1643/CH-08-180). I'll post a nice summary of it in an few days, also. Hopefully that will be somewhat illuminating, as I've known about this project (and helped a little bit) for 3-4 years now!
Now, I just need to get myself in gear and get *my* paper out. 9 months is just embarassing.
I find this incredibly entertaining:
Arguably the greatest problem with it is that we're programmed from a young age to think of left-to-right as increasing on a given axis, though obviously this is meant to be read from right-to-left.
In other news, this "weird science" post from Ars Technica comes with this entertaining gem:
This is little more than a press release on some research in progress. Still, even before the results are in, the process of setting up the experiment turned out to be rather informative. The study, you see, is on porn consumption, and it looks like the researchers will be stuck working without anybody to act as a negative control. "We started our research seeking men in their twenties who had never consumed pornography," said Simon Louis Lajeunesse. "We couldn't find any."
Time to stop procrastinating and start properly bolting out those grad school applications.
I realized that the Zooseum has the flaw that on wet, cold, days, neither aspect of the zooseum would attract customers. However, this problem is easily rectified by having an underground portion of the zooseum.
Located centrally under the zooseum, you can locate the food court and a few stores (with, of course, others by the entrance/exit). Throw in some paths with moving walkways to connect exhibit to exhibit, and arial enclosed connections for nearby exhibits (think Birge-LeConte, or parking structure-airport in L4D's "Dead Air").
This provides an all-weather aspect to the attraction, and means that unlike most zoos, the hours of operation don't need to be strictly confined to animal activity. With hidden paths, lighting does not need to account for disturbance to the animals, as the interconnects can be well-lit, but being underground, should provide little to no animal irritation. Though animal activity will drop off, all that becomes needed are suggestions or notices that there will be reduced animal activity after a certain time can be made, and with longer operating hours, the zooseum should see a higher profit than a standard zoo *or* museum.
Zoos are awesome, and so are museums. So, I wonder, why has no one taken the obvious step and combined natural history museums and zoos?
I think the way you do this is that the physical layout of the "zooseum" echos a phylogenetic tree. Different branches are linked up by aerial cable cars, giving a nice set of sightlines while preserving the message of evolution and interrelatedness of animals. Along these branching paths, there are interspersed buildings with fossil representations and extinct members of lineages.
In addition to this being a largely natural layout for the animals and fossils on display, this also helps instill a proper phylogenetic way of thinking for visitors. Thus, aviaries would be most closely placed to crocodile and alligator enclosures, and between the two would be exhibits on non-avian dinosaurs and pterosaurs. Additionally, finally, Dimetrodon would be placed in fossil exhibits on the ways to the mammal section of the "zoo", and any oceangoing mammals (ie, dolphins or porpoises, with whales being obviously unfeasible) would be most adjacent to hippos, pigs, and cervids, and bovids.
Despite the "unusual" layouts mentioned in the last paragraph, much of the layouts are quite natural. The cats are together, birds of prey are together, snakes are together (and closest to varanids), etcetera. This also provides the unique opportunity to provide an insect/arthropod exhibit that presents relations of these generally underdescribed (both in the literature and in the public) animals.
This "zooseum", then, is effectively a one-stop shop for the natural world. The unique display mechanism and unique content could also provide a draw for personnel, and good merchandising opportunities. The purpose of the museum portions would be more education than research, with (therefore) few real fossils and mostly casts, emphasizing comparative biology and morphologies. The aerial paths connecting various groups could be centered around the amniote split, acting like a hub.
Perhaps this entry was kind of rambly, but I felt like this is a nifty idea, and I wanted to post it — any thoughts?
I've been a bit quiet lately, mostly because of work I've been putting into Velociraptor Systems. Last week's skipped Tuesday Tet was especially tragic, as it was half-composed the Wednesday before that!
I'll get that entry, and second one, up later today. However, it's also good to note that today is the 150th anniversary of the publication of Darwin's "On the Origin of Species, by means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life". It is arguably the most significant single text to change how we live, with evolutionary based insights leading to models of heritibility and research into the genome.
I'll link you to Dawkins discussing the subject on CNN's site (note: they either misquoted Dawkins on "over 300,000 million years", or the publication was in error; that number equates to 300 billion years, well older than our universe). But I'll close this entry with a quote:
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and Dependant on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost certainly implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
Darwin, Charles. "On the Origin of Species". 1859.
A surprising amount of this weekend was dedicated to working on phylogenies. I updated non-eusuchian crocodylomorphs, avialae through neoaves to at least extant order; minor updates to sauropoda, and an update on sauropterygia.
The site also finally got a long-needed search engine. It's not the most efficient thing in the world, but doing a binary search is essentially useless. I made it modular, so I may still end up seeing how a sort + binary search with preserved keys turns out, or cut out the cruft (change the amount of the document searched).
I finally also added a dirty implementation of tagging. I used the <tt> (teletype) tag and changed its contents to not display (CSS display:none). Thus, tags for an entry can be hidden in this element, and will be read by the search engine, but not displayed.
I also noticed that it was hard to find some of the sources I cited with just name and year — so I've started adding linkouts, DOIs, or ISBNs too all sources provided, to make it easier in the future.
Kind of looks less in writing than it felt like ... but I'm happy with the way it's going.
Since I've wasted most of today on this (oh feature creep. And an extra "-1".), I thought I'd share. Reading around on Pharyngula, I found myself wanting to make a more customizable, even-less-preprogrammed version of Richard Dawkin's WEASEL program. So, I present you with a Python 3.0+ version of Dawkin's "Methinks it is a weasel" program. It will take any nonzero length starting string, has a maximum generational cap for local maxima, with customizable rates for single-bit errors (like SNPs), duplication errors, number of offspring, weighting for approaching the target sequence, and accepted variability, and whether bad mutations are penalized or not.
The point of the program, as published in The Blind Watchmaker, is to show that with random mutations over time you can expect to see something like order pop out of a random test string. The version I have below takes the genetic modelling a bit further, starting with any string, regardless of length, and duplication / omission errors will trim down to the right solution. In debug mode, there's an additional completely random selection every 500 generations to help pull the program out of local maxima, but it is not in the primary program.
Click the fold to read the source, or download it here(More)
I've finally ported over my work on phylogenetics that I did for the UCMP to its own dedicated site: http://phylogeny.revealedsingularity.net. I've tried to compile this with sources from multiple papers and college levels textbooks, which gives even it's current status a unique place on what I've found on the internet. As a tetrapod phylogeny, it is complete (excepting avilae and rodentia), but my goal is to eventually have all extant organisms down to family, and include important extinct outgroups.
This is a very very tall order, and a planned multi-year project, but I encourage anyone running across it to contribute or to comment.
While there are other places on the internet with phylogenies, this is different than most of those. It is more complete in certain respects than the Tree of Life, but lacks accounts at the various levels. On the other hand, it is all contained on a single page which allows comparisons not possible on other pages, and the citations provide the ability to double-check the phylogeny posted.
Finally, I've published the source code, so people can contribute more to the phylogeny, and improve functionality in a crowdsourcing effort. My goal? Reach a tentative family level completion in five years. Lets see if we can do it. Share, help out, and encourage others to help!
A quicky today — prompted by Darren's post over at TetZoo, I went on a hunt for US-visible versions of the UK series "Inside Nature's Giants". Here's a snippet from YouTube on the second episode on whales:
Rather than a longish comment on Rachael's latest post, I thought I'd write up a brief entry on Ensatina.
First, the picture:
Ensatina eschscholtzii eschscholtzii, or Monterey subspecies of E. escscholtzii. The "Monterey Salamander", found near Monterey, CA.
Ensatina are an interesting species of salamander in that they are a "ring species", or, they have a sequence of morphotypes that gradually change regionally, and these morphotypes overlap but do not interbreed. There are two terminal morphotypes that are too distantly related to be capable of interbreeding (see Wikipedia's discussion of the subject). The beauty of ring species is that they provide a living sample of speciation and evolution.
In particular, Ensatina in the Bay Area differ from the Monterey morphotype in that they are very morphologically similar to the non-terrestrial stage of Taricha torosa, which are highly toxic to ingest. The tetrodotoxin they produce is a neurotoxin that is potent enough to kill most vertebrates (though some Thamnophis (Garter snakes) have evolved modified sodium channels to enable consumption of them as prey items; see this paper and others for more) (DOI: 10.1007/s10886-005-1345-x). Thus, Ensatina in the Bay Area mimic Taricha presumably to avoid predation.
For those of you curious about the diagnostic differences, an Ensatina is generally smoother than a Taricha, with more prominent costal grooves (the grooves along the side), has nasolabial grooves, and has a constricted base at its tail. The Monterey specimen here lacks the yellow eyes of Taricha, though the Bay Area ecomorph has eyes that are quiet similar to those of Taricha.
Suggested Thamnophis/Taricha studies:
- Brodie and Brodie. Tetrodotoxin Resistance in Garter Snakes: An Evolutionary Response of Predators to Dangerous Prey. Evolution, Vol. 44 No. 3 (May 1990).
- Brodie and Brodie. The Evolutionary Response of Predators to Dangerous Prey: Hotspots and Coldspots in the Geographic Mosaic of Coevolution between Garter Snakes and Newts. Evolution, Vol. 56, No. 10 (October 2002).
- Brodie et al. Parallel Arms Races between Garter Snakes and Newts Involving Tetrodotoxin as the Phenotypic Interface of Coevolution. Journal of Chemical Ecology, 2005. DOI: 10.1007/s10886-005-1345-x
- Geffeney et al. Mechanisms of Adaptation in a Predator-Prey Arms Race: TTX-Resistant Sodium Channels. Science 2002. DOI: 10.1126/science.1074310.
Recently, Taylor, Wedel, and Naish published a paper on sauropod postures (SV-POW, TetZoo), which challenges a paradigm established by Stevens and Parrish's paper on DinoMorph modeling which states that based on the way the cervical vertebrae articulate together, certain postures are prohibited and thus you get the current model of low-slung necks for the majority of diplodocids. This works out nicely with authors who worry about the blood pressures required to pump blood up to a neck that is elevated so high off the ground. Now, given that only a few posts ago I talked about phylogenetic bracketing and its usefulness, it's appropriate that I talk about the problems in overusing it, and step into dangerously clichéd territory while talking about the paper I am working on.
First, right off the bat, I want to say that I think this is an excellent piece of work. I think it has a good place in the literature, and that more than studies of giraffe blood pressure is needed to be convincing about the blood supply issues for diplodocids (I am pretty sure I've talked about this before, but if nothing else, let me reiterate that mammals are not necessarily a good model for archosaurs). The crux of Taylor et al's argument is that extant tetrapods from all groups have strongly inclined cervical vertebrae, and that in modern animals, yes, the most favorable position is in fact a horizontal neutral one. However, soft tissues mean that this is actually not the most neutral position, and only using the vertebrae is misleading. Absolutely true, good work, and I'm amazed this hasn't been looked at before. I've even worked with Matt Wedel in writing up my paper (though I'm sure he doesn't recall by now), and I value his opinion.
So, the argument goes, based on phylogenetic bracketing, you would expect sauropod necks to not be held horizontal, regardless of what the cervical vertebrae show. While this might be largely true, I will attempt to briefly, in this blog entry, illustrate why this doesn't have to be true, and give a bit of a preview into my work-in-progress (post-editor revisions) to demonstrate why I don't think this is true for diplodocids (without spoiling my paper. Sadly, something I must take care not to do).
First, it is important to note that phylogenetic bracketing can never tell the whole story. We are the only extant tetrapod that is fully bipedal with an entirely erect vetebral column, and possibly the only one that has yet evolved. No number of examining outgroups will tell you that Homo sapiens bones should be this way; this has to be inferred from our morphology. This is a fact of essentially all novel traits. Just relying on phylogenetic bracketing prohibits you from inferring novel postures based on morphology that have no extant representatives. Second, it's possible that there was something completely bizzarre going on that we just don't know about. As Matt's SV-POW entry very clearly demonstrates, finding the fossil of, say, a budgie 200 MY from now, with no birds, you might guess it has a crazy neck like a flamingo. Sometimes, you just can't tell. That is not to say it is a very good guideline, that is very often right and instrumental in a lot of work; but it is not perfect. They even address this fact:
Can the habitual posture of
extant amniotes be expected to apply to sauropods? Phylogenetic bracketing strongly supports this hypothesis as the neck
posture described by Vidal et al. (1986) is found in both Aves
and Crocodylia, the nearest extant outgroups of Sauropoda, as
well as in the increasingly remote outgroups Squamata, Testudines and Lissamphibia.
However, some authors have postulated that the necks of sauropods, rather than representing an extreme development of mechanisms found in other vertebrates, were anomalous structures maintained using novel mechanisms. If this were so, then it would not be surprising if the habitual posture of sauropod necks was different from that of other vertebrates.
Now, it is my personal opinion that Taylor et al. is probably right in the majority of the cases. Among other things, the construction of, say, Brachiosaurus would suggest strongly inclined necks, and I suspect that all sauropods would be able to list their heads like this, at least for moderate periods — it seems the obvious, niche-opening thing to do. Even in diplodocids, it seems that a completely flat neck is not necessarily correct, and I personally favor a slightly cantilevered position (this partially addresses their comments about the orientation of semicircular canals, by coincidence). However, according to their paper:
In all four sauropodomorphs figured by Sereno et al. (2007: fig. 1G), the occipital condyle is directed postero-ventrally when the HSCCs are horizontal. If the HSCCs were inclined upwards, as in most birds and mammals, the down? ward tilt of the occipital condyles would be even greater. Therefore, even if the cranio-cervical joints were held in ONP, the anterior part of the neck would be inclined in all four taxa.If the cranio-cervical joints were flexed as in extant terrestrial amniotes, the anterior portion of the neck would need to be even more steeply inclined in order to hold the HSSC horizontal, and would possibly have approached vertical in Camarasaurus and Diplodocus (Fig. 4B, C). Taylor et al. 2009
My own paper works on estimating the sizes of diplodocids, with biomechanical parameters based on the assumption that they held their necks roughly horizontal, as estimated by Stevens and Parrish's work in line with the accessible ranges in Stevens and Parrish's work. Most accurately, the level of the "bridge" is the same as the level of the acetabulum (thanks to Matt for pointing out the error in this statement). The upshot of this is, when you assume this for diplodocids, you get the correct length popping out of the math. This is very strong evidence, in my opinion, that for at least that clade the neutral position was holding the neck horizontal. This model, in fact, pulls within 4.3% of of current restoration lengths.
Now, I really want to write more — but it probably lives somewhere in that mystical realm where Bad Ideas come from. I'm slowly working on an extensive rewrite of my opening, which does not lead to quick work! But with luck, the pace will pick up soon. I should talk to Matt and see if he is interested in taking a look at what I have so far — and if Darren or Mike is interested, as well. Hopefully I can revisit this in a few months, and talk about it more!