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- June 21, 2011
- 01:09 PM
- 393 views
The oceans rise, even as they decline... so long, fish!
by Madhu in Reconciliation Ecology
Two interesting, alarming reports this week about what's happening (no small thanks to us) to the dominant habitat on this watery planet. First, that habitat is becoming even more dominant: a paper...
... Read more »
Kemp, A., Horton, B., Donnelly, J., Mann, M., Vermeer, M., & Rahmstorf, S. (2011) Climate related sea-level variations over the past two millennia. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015619108
- June 21, 2011
- 12:28 PM
- 287 views
The oceans rise, even as they decline... so long, fish!
by Madhusudan Katti in a leafwarbler's gleanings
Two interesting, alarming reports this week about what's happening (no small thanks to us) to the dominant habitat on this watery planet. First, that habitat is becoming even more dominant: a paper in PNAS meticulously reconstructs global sea-levels over the past two millenia to show that the oceans have been steadily rising, in concert with climatic changes, and that their rise has accelerated in recent years. This figure ought to worry you:
via realclimate.org
Meanwhile, though, that dominant habitat is also becoming emptier of inhabitants, as we continue to deplete marine wildlife in alarming ways.
via bbc.co.uk
So concludes an international panel of marine scientists convened by the International Programme on the State of the Ocean (IPSO). Even though conservation biologists have a reputation for being alarmists, this statement from one of the panelists, should worry you:
"The findings are shocking," said Alex Rogers, IPSO's scientific director and professor of conservation biology at Oxford University.
"As we considered the cumulative effect of what humankind does to the oceans, the implications became far worse than we had individually realised.
"We've sat in one forum and spoken to each other about what we're seeing, and we've ended up with a picture showing that almost right across the board we're seeing changes that are happening faster than we'd thought, or in ways that we didn't expect to see for hundreds of years."
via bbc.co.uk
There's more:
"The rate of change is vastly exceeding what we were expecting even a couple of years ago," said Ove Hoegh-Guldberg, a coral specialist from the University of Queensland in Australia.
"So if you look at almost everything, whether it's fisheries in temperate zones or coral reefs or Arctic sea ice, all of this is undergoing changes, but at a much faster rate than we had thought."
But more worrying than this, the team noted, are the ways in which different issues act synergistically to increase threats to marine life.
Those "different issues" include, of course, overfishing, pollution - especially from nasty plastics - ocean acidification, and warming. All adding up to the next mass extinction, one we are living through, unprecedented in being caused largely by a single species - us. So what are we to do?
IPSO's immediate recommendations include:
stopping exploitative fishing now, with special emphasis on the high seas where currently there is little effective regulation
mapping and then reducing the input of pollutants including plastics, agricultural fertilisers and human waste
making sharp reductions in greenhouse gas emissions.
Sounds simple enough, right? Clean up our act and take responsibility? So, we may know the way to back away from this rising, empty tide. Do we have the will?
Reference:
Kemp, A., Horton, B., Donnelly, J., Mann, M., Vermeer, M., & Rahmstorf, S. (2011). Climate related sea-level variations over the past two millennia Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1015619108
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Kemp, A., Horton, B., Donnelly, J., Mann, M., Vermeer, M., & Rahmstorf, S. (2011) Climate related sea-level variations over the past two millennia. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015619108
- June 21, 2011
- 12:28 PM
- 331 views
The oceans rise, even as they decline... so long, fish!
by Madhusudan Katti in a leafwarbler's gleanings
Two interesting, alarming reports this week about what's happening (no small thanks to us) to the dominant habitat on this watery planet. First, that habitat is becoming even more dominant: a paper in PNAS meticulously reconstructs global sea-levels over the past two millenia to show that the oceans have been steadily rising, in concert with climatic changes, and that their rise has accelerated in recent years. This figure ought to worry you:
via realclimate.org
Meanwhile, though, that dominant habitat is also becoming emptier of inhabitants, as we continue to deplete marine wildlife in alarming ways.
via bbc.co.uk
So concludes an international panel of marine scientists convened by the International Programme on the State of the Ocean (IPSO). Even though conservation biologists have a reputation for being alarmists, this statement from one of the panelists, should worry you:
"The findings are shocking," said Alex Rogers, IPSO's scientific director and professor of conservation biology at Oxford University.
"As we considered the cumulative effect of what humankind does to the oceans, the implications became far worse than we had individually realised.
"We've sat in one forum and spoken to each other about what we're seeing, and we've ended up with a picture showing that almost right across the board we're seeing changes that are happening faster than we'd thought, or in ways that we didn't expect to see for hundreds of years."
via bbc.co.uk
There's more:
"The rate of change is vastly exceeding what we were expecting even a couple of years ago," said Ove Hoegh-Guldberg, a coral specialist from the University of Queensland in Australia.
"So if you look at almost everything, whether it's fisheries in temperate zones or coral reefs or Arctic sea ice, all of this is undergoing changes, but at a much faster rate than we had thought."
But more worrying than this, the team noted, are the ways in which different issues act synergistically to increase threats to marine life.
Those "different issues" include, of course, overfishing, pollution - especially from nasty plastics - ocean acidification, and warming. All adding up to the next mass extinction, one we are living through, unprecedented in being caused largely by a single species - us. So what are we to do?
IPSO's immediate recommendations include:
stopping exploitative fishing now, with special emphasis on the high seas where currently there is little effective regulation
mapping and then reducing the input of pollutants including plastics, agricultural fertilisers and human waste
making sharp reductions in greenhouse gas emissions.
Sounds simple enough, right? Clean up our act and take responsibility? So, we may know the way to back away from this rising, empty tide. Do we have the will?
Reference:
Kemp, A., Horton, B., Donnelly, J., Mann, M., Vermeer, M., & Rahmstorf, S. (2011). Climate related sea-level variations over the past two millennia Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1015619108
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Kemp, A., Horton, B., Donnelly, J., Mann, M., Vermeer, M., & Rahmstorf, S. (2011) Climate related sea-level variations over the past two millennia. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015619108
- December 2, 2010
- 07:02 PM
- 403 views
Arsenic and Old Lace
by Madhusudan Katti in a leafwarbler's gleanings
As you may very well have heard by now, NASA made a bit of a splash today in the mainstream media and especially the science (and sci-fi too, of course) blogosphere / twitterverse through its press conference about a fascinating biological discovery with potential astrobiological significance. An "alien" life-form that incorporates Arsenic (which normally kills our kind of life-form) instead of Phosphorus in the "backbone" of its very DNA. Actually its a bacterium from the mud at the bottom of Mono Lake, east of the Sierra Nevada in California, not some bug-eyed green monster from your sci-fi imagination, even though the lakescape itself has an otherworldly quality to it:
So, a bacterium that uses Arsenic is found in an old lake... well, the poor joke (and the title of this blog post) practically writes itself doesn't it? Maybe they should name this bacterium "old lace", as someone tweeted. Here's what the wee beastie looks like:
NASA's press conference was timed to coincide with the publication of a paper about this discovery, but the advance notice from NASA generated a fair amount of hype and breathless anticipation about "alien life" and so forth. The paper itself is now available at Science (perhaps behind a pay firewall, but maybe not), so you can read it and make up your own mind. The paper is very interesting indeed and the central discovery of this strange form of DNA in the bacterium leads to endlessly fascinating questions and speculations about the origin and evolution of life on this planet, and perhaps on others. The media hype surrounding the discovery, though... well, what can one say about media hype about such stories?
Rather than try to translate the paper for you poorly (me not being a microbiologist and all) or engage in more poorly-informed speculation, let me point you instead to several good blog posts that do a much better job than I ever could, and also offer a more balanced perspective to keep the hype in check but also share the excitement of such a fascinating discovery. To start with what's actually in the paper itself, Bhalomanush does a good job of describing the methodology underlying the discovery, while asking "Dude, where's my alien life?". Bad Astronomer Phil Plait, who had been urging caution to cool the hype building up in anticipation of NASA's announcement, offers a typically readable perspective on the real news. His fellow Discover magazine blogger Ed Yong offers perhaps the best commentary I have read on the whole discovery and pours some well-deserved cold water on some of the breathless hype. Over on ScienceBlogs, Greg Laden takes a more evolutionary perspective and places this study in the context of what it might—and might not—mean for the origin of life on our planet as well as Charlie Darwin's second theory about a common ancestor shared among all known lifeforms. Even if the paper is too much for you (some of it is for me because my PhD is in the wrong kind of biology for this stuff!), you'll do much better to read these blog posts rather than the more mainstream media accounts, I think.
Let's cool the hype a bit shall we, down to just the right level of simmering excitement at which the science can really thrive.
Reference:
Wolfe-Simon, F., Blum, J.S., Kulp, T.R., Gordon. G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., and, Oremland, R.S. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science (early release on Dec 2, 2010).
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Wolfe-Simon, F., Blum, J.S., Kulp, T.R., Gordon. G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., and, Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/
- August 23, 2010
- 05:47 AM
- 533 views
Overlooking the familiar in cataloging biodiversity
by Madhu in Reconciliation Ecology
via myrmecos.net
Familiarity, they say, breeds contempt. Or, even if we aren't actually contemptuous of the familiar, we often simply ignore it. It is not surprising, then—although it should...
... Read more »
Hamm, C. (2010) Multivariate Discrimination and Description of a New Species of Tapinoma from the Western United States . Annals of the Entomological Society of America, 103(1), 20-29. DOI: 10.1603/008.103.0104
- August 23, 2010
- 05:22 AM
- 404 views
Overlooking the familiar in cataloging biodiversity
by Madhusudan Katti in a leafwarbler's gleanings
via myrmecos.net
Familiarity, they say, breeds contempt. Or, even if we aren't actually contemptuous of the familiar, we often simply ignore it. It is not surprising, then—although it should be—that Tapinoma sessile, the odorous house ant of North America, the very same little brown one that is pictured above, and that you may well have swept off your kitchen counter today, remains relatively poorly studied! It is so widespread and common across a variety of habitats in North America, it seems, that entomologists haven't really bothered to study it all that much since it was first described by Thomas Say, considered a father of American entomology.
So much so, that they even lost track of the original type specimen used to describe the species. How odd is that, for a widespread species not to have its identity securely moored to a type specimen enshrined in a museum somewhere? Almost like a nation's President not having a birth certificate!
When I accepted the offer of a faculty position in my current department here at CSU-Fresno six years ago, among other items on the startup list of equipment for my laboratory, I had (only half-jokingly) requested an espresso machine to boost my productivity. Hey, it had worked for my last postdoc advisor! But my then department chair, Dr. Fred Schreiber, only got a chuckle out of that one, and we moved on. A couple of years later, Fred called me up one afternoon to ask if I still wanted that espresso machine! A graduate student working in his lab had left one behind while moving on to the next stage of his career, and Fred had no use for it. That Starbucks Barista has since sat on a counter in my lab keeping me caffienated enough to get tenure and keep a research program afloat.
It so happened that, Chris Hamm, that graduate student who is now in the Ph.D. program at Michigan State University, had been studying the common odorous house ant, that same rootless species, for his masters thesis. While collecting specimens in California, he discovered a two-toned (or bicolored) variant that looked similar, yet rather different from the descriptions of T. sessile. So he carefully measured the two different morphs and compared their morphologies to find that they differ consistently (and statistically significantly) across a range of characteristics. So much so, that the bicolored morph must be recognized as a new species of ant!
A brand new species that was being trod underfoot daily in households across California, but had apparently never been looked at all that carefully by any entomologist in a region full of so many biologists! And we fret about losing biodiversity in remote corners of the world.
Chris has honored Fred by naming the new ant after him. Tapinoma schreiberi will forever mark the legacy of the man who has mentored so many in our department (including me as a greenhorn faculty member) over the past 3+ decades. How fitting that the paper was published the very year that Fred has taken early retirement, as of last week.
In the process of searching for the identity of this new ant, Chris also discovered the shaky foundation upon which rested the identity of T. sessile—and has done his bit to correct that injustice as well. He collected a new type specimen, from near the grave of its original discoverer, Thomas Say, to fill that huge hole in its taxonomic origin, even as he was giving it a new cousin! Alex Wild has more on that story at Myrmecos.
Now I find myself looking closely at ants around here, even as I sip my espresso and thank Chris for a good story, and for my morning/afternoon cuppa joe!
Reference:
Hamm, C. (2010). Multivariate Discrimination and Description of a New Species of Tapinoma from the Western United States Annals of the Entomological Society of America, 103 (1), 20-29 DOI: 10.1603/008.103.0104
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Hamm, C. (2010) Multivariate Discrimination and Description of a New Species of Tapinoma from the Western United States . Annals of the Entomological Society of America, 103(1), 20-29. DOI: 10.1603/008.103.0104
- June 3, 2010
- 04:39 AM
- 452 views
Where in the world is the Yellow-billed Magpie? Help us find out this weekend!
by Madhu in Reconciliation Ecology
See and download the full gallery on posterous
What a handsome corvid, the Yellow-billed Magpie. How curiously restricted, its global range:
This lovely bird is another one I consider...
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Reynolds, M. (1995) Yellow-billed Magpie (Pica nuttalli). The Birds of North America Online. DOI: 10.2173/bna.180
- May 21, 2010
- 05:59 PM
- 807 views
Twist it, shake it, shake it, shake it, shake it, baby!
by Madhu in Reconciliation Ecology
You are brightly colored - enough to be considered charismatic even by humans who like to keep you as a pet! You can make fairly loud calls. So how do you communicate with each other? Especially in...
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Caldwell, M., Johnston, G., McDaniel, J., & Warkentin, K. (2010) Vibrational Signaling in the Agonistic Interactions of Red-Eyed Treefrogs. Current Biology. DOI: 10.1016/j.cub.2010.03.069
Robertson, J., & Zamudio, K. (2009) Genetic Diversification, Vicariance, and Selection in a Polytypic Frog. Journal of Heredity, 100(6), 715-731. DOI: 10.1093/jhered/esp041
- May 13, 2010
- 04:18 AM
- 404 views
Even waterfowl like the green. Of the $$ kind, that is, it seems.
by Madhu in Reconciliation Ecology
I've noted the so-called "luxury effect" in the distribution of biodiversity in urban areas on this blog before, as seen in the pattern of higher bird diversity in the more affluent areas of...
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Ann P. Kinzig, Paige Warren, Chris Martin, Diane Hope, & Madhusudan Katti. (2005) The Effects of Human Socioeconomic Status and Cultural Characteristics on Urban Patterns of Biodiversity. Ecology and Society, 10(1). info:other/
- March 6, 2010
- 04:51 PM
- 460 views
Ooze like an amoeba, float like a bird - wish we could still do that when stressed!
by Student @ Fresno State in Darwin's Bulldogs
Here's another fun weird science story from NPR, about a creature that might be in the dirt in your own backyard:
20100305 Me 03 by Npr
Download now or listen on posterous
Naegleria-NPR.mp3 (1426 KB)
Courtesy of Lillian Fritz-Laylan
Naegleria gruberi grows a pair of flagella when under stress. But unlike a sperm tail, it puts these appendages out front, and swims by breast stroke. The organism is stained to emphasize its anatomy.
If you prefer to read the story rather than listen to it aloud, here's the transcript via npr.org.
While that behavioral and morphological flexibility is remarkable enough in something we might, from our lofty hominid perch, consider rather "primitive" and "simple", what graduate student Lillian Fritz-Laylan and colleagues found in its genome is perhaps even more surprising. Whle the NPR story focuses on the physical transformation of the organism, cool as that is, the full story is much richer and has far more significance for our own origins from a common eukaryotic ancestor. As they describe in their paper in the current issue of Cell, Naegleria gruberi turns out to have almost 16000 protein-coding genes, which is over two-thirds of what you and I have! A single celled organism with that many genes - no wonder it can transform itself so radically.
Here's an image from the paper illustrating that transformation, which takes a mere 90 minutes or so (far cooler special effects at half the duration of Avatar, if you ask me!):
Figure 1: Schematic of Naegleria Amoeba and Flagellate Forms. Naegleria amoebae move along a surface with a large blunt pseudopod. Changing direction (arrows) follows the eruption of a new, usually anterior, pseudopod. Naegleria maintains fluid balance using a contractile vacuole. The nucleus contains a large nucleolus. The cytoplasm has many mitochondria and food vacuoles that are excluded from pseudopods. Flagellates also contain canonical basal bodies and flagella (insets). Basal bodies are connected to the nuclear envelope via a single striated rootlet.
Is it just me, or does that upper image, of the amoeboid form, remind you of someone? And... I just realized... that someone also has two apparent flagellae at the top of his head, which unfurl during times of stress!! What better proof do you want of our shared ancestry with Naegleria, eh? No? Oh, what - you mean citing widely published and viewed cartoons is not good enough evidence for you (even though that is a standard of evidence good enough for a third of the good people of Texas)? You want all the boring science-y stuff instead? Well, go read the paper then, which the journal Cell has graciously made freely available!
The paper (luckily for you) turns out to be far from boring. It is indeed quite fascinating because, apart from presenting the complete genome sequence of this remarkable free-living protist, Fritz-Laylan et al also describe several genetic modules for aerobic and anaerobic metabolism (for these guys can do both), amoeboid motility, and a number of other structural and functional necessities of the ecologically diverse lifestyles common to their clade. Further, comparisons with genomes of other protists allow them to predict which genes might have been present in the genome of the common ancestor to all eukaryotes. As the first representative of a fifth (out of 6) major clade of eukaryotes whose genomes have been sequenced thus far, Naegleria holds great promise of generating fresh insights into the early evolution and diversificatiion of eukaryotes. While their lineage diverged from the one we hail from about, oh, a billion or so years ago, understanding their genome brings us closer to understanding and reconstructing the genome of our shared ancestors, those early free-living eukaryotes that gave rise to us both. For it turns out that they contain over 4000 protein families that are similar to ones we have, and therefore were likely found in that common ancestor! That ancestor was presumably also quite versatile and equipped with a set of flexible modules to deal with the diverse environments of that time. And that remarkable flexibility probably underlies the extraordinary diversity of organisms that subsequently evolved from that ancestor. How fascinating and wonderful is that! (Even if some of us later lost the ability to transform ourselves and float away when under stress!)
Let me end with a video where the lead authors talk about what Nargleria's genome can tell us about our own ancestry:
Reference:
Fritz-Laylin, L., Prochnik, S., Ginger, M., Dacks, J., Carpenter, M., Field, M., Kuo, A., Paredez, A., Chapman, J., & Pham, J. (2010). The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility Cell, 140 (5), 631-642 DOI: 10.1016/j.cell.2010.01.032
Posted via email from a leaf warbler's gleanings
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Fritz-Laylin, L., Prochnik, S., Ginger, M., Dacks, J., Carpenter, M., Field, M., Kuo, A., Paredez, A., Chapman, J., & Pham, J. (2010) The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility. Cell, 140(5), 631-642. DOI: 10.1016/j.cell.2010.01.032
- September 20, 2009
- 08:16 PM
- 886 views
A punk-size T-rex and an Eagle that ate children?!
by Student @ Fresno State in Darwin's Bulldogs
One trait that shows interesting evolutionary trends is the size of animals. Body size plays a significant role in the most important interactions between animals: competition (for resources or mates) and predation (for both predator and prey). Body size is also, of course, significant for a variety of physiological reasons. It's no surprise, therefore, that biologists spend a lot of time thinking about body size, and have discovered some intriguing patterns. For instance the so-called island rule in biogeography includes both insular gigantism (relatives of smaller-bodied mainland species tend to be larger in island populations) and insular dwarfism (relatives of larger-bodied mainland species tend to be smaller on islands!) - and both of these patterns are well supported empirically. We also have apparent body size trends in some lineages where successive descendants keep getting bigger and bigger until they reach some apparent limit and go extinct. This might happen because of predator-prey arms races, competition, or runaway sexual selection where female preference drives the exaggeration of a trait (e.g., antlers) in turn selecting for larger body size to support that exaggerated trait.Our understanding of how large some species can get and still function well is somewhat limited by the fact that many of the largest species ever to have evolved have gone extinct, leaving us to speculate whether their very size led to their extinction. Were the giant Haast's Eagles of New Zealand reduced to scavenging because they evolved too rapidly to become too big to be able to hunt? On the other hand, did Tyrannosaurus rex not become a good predator until it attained a sufficiently large body size? Our hypotheses about body size can thus go in different directions depending upon taxon and ecological circumstances. After all, we can only infer so much from reconstructing the anatomy of some of these giant beasts from their fossilized skeletal remains - but we are getting better at studying the fossils and visualizing their functions, by adapting technologies such as CAT (computed axial tomography) scans. This week some of the media picked up two papers reporting interesting findings about the two taxa mentioned above. The AP and several websites who picked it up from there got all excited about how the Haast's Eagle may have been the fearsome aerial predator of Maori legend as it might have hunted humans - especially (oh the horror) children! The original paper by Scofield and Ashwell while generating that sensational headline, is actually more interesting because of its approach and analysis of skeletal material, and in suggesting greater flexibility in the allometry of body size evolution. The authors used CAT scans to reconstruct and analyze the brain structure of the eagle to show that while the body of this species increased rapidly in size upon their arrival in New Zealand - presumably because of the lack of mammalian predators and the presence of a giant prey, the Moa - their brains did not increase in proportion! They use allometric analysis to show that these birds have much smaller brains for their body size compared to other Falconiformes, and this large size seems to have evolved rapidly: Haast's Eagle became 10-times the size of its putative ancestral lineage within a short 1.8 million years! That's what going after Moas, as seen in the above painting, meant for the evolution of this bird!! But wait, weren't these birds too big to hunt actively, instead scavenging off Moa carcasses like Condors and other large vultures? The large morphological size of Haast’s eagle has led to competing hypotheses concerning its life style and behavior. Here we analyse neuroanatomical indicators to address questions concerning the behavior of Haast’s eagle: (1) was it an active predator or merely a scavenger of carcasses; (2) was it most likely to inhabit forest or open places; and (3) did its large body weight allow strong active flight?And therefore:We predict that if this eagle had vulturine habits it would show a combination of all, or some of, the following: (1) somatic evidence that it made significant use of olfaction; (2) adaptations indicative of an ability to undertake sustained gliding flight; (3) large eyes adapted to locate prey from considerable distances; and (4) a lack of evidence for the ability to attack and kill prey with its legs and talons. Alternately, if these features were not found to be present, we would suggest that Haast’s eagle was most likely an active hunter.To do this, they look not just at the whole brain, but specific relevant regions of the brain where the size can be inferred from their scans, as well the anatomy of the eye and the optic nerve. They found that the olfactory system of the Haast eagle's brain was proportionally similar to smaller eagles from the Accipitridae and much smaller than in vultures. So these birds probably did not rely so much on smell to find food! Further, the visual system also remained similar to the Eagles, not apparently gaining any further acuity like we find in the vultures.We suggest this disproportionate growth was only possible in the unique New Zealand environment where Harpagornis was not threatened by mammalian predation or competitors and was able to develop specific adaptations to predating on a particular prey, the moa, by evolving a bigger head and more robust talons. Also we prefer this interpretation rather than the alternative of Harpagornis evolving from a similar sized ancestor and in doing so undertaking a reduction in endocranial capacity, and degradation of the optic and olfactory lobes.They then examined flight morphology to conclude that here the bird was more like vultures in being better adapted to soaring (despite its relatively short wings) than the fine control exhibited by its forest dwelling cousins. It may have dwelt more in open grassland habitats where it could swoop down upon its prey from cliffside perches. And here they draw upon corroborative evidence from Maori legend - for this fearsome beast went extinct from NZ skies only about 500 years ago!Although no European scientist ever observed Haast’s eagle hunting, Maori oral tradition provides some evidence to support our behavioral reconstruction. One description given to Sir George Grey in 1872 (Grey, 1873, pg 435) states: “This bird, the Hokioi, was seen by our ancestors. We (of the present day) have not seen it. That bird has disappeared now-a-days. The statement of our ancestor was that it was a powerful bird, a very powerful bird. It was a very large hawk. Its resting place was on the top of the mountains; it did not rest on the plains. On the days in which it was on the wing our ancestors saw it; it was not seen every day as its abiding place was in the mountains. Its colour was red and black and white. It was a bird of (black) feathers, tinged with yellow and green; it had a bunch of red feathers on the top of its head. It was a large bird, as large as the moa”. Another description reported by the Reverend Stack (Stack, 1878, pg 63) said: “A Pouakai had built its nest on a spur of Mount Tawera, and darting down from thence it seized and carried off men, women, and children, as food for itself and its young. For, though its wings made a loud noise as it flew through the air, it rushed with such rapidity upon its prey that none could escape from its talons”. The carrying off of men and women is undoubtedly an exaggeration, but the description of its presence over open ground and mountainous terrain is consistent with our deductions.So that is the sensational tidbit that the media can run with - this was a terrifying eagle that carried off children!! But the main thrust of the paper itself is in demonstrating that Haast's eagle was an active predator, with an oversized skull (hence disproportionately smaller brain) that attacked moas from the air, striking them with its strong, sensitive talons in the lower back over the kidneys and at the base of the skull. In the bigger evolutionary picture, this is a fascinating case study showing that neurological (brain) and somatic (body) expansion can be mismatched even in cases of island gigantism - there appears to be considerable flexibility in how natural selection affects different parts of the brain and body under different ecological conditions (such as the lack of predators or presence of new bigger prey).Meanwhile, the other ... Read more »
G. Grey. (1873) Description of the extinct gigantic bird of prey, Hokioi, by a Maori. Transactions of the New Zealand Institute, 435. info:/
Scofield, R., & Ashwell, K. (2009) Rapid Somatic Expansion Causes the Brain to Lag Behind: The Case of the Brain and Behavior of New Zealand's Haast's Eagle ( ) . Journal of Vertebrate Paleontology, 29(3), 637-649. DOI: 10.1671/039.029.0325
Sereno, P., Tan, L., Brusatte, S., Kriegstein, H., Zhao, X., & Cloward, K. (2009) Tyrannosaurid Skeletal Design First Evolved at Small Body Size. Science. DOI: 10.1126/science.1177428
- August 23, 2009
- 11:12 PM
- 527 views
Science knows it doesn't know everything... and neither did Darwin
by Student @ Fresno State in Darwin's Bulldogs
A couple of interesting examples of the self-correcting nature of Science today:1. It turns out that good ol' Charlie Darwin was wrong about the human appendix! Bollinger and colleagues reported several years ago that this sometime exemplar of vestigial organs is not so useless after all: The human vermiform (“worm-like”) appendix is a 5–10 cm long and 0.5–1 cm wide pouch that extends from the cecum of the large bowel. The architecture of the human appendix is unique among mammals, and few mammals other than humans have an appendix at all. The function of the human appendix has long been a matter of debate, with the structure often considered to be a vestige of evolutionary development despite evidence to the contrary based on comparative primate anatomy. The appendix is thought to have some immune function based on its association with substantial lymphatic tissue, although the specific nature of that putative function is unknown. Based (a) on a recently acquired understanding of immune-mediated biofilm formation by commensal bacteria in the mammalian gut, (b) on biofilm distribution in the large bowel, (c) the association of lymphoid tissue with the appendix, (d) the potential for biofilms to protect and support colonization by commensal bacteria, and (e) on the architecture of the human bowel, we propose that the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.Now we have a broader comparative phylogenetic analysis by Smith et al (incl. two of the authors of the 2007 paper) where they looked at the distribution of similar structures across the mammalian phylogeny to report: A recently improved understanding of gut immunity has merged with current thinking in biological and medical science, pointing to an apparent function of the mammalian cecal appendix as a safe-house for symbiotic gut microbes, preserving the flora during times of gastrointestinal infection in societies without modern medicine. This function is potentially a selective force for the evolution and maintenance of the appendix, and provides an impetus for reassessment of the evolution of the appendix. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.How exciting: the appendix has evolved and been maintained multiple times among different mammal lineages likely because if confers some selective advantage; and it continues to serve a useful function in the human body too! Tell that to the surgeon who offers to remove yours as an elective procedure while he has you opened up for some other reason (e.g. a cesarean section)!So Darwin, who didn't know about appendix like structures in other mammals, and didn't have access to phylogenetic analyses of the sort that is routine these days, wrote that the appendix was useless, and even a cause of death (which it still is sometimes, when infected). A classic "vestigial" organ. Now we know he was wrong - as he was about some other things too; but not about his theory of evolution by natural selection. As I try to impress upon my students every year, scientists have been trying to prove Darwin wrong for 150 years, but have only ended up strengthening the evidence for his theory of evolution. So it is only natural that when someone finds something, anything, in the details that Darwin was wrong about, there is some excitement. Understandable, really, for this is how science works - we don't venerate our authority figures, but try to prove them wrong, and respect only those theories that can withstand such relentless questioning. What I don't understand, however, is PZ's reaction over on Pharyngula, where he's taken the authors of these studies to task for suggesting Darwin was wrong! Surely PZ knows better - even Darwin would have reveled in the evidence we now have, and gladly accepted his error! So I share my bafflement over PZ's rather odd interpretation of what is "vestigial" with Bjørn Østman of Pleiotropy. If an organ has a function that contributes to current fitness, its hardly "vestigial" now, is it?.And those that berate us as adherents of "scientism" or "Darwinism", take note: we are quite happy to prove even Darwin wrong, and not afraid to stand up to the fierce atheist PZ neither! (and may PZ's octopod friends and minions never find this obscure little blog...)2. The other example of science's self correcting ways comes in the form of a mea culpa by L. David Mech, the leading wolf expert who once suggested that wolf packs are organized in dominance hierarchies with "alpha males" leading the pack - except that most natural wolf packs aren't like that at all! Having continued studying wolves for some 4 decades since he suggested the "alpha male" notion, and increasingly concerned about the population status of wolves in the wild, Mech now admits he was wrong about their social organization, and would like to undo the damage his initial descriptions may have caused to the wolf's reputation. His initial conclusions were biased by studies of artificial wolf groups in captivity, where such dominance hierarchies formed; in natural packs, familial relationships and lineage play a bigger role than combat for leadership (sound familiar?). Mech, therefore, would like us to stop using the "alpha male" terminology which has taken a metaphoric life of its own in popular culture.And rather unlike its depictions in said popular culture, this is exactly how science is supposed to work: through constant self-examination and self-correction! So let me leave you with another video, from a British comedian, who puts it best: "Science Knows It Doesn't Know Everything, Otherwise It Would Stop". Let that be the take-home message this Sunday; and don't stop the questioning!References:Randal Bollinger, R., Barbas, A., Bush, E., Lin, S., & Parker, W. (2007). Biofilms in the large bowel suggest an apparent function of the human vermiform appendix Journal of Theoretical Biology, 249 (4), 826-831 DOI: 10.1016/j.jtbi.2007.08.032... Read more »
Randal Bollinger, R., Barbas, A., Bush, E., Lin, S., & Parker, W. (2007) Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology, 249(4), 826-831. DOI: 10.1016/j.jtbi.2007.08.032
SMITH, H., FISHER, R., EVERETT, M., THOMAS, A., RANDAL BOLLINGER, R., & PARKER, W. (2009) Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology. DOI: 10.1111/j.1420-9101.2009.01809.x
- June 13, 2009
- 04:43 AM
- 922 views
Lost Sounds
by Madhu in Reconciliation Ecology
Deep in the mountains of Arunachal Pradesh, where the mighty Siang river carves its way through the Himalayan wall, nestled the Adi hamlet of Tuting, surrounded by a sea of green—overgrown fields, verdant mountains, the river itself deep green. The very moonlight seemed green as it shone on the ghostly mist rising from the gorge. Eighteen years ago, a search for India's last Takin—that... Read more »
Madhusudan Katti. (2001) Vocal communication and territoriality during the non-breeding season in a migrant warbler. Current Science, 80(3), 419-423. DOI: http://www.ias.ac.in/currsci/feb102001/419.pdf
WARREN, P., KATTI, M., ERMANN, M., & BRAZEL, A. (2006) Urban bioacoustics: it's not just noise. Animal Behaviour, 71(3), 491-502. DOI: 10.1016/j.anbehav.2005.07.014
SWADDLE, J., & PAGE, L. (2007) High levels of environmental noise erode pair preferences in zebra finches: implications for noise pollution. Animal Behaviour, 74(3), 363-368. DOI: 10.1016/j.anbehav.2007.01.004
Slabbekoorn, H., & Peet, M. (2003) Birds sing at a higher pitch in urban noise. Nature, 424(6946), 267-267. DOI: 10.1038/424267a
Fuller, R., Warren, P., & Gaston, K. (2007) Daytime noise predicts nocturnal singing in urban robins. Biology Letters, 3(4), 368-370. DOI: 10.1098/rsbl.2007.0134
- May 9, 2009
- 05:06 AM
- 1,416 views
Plagiarism, peer-review, and protecting the integrity of science
by Madhu in Reconciliation Ecology
I am, (it seems) almost constantly reading, evaluating, and passing judgment on, material written by others: not just when I'm synthesizing material for my own papers or blog essays, but as a peer reviewing manuscripts and grants written by colleagues, or as a teacher grading student papers. Comes with the territory of being a professor, or course. As it happens, its that time of year again when... Read more »
Dove, A. (2009) Regulators confront blind spots in research oversight. Nature Medicine, 15(5), 469-469. DOI: 10.1038/nm0509-469a
Errami, M., Sun, Z., Long, T., George, A., & Garner, H. (2009) Deja vu: a database of highly similar citations in the scientific literature. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn546
Long, T., Errami, M., George, A., Sun, Z., & Garner, H. (2009) SCIENTIFIC INTEGRITY: Responding to Possible Plagiarism. Science, 323(5919), 1293-1294. DOI: 10.1126/science.1167408
- March 18, 2009
- 09:08 PM
- 1,861 views
Urban forestry through the lens of "socio-ecological systems"
by Madhu in Reconciliation Ecology
Contributed by Seth Reid, following a vigorous class discussion with guest presentation by Genevra Ornelas.
Our March 4th class discussion revolved around urban forestry and how it pertained to an article written by John M. Anderis, Marcos A. Jannsen, and Elinor Ostrom. This article provided, “A Framework to Analyze the Robustness of Social-ecologcial Sytems from an Institutional Perspective.”... Read more »
Anderies, J. M., Janssen, M. A., & Ostrom, E. (2004) A Framework to Analyze the Robustness of Social-ecological Systems from an Institutional Perspective. Ecology and Society, 9(1), 18. DOI: http://www.ecologyandsociety.org/vol9/iss1/art18/
- March 18, 2009
- 08:38 PM
- 1,807 views
Ecosystem services, biodiversity conservation, and how to pay for them
by Madhu in Reconciliation Ecology
Brad Schleder shares this summary of class discussion of two very interesting papers that Brett Moore brought to the table.
Modeling multiple ecosystem services, biodiversity conservation, commodity production, and tradeoffs at landscape scales
Erik Nelson, Guillermo Mendoza, James Regetz, Stephen Polasky, Heather Tallis, D. Richard Cameron, Kai MA Chan, Gretchen C. Daily, Joshua Goldstein,... Read more »
Nelson, E., Mendoza, G., Regetz, J., Polasky, S., Tallis, H., Cameron, D., Chan, K., Daily, G., Goldstein, J., Kareiva, P.... (2009) Modeling multiple ecosystem services, biodiversity conservation, commodity production, and tradeoffs at landscape scales. Frontiers in Ecology and the Environment, 7(1), 4-11. DOI: 10.1890/080023
Bohlen, P., Lynch, S., Shabman, L., Clark, M., Shukla, S., & Swain, H. (2009) Paying for environmental services from agricultural lands: an example from the northern Everglades. Frontiers in Ecology and the Environment, 7(1), 46-55. DOI: 10.1890/080107
- March 16, 2009
- 07:48 PM
- 837 views
Why are all earthly lifeforms lefties?
by Student @ Fresno State in Darwin's Bulldogs
What, you think you are not left-handed? Just because you favor your right hand to write/eat/pitch that baseball, etc.? Actually, in case you didn't already know this: deep down, at the amino acid level, we are all lefties! Southpaws, each and every one of us! That's just another one of those wonderfully weird arbitrary fact about life on earth! Amino acids, the building blocks of proteins, are fundamental to the structure and function of life as we know it on our planet (which is pretty much how we know life at all, because we haven't found any other kind - yet!) - and the atoms making up each molecule can be put together in different ways to produce configurations which are mirror-images of each other (chirality, as the chemists call it); we know this because we can make amino acids in the lab. Yet, all life-forms we know of only contain one version of the amino acids - the left-handed one from the mirror-image pair! So this is another deep molecular homology involving amino acids (like the language of the genetic code we discuss in Evolution class), which unites all life-forms on this planet with a shared common ancestor. But there is no inherent reason why that ancestor had to be a southpaw in its use of amino acids. Was it just a random accident that that is how we turned out? A new study of the famous Murchison meteorite takes on the question...Did lefty molecules seed life? (as reported in The Scientist today): "Amino acids come in left-handed and right-handed forms, which, like a pair of human hands, are mirror images that cannot be superimposed onto each other. Yet living organisms use only the left-handed version, which presents a conundrum: There's no biochemical reason why one mirror image should be better than the other, so scientists have long debated whether life's left-handed leaning arose because of random processes or whether rocks from outer space seeded a southpaw solar system."...and suggests an explanation: that there was a left-bias in the amino acids that rained onto early earth from our solar system!The current study argues for the latter possibility by showing that some extraterrestrial meteorites contain an abundance of left-handed molecules. "The implications are that all life in our solar system could be the same handedness as life on Earth," Jeffrey Bada, a geochemist at the Scripps Institution of Oceanography in La Jolla, Calif., who was not involved in the research, told The Scientist. Daniel Glavin and Jason Dworkin, astrobiologists at NASA's Goddard Space Flight Center in Greenbelt, MD, compared the ratio of left- and right-handed 5-carbon amino acids found in six primitive, carbon-rich meteorites that have an elemental composition similar to that presumably found in the early solar system. Three of these rocks were heavily left-skewed, while the remaining three showed equal handedness, or chirality, the researchers found. Of the lefty rocks, the meteorite that fell on Murchison, Australia, in 1969 -- arguably the most widely studied carbonaceous meteorite in the world -- contained the largest imbalance ever observed: a 18.5% excess of the left-handed form of the amino acid isovaline. Or, in their own words from the abstract of the PNAS paper: The large asymmetry in isovaline and other α-dialkyl amino acids found in altered CI and CM meteorites suggests that amino acids delivered by asteroids, comets, and their fragments would have biased the Earth's prebiotic organic inventory with left-handed molecules before the origin of life.Amino acids found in these and other meteorites landing on earth tend to exhibit a bias favoring left chirality, suggesting our entire solar system has the same left-bias, setting life as we know it on its lefty path. And Glavin & Dworkin think they know what favored left chirality in the meteorites: The mechanism that Glavin and Dworkin propose to explain the observed left-handed excess is that polarized light -- which is twisted and can rotate molecules -- probably set the imbalance in motion. Then, once the balance was slightly askew, water within the meteorites further drove an enrichment of left-handed amino acids in the liquid phase and relegated right-handed molecules to the solid phase. "The whole amplification is due to this process of aqueous alteration," said Dworkin. Not everyone is convinced, yet, but the search for answers to these puzzles about life's origin continues. (Or we could simply say goddidit, and stop asking any further questions, couldn't we? but where's the fun in that?)Reference:Glavin, D. P., & Dworkin, J. P. (2009). Enrichment of the amino acid l-isovaline by aqueous alteration on CI and CM meteorite parent bodies Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811618106... Read more »
Glavin, D. P., & Dworkin, J. P. (2009) Enrichment of the amino acid l-isovaline by aqueous alteration on CI and CM meteorite parent bodies. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0811618106
- March 16, 2009
- 06:11 AM
- 1,602 views
Coupled Human And Natural Systems - a class discussion
by Madhu in Reconciliation Ecology
Heather Hanlin wrote the following summary of our class discussion on Feb 17th:
We discussed two different papers: “Coupled Human and Natural Systems,” by Jianguo Liu et al (2007), and “The Effects of Human Socioeconomic Status and Cultural Characteristics on Urban Patterns of Biodiversity” by Ann Kinzig et al (2005). The “Coupled Human and Natural Systems,” are referred to as CHANS. CHANS are... Read more »
Liu, J., Dietz, T., Carpenter, S., Folke, C., Alberti, M., Redman, C., Schneider, S., Ostrom, E., Pell, A., Lubchenco, J.... (2007) Coupled Human and Natural Systems. AMBIO: A Journal of the Human Environment, 36(8), 639-649. DOI: 10.1579/0044-7447(2007)36[639:CHANS]2.0.CO;2
Ann P. Kinzig, Paige Warren, Chris Martin, Diane Hope and Madhusudan Katti. (2005) The Effects of Human Socioeconomic Status and Cultural Characteristics on Urban Patterns of Biodiversity. Ecology and Society, 10(1), 23. DOI: http://www.ecologyandsociety.org/vol10/iss1/art23/
- December 22, 2008
- 06:31 AM
- 1,797 views
Phylogenomics suggest ratites lost flight multiple times
by Student @ Fresno State in Darwin's Bulldogs
Rebekah Wukits discusses recent findings about ratite evolution for Bio 135.Ratite evolution has been debated for centuries. Some of the earliest evolutionary biologists questioned whether or not ratites had a linear evolution or if the major groups had had independent origins. Richard Owen proposed that living ratites had much more in common with other flight capable groups while being united by the “arrested development of wings unfitting them for flight”. In 1951, two ornithologists, Mayr and Amadon, stated that, “the present consensus is that the main groups of these birds are of independent origins”.Traditionally, ratites have been considered to be monophyletic, or ascending from a common ancestor. They are placed in the major group Noegnathae, with the flight-capable tinamous as a sister group. Since the extinct tinamous were capable of flight, it has been thought that the ratites lost flight once in their history, then diversified. Unfortunately, simple geography contradicted this theory. All living ratites (rheas, cassowaries, emus, ostriches and kiwis) are isolated on different southern continents. Rheas are found in South America. Ostriches reside in Africa. Emus and cassowaries are found only in Australia and kiwis can be found in New Zealand. Extinct species of ratites follow the same pattern. Moas were also found in New Zealand, and elephant birds lived in Madagascar. The question became that if flight was lost once early in ratite evolution, how did they become so spread out and isolated? The perfect answer seemed to reside in the theory of continental drift. Ratites came from a single ancestor, lost flight and were then isolated when Gondwana broke up.Though most of the recent studies of morphological and molecular ratite characteristics have supported the monophyletic theory, many still debate it. Rarely challenged is the fact that adaptations to a cursorial lifestyle, one that is adapted to running, can lead to convergent evolution, and can be misleading when basing phylogeny on morphology. This led scientists to do further phylogenomic studies in order to test the prevailing theories. These studies include data taken from genetic loci that represent the entire avian genome. In this particular study, data was taken from 20 loci that are dispersed widely throughout the avian genome. The data set included all living ratites and eight outgroup taxa. Previously done similar genetic tests have supported ratite monophyly, however these tests were more sophisticated and advanced and supported a different conclusion.The results are as follows: analysis of the data strongly supports placing the flight capable tinamous within ratites and ostriches as the sister group. If this new phylogeny is correct, the single loss of flight in ratites is unlikely. In order for all ratites to have lost flight in a common ancestor, the tinamous would have had to regain flight at a later time. It is much more likely that flight was lost multiple times do to convergent evolution than to have gained flight in the earliest ancestors, lost flight in the common ancestor of ratites, than gain flight again in tinamous.It seems more likely that ratites descended from a single ancestor, than diversified when gondwana broke up. Flight was lost in each family and convergent evolution occurred due to similar environmental conditions. Flight is very costly both energetically and morphologically. Ratites had little pressure to fly and since these features are costly to maintain, they became reduced over time. The theories of this paper seem concrete however more study is needed. Their own genetic studies produced conflicting results. Placing tinamous within ratites has great implications for their evolution and dispersal. This idea needs to be further developed and supported.Reference:J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, K. J. Miglia, W. S. Moore, S. Reddy, F. H. Sheldon, D. W. Steadman, S. J. Steppan, C. C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds Proceedings of the National Academy of Sciences, 105 (36), 13462-13467 DOI: 10.1073/pnas.0803242105... Read more »
J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks.... (2008) Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences, 105(36), 13462-13467. DOI: 10.1073/pnas.0803242105
- December 3, 2008
- 05:33 AM
- 1,018 views
Modeling the emergence of multi-drug resistant TB hot zones
by Student @ Fresno State in Darwin's Bulldogs
Rebecca Freeman submitted this essay for the Evolution class.According to the World Health Organization (WHO), a “hot zone” is an area with >5% prevalence (or incidence) of Multi-Drug Resistant Tuberculosis (MDRtb). Sally M Blower and Tom Chou have been using a mathematical method to track the emergence and evolution of multiple strains of drug resistant tuberculosis, but they have now developed a new, more complex mathematical model. Before this model, there was only a two strain model, meaning it was only relevant to individuals that can be infected with a wild type pansensitive strain or a drug resistant strain, but there are many more strains then this. There are a resistant strains only to one drug and some resistant to multiple drugs. This means there is a multitude of strains in these hot zones and there was a need for a better way to track this (Blower and Chou 2004). Blower and Chou realized that a more complex mathematical model is necessary to capture the complexity of the epidemiology of the hot zones, and the evolution of hot zones was very unclearUnderstanding drug resistance is important to understanding the, and Blower and Chou explain the evolving of resistance very well. They give three processes that are involved in generating drug resistance: Transmission of drug resistant strains to uninfected individuals, which is transmitted resistance; Conversion of wild pansensitive cases to drug resistant cases, which is acquired resistance; finally, cases where they have drug resistant strains and it becomes resistant to more antibiotics during treatment, which is amplified resistance. What everyone has had to do in the past is just study acquired and transmitted resistance, and now with the new model, they can incorporate amplification resistance. This was a big problem because it has been shown that inadequate treatment of DRtb can result in the amplification of drug resistant strains, which may be an important process of MDR epidemics (Blower and Chou 2004). So this is where Blower and Chou came in. They created a model, the call the amplifier model, that enables the tracking of emergence and evolution of MDR strains, the transmission of these strains and the amplification of these strains during repeated episodes of treatment.Blower and Chou are really studying the effects of inadequate treatment programs, and how this may lead to a higher prevalence in MDRtb. One problem that this research cannot completely take into account yet is the transmittance ability of MDRtb compared to pansensitive tuberculosis. This is an area that is hazy right now, and so this cannot completely be incorporated into the model. Amazingly, they have measured a general fitness of MDRtb vs. pansensitive tuberculosis, by calculating the treatment fail rates and treatment cure rates of the each category of strains.The authors were very clear with the purpose of the model. Even though the mathematical model is very complex, the idea and how they explain it is easily understandable. They use R0 to stand for the average number of secondary cases caused by one infectious case in a population where treatments are available. Their model breaks this up into four categories of strains: The wild type pansensitive [R0(1)], which is sensitive to all drugs; Pre-MDR [R0(2)], which is sensitive to one of the main drugs used to treat tuberculosis; MDR [R0(3)], which is resistant to both of the main treatment drugs; and post-MDR [R0(4)], which is resistant to both of the main antibiotics and others as well (Blower and Chou 2004). With the information gathered from over 30 years of date they constructed likely evolutionary trajectories of hot zones, and with this they also took into account low cure rates vs. high amplification probabilities in many areas. They also tried to incorporate which strains are more transmissible, but as I said before this was not really possible with their model and there was a large degree of uncertainty.The results of their model matched the WHO predictions well, but there were some distinct differences, and I think these differences are what make this research so important. By using all for types (R01-4) they found great variability in incidence and prevalence. When treatments were originally started strains of pre-MDR strains emerged quickly, so incidence and prevalence of pre-MDR strains increased, and this subsequently led to possible amplification of resistance and MDRtb epidemics in certain areas. The question is: Why certain areas and not others? This question is explained by Blower and Chou. Interestingly, areas with bad treatment programs do not necessarily have a really high incidence of MDRtb, it has stayed pretty steady at a 5%-14% (Blower and Chou 2004). This to me seems like an argument that MDRtb is not as easily transmissible, because its rates overall have stayed pretty low, but there was no significant evidence for this. The WHO predictions state that a >5% prevalence OR incidence in MDRtb equals a hot zone. Blower and Chou found the mathematical relationship between MDR prevalence and incidence. MDR prevalence can be three times greater then MDR incidence. They used the results to evaluate the hot zones on prevalence or incidence. If it is by incidence then only 20% of those areas would be considered hot zones and 51% if criterion is prevalence (Blower and Chou 2004). I see this as an argument for the fitness of MDRtb to be very high and transmissible ability to be lower, because there are less new cases, and more cases that have just become more resistant.When looking at the four strains the hot zones had a much lower R0 for pansensitive strains (median=.82), which suggests that the wild type strain should be slowly eradicated. The R0 for the pansensitive strains in non-hot zones were all above 1 (median=1.39) Looking at the rate of detection of cases and treatment rates in hot zones versus non-hot zones it is 55% to 25% (Blower and Chou 2004). This shows that places where they have control programs were successful at fighting pansensitive strains but ironically it created more MDRtb strains, making it more likely to become a hot zone.The importance of this research is that they have figured out that the difference between incidence and prevalence rates is significant enough to change the view of an area as being a hot zone or not. Their research looks at many factors that go into the evolution of these hot zones. Out of the many factors they actually saw that case detection and treatment rates were the most important factors. They came to this conclusion because if case detection and treatment rates were low, and the amplification was high, it still did not generate a hot zone. Vise versa, if the case detection and treatment rates were high and the amplification rates were low; it was likely to become a hot zone. The point is that these areas with high case detection and treatment rates should not increase these rates unless high cure rates are achieved first. Blower and Chou have created a model that has multiple dimensions and can help the WHO in the future to prevent hot zones from popping up in high risk regions. The WHO already had a model for this but it was nowhere complex enough to correctly calculate prevalence and incidence of MDRtb, and how their mathematical relationship.Reference: Sally M Blower, Tom Chou (2004). Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance Nature Medicine, 10 (10), 1111-1116 DOI: 10.1038/nm1102... Read more »
Sally M Blower, & Tom Chou. (2004) Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance. Nature Medicine, 10(10), 1111-1116. DOI: 10.1038/nm1102
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