Post List

  • October 20, 2010
  • 02:32 PM

The Allee effect in action: why endangered Vancouver Island marmots are struggling to recover

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

There are under 200 California condors alive in the wild.  There are under 600 wild Ethiopian wolves.  There are around 3500 wild tigers and under 5500 African wild dogs outside of zoos. It has been ingrained in all of us … Continue reading →... Read more »

  • October 20, 2010
  • 02:29 PM

Wild, Wild Webs – the impact of artificial changes of productivity on a natural bipartite network

by Timothée Poisot in Timothée Poisot

While we know that food webs are structured in nature, information about how their structure is influenced by environmental conditions is scarce. Given that network structure is associated with more applied properties, such as resilience (Dunne et al. 2002a; Dunne et al. 2002b) and vulnerability to extinction (Memmott et al. 2004), an important research goal is to characterize how environmental changes can affect these properties. In an article published today in Biology Letters, we show how resource availability (a proxy for patch productivity) affects different structural features of a bacteria–bacteriophage bipartite network.... Read more »

Timothée Poisot, Gildas Lepennetier, Esteban Martinez, Johan Ramsayer, & Michael E Hochberg. (2010) Resource availability affects the structure of a natural bacteria–bacteriophage community. Biology Letters. info:/

  • October 20, 2010
  • 02:02 PM

Whale poop can enhance ocean productivity

by Uncharted Atolls in Uncharted Atolls

The biological pump, a way of moving nutrients and carbon down the water column, in the ocean is fairly straight-forward.  Phytoplankton–tiny, photosynthesizing critters bobbing around in the surface ocean–are eaten by larger organisms, like zooplankton and fish.  When the zooplankton … Continue reading →... Read more »

  • October 20, 2010
  • 01:26 PM

Google As a Medical Diagnostic Tool

by William Yates, M.D. in Brain Posts

My Google Reader accidentally picked up an intriguing abstract that examined a research study of resources that medical students use in solving diagnostic cases.  The abstract was picked up because it contained the word “exercise” that is one of my PubMed filter queries.  Although we often think that most diagnostic decision-making occurs from learned information stored in physician’s brains, information resources can be very helpful.  What information resources are medical students using to help them with the diagnostic process?Graber and colleagues asked this question and designed a learning experiment.  One hundred and seventeen medical students were presented a challenging case and asked to provide their top three diagnoses as well as listing all the resources they used and the helpfulness of each resource.  This experiment occurred as part of a examination of the web-based decision support system known as Isabel.  The top six most used resources (and the percent of medical students who used the resource in the experiment) were:Medical books (73%)Google (70%)Other students (69%)Journals (49%)Residents and attending (29%)Isabel (28%) Of note, here were the students ratings of the top resources by usefulness (Likert Scale 1-not helpful to 5=extremely helpful:eMedicine (4.0)Medical books (3.9)Up-to-Date (3.8)Google (3.6)Other students (3.5)Journals (3.4)Residents and attending (3.4)So this group of medical students reported frequently using Google to assist in a diagnostic assignment and they rate it as extremely useful.  The students also endorsed eMedicine a web-based medical information resource and the Up-to-Date subscription medical information resource.  (Disclosure: I have written two chapters published by eMedicine).  It is not clear how the students defined using “journals” in this study.  I would have thought that PubMed would be a particularly good gateway for searching for diagnostic information by finding journals relevant to a specific clinical case presentation.The use of Google for aiding in diagnosis is not limited to medical students and physicians.  Bouwman and colleagues describe two cases where parents were able to diagnose their child’s rare lysosomal storage disorder using Google.   Both cases had received extensive evaluation by medical personnel that did not result in a correct specific diagnosis.  Both child’s parents arrived at a correct diagnosis by using Google search.  In case one, the parents searched for “unexplained recurrent fever”, “pain in feet” and “skin rash” leading them to a site describing Fabry disease.   In the second case, parents typed in a sign their son exhibited “bowed fingers” and were led to a site for their son’s correct diagnosis of mucopolysaccharidosis.Google can also provide false, irrelevant medical information when it comes to diagnosis.  Most clinicians have experienced patient’s making an incorrect self-diagnosis from information they obtained on the web.  It is best to use multiple sources of information when puzzled by a case presentation.  However, it appears that Google Search is playing an important role in how clinicians and the general public collect diagnostic information.  We need more research examining the potential power of this tool and the limitations. Photo of Vijay Singh practicing putting at the 2010 PGA Championship courtesy of Yates PhotographyGraber ML, Tompkins D, & Holland JJ (2009). Resources medical students use to derive a differential diagnosis. Medical teacher, 31 (6), 522-7 PMID: 19811168Bouwman MG, Teunissen QG, Wijburg FA, & Linthorst GE (2010). 'Doctor Google' ending the diagnostic odyssey in lysosomal storage disorders: parents using internet search engines as an efficient diagnostic strategy in rare diseases. Archives of disease in childhood, 95 (8), 642-4 PMID: 20418338... Read more »

  • October 20, 2010
  • 01:19 PM

The regulatory bottleneck for biotech specialty crops

by Anastasia Bodnar in Biofortified

We often hear that there are only two genetically engineered traits on the market – Roundup Ready and Bt. And, for the most part, that’s correct. There are a few other commercialized traits, such as virus resistant papaya and squash, but why aren’t there more? We see all sorts of papers about awesome genetically engineered traits, from nemotode resistance to nutritional enhancement to really specialized traits like nicotine free tobacco and allergen free Continue reading...... Read more »

Miller JK, & Bradford KJ. (2010) The regulatory bottleneck for biotech specialty crops. Nature biotechnology, 28(10), 1012-4. PMID: 20944582  

  • October 20, 2010
  • 01:00 PM

Color Me Aphid

by Moselio Schaechter in Small Things Considered

Is it OK with you if on Fungus Week we post an item that deals with fungal genes instead of whole fungi? We want to do this because of a startling finding, that some aphids are colored because they possess fungus-derived genes for making carotenoids. This is news because until now it was thought that animals cannot synthesize such pigments—only prokaryotes, fungi and plants can (which is why vitamin A—a carotenoid—is a vitamin). But there you have it, some aphids are green and others are reddish depending on which carotenoids they make. It had been thought that these animals get their carotenoids either from their diet or from bacterial endosymbionts. However the sap they live on has no such things, and their symbionts lack the genes for carotenoid biosynthesis. In addition, curing the insects of the symbionts does not affect the color. Lastly, the symbionts are inherited maternally, whereas color follows Mendelian inheritance.... Read more »

  • October 20, 2010
  • 12:00 PM

Methuselah the tree

by beredim in Strange Animals

Methuselah is currently the oldest verified living non-clonal organism known in our planet.... Read more »

  • October 20, 2010
  • 11:57 AM

Don’t Touch That Dock!

by Journal Watch Online in Journal Watch Online

Marine biologists typically frown on construction projects, such as giant docks and seawalls, that bury sensitive coastal ecosystems under tons of steel and concrete. But a quintet of Spanish ecologists is now calling for protecting some of these structures in the name of saving an endangered shellfish. And they argue that “artificial marine micro-reserves” (AMMRs) […] Read More »... Read more »

  • October 20, 2010
  • 11:55 AM

Structural Contributors to Selective Drug-Protein Binding

by Michael Long in Phased

Are there any chemical features which need to be incorporated into an effective drug molecule? If so, what are they? Paul Clemons, Stuart Schreiber (Harvard University and Massachusetts Institute of Technology, United States), and coworkers have answered these questions on a fundamental level, although more pieces to the puzzle will undoubtedly be uncovered in the future. This news feature was written on October 20, 2010.... Read more »

Clemons, P. A., Bodycombe, N. E., Carrinski, H. A., Wilson, J. A., Shamji, A. F., Wagner, B. K., Koehler, A. N., & Schreiber, S. L. (2010) Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1012741107  

  • October 20, 2010
  • 11:45 AM

Genomic Evolution in the Blink of an Eye

by avi_wener in American Biotechnologist

If you think that genetic evolutionary processes take Milena….think again. Scientists at Allegheny General Hospital’s Center for Genomic Sciences have found that through a process known as horizontal gene transfer (HGT), bacterial pathogens can mutate multiple times during the course of a bacterial infection. In a study published by Hiller et. al. in PLoS Pathogens [...]... Read more »

  • October 20, 2010
  • 10:22 AM

Universal Grammar is dead. Long live Universal Grammar.

by gameswithwords in Games with Words

Last year, in a commentary on Evans and Levinson's "The myth of language universals: Language diversity and its importance for cognitive science" in Behavioral and Brain Sciences (a journal which published one target paper and dozens of commentaries in each issue), Michael Tomasello wrote:
I am told that a number of supporters of universal grammar will be writing commentaries on this article. Though I have not seen them, here is what is certain. You will not be seeing arguments of the following type: I have systematically looked at a well-chosen sample of the world's languages, and I have discerned the following universals ... And you will not even be seeing specific hypotheses about what we might find in universal grammar if we followed such a procedure.Hmmm. There are no specific proposals about what might be in UG... Clearly Tomasello doesn't read this blog much. Granted, for that he should probably be forgiven. But he also clearly hasn't read Chomsky lately. Here's the abstract of the well-known Hauser, Chomsky & Fitch (2002):
We submit that a distinction should be made between the faculty of language in the broad sense (FLB) and in the narrow sense (FLN). FLB includes a sensory-motor system, a conceptual-intentional system, and the computational mechanisms for recursion, providing the capacity to generate an infinite range of expressions from a finite set of elements. We hypothesize that FLN only includes recursion and is the only uniquely human component of the faculty of language.Later on, HCF make it clear that FLN is another way of thinking about what elsewhere is called "universal grammar" -- that is, constraints on learning that allow the learning of language.

Tomasello's claim about the other commentaries (that they won't make specific claims about what is in UG) is also quickly falsified, and by the usual suspects. For instance, Steve Pinker and Ray Jackendoff devote much of their commentary to describing grammatical principles that could be -- but aren't -- instantiated in any language.

Tomasello's thinking is perhaps made more clear by a later comment later in his commentary:
For sure, all fo the world's languages have things in common, and [Evans and Levinson] document a number of them. But these commonalities come not from any universal grammar, but rather from universal aspects of human cognition, social interaction, and information processing...Thus, it seems he agrees that there are constraints on language learning that shape what languages exist. This, for instance, is the usual counter-argument to Pinker and Jackendoff's nonexistent languages: those languages don't exist because they're really stupid languages to have. I doubt Pinker or Jackendoff are particular fazed by those critiques, since they are interested in constraints on language learning, and this proposed Stupidity Constraint is still a constraint. Even Hauser, Chomsky and Fitch (2002) allow for constraints on language that are not specific to language (that's their FLB).

So perhaps Tomasello fundamentally agrees with people who argue for Universal Grammar, this is just a terminology war. They call fundamental cognitive constraints on language learning "Universal Grammar" and he uses the term to refer to something else: for instance, proposals about specific grammatical rules that we are born knowing. Then, his claim is that nobody has any proposals about such rules.

If that is what he is claiming, that is also quickly falsified (if it hasn't already been falsified by HCF's claims about recursion). Mark C. Baker, by the third paragraph of his commentary, is already quoting one of his well-known suggested language universals:
(1) The Verb-Object Constraint (VOC): A nominal that expresses the theme/patient of an event combines with the event-denoting verb before a nominal that expresses the agent/cause does.And I could keep on picking examples. For those outside of the field, it's important to point out that there wasn't anything surprising in the Baker commentary or the Pinker and Jackendoff commentary. They were simply repeating well-known arguments they (and others) have made many times before. And these are not obscure arguments. Writing an article about Universal Grammar that fails to mention Chomsky, Pinker, Jackendoff or Baker would be like writing an article about major American cities without mentioning New York, Boston, San Francisco or Los Angeles.

Don't get me wrong. Tomasello has produced absurd numbers of high-quality studies and I am a big admirer of his work. But if he is going to make blanket statements about an entire literature, he might want to read one or two of the papers in that literature first.
Tomasello, M. (2009). Universal grammar is dead Behavioral and Brain Sciences, 32 (05) DOI: 10.1017/S0140525X09990744

Evans, N., & Levinson, S. (2009). The myth of language universals: Language diversity and its importance for cognitive science Behavioral and Brain Sciences, 32 (05) DOI: 10.1017/S0140525X0999094X

Hauser MD, Chomsky N, & Fitch WT (2002). The faculty of language: what is it, who has it, and how did it evolve? Science (New York, N.Y.), 298 (5598), 1569-79 PMID: 12446899

Baker, M. (2009). Language universals: Abstract but not mythological Behavioral and Brain Sciences, 32 (05) DOI: 10.1017/S0140525X09990604

Pinker, S., & Jackendoff, R. (2009). The reality of a universal language faculty Behavioral and Brain Sciences, 32 (05) DOI: 10.1017/S0140525X09990720... Read more »

  • October 20, 2010
  • 10:15 AM

What Caused the Black Death?

by Sara Klink in Promega Connections

I was confident I knew a few things about the bubonic plague: It was caused by the bacterium Yersinia pestis, which was transmitted to humans by fleas hitching a ride on the back of traveling rats; it spread rapidly and devastated populations around the globe, and because cats, a natural predator of scurrying rodents, had [...]... Read more »

Haensch S, Bianucci R, Signoli M, Rajerison M, Schultz M, Kacki S, Vermunt M, Weston DA, Hurst D, Achtman M.... (2010) Distinct Clones of Yersinia pestis Caused the Black Death. PLoS pathogens, 6(10). PMID: 20949072  

  • October 20, 2010
  • 09:58 AM

The werewolf is dead, long live the werewolf, or: The co-existence of lycanthropy and Cotard’s syndrome

by Matt Soniak in

“I speak, breathe and eat but I am dead,” said the patient. The man, a 32-year-old high school dropout, laborer and family man, had been brought to Kerman Psychiatric Hospital in southern Iran by his relatives after he refused to go to work for two straight weeks. Two years before that, the symptoms started. At [...]... Read more »

  • October 20, 2010
  • 09:50 AM

We're Walking Here - and feeling much better as a result: walking to rep in performance improvements

by mc in begin to dig (b2d)

Walking is an action most of us take for granted. It's such an automatic, effortless, thoughtless practice that we tend to forget it's actually a learned, practiced, skill. But it's this natural effortlessness of this deeply rep'ed & acquired practice that makes it so valuable for locking in better movement practice - what we practice when say working with a coach to tune dynamic joint movements... Read more »

  • October 20, 2010
  • 09:45 AM

Running With Arenahippus

by Laelaps in Laelaps

No matter what you call them – Eohippus, Hyracotherium, or something else – most everyone is familiar with the diminutive “dawn horses” of the Eocene. Sure, dinosaurs get better press, but the connection of these small hoofed mammals to the modern horse (Equus) has turned them into minor paleontological celebrities. In fact, these horses have [...]... Read more »

  • October 20, 2010
  • 09:12 AM

Young Children Hear It to Believe It

by APS Daily Observations in Daily Observations

Santa Claus, the tooth fairy, the Easter bunny…you name it and little kids believe it. However, a new study of three-year-olds, published in Psychological Science, finds that they aren’t just ... Read more »

Jaswal, V.K., Croft, A.C., Setia, A.R., & Cole, C.A. (2010) Young children have a specific, highly robust bias to trust testimony. Psychological science : a journal of the Association for Psychological Science/ APS. PMID: 20855905  

  • October 20, 2010
  • 09:09 AM

Tip of the Week: Comparing Microbial Databases

by Jennifer in OpenHelix

A few weeks ago a commenter asked me to compare IMG (Integrated Microbial Genomes) to the UCSC Microbial Genome browser. I’ve been exploring & thinking since then & am going to give a very brief comparison of those two resources in today’s tip & I’ll expand the comparison to other resources here in the text of this post.
Each of these resources could (and does in many cases) have an hour long tutorial devoted to it so I will only be able to give the briefest of overviews in this 5 minute tip, but I think (hope) it will be enough to get you thinking and exploring. The way I see things, comparing these two resources is kind of like comparing apples and aardvarks: they start with the same thing – namely microbial genome information from NCBI’s RefSeq database – but after that they are very different organisms.
* The UCSC Microbial Genome browser includes archaea, bacteria and archaeal virus genomes, and is based on a slightly modified version of the UCSC Genome Browser system, which is an amazingly powerful browser that we know and love here at OpenHelix. On their homepage they describe the resource as:
The UCSC Microbial Genome Browser is a window on the biology of more than 300 microbial species from Bacteria and Archaea domains. Basic gene annotaiton is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data, and soon, high-throughput RNA sequencing. Direct contributions of functional genomic data or bioinformatic analyses are welcome.
Information is presented as ‘tracks’ aligned along the sequence of the genome. These tracks can be hidden, expanded and customized to display exactly the information a researcher is interested in, in the exact format that the researcher would like it. The database contains hundreds of microbial genomes and information from these genomes can be retrieved and analyzed by intersecting datasets using UCSC’s powerful Table Browser resource. We have multiple free tutorials on the general UCSC Genome Browser which would be applicable to using the UCSC Microbial Browser.
* The UCSC Archaeal Genome Browser is another microbial resource based on the general UCSC Genome Browser & displays information very similarly to that of the UCSC Microbial Genome Browser, but the two offer differences in the information tracks and species available. We just created a full tutorial on this resource in July of this year & the homepage has been updated significantly since then, so this group must really be active! (Watch for an announcement of our updated tutorial in the near future…)
* The Integrated Microbial Genomes resource is from the Joint Genome Institute, and also obtains its sequences from NCBI’s RefSeq database, as well as from their own sequencing efforts. It contains sequence data on archaea, bacteria, eukaryotes (for comparative purposes), viruses and plasmids. To quote the IMG homepage:
The Integrated Microbial Genomes (IMG) system ( Nucleic Acids Research, 2010, Vol. 38) serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context…
… The IMG user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools.
However, rather than presenting vast amounts of information aligned along a sequence, this resource aims to provide researchers with the most state-of-the-art technology for microbial comparative analyses. They provide an array of tools for finding precise sets of genomes, genes of functions according to various characteristics. The researcher is then able to use Abundance profilers, functional alignment tools, analysis carts and more to compare the items within the set to one another. Visualizations present the comparative information beautifully and clearly, but are not flexible in the same way that UCSC browser displays are using the track controls.
* The Integrated Microbial Genomes with Microbiome samples (IMG/M) resource is a Data Management & Analysis System that is related to IMG (which I bet you guessed) that specializes in the unique issues surrounding metagenomic sequences. It currently contains metagenome data on 133 microbiomes, specialized tools for metagenomic analyses, and all of the IMG data for reference in comparisons.
* The Complete Microbial Resource, or CMR, from the J. Craig Venter Institute is another general microbial resource, with archaeal, bacterial, and viral genomes. Its genome browser and comparative functions put it somewhere between the UCSC Microbial Browser & IMG, but with a real emphasis on the ability to easily download lists of genes, evidence or genomic elements as well as sequences, etc. that result from you analyses.
* The Complete Microbial Genomes database is from NCBI and offers an extensive collection of data, resources and tools for prokaryotic genomic analysis. Data and tools are organized into three major tables, including Organism info, Complete genomes, and Genomes in progress. Sequence information is available for over 1000 archaeal and bacterial genomes and utilizes NCBI’s extensive resources to provide extensive linkout options to additional information. Complete Microbial Genomes is one of NCBI’s many Entrez Genome Projects.
These resources are just a few of the many general microbial resources publicly available to researchers. Then there are species specific resources such as EcoliHub, subject specific resources such as MiST (Microbial Signal Transduction Database), and resources associated with specific projects such as the Human Microbiome Project (HMP) resources: Data Analysis and Coordination Center (DACC) for the Human Microbiome Project (HMP), the NIH Human Microbiome Project (HMP) Roadmap Project, and the HMP NIH Intramural Skin Microbiome Consortium (NISMC) data at dbGaP, which Mary heard about at a recent meeting. I think I’ll leave exploration of these specialized projects to another day though.
UCSC Microbial Genome Browser and UCSC Archaeal Browser:
Schneider, K. (2006). The UCSC Archaeal Genome Browser Nucleic Acids Research, 34 (90001) DOI: 10.1093/nar/gkj134
... Read more »

Schneider, K. (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Research, 34(90001). DOI: 10.1093/nar/gkj134  

Markowitz, V., Chen, I., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Anderson, I., Lykidis, A., Mavromatis, K.... (2009) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp887  

Markowitz, V., Ivanova, N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I., Grechkin, Y., Dubchak, I., Anderson, I.... (2007) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research, 36(Database). DOI: 10.1093/nar/gkm869  

Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O.... (2009) The comprehensive microbial resource. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp912  

Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S.... (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp967  

  • October 20, 2010
  • 08:43 AM

Earthquakes and Volcanoes in Saudi Arabia!

by geophilo in Traversing the Razor

Many people might not associate Saudi Arabia with volcanoes and earthquakes. A more common image might be miles upon miles of sandy desert. However, the Arabian region is home to some large fields of volcanoes that have erupted in the last thousand years or so. In May 2009, 40,000 people were evacuated from the Harrat [...]... Read more »

Pallister, J., McCausland, W., Jónsson, S., Lu, Z., Zahran, H., Hadidy, S., Aburukbah, A., Stewart, I., Lundgren, P., White, R.... (2010) Broad accommodation of rift-related extension recorded by dyke intrusion in Saudi Arabia. Nature Geoscience, 3(10), 705-712. DOI: 10.1038/ngeo966  

  • October 20, 2010
  • 08:39 AM

Did I mention that Caperea is really, really weird? [Tetrapod Zoology]

by Darren Naish in We Beasties

The recent discussion of Caperea's skeletal morphology (Caperea = Pygmy right whale) inspired Joy Reidenberg to send these photos of a Caperea skeleton, taken in New Zealand and used here with her permission.

In this view of the whale's thoracic region (we're standing beneath the whale, looking up into its ribcage), you can see that the transverse processes (the wing-shaped structures that project from both sides of each vertebra) are proportionally huge: so big that many of them overlap. The dorsal ends of the ribs - the parts of the ribs that contact the transverse processes - look strangely small and narrow by comparison, and also seem to have really loose connections with the transverse processes. Compare this with the ribcage of a North Atlantic right whale Eubalaena glacialis... Read the rest of this post... | Read the comments on this post...

... Read more »

  • October 20, 2010
  • 08:38 AM

Lessons of Dodge Ball: Pay Attention and Keep Your Hands Up

by Psychology 379 bloggers in Cognition & the Arts

If you have ever had the luxury of participating in a good old fashioned game of dodge ball in gym class or just happen to a fan of the movie DodgeBall, you are probably aware that keeping your hands ready to catch a ball is key to staying in the game.  You may not look as [...]... Read more »

Reed, C., Betz, R., Garza, J., & Roberts, R. (2009) Grab it! Biased attention in functional hand and tool space. Attention, Perception , 72(1), 236-245. DOI: 10.3758/APP.72.1.236  

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