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  • October 13, 2010
  • 03:08 PM
  • 935 views

Altruism as a result of sexual selection

by sandygautam in The Mouse Trap

Image via Wikipedia There is a new article in BPS, that has found some evidence for the fact that altruism may have evolved by the process of sexual selection. There are many mechanisms that underlie exactly how and why sexual selection takes place- one is the ‘handicap’ /’costly honest signal‘ theory according to which aRating: 0.0/10 (0 votes cast)... Read more »

  • October 13, 2010
  • 02:59 PM
  • 1,248 views

Caffeine makes us Crazy - or at least messes with our sleep

by mc in begin to dig (b2d)

i *love* good coffee. You? Do you know how you react to coffee? Do you find caffeine keeps you awake/alert? Yes? or maybe you find it doesn't affect your getting to sleep? We know that the magic in coffee is caffeine. Guess what? apparently whether or not we can fall asleep with caffeine is less of an issue than what it does to our sleep quality, in particular, our deep sleep state. That is, it ... Read more »

  • October 13, 2010
  • 02:45 PM
  • 606 views

Babies, balls and creationists

by Daniel in Ego sum Daniel

A recently published study in PNAS explores how small babies relate order and disorder, or entropy, to the different types of things that may cause them. Amazingly, babies as small as 12 months old show some understanding of the difference between the deliberate and goal-directed "agents" that can cause order, such as a person, and those randomly acting inanimate objects that cannot, such as a bouncing ball. This means that we have some sort of general understanding that the way agents act on the world is completely different from the way inanimate objects act on the world from a very early age. Long before we're able to articulate why we would believe such a thing. Read more about the experiments from this summary at Ars Technica: Toddlers recognize entropy from messy bedrooms. The extraordinary thing here is that the authors of the study don't limit themselves to stating this fact regarding the cognitive development of human beings, but weave in several references to creationism in the article. Although the Second Law of Thermodynamics is often understood as stating that isolated systems tend to move from order to disorder in a manner that increases entropy, we frequently encounter cases where an external entity can take a system from relative disorder to order. Most of the time, the entity is an “agent,” meaning a goal-directed actor, and very often that agent is thought of as having intentions to bring order to the system...The second law of thermodynamics often fallaciously used by creationists as an argument against evolution, based exactly on the temptation to think of evolution as a process that "wants to bring order to the system". This inability of imagining evolutionary processes as completely devoid or intentions or goals underlies many misconceptions about evolution. As adults, however, we do not typically see inanimate objects as capable of having such effects. It is highly unlikely that a rolling ball or falling stone could increase the orderliness of a system.Or indeed a tornado in a junkyard, again a creationist fallacy.We would be surprised to see such an event because we normally assume that order arises from the actions of agents, not inanimate objects. <...> Thus, as adults, we appreciate that one major division in the world of causal entities is between those that are generally capable of “reversing local entropy” and those that are not. Having set the stage, the authors deliver their crushing blow. Although previous work has established that adults, infants, and even nonhuman primates are often remarkably accurate at identifying appropriate causal agents, there also appear to be systematic ways in which children and adults are prone to agentic or teleological explanations. For example, 4-y-old children will report that lakes are “for swimming,” or when asked about the origins of animals and people, tend to endorse explanations that include an intentional creator. In addition, cross-cultural work finds striking commonalities in the prevalence of “intelligent design” arguments among children and adults.One explanation for these types of inferences is that, in our everyday experiences, ordered phenomena do tend to result only from other agents. The correlation is simply too strong and salient to ignore. Moreover, it is well known that adults and children often have a difficult time reasoning about randomness and its effects. Thus, in certain situations, we may overextend a causal framework that includes strong connections between agents and order to erroneously see some ordered patterns as intentionally created by an agent, even when the ordered pattern is actually created by an unintentional, inanimate process.(My emphasis.) So the common fallacy of imagining evolution as a directed process is probably a reflection of how we otherwise cognize about agents and their actions on the world. In turn this makes some of us imagine that there must be an agent behind it. Evolution appears as though it is generating order, or "reversing entropy", therefore it is impossible or it must be caused by an intelligent actor with set goals, depending of which particular flavor of creationism/intelligent design you find most appealing. It might be the reason why intelligent design is so tempting to some. The authors of this study have shown that these cognitive processes, that for the most part lead us to make correct assumptions but that can also cause us to "over-interpret" apparent order, arise very early in our development, before many other cognitive abilities. This can be used as an argument for two statements: That these cognitive processes are absolutely central to our way of relating to the world, which makes them difficult to shake. And that the type of arguments used by intelligent design proponents, who presumably are mostly adults, are based on pretty naïve assumptions made by children and not on the type of reasoning adults use. It also pinpoints something many evolutionary biologists have been saying for a while; that thinking correctly about evolution is actually quite difficult and counterintuitive. Newman, G., Keil, F., Kuhlmeier, V., & Wynn, K. (2010). Early understandings of the link between agents and order Proceedings of the National Academy of Sciences, 107 (40), 17140-17145 DOI: 10.1073/pnas.0914056107... Read more »

Newman, G., Keil, F., Kuhlmeier, V., & Wynn, K. (2010) Early understandings of the link between agents and order. Proceedings of the National Academy of Sciences, 107(40), 17140-17145. DOI: 10.1073/pnas.0914056107  

  • October 13, 2010
  • 02:31 PM
  • 1,005 views

Mutation Detection in Rare Disease by Pooled Sequencing

by Daniel Koboldt in Massgenomics

When it comes to massively parallel sequencing, few areas of human health stand to benefit as much as rare genetic diseases. Indeed, both whole-genome and exome sequencing strategies have identified disease-causing mutations in probands with Charcot-Marie Tooth disease, Miller syndrome, severe brain malformations, and a few other disorders. The Mito10K project took a different approach. [...]... Read more »

Calvo, S., Tucker, E., Compton, A., Kirby, D., Crawford, G., Burtt, N., Rivas, M., Guiducci, C., Bruno, D., Goldberger, O.... (2010) High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nature Genetics, 42(10), 851-858. DOI: 10.1038/ng.659  

Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA.... (2010) Exome sequencing identifies the cause of a mendelian disorder. Nature genetics, 42(1), 30-5. PMID: 19915526  

Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoğlu D, Tüysüz B, Cağlayan AO, Gökben S.... (2010) Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature, 467(7312), 207-10. PMID: 20729831  

Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA.... (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. The New England journal of medicine, 362(13), 1181-91. PMID: 20220177  

  • October 13, 2010
  • 02:23 PM
  • 900 views

BARP Goes the Weasel!

by Kristopher Hite in Tom Paine's Ghost

By Kristopher Hite



Looking back at discoveries of the past year the one that sticks out above all others to me was the identification of a single protein; a bacterial actin homologue dubbed BARP - Bacterial Actin Related Protein. The brilliance of this discovery comes from its directly contributing to our understanding of evolution, overturning decades of dogma, and providing a shiny new teaching tool.  The discovery was published in late 2009 as part of a massive sequencing project to fill in gaps of knowledge among bacterial and archael genomes.

With all the other sexy and more controversial stories about evolution - Ardi, Ida and so on, why do I pick this one? Aside from my biochemical inclination I thought this little piece of biological hardware deserved more exposure.  Though the paper was covered and lead author Jonathan Eisen interviewed for the nature podcast, it received relatively little coverage on the science blogs. Yes, the prolific science writer Carl Zimmer wrote a nice summary for the New York Times but the BARP bit is mentioned only briefly. I don't know if anyone realized what a great tool this discovery is to hammer even more nails in the coffin of the "irreducible complexity" argument for intelligent design. 



In January 2010 I had the pleasure to sit down and interview Eugenie Scott - executive director of the National Center for Science Education (NSCE).  As she explained the history of science education in the United States we came to an agreement on what one "take home" message should be for the average high school student - that all living things on earth share common ancestors, that all species have a common descent. This point may not seem earth-shattering to comprehend but I think many in America fail to realize the significance of this fact. The procession of science has uncovered an armory of teaching tools - fossilized trilobites, floating whale hip bones, and common DNA sequences. The more is known about the inner workings of the natural world the easier it should be for students to see and accept the facts. What then is the barrier to getting students to accept take-home messages like common descent? I would posit that fundamentalist opposition to evolution and the idea of the rapture have more than a little to do with it. Proponents of intelligent design often use a phrase coined by Lehigh University professor Michael Behe - irreducible complexity - in their defense of a necessary designer. This was a large part of Behe's arguments against teaching evolution as fact in the Kitzmiller vs. Dover, PA landmark court case.



Behe defines an irreducibly complex system as one "composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning." Brown University Biology Professor Ken Miller uses the analogy of a mouse trap to explain away irreducible complexity. Yes, all components of a mouse trap are necessary for overall function but each component can be have alternate uses.



In the logical chronology of evolution complexity emerges incrementally by the acquisition of functional structures that appear by chance and remain due to conferred advantage. Behe has tried over and over to use the molecular structure of the bacterial flagellum as an example of an irreducibly complex system.  In response Ken Miller did an excellent job explaining how the components of bacterial flagella could emerge incrementally.



So what IS actin and how does its showing up in a bacterial specimen add to the arsenal of teaching tools against irreducible complexity?



actin filament







As you move your cursor around this page your muscles are contracting and relaxing, your brain is sending signals along tiny electrified
strands called axons guiding these contractions. Among the myriad
things that make this possible is the little protein called actin. 
Deriving its name from the word "activating" actin enables muscular
motion, provides train tracks inside each cell for directional transportation of other tools, and gives shape to most cells in your body.  Like oddly
shaped legos these tiny building blocks bind to each other and form long
filaments that grow and shrink.  A mesh-work of actin filaments push on
the perimeter of each cell establishing shape.  Those long axons I
mentioned before are extensions of brain cells (neurons). During
development neurons send out these long extensions and it is the mesh-work of actin that leads the charge enabling all those millions of
electronic connections between brain and body to form. 



The
gene that codes for this little protein exists without much variation
in all eukaryotic organisms. Eukaryote means simply "true nucleus." The distinction is made because the more
ancient but still surviving bacteria do not have "true nuclei" they
are therefore dubbed prokaryotes. The moment at which the first
eukaryote appeared on earth marked the beginning of an explosion of diversity, and a
fundamental branch point in the phylogenetic tree of life.




(Haliangium ochraceum)


 Unlike the carefully crafted nuts and bolts you can pick up at the hardware store cellular machinery is not designed for a purpose, it just appears by duplication, mutation, or other spontaneous variations of genetic material.  If it works it is retained, if its merely eating up metabolic resources it usually goes extinct.  This represents an important variation on pure chance that the process of evolution carries with it.  Richard Dawkins has illustrated the power of evolving systems to accumulate positive variation in his classic "Weseal" thought experiment. Self-replicating systems have the ability to retain random variation in their code by copying themselves. When a variation carries a positive effect for the code carrier (organism) then that carrier is more likely to make more copies of that advantageous variation.  New variation is possible because there are usually redundant bits of cellular machinery.  This is exactly what we see in the case of BARP.

If you asked any professor of cell biology any time prior to a year ago "Do bacteria contain a gene for actin?" they would, without hesitation, say "of course not." It was understood that the gene for actin was one that separated eukaryote from prokaryote. Bacteria have an unrelated gene  - MreB - that has a scaffolding function. They don't need actin.   Now it is shown that the gene for actin showed up in  marine bacteria (specifically the one named Haliangium ochraceum)... Read more »

Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.... (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276), 1056-1060. DOI: 10.1038/nature08656  

  • October 13, 2010
  • 12:01 PM
  • 584 views

SVP Dispatch, Part 2: Did Sea Level Influence Dinosaur Diversity?

by Brian Switek in Dinosaur Tracking


Paleontologists are constantly reminding themselves of the incompleteness of the fossil record. What has been preserved is only a small fraction of all the organisms and environments that have ever existed. This makes detecting evolutionary patterns a bit of a challenge. In a presentation given at this year’s Society of Vertebrate Paleontology conference, Smithsonian paleontologist [...]... Read more »

  • October 13, 2010
  • 11:55 AM
  • 796 views

Defending the Sensible: Charles Darwin and the Anti-Vivisection Controversy

by Eric Michael Johnson in The Primate Diaries

The latest stop in the #PDEx tour is being hosted at The Dispersal of Darwin:According to the British Medical Journal it resembled a crucifixion. The dogs were strapped to boards, backs down, and with their legs cinched outwards. In the stifling August heat their heavy panting was made only more intense by a suffocating fear. The accused was described as wearing a white apron “that was afterwards covered with blood” as he approached one of the struggling animals. His mouth was tied shut but when the blade entered the thin, pink flesh of his inner thigh the animal’s cries of agony were too much to bear.Experienced medical men in attendance, including some of the nineteenth century’s top surgeons, were outraged and demanded that the animal’s torture cease. Thomas Joliffe Tufnell, President of the Royal College of Surgeons in Ireland, denounced the demonstration as a “cruel proceeding” and stormed to the operating table to cut the animal loose. Other physiologists objected to the interruption with one insisting, “That dog is insensible; he is not suffering anything.” But Tufnell held firm, “The dog is struggling hard to get free. I am a sportsman as well as a surgeon, and I will never see a dog bullied.” However, a vote was taken among the assembled members of the British Medical Association and the demonstration was allowed to continue.A tube was then forced into the conscious animal’s femoral artery, the white hair of his belly stained red as the arterial pressure caused blood to spurt from the incision. Into the tube the accused injected pure alcohol. The result, continued the Journal, “was an immediate struggle, which almost immediately subsided. The animal became dead drunk.”“Now, you see he’s insensible,” a physician snidely remarked to Tufnell.“Yes,” Tufnell replied, “and he’ll never be sensible again, for he will die.”Read the rest of the post here and stay tuned for the next entry in The Primate Diaries in Exile tour.Feller, D. (2009). Dog fight: Darwin as animal advocate in the antivivisection controversy of 1875 Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 40 (4), 265-271 DOI: 10.1016/j.shpsc.2009.09.004... Read more »

Feller, D. (2009) Dog fight: Darwin as animal advocate in the antivivisection controversy of 1875. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 40(4), 265-271. DOI: 10.1016/j.shpsc.2009.09.004  

  • October 13, 2010
  • 11:55 AM
  • 671 views

Defending the Sensible: Charles Darwin and the Anti-Vivisection Controversy

by Eric Michael Johnson in The Primate Diaries in Exile

The latest stop in the #PDEx tour is being hosted at The Dispersal of Darwin:According to the British Medical Journal it resembled a crucifixion. The dogs were strapped to boards, backs down, and with their legs cinched outwards. In the stifling August heat their heavy panting was made only more intense by a suffocating fear. The accused was described as wearing a white apron “that was afterwards covered with blood” as he approached one of the struggling animals. His mouth was tied shut but when the blade entered the thin, pink flesh of his inner thigh the animal’s cries of agony were too much to bear.Experienced medical men in attendance, including some of the nineteenth century’s top surgeons, were outraged and demanded that the animal’s torture cease. Thomas Joliffe Tufnell, President of the Royal College of Surgeons in Ireland, denounced the demonstration as a “cruel proceeding” and stormed to the operating table to cut the animal loose. Other physiologists objected to the interruption with one insisting, “That dog is insensible; he is not suffering anything.” But Tufnell held firm, “The dog is struggling hard to get free. I am a sportsman as well as a surgeon, and I will never see a dog bullied.” However, a vote was taken among the assembled members of the British Medical Association and the demonstration was allowed to continue.A tube was then forced into the conscious animal’s femoral artery, the white hair of his belly stained red as the arterial pressure caused blood to spurt from the incision. Into the tube the accused injected pure alcohol. The result, continued the Journal, “was an immediate struggle, which almost immediately subsided. The animal became dead drunk.”“Now, you see he’s insensible,” a physician snidely remarked to Tufnell.“Yes,” Tufnell replied, “and he’ll never be sensible again, for he will die.”Read the rest of the post here and stay tuned for the next entry in The Primate Diaries in Exile tour.Feller, D. (2009). Dog fight: Darwin as animal advocate in the antivivisection controversy of 1875 Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 40 (4), 265-271 DOI: 10.1016/j.shpsc.2009.09.004... Read more »

Feller, D. (2009) Dog fight: Darwin as animal advocate in the antivivisection controversy of 1875. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 40(4), 265-271. DOI: 10.1016/j.shpsc.2009.09.004  

  • October 13, 2010
  • 11:05 AM
  • 1,923 views

Seeking Authenticity in Facebook Profiles

by Krystal D'Costa in Anthropology in Practice


I was chatting with a friend who is in the process of job hunting the other day and he told me that he friended a recruiter on Facebook. Perplexed, I asked if he was concerned about the information the recruiter might see. "No," he said. "I'm not really the drunken reverie poster." He also does not use features such as lists to organize contacts and restrict access to parts of his profile.
This exchange suggests to me that the boundaries between online social networks are still in flux. So far, the general suggestion has been that users should use LinkedIn for professional contacts and keep Facebook for personal ones—or make use of the lists feature to set privacy settings accordingly. We've heard the horror stories about the times when friending a supervisor went astray (seriously, Google Facebook fired—there's even a group!), and we're learning that HR is increasingly reviewing the social media profiles of applicants before they're even invited for an interview. Sites like Facebook allow users to craft a personalized image of themselves—does this personalization suggest a more authentic self? And if so, does that make Facebook a more desirable point of contact for a more "complete" view of a person?
Researcher Soraya Mehdizadeh (2010) proposes that sites like Facebook and MySpace have contributed to the rise of narcissistic tendencies. As Facebook has surpassed MySpace in overall general use and has a wider base of potential contacts (e.g., recruiters and applicants, supervisors and employees), I'll focus this discussion on Facebook. In my opinion, it seems to be the more "serious" of the two—at least, it appears to be the more trustworthy for authentic representations, which we'll explore in bit. First, what does Mehdizadeh mean by narcissism online?
She define narcissists as individuals who seek superficial relationships with high status individuals who can contribute to public glory (2010: 358). Online social networking sites encourage these sorts of relationships:First, this setting offers a gateway for hundreds of shallow relationships (i.e., virtual friends), and emotionally detached communication (i.e., wall posts, comments). While these sites do indeed serve a communicative purpose among friends, colleagues, and family, other registered users can initiate requests to be friends, and one's social network often snowballs rapidly across institutions in this fashion (358).One way this sort of relationships is achieved is through the presentation of an attractive self—the user must reveal something that encourages the connection. this connection may be emotionally appealing (e.g., a shared history: attending the same high school or college) or physically appealing (e.g., an enticing photo, a pleasant demeanor). The latter seems particularly important once the user moves past first tier connections and begins to add connections from the second tier (i.e., friend of a friend) and beyond. According to Mehdizadeh, this opens the door for a showing of the "hoped for possible self," which "emphasizes realistic socially desirable identities an individual would like to establish given the right circumstances" (358).
Facebook is a "nonymous" online environment—it requires the user to reveal herself. Users have to enter their real names, for example, although an increasing number of users are slightly tweaking their names to make themselves unsearchable. But it also requires users to place themselves within a physical network, whether that be an academic circle or a geographic one. And while a small number of users choose not to have a photo, many have some sort of pictorial representation associated with their name. Frequently, this is a photograph although in some cases avatars or other icons may be used, however, the representation is true in that it represents the user in some way. That is to say, Jane Doe does not use Mary Smith's image as her own. Nonymous environments require a degree of truth. The personal nature of Facebook adds another layer to that sense of truth which distinguishes the network from the likes of LinkedIn. Users are not free to simple pretend to be someone they are not.
Mehdizadeh correctly states that users are actively engaged in constructing their identity in nonymous settings:While the nonymity of this environment places constraint on the freedom of the individual identity claims, this setting also enables users to control the information projected about themselves. In particular, users can select attractive photographs and write self descriptions that are self-promoting in an effort to project an enhanced sense of self. Furthermore, Facebook users can receive public feedback on profile features from other users, which can act as a positive regulator of narcissistic esteem (360).Though she views the interaction between users and their connections as confirming narcissistic behaviors, I want to propose that Facebook relationships also help vet the image projected by calling attention to anomalies. For example, if a user posts a photo showing themselves in a new, unexplained location, someone will usually ask where the user was and what he was doing at the time.
In this sort of setting, it may be possible to expand your network to include business and other professional contacts. In this setting, would a drunken reverie poster get a pass because it would seem out of character? It may mean a more open social web.

Cited:Mehdizadeh S (2010). Self-presentation 2.0: narcissism and self-esteem on Facebook. Cyberpsychology, behavior and social networking, 13 (4), 357-64 PMID: 20712493
... Read more »

Mehdizadeh S. (2010) Self-presentation 2.0: narcissism and self-esteem on Facebook. Cyberpsychology, behavior and social networking, 13(4), 357-64. PMID: 20712493  

  • October 13, 2010
  • 11:05 AM
  • 1,477 views

Pessimistic Pooches? Depressed Doggies? Not So Fast!

by Jason Goldman in The Thoughtful Animal



Does Fido see the cup as half full? Is your dog pessimistic? Last time we saw headlines like these they were about a certain barnyard animal. Remember "Pampered pigs 'feel optimistic'"? I didn't like it then, and I don't like it now.

Roughly half of the population of dogs in the UK are likely to - at some point in their lives - exhibit "undesirable separation-related behavior (SRB)." These are things that sometimes happen when left alone, like barking, chewing up or otherwise destroying objects, and urinating (or worse!) inside the house. While some owners view these behaviors as fine and normative, and while some will seek out professional guidance, many are motivated to give up the dog. In this paper, veterinary scientist Michael Mendl and colleagues were interested in what makes people surrender their pet dogs for adoption (or, as they call it across the pond, "re-homing.") They wondered: do the dogs with the most SRB have some kind of negative underlying affect? Are they grumpy? Can dogs be, essentially, depressed?
Read the rest of this post... | Read the comments on this post...... Read more »

Mendl, M., Brooks, J., Basse, C., Burman, O., Paul, E., Blackwell, E., & Casey, R. (2010) Dogs showing separation-related behaviour exhibit a 'pessimistic' cognitive bias. Current Biology, 20(19). info:/10.1016/j.cub.2010.08.030

  • October 13, 2010
  • 10:57 AM
  • 465 views

Bad Assessment

by Journal Watch Online in Journal Watch Online

Need another reason to loathe invasive species? How about plummeting property values? An invading aquatic weed that creates impenetrable mats of vegetation appears to be dinging lakefront property values in Vermont, researchers say. The slump highlights the costs of exotic invaders, and has implications for communities that depend on property taxes to fund schools, fire […] Read More »... Read more »

  • October 13, 2010
  • 10:35 AM
  • 1,048 views

Universal influenza vaccines

by Vincent Racaniello in virology blog

The need to re-formulate the influenza virus vaccine in response to viral antigenic drift and shift makes for complex logistics of vaccine production and administration. Surveillance programs must be conducted each year to identify strains that are likely to predominate and cause disease. Wouldn’t it be simpler if a single vaccine could be developed that [...]... Read more »

  • October 13, 2010
  • 09:28 AM
  • 832 views

Supply Chain Risk Management Dissertations (No. 3)

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management


This is the third contribution to my series on doctoral dissertations on Supply Chain Risk Management. An immense effort and dedication is spent on these works only to find the results hidden in the libraries. So the goal is raise interest in the research of my peers.

Author / Topic
This dissertation was written by Stephanie Freiwald in 2005 as her doctoral thesis at the University of Bochum. It was published by Peter Lang, Frankfurt a.M. and can be ordered here from amazon.de or your local library. The title can be translated as:
Supply Chain Design - Robust Planning with differentiated Supplier Selection Continue reading "Supply Chain Risk Management Dissertations (No. 3)"
... Read more »

Stephanie Freiwald. (2005) Supply Chain Design - Robuste Planung mit differenzierter Auswahl der Zulieferer. Peter Lang, Frankfurt a.M., Dissertation. info:/

  • October 13, 2010
  • 09:28 AM
  • 809 views

Supply Chain Risk Management Dissertations (Supply Chain Design - Robust Planning with differentiated Supplier Selection)

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management


This is the third contribution to my series on doctoral dissertations on Supply Chain Risk Management. An immense effort and dedication is spent on these works only to find the results hidden in the libraries. So the goal is raise interest in the research of my peers.

Author / Topic
This dissertation was written by Stephanie Freiwald in 2005 as her doctoral thesis at the University of Bochum. It was published by Peter Lang, Frankfurt a.M. and can be ordered here from amazon.de or your local library. The title can be translated as:
Supply Chain Design - Robust Planning with differentiated Supplier Selection Continue reading "Supply Chain Risk Management Dissertations (Supply Chain Design - Robust Planning with differentiated Supplier Selection)"
... Read more »

Stephanie Freiwald. (2005) Supply Chain Design - Robuste Planung mit differenzierter Auswahl der Zulieferer. Peter Lang, Frankfurt a.M., Dissertation. info:/

  • October 13, 2010
  • 09:07 AM
  • 1,292 views

Autism, vaccines, and thimerasol: A review of the latest Pediatrics study.

by Nestor Lopez-Duran PhD in Child-Psych

By now most of you are likely familiar with the background on the controversy regarding the proposed link between vaccines and autism. But briefly, there are a significant number of parents who believe that vaccines cause, or at least play a role in, autism and a growing research library of studies that find no link [...]... Read more »

Price, C., Thompson, W., Goodson, B., Weintraub, E., Croen, L., Hinrichsen, V., Marcy, M., Robertson, A., Eriksen, E., Lewis, E.... (2010) Prenatal and Infant Exposure to Thimerosal From Vaccines and Immunoglobulins and Risk of Autism. PEDIATRICS, 126(4), 656-664. DOI: 10.1542/peds.2010-0309  

  • October 13, 2010
  • 09:05 AM
  • 1,196 views

Tip of the Week: NCBI Epigenomics “Beyond the Genome”

by Mary in OpenHelix


We spend a lot of time talking about sequence data: where to find it, how to analyze it, etc. But increasingly we are seeing more and more data that comes from epigenomics projects. Recently a tweet from NCBI got me to look at their Epigenetics site again.  http://www.ncbi.nlm.nih.gov/epigenomics
Their definition of epigenetics is:
What is Epigenetics?
Interest in epigenetics has exploded in recent years, but the central question it aims to answer has been with us for decades: how do the many cell types of the body maintain drastically different gene expression patterns while sharing exactly the same DNA?
Epigenetics refers to a gene activity state that may be stable over long periods of time, persist through many cell divisions, or even be inherited through several generations, all without any change to the primary DNA sequence (Roloff and Nuber 2005, Ng and Gurdon 2008, Probst, et al. 2009).
This is a nice site that offers a lot of helpful background, project information about the NIH Roadmap for Epigenomics, and then of course access to the data itself.  They have separate guidance on the types of data that you will find in here: About DNA Methylation, About Histone Modification, and About Chromatin Structure. So if you are ready to go “Beyond the Genome” as their tag line indicates, you can learn about the data types and find the data too.
This tip of the week will take a look at access to the data. I’ll be taking a look at what happens when you use the Sample Browser as a starting point to see some of the data via browsing. You can do more complex and custom queries with the Advanced Query form, which looks like other query building tools at NCBI. I won’t have time to cover that, but I wanted you to know it was available.
For my example I just chose the top sample that was in the list at the time I did this tip. And it was fortuitous for a couple of reasons.  First it was exactly the kind of paper that I was talking about in my recent post (The data isn’t in the papers anymore, you know.) This paper (referenced below) has a huge volume of data. It looks at 39 types of histone modifications, and looks at them genome wide.  There’s no way to publish all that as figures in this paper.  There are summary figures, but not individual ones for that data collection. You’d have to visualize this yourself elsewhere.  The second reason it was cool was because the data perfectly validates some of the data I’ve been using to develop the ENCODE project tutorial we’ve just created with the UCSC ENCODE team.
Anyway–check out the NCBI Epigenomics resource for a great way to visualize data on this topic. Data that you will not find in the papers.
Quick links:
NCBI Epigenomics (the tip site): http://www.ncbi.nlm.nih.gov/epigenomics
Roadmap: http://www.roadmapepigenomics.org/
Epigenome Browser: http://www.epigenomebrowser.org/
ENCODE: http://encodeproject.org/
By the way: I also asked the hive mind at BioStar what tools they are using for epigenomics, and you can go and see that question over there. People told me about the Epigenome Atlas and EPIGRAPH. And as I was researching this tip I came across a Roadmap Epigenomics site, that offers a link to a browser. It’s a UCSC Genome Browser framework focused on this kind of data: Epigenome Browser–but that’s a different installation than the main UCSC Genome Browser that I illustrate from this tip.
Reference for data used and shown in the tip:
Wang, Z., Zang, C., Rosenfeld, J., Schones, D., Barski, A., Cuddapah, S., Cui, K., Roh, T., Peng, W., Zhang, M., & Zhao, K. (2008). Combinatorial patterns of histone acetylations and methylations in the human genome Nature Genetics, 40 (7), 897-903 DOI: 10.1038/ng.154
Currently there’s isn’t a reference for NCBI Epigenomics. I contacted the Help Desk to be sure, and they told me it’s been submitted but isn’t out yet. I’ll update this when that reference becomes available.



... Read more »

Wang, Z., Zang, C., Rosenfeld, J., Schones, D., Barski, A., Cuddapah, S., Cui, K., Roh, T., Peng, W., Zhang, M.... (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics, 40(7), 897-903. DOI: 10.1038/ng.154  

  • October 13, 2010
  • 09:04 AM
  • 476 views

Sensation Seeking Could Be in Your Genes

by APS Daily Observations in Daily Observations

Do you enjoy rock climbing, sky diving, and extreme sports? If so, you are likely a “sensation seeker,” a person who has the urge to do exciting, possibly dangerous things. ... Read more »

Derringer, J., Krueger, R.F., Dick, D.M., Saccone, .S, Grucza, R.A., & Agrawal, A. (2010) Predicting sensation seeking from dopamine genes: a candidate-system approach. Psychological science : a journal of the Association for Psychological Science/ APS. PMID: 20732903  

  • October 13, 2010
  • 09:00 AM
  • 647 views

Blog: The Spider Sexual Battlefield

by Torah Kachur, Rheanna Sand and Brit Trogen in Science in Seconds


Generally, sex is a risk free pastime of many people - we've got the pill to prevent pregnancy and condoms to prevent disease.  And, we don't need to worry about decapitation at the end.

 

Not true for a male orb spider.  If the woman's thirst for sex isn't satisfied, she satisfies her belly by eating him.  Talk about sex wars.

 

Mmmmmm.... previous sex partners are yummy

         

 

The cannibalistic behaviour of the female orb spider seems like the ultimate price to pay if you aren't good in the sack.  But, the research suggests otherwise: male spiders that can copulate for longer are actually the ones that get sacrificed.  The 'premie' spiders can have sex, deposit sperm and take off before she gets annoyed.  So it's the ones that can last that become lunch.

 

The reasoning is simple "Females should always cannibalize a male".  That is probably the wisest thing ever said in a piece of scientific literature.  What it really means is that it is advantageous for a female to eat mates because it provides a source of food and therefore improves the fecundity of the female by ensuring she is nice and well fed.  He could also just cook for once, but researchers haven't explored that yet.

 

New research published this week in Biology Letters suggests that the degree of relatedness also influences mating time and whether he becomes the next meal.  In an experiment akin to the next MMA fighting championships or cock-fighting, researchers got to put a female Argiope spider with either a sibling or non-sibling males.  And then they got to watch!

 

 

Did he survive?  Did he copulate?  Who won?

 

Winning is maybe in the eye of the beholder on this one.  When females mated with their brothers, the brothers were obviously disgusted at the prospect and had reduced mating time which allowed them to escape sexual cannibalism.  While unrelated males were a bit more enthusiastic and mated longer....resulting in their ultimate demise.  The researchers concluded that spider-sex-fighting will be the next wave of online betting matches, and that the brothers survival allowed him to go off and find a more appropriate mate.

 

Sexual cannibalism is not common in nature, resulting in comments from great evolutionary biologists like Stephen Jay Gould to claim that it's importance is overestimated.  However, it's pretty cool and it is sure to make females of many species a little bit jealous. 

 

"Oh...... hi honey.. love you"

 

Welke, K., & Schneider, J. (2010). Males of the orb-web spider Argiope bruennichi sacrifice themselves to unrelated females Biology Letters, 6 (5), 585-588 DOI: 10.1098/rsbl.2010.0214
... Read more »

  • October 13, 2010
  • 08:16 AM
  • 618 views

Cannabinoids in Huntington's Disease

by Neuroskeptic in Neuroskeptic

Two recent papers have provided strong evidence that the brain's endocannabinoid system is dysfunctional in Huntington's Disease, paving the way to possible new treatments.Huntington's Disease is a genetic neurological disorder. Symptoms generally appear around age 40, and progress gradually from subtle movement abnormalities to dementia and complete loss of motor control. It's incurable, although medication can mask some of the symptoms. Singer Woodie Guthrie is perhaps the disease's best known victim: he ended his days in a mental institution.The biology of Huntington's is only partially understood. It's caused by mutations in the huntingtin gene, which lead to the build-up of damaging proteins in brain cells, especially in the striatum. But exactly how this produces symptoms is unclear.The two new papers show that cannabinoids play an important role. First off, Van Laere et al used PET imaging to measure levels of CB1 receptors in the brain of patients in various stages of Huntington's. CB1 is the main cannabinoid receptor in the brain; it responds to natural endocannabinoid neurotransmitters, and also to THC, the active ingredient in marijuana.They found serious reductions in all areas of the brain compared to healthy people, and interestingly, the loss of CB1 receptors occurred early in the course of the disease:That was an important finding, but it didn't prove that CB1 loss was causing any problems: it might have just been a side-effect of the disease. Now another study using animals has shown that it's not: Blazquez et al. They studied mice with the same mutation that causes Huntington's in humans. These unfortunate rodents develop Huntington's, unsurprisingly.They found that Huntington's mice who also had a mutation eliminating the CB1 receptor suffered more severe symptoms, which appeared earlier, and progressed faster. This suggests that CB1 plays a neuroprotective role, which is consistent with lots of earlier studies in other disorders.If so, drugs that activate CB1 - like THC - might be able to slow down the progression of the disease, and indeed it did: Huntington's mice given THC injections stayed healthier for longer, although they eventually succumbed to the disease. Further experiments showed that mutant huntingtin switches off expression of the CB1 receptor gene, explaining the loss of CB1.This graph shows performance on the RotaRod test of co-ordination: mice with Huntington's (R6/2) got worse and worse starting at 6 weeks of age (white bars), but THC slowed down the decline (black bars). The story was similar for other symptoms, and for the neural damage seen in the disease.They conclude that:Altogether, these results support the notion that downregulation of type 1 cannabinoid receptors is a key pathogenic event in Huntington’s disease, and suggest that activation of these receptors in patients with Huntington’s disease may attenuate disease progression.Now, this doesn't mean people with Huntington's should be heading out to buy Bob Marley posters and bongs just yet. For one thing, Huntington's disease often causes psychiatric symptoms, including depression and psychosis. Cannabis use has been linked to psychosis fairly convincingly, so marijuana might make those symptoms worse.Still, it's very promising. In particular, it will be interesting to try out next-generation endocannabinoid boosting drugs, such as FAAH inhibitors, which block the breakdown of anandamide, one of the most important endocannabinoids.In animals FAAH inhibitors have pain relieving, anti-anxiety, and other beneficial effects, but they don't cause the same behavioural disruptions that THC does. This suggests that they wouldn't get people high, either, but there's no published data on what they do in humans yet...Van Laere K, et al. (2010). Widespread decrease of type 1 cannabinoid receptor availability in Huntington disease in vivo. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 51 (9), 1413-7 PMID: 20720046Blázquez C, et al. (2010). Loss of striatal type 1 cannabinoid receptors is a key pathogenic factor in Huntington's disease. Brain : a journal of neurology PMID: 20929960... Read more »

Van Laere K, Casteels C, Dhollander I, Goffin K, Grachev I, Bormans G, & Vandenberghe W. (2010) Widespread decrease of type 1 cannabinoid receptor availability in Huntington disease in vivo. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 51(9), 1413-7. PMID: 20720046  

Blázquez C, Chiarlone A, Sagredo O, Aguado T, Pazos MR, Resel E, Palazuelos J, Julien B, Salazar M, Börner C.... (2010) Loss of striatal type 1 cannabinoid receptors is a key pathogenic factor in Huntington's disease. Brain : a journal of neurology. PMID: 20929960  

  • October 13, 2010
  • 08:00 AM
  • 1,534 views

Cognitive Behavioural Therapy for Attention Deficit Disorder

by Arya M. Sharma in Dr. Sharma's Obesity Notes

Regular readers will recall that almost 30% of adults with severe obesity may have signs of attention hyperactivity deficit disorder (ADHD) and, when present, this can be a major barrier to weight management.
Thus, all patient in our obesity clinic are routinely screened for ADHD and often treating this condition is the first step to successful [...]... Read more »

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