Biology posts

August 16, 2009
03:12 AM
787 views

Of Twinkling Nanostars and the Possible Application of Stroboscopes in Biological Imaging

by Amiya in Physiology physics woven fine

Imagine a strong crowd, as you see in a Manchester United versus Liverpool football match and you wished to concentrate on a particular person. How would you do it? Make him wear a fluorescent shirt and dye his hair (don’t do it in the middle of the crowd, I can’t guarantee your safety).Purdue University researchers have been successful in focusing at the cell of interest among a background of equally noisy and boisterous biomolecules and other metabolically active cells. Currently, researchers use immunological techniques to create an antibody to a molecule and then visualize the ‘molecule of interest’ by tagging the antibody to a radioisotope or a fluorescent dye; and flow cytometry can sort out different types of cells.The Purdue University team used gold coated nanoparticles with an iron oxide core that was impregnated in the cell they wished to see. They then subjected the specimen to a periodically changing magnetic field. The superparamagnetic cores (superparamagnetic nanoparticles have no net magnetization, but an external magnetic field can magnetize them) responded by rotating as the magnetic field rotated around them. The rotation could be seen in the ‘near infra-red’ light spectrum, as the incident light bounced off (scattered) the specially designed arms of the gold nanostar as it revolved. The rate (rpm) of this gyromagnetic (gyros means to rotate) twinkling could be externally controlled by varying the rate of the externally applied field. You now could identify the cell by its characteristic ‘twinkling’ (lighthouse type) effect.I am tempted to go beyond what’s been achieved so far. Here I go. I guess you are all familiar what happens to the rotating ceiling fan blades when you turn on a fluorescent lamp. Don’t you see a momentary snapshot of the three blades (some have 4)? That’s what where stroboscope comes in. It consists of a Xenon lamp (ordinary fluorescent lamps could do, but incandescent lamps won’t work as the glowing filament takes time to extinguish) flashing at a controllable rate. The electronic circuitry may be had here.Suppose that the fan is revolving at 1200 RPM and it is not changing. Set your stroboscope to flash at this rate. You’ll ‘see’ that the fan blades are absolutely not moving, which is certainly not true! But be there any mechanical defect in the fan, it will stand out as the centrifugal force widens it (provided that the fault is more or less tangential to the axis of rotation). Here also we are looking at our object of interest, aren’t we?Now lets look what implication it might have in biological imaging. We now know that the gamma subunit of mitochondrial F type ATP Synthase ‘actually’ rotates when it is synthesizing ATP (reverse rotation occurs when ATP is hydrolyzed). There are other locomotive units within the cell as well. They comprise of actin and myosin based molecular motors. Could we study them using an externally adjustable stroboscope? The optical (electromagnetic) signals so obtained may then be similarly broken down into simpler trigonometric (sine and cosine) functions by Fourier analysis (Fourier transform) as was done in the ‘twinkling nanostars’ experiment. At least, we expect to get rid of some 'noise' and some good still photos. But if we wanted better resolution and used higher frequency (electromagnetic) for it, some extraneous error will be introduced. It's a trade-off!Last modified: neverReference: hyper-links, unless specifically mentionedPrinciples of Biochemistry, Lehninger, 4th edhttp://en.wikipedia.org/wiki/ATP_synthaseWei, Q., Song, H., Leonov, A., Hale, J., Oh, D., Ong, Q., Ritchie, K., & Wei, A. (2009). Gyromagnetic Imaging: Dynamic Optical Contrast Using Gold Nanostars with Magnetic Cores Journal of the American Chemical Society, 131 (28), 9728-9734 DOI: 10.1021/ja901562j... Read more »

Wei, Q., Song, H., Leonov, A., Hale, J., Oh, D., Ong, Q., Ritchie, K., & Wei, A. (2009) Gyromagnetic Imaging: Dynamic Optical Contrast Using Gold Nanostars with Magnetic Cores. Journal of the American Chemical Society, 131(28), 9728-9734. DOI: 10.1021/ja901562j

August 15, 2009
02:31 PM
1,007 views

PopABC: a program to infer historical demographic parameters

by Thomas Mailund in Mailund on the Internet

Just saw this paper in Bioinformatics today:
PopABC: A program to infer historical demographics parameters
Lopes, Balding and Beaumont
Abstract
Summary: PopABC is a computer package for inferring the pattern of demographic divergence of closely related populations and species. The software performs coalescent simulation in the framework of approximate Bayesian computation (ABC). PopABC can also be used to perform [...]... Read more »

Lopes, J., Balding, D., & Beaumont, M. (2009) PopABC: a program to infer historical demographic parameters. Bioinformatics. DOI: 10.1093/bioinformatics/btp487

August 15, 2009
07:36 AM
1,924 views

Unconscious Cognition 1-Simple Dissociation

by Varun in Wissenschaft

Attempts to demonstrate unconscious processing of visual stimuli are very old and riddled in controversies, but the controversy does not so much concern the existence of unconscious processing (most researchers seem to be convinced of this), but rather the question of how to demonstrate unconscious processing in a given experiment. If one needs to demonstrate it, one has to make sure that a critical stimulus was completely outside of awareness (the so called zero-awareness criterion). Schmidt (2007) poposes two lines of attack for establishing unconscious processing beyond the zero-awareness criterion. The paper deals with different types of dissociation between measures of awareness and measures of processing.Simple DissociationsTo demonstrate that a critical stimulus was processed unconsciously, one usually produces some dissociation between different behavioral measures of performance. This is done by comparing two measures obtained from different tasks. One measure (called the direct measure, D) signals the observer's awareness of a critical stimulus. For example, consider a visual perception experiment, where the task is to detect the offset of a vernier (a vernier is simply a set of two vertical lines, one below the other, where the lower line can be offset either to the right or left of the upper line). However, before the vernier is shown (let's say for 25 msec), a prime is flashed for a short period of time (say 15 msec). This prime could be, for example, arrows pointing to the right or left. A forced-choice prime discrimination task ("Was the arrow to the right or left" ) would measure if the observer was aware of the stimulus, and hence would comprise the direct measure. The second measure (called the indirect measure, I) would indicate that the primes themselves are not consciously detected, but they are involved in a priming effect, and hence affect the reaction times of responding to whether the target vernier is offset to the right or left. For example, if the prime and vernier are both congruent (i.e. the arrow points to the right and the vernier is also offset to the right) and if the subject cannot consciously detect the direction of the prime but the reaction times during the congruent cases are always shorter than the reaction times during the incongruent cases (prime pointing to the right but vernier offset to the left), then this would comprise the indirect measure.Schmidt and Vorberg (2006) examined the assumptions required by the zero-awareness criterion and other approaches. They start by assuming that the direct and indirect measures may depend on two sources of information labeled conscious (c)and unconscious (u). In other words, D = D(c,u)... Read more »

Schmidt, T. (2007) Measuring unconscious cognition: Beyond the zero-awareness criterion. Advances in Cognitive Psychology, 3(1), 275-287. DOI: 10.2478/v10053-008-0030-3

August 14, 2009
11:43 PM
729 views

On Photoaging of Skin

by Reason in Fight Aging!

The latest issue of the Journal of Investigative Dematology Symposium Proceedings includes a set of papers theorizing on the mechanisms by which exposure to sunlight accelerates the characteristic ways in which skin changes with age. In many ways its a good illustration of just how far there is to go in pulling together present knowledge of aging biochemistry into theories that are both unifying and specific: the researchers here argue on mechanisms from a number of quite different and distinct viewpoints. Some of the papers are presently free to read, so take a look while that lasts. Telomere-Mediated Effects on Melanogenesis and Skin Aging UV-induced melanogenesis (tanning) and "premature aging" or photoaging result in large part from DNA damage. This article reviews data tying both phenomena to telomere-based DNA damage signaling and develops a conceptual framework in which both responses may be understood as cancer-avoidance protective mechanisms. Role of Mitochondria in Photoaging of Human Skin: The Defective Powerhouse Model The exact pathogenesis of photoaging of the skin is not yet known. Earlier, a number of molecular pathways explaining one or more characteristics of photoaged skin have been described, but a unifying mechanistic concept is still missing. Here we propose the...... Read more »

Krutmann, J., & Schroeder, P. (2009) Role of Mitochondria in Photoaging of Human Skin: The Defective Powerhouse Model. Journal of Investigative Dermatology Symposium Proceedings, 14(1), 44-49. DOI: 10.1038/jidsymp.2009.1

August 14, 2009
07:05 PM
1,065 views

Did knuckle-walking evolve twice?

by zinjanthropus in A Primate of Modern Aspect

Knuckle-walking is a pretty special mode of locomotion. Amongst primates, only the African apes do it habitually, and anteaters are the only other mammal who does it. It would seem, then, that the most parsimonious explanation for such a specialized form of locomotion would be that the African apes all share a common [...]... Read more »

Kivell, T., & Schmitt, D. (2009) Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0901280106

RENDALL, D., & DIFIORE, A. (2007) Homoplasy, homology, and the perceived special status of behavior in evolution. Journal of Human Evolution, 52(5), 504-521. DOI: 10.1016/j.jhevol.2006.11.014

Dainton, M., & Macho, G. (1999) Did knuckle walking evolve twice?. Journal of Human Evolution, 36(2), 171-194. DOI: 10.1006/jhev.1998.0265

August 14, 2009
04:54 PM
514 views

The bat and the moth, and the ant and the butterfly

by Sunil in Balancing life

What better way to resume blogging after a break than with a couple of fascinating stories from the natural world, about predator and prey, defensive arms races and survival cues?Bats invoke a variety of emotions from people, ranging from disgust and (unfounded) fear to “they’re cool”. At least the Batman sometimes did some good in helping kids get rid of their fear or paranoia of bats. But while bats might look like silly rats with wings, they are indeed supremely efficient hunting machines. While some bats eat fruit, a majority of them hunt flying insects in the dark, and eat vast quantities of moths, locusts, flies, mosquitoes and any other bug that flies. In order to do this efficiently in the dark, they have a fabulously developed system of “echolocation”, a better sonar system than most battleships. This is great for the bat, and allows them to locate flying insects with pin-point accuracy. But what about the insects? Obviously, they have a pressing need to survive and need to escape bats. Therefore many insects have evolved remarkable ways to evade their hunters.Some insects have developed evasive flying maneuvers, others just taste bad and the bats learn to avoid them, while others yet have evolved a neuronal auditory system that can detect the bat sonar frequency and allow them to escape. So there is this constant fight between bat and insect in evolving better sonar or ways to evade it. But, taking a cue from standard defense technology, do any insects actually jam or disrupt bat sonar? It appears that a certain species of tiger moth can do precisely this.The tiger moth is a perfectly edible snack for the echolocating bat. But some tiger moths emit specific ultrasonic clicks in the presence of attacking bats. These clicks could potentially serve as a warning sound, or perhaps be used to startle bats (thus giving the moth time to escape), or perhaps affect the bat sonar. A group of researchers decided to investigate this phenomenon in a tiger moth species called B. trigona, and used an ingenious test to determine what role these ultrasonic clicks were playing. They pitted moths against bats in a closed chamber and precisely observed what the bats did. If the click was a warning sound (for say a poisonous or distasteful insect), the bat would at first attack the insect, but drop it or spit it out, and then learn to avoid the insect. If it was a startling sound, the bat would at first be startled, but would learn to avoid it. If the click was indeed a sonar jamming sound, the bats would continue to be confused by the clicking over time. In their experiments, the researchers used a bunch of juvenile or adult bats and presented them with either the clicking moths, or other moths of the same size that didn’t click, or just a different type of edible, non-clicking moth. What they found was fascinating. The bats indeed did eat the clicking moths. However, the bats were 400% more likely to eat a non-clicking moth than the clicking B. trigona. But what if these clicking moths just tasted worse? To make sure that this wasn’t the case, the researchers disrupted the clicking mechanisms of these moths, and then let them out with the bats. This time, the bats hunted them down as well as the other non-clicking moths. It became very apparent that the moths used the clicking sound in order to disrupt the bat sonar.As far as the moths go, the evolutionary race for survival is pretty simple. Out in the wild, they don’t need to develop a fantastic sonar jamming device to completely disrupt the bat sonar. All they need to do to get a huge survival edge is to be able to disrupt the bat echolocator just a little bit (but more than any other insect around), so that they can get away and the other insect gets eaten. To do this, they only needed to develop a simple tymbal structure, and this structure is now widespread amongst some tiger moth species. And by doing that, they haven’t evolved to escape all bats, but have just enough to gain that much needed survival edge over other bat prey.(Original reference: Corcoran, A., Barber, J., & Conner, W. (2009). Tiger Moth Jams Bat Sonar Science, 325 (5938), 325-327 DOI: 10.1126/science.1174096)**********This next story is just as fascinating, though more incomplete and raising more questions. Plants obviously are under constant risk of being eaten by some herbivore or the other. So some plants have a very effective defense strategy. They secrete sugars onto their stem or leaves so that they can attract ants. These ants then stay on the plant, and serve as a nice, natural defense against other plant eating insects or animals. Butterflies, on the other hand, are insects that plants share a love-hate relationship with. On one hand, the butterfly pollinates the flowers, allowing the transfer of genetic material from one plant to the other, thus enabling reproduction. On the other hand, butterflies lay their eggs on plant leaves and the caterpillars then devour the leaves. And for the butterfly itself, the last place it wants to lay eggs on is a leaf full of predatory ants which would eat up the eggs or caterpillars.But can a butterfly, a mere non-thinking insect, know not to lay eggs on leaves with ants? The answer, surprisingly, is yes. In this little paper in The American Naturalist, some researchers devised ingenious experiments to see if butterflies would distinguish between leaves that had ants, or didn’t have ants on them, in order to decide which leaves to lay their eggs on. In their experiment, the researchers took dead specimens of three species of ants, two of which were predatory (and would eat the eggs/caterpillars) and one of which was a bug of a similar size and shape, but a harmless herbivores. Then, they pinned these ants on different leaves, and let the butterflies decide where they laid their eggs. What they saw was surprising, to say the least. The butterflies not only avoided the leaves with the predatory ants, but also didn’t mind laying eggs on the leaves which had the harmless bug on them. So it wasn’t as if the butterfly was just laying eggs on leaves with no ants on them, but actually seemed to know that laying eggs on leaves with the herbivorous bug wouldn’t hurt their eggs and so ignored the innocuous bug. Clearly, it appears that butterflies can use visual clues and decide where to lay their eggs.What is particularly fascinating to me though is not the fact that butterflies can distinguish between predatory and non-predatory ants, but the fact that they know how to do so without any prior “training”. After all, butterflies are far away from animals or birds which care for their young and potentially teach them about predators or food. Butterflies aren’t even social insects, to have groups to collectively “learn” from. So what is the internal wiring they are born with that tells them some ants are dangerous, while others aren’t? What neuronal and signaling pathways do visual cues of predatory ants activate, while those of innocuous bugs do not? And how does that happen? Do other things, like smell, also influence the butterflies? There is a whole world of questions out there, waiting to be answered. Original reference: Sendoya, S., Freitas, A., & Oliveira, P. (2009). Egg‐Laying Butterflies Distinguish Predaceous Ants by Sight The American Naturalist, 174 (1), 134-140 DOI: 10.1086/599302)
... Read more »

Corcoran, A., Barber, J., & Conner, W. (2009) Tiger Moth Jams Bat Sonar. Science, 325(5938), 325-327. DOI: 10.1126/science.1174096

Sendoya, S., Freitas, A., & Oliveira, P. (2009) Egg‐Laying Butterflies Distinguish Predaceous Ants by Sight. The American Naturalist, 174(1), 134-140. DOI: 10.1086/599302

August 14, 2009
10:45 AM
822 views

Making sense of changing risk predictions from personal genomics

by dgmacarthur in Genetic Future

Mihaescu, R., van Hoek, M., Sijbrands, E., Uitterlinden, A., Witteman, J., Hofman, A., van Duijn, C., & Janssens, A. (2009). Evaluation of risk prediction updates from commercial genome-wide scans Genetics in Medicine, 11 (8), 588-594 DOI: 10.1097/GIM.0b013e3181b13a4fCaroline Wright from the Public Health Genomics Foundation has a concise post describing the results from a recent paper in Genetic Medicine. The paper evaluates the probability that personal genomics customers will find that their predicted risk of a common disease changes significantly over time as their genetic data are updated, using data on known type 2 diabetes risk variants as a case study. Read the rest of this post... | Read the comments on this post...

... Read more »

Mihaescu, R., van Hoek, M., Sijbrands, E., Uitterlinden, A., Witteman, J., Hofman, A., van Duijn, C., & Janssens, A. (2009) Evaluation of risk prediction updates from commercial genome-wide scans. Genetics in Medicine, 11(8), 588-594. DOI: 10.1097/GIM.0b013e3181b13a4f

August 14, 2009
08:41 AM
1,487 views

Bipedalism: From the ground-up or trees-down?

by Laelaps in Laelaps

A male western gorilla (Gorilla gorilla), photographed at the Bronx Zoo.

The origin of human bipedalism has long been a hot topic among paleoanthropologists. At the very least it is seen as something of a marker for the emergence of the first hominin, yet it remains unclear whether the earliest hominins evolved from a terrestrial, knuckle-walking ancestor or a more arboreal ape. A common interpretation is that since our closest living relatives, gorillas and chimpanzees, are both knuckle-walkers then the first hominins, too, evolved from a knuckle-walking ancestor. As Tracy Kivell and Daniel Schmitt explain in a new PNAS paper, though, this idea may overlook subtle differences between chimpanzees and gorillas that may help us understand the evolution of the earliest hominins.

Gorillas are physically larger than chimpanzees, so it might be expected that they would have more rigid wrists that would help stabilize them as they walked around on their knuckles. This is not what Kivell and Schmitt found. Not only did gorillas have a much greater range of wrist motion than chimpanzees, but it was the chimpanzees that had adaptations in their wrists to increase stability. Despite being more terrestrial and knuckle-walking on the ground more often gorillas actually showed fewer "classic" knuckle-walking adaptations in their wrist bones than chimpanzees did! Read the rest of this post... | Read the comments on this post...... Read more »

Kivell TL, & Schmitt D. (2009) Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor. Proceedings of the National Academy of Sciences of the United States of America. PMID: 19667206

August 14, 2009
08:40 AM
836 views

How does your brain work out what’s alive?

by Jacob Aron in Just A Theory

Picture a dog playing with a ball. The dog is alive, and the ball is inanimate. Obvious stuff, but how do we know? You might think our brains use visual cues to sort the living from the non-living, but research published in the journal Neuron this week proves it’s a little more complicated.
A team of [...]... Read more »

Mahon, B., Anzellotti, S., Schwarzbach, J., Zampini, M., & Caramazza, A. (2009) Category-Specific Organization in the Human Brain Does Not Require Visual Experience. Neuron, 63(3), 397-405. DOI: 10.1016/j.neuron.2009.07.012

August 14, 2009
07:30 AM
780 views

On cancer mortality

by iayork in Mystery Rays from Outer Space

[Cancer] mortality has been systematically decreasing among younger individuals for many decades. … the cancer mortality rates for 30 to 59 year olds born between 1945 and 1954 was 29% lower than for people of the same age born three decades earlier. … substantial changes in cancer mortality risk across the life span have been [...]... Read more »

Kort, E., Paneth, N., & Vande Woude, G. (2009) The Decline in U.S. Cancer Mortality in People Born since 1925. Cancer Research, 69(16), 6500-6505. DOI: 10.1158/0008-5472.CAN-09-0357

August 14, 2009
05:48 AM
1,913 views

On the Integration of Tactile, Proprioceptive and Visual Signals by the Brain

by Varun in Wissenschaft

The integration of different sensory inputs in the brain is crucial not only for taking appropriate motor actions but also for body perception and awareness of the bodily self. Integration occurs in higher areas in the brain usually in areas belonging to the parietal lobe1) Integrating Vision and Proprioception in Area 5 ( Graziano et. al (2000))Brodmann Area 5 (or Area 5) is part of the parietal cortex in humans, and in monkeys, is a subdivision of the parietal lobe, occupying primarily the superior parietal lobule. Graziano et. al (2000) studied single neuron responses from Area 5 of monkeys. In their experiments, the arm contralateral to the recording site was outstretched. The real arm of the monkey was covered, and instead a realistic fake hand was kept in view. The experimental design was 2 x 22 x 2 experimental design. Cross indicates fixation spot. The gray arm is the fake arm. The real arm is covered in the experiment (Graziano et. al (2000))Single neuron recordings indicated that the firing rate of individual neurons depends not only on the position of the real arm, but also on the position of the fake arm. The neuron is significantly affected by the position of the real arm, firing more when he real arm is to the left. Additionally, the firing rate further increases when the fake arm is also to the left. Single neuron recording from Area 5. The firing rate is maximum when the real and the fake arms are in congruent position (Graziano et. al (2000))2) Integrating Vision and Touch in Ventral Intraparietal Area (Duhamel et. al (1998))The Ventral Intraparietal Area (or VIP) is a discrete area in the depths of the intraparietal sulcus. Duhamel et. al carried out single neuron recordings in the VIP. They found the neurons to possess a bimodal receptive field. Not only did they respond to a combination of visual and tactile stimuli, but the bimodal receptive fields were arranged in an orderly manner.Bimodal receptive fields of VIP neurons (Duhamel et. al (1998))Small central visual receptive fields were associated with small tactile receptive fields on the muzzle, whereas large peripheral receptive fields were associated with large tactile receptive fields on the side of the head or body. The neurons also demonstrated direction selectivity, in the sense that a visual or tactile stimulus moving in one direction was preferred over the other, and this preferred direction of visual and tactile stimuli coincided in the majority of cells. Direction selectivity of VIP neurons (Duhamel et. al (1998))ReferencesGraziano, M. (2000). Coding the Location of the Arm by Sight Science, 290 (5497), 1782-1786 DOI: 10.1126/science.290.5497.1782Duhamel JR, Colby CL, & Goldberg ME (1998). Ventral intraparietal area of the macaque: congruent visual and somatic response properties. Journal of neurophysiology, 79 (1), 126-36 PMID: 9425183 ... Read more »

Graziano, M. (2000) Coding the Location of the Arm by Sight. Science, 290(5497), 1782-1786. DOI: 10.1126/science.290.5497.1782

Duhamel JR, Colby CL, & Goldberg ME. (1998) Ventral intraparietal area of the macaque: congruent visual and somatic response properties. Journal of neurophysiology, 79(1), 126-36. PMID: 9425183

August 13, 2009
05:18 PM
767 views

Boobies!

by TomJoe in (It's a ...) Micro World (... after all)

Came across this article in the New Scientist. It's a lovely piece of modern day molecular biology doing some forensic work to rediscover a species that was thought to have died out a couple of hundred years ago. The bird in question is the Tasman Booby (Sula tasmani).It has been speculated that this bird has been extinct since around 1790, though evidence has suggested that these birds might still be around. From my reading of the papers, it appears that the call for extinction of the Tasman Booby was based on the examination of fossil material. However the authors believe that the previous study was instead looking at fossil remains of S. dactylatra, the Masked Booby, that were in the upper size range of that species.The authors first performed morphometric data. Their results were presented as follows:Contrary to van Tets et al. (1988), our comparison of new skeletal material revealed a size overlap between modern and fossil specimens for all standard humerus measurements.Such an overlap was not seen by van Tets et al. (see Table 1 reproduced below).So how does that happen? The authors of this manuscript state that van Tets et al. in their studies made a bit of a faux pas. Seems that they "failed to acknowledge" the fact that all the fossil specimens in their study were female, and the modern specimens in their study were male. Like a number of birds, the Booby presents with what is known as reversed sexual size dimorphism. In other words, the females are larger than the males. Whoops.Anywhoo ... Steeves et al. complement the morphometric data with genetic data by performing mitochondrial DNA sequencing. Phylogenetic analysis of these sequences revealed that mitochondrial DNA extracted from three of the six fossil specimens (nothing was recoved from the remaining fossils) were identical to an existing species of Booby, Sula dactylatra fullagari. Based on this, they proposed that all North Tasman Sea boobies should be known as Sula dactylatra tasmani. With this Steeves et al. have extracted the Tasman Booby from the Book of the Dead!ReferenceSteeves, T., Holdaway, R., Hale, M., McLay, E., McAllan, I., Christian, M., Hauber, M., & Bunce, M. (2009). Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea Biology Letters DOI: 10.1098/rsbl.2009.0478... Read more »

Steeves, T., Holdaway, R., Hale, M., McLay, E., McAllan, I., Christian, M., Hauber, M., & Bunce, M. (2009) Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea. Biology Letters. DOI: 10.1098/rsbl.2009.0478

Biology

August 13, 2009
05:18 PM
728 views

A Big Boost for a Revolutionary Theory

by AK in AK's Rambling Thoughts

One of my more favorite reads was Aaron Filler's Upright Ape: A New Origin of the Species[3], shortly after it was published. The suggestion(s) regarding human evolution were attractive and revolutionary, while the discussions of homeotic mutations and their mechanisms (based upon peer-reviewed work[4]) were enlightening and form part of the foundation of my own approach to understanding how mutation, development, and Darwinian selection work together (a subject I haven't blogged much about although it underlies much of my writing here).Filler's primary suggestion is that the main stem lineage of the Great Apes has been walking upright since shortly after it diverged from the ancestors of the ancestors of the gibbons and siamangs due to a homeotic mutation that modified the spine to give it the potential to support an upright stance for long periods, something the gibbons and siamangs lack. (Although they can and do walk upright, both in the canopy and on the ground.) One of the implications of this theory is that the common ancestor of humans, gorillas, chimpanzees, and bonobos walked upright, and that knuckle-walking behavior evolved independently in the lineage leading to gorillas from that leading to chimpanzees and bonobos.Figure 1: Example of the detailed anatomical discussion of the proposed homeotic mutation that lead to the human/great ape backbone structure. Click on image to see illustration and caption at the book's website. (From Reference 3, figure 9-5.)Now, in the advance online Early Edition of PNAS, we find Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor[2] (by Tracy L. Kivell and Daniel Schmitt), unfortunately behind a paywall, that describes research thoroughly undermining the notion that humans evolved from a knuckle-walking ancestor. Let's look at the research first: ...What Kivell and Schmitt did was examine the "features most commonly thought to reflect knucklewalking behavior in the African ape wrist", in terms of their occurrence and development in many primates, and especially gorillas as well as chimpanzees and bonobos. They found "(i) that most gorillas lack key features that have been assumed to be critical for limiting extension of the wrist during knuckle-walking ([refs]), and (ii) these features are found in monkeys that use a variety of different hand postures and substrates."Assuming that such features are necessary (or highly desirable) for knuckle-walking, we should find them emphasized in gorillas, and at earlier ages, since gorillas are larger, thus putting more stress on the bones of their hands during knuckle-walking, and normally start earlier during development. Instead: In addition, the ontogenetic analysis shows that the features of the scaphoid that are assumed to be essential for knuckle-walking ([refs]) are not only inconsistently developed in Gorilla, but, when present, do not appear relatively earlier in development in gorillas (Table 2). Therefore, using the traditional functional interpretation of these features ([ref]), it would appear that the Gorilla radiocarpal joint may be actually less, rather than more, stable in extension throughout ontogeny compared to Pan. The mention of stability during extension of the radiocarpal joint (bending back the wrist) leads to the next important feature of this report: the proposal that the method of knuckle-walking used by gorillas is different from that of chimpanzees and bonobos. We propose that Gorilla uses a relative ‘‘columnar’’ forelimb posture during knuckle-walking in which the hand and wrist joints are aligned in a relatively straight, neutral posture compared to the more extended postures adopted by Pan (Fig. 3). Animals using a relatively columnar wrist and hand posture would have carpal joints that are in line with the hand and forearm, similar to limb joint position in large graviportal animals such as elephants ([ref]). Supporting loads directly over more vertically-oriented forelimb joints during support phase explains the absence of posited bony adaptations to bending loads in gorillas and also permits more mobility at the joint ([ref]). By contrast, Pan, which exhibit extended wrist postures (Fig. 3), will experience higher bending loads. Thus Pan carpal bones have relatively prominent osteological features that have traditionally, but mistakenly, been interpreted simply as features associated with knuckle-walking in general rather than with a specific posture. The notion that Pan and Gorilla use different wrist postures is consistent with the morphometric data presented here. Although this hypothesis has yet to be explored in detail with videographic data, this idea is further supported by previous research showing that Gorilla exhibits increased wrist mobility compared to Pan ([ref]), a more hyperextended elbow joint ([ref]) and relatively equal length of rays 2 through 4, which creates a larger, more stable area over which to disperse axial loads ([ref]). Imagine the difference between doing push-ups on your fists and on a steel bar you've got your hand wrapped around with your wrist bent back. This is sort of what the difference is, but only sort of. Unfortunately, their "figure 3" is behind a paywall, but the important takeaway is that there is a difference in mechanism, the details of that difference, while important, aren't necessary to the wider implications.Kivell and Schmitt have provided very strong support for the idea that knuckle-walking works differently, is used differently, and probably evolved independently in these two lineages. A less technically oriented discussion (than the paper) is provided by Science Daily[1], I'm not going to try to replicate their work. (afarensis, FCD is not really convinced, I've discussed Filler's theory in comments on his (old) blog, and I've expanded and modified some of my arguments there in this post.)Support for the Upright ApeInstead, I'm going to discuss how this new research relates to the "Upright Ape" hypothesis. One key hypothesis here is that the homeotic mutation to the spine "pre-adapted" it to support the upper body when standing, walking, or running upright. I won't go into the details, but with this adaptation in place, we need to ask precisely why any possessor would go in for knuckle-walking. The answer is that the requirements of brachiation (swinging from the arms) include suppressing a twisting movement between the hips and the shoulders, a need that grows greater with greater size (mass). An ancestral "Great Ape" weighing no more than a typical gibbon might have found this movement easy to suppress, but a larger ape that depended on brachiation would have been under some selective pressure to suppress this movement.(Another possibility, IMO, is that the lumbar structure of gibbons has actually become adapted to use the springy structures of the lumbar transverse process (LTP) to provide energy storage from/to this twising moment, which in Great apes must be suppressed by muscular action at the cost of energy. AFAIK no research has been done into this possibility. I'll mention that the springy structures involved are used in most mammals to counter the drop of the belly, allowing it to be suspended during walking and storing energy during running/leaping, while in Great apes it tends to counter the forward droop of the upper body while standing upright (because it has been moved dorsally of the center of flexion (bending) of the backbone by the homeotic mutation). For more detail, I must refer you to the book,[3] I just don't have the expertise, and haven't done the detailed research, to attempt it. Thus I must also leave my suggestion regarding the gibbons as a possibility, until I find research (if any) into th... Read more »

Kivell, T., & Schmitt, D. (2009) Independent evolution of knuckle-walking in African apes shows that humans did not evolve from a knuckle-walking ancestor. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0901280106

August 13, 2009
02:53 PM
1,290 views

Climate change and coffee pests

by Julie Craves in Coffee & Conservation

A paper just published in the journal PLoS ONE explores the impact of climate change on the life history and distribution of the world's worst coffee pest, a minute beetle called the coffee berry borer (CBB), Hypothenemus hampei.

... Read more »

Jaramillo, J., Chabi-Olaye, A., Kamonjo, C., Jaramillo, A., Vega, F., Poehling, H., & Borgemeister, C. (2009) Thermal Tolerance of the Coffee Berry Borer Hypothenemus hampei: Predictions of Climate Change Impact on a Tropical Insect Pest. PLoS ONE, 4(8). DOI: 10.1371/journal.pone.0006487

August 13, 2009
12:35 PM
890 views

The Versatile GABAa Chloride Channel Receptor Complex

by Amiya in Physiology physics woven fine

In today’s industrialized society we are constantly exposed to work related stresses. Consequently, anxiety and insomnia (sleeplessness) have become quite common. No wonder, we are using anxiolytics and sedatives more often; to get relief from the anxiety and insomnia respectively.Benzodiazepines such as diazepam (Valium), chlordiazepoxide (Librium) can effectively treat anxiety and insomnia. They do so by binding with a receptor (called Benzodiazepine-GABAa-chloride ion channel complex [henceforth to be referred to simply as GABAa receptor]) in nerve cell membranes. It is known that most drugs (medicines) exert their actions by combining with receptors: macromolecular complexes present in the cell membrane or within the cytosol or the nucleus.The GABAa receptor is a very versatile receptor complex (a hypothetical model is shown at the bottom). Its main action is to inhibit transmission along neurons in which they are present. Normally, proper functioning of the brain is ensured by a balance between the action of excitatory and inhibitory neurotransmitters [henceforth to be referred to simply as NTs]. Simply put, excitatory NTs (for example, glutamate) give a green or go signal; while inhibitory NTs (such as GABA) tell the nerve not to fire (red or stop signal). In this connection, it must be said that GABA (gamma amino butyric acid) is the most important inhibitory NT. When GABA binds with the GABA receptor ionophore complex, the receptor changes shape (conformation); and then a centrally located chloride channel, that is a part of the receptor itself, opens. Since the concentration of the chloride ions (Cl-) is much more on the outside of the cell than on the inside, Cl- now rushes in due to the increase in chloride conductance. The cell voltage goes further down and the interior of the cell becomes more negative (hyperpolarized) with respect to the outside. The cell becomes less excitable and is thus inhibited.Apart from maintaining the much needed critical balance already mentioned, they also ensure that the brain works in a relatively noise free environment. Billions of neuronal units are always firing in the background creating a constant ‘noise’. A constant release of GABA by the brain drowns out this noise thus improving the ‘signal to noise’ ratio, making the brain’s task of finding the proverbial ‘needle in a haystack’ a lot easier.The GABAa receptor not only binds with GABA, but it is a binding site for various other ligands. But before we discuss them, let us briefly analyze its structure first. The receptor has a pentameric structure which means that it consists of five subunits, and each subunit has four membrane-spanning (transmembrane) domains (see picture). And there are many of the polypeptide subunits to choose from a vast array consisting of alpha, beta, gamma, delta, pi, rho and so on. (In addition, there are six different forms of alpha, 4 beta and 3 gamma subunits). Thus, it’s no wonder that a great variety of GABAa receptors will be found, given the possible permutations!This receptor heterogeneity explains actions of various pharmaceuticals on the receptor. One major form of GABAa receptor (found throughout the brain) consists of two alpha1, two beta2 and one gamma2 subunits. In this isoform, GABA ‘somewhere’ between alpha1 and beta2 subunits, and benzodiazepines bind with the BZ1 (also called omega1) pockets located between alpha1 and gamma2 subunits. Benzodiazepines act only when the receptor isoform has one of the following alpha subunits: 1, 2, 3 or 5 and the subunit should have a conserved histidine residue in the N-terminal domain. In ‘knock-in’ mice where histidine has been replaced by arginine in the alpha1 subunit (alpha1H101R; H for histidine and R for arginine in the 101st residue of alpha1 subunit) there was no sedation or amnesia (as evidenced by their unchanged ‘energy’ and memory to electric shocks). It may be mentioned at this moment that the so called ‘date rape’ pills exploit the amnestic properties of benzodiazepines. The drug plays tricks with the victims’ memories. However, the anxiolytic and muscle relaxant properties were retained in these mice.These mice also do not respond to the hypnotic effects of zolpidem and zaleplon, non-benzodiazepines that act at GABAa receptors containing alpha1 subunits. But in mice with selective histidine arginine mutation in the alpha2 subunit of GABAa receptors, resistance to the antianxiety action of benzodiazepines has been seen. Based on these observations, it is thought that alpha1 subunit mediates sedative and amnestic effects, while alpha2 takes care of the anxiolytic and muscle relaxant ones. It also seems that we are poised to make better benzodiazepines in future (like one that works in anxiety but doesn’t wreak the patients’ memory).Lastly, the versatility. The GABAa receptor also binds barbiturates (urea derivatives used as anesthetics, anticonvulsants, Marilyn Monroe supposedly died of its overdose) in addition to the benzos. Alcohol, alphaxolone (a steroid anesthetic), etomidate (a short acting anesthetic), propofol (diprivan, Michael Jackson supposedly used it), volatile anesthetics like halothane, anticonvulsants like gabapentin and vigabatrin, anthelminthics like ivermectin, and neurosteroids (metabolites of androgen and progesterone) exert part or all of their actions by acting through this receptor, thereby hyperpolarizing the neuron. Conversely, convulsants picrotoxin blocks the chloride channel directly, while bicuculline blocks the receptor’s GABAa binding site causing depolarization and convulsion. There's a lot more than this mere exegesis, and I hope to discuss about it furher later.Last modified: neverReference: Bertram G. Katzung, Basic and Clinical Pharmacology, ninth editionPharmacology: Rang, Dale, Ritter, MooreWisden, W., & Stephens, D. (1999). Pharmacology: Towards better benzodiazepines Nature, 401 (6755), 751-752 DOI: 10.1038/44482... Read more »

Wisden, W., & Stephens, D. (1999) Pharmacology: Towards better benzodiazepines. Nature, 401(6755), 751-752. DOI: 10.1038/44482

August 13, 2009
12:10 PM
1,230 views

A helpful invasive species?

by Jeremy Yoder in Denim and Tweed

Introduced species can wreak havoc on the ecosystems they invade. But what happens after they've been established for centuries? A new study in the latest Proceedings of the Royal Society suggests that, in one case, an introduced species has actually become an important part of the native ecosystem -- and helps protect native species from another invader [$-a].

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Dingoes (above) control red
foxes, which is good for native
critters. Photos by ogwen and
HyperViper.The introduced species in question is the Australian dingo, the wild descendant of domestic dogs [$-a] that moved Down Under with the first humans to settle the continent. Today, 5,000 years after their introduction, dingoes are the largest predator in much of Australia, and they were a prominent part of the ecosystem encountered by European settlers. Europeans, like previous waves of human arrivals, brought their own domestic and semi-domestic animals -- including red foxes, which prey on small native mammals.

The new study's authors hypothesized that because dingoes reduce red fox activity both through direct predation and through competition for larger prey species, dingoes should reduce fox predation on the smallest native mammals. At the same time, dingoes prey on kangaroos, the largest herbivore in the Australian bush -- and reducing kangaroo populations should increase grass cover, providing more habitat for small native mammals. When the authors compared study sites with dingoes present to sites where dingoes had been excluded to protect livestock, this is what they found: increased grass cover, and greater diversity of small native mammals where dingoes were present.

Recently a news article in Nature discussed ragamuffin earth [$-a] -- the idea that human interference in nature has so dramatically changed natural systems that it may often be impossible to restore "pristine" ecological communities. In these cases, some ecologists say, conservation efforts might be better focused on how to maintain and improve the diversity and productivity of the novel ecosystems we've inadvertently created. It looks as though the dingo could be a poster child for exactly this approach.

References

Letnic, M., Koch, F., Gordon, C., Crowther, M., & Dickman, C. (2009). Keystone effects of an alien top-predator stem extinctions of native mammals Proc. R. Soc. B, 276 (1671), 3249-3256 DOI: 10.1098/rspb.2009.0574

Marris, E. (2009). Ecology: Ragamuffin Earth Nature, 460 (7254), 450-3 DOI: 10.1038/460450a

Savolainen, P. (2004). A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA Proc. Nat. Acad. Sci. USA, 101 (33), 12387-90 DOI: 10.1073/pnas.0401814101

... Read more »

Letnic, M., Koch, F., Gordon, C., Crowther, M., & Dickman, C. (2009) Keystone effects of an alien top-predator stem extinctions of native mammals. Proc. R. Soc. B, 276(1671), 3249-3256. DOI: 10.1098/rspb.2009.0574

Marris, E. (2009) Ecology: Ragamuffin Earth. Nature, 460(7254), 450-3. DOI: 10.1038/460450a

Savolainen, P. (2004) A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc. Nat. Acad. Sci. USA, 101(33), 12387-90. DOI: 10.1073/pnas.0401814101

August 13, 2009
11:10 AM
1,178 views

Personal protective equipment and influenza

by Vincent Racaniello in virology blog

We’ve had several discussions on the value of personal protective equipment (PPE) in preventing influenza infection. CIDRAP has an excellent summary of an Institute of Medicine meeting on this subject. The IOM has been asked to make recommendations about how to protect healthcare workers against swine-origin H1N1 influenza.
An unpublished study of respiratory protection in hospital [...]... Read more »

MacIntyre, C. (2009) Face Mask Use and Control of Respiratory Virus Transmission in Households. Emerging Infectious Diseases, 15(2), 233-241. DOI: 10.3201/eid1502.081167

August 13, 2009
06:48 AM
640 views

Scaredy Cat? Blame it on your genes (Again!!)

by Varun in Wissenschaft

Serotonin (5-Hydroxytryptamine or 5-HT), as some of us may know, is a neurotransmitter that is involved in modulation of moods such as anger. The level of re-uptake of serotonin by the presynaptic neuron is crucial and abnormal functioning of the serotonin transporter has been implicated in different neurological diseases. The human 5-HT transporter (5-HTT) gene transcription is modulated by a common polymorphism in the upstream regulatory region and the short variant of the polymorphism reduces 5-HTT transcription and hence reduces 5-HT uptake by lymphoblasts. In this paper, the authors (Lesch et. al (1996)) report association studies demonstrating that the presence of the short variant pre-disposes the individual towards anxiety related personality traits.Neuroticism scores (seperated into eight groups) and percentages of subjects from L(n=163) and S(n=342)groups in each of the eight T-score groups. Notice that the S percentage is higher than L percentagein all T-score groups above 54 (Lesch et. al (1996))ReferenceLesch, K., Bengel, D., Heils, A., Sabol, S., Greenberg, B., Petri, S., Benjamin, J., Muller, C., Hamer, D., & Murphy, D. (1996). Association of Anxiety-Related Traits with a Polymorphism in the Serotonin Transporter Gene Regulatory Region Science, 274 (5292), 1527-1531 DOI: 10.1126/science.274.5292.1527... Read more »

Lesch, K., Bengel, D., Heils, A., Sabol, S., Greenberg, B., Petri, S., Benjamin, J., Muller, C., Hamer, D., & Murphy, D. (1996) Association of Anxiety-Related Traits with a Polymorphism in the Serotonin Transporter Gene Regulatory Region. Science, 274(5292), 1527-1531. DOI: 10.1126/science.274.5292.1527

August 12, 2009
02:37 PM
985 views

Some Thoughts on P-Zombies and the Gap Explanatory Argument

by Varun in Wissenschaft

Dedicated to Anna Traußnig...for the several hours of intellectual orgasms, as she likes to call itParts of this article have been inspired by the writings of Robert Kirk, William Seager and Daniel DennettA philosophical zombie (or p-zombie as it is often called), is a curious creature that is central to the basic idea of the explanatory gap. It is a hypothetical being that is indistinguishable from you and I, or any normal human being for that matter, except for one fundamental detail. Such a zombie, for example, cries in pain (when you kick it), but it feels no pain. In other words it lacks any conscious experience. But, given their definition, this singular fact will have no bearing on the physical processes that the zombie will undergo in it's own world. Put another way, a zombie's behaviour should be indistinguishable from the behaviour and physical state of a genuine human being. This first case is the well known "zombie duplicate" -There exists a philosophical zombie that is physically indistinguishable from me , assuming of course that I can be granted consciousness. Let's stick with that for the moment. We shall come back to this point later.Now I could argue that a perfectly physical duplicate of me should live in a perfectly duplicate realm of reality. It could also be argued that the only possible world that could have a perfectly physical duplicate of me is one which is perfectly duplicated , which might be the very same possible world. Are zombies nomologically or even physically possible? To state that they are nomologically possible would be to state that in some world that shares all physical and natural laws of this world, there exists a "human being" who lacks consciousness. But wait, what happens if certain natural and physical laws do not bear any causal relation? If all natural laws are physical laws or at least dictate physical laws and if, consciousness is causally related to physical states (and there is some evidence for that), then there cannot exist any world with the same physical and natural laws as ours and yet have a zombie. It's not possible. On the other hand, if physical laws were dissociated from natural laws, then zombies could exist by breaking natural laws but not the physical ones. Remember, we have access only to physical laws (which we assume, by default to be natural laws, although this may not necessarily be true). Going further, if mental states (such as consciousness) were non physical, it seems reasonable to claim that zombies are not only nomologically possible but even logically (or physically) possible. Of course, the question still remains whether such another distinct reality, separate from ours does exist (this in itself is another huge philosophical debate). Now if this were the case, one would have a tough time proving what consciousness really is (or is not). It raises another question. How are we to assume that a zombie that exists in another physical realm sharing the same physical laws as ours but not the natural laws does not have consciousness? It may possess a different kind of consciousness that is drawn from the natural laws that govern it's world.In 1999, Robert Kirk, presented an argument which attempted to demonstrate that philosophical zombies are logically impossible. He starts by assuming that a zombie suddenly acquires non-physical qualia. A weak definition of qualia would be the property that distinguishes us from zombies (consciousness if you will). Parts of his argument are as follows:My zombie twin is unaffected by anything non-physicalSo he remains unaffected when he acquires non-physical qualiaIn order to become conscious following acquisition of this non-physical qualia, he must be affected by it in some wayBut nothing non-physical affects him. So he doesn't become conscious.To tell the difference between the subjective character of two different perceptual experiences, he must be sensitive to them or detect them in some wayIn any case, nothing non-physical affects the zombie, so he cannot distinguish non-physical qualia from having no qualiaFriends of the zombie maintain that a "conscious" being is simply the zombie component with non-physical qualia. This position entails that "conscious" humans cannot tell the difference between tea and coffe, for example.But we can tell the difference between tea and coffee.Hence, we are nothing of the sort that friends of zombies maintain we are and hence zombies in their sense are not genuinely possibleKirk's paper has been criticized but it presents an interesting case.One final word on physicalism. In short, there are no kinds of things other than physical things (including consciousness). Daniel Dennett argues that even if consciousness were purely physical, our own conviction that we are not zombies, is simply a product on the external physical world. But, we could still be zombies who think we're conscious, who think we have qualia and who think we feel pain, in ways that are we could never discover. If such were the case, it wouldn't be careless to say that "consciousness" could never be defined or understood or even proved. I for one remain hopeful that science may one day provide a good theory on how consciousness works, but Anna and I both think that even if one ends up showing how it works, one would never be able to show what it really is. ReferencesKirk, R. (1999). The Inaugural Address: Why There Couldn't Be Zombies Aristotelian Society Supplementary Volume, 73 (1), 1-16 DOI: 10.1111/1467-8349.00046Seager, W.E., Are Zombies Logically Possible?-And Why it Mattershttp://www.scar.utoronto.ca/~... Read more »

Kirk, R. (1999) The Inaugural Address: Why There Couldn't Be Zombies. Aristotelian Society Supplementary Volume, 73(1), 1-16. DOI: 10.1111/1467-8349.00046

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