Kambiz attended the Humanity’s Genes and the Human Condition, and he reports some interesting goings on. Sydney Brenner, Nobel Laureate 2002, had this to say this about human evolution:

Starts off with a zinger: “Biological evolution for humans has stopped.” Uhh, really Sydney? You better do better than that. He uses an analogy about how if we feel cold, we don’t ‘adapt’ we just kill an animal, skin it, and wear its pelt as evidence of relaxed natural selection.

I wonder if this the malevolent influence of Steve Jones, but I doubt it. But that wasn’t the weird stuff:

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“Oil Change International campaigns to expose the true costs of oil and facilitate the coming transition towards clean energy. We are dedicated to identifying and overcoming political barriers to that transition.” That’s what they’re saying about themselves. This is a worthy goal as I think most people just fill up their tanks and don’t think a thing about what they’re doing.

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Greenpeace Africa opened its first office in Johannesburg today, announcing a long-term commitment to building a strong presence in Africa dedicated to tackling the most urgent environmental problems facing the continent - climate change, deforestation and overfishing.     Full Story…

There are 11 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:

Global Taxonomic Diversity of Anomodonts (Tetrapoda, Therapsida) and the Terrestrial Rock Record Across the Permian-Triassic Boundary:

The end-Permian biotic crisis (~252.5 Ma) represents the most severe extinction event in Earth’s history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids (’mammal-like reptiles’), through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction) indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates.

Ordered Patterns of Cell Shape and Orientational Correlation during Spontaneous Cell Migration:

In the absence of stimuli, most motile eukaryotic cells move by spontaneously coordinating cell deformation with cell movement in the absence of stimuli. Yet little is known about how cells change their own shape and how cells coordinate the deformation and movement. Here, we investigated the mechanism of spontaneous cell migration by using computational analyses. We observed spontaneously migrating Dictyostelium cells in both a vegetative state (round cell shape and slow motion) and starved one (elongated cell shape and fast motion). We then extracted regular patterns of morphological dynamics and the pattern-dependent systematic coordination with filamentous actin (F-actin) and cell movement by statistical dynamic analyses. We found that Dictyostelium cells in both vegetative and starved states commonly organize their own shape into three ordered patterns, elongation, rotation, and oscillation, in the absence of external stimuli. Further, cells inactivated for PI3-kinase (PI3K) and/or PTEN did not show ordered patterns due to the lack of spatial control in pseudopodial formation in both the vegetative and starved states. We also found that spontaneous polarization was achieved in starved cells by asymmetric localization of PTEN and F-actin. This breaking of the symmetry of protein localization maintained the leading edge and considerably enhanced the persistence of directed migration, and overall random exploration was ensured by switching among the different ordered patterns. Our findings suggest that Dictyostelium cells spontaneously create the ordered patterns of cell shape mediated by PI3K/PTEN/F-actin and control the direction of cell movement by coordination with these patterns even in the absence of external stimuli.

Rapid Experimental Evolution of Pesticide Resistance in C. elegans Entails No Costs and Affects the Mating System:

Pesticide resistance is a major concern in natural populations and a model trait to study adaptation. Despite the importance of this trait, the dynamics of its evolution and of its ecological consequences remain largely unstudied. To fill this gap, we performed experimental evolution with replicated populations of Caenorhabditis elegans exposed to the pesticide Levamisole during 20 generations. Exposure to Levamisole resulted in decreased survival, fecundity and male frequency, which declined from 30% to zero. This was not due to differential susceptibility of males. Rather, the drug affected mobility, resulting in fewer encounters, probably leading to reduced outcrossing rates. Adaptation, i.e., increased survival and fecundity, occurred within 10 and 20 generations, respectively. Male frequency also increased by generation 20. Adaptation costs were undetected in the ancestral environment and in presence of Ivermectin, another widely-used pesticide with an opposite physiological effect. Our results demonstrate that pesticide resistance can evolve at an extremely rapid pace. Furthermore, we unravel the effects of behaviour on life-history traits and test the environmental dependence of adaptation costs. This study establishes experimental evolution as a powerful tool to tackle pesticide resistance, and paves the way to further investigations manipulating environmental and/or genetic factors underlying adaptation to pesticides.

Sexual Behaviour and HPV Infections in 18 to 29 Year Old Women in the Pre-Vaccine Era in the Netherlands:

Infection with Human Papillomavirus (HPV) is a necessary event in the multi-step process of cervical carcinogenesis. Little is known about the natural history of HPV infection among unscreened young adults. As prophylactic vaccines are being developed to prevent specifically HPV 16 and 18 infections, shifts in prevalence in the post vaccine era may be expected. This study provides a unique opportunity to gather baseline data before changes by nationwide vaccination occur. This cross-sectional study is part of a large prospective epidemiologic study performed among 2065 unscreened women aged 18 to 29 years. Women returned a self-collected cervico-vaginal specimen and filled out a questionnaire. All HPV DNA-positive samples (by SPF10 DEIA) were genotyped using the INNO-LiPA HPV genotyping assay. HPV point prevalence in this sample was 19%. Low and high risk HPV prevalence was 9.1% and 11.8%, respectively. A single HPV-type was detected in 14.9% of all women, while multiple types were found in 4.1%. HPV-types 16 (2.8%) and 18 (1.4%) were found concomitantly in only 3 women (0.1%). There was an increase in HPV prevalence till 22 years. Multivariate analysis showed that number of lifetime sexual partners was the most powerful predictor of HPV positivity, followed by type of relationship, frequency of sexual contact, age, and number of sexual partners over the past 6 months. This study shows that factors independently associated with HPV prevalence are mainly related to sexual behaviour. Combination of these results with the relative low prevalence of HPV 16 and/or 18 may be promising for expanding the future target group for catch up vaccination. Furthermore, these results provide a basis for research on possible future shifts in HPV genotype prevalence, and enable a better estimate of the effect of HPV 16-18 vaccination on cervical cancer incidence.

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I’ve been away from the blog for a while, working on fellowship applications and riding the wave of the ICU. Thank you for your patience, as ever.

As you might remember from my days as an intern, I used to love the ICU. That love is no longer: doing procedures to people whose fate is inevitable isn’t as much fun as it used to be, and I feel powerless in the face of a culture that doesn’t exactly embrace the avoidance of unnecessary intervention.

This most recent time in the ICU, I worked with an intern who seemed to me less eager than some to take on the burden of her responsibility. About three days into the rotation, she–let’s call her Dawanna–remarked to me with some irritation that “all I ever do is put in orders.”

“Yes,” I replied. “That’s kind of your job.”

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The Green-e program is meant to bolster customer confidence in the reliability of retail electricity products reflecting renewable energy generation, expand the retail market for electricity products incorporating renewable energy, provide customers clear information about retail “green” electricity products to enable them to make informed purchasing decisions, and encourage the deployment of electricity products that minimize air pollution and reduce greenhouse gas emissions.

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A few months ago I was at a workshop in which we were asked to do something a bit outrageous. Some folks sat out and watched the braver souls carry out the exercise. Others quickly fled the room to hide until the exercise was over. While some jumped right in — enthusiastically. I stayed and did the exercise, as I’ll usually try just about anything at least once.

Still, it was interesting to notice the process that occurred — my first reaction was that of a truculent toddler — “NO!” I got over that and then my prim-and-proper-follow-the-rules-stickler showed up — “That’s weird! You can’t do that! What your friends/parents/partner think if they found out you did this?!?!” After listening to these two voices in my mind, I proceeded to ignore them and carry on. I’m so glad I did because the experience was fun and quite enlightening.

Like it often does, this shows up in my yoga practice. I’ve spoken about this before — how you show up in your yoga practice is how you show up in your life. So, if you’re often distracted and have trouble focusing, you’ll be the same way during your yoga practice. If you get caught up in your thoughts, then you might lose track of your breath or you might find yourself saying no to certain poses rather than flowing. I’ve learned that I often have thoughts of wanting to quit, wanting to escape discomfort and doubting whether or not I can do a more difficult pose. Rather than get all pissy about it, I just acknowledge that those thoughts are there.

The thoughts being there isn’t the problem — it’s when you start listening to them and allowing them to dictate your experience. Not good. Now I’m not saying that you shouldn’t listen to yourself and force your body into a pose that it’s neither willing nor able to go into - although usually something like that originates from a gut feeling rather than the thinking mind. What I’m saying is to notice without letting it pull your out of your natural flow. The flow is life in this present moment. When you start making judgments about the present in your mind, your mind starts creating stories and pulls you very far out of the moment.

When I first started practicing yoga, I was a bit too taken with doing fancy stuff. I tried all of the arm balances as well as other poses that required balance, strength, and flexibility. If it was challenging, I attempted it. As I look back I realize that I was simply curious about yoga and was trying to throw myself wholeheartedly into the practice of it. Of course my ego won out at times and I experienced quite a few ouchies.

One class in particular comes to mind. It was a great flow class that appealed to the athletic part of me. After completing some warm ups, the teacher took us into some more difficult binds and balance postures. I can’t remember the exact pose, but I remember that it was one that I had never done before. It required starting from a squat position and placing your leg somewhere in the vicinity of your shoulder and upper arm. Getting into the pose was only the beginning — once you had the bind, you were to stand up while holding it. The truculent child must have been at recess that day because I didn’t even think about not attempting the pose, nor did I think I couldn’t do it. I simply did it.

As I stood up the truculent child came roaring to the surface with a vengeance — “you can’t do that!” That thought totally knocked me off my game and took over. I immediately released the pose. Interesting, since I had already gotten into the pose and stood up while maintaining the hold. Ah, but the mind can be a powerful thing when you let it have its way. After that experience, I found myself letting my thoughts get the best of me when I attempted poses similar to that one.

Over the years I’ve gotten better at letting the thoughts be there without allowing them to take over my experience. Being in my head too much during my yoga practice isn’t safe for me because it pulls my attention away from what I’m feeling. It takes me out of my experience in the poses which wreaks havoc on my breathing and the quality of my practice. Essentially, it morphs my yoga practice into exercise. This is one of the reasons I prefer a home practice to group classes — during a class, my mind is much more engaged. My attention is divided between my environment, the dialogue from the teacher, and any distractions that can come up during the course of a class. [Blogger’s Note: No, I’m not saying that yoga classes are bad. I’m saying that I PERSONALLY find them distracting. It’s my personal preference to practice on my own. Many people love classes. It’s these folks that keep me in business.]

So how do you stay in the moment and keep yourself from getting sucked into the whirlwind of your thoughts? Here are a few things that work for me:

• Tune into your anchor — your breath. Your breath is always there for you, so use it! Notice what’s going on with it — is it flowing or are you holding it? Are you finding that your breath is getting “stuck” in a certain area of your body? Is your breathing fast or slow, deep or shallow? Tune in and stay focused on it.
• Notice the sensations in your body — how is your body feeling? Is it tense or loose? Are you feeling tired or energized? Does your body need to make a micromovement to bring more pleasure or comfort? 
• Look at your environment — if your mind is wandering bring it back by taking inventory of your physical environment. Notice the floor, the walls, room decoration, etc. You might find that you feel as though you’re noticing what’s around you for the very first time.’
• Feel your feet/hands — outside of focusing on my breath, this one is my favorite. It grounds me to notice how my feet feel on the ground. It brings my focus back from wherever it’s been roaming.

It’s all about noticing the thoughts and continuing to flow in the present — whether in your yoga practice or in life. Sometimes when you hear your thoughts but ignore them you wind up doing things that you never could have believed you could do. Be here now.

Namaste!

A few months ago I was at a workshop in which we were asked to do something a bit outrageous. Some folks sat out and watched the braver souls carry out the exercise. Others quickly fled the room to hide until the exercise was over. While some jumped right in — enthusiastically. I stayed and did the exercise, as I’ll usually try just about anything at least once.

Still, it was interesting to notice the process that occurred — my first reaction was that of a truculent toddler — “NO!” I got over that and then my prim-and-proper-follow-the-rules-stickler showed up — “That’s weird! You can’t do that! What your friends/parents/partner think if they found out you did this?!?!” After listening to these two voices in my mind, I proceeded to ignore them and carry on. I’m so glad I did because the experience was fun and quite enlightening.

Like it often does, this shows up in my yoga practice. I’ve spoken about this before — how you show up in your yoga practice is how you show up in your life. So, if you’re often distracted and have trouble focusing, you’ll be the same way during your yoga practice. If you get caught up in your thoughts, then you might lose track of your breath or you might find yourself saying no to certain poses rather than flowing. I’ve learned that I often have thoughts of wanting to quit, wanting to escape discomfort and doubting whether or not I can do a more difficult pose. Rather than get all pissy about it, I just acknowledge that those thoughts are there.

The thoughts being there isn’t the problem — it’s when you start listening to them and allowing them to dictate your experience. Not good. Now I’m not saying that you shouldn’t listen to yourself and force your body into a pose that it’s neither willing nor able to go into - although usually something like that originates from a gut feeling rather than the thinking mind. What I’m saying is to notice without letting it pull your out of your natural flow. The flow is life in this present moment. When you start making judgments about the present in your mind, your mind starts creating stories and pulls you very far out of the moment.

When I first started practicing yoga, I was a bit too taken with doing fancy stuff. I tried all of the arm balances as well as other poses that required balance, strength, and flexibility. If it was challenging, I attempted it. As I look back I realize that I was simply curious about yoga and was trying to throw myself wholeheartedly into the practice of it. Of course my ego won out at times and I experienced quite a few ouchies.

One class in particular comes to mind. It was a great flow class that appealed to the athletic part of me. After completing some warm ups, the teacher took us into some more difficult binds and balance postures. I can’t remember the exact pose, but I remember that it was one that I had never done before. It required starting from a squat position and placing your leg somewhere in the vicinity of your shoulder and upper arm. Getting into the pose was only the beginning — once you had the bind, you were to stand up while holding it. The truculent child must have been at recess that day because I didn’t even think about not attempting the pose, nor did I think I couldn’t do it. I simply did it.

As I stood up the truculent child came roaring to the surface with a vengeance — “you can’t do that!” That thought totally knocked me off my game and took over. I immediately released the pose. Interesting, since I had already gotten into the pose and stood up while maintaining the hold. Ah, but the mind can be a powerful thing when you let it have its way. After that experience, I found myself letting my thoughts get the best of me when I attempted poses similar to that one.

Over the years I’ve gotten better at letting the thoughts be there without allowing them to take over my experience. Being in my head too much during my yoga practice isn’t safe for me because it pulls my attention away from what I’m feeling. It takes me out of my experience in the poses which wreaks havoc on my breathing and the quality of my practice. Essentially, it morphs my yoga practice into exercise. This is one of the reasons I prefer a home practice to group classes — during a class, my mind is much more engaged. My attention is divided between my environment, the dialogue from the teacher, and any distractions that can come up during the course of a class. [Blogger’s Note: No, I’m not saying that yoga classes are bad. I’m saying that I PERSONALLY find them distracting. It’s my personal preference to practice on my own. Many people love classes. It’s these folks that keep me in business.]

So how do you stay in the moment and keep yourself from getting sucked into the whirlwind of your thoughts? Here are a few things that work for me:

• Tune into your anchor — your breath. Your breath is always there for you, so use it! Notice what’s going on with it — is it flowing or are you holding it? Are you finding that your breath is getting “stuck” in a certain area of your body? Is your breathing fast or slow, deep or shallow? Tune in and stay focused on it.
• Notice the sensations in your body — how is your body feeling? Is it tense or loose? Are you feeling tired or energized? Does your body need to make a micromovement to bring more pleasure or comfort? 
• Look at your environment — if your mind is wandering bring it back by taking inventory of your physical environment. Notice the floor, the walls, room decoration, etc. You might find that you feel as though you’re noticing what’s around you for the very first time.’
• Feel your feet/hands — outside of focusing on my breath, this one is my favorite. It grounds me to notice how my feet feel on the ground. It brings my focus back from wherever it’s been roaming.

It’s all about noticing the thoughts and continuing to flow in the present — whether in your yoga practice or in life. Sometimes when you hear your thoughts but ignore them you wind up doing things that you never could have believed you could do. Be here now.

Namaste!

This article originally appeared on the old bioephemera September 9, 2007.

Syphilitic skull with three trephine holes and osteomyelitic lesions
Hunterian museum

One of my favorite London experiences was my visit to the Hunterian museum. If only I had more time there! I liked it so much, I returned on my last day, procrastinating my departure for Heathrow as long as possible.

The Hunterian is tucked away inside the Royal College of Surgeons of England, on Lincoln’s Inn Fields. In its Victorian incarnation, it was a wonderful multi-tiered gallery with railings, balconies, and suspended skeletons:

Illustrated London News, 1845

The Hunterian Gallery before the wars (source)

So I was shocked when I entered the grey, columned Royal College, climbed a graciously curving stairway, and found this extremely modern, two-story crystal-and-glass atrium:

The Crystal Gallery at the Hunterian Museum, Royal College of Surgeons

Definitely not what I was expecting! But it grew on me. I love ornate curiosity cabinets, but there is something very elegant about unadorned bones, and simple glass jars. Biological structures are so rich with intrinsic beauty, there’s no real need to gild the lily (that means you, Damien Hirst).

Though the new Hunterian galleries are peaceful and refined, I felt a slight pang of regret for the railings and wood cabinetry Darwin would have touched, when he studied here in the 1830s and 40s. Unfortunately, many of the specimens Darwin saw were destroyed when the Royal College of Surgeons was bombed in 1941. Like the gallery housing it, John Hunter’s collection is no longer what it once was. But what remains is still pretty darn amazing.

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