Bears in wolf clothing

Reported in May 23' 2013' issue of Nature journal:

Hot topic, scalding hot, is the observed decrease in elk population in Yellowstone Nation Park. "It's those damned wolves!!!" Wolves, the ancient scapegoat for everything. Let's look underneath the wolf clothing.

In an attempt to 'reclaim' the trout population in the park lakes, 'humans' (clarification of which humans are not mentioned in the report) restocked the lakes with lake trout. Instead of the native trout. A detail missing from the original ecological assessment was that the lake trout spawn on the bottom of the lakes, unlike the natives, which do not. The introduced non-native fish are unable to be harvested by grizzly bears. Since fish are a major dietary source for grizzlies, the bears look for alternative food sources. Elk calves.

A research team in Wyoming estimated that this dietary shift accounts for as much as 11 percent reduction in the elk population, even elk that winter outside the park. "The decline of these elk is often blamed, perhaps erroneously, on the reintroduction of wolves."

But we do so love our scapegoats, don't we?

Which came first: obese chicken or its obese microflora?

Which came first: The obese chicken or its obese microbiota? « Nothing in Biology Makes Sense!

Good summary of a recently published paper on how our gut microflora influences metabolism of the entire organism. Most people tend to think of the gut simply as a container to periodically fill and empty. Only until recent years has science demonstrated that our gut is an organ actively involved in our entire physiology, including communication with the brain and immune system. In fact, just as our body fat is an endocrine organ, the gut is also involved in our endocrine system, including inflammation.

While we consciously or subconsciously interact with thousands of environment components on a daily basis, our gut contains another environment, the microflora, which interacts in ways we are unaware of. Part of that is comprised of what we swallow, sometimes microbes that hitch a ride on food we eat or drink. But that is why we have such a complex environment inside our gut. Hordes of 'good' bacteria often battle with 'bad' bacteria, and sometimes the latter may win. We usually become aware of those battle victories. Others are minor skirmishes that go unnoticed.

It is the chronic battles that alert the big army of our defenses, the immune system. And when the balance is continually upset, the rest of the body responds and other systems may malfunction.

Although epidemiological studies have suggested that some enteric bacteria are associated with obesity and chronic inflammation, the authors of this study demonstrated that a specific bacteria strain causes obesity. (Remember that association is not proof of causation.) However, a limitation of this study is the model: gnotobiotic (aka germ-free) mice. Regardless, it is a logical progression from in vitro models to study interactions of the gut microflora and metabolism. But we have more work to do on this.

My comments submitted on the website's post:

Gnotobiotic studies have their limitations despite that they are a logical progression from in vitro studies and isolate otherwise complex immune and intestinal interactions. Gnotobiotic animals typically have immune systems and intestinal walls that are under-developed. Also, all the food must be antigen free, which is difficult to achieve. Often, secondary infections can rapidly kill off an entire gnotobiotic colony or mask effects of controlled dietary variables. In our experience with gnotobiotic pigs (which are more relevant to human nutrition and gut microflora), administered probiotics had no effect on morbidity when challenged by a single-strain pathogen, whereas pigs in conventional state (non-gnotobiotic conditions) fared significantly better. Animals in a germ-free environment do not fully represent their counterparts in a conventional environment ,and variables in studies with gnotobiotic animals must be strictly controlled (and are very expensive).

I found it interesting that in neither the paper or the supplementary information was provided the specific ingredients of the ‘WTP’ diet except for the major nutrient composition. ‘Chinese medicinal medicine’? ‘Prebiotics’? As a reviewer, I would have requested this information be more specific.

Academic Assholiness

"As we talked we started to wonder: do you get further in academia if you are a jerk?"

A recent blog post, Academic assholes and the circle of niceness, on the Thesis Whisperer examines the increasing trend of academic snobbery, arrogance, and, aptly termed, 'assholiness'.

Some people ask me why I retired early from academia. Depending on the inquirer, my responses range from "It was just time to do so," to a rant on the trend of academic assholiness.

During the last nine years at a large self-inflated university that trend has increased, and, in fact, has been selected for, intentionally or not. After being recruited for a research position there, I was genuinely excited and passionate about my work. Over the next nine years of experience and observations in two departments, that dwindled to waking up every weekday morning and forcing myself to go through the motions. The last two years were simply a job while I prepared to walk away from the Academic Empire.

This is not the only university in which I have observed and experienced Academic Assholiness. Nor have I been close-mouthed about specific examples like many others that endure it and trudge on. My grievances were nodded at, checked off and ignored. I watched with anger as a research lab manager fought for her job with a lawsuit because a department head covertly attempted to have her fired. In this case, it was a prompted by an illness resulting from unhealthy environmental conditions in the department. This was an ongoing complaint by several staff and researchers over several years, but was repeatedly ignored.

Another example was a research scientist that continuously discriminated against gender and race of staff and graduate students in his laboratory. Grievances related to this individual were overtly ignored. Additionally, an academic scientist nearly destroyed the career of a young and brilliant scientist because of a personal dislike for her national affiliation and origin. And another scientist who intentionally recruited foreign graduate students to demand unreasonably long working hours, even threatening their educational and visa status if they complained. Then there's the junior scientist who feels that unrelenting humiliation of graduate and undergraduate students during their seminars or presentations elevates his own academic standing. And, lastly, the arrogant yelling at janitorial and service staff as if they were kicking a dog, or, mostly, their prevalent treatment of them as the Invisibles and Untouchables.

Finally, there is the Nobel Prize researchers recruited and installed in university departments at the expense -their research space and equipment- of other well-established and equally successful (without the NP recognition) academics, and whose snobbery and academic arrogance is overlooked and even smiled upon by university administration.

These are members of the increasing species of Academia assholiata that I see rapidly evolving in our social environment. I could continue with examples from 28 years in academic halls and three universities. Only one of these institutions, a small university, had a credible and effective process for grievances. The other two institutions had sham committees. Speaking openly meant being blacklisted. In the past four years I have seen too many young and bright scientists leave academia, and am now seeing a flood of older scientists flee, some jaded and bitter.I left last year without looking back.

I am heartened and pleased to see more public discourse like this post on these issues, and I encourage others in all levels of academia to be more outspoken.

KcD Studios: senior thesis

KcD Studios: senior thesis

 A brilliant idea and wonderful artistic imaginative renditions. A great idea to incorporate into teaching chemistry!

Visit Kacie's website and blog to see more artistic renditions of the periodic elements.

Treat obesity as physiology, not physics : Nature News & Comment

I find it sadly amusing that we still strive to reduce the obesity/diabetes problem down to one cause. As if reality and the world were binary: either/or. Instead of a very complex and dynamic network of factors involved with obesity and associated diseases. Until a human being is viewed holistically as a dynamic organism that responds to its intrinsic and extrinsic environment, and that the process to a state of obesity and diabetes is multifactorial, we will continue to blunder along as if blindfolded.


Treat obesity as physiology, not physics : Nature News & Comment

Precious Proteins

There I was; leading a small team of scientists to save these precious proteins for the world. For the future. Ice cream proteins. We had two of these rare proteins that expressed smooth, creamy, flavorful ice cream. And recovered another from an evil group of industrial men. It had been stolen from a collaborator; this one expressed rich butterscotch ice cream.

I had hidden these proteins in a house. But as the private industry group of men were surrounding us, I distributed the three precious proteins to three individuals in our small group (one looked like Albert Einstein). And told them to run. Run, hide; don't let ourselves, and the proteins be caught. Faint, punt, divert those bad men away from each of us. Don't listen to their pleas and lies.

We must preserve and keep these proteins safe. Safe for all to access in the future. Without modifications, without capitalization; free for all mankind. 'Run, and protect them with your lives.' For these are the keys to the Perfect Ice Cream. RUN!!!!

Then there was a small party outside, a gathering of friends to share food and music. Graeme playing guitar (I didn't think he had a music bone in his body), a girl with short blond hair and fine voice, and I thank John and Tracy for coming all the way from Indiana to play bass and share in the celebration. Of ice cream.

Full moon triggers wild and vivid dreams at night.

To mouse, or not to mouse. What is the question?

After many years in medical and veterinary biology, I always questioned the (rather blind) reliance on the mouse model by modern science. I was glad to see I am not the only one.

Sometimes, there is a 800-pound silverback gorilla in the room and he is 'invisible'. This article exposes the gorilla and shows that the problem animal is not the gorilla but in fact a big fat rodent! An often overlooked aspect of research studies using rodents is that these animals tend to be sedentary, mentally stagnant and overfed. This life style results in obesity and a range of consequent pathologies, including cardiovascular disease, cancer, diabetes, accelerated neurodegeneration and renal failure. This article details the fact that animals in such an unhealthy state do not qualify as appropriate research models for anything other than the study of 'couch potatoes'. 
This is a major wake-up call for the research community and easily addressed by portioned feeding of laboratory rodents and by putting a running wheel in their cages.

Citation: Shelley C, Marshansky V: "Sometimes, there is a 800-pound silverback gorilla in the room and he is..." Evaluation of: [Martin B et al. "Control" laboratory rodents are metabolically morbid: why it matters. Proc Natl Acad Sci U S A. 2010 Apr 6; 107(14):6127-33; doi: 10.1073/pnas.0912955107]. 

Faculty of 1000, 22 Jul 2010. F1000.com/3078978