Annual BMCDB Business Meeting @11AM in 1022 LSA

June 12, 2014 Leave a comment

Just FYI. There will also be an ice cream social in the courtyard after the meeting.

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Got ugly mug, at least you can take a punch! Males have facial features that were selected to stand up to getting punched

June 9, 2014 Leave a comment

Interesting, if slightly controversial argument that male faces (and other features) were selected through the course of evolution to be more resistant to impacts from violent altercations. Fascinating idea, but I would still cry like a baby if you clocked me right in the face.

Excerpt from “Male faces ‘buttressed against punches’ by evolution” By Jonathan Webb

Fossil records show that the australopiths, immediate predecessors of the human genus Homo, had strikingly robust facial structures.

For many years, this extra strength was seen as an adaptation to a tough diet including nuts, seeds and grasses. But more recent findings, examining the wear pattern and carbon isotopes in australopith teeth, have cast some doubt on this “feeding hypothesis”.

Instead of diet, Prof Carrier and his co-author, physician Dr Michael Morgan, propose that violent competition demanded the development of these facial fortifications: what they call the “protective buttressing hypothesis”.

“Jaws are one of the most frequent bones to break – and it’s not the end of the world now, because we have surgeons, we have modern medicine,” Prof Carrier explained. “But four million years ago, if you broke your jaw, it was probably a fatal injury. You wouldn’t be able to chew food… You’d just starve to death.”

The jaw, cheek, eye and nose structures that most commonly come to grief in modern fist fights were also the most protected by evolutionary changes seen in the australopiths.

Furthermore, these are the bones that show the most differences between men and women, as well as between our male and female forebears. That is how you would expect defensive armour to evolve, Prof Carrier points out.

“In humans and in great apes in general… it’s males that are most likely to get into fights, and it’s also males that are most likely to get injured,” he told BBC News.



Related articles:

Protective buttressing of the hominin face 

David R. Carrier and Michael H. Morgan

When humans fight hand-to-hand the face is usually the primary target and the bones that suffer the highest rates of fracture are the parts of the skull that exhibit the greatest increase in robusticity during the evolution of basal hominins. These bones are also the most sexually dimorphic parts of the skull in both australopiths and humans. In this review, we suggest that many of the facial features that characterize early hominins evolved to protect the face from injury during fighting with fists. Specifically, the trend towards a more orthognathic face; the bunodont form and expansion of the postcanine teeth; the increased robusticity of the orbit; the increased robusticity of the masticatory system, including the mandibular corpus and condyle, zygoma, and anterior pillars of the maxilla; and the enlarged jaw adductor musculature are traits that may represent protective buttressing of the face. If the protective buttressing hypothesis is correct, the primary differences in the face of robust versus gracile australopiths may be more a function of differences in mating system than differences in diet as is generally assumed. In this scenario, the evolution of reduced facial robusticity in Homo is associated with the evolution of reduced strength of the upper body and, therefore, with reduced striking power. The protective buttressing hypothesis provides a functional explanation for the puzzling observation that although humans do not fight by biting our species exhibits pronounced sexual dimorphism in the strength and power of the jaw and neck musculature. The protective buttressing hypothesis is also consistent with observations that modern humans can accurately assess a male’s strength and fighting ability from facial shape and voice quality.



Pattern, severity and aetiology of injuries in victims of assault.

Although the incidence of assault and other violent crime is increasing in the UK, the cause and overall pattern of injury, and the need for admission have not been defined in adult victims who attend hospital. In a prospective study, all 539 adult victims of assault attending a major city centre Accident & Emergency department in 1986 were therefore interviewed and examined. Facial injury was extremely common: 83% of all fractures, 66% of all lacerations and 53% of all haematomas were facial. The upper limb was the next most common site of injury (14% of all injuries). Twenty-six per cent of victims sustained at least one fracture and nasal fractures were the most frequently observed skeletal injuries (27%) followed by zygomatic fractures (22%) and mandibular body (12%), angle (12%) and condyle (9%) fractures. Seventeen per cent of victims required hospital admission. Overall, the type of injury observed correlated with the alleged weapon used (P = less than 0.001) though 20% of victims who reported attacks with sharp weapons sustained only haematomas or fractures. Injury most often resulted from punching (72% of assaults) or kicking (42% of assaults). Only 6% of victims reported injury with knives but 11% were injured by broken drinking glasses. Those who were kicked were most likely to need hospital admission.


The soap and skin paradox: the human skin microbiome may have changed drastically with the use of detergents

May 28, 2014 Leave a comment

This is a pretty interesting concept, essentially that we used to have bacteria capable of metabolizing ammonia and making our BO less offense. The science seems relatively compelling, however I’m still not entirely sold on the idea of foregoing a nice long hot shower for spraying myself twice daily with a suspension of bacteria. Certainly an interesting concept but I’ll stick to soap for the time being.

Like with most probiotic/microbiome products the biggest hurdle will be getting permanent colonization of the environment after the product is not longer being used, or the environment faces a disruption.

Maybe for a backpacking trip where I can experiment away from civilized society. Cool stuff.

Excerpt from “My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment” by By Julia Scott

Whitlock gathered his samples and brought them back to his makeshift home laboratory, where he skimmed off the dirt and grew the bacteria in an ammonia solution (to simulate sweat). The strain that emerged as the hardiest was indeed an ammonia oxidizer: N. eutropha. Here was one way to test his “clean dirt” theory: Whitlock put the bacteria in water and dumped them onto his head and body.

Some skin bacteria species double every 20 minutes; ammonia-oxidizing bacteria are much slower, doubling only every 10 hours. They are delicate creatures, so Whitlock decided to avoid showering to simulate a pre-soap living condition. “I wasn’t sure what would happen,” he said, “but I knew it would be good.”

The bacteria thrived on Whitlock. AO+ was created using bacterial cultures from his skin.

And now the bacteria were on my skin.

I had warned my friends and co-workers about my experiment, and while there were plenty of jokes — someone left a stick of deodorant on my desk; people started referring to me as “Teen Spirit” — when I pressed them to sniff me after a few soap-free days, no one could detect a difference. Aside from my increasingly greasy hair, the real changes were invisible. By the end of the week, Jamas was happy to see test results that showed the N. eutropha had begun to settle in, finding a friendly niche within my biome.



The company website AOBiome

BMCDB Group Retreat March 2014

May 28, 2014 Leave a comment
Jesuit Center up near Auburn

Jesuit Center up near Auburn

Categories: Social Events, UC Davis

BMCDB End of the Year BBQ 2013

September 12, 2013 1 comment

BMCDB End of the Year BBQ 2013

Great fun and food for all!

Categories: Uncategorized

Reasons for a Nightmare PhD

September 12, 2013 Leave a comment

Common Reasons for Nightmare PhDs by 

From pre-doc to postdoc, there are many instances that can transform a perfectly good PhD program into a nightmarish one. Here are the most common scenarios to watch out for in graduate school – and some ideas about how to deal with them when they pop up.

I wanted to get my PhD but didn’t realize how much work was involved!

Few leap into graduate programs just for the final prize, only to discover that the workload is more than they bargained for. Looking back, the student realizes their heart wasn’t in it from the start. And while they may still be determined to finish, the five years program now feels as if it will take 50.

Is science your passion? Live vicariously through a graduate student while working in a lab as a research assistant for a year. You’ll share in their joys, their trials, and discover if you’re ready to take on your own gauntlet of unpredictable late night and weekend work, and writing (lots of writing!). The transition from research staff to grad student is easy. And if you come to the realization that graduate school isn’t the route for you, that’s OK too!

I really don’t like my current project anymore…

You love being a graduate student, but the current project is about as exciting as watching paint dry. It’s hard to be motivated when your heart isn’t in it, although in grad school there’s lots of help! First and second year projects are to expose you to a variety of new experiences. Your thesis project is longer. And if parts of that become mundane, seek out more established scientists to glimpse the bigger picture, including the societal impact that your work will have. That’s inspirational!

My project is a disaster! If only it were planned and executed properly.

Suppose you’re learning a new technique and decide to use the most valuable samples. You hope everything will run perfectly but with one misstep you’ve suddenly set yourself back by months. Time and reagents are wasted…now you have to start again from the very beginning, hoping not to make the same mistake twice!

With a good plan every experiment can be a success. Consider these ideas before executing your next experiment:

ñ Projects can easily take on a life of their own so define endpoints where no matter the outcome you know comfortable places to stop experimentation

ñ Remember your positive & negative controls

ñ While the experiment is fresh on your mind, make a goal to analyze raw data soon after it’s collected

ñ You can save $$$ or time when ordering supplies, but usually not both

ñ Think ahead: Murphy’s Law is ruthless.

ñ Lab calendars make equipment scheduling simple

And of course, practice makes perfect. Master new techniques using samples set aside just for practice.

Arrgh!!! These experiments just don’t work. At all.

Experimental design looked impressive on paper, but in practice it didn’t pan out. After burning the midnight oil for countless nights you realize that the experiments aren’t novel enough for your thesis. You had a backup plan, right? No? Oh…

Time to switch gears quickly, lest you spend even more years working towards the PhD. Instead of a frantic scramble to plan and execute last minute experiments, take some time at the beginning of your program to design a second project. It may be that you’ll never have to use it, but it’s there for your peace of mind to fall back on, just in case.

My advisor and I rarely see eye-to-eye…

Because sometimes personalities clash. And sometimes the advisor wants to keep a student in the lab as long as possible (as inexpensive labor). Whatever the reason, the student/advisor relationship is toxic and forward progress is stalled.

Thankfully you have an advising team and can turn to the others for guidance. In the rare case that your differences are irreconcilable, there is one last ditch option: pull together a new advising team, seek out a new lab that is willing to take you on as a graduate student, and effectively “fire” those that are stunting your educational growth. Do note that is quite an unpopular choice to have to make, and one not to be made lightly.

My advisor is never around when I need them most!

What can be more agonizing than a floundering graduate program is one where the Advisor has vanished, leaving you with a foreboding sense of abandonment. Whether they’re taking every Friday off, whether they’re vacationing halfway around the world, they remain your Advisor and mentor until the very end.

Don’t wait for their reappearance to flood them with questions, data, and meetings; instead, keep a steady line of communication going. In today’s ever connected world, that’s easy to do: E-mail for casual correspondence and for submitting data and writing samples; phone calls for the more immediate lab matters; and face-to-face Internet video conferencing for the full experience of praise, lively discussion, and furrowed brows.

Finally! Is there enough time to start…and finish…writing my thesis?

Graduation is so close, but what holds you back now is the written portion of your thesis. In the span of a month you’ll develop a solid writer’s block, maybe even overdose on caffeine while trying to write 24/7. Did you leave yourself enough time to make edits based on advisor feedback?

When you do 5 minutes of experimental work to wait 30 on incubation, dedicate the extra time to writing. For thesis sections like the introduction, background, and experimental design, that can be started early on, leaving individual experiments, data and discussion, conclusion and a polishing touch towards the end. Good luck

Categories: Interesting link Tags: ,

Tannisomes: Tannin producing organelles identified in plants

September 12, 2013 1 comment

Very cool discovery!

New Cell Component Important to Tea and Wine-Making

The international team, headquartered at INRA in Montpellier, used a number of techniques to examine the cells in action. In some cases they fixed cells into place, in others they introduced dyes and in more samples they examined spectra, light signatures of chemicals. What they found was that these strange organelles were producing tannins. Until now, no one has known exactly where in the cell tannins have been made. People could see them stored in the vacuole, another organelle in the plant cell, but couldn’t work out how they got there.

Geneviève Conéjéro said: “Tannins, also called condensed tannins or proanthocyanidins, are thought to play diverse roles such as defense against herbivores and pathogens or ultraviolet protection. They give feeling of pungency in the mouth, the feel of a cat’s tongue licking your hand. Common sense associates tannins with immature unripe fruit, and people ironically say ‘this fruit is too green’. More seriously, plant tannins have been used since the Neolithic times to prevent spoilage of animal skins, and therefore first to manufacture leather laces and soles protecting feet of rough ground.”


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