Thursday, February 28, 2013

Natural History of Nitrogen Fixation

I think this paper, the Natural History of Nitrogen Fixation, provides most of the answers I was looking for - but then it raises further questions.

It has been suggested that abiotic sources of fixed nitrogen on the early Earth, supplied through endogenous/abiotic synthesis and exogenous delivery, were most likely limiting (Raven and Yin 1998; Kasting and Siefert 2001; Navarro-Gonzalez, McKay, and Mvondo 2001). At some point, dwindling concentrations of reduced nitrogen would have become insufficient for an expanding microbial biomass, precipitating the evolution of biological nitrogen fixation (Towe 2002). These prevailing conditions have been used to argue that the innovation of biological nitrogen fixation occurred early in prokaryotic evolution, and indeed the ability to fix nitrogen is found exclusively among members of the bacteria and archaea.

So usable nitrogen probably was limiting to early microbes. But questions remain about how such an expensive and complex metabolic process evolved.

We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.

Wednesday, February 27, 2013

Pollination syndromes (or not)

A bee that's not following the rules. For an explanation see 'Bees use achromatic contrast to see red.'

‘Pollination syndromes’ are suites of phenotypic traits reflecting convergent adaptations of flowers for pollination by specific types of animals. It's easy to find examples that fit the theory but are the syndromes testable?

In a 2009 paper in Annals of Botany Jeff Ollerton and colleagues use flowers from six communities on three continents and score them for the expression of floral traits used in published descriptions of the pollination syndromes. They then compare these to the actual pollinators.

Bottom line:

(I)n approximately two-thirds of plant species, the most common pollinator could not be successfully predicted by assuming that each plant species belongs to the syndrome closest to it in phenotype space.

Tuesday, February 26, 2013

Orchid moth

This video always makes me think of that great Skinner quote from the Simpsons:
There's nothing more exciting than science. You get all the fun of sitting still, being quiet, writing down numbers, paying attention. Science has it all.

Monday, February 25, 2013

Swallowing a grenade

Still on the topic of the microbiome Carl Zimmer has another insightful article on his blog about antibiotics and their effect on our microbiome: When you swallow a grenade.


What made antibiotics so wildly successful was the way they attacked bacteria while sparing us. Penicillin, for example, stops many types of bacteria from building their cell walls. Our own cells are built in a fundamentally different way, and so the drug has no effect. While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.

Read it to learn about some recent research but also to learn from a master at how to communicate science.

Sunday, February 24, 2013

Depauperate dental flora

Going back to an earlier class here's a news article from Science this week on two recent papers that describe the origin of our depauperate dental flora:

How Sweet It Is: Genes Show How Bacteria Colonized Human Teeth
When humans invented farming 10,000 years ago, they weren't the only ones to get a boost from the new starchy diet. Some microbes that had lurked at low levels in the mouths of hunter-gatherers bloomed on the sugary films coating the teeth of farmers who munched cereal grains. Eventually the cavity-causing Streptococcus mutans, for one, took root. It adapted to the sweet life, multiplying like a weed and edging out many other species of bacteria. That leaves the modern mouth a depauperate ecosystem, according to two new genetic studies.

Saturday, February 23, 2013

More Nemo

The first in series of job candidates for a marine ecology position.

MARINE ECOLOGY JOB SEMINAR

Monday Feb 25, Noon, MSB Auditorium

Dr. Michael Berumen (KAUST)
Movement ecology in reef systems: from finding Nemo to metapopulation dynamics

Dr. Berumen is an Assistant Professor of Marine Science and Engineering at the Red Sea Research Center of the (KAUST), and an Adjunct Scientist at the Woods Hole Oceanographic Institution. He is a population and community ecologist whose research interests include population connectivity of marine organisms in benthic marine systems.

More Weird Sex

Male pipefish get “pregnant,” and Atlantic slippersnails change sexes as they grow. Researchers are now uncovering how and why these bizarre sex strategies occur.

There is some recent research about the intricacies of some of the weirder animal sexual strategies, including but not limited to, the pipefish. These male pipefish "get pregnant" as the females pass the eggs off into their brood pouch. But more interesting, they can either care for the eggs diligently, or fail to take good care of them, resulting in fewer viable offspring.

Here's the article I found

Here's the original paper in Nature about pipefish

Friday, February 22, 2013

Haplodiploidy

Also in Science this week: Why Queens Prefer Daughters A comment on a recent paper in the American Naturalist that investigates the relationship between sociality, sex ratio adjustment and haplodiploidy.

Hamilton’s “haplodiploidy hypothesis” holds that inflated sororal relatedness has promoted altruistic sib rearing in haplodiploids, potentially explaining their apparent predisposition to eusociality. Here, we suggest that haplodiploidy may instead promote eusociality simply by facilitating sex-ratio adjustment. Specifically, haplodiploidy may enable sex-ratio bias toward the more helpful sex, owing to “local resource enhancement,” and such sex-ratio bias may promote the evolution of helping by individuals of that sex, owing to the “rarer-sex effect.” This could explain why haplodiploidy appears to have been important for eusociality in taxa with only female helpers, such as ants, wasps, and bees, but not in taxa with both male and female helpers, such as termites.

Honey, It's Electric: Bees Sense Charge On Flowers


I thought that flowers' use of patterns in the ultraviolet spectrum to attract bees was pretty amazing. Turns out that flowers utilize even crazier means of getting bees' attention!

Flowers are nature's ad men. They'll do anything to attract the attention of the pollinators that help them reproduce. That means spending precious energy on bright pigments, enticing fragrances and dazzling patterns. Now, scientists have found another element that contributes to flowers' brand: their distinct electric field.


Thursday, February 21, 2013

Pollen & Forensics



I think on Tuesday, John mentioned that the pollen of different plant species have a vast array of different structures. This TED talk (Every Pollen Grain Has a Story) by Jonathan Drori highlights some of the stranger forms of pollen and their various uses, and as Drori points out:

"Perhaps you didn't realize that plants have sex. They have rampant, promiscuous and really quite interesting and curious sex. Really, a lot."

Then the talk takes a twist. Drori illuminates the use of pollen in the field of forensics (I know, I was like "What?!?"). Just as Jennifer mentioned at CCBER today, plants have a huge variety of uses in forensics. Apparently, experts in the field of pollen physiology and ecology are being called to identify species of pollen from different crime scenes and the implications of those species to the location of the committed crime. Proportions of pollen species found on articles of clothing can identify a geographic location to within 1 kilometer. This means that:

"Plant forensics are being used now to track where counterfeit drugs have been made, and where banknotes have come from."

Pretty cool stuff, so check out the video.


Watermelon

I mentioned that there were several ways to get seedless fruit. There's the 'trick the plant with auxin method' I mentioned in class. There's the 'find a genetic mutant' in the orange example below and when you look into seedless watermelons you find yet another method - create a mule.

The watermelon, or Citrullus lanatus, belongs to a family of climbing vines that include cucumbers and gourds. And like all fruits, they naturally have seeds. The seedless versions are not genetically modified, as some might assume, but are hybrids that have been grown in the United States since the middle of the 20th century. Breeders match the pollen from a diploid plant, one that contains 22 chromosomes per cell, and the flower of a tetraploid plant, which contains 44 chromosomes per cell. The result is a triploid with 33 chromosomes that is incapable of producing seeds. (The tiny white ones you sometimes find are seed coats, where a seed did not mature.) Breeders call it the mule of the watermelon world.

From a Washington Post article, Watermelons: What happened to the seeds?

Wednesday, February 20, 2013

A little history on seedless navel oranges

John talked about seedless fruits and mentioned that the type of oranges that are seedless are all clones from one mutant individual found long ago...  Here is a fun NPR article on Navel Oranges and their interesting history (and the source of their navels...):  "Who Put the Navel in  Navel Oranges"

Saving Babies


Short notice but this event tonight looks very interesting:

Seminar:
Wed Feb 20, 8pm, room 1104 Harold Frank Hall, UCSB
Speaker: Stefan Timmermans, Ph.D. (UCLA)
Title: Saving Babies? The Consequences of Newborn Genetic Screening

Sponsored by the Capps Forum on Ethics & Public Policy
More information about the speaker:
 Saving Babies? The Consequences of Newborn Genetic Screening 
It has been close to six decades since Watson and Crick discovered the structure of DNA and more than ten years since the human genome was decoded. Today, through the collection and analysis of a small blood sample, every baby born in the United States is screened for more than fifty genetic disorders. Though the early detection of these abnormalities can potentially save lives, the test also has a high percentage of false positives—inaccurate results that can take a brutal emotional toll on parents before they are corrected. Now some doctors are questioning whether the benefits of these screenings outweigh the stress and pain they sometimes produce. In Saving Babies?, Stefan Timmermans and Mara Buchbinder evaluate the consequences and benefits of state-mandated newborn screening—and the larger policy questions they raise about the inherent inequalities in American medical care that limit the effectiveness of this potentially lifesaving technology.
Drawing on observations and interviews with families, doctors, and policy actors, Timmermans and Buchbinder have given us the first ethnographic study of how parents and geneticists resolve the many uncertainties in screening newborns. Ideal for scholars of medicine, public health, and public policy, this book is destined to become a classic in its field.
Speaker Profile:
Stefan Timmermans is chair and professor of the sociology department at UCLA.  His research draws from medical sociology and science studies and uses ethnographic and historical methods to address key issues in the for-profit U.S. health care system. He has conducted research on medical technologies, health professions, death and dying, and population health. He is currently working on an ethnographic study of the expansion of newborn screening. His next projects will be about the community spillover effects of lack of health insurance and whole exome sequencing. His goal is to conduct robust qualitative research that reveals the invisible benefits and costs of the U.S. health care system. He is the author of Sudden Death and the Myth of CPR (Temple 1999), The Gold Standard: The Challenge of Evidence-Based Medicine and Standardization in Health Care (Temple, 2003, with Marc Berg), and Postmortem: How Medical Examiners Explain Suspicious Deaths (Chicago, 2006). His book Saving Babies? The Consequences of Newborn Genetic Screening (with Mara Buchbinder) is forthcoming from University of Chicago Press. He is also senior editor medical sociology for the journal Social Science and Medicine.

Tuesday, February 19, 2013

Why don't we all do it?

One of the cool things about biology is that as soon as you come up with a satisfactory explanation for an apparently strange phenomenon (eg gender change in some species) you have new question - if it's such a good idea why don't more species do it?

This is exactly the question asked by Yale University researchers:
Why Don’t More Animals Change Their Sex?
While the adaptive advantage of sex change is well understood, it is not clear why relatively few animals change sex. According to Alonzo, “An intuitive, yet rarely studied, explanation is that the considerable time or energy it takes to change sex make hermaphroditism unfeasible for most animals.”

Others have pointed out the errors in Finding Nemo eg:

Clownfish, of Finding Nemo fame, are a good example of a protandrous hermaphrodite: the largest individual fish in a group is female, the next smallest is the reproductive male, and the rest are typically non-reproductive. When the largest female is removed from the population the male becomes female, and a non-breeder becomes male. Thus, in Nemo's case Marlin (Nemo's father) should have turned into Marla once Coral (Nemo's mother) disappeared. 

Monday, February 18, 2013

Fun with spores


I posted this before but since I mentioned it in class I thought I'd post it again.
Lycopodium is actually a type of club moss - which, as you may remember, is not a moss at all but a group of the seedless tracheophytes. Their very fine spores have been used for many purposes including early flash photography and as a fuel source in the first internal; combustion engine!
When mixed with air, the spores are highly flammable because of their high fat content and their large surface area per unit of volume — a single spore's diameter is about 33 micrometers requiring about 30 laid side by side to span a millimeter and so 30x30x30=27,000 could be packed into a single cubic millimeter!

Sunday, February 17, 2013

The larch


It is a sad indication of the state of education these days when students are not grounded in the fundamentals of Monty Python.

Season 1, episode 3 from 1969: How to Recognise Different Types of Trees From Quite a Long Way Away.

And what a great episode this is too, not only the Larch but Cardinal Richelieu, Superman's alter-ego Bicycle Repair man and nudge, nudge, wink, wink.

The larch re-appears in the closing sequence although I do feel compelled to point out that doesn't look like a larch trunk, I think its a birch - almost all the other trees around it are clearly silver birch. And look at all those wonderful ferns. Just look at them!

Saturday, February 16, 2013

Interspecies signalling

In the journal Cell this week (with this neat 'graphical abstract'):
Bacterial Nitric Oxide Extends the Lifespan of C. elegans

Nitric oxide (NO) is an important signaling molecule in multicellular organisms. Most animals produce NO from L-arginine via a family of dedicated enzymes known as NO synthases (NOSes). A rare exception is the roundworm Caenorhabditis elegans, which lacks its own NOS. However, in its natural environment, C. elegans feeds on Bacilli that possess functional NOS. Here, we demonstrate that bacterially derived NO enhances C. elegans longevity and stress resistance via a defined group of genes that function under the dual control of HSF-1 and DAF-16 transcription factors. Our work provides an example of interspecies signaling by a small molecule and illustrates the lifelong value of commensal bacteria to their host.

Science Daily has a report as well: Nitric Oxide: A Little Molecule's Remarkable Feat -- Prolonging Life, Worm Study Shows
Nitric oxide, the versatile gas that helps increase blood flow, transmit nerve signals, and regulate immune function, appears to perform one more biological feat -- prolonging the life of an organism and fortifying it against environmental stress, according to a new study.

Nitric oxide is why all the cool kids, well the athletic ones anyway, are drinking beet juice. Beet juice has large amounts of nitrate which bacteria in you mouth and intestines convert to nitrites which is converted to nitric oxide. This lowers blood pressure and increases oxygen supply to tissues: All the Olympic Athletes Are Guzzling Beet Juice. The only downsides are that beet juice is an acquired taste (although beet-carrot-apple is pretty good), and that it colors your urine a disturbing bright red.

Friday, February 15, 2013

Perpetual Ocean

This is a beautiful visualization of the world's ocean surface currents from 2005-2007. It is sort of like a wind map. Impressive.


Rockfish Recompression


I know some of you are interested in marine biology so I thought I'd share this gem from the Love lab right here on campus (see Chadler's post below for more from the Love lab). It's also a handy reminder of the wealth of talent (!) on campus outside of the faculty. Many of these talented individuals were mentioned to you in the Colloquium but don't forget about them when you are looking for research opportunities.

Thursday, February 14, 2013

Gymnosperm reproduction

Here are the Gymnosperm reproduction videos I mentioned. The first one is very short and a little obvious but I liked the second and third ones a lot. I thought they really helped in visualizing what is going on.











Wednesday, February 13, 2013

Donor feces

I've been reading a lot about clinical trials lately. The press tend to make too much out of small effects that may not mean very much and a great many of our drugs, even well known and very popular ones, are little better than a placebo.

In any double-blind clinical trial the results are monitored by an outside body to ensure, for example, that any dangerous side-effect of the drug or treatment, is noticed and the trial can be stopped. In rare instances they also decide the drug, or treatment, is so successful that they also stop the trial so that everyone can benefit. When they do this it's usually a good sign the researchers are onto something big.

That's what happened in one of the first clinical trials of fecal transplants published last month in the New England Journal of Medicine:
Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

There's a description of the issue and the research at Wired's Superbug blog. They link to an NPR article that describes the work of a Canadian team to come up with synthetic feces called RePOOPulate.




Meow, meow, meow

Whatcha lookin' at?!?!?
I heard this article on the radio a couple of years ago and decided to look at it again for some reason. The name of the article is "Glowing Kittens Help in Fighting AIDS".

The idea behind this article is that you have a mixture consisting of monkey genes, used to block the HIV infection, and jellyfish genes, used to see whether the gene concoction was taken up by the cells. This concoction is injected into cat eggs. When the cat is growing up, the cat will produce the proteins that are feline "AIDS-resistant". In order to tell whether the kitten is feline AIDS resistant, you shine a blue light, in the dark, on these little critters and they glow green.These genes are passed on to the offspring; thus, protecting the offspring from feline AIDS as well.

Using these kittens as a model system, one of the doctors, Dr. Eric Poeschla, is hoping that they can get insight into how to human gene therapy can use this technology.

As a side note, who wouldn't want a glow-in-the-dark cat?... Or any glow-in-the-dark pet, if you happen to be allergic to cats.

Tuesday, February 12, 2013

Life under ice


In Nature this week:
Lake-drilling team discovers life under the ice
Host of microbes found in lake deep under Antarctica's ice sheet.

The lake in question is a 60-square-kilometre body of water that sits on the edge of the Ross Ice shelf in West Antarctica. To reach it, Priscu, a glaciologist at Montana State University in Bozeman, and his team had to drill down 800 metres of ice.
...
Both water and sediment contained an array of microbes that did not need sunlight to survive. The scientists counted about 1,000 bacteria per millilitre of lake water — roughly one-tenth the abundance of microbes in the oceans. In Petri dishes, the bacteria show a “really good growth rate”, says Priscu.
...

The exact nature of the life unearthed by the US team will now be established by DNA sequencing and other tests. It will take at least a month to do the basic work, says Priscu.

“What we are all dying to find out now is, of course, ‘who’s there’ and ‘what’s their life style',” he says.

Researchers hope that the survival strategies of the subglacial microbes might offer clues to what the biology of extraterrestrial life might be like — Jupiter’s moon Europa, for instance, is thought to host a large sub-surface ocean of water where such life might be able to exist.


As photosynthesis is impossible without sunlight, the Lake Whillans bacteria must get their energy from a different source. This could be existing organic material, or, like the ‘chemotrophs’ found in gold mines and near deep-sea hydrothermal vents, the bacteria might run on chemical reactions involving minerals in the Antarctic bedrock and carbon dioxide dissolved in lake water.

“We have been allowed a glimpse into Antarctica’s subglacial world,” Priscu says. “I’m sure our results will change the way we view that continent.”

Monday, February 11, 2013

Ockham’s razor

An interesting article on William of Ockham (of Ockham’s razor fame) on BoingBoing today.

Here's the conventional translation:


plurality should not be posited without necessity,"

Wikipedia defines Ockham's razor as:

Among competing hypotheses, the one that makes the fewest assumptions should be selected.

Except that's not what Ockham actually said. He's been the victim of selective editing. What he really said is:

“Nothing ought to be posited without a reason given, unless it is self-evident or known by experience or proved by the authority of Sacred Scripture.”

Hmmm

Saturday, February 9, 2013

Moss carpet

Do you think this would work? I doubt it would last more than a few weeks unless you have a nice skylight but it's a nice idea.

La Chanh Nguyen’s moss carpet brings a little green into your bathroom in an unconventionally natural way. This living bathmat features three types of green mosses — forest moss, island moss and ball moss — that grow in plastazote, a decay-free, recycled latex foam. This mat will certainly liven up your shower space, and it’s wonderfully low maintenance. Because moss flourishes in damp, humid places, your bathroom is the ideal location for the moss carpet — even the green-thumb challenged can keep it alive!

Friday, February 8, 2013

Insect Astronomers

Not really relevant to anything we are talking about right now but I thought this was cool and that some of you might enjoy it.

Lowly Dung Beetles Are Insect Astronomers

Even the humble dung beetle, its life spent barely an inch above the ground, pushing balls of waste, steers by starlight.

This unsuspected navigational mechanism, described Jan. 24 in Current Biology, is likely not limited to the Scarabaeus satyrus examined by the researchers.

Peering through compound eyes into the darkness of night, insects around the world may be guided by stars.

Thursday, February 7, 2013

Moss cam no more

Sadly the moss cam appears to no longer be online although the James Reserve website suggests it is still operational.

Even the old page with all the information is gone although the Internet archive does bring it back with a lot of pictures and the answers to most questions you might want to ask about a moss cam.


  • 'what does it look like at night?' (ans=dark)
  • 'how much did it cost' (ans=$1832.72) 
  • 'what happens if a chipmunk comes by?' (ans= dangerous levels of excitement). 

Check out the hydrated and dehydrated pictures of the moss.

Wednesday, February 6, 2013

So you want to be a marine biologist?

So I was researching stuff about marine biology and different biologists' opinions how to succeed as one (for my Writing 2 class) and I came accross this.  This is posted on the Love Lab webpage.  It's quite entertaining, especially if you want to be a "real" marine biologist, and not work at SeaWorld.  I appologize if this post seems harsh to anyone.  I did not write it, the people from the Love Lab wrote it.  I am merely reposting it for entertainment.
 
Three Really, Really Bad Reasons to Want to Be a Marine Biologist

Reason Number One: "I want to be a marine biologist so that I can talk to dolphins."


Believing this is simply the Kiss of Death. This is the verbal equivalent of reaching down your throat, pulling out your own intestines, wrapping them around your neck and choking yourself. When we hear this our impulse is to thwack you a good one on your keester with the frozen haddock we keep within arm’s reach just for this occasion.

And why is that? It is because, and please listen carefully, while you may want to talk to dolphins, dolphins do not want to talk to you. That’s right. Mostly, dolphins want to eat fishes and have sex with other dolphins. And that pretty much cuts you out of the loop, doesn’t it? Oh, I know that there are the occasional dolphins that hang around beaches, swim with humans and seem to be chummy, but these are the exceptions. You don’t judge the whole human race by the people who attend monster car rallies, do you?

Just be honest with yourself. If you want to talk to dolphins you don’t want to be a biologist. What you really want to do is explore your past lives, get in touch with the Cosmic Oneness and conduct similar-minded individuals on tours to Central America looking for evidence that We Are Not Alone. Our experience is that people who feel this way last about 6.5 minutes in any biology program.

Reason Number Two: "I want to be a marine biologist because I really like Jacques Cousteau."


That’s nice. We really like Jacques Cousteau, too. But, drinking thousands of gallons of red wine while scuba diving around the world does not make you a marine biologist. It makes you a wonderful and effective spokesperson for the sea, and gives you a liver with the consistency of a chocolate necco wafer, but it does not make you a marine biologist.

Reason Number Three: "I want to be a marine biologist because I want to make big bucks."


Okay, here’s the bottom line. By Federal law, marine biologists have to take a vow of poverty and chastity. Poverty, because you are not going to make squat-j-doodly in this job. Just how squat is the doodly we are talking about? Well, five years after finishing my PhD I was making slightly less than a beginning manager at McDonalds. Ooh, a 36 year old guy with 13 years of college and 5 years of post-doctoral experience making just about as much as a semi-literate 19 year old with pimples the size of Bolivia, who can speak perhaps 3 words at a time before the term "you know" enters the conversation.

And chastity because, well, who’s going to date a marine biologist? The smell alone tends to dissuade a large proportion of the opposite sex.
 
Two Really, Really Good Reasons to Want to Be a Marine Biologist

Reason Number One: "You can dress and act almost any way you want."


This is true. Marine biologists are almost entirely free of any of those silly restrictions that blight the professional landscape of our fellow proletarians. This is because no one really cares about what we do or what we say. You want to come to work dressed in scabrous khaki shorts and a torn black Sandman shirt? Fine. You want to grow a scruffy beard, get a tattoo of a gooseneck barnacle on your arm or burp at inopportune moments? No problem, just do good work.

Reason Number Two: "If you like it, just do it."


Look, the reality is that you only go around once in life and if, by chance, you do come back, knowing how you have behaved in this life, you will undoubtedly come back as a slime mold. And most slime molds cannot be marine biologists. So just go out there and do what you enjoy. Marine biology is a wonderful profession. You want to find cancer cures by grinding up sponges? How about figuring out why hammerhead sharks always come back to the same seamount? Or where is the missing carbon dioxide that industries are producing; could the ocean be soaking it up? All neat projects. But pay attention here. None of this involves drinking copious quantities of fermented grape juice, while intoning "The ocean, she is strange and wondrous, filled with animals that disturb even a Frenchman."

The ocean is an exciting, never-dull place that is perfect for piddling away your existence. And just think, you actually get paid to think cool thoughts and do cool things.

Learn about research at the UC Reserves

On Friday there will be an all day conference highlighting some of the work/research that is being conducted at the UC Natural Reserves.  You can come to any or all of it, so check out the schedule.  Everything from sea otters to parasites to painting, and lots of interesting work presented at the 2 poster sessions.   It's on campus in the Bren building.

Two minutes



Can you describe your thesis in two minutes?

From the 2 minute thesis content at PhD comics.

Tuesday, February 5, 2013

New Research is redefining "normal" sexual behavior.


I came across this recently and have come back to it for this post because I thought it might prove interesting as we study speciation and because it's really just hilarious to read. The Australian splendid-fairy wren has to be in the top ten (along with the honey badger) for most hardcore animal. 
It also brings up the interesting social question of, if the animals do it on the daily, can we even look down on this behavior?

Arsenic Life Redux

Nov. 29, 2010. NASA announces a news conference "to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life."

If you don't remember this then read the story as it unfolded here: The Arsenic Chronicles
A humble arsenic-friendly microbe from Mono Lake, Calif., has recently stirred a tempest in the science world's teapot. Here's the story as it played out over the last two weeks in tweets, blogs and news conferences, of course.

Now, with that background, you may enjoy this article from USA Today a few days ago:
Glowing reviews on 'arseniclife' spurred NASA's embrace
USA Today reporters got hold of Science's reviews of the original article via a Freedom of Information Request.

Pace says there was "poor judgment at multiple levels" in the arseniclife case, from an "overly exuberant" interpretation of the study results by the authors to the peer reviewers missing "the big crux of the results: the claim of absence of phosphorus," to NASA repeating some of the mistakes that caused the agency trouble in 1996, when it publicized results suggesting a Martian meteorite contained microscopic signs of life. 

Monday, February 4, 2013

The punchline

Josh Schimel (faculty member in EEMB and ES) has an interesting post on his blog about a recent trend in talks.

(I)t has become common to end with an acknowledgements slide, usually that has a long list of funders, advisors, students who helped in the lab, etc. And since speakers are usually running out of time, they often skim over the list, almost dismissively, which does little to honor the contributors. In any case, to borrow a famous quote “Frankly my dear, I don’t give a damn.” What we want to learn from your talk is not your assistants’ names, but your science.

A final acknowledgements slide shuts off the conclusions before we've had a chance to assimilate them or to write them down—it undermines the message. That is shooting yourself in the foot, or maybe some part of your anatomy higher up and more vital.



I aint saying bacteria be gold diggers!

Gold Digging Bacterium Makes Precious Particles

We have learned in class that life can come in all sort of crazy shapes and sizes, as well as being able to live in conditions that most would not consider possible for life to even exist.  Historically gold ions have been shown to effectively prevent microbial growth, however a newly discovered bacterium Delftia acidovorans can survive conditions with high quantities of gold ions by creating solid gold forms.  They do this by creating a secondary metabolite which reduces gold in its ion form to its solid atomic form. 

So stop what your doing, because there is gold in these petri dishes!

Sunday, February 3, 2013

Superb Owl Sunday



Not my idea. Shamelessly stolen from BoingBoing and I'm sure it didn't start there. Check out all the Superb Owl pictures and videos people have posted in the thread. I love this Northern White-Faced Owl video which I haven't seen before - although the Japanese TV show is a bit distracting. If you are curious why the owl transforms itself into 'evil-owl' then Wikipedia provides a logical explanation:

  As shown, the owl has a rather notable defense mechanism. When faced with another owl slightly larger than it, the bird flares its wings to appear larger. When faced with something much larger than itself, it pulls its feathers inwards, elongates its body, and narrows its eyes to thin slits. It is thought that it uses this ability to camouflage itself,and it shares the ability with relatives like the African Scops Owl. In fact, many different types of owls have some ability to adopt a "concealing posture", also known by the German word Tarnstellung, in which they squeeze and thin their body to look like a broken tree branch, and some types may also narrow their eyes to slits and fold a wing sideways across their chest in a Dracula-like manner to hide the lighter-colored feathers on their underparts. Such behavior has also been documented in Eastern Screech Owls in a natural setting reacting to threats.

This video shows some Eastern Screech Owl's doing the same trick in a more natural setting so you can see how the camouflage works.

Owls are awesome.

Saturday, February 2, 2013

Great mechanical bird

I was browsing through the website of Erasmus Darwin House (that celebrates the amazing Erasmus) when I came upon an irresistible link to "Great mechanical bird". Erasmus just rose further in my estimation and I didn't think that was possible.


In the 18th century there was still no satisfactory explanation for the mechanics of flight and, inquisitive by nature, Darwin appears to have set himself to the task. Sketched out in his commonplace book in 1777 at the height of the 18th century quest for automata and artificial life, the bird (technically a goose) will be brought to life in a steam punk style reminiscent of the era. Using a small reservoir of compressed air as the in-flight rewinding mechanism in the book, Darwin’s description of a bird’s flight is very close to reality, and appears to be the first complete account of a power-plant and the necessary cycle of the wings’ movement – fascinating stuff! We’re working away at ensuring our model does this incredible invention justice.


Friday, February 1, 2013

Communication crisis

From Kathy, and well worth a read.


Opinion: Communication Crisis in Research
The problem threatens progress and stems from both a lack of attention to clear discourse and a scientific culture not focused on critical challenges.
...

It is often acknowledged that scientists don't communicate well with the public, but increasingly they don't communicate well with each other. The typical biomedical research presentation has become a dizzying whirlwind of incomprehensible slides, presented at lightening speed and labeled with unreadable font sizes and abbreviations known only to the speaker. Publications also pose problems. Many scientists report they don't have time to evaluate or even read the deluge of articles coming from the growing number of print and on-line journals. A recent New York Times article argued that the problem of scientific retractions is reaching a critical point. While many factors contribute to scientific inaccuracy, the sheer volume of publications and the obliqueness with which many are written, clearly play a role.  

This crisis of communication has developed slowly and almost imperceptibly. During the last 40 years the need for effective communication has increased while the quality of that communication has declined. This growing gap threatens progress.

What Is Life?















Two interesting articles on man-made chemical systems with strikingly lifelike characteristics. This relates more to the first few weeks, but it's still really cool. Check out the video on the first link. It's hard to believe those little guys aren't "alive."

It’s (Almost) Alive! Scientists Create a Near-Living Crystal

The ultimate goal of the work is to study how complicated collective behaviors arise from simple individual properties, perhaps informing molecular self-assembly projects, but it’s hard not to think about the origin-of-life implications.
“Here we show that with a simple, synthetic active system, we can reproduce some features of living systems,” Palacci said. “I do not think this makes our systems alive, but it stresses the fact that the limit between the two is somewhat arbitrary.”
Self-Replication Chemicals Evolve into Lifelike Ecosystem

Life makes more of itself. And now so can a set of custom-designed chemicals. Chemists have shown that a group of synthetic enzymes replicated, competed and evolved much like a natural ecosystem, but without life or cells.
"So long as you provide the building blocks and the starter seed, it goes forever," said Gerald Joyce, a chemist at the Scripps Research Institute and co-author of the paper published Thursday in Science. "It is immortalized molecular information."
Joyce’s chemicals are technically hacked RNA enzymes, much like the ones we have in our bodies, but they don’t behave anything like those in living creatures. But, these synthetic RNA replicators do provide a model for evolution — and shed light on one step in the development of early living systems from on a lifeless globe.