ScienceBlogs Channel : Life Science

Friday Cephalopod: For Monty [Pharyngula]

PZ Myers none@example.com — Fri, 10 Sep 2010 14:57:57 -0500

Mark (Monty) Montague was an occasional commenter here, and a major contributor at TONMO with a passion for cephalopods. I'm sorry to report that he died in in a diving accident this summer. There will be a memorial service on 2 October at Caltech.

Sepioteuthis sepioidea

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We've lost one of the greats: George C. Williams [Pharyngula]

PZ Myers none@example.com — Fri, 10 Sep 2010 12:22:21 -0500

Williams was one of the giants of 20th century evolutionary biology, and he died on Wednesday. Michael Ruse offers a brief summary of his career, while Edge has personal testimonials from people who knew him. I never met him, to my regret, but knew his work, which was enormously influential.

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Bring in the Noise [Oscillator]

Christina Agapakis none@example.com — Fri, 10 Sep 2010 09:48:10 -0500

Noise obscures meaningful information. Noise is what ruins your carefully designed synthetic biology gene circuit. But noise is part of life and life, it turns out, needs noise. There's a terrific review article in this week's Nature discussing recent theoretical and experimental work on biological noise showing functional roles for molecular, genetic, and evolutionary noise.

From the abstract:

The genetic circuits that regulate cellular functions are subject to stochastic fluctuations, or 'noise', in the levels of their components. Noise, far from just a nuisance, has begun to be appreciated for its essential role in key cellular activities. Noise functions in both microbial and eukaryotic cells, in multicellular development, and in evolution. It enables coordination of gene expression across large regulons, as well as probabilistic differentiation strategies that function across cell populations. At the longest timescales, noise may facilitate evolutionary transitions.

Of course I am most interested in what this research means for synthetic biology, where the focus often lies on the elimination or reduction of noise through buffered genetic feedback circuits. But what if noise has to be part of a circuit in order for proper function?

As an impediment to the design of deterministic circuits, noise is a nuisance. But a new wave of studies is showing how noise can, and does, provide critical functions that would be difficult or impossible to achieve by (hypothetical) deterministic gene circuits.

Maybe gene expression stochasticity ain't noise pollution after all!

Thanks for the link Michael!

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Origins of Mind 101 [The Thoughtful Animal]

Jason G. Goldman none@example.com — Fri, 10 Sep 2010 08:35:00 -0500

If I had to describe the mission, the point, the raison d'etre of the entire field of psychology in just one sentence, I would say: Psychology aims to determine the relative extents to which biology and experience determine cognition and behavior." And, as you might expect, there are widely differing schools of thought. Nativists emphasize genetics, biology, and innate mechanisms. By contrast, the empiricists insist that babies are born into the world with no a priori knowledge thereof, and just a powerful statistical associative learning mechanism by which they piece together their understanding of reality. In reality, it is likely that there are some things that are innate and some things that require learning. Other mechanisms are probably innate but require experience or learning to properly "tune" or "sharpen" the system.

Rene Descartes speculated that the self (or more specifically, the mind) perceives its own body due to the senses. However, he was aware that the senses could be fooled, and explained the apparent limits of sensory perception with the wax argument: Consider a piece of wax. You perceive certain characteristics about it, such as shape, texture, size, color, smell, etc. But when you move the wax towards a flame, the perceived characteristics change as the wax begins to melt. You know it is still the same piece of wax, but the senses inform you however that the characteristics have changed. So, Descartes argued, sensory perception is not sufficient to properly understand the nature of the wax; instead, he must use his mind. He wrote "...And so something which I thought I was seeing with my eyes is in fact grasped solely by the faculty of judgment which is in my mind." Descartes thus discarded perception and focused solely on deduction as a useful method by which we can come to know the world.

Figure 1: Rene Descartes, 1596-1650.

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Testosterone Levels In Carcharhinus leucas: Is It All Bull? [Observations of a Nerd]

Christie Wilcox none@example.com — Fri, 10 Sep 2010 04:19:08 -1000

So, Shark Diver set out a challenge for Ocean of Pseudoscience Week that I simply had to look into. He wanted to know whether there's any science backing the notion that Bull Sharks, Carcharhinus leucas, have extraordinarily high testosterone levels and might thus be usable as a source for legally obtainable steroids - an idea, apparently, started by some video game.

The rumor, as I'd heard it, is that the fierce attitudes of these large and aggressive sharks is due to unfathomably high circulating levels of testosterone. Specifically, these menacing monsters supposedly have higher serum testosterone levels than any species on the planet, land or sea, and that even a female bull shark has higher levels than a testosterone-raged male elephant in musth.

I know I'm as much to blame as anyone, as I've repeated that line myself. But suddenly, I realized, I don't know if it's true. How do the circulating testosterone levels compare between bull sharks and other species? Could you procure enough testosterone by catching and eating bull sharks to beef up your body? I simply couldn't let Shark Diver's challenge go unanswered.

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Feathers are Not Just for Flying [Life Lines]

dolittle none@example.com — Thu, 09 Sep 2010 17:46:04 -0500

In a recent issue of Science magazine, researchers Li et al., were able to determine the plumage color of an extinct non-avian theropod dinosaur. This was possible due to the presence of melanin-containing melanosomes, which were preserved in the fossilized feathers. The fossilized remains were from a Jurassic troodontid, Anchiornis huxleyi, an ancestor of Archaeopteryx and modern birds. The presence of colored feather patterns in a bird prior to the evolution of true flight, suggests that feather coloration may have evolved for reproductive or communication purposes.

Click here for more information.

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One could say that bats evolved twice [Greg Laden's Blog]

Greg Laden none@example.com — Thu, 09 Sep 2010 16:28:53 -0500

Much in the same way that "woodpeckers" have evolved several times (most are birds that look like each other, but then there is the aye-aye and Darwin's finch), one can say that the nightjars are birds poking around in the insect-eating bat niche.

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Concavenator: an incredible allosauroid with a weird sail (or hump)... and proto-feathers? [Tetrapod Zoology]

Darren Naish none@example.com — Thu, 09 Sep 2010 09:49:00 -0500

The last few weeks have been pretty exciting for people interested in theropod dinosaurs.... but then, you could say this about most weeks: new theropods are constantly being published.

Last week saw the publication of the weird, functionally two-fingered, short-footed maniraptoran Balaur bondoc from the latest Cretaceous of the Haţeg Basin in Romania (Csiki et al. 2010) [left foot of Balaur shown here, from BBC News]. When Balaur was alive, the Hateg region was an island, so this was another of those weird, island-dwelling dinosaurs we've often hoped would exist. I have a vested personal interest, given that its discovery has implications for work I've published on Haţeg maniraptorans (Naish & Dyke 2004).

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What is the oldest living organism? [Greg Laden's Blog]

Greg Laden none@example.com — Thu, 09 Sep 2010 09:33:58 -0500

Rachel Sussman shows photographs of the world's oldest continuously living organisms -- from 2,000-year-old brain coral off Tobago's coast to an "underground forest" in South Africa that has lived since before the dawn of agriculture.

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... but mostly, I'm a grad student. [Observations of a Nerd]

Christie Wilcox none@example.com — Thu, 09 Sep 2010 06:29:28 -1000

Sure, the field days sound exciting and magical, don't they? So, of course, it's hard not to want to paint the picture that that is what it's like to be a marine biologist. But I don't get to do that kind of work often. Here's an average day in my life, a work day, is like:

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[Pharyngula]

PZ Myers none@example.com — Wed, 08 Sep 2010 16:11:49 -0500

Water lily

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Shrooms [Aardvarchaeology]

Martin R none@example.com — Wed, 08 Sep 2010 14:25:35 -0500

At my wife's suggestion, I quit work 1½ hour early today and cycled with her and the kids into the woods to pick mushrooms. Lovely sunny afternoon, and I can report that the hills between Lakes Lundsjön and Trehörningen are rich in boletes right now. Here are the species we got:

King bolete, Stensopp/Karl Johan, Boletus edulis
Velvet bolete, Sandsopp, Suillus variegatus
Orange Birch Bolete, Tegelsopp, Leccinum versepelle
Copper brittlegill, Tegelkremla, Russula decolorans
Chanterelle, Kantarell, Cantharellus cibarius
Fårticka, Albatrellus ovinus

Wireless Cellular Communication [Oscillator]

Christina Agapakis none@example.com — Wed, 08 Sep 2010 11:40:33 -0500

Cells are constantly jibber jabbering, sending messages to each other to coordinate behavior, both within a population of single-celled organisms or between cells of an individual multicellular organism. Most of these signals are chemicals that float around in the liquid that surrounds the cells but there recently has been an increased appreciation for cells' sense of "smell"--how cells respond to chemicals that are present as gasses.

A brand new paper outlines the discovery of "olfaction" in a species of bacteria, Bacillus licheniformis. Trying to save space on a 96 well dish by putting different experiments side by side, the researchers accidentally discovered that even though each experimental strain was separated in its own plastic well, bacteria growing closer to wells that were producing gaseous ammonia were forming more pigment and more vigorous biofilms. As olfaction can be defined at its simplest as responding in some way to volatile chemicals, these bacteria seem to display olfaction, although the details of how the ammonia to biofilm response occurs have not yet been explored.

In higher organisms such as fungi, response to gasses has been better studied, allowing for the creation of genetic parts for synthetic biology that turn on in the presence of volatile acetaldehyde. When the DNA sequence responsible for sensing acetaldehyde from the fungus Aspergillus nidulans is engineered into cultured hamster cells, gene activation can be measured as a function of distance away from the source of acetaldehyde on a plate:

The acetaldehyde-smelling part can be used to activate any gene that the researcher wants, including genes that are required for the cell's survival. Such a strain would require an acetaldehyde producing strain nearby in order to survive, creating a synthetic ecosystem that communicates through the air!

Being able to listen in to cellular conversations and understanding all the ways that organisms can sense and interact with their environment is amazing and incredibly powerful for the synthetic biology toolbox. Like natural ecosystems, synthetic biological systems made up of multiple engineered strains or even species can create ecosystems that together can do much more than any one species alone.

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Was the Era of Widespread Antibiotic Use Much Earlier Than Previously Thought? [Mike the Mad Biologist]

Mike none@example.com — Wed, 08 Sep 2010 10:19:15 -0500

One of the constant assumptions in the field of antibiotic resistance is that the massive exposure of bacteria to antibiotics, and the evolution of resistance to these antibiotics, didn't occur until after the widespread introduction of penicillin and other antibiotics less than a century ago. But ScienceDaily reports that we might have to rethink this:

A chemical analysis of the bones of ancient Nubians shows that they were regularly consuming tetracycline, most likely in their beer....

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Ele-Comm: Short for Elephant Communication [Life Lines]

dolittle none@example.com — Wed, 08 Sep 2010 09:01:21 -0500

Caitlin O'Connell-Rodwell is a Stanford University professor whose research focuses on how elephant vocalizations travel through the ground for great distances, and how other elephants can understand them, just as they understand acoustic sound, which travels through the air. O'Connell-Rodwell is the author of The Elephant's Secret Sense. You can see videos of some of the elephant communication experiments she describes in the podcast on her Utopia Scientific site. The links to the videos are on this page.

Early in her research, O'Connell-Rodwell noticed behavior that indicates elephants are listening to acoustic (airborne) sounds by putting their ears out and orienting toward the sound's source. At other times, she also noticed a more puzzling behavior: Several elephants would freeze simultaneously, sometimes in mid-stride, and would press their front feet into the ground. They might also roll a foot forward so that only their toes touched the ground. At other times, they would lift a front leg. The behavior reminded her of the behavior she saw in insects that communicate seismically.

She began a series of experiments that eventually found that:

Low-frequency elephant vocalizations, which are below the threshold of human hearing, travel through the ground in the same waveform as they do in the air. The ground vocalization can travel faster or more slowly than acoustic sound, depending on soil conditions, but has the potential of travelling further as there is no outer limit to how far sounds can travel through the earth.

When she played a recorded elephant vocalization through the ground only (not through the air), other elephants detected the vocalization.

Elephants understood the ground-borne vocalizations. For example, they responded appropriately to an alarm call from another elephant by assuming their defensive posture of bunching and freezing. They also responded only to alarm calls of elephants living in the area rather than those made from elephants elsewhere.

Further research revealed that there are two ways elephants 'hear' sound waves traveling through the ground:

They have an enlarged malleus, a middle ear bone that plays an important role in hearing. Animals that communicate seismically often have an enlarged malleus as it also facilitates bone conducted detection of vibrations.

Elephants can close their middle ear canal, forming a closed acoustic tube which enhances bone conduction and blocks out acoustic sound, helping the elephant focus on the vibration pathway.

They have an acoustically designed foot, with a thick fat pad that perhaps helps in the transmission or conduction of vibrations.

O'Connell-Rodwell was interviewed in LifeLines podcast episode 25. In the first segment, she discusses how elephants communicate seismically during migration. In the second segment, she describes how they sense these seismic vibrations using their feet and trunks. Click here to listen to the full podcast.

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A marine biologist sounds good... [Observations of a Nerd]

Christie Wilcox none@example.com — Wed, 08 Sep 2010 04:56:01 -1000

Graduate Student. Marine Biologist. Science Blogger.

I put on a lot of hats in my daily life, and the end result is that when someone asks me what I do for a living, I usually want to answer "I'm a Marine Biologist." Sounds good, doesn't it? Recently I've had a few people ask to interview me, and when I agree they all ask what it is like to be me. A Marine Biologist! It sounds so exciting! So...what do you do, anyway?

Truth is, what I do depends a lot on what day it is. There are class days - those are fairly self-explanitory. There are work days, which make up the majority of my daily life. And there are field days. I love field days. They're the fun ones to talk about. So why don't we start there? Here are some examples of a typical field day... Let's see if you still think being a marine biologist is glamorous after these.

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Dr. Isis's Shoe of the Week [On Becoming a Domestic and Laboratory Goddess]

Isis the Scientist none@example.com — Tue, 07 Sep 2010 22:06:45 -0500

The fine folks who are handling the lab remodel told me that my office would be done today. I walked up to find a desk and painted walls. It did not occur to them, however, that I might need a chair. I have no chair.

So, I bought these...

Figure 1: The Catwalk Boot. $39.95 at ShoeDazzle.

I won't lie though. My attention was more focused on her chair.

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Edible Symbiosis [Oscillator]

Christina Agapakis none@example.com — Tue, 07 Sep 2010 13:27:28 -0500

A delightful lunch conversation about fruits introduced me to what may be my new favorite symbiotic relationship! Figs are not actually fruits but a mass of inverted flowers and seeds that are pollinated by a species of tiny symbiotic wasps. The male fig flower is the only place where the female wasp can lay her eggs, at the bottom of a narrow opening in the fruit that she shimmies her way through. The baby wasps mature inside the fig into males that have sharp teeth but no wings and females ready to fly. They mate, the males chew through the special fig pollen holders and drop them down to the females, chew holes in the skin of the fig to let the females out, and then die. The females, armed with the pollen, fly off in search of new male figs to lay her eggs in. In the process some of the female wasps land on female figs that don't have the special egg receptacle but trick the female into shimmying inside. As the female wasp slides through the narrow passage in the fig her wings are ripped off (egg laying is a one-way mission) and while she is unsuccessful in laying her eggs, she successfully pollinates the female flower. The female flower then ripens into the fig that you can get at the supermarket, digesting the trapped wasp inside with specialized enzymes! For the females that managed to lay their eggs the life cycle continues with a new brood of tiny wasps ready to mate and pollinate.

There is a whole PBS special about figs that I really want to watch now, here are some clips from youtube:

Thanks to Mara for teaching me about the wonders of figs!

UPDATE: Oooh ooh also check out this great post about mutualism and active vs. passive pollination of figs over at Observations of a Nerd!

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The Irish Genome [Pharyngula]

PZ Myers none@example.com — Tue, 07 Sep 2010 13:22:27 -0500

What a curious paper — it's fine research, and it's a useful dollop of data, but it's simultaneously so 21st century and on the edge of being completely trivial. It's like a tiny shard of the future whipping by on its way to quaintness.

Researchers have for the first time sequenced the genome of an Irishman, a fellow confirmed to be the product of at least 3 generations of fully Irish ancestors.

It's a good piece of work, another piece in the puzzle of human genomics, but it's also a little bit odd. I'm always excited to see another organism's genome sequenced, the first marsupial, the first sea anemone, the first avian, etc., and it's also become a bit commonplace (oh, another bacterium sequenced…); it's just weird to see "Irish" announced as a new novel addition to the ranks of sequenced organisms, as if it were Capitella or something. Cool, but a little jarring.

It's also a genre with limited prospects. If you're busy sequencing the first Armenian or the first New Guinean or the first Luxembourger, work fast — I can't quite imagine that most will warrant a publication, except as a formality, as I imagine this paper is. We're entering the era of personalized genomics, when anyone will be able to get their sequence done for under a thousand dollars. I don't imagine that a paper titled "Sequencing and analysis of PZ Myers' human genome" will get published in Nature. But if anyone wants to try, I'll gladly send them a few cells and my permission.

Anyway, the paper got the sequence of this Irish fella. They identified many unique single nucleotide polymorphisms that may be useful molecular markers of Irish ancestry; a few of the new alleles seem to be associated with diseases like inflammatory bowel and chronic liver problems. They identified a few genes bearing the signature of positive selection. Here are their conclusions:

The first Irish human genome sequence provides insight into the population structure of this branch of the European lineage which has a distinct ancestry from other published genomes. At 11 fold genome coverage approximately 99.3% of the reference genome was covered and more than 3 million SNPs were detected, of which 13% were novel and may include specific markers of Irish ancestry. We provide a novel technique for SNP calling in human genome sequence using haplotype data and validate the imputation of Irish haplotypes using data from the current Human Genome Diversity Panel (HGDP-CEPH). Our analysis has implications for future re-sequencing studies and suggests that relatively low levels of genome coverage, such as that being used by the 1000 genomes project, should provide relatively accurate genotyping data. Using novel variants identified within the study, which are in linkage disequilibrium with already known disease associated SNPs, we illustrate how these novel variants may point towards potential causative risk factors for important diseases. Comparisons with other sequenced human genomes allowed us to address positive selection in the human lineage and to examine the relative contributions of gene function and gene duplication events. Our findings point towards the possible primacy of recent duplication events over gene function as indicative of a genes likelihood of being under positive selection. Overall we demonstrate the utility of generating targeted whole genome sequence data in helping to address general questions of human biology as well as providing data to answer more lineage-restricted questions.

Hey, it's data. But I think it will be made much more interesting when it acquires more context. One Irish genome doesn't give us much information on Irish variation. It's information to complement the 1000 Genomes Project (the Irish study is not part of that bigger project), which intends to take a nice snapshot of human genetic diversity by sampling 100 individuals from each of 10 distinct populations. Then the hard part comes: comparing and analyzing everything.

Oh, and the digging out from all the ethnic jokes that will appear in the comments.

Tong P, Prendergast JGD, Lohan AL, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF and Loftus BJ (2010) Sequencing and analysis of an Irish human genome. Genome Biology (in press)

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Editor's Selections: Katrina, Music, Crickets, and Artificial Movement [The Thoughtful Animal]

Jason G. Goldman none@example.com — Tue, 07 Sep 2010 11:15:00 -0500

Here are my Research Blogging Editor's Selections for this week:

"Now, five years later, there's new evidence of the significant, negative impact of Hurricane Katrina on children's mental health." Many Children Still Haven't Recovered from Katrina.
"Congenital amusia is one of several different types of music perception impairments. A person with the disorder is born with a variety of symptoms, including an inability to recognize a familiar song without hearing the lyrics, an inability to discern the difference between two melodies, and difficulty perceiving when he or she is singing or hearing music performed out of tune." Sarah Stanley of the Curious! blog writes about congenital amusia.
"Working on an animal in a lab is a little like assuming a cow is a perfect sphere." In a post called Neurons in the Wild, Doctor Zen of NeuroDojo writes about field studies of crickets.
Over at Greta Munger's "Cognition and the Arts" course blog, check out What makes movement seem artificial?

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