Posts Tagged ‘Yale University’

Structure of color

Thursday, February 7th, 2013

AGELESS BRILLIANCE: Although the pigment-derived leaf color of this decades-old specimen of the African perennial Pollia condensata has faded, the fruit still maintains its intense metallic-blue iridescence.COURTESY OF P.J. RUDALL [downloaded from http://www.the-scientist.com/?articles.view/articleNo/34200/title/Color-from-Structure/]

AGELESS BRILLIANCE: Although the pigment-derived leaf color of this decades-old specimen of the African perennial Pollia condensata has faded, the fruit still maintains its intense metallic-blue iridescence.COURTESY OF P.J. RUDALL [downloaded from http://www.the-scientist.com/?articles.view/articleNo/34200/title/Color-from-Structure/]

Hard to believe those berries were collected more than four decades ago, according to Cristina Luiggi in her Feb. 1, 2013 article, Color from Structure, for The Scientist magazine. Her focus is on biological nanostructures and it is a fascinating article which I urge you to read in its entirety if you have the time and this kind of thing interests you. As you can see, the pictures are great.

Here are a few excerpts from the piece,

Colors may be evolution’s most beautiful accident. Spontaneous mutations that perturbed the arrangement of structural components, such as cellulose, collagen, chitin, and keratin, inadvertently created nanoscale landscapes that catch light in the most vibrantly diverse ways—producing iridescent greens, fiery reds, brilliant blues, opalescent whites, glossy silvers, and ebony blacks.

Structural colors, in contrast to those produced by pigments or dyes, arise from the physical interaction of light with biological nanostructures. These color-creating structures likely developed as an important phenotype during the Cambrian explosion more than 500 million years ago, when organisms developed the first eyes and the ability to detect light, color, shade, and contrast. “As soon as you had visual predators, there were organisms that were either trying to distract, avoid, or communicate with those predators using structural coloration,” says Yale University evolutionary ornithologist Richard Prum.

Ever since, structural coloration has evolved multiple times across the tree of life, as a wide range of organisms developed ways to fine-tune the geometry of some of the most abundant (and often colorless) biomaterials on Earth, engineering grooves, pockets, and films that scatter light waves and cause them to interfere with each other in ways we humans happen to find aesthetically pleasing.

Here’s why color derived from structure doesn’t fade, from Luiggi’s article,

Pigments and dyes are molecules that produce colors by the selective absorption and reflection of specific wavelengths of electromagnetic radiation. Structural colors, on the other hand, rely exclusively on the shape of the material and not its chemical properties. While pigments and dyes degrade and their colors fade over time, some types of structural coloration, which rely on the same materials that make up tree bark, insect exoskeletons, and claws or nails, can persist hundreds, thousands, and even millions of years after the death of the organism.

Structural color can be found in a lot of plant life,

Although there are only a handful of known examples of structural colors in fruits, there are plenty to be found in the leaves and petals of plants. Within every family of flowering plants, there is at least one species that displays structural colors.

“The presence of structural colors, especially in flowers, is likely used by pollinators to spot the position of the flower and to recognize it better,” Vignolini [Silvia Vignolini, a physics postdoc at the University of Cambridge] explains. But in some plants, the evolutionary purpose of structural coloration is harder to pin down. The leaves of the low-lying tropical spikemoss Selaginella willdenowii, for example, produce blue-green iridescence when young and growing in the shade, and tend to lose the structural coloration with age and when exposed to high levels of light. The iridescence is achieved by cells in the leaves’ upper epidermis, which contain a few layers of cellulose microfibrils packed with different amounts of water. This ultrastructure is often absent in the leaves of the same species growing in direct sunlight. Researchers hypothesize that the spikemoss turns off its iridescence by changing the water content of the leaves’ cell walls, says Heather Whitney, a research fellow at the University of Bristol who studies iridescence in plants.

This capability is not limited to plants. Insects (jewel beetles and the morpho butterfly are often cited) and fish also have evolved to include structural color as protective or attractive devices, from Luiggi’s article,

The brightest living tissues on the planet are found in fish. Under ideal conditions, for example, the silvery scales of the European sardine and the Atlantic herring can act like near-perfect mirrors—reflecting up to 90 percent of incoming light. It is an irony of nature that these shiniest of structures are not meant to be flaunted, but are intended as camouflage.

“When you’re out in the open water, if you drop down below 10 to 30 meters, in any direction you look, the intensity of light is the same,” explains Nicholas Roberts, a physicist at the University of Bristol who specializes in bio-optics. At that depth, a perfect reflector, or mirror, would seem invisible, because light is equally reflected from all sides and angles.

It will be interesting to see if there’s any future discussion of the giant squid in the context of structural color since, according to very recent research (as per my Feb. 1, 2013 posting), it appears to be covered in gold leaf when observed in its habitat.

Luiggi’s article starts with an ornithologist and circles back in a discussion about the difficulty of creating nanostructures, soft matter condensed physics, and birds,

To create structural colors, organisms must master architecture at the nanoscale—the size of visible-light wavelengths. “But it turns out that biology doesn’t do a good job of creating nanostructures,” Prum says.

Instead, organisms create the initial conditions that allow those nanostructures to grow using self-organizing physical processes. Thus, organisms exploit what’s known as soft condensed matter physics, or “the physics of squishy stuff,” as Prum likes to call it. This relatively new field of physics deals with materials that are right at the boundaries of hard solids, liquids, and gases.

“There’ve been huge advances in this field in the last 30 years which have created rich theories of how structure can arise at the nanoscale,” Prum says. “It has been very applicable to the understanding of how structural colors grow.”

Soft condensed matter physics has been particularly useful in understanding the production of the amorphous nanostructures that imbue the feathers of certain bird species with intensely vibrant hues. The blue color of the male Eastern bluebird (Sialia sialis), for example, is produced by the selective scattering of blue light from a complex nanostructure of b-keratin channels and air pockets in the hairlike branches called feather barbs that give the quill its lift. The size of the air pockets determines the wavelengths that are selectively amplified.

While there’s better understanding of the mechanisms involved in structural color, scientists are a long way from replicating the processes, from the article,

“The three-dimensional nature of the structures themselves is just so complex,” says Vukusic. [physicist Peter Vukusic, a professor of natural photonics at the University of Exeter, UK] “Were it to be a simple periodic system with a regular geometry, you could easily put that into a computer model and run simulations all day. But the problem is that they are never perfectly periodic.”

This article is open access so, as I noted earlier, all you need is the time. As of my Feb. 6, 2013 posting, there was some new research announced about scientists making observations about the structural color in peacock feathers and applying some of those ideas to develop better resolution in e-readers.

Phyto-mining; using plants to extract minerals

Wednesday, September 26th, 2012

Plants do it anyway, so, why not harness their ability to absorb nutrients and transform them into various materials for the mining industry? In the scientists at the University of York (UK) mentioned in a Sept. 20, 2012 news item on Nanowerk are doing precisely that,

Scientists at the University of York are to lead an international team that will explore the use of plants to recover precious metals from mine tailings around the world.

Researchers in the University’s Green Chemistry Centre of Excellence and the Centre for Novel Agricultural Products (CNAP) aim to develop ways to extract platinum group metals (PGM) discarded during mine processing which might then be used in catalysis. The research will investigate “phyto-mining,” which involves growing plants on mine waste materials to sponge up PGM into their cellular structure.

Initial studies show that plant cells used to phyto-mine PGM can be turned into materials for a variety of industrial applications – the one in most demand being catalytic converters for vehicle emissions control.

The Sept. 20, 2012 University of York news release (which originated the news item) notes,

The $1.4 million PHYTOCAT project is supported by the G8 Research Councils Initiative on Multilateral Research Funding. The team is led by the University of York in the UK with support from Yale University, the University of British Columbia and Massey University in New Zealand. [emphasis mine]

Professor James Clark, the Director of the Green Chemistry Centre of Excellence at York, says: “We are looking at ways of turning these residual metals into their catalytically active form using the plants to extract them from the mine waste. The plant is heated in a controlled way with the result that the metal is embedded in a nano-form in the carbonised plant.

“The trick is to control the decomposition of the plant in a way which keeps the metal in its nano-particulate or catalytically active form. Catalysis is being used more and more in industrial processes and particularly for emission control because of the demand for cleaners cars, so ‘phyto-mining’ could provide a sustainable supply of catalytically active metals.”

For PGM phyto-mining, the researchers will investigate plants known as hyperaccumulators which include about 400 species from more than 40 plant families. Plants such as willow, corn and mustard have evolved a resistance to specific metals and can accumulate relatively large amounts of these metals, which once absorbed into the plants’ cellular structure form nano-scale clusters than can then be used directly as a catalyst.

Professor Neil Bruce, of CNAP, added: “The ability of plants to extract PGMs from soil and redeposit the metal as nanoparticles in cells is remarkable. This project will allow us to investigate the mechanisms behind this process and provide a green method for extracting metals from mine tailings that are currently uneconomical to recover.”

(It makes sense that the University of British Columbia from my home province is participating, given the province’s heavy involvement in the mining industry.)

This proposed phyto-mining process has much in common with phytoremediation where plants are grown in polluted areas so they can absorb the pollutants from the soil as per my March 30, 2012 posting, which featured a guest writer, Joe Martin on the topic of phytoremediation.

I wonder what they will be doing to the plants for make them more suitable for the phyto-mining process.

Uncomfortable truths; favouring males a gender bias practiced by male and female scientists

Monday, September 24th, 2012

Nancy Owano’s Sept. 21, 2012 phy.org article on a study about gender bias (early publication Sept. 17, 2012 in the Proceedings of the National Academy of Sciences) describes a situation that can be summed up with this saying ‘we women eat our own’.

The Yale University researchers developed applications for a supposed position in a science faculty and had faculty members assess the applicants’ paper submissions.  From Owano’s article,

Applications were all identical except for the male names and female names. Even though the male and female name applications were identical in competencies, the female student was less likely to be hired, being viewed as less competent and desirable as a new-hire.

Results further showed the faculty members chose higher starting salaries and more career mentoring for applicants with male names.

Interestingly, it made no difference on hiring decisions as to whether the faculty member was male or female. Bias was just as likely to occur at the hands of a female as well as male faculty member.

I tracked down the paper (which is open access), Science faculty’s subtle gender biases favor male students by Corinne A. Moss-Racusin, John F. Dovidio, Victoria L. Bescroll, Mark J. Graham, and Jo Handelsman and found some figures in a table which I can’t reproduce here but suggest the saying ‘we women eat their own’ isn’t far off the mark. In it, you’ll see that while women faculty members will offer less to both genders, they offer significantly less to female applicants.

For a male applicant, here’s the salary offer,

Male Faculty               Female Faculty

30,520.82                    29, 333.33

 

For a female applicant, here’s the salary offer,

Male Faculty               Female Faculty

27,111.11                    25,000.00

To sum this up, the men offered approximately $3000 (9.25%) less to female applicants while the women offered approximately $4000 (14.6%) less. It’s uncomfortable to admit that women may be just as much or even more at fault as men where gender bias is concerned. However, it is necessary if the situation is ever going to change.

The Sept. 24, 2012 news release from Yale University features a quote from the lead author (Note: I have removed a link),

Yale University researchers asked 127 scientists to review a job application of identically qualified male and female students and found that the faculty members – both men and women – consistently scored a male candidate higher on a number of criteria such as competency and were more likely to hire the male. The result came as no surprise to Jo Handelsman, professor of molecular, cellular, and developmental biology (MCDB), a leading microbiologist, and national expert on science education. She is the lead author of the study scheduled to be published the week of Sept. 24 in the Proceedings of the National Academy of Sciences.

“Whenever I give a talk that mentions past findings of implicit gender bias in hiring, inevitably a scientist will say that can’t happen in our labs because we are trained to be objective. I had hoped that they were right,” said Handelsman, who is also a Howard Hughes Medical Institute Professor.

So Handelsman and Corinne A. Moss-Racusin, a postdoctoral associate in MCDB and psychology, as well as colleagues in social psychology decided to test whether this bias among researchers might help explain why fewer women than men have careers in science. They provided about 200 academic researchers with an application from a senior undergraduate student ostensibly applying for a job as lab manager. The faculty participants all received the same application, which was randomly assigned a male or female name. The faculty were asked to judge the applicants’ competency, how much they should be paid, and whether or not they would be willing to mentor the student.

In the end, scientists responded no differently than other groups tested for bias. Both men and women science faculty were more likely to hire the male, ranked him higher in competency, and were willing to pay him $4000 more than the woman. [emphasis mine] They were also more willing to provide mentoring to the male than to the female candidate.

I highlighted the sentence in the excerpt since the portion about the salary difference somewhat contradicts my own reading of the information in the study. If you are female, you will still be offered less money by male faculty but the percentage (9% less) is an improvement over the 14% differential offered by female faculty.  I do appreciate that these numbers have been crunched together and there will be individual differences, as well as, outliers but this finding certainly confirms ‘folk wisdom’ and points to the difficulty of facing uncomfortable truths for even the researchers and their sponsoring institutions.

ETA Sept. 25, 2012: There have been some comments about the research and the methodology on Uta Frith’s Science&shopping website:

Research on gender bias

Comments by David Attwell on Moss-Racusin et al. ‘Science faculty’s subtle gender biases’

Comments on comments by Virginia Valian

Comments on comments by Dorothy Bishop

H/T to Jenny Rohn for the information about Uta Frith’s coverage of the issue which I found in Rohn’s Sept. 25, 2012 posting about women, science, and bias (she mentions this recent research from Yale but in the context of other research and broader issues of gender bias in the sciences) for the Guardian science blogs.

ETA Sept. 26, 2012: The Canadian Broadcasting Corporation’s As It Happens radio show features an interview with Corinne A. Moss-Racusin about the paper in their Sept. 25, 2012 broadcast. Click here and scroll down to the Sept. 25, 2012 entry and keep scrolling until you see the speaker icon and Listen, click on Listen and the popup menu will appear. Scroll down to part 3 and click again (it’s the second interview). There’s also a Sept. 25, 2012 podcast in the left column of today’s front page screen of As It Happens, which I did not test.

It’s a bird. It’s a plane. No, it’s a laser!

Friday, October 14th, 2011

I couldn’t resist the Superman reference although it really should have been a Morpho butterfly or a jewel beetle reference since these are two other animals/insects that also display unusual optical properties courtesy of nanoscale structures.

Top: Male eastern bluebird (Sialia sialis, Turdidae). Credit: Ken Thomas (image in public domain). Published in Soft Matter, 2009, 5, 1792-1795. E.R. Dufresne et al., “Self-assembly of amorphous biophotonic nanostructures by phase separation.” Royal Society of Chemistry. http://dx.doi.org/10.1039/B902775K

According to the Oct. 12, 2011 news item on Nanowerk,

Researchers at Yale University are studying how two types of nanoscale structures on the feathers of birds produce brilliant and distinctive colors. The researchers are hoping that by borrowing these nanoscale tricks from nature they will be able to produce new types of lasers—ones that can assemble themselves by natural processes. The team will present their findings at the Optical Society’s (OSA) Annual Meeting, Frontiers in Optics (FiO) 2011, taking place in San Jose, Calif. next week. [It starts Sunday, Oct. 16, 2011.]

Devin Powell, in a May 13, 2011 article for Science News provides some additional detail,

The barbs of these feathers [from bluebirds, blue jays, and parrots] contain tiny pockets of air. Light striking the tightly packed air bubbles scatters, bringing out deep shades of blues and ultraviolet (which birds can see but humans can’t).

“Birds use these structures to create colors that they can’t make in other ways,” says Richard Prum, an  ornithologist at Yale University who discovered the mechanism behind this color.

To make a two-dimensional imitation of a bird feather, Yale physicist Hui Cao and her colleagues punched holes into a thin slice of gallium arsenide semiconductor. The holes were arranged like people in a crowd — somewhat haphazardly but with small-scale patterns that dictate roughly how far each hole is from its neighbor.

“The lesson we learned from nature is that we don’t need something perfect to get control,” says Cao, whose team describes their laser in the May 6 [2011] Physical Review Letters.

The latest work being presented is described this way in an Oct. 2011 news release (why aren’t people putting dates on their news releases????) from the Optical Society of America,

Inspired by feathers, the Yale physicists created two lasers that use this short-range order to control light. One model is based on feathers with tiny spherical air cavities packed in a protein called beta-keratin. The laser based on this model consists of a semiconductor membrane full of tiny air holes that trap light at certain frequencies. Quantum dots embedded between the holes amplify the light and produce the coherent beam that is the hallmark of a laser. The researchers also built a network laser using a series of interconnecting nano-channels, based on their observations of feathers whose beta-keratin takes the form of interconnecting channels in “tortuous and twisting forms.” The network laser produces its emission by blocking certain colors of light while allowing others to propagate. In both cases, researchers can manipulate the lasers’ colors by changing the width of the nano-channels or the spacing between the nano-holes.

What makes these short-range-ordered, bio-inspired structures different from traditional lasers is that, in principle, they can self-assemble, through natural processes similar to the formation of gas bubbles in a liquid. This means that engineers would not have to worry about the nanofabrication of the large-scale structure of the materials they design, resulting in cheaper, faster, and easier production of lasers and light-emitting devices.

Here’s an image of a ‘feather-based laser’,

Top: A laser based on feathers with the sphere-type nanostructure. This laser consists of tiny air holes (black) in a semiconductor membrane; each hole is about 77 nanometers across. (Scale bar = 5 micrometers.) Credit: Hui Cao Research Laboratory / Yale University.

As for the Morpho butterfly and jewel beetle, I last posted about gaining inspiration from these insects (biomimicry) in my May 20, 2011 posting in the context of some anti-counterfeiting strategies.

I first came across some of this work on the optical properties of nanostructures in nature in a notice about a 2008 conference on iridescence at Arizona State University. Here’s the stated purpose for the conference (from the conference page),

A unique, integrative 4–day conference on iridescent colors in nature, Iridescence: More than Meets the Eye is a graduate student proposed and organized conference supported by the Frontiers in Life Sciences program in Arizona State University’s School of Life Sciences. This conference intends to connect diverse groups of researchers to catalyze synthetic cross–disciplinary discussions regarding iridescent coloration in nature, identify new avenues of research, and explore the potential for these stunning natural phenomena to provide novel insights in fields as divergent as materials science, sexual selection and primary science education.