Much ado about sitting

A few years ago, athletic shoe companies began to cash in on a study or two suggesting that running in shoes was dangerous, guaranteed to ruin your joints and your life, make you less attractive and confident, etc. (at least, that’s how it was translated to press coverage). The only viable answer, vested marketing implied, was to buy a new pair of shoes with less shoe in them.

Despite the obvious irony, consumers flocked in droves to purchase sweet new kicks and rectify their embarrassing running habits. Much like any other fitness craze, popular active-lifestyle magazines ran articles about the trend spinning a small amount of scientific research into definitive conclusions right next to advertisements for the shoes themselves. Fast forward to 2014 wherein the makers of arguably the most notorious shoes in the minimalist sector, the Vibram Five Fingers line, have moved to settle a lawsuit alleging the claimed health benefits of the shoes were not based on evidence. The market frenzy for minimalist footwear appears to have sharply abated. There are even blatant examples of market backlash in the introduction of what could be described as “marshmallow shoes,” such as the Hakko, with even more padding than runners were used to before the barefoot revolution.

An eerily similar phenomenon has appeared, i.e. market capitalisation on nascent scientific evidence, in the latest demon threatening our health: sitting. At the bottom of the orogenic marketplace for accessories designed to get workers a bit less semi-recumbent in the workplace. This market was virtually non-existent only a few years ago, yet now is substantial enough to have spawned an entire genre of internet article.

There is even a new term gaining traction for the condition: “sitting disease.” I sure hope it’s not catching. For now at least the term seems to remain quarantined in quotation marks most places it is used.

Many of the underlying articles in science journals are what is euphemistically referred to as survey science. Long generational time, lack of uniform cultivation standards and potential ethical considerations make Homo sapiens a rather poor model organism. Even if survey data were considered reliable (a dubious assumption), this only reveals associations. Even accelerometer studies, like those at the Mayo Clinic, only measure activity for a few weeks. The results can’t tell you that sitting alone causes obesity. An equally fair hypothesis would be that obesity increase the likelihood to stay sitting, but that’s just called inertia.

Although the studies and their press coverage motivate a burgeoning marketplace for NEAT accessories they don’t actually tell us much in the way of new information. A sedentary lifestyle is unhealthy. Attempts to increase the amount of low-intensity activity throughout the day, such as using a walking desk, are likely to motivate appetite. Without considering diet (and downplaying the importance of exercise), a standing desk, sitting ball, or occasional walking meeting is not likely to have tremendous health benefits when taken alone. And despite the rhetoric, maintaining a smoking habit to break up your sit-time with walks to the outdoors is probably not an equivalent trade-off. Presenting health management in such an unbalanced, single-variable way seems more motivated by trendiness for some, revenue for others, and both for the press. It is not that sitting is actually good for you, it’s just myopic to focus solely on that one health factor. As part of a a sedentary lifestyle gestalt, yes, it does play a role in promoting ill-health. Then again, if you think about it, you probably already knew that before it was cool.


Avoid sensationalist science journalism, consider the sources:
Ford, E.S., and Caspersen, C.J. (2012). Sedentary behaviour and cardiovascular disease: a review of prospective studies. Int J Epidemiol 41, 1338–1353.
Hamilton, M.T., Hamilton, D.G., and Zderic, T.W. (2007). Role of low energy expenditure and sitting in obesity, metabolic syndrome, type 2 diabetes, and cardiovascular disease. Diabetes 56, 2655–2667.
Katzmarzyk, P.T., Church, T.S., Craig, C.L., and Bouchard, C. (2009). Sitting time and mortality from all causes, cardiovascular disease, and cancer. Med Sci Sports Exerc 41, 998–1005.
Rosenkranz, R.R., Duncan, M.J., Rosenkranz, S.K., and Kolt, G.S. (2013). Active lifestyles related to excellent self-rated health and quality of life: cross sectional findings from 194,545 participants in The 45 and Up Study. BMC Public Health 13, 1071.
Rovniak, L.S., Denlinger, L., Duveneck, E., Sciamanna, C.N., Kong, L., Freivalds, A., and Ray, C.A. (2014). Feasibility of using a compact elliptical device to increase energy expenditure during sedentary activities. Journal of Science and Medicine in Sport 17, 376–380.
Schmid, D., and Leitzmann, M.F. (2014). Television Viewing and Time Spent Sedentary in Relation to Cancer Risk: A Meta-analysis. JNCI J Natl Cancer Inst 106, dju098.
Young, D.R., Reynolds, K., Sidell, M., Brar, S., Ghai, N.R., Sternfeld, B., Jacobsen, S.J., Slezak, J.M., Caan, B., and Quinn, V.P. (2014). Effects of Physical Activity and Sedentary Time on the Risk of Heart Failure. Circ Heart Fail 7, 21–27.

“Where is everybody?”

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Don’t get too excited about finding E.T. just yet. Get excited about the engineering.

A few days ago NASA had a press conference moderated by NASA Chief Scientist Ellen Stofan. The filtered headline that eventually made its way into the popular consciousness of the internet is that the discovery of extraterrestrial life is a paltry couple decades away. The way the conference was parsed into news form range from the relatively guarded “NASA scientists say they’re closer than ever to finding life beyond Earth” at the LA Times to the more sensational “NASA: ALIENS and NEW EARTHS will be ours inside 20 years” at the The Register. As statements, the former headline is almost unavoidably true given an assumption that humans eventually stumble upon life off-planet, and the latter is only one more over-capitalised word from being wholly fantastic. Neither actually touches on the content of the NASA press conference.

The impetus of the conference was partially fueled by an April announcement of a discovery by the Kepler program of the Earth-similar Kepler 186f, which happens to reside in the habitable zone of its siminymous parent star. Although Kepler 186f definitely might be sort of a bit more Earth-like, its discovery was only the latest in a long list of over 1800 exoplanets posited to exist to date. Although the techniques for exoplanet discovery planetary transit attributable stellar dimming, are not infalliable [paywalled primary source], the continued refinement of modern signal processing for unearthing (heh) exoplanet planet signatures makes this an exciting time to look skyward.

The speakers took a broad view of progression toward answering the question “are we alone?” John Grunsfeld, Hubble mechanic extraordinaire, emphasised the approach of looking for spectral signals corresponding to bio-signatures with the upcoming James Webb telescope. Of course, the terracentric focus shared by the panel means that NASA plans to look for signals associated with Earth life: water, methane, oxygen, etc. Carl Sagan et al. considered the task of finding similar biosignatures on Earth itself. Looking for signs we know to be associated with our own personal experience of life is our best current guess for what we should be looking for, but no guarantee exists that it is the right one. We are no longer too enthralled by the idea of trading arsenate for phosphate, but our own planet has plenty of examples of strange metabolism, that we should expect life off planet to consist of more peculiar possibilities. Imagine our chagrin if we spend a few centuries looking for spectral signatures of water before stumbling across hydrophobic biochemistry on Titan.

Many of us may remember the nanobe-laden Martian meteorite ALH84001 that touched off a burst of interest and a flurry of Mars probes in the latter half of the 1990s. Like the 100-200 nm fossilised “bacteria” in the Mars meteorite, the tone suggesting imminent discovery of extraterrestrial life (particularly the sensationalist coverage by the lay press) serves as nothing more than hyperbolic rhetoric. If this effect carries over to those with a hand on the purse-strings, so much the better, but don’t get too caught up as a member of the scientifically literate and generally curious public. The likelihood of finding life outside our own planet in a given time span is essentially impossible to predict with no priors, hence the famous Fermi’s paradox which graces the title of this post. The actual content of the video is much more important than the wanton speculation that fuels its press coverage.

A major advantage of placing the Hubble space telescope above the atmosphere was to avoid optical aberrations generated by atmospheric turbulence. The present state of the art in adaptive optics and signal processing essentially obviates this need, as ground-based telescopes such as the Magellan II in Chile can now outperform the Hubble in terms of resolution. The James Webb will offer some fundamentally novel capabilities in what it can see, with a 6.5m primary mirror and sensors sensitive to wavelengths from 600 nanometre red to the mid infrared at 28 microns.

The upcoming TESS survey, described by McArthur Fellow Sarah Seager, will use the same basic technique-observing planetary transits-as the Kepler mission to look for exoplanets. TESS will launch in 2017, slightly in advance of the main attraction of JWST. Looking for planetary transits has served us well in the past, but direct imaging is the holy grail. Seager described a starshade for occluding bright, planet-hosting stars to further that goal as part of the New Worlds mission. The design resembles a sunflower in pattern rather than a circular shade, the latter would introduce airy rings from diffaction around the edges, and desert tests of the prototypes have been encouraging so far. The precision engineering of the shade unfolding is another masterpiece. Due to its size, deployment cannot be tested in a terrestrial vacuum chamber, requiring its engineering to be all the more precise. I could see scale versions of the design as parasols doing quite well in the gift shop.

800px-Artist's_concept_of_the_New_Worlds_Observatory

Image from NASA via Wikipedia

The natural philosophy that we now call science has roots in the same fundamental questions as “regular” philosophy. “Are we alone?” Is really just a proxy for “Where are we, how does it work, and why are we here?” Without any definitive answers to these questions on the horizon, I think we can safely say that building the machines that allow us to explore them and conditioning our minds in order to think about our universe is a pretty good way to spend our time. It will be a lonely universe if we find ourselves to be a truly unique example of biogenesis, but not so lonely in the looking.

As for yours truly, I’m looking forward to the “Two Months of Terror” (to quote Grunsfeld), October-December 2018, as the James Webb telescope makes its way to the L2 Lagrange point to unfold and cool in preparation for a working life of precipitous discovery.

Link to video

Panel:
Ellen Stofan- Chief Scientist, NASA
John Grunsfeld- Astrophysicist, former astronaut, Hubble mechanic
Matt Mountain- Director: Space telescope Science Institute
John Mather- Project scientist James Webb telescope, 2006 physics Nobel laureate
Sarah Seager- Astrophysicist, MIT Principal Investigator, McArthuer fellow 2013
Dave Gallagher Electrical Engineer, Director of Astronomy and Physics at Jet Propulison Laboratory

Also read up on ESA projects: the Herschel Space Observatory, observing at 60 to 500 microns, and Gaia, a satellite set to use parallax to generate a precise galactic census.

Top image by the author

Good Seeing

1280px-Van_Gogh_-_Starry_Night_-_Google_Art_ProjectPLusAO

Long the purview of telescopes, the dynamic mirrors and wavefront engineering that enables astronomers to calm the night sky’s twinkle are now founding applications in biological microscopy as well. The techniques, termed adaptive optics, are leading to major improvents in the clarity and depth imaging capabilities of today’s microscopes.

The eyes may or may not be the windows to the soul, but our ocular world plays a central role in how our minds are built. Of all human senses, sight is the most influential to our worldview, the most relied-upon to ascertain the validity of our guesses about reality. Galileo’s observations showed us our place in the cosmos by providing the givens to test the conflicting ideas from Ptolemy and Aristotle against Copernicus and Kepler. Hooke, Leeuwenhoek, and Spinoza seeded the scientific landscape with observations that would provide an alternative to the commonly held belief that disease causes were malarial, that is a result of “bad air,” and preventable by applied fragrance. Even the word “cell,” the fundamental building block of life, was concocted as Robert Hooke viewed the organization of a slice of cork through the lens of a microscope.

Humans are lucky to live under a dense atmosphere, keeping us warm and respiring while it protects us from (most) meteors drawn to our gravity well. The downside is that Earthbound astronomers are like a swimmer watching a birthday party from the bottom of a pool, an assuredly poor choice of viewpoints. The dense, turbulent atmosphere of the Earth confounded observation of especially dim extraterrestrial objects, until a few decades ago when deformable mirrors were introduced to astronomical telescopes to counteract atmospheric aberration. Before adaptive optics, astronomers were limited in the tools available to counteract the atmosphere, and made do by building observation centres at high-altitudes and waiting for “good seeing” conditions to attenuate the blurring of active air. In contrast, a modern adaptive optics telescope can best the resolution of the famous Hubble space telescope, as in the case of the adaptive optics-enabled Magellan II located in Chile.
Astronomers have to look out through the thick soup of the atmosphere, but biological microscopists looking into tissues have even more challenges to contend with. Like trying to peer through a nice cup of milky chai, trying to look at living cells in vivo is a major hurdle to determining the nature of life intact and in action. This has led to the adaptation of the same techniques previously developed to take out the night’s twinkle for use in microscopy, now used to obviate the blur of microscopical imaging at depth.

The problem of imaging through a highly aberrating medium is experienced twice when imaging into tissues: once on the illumination side of the path and again as the signal leaves the sample. Optimising the amount of light that illuminates the desired depth and location and then successfully making it back to a point detector or image sensor determines the clarity and speed with which an image can be formed.

In microscope design there are three characteristics to optimise: temporal resolution (speed), spatial resolution, and depth (signal to noise). Improving one aspect of an instrument invariably leads to a decrease in another quality. Anton van Leuwenhoek made incredible observations using instruments made by carefully melting pulled strands of glass in a flame, and setting the resulting aspherical lenses in pinhole brass frames. The tiny, single lens instruments bear more resemblance to a magnifying glass than to a modern compound microscope. Using one was a matter of holding the entire instrument a few centimetres from the eye and squinting through a tiny aperture at the subject, generally illuminated by sunlight. Game changing innovations that lead the way to improve the overall capability of microscopy beyond zero-sum trade-offs in design optimization are few and far between. It is becoming increasingly clear as the technology matures that adaptive optics is fundamentally enabling for imaging tasks that were not possible with the instruments of a decade ago.

One realm in which adaptive optics is finding ready application is in optical imaging of the living brains of model organisms. Brain imaging was the same inspiration that led Marvin Minsky to invent the confocal microscope in the late 1950s. In confocal microscopy, a pinhole plate rejects the majority of light arising from out of focus areas as the microscope beam is scanned throughout the sample of interest. The pinhole plate ensures that out-of-focus light is rejected, but there is a fundamental limit to how much total optical power can be pumped into tissue before damage occurs. Thanks to the pinhole plate, improving confocal imaging with adaptive optics is straightforward as: any increase in the signal making it to the detector indicates a positive correction for aberrations. Therefore, optimising the dynamic elements of the microscope is a matter of producing the maximum signal.

psfSpiralGrad

Beam shaping and point-spread function engineering enable new imaging modalities in microscopy.

The application of adaptive optics to neuroimaging instills a strong sense of the cutting-edge, combining brain science with optical physics, but some areas adaptive optics has made a striking impact may seem are much more domestic. Researchers at Durham Univerity, UK employed adaptive optics confocal microscopy to measure the effects of temperature on the activity of cold-water lipases, enzymes that break down fat and grease. Enzyme names are one of the rare cases of scientific nomenclature being intuitive and informative, the name ‘lipase’ identifies the enzyme’s substrate as lipids, or fats, and the activity as cutting them apart is denoted by the suffix “-ase”. Much like a greasy fingerprint on a pair of sunglasses, the very presence of the substrate induces unwanted blurring amenable to correction with dynamic optical elements.

The state of the art is no longer limited to improving the precision and design of static optics. Dynamic elements allow the microscope and the microscopist to adapt to specific imaging situations, a task for which algorithms and image processing are essential. The computational brains of modern microscopes are integral components of the optical system, as essential as the lenses and mirrors that make up the physical hardware.

In pushing the limits of the types of scientific questions that can be addressed with light, there’s no requirement to generate a two-dimensional image. Rather, the data required to test a given hypothesis may exist as a three-dimensional construct, four-dimensional volume plus time, or even higher dimensionality. Although visualisation of data will continue to be important for science communication, the central role of the image in science may soon take a back seat to generalised, multidimensional data. Paralleling this shift, the next generation of light microscopes will also look radically different than our conventional expectations. The shift has already appeared in commercially available microscopes: the computer is so integral to the light sheet microscope made by German optics giant Zeiss, that the instrument does not have eyepieces. The microscopes we use tomorrow will resemble modern microscopes to the same extent as modern microscopes remind us of Leuwenhoek’s handlenses.

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In short order that shiny new confocal system may share the fate of this Leuwenhoek replica. This piece is part of the collection at the Oxford Museum of the History of Science.

Adaptive optics links:

http://www.nature.com/lsa/journal/v3/n4/fig_tab/lsa201446f3.html#figure-title

http://www.nature.com/lsa/journal/v3/n4/full/lsa201446a.html

http://www.iop.org/careers/working-life/articles/page_59193.html

Edit 2014/06/24: Fixed links

Rose gall wasp pupae and new lens caps

I dissected a set of wild rose bush galls to discover minuscule wasps in various stages of development. These shots were taken with a 25mm f/3.5 macro lens and Lieberkühn reflector. Appropriately, this subset of gall wasps are colloquially known as rose gall wasps or mis-known as gallflies. They gain some control over the host plant, inducing the characteristic gall they live in during early development, but I am uncertain as to how much this may harm the plant and if they perform any significant pollination services.

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I have also been working on increasing the utility of my 3D printed lens caps. These are now available to fit two sizes of filter threads in a single lens cap-ideal for a day of shooting split between two lenses. And they still stay affixed better than squeeze style caps.

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The Color Coded Tiers of Open Access

Open Access, or OA, in scientific publishing is bringing long-due attention to the question of availability. University libraries pay millions of dollars per year on subscriptions, sometimes under the influence of coercive package deals which encourage libraries to subscribe to a lump of journals rather than pick and choose the most relevant. Tim Gower, a fellow at Trinity College, Cambridge, reports that UK university libraries pay anywhere from £234,126 (Exeter) to £1,381,380 (University College London) in subscription costs to Elsevier alone. The excessive cost increases in journal subscriptions have led to substantial actions by some universities, including a cancellation of Elsevier subscriptions by Harvard, MIT avoiding a 3-year renewal commitment with Wiley and Elsevier, and selective cancellation of Elsevier journals by Cornell, to name a few.

The debate over the efficacy of the scientific publishing status quo is alive and well. By most counts the rate of retractions has increased, although it is not clear if more retractions are caused by more misconduct or better vigilance. eLife editor and Nobel Laureate Randy Schekman, among others, suspect the pressure to publish in superstar journals and over-reliance on impact factor leads to misplaced incentives and rewards showy failures. For example, the infamous “arsenic life” paper has amassed 287 citations as of this writing, as indexed by Google Scholar, and is unlikely to be retracted by Science as a result; the 287 references to the article could buoy an additional 8 articles, each with little to no citations, and still maintain Science’s impact factor of ~32.

So maybe you’ve become a bit frustrated with paywalls and the relative attention (and citation) monoply enjoyed by top-brand journals. Perhaps you are tired of your library paying exorbitant fees for bundled subscriptions. In any case, you’re considering pursuing open access for some of your work. It may be as simple as hosting PDFs of your articles on your own, but the options are diverse, as are the costs. OA is typically differentiated into two major types, designated by color: gold and green.

Green OA refers to self-hosting of copies by a person, lab, or university. These can be archived and made avaible as pre-prints, post-prints, or in the final, formatted version published by the journal. The latter method can be contentious with some publishers (see the recent spate at Nature over Duke University’s open access mandate). SHERPA/RoMEO further differentiates green OA friendliness of journals according to a range of colors according to what is allowed by a journal or publishers copyright transfer agreement.

  • green pre-print, post-print and publisher’s version
  • blue post-print and publisher’s version
  • yellow pre-print and publisher’s version
  • white not designated/not allowed

Gold OA is driven by the journal or publisher, rather than the author or university. These are the journals typically associated as open access, and they usually, but not always, charge a hefty fee to authors. Journals under the PLOS umbrella belong to this category, and big name publishers have been dipping their toes into gold open access as well.

A hybrid approach to publishing is becoming widespread. This is often implemented as making optional OA available at a few thousand dollars charged to the author, such as the policy employed by the Journal of Visual Experimentation or Optical Society publications. Other journals make the headline article for an issue freely available, often in advance of print publication, to draw interest. Many journals have explicit policies that OK green OA after a designated grace period, e.g. according to their policy Science allows free access to articles 12 months after initial publication.

OA has a role to play in the changing landscape of scientific publishing but there are still plenty of variations to be tried, and OA is no silver bullet for all that ails publication, funding, and promotion in science careers. Web resources such as figshare expand the role of data and figures, while online lab notebooks like OpenWetWare increase transparency. F1000 Research is experimenting with citeable, viewable, open peer review. OA won’t stop the occasional “arsenic life” paper from stealing headlines, but it definitely has a role to play in the future of access.

Additional OA resources:

The University of California Berkeley Library maintains an index of publishers with gold open access options and their associated publishing fees.

Duke University OA mandates versus Nature Publishing Group:
Duke Libraries take by Kevin Smith, JD: https://blogs.library.duke.edu/scholcomm/2014/03/27/attacking-academic-values/
Nature Publishing Group’s take by Grace Baynes http://blogs.nature.com/ofschemesandmemes/2014/03/28/clarifying-npgs-views-on-moral-rights-and-institutional-open-access-mandates

SHERPA/RoMEO. Provides shades of green to denote publisher’s OA archiving policies: http://www.sherpa.ac.uk/romeoinfo.html

Directory of Open Access Journals: http://doaj.org/

University of Colorado Denver Librarian Jeffrey Beall’s site: http://scholarlyoa.com/
Beall’s blog includes his list of potentially predatory publishers (http://scholarlyoa.com/publishers/), potentially predatory journals (http://scholarlyoa.com/individual-journals/), and the newer list of exploitative metric indexes (http://scholarlyoa.com/other-pages/misleading-metrics/). These are essential resources, particularly useful when conventional publishers conflate known exploitative publishers with OA as a whole.

How to win the Nikon Small World photomicrography competition

The deadline for the Nikon Small World photomicrography competition is fast approaching (April 30th), and I’ve parsed some data on what types of images tend to win over since the contest’s inception in the late 1970s. The graphs below include data from both the stills and the newly minted video competition.

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Figure 1: The total number of images utilizing each technique for places 1-20, Honorable Mentions, and Images of Distinction.

Right away we see that polarized light techniques have a distinct advantage in terms of how often we see them on the winners podium. This was a bit of a surprise. I’m always left with the impression of a preponderance of confocal images after each year’s announcement of winners, but I suppose confocal would have not been seeing much use until the 80s.

nikonHeatMapWinners

Figure 2: Heat map of the total number of images from 1st to 20th place.

Polarized light still easily dominates the field, with fluorescence and confocal making strong showings (you’ll notice many of the technique categories for NSW are overlapping). Techniques grouped under fluorescence do have a slightly higher number of 1st place finishes at 9 versus 8, and of total top 5 finishes (41 vs. 40). Beyond the top 5, polarized light has essentially more placers at every position.

Good luck to everyone who enters. I don’t have the rights to display my favorites from previous contests (e.g. this, this, or this), but I will display a few of my own, non-winner, images.

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Freshwater ostracod

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Freshwater copepod (cyclops)

 

Teaser photomicrography

Here’s something you may not know about the old manual Canon auto bellows and macro lens: the threaded adapter that connects a 20mm f3.5 (or 35mm f2.8) macro lens to the bellows employs the same threading standard as the typical microscope objective, known as the Royal Microscopical Society standard, 20.32 mm diameter with a pitch of 0.706 mm per turn, dates back to 1896 when it replaced an earlier standard.

The impact of this design choice for macrophotographers is that one can use any standard microscope objective, adding a great deal of options for imaging with the auto bellows and potentially pushing the capabilities of bellows macro into photomicrography. This can result in some very short working distances, and the sterics of the objective and subject mean there won’t generally be a lot of room for illumination sources. I designed this simple 3D printed microphotography objective hood for use with bright transverse illumination such as from a fiber optic illuminator. You may be familiar with the type of lens flare that can arise from this illumination setup-typically a haze effect that decreases the overall contrast of the image while increasing the brightness, particular toward the middle of the image.

I took the images below through a 10X NA = 0.25 objective (on the right, with lens hood).

hoodOn10xObjective

My camera battery is charging, no spare, and I don’t have a worthwhile illumination source handy to shoot proper test shots (these were illuminated with a handheld torch). Nonetheless, I couldn’t resist taking these half-portraits, and I’ll post them here as a teaser. I will use these gorgeous metallic bees for Lieberkühn tests as well. For now, enjoy these Osmia aglaia photos while my camera charges.

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Is the future of scientific publishing in-house open access?

WeirdFuture
Photo from flickr user Tom Marxchivist, 1952 cover by Basil Wolverton, used under CC attribution license.

Those of you that frequent theScinder know that I am pretty passionate about how science is disseminated, and you have probably noticed that, like their brethren in newsprint and magazine before them, the big-name publishers don’t know exactly how to react to a changing future, and despite what traditional publishers would have you believe, they are not immune to publishing tripe.

Nature may be butting heads with Duke University over requesting waivers for the open access policy in place there. Apparently the waiver request isn’t even necessarily based on the practical implementation of Duke’s open access policy (Nature allows articles to be made freely available in their final version 6 months after publication), but it does raise the question: how much hassle will universities and their faculty put up with before they take matters into their own hands? As MIT’s Samuel Gershman points out, modern publishing doesn’t cost all that much. Even the fairly exorbitant fees charged to authors by the “gold standard” of open access publishers may be a transient relic of the conventional (turning archaic?) publishing business model. This provides incentive for predatory publishing (as discussed in this article at The Scientist and the basis for the Bohannon article published in Science last October) But if peer review and editing is largely volunteer labour, performed as an essential component of the role of a researcher and with the bill largely footed as a public expenditure, why keep paying enormous subscription fees for traditional publishing? If the trend catches on, as it almost certainly will, leading institutions will continue to adopt open access policies and libraries will see less and less reason to keep paying for outdated subscriptions.

Relevant links:

Scholarly Publishing: Where is Plan B?

California univerisity system consider boycotting Nature Publishing Group

Samuel Gershman’s ideal publishing model, the Journal of Machine Learning Research

Quantitative comparisons of macrophotography with and without Lieberkühn reflectors

In order to quantitatively examine the effect of the the 3D printed Lieberkühn reflectors I described previously, I came up with two image quality metrics relevant to their use, both measured on the “dark side” of the image subject. The metrics we will look at today are average intensity and, as a measure of contrast, the standard deviation of pixel values on a line trace.

I’ll be using the Megachile photo from the previous post for these analyses.

The first line trace begins at right eye and extends back behind the wing:

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RightEyeTraceValues

If we plot these values together, we see that the photo taken with the Lieberkühn (values in black) is brighter and brings out a lot more detail, while the photo taken without is relatively flat and dark. We see similar results for second and third traces, taken across the tegula and along the wing.

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AcrossThoraxTraceValues

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If we compare the average values:

octave3.2:25> mean(RE523(:,2)) %with Lieberkühn, right eye trace
ans = 102.00
octave3.2:26> mean(RE524(:,2))%w/o Lieberkühn, right eye trace
ans = 54.093
octave3.2:28> mean(AT523(:,2))%with Lieberkühn, trace across tegula
ans = 81.553
octave3.2:27> mean(AT524(:,2))%w/o Lieberkühn, trace across tegula
ans = 51.288
octave3.2:29> mean(W523(:,2))%with Lieberkühn, across the wing
ans = 103.85
octave3.2:30> mean(W524(:,2))%w/o Lieberkühn, across the wing
ans = 53.045

We see that taken together, the averages of the plots from the photo taken with the Lieberkühn are about 80% brighter than those without.

mean(Lieberkühn)/mean(no Lieberkühn) = 1.8142

octave3.2:56> std(RE523(:,2)))%with Lieberkühn, right eye trace
ans = 20.316
octave3.2:55> std(RE524(:,2))%w/o Lieberkühn, right eye trace
ans = 7.3926

octave3.2:54> std(AT523(:,2))%with Lieberkühn, trace across tegula
ans = 17.737
octave3.2:53> std(AT524(:,2))%w/o Lieberkühn, trace across tegula
ans = 13.227

octave3.2:52> std(W523(:,2))%with Lieberkühn, across the wing
ans = 12.746
octave3.2:51> std(W524(:,2))%w/o Lieberkühn, across the wing
ans = 8.2902

Using standard deviation as a metric for image detail, we get an increase of about 75% in standard deviation over the dark photo by using the reflector.

octave3.2:30> (20.316+17.737+12.746)/(7.3926+13.227+8.2902)
ans = 1.7572

The averages, standard deviation etc. may seem a bit redundant at this point; you don’t need to plot a pixel-value profile to see that the image with the reflector is much brighter and more detailed than the photo taken without.

Lens caps that screw on

Most lenses already have a standard, secure method for attaching accessories to the distal end. So why do we still put up with the infamy of squeeze-style caps that are so easily lost? Below are some iterations of my designs for threaded lens caps, designed with information on the lens filter thread standards from Wikipedia, and printed in various colors of Shapeways basic sintered plastic. They’re durable, can be colorful, and it’s possible to emboss custom text or an image on the front. Oh, and I never worry about them falling off in the bag.

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