Waves, Satellites, and an Oceanographer at Sea: Annual Review of Marine Science Volume 10

January 26, 2018 Suzanne K. Moses Volume Annoucement marine

Browse the Annual Review of Marine Science Volume 10 table of contents.

ma10-waves “The Fate and Impact of Internal Waves in Nearshore Ecosystems” by C.B. Woodson introduced me to the wonder and science of internal waves. Like the surface waves most people are accustomed to thinking about, these internal waves also break as they near land and can bring of deep offshore waters into the nearshore environment:

These deeper waters are often colder, lower in oxygen, higher in CO₂concentration (lower pH), and nutrient enriched. Consequently, internal waves can dramatically change the ambient environment, leading to either extreme oxygen (hypoxia) or pH (acidification) events. However, they can also mediate extreme heating events by providing a temporary reprieve from high temperatures. Deep offshore waters can also provide nutrients and food subsidies to nearshore ecosystems. Nutrient-deprived nearshore ecosystems, namely coral reefs, can be highly dependent on such subsidies.

ma-dugdale Richard Dugdale credits mentoring with influencing his path from electrical engineering to oceanographer in his autobiography “A Biogeochemical Oceanographer at Sea: My Life with Nitrogen and a Nod to Silica” He has a warm writing style and I enjoyed reading about the history of this field through his experiences, especially about the changing technology:

…this field rapidly developed both analytically, starting with the use of stable and radioactive tracers, and computationally, from the use of slide rules to the development of onboard computers with disk drives (with 250 KB of storage!) and the era of smartphones. Also changing has been the mode of communication between oceanographers—from handwritten or mimeographed notes to faxes to the early email and Internet (telemail) used by oceanographers in the 1980s to today’s email and social media. What follows, then, is a biased (biological/chemical) history of a period in which modern oceanography was largely developed and in which I had the great fortune to be a player.

“Spaceborne Lidar in the Study of Marine Systems” by Hostetler et al. is one of several articles in this volume that report on the use of satellites in marine research. This article reviews the use of passive color analysis to observe chlorophyll levels among many other topics and looks forward to an upcoming PACE mission which pairs the color observations with new tools:

Satellite passive ocean color observations have vastly improved our understanding of global links between biodiversity, ecosystem structure, and ecological and biogeochemical function. However, there are fundamental geophysical properties that simply cannot be characterized with ocean color technology alone. Addressing these issues requires additional tools in space. For example, the Plankton, Aerosol, Cloud, and Marine Ecosystem (PACE) mission aims to co-deploy a multi-angle polarimeter with a hyperspectral ocean color sensor, with the polarimetry enabling more accurate atmospheric corrections and advanced characterization of ocean particle types. Here, we describe how even greater synergies may be achieved by combining a passive ocean color sensor with an ocean-optimized satellite profiling lidar.

Annual Review of Psychology Volume 69: Language, Gender, and Replication

January 24, 2018January 26, 2018 Suzanne K. Moses Volume Annoucement psych

Browse the Annual Review of Psychology Volume 69 table of contents.

ps69-lang While I’m used to thinking about language as a way of gauging cognitive development “Linking Language and Cognition in Infancy” by Perszyk and Waxman had me thinking about the ways language influences cognition. For instance:

…more recent developmental evidence reveals that, even before infants begin to speak, words invite them to form categories. The evidence for this claim comes from a robust behavioral paradigm, elegant in its simplicity. It is essentially an object categorization task with two phases. During the familiarization phase, infants view a series of discriminably different objects (e.g., dog, horse, duck) from a given object category (e.g., animal). Next, during the test phase, infants view two new objects—one a member of the now-familiar category (e.g., a cat) and the other a member of an entirely different category (e.g., an apple). The logic of this paradigm is straightforward: If infants detect the category-based commonalities among the familiarization objects, then they should distinguish the novel test image from the familiar; if they fail to detect these commonalities, then they should perform at chance levels ….The evidence reveals that, by 12 months of age, even before they produce more than a few words on their own, infants have established a principled link between object naming and object categorization.

I found “Gender Stereotypes” by Ellemers quite an interesting read. I particularly responded to the summation in the section “How We Can Benefit From This Knowledge”:

Gender stereotypes prevent women and men from equally sharing the care for children and family members and from equally benefiting from the interpersonal connections made through these activities. Gender stereotypes prevent women with successful careers from finding a romantic partner and men without employment from feeling valued. They cause us to underestimate the emotional burden of care functions for women and the physical burden of strenuous labor for men. This is not only costly for the individuals involved but also for society, as it impacts the psychological and physical well-being of individuals, the resilience of families, and the long-term availability and contributions of workers in the labor market. We are only human and have to accept that we are subject to stereotypical thinking and gendered expectations. Accepting our fallibility in this way, rather than denying that gender stereotypes play a role while implicitly reproducing them, makes it easier to correct for any undesired outcomes that may result.

Shrout and Rodgers’ article “ Psychology, Science, and Knowledge Construction: Broadening Perspectives from the Replication Crisis” is a good overview of the history of evaluating results, the problems with current practices, and steps that have been taken to verify findings. I was particularly interested in how the changes in research procedure have affected scientists:

As calls have been made to change the way science is conducted in psychology by preregistering designs and analyses and increasing sample sizes, some authors have noted what might be called collateral damage. The three types of damage that have been identified are (a) slowing and ultimate reduction of new findings and phenomena, (b) penalizing different subfields with the imposition of one-size-fits-all norms, and (c) discouraging young scientists from staying in the field because of the higher bar for publication and professional advancement.

Fire, Explosions, and Lymphatic Systems: Annual Review of Fluid Mechanics Volume 50

January 23, 2018January 26, 2018 Suzanne K. Moses Volume Annoucement fluid

Browse the Annual Review of Fluid Mechanics Volume 50 table of contents.

Before I get to the fire and explosions I want to highlight the lovely article “John Leask Lumley: Whither Turbulence?” by Leibovich and Warhaft that begins this volume. This biography includes sections about Dr. Lumley’s love and appreciation for vintage cars and good food and wine as well as a look at his contributions to fluid mechanics. It’s a remarkable tribute and a worthwhile read.

Tohidi, Gollner, and Xiao wrote “Fire Whirls” which I found myself thinking about as I watched coverage of the California wildfires:

fl50-fire whirls

Throughout the literature, fire whirls have been identified by a variety of names, including devil, tornado, twister, whirlwind, or even dragon twist (Japanese). Regardless of the name, when the right combination of wind and fire interact, the result is an intensification of combustion with whirling flames that we call the fire whirl. Although the fire whirl or fire tornado shares some features with its atmospheric counterparts, it remains distinct in its source of buoyancy, combusting fuel, structure, and formation patterns. In nature, fire whirls are most often observed in mass fires. These include both large wildland (also known as forest fires or bushfires) and urban conflagrations, such as the burning of cities or towns…

fl50-detonation While action movie explosions make it seem easy, a controlled detonation that accomplishes more than looking good on film is difficult and complex to model. “High Explosive Detonation-Conifer Interactions” by Short and Quirk begins by explaining some of the complexity:

The dynamics of a given HE–confiner system depend on the pressure-loading properties of the explosive (magnitude and timescale), while in turn the structure and speed of the detonation reaction zone and the lateral confinement of explosive products are dependent on the material properties of the confining material, such as its density and sound speed. The ability to predict the motion of a detonation in an explosive system (known as the timing) and the response of the confiner to the HE detonation pressure loading depend on our ability to model and understand this detonation–confiner flow coupling…

I found “Lymphatic System Flows” by Moore and Bertram quite interesting especially as it explained the importance of several organs I’d always been curious about:

The lymphatic system as a functional whole includes several organs whose association as a system is not readily apparent. Lymphoid organs include the spleen, thymus, and tonsils; another vital component is the bone marrow where white cells are manufactured…. Functionally, the lymphatic vascular system runs in parallel to the blood venous system, in that both return fluids centrally. Lymphatic vessels carry lymph, which is largely water gathered from interstitial tissue spaces. Fluid appears in the interstitial spaces because blood capillary walls are somewhat leaky, allowing part of the aqueous component of blood to escape, along with some proteins…. The lymphatic vascular system scavenges this water and protein, ultimately returning it to the venous circulation via junctions with the subclavian veins at shoulder level. The maintenance of the interstitial milieu is one of its vital functions; if fluid is not returned to the blood system at the same rate as it leaves, the painful and debilitating condition of edema can develop.

The Grand Finale – Farewell to Cassini

September 14, 2017 Suzanne K. Moses News EA

On September 15, 2017, Cassini will enter Saturn’s atmosphere and break into very small pieces before burning up entirely. For the past 7 years, the satellite’s exploration of Saturn and its moons has resulted in valuable data and glorious images. Now as it runs out of fuel it will begin it’s final mission—a deep dive into Saturn’s atmosphere sending data back to Earth for as long as it can.

Personally, I find it difficult to avoid anthropomorphizing these space vehicles, especially one I have observed closely for so long, and watching this final mission continues to be quite moving to me. The remarkable images of Saturn’s rings were my desktop background and I closely watched the craft travel to the moons. I followed Cassini’s Twitter feed (CassiniSaturn) and saw the images and data come in daily. Now this week I watch it end, and as NASA said in one of their animations, Cassini will become part of Saturn itself. (To see details and to watch the amazing animation, see NASA’s “Grand Finale Toolkit.”)

Here at Annual Reviews, our authors have been using the data from Cassini’s exploration of Saturn for many years, and we are highlighting some of those articles during the culmination of Cassini’s mission.

Thank you, Cassini.

spencer-cassini “Enceladus: An Active Ice World in the Saturn System” by John R. Spencer and Francis Nimmo. Annual Review of Earth and Planetary Sciences, Volume 41

“Planetary Reorientation” by Isamu Matsuyama, Fancis Nimmo, and Jerry X. Mitrovica. Annual Review of Earth and Planetary Sciences, Volume 42

mitchell-cassini “The Climate of Titan” by Jonathan L. Mitchell and Juan M. Lora Annual Review of Earth and Planetary Sciences, Volume 44

“Shape, Internal Structure, Zonal Winds, and Gravitational Field of Rapidly Rotating Jupiter-Like Planets” by Keke Zhang, Dali Kong, and Gerald Schubert. Annual Review of Earth and Planetary Sciences, Volume 45

Hayes-cassini

“The Lakes and Seas of Titan” by Alexander G. Hayes Annual Review of Earth and Planetary Sciences, Volume 44

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

The Science of Art and Plant Monitoring: Annual Review of Analytical Chemistry Volume 10

August 18, 2017 Suzanne K. Moses Volume Annoucement anchem

Browse the Annual Review of Analytical Chemistry Volume 10 table of contents.

AC10-art There’s something magical about how scientific technology and techniques can peel back layers of paint and dust to reveal new information about an object or artist. Karen Trentelman’s article “Analyzing the Heterogeneous Hierarchy of Cultural Heritage Materials: Analytical Imaging” only increased my enjoyment of the topic. I was especially intrigued by the approach laid out in the introduction:

“In the creation of works of art, the extent to which human activity is necessary or able to control the final product can also be considered in terms of different length scales. Generally, the most important macroscale property, and the one entirely controlled (or at least actively sought) by the artist, is the overall appearance, broadly understood to include qualities such as color, texture, sheen, and shape. However, although the artist may control the final appearance through the selection and exploitation (whether deliberate or incidental) of specific mesoscale (or smaller) properties, the intrinsic micro- to nanoscale physics and chemistry that produce the desired macroscale appearance are out of the artist’s control. For example, a layer of varnish only a few tens of microns thick can dramatically change the appearance of a painting; the artist can control the choice of varnish and the thickness and method of application, but the index of refraction and surface tension properties that impart the desired saturation of color and surface appearance are controlled by nature.”

The ideas in Kwak et al.’s article “Nanosensor Technology Applied to Living Plant Systems” took me a bit by surprise. I knew that there was research that involved precision monitoring of agriculture, but I didn’t realize that plants could be actively managed at this level with great potential to change the way agriculture works:

“In the field of plant biology or agriculture, nanosensors have been used as nanobiosensors environmental pollution (25). Several nanosensors have been developed to detect contaminants, such as crystal violet or malachite green concentrations in seafood, and parathion residues or residues of organophosphorus pesticides on vegetables)…. The installation of nanosensors or nanoscale wireless sensors in living plants is currently applied to enable the real-time monitoring and early detection of potential problems related to biochemistry and metabolism.”

Historical Context: Annual Review of Biochemistry Volume 86

August 17, 2017 Suzanne K. Moses Volume Annoucement biochem

Browse the Annual Review of Biochemistry Volume 86 table of contents.

This volume of the Annual Review of Biochemistry opens with an autobiography by Christopher Walsh, titled “At the Intersection of Chemistry, Biology, and Medicine.” I especially enjoyed his memories of his early days in research and how these early projects shaped his long-term research:

“Two epiphanies turned my attention away from medical school, which had
been my default expectation, to biomedical research as a career option. The
first came from research on fire ant trail substance pheromone. I was involved
in a joint project between Professor Law and Professor E.O. Wilson in the
Biology Department. Wilson has been the world’s expert in ant biology and the
lessons learned from their interdependent society for the past 60-plus years.
My efforts at partial purification resulted in my initial research paper,
published in Nature no less. Although it would be another 30 years before I
published in Nature again, in my callow enthusiasm I thought from this
encounter that the research enterprise would be exciting.”

I also liked the description of his first research group:

“Starting a research group is like diving into the deep end of a pool to find out if you can swim, with no prior instructions on what keeps people afloat. At the outset, aged 28, I was at most 5 years older than the students in my group. The sales and instrument people who would drop by would ask me all the time if Professor Walsh was in. I usually replied that unfortunately he was otherwise occupied.”

Nielsen’s article “Systems Biology of Metabolism” is a wide-ranging article that gave me a better understanding of metabolism—a subject I’m interested in but find very complicated. I especially enjoyed the history of the subject in the Introduction to the article, including the “golden age of metabolism studies.” These bits of history are very useful context.
bi-ribosomal rna I discovered another historical section in Matzov’s article, “A Bright Future for
Antibiotics?”

“This article addresses a major problem in modern medicine: resistance of pathogens to antibiotics. It focuses on how antibiotics paralyze ribosomes, the universal multicomponent cellular particles that translate the genetic code into proteins. It highlights conventional and nonconventional suggestions that may relieve, to some extent, the current problematic medical situation and shows how we may benefit from the vast amount of available structural information. Notably, understanding the mechanisms of resistance to antibiotics could not even be dreamt about when a project aimed at the determination of the atomic structure of ribosomes was started during the last two weeks of November 1979.”

Ice Crystals and Ice Cream: Annual Review of Materials Research Volume 47

August 16, 2017 Suzanne K. Moses Volume Annoucement matsci

Browse the Annual Review of Materials Research Volume 47 table of contents.

I am thrilled to introduce you to “Physical Dynamics of Ice Crystal Growth” by Libbrecht. This article provided me with a welcome break from the heat and inspired a great deal of respect for this field (as well as a snow dance in my office chair). It’s a really great article and I hope you go take a look—even if just to gaze in wonder at the figures.

MR47-ice

“The winter clouds produce a great diversity of snow-crystal forms, from slender columns to thin plates, at times branched, sectored, hollowed, and faceted, as shown in Figure 1. Yet extensive laboratory and theoretical investigations have still not determined why these varied structures appear under different growth conditions. For example, we do not yet possess even a qualitative understanding of why snow crystal growth alternates between plate-like and columnar forms as a function of temperature, as seen in Figure 1, although this behavior was first observed more than 75 years ago.”

I would be willing to bet that most of us have bent a spoon while attempting to scoop hard ice cream. A few of us have gone on to write scientific papers about it, as I discovered in the article by Sethna et al. “Deformation of Crystals: Connections with Statistical Physics.”

“A metal spoon will spring back into its original shape under ordinary use, but when scooping hard ice cream, one may bend the spoon too far for it to recover (Figure 1). The spoon is made up of many crystalline grains, each of which has a regular grid of atoms. To permanently deform the spoon, atomic planes must slide past one another. Such glide happens through the motion of dislocation lines. The dynamics, interactions, and entanglement of these dislocation lines form the microscopic underpinnings of crystal plasticity, inspiring this review.”

It’s a noisy world out there and I’ve often wished for better soundproofing. I was not aware of the complexity of those sound barriers until discovering Yang & Sheng’s article, “Sound Absorption Structures: From Porous Media to Acoustic Metamaterials.” I particularly enjoyed the early section on “traditional porous materials such as plastic foam, fiber glass, and mineral wool.”

“Because sound is associated with very small air displacement velocities, its dissipation as a function of frequency must obey the linear response theory, in which the generalized flux (e.g., electrical current density, flow rate, heat flux) is linearly proportional to the generalized force (e.g., gradients of electrical potential, pressure, temperature). Because dissipative force varies linearly as function of the rate (e.g., dynamic friction varies linearly as a function of relative velocity) and dissipated power is given by the product of force and flux, it follows that sound dissipation is a quadratic function of frequency, as shown below. Hence, for low frequency sound, dissipation is inherently much weaker than for high-frequency sound.”

Brewing Science and a Fantastic Interview: Annual Review of Chemical and Biomolecular Engineering Volume 8

August 15, 2017 Suzanne K. Moses Volume Annoucement chembioeng

Browse the Annual Review of Chemical and Biomolecular Engineering Volume 8 table of contents.

While some home brewers may appreciate the more detailed breakdown of the various ingredients and each stage of the brewing process in the article by Dr. Bamforth, “Progress in Brewing Science and Beer Production,” I enjoyed the opening section on the history of brewing:

“Despite the enormous depths of understanding of the brewing process, it is nevertheless a fact that the fundamental shape of the brewing process has not changed in millennia. Were one to be time-transported to the Middle Ages, one would find fundamentally the same unit operations that continue to be employed in the brewing of beer.”

CH9-McKetta I’m always delighted to read the autobiographies, or watch the video interviews, especially when the subject turns out to be a wonderful storyteller. I really enjoyed “A Conversation with John McKetta” by Thomas Truskett. The questions were interesting and the answers revealed a few of McKetta’s extraordinary experiences:

“I looked forward to the time when I could work in the mine because they paid you $0.25 for every ton that you brought to the surface. And I did this after I graduated from high school. I just couldn’t wait until the day that I could go into the mines…until I went that first day, and then I hated it. I never liked it all. What happened was, our mine was 100 and some feet deep—that’s kind of shallow. And the first day that we were in the mines, the couple working right next to us were under a fall. There was a rock fall over their heads. And it took us a couple of days to scrape away the dirt and get them out as well as we could. And of course, they were dead the minute the rock hit them. So I just hated it.”

I’ve been hearing about the possibility of making oil from algae since childhood when my grandfather mentioned it as we were fishing at a local pond with some spectacular algae infestations. I found the note in the abstract of “Algae to Economically Viable Low-Carbon-Footprint Oil” by Bhujade, Chidambaram, Kumar & Sapre about the historically cyclical research really interesting:

“Whenever crude prices declined, research on algae stopped. The scenario today is different. Even given low and volatile crude prices ($30–$50/barrel), interest in algae continues all over the world. Algae, with their cure-all characteristics, have the potential to provide sustainable solutions to problems in the energy-food-climate nexus. However, after years of effort, there are no signs of algae-to-biofuel technology being commercialized.”

Annual Review of Biomedical Engineering Volume 19

August 10, 2017 Suzanne K. Moses Volume Annoucement bioeng

Browse the Annual Review of Biomedical Engineering Volume 19 table of contents.

I’ve noticed a lot of articles recently about wearable and insertable technologies. “Energy Harvesting from the Animal/Human Body for Self-Powered Electronics” by Dagdeviren, Li & Wang is the first article I recall discussing how to use the subjects wearing the technology to power the batteries as well! Personally, I love the idea of charging my cellphone via a brisk walk around the block. The authors point out there are many energy sources available:

“Although there are various applicable energy sources for harvesters, including sunlight, IR light from the environment, and radio-frequency power sources through inductive coupling, the body of a living subject is a particularly favorable energy source, given the vast number and wide variety of available energies. For instance, theoretical calculations have demonstrated that body heat, breathing, and arm movements can generate 2.8–4.8 W, 0.83 W, and 60 W, respectively. Although these power sources could offer a compelling way to accommodate the operation of a cardiac pacemaker (50 μW for 7 years), a hearing aid (1 mW for 5 days), and a smartphone (1 W for 5 h), practical demonstrations are needed to show the feasibility of powering such electronics.”

I feel like I have followed many of the ideas presented in Black, Perez-Pinera & Gersbach’s article “Mammalian Synthetic Biology: Engineering Biological Systems” from science fiction to reality. These synthetic circuits could offer new ways to treat many diseases and genetic problems:

“Synthetic biology aims to create new biological functions through the design and controlled assembly of genetic circuits. A genetic circuit is a combination of biological parts that together execute a defined function within a host organism. By deconstructing natural genetic circuits that have been refined by evolution and reconstructing them from modular components, synthetic biologists can gain insight into the structure–function relationship of natural biological systems and use this information to build systems with novel activity.”

The Complicated Immune Response: Annual Review of Immunology, Volume 35

May 11, 2017 Suzanne K. Moses Volume Annoucement immunol

Browse the Annual Review of Immunology, Volume 35 table of contents.

While proofing this volume, I was impressed again by how complicated the immune system is. It seemed so very simple in high school biology! But there are so many related actions that have to happen in precise sequences, and even systems that I thought were disconnected from immunity turn out to be quite important. For instance, see the abstract of “The Lymphatic System: Integral Roles in Immunity” by Gwendalyn Randolph et al.: IY35-lymphatic

The lymphatic vasculature is not considered a formal part of the immune system, but it is critical to immunity. One of its major roles is in the coordination of the trafficking of antigen and immune cells. However, other roles in immunity are emerging. Lymphatic endothelial cells, for example, directly present antigen or express factors that greatly influence the local environment.

The study of immunology has progressed in recent years and is producing huge amounts of data—as I discovered in Arup K. Chakraborty’s article, “A Perspective on the Role of Computational Models in Immunology.” To make use of that data, because the processes are so complex, researchers are using computational models:

Computational or theoretical studies of the model can keep track of every possible event that can occur consistent with a hypothesis and reveal whether a particular hypothesis is plausible. Hypotheses that appear feasible at first glance can be incorrect because of the complexity of the underlying phenomena. Computational biophysics–based models not only can screen out these hypotheses prior to fruitless experimental tests, but also can shed light on the reason a hypothesis is unlikely to be right and thus guide the choice of other feasible hypotheses. Such computational studies are not exercises in fitting parameters to quantitate known mechanistic models. Rather they offer ways to obtain mechanistic insights and guide the choice of meaningful hypotheses underlying puzzling observations and the design of realistic experiments that can test the hypotheses.

Another article that caught my interest was Kole T. Roybal &Wendell A. Lim’s “Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities.” I was intrigued by the title’s use of “hacking” in a biomedical context and the article itself proved to be fascinating!

[I]mmune cells are relatively easy to remove, modify, and transfer back into a patient. Given these unique properties, immune cells provide a remarkable platform for interfacing with and treating disease. There are many complex diseases, such as cancer and autoimmunity, that our natural immune systems either cannot handle or pathologically contribute to. Thus, there is a strong rationale to engineer new disease sensing and response behaviors in immune cells, especially given recent powerful advances in synthetic biology and genome editing, which give us unprecedented ability to modify and engineer cellular functions.

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Author: Suzanne K. Moses