Physical Sciences and Mathematics Commons^™

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …

Students Arts Participation Increases Stem Motivation Via Self-Efficacy, Stephen M. Dahlem

The STEAM Journal

This work found that there exists a correlation between student motivation in science, technology, engineering and mathematics (STEM) and student participation in the arts during high school with self-efficacy being a mediator. STEM is an important component of student success from a broad, national, perspective, as well as from a domain-specific point of view. The results of this work may provide aid to teachers, parents, administrators, and even students seeking to find ways to increase student motivation and performance in the STEM subjects. Additionally, this work may be of interest to advocates of the arts. This quantitative correlational study was …

Natural By Design, Craig Steele

Journal of Humanistic Mathematics

I’m a professor in the Department of Biology and Health Sciences at Edinboro University, in Edinboro, Pennsylvania, a small, comprehensive liberal arts institution within the Pennsylvania State System of Higher Education. My major teaching duties involve environmental biology, zoology, and ichthyology. I emphasize to my students how mathematics underlies the natural world of plants and animals, pointing out to them how many of “our” most amazing engineering and constructional achievements are copied from nature (from geodesic domes to the fusiform bows of modern commercial ships), as well as how plant and animal physiology and animal behavior (of individuals and of …

In The Eye Of The Storm: Houston After Hurricane Harvey, Brandon Tolentino-Serrano

Pomona Senior Theses

Situated in one of the wettest climates in America, Houston, TX has had a long history of heavy rains and unprecedented floods. Unfortunately, floods have become more common over the last few decades as climate change increases the frequency and intensity of hurricanes around the globe. To complicate matters further, Houston has quickly sprawled to accommodate over 2.5 billion people. Rapid urbanization has rendered the landscape even more susceptible to floods through excess concretization and watershed disturbance. This thesis traces the history of the Bayou City in relation to the damages caused by Hurricane Harvey. By mapping out the original …

Social Aggregation In Pea Aphids: Experiment And Random Walk Modeling, Christa Nilsen, John Paige, Olivia Warner, Benjamin Mayhew, Ryan Sutley, Matthew Lam '15, Andrew J. Bernoff, Chad M. Topaz

All HMC Faculty Publications and Research

From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. …

Post-Speleogenetic Biogenic Modification Of Gomantong Caves, Sabah, Borneo, Joyce Lundberg, Donald A. Mcfarlane

WM Keck Science Faculty Papers

The Gomantong cave system of eastern Sabah, Malaysia, is well-known as an important site for harvesting edible bird-nests and, more recently, as a tourist attraction. Although the biology of the Gomantong system has been repeatedly studied, very little attention has been given to the geomorphology. Here, we report on the impact of geobiological modification in the development of the modern aspect of the cave, an important but little recognized feature of tropical caves. Basic modeling of the metabolic outputs from bats and birds (CO₂, H₂O, heat) reveals that post-speleogenetic biogenic corrosion can erode bedrock by between …

Subaerial Freshwater Stromatolites In Deer Cave, Sarawak – A Unique Geobiological Cave Formation, Joyce Lundberg, Donald A. Mcfarlane

WM Keck Science Faculty Papers

A suite of distinctive freshwater subaerial phosphatic stromatolites is developed close to the northeastern entrance of Deer Cave, Gunung Mulu National Park, Sarawak, Borneo, in conditions of very low light but ample supply of nutrients from guano. These stromatolites are not particulate; they are composed of alternating layers of more porous and more dense amorphous hydroxylapatite. This biomineralization occurs as moulds of coccoid (the majority) and filamentous (less abundant) cyanobacteria. Mineralization occurs at a pH of ~ 7.0 in the extracellular sheaths and in micro-domains of varying carbonate content in the surrounding mucus of the biofilm. The most recent surfaces …

Effect Of Substrate Composition And Alignment On Corneal Cell Phenotype, Donna Phu '09, Lindsay S. Wray '08, Robert V. Warren '10, Richard C. Haskell, Elizabeth J. Orwin

All HMC Faculty Publications and Research

Corneal blindness is a significant problem treated primarily by corneal transplants. Donor tissue supply is low, creating a growing need for an alternative. A tissue-engineered cornea made from patient-derived cells and biopolymer scaffold materials would be widely accessible to all patients and would alleviate the need for donor sources. Previous work in this lab led to a method for electrospinning type I collagen scaffolds for culturing corneal fibroblasts ex vivo that mimics the microenvironment in the native cornea. This electrospun scaffold is composed of small-diameter, aligned collagen fibers. In this study, we investigate the effect of scaffold nanostructure and composition …

"Toward Integration: From Quantitative Biology To Mathbio-Biomath?", Pat Marsteller, Lisette G. De Pillis, Ann Findley, Karl Joplin, John Pelesko, Karen Nelson, Katerina Thompson, David Usher, Joseph Watkins

All HMC Faculty Publications and Research

In response to the call of BIO2010 for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and biology. With the assistance of an HHMI-funded mini-grant, led by Karl Joplin of East Tennessee State University, and support in institutional HHMI grants at Emory and University of Delaware, these institutions held a series of summer institutes and workshops to document progress toward and address the challenges of implementing a more quantitative …

Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn

All HMC Faculty Publications and Research

Locomotory muscles typically operate over a narrow range of contraction frequencies, characterized by the predominant fiber types and functional roles. The highest documented frequencies in the synchronous sound-producing muscles of insects (550 Hz) and toadfish (200 Hz) far exceed the contraction frequencies observed in weight-bearing locomotory muscles, which have maximum documented frequencies below 15-30 Hz. Laws of scaling, however, predict that smaller arthropods may employ stride frequencies exceeding this range. In this study we measured running speed and stride frequency in two undescribed species of teneriffiid mites from the coastal sage scrub of southern California. Relative speeds of both species …

An Extraordinary Example Of Photokarren In A Sandstone Cave, Cueva Charles Brewer, Chimantá Plateau, Venezuela: Biogeomorphology On A Small Scale, Joyce Lundberg, Donald A. Mcfarlane, Charles Brewer-Carias

WM Keck Science Faculty Papers

A distinctive suite of small-scale erosional forms that are oriented towards the light occur close to the entrance of Cueva Charles Brewer, a large cave in a sandstone tepui, in SE Venezuela. These are the third example of photokarren ever studied in the world, the other two being from Borneo and Ireland. They are the only photokarren ever described from sandstone, and the only example from a non-carbonate environment. The host rock is a poorly-lithified unit of the Precambrian quartz arenite of the Roraima Supergroup. The forms are all oriented towards the light at 30° regardless of rock surface orientation. …

A Unique Population Of Cave Bears (Carnivora: Ursidae) From The Middle Pleistocene Of Kents Cavern, England, Based On Dental Morphometrics, Donald A. Mcfarlane, Martin Sabol, Joyce Lundberg

WM Keck Science Faculty Papers

The ‘breccia’ stratum from Kents (we follow local tradition in using the form ‘Kents’, without an apostrophe) Cavern, England, has been well known for its rich yield of cave-bear material since excavations began in the mid-19th century. Recent work has established that the bears are of latest MIS 12 or earliest MIS 11 age. A life table based on a collection of 67 molariform teeth is consistent with the use of the cave as a hibernaculum. Univariate and morphological assessment of the teeth shows an unusual range of primitive and more derived characters. Multivariate morphometric analysis of cave-bear teeth from …

Jane: A New Tool For The Cophylogeny Reconstruction Problem, Chris Conow, Daniel Fielder '11, Yaniv J. Ovadia '10, Ran Libeskind-Hadas

All HMC Faculty Publications and Research

Background

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.

Results

The Jane software tool uses a polynomial time dynamic …

Mathematical Biology At An Undergraduate Liberal Arts College, Stephen C. Adolph, Lisette G. De Pillis

All HMC Faculty Publications and Research

Since 2002 we have offered an undergraduate major in Mathematical Biology at Harvey Mudd College. The major was developed and is administered jointly by the mathematics and biology faculty. In this paper we describe the major, courses, and faculty and student research and discuss some of the challenges and opportunities we have experienced.

Thermal Links For The Implementation Of An Optical Refrigerator, John Parker, David Mar, Steven Von Der Porten, John Hankinson, Kevin Byram, Chris Lee, Michael K. Mayeda, Richard C. Haskell, Qimin Yang, Scott R. Greenfield, Richard I. Epstein

All HMC Faculty Publications and Research

Optical refrigeration has been demonstrated by several groups of researchers, but the cooling elements have not been thermally linked to realistic heat loads in ways that achieve the desired temperatures. The ideal thermal link will have minimal surface area, provide complete optical isolation for the load, and possess high thermal conductivity. We have designed thermal links that minimize the absorption of fluoresced photons by the heat load using multiple mirrors and geometric shapes including a hemisphere, a kinked waveguide, and a tapered waveguide. While total link performance is dependent on additional factors, we have observed net transmission of photons with …

An Undescribed Gecko (Gekkonidae: Cyrtodactylus) From Deer Cave, Gunung Mulu National Park, Sarawak, With Comments On The Distribution Of Bornean Cave Geckos, Donald A. Mcfarlane, Joyce Lundberg, Keith Christenson

WM Keck Science Faculty Papers

Geckos of the genus Cyrtodactylus are a speciose group in Southeast Asia, with at least nine species known from the island of Borneo (Das & Ismail, 2001; Das, 2006). Of these species, Cyrtodactylus cavernicolus has the smallest known range and is therefore the most vulnerable, a status that is reflected in the species having been designated a Totally Protected Species in Sarawak. Confirmed records of C. cavernicolus are known only from Niah Cave, located in an isolated limestone block known as the Gunung Subis massif, approximately 13 km² in extent. The Niah Cave Gecko is presumed to be dependent on …

Bats And Bell Holes: The Microclimatic Impact Of Bat Roosting, Using A Case Study From Runaway Bay Caves, Jamaica, Joyce Lundberg, Donald A. Mcfarlane

WM Keck Science Faculty Papers

The microclimatic effect of bats roosting in bell holes (blind vertical cylindrical cavities in cave roofs) in Runaway Bay Caves, Jamaica, was measured and the potential impact of their metabolism on dissolution modelled. Rock temperature measurements showed that bell holes with bats get significantly hotter than those without bats during bat roosting periods (by an average of 1.1 °C). The relationship is clearest for bell holes with more than about 300 g aggregate bat body mass and for bell holes that are moderately wide and deep, of W:D ratio between 0.8 and 1.6. Measurement of temperature decay after abandonment showed …

The Shapley Value Of Phylogenetic Trees, Claus-Jochen Haake, Akemi Kashiwada '05, Francis E. Su

All HMC Faculty Publications and Research

Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space …

Spatial And Temporal Expression Of Vegetation And Atmospheric Variability From Stable Carbon And Nitrogen Isotope Analysis Of Bat Guano In The Southern United States, Christopher M. Wurster, Donald A. Mcfarlane, Michael I. Bird

WM Keck Science Faculty Papers

Stable isotopes of faeces contain information related to the animals feeding ecology. The use of stable isotope values from subfossil faeces as a palaeoenvironmental indicator depends on how faithfully the animal records their local environment. Here we present insectivorous bat guano δ¹³C and δ¹⁵N values from a precipitation gradient across the southern United States and northern Mexico to compare with local vegetation and climate. We find δ¹³C values to be an excellent predictor of expected C₄/CAM vegetation, indicating that the bats are non-selective in their diet. Moreover, we find bat guano δ …

Motion-Sensitive 3-D Optical Coherence Microscope Operating At 1300 Nm For The Visualization Of Early Frog Development, Barbara M. Hoeling, Stephanie S. Feldman, Daniel T. Strenge, Aaron Bernard, Emily R. Hogan, Daniel C. Petersen, Scott E. Fraser, Yun Kee, J. Michael Tyszka, Richard C. Haskell

All HMC Faculty Publications and Research

We present 3-dimensional volume-rendered in vivo images of developing embryos of the African clawed frog Xenopus laevis taken with our new en-face-scanning, focus-tracking OCM system at 1300 nm wavelength. Compared to our older instrument which operates at 850 nm, we measure a decrease in the attenuation coefficient by 33%, leading to a substantial improvement in depth penetration. Both instruments have motion-sensitivity capability. By evaluating the fast Fourier transform of the fringe signal, we can produce simultaneously images displaying the fringe amplitude of the backscattered light and images showing the random Brownian motion of the scatterers. We present time-lapse movies of …

Is A Basketball Free-Throw Sequence Nonrandom? A Group Exercise For Undergraduate Statistics Students, Stephen C. Adolph

All HMC Faculty Publications and Research

I describe a group exercise that I give to my undergraduate biostatistics class. The exercise involves analyzing a series of 200 consecutive basketball free-throw attempts to determine whether there is any evidence for sequential dependence in the probability of making a free-throw. The students are given the exercise before they have learned the appropriate statistical tests, so that they can come up with ideas on their own. Students spend a full class period working on the problem, with my guidance and hints. In the next class period, we discuss how each student group approached the problem. I then present several …

Analyzing Dna Microarrays With Undergraduate Statisticians, Johanna S. Hardin, Laura Hoopes, Ryan Murphy '06

Pomona Faculty Publications and Research

With advances in technology, biologists have been saddled with high dimensional data that need modern statistical methodology for analysis. DNA microarrays are able to simultaneously measure thousands of genes (and the activity of those genes) in a single sample. Biologists use microarrays to trace connections between pathways or to identify all genes that respond to a signal. The statistical tools we usually teach our undergraduates are inadequate for analyzing thousands of measurements on tens of samples. The project materials include readings on microarrays as well as computer lab activities. The topics covered include image analysis, filtering and normalization techniques, and …

The 19th Century Excavation Of Kent's Cavern, England, Donald A. Mcfarlane, Joyce Lundberg

WM Keck Science Faculty Papers

Between 1858 and 1880, William Pengelly developed revolutionary new techniques for the archeological and paleontological excavation of cave deposits. His work at Brixham Cave and Kent’s Cavern, England, yielded tens of thousands of specimens from the mid-Pleistocene to the Holocene, settled the intellectual debate over the co-existence of humans and extinct mammals, and accumulated an unparalleled resource for continued study. Although the Brixham Cave work was thoroughly summarized in print, Pengelly never published the plans of his much more thorough and extensive excavations at Kent’s Cavern. Here we present a reconstructed plan of the Pengelly excavations that we hope will …

Immunogold Labeling To Enhance Contrast In Optical Coherence Microscopy Of Tissue Engineered Corneal Constructs, Chris B. Raub, Elizabeth J. Orwin, Richard C. Haskell

All HMC Faculty Publications and Research

Our lab has used an optical coherence microscope (OCM) to assess both the structure of tissue-engineered corneal constructs and their transparency. Currently, we are not able to resolve cells versus collagen matrix material in the images produced. We would like to distinguish cells in order to determine if they are viable while growing in culture and also if they are significantly contributing to the light scattering in the tissue. In order to do this, we are currently investigating the use of immunogold labeling. Gold nanoparticles are high scatterers and can create contrast in images. We have conjugated gold nanoparticles to …

Visualizing Early Frog Development With Motion-Sensitive 3-D Optical Coherence Microscopy, Richard C. Haskell, Mary E. Williams, Daniel C. Petersen, Barbara M. Hoeling, Andrew J. Schile, J. D. Pennington, M. G. Seetin, J. M. Castelaz, Scott E. Fraser, Cyrus Papan, Hongwu Ren, Johannes F. De Boer, Zhongping Chen

All HMC Faculty Publications and Research

A motion-sensitive en-face-scanning 3-D optical coherence microscope (OCM) has been designed and constructed to study critical events in the early development of plants and animals. We describe the OCM instrument and present time-lapse movies of frog gastrulation, an early developmental event in which three distinct tissue layers are established that later give rise to all major organ systems. OCM images constructed with fringe-amplitude data show the mesendoderm migrating up along the blastocoel roof, thus forming the inner two tissue layers. Motion-sigma data, measuring the random motion of scatterers, is used to construct complementary images that indicate the presence of Brownian …

An Unusual Lava Cave From Ol Doinyo Lengai, Tanzania, Donald A. Mcfarlane, Joyce Lundberg, Frederick Belton

WM Keck Science Faculty Papers

A new type of lava cave is described from the summit crater of Ol Doinyo Lengai, a unique active carbonatite volcano in Tanzania. This and other similar caves on Ol Doinyo Lengai are formed by thermal erosion and aqueous dissolution of otherwise solid spatter cones. Meteoritic water and endogenous condensates act to form speleothems of complex mineralogy up to 3 m in length. We propose the new classification of “polygenetic spatter cone cave”.

Guano, Donald A. Mcfarlane

WM Keck Science Faculty Papers

This is an encyclopedia article.

A New Megalonychid Sloth From The Late Wisconsinan Of The Dominican Republic, Elizabeth Rega, Donald A. Mcfarlane, Joyce Lundberg, Keith Christenson

WM Keck Science Faculty Papers

An unusually well preserved skull, mandible, and indisputably associated post-cranial elements of new sloth, Acratocnus (Miocnus), were recovered from a cave in Jaragua National Park, Dominican Republic. The animal died lying in a rimstone pool and was rapidly coated with a thin calcite patina. We have documented a late Wisconsinan age for this specimen by inorganic 14C radiometric dating of the patina, with supporting data on the carbon systematics of the speleothems in this cave. This sloth is described as a new species on the basis of the distinctive morphology and relative size of cranial and mandibular features. We consider …

A Middle Pleistocene Age And Biogeography For The Extinct Rodent Megalomys Curazensis From Curaçao, Netherlands Antilles, Donald A. Mcfarlane, Joyce Lundberg

WM Keck Science Faculty Papers

The extinct oryzomyine rodent Megalomys curazensis has been known from abundant but fragmentary remains on the island of Curaçao since 1959. Here we demonstrate an age of 130 000 to 400 000 years before present based on geomorphological context, and propose a biogeographical model for the genus.

A Late Quaternary Paleoecological Record From Caves Of Southern Jamaica, West Indies, Donald A. Mcfarlane, Joyce Lundberg, A.G. Fincham

WM Keck Science Faculty Papers

Studies of an unusual and diverse system of caves in coastal southern Jamaica have yielded a paleoclimatic record associated with a fossil vertebrate record that provides useful insights into the poorly documented paleoecology of latest Wisconsinan and Holocene Jamaica. Episodes of significantly increased precipitation during the Holocene have left characteristic deposits of speleothems, and have supported both faunal and archaeological communities that were dependent on these mesic conditions. Deposits of fossil bat guano preserved in the caves provide a δ¹³C record of alternating mesic and xeric climatic episodes that supports the interpretation of the faunal and archaeological record.