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The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.

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12 Jun 2018

 

2018-05-14
Create/Update Page ESP Digital Book: The Cell in Development and Inheritance, 2nd Edition — Edmund B. Wilson was the leading cytologist of his time and The Cell in Development and Inheritance was the definitive text on cytology from 1896 into the 1930's. A modern reader will be surprised to see how many of the illustrations in the book seem familiar – versions of many of them still appear in textbooks of introductory biology. The last chapter in the book is entitled "Theories of Inheritance and Development:, and it begins: Every discussion of inheritance and development must take as its point of departure the fact that the germ is a single cell similar in its essential nature to any one of the tissue-cells of which the body is composed. That a cell can carry with it the sum total of the heritage of the species, that it can in the course of a few days or weeks give rise to a mollusk or a man, is the greatest marvel of biological science. In attempting to analyze the problems that it involves, we must from the outset hold fast to the fact, on which Huxley insisted, that the wonderful formative energy of the germ is not impressed upon it from without, but is inherent in the egg as a heritage from the parental life of which it was originally a part. The development of the embryo is nothing new. It involves no breach of continuity, and is but a continuation of the vital processes going on in the parental body. What gives development its marvelous character is the rapidity with which it proceeds and the diversity of the results attained in a span so brief. But when we have grasped this cardinal fact, we have but focussed our instruments for a study of the real problem. How do the adult characteristics lie latent in the germ-cell
2018-04-14
Create/Update Bibliography Classical Genetics: Drosophila Wikipedia: Drosophila is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many species to linger around overripe or rotting fruit. One species of Drosophila in particular, D. melanogaster, has been heavily used in research in genetics and is a common model organism in developmental biology. The terms "fruit fly" and "Drosophila" are often used synonymously with D. melanogaster in modern biological literature. The entire genus, however, contains more than 1,500 species and is very diverse in appearance, behavior, and breeding habitat. D. melanogaster is a popular experimental animal because it is easily cultured en masse out of the wild, has a short generation time, and mutant animals are readily obtainable. In 1906, Thomas Hunt Morgan began his work on D. melanogaster and reported his first finding of a 'white' (eyed) mutant in 1910 to the academic community. He was in search of a model organism to study genetic heredity and required a species that could randomly acquire genetic mutation that would visibly manifest as morphological changes in the adult animal. His work on Drosophila earned him the 1933 Nobel Prize in Medicine for identifying chromosomes as the vector of inheritance for genes.
2018-04-14
Create/Update Bibliography Classical Genetics: Sex Determination Scitable: In humans and many other animal species, sex is determined by specific chromosomes. The first inkling that sex chromosomes were unique from all other chromosomes came from experiments conducted by German biologist Hermann Henking in 1891. While studying sperm formation in wasps, Henking saw that some wasp sperm cells had 12 chromosomes, while others had only 11. Moreover, while observing the stages of meiosis that formed these sperm cells, Henking noticed that the mysterious twelfth chromosome looked different from all the others. He thus named this chromosome the "X element," to represent its unknown nature. nce that supported this hypothesis. About 10 years after Henking's studies, American zoologist C. E. McClung began extensive research into the idea that the X element must have something to do with sex determination. First, McClung asserted that this strange chromosome be called the "accessory chromosome," because it appeared to have a separate purpose compared to the other chromosomes. Next, he decided to undertake a wide comparative study of spermatogenesis not just in insects but in many different organisms, including spiders and mice. While observing sperm generation in grasshoppers, McClung noted that the accessory chromosome did not behave as the other chromosomes did during the first meiotic division. Specifically, this "twelfth chromosome" was not distributed equally to the four sperm cells that arose from one grasshopper spermatogonium; instead, it was present in only half of them. This consistent pattern of segregation in the spermatogenesis of many different organisms caused McClung to speculate that there must be some fundamental reason for the generation of two types of sperm cells. McClung thought about the consequences of this 50/50 distribution of the accessory chromosome, and he pondered how this distribution probably resulted in two different kinds of zygotes. He also noted that there was really only one characteristic that varied among zygotes of many different species in 50/50 proportions, and that characteristic was sex.
2018-04-14
Create/Update Bibliography Classical Genetics Wikipedia: Classical genetics is often referred to as the oldest form of genetics, and began with Gregor Mendel's experiments that formulated and defined a fundamental biological concept known as Mendelian Inheritance. Mendelian Inheritance is the process in which genes and traits are passed from a set of parents to their offspring. These inherited traits are passed down mechanistically with one gene from one parent and the second gene from another parent in sexually reproducing organisms. This creates the pair of genes in diploid organisms. Gregor Mendel started his experimentation and study of inheritance with phenotypes of garden peas and continued the experiments with plants. He focused on the patterns of the traits that were being passed down from one generation to the next generation. This was assessed by test-crossing two peas of different colors and observing the resulting phenotypes. After determining how the traits were likely inherited, he began to expand the amount of traits observed and tested and eventually expanded his experimentation by increasing the number of different organisms he tested.
2018-04-14
Create/Update Bibliography Classical Genetics: Mutation Wikipedia: We now know that, in biology, a mutation is the process that produces heritable change via the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations result from errors during DNA replication or other types of damage to DNA (such as may be caused by exposure to radiation or carcinogens), which then may undergo error-prone repair, or cause an error during other forms of repair, or else may cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements. Mutations may or may not produce discernible changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system, including junctional diversity. In the early days of classical genetics, work to characterize, model, and understand the phenomenology of mutation were critically important for developing the foundations of modern molecular genetics.
2017-12-07
2017-11-09
Create/Update Page ESP Digital Book: Vestiges of the Natural History of Creation — When it first appeared in 1844, Vestiges brought together various ideas of stellar evolution with the progressive transmutation of species in an accessible narrative which tied together numerous scientific theories of the age. The book was initially well received and became an international bestseller, but its unorthodox themes contradicted the natural theology fashionable at the time and were reviled by clergymen - and subsequently by scientists who readily found fault with its amateurish deficiencies. Vestiges caused a shift in popular opinion which - Charles Darwin believed - prepared the public mind for the scientific theories of evolution by natural selection which followed from the publication of On the Origin of Species in 1859.
2017-11-09
Create/Update Page ESP Digital Book: Materials for the Study of Variation — In Materials for the Study of Variation, Bateson was concerned to show that biological variation exists both continuously, for some characters, and discontinuously for others, and coined the terms "meristic" and "substantive" for the two types. In common with Darwin, he felt that quantitative characters could not easily be "perfected" by the selective force of evolution, because of the perceived problem of the "swamping effect of intercrossing", but proposed that discontinuously varying characters could. Amongst other interesting observations he noted variations in which an expected body-part has been replaced by another (which he called homeotic).
2017-11-09
Create/Update Page ESP Digital Book: A History of Genetics — In the small "Fly Room" at Columbia University, T. H. Morgan and his students, A. H. Sturtevant, C. B. Bridges, and H. J. Muller, carried out the work that laid the foundations of modern, chromosomal genetics. The excitement of those times, when the whole field of genetics was being created, is captured in this book, written by one of those present at the beginning.
2017-11-08
Create/Update Page ESP Digital Book: A History of Genetics — In the small "Fly Room" at Columbia University, T. H. Morgan and his students, A. H. Sturtevant, C. B. Bridges, and H. J. Muller, carried out the work that laid the foundations of modern, chromosomal genetics. The excitement of those times, when the whole field of genetics was being created, is captured in this book, written by one of those present at the beginning.
2017-10-27
Create/Update Bibliography Biofilm Wikipedia: Biofilm A biofilm is any group of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPS). The EPS components are produced by the cells within the biofilm and are typically a polymeric conglomeration of extracellular DNA, proteins, and polysaccharides. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, biofilms are frequently described metaphorically as cities for microbes. Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial and hospital settings. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single-cells that may float or swim in a liquid medium. Biofilms can be present on the teeth of most animals as dental plaque, where they may cause tooth decay and gum disease. Microbes form a biofilm in response to many factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of antibiotics. When a cell switches to the biofilm mode of growth, it undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated.
2017-10-08
Create/Update Bibliography Long Term Ecological Research The LTER Network: The US. long-term ecological research network consists of 28 sites with a rich history of ecological inquiry, collaboration across a wide range of research topics, and engagement with students, educators, and community members. Bringing together diverse groups of researchers with sustained data collection, ecosystem manipulation experiments, and modeling, these sites allow scientists to apply new tools and explore new questions in systems where the context is well understood, shared, and thoroughly documented.
2017-10-08
Create/Update Bibliography Ecological Informatics Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE and Data Conservancy.
2017-07-02
2017-06-18
Create/Update Page Genetics and History — Late in the summer of 1818, a human sperm and egg united to form a human zygote. One of those gametes, we don't know which, was carrying a newly mutated gene. A century later, after passing through three generations, a copy of that mutation contributed to the overthrow of the Tsar and the emergence of communism in Russia.
2017-04-23
Create/Update Bibliography Microbial Ecology Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.
2017-04-23
Create/Update Bibliography Microbiome Project(s) — For many multicellular organisms, a microscopic study shows that microbial cells outnumber host cells by perhaps ten to one. Until recently, these abundant communities of host-associated microbes were largely unstudied, often for lack of analytical tools or conceptual frameworks. The advent of new tools is rendering visible this previously ignored biosphere and the results have been startling. Many facets of host biology have proven to be profoundly affected by the associated microbiomes. As a result, several large-scale projects — such as the Human Microbiome Project — have been undertaken to jump start an understanding of this critical component of the biosphere.
2017-03-20
Create/Update Page General Publications — The miscellaneous page is just that: a grab bag of items that just don't fit anywhere else. Over time, the content might include humor, items of interest from the news, general commentaries, or pretty much anything.
2017-03-19
Create/Update Page Miscellaneous — The miscellaneous page is just that: a grab bag of items that just don't fit anywhere else. Over time, the content might include humor, items of interest from the news, general commentaries, or pretty much anything.
2017-03-19
Create/Update Page Humor — The miscellaneous page is just that: a grab bag of items that just don't fit anywhere else. Over time, the content might include humor, items of interest from the news, general commentaries, or pretty much anything.
2017-03-13
Create/Update Graphic Arts Gallery IRO Cover — By 2009, my hobby of creating parody magazine covers had become well known at work. As a result, I was recruited to provide my services as a door prize to be awarded during an all-management retreat of the Fred Hutchinson Cancer Research Center. Karen Hansen, the Director of the Institutional Review Office, won the prize. I told Karen that I would design the cover, without telling her its contents, and present it to her, in the form of a large poster, when it was done. All she had to do was help me obtain a starting photograph. She opted to involve her entire staff, and so we started by arranging to have a group photo taken by Phil Meadows. Then I got to work. Lots of people helped come up with ideas for the table of contents. When delivered, the poster was a hit and was immediately hung on the IRO office wall. done in Photoshop
2017-03-06
Create/Update Bibliography Current Literature — Recent Full Contents Current Literature: Full, recent table-of-contents listings for a few selected journals.
2017-03-06
Create/Update Bibliography Misophonia — Cannot Stand the Sound of Chewing Wikipedia: Misophonia, literally "hatred of sound," was proposed in 2000 as a condition in which negative emotions, thoughts, and physical reactions are triggered by specific sounds. It is also called "select sound sensitivity syndrome" and "sound-rage." Misophonia has no classification as an auditory, neurological, or psychiatric condition, there are no standard diagnostic criteria, it is not recognized in the DSM-IV or the ICD-10, and there is little research on its prevalence or treatment. Proponents suggest misophonia can adversely affect ability to achieve life goals and to enjoy social situations. Treatment consists of developing coping strategies such as cognitive behavioral therapy and exposure therapy. As of 2016 the literature on misophonia was very limited (see below). Some small studies show that people with misophonia generally have strong negative feelings, thoughts, and physical reactions to specific sounds, which the literature calls "trigger sounds." One study found that around 80% of the sounds were related to the mouth (eating, yawning, etc.), and around 60% were repetitive.
2017-03-02
Create/Update Bibliography Publications by FHCRC Researchers — The Fred Hutchinson Cancer Research Center began in 1975, with critical help from Washington State's U.S. Senator Warren Magnuson. Fred Hutch quickly became the permanent home to Dr. E. Donnall Thomas, who had spent decades developing an innovative treatment for leukemia and other blood cancers. Thomas and his colleagues were working to cure cancer by transplanting human bone marrow after otherwise lethal doses of chemotherapy and radiation. At the Hutch, Thomas improved this treatment and readied it for widespread use. Since then, the pioneering procedure has saved hundreds of thousands of lives worldwide. While improving bone marrow transplantation remains central to Fred Hutch's research, it is now only part of its efforts. The Hutch is home to five scientific divisions, three Nobel laureates and more than 2,700 faculty, who collectively have published more than 10,000 scientific papers, presented here as a full bibliography.

NOTE: From 1995 to 2009 I served as the Hutch's vice president for information technology — hence my interest in the organization. Although my role was in the admin division, if you dig through this bibliography, you will find a couple of papers with me as an author.
2017-02-01
Create/Update Bibliography Telomeres — Wikipedia: A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos (τέλος) "end" and merοs (μέρος, root: μερ-) "part". For vertebrates, the sequence of nucleotides in telomeres is TTAGGG, with the complementary DNA strand being AATCCC, with a single-stranded TTAGGG overhang. This sequence of TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth to less than 4 kilobases in old age,[3] with average rate of decline being greater in men than in women. During chromosome replication, the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome, so in each duplication the end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). The telomeres are disposable buffers at the ends of chromosomes which are truncated during cell division; their presence protects the genes before them on the chromosome from being truncated instead. The telomeres themselves are protected by a complex of shelterin proteins, as well as by the RNA that telomeric DNA encodes.
2017-02-01
Create/Update Bibliography Sociobiology Sociobiology is a field of scientific study that is based on the hypothesis that social behavior has resulted from evolution and attempts to examine and explain social behavior within that context. Sociobiology investigates social behaviors, such as mating patterns, territorial fights, pack hunting, and the hive society of social insects. It argues that just as selection pressure led to animals evolving useful ways of interacting with the natural environment, it led to the genetic evolution of advantageous social behavior. While the term "sociobiology" can be traced to the 1940s, the concept did not gain major recognition until the publication of Edward O. Wilson's book Sociobiology: The New Synthesis in 1975.
2017-01-30
Create/Update Bibliography Kin Selection Wikipedia: Kin selection is the evolutionary strategy that favours the reproductive success of an organism's relatives, even at a cost to the organism's own survival and reproduction. Kin altruism is altruistic behaviour whose evolution is driven by kin selection. Kin selection is an instance of inclusive fitness, which combines the number of offspring produced with the number an individual can produce by supporting others, such as siblings. Charles Darwin discussed the concept of kin selection in his 1859 book, The Origin of Species, where he reflected on the puzzle of sterile social insects, such as honey bees, which leave reproduction to their mothers, arguing that a selection benefit to related organisms (the same "stock") would allow the evolution of a trait that confers the benefit but destroys an individual at the same time. R.A. Fisher in 1930 and J.B.S. Haldane in 1932 set out the mathematics of kin selection, with Haldane famously joking that he would willingly die for two brothers or eight cousins. In 1964, W.D. Hamilton popularised the concept and the major advance in the mathematical treatment of the phenomenon by George R. Price which has become known as "Hamilton's rule". In the same year John Maynard Smith used the actual term kin selection for the first time. According to Hamilton's rule, kin selection causes genes to increase in frequency when the genetic relatedness of a recipient to an actor multiplied by the benefit to the recipient is greater than the reproductive cost to the actor.
2017-01-21
Create/Update Photo Gallery Test Caption Gallery — A test gallery consisting of pictures that have no other purpose than to test the layout of the gallery slide-show system. The individual pics are of no consequence, the captions are of no consequence. The truth is of no consequence. No truth, no consequences. shot with view camera once owned by Ansel Adams
2017-01-19
Create/Update Page Consulting Services — RJ Robbins engages in consulting and/or collaboration services on a variety or projects, including things such as Cancer Center Core Grant preparation, meeting facilitation, publishing and typesetting, and biodiversity informatics. Fees are negotiated on a project-by-project basis. Anyone with a need for consulting or collaborative activities in any area in which Robbins might be of assistance should click here to send him an email describing the project.
2017-01-16
Create/Update Photo Gallery Bahia la Choya, Sonora, Mexico — Cholla Bay (Bahia la Choya) is a small village, near Puerto Peñasco, a city located in the northwest of the Mexican state of Sonora, about 100 km from the border with the U.S. state of Arizona. The village is both on the water (the northern end of the Sea of Cortez) and in a desert. In the village, one often sees water in the distance and dry, dusty soil in the foreground, giving the whole place an eerie feel. The colorful, and sometimes exotic architecture add to the mood, sometimes suggesting Tatooine with a beach. Canon 5D Mark II, various lenses ...
2017-01-15
Create/Update Page Miscellaneous — The miscellaneous page is just that: a grab bag of items that just don't fit anywhere else. Over time, the content might include humor, items of interest from the news, general commentaries, or pretty much anything.
2017-01-15
Create/Update Page Six-legged Mouse — In a breeding colony of deermice at Michigan State, a six-legged pup was produced. A photograph of the pup is shown and some comments offered.
2017-01-07
Create/Update Photo Gallery Experiments in Olympus Macrophotography — Experiments in macrophotography, with new lens: I acquired a new macro lens, so decided to walk around the house taking a snap here and there. The Pen E-P5 was the first camera I had used for macro photography that allowed you to focus and take the shot by touching the display screen. This is especially useful for macrophography where autofocus is not likely to focus on the part of the image you had in mind. Olympus Pen E-P5, M.Zuiko ED 60mm f2.8 Macro Lens
2017-01-03
Create/Update Graphic Arts Gallery Nakaturibu: Creating an Image — In 2007, I received an important request from my boss, the Chief Operating Officer. The COO explained that the VP for HR, Han Nachtrieb, was on vacation in Japan, and that it was imperative that something be done to celebrate his return. I opted to create a poster-sized print of him in Japanese regalia. Starting with an image found on-line, I stripped out some faces and other material, added Han's head and a helmet to the top, replaced a face at the lower left with that of Lee Hartwell (our center President and Director), and replaced the text on the vertical sign. done in Photoshop
2017-01-02
Create/Update Photo Gallery Small Town Pool Hall, 1960s — Around fifty or sixty years ago, in Niles, Michigan, there was a small "pool hall" (actually just two tables in repurposed garage), located near the east bank of the river, towards the end of Sycamore Street. It was nothing fancy and served no other purpose than to provide a place for people to play pool — usually 8-ball or 9-ball or 6-ball, or some variant on those games. Every once in a while somebody would play some straight pool. The proprietor (shown in these pictures sitting with a cigarette or racking balls) was John Billups, better known as Skip. Skip had an old, horizontal vending machine (that cooled by keeping the bottles immersed in cold water) for soda pop. I don't remember whether they were a nickel or a dime each. Minolta SRT-101, 50mm F1.4 normal lens
2017-01-01
Create/Update Bibliography Microbiome It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.
2017-01-01
Create/Update Bibliography Archaea In 1977, Carl Woese and George Fox applied molecular techniques to biodiversity and discovered that life on Earth consisted of three, not two (prokaryotes and eukaryotes), major lineages, tracing back nearly to the very origin of life on Earth. The third lineage has come to be known as the Archaea. Organisms now considered Archaea were originally thought to be a kind of prokaryote, but Woese and Fox showed that they were as different from prokaryotes as they were from eukaryotes. To understand life on Earth one must also understand the Archaea .
2017-01-01
Create/Update Bibliography Climate Change The year 2014 was the hottest year on record, since the beginning of record keeping over 100 years ago. The year 2015 broke that record, and 2016 will break the record of 2015. The Earth seems to be on a significant warming trend.
2017-01-01
Create/Update Bibliography Metagenomics While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.
2017-01-01
Create/Update Bibliography Mitochondrial Evolution The endosymbiotic hypothesis for the origin of mitochondria (and chloroplasts) suggests that mitochondria are descended from specialized bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm.
2017-01-01
Create/Update Bibliography Neanderthals Wikipedia: Neanderthals or Neandertals — named for the Neandertal region in Germany — were a species or subspecies of archaic human, in the genus Homo. Neanderthals became extinct around 40,000 years ago. They were closely related to modern humans, sharing 99.7% of DNA. Remains left by Neanderthals include bone and stone tools, which are found in Eurasia, from Western Europe to Central and Northern Asia. Neanderthals are generally classified by paleontologists as the species Homo neanderthalensis, having separated from the Homo sapiens lineage 600,000 years ago, but a minority consider them to be a subspecies of Homo sapiens (Homo sapiens neanderthalensis). Several cultural assemblages have been linked to the Neanderthals in Europe. The earliest, the Mousterian stone tool culture, dates to about 160,000 years ago. Late Mousterian artifacts were found in Gorham's Cave on the south-facing coast of Gibraltar. Compared to Homo sapiens, Neanderthals had a lower surface-to-volume ratio, with shorter legs and a bigger body, in conformance with Bergmann's rule, as an energy-loss reduction adaptation to life in a high-latitude (i.e. seasonally cold) climate. Their average cranial capacity was notably larger than typical for modern humans: 1600 cm3 vs. 1250-1400 cm3. The Neanderthal genome project published papers in 2010 and 2014 stating that Neanderthals contributed to the DNA of modern humans, including most humans outside sub-Saharan Africa, as well as a few populations in sub-Saharan Africa, through interbreeding, likely between 50,000 and 60,000 years ago.
2017-01-01
Create/Update Bibliography Invasive Species Standard Definition: Invasive species are plants, animals, or pathogens that are non-native (or alien) to the ecosystem under consideration and whose introduction causes or is likely to cause harm. Although that definition allows a logical possibility that some species might be non-native and harmless, most of time it seems that invasive species and really bad critter (or weed) that should be eradicated are seen as equivalent phrases. But, there is a big conceptual problem with that notion: every species in every ecosystem started out in that ecosystem as an invader. If there were no invasive species, all of Hawaii would be nothing but bare volcanic rock. Without an invasion of species onto land, there would be no terrestrial ecosystems at all. For the entire history of life on Earth, the biosphere has responded to perturbation and to opportunity with evolutionary innovation and with physical movement. While one may raise economic or aesthetic arguments against invasive species, it is impossible to make such an argument on scientific grounds. Species movement — the occurrence of invasive species — is the way the biosphere responds to perturbation. One might even argue that species movement is the primary, short-term "healing" mechanism employed by the biosphere to respond to perturbation — to "damage." As with any healing process, the short-term effect may be aesthetically unappealing (who thinks scabs are appealing?), but the long-term effects can be glorious.
2017-01-01
Create/Update Bibliography Taste-Aversion Learning — The notion of "conditioned taste aversions" refers to animals' ability to preferentially associate taste with illness, despite the passage of a significant time between ingestion and illness. When first described, this pattern seemed so at variance with the tenets of classical learning theory that one early reviewer claimed "results like that are no more likely than birdshit in a cuckoo clock." Now, however, the reality of the phenomenon is well established and has demonstrated relevance in practical areas ranging from rodent control to chemotherapy.
2017-01-01
Create/Update Bibliography Origin of Eukaryotes The evolutionary origin of eukaryotes is a critically important, yet poorly understood event in the history of life on earth. The endosymbiotic origin of mitochondria allowed cells to become sufficiently large that they could begin to interact mechanically with their surrounding environment, thereby allowing evolution to create the visible biosphere of multicellular eukaryotes.
2017-01-01
Create/Update Bibliography Biodiversity and Metagenomics If evolution is the only light in which biology makes sense, and if variation is the raw material upon which selection works, then variety is not merely the spice of life, it is the essence of life — the sine qua non without which life could not exist. To understand biology, one must understand its diversity. Historically, studies of biodiversity were directed primarily at the realm of multicellular eukaryotes, since few tools existed to allow the study of non-eukaryotes. Because metagenomics allows the study of intact microbial communities, without requiring individual cultures, it provides a tool for understanding this huge, hitherto invisible pool of biodiversity, whether it occurs in free-living communities or in commensal microbiomes associated with larger organisms.
2017-01-01
Create/Update Bibliography Endosymbiosis — A symbiotic relationship in which one of the partners lives within the other, especially if it lives within the cells of the other, is known as endosymbiosis. Mitochondria, chloroplasts, and perhaps other cellular organelles are believed to have originated from a form of endosymbiosis. The endosymbiotic origin of eukaryotes seems to have been a biological singularity — that is, it happened once, and only once, in the history of life on Earth.
2017-01-01
Create/Update Bibliography Horizontal Gene Transfer The pathology-inducing genes of O157:H7 appear to have been acquired, likely via prophage, by a nonpathogenic E. coli ancestor, perhaps 20,000 years ago. That is, horizontal gene transfer (HGT) can lead to the profound phenotypic change from benign commensal to lethal pathogen. "Horizontal" in this context refers to the lateral or "sideways" movement of genes between microbes via mechanisms not directly associated with reproduction. HGT among prokaryotes can occur between members of the same "species" as well as between microbes separated by vast taxonomic distances. As such, much prokaryotic genetic diversity is both created and sustained by high levels of HGT. Although HGT can occur for genes in the core-genome component of a pan-genome, it occurs much more frequently among genes in the optional, flex-genome component. In some cases, HGT has become so common that it is possible to think of some "floating" genes more as attributes of the environment in which they are useful rather than as attributes of any individual bacterium or strain or "species" that happens to carry them. For example, bacterial plasmids that occur in hospitals are capable of conferring pathogenicity on any bacterium that successfully takes them up. This kind of genetic exchange can occur between widely unrelated taxa.
2017-01-01
Create/Update Bibliography Did Mendel Cheat? In 1936, R. A. Fisher noted that Mendel's results seem to come too close to the expected value too often, leading him to conclude "the general level of agreement between Mendel's expectations and his reported results shows that it is closer than would be expected in the best of several thousand repetitions. The data have evidently been sophisticated systematically..." That is, Mendel's data had been fiddled with. A small industry has grown up, with various authors taking sides on the controversy.
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Create/Update Bibliography Topologically Associating Domains "Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization." QUOTE FROM: Dekker Job and Heard Edith (2015), Structural and functional diversity of Topologically Associating Domains, FEBS Letters, 589, doi: 10.1016/j.febslet.2015.08.044
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Create/Update Bibliography Paleonotology Meets Genomics — Sequencing Ancient DNA The ideas behind Jurassic Park have become real, kinda sorta. It is now possible to retrieve and sequence DNA from ancient specimens. Although these sequences are based on poor quality DNA and thus have many inferential steps (i,e, the resulting sequence is not likely to be a perfect replica of the living DNA), the insights to be gained from paleosequentcing are nonetheless great. For example, paleo-sequencing has shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.
2017-01-01
Create/Update Bibliography Squid-Vibrio Symbiosis The small bobtail squid (Euprymna scolopes) has a mutually beneficial relationship with bacteria called Vibrio fischeri that live on the squid's underside. The bacteria allow the squid to produce light, which then allows the squid to escape from things that might want to eat it. "The squid emit ventral luminescence that is often very, very close to the quality of light coming from the moon and stars at night," explains Margaret McFall-Ngai, Margaret McFall-Ngai, professor of medical microbiology and immunology at the University of Wisconsin-Madison. For fish looking up from below for something to eat, the squid are camouflaged against the moon or the starlight because they don't cast a shadow. "It's like a 'Klingon' cloaking device," she notes. But the Vibrio fischeri don't stay in the squid continuously. Every day, in response to the light cue of dawn, the squid vents 90 percent of the bacteria back into the seawater. "And then, while it's sitting quiescent in the sand, the bacteria grow up in the crypt so that when [the squid] comes out in the evening, it will have a full complement of luminous Vibrio fischeri," says McFall-Ngai.
2017-01-01
Create/Update Bibliography Fecal Transplantation Fecal Transplantion is a procedure in which fecal matter is collected from a tested donor, mixed with a saline or other solution, strained, and placed in a patient, by colonoscopy, endoscopy, sigmoidoscopy, or enema. The theory behind the procedure is that a normal gut microbial ecosystem is required for good health and that sometimes a benefucuial ecosystem can be destroyed, perhaps by antibiotics, allowing other bacteria, specifically Clostridium difficile to over-populate the colon, causing debilitating, sometimes fatal diarrhea. C. diff. is on the rise throughout the world. The CDC reports that approximately 347,000 people in the U.S. alone were diagnosed with this infection in 2012. Of those, at least 14,000 died. Fecal transplant has also had promising results with many other digestive or auto-immune diseases, including Irritable Bowel Syndrome, Crohn's Disease, and Ulcerative Colitis. It has also been used around the world to treat other conditions, although more research in other areas is needed. Fecal transplant was first documented in 4th century China, where the treatment was known as yellow soup.
2017-01-01
Create/Update Bibliography Energetics and Mitochondrial Evolution Mitochondria are the energy-producing "engines" that provide the power to drive eukaryotic cells. The energy output of hundreds, or thousands, of mitochondria allowed eukaryotic cells to increase in size 1000-fold, or more, over the size of prokaryotics cells. This increase in size allowed an escape from the constraints of low Reynolds numbers and, for the first time, life could function in a way where mechanism, and thus morphology, mattered. Evolution began to shape morphology, allowing the emergence of the multicellular eukaryotic biosphere — the visible living world.
2017-01-01
Create/Update Bibliography The Denisovans, Another Human Ancestor Wikipedia: The Denisovans are an extinct species or subspecies of human in the genus Homo. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. Two teeth belonging to different members of the same population have since been reported. In November 2015, a tooth fossil containing DNA was reported to have been found and studied. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known. Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from the mtDNAs of Neanderthals and modern humans. Subsequent study of the nuclear genome from this specimen suggests that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans. A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.
2017-01-01
Create/Update Bibliography Mesothelioma and Asbestos Mesothelioma is a rare, but deadly form of cancer that is often (nearly always) associated with prior exposure to asbestos. The latency between exposure and disease onset is long, usually 20-50 years, making this a difficult cause-effect system to study.
2017-01-01
Create/Update Bibliography Drosophila: The Fly Room In the small "Fly Room" at Columbia University, T. H. Morgan and his students, A. H. Sturtevant, C. B. Bridges, H. J. Muller, carried out the work that laid the foundations of modern, chromosomal genetics. The excitement of those times, when the whole field of genetics was being created, is captured in this book, written by one of those present at the beginning. In a time when genomics and genetics maps are discussed almost daily in the popular press, it is worth remembering that the world's first genetic map was created in 1913 by A. H. Sturtevant, then a sophomore in college. In 1933, Morgan received the Nobel Prize in medicine, for his "discoveries concerning the role played by the chro- mosome in heredity." In the 67 years since, genetics has continued to advance, leaving behind a fascinating history. The year 2000 was the 100th anniversary of the founding of modern genetics with the rediscovery of Mendel' work and it is the year in which the full DNA sequence of the Drosophila genome was obtained. The fruit fly is still at the center of genetic research, just as it was in 1910 when work first began in Morgan's fly room.
2017-01-01
Create/Update Bibliography Homo floresiensis, The Hobbit Wikipedia: Homo floresiensis ("Flores Man"; nicknamed "hobbit" for its small stature) is an extinct species in the genus Homo. The remains of an individual that would have stood about 3.5 feet (1.1 m) in height were discovered in 2003 at Liang Bua on the island of Flores in Indonesia. Partial skeletons of nine individuals have been recovered, including one complete skull, referred to as "LB1".These remains have been the subject of intense research to determine whether they represent a species distinct from modern humans. This hominin had originally been considered to be remarkable for its survival until relatively recent times, only 12,000 years ago. However, more extensive stratigraphic and chronological work has pushed the dating of the most recent evidence of their existence back to 50,000 years ago. Their skeletal material is now dated to from 100,000 to 60,000 years ago; stone tools recovered alongside the skeletal remains were from archaeological horizons ranging from 190,000 to 50,000 years ago. Fossil teeth and a partial jaw from hominins believed ancestral to H. floresiensis were discovered in 2014 and described in 2016. These remains are from a site on Flores called Mata Menge, about 74 km from Liang Bua. They date to about 700,000 years ago and are even smaller than the later fossils. The form of the fossils has been interpreted as suggesting that they are derived from a population of H. erectus that arrived on Flores about a million years ago (as indicated by the oldest artifacts excavated on the island) and rapidly became dwarfed. The discoverers (archaeologist Mike Morwood and colleagues) proposed that a variety of features, both primitive and derived, identify these individuals as belonging to a new species, H. floresiensis, within the taxonomic tribe of Hominini, which includes all species that are more closely related to humans than to chimpanzees. Based on previous date estimates, the discoverers also proposed that H. floresiensis lived contemporaneously with modern humans on Flores. Two orthopedic researches published in 2007 reported evidence to support species status for H. floresiensis. A study of three tokens of carpal (wrist) bones concluded there were differences from the carpal bones of modern humans and similarities to those of a chimpanzee or an early hominin such as Australopithecus. A study of the bones and joints of the arm, shoulder, and lower limbs also concluded that H. floresiensis was more similar to early humans and other apes than modern humans. In 2009, the publication of a cladistic analysis and a study of comparative body measurements provided further support for the hypothesis that H. floresiensis and Homo sapiens are separate species.
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Create/Update Bibliography Feathered Dinosaurs "A feathered dinosaur is any species of dinosaur possessing feathers. For over 150 years, since scientific research began on dinosaurs in the early 1800s, dinosaurs were generally believed to be related to the reptile family; the word "dinosaur", coined in 1842 by paleontologist Richard Owen, comes from the Greek for "formidable lizard". This view began to shift during the so-called dinosaur renaissance in scientific research in the late 1960s, and by the mid-1990s significant evidence had emerged that dinosaurs are much more closely related to birds. In fact, birds are now believed to have descended directly from the theropod group of dinosaurs, and are thus classified as dinosaurs themselves, meaning that any modern bird can be considered a feathered dinosaur, since all modern birds possess feathers (with the exception of a few artificially selected chickens). Among extinct dinosaurs, feathers or feather-like integument have been discovered on dozens of genera via both direct and indirect fossil evidence. The vast majority of feather discoveries have been for coelurosaurian theropods. However, integument has also been discovered on at least three ornithischians, raising the likelihood that proto-feathers were also present in earlier dinosaurs." QUOTE FROM: Wikipedia
2017-01-01
Create/Update Bibliography Symbiosis Symbiosis refers to an interaction between two or more different organisms living in close physical association, typically to the advantage of both. Symbiotic relationships were once thought to be exceptional situations. Recent studies, however, have shown that every multicellular eukaryote exists in a tight symbiotic relationship with billions of microbes. The associated microbial ecosystems are referred to as microbiome and the combination of a multicellular organism and its microbiota has been described as a holobiont. It seems "we are all lichens now."
2017-01-01
Create/Update Bibliography Reynolds Number It is well known that relative size greatly affects how organisms interact with the world. Less well known, at least among biologists, is that at sufficiently small sizes, mechanical interaction with the environment becomes difficult and then virtually impossible. In fluid dynamics, an important dimensionless parameter is the Reynolds Number (abbreviated Re), which is the ratio of inertial to viscous forces affecting the movement of objects in a fluid medium (or the movement of a fluid in a pipe). Since Re is determined mainly by the size of the object (pipe) and the properties (density and viscosity) of the fluid, organisms of different sizes exhibit significantly different Re values when moving through air or water. A fish, swimming at a high ratio of inertial to viscous forces, gives a flick of its tail and then glides for several body lengths. A bacterium, "swimming" in an environment dominated by viscosity, possesses virtually no inertia. When the bacterium stops moving its flagellum, the bacterium "coasts" for about a half of a microsecond, coming to a stop in a distance less than a tenth the diameter of a hydrogen atom. Similarly, the movement of molecules (nutrients toward, wastes away) in the vicinity of a bacterium is dominated by diffusion. Effective stirring — the generation of bulk flow through mechanical means — is impossible at very low Re. An understanding of the constraints imposed by life at low Reynolds numbers is essentially for understanding the prokaryotic biosphere.
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Create/Update Bibliography Pangenome Although the enforced stability of genomic content is ubiquitous among MCEs, the opposite is proving to be the case among prokaryotes, which exhibit remarkable and adaptive plasticity of genomic content. Early bacterial whole-genome sequencing efforts discovered that whenever a particular "species" was re-sequenced, new genes were found that had not been detected earlier — entirely new genes, not merely new alleles. This led to the concepts of the bacterial core-genome, the set of genes found in all members of a particular "species", and the flex-genome, the set of genes found in some, but not all members of the "species". Together these make up the species' pan-genome.
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Create/Update Bibliography CRISPR-Cas Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced crisper) are segments of prokaryotic DNA containing short repetitions of base sequences. Each repetition is followed by short segments of "spacer DNA" from previous exposures to foreign DNA (e.g a virus or plasmid). The CRISPR/Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides a form of acquired immunity. CRISPR associated proteins (Cas) use the CRISPR spacers to recognize and cut these exogenous genetic elements in a manner analogous to RNA interference in eukaryotic organisms. CRISPRs are found in approximately 40% of sequenced bacterial genomes and 90% of sequenced archaea. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added. The Cas9-gRNA complex corresponds with the CAS III crRNA complex in the above diagram. CRISPR/Cas genome editing techniques have many potential applications, including altering the germline of humans, animals, and food crops. The use of CRISPR Cas9-gRNA complex for genome editing was the AAAS's choice for breakthrough of the year in 2015.
2017-01-01
Create/Update Bibliography Holobiont — Holobionts are assemblages of different species that form ecological units. Lynn Margulis proposed that any physical association between individuals of different species for significant portions of their life history is a symbiosis. All participants in the symbiosis are bionts, and therefore the resulting assemblage was first coined a holobiont by Lynn Margulis in 1991 in the book Symbiosis as a Source of Evolutionary Innovation. Holo is derived from the Ancient Greek word ὅλος (hólos) for “whole”. The entire assemblage of genomes in the holobiont is termed a hologenome.
2017-01-01
Create/Update Bibliography Wolbachia WIKIPEDIA: Wolbachia is a genus of bacteria which "infects" (usually as intracellular symbionts) arthropod species, including a high proportion of insects, as well as some nematodes. It is one of the world's most common parasitic microbes and is possibly the most common reproductive parasite in the biosphere. Its interactions with its hosts are often complex, and in some cases have evolved to be mutualistic rather than parasitic. Some host species cannot reproduce, or even survive, without Wolbachia infection. One study concluded that more than 16% of neotropical insect species carry bacteria of this genus, and as many as 25 to 70 percent of all insect species are estimated to be potential hosts. Wolbachia also harbor a temperate bacteriophage called WO. Comparative sequence analyses of bacteriophage WO offer some of the most compelling examples of large-scale horizontal gene transfer between Wolbachia coinfections in the same host. It is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that were previously considered highly stable or prone to loss of genes overtime. Outside of insects, Wolbachia infects a variety of isopod species, spiders, mites, and many species of filarial nematodes (a type of parasitic worm), including those causing onchocerciasis ("River Blindness") and elephantiasis in humans as well as heartworms in dogs. Not only are these disease-causing filarial worms infected with Wolbachia, but Wolbachia seem to play an inordinate role in these diseases. A large part of the pathogenicity of filarial nematodes is due to host immune response toward their Wolbachia. Elimination of Wolbachia from filarial nematodes generally results in either death or sterility of the nematode.
2017-01-01
Create/Update Bibliography Human Microbiome — The human microbiome is the set of all microbes that live on or in humans. Together, a human body and its associated microbiomes constitute a human holobiont. Although a human holobiont is mostly mammal by weight, by cell count it is mostly microbial. The number of microbial genes in the associated microbiomes far outnumber the number of human genes in the human genome. Just as humans (and other multicellular eukaryotes) evolved in the constant presence of gravity, so they also evolved in the constant presence of microbes. Consequently, nearly every aspect of human biology has evolved to deal with, and to take advantage of, the existence of associated microbiota. In some cases, the absence of a "normal microbiome" can cause disease, which can be treated by the transplant of a correct microbiome from a healthy donor. For example, fecal transplants are an effective treatment for chronic diarrhea from over abundant Clostridium difficile bacteria in the gut.
2017-01-01
Create/Update Bibliography Gregor Mendel In 1865, Gregor Mendel reported the results of his experiments with peas and in so doing laid the foundations of what has become the modern science of genetics. There are few examples of entire fields having been so clearly founded upon the works of one man.
2017-01-01
Create/Update Bibliography Genomic Standards Consortium The Genomic Standards Consortium (GSC) is an open-membership working body formed in September 2005. The aim of the GSC is making genomic data discoverable. The GSC enables genomic data integration, discovery and comparison through international community-driven standards.
2016-12-31
Create/Update Photo Gallery Desert Garden, Balboa Park, San Diego, CA — The Desert Garden contains more than 1,300 plants, including succulents and drought-resistant plants from around the world, within its 2.5 acres. The peak blooming period is January through March; however, these plants are interesting at any time of year because of their unusual shapes. Because the light at the park can be flat or harsh, I used a set of twin flashes, one on the camera and one hand held. Canon 5D Mk II, macro lens
2016-12-31
Create/Update Photo Gallery Desert Garden, Balboa Park, San Diego, CA — The Desert Garden contains more than 1,300 plants, including succulents and drought-resistant plants from around the world, within its 2.5 acres. The peak blooming period is January through March; however, these plants are interesting at any time of year because of their unusual shapes. Because the light at the park can be flat or harsh, I used a set of twin flashes, one on the camera and one hand held. Canon 5D Mk II, macro lens

 

2017: 01/04
Modified pop-up menus to include a translucent white-out background while the menu is being displayed..
2017: 01/04
Modified and unified the design of the pop-up menus for socia-media sharing and for finer-resolution control of bibliography displays.
2016: 11/04
Develop the overall design, with black headers and footers.
2016: 11/03
Start work on new main css file for the site, RJR-flat-responsive.css.
2016: 11/01
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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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In the small "Fly Room" at Columbia University, T.H. Morgan and his students, A.H. Sturtevant, C.B. Bridges, and H.J. Muller, carried out the work that laid the foundations of modern, chromosomal genetics. The excitement of those times, when the whole field of genetics was being created, is captured in this book, written in 1965 by one of those present at the beginning. R. Robbins

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