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New Look, New Capabilities
In 2018, the Electronic Scholarly Publishing Project received a complete facelift. All of the old content and functionality were preserved, now wrapped in a new look. Additional features and content were also added.
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Examples of ESP Content
The Electronic Scholarly Publishing Project
The original goal of the ESP Project was simple — we wished to provide free, world-wide access to materials that make it easier to appreciate and understand the field of classical genetics.
Why classical genetics?
For several reasons:
• A real understanding of classical genetics provides a strong (and necessary) foundation for understanding molecular genetics. That is, classical genetics provides the question for which molecular genetics is the answer.
• Understanding the logic of classical genetics is still necessary to understand the many ways that genetics affects our everyday lives.
• The rapid, logical unfolding of classical genetic knowledge (from the rediscovery of Mendel's work to the development of the chromosomal model of heredity in less than twenty years) provides a nearly perfect example of the scientific method in action.
If science is taught primarily as a collection of facts, the process becomes virtually indistinguishable from any other faith-based catechism. If science education is to produce scientific literacy, then science education must emphasize the process by which scientific beliefs are acquired, not merely the beliefs themselves.
Detailed presentations of molecular biological findings only show what we scientists believe. Why we believe remains inaccessible to students, unless we help them grasp the process of scientific investigation and reasoning. Textbooks and monographs offer excellent summaries of what we know, but really understanding why we believe requires contact with original literature.
The example of classical genetics provides powerful pedagogical tools for helping students understand the process of scientific investigation and the basis of scientific belief. Basic experiments in classical genetics can be appreciated by students with little or no formal scientific training. In these experiments, one crosses two individuals that differ in a single trait, counts the progeny, then draws inferences regarding the possible mechanisms of heredity. Although the first works are intellectually accessible to all, as the evidence mounts, the model becomes more complex, drawing one inexorably toward molecular explanations.
Although historical treatments run the risk of being seen as dry and dusty (especially if the "historical" treatment is merely a chronologically ordered recitation of facts), in my experience, if the foundations of classical genetics are presented with an eye on both the process and the excitement of discovery, students follow the material with great interest. Soon, they find themselves not only ready for, but demanding molecular explanations for genetic models they now are prepared both to understand and to believe.
For example, by 1950, classical genetic analysis had shown that the chemical gene, if there was such a thing, would have to possess two traits that seemed to be mutually exclusive:
1. The gene must be heterocatalytic — that is, it must be able to control the synthesis of other molecules of arbitrary complexity and detail.
2. The gene must be autocatalytic — that is, it must be able to control the synthesis of its own descendants with perfect fidelity.
Most surprisingly, the heterocatalylic function was known to be readily susceptible to mutation, yet the autocatalytic function was wholly resistant to mutation. Genes whose heterocatalytic function had been profoundly altered by mutation replicated as well as any normal gene.
These almost paradoxical requirements defined the necessary attributes of the chemical gene on the eve of the molecular revolution. By the early 1950's, evidence suggested that DNA might be the hereditary substance, but the current tetranucleotide model for the structure of DNA (a dull polymer of repeating identical tetramers) seemed to rule it out. Then, Watson and Crick proposed a model for DNA structure (Watson and Crick, 1953a) that transformed our thinking about biological molecules.
The significance of the Watson-Crick model for DNA structure can only be fully appreciated by someone familiar with the apparent paradox in the simultaneous requirement for hetero- and autocatalysis. Watson-Crick DNA is wholly unconstrained in one dimension (where four different nucleotides may be arrayed in any possible order along one strand), but totally constrained in another dimension (where base pairs in one strand must be perfectly complementary to their partners in the other strand).
Clearly, the heterocatalytic function must reside in the unconstrained linear ordering of nucleotides, while the autocatalytic function must reside in the totally constrained base-pairing between strands. Watson and Crick (1953b) explicitly noted this in their second paper:
The phosphate-sugar backbone of our model is completely regular, but any sequence of the pairs of bases can fit into the structure. It follows that in a long molecule many different permutations are possible, and it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information. If the actual order of the bases on one of the pair of chains were given, one could write down the exact order of the bases on the other one, because of the specific pairing. Thus one chain is, as it were, the complement of the other, and it is this feature which suggests how the deoxyribonucleic acid molecule might duplicate itself.
Watson JD and Crick FHC. 1953. Genetical implications of the
of deoxyribonucleic acid.
The point of this aside on the structure of DNA is to show that a grounding in classical genetics provides an excellent foundation for an appreciation of molecular genetics. And, the best way to gain a true scientific grounding in classical genetics is through reading and understanding the early literature.
Hence, the focus of The Electronic Scholarly Publishing Project.
This analysis and more is presented in the Narrative of the 1996 ESP Proposal — the proposal that resulted in the original funding for ESP.
ESP Quick Facts
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.
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.
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.
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.
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.
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.
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.
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.
ESP Picks from Around the Web (updated 07 JUL 2018 )
CRISPR-Cas: Bringing precise editing to DNA manipulation.
Treating Disease with Fecal Transplantation
Fossils of miniature humans (hobbits) discovered in Indonesia
Using DNA as a mass-storage device for digital data.
Researchers have used the microbial immune system CRISPR-Cas to encode a movie into the genome of the bacterium Escherichia coli.
Science Policy & Funding
Overbuilding Research Capacity: an important editorial in which Bruce Alberts argues that the current funding trajectory is unsustainable.
Rescuing US biomedical research from its systemic flaws: Bruce Alberts and others argue that "it is time to rethink some fundamental features of the US biomedical research ecosystem."
Gates Foundation research can't be published in top journals
DNA barcoding shows that restaurant seafood is often not what it seems
Dinosaur tail, complete with feathers, found preserved in amber.
Dinosaurs and Feathers: A Bibliography
Mysterious fast radio burst (FRB) detected in the distant universe.
Colliding stars will light up the night sky in 2022
Big Data & Informatics
Big Data: Buzzword or Big Deal?
Hacking the genome: Identifying anonymized human subjects using publicly available data.
Using DNA as a mass-storage device for digital data.
Six-legged mouse discovered. No joke, no click-bait material. Just a real mouse with six legs.
A red Tesla convertible is launched into space, just for fun...
Apple's Siri, Amazon's Alexa, and Google's Assistant all can respond to commands you can't hear. Commands coming in the window or over the radio or out of the television. Oops...
Robot dogs, walking around and opening doors. Cool. What's not to like?