1. PAPER: Mendel, Gregor. (1865): Experiments in plant hybridization.

In February and March of 1865, Gregor Mendel presented the Brünn Natural History Society in Brünn, Czechoslovakia, with the results of his investigations into the mechanisms governing inheritance in pea plants. The next year, the work was published as Mendel, Gregor. 1866. "Versuche über Pflanzen Hybriden." Verhandlungen des naturforschenden Vereines in Brünn, 4:3-47.

In this remarkable paper, Mendel laid the groundwork for what later became the science of genetics. However, the work was largely ignored when it appeared and Mendel moved on to other things. He died in 1884.

His work was rediscovered at the turn of the century and its significance immediately recognized. Genetics, as a formal scientific discipline, exploded into activity in 1900.

An annotated version of Mendel's paper is also available. The annotated version contains explanatory notes throughout the document. This can be useful to those reading Mendel's paper for the first time.

For those wishing to see and read Mendel in the original, a facsimile reprint edition is available. This version is in Adobe PDF format, but the pages are images of the original publication, not a new type-setting of the material.

You may also wish to visit The Mendel Web site, created by Roger Blumberg. The site offers many additional resources for the Mendel scholar.

2. PAPER: Hardy, G. H. (1908): Mendelian Proportions in a Mixed Population.

Every geneticist has heard of the Hardy-Weinberg Law and of Hardy-Weinberg Equilibrium, and nearly all basic biology texts teach that G. H. Hardy played a seminal role in founding population genetics. But, what most biologists don't realize is that Hardy's total contribution to biology consisted of a single letter to the editor in Science. The letter began,

I am reluctant to intrude in a discussion concerning matters of which I have no expert knowledge, and I should have expected the very simple point which I wish to make to have been familiar to biologists. However, some remarks of Mr. Udny Yule, to which Mr. R. C. Punnett has called my attention, suggest that it may still be worth making.

With that, Hardy offered his "simple point" and then washed his hands of biology. His autobiography, A Mathematician's Apology, makes no mention of population genetics.

3. PAPER: Morgan, Thomas H. (1910): Sex-limited inheritance in Drosophila.

(with an explanatory introduction by R. J. Robbins)

After Mendel's work was rediscovered in 1900, many researchers worked to confirm and extend his findings. Although a possible relationship between genes and chromosomes was suggested almost immediately, proof of that relationship, or even evidence that genes were physical objects, remained elusive. To many, the gene served only as a theoretical construct, conveniently invoked to explain observed inheritance patterns. In 1909, Morgan himself published a paper in which he expressed his skepticism about the facility with which Mendelian explanations were adjusted to fit the facts.

Just one year later, however, Morgan published the results of his work on an atypical male fruit fly that appeared in his laboratory, and all this began to change. Normally Drosophila melanogaster have red eyes, but Morgan's new fly had white eyes. The inheritance pattern for this new eye-color trait suggested strongly that the gene for eye-color was physically attached to the X-chromosome. In the paper, Morgan concluded:

It now becomes evident why we found it necessary to assume a coupling of [the eye-color gene] and X in one of the spermatozoa of the red-eyed F₁ hybrid. The fact is that this R and X are combined, and have never existed apart.

In this present paper, Morgan offered the first evidence that genes are real, physical objects, located on chromosomes, with properties that could be manipulated and studied experimentally. The white-eyed fly provided the foundation upon which Morgan and his students established the modern theory of the gene.

4. PAPER: Garrod, Archibald E. (1902): The incidence of alkaptonuria: A study in chemical individuality.

This paper is a true classic. Like Mendel's own work, this report offers insights so far ahead of its time that it, and Garrod's follow-on work, were largely neglected, until later efforts to elucidate the physiological functioning of genes led to the Nobel-prize-winning one-gene, one-enzyme hypothesis.

Less than two years after the rediscovery of Mendelism and just a few years after the word biochemistry was first coined, Garrod reports on alkaptonuria in humans and comes to the conclusion that it is inherited as a Mendelian recessive and that the occurrence of mutations (sports in the word of the time) in metabolic function should be no more surprising than inherited variations in morphology.

5. PAPER: Sturtevant, Alfred H. (1913): The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association.

(with an explanatory introduction by R. J. Robbins)

Today, with genome projects routinely producing detailed genetics maps of mice and men and every other sort of organism, it can be difficult to imagine a time when there were no genetic maps. The idea that individual genes occupy regular positions on chromosomes was one of the great insights of early genetics, and the very first genetic map was published in 1913 by Alfred H. Sturtevant, who was working on fruit flies in the laboratory of Thomas H. Morgan at Columbia University.

Sturtevant is now well known as one of the most important early pioneers in genetic research. However, at the time he produced the first map, he was an undergraduate. Many years later, Sturtevant ( A History of Genetics ) described how an undergraduate came to be crucially involved in establishing the very foundations of classical genetics:

In 1909, the only time during his twenty-four years at Columbia, Morgan gave the opening lectures in the undergraduate course in beginning zoology. It so happened that C. B. Bridges and I were both in the class. While genetics was not mentioned, we were both attracted to Morgan and were fortunate enough, though both still undergraduates, to be given desks in his laboratory the following year (1910-1911). The possibilities of the genetic study of Drosophila were then just beginning to be apparent; we were at the right place at the right time. In the latter part of 1911, in conversation with Morgan, I suddenly realized that the variations in strength of linkage, already attributed by Morgan to differences in the spatial separation of the genes, offered the possibility of determining sequences in the linear dimension of a chromosome. I went home and spent most of the night (to the neglect of my undergraduate homework) in producing the first chromosome map, which included the sex-linked genes y, w, v, m, and r, in the order and approximately the relative spacing that they still appear on the standard maps (Sturtevant, 1913).

6. PAPER: Muller, Hermann J. (1927): Artificial transmutation of the gene.

7. PAPER: Wright, Sewall. (1931): Evolution in Mendelian populations.

Soon after the establishment of Mendelian genetics, several workers began to explore how Mendelian mechanisms would affect changes in gene frequencies in populations — that is, they began to explore the implications of Mendelism for evolution.

Sewall Wright became one of the leading theoreticians who studied Mendelism in the context of population genetics. This paper is a key presentation of his thinking on how Mendelism and evolution might interact.

8. Mendel, Gregor (1866): Gregor Mendel's letters to Carl Nägeli, 1866-1873.

After his original paper on peas, Mendel published only one other paper on genetics, that one on Hieracium. These letters to Nägeli provide a rare additional glimpse into Mendel's thinking as he pursued his investigations on heredity.

9. PAPER: Muller, Hermann J. (1922): Variation due to change in the individual gene.

This paper is from an address given by to the thirty-ninth annual meeting of the American Society of Naturalists, held in Toronto on 29 December 29 1921.

In this remarkably prescient analysis, Muller lays out the paradoxical nature of the genetic material. It is apparently both autocatalytic (i.e., directs its own synthesis) and heterocatalytic (i.e., directs the synthesis of other molecules), yet only the heterocatalytic function seems subject to mutation. With this, he defines the key problems that must be solved for a successful chemical model of the gene.

Muller also anticipated the ultimate development of molecular genetics:

That two distinct kinds of substances — the d'Hérelle substances (NOTE: viruses) and the genes — should both possess this most remarkable property of heritable variation or "mutability," each working by a totally different mechanism, is quite conceivable, considering the complexity of protoplasm, yet it would seem a curious coincidence indeed. It would open up the possibility of two totally different kinds of life, working by different mechanisms. On the other hand, if these d'Hérelle bodies were really genes, fundamentally like our chromosome genes, they would give us an utterly new angle from which to attack the gene problem. They are filterable, to some extent isolable, can be handled in test tubes, and their properties, as shown by their effects on the bacteria, can then be studied after treatment. It would be very rash to call these bodies genes, and yet at present we must confess that there is no distinction known between the genes and them. Hence we cannot categorically deny that perhaps we may be able to grind genes in a mortar and cook them in a beaker after all. Must we geneticists become bacteriologists, physiological chemists and physicists, simultaneously with being zoologists and botanists? Let us hope so.

10. PAPER: Sutton, Walter S. (1902): On the morphology of the chromosome group in Brachystola magna.

In this paper, Sutton reports cytological studies of grasshopper chromosomes that lead him to conclude that (a) chromosomes have individuality, (b) that they occur in pairs, with one member of each pair contributed by each parent, and (c) that the paired chromosomes separate from each other during meiosis.

After presenting considerable evidence for his assertions, Sutton closes his paper with a sly reference to its undoubted significance:

I may finally call attention to the probability that the association of paternal and maternal chromosomes in pairs and their subsequent separation during the reducing division as indicated above may constitute the physical basis of the Mendelian law of heredity. To this subject I hope soon to return in another place.

11. PAPER: Morgan, T. H. and Bridges, C. B. (1916): Sex-linked Inheritance in Drosophila.

In this special publication from the Carnegie Institution of Washington, Morgan and Bridges review and summarize what was then known about sex-linked traits in Drosophila. It is interesting to note that this was written early enough that they use the word gen instread of the later word gene.

12. PAPER: Correns, Carl (1900): G. Mendel's law concerning the behavior of progeny of varietal hybrids.

Correns, along with Hugo de Vries and Erik von Tschermak, is considered to be one of the three co-discovers of Mendel's work in 1900. Correns was the only one of the three to acknowledge Mendel in the title of his paper. Correns' paper begins:

The latest publication of Hugo de Vries: Sur la loi de disjonction des hybrides, which through the courtesy of the author reached me yesterday, prompts me to make the following statement: In my hybridization experiments with varieties of maize and peas, I have come to the same results as de Vries, who experimented with varieties of many different kinds of plants, among them two varieties of maize. When I discovered the regularity of the phenomena, and the explanation thereof - to which I shall return presently - the same thing happened to me which now seems to be happening to de Vries: I thought that I had found something new. But then I convinced myself that the Abbot Gregor Mendel in Brünn, had, during the sixties, not only obtained the same result through extensive experiments with peas, which lasted for many years, as did de Vries and I, but had also given exactly the same explanation, as far as that was possible in 1866.

13. PAPER: Sutton, Walter S. (1903): The chromosomes in heredity.

Early on, some researchers noticed that Mendel's theory required that some kind of hereditary unit segregate in pairs to offspring. Sutton was one of the first to note that the chromosomes behaved in exactly a manner to match this requirement.

The opening lines of his paper show that he is aware of the significance of his observations:

In a recent announcement of some results of a critical study of the chromosomes in the various cell generations of Brachystola the author briefly called attention to a possible relation between the phenomena there described and certain conclusions first drawn from observations on plant hybrids by Gregor Mendel in 1865, and recently confirmed by a number of able investigators. Further attention has already been called to the theoretical aspects of the subject in a brief communication by Professor E. B. Wilson. The present paper is devoted to a more detailed discussion of these aspects, the speculative character of which may be justified by the attempt to indicate certain lines of work calculated to test the validity of the conclusions drawn. The general conceptions here advanced were evolved purely from cytological data, before the author had knowledge of the Mendelian principles, and are now presented as the contribution of a cytologist who can make no pretensions to complete familiarity with the results of experimental studies on heredity. As will appear hereafter, they completely satisfy the conditions in typical Mendelian cases, and it seems that many of the known deviations from the Mendelian type may be explained by easily conceivable variations from the normal chromosomic processes.

14. PAPER: Stevens, Nettie M. (1905): Studies in Spermatogenesis with especial reference to the "accessory chromosome".

Nettie Stevens was one of the first female scientists to make a name for herself in the biological sciences. In 1896, Stevens went to California to attend Leland Stanford Jr. University, where she obtained first a bachelor's and then a masters in biology. Her masters thesis involved microscopic work and precise, careful detailing of new species of marine life. This training was a factor in her success with later investigations of chromosomal behavior. After Stanford, Stevens pursued a PhD. at Bryn Mawr College, where Thomas Hunt Morgan was still teaching and was one of her professors. Stevens again did so well that she was awarded a fellowship to study abroad. She traveled to Europe and spent time in Theodor Boveri's lab at the Zoological Institute at Würzburg, Germany. Boveri was working on the problem of the role of chromosomes in heredity and Stevens likely developed an interest in the subject from her stay.

In 1903, after receiving her Ph.D from Bryn Mawr, Stevens was given an assistantship by the Carnegie Institute after glowing recommendations from Thomas Hunt Morgan, Edmund Wilson and M. Carey Thomas, the president of Bryn Mawr. Her work on sex determination was published as a Carnegie Institute report in 1905. In this first study she looked at sex determination in meal worms. Later, she studied sex determination in many different species of insects. Stevens' assistantship at Bryn Mawr still meant that she had to teach. desiring a pure research position, Stevens wrote to Charles Davenport at Cold Spring Harbor to see if it was possible for her to work at his Station for Experimental Biology. Unfortunately, Stevens died of breast cancer in 1912 before she could occupy the research professorship created for her at Bryn Mawr, or work with Davenport at Cold Spring Harbor.

15. /foundations/genetics/classical/holdings/o/ostrom-1969.pdf

16. PAPER: Morgan, Thomas H. (1909): What are "factors" in Mendelian explanations?

Although T. H. Morgan is best known for heading the genetics laboratory at Columbia University (later at Cal Tech) that essentially defined American genetics research for decades, he was initially skeptical of the facile manner in which combinations of alleged Mendelian factors were being invoked to explain all manner of heritable traits.

This paper begins with a wonderful debunking of easy explanation:

In the modern interpretation of Mendelism, facts are being transformed into factors at a rapid rate. If one factor will not explain the facts, then two are invoked; if two prove insufficient, three will sometimes work out. The superior jugglery sometimes necessary to account for the result, may blind us, if taken too naïvely, to the common-place that the results are often so excellently "explained" because the explanation was invented to explain them. We work backwards from the facts to the factors, and then, presto! explain the facts by the very factors that we invented to account for them.

17. PAPER: Vries, Hugo de (1900): Concerning the law of segregation of hybrids.

18. PAPER: Weldon, W. F. R. (1902): Mendel's laws of alternative inheritance in peas.

Textbook treatments of genetics often give the impression that upon being rediscovered Mendel's dominated the field. This is not so. Galton and his followers had been working for decades studying patterns of inheritance and had developed a formal quantitative model for the inheritance of "natural" (i.e., continuous) traits.

The biometricians, as they were called, felt that Mendel's work was a special case, valid only when applied to discontinuous traits in domesticated species. Weldon was a leading proponent of the biometrician school. This paper provides a strong summary of why the biometricians believed Mendel's work to be fundamentally flawed and of no general consequence. The paper concludes:

The fundamental mistake which vitiates all work based upon Mendel's method is the neglect of ancestry, and the attempt to regard the whole effect upon offspring, produced by a particular parent, as due to the existence in the parent of particular structural characters; while the contradictory results obtained by those who have observed the offspring of parents apparently identical in certain characters show clearly enough that not only the parents themselves, but their race, that is their ancestry, must be taken into account before the result of pairing them can be predicted.

19. PAPER: Bateson, William, and Saunders, E. R. (1902): The facts of heredity in the light of Mendel's discovery.

William Bateson was the first English-speaking scientist to appreciate the potential significance of Mendel's work. He began working immediately to confirm and extend Mendel's findings. This report to the evolution committee of the Royal Society represents one of the very first systematic investigations into Mendelism as a possible general explanation for the fundamental mechanisms of heredity.

20. PAPER: Cook, Robert. (1937): A chronology of genetics.

Robert Cook, as editor of The Journal of Heredity, was especially well positioned to appreciate how the new science of genetics developed after the rediscovery of Mendel in 1900 and the establishment of the chromosome theory of inheritance by T. H. Morgan and his students.

In this essay, Cook traces the history of genetics to four main roots - mathematics, plant breeding, animal breeding, and cytology.

21. PAPER: Muller, Hermann J. (1928): The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature.

22. PAPER: Luria, S. E., and Delbrück, M. (1943): Mutations of bacteria from virus sensitivity to virus resistance.

(with an explanatory introduction by R. J. Robbins)

This classic paper is the "fluctuation test" in which Luria and Delbrück first demonstrated the occurrence of microbial genetics. In fact, the fluctuation test must be regarded as the founding of bacterial genetics since it gave the first real proof that bacteria both possessed genes and experienced mutation. Luria and Delbrück shared the 1969 Nobel Prize with Alfred Hershey.

Luria and Delbrück were also able to use their data to calculate the actual mutation rate per bacterial cell division. Averaged across all of their experiments, this came to approximately 2.45 x 10^-8. Thus, they not only proved that true genetic mutations occurred in bacteria, but also that such mutations were just as rare in bacteria as they were in higher organisms. Their work demonstrated that heritable variation in bacteria could be attributed to mechanisms similar to those in higher organisms. The previously puzzling ability of bacteria to respond rapidly and adaptively to changes in the environment could now be recognized as nothing more than the normal consequence of random gene mutation, followed by selection, in huge, rapidly reproducing populations.

Following this discovery, many researchers hurried to determine the range of true genetic mutation occurring in bacteria. Soon, such variation was detected in virtually every trait that could be studied, such as color, colony morphology, virulence (ability to infect a host), resistance to antimicrobial agents, nutritional requirements, and fermentation abilities (i.e., the ability to use different compounds as carbon sources).

23. BOOK: Bateson, William. (1908): The Methods and Scope of Genetics.

This short book is a copy of the Inaugural Address, given by Bateson upon the creation of the Professorship of Biology at Cambridge. In his introduction, Bateson notes:

The Professorship of Biology was founded in 1908 for a period of five years partly by the generosity of an anonymous benefactor, and partly by the University of Cambridge. The object of the endowment was the promotion of inquiries into the physiology of Heredity and Variation, a study now spoken of as Genetics.

It is now recognized that the progress of such inquiries will chiefly be accomplished by the application of experimental methods, especially those which Mendel's discovery has suggested. The purpose of this inaugural lecture is to describe the outlook over this field of research in a manner intelligible to students of other parts of knowledge.

Here then is a view of how one of the very first practitioners of genetics conceived of the "Methods and Scope of Genetics".

24. PAPER: Mendel, Gregor. (1865): Experiments in plant hybridization. (annotated)

(with explanatory side-note annotations by R. J. Robbins)

In February and March of 1865, Gregor Mendel presented the Brünn Natural History Society in Brünn, Czechoslovakia, with the results of his investigations into the mechanisms governing inheritance in pea plants. The next year, the work was published as Mendel, Gregor. 1866. "Versuche über Pflanzen Hybriden." Verhandlungen des naturforschenden Vereines in Brünn, 4:3-47.

In this remarkable paper, Mendel laid the groundwork for what later became the science of genetics. However, the work was largely ignored when it appeared and Mendel moved on to other things. He died in 1884.

His work was rediscovered at the turn of the century and its significance immediately recognized. Genetics, as a formal scientific discipline, exploded into activity in 1900.

A non-annotated version of Mendel's paper is also available.

For those wishing to see and read Mendel in the original, a facsimile reprint edition is available. This version is in Adobe PDF format, but the pages are images of the original publication, not a new type-setting of the material.

You may also wish to visit The Mendel Web site, created by Roger Blumberg. The site offers many additional resources for the Mendel scholar.

25. PAPER: Morgan, Thomas H. (1917): The Theory of the Gene.

In 1909, Morgan expressed doubts about the methods of Mendelian inheritance. Then, in 1910, a white-eyed mutant fly turned up in Morgan's laboratory and studies on the inheritance of the white-eyed trait suggested that the gene producing the trait was carried on the X-chromosome. This strongly suggested that Mendelian genes were real, not theoretical, objects. Suddenly, Morgan became a Mendelian. Within a few years, Morgan and his students in The Fly Room had established a remarkably thorough understanding of The Mechanism of Mendelian Heredity.

In this paper, Morgan discusses The Theory of the Gene, as established in his laboratory.

26. PAPER: Morgan, Thomas H (1910): Chromosomes and Heredity.

Work in the laboratory of T. H. Morgan was critical in establishing that genes are real, physical entities and that they are arranged in a linear order on chromosomes. In this early, analytical paper, Morgan considers whether or not chromosomes might be carriers of the hereditary material and whether or not they might control sex determination.

Morgan's careful and logical approach is captured in his final comments on sex determination:

Science advances by carefully weighing all of the evidence at her command. When a decision is not warranted by the facts, experience teaches that it is wise to suspend judgment, until the evidence can be put to further test. This is the position we are in today concerning the interpretation of the mechanism that we have found by means of which sex is determined. I could, by ignoring the difficulties and by emphasizing the important discoveries that have been made, have implied that the problem of sex determination has been solved. I have tried rather to weigh the evidence, as it stands, in the spirit of the judge rather than in that of the advocate. One point at least I hope to have made evident, that we have discovered in the microscopic study of the germ cells a mechanism that is connected in some way with sex determination; and I have tried to show, also, that this mechanism accords precisely with that the experimental results seem to call for. The old view that sex is determined by external conditions is entirely disproven, and we have discovered an internal mechanism by means of which the equality of the sexes where equality exists is attained. We see how the results are automatically reached even if we can not entirely understand the details of the process. These discoveries mark a distinct advance in our study of this difficult problem.

27. PAPER: Beadle, G. W. and Ephrussi, Boris (1937): Development of Eye Colors in Drosophila: Diffusible Substances and Their Interrelations

28. PAPER: Tschermak, Erik von (1900): Concerning artificial crossing in Pisum sativum

Tschermak, along with Carl Correns and Hugo de Vries, is considered to be one of the three co-discovers of Mendel's work in 1900. He had been working himself with garden peas when he rediscovered Mendel's prior contributions. In a postscript to his paper, he wrote:

Correns has just published experiments which also deal with artificial hybridization of different varieties of Pisum sativum and observations of the hybrids left to self-fertilization through several generations. They confirm, just as my own, Mendel's teachings. The simultaneous "discovery" of Mendel by Correns, de Vries, and myself appears to me especially gratifying. Even in the second year of experimentation, I too still believed that I had found something new.

29. PAPER: Wright, Sewall (1935): A Mutation of the Guinea Pig, Tending to Restore the Pentadactyl Foot When Heterozygous, Producing a Monstrosity When Homozygous

30. PAPER: Demerec, Milislav (1933): What is a Gene?

Once the foundations of transmission genetics had been worked out, researchers began to consider what the chemical nature of the gene might be. Here Milislav Demerec offers one of the first such efforts. He concludes that the gene is a minute organic particle, capable of reproduction, located in a chromosome and responsible for the transmission of a hereditary characteristic. Moreover, he states that the available evidence suggests that genes are uni-molecular, and he notes:

If a gene is a complex organic molecule it would be expected to be similar in composition to other complex molecules, viz. molecular groups constituting this molecule (whatever these groups may be) would he arranged in chains and side chains. He then offers a drawing of the structure of DNA (!) as an example of a complex organic molecule, but is quick to add that The diagram is not intended to give any implication as to the number, the type, or the arrangement of the molecules in a gene group. Its purpose is to illustrate the molecular structure of a complex organic molecule.

Another 20 years would have to pass before the true chemical nature of the gene would be established.

31. PAPER: Hurst, C. C. (1904): Experiments with Poultry.

William Bateson was the first English-speaking scientist to appreciate the potential significance of Mendel's work. He and his co-workers began immediately to confirm and extend Mendel's findings. C. C. Hurst was one of Wm Bateson's early co-workers. Bateson and Hurst collaborated in the battle against the biometricians Karl Pearson and Walter Frank Raphael Weldon, with Hurst generating much data from experimental crosses of different plant varieties and animal colour variants, including chickens, horses, and man. Together they practically proved that Mendelian genetics could be extended to many different systems. Hurst was much younger than Bateson, but had a fiery passion for genetics, great skill in debate, and an approachableness lacking in some of his older peers which meant he was well respected within the scientific and lay community.

Hurst adopted the chromosome theory of inheritance whole-heartedly referring copiously to Thomas Hunt Morgan's Drosophila work, and he was also clearly a staunch Darwinist. He believed that natural selection and Mendelian genetics were compatible, and referred to the theoretical work of Sewall Wright, R.A. Fisher, and J.B.S. Haldane, which proved that quantitative traits and natural selection were compatible with Mendelism. Hurst was also a major initiator of the modern "genetical species concept" later known as the biological species concept. Here is Hurst's concept of species in Creative Evolution (1932), p. 66-67.

A species is a group of individuals of common descent, with certain constant specific characters in common which are represented in the nucleus of each cell by constant and characteristic sets of chromosomes carrying homozygous specific genes, causing as a rule intra-fertility and inter-sterility. On this view the species is no longer an arbitrary conception convenient to the taxonomist, a mere new name or label, but rather a real specific entity which can be experimentally demonstrated genetically and cytologically. Once the true nature of species is realised and recognised in terms of genes and chromosomes, the way is open to trace its evolution and origin, and the genetical species becomes a measurable and experimental unit of evolution.

This report — Experiments with Poultry ‐ to the evolution committee of the Royal Society represents one of the very first systematic investigations into Mendelism as a possible general explanation for the fundamental mechanisms of heredity.

32. PAPER: Bridges, Calvin B. (1916b): Non-disjunction as proof of the chromosome theory of heredity (part 2).

This paper was published as the first article in the first volume the new journal genetics. As the title states, the paper offered PROOF that genes are real, physical things that are carried on chromosomes.

This article was scanned from Alfred Sturtevant's personal copy of Genetics. Access to the journal was provided by Edward B. Lewis and Elliot M. Meyerowitz of the California Institute of Technology.

33. PAPER: Dobzhansky, Th. (1936): Studies on Hybrid Sterility. II. Localization of Sterility Factors in Drosophila Pseudoobscura Hybrids

34. PAPER: Macarthur, John W. (1933): Sex-linked Genes in the Fowl

35. PAPER: Ibsen, Heman L. (1916): Tricolor Inheritance. II. the Basset Hound

36. PAPER: Mendel, Gregor. (1865): Experiments in plant hybridization. (facsimile of first edition)

For those wishing to see and read Mendel in the original, this provides an image facsimile of the original paper as it was published in German.

37. PAPER: McClung, C. E. (1902): The accessory chromosome - Sex determinant?

(with an explanatory introduction by R. J. Robbins)

In this paper, McClung analyzes the evidence that male and female insects exhibit different chromosomal structures in their nuclei and that spermatozoa fall into two types - those that carry the "accessory chromosome" and those that do not.

Based on this analysis, McClung offers the bold hypothesis that the presence or absence of the "accessory chromosome" in spermatozoa may determine the sex of the progeny:

A most significant fact ... is that the [accessory chromosome] is apportioned to but one half of the spermatozoa. Assuming it to be true that the chromatin is the important part of the cell in the matter of heredity, then it follows that we have two kinds of spermatozoa that differ from each other in a vital matter. We expect, therefore, to find in the offspring two sorts of individuals in approximately equal numbers. ... [Since] nothing but sexual characters ... divides the members of a species into two well-defined groups, ... we are logically forced to the conclusion that the [accessory] chromosome has some bearing upon this arrangement.

That is, McClung hypothesizes that a difference in chromosome number is the cause, not an effect, of sex determination. This paper represents the first effort to associate the determination of a particular trait with a particular chromosome.

38. PAPER: Wright, Sewall (1932): General, Group and Special Size Factors

39. PAPER: Cannon, W. A. (1902): A cytological basis for the Mendelian laws.

40. PAPER: Mendel - de Vries - Correns - Tschermak (1950): The Birth of Genetics

To celebrate the fiftieth anniversary of the rediscovery of Mendel's work, the Genetics Society of America published this special supplement, containing translations of the original papers by the rediscovers of Mendel - Carl Correns, Erik von Tschermak, and Hugo de Vries. It also contains letters written by Mendel and sent to Carl Nägeli, a leading botanist.

This was the first time these key works were made available in English translation.

41. PAPER: Wilson, Edmund B. (1905): The chromosomes in relation to the determination of sex in insects.

(with an explanatory introduction by R. J. Robbins)

In this short note, Wilson (a leading cell biologist of his time) offers his endorsement of the idea that there is a relationship between specific chromosomes and the determination of sex in insects:

Material procured during the past summer demonstrates with great clearness that the sexes of Hemiptera show constant and characteristic differences in the chromosome groups, which are of such a nature as to leave no doubt that a definite connection of some kind between the chromosomes and the determination of sex exists in these animals. These differences are of two types. In one of these, the cells of the female possess one more chromosome than those of the male; in the other, both sexes possess the same number of chromosomes, but one of the chromosomes in the male is much smaller than the corresponding one in the female (which is in agreement with the observations of Stevens on the beetle Tenebrio).

Wilson's contribution is the observation that the various cases all seem to fall cleanly into one of two types — those in which the male seems to be missing a chromosome, and those in which the male is carrying a pair of mis-matched chromosomes. Wilson's goes on to note that he does not believe that the 'accessory chromosomes' are actual sex determinants as conjectured by McClung, but rather that they probably act in a quantitative, not qualitative manner.

Wilson's endorsement of the idea that chromosome make-up is related to sex determination greatly facilitated the later general acceptance of the notion that individual chromosomes might be related to individual traits. Of course, sex is not a simple Mendelian trait, such as round or wrinkled peas, but nonetheless the evidence that some aspect of phenotype (sex) was related to some aspect of genotype was an important initial step in bringing genetics together with cytology.

42. PAPER: Bateson, William. (1900): Problems of heredity as a subject for horticultural investigation.

Mendel's work of 1865 was largely neglected, until 1900 when it was simultaneously rediscovered by Hugo de Vries, Carl Correns, and Erik von Tschermak. When Mendel's work came to the attention of William Bateson (who himself had already been advocating controlled crosses as an approach to studying heredity), he was convinced that Mendel's work was of major importance:

That we are in the presence of a new principle of the highest importance is, I think, manifest. To what further conclusions it may lead us cannot yet be foretold.

Bateson devoted the remainder of his scientific career to further elucidations of "Mendelism." This present paper captures the enthusiasm of Bateson's first encounter with the works of Mendel.

43. PAPER: Weinberg, Wilhelm (1908): Über Vererbungsgesetze beim Menschen.

An early contribution from Weinberg on the study of inheritance in humans.

44. PAPER: Shull, George Harrison (1909): The "Presence and Absence" Hypothesis.

45. PAPER: Morgan, Thomas H. (1911): Random segregation versus coupling in Mendelian inheritance

46. PAPER: Morgan, Thomas H. (1911): The origin of five mutations in eye color in Drosophila and their modes of inheritance.

47. PAPER: Shull, G. H. (1915): Genetic Definitions in the New Standard Dictionary.

(with an explanatory introduction by R. J. Robbins)

In this short paper, Shull takes exception to some recently published dictionary definitions of many technical genetics terms and he offers corrected definitions in their stead. The main value of this paper to modern readers is that it gives a very good idea of what geneticists (or at least this geneticist) meant by their use of genetic terminology at the time. Although many of Shull's proffered definitions would be at home in a modern biology text, some are no longer in current usage.

Shull could have done a better job of defining "alternative inheritance" by adding "contrast with continuous inheritance," since at the time of his writing there was still a school of thought that argued that most heritable variation was continuous but that Mendelian theories provided explanations only for cases of "alternative inheritance," which were rare in nature and might only represent artifacts of inheritance in domesticated organisms.

For just such a criticism of alternative inheritance, see Weldon, W. F. R. 1902 Mendel's laws of alternative inheritance in peas. Biometrika, 1:228-254.

48. PAPER: McClung, C. E. (1901): Notes on the accessory chromosome.

(with an explanatory introduction by R. J. Robbins)

In this brief paper, McClung introduces the evidence that male and female insects exhibit different chromosomal structures in their nuclei and that spermatozoa fall into two types &,mdash; those that carry the "accessory chromosome" and those that do not.

Based on this analysis, McClung suggests that the presence or absence of the "accessory chromosome" in spermatozoa may determine the sex of the progeny. McClung published this short note in 1901 to alert the scientific community of his findings and to alert them to a more detailed argument that he had already submitted for publication elsewhere and that he knew would appear a year later, in McClung, C. E. 1902. The accessory chromosome - Sex determinant? Biological Bulletin, 3:43-84.

49. PAPER: Bridges, Calvin B. (1914): Direct proof through non-disjunction that the sex-linked genes of Drosophila are borne on the X-chromosome.

Although Bridges' longer 1916 Genetics paper (vol 1, page 1) on the same topic is better known and treats the issue at much greater length, this short communication in Science contains the same argument and is equally persuasive.

By 1910, much evidence had been presented to demonstrate that sexual phenotype (i.e., maleness or femaleness) was determined by chromosomes. And, as early as 1902 Sutton noted that similarities in the behavior of genes and chromosomes suggested that Mendelian factors might be carried on chromosomes.

Here, Bridges shows that mis-assortment of the sex chromosomes is accompanied by atypical inheritance patterns for sex-linked traits and he argues that this proves that genes are carried on chromosomes. He concludes his paper: "there can be no doubt that the complete parallelism between the unique behavior of the chromosomes and the behavior of sex-linked genes and sex in this case means that the sex-linked genes are located in and borne by the X-chromosomes."

50. PAPER: Wright, Sewall (1931): Evolution in Mendelian populations.

51. PAPER: Painter, Theophilus S. (1934): The Morphology of the X Chromosome in Salivary Glands of Drosophila melanogaster and a New Type of Chromosome Map for this Element.

In this paper, Painter follows up on his earlier publication describing Drosophila giant salivary-gland chromosomes and here shows how genetics maps, obtained from crossing studies, can be placed on a morphological map obtained from cytological studies.

52. BOOK: Punnett, R. C. (1907): Mendelism, 2nd Edition.

Reginald Punnett was born in 1875 in the town of Tonbridge in Kent, England. Attending Gonville and Caius College, Cambridge, Punnett earned a bachelor's degree in zoology in 1898 and a master's degree in 1901. Between these degrees he worked as a demonstrator and part-time lecturer at the University of St. Andrews' Natural History Department. In October 1901, Punnett was back at Cambridge when he was elected to a Fellowship at Gonville and Caius College, working in zoology, primarily the study of worms, specifically nemerteans. It was during this time that he and William Bateson began a research collaboration, which lasted several years. When Punnett was an undergraduate, Gregor Mendel's work on inheritance was largely unknown and unappreciated by scientists. However, in 1900, Mendel's work was rediscovered by Carl Correns, Erich Tschermak von Seysenegg, and Hugo de Vries. William Bateson became a proponent of Mendelian genetics, and had Mendel's work translated into English and published as a chapter in Mendel's Principles of Heredity: A Defence. It was with Bateson that Reginald Punnett helped established the new science of genetics at Cambridge. He, Bateson and Saunders co-discovered genetic linkage through experiments with chickens and sweet peas.

This second edition of Punnett's text on Mendelism came out just two years after the first edition. In this new edition, Punnett Squares appeared for the first time. Also, the author included an index (that could fit on a single page with room left over).

53. PAPER: Morgan, Thomas H. (1922): Croonian Lecture: On the Mechanism of Heredity.

The Croonian Lecture is the Royal Society's premier lecture in the biological sciences. Dr Croone, one of the original members of the Society, left on his death in 1684 a scheme for two lectureships, one at the Royal Society and the other at the Royal College of Physicians

Morgan was invited to give the Croonian lecture in 1922 - a recognition of his pioneering work in elucidating the physical basis of heredity.

54. PAPER: Creighton, Harriet B., and McClintock, Barbara. (1931): A correlation of cytological and genetical crossing-over in Zea mays.

(with an explanatory introduction by R. J. Robbins)

When Alfred Sturtevant created the first genetic map, he hypothesized that genetic recombination resulted from the actual exchange of chromatid fragments. However, at the time there was no hard evidence that proved recombination is accomplished via such a mechanism. The same genetic results could be explained if only alleles are exchanged during recombination, leaving the bulk of the chromatid arm unaffected. Since the two hypotheses make equivalent predictions regarding the distribution of alleles, they cannot be distinguished using purely genetic methods.

Attempting to demonstrate that genetic recombination is accomplished via the physical exchange of chromatid arms poses a problem similar to that encountered by Thomas H. Morgan when he first hypothesized that genes might be carried on the X chromosome. Although Morgan's genetic hypothesis of X-linkage provided an explanation for the inheritance of the white-eye allele in Drosophila, the notion that genes are actually carried on the X chromosome was not proven until Calvin Bridges provided cytological evidence to confirm the genetic observations. Bridges established a one-to-one correspondence between the abnormal distribution of eye-color alleles and the abnormal distribution of X chromosomes. That is, he established a relationship between genetic markers (the eye color alleles and their associated inheritance patterns) and cytological markers (the presence of abnormal sets of sex chromosomes).

In this paper, Creighton and McClintock present work in which they use a combination of cytological and genetic markers to show that cytological crossing-over occurs and that it is accompanied by genetical crossing-over. In just a few pages the authors accomplish their goal of establishing the reality of cytological recombination and of showing that it is associated with genetic recombination. This paper is truly a classic.

If this paper is read in isolation, the authors' discussion of their results can, at times, be difficult to follow. When this paper was originally published, however, it was accompanied by another paper (by McClintock) that immediately preceded it in the journal and that was intended to serve as an introduction to this paper. In the preceding paper, McClintock provided the basic genetic and cytological information necessary to understand the experimental logic of this paper. The background paper is The order of the genes C, Sh, and Wx in Zea mays with reference to a cytologically known point in the chromosome. The two papers should be read together, with the first, descriptive paper serving as a critical and necessary introduction to the second, experimental work.

For additional commentary on Creighton and McClintock's important work, see Edward Coe and Lee B. Kass (2005) Proof of physical exchange of genes on the chromosomes. Proceedings of the National Academy of Sciences, USA. 102:6641-6646.

55. PAPER: Castle, W. E. and Reed, S. C. (1936): Studies of Inheritance in Lop-eared Rabbits

56. PAPER: Galton, Francis. (1898): A Diagram of Heredity.

Some standard textbook descriptions of early genetics give the impression that, besides Mendel, no one attempted any genetic analysis in the entire nineteenth century. This is far from the truth, with Francis Galton offering a fine refutation. Starting just a few years after Mendel (and also working with peas), Galton carried out a series of well-received studies that resulted in his "Ancestral Law of Heredity," summarized diagrammatically in this brief communication. Galton's "Law" was so firmly established in some circles, that many adherents did not accept Mendelism until 1918, when R. A. Fisher showed that Galton's Law was in fact a natural consequence of Mendelian inheritance for polygenic traits.

57. PAPER: Stevens, Nettie M. (1906): Studies in Spermatogenesis Part II., A comparative study of the heterochromosomes in certain species of coleoptera, hemiptera and lepidoptera, with especial reference to sex determination.

Nettie Stevens was one of the first female scientists to make a name for herself in the biological sciences. In 1896, Stevens went to California to attend Leland Stanford Jr. University, where she obtained first a bachelor's and then a masters in biology. Her masters thesis involved microscopic work and precise, careful detailing of new species of marine life. This training was a factor in her success with later investigations of chromosomal behavior. After Stanford, Stevens pursued a PhD. at Bryn Mawr College, where Thomas Hunt Morgan was still teaching and was one of her professors. Stevens again did so well that she was awarded a fellowship to study abroad. She traveled to Europe and spent time in Theodor Boveri's lab at the Zoological Institute at Würzburg, Germany. Boveri was working on the problem of the role of chromosomes in heredity and Stevens likely developed an interest in the subject from her stay.

In 1903, after receiving her Ph.D from Bryn Mawr, Stevens was given an assistantship by the Carnegie Institute after glowing recommendations from Thomas Hunt Morgan, Edmund Wilson and M. Carey Thomas, the president of Bryn Mawr. Her work on sex determination was published as a Carnegie Institute report in 1905. In this first study she looked at sex determination in meal worms. Later, she studied sex determination in many different species of insects. Stevens' assistantship at Bryn Mawr still meant that she had to teach. desiring a pure research position, Stevens wrote to Charles Davenport at Cold Spring Harbor to see if it was possible for her to work at his Station for Experimental Biology. Unfortunately, Stevens died of breast cancer in 1912 before she could occupy the research professorship created for her at Bryn Mawr, or work with Davenport at Cold Spring Harbor.

58. PAPER: Sturtevant, Alfred H. (1925): The effects of unequal crossing over at the bar locus in Drosophila.

59. BOOK: Punnett, R. C. (1905): Mendelism, 1st Edition.

Reginald Punnett was born in 1875 in the town of Tonbridge in Kent, England. Attending Gonville and Caius College, Cambridge, Punnett earned a bachelor's degree in zoology in 1898 and a master's degree in 1901. Between these degrees he worked as a demonstrator and part-time lecturer at the University of St. Andrews' Natural History Department. In October 1901, Punnett was back at Cambridge when he was elected to a Fellowship at Gonville and Caius College, working in zoology, primarily the study of worms, specifically nemerteans. It was during this time that he and William Bateson began a research collaboration, which lasted several years. When Punnett was an undergraduate, Gregor Mendel's work on inheritance was largely unknown and unappreciated by scientists. However, in 1900, Mendel's work was rediscovered by Carl Correns, Erich Tschermak von Seysenegg, and Hugo de Vries. William Bateson became a proponent of Mendelian genetics, and had Mendel's work translated into English and published as a chapter in Mendel's Principles of Heredity: A Defence. It was with Bateson that Reginald Punnett helped established the new science of genetics at Cambridge. He, Bateson and Saunders co-discovered genetic linkage through experiments with chickens and sweet peas.

Punnett's little book — Mendelism — is the first edition of the first genetics textbook ever written. It was published just five years after Mendel's work was rediscovered.

60. PAPER: Sturtevant, A. H. and Dobzhansky, Th. (1936): Geographical Distribution and Cytology of "sex Ratio" in Drosophila Pseudoobscura and Related Species

61. PAPER: Bridges, Calvin. (1921): Triploid intersexes in Drosophila melanogaster.

Work in the laboratory of T. H. Morgan was critical in establishing that genes are real, physical entities and that they are arranged in a linear order on chromosomes. Calvin Bridges was a key player in the Morgan group. In 1914, Bridges first demonstrated that a correlation existed between the incorrect assortment of X chromosomes and the incorrect assortment of some genes. In 1916, he expanded on that work to "prove" that sex-linked genes in Drosophila are carried on the X chromosome.

In this paper, Bridges shows that the correlation between mis-assortment of genes and chromosomes applies to the autosomes as well as to the sex chromosomes. In addition, he shows that sex determination in Drosophila appears to be driven by the ratio of X chromosomes to autosomes, not by the absolute number of X chromosomes.

62. PAPER: Bateson, William. (1899): Hybridisation and cross-breeding as a method of scientific investigation.

In this talk, given in 1899, before Mendel's work had been rediscovered, Bateson gives his vision of what kind of research will be necessary to shed light on the processes of inheritance and evolution:

What we first require is to know what happens when a variety is crossed with its nearest allies. If the result is to have a scientific value, it is almost absolutely necessary that the offspring of such crossing should then be examined statistically. It must be recorded how many of the offspring resembled each parent and how many shewed characters intermediate between those of the parents. If the parents differ in several characters, the offspring must be examined statistically, and marshalled, as it is called, in respect of each of those characters separately.

One would be hard pressed to provide a better anticipation of the experimental approach of Gregor Mendel. Small wonder that Bateson, upon encountering Mendel's work, quickly became convinced that the correct method for studying inheritance was finally at hand.

63. PAPER: Wilson, Edmund B. (1902): Mendel's principles of heredity and the maturation of the germ cells.

In this short note, E. B. Wilson calls attention to the possible relationship between Mendelian patterns of inheritance and the assortment of chromosomes in meiosis.

64. PAPER: East - Morgan - Harris - Shull (1923): The Centenary of Gregor Mendel and of Francis Galton.

In December of 1922, the American Society of Naturalists held a special session to honor the centenaries of the birth of Gregor Mendel and of Francis Galton. This is the collection of the four papers presented at that session and later published in the The Scientific Monthly.

65. PAPER: Weinstein, Alexander (1936): The Theory of Multiple-strand Crossing Over

66. PAPER: Wright, Sewall (1934): On the Genetics of Subnormal Development of the Head (otocephaly) in the Guinea Pig

67. PAPER: Schultz, Jack, and Dobzhansky, Th. (1934): The Relation of a Dominant Eye Color in Drosophila Melanogaster to the Associated Chromosome Rearrangement

68. PAPER: Morgan, L. V. (1925): Polyploidy in Drosophila melanogaster with Two Attached X Chromosomes

69. PAPER: Morgan, Thomas H. (1909): Breeding Experiments with Rats

70. PAPER: Wright, Sewall (1921): Systems of mating. V. General considerations.

Sewall Green Wright was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. Sewall Wright was born in Melrose, Massachusetts to Philip Green Wright and Elizabeth Quincy Sewall Wright. His parents were first cousins, an interesting fact in light of Wright's later research on inbreeding. The family moved three years later after Philip accepted a teaching job at Lombard College, a Universalist college in Galesburg, Illinois. As a child, Wright helped his father and brother print and publish an early book of poems by his father's student Carl Sandburg. Sewall was the oldest of three gifted brothers — the others being the aeronautical engineer Theodore Paul Wright and the political scientist Quincy Wright. From an early age Wright had a love and talent for mathematics and biology.

Wright received his Ph.D. from Harvard University, where he worked at the Bussey Institute with the pioneering mammalian geneticist William Ernest Castle investigating the inheritance of coat colors in mammals. He worked for the U.S. Department of Agriculture until 1925, when he joined the Department of Zoology at the University of Chicago. He remained there until his retirement in 1955, when he moved to the University of Wisconsin–Madison.

Wright was a founder of population genetics alongside Ronald Fisher and J.B.S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution. He discovered the inbreeding coefficient and methods of computing it in pedigree animals. He extended this work to populations, computing the amount of inbreeding between members of populations as a result of random genetic drift, and along with Fisher he pioneered methods for computing the distribution of gene frequencies among populations as a result of the interaction of natural selection, mutation, migration and genetic drift. Wright also made major contributions to mammalian and biochemical genetics.

In 1921, Wright published a series of five papers (of which this is the fifth) on Systems of Mating. In these papers Wright used his method of path coefficients to consider the effect of mating systems on patterns of inheritance.

Path coefficients are standardized versions of linear regression weights which can be used in examining the possible causal linkage between statistical variables in the structural equation modeling approach. The standardization involves multiplying the ordinary regression coefficient by the standard deviations of the corresponding explanatory variable: these can then be compared to assess the relative effects of the variables within the fitted regression model. The idea of standardization can be extended to apply to partial regression coefficients. The term "path coefficient" derives from Wright's 1921 paper, "Correlation and causation", Journal of Agricultural Research, 20, 557–585, where a particular diagram-based approach was used to consider the relations between variables in a multivariate system.

71. PAPER: Wright, Sewall (1921): Systems of mating. I. The biometric relations between parent and offspring.

Sewall Green Wright was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. Sewall Wright was born in Melrose, Massachusetts to Philip Green Wright and Elizabeth Quincy Sewall Wright. His parents were first cousins, an interesting fact in light of Wright's later research on inbreeding. The family moved three years later after Philip accepted a teaching job at Lombard College, a Universalist college in Galesburg, Illinois. As a child, Wright helped his father and brother print and publish an early book of poems by his father's student Carl Sandburg. Sewall was the oldest of three gifted brothers — the others being the aeronautical engineer Theodore Paul Wright and the political scientist Quincy Wright. From an early age Wright had a love and talent for mathematics and biology.

Wright received his Ph.D. from Harvard University, where he worked at the Bussey Institute with the pioneering mammalian geneticist William Ernest Castle investigating the inheritance of coat colors in mammals. He worked for the U.S. Department of Agriculture until 1925, when he joined the Department of Zoology at the University of Chicago. He remained there until his retirement in 1955, when he moved to the University of Wisconsin–Madison.

Wright was a founder of population genetics alongside Ronald Fisher and J.B.S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution. He discovered the inbreeding coefficient and methods of computing it in pedigree animals. He extended this work to populations, computing the amount of inbreeding between members of populations as a result of random genetic drift, and along with Fisher he pioneered methods for computing the distribution of gene frequencies among populations as a result of the interaction of natural selection, mutation, migration and genetic drift. Wright also made major contributions to mammalian and biochemical genetics.

In 1921, Wright published a series of five papers (of which this is the first) on Systems of Mating. In these papers Wright used his method of path coefficients to consider the effect of mating systems on patterns of inheritance.

Path coefficients are standardized versions of linear regression weights which can be used in examining the possible causal linkage between statistical variables in the structural equation modeling approach. The standardization involves multiplying the ordinary regression coefficient by the standard deviations of the corresponding explanatory variable: these can then be compared to assess the relative effects of the variables within the fitted regression model. The idea of standardization can be extended to apply to partial regression coefficients. The term "path coefficient" derives from Wright's 1921 paper, "Correlation and causation", Journal of Agricultural Research, 20, 557–585, where a particular diagram-based approach was used to consider the relations between variables in a multivariate system.

72. PAPER: Sturtevant, Alfred H. (1923): Inheritance of the direction of coiling in Limnaea.

(with an explanatory introduction by R. J. Robbins)

As evidence mounted for the chromosomal basis of inheritance, occasional examples were discovered that seemed to challenge the Mendelian model, as mapped to the chromosomes by T. H, Morgan and his students. In this paper, A. H. Sturtevant (one of Morgan's students) shows that apparently aberrant patterns of inheritance can be seen to correspond to the Mendelian model, if care is taken to assign phenotype to the correct individual.

The case in question is the direction of shell coiling in snails of the genus Limnaea. These shells can either coil to the right (dextral) or left (sinistral). Coiling seemed to be an inherited trait, except that the observed patterns of inheritance were strange. Broods of offspring from sinistral snails, produced by self-fertilization (these snails are hermaphroditic) were either all sinistral or all dextral (never some of each). The same was found true if the single parent was dextral. Complicated models had been offered to explain these results, but here Sturtevant shows that a much simpler model is equally effective:

An analysis of the data presented suggests that the case is a simple Mendelian one, with the dextral character dominant, but with the nature of a given individual determined, not by its own constitution but by that of the unreduced egg from which it arose.

A similar problem exists with the color of bird eggs. Chickens, for example, can produce eggs that are either brown or white, and these colors are genetically determined. However, the trait "shell color" is an attribute of the hen laying the eggs, not of the chick that hatches out of the egg. When you realize that the shell is created as a secretion in the hen's oviducts, this makes perfect sense, even though the actual egg shell is ultimately separate from the body of the hen and is part of the egg from which the chick hatches.

The direction of shell coiling is now known to be controlled by specific proteins present in the cytoplasm of the egg. These proteins are produced early in egg development, prior to fertilization, and so are produced solely from genes present in the mother. Just as with the color of egg shells in chickens, the direction of shell coiling in Limnaea is really part of the phenotype of the mother of the snail, not of the snail actually wearing the shell.

73. PAPER: Mendel, Gregor (1869): On Hieracium-hybrids obtained by artificial fertilisation.

After his original paper on peas, Mendel published only one other paper on genetics, this one on Hieracium. Unknown to Mendel, Hieracium does not experience normal sexual fertilization, making it impossible for him to confirm the findings that he had obtained earlier with peas.

74. PAPER: Dobzhansky, Th. (1935): The Y Chromosome of Drosophila Pseudoobscura

75. PAPER: Wright, Sewall (1934): An Analysis of Variability in Number of Digits in an Inbred Strain of Guinea Pigs

76. PAPER: Belling, John (1933): Crossing Over and Gene Rearrangement in Flowering Plants

77. PAPER: Patterson, J. T. and Muller, H. J. (1930): Are "progressive" mutations produced by X-rays?

78. PAPER: Altenburg, Edgar and Muller, Hermann J. (1920): The Genetic Basis of Truncate Wing,—an Inconstant and Modifiable Character in Drosophila

79. PAPER: Wright, Sewall. (1932): Complementary Factors for Eye Color in Drosophila.

There are two distinct biochemical pathways producing pigments that color the eyes of Drosophila melanogaster — one yields a bright red pigment, the other brown. When both are present, the eyes are dark-red. When one is present and the other absent, flies have brown or bright red eyes. When both are missing, flies have white eyes.

In 1932, Sewall Wright reported the first case where a cross between red-eyed and brown-eyed flies yielded double-recessive progeny with white eyes. What makes this observation interesting is that the work occurred as part of a class exercise in an undergraduate teaching laboratory at the University of Chicago. Not many modern undergraduate lab exercises yield publishable results.

80. PAPER: Sturtevant, Alfred H. (1920): Genetic studies on Drosophila simulans. I. Introduction. Hybrids with Drosophila melanogaster.

81. PAPER: Sturtevant, A. H., Bridges, C. B., and Morgan, T. H. (1919): The spatial relations of genes.

82. PAPER: Ephrussi, Boris and Beadle, G. W. (1937): Development of Eye Colors in Drosophila: Production and Release of cn⁺ Substance by the Eyes of Different Eye Color Mutants

83. PAPER: Harnly, Morris Henry and Ephrussi, Boris (1937): Development of Eye Colors in Drosophila: Time of Action of Body Fluid on Cinnabar

84. PAPER: Haldane, J. B. S. (1934): A Mathematical Theory of Natural and Artificial Selection Part X. Some Theorems on Artificial Selection

85. PAPER: Thompson, David H. (1931): The side-chain theory of the structure of the Gene

86. PAPER: McClintock, Barbara and Hill, Henry E. (1931): The cytological identification of the chromosome associated with the r-g linkage group in Zea mays

87. PAPER: Davenport, C. B. (1930): Sex linkage in man

88. PAPER: Schultz, Jack (1929): The minute reaction in the development of Drosophila melanogaster

89. PAPER: Castle, W. E., and Wachter, W. L. (1924): Variations of Linkage in Rats and Mice

90. PAPER: Davenport, Charles B. (1917): Inheritance of Stature

91. PAPER: Montgomery, Thos. H., Jr. (1910): ARE PARTICULAR CHROMOSOMES SEX DETERMINANTS?

92. PAPER: Bridges, Calvin B. (1916a): Non-disjunction as proof of the chromosome theory of heredity (part 1).

This paper was published as the first article in the first volume the new journal genetics. As the title states, the paper offered PROOF that genes are real, physical things that are carried on chromosomes.

This article was scanned from Alfred Sturtevant's personal copy of Genetics. Access to the journal was provided by Edward B. Lewis and Elliot M. Meyerowitz of the California Institute of Technology.

93. PAPER: Riddle, Oscar. (1924): Any Hereditary Character and the Kinds of Things We Need to Know About It.

This does not qualify as a classic genetics paper and I suspect that it has never before been included in a collection of important papers. In his time, Riddle was one of the top biologists in the United States. His research spanned endocrinology, the physiology of reproduction, animal pigmentation, and the nature and functional basis of sex. He is most remembered for his research into the major pituitary hormone prolactin. Riddle studied under Jacques Loeb, and he and his colleagues were the first to isolate prolactin, which was named by Riddle in 1932. Because Riddle was not focussed on researching heredity, his comments offer an interesting general perspective on the questions of heredity in the 1920s.

The paper begins: No one seems ever to have written the results of a serious inquiry as to which are the distinctly different kinds of knowledge that will be required for the adequate comprehension of a (any) hereditary character. It is possible that studies in heredity have lost and now lose something of perspective and of balance by the absence of some sort of gauge against which actual accomplishment in this subject can be measured against the total necessary accomplishment. The older and more inclusive science of biology has made far more definite and helpful classifications of its constituent aspects as applied to organisms and to groups of organisms than has heredity. These divisions or aspects of biological science comparative anatomy, systematics, biochemistry, paleontology, behavior, embryology, evolution, pathology, ecology, microanatomy, physiology and distribution are at once frank recognitions of the kinds of knowledge necessary to a comprehension of the organism, and of the limited scope and value of any single type of information. Heredity, or evolution, like biology as a whole, possesses an integrity which upon examination immediately dissolves into diversity. It is a crystal of many facies. The first purpose here is to attempt the identification of the radically diverse aspects presented by any single hereditary character. This attempt is the more opportune because some recent developments in sex studies now make it fairly clear that one or two new or hitherto imperfectly conceived aspects of a hereditary character can be identified as distinct and utilizable aspects of any hereditary character.

The premise of this essay is essentially that, as of its writing, "studies on heredity and evolution offer what is mainly a two-sided attack on a many-sided problem." This argument was well taken, but the modern reader may have difficulty appreciating other concerns of the essay. At the same time, appreciating works in the history of science require appreciating the general mindset, concerns, and zeitgeist extant at the time a paper was written.

94. PAPER: Vries, Hugo de, and Boedijn, K. (1923): On the distribution of mutant characters among the chromosomes of Oenothera lamarckiana.

95. PAPER: Sturtevant, A. H. (1928): A Further Study of the So-called Mutation at the Bar Locus of Drosophila

96. PAPER: Sturtevant, A. H. (1917): Crossing Over without Chiasmatype?

97. PAPER: Painter, Theophilus S. (1934): A New Method For the Study of Chromosome Aberrations and the Plotting of Chromosome Maps in Drosophila melanogaster.

Now, almost any reference to the genetics of Drosophila includes some illustration of the giant salivary gland chromosomes found in these flies. Although Drosophila had been used effectively since 1910, it was this paper by Painter that first showed the tremendous potential of these chromosomes for cytogenetic research. New discovery often hinges on new methods and this paper is truly a break-through study in genetic methodology.

98. PAPER: Muller, Hermann J. (1918): Genetic variability, twin hybrids and constant hybrids, in a case of balanced lethal factors.

99. PAPER: Muller, Hermann J. (1925): The regionally differential effect of X rays on crossing over in autosomes of Drosophila.

100. PAPER: Painter, Theophilus S. and Griffen, Allen B. (1937): The Structure and the Development of the Salivary Gland Chromosomes of Simulium

1. BOOK: Voltaire. (1759): Candide.

Is there a more classic piece of humor than this? Besides it is in keeping with the biological orientation of this site, since it offers an alternative to evolution in explaining adaptation: "It is demonstrable," Pangloss said, "that things cannot be otherwise than as they are; for as all things have been created for some end, they must necessarily be created for the best end. Observe, for instance, the nose is formed for spectacles, therefore we wear spectacles. The legs are visibly designed for stockings, accordingly we wear stockings."

In any event, the book is a delightful read and provides both an antidote to excessive optimism and a basis for ultimate hope. "Excellently observed," answered Candide, "but let us cultivate out garden."

2. BOOK: Malthus, T. (1798): An Essay on the Principle of Population.

This book was first published anonymously in 1798, but the author was soon identified as Thomas Robert Malthus. The book predicted a grim future, as population would increase geometrically, doubling every 25 years, but food production would only grow arithmetically, which would result in famine and starvation, unless births were controlled. While it was not the first book on population, it was revised for over 28 years and has been acknowledged as the most influential work of its era. Malthus's book fuelled debate about the size of the population in the Kingdom of Great Britain and contributed to the passing of the Census Act 1800. This Act enabled the holding of a national census in England, Wales and Scotland, starting in 1801 and continuing every ten years to the present. The book's 6th edition (1826) was independently cited as a key influence by both Charles Darwin and Alfred Russel Wallace in developing the theory of natural selection.
rb> This book had a significant influence on Darwin as he looked for mechanisms that might explain evolutionary change. The influence shows, with Chapter Three of Darwin's Origin of Species entitled "Struggle for Existence".

3. /books/bacon/essays/contents/essay27.pdf

4. /books/bacon/essays/contents/essay50.pdf

5. BOOK: A. H. Sturtevant (1965): A History of Genetics

6. BOOKS: Browse Page for the ESP collection of digital books, sorted by author name (short format)

7. BOOK: Charles Lyell (1830): Principles of Geology, Volumes 1 - 3

8. /books/bacon/essays/contents/essay04.pdf

9. BOOK: Charles Darwin (1859): On THE ORIGIN OF SPECIES By Means of Natural Selection, First Edition

10. BOOK: Hugo De Vries (1910): Intracellular Pangenesis, Including a paper on Fertilization and Hybridization

11. /books/bacon/essays/contents/essay02.pdf

12. /books/bacon/essays/contents/essay05.pdf

13. /books/bacon/essays/contents/essay08.pdf

14. BOOK: Herman Melville (1856): The Piazza Tales

The Piazza Tales is a collection of six short stories, published by Dix & Edwards in the United States in May 1856 and in Britain in June. Except for the newly written title story, "The Piazza," all of the stories had appeared in Putnam's Monthly in 1853-1855. The collection includes what has long been regarded as three of the Melville's most important achievements in the genre of short fiction, "Bartleby, the Scrivener", "Benito Cereno", and "The Encantadas", his sketches of the Galápagos Islands. Like Darwin, Melville was struck with the islands' barren nature:

Take five-and-twenty heaps of cinders dumped here and there in an outside city lot, imagine some of them magnified into mountains, and the vacant lot the sea, and you will have a fit idea of the general aspect of the Encantadas, or Enchanted Isles. A group rather of extinct volcanoes than of isles, looking much as the world at large might after a penal conflagration. It is to be doubted whether any spot on earth can, in desolateness, furnish a parallel to this group.

15. BOOK CHAPTER: Sewall Wright (1932): The Roles of Mutation, Inbreeding, Crossbreeding, and Selection in Evolution, in Proceedings of the Sixth International Congress of Genetics

16. BOOK: Archibald Garrod (1923): Inborn Errors of Metabolism, Second Edition

17. BOOK: August Weismann (1893): The Germ-Plasm: A Theory of Heredity

18. BOOK: Charles Darwin (1883): The Variation of Animals and Plants Under Domestication, Second Edition, Revised

19. BOOK: T. H. Morgan, A. H. Sturtevant, H. J. Muller, C. B. Bridges (1915): The Mechanism of Mendelian Heredity

This book, by T. H. Morgan and his students, was the first work to articulate a comprehensive, mechanistic model to explain Mendelian patterns of inheritance. Although Mendelism had quickly been accepted as a good phenomenological explanation for the patterns seen in Mendelian crosses, until the work of Morgan's group, it was still possible to consider Mendelism to be a purely theoretical model of heredity. As Morgan's group first established the relationship of genes to chromosomes, then developed the first genetic map, and went on to describe a variety of interactions between chromosomes and Mendelian factors, the conclusions they offered became inescapable — genes are physical objects, carried on chromosomes in static locations. Morgan's group made genes real and this book is the first full-length presentation of their findings. It revolutionized the study of heredity.

This is a full-text PDF image facsimile version of the entire 262-page original book.

20. BOOK: Charles Darwin (1845): Journal of Researches into the Natural History and Geology of the Countries Visited During the Voyages of the H.M.S. Beagle Around the World, Second Edition, Corrected, with Additions

21. /books/aristotle/generation-of-animals/

22. /books/bacon/essays/contents/essay01.pdf

23. /books/bacon/essays/contents/essay56.pdf

24. /books/bacon/essays/contents/essay10.pdf

25. BOOK: W. Bateson (1902): Mendel's Principles of Heredity: A Defence

26. /books/bacon/essays/contents/essay36.pdf

27. BOOK: Sandburg, Carl (1916): Chicago Poems.

28. /books/bacon/essays/contents/essay06.pdf

29. /books/bacon/essays/contents/essay03.pdf

30. /web/viewer.html?file=/books/sturt/history/contents/cover.pdf

31. BOOK: E. B. Wilson (1900): The Cell in Development and Inheritance, Second Edition, Revised and Enlarged

32. BOOK: August Weismann (1889): Essays Upon Heredity, Volumes 1 and 2

33. BOOK: Anonymous (1844): Vestiges of The Natural History of Creation

34. /books/aristotle/generation-of-animals/contents/cover.pdf

35. BOOK: Donald F. Jones (ed.): Proceedings of the Sixth International Congress of Genetics, 1932

36. /web/viewer.html?file=/books/aristotle/generation-of-animals/contents/cover.pdf

37. /books/sturt/history/contents/cover.pdf

38. BOOK: T. H. Morgan (1928): The Theory of the Gene, Revised and Enlarged Edition

39. BOOK: W. K. Brooks (1883): The Law of Heredity, A Study of the Cause of Variation and the Origin of Living Organisms, Second Edition, Revised

40. BOOK: Morgan, Thomas H. (1919): The Physical Basis of Heredity.

In this book, T. H. Morgan (who would later receive the first Nobel Prize for genetics research) describes the model of heredity developed at Columbia by Morgan and his students.

The foundations of genetics were laid down by Mendel, and these were brought to the world's attention when his work was rediscovered by Correns, de Vries, and von Tschermak in 1900. But the real establishment of genetics as a real science, with a known physical basis, did not occur until the work outlined in this book became generally known.

To understand the true conceptual underpinnings of classical genetics, one must read the publications from "The Fly Room" at Columbia.

41. RECOMMENDATIONS: Books

We offer a few recommendations of interesting books.

42. /web/viewer.html?file=/books/devries/pangenesis/facsimile/contents/pangenesis-fm-i.pdf

43. /books/devries/pangenesis/facsimile/contents/pangenesis-fm-i.pdf

44. /books/bacon/essays/contents/essay07.pdf

45. /books/bacon/essays/

46. BOOK: Galton, Francis (1889): Natural Inheritance.

47. /books/garrod/inborn-errors/facsimile/contents/garrod-inborn-fm-i.pdf

48. /web/viewer.html?file=/books/garrod/inborn-errors/facsimile/contents/garrod-inborn-fm-i.pdf

49. PAPER: Wallace. A. R. (1855): On the law which has regulated the introduction of new species.

Today Darwin's name is known to everyone, while Alfred Russel Wallace is familiar to only a few. Yet the concept of evolution by natural selection was independently developed by Wallace and Darwin, with Wallace publishing first. This paper, and the 1858 manuscript he sent directly to Darwin, show clearly that, prior to Darwin's publication, Wallace had a firm grasp on the concept of evolution.

50. /books/bacon/essays/contents/essay48.pdf

1. TIMELINE (1540-2019): History of Freedom vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Freedom with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

2. TIMELINES BROWSE PAGE: Genetics in Context, a collection of side-by-side timelines that show scientific events next to representative events from the rest of world history.

3. TIMELINE (1540-2019): All Science vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Science with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

4. TIMELINE (1540-2019): Evolutionary Biology vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Evolutionary Biology with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

5. TIMELINE (1540-2019): American Literature vs All Other Categories

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6. TIMELINE (1540-2019): All Other Categories vs All Science

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7. TIMELINE (1540-2019): Physics vs All Other Categories

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8. TIMELINE (1540-2019): All Other Categories vs History

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of History. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

9. TIMELINE (1540-2019): History of Technology vs Visual Arts

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Technology with events from the topic of Visual Arts. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

10. TIMELINE (1540-2019): All Other Categories vs Physics

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11. TIMELINE (1540-2019): Arts and Culture vs History

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Arts and Culture with events from the topic of History. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

12. TIMELINE (1540-2019): Arts and Culture vs All Science

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Arts and Culture with events from the topic of All Science. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

13. TIMELINE (1540-2019): Visual Arts vs All Other Categories

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14. TIMELINE (1540-2019): Biology vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Biology with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

15. TIMELINE (1540-2019): All Other Categories vs History of Technology

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of History of Technology. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

16. TIMELINE (1540-2019): History of Technology vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Technology with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

17. TIMELINE (1540-2019): All Other Categories vs Arts and Culture

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of Arts and Culture. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

18. TIMELINE (1540-2019): History of Photographic Technology vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Photographic Technology with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

19. TIMELINE (1540-2019): Genetics, Development, and Evolution vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Genetics, Development, and Evolution with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

20. TIMELINE (1860-1869): Genetics, Development, and Evolution vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Genetics, Development, and Evolution with events from the topic of All Other Categories.

21. TIMELINE (1540-2019): All Other Categories vs Visual Arts

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of Visual Arts. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

22. TIMELINE (1540-2019): All Other Categories vs Biology

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of Biology. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

23. TIMELINE (1540-2019): Arts and Culture vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of Arts and Culture with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

24. TIMELINE (1540-2019): All Other Categories vs History of Photographic Technology

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of History of Photographic Technology. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

25. TIMELINE (1540-2019): All Other Categories vs History of Freedom

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Other Categories with events from the topic of History of Freedom. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

1. AUTOMATED BIBLIOGRAPHY: History of Genetics (bibtex file)

(plain text bibliography in readable bibtex format)

2. AUTOMATED BIBLIOGRAPHY: Symbiosis

Symbiosis refers to an interaction between two or moredifferent organisms living in close physical association, typically tothe advantage of both. Symbiotic relationships were once thought to beexceptional situations. Recent studies, however, have shown thatevery multicellular eukaryote exists in a tight symbioticrelationship with billions of microbes. The associated microbial ecosystemsare 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."

3. AUTOMATED 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 wasknown as yellow soup.

4. AUTOMATED 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.

5. AUTOMATED 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.

6. AUTOMATED 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 arebased on poor quality DNA and thus have many inferential steps (i,e, the resultingsequence is not likely to be a perfect replica of the living DNA), the insights tobe gained from paleosequentcing are nonetheless great. For example, paleo-sequencinghas shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

7. AUTOMATED 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.

8. AUTOMATED 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.

9. AUTOMATED 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

10. AUTOMATED 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.

11. AUTOMATED 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

12. AUTOMATED BIBLIOGRAPHY: Brain-Computer Interface

Wikipedia: A brainG€“computer interface (BCI), sometimes called a neural control interface (NCI), mindG€“machine interface (MMI), direct neural interface (DNI), or brainG€“machine interface (BMI), is a direct communication pathway between an enhanced or wired brain and an external device. BCIs are often directed at researching, mapping, assisting, augmenting, or repairing human cognitive or sensory-motor functions.Research on BCIs began in the 1970s at the University of California, Los Angeles (UCLA) under a grant from the National Science Foundation, followed by a contract from DARPA. The papers published after this research also mark the first appearance of the expression brainG€“computer interface in scientific literature.BCI-effected sensory input: Due to the cortical plasticity of the brain, signals from implanted prostheses can, after adaptation, be handled by the brain like natural sensor or effector channels. Following years of animal experimentation, the first neuroprosthetic devices implanted in humans appeared in the mid-1990s.BCI-effected motor output: When artificial intelligence is used to decode neural activity, then send that decoded information to some kind of effector device, BCIs have the potential to restore communication to people who have lost the ability to move or speak. To date, the focus has largely been on motor skills such as reaching or grasping. However, in May of 2021 a study showed that an AI/BCI system could be use to translate thoughts about handwriting into the output of legible characters at a usable rate (90 characters per minute with 94% accuracy).

13. AUTOMATED 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.

14. AUTOMATED 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.

15. AUTOMATED 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.

16. RECOMMENDED BIBLIOGRAPHIES: Keeping up with the literature can be challenging. On this page we offer several automatically-created bibliographies on selected topics, with links out to the original document (via the publisher's DOI), to PubMed, to Google Scholar, etc. The bibliographies are updated regularly and are sorted to show the most recent at the top. For long bibliographies the first link is to a page containing only the most recent 100 entries, with options to access the remaining entries. It is also possible, via the bibliography options menu, to access the entire bibliography in bibtex format, for easy loading into reference-management software.

17. AUTOMATED 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.

18. AUTOMATED 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.

19. AUTOMATED BIBLIOGRAPHY: Biofilm

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.

20. AUTOMATED 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, microorganismal key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganismal production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

21. AUTOMATED BIBLIOGRAPHY: COVID-19 / Review Papers (bibtex file)

(plain text bibliography in readable bibtex format)

NOTE: As of 2 Jan 2021, this bibliography contains only review papers.When the bibliography was first created, there were only 774 entries. Withthe published and pre-print literature now containing 100,000 papers, thedecision was made to limit this bibliography to REVIEWS only.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, or SARS-CoV-2), a virus closely related to the SARS virus. The disease was discovered and named during the 2019-20 coronavirus outbreak. Those affected may develop a fever, dry cough, fatigue, and shortness of breath. A sore throat, runny nose or sneezing is less common. While the majority of cases result in mild symptoms, some can progress to pneumonia and multi-organ failure.The infection is spread from one person to others via respiratory droplets produced from the airways, often during coughing or sneezing. Time from exposure to onset of symptoms is generally between 2 and 14 days, with an average of 5 days. The standard method of diagnosis is by reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab or sputum sample, with results within a few hours to 2 days. Antibody assays can also be used, using a blood serum sample, with results within a few days. The infection can also be diagnosed from a combination of symptoms, risk factors and a chest CT scan showing features of pneumonia.Correct handwashing technique, maintaining distance from people who are coughing and not touching one's face with unwashed hands are measures recommended to prevent the disease. It is also recommended to cover one's nose and mouth with a tissue or a bent elbow when coughing. Those who suspect they carry the virus are recommended to wear a surgical face mask and seek medical advice by calling a doctor rather than visiting a clinic in person. Masks are also recommended for those who are taking care of someone with a suspected infection but not for the general public. There is no vaccine or specific antiviral treatment, with management involving treatment of symptoms, supportive care and experimental measures. The case fatality rate is estimated at between 1% and 3%.The World Health Organization (WHO) has declared the 2019-20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC). As of 29 February 2020, China, Hong Kong, Iran, Italy, Japan, Singapore, South Korea and the United States are areas having evidence of community transmission of the disease.

22. AUTOMATED BIBLIOGRAPHY: COVID-19 / Review Papers

NOTE: As of 2 Jan 2021, this bibliography contains only review papers.When the bibliography was first created, there were only 774 entries. Withthe published and pre-print literature now containing 100,000 papers, thedecision was made to limit this bibliography to REVIEWS only.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, or SARS-CoV-2), a virus closely related to the SARS virus. The disease was discovered and named during the 2019-20 coronavirus outbreak. Those affected may develop a fever, dry cough, fatigue, and shortness of breath. A sore throat, runny nose or sneezing is less common. While the majority of cases result in mild symptoms, some can progress to pneumonia and multi-organ failure.The infection is spread from one person to others via respiratory droplets produced from the airways, often during coughing or sneezing. Time from exposure to onset of symptoms is generally between 2 and 14 days, with an average of 5 days. The standard method of diagnosis is by reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab or sputum sample, with results within a few hours to 2 days. Antibody assays can also be used, using a blood serum sample, with results within a few days. The infection can also be diagnosed from a combination of symptoms, risk factors and a chest CT scan showing features of pneumonia.Correct handwashing technique, maintaining distance from people who are coughing and not touching one's face with unwashed hands are measures recommended to prevent the disease. It is also recommended to cover one's nose and mouth with a tissue or a bent elbow when coughing. Those who suspect they carry the virus are recommended to wear a surgical face mask and seek medical advice by calling a doctor rather than visiting a clinic in person. Masks are also recommended for those who are taking care of someone with a suspected infection but not for the general public. There is no vaccine or specific antiviral treatment, with management involving treatment of symptoms, supportive care and experimental measures. The case fatality rate is estimated at between 1% and 3%.The World Health Organization (WHO) has declared the 2019-20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC). As of 29 February 2020, China, Hong Kong, Iran, Italy, Japan, Singapore, South Korea and the United States are areas having evidence of community transmission of the disease.

23. AUTOMATED 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 realmof 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.

24. AUTOMATED BIBLIOGRAPHY: Holobiont

n++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 for "whole". The entire assemblage of genomes in the holobiont is termed a hologenome.

25. AUTOMATED 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.

1. Subprime Loans: A Primer (edgy language, NSFW)

This little cartoon primer provided a first-rate explanation about what went wrong in the financial markets before the 2009 meltdown. Now that we are beginning to forget the lessons of 2009 and are starting to remove regulations and safeguards, it may be a good idea to revisit some of those issues.

2. Dave Barry: How to Attend a Meeting

3. Jonathan Swift (1729): A Modest Proposal for Preventing the Poor People in Ireland from being a Burden to their Parents or Country, and for Making them Beneficial to the Public

A Modest Proposal, is a satirical essay written and published anonymously by Jonathan Swift in 1729. The essay suggests that the impoverished Irish might ease their economic troubles by selling their children as food for rich gentlemen and ladies. This satirical hyperbole mocked heartless attitudes towards the poor, as well as British policy toward the Irish in general. The primary target of Swift's satire was the rationalism of modern economics, and the growth of rationalistic modes of thinking in modern life at the expense of more traditional human values.

4. HUMOR: Home Directory (browse the ESP collection of frivolity)

5. R. J. Robbins. 1997. Believe It, or Else!

Scientific publishing is always a challenge, especially in a premier venue. Here's the story of what it took to get a major finding in human genomics published in Ripley's Believe It or Not!

6. Warning-Protocol (WP) Login

Every hour of every day, most websites (including this one) are inundated with requests for wp-login.php, sent by lame hackers who keep flogging away on the assumption that every website is based on a poorly protected WordPress installation. This is our version of wp-login.php...

7. Hu's On First

Playwrite Jim Sherman imagines Condi Rice trying to explain to George Bush that Hu Jintao has just been named the head of the communist party in China, resulting in an international-diplomacy version of who's on first.

8. If Airlines Were Based on Computer Operating Systems

9. Moving to Seattle

10. WHAM! An Asteroid Comes to Portland

If an asteroid the size of 4179 Toutatis (2.5 km diameter) were to hit Portland, the impact would release about 13 million megatons of energy. Result: Portland would be inconvenienced. Specifically, in few seconds Portland would be replaced by a hole two-thirds of a mile deep and 45 miles in diameter. But what would be the effect on Seattle?

11. Historical Perspective: Teaching Mathematics Through the Years

12. Mark Twain (1897) "Horrors of the German Language"

A side-by-side literal translation of an address given (in German) to the Vienna Press Club

13. PRESS RELEASE: President Clinton signs the Americans With No Abilities Act into law.

14. Real College Essay, Written by Real Student

15. Presidential Statements

When President, George W. Bush sometimes made statements that seemed, well, a little mangled. Here, to set the record straight, is an analysis showing how Bush's apparent misstatements, upon closer consideration, turn out to be just right.

1. US DOE Human Genome Program Report, Part 2, 1996 Research Abstracts

2. HUMOR: Home Directory (browse the ESP collection of frivolity)

3. MISC: Browse Our Miscellany (including a real six-legged mouse)

4. ESP General Publications: Papers and Other Material of Interest

5. US DOE OBER: Program Management

6. US DOE: To Know Ourselves

7. USCA-DC_00-5212: United States of America, Appellee, v. Microsoft Corporation, Appellant. Argued 26-27 FEB 2001 : Decided 28 JUN 2001

8. Catherine Baker: Your Genes, Your Choices: Exploring the Issues Raised by Genetic Research

9. US DOE: Primer on Molecular Genetics

10. Francis Collins and David Galas (1993): A New Five-Year Plan for the U.S. Human Genome Project

1. BOOK: Voltaire. (1759): Candide.

Is there a more classic piece of humor than this? Besides it is in keeping with the biological orientation of this site, since it offers an alternative to evolution in explaining adaptation: "It is demonstrable," Pangloss said, "that things cannot be otherwise than as they are; for as all things have been created for some end, they must necessarily be created for the best end. Observe, for instance, the nose is formed for spectacles, therefore we wear spectacles. The legs are visibly designed for stockings, accordingly we wear stockings."

In any event, the book is a delightful read and provides both an antidote to excessive optimism and a basis for ultimate hope. "Excellently observed," answered Candide, "but let us cultivate out garden."

2. BOOK: Malthus, T. (1798): An Essay on the Principle of Population.

This book was first published anonymously in 1798, but the author was soon identified as Thomas Robert Malthus. The book predicted a grim future, as population would increase geometrically, doubling every 25 years, but food production would only grow arithmetically, which would result in famine and starvation, unless births were controlled. While it was not the first book on population, it was revised for over 28 years and has been acknowledged as the most influential work of its era. Malthus's book fuelled debate about the size of the population in the Kingdom of Great Britain and contributed to the passing of the Census Act 1800. This Act enabled the holding of a national census in England, Wales and Scotland, starting in 1801 and continuing every ten years to the present. The book's 6th edition (1826) was independently cited as a key influence by both Charles Darwin and Alfred Russel Wallace in developing the theory of natural selection.
rb> This book had a significant influence on Darwin as he looked for mechanisms that might explain evolutionary change. The influence shows, with Chapter Three of Darwin's Origin of Species entitled "Struggle for Existence".

3. US DOE Human Genome Program Report, Part 2, 1996 Research Abstracts

4. /viewimage/

5. PAPER: Mendel, Gregor. (1865): Experiments in plant hybridization.

In February and March of 1865, Gregor Mendel presented the Brünn Natural History Society in Brünn, Czechoslovakia, with the results of his investigations into the mechanisms governing inheritance in pea plants. The next year, the work was published as Mendel, Gregor. 1866. "Versuche über Pflanzen Hybriden." Verhandlungen des naturforschenden Vereines in Brünn, 4:3-47.

In this remarkable paper, Mendel laid the groundwork for what later became the science of genetics. However, the work was largely ignored when it appeared and Mendel moved on to other things. He died in 1884.

His work was rediscovered at the turn of the century and its significance immediately recognized. Genetics, as a formal scientific discipline, exploded into activity in 1900.

An annotated version of Mendel's paper is also available. The annotated version contains explanatory notes throughout the document. This can be useful to those reading Mendel's paper for the first time.

For those wishing to see and read Mendel in the original, a facsimile reprint edition is available. This version is in Adobe PDF format, but the pages are images of the original publication, not a new type-setting of the material.

You may also wish to visit The Mendel Web site, created by Roger Blumberg. The site offers many additional resources for the Mendel scholar.

6. /books/bacon/essays/contents/essay27.pdf

7. AUTOMATED BIBLIOGRAPHY: History of Genetics (bibtex file)

(plain text bibliography in readable bibtex format)

8. /books/bacon/essays/contents/essay50.pdf

9. BOOK: A. H. Sturtevant (1965): A History of Genetics

10. FOUNDATIONS OF CLASSICAL GENETICS: The Home Page for the Electronic Scholarly Publishing Project's collection of material relating to classical genetics.

11. BOOKS: Browse Page for the ESP collection of digital books, sorted by author name (short format)

12. BOOK: Charles Lyell (1830): Principles of Geology, Volumes 1 - 3

13. /books/bacon/essays/contents/essay04.pdf

14. BOOK: Charles Darwin (1859): On THE ORIGIN OF SPECIES By Means of Natural Selection, First Edition

15. BOOK: Hugo De Vries (1910): Intracellular Pangenesis, Including a paper on Fertilization and Hybridization

16. /books/bacon/essays/contents/essay02.pdf

17. /books/bacon/essays/contents/essay05.pdf

18. AUTOMATED BIBLIOGRAPHY: Symbiosis

Symbiosis refers to an interaction between two or moredifferent organisms living in close physical association, typically tothe advantage of both. Symbiotic relationships were once thought to beexceptional situations. Recent studies, however, have shown thatevery multicellular eukaryote exists in a tight symbioticrelationship with billions of microbes. The associated microbial ecosystemsare 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."

19. /books/bacon/essays/contents/essay08.pdf

20. AUTOMATED 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 wasknown as yellow soup.

21. BOOK: Herman Melville (1856): The Piazza Tales

The Piazza Tales is a collection of six short stories, published by Dix & Edwards in the United States in May 1856 and in Britain in June. Except for the newly written title story, "The Piazza," all of the stories had appeared in Putnam's Monthly in 1853-1855. The collection includes what has long been regarded as three of the Melville's most important achievements in the genre of short fiction, "Bartleby, the Scrivener", "Benito Cereno", and "The Encantadas", his sketches of the Galápagos Islands. Like Darwin, Melville was struck with the islands' barren nature:

Take five-and-twenty heaps of cinders dumped here and there in an outside city lot, imagine some of them magnified into mountains, and the vacant lot the sea, and you will have a fit idea of the general aspect of the Encantadas, or Enchanted Isles. A group rather of extinct volcanoes than of isles, looking much as the world at large might after a penal conflagration. It is to be doubted whether any spot on earth can, in desolateness, furnish a parallel to this group.

22. TIMELINE (1540-2019): History of Freedom vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Freedom with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

23. BOOK CHAPTER: Sewall Wright (1932): The Roles of Mutation, Inbreeding, Crossbreeding, and Selection in Evolution, in Proceedings of the Sixth International Congress of Genetics

24. FOUNDATIONS OF CLASSICAL GENETICS: Browse Page for the literature of classical genetics, sorted by author name (short format)

25. AUTOMATED 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.

26. AUTOMATED 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.

27. BOOK: Archibald Garrod (1923): Inborn Errors of Metabolism, Second Edition

28. AUTOMATED 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 arebased on poor quality DNA and thus have many inferential steps (i,e, the resultingsequence is not likely to be a perfect replica of the living DNA), the insights tobe gained from paleosequentcing are nonetheless great. For example, paleo-sequencinghas shown that Neanderthal DNA is sufficiently different from human DNA as to be reasonably considered as coming from a different species.

29. BOOK: August Weismann (1893): The Germ-Plasm: A Theory of Heredity

30. ESSAY: R. J. Robbins: GENETICS AND HISTORY — How a Single Gene Mutation Affected the Entire World

31. BOOK: Charles Darwin (1883): The Variation of Animals and Plants Under Domestication, Second Edition, Revised

32. PAPER: Hardy, G. H. (1908): Mendelian Proportions in a Mixed Population.

Every geneticist has heard of the Hardy-Weinberg Law and of Hardy-Weinberg Equilibrium, and nearly all basic biology texts teach that G. H. Hardy played a seminal role in founding population genetics. But, what most biologists don't realize is that Hardy's total contribution to biology consisted of a single letter to the editor in Science. The letter began,

I am reluctant to intrude in a discussion concerning matters of which I have no expert knowledge, and I should have expected the very simple point which I wish to make to have been familiar to biologists. However, some remarks of Mr. Udny Yule, to which Mr. R. C. Punnett has called my attention, suggest that it may still be worth making.

With that, Hardy offered his "simple point" and then washed his hands of biology. His autobiography, A Mathematician's Apology, makes no mention of population genetics.

33. AUTOMATED 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.

34. BOOK: T. H. Morgan, A. H. Sturtevant, H. J. Muller, C. B. Bridges (1915): The Mechanism of Mendelian Heredity

This book, by T. H. Morgan and his students, was the first work to articulate a comprehensive, mechanistic model to explain Mendelian patterns of inheritance. Although Mendelism had quickly been accepted as a good phenomenological explanation for the patterns seen in Mendelian crosses, until the work of Morgan's group, it was still possible to consider Mendelism to be a purely theoretical model of heredity. As Morgan's group first established the relationship of genes to chromosomes, then developed the first genetic map, and went on to describe a variety of interactions between chromosomes and Mendelian factors, the conclusions they offered became inescapable — genes are physical objects, carried on chromosomes in static locations. Morgan's group made genes real and this book is the first full-length presentation of their findings. It revolutionized the study of heredity.

This is a full-text PDF image facsimile version of the entire 262-page original book.

35. BOOK: Charles Darwin (1845): Journal of Researches into the Natural History and Geology of the Countries Visited During the Voyages of the H.M.S. Beagle Around the World, Second Edition, Corrected, with Additions

36. /books/aristotle/generation-of-animals/

37. /books/bacon/essays/contents/essay01.pdf

38. /books/bacon/essays/contents/essay56.pdf

39. AUTOMATED 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.

40. /books/bacon/essays/contents/essay10.pdf

41. AUTOMATED 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

42. PAPER: Morgan, Thomas H. (1910): Sex-limited inheritance in Drosophila.

(with an explanatory introduction by R. J. Robbins)

After Mendel's work was rediscovered in 1900, many researchers worked to confirm and extend his findings. Although a possible relationship between genes and chromosomes was suggested almost immediately, proof of that relationship, or even evidence that genes were physical objects, remained elusive. To many, the gene served only as a theoretical construct, conveniently invoked to explain observed inheritance patterns. In 1909, Morgan himself published a paper in which he expressed his skepticism about the facility with which Mendelian explanations were adjusted to fit the facts.

Just one year later, however, Morgan published the results of his work on an atypical male fruit fly that appeared in his laboratory, and all this began to change. Normally Drosophila melanogaster have red eyes, but Morgan's new fly had white eyes. The inheritance pattern for this new eye-color trait suggested strongly that the gene for eye-color was physically attached to the X-chromosome. In the paper, Morgan concluded:

It now becomes evident why we found it necessary to assume a coupling of [the eye-color gene] and X in one of the spermatozoa of the red-eyed F₁ hybrid. The fact is that this R and X are combined, and have never existed apart.

In this present paper, Morgan offered the first evidence that genes are real, physical objects, located on chromosomes, with properties that could be manipulated and studied experimentally. The white-eyed fly provided the foundation upon which Morgan and his students established the modern theory of the gene.

43. Subprime Loans: A Primer (edgy language, NSFW)

This little cartoon primer provided a first-rate explanation about what went wrong in the financial markets before the 2009 meltdown. Now that we are beginning to forget the lessons of 2009 and are starting to remove regulations and safeguards, it may be a good idea to revisit some of those issues.

44. R. J. Robbins (1995): Database Fundamentals

At Johns Hopkins, while serving at the director of the informatics core of GDB (the human gene-mapping database that was part of the US Human Genome Project), Robbins co-taught a course in the computer-science department, entitled Computational Biology and Medical Informatics. That class was intended for computer-science majors, nearly all of whom had had no prior course work in biology and no prior experience with database theory or design.

This material, originally prepared as a handout for that class, was designed to provide a working, introductory presentation ofdatabase theory and design, so that students could better understand the challenges of representing biological and biomedical data in a formal information-management system.

45. BOOK: W. Bateson (1902): Mendel's Principles of Heredity: A Defence

46. ESSAYS: Six-legged Mouse

While on the faculty at Michigan State, R. J. Robbins (ESP's founder, editor, and technical developer) did research on deermice (Peromyscus) and this required maintaining a breeding colony of those mice. With a large enough breeding colony, the possibility of seeing the occasional new mutation or developmental abnormality is reasonably high. Once a pup was produced with a distinctly atypical appearance: it had six legs.

47. /books/bacon/essays/contents/essay36.pdf

48. ABOUT: R. J. Robbins

49. PAPER: Garrod, Archibald E. (1902): The incidence of alkaptonuria: A study in chemical individuality.

This paper is a true classic. Like Mendel's own work, this report offers insights so far ahead of its time that it, and Garrod's follow-on work, were largely neglected, until later efforts to elucidate the physiological functioning of genes led to the Nobel-prize-winning one-gene, one-enzyme hypothesis.

Less than two years after the rediscovery of Mendelism and just a few years after the word biochemistry was first coined, Garrod reports on alkaptonuria in humans and comes to the conclusion that it is inherited as a Mendelian recessive and that the occurrence of mutations (sports in the word of the time) in metabolic function should be no more surprising than inherited variations in morphology.

50. WHAT'S Hot: A compendium of the most popular contents of the site, arranged into a few categories, and presented in descending order of popularity

51. BOOK: Sandburg, Carl (1916): Chicago Poems.

52. /books/bacon/essays/contents/essay06.pdf

53. AUTOMATED 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.

54. PAPER: Sturtevant, Alfred H. (1913): The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association.

(with an explanatory introduction by R. J. Robbins)

Today, with genome projects routinely producing detailed genetics maps of mice and men and every other sort of organism, it can be difficult to imagine a time when there were no genetic maps. The idea that individual genes occupy regular positions on chromosomes was one of the great insights of early genetics, and the very first genetic map was published in 1913 by Alfred H. Sturtevant, who was working on fruit flies in the laboratory of Thomas H. Morgan at Columbia University.

Sturtevant is now well known as one of the most important early pioneers in genetic research. However, at the time he produced the first map, he was an undergraduate. Many years later, Sturtevant ( A History of Genetics ) described how an undergraduate came to be crucially involved in establishing the very foundations of classical genetics:

In 1909, the only time during his twenty-four years at Columbia, Morgan gave the opening lectures in the undergraduate course in beginning zoology. It so happened that C. B. Bridges and I were both in the class. While genetics was not mentioned, we were both attracted to Morgan and were fortunate enough, though both still undergraduates, to be given desks in his laboratory the following year (1910-1911). The possibilities of the genetic study of Drosophila were then just beginning to be apparent; we were at the right place at the right time. In the latter part of 1911, in conversation with Morgan, I suddenly realized that the variations in strength of linkage, already attributed by Morgan to differences in the spatial separation of the genes, offered the possibility of determining sequences in the linear dimension of a chromosome. I went home and spent most of the night (to the neglect of my undergraduate homework) in producing the first chromosome map, which included the sex-linked genes y, w, v, m, and r, in the order and approximately the relative spacing that they still appear on the standard maps (Sturtevant, 1913).

55. Foundations of Freedom: An Act for the Abolition of the Slave Trade

The Slave Trade Act 1807 was an Act of the Parliament of the United Kingdom prohibiting the slave trade in the British Empire. Although it did not abolish the practice of slavery, it did encourage British action to press other nations states to abolish their own slave trades. Full abolition in the British Empire did not occur until the Slavery Abolition Act in 1833.

56. AUTOMATED 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

57. /books/bacon/essays/contents/essay03.pdf

58. ABOUT: ESP Content

59. AUTOMATED BIBLIOGRAPHY: Brain-Computer Interface

Wikipedia: A brainG€“computer interface (BCI), sometimes called a neural control interface (NCI), mindG€“machine interface (MMI), direct neural interface (DNI), or brainG€“machine interface (BMI), is a direct communication pathway between an enhanced or wired brain and an external device. BCIs are often directed at researching, mapping, assisting, augmenting, or repairing human cognitive or sensory-motor functions.Research on BCIs began in the 1970s at the University of California, Los Angeles (UCLA) under a grant from the National Science Foundation, followed by a contract from DARPA. The papers published after this research also mark the first appearance of the expression brainG€“computer interface in scientific literature.BCI-effected sensory input: Due to the cortical plasticity of the brain, signals from implanted prostheses can, after adaptation, be handled by the brain like natural sensor or effector channels. Following years of animal experimentation, the first neuroprosthetic devices implanted in humans appeared in the mid-1990s.BCI-effected motor output: When artificial intelligence is used to decode neural activity, then send that decoded information to some kind of effector device, BCIs have the potential to restore communication to people who have lost the ability to move or speak. To date, the focus has largely been on motor skills such as reaching or grasping. However, in May of 2021 a study showed that an AI/BCI system could be use to translate thoughts about handwriting into the output of legible characters at a usable rate (90 characters per minute with 94% accuracy).

60. /web/viewer.html?file=/books/sturt/history/contents/cover.pdf

61. AUTOMATED 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.

62. TIMELINES BROWSE PAGE: Genetics in Context, a collection of side-by-side timelines that show scientific events next to representative events from the rest of world history.

63. BOOK: E. B. Wilson (1900): The Cell in Development and Inheritance, Second Edition, Revised and Enlarged

64. AUTOMATED 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.

65. R. J. Robbins (1995): Molecular Biology Fundamentals

At Johns Hopkins, while serving at the director of the informatics core of GDB (the human gene-mapping database that was part of the US Human Genome Project), Robbins co-taught a course in the computer-science department, entitled Computational Biology and Medical Informatics. That class was intended for computer-science majors, nearly all of whom had had no prior course work in biology and no prior experience with database theory or design.

This material, originally prepared as a handout for that class, was designed to provide a working, introductory presentation ofbasic concepts in molecular biology, so that students could better understand the challenges of representing biological and biomedical data in a formal information-management system.

66. BOOK: August Weismann (1889): Essays Upon Heredity, Volumes 1 and 2

67. BOOK: Anonymous (1844): Vestiges of The Natural History of Creation

68. ABOUT: This Website

69. AUTOMATED 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.

70. RECOMMENDED BIBLIOGRAPHIES: Keeping up with the literature can be challenging. On this page we offer several automatically-created bibliographies on selected topics, with links out to the original document (via the publisher's DOI), to PubMed, to Google Scholar, etc. The bibliographies are updated regularly and are sorted to show the most recent at the top. For long bibliographies the first link is to a page containing only the most recent 100 entries, with options to access the remaining entries. It is also possible, via the bibliography options menu, to access the entire bibliography in bibtex format, for easy loading into reference-management software.

71. /sitemap.xml

72. /books/aristotle/generation-of-animals/contents/cover.pdf

73. AUTOMATED 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.

74. BOOK: Donald F. Jones (ed.): Proceedings of the Sixth International Congress of Genetics, 1932

75. WHAT'S NEW: A cumulative presentation of additions, updates, and changes to the site

76. ESSAYS: The base browsing page for our collection of essays and vignettes.

In addition to providing access to the literature of classical genetics and other scientific fields, ESP will occasionally offer essays, vignettes, annotated bibliographies, and other material to help the reader understand and appreciate the meaning and significance of these fields.

77. /web/viewer.html?file=/books/aristotle/generation-of-animals/contents/cover.pdf

78. TIMELINE (1540-2019): All Science vs All Other Categories

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Science with events from the topic of All Other Categories. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

79. EXTERNAL REFERENCES: WWW Resources

80. /books/sturt/history/contents/cover.pdf

81. PEOPLE: Scientific Biographies

Here we offer access to biographical materials for a number of scientists who have worked in fields relevant to the contents of The Electronic Scholarly Publishing Project. The materials are presented under tabs, sorted in more or less chronological order, grouped by topics: A = All Science, G = Genetics, Me = Mendelian Genetics, etc.

82. BOOK: T. H. Morgan (1928): The Theory of the Gene, Revised and Enlarged Edition

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84. BOOK: W. K. Brooks (1883): The Law of Heredity, A Study of the Cause of Variation and the Origin of Living Organisms, Second Edition, Revised

85. AUTOMATED 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.

86. PAPER: Muller, Hermann J. (1927): Artificial transmutation of the gene.

87. BOOK: Morgan, Thomas H. (1919): The Physical Basis of Heredity.

In this book, T. H. Morgan (who would later receive the first Nobel Prize for genetics research) describes the model of heredity developed at Columbia by Morgan and his students.

The foundations of genetics were laid down by Mendel, and these were brought to the world's attention when his work was rediscovered by Correns, de Vries, and von Tschermak in 1900. But the real establishment of genetics as a real science, with a known physical basis, did not occur until the work outlined in this book became generally known.

To understand the true conceptual underpinnings of classical genetics, one must read the publications from "The Fly Room" at Columbia.

88. AUTOMATED BIBLIOGRAPHY: Biofilm

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.

89. ABOUT: ESP Needs

This page outlines some needs of the ESP Project, including documents to be acquired and work to be undertaken. If you are interested in becoming an active member of the ESP support community, read on.

90. RECOMMENDATIONS: Books

We offer a few recommendations of interesting books.

91. TIMELINE (1540-2019): Evolutionary Biology vs All Other Categories

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92. Dave Barry: How to Attend a Meeting

93. AUTOMATED 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, microorganismal key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganismal production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

94. /web/viewer.html?file=/books/devries/pangenesis/facsimile/contents/pangenesis-fm-i.pdf

95. TIMELINE (1540-2019): American Literature vs All Other Categories

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96. TIMELINE (1540-2019): All Other Categories vs All Science

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97. PEOPLE: Walter S. Sutton

Walter Stanborough Sutton was an American geneticist and physician whose most significant contribution to present-day biology was his theory that the Mendelian laws of inheritance could be applied to chromosomes at the cellular level of living organisms. This is now known as the Boveri-Sutton chromosome theory.

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99. TIMELINE (1540-2019): Physics vs All Other Categories

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100. TIMELINE (1540-2019): All Other Categories vs History

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104. /books/bacon/essays/

105. TIMELINE (1540-2019): History of Technology vs Visual Arts

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of History of Technology with events from the topic of Visual Arts. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

106. TIMELINE (1540-2019): All Other Categories vs Physics

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107. AUTOMATED BIBLIOGRAPHY: COVID-19 / Review Papers (bibtex file)

(plain text bibliography in readable bibtex format)

NOTE: As of 2 Jan 2021, this bibliography contains only review papers.When the bibliography was first created, there were only 774 entries. Withthe published and pre-print literature now containing 100,000 papers, thedecision was made to limit this bibliography to REVIEWS only.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, or SARS-CoV-2), a virus closely related to the SARS virus. The disease was discovered and named during the 2019-20 coronavirus outbreak. Those affected may develop a fever, dry cough, fatigue, and shortness of breath. A sore throat, runny nose or sneezing is less common. While the majority of cases result in mild symptoms, some can progress to pneumonia and multi-organ failure.The infection is spread from one person to others via respiratory droplets produced from the airways, often during coughing or sneezing. Time from exposure to onset of symptoms is generally between 2 and 14 days, with an average of 5 days. The standard method of diagnosis is by reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab or sputum sample, with results within a few hours to 2 days. Antibody assays can also be used, using a blood serum sample, with results within a few days. The infection can also be diagnosed from a combination of symptoms, risk factors and a chest CT scan showing features of pneumonia.Correct handwashing technique, maintaining distance from people who are coughing and not touching one's face with unwashed hands are measures recommended to prevent the disease. It is also recommended to cover one's nose and mouth with a tissue or a bent elbow when coughing. Those who suspect they carry the virus are recommended to wear a surgical face mask and seek medical advice by calling a doctor rather than visiting a clinic in person. Masks are also recommended for those who are taking care of someone with a suspected infection but not for the general public. There is no vaccine or specific antiviral treatment, with management involving treatment of symptoms, supportive care and experimental measures. The case fatality rate is estimated at between 1% and 3%.The World Health Organization (WHO) has declared the 2019-20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC). As of 29 February 2020, China, Hong Kong, Iran, Italy, Japan, Singapore, South Korea and the United States are areas having evidence of community transmission of the disease.

108. AUTOMATED BIBLIOGRAPHY: COVID-19 / Review Papers

NOTE: As of 2 Jan 2021, this bibliography contains only review papers.When the bibliography was first created, there were only 774 entries. Withthe published and pre-print literature now containing 100,000 papers, thedecision was made to limit this bibliography to REVIEWS only.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, or SARS-CoV-2), a virus closely related to the SARS virus. The disease was discovered and named during the 2019-20 coronavirus outbreak. Those affected may develop a fever, dry cough, fatigue, and shortness of breath. A sore throat, runny nose or sneezing is less common. While the majority of cases result in mild symptoms, some can progress to pneumonia and multi-organ failure.The infection is spread from one person to others via respiratory droplets produced from the airways, often during coughing or sneezing. Time from exposure to onset of symptoms is generally between 2 and 14 days, with an average of 5 days. The standard method of diagnosis is by reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab or sputum sample, with results within a few hours to 2 days. Antibody assays can also be used, using a blood serum sample, with results within a few days. The infection can also be diagnosed from a combination of symptoms, risk factors and a chest CT scan showing features of pneumonia.Correct handwashing technique, maintaining distance from people who are coughing and not touching one's face with unwashed hands are measures recommended to prevent the disease. It is also recommended to cover one's nose and mouth with a tissue or a bent elbow when coughing. Those who suspect they carry the virus are recommended to wear a surgical face mask and seek medical advice by calling a doctor rather than visiting a clinic in person. Masks are also recommended for those who are taking care of someone with a suspected infection but not for the general public. There is no vaccine or specific antiviral treatment, with management involving treatment of symptoms, supportive care and experimental measures. The case fatality rate is estimated at between 1% and 3%.The World Health Organization (WHO) has declared the 2019-20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC). As of 29 February 2020, China, Hong Kong, Iran, Italy, Japan, Singapore, South Korea and the United States are areas having evidence of community transmission of the disease.

109. AUTOMATED 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 realmof 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.

110. AUTOMATED BIBLIOGRAPHY: Holobiont

n++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 for "whole". The entire assemblage of genomes in the holobiont is termed a hologenome.

111. RECOMMENDATIONS: Home Page

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113. TIMELINE (1540-2019): Arts and Culture vs History

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114. HUMOR: Home Directory (browse the ESP collection of frivolity)

115. BOOK: Galton, Francis (1889): Natural Inheritance.

116. TIMELINE (1540-2019): Arts and Culture vs All Science

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117. VIDEOS: Browse Our List of Recommended Videos

118. AUTOMATED 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.

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122. MISC: Browse Our Miscellany (including a real six-legged mouse)

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124. VIDEO: Margaret McFall-Ngai (2016) Lectures on squid-vibrio symbiosis

Two iBioSeminars on symbiosis. In her first lecture, Dr. Margaret McFall-Ngai provides an overview of the three main types of symbiosis: mutualism (both partners benefit), commensalism (only one partner benefit), and parasitism (one partner benefits, but the other partner is harmed). In her second talk, McFall-Ngai tells the story of a symbiosis between the Hawaiian bobtail squid and Vibrio fischeri, a type of luminescent bacteria that enables the squid to hunt at night.

125. HELP: Video Tour of New Design of ESP Website

For more than 20 years, the Electronic Scholarly Publishing Project has been making scientific literature available on line in digital format. Now the web site itself has undergone a major redesign and upgrade to its look and feel. This video provides a quick tour of the new design.

126. AUTOMATED BIBLIOGRAPHY: Neanderthals (bibtex file)

(plain text bibliography in flat bibtex format)

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.

127. AUTOMATED 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.

128. AUTOMATED 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 humanholobiont.Although a human holobiont is mostly mammal by weight, by cell count it ismostly microbial. The number of microbial genes in the associated microbiomes faroutnumber 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.

129. PAPER: Wallace. A. R. (1855): On the law which has regulated the introduction of new species.

Today Darwin's name is known to everyone, while Alfred Russel Wallace is familiar to only a few. Yet the concept of evolution by natural selection was independently developed by Wallace and Darwin, with Wallace publishing first. This paper, and the 1858 manuscript he sent directly to Darwin, show clearly that, prior to Darwin's publication, Wallace had a firm grasp on the concept of evolution.

130. TIMELINE (1540-2019): Visual Arts vs All Other Categories

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131. ESP General Publications: Papers and Other Material of Interest

132. Jonathan Swift (1729): A Modest Proposal for Preventing the Poor People in Ireland from being a Burden to their Parents or Country, and for Making them Beneficial to the Public

A Modest Proposal, is a satirical essay written and published anonymously by Jonathan Swift in 1729. The essay suggests that the impoverished Irish might ease their economic troubles by selling their children as food for rich gentlemen and ladies. This satirical hyperbole mocked heartless attitudes towards the poor, as well as British policy toward the Irish in general. The primary target of Swift's satire was the rationalism of modern economics, and the growth of rationalistic modes of thinking in modern life at the expense of more traditional human values.

133. /books/bacon/essays/contents/essay48.pdf

134. TIMELINE (1540-2019): Biology vs All Other Categories

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135. TIMELINE (1540-2019): All Other Categories vs History of Technology

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136. BOOK: Bateson, William (1894): Materials for the Study of Variation, Treated with Especial Regard to DISCONTINUITY in the Origin of Species

137. TIMELINE (1540-2019): History of Technology vs All Other Categories

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138. VIDEO: Robbins, RJ 2016. Big Data: Yet Another Buzzword or Actual Big Deal?

139. AUTOMATED BIBLIOGRAPHY: Climate Change (ALL)

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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.

140. HUMOR: Home Directory (browse the ESP collection of frivolity)

141. /books/muller/x-over/facsimile/

142. /books/lyell/principles/facsimile/contents/cover.pdf

143. BOOK: Francis Bacon (1601): The Essays

144. /books/aristotle/generation-of-animals/contents/book2.pdf

145. /books/aristotle/generation-of-animals/contents/book1.pdf

146. TIMELINE (1540-2019): All Other Categories vs Arts and Culture

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147. TIMELINE (1540-2019): History of Photographic Technology vs All Other Categories

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148. TIMELINE (1540-2019): Genetics, Development, and Evolution vs All Other Categories

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149. TIMELINE (1860-1869): Genetics, Development, and Evolution vs All Other Categories

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150. AUTOMATED 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.

151. PAPER: Wright, Sewall. (1931): Evolution in Mendelian populations.

Soon after the establishment of Mendelian genetics, several workers began to explore how Mendelian mechanisms would affect changes in gene frequencies in populations — that is, they began to explore the implications of Mendelism for evolution.

Sewall Wright became one of the leading theoreticians who studied Mendelism in the context of population genetics. This paper is a key presentation of his thinking on how Mendelism and evolution might interact.

152. Mendel, Gregor (1866): Gregor Mendel's letters to Carl Nägeli, 1866-1873.

After his original paper on peas, Mendel published only one other paper on genetics, that one on Hieracium. These letters to Nägeli provide a rare additional glimpse into Mendel's thinking as he pursued his investigations on heredity.

153. TIMELINE (1540-2019): All Other Categories vs Visual Arts

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154. AUTOMATED BIBLIOGRAPHY: Telomeres (ALL)

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n++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 "end" and meros "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, with the 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.

155. AUTOMATED BIBLIOGRAPHY: Topologically Associating Domains (ALL)

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"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

156. AUTOMATED 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.

157. /news/

158. /web/viewer.html?file=/books/lyell/principles/facsimile/contents/cover.pdf

159. TIMELINE (1540-2019): All Other Categories vs Biology

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160. AUTOMATED 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 organellesare believed to have originated from a form of endosymbiosis. The endosymbioticorigin of eukaryotes seems to have been a biological singularity — that is,it happened once, and only once, in the history of life on Earth.

161. AUTOMATED BIBLIOGRAPHY: Microbiome Projects

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 lackof 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 asthe Human Microbiome Project — have been undertaken to jump start an understandingof this critical component of the biosphere.

162. AUTOMATED BIBLIOGRAPHY: Pangenome

Although the enforced stability of genomic content is ubiquitous among multi-cellular eukaryotes, 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.

163. TIMELINE (1540-2019): Arts and Culture vs All Other Categories

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164. /web/viewer.html?file=/books/melville/piazza/contents/cover.pdf

165. TIMELINE (1540-2019): All Other Categories vs History of Photographic Technology

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166. VIDEO: Robot Dogs Walk Around, Open a Door

167. AUTOMATED BIBLIOGRAPHY: The Denisovans, Another Human Ancestor (ALL)

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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.

168. AUTOMATED BIBLIOGRAPHY: Origin of Multicellular Eukaryotes

169. AUTOMATED BIBLIOGRAPHY: Kin Selection (ALL)

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170. AUTOMATED 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 speciesmight 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 ecosystemstarted 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 invasionof 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 isimpossible 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 aestheticallyunappealing (who thinks scabs are appealing?), but the long-term effects can be glorious.

171. AUTOMATED BIBLIOGRAPHY: Gregor Mendel (ALL)

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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.

172. AUTOMATED 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.

173. AUTOMATED BIBLIOGRAPHY: Classical Genetics: Drosophila (ALL)

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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.

174. AUTOMATED 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.

175. US DOE OBER: Program Management

176. BOOK: J. Arthur Thomson(1908): Heredity

This book is one of the first textbook treatments of heredity after the rediscovery of Mendel's work. Thomson provides his analysis in the context of the understanding of inheritance in the pre-Mendelian late nineteenth century. Chapter 11, History of Theories of Heredity and Inheritance summarizes many of the nineteenth-century theories of heredity.

In his bibliography, Thomson cites many nineteenth-century works. He also provides a subject-index to the bibliography, making this collection of citations especially valuable.

177. /books/darwin/origin/facsimile/contents/cover.pdf

178. PAPER: R. J. Robbins (1992): Challenges in the Human Genome Project

179. TIMELINE (1540-2019): All Other Categories vs History of Freedom

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180. VIDEO: Tesla Roadster + Starman in Space, Orbiting Earth

181. AUTOMATED BIBLIOGRAPHY: Sociobiology (ALL)

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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.

182. AUTOMATED BIBLIOGRAPHY: Horizontal Gene Transfer (ALL)

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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.

183. PAPER: Muller, Hermann J. (1922): Variation due to change in the individual gene.

This paper is from an address given by to the thirty-ninth annual meeting of the American Society of Naturalists, held in Toronto on 29 December 29 1921.

In this remarkably prescient analysis, Muller lays out the paradoxical nature of the genetic material. It is apparently both autocatalytic (i.e., directs its own synthesis) and heterocatalytic (i.e., directs the synthesis of other molecules), yet only the heterocatalytic function seems subject to mutation. With this, he defines the key problems that must be solved for a successful chemical model of the gene.

Muller also anticipated the ultimate development of molecular genetics:

That two distinct kinds of substances — the d'Hérelle substances (NOTE: viruses) and the genes — should both possess this most remarkable property of heritable variation or "mutability," each working by a totally different mechanism, is quite conceivable, considering the complexity of protoplasm, yet it would seem a curious coincidence indeed. It would open up the possibility of two totally different kinds of life, working by different mechanisms. On the other hand, if these d'Hérelle bodies were really genes, fundamentally like our chromosome genes, they would give us an utterly new angle from which to attack the gene problem. They are filterable, to some extent isolable, can be handled in test tubes, and their properties, as shown by their effects on the bacteria, can then be studied after treatment. It would be very rash to call these bodies genes, and yet at present we must confess that there is no distinction known between the genes and them. Hence we cannot categorically deny that perhaps we may be able to grind genes in a mortar and cook them in a beaker after all. Must we geneticists become bacteriologists, physiological chemists and physicists, simultaneously with being zoologists and botanists? Let us hope so.

184. BOOK: Aristotle (350BC): The History of Animals

185. ABOUT: ESP website in 1998 — a view from the Wayback Machine

186. /web/viewer.html?file=/books/aristotle/generation-of-animals/contents/book1.pdf

187. AUTOMATED BIBLIOGRAPHY: Misophonia — Cannot Stand the Sound of Chewing (ALL)

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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 physica 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.

188. AUTOMATED BIBLIOGRAPHY: Did Mendel Cheat? (related papers) (ALL)

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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.

189. AUTOMATED BIBLIOGRAPHY: History of Genetics

190. BOOK: Aristotle (350BC): On the Generation of Animals

191. /web/viewer.html?file=/books/weismann/germ-plasm/facsimile/contents/cover.pdf

192. /web/viewer.html?file=/books/aristotle/generation-of-animals/contents/book2.pdf

193. AUTOMATED BIBLIOGRAPHY: Telomeres

n++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 "end" and meros "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, with the 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.

194. AUTOMATED 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.

195. AUTOMATED BIBLIOGRAPHY: Fecal Transplantation (ALL)

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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 wasknown as yellow soup.

196. AUTOMATED BIBLIOGRAPHY: Archaea (ALL)

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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 lineagehas 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 Earthone must also understand the Archaea.

197. PAPER: Sutton, Walter S. (1902): On the morphology of the chromosome group in Brachystola magna.

In this paper, Sutton reports cytological studies of grasshopper chromosomes that lead him to conclude that (a) chromosomes have individuality, (b) that they occur in pairs, with one member of each pair contributed by each parent, and (c) that the paired chromosomes separate from each other during meiosis.

After presenting considerable evidence for his assertions, Sutton closes his paper with a sly reference to its undoubted significance:

I may finally call attention to the probability that the association of paternal and maternal chromosomes in pairs and their subsequent separation during the reducing division as indicated above may constitute the physical basis of the Mendelian law of heredity. To this subject I hope soon to return in another place.

198. PAPER: Morgan, T. H. and Bridges, C. B. (1916): Sex-linked Inheritance in Drosophila.

In this special publication from the Carnegie Institution of Washington, Morgan and Bridges review and summarize what was then known about sex-linked traits in Drosophila. It is interesting to note that this was written early enough that they use the word gen instread of the later word gene.

199. /books/melville/piazza/contents/cover.pdf

200. /books/bacon/essays/html/index.p.6.html

201. /books/aristotle/history-of-animals/

202. TIMELINE (1540-2019): All Other Categories vs American Literature

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203. /rjr/canberra/old/canberra.pdf

204. AUTOMATED BIBLIOGRAPHY: Kin Selection

205. AUTOMATED BIBLIOGRAPHY: Classical Genetics: Mutation (ALL)

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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.

206. /books/melville/piazza/contents/05-encantadas-fin-book.pdf

207. /books/darwin/beagle/contents/cover-fin.pdf

208. TIMELINE (1540-2019): All Science vs Arts and Culture

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Science with events from the topic of Arts and Culture. This particular timeline is large and may be slow to load, as it contains almost five hundred years worth of data.

209. AUTOMATED BIBLIOGRAPHY: Endosymbiosis (ALL)

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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 organellesare believed to have originated from a form of endosymbiosis. The endosymbioticorigin of eukaryotes seems to have been a biological singularity — that is,it happened once, and only once, in the history of life on Earth.

210. AUTOMATED BIBLIOGRAPHY: Publications by FHCRC Researchers

The Fred Hutchinson Cancer Research Center began in 1975,with critical help from Washington State's U.S. SenatorWarren Magnuson.Fred Hutch quickly became the permanent home to Dr. E.Donnall Thomas, who had spent decades developing aninnovative treatment for leukemia and other bloodcancers. Thomas and his colleagues were working to curecancer by transplanting human bone marrow after otherwiselethal doses of chemotherapy and radiation. At the Hutch,Thomas improved this treatment and readied it forwidespread use. Since then, the pioneering procedurehas saved hundreds of thousands of lives worldwide.While improving bone marrow transplantation remainscentral to Fred Hutch's research, it is now only partof its efforts. The Hutch is home to five scientificdivisions, three Nobel laureates and more than 2,700faculty, who collectively have published more than 10,000scientific papers, presented here as a full bibliography.

NOTE: From 1995 to 2009 I served as the Hutch's vicepresident for information technology — hence myinterest in the organization. Although my role was inthe admin division, if you dig through this bibliography,you will find a couple of papers with me as an author.

211. /books/weismann/germ-plasm/facsimile/contents/cover.pdf

212. TIMELINE (1860-1869): All Science vs History

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of All Science with events from the topic of History.

213. TIMELINE (1540-2019): All Other Categories vs Genetics, Development, and Evolution

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214. AUTOMATED BIBLIOGRAPHY: Microbial Ecology (ALL)

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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, microorganismal key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganismal production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

215. AUTOMATED BIBLIOGRAPHY: Long Term Ecological Research (LTER)

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.

216. AUTOMATED BIBLIOGRAPHY: The Evolution of Multicellularity

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.

217. AUTOMATED 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 lineagehas 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 Earthone must also understand the Archaea.

218. PAPER: Correns, Carl (1900): G. Mendel's law concerning the behavior of progeny of varietal hybrids.

Correns, along with Hugo de Vries and Erik von Tschermak, is considered to be one of the three co-discovers of Mendel's work in 1900. Correns was the only one of the three to acknowledge Mendel in the title of his paper. Correns' paper begins:

The latest publication of Hugo de Vries: Sur la loi de disjonction des hybrides, which through the courtesy of the author reached me yesterday, prompts me to make the following statement: In my hybridization experiments with varieties of maize and peas, I have come to the same results as de Vries, who experimented with varieties of many different kinds of plants, among them two varieties of maize. When I discovered the regularity of the phenomena, and the explanation thereof - to which I shall return presently - the same thing happened to me which now seems to be happening to de Vries: I thought that I had found something new. But then I convinced myself that the Abbot Gregor Mendel in Brünn, had, during the sixties, not only obtained the same result through extensive experiments with peas, which lasted for many years, as did de Vries and I, but had also given exactly the same explanation, as far as that was possible in 1866.

219. /books/6th-congress/facsimile/contents/6th-cong-aa-fm-01.pdf

220. TIMELINE (): vs

A side-by-side illustrated timeline (with links to sources) that compares events from the topic of with events from the topic of .

221. AUTOMATED 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.

222. AUTOMATED BIBLIOGRAPHY: Publications by FHCRC Researchers (ALL)

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The Fred Hutchinson Cancer Research Center began in 1975,with critical help from Washington State's U.S. SenatorWarren Magnuson.Fred Hutch quickly became the permanent home to Dr. E.Donnall Thomas, who had spent decades developing aninnovative treatment for leukemia and other bloodcancers. Thomas and his colleagues were working to curecancer by transplanting human bone marrow after otherwiselethal doses of chemotherapy and radiation. At the Hutch,Thomas improved this treatment and readied it forwidespread use. Since then, the pioneering procedurehas saved hundreds of thousands of lives worldwide.While improving bone marrow transplantation remainscentral to Fred Hutch's research, it is now only partof its efforts. The Hutch is home to five scientificdivisions, three Nobel laureates and more than 2,700faculty, who collectively have published more than 10,000scientific papers, presented here as a full bibliography.

NOTE: From 1995 to 2009 I served as the Hutch's vicepresident for information technology — hence myinterest in the organization. Although my role was inthe admin division, if you dig through this bibliography,you will find a couple of papers with me as an author.

223. /books/bacon/essays/contents/essay17.pdf

224. /web/viewer.html?file=/books/weismann/essays/facsimile/contents/weismann-essays-1-a-fm.pdf

225. TIMELINE (1540-2019): All Science vs History of Technology

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226. TIMELINE (1540-2019): History vs All Other Categories

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227. TIMELINE (1880-1889): Arts and Culture vs History

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228. /recommended/literature//microbiome/all.html (ALL)

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229. AUTOMATED BIBLIOGRAPHY: Long Term Ecological Research (LTER) (ALL)

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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.

230. AUTOMATED BIBLIOGRAPHY: Invasive Species (ALL)

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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 speciesmight 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 ecosystemstarted 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 invasionof 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 isimpossible 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 aestheticallyunappealing (who thinks scabs are appealing?), but the long-term effects can be glorious.

231. /recommended/literature//invasive/

232. AUTOMATED BIBLIOGRAPHY: Ecological Informatics (ALL)

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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 the Datanet, DataONE and Data Conservancy projects sponsored by the National Science Foundation.

233. AUTOMATED BIBLIOGRAPHY: Classical Genetics: Sex Determination

234. R. J. Robbins. 1997. Believe It, or Else!

Scientific publishing is always a challenge, especially in a premier venue. Here's the story of what it took to get a major finding in human genomics published in Ripley's Believe It or Not!

235. PAPER: Sutton, Walter S. (1903): The chromosomes in heredity.

Early on, some researchers noticed that Mendel's theory required that some kind of hereditary unit segregate in pairs to offspring. Sutton was one of the first to note that the chromosomes behaved in exactly a manner to match this requirement.

The opening lines of his paper show that he is aware of the significance of his observations:

In a recent announcement of some results of a critical study of the chromosomes in the various cell generations of Brachystola the author briefly called attention to a possible relation between the phenomena there described and certain conclusions first drawn from observations on plant hybrids by Gregor Mendel in 1865, and recently confirmed by a number of able investigators. Further attention has already been called to the theoretical aspects of the subject in a brief communication by Professor E. B. Wilson. The present paper is devoted to a more detailed discussion of these aspects, the speculative character of which may be justified by the attempt to indicate certain lines of work calculated to test the validity of the conclusions drawn. The general conceptions here advanced were evolved purely from cytological data, before the author had knowledge of the Mendelian principles, and are now presented as the contribution of a cytologist who can make no pretensions to complete familiarity with the results of experimental studies on heredity. As will appear hereafter, they completely satisfy the conditions in typical Mendelian cases, and it seems that many of the known deviations from the Mendelian type may be explained by easily conceivable variations from the normal chromosomic processes.

236. PAPER: Stevens, Nettie M. (1905): Studies in Spermatogenesis with especial reference to the "accessory chromosome".

Nettie Stevens was one of the first female scientists to make a name for herself in the biological sciences. In 1896, Stevens went to California to attend Leland Stanford Jr. University, where she obtained first a bachelor's and then a masters in biology. Her masters thesis involved microscopic work and precise, careful detailing of new species of marine life. This training was a factor in her success with later investigations of chromosomal behavior. After Stanford, Stevens pursued a PhD. at Bryn Mawr College, where Thomas Hunt Morgan was still teaching and was one of her professors. Stevens again did so well that she was awarded a fellowship to study abroad. She traveled to Europe and spent time in Theodor Boveri's lab at the Zoological Institute at Würzburg, Germany. Boveri was working on the problem of the role of chromosomes in heredity and Stevens likely developed an interest in the subject from her stay.

In 1903, after receiving her Ph.D from Bryn Mawr, Stevens was given an assistantship by the Carnegie Institute after glowing recommendations from Thomas Hunt Morgan, Edmund Wilson and M. Carey Thomas, the president of Bryn Mawr. Her work on sex determination was published as a Carnegie Institute report in 1905. In this first study she looked at sex determination in meal worms. Later, she studied sex determination in many different species of insects. Stevens' assistantship at Bryn Mawr still meant that she had to teach. desiring a pure research position, Stevens wrote to Charles Davenport at Cold Spring Harbor to see if it was possible for her to work at his Station for Experimental Biology. Unfortunately, Stevens died of breast cancer in 1912 before she could occupy the research professorship created for her at Bryn Mawr, or work with Davenport at Cold Spring Harbor.

237. /foundations/genetics/classical/holdings/o/ostrom-1969.pdf

238. BOOK CHAPTER: A. H. Sturtevant (1965): A History of Genetics, Front Matter

239. BOOK CHAPTER: A. H. Sturtevant (1965): A History of Genetics, Chapter 17, Population Genetics and Evolution

240. BOOK CHAPTER: A. H. Sturtevant (1965): A History of Genetics, Chapter 1, Before Mendel

241. BOOK: L. Doncaster (1911): Heredity In the Light of Recent Research

242. BOOK: William Castle (1911): Heredity in Relation to Evolution and Animal Breeding

243. /web/viewer.html?file=/books/chambers/vestiges/facsimile/contents/chambers-vestiges-cover.pdf

244. TIMELINE (1860-1869): Biology vs All Other Categories

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245. TIMELINE (1540-2019): Arts and Culture vs History of Photographic Technology

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246. AUTOMATED 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.

247. AUTOMATED 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 physica 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.

248. AUTOMATED BIBLIOGRAPHY: Did Mendel Cheat? (related papers)

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.

249. PAPER: Morgan, Thomas H. (1909): What are "factors" in Mendelian explanations?

Although T. H. Morgan is best known for heading the genetics laboratory at Columbia University (later at Cal Tech) that essentially defined American genetics research for decades, he was initially skeptical of the facile manner in which combinations of alleged Mendelian factors were being invoked to explain all manner of heritable traits.

This paper begins with a wonderful debunking of easy explanation:

In the modern interpretation of Mendelism, facts are being transformed into factors at a rapid rate. If one factor will not explain the facts, then two are invoked; if two prove insufficient, three will sometimes work out. The superior jugglery sometimes necessary to account for the result, may blind us, if taken too naïvely, to the common-place that the results are often so excellently "explained" because the explanation was invented to explain them. We work backwards from the facts to the factors, and then, presto! explain the facts by the very factors that we invented to account for them.

250. PAPER: Vries, Hugo de (1900): Concerning the law of segregation of hybrids.