Tag Archives: Genetics

The Origin of Syphilis

Blogging on Peer-Reviewed ResearchSyphilis is first clearly seen in Europe in 1495, when it appeared as a plague (though it was not “the plague” … Yersinia pestis) among Charles VIII’s troops. When these troops went home shortly after the fall of Naples, they brought this disease with them, staring an epidemic. The level of mortality in Europe was truly devastating. Is it the case that syphilis was brought to Europe by Columbus and his men just prior to the plague-like outbreak of 1495?

The origin of syphilis has been debated for years, really since the actual 1495 event itself. Some researchers have asserted that syphilis is present in the writings of Hippocrates, placing it squarely in the old world thousands of years prior to Columbus. Others, as suggested above, have argued that Columbus brought syphilis over to the Old World . A third (Crosby’s “combination theory”) asserts, essentially, that syphilis is both an Old World and New World disease, and that the history of the disease is complicated by the innately complex relationship between any pathogen and human populations with variable immunities, both of which tend to evolve.

A new paper is being published as we speak in PLoS Neglected Tropical Diseases, by Harper et al , called “On the Origin of the Treponematoses: A Phylogenetic Approach.” Studiously ignoring Crosby’s discussion (and I’m sure there is some unseemly story of academic infighting to explain that), the paper examines the Old World vs. New World origins hypotheses.Here is the author’s summary from the paper:

 

For 500 years, controversy has raged around the origin of T. pallidum subsp. pallidum, the bacterium responsible for syphilis. Did Christopher Columbus and his men introduce this pathogen into Renaissance Europe, after contracting it during their voyage to the New World? Or does syphilis have a much older history in the Old World? This paper represents the first attempt to use a phylogenetic approach to solve this question. In addition, it clarifies the evolutionary relationships between the pathogen that causes syphilis and the other T. pallidum subspecies, which cause the neglected tropical diseases yaws and endemic syphilis. Using a collection of pathogenic Treponema strains that is unprecedented in size, we show that yaws appears to be an ancient infection in humans while venereal syphilis arose relatively recently in human history. In addition, the closest relatives of syphilis-causing strains identified in this study were found in South America, providing support for the Columbian theory of syphilis’s origin.

 

The authors looked at 21 strains of the bacterium Treponematoses pallidum and conducted a detailed genetic (phylogenetic) study of these genomes to come to the conclusion that syphilis originates in the new world. However, a commentary on the paper, published along side it in PLoS, brings the conclusion into question. The commentary by Lukehart and Norris notes that the genetic data from the New World (which the main paper’s authors assert points to a New World origin) is weak. In addition, there are problems, partly outlined in the commentary and partly fairly obvious to anyone who reads the paper, that the issue of evolutionary change in both the pathogens and the humans who harbor them has not been sufficiently taken into account.In my view, a detailed phylogenetic study such as the one presented here is fundamentally important, but is very unlikely on its own to definitively answer the question of origin and evolution of syphilis.Need more research…

Updated: See The Science Behind Pre-Columbian Evidence of Syphilis in Europe: Research by Documentary, by Armelagos, Zuckerman, and Harper, on “Science by documentary” and “Science by press release”

This article discusses the presentation of scientific findings by documentary, without the process of peer review. We use, as an example, PBS’s “The Syphilis Enigma,” in which researchers presented novel evidence concerning the origin of syphilis that had never been reviewed by other scientists. These “findings” then entered the world of peer-reviewed literature through citations of the documentary itself or material associated with it. Here, we demonstrate that the case for pre-Columbian syphilis in Europe that was made in the documentary does not withstand scientific scrutiny. We also situate this example from paleopathology within a larger trend of “science by documentary” or “science by press conference,” in which researchers seek to bypass the peer review process by presenting unvetted findings directly to the public. © 2012 Wiley Periodicals, Inc.

See: Syphilis May Have Spread Through Europe Before Columbus.

Summary: A recent study conducted at the University of Zurich now indicates that Europeans could already have been infected with this sexually transmitted disease before the 15th century. In addition, researchers have discovered a hitherto unknown pathogen causing a related disease. The predecessor of syphilis and its related diseases could be over 2,500 years old.

Lukehart S, Mulligan C, Norris S (2008) Molecular Studies in Treponema pallidum Evolution: Toward Clarity? PLoS Negl Trop Dis 2(1).Harper KN, Ocampo PS, Steiner BM, George RW, Silverman MS, et al. (2008) On the Origin of the Treponematoses: A Phylogenetic Approach. PLoS Negl Trop Dis 2(1): e148. doi:10.1371/journal.pntd.0000148

New Twist in microRNA biology

MIT scientists have found a new way that DNA can carry out its work that is about as surprising as discovering that a mold used to cast a metal tool can also serve as a tool itself, with two complementary shapes each showing distinct functional roles.Professor Manolis Kellis and postdoctoral research fellow Alexander Stark report in the Jan. 1 issue of the journal Genes & Development that in certain DNA sequences, both strands of a DNA segment can perform useful functions, each encoding a distinct molecule that helps control cell functions.

There is a full press report here.

Lamarckian Mechanism in Ciliates

A group of scientists … has uncovered a new biological mechanism that could provide a clearer window into a cell’s inner workings…..What’s more, this mechanism could represent an “epigenetic” pathway — a route that bypasses an organism’s normal DNA genetic program — for so-called Lamarckian evolution, enabling an organism to pass on to its offspring characteristics acquired during its lifetime to improve their chances for survival.

Continue reading Lamarckian Mechanism in Ciliates

Race is a social construct and a self fulfilling prophecy all wrapped up together

Gene Expression has the second in a pair of posts on race that is worth a close look. In Why phenotypic races may not disappear, G.E. speaks of the particulate nature of inheritance in relation to culturally defined racial types (that are in turn based on appearance). Continue reading Race is a social construct and a self fulfilling prophecy all wrapped up together

Heritability of Magical Powers Investigated

A multilocus model with a dominant gene for magic might exist, controlled epistatically by one or more loci, possibly recessive in nature. Magical enhancers regulating gene expressionmay be involved, combined with mutations at specific genes implicated in speech and hair colour such as FOXP2 and MCR1.

The most important thing about this study is not its conclusion, but what we will do with it. Continue reading Heritability of Magical Powers Investigated

Reduced Verbal Ability in African American Children

Blogging on Peer-Reviewed ResearchAfrican American children may have reduced verbal ability compared to other children to a degree that is roughly equivalent to missing a year in school, according to a recently published paper. Is this evidence of a racial difference?The study by Sampson et.al., published in the Proceedings of the National Academy of Sciences included more than 200 children aged 6-12 living in Chicago, and followed these children over seven years. The study controlled for poverty, and interestingly, poverty was not found to be a good predictor of differences in verbal ability. Continue reading Reduced Verbal Ability in African American Children

Life history trade-offs and human pygmies

Blogging on Peer-Reviewed Research

Every few years a paper comes out “explaining” short stature in one or more Pygmy groups. Most of the time the new work ads new information and new ideas but fails to be convincing. This is the case with the recent PNAS paper by Migliano et al.

From the abstract:

Continue reading Life history trade-offs and human pygmies

Japanese Develop Fearless Mouse

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In this undated photo released by Tokyo University’s Department of Biophysics and Biochemistry Graduate School of Science, a genetically modified mouse stays near a cat in Tokyo. Using genetic engineering, scientists at Tokyo University say they have successfully switched off the rodents’ instinct to cower at the smell or presence of cats, showing that fear is genetically hardwired and not leaned through experience, as commonly believed. (AP Photo/Ko and Reiko Kobayakawa, Tokyo University Department of Biophysics and Biochemistry Graduate School of Science)[source]

… This could lead to a better mouse trap. Or at least, a whole new world of Friday cat-blogging.

Scientists Investigate Gorilla Biogeography

Blogging on Peer-Reviewed ResearchThe Central African Rainforest (as distinct from the West African Rain Forest) spans an area from the Atlantic coast to nearly Lake Victoria in Uganda and Tanzania. In fairly recent times (the mid Holocene) this forest was probably continuous all the way to Victoria, and probably extended farther north and south than one might imagine from looking at its current distribution.Within the forest are major rivers, including the Congo. The Congo River is the only major river in the world that crosses the Equator twice. This trans-equatorial configuration guarantees that the rivers picks up rain from both of the equatorial rainy seasons, making it a huge and virtually uncrossable barrier for terrestrial mammals. During glaical periods, the forest is believed to have shrunk to either small refugia, or to have virtually disappeared entirely with only riverine forest remaining. Between the shrinkage of the forest and the major riverine barriers, terrestrial (non-flying, non-swimming) forest-dwelling animals that might have had a more continuous distribution would have been broken into many smaller units. Likely, many of these small populations would have gone extinct, but others may have changed over time such that when the forest was re-established, they may have constituted different subspecies or species. This breaking up and rejoining of the rain forest, over and over again, during the Pleistocene is thought to have caused much of the modern day variation we see among closely related forest species of primates, small carnivores, and forest ungulates such as duikers. Continue reading Scientists Investigate Gorilla Biogeography

More “Junk” DNA is Not

Blogging on Peer-Reviewed ResearchSome of the base pairs in a given genome are strung together into templates that code for proteins or RNA molecules. These are the classic “genes.” Other base pairs probably have little or no function. Among the DNA that is not in classic gene-templates, however, there is a lot of important information, including “control regions.”

How much of each “type” of DNA exists in a particular genome varies. A recent study suggests that the currently used methods for scanning DNA for regulatory sequences may systematically m miss more than half of that information.

Continue reading More “Junk” DNA is Not