Biotechnology in the News (BITN)

Other topics

This page contains brief sections on several "miscellaneous" topics. The topics are listed immediately below. The rest of the "Table of Contents" section below lists other BITN pages, including major topics with their own pages.

I now maintain a newsletter on a broad range of current science. In many cases, I add new things to the Musings newsletter, rather than to the BITN pages. BITN pages -- including some topics below -- have some cross-links to the Musings newsletter. To go directly to the Musings newsletter and browse: Musings newsletter.

Other topics

Aging + New 1/24/24
Alzheimer's disease + New 4/9/24, 4/12/24
Bio-inspiration (biomimetics)
Brain + New 2/7/24, 2/20/24
Cancer (Chinese, Italian, Russian, Spanish)
COVID: See SARS (next column)
Dengue virus (and miscellaneous flaviviruses)
Ebola and Marburg (and Lassa)

Emerging diseases (general) (Arabic, Chinese, French, Japanese, Portuguese, Russian, Spanish)
Ethical and social issues; the nature of science
Hormone replacement therapy
HPV (Human papillomavirus)
Malaria + New 3/20/24
Protein Folding -- and diseases
RNAi (RNA interference or silencing)
SARS, MERS (coronaviruses) (Arabic, Chinese, French, Greek, Italian, Portuguese, Romanian, Spanish, Vietnamese) + New 6/7/23, 4/17/24. Includes COVID-19.
Smallpox (poxviruses) (Spanish)
Sudden Oak Death
Synthetic biology
TGN1412: The clinical trial disaster
Vaccines (general) + New 6/14/23
West Nile Virus
  Links to external sites will open in a new window.
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BITN home page. General information about BITN, including some resources that may be useful for your own explorations of biotechnology. Also includes some background information about the original BITN course.
   Sections on general resources include:    Introduction    Magazines and journals    Local libraries    Local research    Web sites    Books    Glossaries

BITN topics (major topics, each with its own page):
DNA and the genome
Cloning and stem cells
Agricultural biotechnology (GM foods) and Gene therapy
Prions (BSE, CJD, etc)
Influenza (Bird flu)
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The section was previously labeled Aging (including Alzheimer's disease). It is now split into two separate sections, one each on Aging and on Alzheimer's disease.

Also see other sections of this page:
* Alzheimer's disease
* Autism
* Brain

My Musings newsletter includes posts on various aspects on aging. Many of these are listed below, in two lists. List 2 is for posts about people who have lived to age 100. List 1 is general.

List 1. Musings posts on aging (general)...
* Briefly noted... A good role for "senescent cells"? (February 1, 2023).
* If a cell needs more telomeres, can it get some from another cell? (November 15, 2022).
* Physiological effects of blue light (September 10, 2022).
* How oocytes limit oxygen-induced aging (August 20, 2022).
* Briefly noted... The gut microbiome and aging - in mice (April 13, 2022).
* Briefly noted... Why some species of rockfish live for 200 years (April 6, 2022).
* Fidelity of protein synthesis: a factor in aging? (November 13, 2021).
* A senolytic treatment for severe COVID (August 21, 2021).
* Treating progeria by editing the gene (March 23, 2021).
* Briefly noted... How flies protect their aging brains (January 6, 2021).
* How about having your immune system remove senescent cells? (September 27, 2020). Update added January 24, 2024: Hydrogen as an anti-aging agent?
* What if we just gently nudge old cells a little bit toward pluripotency? (May 9, 2020).
* Comparing the death rates of American football and baseball players (July 2, 2019).
* The genetic basis of why parrots seem so human (March 31, 2019).
* Do naked mole rats get old? (April 20, 2018).
* A mutation, found in a human population, that extends the human lifespan (February 2, 2018).
* Treating senescent cells: an overview (November 29, 2017).
* A treatment for senescence? (June 4, 2017).
* What to do if your telomeres get too long (March 19, 2017).
* Age-related development of far-sightedness in bonobos (January 10, 2017).
* How long can humans live? (November 29, 2016). (A follow-up post is included in List 2, below.)
* Extending lifespan by dietary restriction: can we fake it? (August 10, 2016).
* Drug may extend life in progeria patients (October 17, 2014).
* Extending lifespan -- five-fold (January 12, 2014).
* Premature aging: a treatment? (January 5, 2014).
* A drug that delays neurodegeneration? (June 14, 2013).
* Would young blood be good for your brain? (October 21, 2011).
* Methuselah's secret: methionine? (February 12, 2010).

List 2. Musings has also noted some individuals who reached age 100...
* Briefly noted... James Lovelock, 1919-2022 (August 1, 2022).
* Follow-up: How long can humans live? (July 23, 2018). (The original post is included in List 1, above.)
* A 115-year-old person: What do we learn from her blood? (November 18, 2014). This really is a biology research item.
* Living to 100 (April 22, 2009).
* Elliott Carter: 100th birthday (December 23, 2008).

A very famous non-human centenarian. Analysis of the genome of Lonesome George, after his death at an age probably above 100, offers some clues about the longevity of tortoises, as well as their low cancer incidence.
* News story: Scientists sequence Lonesome George's genome, find genes associated with long life and giant size. (T Puiu, ZME Science, December 3, 2018.)
* The article, which is freely available: Giant tortoise genomes provide insights into longevity and age-related disease. (V Quesada et al, Nature Ecology & Evolution 3:87, January 2019.)

C Rundel, Genes, aging, and the future of longevity. Engineering & Science LXV #4, 12/02, p 36. A delightful essay on some issues of aging, written by a Caltech undergraduate as part of a science writing class -- and then published in the Caltech magazine. The article is available online at The article discusses some genes that are known to affect aging in simple model organisms, and even a drug which seems to extend the life of fruit flies.

An intriguing result has recently been published: A team at Scripps Research Institute (La Jolla, California) has engineered mice to have a slightly lower core body temperature (by about 0.5 degree Celsius). These mice lived longer (by about 15%) than the "normal" mice. How did they lower the body temperature? By engineering the mice to make a heat-producing protein (uncoupling protein) in the hypothalamus -- where the body senses and regulates its temperature. The cooler mice ate and exercised normally, had somewhat higher weight (since they were producing less heat from the same food) -- and lived longer. Interestingly, one effect of severe caloric restriction, which is known to increase lifespan, is lowering the body temperature. So this work may give us one more piece of a complex puzzle. Its practical significance for now is purely speculative: there is no known way to reduce human body temperature, and of course we know nothing about what the side effects might be.
* The paper is B Conti et al, Transgenic mice with a reduced core body temperature have an increased life span. Science 314:825, 11/3/06. The paper is accompanied by a "perspective" article: C B Saper, Biomedicine: Life, the universe, and body temperature. Science 314:773, 11/3/06. These are online at (perspective, probably the best place to start) and (article).

SAGE KE, the Science of Aging Knowledge Environment Archive Site, from Science magazine. "From October 2001 to June 2006, Science's SAGE KE provided news, reviews, commentaries, disease case studies, databases, and other resources pertaining to aging-related research. Although SAGE KE has now ceased publication, we invite you to search and browse the article content on this archive site."

Nature web focus sites on aging: Senescence: Cells, ageing and cancer. (August 2005) Determining lifespan. (September 2003)

Book. Stephen S Hall, Merchants of Immortality - Chasing the dream of human life extension. Houghton Mifflin, 2003. ISBN 0-618-09524-1. For more about this book, see the listing of it under Cloning and stem cells. The "aging" parts of the book largely deal with telomerase, a fascinating scientific topic which probably is not a key limiting factor in human aging. In fact, much of the book deals with the hype surrounding telomerase -- and attempts to commercialize telomerase technologies.

Book. Lenny Guarente, Ageless Quest - One scientist's search for genes that prolong youth. Cold Spring Harbor Lab Press, 2003. ISBN 0-87969-652-4. Guarente is a biologist at MIT. In this short book, he talks about finding a gene that extends the life of simple yeast -- and of worms. The question, then, is whether it is relevant to aging in higher organisms, including humans. He discusses evidence that it may be, though conclusive evidence is not yet available. This story is a good testimonial to the importance of basic research -- how studying simple model systems leads to insights that guide work in more complex systems. It is also a good story of how scientists develop and pursue leads -- some of which work out and some of which do not; that is how science works. It is an optimistic book -- perhaps too optimistic, since the gap between what has been shown and what is needed is still quite large. Enjoy the story, and Guarante's enthusiasm. But be careful to distinguish what turns out to work from the exciting discussions of what might be.

The books listed above are also listed on my page Books: Suggestions for general science reading.

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Alzheimer's disease

The section previously labeled Aging (including Alzheimer's disease) is now split into two separate sections, one each on Aging and on Alzheimer's disease.

Also see other sections of this page:
* Aging
* Autism
* Brain
* Protein Folding -- and diseases
* and the page Prions (BSE, CJD, etc)

My Musings newsletter includes posts on Alzheimer's disease and related issues. Examples...
* Briefly noted... Viruses and Alzheimer's disease (and other neurodegenerative diseases)? (May 3, 2023).
* Features of Alzheimer's disease in dolphins? (April 24, 2023).
* The importance of choline as a dietary nutrient (April 15, 2023).
* Biomarkers for Alzheimer's disease (March 13, 2023).
* SNO and the higher prevalence of Alzheimer's disease in women (January 14, 2023).
* Alzheimer's disease: a blood treatment? (January 9, 2023).
* What's the connection: Alzheimer's disease and cancer? (October 31, 2022).
* Heat production by aggregation of amyloid-beta in Alzheimer's disease (September 13, 2022).
* Briefly noted... Faked data and the status of research on Alzheimer's disease (August 3, 2022).
* Sleep genes and Alzheimer's disease? (May 28, 2022).
* How many types of Alzheimer's disease are there? (June 15, 2021).
* Brain imaging to detect and distinguish tauopathies, including Alzheimer's disease (January 18, 2021).
* Alzheimer's disease: a blood test that might be used for people with some signs of cognitive decline (January 16, 2021).
* How tau gets around (June 28, 2020).
* A mutation in ApoE that protects against Alzheimer's disease? (February 22, 2020).
* Alzheimer's disease: a role for inflammation? (January 18, 2020).
* Alzheimer's disease: The role of vascular damage? (August 13, 2019).
* Formation of new neurons in adults: relevance to Alzheimer's disease? (May 21, 2019)
* Briefly noted... Role of senescent cells in neurodegeneration? (March 13, 2019).
* Games genes play -- Alzheimer genes, in your brain (January 4, 2019).
* Alzheimer's disease: What is the role of ApoE? (November 6, 2017).
* Do chimpanzees get Alzheimer's disease? (October 17, 2017).
* An antibody to treat Alzheimer's disease: early clinical trial results (September 26, 2016).
* Transmissibility of Alzheimer's disease? (June 1, 2016). Overview.
* BRCA1 (the breast cancer gene) and Alzheimer's disease? (February 8, 2016).
* Transmission of Alzheimer's disease in humans? (September 27, 2015). Two updates added April 9 & 12, 2024: Evidence for transmission of Alzheimer's disease by medical procedures. The gut microbiome and Alzheimer's disease.
* Early detection of brain damage in football players? A breakthrough, or not? (September 14, 2015).
* A better way to un-boil an egg -- and why it might be useful (March 20, 2015).
* An early-detection system for Alzheimer's disease? (June 28, 2014).
* Making stem cells using brain tissue from dead people (June 2, 2014).
* Sleep and the brain drain (November 17, 2013).
* Male DNA found in human female brains (October 8, 2012).
* A mutation that reduces the chances of Alzheimer's disease (September 18, 2012).
* A drug trial to prevent Alzheimer's disease (May 23, 2012).
* Using patient-specific stem cells to study Alzheimer's disease (February 24, 2012).
* Insulin as a treatment for Alzheimer's disease? (January 28, 2012).
* Reversing Alzheimer's disease (March 4, 2011).
* Alzheimer's disease may be delayed in people who are actively bilingual (March 1, 2011).
* Is Alzheimer's disease transmissible? (February 4, 2011).
* The Alzheimer's disease peptide: Why does it accumulate? (January 22, 2011).
* GSAP -- a clue to treating Alzheimer's disease? (October 2, 2010).
* Do cell phones prevent Alzheimer's disease? (January 13, 2010).
* Curry and Alzheimer's disease (June 15, 2009).

Nature web focus site on Alzheimer's disease: Alzheimer's disease. (June 2006)

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My Musings newsletter includes posts on anthrax...
* Is Bcbva anthrax a threat to wild populations of chimpanzees? (September 8, 2017).
* Playing music can make you sick (July 31, 2010).

Researchers, including a group from UC Berkeley, have explored the tricks that the anthrax bacteria use to get the iron they need for growth. They found that these bacteria make two chemicals designed to steal iron from their host; such chemicals are generically called siderophores. One of these is attacked by the human immune system; however, the other -- the more novel one -- evades it, and actually succeeds in supplying iron to the bacteria. They suggest that this novel siderophore might be a good target for anti-anthrax drugs, or simply a marker for detection of this pathogen.
* The work was featured in the student newspaper, December 8, 2006: Researchers Find Possible Way to Block Anthrax, (now archived).
* The work was published as R J Abergel et al, Anthrax pathogen evades the mammalian immune system through stealth siderophore production. PNAS 103:18499, December 5, 2006. Online at
* This work is also briefly noted on my Intro Chem Internet Resources page under solutions.

Book. For some interesting history, see the listing for Thomas D Brock, Robert Koch - A Life in Medicine and Bacteriology (1988) on my page Books: Suggestions for general science reading -- Brock. One major story is the first clear elucidation of the life cycle of a pathogenic bacterium -- anthrax. Those interested in bacteria, especially as agents of disease, will enjoy this fascinating tale of the origins of modern medical microbiology.

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My Musings newsletter includes posts on antibiotics and the broader issues of reducing bacterial growth. Topics include disinfectants and biofilms. Examples...
* Water disinfection in nanoseconds (April 3, 2023).
* What if infection triggered a treatment? (August 2, 2022).
* Graphdiyne: helping make silver a better anti-bacterial agent (June 11, 2022).
* Air filters that can kill (March 19, 2022).
* Triclosan: an explanation for its gut toxicity (January 30, 2022).
* Antibiotic action: effect of hydrogen sulfide (July 9, 2021).
* Strawberries, bees, and their bacteria: a complex alliance (January 11, 2020).
* How to preserve dead mice so they stay fresh and edible (January 18, 2019).
* Antibiotic prophylaxis: a useful tool to reduce childhood mortality? (July 9, 2018).
* Antibiotics and viruses: An example of harm (May 6, 2018).
* Antibiotics and viruses: An example of effectiveness (May 5, 2018).
* On completing the course of the antibiotic treatment (September 19, 2017).
* Staph fighting Staph: a small clinical trial (April 8, 2017).
* Antibiotic resistance genes in "ancient" bacteria (February 11, 2017).
* Staph in your nose -- making antibiotics (October 9, 2016).
* Resistance to Bt toxin: What next? (July 15, 2016).
* Humans resistant to arsenic? (June 16, 2015).
* Designing a less toxic form of an antibiotic (April 19, 2015).
* Shark skin inspires design of a new material to reduce bacterial growth (March 13, 2015).
* A new antibiotic: an interesting story about the discovery and action of teixobactin (March 7, 2015).
* How our immune system may enhance bacterial infection (September 19, 2014).
* Does Triclosan in antibacterial soaps promote infection? (May 19, 2014).
* Salmonella and food contamination; the biofilm problem (April 28, 2014).
* Theonella's secret: Entotheonella (March 18, 2014).
* Black silicon and dragonfly wings kill bacteria by punching holes in them (January 28, 2014).
* Killing persisters -- a new type of antibiotic (January 3, 2014).
* A rapid test for antibiotic sensitivity? (July 19, 2013).
* Cockroach should be disinfected before eating it (February 12, 2013).
* Antibiotics and obesity: Is there a causal connection? (October 15, 2012).
* Scorpion venom: a source of a novel antibiotic? (August 3, 2012)
* Using viruses to make a better disinfectant (April 22, 2012)
* Antibiotics in ancient times (January 10, 2011).
* Restricting excessive use of antibiotics on the farm (September 25, 2010). With follow-up posts listed there.
* Antibiotic resistance: A new concern from New Delhi (August 24, 2010).
* Can the Staph solve the Staph problem? (July 12, 2010).
* The Scientist: open access (temporary) (May 22, 2010). See listed item by Julian Davies.

Books. The following books that deal with antibiotics are listed on my page of Books: Suggestions for general science reading...
* Blaser, Missing Microbes -- How the overuse of antibiotics is fueling our modern plagues (2014).
* Hopwood, Streptomyces in Nature and Medicine -- The antibiotic makers (2007).

Bacterial 'battle for survival' leads to new antibiotic -- Holds promise for treating stomach ulcers. A press release from MIT, Feb 2008, on a new approach for discovering new antibiotics. Briefly, they force bacteria not known to make antibiotics to compete with other bacteria. One possible response is for them to develop the ability to make antibiotics. This should be considered interesting lab work at this point. The potential of the new antibiotics is unknown.

Alliance for the Prudent Use of Antibiotics. This site has "an agenda" -- trying to reduce "inappropriate" use of antibiotics. A particular concern is the use of vast amounts of antibiotics with farm animals, sometimes with minimal justification. The site also contains a lot of general information about antibiotics, aimed at the consumer and at doctors.

A local angle. The July 24, 2003, issue of the Berkeleyan (a campus newspaper for staff) published part of an interview with science writer and UCB journalism professor Michael Pollan on the subject of antibiotics in beef farming, with a focus on McDonald's announcement of favoring suppliers that use less antibiotics. The article title is Prof has a beef with McDonald's antibiotics announcement. The entire interview is online at Very readable, with a useful general overview of why antibiotics are used in commercial production of animals. Pollan also expresses reservations about how significant the policy announcement will be.

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The DNA double helix has become a popular icon, known well beyond the circles of those who know anything about biology. And of course, some artists are attracted to social issues. Thus it should not be surprising that DNA and genes and genomes and related issues have become the subject of artistic efforts.

John Sulston was the head of the British lab working on the human genome. Provocatively and/or appropriately, artist Marc Quinn did a "portrait" of Sulston -- using his DNA. For a news article on this, which includes the "portrait", see If you have access to Nature, see Martin Kemp's article about the portrait in the October 25, 2001, issue (413:778). (The printed article and the online PDF file contain the "portrait"; however the online HTML file does not.) This article is part of Nature's regular series, Science and Culture; art historian Kemp is a regular contributor.

Sulston shared the 2002 Nobel prize for his work on development in the worm Caenorhabditis elegans. In the course of that work, he played a key role in discovering the phenomenon of programmed cell death, now called apoptosis.

England issued a coin to commemorate the 50th anniversary of the DNA structure (which was developed at Cambridge Univ in England); it shows a DNA double helix on one side. (The other side shows the Queen, who coincidentally is celebrating her 50th anniversary as monarch.) For pictures of the coin, plus some information:

Also see L Gamwell, Science in culture: Art after DNA. Nature 422:817, 4/24/03. The subtitle notes "The double helix has inspired scientists and artists alike."

On my page Internet resources: Miscellaneous there is a section for Art and Music. Some of the items there are science-based. That section includes a list of relevant posts in my Musings newsletter.

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Earlier, items on autism were included in the section below on Brain.

Also see other sections of this page:
* Aging
* Alzheimer's disease
* Brain
* Protein Folding -- and diseases
* and the page Prions (BSE, CJD, etc)

Posts in my Musings newsletter on autism include...

* Human cortical organoids can survive -- and function -- in rat brains (October 22, 2022).
* The autism-Angelman connection: a single enzyme involved in two brain disorders (November 9, 2015).
* Autism in a dish? (September 4, 2015).
* Can we make sense of the many genes involved in autism? (January 16, 2015).
* Signs of autism in 2-month-old babies (February 7, 2014).
* Suggested genes for autism challenged (November 18, 2013).
* DNA twisting and long genes -- and autism: Are there connections? (November 8, 2013).
* A blood test for autism? (December 11, 2012).
* A drug treatment for an autism-like condition in mice (November 9, 2012).
* A mouse carrying a serotonin-transport gene that contributes to human autism (May 18, 2012).
* Early detection of autism (June 14, 2011).
* Is the incidence of autism increasing? (November 6, 2009).

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Bio-inspiration (biomimetics)

My Musings newsletter includes posts on biomimetics. Examples...
* Would moth wings make good sound absorbers? (July 19, 2022).
* Environmental sensors that can be dispersed by the wind and land upright (May 9, 2022).
* The smallest manmade flying devices (December 12, 2021).
* A mosquito-like robot (August 18, 2020).
* A new way to make impact-resistant glass (August 9, 2019).
* Staying warm -- polar-bear style (July 23, 2019).
* Crashworthy drones, wasp-inspired (October 16, 2017).
* What if you pulled on the ends of a ladderene? (September 26, 2017).
* Coloring with graphene: making a warning system for structural cracks? (June 2, 2017).
* Biomimetics -- an overview (December 9, 2015).
* Shark skin inspires design of a new material to reduce bacterial growth (March 13, 2015).
* How to climb a pile of sand (November 7, 2014).
* Fixing the heart with some glue and light (July 27, 2014).
* Black silicon and dragonfly wings kill bacteria by punching holes in them (January 28, 2014).
* Progress toward an artificial fly (December 6, 2013).
* An artificial forest with artificial trees (June 7, 2013).
* Bending a rigid rod (May 17, 2013).
* How porcupine quills work (January 5, 2013).
* Acrobatic cockroaches inspire robot design (September 16, 2012).
* See cat run (March 14, 2012).
* Wings for better walking (November 5, 2011).
* Why don't woodpeckers get headaches? Designing better shock absorbers (April 18, 2011).
* Robots should learn to crawl first, then walk (February 27, 2011).
* Armor (February 5, 2010).

Book. Peter Forbes, The Gecko's Foot - Bio-inspiration: Engineering new materials from nature. Norton, 2005. The lotus leaf is easily rinsed clean; the gecko can climb a glass wall. Why? And, can we make use of the principles that Nature has used to achieve these remarkable accomplishments? Those are just two of the topics in this delightful book -- one of which is reflected in its title. The theme is bio-inspiration (sometimes called biomimetics), in which we look to Nature for an idea about how to do something. The hook-and-loop fastener, popularly known by the tradename Velcro, is an example of old, but the field has now taken on an identity that reflects a more focused effort to discover and exploit what Nature has already learned. Forbes emphasizes work at the "nano" level, where recent advances in instrumentation, such as the scanning electron microscope (SEM), helped us unlock Nature's secrets. Commercial importance? Well, products based on the self-cleaning lotus leaf and the sticky gecko foot are on the market. They are not yet big successes; perhaps that will take time, or perhaps there is less here of commercial importance than we would like to believe. In any case, the book is delightful biology, delightfully presented. It is suited for the scientific novice, but even biologists are likely to find it rewarding. This book is listed on my Book suggestions page, and as further reading for Intro Chem Ch 15, re intermolecular forces, and for Organic/Biochem Ch 15, re spider silk. In fact, it was reading this book that prompted me to start this BITN section.

Plant-inspired robot. A robot that moves like a plant. Very slowly, of course. But the point is that it moves based on osmotic changes, which is how plant tendrils wrap around a host structure, for example. Why? It offers potential advantages in terms of delicate handling. The new work makes progress in showing that such a system can operate reversibly under practical conditions.
* News story: Researchers design the first soft robot that moves like a plant. (A Micu, ZME Science, January 29, 2019.) Links to the article, which is freely available. The article includes three movie files (about 1 minute each, no sound). The first two show how the device works; the third is on how it is made.

Ask Nature. A site that explores how Nature does things. It includes examples of how people have already made use of the ideas, but a major goal is to inspire more such developments. It's a serious academic site -- with plenty to please the casual reader. From the Biomimicry 3.8 Institute; the number in their name refers to the number of billions of years Nature has been working on this issue.

From University of California, Berkeley:
* Biomimetic Millisystems Lab. "The goal of the Biomimetic Millisystems Lab is to harness features of animal manipulation, locomotion, sensing, actuation, mechanics, dynamics, and control strategies to radically improve millirobot capabilities. Research in the lab ranges from fundamental understanding of mechanical principles to novel fabrication techniques to system integration of autonomous millirobots. The lab works closely with biologists to develop models of function which can be tested on engineered and natural systems. The lab's current research is centered on fly-size flapping flight, and all-terrain crawling using nanostructured adhesives." The "Current Research Projects" listed in January 2008 include: Micromechanical Flying Insect, Biologically Inspired Synthetic Gecko Adhesives, Millirobot Rapid Prototyping, Micro-Robots and Microassembly. This page is from Ronald Fearing, in EECS (Electrical engineering and computer science). However, a glance at the people shows that this is a collaboration that also includes the Departments of Integrative Biology and Chemical Engineering.
* CIBER. The Center for Interdisciplinary Bio-inspiration in Education & Research. A new center at Berkeley, headed by Dr Robert Full, of Integrative Biology. From "Objectives": CIBER "will innovate methods to extract principles in biology that inspire novel design in engineering and train the next generation of scientists and engineers to collaborate in mutually beneficial relationships. ... Biologists working with engineers, computer scientists and mathematicians are discovering general principles of nature from the level of molecules to behavior at an ever-increasing pace. Now more than ever before, nature can instruct us on how to best use new materials and manufacturing processes discovered by engineers, because these human technologies have more of the characteristics of life. This effort will require unprecedented integration among disciplines that include biology, psychology, engineering, physics, chemistry, computer science and mathematics." Choose Publications & Journals for good information on the work going on.
* News story in the Daily Cal, the student newspaper, February 12, 2008. Mimicking the geckos' ability to defy gravity - From geckos to humans to robots: new adhesive tape makes the vertical horizontal. (Now archived.)
* News release: Engineers create gecko-inspired high-friction micro-fibers, August 2006. As you read the item, note that they are not making synthetic gecko feet, but rather using some of what they learned about gecko feet to help them design a new material.

'Gecko foot' band-aids could promote healing. A news story in New Scientist, February 19, 2008, about the development of a new type of adhesive tape, which may be suitable for not only band-aids but also sutures. It is based in part on the structure of the gecko foot. Importantly, the work does not simply mimic the gecko foot, but builds on it, to develop a material suitable for the intended use. The story is online at The work referred to is published as: A Mahdavi et al, A biodegradable and biocompatible gecko-inspired tissue adhesive. PNAS 105:2307, 2/19/08. There is a link to the article at the end of the news story.

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The scope of this section has varied over the years. Some brain-related topics have been split off to separate sections, as noted below. This section remains for general brain topics. Some items more generally on the nervous system may be included. Cross links to this section may show older versions of the section title, but should always start with "Brain". Most entries here point to posts in my Musings newsletter; there is a little more at the end of that list.

Also see other sections of this page:
* Aging
* Alzheimer's disease
* Autism
* and the page Prions (BSE, CJD, etc)

My Musings newsletter includes posts on various brain issues. Many of these are listed below.

* Effect of corticosteroids on brain function (May 20, 2023).
* Graphene-based sensors for capturing your brain waves (April 22, 2023).
* Briefly noted... Neurons at play (April 12, 2023).
* What's the connection: Alzheimer's disease and cancer? (October 31, 2022).
* Human cortical organoids can survive -- and function -- in rat brains (October 22, 2022).
* Physiological effects of blue light (September 10, 2022).
* A bio-marker for SIDS? (June 27, 2022).
* Selenium and neurodegenerative diseases? (June 25, 2022).
* Sleep genes and Alzheimer's disease? (May 28, 2022). Update added February 20, 2024: Includes an "update" about an unusual sleep behavior in penguins.
* Briefly noted... Exploring the mind of a jellyfish (April 20, 2022).
* Briefly noted... Brain organoids grow eye precursor structures (March 2, 2022).
* Briefly noted... Synapses in a sponge? (February 23, 2022).
* Tau and ALS (February 19, 2022).
* Briefly noted... Bird song from brain waves (January 13, 2022).
* Could a better gut microbiome improve memory? (December 6, 2021).
* Treating epilepsy with Mozart (December 4, 2021).
* Briefly noted... A non-invasive test for concussion (November 9, 2021).
* What happens to capillary blood flow in the brain during sleep -- and why? (November 8, 2021).
* Aging without memory loss in cuttlefish (October 4, 2021).
* Briefly noted... Concussions in women athletes (August 18, 2021).
* Sleep stages in octopuses -- do they dream? (July 13, 2021).
* Conversing with dreamers (July 6, 2021).
* Could tomatoes be used as the source of a common drug for Parkinson's disease? (April 24, 2021).
* Shrews downsize part of the brain for the winter (March 13, 2021).
* Studying concussions in egg yolks (February 28, 2021).
* Right-hemisphere processing of language in children (October 3, 2020).
* How exercise benefits the brain (August 9, 2020).
* A sniff test to see if a person is conscious (August 4, 2020).
* A new brain study (March 3, 2020).
* An "antidote" for Huntington's disease? (February 29, 2020).
* Is it possible to have a normal sense of smell without olfactory bulbs? (January 28, 2020).
* Brain development: comparing human and chimpanzee lab-grown brain organoids (November 5, 2019).
* Traumatic brain injury: long term effects? (October 8, 2019).
* Briefly noted... (two items about brain-computer interfaces) (August 14, 2019). One item is from Neuralink, a company founded by Elon Musk. The other is an "opinion" piece about the field.
* Metabolism of the Parkinson's disease drug L-DOPA by the gut microbiota (July 26, 2019).
* Using a brain-computer interface to direct synthetic speech (July 16, 2019).
* Developing a monkey with a gene for a human brain protein (July 6, 2019).
* Comparing the death rates of American football and baseball players (July 2, 2019).
* How slime molds learn (June 11, 2019).
* What can a brain do after death? (June 3, 2019).
* Using caffeine to treat premature babies: risk of neurological effects? (April 27, 2019).
* The genetic basis of why parrots seem so human (March 31, 2019).
* Role of a receptor for HIV in stroke recovery (March 23, 2019).
* Involvement of the non-pregnant uterus in brain function? (February 11, 2019).
* Does the appendix affect the development of Parkinson's disease? (December 11, 2018).
* Brain imaging, with minimal restraint (June 2, 2018).
* When do jellyfish sleep? (September 29, 2017).
* Triplet-repeats: Do they act through the RNA? (September 24, 2017).
* Ravens: planning for the future? (September 11, 2017).
* Evidence for brain damage in players of (American) football at the high school level (August 23, 2017).
* RNA editing is a major contributor to protein diversity in cephalopod brains (June 3, 2017).
* A step toward doing cephalosomatic anastomosis in humans? (May 31, 2017).
* If you are talking with someone, how can you tell if they are paying attention? (May 8, 2017).
* A possible genetic cause for the large human brain (March 25, 2017).
* Possible role of gut bacteria in Parkinson's disease? (March 17, 2017).
* Imaging of fetal human brains: evidence that babies born prematurely may already have brain problems (March 10, 2017).
* Can we predict whether a person will respond to a placebo by looking at the brain? (February 21, 2017).
* Do apes have a "theory of mind"? (February 19, 2017).
* Brain-computer interface -- without invasive electrodes (December 28, 2016).
* How long is a yawn? (December 16, 2016).
* Bird brains -- better than mammalian brains? (June 24, 2016).
* Nerves a half billion years old (June 20, 2016).
* Measuring brain injury after head trauma? (April 25, 2016).
* Huntington's disease: Mutant human protein disrupts singing in birds (April 18, 2016).
* Biodegradation of an implant in the brain (April 5, 2016).
* Progress toward a practical brain-computer interface: self-calibrating software (March 28, 2016).
* Sliced meat: implications for size of human mouth and brain? (March 23, 2016).
* Is a "dead" virus in the human genome contributing to the neurological disease ALS? (January 11, 2016).
* An artificial neuron? (November 6, 2015).
* How much would it cost to make a brain? (November 1, 2015).
* Early detection of brain damage in football players? A breakthrough, or not? (September 14, 2015).
* As we add human cells to the mouse brain, at what point ... (August 3, 2015).
* Can blind rats learn to use a geomagnetic compass? (June 29, 2015).
* Should you give Librium -- an anti-anxiety drug -- to crayfish? (October 6, 2014).
* Huntington's disease: Is it an amino acid deficiency? (October 4, 2014).
* A novel nervous system? (July 20, 2014).
* How BMAA may cause motor neuron disease -- a clue? (July 1, 2014).
* "Moonwalkers" -- flies that walk backwards (May 28, 2014).
* Brain activity at the time of death: Do rats have "near-death experiences"? (March 8, 2014).
* 3D printing: Neurosurgeons can practice on a printed model of a specific patient's head (December 16, 2013).
* Can memories survive if head is lost? (November 23, 2013).
* Sleep and the brain drain (November 17, 2013).
* Down syndrome: Could we turn off the extra chromosome? (November 15, 2013).
* Atomic bombs and growing new brain cells (November 1, 2013).
* Artificial brain-like structures grown from human stem cells in the lab (October 1, 2013).
* On handedness in humans (September 30, 2013).
* Computer scientist thinks; psychologist moves finger (September 24, 2013).
* False memories in the courtroom (September 10, 2013).
* A mouse that remembers an event that did not happen (September 3, 2013).
* Near-death experiences: are the memories real? (August 11, 2013).
* What if you had eyes on your tail? (July 27, 2013).
* Can we predict the proper treatment for depression? (June 24, 2013).
* A drug that delays neurodegeneration? (June 14, 2013).
* Using your brain waves to log on to the computer (April 29, 2013).
* Mice with human brain cells (April 13, 2013).
* Can one rat know what another rat is thinking? (April 8, 2013).
* Can rats touch infrared light? (February 25, 2013).
* Fish with bigger brains may be smarter, but ... (January 25, 2013).
* Is it possible that mental retardation could be prevented by a simple prenatal treatment? (January 14, 2013).
* Brain-computer interface: Paralyzed patients control robotic arm by their thoughts (June 16, 2012).
* Dog fMRI (June 8, 2012).
* Novelty-seeking behavior (May 26, 2012).
* Music-making technology -- for the physically disabled (April 23, 2011).
* Effect of cell phone on your brain (April 11, 2011).
* Reading the brain waves from speech (October 17, 2010).
* Swarming locusts have bigger brains (August 29, 2010).
* Near-death experiences: the CO2 connection (April 28, 2010).
* A smart rat (November 30, 2009).
* Athletes: Head injuries (October 5, 2009).
* Self (October 8, 2008).

Added February 7, 2024.
Enhancing hypnotizability. A new article reports transient enhancement of the ability of people to be hypnotized, by magnetic stimulation of the brain. The treatment is guided by neuroimaging of the individual, and is non-invasive. The induced hypnotizability was reported in a sample of people with the chronic pain disorder fibromyalgia. The hope is that stimulating hypnotizability may allow the use of hypnosis, an effective treatment, on more people.
* News story: Stanford scientists boost hypnotizability with transcranial magnetic brain stimulation. (Eric W Dolan, PsyPost, January 4, 2024.)
* The article, which is open access: Stanford Hypnosis Integrated with Functional Connectivity-targeted Transcranial Stimulation (SHIFT): a preregistered randomized controlled trial. (Afik Faerman et al, Nature Mental Health 2:96, January 2024.)
* This item is listed on my Musings page as an "update".

Gut microbes and the brain? Microbes grow in your gut. How could they affect your brain? Well, as one example, they secrete metabolic products, as do any cells. And some of those get into the bloodstream, and can get to the brain. It is a controversial field, with a variety of claims, some not standing up to further work. A recent news feature gives an overview of the field. Useful for perspective; don't get too bogged down in specifics.
* News feature, which is freely available: How gut microbes could drive brain disorders. (Cassandra Willyard, Nature, February 3, 2021. In print, with a different title: Nature 590:22, February 4, 2021.)

There is evidence to suggest that infection of the mother during pregnancy may increase the chances of some brain diseases, including autism and schizophrenia. The effects seem to be due not to the infectious agent per se, but to the host response. Now, work with a mouse model system points to one specific component, the cytokine IL-6, as promoting the brain mis-development. Remember, this is with mice; the work generates some leads that must be followed up to see if they are relevant to humans.
* A press release about this work: "Researchers discover link between schizophrenia, autism and maternal flu", October 1, 2007:
* The paper is: S E P Smith et al, Maternal immune activation alters fetal brain development through interleukin-6. Journal of Neuroscience, 27:10695, October 3, 2007. online.

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This is a broad topic. I have no intention of trying to cover it comprehensively, but merely want to occasionally note some things of interest.

Recent news (2019-)

Transmissible cancers. These are cancers that can be transmitted from one animal to another. Not common, but there are now examples in diverse organisms, and considerable study of what is going on for at least one case. A recent news feature in The Scientist is a nice overview and update.
* News feature: Some Cancers Become Contagious -- So far, six animal species are known to carry transmissible, "parasitic" forms of cancer, but researchers are still mystified as to how cancer can become infectious. (K Zimmer, The Scientist, April 1, 2019. Now archived.) In print, with a slightly different title... p 36 of April 2019 issue.
* The list of Musings posts, immediately below, includes several on transmissible cancers. You can scan/search that list for 'devil' or 'clam' to get some of them, which link to others.

Musings posts

There are posts in my Musings newsletter on cancer. Among them...
* Briefly noted... Toxic chemicals in household cleaning products: ordinary vs "green" (March 1, 2023).
* X-chromosome inactivation in males -- in cancer (February 6, 2023).
* What's the connection: Alzheimer's disease and cancer? (October 31, 2022).
* More about elephants, cancer, and p53 (August 30, 2022).
* Engineering a worm to treat cancer (July 23, 2022).
* A connection between eating fish and skin cancer? (June 20, 2022).
* A protein that can assist with handling actinium (January 9, 2022).
* Can fecal transplantation be useful in treating cancer? (April 27, 2021).
* Can a "silent" mutation be harmful? (April 17, 2021).
* How about having your immune system remove senescent cells? (September 27, 2020).
* Pancreatic cancer: another trick for immune evasion (August 1, 2020).
* Men are losing their Y chromosomes, and some men are losing them faster than others -- does it matter? (February 25, 2020).
* Distinguishing pathogenic and benign BRCA1 mutants: a high-throughput test (January 26, 2019).
* CRISPR connections: p53? cancer? (October 6, 2018).
* A blood test that detects multiple types of cancer (March 30, 2018).
* Role of neoantigens in surviving pancreatic cancer? (February 4, 2018).
* Does using printer toner lead to carcinogens? (October 31, 2017).
* What if zebrafish could get human cancer? (October 25, 2017).
* Predicting who will respond to cancer immunotherapy: role of high mutation rate? (October 6, 2017).
* Cancer and pain -- and immunotherapy (July 7, 2017).
* Immunization of devils: a treatment for a transmissible cancer? (April 24, 2017).
* Why some viruses may be less virulent in women (March 1, 2017).
* CRISPR: First clinical trial in humans (November 28, 2016).
* Tasmanian devils: Are they developing resistance to the contagious cancer? (September 6, 2016).
* Did the Fukushima nuclear accident lead to a burst of thyroid cancer? (July 17, 2016).
* Is clam cancer contagious? Follow-up (July 2, 2016).
* Is glyphosate (Roundup) a carcinogen? Follow-up (June 7, 2016).
* Metastasis: How clusters of tumor cells get through narrow capillaries (June 3, 2016).
* Why do elephants have a low incidence of cancer? (March 20, 2016).
* Is glyphosate (Roundup) a carcinogen? (March 6, 2016).
* BRCA1 (the breast cancer gene) and Alzheimer's disease? (February 8, 2016).
* Why are some types of cancer more common than others? Follow-up (January 24, 2016).
* Can pigeons diagnose cancer by reading patient X-rays? (December 29, 2015).
* How vitamin C kills cancer (December 15, 2015).
* The WHO report on the possible carcinogenicity of meat (December 12, 2015).
* Could a tapeworm with cancer transmit the cancer to its human host? (November 16, 2015).
* Cancer metastasis: An early detection system? (October 20, 2015).
* Anti-oxidants and cancer? (October 18, 2015).
* The role of combinations of chemicals in causing cancer? (September 21, 2015).
* Effect of low dose radiation on humans: some real data, at long last (July 24, 2015).
* SyAMs: Synthetic drugs that act like antibodies (May 31, 2015).
* Is clam cancer contagious? (April 21, 2015).
* Why are some types of cancer more common than others? (February 6, 2015).
* Cachexia: is it BAT run amok? (September 22, 2014).
* A clue about cancer from the naked mole rat? (January 18, 2014).
* 3D printing: Neurosurgeons can practice on a printed model of a specific patient's head (December 16, 2013).
* Coupling the surgeon's knife to a mass spectrometer (August 13, 2013).
* A tumor in a Neandertal (July 8, 2013).
* Fair skin and cancer: What is the connection? (March 12, 2013).
* Is Helicobacter pylori good for you or bad? (April 10, 2012).
* Does dry cleaning cause cancer? (November 30, 2011).
* Diagnosis of prostate cancer in a 2100 year old man (November 8, 2011).
* The devil has cancer -- and it is contagious (June 6, 2011).
* Does radiation treatment of cancer cause new cancers? (April 8, 2011).
* Targeting cancers (January 15, 2011).
* Cancer in the ancient world (November 1, 2010).
* A cancer drug with a switch: it acts only in a cancer cell (September 26, 2010).
* A gene for breast cancer: what does it do? (May 4, 2010).
* Can genes be patented? The Myriad case (April 2, 2010). Follow-up posts are linked there.
* NOTCH drugging (December 1, 2009).
* Personalized medicine: cancer therapy (November 9, 2009).


Some cancer-related books are listed on my page Books: Suggestions for general science reading. They include...
* Graeber, The Breakthrough: Immunotherapy and the Race to Cure Cancer. 2018.
* Wapner, The Philadelphia Chromosome -- A mutant gene and the quest to cure cancer at the genetic level. 2013.
* Bishop, How to win the Nobel prize -- An unexpected life in science. 2003.

Some general educational resources

Inside Cancer. Educational materials, for the general public. Sections include: hallmarks, causes and prevention, diagnosis and treatment, pathways. Some materials are specifically for teachers. This is from the Dolan DNA Learning Center, Cold Spring Harbor Laboratory: Other parts of the Dolan DNA Learning Center are referred to under BITN Resources: DNA and the genome and Molecular Biology Internet Resources: Methods.

Cancer Topics. A series of informational web pages for the general public, from the National Cancer Institute (NCI). Also in Spanish.

Cancer Quest, a broad informational resource, largely organized as a tutorial, from G Orloff, Emory Univ. Topics range from the basic underlying biology to clinical issues. Special pages offer guidance to patients, educators, students, and health professionals. Also available in Chinese, Italian, Russian, Spanish.


Personalized cancer vaccine made in plants. This work deals with a cancer of the immune system, called follicular B cell lymphoma. An important characteristic of this cancer is that each case expresses a unique antigen, reflecting its development from a single immune system cell. The goal is to make a vaccine that targets this particular antigen. Here, they show that they can do this in a plant system -- which is both faster and cheaper than animal systems previously tried. The resulting vaccines do elicit an immune response in [most of] the patients, though no therapeutic benefit was seen in this small early study. The work is of note both for the special approach of making a personalized vaccine, and for the broader issue of making vaccines in plants. News story, from Stanford: Plants can be factories making vaccine to treat cancer, July 23, 2008. The paper: A A McCormick et al, Plant-produced idiotype vaccines for the treatment of non-Hodgkin's lymphoma: Safety and immunogenicity in a phase I clinical study. PNAS 105:10131, 7/22/08. Free online:

Drug targeting. A group from UC Berkeley and San Francisco reported making a new drug delivery system. The active drug is attached to a large molecule called a dendrimer. Because the blood system in tumors tends to be leaky, the large drug complex is taken up by the tumor selectively, and then hydrolyzed. They report promising results in a mouse model system. Both the article and the story about it discuss some of the logic of the system. The paper: C C Lee et al, A single dose of doxorubicin-functionalized bow-tie dendrimer cures mice bearing C-26 colon carcinomas. PNAS 103:16649, 11/7/06. Free online: News story, with the same title... News-Medical.Net, November 13, 2006:

Irreversible electroporation. UC Berkeley scientists, led by B Rubinsky, are working on a new approach to treating solid tumors. A new paper is on the use of the method with pigs, the first large animal tests. The method is a variation of the common electroporation used in laboratory work to make transient membrane pores that can allow uptake of drugs or even DNA. The key difference is that the conditions are chosen so that the pores do not quickly reseal; thus the cells "leak to death". In this method, the electrical pulse is delivered directly to tumor cells, in a surgical procedure. News story, "A breakthrough treatment for tumors? New medical technique uses electrical pulses to punch holes in target cell membrane." February 14, 2007. Online:

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Dengue virus (and miscellaneous flaviviruses)

Two other flaviviruses have their own sections:
West Nile Virus

There are also more general sections that may overlap with this section:
Emerging diseases (general)
Vaccines (general)

Here is a list of posts in my Musings newsletter about dengue virus. The list also includes posts about flaviviruses in general. It may also contain posts about mosquitoes in general, if there is some emphasis on those that carry dengue or miscellaneous flaviviruses. The list is currently "in progress".
* Virus infection may make you more attractive to mosquitoes (July 16, 2022).
* Effect of the COVID pandemic on the incidence of dengue (May 24, 2022).
* What if the mosquitoes carried immunity to the dengue virus? (March 8, 2020).
* A new dengue vaccine (November 16, 2019).
* Does vaccination against yellow fever affect incidence of severe dengue? (October 4, 2019).
* Could we repel mosquitoes by playing loud music they don't like? (May 18, 2019).
* The effect of prior dengue infection on Zika infection (April 20, 2019).
* Can Wolbachia reduce transmission of mosquito-borne diseases? 3. A field trial, vs dengue (August 10, 2018).
* Antibiotics and viruses: An example of harm (May 6, 2018).
* Dengue vaccine: a step backwards? (December 6, 2017).
* Dengue vaccine follow-up: Phase 3 trial (September 15, 2014).
* A new type of dengue virus (October 27, 2013).
* A dengue vaccine trial (December 1, 2012).
* Dengue fever: an overview (February 28, 2011).
* Dengue fever -- Two strikes and you're out (August 10, 2010).
* Science: Love songs (March 26, 2009).

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My Musings newsletter includes posts on diabetes and related issues such as insulin. Among them...
* FGF1 and insulin? (February 5, 2022).
* Diabetes type 1: an immunotherapy to delay onset? (April 20, 2021).
* Insulin: role in reproduction in ants (October 2, 2018).
* Diabetes: types 1, 2, 3, 4, 5 (March 16, 2018).
* Treating obesity: A microneedle patch to induce local fat browning (January 5, 2018).
* Diagnosing diabetes in people of African ancestry: a race-dependent variable (January 3, 2018).
* Making a functional mouse pancreas in a rat (February 17, 2017).
* Treatment of Type 1 diabetes with encapsulated insulin-producing cells derived from stem cells (March 11, 2016).
* A smart insulin patch that rapidly responds to glucose level (October 26, 2015).
* Artificial sweeteners: Saccharin and high blood sugar levels (December 7, 2014).
* Chelation therapy -- a controversial clinical trial (December 13, 2013).
* Insulin as a treatment for Alzheimer's disease? (January 28, 2012).
* What color is your rice? Rice, diabetes, and arsenic. (December 12, 2010)
* Making replacement insulin-producing cells: another way (May 14, 2010).

J Diamond, The double puzzle of diabetes. Nature 423:599, 6/5/03. Feature. Nature's blurb for this article: "Why is the prevalence of type 2 diabetes now exploding in most populations, but not in Europeans? The genetic and evolutionary consequences of geographical differences in food history may provide the answer." The article gives an overview of the types of diabetes, and their incidence. The main purpose is to propose an explanation of why diabetes is not rampant among Europeans. As you read this, remember that he is proposing a hypothesis -- and some tests of it; be careful about remembering his "answer" as if it were true. Reading the article for its background information can be good. Online at

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Ebola and Marburg (and Lassa)

August 25, 2015... I have added Lassa to the scope of this section.

Some news...

Ebola vaccine. The Ebola news from the current outbreak in the Democratic Republic of the Congo (DRC) is mostly depressing. However, results from vaccination, announced recently, are encouraging. The vaccination work was done by the ring strategy discussed in earlier Musings posts (listed below), administering vaccine to contacts of known cases. Analysis suggests that the vaccine is 97% effective. Further, the death rate of those who do get the disease after vaccination is very low. The announcement, from the DRC and WHO, is preliminary; a proper scientific article is promised.
* News story: Ebola cases climb by 44 as vaccine trial affirms high efficacy. (L Schnirring, CIDRAP, April 15, 2019.) Links to the report, which is freely available; see the item near the end "Apr 13 INRB WHO preliminary VSV-EBOV results".
* To be clear... This is about the second outbreak of Ebola in the DRC in 2018. It is alluded to briefly at the end of the next item here.

The May 2018 Ebola outbreak in the Democratic Republic of the Congo (DRC) is over. About three months from first reported cases to a formal declaration of the end. In general, the DRC and partners around the world are getting high marks for how they handled the outbreak, which seemed to have the potential to become very serious. The experimental vaccine and ring vaccination protocol were used here. As far as we know, no vaccinated individuals got Ebola; it is hard to know the significance of that result, since there was no control group.
* News story: DRC declares end to Ebola outbreak. (L Schnirring, CIDRAP, July 24, 2018.) The bad news... A few days after the official end of the May outbreak, a new Ebola outbreak in the DRC was reported; it is an independent outbreak -- and shows signs of becoming very serious.

Posts in my Musings newsletter about these viruses include:
* Briefly noted... Ebola transmission from long-term survivors? (October 20, 2021).
* Ebola vaccines: two brief updates (December 15, 2017).
* The new Ebola outbreak (June 6, 2017).
* An antibody treatment for Marburg virus disease? (May 14, 2017).
* Update: Ebola vaccine trial (January 24, 2017).
* Ebola survivors: are they a risk to others? (June 5, 2016).
* The role of WHO: the view of its director (December 1, 2015).
* After Ebola, what next? and how will we react? (September 5, 2015).
* In the shadow of Ebola: The story of Lassa virus (August 26, 2015).
* An Ebola vaccine: 100% effective? (August 7, 2015).
* Fallout from the Ebola outbreak: more measles? (April 28, 2015).
* The tree where the West Africa Ebola outbreak began? (January 12, 2015).
* Ebola in the United States: the "suspicion" factor (December 15, 2014).
* How Ebola kills: a clue about a key protein (December 5, 2014).
* Ebola virus: ancient origins? (November 4, 2014).
* A broad-spectrum antiviral drug candidate that may be active against Ebola, MERS, and more (October 18, 2014).
* Drug may extend life in progeria patients (October 17, 2014).
* The new Ebola virus (August 19, 2014).

Ebola and Marburg are related viruses. Lassa is a distinct type of virus, but also causes a hemorrhagic fever.

The CIDRAP site is a good source of current news as well as background for these viruses. The CIDRAP main page for Ebola is: You can sign up for a daily e-mail from CIDRAP; in mid 2014, it has a lot of Ebola news.

CDC sites:
* Ebola:
* Lassa:

Both CIDRAP and the CDC are good sources of information, on an almost daily basis, about the current (2014) outbreak of Ebola in West Africa. Remember that the CDC is an official government site, and CIDRAP is a news site, one specializing in infectious diseases.

Treatments? A CDC page, dated, as I post this, August 29, 2014. Questions and Answers on Experimental Treatments and Vaccines for Ebola.

Ebola has been observed to emerge "from the jungle" from time to time. A major -- and important -- mystery is where is it "hiding". That is, what is the "reservoir" (likely an animal) from which the virus emerges? Now there is evidence that bats may be the culprit; the bats carrying the virus show no symptoms. It is important to emphasize that this is a new finding, subject to further work. Even if correct, it only shows that the bats are a part of the story; there may be more to it.
* The article is: E M Leroy et al, Fruit bats as reservoirs of Ebola virus. Nature 438:575, 12/1/05. The abstract is at
* Here are two news stories on this finding: and

Now there is a report of Marburg virus being detected in bats. The work is published: J S Towner et al, Marburg virus infection detected in a common African bat. PLoS ONE 2(8):e764, 8/22/07. There is a news story, August 2007: Scientists detect presence of Marburg virus in African fruit bats, at: This has a link to the article, which is freely available.

Progress with efforts to control Ebola, Marburg viruses. Microbe 1:217, 5/06. Discusses both vaccines and drugs.

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Emerging diseases (general)

My Musings newsletter includes posts on emerging diseases. Examples...
* SpillOver: predicting zoonoses (July 20, 2021).
* What is in the rubella virus family? (November 15, 2020).
* WHO: We need to prepare for Disease X (May 13, 2018).
* After Ebola, what next? and how will we react? (September 5, 2015).
* Chikungunya in the Americas, 1827 -- and the dengue confusion (April 3, 2015).
* Disease outbreaks: Trends and perspective (March 31, 2015).
* Chikungunya in the Americas -- are vaccines near? (March 17, 2015).
* The new Ebola virus (August 19, 2014).
* MERS in the United States (May 18, 2014).
* The Heartland virus -- follow-up (March 30, 2014).
* Polio-like disease without polio virus? (March 17, 2014).
* Where is the MERS virus coming from? (September 22, 2013).
* Face masks and flu virus transmission on airplanes: an analysis of a flight (August 27, 2013).
* A new SARS-related virus seems to be emerging -- and an "ethics" story (February 4, 2013).
* The Heartland virus (October 2, 2012)
* Is the Schmallenberg virus episode dying out on its own? (October 2, 2012)
* Schmallenberg virus (January 20, 2012)
* One health (November 15, 2010)
* Both ways (November 18, 2008).

In the Spring of 2003, as I started to put together a BITN web site, one dominant news story was a new illness, called SARS (severe acute respiratory syndrome). Our fears of SARS are enhanced by our ignorance. And that is not just the ignorance of the general public, but also the ignorance of the medical and scientific communities. SARS is a new disease. At least at the start, we do not know what causes it, how it is transmitted, how to contain or treat it -- even how to diagnose or define it, or what its risks are. Of course, over time, answers to some of these questions are developed. It is actually quite amazing how fast some of the answers come in. On the other hand, not all the answers we hear are correct. (For example, three different organisms were quickly "identified" as the cause of SARS. Obviously, two of those were likely to be incorrect.)

By mid-summer, we may have the disease under control. Yet, we still have little idea how the disease started -- and if/when it may return.

SARS is an example of an emerging disease -- a new disease, or at least one that has moved from obscurity to some prominence. MERS is a related disease that emerged more recently; it is now included in the section on SARS. which is now called "SARS, MERS (coronaviruses)". Other diseases that have emerged over the last 30 years include Legionnaire's diseases, AIDS, toxic shock syndrome, Ebola, West Nile Virus, Zika -- and perhaps a new strain of Influenza each year. Both SARS and the broader topic raise lots of questions about how we deal with a disease that has emerged, and how we might predict or prevent new emerging diseases.

M E J Woolhouse, Where Do Emerging Pathogens Come from? Microbe 1:511, 11/06. (or check Google Scholar). A discussion of the factors involved in the emergence of new diseases.

Why do so many pathogenic viruses come from bats? Evidence is accumulating that the immune system of the bats plays a role. The bat immune system is unusually strong, and puts a strong selective pressure on the viruses. Any virus that can thrive in the bats has a headstart when it moves to a host with a more ordinary immune system. A recent article discusses the evidence -- and the nuances. Much of the current article is modeling, and the core of the paper may be less interesting than the sections that explore the ideas (Introduction and Discussion).
* News stories. Both link to the article, which is freely available.
- Immune arms-race in bats may make their viruses deadly to people -- Strong immune system may save bats but make their germs harder for humans and others to survive. (E Garcia de Jesus, Science News Explores, February 12, 2020.)
- Coronavirus outbreak raises question: Why are bat viruses so deadly? (R Sanders, University of California - Berkeley, February 10, 2020.)

The following sites track emerging diseases:
* CIDRAP -- the Center for Infectious Disease Research and Policy (University of Minnesota). I list specific CIDRAP sections for Ebola and Marburg, Influenza (Bird flu), Prions (BSE, CJD, etc), and SARS, MERS (coronaviruses). Other topic areas here include: Bioterrorism, Biosecurity (e.g., food), Food safety (foodborne illnesses, irradiation), and a miscellaneous section that includes SARS, West Nile, Mpox (Monkeypox), Chemical Terrorism. Useful for the general audience.
* Healthmap, a "Global disease alert map", presents disease reports by country. You can click on a map or chose from a list of countries. From J Brownstein, Harvard Medical School. Also in Arabic, Chinese, French, Portuguese, Russian, Spanish. Caution: loads very slowly.
* ProMED-mail is aimed at medical professionals, informing them about emerging diseases; it is one of the major primary sources underlying the sites listed above. Includes announcements and maps of outbreaks, as well as general information. From the International Society for Infectious Diseases. Parts of the site are also available in Chinese, Japanese, Portuguese, Russian, Spanish.

US government sites with information on emerging diseases:
* CDC.
* NIH.

Book. See the listing for Dorothy H Crawford, Deadly Companions - How microbes shaped our history (2007) on my page Books: Suggestions for general science reading. This book is about the relationship between microbes and man. It starts with a discussion of SARS, and discusses many emergences of the past. Good perspective.

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Ethical and social issues; the nature of science

I have expanded the title of this section, to more accurately show how it is being used. (May 2015)


Direct-to-consumer genetic testing. It's not (quite) practical yet to test your own genes, but it is practical -- and inexpensive -- to pay a company to do genetic tests for you. It has become quite a business. Here is a bioethics column with a skeptical view: Opinion: Consumer DNA Testing Is Crossing into Unethical Territories -- Data don't support many direct-to-consumer products, from telomere assessments to bespoke diets based on genetic sequences. (J D Loike, The Scientist, August 16, 2018. Now archived.) This is one person's view. As so often, it is best read for the questions it raises.

There are many posts in my Musings newsletter that deal with ethical and social issues. Some are broad; some deal with a single piece of work. Some deal with the process of doing science. Here are some of them...

* Briefly noted... How reliable are preprints? (October 26, 2022).
* Developing a monkey with a gene for a human brain protein (July 6, 2019).
* What can a brain do after death? (June 3, 2019).
* Antibiotic prophylaxis: a useful tool to reduce childhood mortality? (July 9, 2018).
* Comparing how true and false news stories spread (June 5, 2018).
* Identifying individuals from their genomes: a controversy (December 5, 2017).
* Zika fallout: Should pregnant women receive immunizations? (September 30, 2017).
* A tale of scientific reproducibility (September 27, 2017).
* Triparental embryos: the FDA and the regulatory dispute (September 12, 2017).
* Peer review of scientific articles -- by crowd reviewing? (June 26, 2017).
* A step toward doing cephalosomatic anastomosis in humans? (May 31, 2017).
* Scientific curiosity -- and politics (May 22, 2017).
* The boy with three parents -- an article is now published (May 17, 2017).
* The quality of science news (April 26, 2017).
* US Presidential candidates weigh in on science questions (October 18, 2016). Links to earlier posts about science and government.
* Tri-parental embryos: the first human birth (October 1, 2016).
* The Berkeley soda tax: does a "fat tax" work? (August 30, 2016).
* Security fences at national borders: implications for wildlife (August 29, 2016).
* The moral car: when is it ok for your car to kill you? (July 23, 2016).
* Women in science: How about at the highest level, the national academies? (April 12, 2016).
* Science myths (February 23, 2016).
* Early detection of brain damage in football players? A breakthrough, or not? (September 14, 2015).
* As we add human cells to the mouse brain, at what point ... (August 3, 2015).
* A new botulinum toxin -- and a story of how we deal with dangerous things (July 11, 2015).
* CRISPR and editing of the human germline: the ethical line? (May 4, 2015).
* On the testability of scientific models (March 14, 2015).
* Media hype about scientific articles: Who is responsible? (March 9, 2015).
* CRISPR: the legal battles begin (February 1, 2015).
* Do variable work schedules, such as shift work, affect cognitive performance? (December 2, 2014).
* Earthquake: Are the geologists responsible for the damage? (November 17, 2014).
* Science in progress. Science in doubt. Is STAP the latest great advance in stem cells -- or not? (July 28, 2014).
* Should physicists be allowed to use lead from ancient Roman shipwrecks? (December 2, 2013).
* Slavery - II (November 5, 2013).
* A new SARS-related virus seems to be emerging -- and an "ethics" story (February 4, 2013).
* Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).
* Who mismeasured man -- and why? (September 9, 2011).
* Medical ethics: pregnancy reduction (August 20, 2011).
* International relations: sharing flu viruses (May 28, 2011).
* US Army attacks colony collapse problem -- and an ethics story (October 25, 2010).
* A bio-ethics controversy: HIV-TB interaction (July 13, 2010).
* Let parents decide (May 14, 2010).
* The promise of science? (November 16, 2009).
* Personalized medicine: Getting your genes checked (October 27, 2009). This is an early post on personalized medicine. It includes an extensive list of related posts, some of which are relevant here. (Some of the relevant posts listed there are not repeated here.)

The following books related to this topic are listed on my page of Books: Suggestions for general science reading:
* Flexner, The Usefulness of Useless Knowledge. With an Introduction, The World of Tomorrow, by Dijkgraaf. 2017 (1939).
* Dreger, Galileo's Middle Finger -- Heretics, activists and the search for justice in science. 2015.
* Cromer, Uncommon Sense: The heretical nature of science. 1993.

As noted in the introductory materials, I intend the main emphasis here to be the scientific issues. Of course, other issues are important parts of the overall story. Some of the topic-specific resources listed include ethical and social issues. But occasionally, I may want to list a site that focuses on these matters.

Bloodlines: Technology Hits Home. The web site was written to accompany a PBS show. It broadly deals with issues arising from reproductive and genetic technologies, and includes interactive questions which you can try to evaluate for yourself.

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HIV-related posts in my Musings newsletter include...
* Briefly noted... A mutation that makes COVID worse protects against HIV (March 9, 2022).
* Why are some people "elite controllers" of HIV? (December 1, 2020).
* The CCR5 mutation that protects against HIV may be bad for people (June 17, 2019).
* Role of a receptor for HIV in stroke recovery (March 23, 2019).
* Genetic clues: Why some monkey species don't get "AIDS" upon infection with the immunodeficiency virus (March 26, 2018).
* Should we make antibodies to HIV in cows? (November 14, 2017).
* It's CRISPR vs HIV -- and HIV might win (April 17, 2016).
* Infant cured of HIV? Follow-up. (July 21, 2014).
* How HIV destroys the immune system (March 3, 2014).
* Infant cured of HIV? (April 15, 2013).
* A simpler assay for detecting low levels of HIV, using gold nanoparticles (January 3, 2013).
* How a drug can cause an autoimmune reaction (September 1, 2012).
* A novel approach to providing immunity to HIV (March 12, 2012).
* Why did the HIV vaccine work for some people? (September 27, 2011).
* A bio-ethics controversy: HIV-TB interaction (July 13, 2010).
* Why are HIV-infected people more susceptible to Salmonella infection? (May 21, 2010).
* HIV vaccine trial -- and quibbling about statistics (November 2, 2009). A broad source of HIV information, from NIH. Also available in Spanish.

The 2008 Nobel prize in Physiology or Medicine was awarded to Harald zur Hausen, "for his discovery of human papilloma viruses causing cervical cancer" and Francoise Barre-Sinoussi and Luc Montagnier, "for their discovery of human immunodeficiency virus". See the Nobel site: This item is listed on this page for HIV and HPV.

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Hormone replacement therapy

A major and continuing news story for 2002-3 was based on some long term studies of the use of replacement hormones by post-menopausal women. The results were not at all what had been commonly expected. One important general point from the story is the problem of knowing what long term effects of a treatment are, especially the smaller effects -- without doing long term studies with large numbers of patients. Lots of info, with regular updates, is available at the home page for the Women's Health Initiative: "The Women's Health Initiative (WHI) is a long-term national health study that focuses on strategies for preventing heart disease, breast and colorectal cancer and fracture in postmenopausal women. This 15-year project involves over 161,000 women ages 50-79, and is one of the most definitive, far reaching programs of research on women's health ever undertaken in the U.S. The purpose of this site is to provide WHI participants [and] others interested in the WHI findings a way of obtaining information about research results directly from the study."

And now, after five more years of data, the advice changes again. It is more detailed, more nuanced. This is common, and emphasizes that we must be cautious about over-interpreting any data set. News story, June 21, 2007, from Brigham and Women's Hospital and Harvard Medical School: "Estrogen Therapy and Coronary Artery Calcification. Women aged 50-59 who took estrogen show a reduced risk of coronary plaque buildup." Now archived.

For an introduction to the use of testosterone supplements in men, see a page from the US National Institute on Aging: NIA statement on IOM testosterone report, 11/12/03 (now archived).

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HPV (Human papillomavirus)

A new vaccine was announced recently. It is widely known by its trade name, Gardasil. It acts to prevent infection by some strains of the human papillomavirus, which cause cervical cancer and genital warts. The vaccine itself is indeed a product of modern biotechnology: it contains only viral proteins (produced in yeast), with no viral genome; thus it cannot grow at all. Here are some materials from the CDC about HPV and this vaccine:
* Human Papillomavirus. About HPV; includes vaccine.
* A more technical report: "Quadrivalent Human Papillomavirus Vaccine -- Recommendations of the Advisory Committee on Immunization Practices (ACIP)", by L E Markowitz et al, dated March 23, 2007. It provides background about the type of virus and its effects, and the nature of the vaccine.


There are many strains of HPV. Only some of them cause cancer or warts. The vaccine is effective against four of these strains. Data so far suggests that the vaccine is extremely effective against those four strains, but it is important to realize that strains other than those in the vaccine are responsible for some cancer. One might be confused by hearing that the virus is "100%" effective or "70%" effective. The former number refers to the apparent effectiveness against the strains included in the vaccine; the latter number refers to the overall effectiveness against cervical cancer, given that the current vaccine works against only some of the relevant strains.

Long term issues about this new vaccine are, of course, not known. For example, how long is it effective?

The May 10, 2007, issue of the New England Journal of Medicine contains several articles on this new vaccine -- with more data and perspectives. I suggest that readers start with two editorials, with differing views. Both are freely available online.
* L R Baden et al, Human papillomavirus vaccine - opportunity and challenge. N Engl J Med 356:1990, 5/10/07.
* G F Sawaya & K Smith-McCune, HPV vaccination - more answers, more questions. N Engl J Med 356:1991, 5/10/07.

The 2008 Nobel prize in Physiology or Medicine was awarded to Harald zur Hausen, "for his discovery of human papilloma viruses causing cervical cancer" and Francoise Barre-Sinoussi and Luc Montagnier, "for their discovery of human immunodeficiency virus". See the Nobel site: This item is listed on this page for HIV and HPV. It is also noted in a Musings post: Nobel prizes (October 8, 2008).

The main emphasis with HPV and cancer has been cervical cancer. However, there is increasing evidence that these viruses, probably the same strains, may cause other cancers. Here is one news story on this: HPV-Linked Oral Cancer In Men Increasing, Feb 4, 2008.

The traditional method of screening for cervical cancer is the pap smear, which looks for abnormal cells; in poor countries, little or no screening may be done. A new study suggests that it might be better to screen for the virus that causes the cancer. Their extensive testing shows that the test for the viral DNA is more effective than the pap smear. They argue that it is also likely to become inexpensive enough to be practical -- and worthwhile -- in poorer countries. A news story on this work: DNA Test Outperforms Pap Smear; April 6, 2009. The paper is: R Sankaranarayanan et al, HPV Screening for Cervical Cancer in Rural India. N Engl J Med 360:1385, April 2, 2009. Freely available at The article is accompanied by an editorial: M Schiffman & S Wacholder, From India to the World - A Better Way to Prevent Cervical Cancer. N Engl J Med 360:1453, April 2, 2009. Freely available at The editorial is a good overview of many issues surrounding cervical cancer.

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There are posts about malaria in my Musings newsletter. There are also some posts about other mosquitoes that transmit disease. Examples of these malaria or mosquito posts include:
* Briefly noted... The mosquito microbiome - inside and out (February 28, 2023). Update added March 20, 2024. Oldest mosquito fossils: bloodsucking males.
* Does the frog population affect the incidence of malaria? (October 17, 2022).
* Do mosquitoes remember encounters with sub-lethal levels of pesticides? (February 26, 2022).
* "Color vision" in mosquitoes? (February 12, 2022).
* An antibody to protect against getting malaria? (November 15, 2021).
* A trap to attract -- and kill -- mosquitoes (October 26, 2021).
* Wind-borne mosquitoes repopulate the Sahel semi-desert after the dry season (October 14, 2019).
* Biological control of mosquitoes, using a modified fungus (July 8, 2019).
* Artemisinin: an improved source? (June 4, 2019).
* What if we gave mosquitoes anti-malarial drugs? (April 7, 2019).
* What if one gave appetite-suppressing pills to mosquitoes? (March 15, 2019).
* Blocking eggshell formation in mosquitoes? (February 8, 2019).
* A mammalian device for repelling mosquitoes (December 10, 2018).
* Walter Clement Noel and his peculiar sickle-shaped blood cells (November 27, 2018).
* Monkey malaria in humans? (January 19, 2018).
* A mosquito map for the United States (October 3, 2017).
* Malaria and bone loss (September 10, 2017).
* A highly effective malaria vaccine -- follow-up (May 3, 2017).
* Malaria history (January 18, 2017).
* Can chickens prevent malaria? (August 12, 2016).
* Can Wolbachia reduce transmission of mosquito-borne diseases? 2. Malaria (June 17, 2016).
* How an American weed might interfere with control of malaria in Africa (November 13, 2015).
* A novel drug candidate that is active against all stages of the malaria parasite (October 10, 2015).
* Chikungunya in the Americas -- are vaccines near? (March 17, 2015).
* Why don't black African mosquitoes bite humans? (December 19, 2014).
* Pop goes the hemozoin: the bubble test for malaria (January 24, 2014).
* A vaccine against malaria -- with 100% efficacy? (October 20, 2013).
* Malaria-infected mosquitoes have greater attraction for people (May 28, 2013).
* An easier way to get infected with malaria (January 18, 2013).
* Checking mosquito saliva (November 19, 2010).
* Using genetically engineered mosquitoes in the real world (October 18, 2010).
* Genes that protect against malaria (January 19, 2010). Discusses resistance both to Plasmodium falciparum and to P vivax.
* Some fun reading: Fuel cell gadget and growing diesel (December 13, 2008). Among other things, this post introduces Keasling's work to make the anti-malaria drug artemisinin.

Malaria is one of the world's great killers. Recent years have seen the analysis of the genome of both the malaria parasite itself and its mosquito vector. Nature has posted a "web focus" on the diverse aspects of this disease, 2008.

A UC Berkeley group led by Jay Keasling is working on production of artemisinin, a new type of anti-malarial drug, in microbes (bacteria and yeast).
* Here is a campus news story on the funding of this project by the Gates Foundation: "QB3 + Gates' millions = a cure? Helped by Microsoft's founder, Jay Keasling and his industry partners hope to create an inexpensive treatment for malaria". January 12, 2005.
* A status report -- a news story, June 4, 2008. "Synthetic yeast to brew up vital malaria drug."
This group of items is also listed for Organic/Biochemistry Internet resources: Alkenes. It is also noted in the Synthetic biology section of this page.


Synthetic biology's first malaria drug meets market resistance. A news story: M Peplow, Nature 530:389, February 23, 2016.

Malaria drug made in yeast causes market ferment. A news story: Nature 494:160, February 14, 2013.

Malaria Vaccine Initiative (MVI).

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Posts in my Musings newsletter about measles and related matters include:
* The measles vaccine: What does it protect against? (June 6, 2015).
* Fallout from the Ebola outbreak: more measles? (April 28, 2015).
* What if Mickey Mouse got measles? (January 27, 2015).
* Silk: Stabilizing vaccines and drugs (July 29, 2012).
* Another disease has been eradicated. GREP (February 2, 2010). This is about the eradication of rinderpest, a cattle disease related to measles.

Measles history. Scientists have reported sequencing a measles virus genome recovered from a hundred-year old tissue sample. It is not only the oldest genome sequence for this virus, but also the oldest for any RNA virus that infects humans. Taken along with other data, it suggests that human measles split off from bovine rinderpest about 2500 years ago, more than a thousand years earlier than previous estimates. (That is when the viruses diverged. The date of first human infection must be more recent, and is not known.)
* News story: Measles Virus Much Older Than Previously Thought - Genome Sequenced From Century-Old Diseased Lung. (SciTechDaily (KU Leuven), June 28, 2020.) Links to the article.

In some ways measles would seem to be a good target for eradication. It occurs only in humans, so there is no need to worry about animal reservoirs. A good vaccine is available. Yet measles remains a major killer. One key reason is that the virus is highly infectious, thus a very high level of population immunity is needed to block its transmission. The following article is a good readable discussion of the issues of measles, its vaccine, and the difficulty of eradicating this disease. D E Griffin & W J Moss, Can We Eradicate Measles? Microbe 1:409, 9/06. Click on the first item there.

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There are posts about polio and polio-like conditions on my Musings newsletter pages. These include:
* An enteric virus has acquired the ability to infect neurons; relevance to emerging polio-like illness? (October 22, 2018).
* An improved polio vaccine? (February 6, 2016).
* Polio eradication: And then there were two (July 27, 2015).
* Chikungunya in the Americas -- are vaccines near? (March 17, 2015).
* Polio-like disease without polio virus? Follow-up (February 11, 2015).
* Polio: Another country may be getting close to eradication (December 8, 2014).
* WHO certifies "South-East Asia" free of polio (November 1, 2014).
* Polio-like disease without polio virus? (March 17, 2014).
* Polio eradication: And then there were three (March 27, 2012).
* Poliovirus eradication: an update, with some good news and some bad news (May 22, 2011).
* Polio: progress toward eradication (November 5, 2010). This discusses the three types of polio viruses (PV), and the merits of using vaccines that lack Type 2 PV.
* Making a wimpy virus (July 23, 2008).

For a site that has current numbers of polio cases by country (and virus type), for this year and last: Polio now. From the Global Polio Eradication Initiative; updated weekly.

A book listed on my page of Book Suggestions... The Cutter Incident: How America's First Polio Vaccine Led to the Growing Vaccine Crisis. The book, by Paul Offit, 2005, is on historical aspects of polio vaccine, focusing on the Cutter incident, involving defective batches of vaccine.

Whatever happened to polio? A history site from the Smithsonian Institution, posted to coincide with the 50th anniversary of the first polio vaccine. Includes information on the current effort to eradicate polio. (February 2024... The site seems to be in transition. It does include a link to an archived version.)

A report from the Institute of Medicine (IOM)... K Stratton et al, Immunization safety review: SV40 Contamination of Polio Vaccine and Cancer, October 2002. Some early batches of the original polio vaccine (the Salk vaccine, with killed virus) were later found to be contaminated with the virus SV40 (which was not killed by the treatment used to kill the poliovirus). SV40 may be a cancer-causing virus. So, inadvertently, we have been running a big test on whether it causes cancer in humans. A long enough time has passed that it is rather clear there is no big problem. Some data has suggested increases in certain very rare cancers. This report analyzes what is known. One of the frustrations, inherent in an accidental test, is that the data is not kept very well. This is an interesting story, but I do suggest you read it for the message about how things should be done, and not try to make SV40 into a big problem.

Nature web focus: End of polio - the final assault. (September 2004)

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Protein Folding -- and diseases

Also see the following, which deal with specific diseases that involve protein folding:
* Alzheimer's disease (a section of this page);
* Prions (BSE, CJD, etc.) (a separate BITN page).

This topic was suggested by a student. It was stimulated in part by the Sept 8, 2003, issue of The Scientist, including a feature article by P Hunter, Protein Folding: Theory meets disease, p 24: (Now archived.)

There are several issues here. The general topic of how proteins fold has long fascinated -- and frustrated -- biologists. But the topic has taken on greater significance with the increasing recognition of how relevant the protein folding problem is to disease. In fact, a good place to start with the Hunter article, listed above, is the side-bar on p 25, "Miss a fold, prompt a disease." Many cases are now known where we realize that the main effect of a mutation that causes a disease is to interfere with protein folding. For example, the major mutation found in cystic fibrosis is of this type. Once/if the mutant protein manages to fold, it works fine, but the mutation greatly slows the folding process.

Another type of folding-disease connection is illustrated by the prions. Although our understanding of prions is still incomplete, it seems that the prion proteins have two stable forms. One is the normal form of the protein, in your cells, and the other form causes disease. See the Prions (BSE, CJD, etc.) page for more.

A classic experiment in the history of studying protein folding was done by Christian Anfinsen, around 1960. Anfinsen showed that a protein could fold up properly in vitro, without any external source of "information" on how to fold. This established the paradigm that the 3D shape of a protein follows from its amino acid sequence. Although there are some nuances, this still underlies our modern understanding of protein folding. Anfinsen shared the 1972 Nobel prize for Chemistry "for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation". See the Nobel site:

A nice review and update on protein folding... K A Dill & J L MacCallum, The Protein-Folding Problem, 50 Years On. Science 338:1042, November 23, 2012. The "50 years" of the title refers to the 1962 Nobel prize to Perutz and Kendrew for the first solved protein structures:

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RNAi (RNA interference or silencing)

Natural small RNA molecules act as gene regulators. Similarly, synthetic small RNA molecules may be useful to biologists to probe gene function -- and may be useful as therapeutic agents. This is a new field. Particularly with regard to actual therapeutic use, there is much promise but little information. Two articles in the March 29, 2004, issue of The Scientist provide a good introduction and overview. The articles are A Adams, RNAi inches toward the clinic (p 32), and A Constans, Concocting a knock-out punch for HIV-1 (p 28). &

The first is available from the archive:

The Scientist for September 2004 (Vol 18 #17) has the feature topic of RNAi, with multiple articles: Again, an excellent introduction and overview.

The idea of using an inhibitory RNA as a therapeutic is simple enough, but there are many technical hurdles. Here is a report of targeting an siRNA (small interfering RNA) to the brain -- by using a protein from rabies virus. Rabies infects the nervous system, and the scientists exploit one part of that virus to deliver the therapeutic RNA across the blood brain barrier. The therapeutic RNA attached to the rabies virus delivery system protects the mice from an experimental viral infection of the brain. Press release, from NIH, June 17, 2007: Blood-Brain Barrier Breached by New Therapeutic Strategy. (Now archived.) The work was published: P Kumar et al, Transvascular delivery of small interfering RNA to the central nervous system . Nature 448:39, 7/5/07. Accompanying news story: E M Cantin & J J Rossi, Molecular medicine: Entry granted. Nature 448:33, 7/5/07.

The 2006 Nobel prize for physiology or medicine was awarded to Andrew Z Fire and Craig C Mello for their discovery of "RNA interference - gene silencing by double-stranded RNA".

See the BITN page Prions (BSE, CJD, etc): Treatment for a paper on the possible use of RNAi to treat a prion disease.

See the BITN page Agricultural biotechnology (GM foods): Recent items for a paper on the use of RNAi, targeted to the seeds, to reduce production of a toxic chemical in cotton seeds.

Nature has a web focus site on this topic. Of particular interest may be a set of animations of how the process works:

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SARS, MERS (coronaviruses)

Information on the SARS-2 virus, causing COVID-19, was added starting January 2020.

The new coronavirus. The big medical story of the new year. (The outbreak began in late 2019.) There is a daily barrage of news, some straightforward, some confusing or even contradictory. The new virus, a coronavirus, is related to those that cause SARS and MERS. The disease is similar, and some of the news is eerily similar to the SARS story of two decades ago. The new disease probably got to humans via markets dealing in live animals, and it is being transmitted worldwide via airplanes.

* The US CDC (Centers for Disease Control and Prevention) has established a page for the new virus: 2019 Novel Coronavirus (2019-nCoV). An excellent official source of information, much of it intended for healthcare workers.

* For the latest, I recommend CIDRAP. They have an update almost every day. Their pages are well-written, and include links to their sources. The CIDRAP page for this disease is You can also sign up for their daily e-mail.

* Official names for the new coronavirus and its disease. The temporary name of the virus has been nCoV (for novel coronavirus). Now, officially... The virus is SARS-CoV-2. The disease is COVID-19; I suspect that COVID stands for COrona VIrus Disease.

There are posts about coronaviruses in my Musings newsletter. They include...
* Added June 7, 2023. Briefly noted... Might the doctor's politics affect how they treat COVID? (June 7, 2023).
* Briefly noted... Making carbon nanotubes out of waste face masks (December 7, 2022).
* How the SARS-2 virus causes heart damage: lessons from fruit flies (November 12, 2022).
* Briefly noted... How reliable are preprints? (October 26, 2022).
* Production of aerosols by the winds of the Philadelphia Orchestra (October 24, 2022).
* COVID and cardiovascular events (blood clots) (October 3, 2022).
* Making decoys that trap the SARS-2 virus (August 10, 2022).
* Inhibiting the TMPRSS in your nose to protect against respiratory viruses (COVID, flu) (July 11, 2022).
* Briefly noted... COVID and pets? (June 22, 2022).
* Effect of the COVID pandemic on the incidence of dengue (May 24, 2022).
* Air filters that can kill (March 19, 2022).
* Targeted degradation of the viral genome as a treatment for COVID? (March 13, 2022).
* Briefly noted... A mutation that makes COVID worse protects against HIV (March 9, 2022).
* Briefly noted... An mRNA vaccine against COVID-19 that didn't work well -- why? (November 10, 2021).
* A novel sensor for infectious viruses, using nanopores lined with aptamers (November 6, 2021).
* Briefly noted... mRNA vaccine history (November 3, 2021). Update added October 5, 2023.
* Briefly noted... The Merck drug for COVID (October 27, 2021).
* Briefly noted... Are birthdays a risk factor for COVID-19? (October 6, 2021).
* Briefly noted... The infection process for the SARS-2 (COVID-19) virus (September 8, 2021).
* A senolytic treatment for severe COVID (August 21, 2021).
* Briefly noted... Vitamin D and COVID-19? (June 23, 2021).
* When did the SARS-2 (COVID-19) virus arise? A window into how a zoonosis starts (June 22, 2021).
* Can you detect the SARS-2 virus with your phone? (March 2, 2021).
* Susceptibility to severe COVID: role of a genetic region from Neandertals (February 20, 2021).
* UV LEDs for the inactivation of viruses? (January 11, 2021).
* Seismologists report that Earth is quieter because of COVID-19 (October 19, 2020).
* How bad will the upcoming COVID-era winter flu season be? (September 25, 2020).
* Briefly noted... Improved ventilation to reduce COVID transmission (September 23, 2020). Update added April 17, 2024: Improving ventilation reduces COVID.
* COVID-19: How well does the virus replicate in children? (September 6, 2020).
* Could we treat COVID by driving it to an error catastrophe? (June 30, 2020).
* Does post-exposure administration of hydroxychloroquine prevent Covid-19? A clinical trial (June 16, 2020).
* Speech droplets: Can you transmit an infection to someone by yelling "Stay healthy" at them? (June 14, 2020). This post contains no work with viruses, but is done within the context of COVID transmission.
* Spike D614G: An emerging mutant strain of the virus that causes COVID-19 (May 12, 2020).
* Prions in camels? (June 18, 2018). Mentions MERS.
* The origin of SARS: getting closer (February 6, 2018).
* Bats and the coronavirus reservoirs (July 25, 2017).
* A MERS vaccine, for camels (January 22, 2016).
* How the MERS virus spread in Korea: role of super-spreaders (November 3, 2015).
* Camels and the transmission of MERS: blame the kids? (March 30, 2015).
* Do camels transmit MERS to humans? (January 21, 2015).
* A broad-spectrum antiviral drug candidate that may be active against Ebola, MERS, and more (October 18, 2014).
* MERS in the United States (May 18, 2014).
* Bats and the origin of SARS (January 25, 2014).
* Where is the MERS virus coming from? (September 22, 2013).
* A new SARS-related virus seems to be emerging -- and an "ethics" story (February 4, 2013).

See Emerging diseases section, above, for perspective.

This section is now being used for items on the following viral infections:
* SARS (Severe acute respiratory syndrome)
* MERS (Middle East respiratory syndrome)
* SARS-2, causing COVID-19. Also known as 2019-nCoV (2019 novel coronavirus).
These diseases are caused by members of the coronavirus family. SARS was first reported in 2002, and was prominent in 2003; no cases have been reported since 2004. MERS appeared in 2012 and is still active into 2020 at this writing. 2019-nCoV appeared at the tail end of 2019, and is a developing story.

* * * * *


This sub-section includes items posted during the COVID-19 outbreak. Some include work on other coronaviruses.

When did COVID-19 come to the United States? The common story is that the first case was reported in China in late December 2019. The first known case in the US is from late January 2020. However, there have been several reports suggesting that there may have been earlier cases -- in various places around the world. We now have an article reporting that some blood samples obtained in the US during mid-December 2019 (and into mid-January 2020), from routine blood donations, contained antibodies to the SARS-2 virus; positives were found among the samples from all states examined. The significance of such findings is open. It is possible that the observed antibodies originated as a response to some other coronavirus. The authors present evidence against this, but it is not conclusive. It is also possible that we still do not understand the origin and early spread of this virus. COVID mysteries abound -- and remain.
* News story: COVID-19 Possibly Arrived in the U.S. in Dec. 2019. (Carolyn Crist, WebMD, December 3, 2020. Now archived.)
* The article, which is open access: Serologic Testing of US Blood Donations to Identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-Reactive Antibodies: December 2019-January 2020. (Sridhar V Basavaraju et al, Clinical Infectious Diseases 72:e1004, June 15, 2021.)
* More about the early history of the virus: When did the SARS-2 (COVID-19) virus arise? A window into how a zoonosis starts (June 22, 2021).

mRNA vaccines. They have been in the news because of the announcements of results for vaccines against COVID-19. Using mRNA to make protein is normal biology. Using mRNA for vaccines has a big appeal: ease of making new versions. However, there have bean technical hurdles, and earlier work gave mixed results. A recent news story provides a nice overview of mRNA vaccines.
* News story: The Promise of mRNA Vaccines -- Long before Moderna and Pfizer's COVID-19 shots, scientists had been considering the use of genetically encoded vaccines in the fight against infectious diseases, cancer, and more. (Diana Kwon, The Scientist, November 25, 2020.) Now archived.
* This item is also noted in the section Vaccines (general).

Why some people get the severe form of COVID -- an interferon clue. Severe COVID seems to be due to an improper response of the immune system. A pair of recent articles provide evidence that about 15% of those with severe COVID have one or another defect in the interferon response. Some have mutations in one of the genes of that system, and some have antibodies to the interferons. Possible implications... People could be screened for their chances of developing severe COVID; the interferons could be useful therapeutically. Further work may well uncover other factors that predict severe COVID.
* One tidbit... Excessive anti-interferon antibodies are found mainly in men. Why is not known, but it does correlate with men having a much higher level of severe COVID.
* News story: Immunity gene mutations and autoantibodies linked to severe COVID-19. (M Krause, BioNews, September 28, 2020.) Links to two other good news stories. Links to the two articles, from the same lab and published together. Both are freely available. Caution, they are complex articles.
* A post about another analysis of a cytokine storm: How does "cytokine storm" work? (April 28, 2020).

Dexamethasone: first drug shown to reduce mortality due to COVID-19 -- and an important caveat.
*** This item was originally posted based on a preprint, prior to peer review. The published article is now included below. Otherwise, the post is largely the original version. ***
It was headline news a few days ago, based simply on a press release. A preprint of the article is now available, prior to peer review. Let's note it. The key finding is that a common anti-inflammatory drug reduces deaths in people with severe COVID-19, especially those on ventilators.
* The caveat is that the drug is probably not appropriate for those with ordinary or mild COVID. The drug reduces the body's response to the virus. During an ordinary infection, that is bad, and the drug could be harmful. But severe COVID may be due to an excessive inflammatory response (a cytokine storm), and reducing the body response may be good. The current work actually shows a small increase in deaths for those with less severe infections who were given the drug. That did not test as significant here, but it is important for further work to dissect the effect of this drug by disease severity.
* Any single article has limitations, and this one is not even a published article at this point. Nevertheless, it appears to be an exciting result, which will get serious follow-up. But it is important to distinguish its effects on the two stages of COVID-19.
* News stories:
- Insight into Dexamethasone's Benefits in Severe COVID-19 -- The steroid's exceptional performance in early results from the RECOVERY clinical trial in the United Kingdom is a rational outcome of the drug's anti-inflammatory effects, experts say. (A Olena, The Scientist, June 19, 2020. Now archived.) Links to the article, which is freely available as a preprint (not peer-reviewed).
- Breakthrough Drug for Covid-19 May Be Risky for Mild Cases. (R C Rabin, New York Times, June 24, 2020.)
* Update March 15, 2021... The article has now been published, and is accompanied by two editorials. All should be freely available, at least temporarily.
- Editorial #1 accompanying the article: Research in the Context of a Pandemic. (H C Lane & A S Fauci, New England Journal of Medicine 384:755, February 25, 2021.)
- Editorial #2 accompanying the article: The RECOVERY Platform. (S-L T Normand, New England Journal of Medicine 384:757, February 25, 2021.)
- The article: Dexamethasone in Hospitalized Patients with Covid-19 -- Preliminary Report. (RECOVERY Collaborative Group, New England Journal of Medicine 384:693, February 25, 2021.) For a quick overview of the results, separated by disease severity, see Figure 3 (page 8 of the pdf).

Coronavirus history -- and a possible human CoV pandemic around 1890. This item has two purposes. First, it starts with a news feature story, for an interesting overview of the SARS-2 virus, with some historical perspective on coronaviruses. But it also raises a specific point that deserves note. Toward the end, the author talks about a possible major human coronavirus incident around 1890. I checked the 2005 article referred to. It reports the genome sequence of a well known human coronavirus, one that causes colds. Comparison of the sequence with that of other coronaviruses suggests it arose from a virus in cows about 1890. Interestingly, there was a major incident of respiratory disease about that time. It is commonly attributed to influenza; however, it predates the discovery of viruses, so there is no real information available about the cause. In the Discussion section of the article, the authors speculate that it might have been due to the emergent coronavirus, not yet adapted to humans. There is no evidence to support this speculation, just the coincidence of timing. Is it possible that evidence might be forthcoming? I don't know. I offer it here for fun; it is not "fact". It also illustrates how one needs to be careful with an intriguing point made in a secondary source.
* News feature: Profile of a killer: the complex biology powering the coronavirus pandemic. Scientists are piecing together how SARS-CoV-2 operates, where it came from and what it might do next -- but pressing questions remain about the source of COVID-19. (D Cyranoski, Nature, May 4, 2020. In print: Nature 581:22, May 7, 2020.) A good overview of the SARS-2 story. And it notes the possibility that an 1890 disease was due to an emerging human coronavirus.
* The article that is the source of the point that an 1890 event might have been due to a coronavirus; it is freely available: Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event. (L Vijgen et al, Journal of Virology 79:1595, February 2005.) This is reference 11 of the news feature listed above. It is fine to skip down to the Discussion section to read about their speculation about the 1890 outbreak.

COVID article retractions (one on hydroxychloroquine). It was a big news story in late May... A big study, published in a top medical journal. Hydroxychloroquine is ineffective at treating COVID-19, and is dangerous. A few days later the article was retracted -- because of concerns about the data source used for the study. (Another article based on the same data source was also retracted.) It is a strange story. If there is any good news in this, it is that science is self-correcting -- even if awkwardly. Unfortunately, the article got broad attention upon publication, and its retraction got less attention. Treatment of COVID is a hot topic, politicized or not. There is considerable effort to expedite new findings being made available, to scientists and to the public. It is inevitable that some bad science will make its way through the system, but it is confusing.
* News story: Lancet, NEJM Retract Surgisphere Studies on COVID-19 Patients. (C Offord, The Scientist, June 4, 2020.) Now archived.

Does chloroquine work against the virus that causes COVID-19? The question has been in the news (partly because some prominent but not necessarily well-informed people have voiced opinions). What's the real story? There are hints that it might work, but there is very little actual testing in humans at this point. Chloroquine is well-known as a drug against malaria. That means much is known about it, including its safety profile (which is not simple). But how it works against a coronavirus will be entirely different than how it works against malaria, so that part of the experience doesn't help. A news story from last week provides a good summary of this interesting but incomplete story.
* News story: Chloroquine for COVID-19: Cutting Through the Hype. (C Baraniuk, The Scientist, March 20, 2020. Now archived.) Links to some articles, but the big message is that the question remains open.

Origin of the virus. This came up in a private discussion. Turns out that Nature just did a nice news summary of the current status of investigating that question (as of the end of February). The virus is apparently new to humans. It probably originated in bats, but got to humans via an intermediate host. Can we get more specific? The approach is to sequence the genomes for many viral samples, and compare them with what is in the databases. As of this news story, there is no clear answer, but the story is a nice overview of how things are done, as well as the current uncertainty.
* News story: Mystery deepens over animal source of coronavirus -- Pangolins are a prime suspect, but a slew of genetic analyses has yet to find conclusive proof. (D Cyranoski, Nature, February 26, 2020. In print: Nature 579:18, March 5, 2020.)

Survival of coronaviruses on surfaces; how to kill them. A new article summarizes what is known about how well coronaviruses survive on surfaces, and about methods for disinfection. The analysis, based on a literature review, includes a range of coronaviruses, but there is no specific data for the new virus (but see #3, immediately below). Not surprisingly, results vary; they depend on the type of surface as well as conditions such as temperature and humidity. In some cases, these viruses can survive for extended periods (several days) on surfaces. They are also easily killed by common disinfecting agents.
* For reference... A 12-hour half-life (in the range found under some conditions) means that the virus level is reduced only 16-fold after two days. It would take 5 days for the virus level to drop by 1000-fold, a common (but arbitrary) cut-off for cleaning. (Those estimates assume first-order (exponential) killing. Real data typically looks close to first-order.)
* A very short journal article, freely available, with a summary of the findings... Potential role of inanimate surfaces for the spread of coronaviruses and their inactivation with disinfectant agents. (G Kampf, Infection Prevention in Practice 2:100044, June 2020.) Reference 7 of this article is a more complete version, with tables and full references. You can link to it directly from the reference list; it may be freely available.

Survival of the COVID-19 virus on surfaces. As I was writing up these items I became aware of a preprint that provides some data specifically for the new virus. The general approach was to compare survival of the original SARS-1 and the new SARS-2 (COVID-19) viruses under various conditions. The general result is that they show similar survival.
* Preprint (my original source; not peer-reviewed): Aerosol and surface stability of HCoV-19 (SARS-CoV-6 2) compared to SARS-CoV-1. (N van Doremalen et al, March 13, 2020 -- date of posting preprint at medRxiv.)
* Published article: Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. (N van Doremalen et al, New England Journal of Medicine 382:1564, April 16, 2020.) It is probably freely available, though that may be temporary.

A reminder... My pages are intended to present scientific developments and to give resources. I do not give medical advice.

* * * * *


This sub-section includes some general resources. Some include COVID-19 sections. There are also some older items, from earlier coronavirus outbreaks.

The web site of the US Centers for Disease Control (CDC) is a good site to keep abreast of these diseases -- and of course of other diseases.
* The CDC SARS page:
* The CDC MERS page: The page links to information about MERS in Spanish and Arabic.
* The CDC page for the 2019 novel coronavirus (2019-nCoV):

The CDC site has links to all local and state public health departments, and also includes travel advisories.

CIDRAP is a good independent news source on infectious diseases. CIDRAP pages for this topic:
* The CIDRAP SARS page:
* The CIDRAP MERS page:
* The CIDRAP page for COVID-19:

SARS Reference, a free online SARS "textbook", from B S Kamps & C Hoffmann. The final version is archived at Also available in Chinese, French, Greek, Italian, Portuguese, Romanian, Spanish, Vietnamese. Also see next item.

COVID Reference, a free online COVID "textbook", from C Hoffmann, R Camp & B S Kamps. Yes, it is a spin-off of the previous item. The final version is at Scroll down to part 2. Available in several languages.

Nature magazine's "web focus" on SARS: This set seems to be freely available.

In July 2003, Nature published a "news feature" called "SARS - What have we learned?" It is in the form of a series of questions, with answers, about various aspects of the SARS story. Among the questions... Was the fuss overblown? Are we prepared for the next viral threat? Where did the SARS virus come from? What about a vaccine? Very readable overview and update. Nature 424:123, 7/10/03; also available at the top of their web focus page, listed above.

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Smallpox (poxviruses)

July 2022... The scope of this section has been expanded, to include pox viruses in general. The current interest in Mpox is the immediate motivation.

The title of the section has been changed to reflect the change. (Some references to the section may use the earlier name, but such references should always start with 'smallpox'.)

The chicken pox virus is actually not a member of the pox family. It is a herpes virus. The site provides a wide range of information, including much history. Some materials are also available here in Spanish.

Mpox (Monkeypox): general resources.
* Mpox. Official information from the US CDC.
* Mpox. CIDRAP. Excellent, as usual for this source. Includes excellent news coverage.

Among posts in my Musings newsletter that mention smallpox or other pox viruses, including strains used for various kinds of vaccines...
* A MERS vaccine, for camels (January 22, 2016).
* Another disease has been eradicated. GREP. (February 2, 2010).

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Sudden Oak Death A range of information, both for the consumer and the scientist. The site is from UC Berkeley.

Sudden larch death (SLD) is due to the same pathogen. Some information on the spread of SLD in Europe is included at this site. Just search on larch.

Posts in my Musings newsletter about SOD and related diseases include:
* The quality of citizen science: the SOD Blitz (September 28, 2015).
* The Irish potato blight was caused by a related organism, another oomycete of the genus Phytophthora. Tracking the pathogen of the Irish potato blight (June 25, 2013).

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Synthetic biology

A nice overview of the field of synthetic biology. M Stone, Life redesigned to suit the engineering crowd. Microbe 1:566, 12/06. Free online:

Craig Venter, of genome sequencing fame, plans to make new organisms. One key step along the way was to take a small bacterium, and determine how many of its -- already small -- gene set are really needed. This sets the stage for making artificial genomes -- and then for designing new organisms to do specific tasks. News has been coming fast and furious from the Venter lab; I list some of the news coverage and some of their own press releases below.

Good news stories:
* Genetic engineers who don't just tinker (7/8/07).
* Tycoon's team finds fewest number of genes needed for life (6/8/07).

Press releases from the J Craig Venter Institute:
* First Self-Replicating Synthetic Bacterial Cell (5/20/10). (Now archived.) Since the terms "synthetic" or "artificial" cells are ambiguous and subject to hype, we should be clear what is accomplished here. They made a synthetic genome; that is, they assembled a new genome without using any natural DNA. They then transplanted this into an existing cell, and the new genome "took over". In this case, the synthetic genome is (substantially) identical to a known genome. That is, this work is proof of principle that a new genome can be made and used.
* Synthetic bacterial genome (1/24/08). (Now archived.)
* JCVI scientists publish first bacterial genome transplantation changing one species to another (6/28/07). (Now archived.)

Jay Keasling's work, at UC Berkeley, to develop a cheaper way to make the anti-malarial drug artemisinin is noted in the Malaria section of this page. The work involves making major changes in the metabolic capabilities of the microbes, and is considered synthetic biology.

A related post in my Musings newsletter... What is the minimal set of genes needed to make a bacterial cell? (July 9, 2016). From the Venter Institute.

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TGN1412: The clinical trial disaster

March 2006. The news media carried a story of a clinical trial gone terribly wrong. Within an hour or so of receiving a drug, all recipients were seriously ill. What happened? Was there some mix-up -- perhaps the wrong drug used? Was the trial not properly planned or executed? Or was this just "one of those things" -- showing why we start with a small test in humans? So far, the evidence suggests that the last possibility is correct. Everything seems to have been done properly. However, given the severe result in this case, people are questioning whether "properly" was good enough. Was there reason to have been more cautious in this case -- more cautious than just following standard procedure? Perhaps -- and people are debating this. The drug was of a new type, one about which we know little, and about which some are very concerned -- despite the good data from animal tests. It is clear that even a simple precaution, of giving the drug to one patient at a time, and watching them for an hour or two, would have been much better in this case.

As to the nature of the drug, it is hard to describe briefly. But a simple start would be that it was designed to stimulate the immune system -- and the problem is that it did so inappropriately in the human subjects.

The analysis of the incident is still in progress. However, some information is now appearing in the literature, so it seems appropriate to share that here. I do encourage people to be cautious in reaching conclusions at this point.

The New England Journal of Medicine published three articles in the September 7 issue on this topic. In the order listed below: one is a perspective (an overview discussion of the topic), one is the main scientific report, and one is a commentary. All are freely available online. For most people, the first item listed below -- the perspective -- may be the best place to start.
* A H Sharpe & A K Abbas, Perspective: T-Cell Costimulation - Biology, Therapeutic Potential, and Challenges. New England Journal of Medicine 355:973, 9/7/06.
* G Suntharalingam et al, Cytokine Storm in a Phase 1 Trial of the Anti-CD28 Monoclonal Antibody TGN1412. New England Journal of Medicine 355:1018, 9/7/06.
* J M Drazen, Commentary: Volunteers at Risk. New England Journal of Medicine 355:1060, 9/7/06.

There is also a government report on the incident. I might cynically comment that it reads like a government report. Nevertheless, browsing it may be useful, at least as a guide to the questions that get raised. The final report (December 2006) is archived at (The link to the preliminary version of the report at the end of the Drazen article listed above is now a dead link.)

A Musings post about a clinical trial that is proceeding cautiously. The caution here follows from the TGN1412 disaster. CRISPR: First clinical trial in humans (November 28, 2016).

A post in my Musings newsletter about another clinical trial that went bad because the animal testing did not reveal an important toxicity: A better mouse -- it has a humanized liver (August 12, 2014). That example is quite different from this one; the test discussed there would not have helped here.

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Vaccines (general)

A general comment and caution... Vaccines seem to be the subject of many controversies. But be particularly careful with any arguments that appear to make criticism of vaccines in general. The diseases against which we have vaccines are diverse, and the vaccines are diverse. Most real vaccine issues are specific to a particular vaccine or type of vaccine.

This section is mainly for sources about vaccines in general, or sources with info about many vaccines. Also see sections for individual diseases for info about specific vaccines. For example, the sections on Anthrax, Dengue virus (and miscellaneous flaviviruses), Ebola, HIV (AIDS), HPV (Human papillomavirus), Malaria, Measles, Polio, SARS, MERS (coronaviruses), Smallpox, and West Nile Virus contain info on vaccines for those diseases. An item listed under Cancer deals with making personalized vaccines in plants.

My Musings newsletter includes posts on vaccines. Examples of posts on general vaccine issues, or on vaccines for diseases not listed above...
* Added June 14, 2023. Briefly noted... Can we make good vaccines and spare the sharks? (June 14, 2023).
* Sleep deprivation and vaccine effectiveness (March 27, 2023).
* Self-boosting vaccines? (August 26, 2022).
* A gastric auto-injector, which gives shots in the stomach lining (January 24, 2022).
* Briefly noted... mRNA vaccine history (November 3, 2021). Update added October 5, 2023.
* Printing microneedle patches for vaccine delivery to the skin (October 5, 2021).
* A vaccine against asthma? (July 3, 2021).
* A better strategy for distributing rabies vaccine? (April 26, 2021).
* An improved procedure for vaccination against tuberculosis? (March 13, 2020).
* A new vaccine against tuberculosis? (November 9, 2018).
* Dengue vaccine: a step backwards? (December 6, 2017).
* Zika fallout: Should pregnant women receive immunizations? (September 30, 2017).
* Clinical trial of self-administered patch for flu immunization (July 31, 2017).
* The nasal spray flu vaccine: it works in the UK (April 12, 2017).
* Is it worthwhile to require flu vaccination for health care workers? (March 6, 2017).
* A quick-response system for making new vaccines (September 24, 2016).
* Why vaccine effectiveness may vary: role of gut microbiome? (February 27, 2015).
* Dengue vaccine follow-up: Phase 3 trial (September 15, 2014).
* Rotavirus: passive immunization via food (January 10, 2014). This involves a rice that has been modified to produce an antibody against the virus.
* A dengue vaccine trial (December 1, 2012).
* Does it matter what time of day you get a vaccine? (October 26, 2012).
* Silk: Stabilizing vaccines and drugs (July 29, 2012).
* Aerospace engineers develop explosive device for supersonic delivery of vaccines (August 2, 2011).
* A better way to deliver a vaccine? (July 25, 2010).

mRNA vaccines. They have been in the news because of the announcements of results for vaccines against COVID-19. Using mRNA to make protein is normal biology. Using mRNA for vaccines has a big appeal: ease of making new versions. However, there have bean technical hurdles, and earlier work gave mixed results. A recent news story provides a nice overview of mRNA vaccines.
* News story: The Promise of mRNA Vaccines -- Long before Moderna and Pfizer's COVID-19 shots, scientists had been considering the use of genetically encoded vaccines in the fight against infectious diseases, cancer, and more. (Diana Kwon, The Scientist, November 25, 2020.) Now archived.
* This item is also noted in the section SARS, MERS (coronaviruses).

Vaccine against African swine fever (ASF). ASF is a viral disease that has recently become of serious economic importance. We now have a preprint reporting a vaccine that is highly effective against the major strain in current Eurasian outbreaks. I suggest reading the abstract and introduction for an overview.
* Here is the preprint, which is freely available: Development of a highly effective African swine fever virus vaccine by deletion of the I177L gene results in sterile immunity against the current epidemic Eurasia strain. (M V Borca et al, BioRxiv, December 2, 2019.)
* A news story: Sterile immunity possible against ASFv, US scientists say. (V ter Beek, Pig Progress, December 9, 2019.)
* Here is the published article: Development of a Highly Effective African Swine Fever Virus Vaccine by Deletion of the I177L Gene Results in Sterile Immunity against the Current Epidemic Eurasia Strain. (M V Borca et al, Journal of Virology 94:e02017-19, April 2020.)

VIOLIN -- the Vaccine Investigation and Online Information Network. A broad-based vaccine resource, from the University of Michigan Medical School...

A report from the Institute of Medicine (IOM)... Adverse Effects of Vaccines: Evidence and Causality, 2012. The report addresses numerous possible side effects of vaccines, and tries to analyze whether evidence supports a causal relationship between vaccine and effect. You can download a pdf file of a "Report Brief", or read the report online.

Making a wimpy virus. One approach to making vaccines is to use an attenuated strain of the infectious agent -- one that can induce an immune response, but not cause disease. Scientists at Stony Brook have developed a new approach to making an attenuated virus for use in a vaccine. They re-code the virus so that it uses codons that are poorly translated. They made a few hundred changes in the poliovirus genome, each one making it harder for the genome to function. The result was a virus that seemed to work well as a vaccine strain in mouse tests. A nice feature of this approach is that it would seem to be of general applicability, though of course it needs to be tested in each case. Press release, summarizing the story: "SBU Team Designs Customized "Wimpy" Polioviruses, A Method That Could Be A New Path To Vaccines. Reported in Science, the 'Save' Computer-driven Method Creates a Weakened Synthetic Virus"; June 26, 2008; now archived: The paper is: J R Coleman et al, Virus attenuation by genome-scale changes in codon pair bias. Science 320:1784, 6/27/08.

Thimerosal in vaccines. Thimerosal is an organic mercury compound, used as a preservative -- including in vaccines. As with any mercury compound, it is toxic. Of course, the fact that it is toxic is why it is used as a preservative. The intent is that it is more toxic to bacteria and fungi than to humans. The available information suggests that the risks from exposure to mercury from thimerosal are quite small. (Exposures from eating fish and from coal-fired power plants are likely to be larger.) As a precaution -- in the US and Europe -- thimerosal is now rarely used in vaccines intended for children; the common Influenza vaccine is the one prominent exception. Note points of uncertainty, especially regarding children (which is why extra precautions are taken with children), but also note that there is really no data suggesting any problem with thimerosal as used in vaccines.
* This FDA web page is a good overview of the use of thimerosal. It should serve as a good framework for further discussion.
* A new study shows that ethyl mercury, the form of mercury from thimerosal, is eliminated from the body much faster than methyl mercury. (Methyl mercury is a more common toxic form of mercury, and has been used as a frame of reference for discussing thimerosal in the absence of more direct information.) Children getting many vaccines containing thimerosal (in Argentina) do not show elevated blood level of mercury. A press release from the University of Rochester accompanying publication of this work: Babies Excrete Vaccine-Mercury Quicker than Originally Thought, January 30, 2008. (now archived). The paper is M E Pichichero et al, Mercury Levels in Newborns and Infants After Receipt of Thimerosal-Containing Vaccines. Pediatrics 121:e208, 2/08. It is freely available at .
* I have posted a page showing the chemical structure of thimerosal and some related compounds, including aspirin: thimerosal.
* This topic is also listed under Introductory Chemistry Internet Resources: Thimerosal and Introduction to Organic and Biochemistry Internet Resources: Alcohols, ethers, sulfur compounds.
* A post in my Musings newsletter on mercury: Mercury pollution from Arctic melting (February 19, 2019).

Growing vaccines in plants. Oral, Plant-Based Vaccine against Shiga Toxin Effective in Mice. A news story about this new approach... Microbe 1:311, 7/06,

The article this news story refers to is S X Wen et al, A plant-based oral vaccine to protect against systemic intoxication by Shiga toxin type. PNAS 103:7082, May 2, 2006. Online at

National Network for Immunization Information (NNii). An excellent general resource on immunizations. Articles address individual vaccines, and some of the news stories you may hear about them (see Immunization Issues). From their introduction: "The mission of the National Network for Immunization Information (NNii) is to provide the public, health professionals, policy makers, and the media with up-to-date, scientifically valid information related to immunization to help them understand the issues and to make informed decisions. The National Network for Immunization Information (NNii) is an affiliation of the Infectious Diseases Society of America, the Pediatric Infectious Diseases Society, the American Academy of Pediatrics, the American Nurses Association, the American Academy of Family Physicians, the National Association of Pediatric Nurse Practitioners, the American College of Obstetricians and Gynecologists and the University of Texas Medical Branch."

Financing Vaccines in the 21st Century: Assuring Access and Availability, a report from the Institute of Medicine, 2004. This report discusses policy issues regarding vaccines. The economics of vaccine production are complex, and in some cases not very good. What role should the government play is assuring vaccine availability even when "ordinary economics" might seem to argue otherwise? As with all IOM reports, you can read it online, or purchase it; a short summary is also available online.

The Jordan Report: Accelerated Development of Vaccines, from the NIAID (National Institute of Allergy and Infectious Diseases). 2012. The purpose of the Jordan Report is "to inform policy-makers, researchers and the public about recent accomplishments and future trends in vaccine research."

A report from the Institute of Medicine (IOM)... K Stratton et al, Immunization safety review: Multiple immunizations and immune dysfunction, February 2002. A short summary is that they found no evidence of vaccine-induced problems, but they also note areas where the evidence is insufficient to reach a conclusion and further study is needed.

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West Nile Virus

Other sections of this page on flaviviruses:
Dengue virus (and miscellaneous flaviviruses)

There are also more general sections that may overlap with this section:
Emerging diseases (general)
Vaccines (general)

The Contra Costa Mosquito & Vector Control District (CCMVCD) has a short flier, which it distributes to all county residents, about West Nile Virus. It is written, of course, for the general public, and contains a range of useful information -- about the disease, the virus, and prevention measures. They also have a website, with much useful information: See menu bar for items about West Nile Virus.

California West Nile Virus (and dead bird surveillance) web site, from the state Department of Health Services:

Some scientists now suggest that the West Nile Virus has "settled in" in North America, and probably peaked. That is, they suggest it is likely to stay, but at the generally low levels now observed. Their view is not entirely accepted at this point. A brief summary, West Nile Virus Settled in, but Perhaps No Longer Expanding in the U.S., is in Microbe (Vol 2, p 167, April 2007): It refers to the primary publication.

Posts in my Musings newsletter that include WNV:
* Antibiotics and viruses: An example of harm (May 6, 2018).
* Finding host genes that are required for growth of Zika virus (and related viruses) (August 8, 2016).

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See Emerging diseases section, above, for perspective.

Sections on other flaviviruses:
Dengue virus (and miscellaneous flaviviruses)
West Nile Virus

The reason that Zika is getting attention is the reported connection to microcephaly. This is a quite serious issue, but also quite mysterious.

Why has microcephaly not previously been reported as being associated with Zika? There are various possible reasons, and we don't know for now. Here are some of the factors to consider...
* In areas where Zika is endemic, most people probably become immune while young. Thus Zika infections of pregnant women may not be common.
* In other places where Zika outbreaks have occurred, there may just not be good data, or enough data.
* In some of the countries where Zika is now prevalent in the current outbreak, it may be there hasn't been time for Zika-associated microcephaly to manifest itself. It may well be that the critical period in pregnancy is fairly early (first trimester). Thus it takes six months or so for after the beginning of an outbreak for Zika-associated microcephaly to appear. It would take even longer for it to be recognized as significant. It may be that Brazil is the only country in the current outbreak to have had the virus long enough to accumulate significant Zika-associated microcephaly.
* On the other hand, it is possible that there is some other factor causing microcephaly in Brazil, either in conjunction with Zika, or alone.
* Finally, there is some question about what the microcephaly incidence really is, and what it was prior to the Zika outbreak. Microcephaly is defined in various ways, and the routine way used in simple screening of newborns correlates only weakly with serious brain problems.

CIDRAP is a good source of current news as well as background. The CIDRAP main page for Zika is: You can sign up for a daily e-mail from CIDRAP; in early 2016, it includes a lot of Zika news.

The (US) CDC is a government agency, and a good source of official information, including travel advisories. The CDC main page for Zika is:

Posts in my Musings newsletter on this topic:
* Virus infection may make you more attractive to mosquitoes (July 16, 2022).
* Are non-African Aedes aegypti mosquitoes better at carrying Zika? (January 5, 2021).
* A Zika vaccine test: protection of the developing fetus? (January 24, 2020).
* Asian Zika in Africa (October 12, 2019).
* The effect of prior dengue infection on Zika infection (April 20, 2019).
* An easier way to tell if a mosquito carries Zika virus? (June 2, 2018).
* Should we screen the blood supply for Zika virus? (May 20, 2018).
* A recent genetic change that enhanced the neurotoxicity of the Zika virus (December 1, 2017).
* Zika fallout: Should pregnant women receive immunizations? (September 30, 2017).
* Why does Zika virus affect brain development? (August 11, 2017).
* Can antibodies to dengue enhance Zika infection -- in vivo? (April 15, 2017).
* Why some viruses may be less virulent in women (March 1, 2017).
* How long is a yawn? (December 16, 2016).
* Finding host genes that are required for growth of Zika virus (and related viruses) (August 8, 2016).
* Can Wolbachia reduce transmission of mosquito-borne diseases? 1. Introduction and Zika virus (June 14, 2016).
* A Zika-dengue connection: Might prior infection with dengue make a Zika infection worse? (May 7, 2016).
* Zika: An estimate of the risk of microcephaly, outside Brazil (March 30, 2016).
* Zika virus can infect and inhibit neural progenitor cells (March 14, 2016).

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