Home » Posts tagged 'Biology' (Page 3)
Tag Archives: Biology
Why don’t we yet have a vaccine for HIV/AIDS?
Intro – What is HIV?
HIV (human immunodeficiency virus) is a virus that attacks cells that help the body fight infection, making a person more vulnerable to other infections and diseases.
It is spread by contact with certain bodily fluids of a person with HIV, most commonly during unprotected sex (sex without a condom or HIV medicine to prevent or treat HIV), or through sharing injection drug equipment.
HIV leads to the disease AIDS (acquired immunodeficiency syndrome).
The human body can’t get rid of HIV and no effective HIV cure exists. So, once you have HIV, you have it for life.
from HIV.Gov
HIV infecting a human cell. Credit: NIH Image Gallery
HIV/AIDS vaccine: Why don’t we have one after 37 years, when we have several for COVID-19 after a few months?
Ronald C. Desrosiers writes
HIV has evolved an ability to generate and to tolerate many mutations in its genetic information. The consequence of this is an enormous amount of variation among strains of the virus not only from one individual to another but even within a single individual.
Let’s use influenza for a comparison. Everyone knows that people need to get revaccinated against influenza virus each season because of season-to-season variability in the influenza strain that is circulating.
Well, the variability of HIV within a single infected individual exceeds the entire worldwide sequence variability in the influenza virus (*) during an entire season.
What are we going to put into a vaccine to cover this extent of strain variability?
HIV has also evolved an incredible ability to shield itself from recognition by antibodies. Enveloped viruses such as coronaviruses and herpes viruses encode a structure on their surface that each virus uses to gain entry into a cell.
This structure is called a “glycoprotein,” meaning that it is composed of both sugars and protein.
But the HIV envelope glycoprotein is extreme. It is the most heavily sugared protein of all viruses in all 22 families. More than half the weight is sugar.
And the virus has figured out a way, meaning the virus has evolved by natural selection, to use these sugars as shields to protect itself from recognition by antibodies that the infected host is trying to make. The host cell adds these sugars and then views them as self.
These properties have important consequences relevant for vaccine development efforts. The antibodies that an HIV-infected person makes typically have only very weak neutralizing activity against the virus.
Furthermore, these antibodies are very strain-specific; they will neutralize the strain with which the individual is infected but not the thousands and thousands of other strains circulating in the population.
Researchers know how to elicit antibodies that will neutralize one strain, but not antibodies with an ability to protect against the thousands and thousands of strains circulating in the population. That’s a major problem for vaccine development efforts.
HIV is continually evolving within a single infected individual to stay one step ahead of the immune responses. The host elicits a particular immune response that attacks the virus. This puts selective pressure on the virus, and through natural selection a mutated virus variant appears that is no longer recognized by the individual’s immune system. The result is continuous unrelenting viral replication.
Life cycle of HIV
Source: HIV/AIDS vaccine: Why don’t we have one after 37 years, when we have several for COVID-19 after a few months? By Ronald C. Desrosiers, TheConversation.com, 5/17/2021
(*) Evolutionary and immunological implications of contemporary HIV-1 variation
Bette Korber, Brian Gaschen, Karina Yusim, Rama Thakallapally, Can Kesmir, Vincent Detours
British Medical Bulletin, Volume 58, Issue 1, September 2001, Pages 19–42, https://doi.org/10.1093/bmb/58.1.19
Learning Standards
Massachusetts Comprehensive Health Curriculum Framework
Students will gain the knowledge and skills to select a diet that supports
health and reduces the risk of illness and future chronic diseases. PreK–12 Standard 4
8.1 Describe how the body fights germs and disease naturally and with medicines and
immunization
8.2 Identify the common symptoms of illness and recognize that being responsible for individual health means alerting caretakers to any symptoms of illness.
8.5 Identify ways individuals can reduce risk factors related to communicable and chronic diseases
8.6 Describe the importance of early detection in preventing the progression of disease.
8.7 Explain the need to follow prescribed health care procedures given by parents and health care providers.
8.8 Describe how to demonstrate safe care and concern toward ill and disabled persons in the family, school, and community.
8.13 Explain how the immune system functions to prevent and combat disease
Interdisciplinary Learning Objectives: Disease Prevention and Control
8.a. (Law & Policy. Connects with History & Social Science: Geography and Civics &
Government) Analyze the influence of factors (such as social and economic) on the treatment and management of illness.
Benchmarks for Science Literacy, AAAS
The immune system functions to protect against microscopic organisms and foreign substances that enter from outside the body and against some cancer cells that arise within. 6C/H1*
Some allergic reactions are caused by the body’s immune responses to usually harmless environmental substances. Sometimes the immune system may attack some of the body’s own cells. 6E/H1
Some viral diseases, such as AIDS, destroy critical cells of the immune system, leaving the body unable to deal with multiple infection agents and cancerous cells. 6E/H4
Vaccines induce the body to build immunity to a disease without actually causing the disease itself. 6E/M7** (BSL)
This website is educational. Materials within it are being used in accord with the Fair Use doctrine, as defined by United States law.
§107. Limitations on Exclusive Rights: Fair Use. Notwithstanding the provisions of section 106, the fair use of a copyrighted work, including such use by reproduction in copies or phone records or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright. In determining whether the use made of a work in any particular case is a fair use, the factors to be considered shall include: the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes; the nature of the copyrighted work; the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and the effect of the use upon the potential market for or value of the copyrighted work. (added pub. l 94-553, Title I, 101, Oct 19, 1976, 90 Stat 2546)
Glycans (polysaccharides and oligosaccharides)
Glycans are polymers of individual sugar molecules (monosaccharides)
Here’s a glucose, a simple sugar monomer (single unit.) Note that there are also many other types of sugars.
What’s the difference between monomers and polymers?
Living things can link many sugars together into a polymer – a glycan.
Here’s one example:
Glycans are made by all living things and by many viruses.
Glycans can be free (not bonded to anything else.) In this state they are often used to store chemical energy, or as building blocks for plant cell walls.
Glycans can be bonded together with a protein or a lipid. In such cases they have specific jobs.
• When bonded with a protein they’re called glycoproteins.
• When bonded with a lipid they’re called glycolipids.
Types of glycans
Cellulose – glucose monosaccharides linked to one another in a long, linear chain.
Used for structural support in cell walls of plants and algae.
Trees and plants use these glycans as building blocks.Here we see them linking together until they build the structure of a leaf, a stem, or branch.
From Direct evidence for α ether linkage between lignin and carbohydrates in wood cell walls, Hiroshi Nishimura et al, Scientific Reports volume 8, Article number: 6538 (2018)
Starch is made in plants. This molecule is used for energy storage.
Glycogen – used for energy storage in fungi and animals.
Comparison of cellulose, starches, and glycogen
from coredifferences.com
Uses of glycans in the body
In breast milk
Human milk oligosaccharides are found in breast milk.
Human milk oligosaccharides(HMOs)
On cell membranes
They are found in cell membranes (lipid bilayers) as glycans attached to proteins – glycoproteins.
Gly-tech.com
Immune system
I don’t know if any glycoproteins evolved to be part of the immune system, but I do know that they became a part of the immune system – various pathogens can recognize some glycans and use them as part of a pathway to infect a cell. Some antibodies interact with them.
Uses in bacteria
We find peptidoglycan in bacterial cell walls.
From Prescott’s Microbiology, McGraw Hill
Medical uses
They are valuable diagnostic and therapeutic targets.
How to draw glycans, the exact way
On the left we see a skeletal drawing of a single sugar molecule, glucose. In the middle we see two sugars bonded together to make a sucrose molecule. (disaccharide, i.e. a molecule with 2 sugars.)
On the right we see a starch, which is a more complex structure of several sugars covalently bonded.
On the bottom we see a much more complex assembly of sugar molecules bonded together N-Glycan, in this case mostly a bunch of sucrose molecules bonded together.
The advantage of drawing glycans this way is that we see their exact structure.
The disadvantage of of drawing glycans this way is that it is super difficult to do when drawing freehand, it ain’t that even easy when using an app, and finally – being “exact” isn’t always an advantage! Look at that last molecule. Yes, if you look at it long enough you might figure out that it is a bunch of sugars.
But what about complex molecules like this that are made of many different types of sugars? It would be very difficult to interpret a drawing. Thus we have developed an easier way to visually represent them!
from GlyTech, Inc
How to draw glycans: the easier way
There is a standard Symbol Nomenclature for Glycans (SNFG).
It is from the National Center for Biotechnology Information, U.S. National Library of Medicine.
Super easy to read, each color and shape represents a different sugar.
On the top is an example of a glycan in which we draw the name of each sugar. Technically correct but hard to read.
So below it we show the easier way to draw and color the glycan, so we can see which sugars it is made of.
from National Center for Biotechnology Information, U.S. National Library of Medicine
Another example: Here are seven sugars (monosaccharides.)
And here they are linked together. The atom by atom details are not necessary.
from glytech-inc
Articles
Recent Advances in Nutritional Sciences: An Overview of Glycans and miRNAs, Marcello Menapace
Ecology and Biology in Science Fiction
Ecology and Biology in Science Fiction
Copyright 1996, 1997, 1998, 1999, 2000 by Magic Dragon Multimedia. All rights reserved Worldwide. May not be reproduced without permission. May be posted electronically provided that it is transmitted unaltered, in its entirety, and without charge.
We examine both works of fiction and important contemporaneous works on non-fiction which set the context for ecological Science Fiction and Fantasy. Some questions that we study include:
- How do living organisms grow and reproduce? (Tribbles, TV: Star Trek)
- What forces shape the evolution of species, including our own? Could humans evolve into something very different? (novel: Galapagos, by Kurt Vonnegut)
- What kind of planet is needed for living things and ecosystems to evolve? (novel: Red Mars, by Kim Stanley Robinson)
- What would a desert planet look like? (novel: Dune, by Frank Herbert)
- How does genetics create us–and recreate living things? (novel: Jurassic Park, by Michael Crichton)
- Could genetics make us immortal? (novel: The Children Star, by Joan Slonczewski)
- What if an alien invader tried to do us in–from within? (novel: Andromeda Strain, by Michael Crichton)
- What if the aliens decide they like us–too well? (novel: Dawn, by Octavia Butler)
Biology in Science Fiction: Syllabus by Prof. Joan Slonczewski. Prof. Joan Slonczewski describes her required reading list as follows (the hotlink shows the color art for each book):
- Barlowe’s Guide to Extraterrestrials, by Wayne Douglas Barlowe [New York: Workman Publishers, 1979] “In his classic guide, Wayne Douglas Barlowe’s brilliant portraits bring to life 50 aliens from science fiction literature: Larry Niven’s Thrint and his Puppeteer, Arthur C. Clarke’s Overlord, Frank Herbert’s Steersman, Robert Silverburg’s Sulidor and more. Humanoids, insectoids, reptillians-even protoplasmic, gaseous, and crystalline life forms-are all faithfully and naturalistically depicted so that you can now visualize what could only before be imagined.”
- The Time Machine, by H.G. Wells [New York: Bantam Books, 1895] “When the Time Traveler courageously stepped out of his machine for the first time, he found himself in the year 802,700 — and everything had changed. In another, more utopian age, creatures seemed to dwell together in perfect harmony. The Time Traveler thought he could study these marvelous beings — unearth their secret and then return to his own time-until he discovered that his invention, his only avenue of escape, had been stolen.”
- Galapagos, by Kurt Vonnegut [New York: Dell Publishing, 1985] “Galapagos takes the reader back one million years, to A.D. 1986. A simple vacation cruise suddenly becomes an evolutionary journey. Thanks to an apocalypse, a small group of survivors stranded on the Galapagos islands are about to become the progenitors of a brave new, and totally different human race. Here, America’s master satirist looks at our world and shows us all that is sadly, madly awry-and all that is worth saving.”
- Dune, by Frank Herbert [New York: Ace Books, 1965] “Set on the desert Planet Arrakis, a world more awesome than any other in literature, Dune begins the story of the man known as Muad’dib-and of a great family’s ambition to bring to fruition humankind’s most ancient and unattainable dream…”
- The Children Star, by Joan Slonczewski [Analog magazine serial; New York: Tor Books, 1999] “The Children Star — A world so alien that only children can be lifeshaped to live there. The Children Star features mind-bending genetic engineering, and tire-shaped creatures that evolved with triplex DNA and exotic amino acids. And which of the many circular- shaped life forms is actually an intelligent species with its own plans for the human colonists?”
- Dawn, by Octavia Butler [New York: Warner Books, 1987] “Xenogenesis: The birth of something new-and foreign. Lilith Iyapo awoke from a centuries long sleep…and found herself aboard the vast living spaceship of the Oankali. Alien creatures covered in writhing tentacles, the Oankali had saved every surviving human from a dying, ruined Earth. They healed the planet, cured cancer, increased human strength and disease resistance, and were now ready to help Lilith lead her people back to the Earth. But for a price. For the Oankali were genetic engineers. DNA manipulators. Gene traders. They planned to give us their alienness. They planned to take our humanity. They planned to interbreed. And there was no way to stop them.”
- Red Mars, by Kim Stanley Robinson [New York: Bantam Books, 1993] “For eons, sandstorms have swept the barren, desolate landscape of the red planet. For centuries, Mars has beckoned to mankind to come and conquer its hostile climate. Now, in the year 2026, a group of one hundred colonists is about to fulfill that destiny. John Boone, Maya Toitovna, Frank Chalmers, and Arkady Bogdanov lead a mission whose ultimate goal is to give Mars an Earth-like atmosphere. They will place giant satellite mirrors in Martian orbit to reflect light to the planet’s surface. Black dust sprinkled on the polar caps will capture warmth and melt the ice. And massive tunnels, kilometers in depth, will be drilled into the Martian mantle to create stupendous vents of hot gases. Against this backdrop of epic upheaval, rivalries, loves, and friendships will form and fall to pieces — for there are those who will fight to the death to prevent Mars from ever being changed.”
- Jurassic Park, by Michael Crichton [New York: Ballantine Books, 1990] “An astonishing technique for recovering and cloning dinosaur DNA has been discovered. Now, one of mankind’s most thrilling fantasies has come true. Creatures extinct for eons now roam Jurassic Park with their awesome presence and profound mystery and all the world can visit them-for a price. Until something goes wrong…”
- The Andromeda Strain, by Michael Crichton [New York: Ballantine Books, 1969] “What if there was a virus so lethal, it could kill people as quickly as they took a breath? What if it spared some people from instant death…but drove them hopelessly insane instead? What if the swiftest acting, deadliest, virus ever known to humankind could be spread, by no more than a gust of wind, from the remote desert site of its first massacre to the busiest cities in America…and the world? What, if anything, could stop it?”
- The Cartoon Guide to Genetics, by Larry Gonick and Mark Wheelis [New York: Harper Perennial, 1991] “Have you ever asked yourself: Are spliced genes the same as mended Levis? Watson and Crick? Aren’t they a team of British detectives? Plant sex? Can they do that? Is genetic mutation the name of one of those heavy metal bands? Asparagine? Which of the four food groups is that in? Then you need “The Cartoon Guide to Genetics” to explain the important concepts of classical and modern genetics.”
- Brain Plague, by Joan Slonczewski [New York: Tor Books, 2000] “What if alien microbes could give us whatever our brains imagined–at a price? ‘Brain Plague’ gives new epic meaning to hearing voices inside your head. Tune in or you’ll be sorry.” — Eva, Fantastica Daily
Joan Slonczewski's Book List
The following list is selected, permuted, and edited from: Themes/Genres in Science Fiction: An idiosyncratic and woefully incomplete list, by Kay Fowler ©All the material in this website is copyrighted to Kathleen L. Fowler unless explicitly indicated otherwise. Permission is granted to use and distribute this material freely but please attribute properly by retaining the full header information. 11/16/99 "This list has been constructed over time based on a list and categories originally constructed by the late Professor Ted Michelfeld and owing debts to a number of other sources including The Encyclopedia of Science Fiction. It is still under construction and by no means complete but it is a starting place. The categories are by no means as distinct as is suggested here. Most every one of these works could appear in multiple categories and in many cases I have assigned them rather arbitrarily to one of the many choices they might occupy."
Plagues/Disease/Epidemics:
- Mary Shelley. The Last Man (1826)
- Jack London. The Scarlet Plague (1915)
- George Stewart. Earth Abides (1949)
- Michael Critchton. The Andromeda Strain. (1969).
- Sherri Tepper. Grass (1989); Raising the Stones (1990) Sideshow (1992). Earth has become “Sanctity” controlled by fundamental relgionists. Rich exploration of themes of religion, ecology, social relationships, etc.
Agricultural/Ecological/Population Disasters:
- George Griffith. Olga Romanoff (1894) comet strike and alien invasion.
- M. P. Shield. The Purple Cloud (1901). poisonous gas.
- Arthur Conan Doyle. The Poison Belt (1913) the Earth passes through a poisonous ether
- J. J. Connington. Nordenholt’s Millions (1923) agricultural disaster
- S. Fowler Wright. Deluge (1928). flood.
- Philip Wylie. When Worlds Collide (1932). dying sun on collision course with Earth. Film: When Worlds Collide (1951).
- John Wyndham. The Day of the Triffids (1951) Venomous Plants.
- Isaac Asimov. Caves of Steel (1954) overpopulation — and a great mystery story
- John Christopher. The Death of Grass (a.k.a. No Blade of Grass) (1957)
- Robert Silverberg. Masters of Life and Death (1957). overpopulation.
- J. G. Ballard. “Billenium” (1961) population
- J. G. Ballard. The Drowned World. (1962). flood
- Kurt Vonnegut, Jr. Cat’s Cradle (1963) Ice-9
- J. G. Ballard, The Drought (aka The Burning World) 1965.
- Harry Harrison. Make Room! Make Room! (1966). Film: Soylent Green (1973).
- William F. Nolan and George Clayton Johnson.Logan’s Run (1967). Film: Logan’s Run (1967) Overpopulation; destruction of those over 30.
- Lee Tang. The Wind Obeys Lama Torus. (1967). From India. Overpopulation.
- John Brunner. Stand on Zanzibar. (1968). Young adult novel on overpopulation.
- James Blish. A Torrent of Faces (1968)
- Fred and Geoffrey Hoyle. The Inferno (1973). Cosmic radiation
- Nancy Bond. The Voyage Begun (1989). Young Adult. In a near future Cape Cod, dwindling resources, unemployment, and ecological damage combine to make the Cape a dangerous, and forlorn world.
- David Brin. Earth. (1990). Black hole.
- Karen Hesse. Phoenix Rising (1994). Young adult. A young girl on a farm in Vermont copes with the consequences of a nuclear accident in Massachusetts. Dedicated to the children of Chernobyl.
- Monica Hughes. Invitation to the Game. 1996. Young Adult. overpopulation and shrinking resources leave most unemployed and without hope — unless they can get into “the game”
- Jack McDevitt. Engines of God. (1997) Alien artifacts related to ancient mass destructions on a number of planets. Should we be worried?
- Mary Sullivan. Earthquake 2099. (1997) Young adult.
Using Science Fiction to Understand Biological Concepts by Tamsen K. Meyer and Cheryl H. Powers ©1994 Woodrow Wilson Biology Institute "Integration of disciplines that involve science, social issues, and literature is an increasingly attractive alternative in curriculum development today." "Science fiction has great appeal to many students who do not necessarily think of themselves as readers nor as the stereotypical 'math/science student.'" "The following is a resource list of science fiction short stories and novels that might be used either as an interdisciplinary teaching unit for teachers, an enrichment exercise in your biology course, or possibly a summer reading list for students entering your course the following year." "It also can serve as a starting point for students to create their own science fiction stories if only selections from these novels or short stories are read. "Students can demonstrate their understanding of complex biological concepts by writing their own short science fiction stories on topics such as 'The Day Diffusion Stopped.' What a difference a gene makes: food in the future, medicine in the future, eugenics revisited, and restoring extinct species are possible genetics ideas that could be developed." "Readings are listed by title rather than author because titles seem more useful. Titles were submitted by several Woodrow Wilson participants. A content summary is included for most of the selections and if there is a film version of the book, the notation FVA (film version available) is added in the following bibliography.
- Andromeda Strain, Michael Crichton. 1969. New York: Knopf, Random House. A returning space capsule releases an alien virus on the earth. FVA
- The Beast, Peter Benchley. 1991. New York: Random House. Coral reef ecology is disturbed and a giant squid picks man as his new prey.
- Blade Runner, The, Alan E. Nourse. 1974. New York: D. McKay & Co. In a future of increased human longevity, doctors struggle to cope with problems of overpopulation, hereditary disorders, and virulent new diseases. FVA [The Ultimate Science Fiction Web Guide says: actually, the title is used in a film based on Philip K. Dick’s ‘Do Androids Dream of Electric Sheep”; see below]
- Boys from Brazil, The, Ira Levin. 1976. New York: Random House. Dr. Mengele attempts to produce cloned copies of Adolf Hitler, but in order to do so he must reproduce the environmental factors which made Hitler the evil genius that he was; deals intelligently with the fashionable subject of cloning. FVA
- Brave New World, Aldous Huxley. 1946. New York: Harper and Bros. Reproductive technology as imagined in the 30’s – this famous satire about a technologically stratified world six centuries in the future helped define 20th-century humanity’s view of itself. FVA
- Clan of the Cave Bear, The, Jean Auel. 1980. New York: Crown. Human evolution at the level of the Cro-Magnon/Neanderthal junction. FVA
- Congo, Michael Crichton. 1980. New York, Knopf: Random House. Animal behavior, primate evolution: near future thriller of African exploration involving a tribe of talking gorillas.
- Deathworld Trilogy, Harry Harrison. 1974. Garden City: Nelson Doubleday. Coevolution and adaptation: mysteries of a planet where every life-form appears to be implacably hostile to human colonists.
- Do Androids Dream of Electric Sheep? Philip K. Dick. 1968. Garden City: Doubleday. After World War Terminus, the Earth is an underpopulated wasteland where people keep electronic animals as pets; killer androids come from off-Earth where most economic activity takes place. Filmed as The Blade Runner.
- Dorsai, Gordon R. Dickson. 1976. New York: Dow Books. Themes of human development and the purpose of life; originally published as The Genetic General.
- Dragonflight, Anne McCaffrey. 1968. New York: Ballantine. A well crafted tale of a planet threatened by spores from space which can only be defeated by taming fire-breathing dragons; first of Dragons of Pern series.
- Dune, Frank Herbert. 1965. Philadelphia: Chilton. Planetary environment and system of cultures much like that which would be present on Earth if Earth had no water. FVA
- Earthclan: Startide Rising, David Brin. 1987. Garden City, NY: Nelson Doubleday. Genetic manipulation, origin of man: intelligent dolphins and chimpanzees cooperate with man in the exploration of space.
- Ender’s Game, Orson Scott Card, 1985. New York: Tor, A Tom Doherty Association Book. Interstellar war, aliens and genocide.
- Fantastic Voyage, Isaac Asimov. 1988. New York: Doubleday and Co. Microminiaturization is used to explore the human body; written originally as a screenplay for the movie of the same name. FVA
- Frankenstein, Mary Shelley. 1980 (1818). James Kinsley and M.K. Joseph eds., Oxford, New York: Oxford University Press. Gothic horror story about a medical student who creates an artificial man; first English science fiction novel. FVA
- Galapagos, Kurt Vonnegut. 1985. New York: Delacorte Press/Seymour Lawrence. An observant ghost haunts the Galapagos Islands for a million years and watches as the descendants of a few marooned humans devolve into a new species – furry, finned, and small of brain; a sadly funny Darwinian fable.
- Genesis Quest, Donald Moffitt. 1986. New York: Ballantine. A species of intelligent starfish in another galaxy use genetic engineering to recreate the extinct human race.
- Human Error, Paul Preuss. 1985. New York: Tor. Scientists produce a biochip or living microcomputer.
- Jurassic Park, Michael Crichton. 1990. New York: Alfred A. Knopf. This fictional account of a theme park featuring dinosaurs cloned from DNA in mosquitoes fossilized in amber lends itself to many interesting discussions of genetic engineering, ethical issues, and chaos. FVA
- “Last Question, The,” Isaac Asimov. 1959. in: Nine Tomorrows: Tales of the Near Future. Garden City, NY: Doubleday. Themes of artificial intelligence and definition(s) of intelligence.
- Mortal Fear, Robin Cook. 1988. New York: G.P. Putnam and Sons. Eyedrops accelerate the aging process.
- Mutants: Eleven Stories of Science Fiction. Robert Silverberg, ed. 1974. Nashville: Thomas Nelson. Anthology of collected works.
- Plague Dogs, The, Richard Addams. 1977. London: Allen Lane, Rex Collings. Issues of animal experimentation, epidemics.
- “Rendevous with Rama,” from 2001: A Space Odyssey, Arthur Clarke. 1985. London: Octopus. Ecosystems necessary for terraforming are described.
- Ringworld, Larry Niven. 1970. New York: Ballantine. Complex artificial world is the main focus of this popular book.
- Science Fiction Adventures in Mutation, Groff Conklin, ed. 1956. New York: Vanguard Press. An anthology of collected works. [the referenced site misspell’s Groff’s name]
- “Sound of Thunder, The,” Ray Bradbury. 1966. in: Science Fiction for People Who Hate Science Fiction, Terry Carr, ed. New York: Doubleday. Ecology, human impact on the environment.
- Sphere, Michael Crichton. 1987. New York: Alfred A. Knopf. The discovery of an ancient spacecraft deep in the ocean is the focus of a scientific probe. [FVA]
- Time Machine, The, H.G. Wells. 1931 New York: Random House. Ecological splitting of society leads to human evolution. FVA
- 20,000 Leagues Under the Sea, Jules Verne. 1908. London/New York: J.M.Dent. Underwater adventures with sea creatures, technology of sea exploration.
- Watchers, The, Dean Koontz. 1987. New York: G.P. Putnam’s Sons. Ethics of genetic engineering and issues of animal welfare.
- West of Eden, Harry Harrison. 1984. New York: Bantam Books. Imagine a world where dinosaurs did not die but survived to develop their own civilization; their culture comes into conflict with an emergent human race.
"An excellent resource for short summaries of works of science fiction is:
The Ultimate Guide to Science Fiction,
David Pringle. 1990. Grafton Books, London; Collins Publishing Group."
"Numerous anthologies of science fiction short stories are available in libraries and science fiction magazines have many interesting
short pieces. Omni, Amazing Stories, Fantasy in Science, and Analog Science Fiction/Science Fact are four that are recommended."
This is by no means a comprehensive list of science fiction that could be used at the secondary level. Hopefully, teachers will use this as a
springboard to generate their own annotated bibliographies that might also include favorite biological literature (books, poems, stories, and essays)
and film resources that are not science fiction."
"A sample writing exercise that might be done after students have read 'The Andromeda Strain':
Support the truth of these quotes as demonstrated by events in the book:
"The survival value of human intelligence has never been satisfactorily demonstrated."
"Increasing vision is increasingly expensive."
In the acknowledgments Crichton states, "We can expect more crises on the pattern of Andromeda." How much truth exists in the novel?
What evidence do you see to support his prediction? (Thanks to Susan Terry for these questions.)
Miscellaneous ecological novels:
BLOOM by Wil McCarthy [New York, Del Rey, 1998, paperback, 303 pages, cover art by Rick Berry] [A New York Times Notable Book] A science fiction book featuring nanotechnology. Reporter John Strasheim, Captain Wallich, bioanalyst Renata Baucum, and the rest of the small crew of the space ship Louis Pasteur travel on a dangerous mission from Jupiter's moon of Ganymede and the Immunity, visiting the Gladholders in the asteroid belt, to the inner solar system, including Earth, which has been taken over by the feared Mycosystem. From the back cover: "Mycora: technogenic life. Fast-reproducing, fast-mutating, and endlessly voracious. In the year 2106, these microscopic machine/ creatures have escaped their creators to populate the inner solar system with a wild, deadly ecology all their own, pushing the tattered remnants of humanity out into the cold and dark of the outer planets. Even huddled beneath the ice of Jupiter's moons, protected by a defensive system known as the Immunity, survivors face the constant risk of mycospores finding their way to the warmth and brightness inside the habitats, resulting in a calamitous 'bloom'" But the human race still has a trick or two up its sleeve: In a ship specially designed to penetrate the deadly Mycosystem, seven astronauts are about to embark on mankind's boldest venture yet -- the perilous journey home to infected Earth. Yet it is in these remote conditions, against a virtually omnipotent foe, that we discover how human nature plays the greatest role in humanity's future." Denver Science Fiction & Fantasy Book Club SCIENCE FICTION BOOK SELECTION
Miscellaneous Biological novels/films:
- Fantastic Voyage, film based on novel by Isaac Asimov, where an (impossibly) miniaturized submarine explores the interior of a living human body.
- Them, film: radiation makes ants grow (impossibly) large.
- The Thing, film (and remake of film) from short novel “Who Goes There” by John Campbell; an alien creature terrifies antarctic expolors with its ability to change shape. How do you know that your partner is not an alien morphed to resemble a human?
- Film: It Came from Beneath the Sea
- Film: Jaws
MANY MORE: {to be done}
Academic Papers on Ecology and Science Fiction "From Earth to Ecosphere: Science Fiction, spaceships, and ecology", by Mark Rich pages 373-93 of: "Science et science-fiction", Actes de 4eme colloque international de science-fiction de Nice, 3-6 Apr 1991, Ed. Denise Terrel, Metaphores, #20-21-22 (sep 1992), 2 vols., 653 pages, 180 ff. Order from J. Emiliana, UFR Lettres, BD Herriot, 06007 Nice Cedex, France
Respiratory viruses (influenza, rhinoviruses, coronaviruses etc)
What is a respiratory virus?
They are viruses that affect your breathing passages.
They cause common cold and flu-like symptoms.
They can cause shortness of breath and in more severe cases cause pneumonia.
Some infect mostly the upper respiratory tract, in the larynx, vocal cords and above.
Others infect mostly the lower respiratory tract symptoms – below the larynx and vocal cords.
and
Symptoms
These vary significantly from person to person.
Aching muscles and joints
Cough and sputum
Fever
Headache
Runny nose
Sneezing
Sore throat
Tiredness
Common complications of respiratory viruses include:
Bronchiolitis – inflammation of small air passages in the lungs
Croup – inflammation and swelling of the voice box (larynx), the windpipe (trachea) and the airways (bronchi)
Pneumonia – lung infection with inflammation
Sinusitis – infection or inflammation of the sinuses
What are the common respiratory viruses?
Influenza virus – “the flu”
The CDC estimates that influenza has resulted in between 9 million – 45 million illnesses, between 140,000 – 810,000 hospitalizations and between 12,000 – 61,000 deaths annually since 2010.
Respiratory syncytial virus
common respiratory virus that usually causes mild, cold-like symptoms. Most people recover in a week or two, but RSV can be serious, especially for infants and older adults.
RSV is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia (infection of the lungs) in children younger than 1 year of age in the United States. – CDC
Human parainfluenza viruses (HPIVs)
Human parainfluenza viruses (HPIVs) commonly cause respiratory illnesses in infants and young children. But anyone can get HPIV illness.
Symptoms may include fever, runny nose, and cough. Patients usually recover on their own. However, HPIVs can also cause more severe illness, such as croup or pneumonia.
Metapneumovirus
MPV is associated with 5% to 40% of respiratory tract infections in hospitalized and outpatient children. It is distributed worldwide and, in temperate regions, has a seasonal distribution generally following that of RSV and influenza virus during late winter and spring.
By the age of five, virtually all children worldwide have been exposed. Despite near universal infection during early life, reinfections are common in older children and adults. They may cause mild upper respiratory tract infection (the common cold).
However, premature infants, immunocompromised persons, and older adults >65 years are at risk for severe disease and hospitalization.
from Wikipedia metapneumovirus
Rhinovirus
The most common viral infectious agent in humans. Main cause of the common cold. Exists in three species with at least 160 recognized types.
Coronaviruses
Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal.
Mild illnesses in humans include some cases of the common cold (which is also caused by other viruses, predominantly rhinoviruses), while more lethal varieties can cause SARS, MERS, and COVID-19.
Adenoviruses
Adenoviruses are a type of virus without an outer lipid bilayer, with a double stranded DNA genome. More than 50 distinct types have been in people.
They usually cause mild respiratory infections, the common cold. But they can cause life-threatening multi-organ disease in people with a weakened immune system.
Human bocavirus (HBoV)
HBoV1 is strongly implicated in causing some cases of lower respiratory tract infection, especially in young children. Discovered in 2005.
These are the fourth most common virus in respiratory samples, behind rhinoviruses, respiratory syncytial virus and adenoviruses. Usually causes the common cold although it can also cause very dangerous illness.
Several versions of this virus have been linked to gastroenteritis.
The full role of this emerging infectious disease remains to be known.
– Wikipedia
Main method of transmission is through the air
See this infographic
Image from paper by Jianjian Wei and Yuguo Li. Airborne spread of infectious agents in the indoor environment
In Deep Cleaning Isn’t a Victimless Crime we read
These days, Goldman is extending his crusade against fomite fear from COVID-19 to other diseases. The old story is that if you make contact with a surface that a sick person touched, and then you touch your eyes or lips, you’ll infect yourself.
While Goldman acknowledges that many diseases, especially bacterial diseases, spread easily from surfaces, he now suspects that most respiratory viruses spread primarily through the air, like SARS-CoV-2 does.
“For most respiratory viruses, the evidence for fomite transmission looks pretty weak,” Goldman said. “With the exception of RSV [respiratory syncytial virus], there are few other respiratory viruses where fomite transmission has been conclusively shown.”
For example, rhinovirus, one of the most common viruses in the world and the predominant cause of the common cold, is probably overwhelmingly spread via aerosols. The same may be true of influenza.
Many experiments that suggest surface transmission of respiratory viruses stack the deck by studying unrealistically large amounts of virus using unrealistically ideal (cold, dry, and dark) conditions for their survival. Based on our experience with SARS-CoV-2, these may not be trustworthy studies.
Deep Cleaning Isn’t a Victimless Crime The CDC has finally said what scientists have been screaming for months: The coronavirus is overwhelmingly spread through the air, not via surfaces. Derek Thompson, The Atlantic, 4/13/2021
Thompson also writes:
It’s quite possible that ALMOST ALL respiratory viruses mostly spread through the air—including rhinovirus (lots of common colds) and the flu. That means the best way to avoid getting sick isn’t power-washing strategies, but ventilation strategies. Think windows over Windex.
Articles
Science Brief: SARS-CoV-2 and Surface (Fomite) Transmission for Indoor Community Environments, CDC, 4/5/2021
People can be infected with SARS-CoV-2 through contact with surfaces. However, based on available epidemiological data and studies of environmental transmission factors, surface transmission is not the main route by which SARS-CoV-2 spreads, and the risk is considered to be low. The principal mode by which people are infected with SARS-CoV-2 is through exposure to respiratory droplets carrying infectious virus.
and
Aerosol Transmission of Rhinovirus Colds, Elliot C. Dick et al., The Journal of Infectious Diseases, Volume 156, Issue 3, September 1987, Pages 442–448, https://doi.org/10.1093/infdis/156.3.442
and
Exaggerated risk of transmission of COVID-19 by fomites, Emanuel Goldman, The Lancet Infectious Diseases, Vol. 20(8), p.892-893, 8/1/2020
Vaccines – what does 95% efficacy actually mean?
Covid-19 is one of many types of respiratory viruses.
The mRNA coronavirus vaccines are 95% effective. What does that mean?
Does this mean that you have a 5% of chance of being infected and getting very sick (or dying) and a 95% chance of being okay?
Not at all! That “95%” figure really means that one is 95% less likely to be infected than compared to someone who hasn’t been vaccinated at at.
How about for a vaccine that is “only” 92% effective? As the math below shows, that means that one only has a 0.04 percent chance of getting COVID!
That’s just a 4 in 10,000 chance – and even then, the majority of those people won’t get it bad. They’ll just have some minor symptoms for a few days.
Let’s see the math!
Image from St. Lawrence University, Mathematics-Economics Combined Major
This section excerpted from Coronavirus FAQs, Sheila Mulrooney Eldred, NPR Goats and Soda, 3/12/2021
…The tendency to oversimplify has led many people to the same — mistaken — conclusion that an efficacy rate of 92 percent would mean that of 100 vaccinated people, 8 of them would get sick during a pandemic.
But that’s not the case. Fortunately, a vaccine with a 92 percent efficacy rate actually means your chances of getting the disease is much, much less than 8 percent.
It means that if you were exposed to the disease, your chances of getting infected would be 92 percent less if you were vaccinated than if you weren’t.
…Say you originally had a 10% chance of getting sick without being vaccinated. If you got that vaccine with an efficacy rate of 92%, your chance of getting sick would drop from 10% to less than 1% — 0.8%, to be exact.
In reality, the trials found that the probability of getting sick in the placebo groups was much less than 10%. In the Pfizer trial, for example, it was 0.79% — or less than one per 100 people.
Participants who got the real vaccine had just a .04 percent chance of getting COVID … that’s 4 in 10,000 people.
Coronavirus FAQs: What Is ‘Vaccine Efficacy’?
What does 95% efficacy actually mean? CDC
Vaccine efficacy and vaccine effectiveness measure the proportionate reduction in cases among vaccinated persons.
Vaccine efficacy is used when a study is carried out under ideal conditions, for example, during a clinical trial.
Vaccine effectiveness is used when a study is carried out under typical field (that is, less than perfectly controlled) conditions.
Vaccine efficacy/effectiveness (VE) is measured by calculating the risk of disease among vaccinated and unvaccinated persons and determining the percentage reduction in risk of disease among vaccinated persons relative to unvaccinated persons.
The greater the percentage reduction of illness in the vaccinated group, the greater the vaccine efficacy/effectiveness. The basic formula is written as:
the numerator (risk among unvaccinated − risk among vaccinated) is sometimes called the risk difference or excess risk.
Vaccine efficacy/effectiveness is interpreted as the proportionate reduction in disease among the vaccinated group.
So a VE of 90% indicates a 90% reduction in disease occurrence among the vaccinated group, or a 90% reduction from the number of cases you would expect if they have not been vaccinated.
from CDC Principles of Epidemiology, Measures of Risk
Related articles
This section has been excerpted from COVID-19 vaccines: What does 95% efficacy actually mean?, Anna Nowogrodzki, Live Science, 2/11/2021
“I think it’s important for people to understand that this is an extremely effective vaccine,” said Brianne Barker, a virologist at Drew University in New Jersey, referring to the Pfizer vaccine. “This is much more effective than you might think.”
One common misunderstanding is that 95% efficacy means that in the Pfizer clinical trial, 5% of vaccinated people got COVID. But that’s not true; the actual percentage of vaccinated people in the Pfizer (and Moderna) trials who got COVID-19 was about a hundred times less than that: 0.04%.
What the 95% actually means is that vaccinated people had a 95% lower risk of getting COVID-19 compared with the control group participants, who weren’t vaccinated.
In other words, vaccinated people in the Pfizer clinical trial were 20 times less likely than the control group to get COVID-19.
That makes the vaccine “one of the most effective vaccines that we have,” Barker told Live Science. For comparison, the two-dose measles, mumps and rubella (MMR) vaccine is 97% effective against measles and 88% effective against mumps, according to the Centers for Disease Control and Prevention (CDC).
The seasonal flu vaccine is between 40% and 60% effective (it varies from year to year, depending on that year’s vaccine and flu strains), but it still prevented an estimated 7.5 million cases of the flu in the U.S. during the 2019-2020 flu season, according to the CDC.
So, if efficacy means some percent fewer cases of COVID-19, what counts as a “case of COVID”? Both Pfizer and Moderna defined a case as having at least one symptom (however mild) and a positive COVID-19 test.
Johnson & Johnson defined a “case” as having a positive COVID-19 test plus at least one moderate symptom (such as shortness of breath, abnormal blood oxygen levels or abnormal respiratory rate) or at least two milder symptoms (such as fever, cough, fatigue, headache, or nausea).
Someone with a moderate case of COVID-19 by this definition could either be mildly affected or be incapacitated and feel pretty sick for a few weeks.
… And none of the three vaccine trials looked at all for asymptomatic COVID-19. “All these efficacy numbers are protection from having symptoms, not protection from being infected,” Barker said.
… But all three trials also used a second, potentially more important, definition of “cases.” What we care most about is protecting people from the worst outcomes of COVID-19: hospitalization and death.
So Moderna, Pfizer and Johnson & Johnson also measured how their vaccines performed against severe disease (which meant severely affected heart or respiratory rate, the need for supplemental oxygen, ICU admission, respiratory failure or death).
All three vaccines were 100% effective at preventing severe disease six weeks after the first dose (for Moderna) or seven weeks after the first dose (for Pfizer and Johnson & Johnson, the latter of which requires only one dose). Zero vaccinated people in any of the trials were hospitalized or died of COVID-19 after the vaccines had fully taken effect.
Beware misleading terminology! The base rate fallacy
Dr. Katelyn Jetelina writes about how newspaper articles and social media discussions about science can be misleading. This is a great example: in countries where many people are already vaccinated against covid-19, some people nonetheless do become infected with various variants of covid-19.
Does this mean that the vaccines are useless? Not at all, in fact quite the opposite. She explains the simple logic of the math:
In Israel, 50% of infected are vaccinated, and base rate bias she writes:
The delta variant of covid-19 has arrived in Israel, and with its arrival, cases are increasing (albeit relatively small). And, this is expected. We’ve seen it in the UK. and India. and Indonesia. And South Africa. And Russia. No country is 100% vaccinated. And this coupled with Delta being more transmissible and preliminary evidence suggesting its ability to escape natural immunity, unvaccinated people and populations are in trouble.
The statistic that’s concerning most (and that’s in the news) is a detail the Director General of the Health Ministry of Israel (Professor Chevy Levy) said during a radio interview. When asked how many of the new COVID19 cases had been vaccinated, Levy said that, “we are looking at a rate of 40 to 50%”.
This must mean the Delta variant is escaping our vaccines, right? When I started digging into the numbers, though, this might not be as alarming as it seems.
This is likely an example of base rate bias in epidemiology (it’s called base rate fallacy in other fields).
Professor Levy said that “half of infected people were vaccinated”. This language is important because it’s very different than “half of vaccinated people were infected”. And this misunderstanding happens all. the. time.
The more vaccinated a population, the more we’ll hear of the vaccinated getting infected. For example, say there’s a community that’s 100% vaccinated. If there’s transmission, we know breakthrough cases will happen. So, by definition, 100% of outbreak cases will be among the vaccinated. It will just be 100% out of a smaller number.
Cue Israel. They are one of the global leaders in vaccinations; 85% of Israeli adults are vaccinated. So, say we have the following scenario:
-100 adult community
-4 COVID19 cases
-50% of cases were among the vaccinated
With an infection rate among the vaccinated of 2% and infection rate of 13% among the unvaccinated, this would give us an efficacy rate of 85%. This is pretty darn close to the clinical trial efficacy rate, meaning the Pfizer vaccine is still working against Delta.
Unfortunately, this gets more complicated. We know the original Israeli outbreaks were in two schools. Because the vast majority of kids in Israel are not vaccinated (only 2-4% because they were just approved), imbalance is introduced. But, I ran the numbers and as long as at least 90% of the adults in the original outbreak were vaccinated, we know the vaccine is still working against Delta. 91% isn’t a farfetched number as teachers (at least in the US) are vaccinated at a much higher rate than the general public.
We need other fundamental details before we start to worry too. Like…
1. What did these outbreaks look like? How many people were at risk? How many people infected? What proportion of the infected were adults vs. kids?
2. How were the cases caught? Was there surveillance testing at the schools? In other words, were these asymptomatic cases? If not, what was the severity of the cases? What was the severity of the vaccinated cases?
3. Were vaccinated cases fully or partially vaccinated? We know 1 dose of vaccines doesn’t work well against Delta.
Bottom Line: I have more questions than answers. And we will (hopefully) get answers to these questions soon. But, there’s a strong possibility that this is a textbook example of base rate bias. Which means I’m optimistic that this is just further evidence the vaccine works against Delta on an individual level. However, this does NOT mean that we should
About the author of this section: Katelyn Jetelina has a Masters in Public Health and PhD in Epidemiology and Biostatistics. She is an Assistant Professor at a School of Public Health where her research lab resides.
High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy
Here’s the good news, take-home message:
The vast majority of fully vaccinated persons who have subsequently been infected are either asymptotic or have very mild symptoms. Only one or two recently infected vaccinated persons have been hospitalized. That’s great news – and exactly what was predicted. This in fact is how all vaccines work. None of them work literally 100%. There will always be a few people who can get infected and then sick, just a tiny percent. And even then, when such people do get sick, most of the time it is very mild and they just stay home for a day or two. Very few become very sick.
More to the point, merely being infected is basically meaninglessness: In fact, a vaccine only works when a person *is* infected. A vaccine (for any virus) doesn’t prevent infection, it protects the person from succumbing to the infection. It’s not a magical protective bubble surrounding a person.
Thinking rationally: examining the base rate fallacy
Why do we rely on specific information over statistics? Base Rate Fallacy explained.
______________________________________________________
This website is educational. Materials within it are being used in accord with the Fair Use doctrine, as defined by United States law.
§107. Limitations on Exclusive Rights: Fair Use. Notwithstanding the provisions of section 106, the fair use of a copyrighted work, including such use by reproduction in copies or phone records or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright. In determining whether the use made of a work in any particular case is a fair use, the factors to be considered shall include: the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes; the nature of the copyrighted work; the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and the effect of the use upon the potential market for or value of the copyrighted work. (added pub. l 94-553, Title I, 101, Oct 19, 1976, 90 Stat 2546)
Seaspiracy – documentary or propaganda?
Seaspiracy is a 2021 documentary about the impact of fishing on marine wildlife directed by Ali Tabrizi. The film investigates the effects of plastic marine debris and overfishing around the world and argues that commercial fisheries are the main driver of marine ecosystem destruction. Is this an even-handed piece of journalism, based on science, or is this propaganda? Here we go through criticism of this movie by scientists working in the field, who see this film as misleading, and intellectually dishonest.
They also discuss implicit (albeit, unintended) racism, with upper middle class white people making movies, demanding that huge numbers of people in the Pacific Islands and off the coasts of Asia and Africa must all lose their jobs, in order to make everyone vegan.
What teachers should say to our students
Be aware that all documentaries come with some view and bias.
Students should take care to see if the film makers make specific claims, citing peer-reviewed sources, or if they just more boardly make statements of fact that are hard to (or impossible) to source.
If the filmmakers do cite a peer-reviewed article, is that article representative of the field, or is it an outlier that the great majority of scientists disagree with.
Are the filmmakers citing papers that were later retracted?
We should discuss how the peer review process is all part of science. This includes papers being revised, or occasionally withdrawn. Revision or withdrawing a paper, by the way, isn’t a sign of a problem: that is exactly what one would expect to find in an open, transparent system. Problems only arise if problems are discovered but the author refuses to revise, or if a paper is retracted, but a documentarian nonetheless cites the retracted paper without noting that it is no longer considered correct.
Global Aquaculture Alliance rebuttal to Seaspiracy
Seaspiracy film assails fishing and aquaculture sectors that seem ready for a good fight, Lauren Kramer, Global Aquaculture Alliance, 3/26/2021
“We know the producer is trying to convince an audience not to eat seafood. He’s gone into filmmaking with a desired outcome for his audience, and that’s not documentary making, it’s propaganda,” Gavin Gibbons, VP, communications at NFI, told the Advocate. “We know from Tabrizi’s previous movies, Cowspiracy and What The Health, that the facts are very relative when it comes to this filmmaker.”
Soon after its release, NFI began debunking some of the key arguments the film makes. “The idea that the oceans will be empty by 2048 is based on a completely debunked 2006 statistic, refuted by the author of the original study. The 2048 statistic was put to rest by a follow-up report in the journal Science released in 2009 under the title New hope for fisheries,” it noted.
New hope for fisheries. Scientists document prospects for recovery, call for more global action, AAAS, 7/30/2009
Seaspiracy director Tabrizi interviews Richard Oppenlander, owner of a vegan company and animal rescue sanctuary, who endorses the call to ban fishing in 30 percent of the oceans by 2030 based on his calculation that “less than 1 percent of our oceans are being regulated,” a point that NFI retorted is “not only inaccurate, it’s nonsensical.”
In his coverage of illegal, unregulated and unreported (IUU) fishing in Africa, Tabrizi claims that one in every three wild caught fish imported into the United States were caught illegally and therefor sold illegally, a statistic that prominent U.S. fisheries researcher Ray Hilborn wrote was not credible, and that the retraction of the approach has been a long, drawn-out process.
Pramod et al. methods to estimate IUU are not credible
Ray Hilborn et al
Marine Policy, Volume 108, October 2019, 103632
https://www.sciencedirect.com/science/article/abs/pii/S0308597X19303318
and
Retraction drama continues, Max Mossler, Sustainable Fisheries, University of Washington, 7/14/2019
Response by Christina Hicks
Environmental social scientist at Lancaster Environment Centre, adjunct at JCU
Unnerving to discover your cameo in a film slamming an industry you love & have committed your career to. I’ve a lot to say about #seaspiracy- but won’t. Yes there are issues but also progress & fish remain critical to food & nutrition security in many vulnerable geographies.
Absolutely they raise important issues that need addressing, but there was no real conversation (intersectional or otherwise) and their conclusion-to stop eating fish a) doesn’t address the systematic injustices & b) threatens livelihoods and food security.
Here is a resource put together by academics at UW. I work on fisheries contributions to food and nutrition security. There are important messages in the film. And we do need to challenge corporate control. I just don’t think all fishers are the villains
Rebuttal by Josette Emlen Genio
Sustainable Markets Consultant at Sustainable Fisheries Partnership (SFP)
She writes
No scientist would support the assertion that all fish stocks will be collapsed by 2048. There are threats, however.
https://sustainablefisheries-uw.org/fisheries-2048/
“The latest FAO State of World Fisheries and Aquaculture report (25) indicates that the fraction of overfished stocks has increased since 2000 (from 27% to 33%), while this study suggests that abundance of stocks is increasing.”
“Effective fisheries management instrumental in improving fish stock status” Ray Hilburn et al., Proc Natl Acad Sci USA, 2020 Jan 28;117(4):2218-2224 doi: 10.1073/pnas.1909726116. Epub 2020 Jan 13.
Thoughts by Francisco Blaha
An institutional fisheries advisor. IUU, PSM & Labor issues for FFA/FAO/NZMFAT & others.
Here it is: for all of those that tell me to watch “Seaspiracy” I started and got feed up very soon… Is a kick in the guts for most of the people I work with here in the WCPO that are doing the right thing and managing their fisheries. Be outside and point fingers stuff. Of course, there are many problems! No one doubts that. But also things progressively working in many regions like the WCPO, I choose to focus my work on those. “Gloom sells but does not help”.
Furthermore. to be totally honest: I’m over the set up where, the “bad guys” are predominantly Asian, the “victims” predominantly black/brown, and the “good guys” talking about it and saving the ocean are predominantly white. While I’m sure is well intended, still drags cliche stereotypes and racist overtones.
As for the science background research of the film… as an example… a couple of minutes on google would have shown him that even the lead author of the paper retracted the claim.
Yes, I understand you may choose to not eat fish for whatever reasons you choose to believe. Is your privilege to have a choice. Yet all food production systems have impacts, and it is easy to dismiss one when your livelihood does not depend on them, like for most Pacific Islands
These countries are managing their fisheries sustainably because they are capable and understand better than anyone else, the implications of a failure. They don’t need the uncalled opinion of privileged people to tell them that doesn’t matter what they can scientifically prove.
FFA 2019 Tuna Economics Indicators Brochure
Click to access FFA%202019%20Tuna%20Economic%20Indicators%20Brochure%202019.pdf
The western and central Pacific tuna fishery: 2019 overview and status of stocks, Fisheries, Aquaculture and Marine Ecosystems
https://fame1.spc.int/en/component/content/article/251
Rebuttal by Josette Emlen Genio
I renewed my Netflix subscription just for this, and I was disappointed. Besides the many inaccuracies, I have a gazillion thoughts and sentiments about this documentary, but I’ll be more interested to hear what my fellow colleagues in marine conservation NGOs, many of which have been discredited in the film, have to say😞 But here’s my 2 cents (beware of spoilers!):
While I agree on several of the cases they presented, you cannot ask people to just “stop eating fish and go vegan” (yes that’s exactly the docu’s message) WITHOUT considering the socio-economic impacts of this in MANY fisheries-dependent, food-deficit communities. Overfishing and Illegal, Unreported and Unregulated (IUU) fishing are not only driven by greed, but also by POVERTY.
There’s a distinct line between industrial and artisanal fishing. It’s easy to say “boycott seafood” when options are afforded to you or you do not understand the complexities of the struggles and plight of fishermen. In many coastal communities in Asia and Latin America, the oceans are their LIFEBLOOD that provides them MAIN source if not the ONLY source of livelihood and food security. More than 90% of world’s fishers are NOT from industrial fishing fleets- they are smallholder, subsistence fishers – and thus stand to benefit from eating more sustainable and responsibly-caught seafood.
When it comes to sustainability, the type, size, source, and harvest method of fish always matter. Eating matang-baka or tanigue vs “industrial” salmon or tuna will GREATLY VARY in terms of impacts. And marine conservation NGOs are working hard, so consumers have informed choices. Drastic, blanket recommendations will have drastic, unimaginable consequences. Remember that.
Accusations of racism
I dare them to tell small-scale fishers, esp the ones in the developing countries that they must stop eat and do something that keeps them alive Face with look of triumph This kind of approach – is just another example of white savior complex. I am still enraged!
The documentary outright says that the large scale fishering fleets are taking the food from the small-scale fishers and causing hunger. The dumb “just don’t eat fish” message is obviously made for the viewers that are 90% first world rich people NOT dependant on fish at all.
Magnus Johnson writes
Intelligence of crows: Research project
How intelligent are corvids/crows? (Rooks, jackdaws, jays, magpies, treepies, etc.)
This image from thecut.com/2016/07/crows-continue-to-be-terrifyingly-intelligent.html
Background
In order to investigate this one must first clearly understand:
(A) What are birds? See – Birds
(B) What are corvids? See – Corvidae
(C) How do we know if they are intelligent, sapient, sentient? You’ll need to look up the scientific definitions of these words.
The main idea: How smart are corvids?
How can we design tests or games to interest them, so we can test their intelligence?
Do they have self-awareness/sentience?
Do they have emotions?
How good are they at recognizing individual human faces?
How good is their memory?
Create your report
Create a written report using MS Word/Google Docs. This will have images, text, perhaps short animations if you like. If you like, you can use the built-in voice-to-text; this will transcribe your words.
Create a video, using your favorite software & apps. This will have images, text, perhaps short animations if you like. You’ll narrate it. Share the project as a video file with us.
Create a PowerPoint/Google Slides presentation. This will have images, text, perhaps short animations if you like.
Create an Infographic. There are many websites and apps out there to do this. Choose your favorite apps. This will have images, text, perhaps short animations if you like.
Cite your sources, avoid plagiarism
See Good writing and avoiding plagiarism
What is genetic material?
What is genetic material? What are genes for?
Look closely inside any living creature – plants, animals, even fungi.
If you use a microscope you can see individual cells.
Looking even more closely you can see that cells have a nucleus
Look even more closely inside the nucleus and you’ll see chromosomes.
(Here the nucleus has been punctured, and chromosomes are spilling out.)
Now if you look with some super sophisticated techniques then you’ll see that these chromosome aren’t solid.
They seem to be made of a kind of thread, something really thin that is wrapped up to make a shape.
Looking even close, this thread is made up of molecules bonded together into a kind of helix (spiral shape.)
Not just that, but two spiral shapes wrapped around each other – a double helix
This beautiful molecule here is DNA.
The DNA wraps itself up to make those chromosomes.
Why is it here? This contains the instructions of life itself.
DNA contains all of the information necessary to build a living thing.
Each separate piece of DNA – each gene – builds a different part of the organism.
So we call this genetic material.
There’s another important type of genetic material, RNA
In most forms of life DNA is the “original copy”, the master blueprint.
Cells work by making a working copy of the blueprint.
This copy is made of mRNA (messenger RNA) molecules.
That RNA then leaves the nucleus (see above animation) and gets used by the cell to build things.
So both DNA and RNA are types of genetic information.
Genetic info in viruses
Although viruses are not alive in the same way that cells are, they also have genetic material.
Some viruses have DNA, others have RNA.
The basic idea is still the same. The DNA, or RNA, in a virus is the instruction set to build more virus particles.
Thanks for visiting. See our articles on
Astronomy, Biology, Chemistry, Earth Science, Mathematics, Physics
Beyond immediate death count: Long Covid and blood clots: Covid-19 as a blood clot disease
Coronavirus disease 2019 (COVID-19 ) is caused by a virus. Its name is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2.) This is one of a number of respiratory viruses.
Myth: Covid only affects the lungs. And only about 0.5% of infected people get sick and die, so the rest of us will be okay.
Fact: Covid-19 is an endothelial blood clot disease as well as a pulmonary disease. Blood clots travel to all other organs in the body, including the brain, and can cause serious damage even in survivors. People are at least ten times more likely to get blood clots issues and neurological issues,than dying.
Many covid-19 survivors report painful and debilitating symptoms. Some report feeling like they were being suffocated. During these episodes their blood oxygen levels drop, which causes biochemical stress in many organs.
The death rate alone is staggeringly higher than what we normally see from influenza.
A death rate of .5% is higher than any other viral pandemic that has hit the United States since the Spanish flu, the 1918 flu pandemic. The United States of America has a population of over three hundred million people. Over eight hundred thousand Americans have already died due to this disease. If left unchecked, Covid-19 would kill millions Americans.
Deaths are just a small part of the coronavirus story: Covid-19 is an endothelial blood clot disease.
Many covid-19 patients have blood clots in the legs, lungs, and cerebral arteries leading to the brain. Likely in other locations as well.
Above image: formation of an occlusive thrombus in a vein.
Take blood clots seriously
Blood clots are no joke. They may lead to.
* strokes
* encephalitis (swelling of the brain)
* heart attacks
* inflammation of the heart
* deep vein thromboses in the legs
* clots in the lungs
* stroke-causing clots in cerebral arteries.
* pain, shortness of breath
* fatigue, dizziness due to lack of oxygen to the brain
* kidney failure
* degradation of kidney dialysis: clots can clog kidney dialysis machines.
Doctors have documented short term neurological damage in covid patients, even in some otherwise asymptomatic people.
It is likely that there is long-term neurological damage as well.
“If you start to put all of the data together that’s emerging, it turns out that this virus is probably a vasculotropic virus, meaning that it affects the [blood vessels],”
In a paper published in April in the scientific journal The Lancet, Mehra and a team of scientists discovered that the SARS-CoV-2 virus can infect the endothelial cells that line the inside of blood vessels.
Endothelial cells protect the cardiovascular system, and they release proteins that influence everything from blood clotting to the immune response. In the paper, the scientists showed damage to endothelial cells in the lungs, heart, kidneys, liver, and intestines in people with Covid-19.
– Covid-19 May Be a Blood Vessel Disease, Dana G. Smith
How covid-19 attacks the brain
John Hamilton writes
Many patients who are hospitalized for COVID-19 are discharged with symptoms such as those associated with a brain injury….
COVID-19 also appears to produce many other brain-related symptoms ranging from seizures to psychosis, a team reports in the Jan. 5 issue of the journal Alzheimer’s & Dementia…. it may even increase a person’s risk of developing Alzheimer’s disease.
For many affected patients, brain function improves as they recover. But some are likely to face long-term disability, de Erausquin says.
… “What we found was that the very small blood vessels in the brain were leaking,” Nath says. “And it wasn’t evenly — you would find a small blood vessel here and a small blood vessel there.” The injuries resembled those from a series of tiny strokes occurring in many different areas of the brain, Nath says.
How COVID-19 Attacks The Brain And May Cause Lasting Damage, Jon Hamilton
Conclusions
Many covid-19 survivors may die many years or decades earlier than they otherwise would have, due to the blood clots and endothelial damage.
The full death toll of Covid-19 will likely be many times higher than the current toll. As 1/2022 over 839,000 Americans have died. It is certain that that over the coming years and decades many more people will die from their covid-19 damage. As such, we should be diligent in protecting ourselves, our loved ones, and everyone in our communities.
How to protect ourselves
Gather knowledge, e.g. Covid 19 is an airborne virus
Wearing masks in certain situations – Unmasking mask myths
Note that vaccinated people can be protected yet still transmit covid-19.
Social distancing
Washing hands
Zinc supplements and coronaviruses, rhinoviruses, common cold
Getting a covid-19 vaccination
Covid-19 Vaccine Tracker, Bloomberg
High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy
References
High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy
What Does COVID Do to Your Blood? John Hopkins Medicine, Panagis Galiatsatos, M.D., M.H.S. and Robert Brodsky, M.D.
Covid-19 May Be a Blood Vessel Disease, Which Explains Everything, Dana G. Smith, Elemental, 5/29/2020
How COVID-19 Attacks The Brain And May Cause Lasting Damage, Jon Hamilton, Shots: NPR Health News, 1/5/2021
Microvascular Injury in the Brains of Patients with Covid-19 Letters, New England Journal of Medicine, Myoung-Hwa Lee et al, DOI: 10.1056/NEJMc2033369
The chronic neuropsychiatric sequelae of COVID‐19: The need for a prospective study of viral impact on brain functioning, Gabriel A. de Erausquin et al, Alzheimer’s & Dementia [journal,] 1/5/2021, https://doi.org/10.1002/alz.12255
Our Covid-19 articles
Respiratory viruses (influenza, rhinoviruses, coronaviruses etc)
How do viruses spread? Airborne vs non-airborne
Beyond immediate death count: Long Covid and blood clots: Covid-19 as a blood clot disease
High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy
How vaccinated people can be protected yet still transmit covid-19
Vaccines – what does 95% efficacy actually mean?
Simple DIY masks could help flatten the curve. We should all wear them in public.
Unmasking mask myths
Zinc supplements and coronaviruses, rhinoviruses, common cold
There is reason to believe that taking over-the-counter Zinc supplements can reduce the severity and duration of infection by respiratory viruses such as coronavirus.
Warning: Like all nutritional and dietary supplement studies, this is a notoriously difficult topic to research, because there’s no way for researchers to be certain of exactly what people do or don’t eat during the period of the study.
Biochemistry
In what forms does Zinc exists in our gut, after digestion, and before absorption:
As the Zinc (II) ion – Zn2+
In what form does Zinc exist in our bloodstream and in our cells?
Same as above – Zn2+
Do we normally need to take zinc supplements?
No. Severe zinc deficiency is rare, usually caused by an inherited condition.
We usually don’t see people deficient in zinc unless they have either a malabsorption syndromes or chronic alcoholism.
The recommended dietary allowance (RDA) for adult men is 11 mg/day; for adult women 8 mg/day of zinc.
For those who do take high doze zinc supplements for a long time (UL; 40 mg/day for adults) we should watch our copper levels. Long term use of higher dose zinc can result in copper deficiency
Zinc dietary supplements
Some doctors recommend taking zinc supplements when one feels the onset of cold, influenza, or covid symptoms.
It is often sold as Zinc gluconate (the zinc salt of gluconic acid.)
This is an ionic compound consisting of two anions of gluconate for each zinc(II) cation.
Zinc gluconate is a popular form for the delivery of zinc as a dietary supplement.
– Zinc and the common cold, Wikipedia
Evidence for using Zinc to treat coronaviruses and rhinoviruses
Many doctors advocate taking zinc lozenges within one day of the onset of symptoms of a cold, coronavirus, or rhinovirus.
Always check with your doctor first; some suggest taking a Zinc supplement every 3 hours (during waking hours) until you feel better.
The following section has been excerpted from Zinc, Linus Pauling Institute, Micronutrient Information Center, Oregon State University.
A 2013 Cochrane review confirmed that oral zinc administrated within 24 hours of symptom onset could reduce the duration of cold symptoms (14 trials, 1,656 participants)
– Singh M, Das RR. Zinc for the common cold. Cochrane Database Syst Rev. 2013(6)
Oral zinc was effective regardless of the age of participants (children or adults) and the type of zinc formulation (gluconate/acetate lozenges or sulfate syrup).
Beneficial effects on cold duration were seen in trials that provided more than 75 mg/day of zinc but not in trials that used lower doses.
The pooled analysis of five trials found no evidence of an effect of oral zinc on the severity of cold symptoms.
The analysis of secondary trial outcomes suggested a faster resolution of specific cold symptoms (cough, nasal congestion, nasal drainage, sore throat) and a lower proportion of participants exhibiting cold symptoms after seven days of treatment in zinc- versus placebo-supplemented participants.
– Singh M, Das RR. Zinc for the common cold. Cochrane Database Syst Rev. 2013(6)
With numerous well-controlled trials and meta-analyses, the efficacy of zinc lozenges or syrup in treating common cold symptoms is no longer questionable.
A meta-analysis of seven trials recently reported a 33% reduction in the duration of cold symptoms with the intake of zinc lozenges (>75 mg/day of elemental zinc)
– Hemila H. Zinc lozenges and the common cold: a meta-analysis comparing zinc acetate and zinc gluconate, and the role of zinc dosage. JRSM Open. 2017;8(5)
However, many supplemental zinc formulations available over-the-counter have been found to release zero zinc ions (i.e., the biologically active form of zinc) or to contain additives (e.g., magnesium, certain amino acids, citric acid) that either cancel out the benefit of zinc or worsen cold symptoms.
– Eby GA, 3rd. Zinc lozenges as cure for the common cold–a review and hypothesis. Med Hypotheses. 2010;74(3):482-492
Although taking zinc lozenges for a cold every two to three hours while awake will result in daily zinc intakes well above the tolerable upper intake level (UL) of 40 mg/day for adults, the use of zinc at daily doses of 50 to 180 mg for one to two weeks has not resulted in serious side effects.
– Eby GA, 3rd. Zinc lozenges as cure for the common cold–a review and hypothesis. Med Hypotheses. 2010; 74(3):482-492
Do not use zinc supplements for long periods of time (6 or more weeks) unless under a doctor’s orders. Long term use could result in copper deficiency.
What about Zinc nasal sprays?
Intranasal zinc preparations: pooled analysis … showed no overall benefit of intranasal zinc on the risk of still experiencing cold symptoms by day 3.
– D’Cruze H, Arroll B, Kenealy T. Is intranasal zinc effective and safe for the common cold? A systematic review and meta-analysis. J Prim Health Care. 2009;1(2):134-139.
Of serious concern are several case reports of individuals experiencing loss of the sense of smell (anosmia) after using intranasal zinc as a cold remedy.
Since zinc-associated anosmia may be irreversible, most doctors hold that intranasal zinc preparations should be avoided.
References
A Guide to Human Zinc Absorption: General Overview and Recent Advances of In Vitro Intestinal Models (great graphics) by Maria Maares and Hajo Haase , Nutrients 2020, 12(3), 762; https://doi.org/10.3390/nu12030762
https://www.mdpi.com/2072-6643/12/3/762/htm
Frederickson, C.J.; Koh, J.Y.; Bush, A.I. The neurobiology of zinc in health and disease.
Nat. Rev. Neurosci. 2005, 6, 449–462 https://www.nature.com/articles/nrn1671
KaiserScience 
