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How antibiotics work
Antibiotics are chemicals that disrupt and kill bacteria.
Note that they don’t kill viruses, fungi, or parasites.
For example, influenza (“the flu”) is a virus, not a bacteria. Therefore antibiotics can’t help fight the influenza virus.
Introduction
Antibiotics work by blocking vital processes in bacteria, killing the bacteria or stopping them from multiplying.
This helps the body’s natural immune system to fight the infection.
Different antibiotics work against different types of bacteria.
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Antibiotics that affect a wide range of bacteria are called broad spectrum antibiotics (eg, amoxicillin and gentamicin).
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Antibiotics that affect only a few types of bacteria are called narrow spectrum antibiotics (eg, penicillin).
Different types of antibiotics work in different ways.
For example, penicillin destroys bacterial cell walls, while other antibiotics can affect the way the bacterial cell works.
Doctors choose an antibiotic according to the bacteria that usually cause a particular infection.
Sometimes your doctor will do a test to identify the exact type of bacteria causing your infection and its sensitivity to particular antibiotics.
Antibiotic medicines may contain one or more active ingredients and be available under different brand names. The medicine label should tell you the active ingredient and the brand name.
_ from NPS MedicineWise, Australian Govt. Dept. of Health
Simple animation showing how an antibiotic disrupts the building of a cell wall.
Once the cell wall is disrupted, water can enter, making the cell swell, and eventually burst.
Image from Waterborne Diseases: Typhoid, By Olivia W.
Ways that antibiotics can disrupt bacteria
You can right-click on each image to expand it, or click here for the original page. It shows us several different types of antibiotics. Each has a different way of disrupting a bacteria,
This image is from “Mechanisms of Bacterial Resistance to Aminoglycoside Antibiotics”, 2019 RCSB PDB Video Challenge for High School Students. from the PDB-101 website. This is an educational portal of the RCSB PDM (protein data bank.)
and
Related content
What is an antibiotic? Form Learn.Genetics, Univ. of Utah
Learning Standards
MassachusettsComprehensive Health
8.1 Describe how the body fights germs and disease naturally and with medicines and
immunization
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
8.13 Explain how the immune system functions to prevent and combat disease
8.19 Explain the prevention and control of common communicable infestations, diseases, and infections
Benchmarks for Science Education, AAAS
Inoculations use weakened germs (or parts of them) to stimulate the body’s immune system to react. This reaction prepares the body to fight subsequent invasions by actual germs of that type. Some inoculations last for life. 8F/H4
If the body’s immune system cannot suppress a bacterial infection, an antibacterial drug may be effective—at least against the types of bacteria it was designed to combat. Less is known about the treatment of viral infections, especially the common cold. However, more recently, useful antiviral drugs have been developed for several major kinds of viral infections, including drugs to fight HIV, the virus that causes AIDS. 8F/M6** (SFAA)
Pasteur found that infection by disease organisms (germs) caused the body to build up an immunity against subsequent infection by the same organisms. He then produced vaccines that would induce the body to build immunity to a disease without actually causing the disease itself. 10I/M3*
Investigations of the germ theory by Pasteur, Koch, and others in the 19th century firmly established the modern idea that many diseases are caused by microorganisms. Acceptance of the germ theory has led to changes in health practices. 10I/M4*
Current health practices emphasize sanitation, the safe handling of food and water, the pasteurization of milk, isolation, and aseptic surgical techniques to keep germs out of the body; vaccinations to strengthen the body’s immune system against subsequent infection by the same kind of microorganisms; and antibiotics and other chemicals and processes to destroy microorganisms. 10I/M7** (BSL)
Zombie based geography
I want to share these ideas with other educators and with students.
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Zombie-Based Learning (ZBL) is the brainchild of David Hunter, former teacher from the Bellevue Big Picture school, in a suburb of Seattle, Washington. It uses Project-Based Learning to encourage active engagement, problem solving and critical thinking skills.
Student photo made available from Zombie-Based Learning (ZBL),
When the zombies attack, where should we run, where regroup, and where rebuild our lives? Those questions, key to survival, can focus student attention on a highly motivating and dangerously overlooked fact: Geography skills can save you from the zombie apocalypse!
Use students’ natural desire to survive zombie assaults to motivate study of a complete curriculum based on the 2012 National Geography Standards, and then to apply those skills in a series of scenarios based on surviving when the attacks come to your own neighborhood.
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Making History is Project-Based Learning curriculum created by award-winning teacher David Hunter, designed for standards-based classrooms. Launched on Kickstarter, it’s nine units with projects for middle school students. Teach cross-content or by individual subject, with a time travel backstory to drive students’ interest and engagement. The narrative follows a group of entrepreneurial and altruistic students who go back in time, and work together to invent or discover critical breakthroughs BEFORE they occur in our true historical timeline.
Handouts
Mysterious link between immune system and mental illness
He Got Schizophrenia. He Got Cancer. And Then He Got Cured.
A bone-marrow transplant treated a patient’s leukemia — and his delusions, too. Some doctors think they know why.
By Moises Velasquez-Manoff
Mr. Velasquez-Manoff is a science writer.
The man was 23 when the delusions came on. He became convinced that his thoughts were leaking out of his head and that other people could hear them. When he watched television, he thought the actors were signaling him, trying to communicate. He became irritable and anxious and couldn’t sleep.
Dr. Tsuyoshi Miyaoka, a psychiatrist treating him at the Shimane University School of Medicine in Japan, eventually diagnosed paranoid schizophrenia. He then prescribed a series of antipsychotic drugs. None helped. The man’s symptoms were, in medical parlance, “treatment resistant.”
A year later, the man’s condition worsened. He developed fatigue, fever and shortness of breath, and it turned out he had a cancer of the blood called acute myeloid leukemia. He’d need a bone-marrow transplant to survive. After the procedure came the miracle. The man’s delusions and paranoia almost completely disappeared. His schizophrenia seemingly vanished.
Years later, “he is completely off all medication and shows no psychiatric symptoms,” Dr. Miyaoka told me in an email. Somehow the transplant cured the man’s schizophrenia.
A bone-marrow transplant essentially reboots the immune system. Chemotherapy kills off your old white blood cells, and new ones sprout from the donor’s transplanted blood stem cells. It’s unwise to extrapolate too much from a single case study, and it’s possible it was the drugs the man took as part of the transplant procedure that helped him. But his recovery suggests that his immune system was somehow driving his psychiatric symptoms.
At first glance, the idea seems bizarre — what does the immune system have to do with the brain? — but it jibes with a growing body of literature suggesting that the immune system is involved in psychiatric disorders from depression to bipolar disorder.
The theory has a long, if somewhat overlooked, history. In the late 19th century, physicians noticed that when infections tore through psychiatric wards, the resulting fevers seemed to cause an improvement in some mentally ill and even catatonic patients.
Inspired by these observations, the Austrian physician Julius Wagner-Jauregg developed a method of deliberate infection of psychiatric patients with malaria to induce fever. Some of his patients died from the treatment, but many others recovered. He won a Nobel Prize in 1927.
One much more recent case study relates how a woman’s psychotic symptoms — she had schizoaffective disorder, which combines symptoms of schizophrenia and a mood disorder such as depression — were gone after a severe infection with high fever.
Modern doctors have also observed that people who suffer from certain autoimmune diseases, like lupus, can develop what looks like psychiatric illness. These symptoms probably result from the immune system attacking the central nervous system or from a more generalized inflammation that affects how the brain works.
Indeed, in the past 15 years or so, a new field has emerged called autoimmune neurology. Some two dozen autoimmune diseases of the brain and nervous system have been described. The best known is probably anti-NMDA-receptor encephalitis, made famous by Susannah Cahalan’s memoir “Brain on Fire.” These disorders can resemble bipolar disorder, epilepsy, even dementia — and that’s often how they’re diagnosed initially. But when promptly treated with powerful immune-suppressing therapies, what looks like dementia often reverses. Psychosis evaporates. Epilepsy stops. Patients who just a decade ago might have been institutionalized, or even died, get better and go home.
Admittedly, these diseases are exceedingly rare, but their existencesuggests there could be other immune disorders of the brain and nervous system we don’t know about yet.
Dr. Robert Yolken, a professor of developmental neurovirology at Johns Hopkins, estimates that about a third of schizophrenia patients show some evidence of immune disturbance. “The role of immune activation in serious psychiatric disorders is probably the most interesting new thing to know about these disorders,” he told me.
Studies on the role of genes in schizophrenia also suggest immune involvement, a finding that, for Dr. Yolken, helps to resolve an old puzzle. People with schizophrenia tend not to have many children. So how have the genes that increase the risk of schizophrenia, assuming they exist, persisted in populations over time? One possibility is that we retain genes that might increase the risk of schizophrenia because those genes helped humans fight off pathogens in the past. Some psychiatric illness may be an inadvertent consequence, in part, of having an aggressive immune system.
Which brings us back to Dr. Miyaoka’s patient. There are other possible explanations for his recovery. Dr. Andrew McKeon, a neurologist at the Mayo Clinic in Rochester, Minn., a center of autoimmune neurology, points out that he could have suffered from a condition called paraneoplastic syndrome. That’s when a cancer patient’s immune system attacks a tumor — in this case, the leukemia — but because some molecule in the central nervous system happens to resemble one on the tumor, the immune system also attacks the brain, causing psychiatric or neurological problems. This condition was important historically because it pushed researchers to consider the immune system as a cause of neurological and psychiatric symptoms. Eventually they discovered that the immune system alone, unprompted by malignancy, could cause psychiatric symptoms.
Another case study from the Netherlands highlights this still-mysterious relationship. In this study, on which Dr. Yolken is a co-author, a man with leukemia received a bone-marrow transplant from a schizophrenic brother. He beat the cancer but developed schizophrenia. Once he had the same immune system, he developed similar psychiatric symptoms.
The bigger question is this: If so many syndromes can produce schizophrenia-like symptoms, should we examine more closely the entity we call schizophrenia?
Some psychiatrists long ago posited that many “schizophrenias” existed — different paths that led to what looked like one disorder. Perhaps one of those paths is autoinflammatory or autoimmune.
If this idea pans out, what can we do about it? Bone marrow transplant is an extreme and risky intervention, and even if the theoretical basis were completely sound — which it’s not yet — it’s unlikely to become a widespread treatment for psychiatric disorders. Dr. Yolken says that for now, doctors treating leukemia patients who also have psychiatric illnesses should monitor their psychiatric progress after transplantation, so that we can learn more.
And there may be other, softer interventions. A decade ago, Dr. Miyaoka accidentally discovered one. He treated two schizophrenia patients who were both institutionalized, and practically catatonic, with minocycline, an old antibiotic usually used for acne. Both completely normalized on the antibiotic. When Dr. Miyaoka stopped it, their psychosis returned. So he prescribed the patients a low dose on a continuing basis and discharged them.
Minocycline has since been studied by others. Larger trials suggest that it’s an effective add-on treatment for schizophrenia. Some have argued that it works because it tamps down inflammation in the brain. But it’s also possible that it affects the microbiome — the community of microbes in the human body — and thus changes how the immune system works.
Dr. Yolken and colleagues recently explored this idea with a different tool: probiotics, microbes thought to improve immune function. He focused on patients with mania, which has a relatively clear immunological signal. During manic episodes, many patients have elevated levels of cytokines, molecules secreted by immune cells. He had 33 mania patients who’d previously been hospitalized take a probiotic prophylactically. Over 24 weeks, patients who took the probiotic (along with their usual medications) were 75 percent less likely to be admitted to the hospital for manic attacks compared with patients who didn’t.
The study is preliminary, but it suggests that targeting immune function may improve mental health outcomes and that tinkering with the microbiome might be a practical, cost-effective way to do this.
Watershed moments occasionally come along in medical history when previously intractable or even deadly conditions suddenly become treatable or preventable. They are sometimes accompanied by a shift in how scientists understand the disorders in question.
We now seem to have reached such a threshold with certain rare autoimmune diseases of the brain. Not long ago, they could be a death sentence or warrant institutionalization. Now, with aggressive treatment directed at the immune system, patients can recover. Does this group encompass a larger chunk of psychiatric disorders? No one knows the answer yet, but it’s an exciting time to watch the question play out.
Moises Velasquez-Manoff, the author of “An Epidemic of Absence: A New Way of Understanding Allergies and Autoimmune Diseases” and an editor at Bay Nature magazine, is a contributing opinion writer.
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Related readings
https://en.wikipedia.org/wiki/Neuroimmunology
Emerging Subspecialties in Neurology: Autoimmune neurology
https://education.questdiagnostics.com/insights/104
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499978/
6 page PDF article. http://www.med.or.jp/english/pdf/2004_09/425_430.pdf
https://www.quora.com/What-are-some-autoimmune-neurological-disorders-How-are-they-treated
Metabolism
What are we learning about?
* Hundreds of chemical reactions occur simultaneously in every living cell.
* The entire set of them are collectively known as metabolism .
* in some reactions, complex molecules are broken down to produce energy
* in other reactions, energy is used to build up complex molecules.
Anabolism
From Greek ἁνά, “upward” and βάλλειν, “to throw”
All the chemical pathways in which cells bond smaller molecules together to make macromolecules (larger ones.)
The energy source is another set of processes, catabolism (see below)
Anabolism is used to
create news cells
build muscles and tissues.
grow and mineralize bone
Catabolism
From the Greek κάτω kato, “downward” and βάλλειν ballein, “to throw”
All the chemical pathways in which cells break down large molecules into smaller ones.
Cells gain energy from the breakdown, or create smaller pieces, which become building materials in anabolism.
Catablism is used to:
break proteins down into amino acids
break DNA molecules down into individual nucelotides
convert sugar into ATP and other small organic molecules
Another way to show these metabolic pathways:
BBC Bitezie revisions
Endocrine hormones regulate our metabolism
Hormones can be classified as anabolic or catabolic.
Anabolic hormones are the anabolic steroids, which stimulate protein synthesis and muscle growth, and insulin.
Catabolic hormones include
cortisol (breaks down large molecules into simple sugars, for quick energy)
glucagon (breaks down large molecules into glucose and fatty acids)
adrenaline – increases blood flow to muscles, output of the heart, blood sugar level.
Our article on the endocrine hormone system.
What does metabolism look like inside a cell? Here’s a simplified view:
Image from An Introduction to Nutrition, v. 1.0. 2012books.lardbucket.org/books/an-introduction-to-nutrition
Metabolic map
This is a metro-style map of the metabolism of most life on Earth.
Image by Bert Chan, Hong Kong, via Wikimedia. https://www.behance.net/bertchan
Interactive Metabolic Pathways Map – New Edition | Sigma-Aldrich
Related articles
Scaling-and-biophysics: As animals get larger and larger, how would their metabolism need to change?
Cellular respiration: An introduction
Interactive metabolism maps or apps
Metabolic pathways from Learn.Genetics
Clickable metabolic map from metabolicpathways.teithe.gr
Wiley college textbook step-by-step animations
Roche biochemical pathway online map
Learning Standards
MS-LS1-3. Use argument supported by evidence for how the body is a system of interacting subsystems composed of groups of cells. Emphasis is on the conceptual understanding that cells form tissues and tissues form organs specialized for particular body functions. Examples could include the interaction of subsystems within a system and the normal functioning of those systems.
MS-LS1-7. Develop a model to describe how food is rearranged through chemical reactions forming new molecules that support growth and/or release energy as this matter moves through an organism. Emphasis is on describing that molecules are broken apart and put back together and that in this process, energy is released.
TBA
Green algae
Are green algae plants?
Red algae and brown algae aren’t plants – they’re protists – an entirely different kingdom of life.
Blue-green algae – photosynthetic bacteria.
But what about green algae – are they plants?
It depends on whom you ask:
Image from Slideshare.net/VijayaraghavanGonuguntla/effluent-treat
Types of algae
Botanists (plant scientists) consider green algae plants:
They perform photosynthesis using chlorophyll.
They are the ancestors of modern day land-plants.
They’re part of the land-plant family tree.
End of story -> Plants! 🙂
Zoologists (animal and protist scientists) classify green algae as protozoans (not plants)
In this view, green algae can’t be plants because:
1) Most are single-celled (unicellular), too small to be seen without a microscope.
2) When not single celled, they live in colonies. Don’t form plant tissue.
3) They can move on their own. Some swim with flagella.
4) They have no vascular system to transport nutrients.
5) They do not have true roots, shoots, or veins.
6) They have no stems, leaves or roots.
Why can’t the answer be a simple “yes they are” or “no they are not?” Because life wasn’t created with well-defined boundaries – and life today still doesn’t have such boundaries.
Life started as simple organisms and developed over time, slowly branching out to create new forms, with new characteristics.
Today’s green algae resembles the early forms of life that later gave rise to both plants and to protists. It is a kind of “living fossil.
Plant and green algae family tree
from Leliaert F., Verbruggen H. & Zechman F.W. (2011) Into the deep: New discoveries at the base of the green plant phylogeny. BioEssays 33: 683-692
This figure shows the phylogenetic relationships among the main lineages of green plants. The tree topology is a composite on accepted relationships based on molecular phylogenetic evidence. Uncertain phylogenetic relationships are indicated by polytomies. The divergence times are rough approximations based on the fossil record and molecular clock estimates. These age estimates should be interpreted with care as different molecular clock studies have shown variation in divergence times between major green plant lineages. Drawings illustrate representatives of each lineage.
Source: Leliaert F., Verbruggen H. & Zechman F.W. (2011) Into the deep: New discoveries at the base of the green plant phylogeny. BioEssays 33: 683-692
Learning Standards
Massachusetts Science and Technology/Engineering Curriculum Framework
Life Science (Biology), Grades 6–8. Classify organisms into the currently recognized kingdoms according to characteristics that they share. Be familiar with organisms from each kingdom.
Biology, High School – 5.2 Describe species as reproductively distinct groups of organisms. Recognize that species are further classified into a hierarchical taxonomic system (kingdom, phylum, class, order, family, genus, species) based on morphological, behavioral, and molecular similarities.
Benchmarks for Science Literacy, American Association for the Advancement of Science
Students should begin to extend their attention from external anatomy to internal structures and functions. Patterns of development may be brought in to further illustrate similarities and differences among organisms. Also, they should move from their invented classification systems to those used in modern biology… A classification system is a framework created by scientists for describing the vast diversity of organisms, indicating the degree of relatedness between organisms, and framing research questions.
Evolution and diversity: Origin of life, evidence of evolution, patterns of evolution, natural selection, speciation, classification and diversity of organisms.
Teaching About Evolution and the Nature of Science, National Academy Press (1998)
Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.
Angiosperms and Gymnosperms
Plant life that exists on land is classified as Embryophyta.
Such life can be divided into vascular and non-vascular plants.
Land plant life can be divided into plants that produce seeds and plants that don’t produce seeds.
Seed plants create soils, forests, and food.
For most people these are the most familiar kinds of plants. (Seedless plants like mosses, liverworts, horsetail are often overlooked because of their size or appearance.)
Conifers are seed plants; they include pines, firs, yew, redwood, and many other large trees.
Other major group of seed-plants are the flowering plants, including plants whose flowers are showy, but also many plants with reduced flowers – such as the oaks, grasses, and palms.
Here we look specifically at vascular plants with seeds. They come in two families – the angiosperms and gymnosperms.
Angiosperms
These produce flowers, develop seeds in a fruit, have an endosperm within their seeds.
The most diverse group of land plants. With 416 families containing 300,000 species.
Includes all plants that we call flowers. Includes Fruits, grains, vegetables, trees, shrubs, grasses and flowers
They make up around 80 percent of all the living plant species on Earth.
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Dicots
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monocots
Angiosperm resources PBS Natureworks: Angiosperms
Gymnosperms
Gymnosperms were the first plants to have seeds.
They have naked seeds (no shells)
The seeds develop on the surface of the reproductive structures of the plants, rather than being contained in a specialized ovary.
These seeds are often found on the surface of cones and short stalks.
They do not have flowers or fruits.
They are pollinated by the wind.
Groups
Cycadophyta, the cycads, a subtropical and tropical group of plants.
Ginkgophyta, only has one living species of tree left, genus Ginkgo.
Pinophyta, the conifers, cone-bearing trees and shrubs. pines, firs, yew, redwood
Gnetophyta, woody plants in these genera – Ephedra (shrubs, vines, and a few small trees), Gnetum ( tropical evergreen trees, shrubs and woody vines.)
Examples include conifers
Gymnosperm resources
Education Portal: Gymnosperms
Study.com gymnosperms-characteristics-definition-types
Monocot versus dicot
Here we break down the angiosperm plants into monocots and dicots.
Let’s look up close at monocot and dicot seeds:
Let’s watch the two types sprout:
Grass (monocot) sprouting on left. The cotyledon remains underground and is not visible).
Compare to a dicot sprouting on the right.
{ http://en.wikipedia.org/wiki/Monocotyledon }
What kinds of plants come from these different types of seeds?
Monocot plants versus dicot plants
Comparison chart
Learning Standards
Massachusetts Science and Technology/Engineering Curriculum Framework
Life Science (Biology), Grades 6–8.
Classify organisms into the currently recognized kingdoms according to characteristics that they share. Be familiar with organisms from each kingdom.
Biology, High School
5.2 Describe species as reproductively distinct groups of organisms. Recognize that species are further classified into a hierarchical taxonomic system (kingdom, phylum, class, order, family, genus, species) based on morphological, behavioral, and molecular similarities.
Benchmarks for Science Literacy, American Association for the Advancement of Science
Students should begin to extend their attention from external anatomy to internal structures and functions. Patterns of development may be brought in to further illustrate similarities and differences among organisms. Also, they should move from their invented classification systems to those used in modern biology… A classification system is a framework created by scientists for describing the vast diversity of organisms, indicating the degree of relatedness between organisms, and framing research questions.
Evolution and diversity: Origin of life, evidence of evolution, patterns of evolution, natural selection, speciation, classification and diversity of organisms.
Teaching About Evolution and the Nature of Science, National Academy Press (1998)
Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.
What are animals
What are we learning?
Classification of animals
Characteristics of animals
The major animal groups
Why are we learning this?
The study of animals is essential to the understanding of life on Earth. Animals are one of the many branches of earth’s life.
Animal kingdom is just one part of the tree of life
We see it here on the far right.
Animals include mammals, including humans, insects, birds, fish and more.
Image by Madeleine Price Ball. Simplified universal phylogenetic tree, made using information from the Interactive Tree of Life. Ciccarelli, et al., Mar 3 2006, Science Vol. 311
Characteristics of animals
Multicellular – animals are made of many cells.
Animals are differentiated into separate tissues. *
* except for the simplest forms, e.g. sea sponges.
Eukaryotic – cells have a nucleus, and many organelles.
Each organelle has its own job.
Cell have flexible cell membranes
(only plants and bacteria have rigid cell walls)
Animals have a body plan that becomes fixed as they develop.
It’s not just random growth of cells.
Animals are motile – they can move (as opposed to plants, which can’t)
Animals are heterotrophs – they must eat other organisms for sustenance.
Classification of animals
Animals are divided into sub-groups.
Vertebrates: animals with a backbone
birds, mammals, amphibians, reptiles (*), fish.
(*) Reptiles, well, they’re kind of not really a meaningful group – we’ll learn about that later.
Invertebrates: animals without a backbone
Coelenterata – comb jellies, coral animals, true jellies (“jellyfish), sea anemones, etc.
Flatworms – Planarians, flukes and tapeworms
Annelids – over 17,000 species including ragworms, earthworms, and leeches.
Mollusks – clams, oysters, octopuses, squid, snails
Arthropods – millipedes, centipedes, insects, spiders, scorpions, crabs, lobsters, shrimp
Arachnids – 100,000 species of spiders, scorpions, ticks, mites, etc.
Crustacean – 17,000 species of crabs, lobsters, crayfish, shrimp, krill and barnacles.
Insects – over a million different species!
Myriapoda – Over 13,000 species of centipedes and millipedes
Sea sponges (not shown on the diagram above)
Learning Standards
Massachusetts Science and Technology/Engineering Curriculum Framework
Life Science (Biology), Grades 6–8.
Classify organisms into the currently recognized kingdoms according to characteristics that they share. Be familiar with organisms from each kingdom.
Biology, High School
5.2 Describe species as reproductively distinct groups of organisms. Recognize that species are further classified into a hierarchical taxonomic system (kingdom, phylum, class, order, family, genus, species) based on morphological, behavioral, and molecular similarities.
Benchmarks for Science Literacy, American Association for the Advancement of Science
Students should begin to extend their attention from external anatomy to internal structures and functions. Patterns of development may be brought in to further illustrate similarities and differences among organisms. Also, they should move from their invented classification systems to those used in modern biology… A classification system is a framework created by scientists for describing the vast diversity of organisms, indicating the degree of relatedness between organisms, and framing research questions.
Evolution and diversity: Origin of life, evidence of evolution, patterns of evolution, natural selection, speciation, classification and diversity of organisms.
Teaching About Evolution and the Nature of Science, National Academy Press (1998)
Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.
What is a species?
What is a species?
It first meant a distinctly-describable type.
Then, a distinct type that could not interbreed;
Then, a distinct types that could breed and produce fertile offspring.
Today, a species is defined as: A group that, in natural surroundings, breeds exclusively within the group.
Like any definition, it has exceptions, such as coyotes, dogs, and wolves, which can interbreed, yet are considered separate species. But this definition works fairly well.
– Adapted from “An Online Introduction to the Biology of Animals and Plants” by Michael McDarby, Fulton-Montgomery Community College.
http://faculty.fmcc.suny.edu/mcdarby/animals&plantsbook/History/02-Explaining-Life-Classification.htm
Example of salamanders evolving today
Happening in the San Joaquin Valley, central California.
…a rare but fascinating phenomenon [is] known as “ring species.” This occurs when a single species becomes geographically distributed in a circular pattern over a large area. Immediately adjacent or neighboring populations of the species vary slightly but can interbreed. But at the extremes of the distribution — the opposite ends of the pattern that link to form a circle — natural variation has produced so much difference between the populations that they function as though they were two separate, non-interbreeding species.
this can be likened to a spiral-shaped parking garage. A driver notices only a gentle rise as he ascends the spiral, but after making one complete circle, he finds himself an entire floor above where he started.
A well-studied example of a ring species is the salamander Ensatina escholtzii of the Pacific Coast region of the United States. In Southern California, naturalists have found what look like two distinct species scrabbling across the ground. One is marked with strong, dark blotches in a cryptic pattern that camouflages it well. The other is more uniform and brighter, with bright yellow eyes, apparently in mimicry of the deadly poisonous western newt. These two populations coexist in some areas but do not interbreed — and evidently cannot do so.
Moving up the state, the two populations are divided geographically, with the dark, cryptic form occupying the inland mountains and the conspicuous mimic living along the coast. Still farther to the north, in northern California and Oregon, the two populations merge, and only one form is found. In this area, it is clear that what looked like two separate species in the south are in fact a single species with several interbreeding subspecies, joined together in one continuous ring.”
– http://www.pbs.org/wgbh/evolution/library/05/2/l_052_05.html
Evolution in action
Did Watson and Crick really steal Rosalind Franklin’s data?
Sexism in science: did Watson and Crick really steal Rosalind Franklin’s data?
The race to uncover the structure of DNA reveals fascinating insights into how Franklin’s data was key to the double helix model, but the ‘stealing’ myth stems from Watson’s memoir and attitude rather than facts.
X-ray diffraction image of the double helix structure of the DNA molecule, taken 1952 by Raymond Gosling, commonly referred to as “Photo 51”, during work by Rosalind Franklin on the structure of DNA (text Wikipedia)
Matthew Cobb, The Guardian, 6/23/15
The wave of protest that followed Sir Tim Hunt’s stupid comments about ‘girls’ in laboratories highlighted many examples of sexism in science. One claim was that during the race to uncover the structure of DNA, Jim Watson and Francis Crick either stole Rosalind Franklin’s data, or ‘forgot’ to credit her. Neither suggestion is true.
In April 1953, the scientific journal Nature published three back-to-back articles on the structure of DNA, the material our genes are made of. Together, they constituted one of the most important scientific discoveries in history.
The first, purely theoretical, article was written by Watson and Crick from the University of Cambridge. Immediately following this article were two data-rich papers by researchers from King’s College London: one by Maurice Wilkins and two colleagues, the other by Franklin and a PhD student, Ray Gosling.
Credit: Vittoria Luzzati/NPG
The model the Cambridge duo put forward did not simply describe the DNA molecule as a double helix. It was extremely precise, based on complex measurements of the angles formed by different chemical bonds, underpinned by some extremely powerful mathematics and based on interpretations that Crick had recently developed as part of his PhD thesis. The historical whodunnit, and the claims of data theft, turn on the origin of those measurements.
The four protagonists would make good characters in a novel – Watson was young, brash, and obsessed with finding the structure of DNA; Crick was brilliant with a magpie mind, and had struck up a friendship with Wilkins, who was shy and diffident. Franklin, an expert in X-ray crystallography, had been recruited to King’s in late 1950. Wilkins expected she would work with him, but the head of the King’s group, John Randall, led her to believe she would be independent.
From the outset, Franklin and Wilkins simply did not get on. Wilkins was quiet and hated arguments; Franklin was forceful and thrived on intellectual debate. Her friend Norma Sutherland recalled: “Her manner was brusque and at times confrontational – she aroused quite a lot of hostility among the people she talked to, and she seemed quite insensitive to this.”
Watson and Crick’s first foray into trying to crack the structure of DNA took place in 1952. It was a disaster. Their three-stranded, inside-out model was hopelessly wrong and was dismissed at a glance by Franklin. Following complaints from the King’s group that Watson and Crick were treading on their toes, Sir Lawrence Bragg, the head of their lab in Cambridge told them to cease all work on DNA.
However, at the beginning of 1953, a US competitor, Linus Pauling, became interested in the structure of DNA, so Bragg decided to set Watson and Crick on the problem once more.
At the end of January 1953, Watson visited King’s, where Wilkins showed him an X-ray photo that was subsequently used in Franklin’s Nature article. This image, often called ‘Photo 51’, had been made by Raymond Gosling, a PhD student who had originally worked with Wilkins, had then been transferred to Franklin (without Wilkins knowing), and was now once more being supervised by Wilkins, as Franklin prepared to leave the terrible atmosphere at King’s and abandon her work on DNA.
Watson recalled that when he saw the photo – which was far clearer than any other he had seen – ‘my mouth fell open and my pulse began to race.’ According to Watson, photo 51 provided the vital clue to the double helix. But despite the excitement that Watson felt, all the main issues, such as the number of strands and above all the precise chemical organisation of the molecule, remained a mystery. A glance at photo 51 could not shed any light on those details.
What Watson and Crick needed was far more than the idea of a helix – they needed precise observations from X-ray crystallography. Those numbers were unwittingly provided by Franklin herself, included in a brief informal report that was given to Max Perutz of Cambridge University.
In February 1953, Perutz passed the report to Bragg, and thence to Watson and Crick.
Crick now had the material he needed to do his calculations. Those numbers, which included the relative distances of the repetitive elements in the DNA molecule, and the dimensions of what is called the monoclinic unit cell – which indicated that the molecule was in two matching parts, running in opposite directions – were decisive.
The report was not confidential, and there is no question that the Cambridge duo acquired the data dishonestly. However, they did not tell anyone at King’s what they were doing, and they did not ask Franklin for permission to interpret her data (something she was particularly prickly about).
Their behaviour was cavalier, to say the least, but there is no evidence that it was driven by sexist disdain: Perutz, Bragg, Watson and Crick would have undoubtedly behaved the same way had the data been produced by Maurice Wilkins.
Ironically, the data provided by Franklin to the MRC were virtually identical to those she presented at a small seminar in King’s in autumn 1951, when Jim Watson was in the audience. Had Watson bothered to take notes during her talk, instead of idly musing about her dress sense and her looks, he would have provided Crick with the vital numerical evidence 15 months before the breakthrough finally came.
By chance, Franklin’s data chimed completely with what Crick had been working on for months: the type of monoclinic unit cell found in DNA was also present in the horse haemoglobin he had been studying for his PhD. This meant that DNA was in two parts or chains, each matching the other. Crick’s expertise explains why he quickly realised the significance of these facts, whereas it took Franklin months to get to the same point.
While Watson and Crick were working feverishly in Cambridge, fearful that Pauling might scoop them, Franklin was finishing up her work on DNA before leaving the lab. The progress she made on her own, increasingly isolated and without the benefit of anyone to exchange ideas with, was simply remarkable.
Franklin’s laboratory notebooks reveal that she initially found it difficult to interpret the outcome of the complex mathematics – like Crick, she was working with nothing more than a slide rule and a pencil – but by 24 February, she had realised that DNA had a double helix structure and that the way the component nucleotides or bases on each strand were connected meant that the two strands were complementary, enabling the molecule to replicate.
Above all, Franklin noted that ‘an infinite variety of nucleotide sequences would be possible to explain the biological specificity of DNA’, thereby showing that she had glimpsed the most decisive secret of DNA: the sequence of bases contains the genetic code.
To prove her point, she would have to convert this insight into a precise, mathematically and chemically rigorous model. She did not get the chance to do this, because Watson and Crick had already crossed the finishing line – the Cambridge duo had rapidly interpreted the double helix structure in terms of precise spatial relationships and chemical bonds, through the construction of a physical model.
In the middle of March 1953, Wilkins and Franklin were invited to Cambridge to see the model, and they immediately agreed it must be right. It was agreed that the model would be published solely as the work of Watson and Crick, while the supporting data would be published by Wilkins and Franklin – separately, of course. On 25 April there was a party at King’s to celebrate the publication of the three articles in Nature. Franklin did not attend. She was now at Birkbeck and had stopped working on DNA.
Franklin died of ovarian cancer in 1958, four years before the Nobel prize was awarded to Watson, Crick and Wilkins for their work on DNA structure. She never learned the full extent to which Watson and Crick had relied on her data to make their model; if she suspected, she did not express any bitterness or frustration, and in subsequent years she became very friendly with Crick and his wife, Odile.
Our picture of how the structure of DNA was discovered, and the myth about Watson and Crick stealing Franklin’s data, is almost entirely framed by Jim Watson’s powerful and influential memoir, The Double Helix. Watson included frank descriptions of his own appalling attitude towards Franklin, whom he tended to dismiss, even down to calling her ‘Rosy’ in the pages of his book – a nickname she never used (her name was pronounced ‘Ros-lind’). The epilogue to the book, which is often overlooked in criticism of Watson’s attitude to Franklin, contains a generous and fair description by Watson of Franklin’s vital contribution and a recognition of his own failures with respect to her – including using her proper name.
It is clear that, had Franklin lived, the Nobel prize committee ought to have awarded her a Nobel prize, too – her conceptual understanding of the structure of the DNA molecule and its significance was on a par with that of Watson and Crick, while her crystallographic data were as good as, if not better, than those of Wilkins. The simple expedient would have been to award Watson and Crick the prize for Physiology or Medicine, while Franklin and Watkins received the prize for Chemistry.
Whether the committee would have been able to recognise Franklin’s contribution is another matter. As the Tim Hunt affair showed, sexist attitudes are ingrained in science, as in the rest of our culture.
By Matthew Cobb
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Epigenetics
Epigenetics is the study of biological mechanisms that switch genes on and off. Epigenetics affects how genes are read by cells, and thus how they produce proteins. Here are a few important points:
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Epigenetics Controls Genes. Certain circumstances in life can cause genes to be silenced or expressed over time. In other words, they can be turned off (becoming dormant) or turned on (becoming active).
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Epigenetics Is Everywhere. What you eat, where you live, who you interact with, when you sleep, how you exercise, even aging – all of these can eventually cause chemical modifications around the genes that will turn those genes on or off over time.
Additionally, in certain diseases such as cancer or Alzheimer’s, various genes will be switched into the opposite state, away from the normal/healthy state.
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Epigenetics Makes Us Unique. Even though we are all human, why do some of us have blonde hair or darker skin? Why do some of us hate the taste of mushrooms or eggplants? Why are some of us more sociable than others? The different combinations of genes that are turned on or off is what makes each one of us unique. Furthermore, there have been indications that some epigenetic changes can be inherited.
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Epigenetics Is Reversible. With 20,000+ genes, what will be the result of the different combinations of genes being turned on or off? The possible arrangements are enormous! But if we could map every single cause and effect of the different combinations, and if we could reverse the gene’s state to keep the good while eliminating the bad… then we could theoretically* cure cancer, slow aging, stop obesity, and so much more.
This introduction has been excerpted from WhatIsEpigenetics.com
How does this happen?
We currently know of three systems that attach to genes, and turn them on or off. More systems may be discovered!
DNA methylation
histone modification
non-coding RNA (ncRNA)-associated gene silencing
More content TBA
Example 1
From The importance of gene–environment interactions in human obesity, Hudson Reddon, Jean-Louis Guéant, David Meyre, Clinical Science Aug 08, 2016, 130
Learning Standards
TBA
KaiserScience 