Chlorine and Bleach terminology
Terminology alert: Sometimes people use the same word to describe different things. For example, “chlorine” can refer to:
Chlorine
a single, neutral, chlorine atom. These are unstable.
We normally never encounter one.
They almost instantly bind to each other to form chlorine molecules.
Chlorine
molecule (Cl2) – deadly gas
Chlorine
A chlorine ion is chlorine atom that has picked up an extra electron.
In small quantities these ions are essential for life.
“Chlorine”
There are many chemicals used to bleach laundry, or disinfect swimming pools.
The most common is “chlorine bleach”, sodium hypochlorite.
Chemical formula is NaOCl
In water this breaks down into a sodium cation (Na+) and a hypochlorite anion (OCl−
or ClO− ).
Visualizing the electron distribution in sodium hypochlorite a little more accurately.
How to make sodium hypochlorite
Add chlorine gas (Cl2) to caustic soda (NaOH).
Then sodium hypochlorite, water (H2O) and salt (NaCl) are produced according to the following reaction:
Cl2 + 2NaOH + → NaOCl + NaCl + H2O
How does sodium hypochlorite disinfection work?
By adding hypochlorite to water, hypochlorous acid (HOCl) is formed:
NaOCl + H2O → HOCl + NaOH–
Hypochlorous acid is divided into hydrochloric acid (HCl) and oxygen (O).
Sodium hypochlorite is effective against bacteria, viruses and fungi.
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
Lenz’s law
Lenz’s law demonstration
Lenz’s law is named after the physicist Heinrich Friedrich Emil Lenz (pronounced /ˈlɛnts/) who formulated it in 1834.
The direction of the electric current induced in a conductor by a changing magnetic field is such that the magnetic field created by the induced current opposes the initial changing magnetic field.
It is a qualitative law that specifies the direction of induced current.
This law tells us nothing about the current’s magnitude.
Lenz’s law predicts the direction of many effects in electromagnetism, such as:
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the direction of voltage induced in an inductor or wire loop by a changing current
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the drag force of eddy currents exerted on moving objects in a magnetic field.
Lenz’s law is not really a law of physics on its own. It is a phenomenon which can be predicted from a more general law of physics, Faraday’s law of induction.
Faraday’s law of induction itself is a subset of the even more fundamental MAXWELL’s EQUATIONS.
Step-by-step explanation
Take a copper tube (conductive but non-magnetic.) Drop a piece of steel down through the tube.
The piece of steel will fall through, as you might expect.
It accelerates very close to the acceleration due to gravity.
Only air friction and possible rubbing against the inside of the tube prevent it from reaching the acceleration due to gravity.
Now take the same copper tube and drop a strong magnet through it
Neodymium or other rare earth magnets work the best. Now the magnet falls very slowly.
This is because the copper tube experiences a changing magnetic field from the falling magnet.
This changing magnetic field induces a current in the copper tube.
The induced current in the copper tube creates its own magnetic field ,
one that opposes the magnetic field that created it!
This lesson has been archived ScienceJoyWagon and from regentsprep.org, Oswego City School District, NY.
TBA – create link to this in Electromagnetic Induction
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
Probiotics and human health
What are probiotics?
Probiotics are live microorganisms that are intended to have health benefits. Products sold as probiotics include foods (such as yogurt), dietary supplements, and products that aren’t used orally, such as skin creams.
Although people often think of bacteria and other microorganisms as harmful “germs,” many microorganisms help our bodies function properly. For example, bacteria that are normally present in our intestines help digest food, destroy disease-causing microorganisms, and produce vitamins. Large numbers of microorganisms live on and in our bodies. Many of the microorganisms in probiotic products are the same as or similar to microorganisms that naturally live in our bodies.
What Kinds of Microorganisms Are In Probiotics?
The most common are bacteria that belong to groups called Lactobacillus and Bifidobacterium. Each of these two broad groups includes many types of bacteria. Other bacteria may also be used as probiotics, and so may yeasts such as Saccharomyces boulardii.
Probiotics, Prebiotics, and Synbiotics
“prebiotics” refers to dietary substances that favor the growth of beneficial bacteria over harmful ones.
“synbiotics” refers to products that combine probiotics and prebiotics.
How Popular Are Probiotics?
Data from the 2012 National Health Interview Survey (NHIS) show that about 4 million (1.6 percent) U.S. adults had used probiotics or prebiotics in the past 30 days. Among adults, probiotics or prebiotics were the third most commonly used dietary supplement other than vitamins and minerals, and the use of probiotics quadrupled between 2007 and 2012.
What the Science Says About the Effectiveness of Probiotics
Researchers have studied probiotics to find out whether they might help prevent or treat a variety of health problems, including:
- Digestive disorders such as diarrhea caused by infections, antibiotic-associated diarrhea, irritable bowel syndrome, and inflammatory bowel disease
- Allergic disorders such as atopic dermatitis (eczema) and allergic rhinitis (hay fever)
- Tooth decay, periodontal disease, and other oral health problems
- Colic in infants
- Liver disease
- The common cold
- Prevention of necrotizing enterocolitis in very low birth weight infants.
There’s preliminary evidence that some probiotics are helpful in preventing diarrhea caused by infections and antibiotics and in improving symptoms of irritable bowel syndrome, but more needs to be learned. We still don’t know which probiotics are helpful and which are not. We also don’t know how much of the probiotic people would have to take or who would most likely benefit from taking probiotics. Even for the conditions that have been studied the most, researchers are still working toward finding the answers to these questions.
Probiotics are not all alike. For example, if a specific kind of Lactobacillus helps prevent an illness, that doesn’t necessarily mean that another kind of Lactobacillus would have the same effect or that any of the Bifidobacterium probiotics would do the same thing.
Although some probiotics have shown promise in research studies, strong scientific evidence to support specific uses of probiotics for most health conditions is lacking. The U.S. Food and Drug Administration (FDA) has not approved any probiotics for preventing or treating any health problem. Some experts have cautioned that the rapid growth in marketing and use of probiotics may have outpaced scientific research for many of their proposed uses and benefits.
How might they work? (What is their causal mechanism?0
Probiotics may have a variety of effects in the body, and different probiotics may act in different ways.
Probiotics might:
- Help to maintain a desirable community of microorganisms
- Stabilize the digestive tract’s barriers against undesirable microorganisms or produce substances that inhibit their growth
- Help the community of microorganisms in the digestive tract return to normal after being disturbed (for example, by an antibiotic or a disease)
- Outcompete undesirable microorganisms
- Stimulate the immune response.
What science says about the safety of probiotics
Whether probiotics are likely to be safe for you depends on the state of your health.
- In people who are generally healthy, probiotics have a good safety record. Side effects, if they occur at all, usually consist only of mild digestive symptoms such as gas.
- On the other hand, there have been reports linking probiotics to severe side effects, such as dangerous infections, in people with serious underlying medical problems. The people who are most at risk of severe side effects include critically ill patients, those who have had surgery, very sick infants, and people with weakened immune systems
Even for healthy people, there are uncertainties about the safety of probiotics. Because many research studies on probiotics haven’t looked closely at safety, there isn’t enough information right now to answer some safety questions. Most of our knowledge about safety comes from studies of Lactobacillus and Bifidobacterium; less is known about other probiotics. Information on the long-term safety of probiotics is limited, and safety may differ from one type of probiotic to another.
Quality Concerns About Probiotic Products
Some probiotic products have been found to contain smaller numbers of live microorganisms than expected. In addition, some products have been found to contain bacterial strains other than those listed on the label.
Source of info: US Dept of Health and Human Services, NIH, NCCIH Pub No. D345
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Where did the idea of using probiotics first develop?
The idea came from Nobel laureate Élie Metchnikoff. He postulated that yogurt-consuming Bulgarian peasants lived longer lives because of that custom. He suggested in 1907 that “the dependence of the intestinal microbes on the food makes it possible to adopt measures to modify the microbiota in our bodies and to replace the harmful microbes by useful microbes”.
There is a growing body of peer-reviewed science which indeed shows that there is a link between our gut flora (varieties of bacteria that live in our gut) and our health. But this link is complex, and it may vary widely from person to person, depending on their genes, and their gut biome.
Studies on gut bacteria and physical health
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Studies on gut bacteria and mental health
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Studies which show that treatment should be personalized
Senior author Eran Elinav, an immunologist at the Weizmann Institute of Science in Israel, and colleagues found that many people’s gastrointestinal tracts reject generic probiotics before they can get to work. Even worse, Elinav’s team found that microbial competition from off-the-shelf probiotics can prevent natural gut bacteria from reestablishing themselves after being wiped out by antibiotic drugs.
“I think our findings call for a fundamental change from the currently utilized one-size-fits-all paradigm, in which we go to the supermarket and buy a formulation of probiotics which is designed by some company, to a new method which is personalized,” Elinav says. “By measuring people in a data-driven way, one would be much better able to harness different probiotic combinations in different clinical contexts.”
… Elinav’s group isn’t claiming that probiotic supplements don’t carry heavy doses of beneficial gut bacteria. In fact, the studies confirm that they do. Because many probiotics are sold as dietary supplements, and thus aren’t subject to approval and regulation by many national drug agencies, including the U.S. Food and Drug Administration, the team first set out to ensure that the probiotic supplements in the study actually contained the 11 main strains they were supposed to deliver.
“All those strains were present and viable to consumption and beyond, following the passage through the GI tract, and even in stool, and they were still viable,” Elinav says.
But uncovering what impact these strains of bacteria have on the people who consume them required more digging, poking through patient’s stool and even inside their guts.
The authors set out to directly measure gut colonization by first finding 25 volunteers to undergo upper endoscopies and colonoscopies to map their baseline microbiomes in different parts of the gut. “Nobody has done anything quite like this before,” says Matthew Ciorba, a gastroenterologist at Washington University in Saint Louis School of Medicine unaffiliated with the study. “This takes some devoted volunteers and some very convincing researchers to get this done.”
Some of the volunteers took generic probiotics, and others a placebo, before undergoing the same procedures two months later. This truly insider’s look at the gut microbiome showed some people were “persisters,” whose guts were successfully colonized by off-the-shelf probiotics, while others, called “resisters,” expelled them before they could become established. The research suggests two reasons for the variability in the natural response of different gastrointestinal tracts to probiotics.
First and foremost is each person’s indigenous microbiome, or the unique assembly of gut bacteria that helps dictate which new strains will or won’t be able to join the party. The authors took gut microbiomes from resistant and persistent humans alike and transferred them into germ-free mice, which had no microbiome of their own. All the mice were then given the same probiotic preparation.
“We were quite surprised to see that the mice that harbored the resistant microbiome resisted the probiotics that were given to them, while mice that were given the permissive microbiome allowed much more of the probiotics to colonize their gastrointestinal tract,” Elinav explains. “This provides evidence that the microbiome contributes to a given person’s resistance or permissiveness to given probiotics.”
The second factor affecting an individual’s response to probiotics was each host’s gene expression profile. Before the probiotics were administered, volunteers who ended up being resistant were shown to have a unique gene signature in their guts—specifically, a more activated state of autoimmune response than those who were permissive to the supplements.
“So it’s probably a combination of the indigenous microbiome and the human immune system profile that team up to determine a person’s specific state of resistance or colonization to probiotics,” Elinav says. These factors were so clear that the team even found that they could predict whether an individual would be resistant or permissive by looking at their baseline microbiome and gut gene expression profile.
This unusual in situ gastrointestinal tract sampling also turned out to be key, because in a number of cases the microbiota composition found in a patient’s stool was only partially correlated with what was found inside the gut. In other words, simply using stool samples as a proxy can be misleading.
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The benefits of probiotics may not be so clear cut
Related articles
Do Probiotics Really Work? Scientific American
Learning Standards
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We don’t always need to make a hypothesis
Newton didn’t frame hypotheses. Why should we?
The success of a grant proposal shouldn’t hinge on whether the research is driven by a hypothesis, especially in the physical sciences.
Scott Milner, Physics Today, 24 Apr 2018
“Not hypothesis driven.” With those words and a fatal grade of “Very Good,” a fellow reviewer on a funding agency panel consigned the proposal we were discussing to the wastebasket. I listened in dismay. Certainly the proposal had hypotheses, though it didn’t have boldface sentences beginning “We hypothesize . . .” as signposts for inattentive readers. Then I remembered the famous words from Isaac Newton’s Principia: Hypotheses non fingo. “I do not frame hypotheses.” If that approach worked for Newton, why do we have such a mania for hypothesis-driven research today?
The emphasis on hypothesis-driven research in proposals is strangely embedded in the scientific community, with no obvious origin in funding agencies. The word hypothesisappears nowhere in the NSF guide to writing and reviewing proposals, and only once in the National Institutes of Health proposal guide. Yet grant-writing experts universally stress that proposals should be built around hypotheses and warn that those not written this way risk rejection as “fishing expeditions.”
In recent years, a few voices in the biosciences community have questioned this exclusive focus on hypothesis-driven research, even as the mania spreads to the physical sciences. Allow me to add my voice. Evaluating grant proposals is hard, but shoehorning every proposal into the language of hypothesis testing benefits neither the prospective grantee nor the evaluator. It can also hinder scientific progress.
Today many high school teachers present the scientific method as synonymous with hypothesis testing. Yet hypotheses are just ideas about how nature works, or what 19th-century scientist and philosopher William Whewell called “happy guesses.” Hypotheses organize our thinking about what might be true, based on what we’ve observed so far. If we have a guess about how nature works, we do experiments to test the guess. In quantitative sciences, the role of theory is to work out consequences of the guess in conjunction with things we know.
Perhaps the most famous hypothesis in all of science is that new species arise from the action of natural selection on random mutations. Charles Darwin based his hypothesis on observations of a few species during his famous voyage to the Galápagos. Charged with predictive power, Darwin’s hypothesis applies to all life, everywhere, at all times. Generations of biologists have tested and built on Darwin’s hypothesis with a vast array of new discoveries. The theory of evolution is now firmly established as the central pillar of biology, as well supported by evidence as any theory in science.
But what would Darwin have written had he been obliged to write a proposal to fund his voyage on HMS Beagle? He didn’t have the hypothesis of natural selection yet—it grew out of the very observations he was setting out to make. If he wrote, truthfully, that “the isolated islands we will visit are excellent natural laboratories to observe what becomes of species introduced to a new locale,” it would be judged by today’s standards as a fishing expedition without a strong hypothesis.
What did Newton hypothesize, despite his protests to the contrary? He identified the right variables for the problem of planetary motion: force and momentum. Newton’s grant proposal might have read: “I hypothesize that momenta and forces are the right variables to describe the motion of the planets. I propose to develop mathematical methods to predict their orbits, which I will compare with existing observations.” That’s not quite a guess about how nature works, but rather the best way to describe motion mathematically, which by its widespread success grew into intuitive concepts of force, momentum, and energy.
Newton wrote hypotheses non fingo because of what he didn’t hypothesize. He wrote in reaction to vortex theories of gravity originated by René Descartes and Christiaan Huygens. They imagined that so-called empty space was actually filled with swirling vortices of invisible particles that swept the planets along in their orbits. The vortex idea is certainly a guess about how gravity works; it’s just not a very helpful guess. The idea of invisible particles that only reveal themselves by effects on unreachably distant planets is too elastic a notion. It’s not specific enough to make testable predictions. In the language of 20th-century philosopher of science Karl Popper, it’s not readily falsifiable.
Newton didn’t provide a just-so story, a fanciful mechanism for why momentum was conserved or how gravity arose. Instead he formulated simple rules that describe how the planets move—and as it turns out, how nearly everything else moves under ordinary circumstances. Powerful as Newton’s insight was, his description of gravity had the unsettling feature of “spooky action at a distance” of the Sun on the planets, and indeed every mass on every other mass. It took another 250 years for an explanation of the physical origin of gravity.
Albert Einstein’s hypothesis about gravity, unlike Newton’s, was mechanistic: Mass curves space, which is slightly elastic; as a result, straight lines bend near massive objects, including the path of light from distant stars passing near the Sun on its way to our telescopes. It took years for Einstein to develop the math to show that Newton’s description, which was consistent with so many observations, was only an approximation—and to make astounding predictions of things that happen to huge masses (collapse into black holes) or when big masses move really fast (gravitational waves).
Setting physical science apart
So why is present-day funding so focused on hypothesis-driven research? A clue is that hypothesis-driven experimental design is best suited to certain influential fields, especially molecular biology and medicine. Researchers in those fields study complicated, irreducible systems (living organisms), have limited experimental probes, and are often forced to work with small data sets. Unavoidably, the most common experimental protocol in these fields is to poke at a complex living system by giving it a drug or chemical and then measuring some indirectly related response. Those experiments live and die by the statistical test. When a scatter plot of stimulus versus response looks like a cloud of angry bees, the formal discipline of testing the null hypothesis is essential.
That is an overly narrow paradigm for what experiments can be. In the physical sciences, we are more able to manipulate and simplify the system of interest. We also enjoy more powerful experimental techniques, in many ways extensions of human senses, allowing us to see into a material, to listen to how it rings in response to being pinged with electromagnetic fields, to feel how it responds to a gentle push on the nanoscale.
When you can do those things, experiments can be so much more than testing whether changing X influences Y with statistical significance. In fact, the history of science can be viewed as the development of new ways to probe nature. The Hubble Space Telescope was not driven by a hypothesis but rather by a desire to see deeper into the universe. Observations from Hubble and other modern telescopes enable new hypotheses about the early universe to be formulated and tested.
Progress in science often depends on advances in how to measure something important. A century after Einstein, ultrasensitive detectors brilliantly confirmed his prediction of gravitational waves. Those detectors rely on clever ideas for using lasers and interferometry to measure extremely tiny changes in the distance between two points on Earth. That work was not hypothesis driven, except in the obvious sense that general relativity predicts gravitational waves. Likewise, progress in quantitative sciences often relies on advances in our ability to compute the consequences of hypotheses that already exist.
Hypotheses are all well and good. But in evaluating research proposals, the key criterion should be: Will the proposed work help us answer an important question or reveal an important new question we should have been asking all along?
Scott Milner is William H. Joyce Chair and Professor of Chemical Engineering at the Pennsylvania State University.
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