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Plant identification apps
Learning objectives
SWBAT (“students will be able to,” content, procedures, skills)
Describe characteristics of seeds and plants, based on observation.
Identify characteristics that are the same or different across various seeds and plants.
Use a dichotomous key
Vocabulary objectives
Tier II: Classify, Differentiate, Analyze
Tier III: Dichotomous key, bryophytes, vascular, seed, confiers, angiosperms, gymnosperms, monocotsm dicots
Connections
Life is classified in kingdoms; that plants are one of the many kingdoms; that this kingdom itself is broken down into many smaller groups. Students should be able to recognize what a plant looks like, and have the prior knowledge that plants need sunlight, space and water to survive.
Why identify plants?
Students should be able to explain several ways that plants are useful.
Answers might include:
Large scale food production
Local, community and home food production
Managing national and state parks
Necessary for a healthy ecosystem (biodiversity)
Necessary for human psychological health (contrast blighted areas with plant, tree and flower-rich yards.)

Biology, Miller and Levine, Chap 4, Pearson.
Use of plants in managing wildlife
From Noble News and Views:
“As natural resource managers, we must understand what we manage, and plant identification is a key component of that understanding.”
“whether you are a cow-calf producer, sheep and goat producer, wildlife manager, or manager of some combination of these enterprises, you should be paying close attention to what your management decisions are doing to the resources that support your enterprises: plants. After all, plants are what produce these products.”
“The ability to know, or identify, plants allows us to assess many important rangeland or pasture variables that are critical to proper management: range condition, proper stocking rates, forage production, wildlife habitat quality, and rangeland trend, either upward or downward.”
Noble.org – Plant-identification-is-it-worth-the-effort
Why use dichotomous keys?
Students often learn how to identify plants with dichotomous keys. This is a math and logic skill, valuable for classifying all forms of life (and any kind of classification system.)
A dichotomy is a partition of a whole (or a set) into two parts. This is an essential part of mathematical logic
The use of a dichotomous key for identification is an algorithm.

Apps
iNaturalist – https://www.inaturalist.org/
“Naturalist helps you identify the plants and animals around you. Get connected with a community of over 400,000 scientists and naturalists who can help you learn more about nature!”
PictureThis – https://www.picturethisai.com/
Helps more than 30,000,000 users identify, learn, and enjoy all kinds of plants: flowers, trees, succulents, cacti and more! Capable of identifying 10,000+ plant species.
Plantix – https://plantix.net/en/
Are you a farmer or hobby gardener and grow vegetables, fruit or arable crops? Are your plants sick; did you have losses in the last harvest? We are Plantix and offer you fast and free help. Whether you grow tomatoes, bananas or rice – Plantix is your interactive plant doctor. “
PlantNet Plant Identification https://plantnet.org/en/
This is a research and a citizen science project. Works on more than 20,000 wild plants, and ornamental and cultivated plants
Google Lens https://lens.google.com/
An image recognition technology developed by Google. Brings up relevant info about objects that it identifies using visual analysis based on a neural network.
External resources
Classification and dichotomous key worksheet
Using Dichotomous Keys Middle School Scientists Curriculum
BioNinja Dichotomous Keys
Cultural and religious importance of plants
Many different cultures and religions have specific uses for particular plants. Certain plants may be used in various holidays or ritual observances.
One of the goals of Social Studies is to expose students to the diversity of ethnic, religious, and cultural observances in our world.
The College, Career, and Civic Life (C3) Framework for Social Studies State Standards notes that students should be able to describe how religions are embedded in culture and cannot only be isolated to the “private” sphere, and identify which religious communities are represented or obscured in public discourse.
Thus, science and social studies teachers can work together to create multi-disciplinary units.
Ethnobotany
The study of a region’s plants and their practical uses through the traditional knowledge of a local culture and people. An ethnobotanist studies local customs involving uses of local flora for many aspects of life, such as plants as medicines, foods, intoxicants and clothing.
Ethnobotany, US Forest Service
Plants in the Jewish tradition
The Sabbath year (shmita; Hebrew: שמיטה, literally “release”), also called the Sabbatical year or Shevi’it (שביעית, literally “seventh”.) This is the seventh year of the seven-year agricultural cycle mandated by the Torah for agriculture by Jewish people living in Israel. During this year the land is left to lie fallow, allowing the soil to regenerate nutrients. With certain exceptions, most agricultural activity is not allowed during this year.
Genesis – Shmitah year covenant, Neohasid.org
What is shmita? My Jewish Learning
Lulav and Etrog, the four species Wikipedia
Trees in Jewish Thought
The Seven Species of plants in the land of Israel.
Plants in the Christian tradition
Trees and plants in the Christian tradition
Trees and religion: Christianity
Plants in the Islamic tradition
Islamic garden
Environmental protection – Islamic shariah
Plants in Buddhist tradition
Ecological significance of plants in Buddhism
Plants in Native American traditions
Native American ethnobotany
Native American Plant Use
Plants in Hinduism
Trees and religion: Hinduism
Plants of religious significance
Thanks for reading. While you’re here see our other articles on astronomy, biology, chemistry, Earth science, mathematics, physics, the scientific method, and making science connections through books, TV and movies.
Learning Standards
Common Core ELA CCSS.ELA-LITERACY.RST.9-10.3
Follow precisely a complex multistep procedure when carrying out experiments, taking measurements, or performing technical tasks, attending to special cases or exceptions defined in the text.
Next Generation Science Standards
2-LS4-1. Make observations of plants and animals to compare the diversity of life in different habitats.
2-PS1-1. Plan and conduct an investigation to describe and classify different kinds of materials by their observable properties.
MS-LS4-2. Apply scientific ideas to construct an explanation for the anatomical similarities and differences among modern organisms and between modern and fossil organisms to infer evolutionary relationships.
National Science Education Standards, The National Academies Press, 1996
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.
[Use of dichotomous key is a math skill] – Use Math in all aspects of scientific inquiry: Mathematics is essential to asking and answering questions about the natural world. Mathematics can be used to ask questions; to gather, organize, and present data; and to structure convincing explanations.
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.
SAT Biology Subject Area Test
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)
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.
Massachusetts Digital Literacy and Computer Science (DLCS) Curriculum Framework
Use of Dichotomous key for identification is an algorithm:
Algorithms [3-5.CT.b]
1. Define an algorithm as a sequence of instructions that can be processed by a computer.
2. Recognize that different solutions exist for the same problem (or sub-problem).
3. Use logical reasoning to predict outcomes of an algorithm.
National Curriculum Standards for Social Studies
3. People, Places, and Environments
The study of people, places, and environments enables us to understand the relationship between human populations and the physical world. Students learn where people and places are located and why they are there. They examine the influence of physical systems, such as climate, weather and seasons, and natural resources, such as land and water, on human populations….
During their studies, learners develop an understanding of spatial perspectives, and examine changes in the relationship between peoples, places and environments….
Immunosenescence (aging of immune system)
Introduction

(In this GIF we see Y-shaped antibodies recognizing and attaching to a pathogen, targeting it for destruction.)
Ed Yong writes, there’s a joke about immunology, which Jessica Metcalf of Princeton recently told me:
An immunologist and a cardiologist are kidnapped. The kidnappers threaten to shoot one of them, but promise to spare whoever has made the greater contribution to humanity. The cardiologist says, “Well, I’ve identified drugs that have saved the lives of millions of people.” Impressed, the kidnappers turn to the immunologist. “What have you done?” they ask. The immunologist says, “The thing is, the immune system is very complicated …” And the cardiologist says, “Just shoot me now.”
Immunology Is Where Intuition Goes to Die, The Atlantic
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Immunosenescence refers to the gradual deterioration of the immune system brought on by natural age advancement.
The adaptive immune system is affected more than the innate immune system. [1]
It deteriorates
* our capacity to respond to infections
* the development of long-term immune memory, especially by vaccination. [2]
This age-associated immune deficiency is ubiquitous. It is found in both long- and short-living species as a function of their age relative to life expectancy rather than chronological time. [3]
It is considered a major contributory factor to the increased frequency of morbidity and mortality among the elderly.
Immunosenescence is not random. It appears to repeat an evolutionary pattern. Most of the parameters affected by immunosenescence appear to be under genetic control. [4]
It is the result of increasing, lifelong exposures to a variety of antigens such as viruses and bacteria. [5]
{This introduction has been adapted from the Wikipedia article, Immunosenescence}
How it works


New medical techniques to fight against Immunosenescence
COVID-19 poses the greatest threat to older people, but vaccines often don’t work well in this group. Scientists hope drugs that rejuvenate the immune system will help.
The text below has been excerpted from How anti-ageing drugs could boost COVID vaccines in older people, Cassandra Willyard, Nature (news feature) 10/14/2020
Immunosenescence explains why older age groups are so hard-hit by COVID-19 [and why] vaccines, which incite the immune system to fight off invaders, often perform poorly in older people. The best strategy for quelling the pandemic might fail in exactly the group that needs it most.
[With aging] some types of immune cell become depleted: for example, older adults have fewer naive T cells that respond to new invaders, and fewer B cells, which produce antibodies that latch on to invading pathogens and target them for destruction.
[With aging] older people also tend to experience chronic, low-grade inflammation [inflammageing.] This constant buzz of internal activation makes the immune system less responsive to external insults.
With many COVID-19 vaccine candidates currently being tested… researchers say it’s not yet clear how they will fare in older adults.
… If COVID-19 vaccines perform less well in older adults, researchers might be able to find ways to tweak the shot itself to elicit a stronger response. Some influenza vaccines, for instance, include immune-boosting ingredients or higher doses of the viral antigen.
But some scientists say there is a better option. They are developing and testing drugs that could improve how older adults respond to vaccines and might also help them fight viruses more effectively in the first place. Rather than working with the limitations of the ageing immune system, they are planning to rejuvenate it.
… One promising class of anti-ageing drug acts on pathways involved in cell growth. These drugs inhibit a protein known as mTOR. In the laboratory, inhibiting mTOR lengthens lifespan in animals from fruit flies to mice.
….The type 2 diabetes drug metformin also dampens down mTOR’s activity, albeit indirectly. Some studies suggest that people who take metformin are less likely to be hospitalized or die if they contract COVID-19.
…diseases such as diabetes and obesity lead to some of the same immune deficits as occur in older age.
… many anti-ageing pathways seem to be linked, says James Kirkland, who studies cellular ageing and disease at the Mayo Clinic in Rochester, Minnesota.
“That is, if you target one, you tend to affect all the rest,” he says. Many of the immune changes that come with ageing lead to the same result: inflammation. So researchers are looking at drugs that will calm this symptom.
… Another class of drug, called senolytics, helps to purge the body of cells that have stopped dividing but won’t die.
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Thanks for reading. While you’re here see our other articles on astronomy, biology, chemistry, Earth science, mathematics, physics, the scientific method, and making science connections through books, TV and movies.
Learning Standards
Next Generation Science Standards (NGSS)
HS-LS1-2 Develop and use a model to illustrate the hierarchical organization of interacting systems that provide specific functions within multicellular organisms.
DCI – LS1.A: Structure and Function – Feedback mechanisms maintain a living system’s internal conditions within certain limits and mediate behaviors, allowing it to remain alive and functional even as external conditions change within some range.
Evidence statements: In the model, students describe the relationships between components, including:
* A system’s function and how that relates both to the system’s parts and to the overall function of the organism.
* Students use the model to illustrate how the interaction between systems provides specific functions in multicellular organisms
Massachusetts Comprehensive Health Curriculum Framework
Students will gain the knowledge and skills to select a diet that supports
health and reduces the risk of illness and future chronic diseases. PreK–12 Standard 4
8.1 Describe how the body fights germs and disease naturally and with medicines and
immunization
8.2 Identify the common symptoms of illness and recognize that being responsible for individual health means alerting caretakers to any symptoms of illness.
8.5 Identify ways individuals can reduce risk factors related to communicable and chronic diseases
8.6 Describe the importance of early detection in preventing the progression of disease.
8.7 Explain the need to follow prescribed health care procedures given by parents and health care providers.
8.8 Describe how to demonstrate safe care and concern toward ill and disabled persons in the family, school, and community.
8.13 Explain how the immune system functions to prevent and combat disease
Interdisciplinary Learning Objectives: Disease Prevention and Control
8.a. (Law & Policy. Connects with History & Social Science: Geography and Civics & Government) Analyze the influence of factors (such as social and economic) on the treatment and management of illness.
Benchmarks for Science Literacy, AAAS
The immune system functions to protect against microscopic organisms and foreign substances that enter from outside the body and against some cancer cells that arise within. 6C/H1*
Some allergic reactions are caused by the body’s immune responses to usually harmless environmental substances. Sometimes the immune system may attack some of the body’s own cells. 6E/H1
Some viral diseases, such as AIDS, destroy critical cells of the immune system, leaving the body unable to deal with multiple infection agents and cancerous cells. 6E/H4
Vaccines induce the body to build immunity to a disease without actually causing the disease itself. 6E/M7** (BSL)
Footnotes
1 Pangrazzi L, Weinberger B (2020). “T cells, aging and senescence”. Experimental Gerontology. 134: 110887. doi:10.1016/j.exger.2020.110887. PMID 32092501. S2CID 211237913.
2. Muszkat, M; E. Greenbaum; A. Ben-Yehuda; M. Oster; E. Yeu’l; S. Heimann; R. Levy; G. Friedman; Z. Zakay-Rones (2003). “Local and systemic immune response in nursing-home elderly following intranasal or intramuscular immunization with inactivated influenza vaccine”. Vaccine. 21(11–12): 1180–1186. doi:10.1016/S0264-410X(02)00481-4. PMID 12559796.
3. Ginaldi, L.; M.F. Loreto; M.P. Corsi; M. Modesti; M. de Martinis (2001). “Immunosenescence and infectious diseases”. Microbes and Infection. 3 (10): 851–857. doi:10.1016/S1286-4579(01)01443-5. PMID 11580980.
4. Franceschi, C.; S. Valensin; F. Fagnoni; C. Barbi; M. Bonafe (1999). “Biomarkers of immunosenescence within an evolutionary perspective: the challenge of heterogeneity and the role of antigenic load”. Experimental Gerontology. 34 (8): 911–921. doi:10.1016/S0531-5565(99)00068-6. PMID 10673145. S2CID 32614875.
5. Franceschi, C.; M. Bonafè; S. Valensin (2000). “Human immunosenescence: the prevailing of innate immunity, the failing of clonotypic immunity, and the filling of immunological space”. Vaccine. 18 (16): 1717–1720. doi:10.1016/S0264-410X(99)00513-7. PMID 10689155.
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Sunrise Sunset The science and culture
One of the goals of science education is to see how just a handful of basic laws of nature allow us to understand all phenomenon in our physical universe, from the simplest examples (how objects move) to the most complex (how planets orbit stars)
One of the goals of Social Studies is to expose students to the diversity of ethnic, religious, and cultural observances in our world. The College, Career, and Civic Life (C3) Framework for Social Studies State Standards notes that students should be able to describe how religions are embedded in culture and cannot only be isolated to the “private” sphere, and identify which religious communities are represented or obscured in public discourse.
Science and social studies teachers can work together to create multi-disciplinary units. Here is one on sunset, also known as sundown The daily disappearance of the Sun below the horizon due to Earth’s rotation is something that needs to be understood scientifically, and has ties to major world cultures.

(This section has been adapted from Sunset, Wikipedia)
The time of sunset is defined in astronomy as the moment when the upper limb of the Sun disappears below the horizon.
Near the horizon, atmospheric refraction causes sunlight rays to be distorted to such an extent that geometrically the solar disk is already about one diameter below the horizon when a sunset is observed.
Sunset is distinct from twilight, which is divided into three stages:
civil twilight, begins once the Sun has disappeared below the horizon, and continues until it descends to 6 degrees below the horizon
nautical twilight, between 6 and 12 degrees below the horizon
astronomical twilight, when the Sun is between 12 and 18 degrees below the horizon.
Dusk = very end of astronomical twilight, the darkest moment of twilight just before night.
Night occurs when the Sun reaches 18 degrees below the horizon and no longer illuminates the sky.

image by TWCarlson from Wikimedia.
Refraction: Appearances versus reality
We actually see the Sun a few minutes before it rises and a few minutes after it sets. This is due to the fact that the Earth’s atmosphere refracts the rays of light from the sun.
We learn about refraction of light in our section on geometric optics.
Looking at the situation from the side:

Standing at the beach, looking out towards the horizon, we would see this:

When sun just disappears, the center of the sun is 56’ below. the horizon (almost one degree!). What you see. True position. 34.5’ True position. What you see. 34.5’ 56’ Moment of sunset. Height = 0.
This image from Latitude and Longitude powerpoint by Darleen Cross.
Refraction of light is the reason for mirages – the naturally occurring phenomenon in which light rays are bent to produce a displaced image of distant objects or the sky.
Here’s a spectacular mirage (magnified) that was seen at the Scottish Open golf tournament in Aberdeen, 2014.

Cultural connections
The significance of sunrise and sunset in cultures around the world:
Jewish
In Jewish culture the precise time of sundown and sunrise is of practical and religious importance.
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Observant Jews pray three times daily, and the first prayer service occurs after sunrise, and the last prayer service must occur before the next one.
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Observance of Shabbat, the Jewish Sabbath, is considered to be one of the most important ethical-ritual practices in Judaism. In order to safeguard its observance the timing of sundown should be known as precisely as possible. To avoid any possible violations of Sabbath laws, observance of the Sabbath begins a number of minutes before this time.
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Observance of Jewish festivals, such as Passover, Sukkot, and Shavuot, begin at nightfall. This is why people commonly say that “Jewish holidays begin on the evening of the day before.”
Daybreak עֲלוֹת הַשַּׁחַר alot ha’shachar) – when the first rays of light are visible in the morning
Sunrise הַנֵץ הַחַמָּה, hanetz ha’chamah – when the entire disc of the sun appears over the horizon.
Sunset שְׁקִיעַת הַחַמָּה, shkiyat ha’chamah – when the disc of the sun falls below the horizon
Twilight – bein ha’shemashot בֵּין הַשְּׁמָשׁוֹת, (between the suns) – the period between sunset and nightfall. The status of this time was never clearly delineated in traditional Jewish law. Therefore, on the Sabbath, festivals, and fast days the stringencies of both the previous and following days usually apply.
Muslim
This section is excerpted from a discussion at Islam.stackexchange.com
During the time of the prophet, as was also the case in the Hebrew world and in pre-Islamic Arabia, the day was not calculated as a twenty-four hour period starting at midnight (as our current system of time does). Rather, each day would marked at sunset, and would consist of two parts, starting with “Night” (ليل) and proceeding to “Day” (نهار).
The Qur’an itself does not define “night” clearly; while there are many references associating “day” with the sun and brightness and associating “night” with darkness and concealment, the exact delineation between the two is not so precise.
In fact, according to the classical text الجامع لأحكام القرآن, Imam Qurtubi claims that God alone knows the exact measure of night, based on the revelation in Surat Al-Muzzammil that “Allah determines the night and the day” (الله يقدر الليل والنهار).
According to Lane’s Lexicon, ليل and نهار are opposites, with no intervening period between them. Day, being defined as “the time from the rising of the dawn to sunset”, would thus perfectly complement night, which would by extension be defined as the time from sunset to the rising of the dawn (i.e. sunset to Fajr).
Similarly, Brill’s Encyclopedia of the Qur’an considers the night to include everything from the “evening twilight” (شفق) until “the breaking of morning” (سحر), which immediately precedes the dawn (فلق) itself.
Surat al-Baqarah regulates the nights of fasting until “the white thread of dawn is distinct from the black thread” (يتبين لكم الخيط الأبيض من الخيط الأسود من الفجر), which correlates strongly with the above definitions.
It is important to note that, colloquially, the word ليل (night) can also be overloaded in a similar manner to the English “day”, wherein it can be used to refer to an entire 24-hour period (more accurately, an entire period from sunset to sunset) rather than the night-time in particular. The intended meaning is usually clear in context, especially when ليل is used in a pluralized form, but this too needs to be kept in mind.
While there has been significant scholarly interest in the exact definitions of night and day, especially in regards to the transitory periods of twilight and dawn, much of this research was not conducted until significantly after the death of the prophet himself. As such, any references to “night” in the hadith literature were not necessarily (or likely) using the the term in any scientifically precise manner.
Hindu
(TBA)
Native American
(TBA)
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Thanks for reading. While you’re here see our other articles on astronomy, biology, chemistry, Earth science, mathematics, physics, the scientific method, and making science connections through books, TV and movies.
Learning Standards
National Curriculum Standards for Social Studies
3. People, Places, and Environments
The study of people, places, and environments enables us to understand the relationship between human populations and the physical world. Students learn where people and places are located and why they are there. They examine the influence of physical systems, such as climate, weather and seasons, and natural resources, such as land and water, on human populations….
During their studies, learners develop an understanding of spatial perspectives, and examine changes in the relationship between peoples, places and environments….
8. Science, Technology, and Society
Science, and its practical application, technology, have had a major influence on social and cultural change, and on the ways people interact with the world….
There are many questions about the role that science and technology play in our lives and in our cultures. What can we learn from the past about how new technologies result in broader social change, some of which is unanticipated?… How can we preserve fundamental values and beliefs in a world that is rapidly becoming one technology-linked village? How do science and technology affect our sense of self and morality?
College, Career, and Civic Life (C3) Framework for Social Studies State Standards
College, Career, and Civic ready students:
D2.Rel.4.9-12: Describe and analyze examples of how religions are embedded in all aspects of culture and cannot only be isolated to the “private” sphere.
D2.Rel.12.9-12: Identify which religious individuals, communities, and institutions are represented in public discourse, and explain how some are obscured.
Next Generation Science Standards
5-ESS1-2 Earth’s Place in the Universe
5-ESS1-2. Represent data in graphical displays to reveal patterns of daily changes in length and direction of shadows, day and night, and the seasonal appearance of some stars in the night sky.
NGSS Evidence Statements – Observable features of the student performance: Using graphical displays (e.g., bar graphs, pictographs), students organize data pertaining to daily and seasonal changes caused by the Earth’s rotation and orbit around the sun. Students organize data that include:
i. The length and direction of shadows observed several times during one day.
ii. The duration of daylight throughout the year, as determined by sunrise and sunset times.
iii. Presence or absence of selected stars and/or groups of stars that are visible in the night sky at different times of the year.
NSES (National Science Education Standards)
Content Standard D – Earth and Space Science: Earth in the Solar System
Grades 5-8, page 160. Most objects in the solar system are in regular and predictable motion. Those motions explain such phenomena as the day, the year, phases of the moon, and eclipses.
The Wave Nature of Matter
Everything is made of particles. Pieces of solid matter. All solids, liquids, and gases – you name it. Dirt, pebbles, and red blood cells. Trees, dust mites, planets, and even the air we breath.
That’s obvious and common sense. We even make models of atoms and molecules with wood or plastic manipulatives like this, so that must mean something, right?
Except… we’re going to learn that all solid particles in the universe have a wave-like behavior.
And oh yes, all wave-like behavior has particle-like behavior?! Yup. For real.
This is the inescapable – and verified – result of the quantum mechanical nature of our world.
In the late 19th and early 20th century, when physicists asked hard questions about matter, they came across unexpected, extraordinary results.
We basically went through Alice’s Looking Glass – into the quantum realm. A realm where all particles have wave-like qualities. And further, all waves have particle-like qualities.
To be clear, none of this is a metaphor – we’re being quite literal.
The classical model of matter
The old model of the atom, and of everything in the universe was classical:
Everything is made of solid matter.
Everything has a definite position, mass, and velocity, at any moment in time.
Everything has a definite momentum at any moment in time.
How could it not? That seems to be true by definition.
We envisioned that there was a positively charged nucleus in the center of atoms.
Electrons (hence e– ) orbited around the nucleus like planets orbit around a start.

And so was everything else in our universe. People, cars, rocks, planets, and stars.
But when we looked more closely at their behavior, we kept seeing evidence that this model couldn’t be correct.
The classical model of atoms was wrong
e– lose energy by giving off photons (particles of light)
e– gain energy by absorbing a photon (and its energy)
If e– behaved like solid objects then they could move to any position (further from nucleus, or closer.)
They should be able to have any amount of energy: From a little to a large amount – and any value in between.
Therefore, when atoms gave off light, it was when e– dropped from one energy level to another.
If e– e could exist at any level then they could emit any energy of light, any color.
Thus atoms should be able to produce a continuous spectrum. Continuous means “all possible colors, smoothly going from one to the next, with no gaps.” Like this:
But experiments always showed otherwise! When individual atoms absorb light (energy) they only absorb photons (particles of light) in certain wavelengths. Yet they never absorb energy in others? How is that possible?
And when individual atoms emit (give off) light (energy), they only give off photons in certain wavelengths, never any others. Again, how is this possible?
No one could come with up with any model of the atom which was consistent with classical physics.
By 1913 Niels Bohr realized that nature was telling us something: Our classical intuition about what an atom was, was simply wrong.
We were forced to listen to what nature was telling us. Out of almost desperation, Bohr listened to nature and created a new, semi-classical model of the atom:
Like the old model, Bohr’s model portrays atoms as having a nucleus in the center and e– orbiting around it.
But in his new model e– could only exist in orbits of a certain radius. Not in any others.
Sure, they could lose energy, and “fall” from one orbit to a lower orbit – yet they didn’t exist anyplace in between?!
It was like they disappeared from kind of orbit – and reappeared in a different one?!
Quantum jumps
In classical physics any orbit is possible. It doesn’t make sense that only some orbits would be “allowed.”
Think of climbing a ladder. You can climb up from one stair to the next stair… and in doing so you obviously must pass all of the positions in-between.
There are an infinite number of positions between one ladder rung and the next. We don’t just disappear at one rung and then appear up at the next one, right?

(This GIF might be by artist Daniela Sherer)
This guy climbing the ladder, above, shows the classical, normal world we know.
We’re at one place, then at another – but only because we pass through every position in between.
The same thing goes for a car driving down the road. It starts at one place, ends up at another – and by definition the car must pass through every position in between.
But now imagine seeing this: the car literally disappears from the universe at one place, and then reappears in another place further down the road.
Without ever being in any of the positions in between?! That’s not possible, right?
Except – that is precisely what e– in atoms seem to do.
Worse, all sub-atomic particles have this quantum leap type of behavior.
This violates common sense. But here’s the kicker – when we look closely, this is how the universe works.
Bohr’s model of the atom
An e– gives off energy in the form of a photon. Photon shown as green squiggly arrow.
Then the e– disappears from where it was and reappears in a lower orbit – without traveling through any position in-between!
Later, the e– absorbs energy from a different photon (another green squiggly arrow.)
Once it absorbs the energy the e- jumps up to a higher orbit – again, without traveling through any of the position in between.
These seemingly impossible jumps are called quantum leaps.
(FYI, e- do not actually circular orbits. Bohr’s model was just the first approximation)

(image Bohr atom animation.gif)
This model was the beginning quantum mechanics.
From the Bohr model to the wave model
The following Socratic-style discussion comes from Physics 2000.
Why should an electron’s angular momentum have only certain values?
Why do electrons emit or absorb radiation only when they jump between energy levels?
Bohr’s theory fits experimental results, but it doesn’t explain why atoms behave the way they do.
In 1923, about ten years after Bohr published his results, Louis de Broglie came up with a fascinating idea to explain them: all matter, he suggested, actually consists of waves.
At first, de Broglie had no idea what he meant by matter being “waves.” It was just a mathematical construct that was helpful.
It was only later that physicists realized that this mathematical construction was telling us something about the true nature of reality itself!
de Broglie’s wave model of particles explains why an electron can only be in certain orbits!
de Broglie’s wave model assumes that any particle – an electron, atom, bowling ball, whatever – had a “wavelength”
Yeah, that’s weird – but let’s just roll with it for the moment.
Why assume such a thing? This assumption wasn’t arbitrary; de Broglie knew that the momentum and wavelength of a photon actually were related.
Hmm, wait a minute…photons don’t have any mass, do they? How can photons have momentum?
Photons don’t have mass, but they do have energy – and as Einstein famously proved, mass and energy are really the same thing.
So photons do have momentum – but what exactly is a photon?
For centuries, a heated debate went on as to whether light is made up of particles or waves.
In some experiments, like Young’s double slit experiment, light clearly showed itself to be a wave.
But other phenomena, such as the photoelectric effect, demonstrated equally clearly that light was a particle.
So which is it? Well, sort of both – or better, it is neither.
Light is a thing that sometimes has particle-like behavior, and sometimes has wave-like behavior.
It all depends on what sort of experiment you’re doing.
This is known as wave/particle duality. Like it or not, physicists have been forced to accept it.
That’s why we sometimes talk about “electromagnetic waves” and sometimes about “photons.”
de Broglie’s big idea was that maybe it’s not just light that has this dual personality; maybe it’s everything!
All right…let’s say I accept this idea. How does it explain Bohr’s energy levels?
If we think of electrons as waves, we change our whole concept of what an “orbit” is.
Instead of having a particle whizzing around the nucleus in a circular path, we’d have a wave existing around the whole circle.
Now, the only way that such a wave could exist is if the wave has constructive interference.
It has to have a whole number of its wavelengths fit exactly around the circle.
If the circumference is exactly as long as two wavelengths, say, or three or four or five, that’s great, but two and a half wavelengths won’t cut it.
If we have fractional amounts of wavelengths then there is destructive interference, and the waves cancel out.
So there could only be orbits of certain sizes, depending on the electrons’ wavelengths –which depend on their momentum.
Apps: Modeling electrons with standing waves
Standing waves in Bohr’s atomic model
Standing waves in Bohr’s atomic model Geogebra.org
How to run CDF demonstrations: worlds of math & physics
Seeing constructive & destructive wave interference in 3 dimensions with DESMOS
More from Physics 2000
Student: But is this just some mathematical trick that happens to work, or do particles actually behave like waves sometimes?
Teacher: They actually do behave like waves! Just a few years after de Broglie published his hypothesis, several experiments were done proving that electrons really do display wavelike properties.
Student: So how come when I look at a bowling ball, I don’t notice it acting in a wavelike manner? You said that everything is affected by wave/particle duality.
Teacher: Think about what the wavelength of the bowling ball would be. According to de Broglie, the wavelength is equal to Planck’s constant divided by the object’s momentum.
Planck’s constant is very, very, very tiny, and the momentum of a bowling ball, relatively speaking, is huge.
If you had a bowling ball with a mass of, say, one kilogram, moving at one meter per second, its wavelength would be about a septillionth of a nanometer.
This is so ridiculously small compared to the size of the bowling ball itself that you’d never notice any wavelike stuff going on.
That’s why we can generally ignore the effects of quantum mechanics when we’re talking about everyday objects.
It’s only at the molecular or atomic level that the waves begin to be large enough (compared to the size of an atom) to have a noticeable effect.
Student: If electrons are waves, then it kind of makes sense that they don’t give off or absorb photons unless they change energy levels.
If it stays in the same energy level, the wave isn’t really orbiting or “vibrating” the way an electron does in Rutherford’s model, so there’s no reason for it to emit any radiation.
And if it drops to a lower energy level… let’s see, the wavelength would be longer, which means the frequency would decrease, so the electron would have less energy.
Then it makes sense that the extra energy would have to go someplace, so it would escape as a photon–and the opposite would happen if a photon came in with the right amount of energy to bump the electron up to a higher level.
Teacher: Very good! Now we can look at how Schrödinger extended de Broglie’s idea of waves into a whole new model for the atom…
What happened next, to finally create Quantum Mechanics, was that Schrödinger extended de Broglie’s idea of waves into a whole new model for the atom.
Related apps
Models of the Hydrogen Atom – PhET
Run this PhET app. Click to change from Experiment to Prediction. Press button to start the electron gun.
Under ‘Atomic model,’ the models of the atom most pertinent to this lesson are the Bohr model and the de Broglie model.

External resources
astronomy.nmsu.edu/agso/spectroscopy.pdf
Continuous spectra vs actual spectra
Emission Spectra: How Atoms Emit and Absorb Light
Emission and absorption spectra
Spectral Classification of Stars
Formation of Spectral Lines, Lumen
Physics 2000. University of Colorado by Prof. Martin V. Goldman. This website no longer exists except as an archived copy.
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Maxwell’s Equations
Introduction
On Quora, Mark Eichenlaub writes –
The history of electromagnetism is one of unification. Over and over, different ideas about how things work were subsumed into the same theoretical framework…. Electromagnetism is an example of a field theory, the central object of study in theoretical physics.
A “field” means that at any point in space and time, there’s an electric and magnetic vector there. These fields pervade all of space – they are in the room around you right now, and in outer space, even within you…
We don’t have a mechanical picture of what the field is, or why it is a certain way. It’s not like waves in the water or anything like that. It just exists, but we do have mathematical rules that describe how it works….
Michael Faraday investigated things like the way a wire carrying electric current deflects a compass needle. His crowning achievement was to discover that changing magnetic fields create electric fields, a phenomenon called induction.
James Clerk Maxwell looked at all that, sat down with pen and papers, and mathematically described Faraday’s results in a complicated set of differential equations, importantly including the idea that changing electric fields would create magnetic fields, completing the symmetry between the two.
When Maxwell finished his theory, he discovered that it allowed waves of electromagnetism to fly off at high speed – when he calculated the speed, it turned out to be the speed of light.
Experiments with radio waves soon verified that light was nothing more than a special form of electricity and magnetism.
You can think of it as if we had been studying the way hot air balloons and airplanes and things work, and so were thinking about the dynamics of air. In the process, we develop equations for air, and figure out that sound is just waves moving through the air.
The theory of sound and the theory of airplanes are actually the same theory, even though they don’t seem very similar. That’s roughly what happened for light, except that unlike for sound, no one expected it. (Or at least it wasn’t obvious beforehand.)
Maxwell’s equations describe how electric and magnetic fields work, but those fields need to interact with matter – that happens via electric charge. Charge is an innate property of matter…
Fields
We keep talking about the electromagnetic field. What exactly is a “field” anyways? See What are fields?
Our articles
Maxwell’s equations (our main article, for now)
Backup: Get to know Maxwell’s Equations
External articles
Get to Know Maxwell’s Equations—You’re Using Them Right Now, Wired
Thanks for reading. While you’re here see our other articles on astronomy, biology, chemistry, Earth science, mathematics, physics, the scientific method, and making science connections through books, TV and movies.
Fun books to inspire science teachers as well as students
Fun books to inspire science teachers as well as students
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Gonzo Gizmos: Projects and Devices to Channel Your Inner Geek, by Simon Quellen Field

Step-by-step instructions to building more than 30 fascinating devices …e.g. how to construct a simple radio with a soldering iron, a few basic circuits, and three shiny pennies. Instructions are included for a rotary steam engine that requires a candle, a soda can, a length of copper tubing, and just 15 minutes. To use optics to roast a hot dog, no electricity or stove is required, just a flexible plastic mirror, a wooden box, a little algebra, and a sunny day. Also included are experiments most science teachers probably never demonstrated, such as magnets that levitate in midair, metals that melt in hot water, a Van de Graaff generator made from a pair of empty soda cans, and lasers that transmit radio signals.
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Physics, Fun, and Beyond: Electrifying Projects and Inventions from Recycled and Low-Cost Materials, by Eduardo de Campos Valadares

Build more than 110 projects that uncover the physics beneath everyday life! Most o are amazingly easy to build: all you’ll need are your everyday household tools and cheap (sometimes free) materials.
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Why Toast Lands Jelly-Side Down: Zen and the Art of Physics Demonstrations, by Robert Ehrlich

A collection of physics demonstrations that prove that physics can, in fact, be “made simple.” Intentionally using low tech and inexpensive materials from everyday life, Why Toast Lands Jelly-Side Down makes key principles of physics surprisingly easy to understand. After laying out the basic principles of what constitutes a successful demonstration, Ehrlich provides more than 100 examples.
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The Prism and the Pendulum: The Ten Most Beautiful Experiments in Science, by Robert Crease

We see the first measurement of the earth’s circumference, accomplished in the third century B.C. by Eratosthenes using sticks, shadows, and simple geometry. We visit Foucault’s mesmerizing pendulum, a cannonball suspended from the dome of the Panthéon in Paris that allows us to see the rotation of the earth on its axis. We meet Galileo – the only scientist with two experiments in the top ten – brilliantly drawing on his musical training to measure the speed of falling bodies. And we travel to the quantum world, in the most beautiful experiment of all.
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How Things Work: The Physics of Everyday Life, by Louis A. Bloomfield
Uses familiar objects to introduce basic physics concepts with real-life examples. For example, discussions of skating, falling balls, and bumper cars are included to explain the laws of motion. Air conditioners and automobiles are used to explore thermodynamics.
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The Way Things Work Now, by David Macaulay
Explainer-in-Chief David Macaulay updates the worldwide bestseller The New Way Things Work to capture the latest developments in the technology that most impacts our lives. Famously packed with information on the inner workings of everything from windmills to Wi-Fi, this extraordinary and humorous book both guides readers through the fundamental principles of machines, and shows how the developments of the past are building the world of tomorrow.
This sweepingly revised edition embraces all of the latest developments, from touchscreens to 3D printer…. What possible link could there be between zippers and plows, dentist drills and windmills? Parking meters and meat grinders, jumbo jets and jackhammers, remote control and rockets, electric guitars and egg beaters? Macaulay explains them all.
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Building Big, by David Macaulay
Why this shape and not that? Why steel instead of concrete or stone? Why put it here and not over there? These are the kinds of questions that David Macaulay asks himself when he observes an architectural wonder. These questions take him back to the basic process of design from which all structures begin, from the realization of a need for the structure to the struggles of the engineers and designers to map out and create the final construction. Macaulay engages readers’ imaginations and gets them thinking about structures they see and use every day — bridges, tunnels, skyscrapers, domes, and dams.
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Insultingly Stupid Movie Physics: Hollywood’s Best Mistakes, Goofs and Flat-Out Destructions of the Basic Laws of the Universe, b y Tom Rogers
Would the bus in Speed really have made that jump? -Could a Star Wars ship actually explode in space? -What really would have happened if you said “Honey, I shrunk the kids”? The companion book to the hit website (www.intui tor.c om/moviephy sics), which boasts more than 1 million visitors per year, Insultingly Stupid Movie Physics is a hilarious guide to the biggest mistakes, most outrageous assumptions, and the outright lunacy at work in Hollywood films that play with the rules of science.
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Don’t Try This At Home!: The Physics of Hollywood Movies, by Adam Weiner
A fresh look at the basics of physics through the filmmaker’s lens. It will deconstruct, demystify, and debunk popular Hollywood films through the scientific explanations of the action genre’s most dynamic and unforgettable scenes.
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The Cosmic Code: Quantum Physics as the Language of Nature, Heinz R. Pagels
One of the best books on quantum mechanics for general readers. Heinz Pagels, an eminent physicist and science writer, discusses the core concepts without resorting to complicated mathematics. He covers the development of quantum physics. And although this is an intellectually challenging topics, he is one of the few popular physics writers to discuss the development and meaning of Bell’s theorem. Anecdotes from the personal documents of Einstein, Oppenheimer, Bohr, and Planck offer intimate glimpses of the scientists whose work forever changed the world.
A reviewer on Goodreads notes – “Pagels assumes a lay audience, but one prepared, after single paragraphs of description, to thereafter carry the technical terms across the finish line. Unlike other popsci, he also favors technical description–albeit written in smooth, clear prose over metaphor… The commitment to not talking down to his audience is rather commendable…
[His] intellectual project [is] reconciling the impossibility of visualizing quantum processes with a remit to communicate the science to non-scientists who, lacking the requisite mathematical literacy, necessarily require metaphor, universal human logics, and everyday comparisons to grasp most science in the first place.”
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Quantum Reality: Beyond the New Physics, Nick Herbert
Herbert brings us from the “we’ve almost solved all of physics!” era of the early 1900s through the unexpected experiments which forced us to develop a new and bizarre model of the universe, quantum mechanics. He starts with unexpected results, such as the “ultraviolet catastrophe,” and then brings us on a tour of the various ways that modern physicists developed quantum mechanics.
And note that there isn’t just one QM theory – there are several! Werner Heisenberg initially developed QM using a type of math called matrix mechanics, while Erwin Schrödinger created an entirely different way of explaining things using wave mechanics. Yet despite their totally different math languages – we soon discovered that both ways of looking at the world were logically equivalent, and made the same predictions. Herbert discussed the ways that Paul Dirac and Richard Feynman saw QM, and he describes eight very different interpretations of quantum mechanics, all of which nonetheless are consistent with observation…
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In Search of Schrödinger’s Cat: Quantum Physics and Reality, John Gribbon
“John Gribbin takes us step by step into an ever more bizarre and fascinating place, requiring only that we approach it with an open mind. He introduces the scientists who developed quantum theory. He investigates the atom, radiation, time travel, the birth of the universe, superconductors and life itself. And in a world full of its own delights, mysteries and surprises, he searches for Schrodinger’s Cat – a search for quantum reality – as he brings every reader to a clear understanding of the most important area of scientific study today – quantum physics.”
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The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory, Brian Greene
“Brian Greene, one of the world’s leading string theorists, peels away the layers of mystery surrounding string theory to reveal a universe that consists of eleven dimensions, where the fabric of space tears and repairs itself, and all matter—from the smallest quarks to the most gargantuan supernovas—is generated by the vibrations of microscopically tiny loops of energy….
Today physicists and mathematicians throughout the world are feverishly working on one of the most ambitious theories ever proposed: superstring theory. String theory, as it is often called, is the key to the Unified Field Theory that eluded Einstein for more than thirty years.
Finally, the century-old antagonism between the large and the small-General Relativity and Quantum Theory-is resolved. String theory proclaims that all of the wondrous happenings in the universe, from the frantic dancing of subatomic quarks to the majestic swirling of heavenly galaxies, are reflections of one grand physical principle and manifestations of one single entity: microscopically tiny vibrating loops of energy, a billionth of a billionth the size of an atom.”
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Thanks for reading. While you’re here see our other articles on astronomy, biology, chemistry, Earth science, mathematics, physics, the scientific method, and making science connections through books, TV and movies.
How can we see photos taken in UV, Infrared or Radio?
How is it possible that we can see photos taken in UV, Infrared or Radio?

Humans can only see visible wavelengths of light. Visible light has 𝜆 (wavelengths) of about 380 to 700 nm (nanometers.)
Yet in science class we often see infrared photos, like this!
Or we see photos taken in ultraviolet light. Bees see UV light, and so see flowers differently than we do. On the left is a primrose in visible light, but on the right we see it in UV light.

We see radar images of the Earth from an orbiting satellite, or radio telescope images of the galaxy. And those wavelengths of light just aren’t visible to humans.

UV light 𝜆 = 100 to 400 nm.
Infrared light 𝜆 = 700 nm to 1 mm
Radio waves 𝜆 = 1 millimeter to 100 kilometers.
Okay, the easy part is the technology: we can build equipment that detect such wavelengths. But what is the resulting image that we are looking at? Something visible to the human eye – which is in the visible spectrum.
So what does it even mean to translate something invisible to something visible?
Think about transposing music on a piano. We can play a melody in the middle of a piano keyboard. Then we can play the exact same melody one octave higher just by moving our hands to the right. We can do this again, and again. Each time the same melody is preserved, just an octave higher.

We can keep doing this until the notes are so high pitched that human ears can’t detect them (although maybe dogs and bats could hear this.) The resulting melody would be the same as the original melody, yet undetectable to us.
We can compare this to “seeing” higher frequencies of light – they get higher and higher until they become ultraviolet or X-rays.
Now, we can do the same thing again, but in reverse. Play a melody in the middle of a piano keyboard. Then we can play the exact same melody one octave lower just by moving our hands to the left. We can do this again, and again. Each time the same melody is preserved, just an octave lower.

We can keep doing this until the notes have such a low pitch that human ears can’t detect them (although whales, elephants, and hippopotamuses could hear this.) The resulting melody would be the same as the original melody, yet undetectable to us.

This is pretty much what is happening when we print out images of data capturing UV, Infrared or Radio!
For high frequency images (like UV light) we are dropping the image by many octaves (so to speak) until we reach the visible spectrum.
For low frequency images (like radio or infrared) we are increasing the image by many octaves (so to speak) until we reach the visible spectrum.
Avoiding misunderstandings
Electromagnetic waves (light, UV, radio) are transverse waves. The direction of particle displacement is perpendicular to the direction of movement.
Sound waves are longitudinal waves.
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Supervolcano
Supervolcano
A volcano which had an eruption of magnitude 8 on the Volcano Explosivity Index (VEI)
Such euprtions send out more than 1,000 cubic kilometers (240 cubic miles) of material.
These are exceedingly voluminous pyroclastic eruptions. They form monstrously huge calderas.
Few are recent. Most are ancient. Examples over the last couple of million years include the ones in Yellowstone National Park, Long Valley in eastern California, Toba in Indonesia, and Taupo in New Zealand.
There are large caldera volcanoes in Japan, Indonesia, and South America.
The most recent supervolcanic eruption on Earth occurred 27,000 years ago at Taupo, New Zealand’s north island.
…In 2005, BBC and the Discovery Channel produced a docudrama and documentary about Yellowstone called Supervolcano.
Below, Yellowstone Volcano Observatory scientists answer questions that arose after this program aired that relate to supervolcanoes, volcanic hazards, and Yellowstone.
The docudrama Supervolcano dramatically explores the impact of a large caldera-forming eruption at Yellowstone. The scale of the portrayed eruption is similar to the eruption of the Huckleberry Ridge Tuff at Yellowstone 2.1 million years ago.
The movie is realistic insofar as depicting what could happen if an eruption of this magnitude were to occur again. .. it does an acceptable job of addressing some of the issues scientists would grapple with if Yellowstone showed signs of an impending eruption.
Questions about supervolcanoes. USGS.
Comparing the volumes of eruptions
Regular eruptions are shown towards the right; super eruptions are shown towards the left.

Ancient supervolcano in Yellowstone Park
Yellowstone National Park is the first national park in the world – located primarily in the U.S. state of Wyoming, extending into Montana and Idaho. It known for its wildlife and its many geothermal features, especially Old Faithful Geyser.
See our article Yellowstone National Park & Caldera

Image by the National Park Service.
Yellowstone, one of the world’s largest active volcanic systems, has produced several giant volcanic eruptions in the past few million years, as well as many smaller eruptions and steam explosions. Although no eruptions of lava or volcanic ash have occurred for many thousands of years, future eruptions are likely.
In the next few hundred years, hazards will most probably be limited to ongoing geyser and hot-spring activity, occasional steam explosions, and moderate to large earthquakes. To better understand Yellowstone’s volcano and earthquake hazards and to help protect the public, the U.S. Geological Survey, the University of Utah, and Yellowstone National Park formed the Yellowstone Volcano Observatory, which continuously monitors activity in the region….
from Steam Explosions, Earthquakes, and Volcanic Eruptions – What’s in Yellowstone’s Future? U.S. Geological Survey Fact Sheet 2005-3024, 2005
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How do we know how atoms are arranged in a crystal?
How do we know how atoms are arranged in a protein, an enzyme, or a fat molecule?
Each individual atom is only a few nanometers (1 x 10-10 m) wide, way too small to photograph directly.
Yet we often see images of how atoms how are arranged, like this.
Just look it this image: We see individual atoms (yellow, red, blue) connected in a precise pattern. How in the world did we see this?
Well, there’s no way to see this, in one step. Too difficult.
But there is a way to accurately visualize this, if we go through a very careful process.
The process is called X-ray crystallography.
We start with a tiny sample of whatever it is we’d like to learn about. For example, a protein or an enzyme.
First, a biochemist needs to purify cells, and extract just the one molecule that we’re interested in.
That, in of itself, is a procedure that needs to be done carefully.
Once we have a pure form of that molecule, we then crystallize it.
Of course, in order for the rest of this lesson to make sense, we need to know what a “crystal” really is. So if you haven’t already learned about this, first check out our lesson on What is a crystal?
Short version: A crystal is solid material, in which the atoms, molecules, or ions are arranged in an orderly repeating pattern.
For instance, on the left is the atom-by-atom structure of a halite crystal.
(Purple is sodium ion, green is chlorine ion.)
This crystal is so tiny, that it would take 10,000 of them to make one tiny grain of salt!
On the right is a visible salt crystal. This contains millions of such crystal units.
Well, if we have a pure chemical from a cell (protein, enzyme, fatty acid, etc.) we can slowly cool and dry this chemical until it crystallizes!
Each different kind of molecule would create a differently shaped and colored crystal.
Please understand that these crystals look tiny – maybe just 1/10 of an inch across.
Yet each crystal contains millions of repeating atomic units.
Figure 22.3. Examples of protein crystals. From left to right: β-secretase inhibitor complex; human farnesyl pyrophosphatase in complex with zoledronic acid; abl kinase domain in complex with imatinib; cdk2 inhibitor complex.
Source – Jean-Michel Rondeau, Herman Schreuder, in The Practice of Medicinal Chemistry (Fourth Edition), 2015
This crystal is then placed in front of an X-ray source.
The X-rays scatter off the atoms in a crystal.
Those X-rays fly onto either a piece of film, or a digital X-ray detector plate.
Either way, we end up with a beautiful array of dots called a diffraction pattern.
This pattern is beautiful – but doesn’t seem to look like anything?
Ah, but there’s a relationship between the placement of the atoms, and where the X-rays deflect off of them – just like there’s a relationship between a pool ball bouncing off of other pool balls.
Think about it: If you know how a pool table is set up, what balls are made of, and see how the balls move after being it, then you could use math to work backwards.
Just by seeing the results of where the balls are scattering to, you could work backwards to figure out where the balls originally where.

from Banks and Kicks in Pool and Billiards, Dr. Dave Alciatore, Billiards and Pool Principles, Techniques, Resources
The same is true here: We can use math to figure out where each individual atom in the molecule is!
Let’s follow the steps below:
On the left, we see X-rays leave a source. Some of these x-rays hit a lead screen. All those X-rays are stopped.
Only a thin, focused beam of X-rays makes it thru the slit.
Those X-rays hit our crystal sample.
The X-rays bounce off the atoms, like pool balls bouncing off of each other.
(This GIF created by Abhijit Poddar, ‘E-learning’ of select topics in solid state physics and quantum mechanics)
Some of the x-rays bounce onto a film plate. This makes an image.
We end up with a diffraction pattern on film.

Figure 11.4, Purves’s Life: The Science of Biology, 7th Edition
Once we have a diffraction pattern, we use math to work backwards:
We figure out where the atoms must have been.
The result is an electron density map.
This traces out the shape of the atoms in the molecule.

Left image: X-ray diffraction pattern, Wikimedia. Right upper image: electron density map. Right lower image: model fitting atoms to the density map.
Appearance of a zone of the electron density map of a protein crystal, before it is interpreted

The same electron density map after its interpretation in terms of a peptidic fragment.

These last two images come from CSIC Crystallography
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External resources
Welcome to the world of Crystallography: The Spanish National Research Council
Cryo Electron Microscopy
Cryo-EM is an electron microscopy (EM) technique applied on samples cooled to cryogenic temperatures and embedded in an environment of vitreous water.
An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane.
While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution.
This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization.
Cryo-electron microscopy wins chemistry Nobel, Nature
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Geography, geology, geometry and geodesy
What’s the difference between geometry, geology, geography and geodesy?
Geometry
the branch of mathematics concerned with the properties and relations of points, lines, surfaces, solids.
Here is a very common example of what one may study in geometry.
In geometry we also learn about things like angles –
And of course geometry has many practical uses in many careers!
It is very useful when designing gears, drills bits, laying out camera lenses, and so much more.
Geology
This is the science that deals with the earth’s physical structure and substance, its history, and the processes that act on it.
Geology includes the study of minerals, crystals and rocks.
Geography
Geography is the the spatial study of Earth’s landscapes, peoples, places and environments.
This includes cartography (map-making.)
Here’s an example of how we use shadow projections in geography to create maps.
Of course, there are many types of maps used in geography.
Geodesy
Geodesy combines applied mathematics and earth sciences to measure and represent the Earth (or any planet.)
Isn’t the Earth a sphere? Well, mostly, sure. But exactly? No, not at all – and sometimes the actual difference matters quite a bit!

NOAA National Geodetic Survey, from a PPT by Hawaii Geographic Information Coordinating Council
Don’t we already know the Earth’s shape and size? To some degree, yes, of course. But how accurate? To the nearest plus or minus 100 feet? Plus or minus ten feet? Plus or minus one foot? Each decade, with new advances in technology, our measurements become more accurate.
And this matters because the Earth’s surface doesn’t always stay the same. Over time – even within a one year period – land can move up or down.

from the National Oceanic and Atmospheric Administration Ocean Service Education page on Geodesy:




















