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Seaport Academy explores with microscopes

At Seaport Academy, science education isn’t about drills and worksheets. We motivate students with hands-on manipulatives, interactive apps, three dimensional animations, connections to the world around then, and labs. Here we’re learning how to explore the microscopic world with a microscope.

Seaport class microscope

Microscope insect bee leg
We examine animal fur, scales and skin, plant pollen, seeds and leaves, and insect parts.

Here we see a student’s point-of-view when discovering the anatomy of a honeybee leg.






Compound microscope

Used when a specimen is translucent (some light passes thru it)

Usually higher power 10x to 300x

The observer sees all the way thru the specimen being studied.

Has more than two sets of lenses.

Has an eyepiece lens  (or ocular) and two or more sets of objective lenses

They sit on on a nosepiece that can revolve

The specimen is placed on the stage of this microscope.

Parts of the microscope

Label Microscope parts

  1. eyepiece (ocular) – where you look through to see the image

  2. body tube – Holds the eyepiece and connects it down to the objectives

  3. fine adjustment knob – Moves the body of the microscope up/down more slowly; fine control. Gets the specimen exactly focused. We only use this after we first use the coarse adjustment knob.

  4. nosepiece – rotating piece at the bottom of the body tube. Lets us choose between several lenses (objectives.)

  5. high power objective — used for high power magnification (the longer objective lens)

  6. low power objective — used for low power magnification

  7. diaphragm – controls amount of light going through the specimen

  8. light/mirror – source of light, usually found near the base of the microscope.

  9. base – supports the microscope

  10. coarse adjustment knob — Moves body of the microscope up/down more quickly; Gets specimen approximately focused.

  11. arm – Holds main part of the microscope to the base.

  12. stage clips – hold the slide in place.

  13. inclination joint – used to tilt the microscope

Learning Standards

College Board Standards for College Success: Science

LSM-PE.2.1.2 Gather data, based on observations of cell functions made using a microscope or on cell descriptions obtained from print material, that can be used as evidence to support the claim that there are a variety of cell types.

LSM-PE.2.2.1 Describe, based on observations of cells made using a microscope and on information gathered from print and electronic resources, the internal structures (and the functions of these structures) of different cell types (e.g., amoeba, fungi, plant root, plant leaf, animal muscle, animal skin).

2006 Massachusetts Science and Technology/Engineering Curriculum Framework

Inquiry, Experimentation, and Design in the Classroom: SIS2. Design and conduct scientific investigations. Properly use instruments, equipment, and materials (e.g., scales, probeware, meter sticks, microscopes, computers) including set-up, calibration (if required), technique, maintenance, and storage.


Lack of exercise is a major cause of chronic diseases

Lack of exercise is a major cause of chronic diseases

Frank W. Booth, Ph.D., Christian K. Roberts, Ph.D., and Matthew J. Laye, Ph.D.

PMC 2014 Nov 23, and Comprehensive Physiology 2012 Apr; 2(2): 1143–1211.5

U.S. Air Force photo by Staff Sgt. Christopher Hubenthal

U.S. Air Force photo by Staff Sgt. Christopher Hubenthal


Chronic diseases are major killers in the modern era. Physical inactivity is a primary cause of most chronic diseases. The initial third of the article considers: activity and prevention definitions; historical evidence showing physical inactivity is detrimental to health and normal organ functional capacities; cause vs. treatment; physical activity and inactivity mechanisms differ; gene-environment interaction [including aerobic training adaptations, personalized medicine, and co-twin physical activity]; and specificity of adaptations to type of training.

Next, physical activity/exercise is examined as primary prevention against 35 chronic conditions

[Accelerated biological aging/premature death, low cardiorespiratory fitness (VO2 max), sarcopenia, metabolic syndrome, obesity, insulin resistance, prediabetes, type 2 diabetes, non-alcoholic fatty liver disease, coronary heart disease, peripheral artery disease, hypertension, stroke, congestive heart failure, endothelial dysfunction, arterial dyslipidemia, hemostasis, deep vein thrombosis, cognitive dysfunction, depression and anxiety, osteoporosis, osteoarthritis, balance, bone fracture/falls, rheumatoid arthritis, colon cancer, breast cancer, endometrial cancer, gestational diabetes, preeclampsia, polycystic ovary syndrome, erectile dysfunction, pain, diverticulitis, constipation, and gallbladder diseases].

The article ends with consideration of deterioration of risk factors in longer-term sedentary groups; clinical consequences of inactive childhood/adolescence; and public policy. In summary, the body rapidly maladapts to insufficient physical activity, and if continued, results in substantial decreases in both total and quality years of life. Taken together, conclusive evidence exists that physical inactivity is one important cause of most chronic diseases. In addition, physical activity primarily prevents, or delays, chronic diseases, implying that chronic disease need not be an inevitable outcome during life.



Detecting genetic disorders with 3d face scans

Detecting genetic disorders with 3d face scans

Johan at the Phineas Gage Fan Club writes:

Following on from last week’s post on smile measuring software, The Scotsman (via Gizmodo) reports on the work by Hammond and colleagues at UCL, who are developing 3d face scans as a quick, inexpensive alternative to genetic testing. This is not as crazy as it sounds at first since it is known that in a number of congenital conditions, the hallmark behavioural, physiological or cognitive deficits are also (conveniently) accompanied by characteristic appearances. The classic example of this is Down syndrome, which you need no software to recognise. More examples appear in the figure above, where you can compare the characteristic appearances of various conditions to the unaffected face in the middle.

Hammond’s software can be used to identify 30 congenital conditions, ranging from Williams syndrome (a sure topic of a future post) to Autism,


Face scan Williams syndrome

Face scan Fragile X and Jacobson


Diagnostically relevant facial gestalt information from ordinary photos

Rare genetic disorders affect around 8% of people, many of whom live with symptoms that greatly reduce their quality of life. Genetic diagnoses can provide doctors with information that cannot be obtained by assessing clinical symptoms, and this allows them to select more suitable treatments for patients. However, only a minority of patients currently receive a genetic diagnosis.

Alterations in the face and skull are present in 30–40% of genetic disorders, and these alterations can help doctors to identify certain disorders, such as Down’s syndrome or Fragile X.

Extending this approach, Ferry et al. trained a computer-based model to identify the patterns of facial abnormalities associated with different genetic disorders. The model compares data extracted from a photograph of the patient’s face with data on the facial characteristics of 91 disorders, and then provides a list of the most likely diagnoses for that individual. The model used 36 points to describe the space, including 7 for the jaw, 6 for the mouth, 7 for the nose, 8 for the eyes and 8 for the brow.

This approach of Ferry et al. has three advantages. First, it provides clinicians with information that can aid their diagnosis of a rare genetic disorder. Second, it can narrow down the range of possible disorders for patients who have the same ultra-rare disorder, even if that disorder is currently unknown. Third, it can identify groups of patients who can have their genomes sequenced in order to identify the genetic variants that are associated with specific disorders.


Quentin Ferry et al, eLife 2014;3:e02020


This App Uses Facial Recognition Software to Help Identify Genetic Conditions

A geneticist uploads a photo of a patient’s face, and Face2Gene gathers data and generates a list of possible syndromes

… Face2Gene, the tool Abdul-Rahman used, was created by the Boston startup, FDNA. The company uses facial recognition software to aid clinical diagnoses of thousands of genetic conditions, such as Sotos syndrome (cerebral gigantism), Kabuki syndrome (a complicated disorder that features developmental delay, intellectual disability and more) and Down syndrome.

This App Uses Facial Recognition Software to Help Identify Genetic Conditions, Smithsonian Magazine


Related resources

How phenotypes lead to genotypes (infographic?)

Scientific journal articles

Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration
Shouneng Peng et al, PLoS Comput Biol. 2013 Dec; 9(12)


Digesting nutrients

This next section comes from BBC KS3 Bitzesize Science, http://www.bbc.co.uk, Organisms, behaviour and health


Special proteins that can break large molecules into small molecules.

Different types of enzymes can break down different nutrients:

  • carbohydrase or amylase ⇒ break down starch into sugar

  • protease ⇒ break down proteins into amino acids

  • lipase ⇒ break down fats into fatty acids and glycerol


Saliva in your mouth contains amylase, which is a starch digesting enzyme.

Diagram shows how carbohydrase molecules break down starch into sugar during digestion


Proteins are digested in the stomach and small intestine.

Protease enzymes break down proteins into amino acids.

Digestion of proteins in the stomach is helped by stomach acid, which is strong hydrochloric acid. This also kills harmful micro-organisms that may be in the food.

Diagram shows protease molecules breaking down proteins into amino acids


Lipase enzymes break down fat into fatty acids and glycerol. Digestion of fat in the small intestine is helped by bile, made in the liver. Bile breaks the fat into small droplets that are easier for the lipase enzymes to work on.

Digestion breaks down fat molecules into fatty acid molecules and glycerol molecules

Things that are not digested

Minerals, vitamins and water are already small enough to be absorbed by the body without being broken down

Fiber – these are carbohydrates that our body can’t digest

How does the digestive system break larger molecules down into smaller molecules?


(adding water molecules as part of a chemical reaction.)



 How does does starch enter the bloodstream

Absorption and egestion


These are the processes that happen in the digestive system:

ingestion (eating) → digestion (breaking down) → absorptionegestion

Digested food molecules are absorbed in the small intestine. This means that they pass through the wall of the small intestine and into ourbloodstream.
Once in the bloodstream, the digested food molecules are carried around the body to where they are needed.

Only small, soluble substances can pass across the wall of the small intestine.
Large insoluble substances cannot pass through.

Absorption into bloodstream

Diagram shows food in the small intestine, and the wall of the small intestine which divides it from the blood stream.

Shows carbohydrase combining with the food in the small intestine.

Shows the food cells passing through the wall of the small intestine into the blood stream

The inside wall of the small intestine needs to be thin, with a really big surface area.

This allows absorption to happen quickly and efficiently. If the small intestine had a thick wall and a small surface area, a lot of digested food might pass out of the body before it had a chance to be absorbed.

To get a big surface area, the inside wall of the small intestine is lined with tiny villi (one of them is called a villus).

These stick out and give a big surface area. They also contain blood capillaries to carry away the absorbed food molecules.

Diagram of villli, showing the walls which are just 1 cell thick, and the network of capillaries, and the blood vessels


Stone walls

Walk into a patch of forest in New England, and chances are you will—almost literally—stumble across a stone wall. According to Robert Thorson, a landscape geologist at University of Connecticut, these walls are “damn near everywhere” in the forests of rural New England.

Jeanna Bryner, in Livescience, writes about the rediscovery of the lost archaeological landscape of New England.

Leaf-off (left) and Leaf-on (right) aerial photographs with a modern road superimposed through the northeast corner of the image for reference .

Aerial New England forest optical stone walls

These stone walls and other archaeological features could not be seen with traditional aerial photographs shown here. This figure illustrates the advantage of LiDAR data with a point spacing of 1 meter or better over traditional map views of the landscape for archaeological purposes.

Examinations of airborne scans, using light detection and ranging (LiDAR), of three New England towns have revealed networks of old stone walls, building foundations, old roads, dams and other features, many of which long were forgotten. Here, stone walls are yellow, abandoned roads are red, and building foundations are outlined by green squares.

Aerial New England forest LIDAR stone walls

LiDAR is not only a powerful tool on its own; it can also be used in conjunction with the many types of historical documents available to those performing research in this geographic area,” Johnson and Ouimet write in the Journal of Archaeological Science.

As an example, this 1934 aerial photograph taken of an area in Preston, Conn., shows a farmstead — cleared fields, forest, stone walls or fences, a house, a barn and other outbuildings, and a road running through the farm.

Aerial forest Connecticut stone walls

Now compare with this aerial image from 2012.

Aerial forest Connecticut stone walls 2012

from Livescience, Images: ‘Lost’ New England Archaeology Sites Revealed in LiDAR Photos, 1/16/14


New England Is Crisscrossed With Thousands of Miles of Stone Walls

That’s enough to circle the globe—four times.

By Anna Kusmer 5/4/18

Walk into a patch of forest in New England, and chances are you will—almost literally—stumble across a stone wall. Thigh-high, perhaps, it is cobbled together with stones of various shapes and sizes, with splotches of lichen and spongy moss instead of mortar. Most of the stones are what are called “two-handers”—light enough to lift, but not with just one hand. The wall winds down a hill and out of sight. According to Robert Thorson, a landscape geologist at University of Connecticut, these walls are “damn near everywhere” in the forests of rural New England.

He estimates that there are more than 100,000 miles of old, disused stone walls out there, or enough to circle the globe four times.

Who would build a stone wall, let alone hundreds of thousands of miles of them, in the middle of the forest? No one. The walls weren’t built in the forest but in and around farms. By the middle of the 19th century, New England was over 70 percent deforested by settlers, a rolling landscape of smallholdings as far as the eye could see. But by the end of the century, industrialization and large-scale farms led to thousands of fields being abandoned, to begin a slow process of reforestation.

“New England had great pastures,” says Thorson. “It was a beef-butter-bacon economy.”

As farmers cleared those New England forests, they found rocks—lots and lots of them. The glaciers that receded at the end of the last Ice Age left behind millions of tons of stone in a range of sizes. New England soils remain notoriously stony today.

When life gives you stones? Build a wall. Farmers pulled these plow-impeding stones from their fields and piled them on the edges. “The farmer’s main interest was his fields,” says Thorson. “The walls are simply a disposal pile. It was routine farm work.” This process was replicated at thousands of farms across the region—a collective act of labor on a glacial scale.

The supply of stone seemed endless. A field would be cleared in the autumn, and there would be a whole new crop of stones in the spring. This is due to a process known as “frost heave.” As deforested soils freeze and thaw, stones shift and migrate to the surface. “People in the Northeast thought that the devil had put them there,” says Susan Allport, author of the book Sermons in Stone: The Stone Walls of New England and New York. “They just kept coming.”

Wall-building peaked in the mid-1800s when, Thorson estimates, there were around 240,000 miles of them in New England. That amounts to roughly 400 million tons of stone, or enough to build the Great Pyramid of Giza—more than 60 times over.

No one dedicates more time to thinking about these walls than Thorson, who has written a children’s book, a field guide, and countless articles about them since he first moved to New England in 1984. Thorson, bald and bearded, a mossy stone himself, is a landscape geologist, and he distinctly remembers his first walks in the New England woods—and coming across one stone wall after another. His mind was full of questions about what they were and who built them, “it was a phenomenon that was extraordinary,” he says. “One thing led to another, and I got obsessed on the topic”.

Thorson started the Stone Wall Initiative in 2002, aimed at educating the public about this distinctive feature of their forests, in addition to conserving the walls and studying how they impact the landscape around them. Thorson has built a reputation as the ultimate expert on this phenomenon. “You know how a natural history museum would have a person who identifies stuff for you? I’m kind of that guy for stone walls,” he says.

Every year he takes his students to a maple-beech forest stand in Storrs, Connecticut, which he calls “The Glen,” to look at a classic farmstead stone wall. This wall is thigh-high, and mostly built of gneiss and schist, metamorphic rocks common in the valley flanks of central New England. With Thorson’s help, one begins to see a little structure in how the stones were stacked—in messy tiers, by a farmer who added one load at a time.

Thorson may be particularly obsessed with the walls, but he’s not alone in the interest. He is constantly invited to speak at garden clubs, historical societies, public libraries, and more. “The interest doesn’t die down,” he says. “Twenty years later, it’s still going on.”

His field guide, Exploring Stone Walls, is a directory of some of the most unusual, interesting, or distinctive walls in the region. The tallest example is a mortared sea wall beneath the Cliff Walk in Newport, Rhode Island, measuring over 100 feet. The oldest wall, in Popham Point, Maine, dates to 1607. Thorson’s favorite historically significant wall is at the Old Manse, a historic home in Concord, Massachusetts. It provided cover for minutemen firing on the British during the Revolutionary War. Thorson also highlights Robert Frost’s “Mending Wall,” located on his farm in Derry, New Hampshire, the inspiration for the famous line, “Good fences make good neighbors.”

Thorson knows about as much as one can know about the world-wonder- scale web of walls across the Northeast, but there remains much to learn, particularly in terms of what they mean for ecosystems, such as their role as both habitat and impediment to wildlife, and their effect on erosion and sedimentation. “It sounds silly,” he says, “but we almost know nothing about them.”

Geographer and landscape archaeologist Katharine Johnson earned her doctorate mapping stone walls from above, using lidar (light detection and ranging) technology. Lidar is similar to radar, only instead of using radio waves to detect objects, it uses light. Laser pulses—thousands per second—are emitted from a specially equipped plane. There are so many of these pulses, that some are able to hit the small spaces between leaves and penetrate all the way to the forest floor, even through thick tree cover. Johnson’s lidar images reveal the exent of those crisscrossing stone walls in a way nothing else can.

Her research shows that, stripped of the region’s resurgent forests, the walls provide a snapshot of 19th-century history—a map of what land was cleared and farmed at the time. Combined with other data on the forests themselves, this can help specialists model historic forest cover and, in turn, help ecologists understand how forests grow back after they have been disturbed or cleared entirely. The walls can hold the key to New England’s social history, including settlement patterns and farming styles. They provide a static backdrop against which change can be measured.

“Stone walls are the most important artifacts in rural New England,” Thorson says. “They’re a visceral connection to the past. They are just as surely a remnant of a former civilization as a ruin in the Amazon rain forest.”

Each of the millions of stones that make up New England stone walls was held by a person, usually a subsistence farmer, or perhaps a hired Native American or a slave. What remains is a trace of countless individual acts etched on the landscape. “Those labors,” says Allport, “hundreds of years later, they endure.”

source atlasobscura.com/articles/new-england-stone-walls

Related references



Scientific articles

Rediscovering the lost archaeological landscape of southern New England using airborne light detection and ranging (LiDAR), Katharine M.Johnson and William B.Ouimet, Journal of Archaeological Science, Volume 43, March 2014, Pages 9-20

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§107. Limitations on Exclusive Rights: Fair Use.  Notwithstanding the provisions of section 106, the fair use of a copyrighted work, including such use by reproduction in copies or phone records or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright. In determining whether the use made of a work in any particular case is a fair use, the factors to be considered shall include: the purpose and character of the use, including whether such use is of a commercial nature or is for nonprofit educational purposes; the nature of the copyrighted work; the amount and substantiality of the portion used in relation to the copyrighted work as a whole; and the effect of the use upon the potential market for or value of the copyrighted work. (added pub. l 94-553, Title I, 101, Oct 19, 1976, 90 Stat 2546)

Learning Standards

Massachusetts History and Social Science Curriculum Framework

1. Use map and globe skills learned in prekindergarten to grade five to interpret different
kinds of projections, as well as topographic, landform, political, population, and climate
maps. (G)
2. Use geographic terms correctly, such as delta, glacier, location, settlement, region,
natural resource, human resource, mountain, hill, plain, plateau, river, island, isthmus,
peninsula, erosion, climate, drought, monsoon, hurricane, ocean and wind currents,
tropics, rain forest, tundra, desert, continent, region, country, nation, and urbanization.
3. Interpret geographic information from a graph or chart and construct a graph or chart
that conveys geographic information (e.g., about rainfall, temperature, or population
size data). (G)


Pancreas has two major jobs: Digestion, and hormonal control of blood sugar levels

I. Releases pancreatic juice


  • released into the duodenum (first part of the small intestine)

  • is alkaline (the opposite of acid).
This neutralizes the acid that had been created by your stomach.

  • contains lipases – enzymes which break down fats

  • contains proteases – enzymes which break down proteins

  • contains amylases – enzymes which break down carbohydrates


II. Pancreas’s endocrine cells release hormones

Hormones regulate your blood sugar levels.

When [blood sugar] too high -> pancreas releases insulin

causes muscle and fat cells to take in more sugar, so this decreases [blood sugar]

promotes glycolysis – conversion of sugar into ATP, also decreases [blood sugar]

makes liver store glucose as glycogen

glycogen glucose

When [blood sugar] too low -> pancreas releases glucagon

tells liver to break down glycogen into glucose, so this increases  [blood sugar]

stops cells taking in more sugar, so this increases [blood sugar]

STOPS glycolysis, so sugar isn’t turned into ATP, so this increases [blood sugar]


Liver pancreas homeostasis GIF

from dynamicscience.com.au, feedbackloops

Organic molecules in smoke

Burning wood produces a wide array of organic compounds. Each type of wood makes many unique compounds, and the specific compounds formed depend on the amount of oxygen available. Here are a few of them.

Description: nutty roasted hazelnut


2-Acetyl-3-methylpyrazine smoke

nutty nut flesh roasted hazelnut toasted grain


Learning Standards

2016 Massachusetts Science and Technology/Engineering Curriculum Framework

HS-LS1-6. Construct an explanation based on evidence that organic molecules are primarily composed of six elements, where carbon, hydrogen, and oxygen atoms may combine with nitrogen, sulfur, and phosphorus to form monomers that can further combine to form large carbon-based macromolecules.