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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.


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)


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

This website is educational. Materials within it are being used in accord with the Fair Use doctrine, as defined by United States law.

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

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)

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.


MCAS Science and Technology

MCAS Science and Technology 8th grade. Spring 2017. Based on learning standards in the four major content strands of the Massachusetts Science and Technology/Engineering Curriculum Framework.

MCAS Science and Tech 8th grade

• Earth and Space Science
• Life Science (Biology)
• Physical Sciences (Chemistry and Physics)
• Technology/Engineering

MCAS Cell biology, mitosis, meiosis, fertilization

Different types of cells in the human body undergo mitosis at different rates. Which of the following statements best explains why skin cells frequently undergo mitosis?

A. Skin cells contain molecules of DNA.
B. Skin cells constantly need to be replaced or repaired.
C. Skin cells have large numbers of sensory nerve receptors.
D. Skin cells constantly need to produce antibodies to fight off infections.


Mice with the same parents can have different traits. Which of the following
best explains how most of these differences occur?

A. Gametes join by binary fission.
B. Cells divide by asexual reproduction.
C. Genes assort independently during meiosis.
D. Spontaneous mutations occur during mitosis.


Which of the following is always part of normal sexual reproduction?

A. The male produces gametes by mitosis.

B. An offspring looks identical to the parents at birth.

C. The female carries only one fertilized egg at a time.

D. An offspring receives half its chromosomes from each parent.


Various MCAS questions may be related to bacteria.

a. Identify the process that bacteria cells use to reproduce.

b. Describe two similarities between the process that skin cells use for cell division and the process that you identified in part (a).


2015 MCAS

The illustration below shows one chromosome pair in a zygote. The zygote was produced by sexual reproduction.

cell 2 chromosomes

Assuming normal meiosis and fertilization occurred, which illustration shows the egg and sperm that produced this zygote?

MCAS zygote fertilization


The diagram below shows a plant cell at a particular stage in the cell cycle. This stage occurs immediately after which cellular process?

MCAS plant cell plate

A. crossing over
B. DNA replication
C. fertilization
D. mitosis


2016 MCAS

Which of the following must occur before mitosis can begin?

A. DNA must be replicated in the nucleus.
B. RNA must move to the center of the nucleus.
C. Chromosomes must attach to the cell membrane.
D. Ribosomes must move to opposite sides of the cell.


Each summer, up to 40% of the lobsters in a certain area lose one of their claws due to injury. By late fall, the missing claw usually begins to grow back. Which of the following describes the process by which lobsters grow new claws?

A. Lysosomes fuse together to recycle matter to build a new claw.
B. Mitotic cell division adds new cells to rebuild the lobster’s claw.
C. Facilitated diffusion moves body cells from the remaining claw to the new claw.
D. Cellular respiration creates nutrients to enlarge existing cells in the lobster’s claw.


2014 MCAS

Sharks typically reproduce sexually. A particular female shark, however, gave birth in a zoo despite having no recent contact with a male shark.

a. Identify the type of cell division that produces eggs and sperm in animals such as sharks.

b. Describe what normally happens during fertilization in animals such as sharks. Be sure to identify the end product of fertilization.

Female sharks can store sperm after mating and then wait to fertilize their eggs.

Scientists investigated whether the female shark in the zoo did this.

c. Describe how DNA analysis can determine if the shark reproduced using stored sperm or if she reproduced asexually. Be sure to include the source(s) of DNA being analyzed and the results of the analysis in your answer.

d. Explain why sexual reproduction is important for the long-term survival of shark species.


2016 MCAS open response question

The diagram below represents a plant cell with three structures labeled X, Y, and Z.

MCAS Plant cell

Plant cells and fungal cells have many of the same types of organelles. Structures X and Y are found in both plant cells and fungal cells. Structure Z is found in plant cells, but not in fungal cells.

a. Identify structure Y and describe its main function.

b. Identify structure Z and explain how plants use this structure to survive.

c. Explain how fungi can survive without structure Z


Each summer, up to 40% of the lobsters in a certain area lose one of their claws due to injury. By late fall, the missing claw usually begins to grow back. Which of the following describes the process by which lobsters grow new claws?

A. Lysosomes fuse together to recycle matter to build a new claw.
B. Mitotic cell division adds new cells to rebuild the lobster’s claw.
C. Facilitated diffusion moves body cells from the remaining claw to the new claw.
D. Cellular respiration creates nutrients to enlarge existing cells in the
lobster’s claw.


2017 MCAS

The diagram below shows a chloroplast and some of the components of the reactions that occur in chloroplasts.


Which of the following is a product of the reactions that take place in a chloroplast?

A. hydrogen gas      B. nitrate      C. oxygen gas       D. protein


In which of the following ways does the plasma membrane regulate the entry of molecules into a cell?

Creative Biomart Lipidsome-Based-Membrane-Protein-Production

A. The membrane allows only certain molecules to move into the cell.
B. The membrane destroys most molecules so that they do not enter the cell.
C. The membrane changes only certain molecules into ions before they move into the cell.
D. The membrane allows most molecules to transfer energy to the cell without entering the cell.


Many  animals  have  either internal  or external  skeletons that  provide  support and  structure. Which  of the  following  parts  of  plant  cells  play  a  similar  role?

A.  cell membranes
B.  cell  walls
C.  chloroplasts
D.  cytoplasm





Sample response: Sharks typically reproduce sexually.



Lectures on the history of physics

Galileo and Einstein: Lectures on the history of physics

Michael Fowler – University of Virginia Physics