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January Meetings for Seniors

Posted on Tuesday, January 17, 2012 by for NYCSEF, Seniors, St. Joseph's.

All seniors must meet with their supervising teacher at some time during this week (as soon as possible). Meetings should only last about 10 minutes. There are 3 purposes for this meeting…

  1. to discuss your NYCSEF Application Status
  2. to register for the St. Joseph’s College High School Poster Session
  3. to compute your final grade for the semester

Ms. Sullivan is available in the Dean’s Office (room 113) periods 3-7. If you cannot meet with her during these periods, please meet with me instead (room A214). I am available periods 3, 4, 7-10 (also period 2 on Wednesday).

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Google Science Fair Announcement

Posted on Thursday, January 12, 2012 by for Google, Seniors.

Google Science Fair

Today is the official launch date for the 2012 Google Science Fair. All seniors will participate in this competition. Projects are entered as web sites that exist in Google’s cloud services network and must include either an embedded YouTube video or Google Docs presentation. You can’t enter without a Gmail account, so set one up now if you haven’t already done so.

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DNA Day Essay Contest

Posted on Thursday, January 12, 2012 by for Extra Credit, Juniors, Seniors.

The DNA Day Essay Contest aims to challenge students to examine, question, and reflect on the important concepts of genetics. Essays are expected to contain substantive, well-reasoned arguments indicative of a depth of understanding of the concepts related to the essay questions. Essays must be less than 750 words (excluding references). Here’s this year’s topics.

DNA Day Essay Contest

Genes exert their influence on organisms by being turned on and off in precise ways and at precise times. Disease can result when problems arise during this process of "gene regulation". The first processes of gene regulation to be discovered involved molecular "switches" that regulate transcription at gene promoters. In the last 20 years, genomic research has uncovered many new types of gene regulation that earlier researchers would have never imagined. Genes can be regulated by repressors, activators, enhancers, epigenetic changes to chromatin, RNA interference, the environment, and other processes. Choose one of the gene regulation processes listed above and, using references to support your argument, explain why/how that regulatory process is critically important to ONE of the following:

  • early development
  • normal cell function
  • causation of disease or cell malfunction

Submission Deadline: March 12, 2012 at 5:00 PM EST.

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Senior Gathering

Posted on Friday, January 6, 2012 by for Seniors.

The Research Room is reserved periods 8, 9, 10 on Tuesday, January 10 for an end-of-the-semester celebration. You made it through the paperwork nightmares that are Intel and NYCSEF. I think it’s time we used A214 for a gathering.

The best thing would be if everyone would contribute something to the cause (main dish, side dish, beverage, etc.). We may have cups, silverware, and napkins left over from last year’s science fair, but I don’t know for sure.

I have arranged for the delivery of a 160 liter tank of liquid nitrogen for educational purposes. One of the more interesting things you can do with it is make ice cream in 30 seconds. I have some of the ingredients (vanilla powder, cocoa powder, peppermint extract, sugar) as well as the necessary utensils. I need a volunteer or two or three to bring cream (light cream works better than heavy cream).

Please visit the spreadsheet and tell me what you’d like to contribute. (Check your email for the link.)

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SEM Image of the Week: Seasons Greetings

Posted on Monday, December 26, 2011 by for SEM.

The subject of this week’s SEM IOTW is a mystery, but I’ll give you a hint. It’s a food that’s really only eaten at this time of year. It’s also SEM friendly (that is, it contains very little moisture.) The pure object didn’t look that interesting — until I decided to break it. Fractures are a great thing to study with an SEM.

whatizit? whatizit?
Two images at nearly the same magnification. The one on the left shows the shattered edge of the mystery object. The one on the right shows the interior that was exposed when the mystery object was broken.
whatizit? whatizit?
A magnified region of the image above. The broken end of the mystery object. A mosaic of four images, rotated 90° counterclockwise relative to the other three images.

Image credit: Glenn Elert

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January Meetings

Posted on Thursday, December 22, 2011 by for Juniors.

January meetings have been scheduled. All students should bring the second draft of the article analysis. The article should be attached as well as the first draft. Be sure to include the reference on your analysis.

Many of you gave me the final draft of the Intel essay, but did not give me the 1st and 2nd drafts. These should be in my mailbox by 9th period on January 3rd, or your grade for that assignment will be lowered.

Students in Lab should bring their lab logs with them to the first meeting in January so I can check logs for November and December.

For the 2nd meeting in January, you should come on whichever of the 2 days is best for you according to whether you are in lab or not.

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SEM Image of the Week: Mussels not from Brussels, Part 2

Posted on Monday, December 19, 2011 by for SEM.

Last week’s SEM images showed the shell of a blue mussel (Mytilus edulis), focusing on the structure of the hard outer shell made of the mineral aragonite (a polymorph of calcium carbonate or CaCO3). This week we’ll be looking at the outside of that same mussel, focusing on a group of microscopic algae whose hard outer shells are made of silicate (also known as hydrated silicon dioxide or H4SiO4).

The little creatures you see below are single celled algae called diatoms. The origin of the word diatom comes from the fact that their shells (called tests or frustules) are made of two interlocking halves. In Greek, dia (διά) means "across" (the diameter of a circle is the measure across it) and tomos (τομος) means "to cut" (atoms are things that can’t be cut), thus diatomos (διάτομος) in Greek or diatoms in English are things that can be "cut across" or "cut in two". Diatoms reproduce asexually by splitting in half. The top half (called the the epitheca) becomes one daughter and the bottom half (called the hypotheca) becomes another. More Greek. The word theca (θήκη) means "case", epi (ἐπί) means "on top", and hypo (ὑπό) means "beneath". Thus, the epitheca (ἐπίθήκη) is the "top case" and the hypotheca (ὑπόθήκη) is the "bottom case".

Diatoms have a light golden brown color due to the presence of chlorophyll a (a green photosynthetic pigment) and chlorophyll c (a yellow photosynthetic pigment). Compare this to trees, grasses, and the other large plants we see around us every day. The leaves of these plants are mostly chlorophyll a and a little bit of chlorophyll b (another yellow photosynthetic pigment). Trees and grasses appear green because the leaves are higher in chlorophyll a than chlorophyll b — 3:1 being a typical a:b ratio. Diatoms appear golden brown because they contain mixtures of chlorophyll a and chlorophyll c that are closer to being equal — a:c ratios from 2:1 (mostly green) all the way to 1:2 (mostly yellow) are found.

Silicon dioxide (SiO2) from sand is the primary raw material for nearly all commercially produced glasses (other ingredients include calcium oxide and sodium carbonate). It is also the primary raw material for the silicate shells of diatoms (the other ingredient is water). In essence, diatoms live in glass houses. Trying to image them with a light microscope is a real challenge. Their clear bodies nearly vanish in the clear liquid they live in. The only thing that makes them stand out is the little bit of yellow-brown pigment in their chloroplasts. To an electron beam, however, these glass housed microalgae are solid as a rock. Light goes through diatoms, but electrons bounce off. A scanning electron microscope is the perfect tool for imaging diatoms and diatoms are the perfect subject for the scanning electron microscope. Enjoy this week’s images and expect to see more diatoms in the future.

diatoms diatoms diatoms
A group of diatoms hanging out together on the back of a blue mussel. The width of this image is about the same as the width of a human hair. The wavy appearance is an artifact that commonly occurs at high magnification with non-conducting materials. All SEM images are made in a vacuum. Two whole diatoms with their top half (epitheca) showing and one with its top half missing. These diatoms are in the genus Cocconeis. Possibly Cocconeis scutellum or Cocconeis stauroneiformis. The bottom half (hypotheca) of one diatom. The top half was blown away by the electron beam. The two halves became negatively charged, like charges repel, and the top half took off.

Image credit: YaQun Zhou and Anastasiya Matveyenko (images 1 and 2); Glenn Elert (image 3). Thanks to Professors John Marra and Brett Branco at Brooklyn College and Professor Edward Theriot at the University of Texas at Austin for help in identifying these creatures.

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NYCSEF forms have been delivered.

Posted on Friday, December 16, 2011 by for NYCSEF, Seniors.

NYCSEF forms have been delivered.

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SEM Image of the Week: Mussels not from Brussels, Part 1

Posted on Monday, December 12, 2011 by for SEM.

Mollusks are invertebrate animals with shells made of calcium carbonate (CaCO3). This phylum includes cephalopods (squid, octopus, cuttlefish), gastropods (snails, slugs), and bivalves (clams, oysters, scallops, and mussels). The subject of this week’s SEM Images of the Week is a mussel shell I saved from dinner a month ago. I bought it at the Whole Foods on Columbus Ave and 97th Street in Manhattan near my apartment. I purposely decided to eat mussels that day just so I would have a shell to place in the SEM. Mussel shells are hard and low in moisture, which makes them perfect for the high voltage, high vacuum environment inside a working SEM.

Calcium carbonate comes in one of two polymorphs — two different geometric arrangements of the calcium and carbonate ions — calcite and aragonite. All mollusk shells are made from aragonite. So are pearls, coral, and bird eggs. Followers of this website should expect to see other examples of aragonite appearing in the future (eggshells leftover from breakfast, snail shells from lunch in Paris, coral from my next trip to the Great Barrier Reef, pearls from Marge Simpson, etc.). The aragonite in this mussel shell formed crystals of varying shapes — prismatic rods; layered sheets; bristly mats; and soft, rounded hexagons.

broken point stacked plates stacked plates
The tip of a broken edge. Zoom in on the broken edge. The shell is made of layers of aragonite
rod ends doormat rounded hexagons
Around the lip of the shell, the aragonite is arranged in rods. In some regions, the aragonite crystals are loosely arranged into short spikes that remind me of a rough doormat. Inside where the mussel lives, the aragonite appears as stacks of soft, rounded hexagons.
single rod tag
A single aragonite rod sitting on a bed of rod ends. Shellfish Harvest ID Tag. These live blue mussels were cultivated on ropes in waters off Prince Edward Island, delivered to a distribution center in Pigeon Cove, then purchased, steamed and eaten in New York City.

Image credit: Glenn Elert

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SEM Image of the Week: Tiny shrimp

Posted on Monday, December 5, 2011 by for SEM.

The Department of Redundancy Department came up with the title of this week’s entry. The objects studied were tiny dried shrimp (蝦米 xiāmi) from an Asian grocery in Brooklyn. None of them was bigger than an adult fingernail. They had bright pink bodies and crazy, blue-black eyes on stalks. I tried to mimic the natural color using Photoshop. Adding color to highlight structure is common in SEM imaging.

top view top view, false color
Top view of the head. False color image
left eye, low vacuum left eye, high vacuum
Left eye, low vacuum mode. Left eye, high vacuum mode.
right eye, low vacuum right eye, high vacuum
Right eye, low vacuum mode. Right eye, high vacuum mode.

Image credit: Glenn Elert. Thanks to Kate Wong for providing the sample.

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Message for My Juniors

Posted on Sunday, December 4, 2011 by for Juniors.

I just completed the schedule for the remainder of the fall semester. Please check the website now. Let me know about problems in advance. There are only 4 meetings left. These are the things we’ll work on at each meeting. All items identified by the word “draft” must be submitted one business day before the meeting.

  1. First December Meeting: Second draft of Intel personal essay; “Classic” paper identified; November lab logs reviewed
  2. Second December Meeting: Final draft of Intel personal essay; First draft of “Classic” paper
  3. First January Meeting: Second draft of “Classic” paper; December lab logs reviewed
  4. Second January Meeting: Final draft of “Classic” paper; Extra credit projects discussed

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Midwood Science Research
Midwood Science Research Program
Glenn Elert — Coordinator
Midwood High School at Brooklyn College   Midwood High School at Brooklyn College
David Cohen — Principal
2839 Bedford Avenue
Brooklyn NY 11210
(718) 724–8500