Sunday, August 31, 2008

A "flatworm" look at stem cells...

More information:

Students present research as do senior faculty. Dr. J's community college students, 4-year college students, high school and even one elementary student have presented research at National scientific meetings. It started with presenting the research in the classroom. Try doing a lab and then holding a mini-meeting on the lab. The above example of a student's presentation on flatworm regeneration is also about a timely topic: stem cells.

Wednesday, August 27, 2008

Monotropa hypopithys

Monotropa hypopithys L was spotted on a recent field trip up Mount Fuji (See earlier post). So, what is it? Well, it may be a mouthful to say, but doing a search to find out more can be exciting. Do you know how to find out more?

The plants database shows the following:
Click it and see some details and another photo.


The Connecticut Botanical Society:

Robert W. Freckmann Herbarium:

There are many sources. How do you evaluate them? What sources are good? Becoming proficient in higher order thinking skills can help you evaluate the value of different sites, or, texts, or journal articles.

Suppose you want to use "Reach Reading(TM)," to read some journal articles? Where and how would you find them? Think about that.

You could just happen upon one, like I did with this one from Japan, for example:
But, how would you go about a systematic search on this topic?
(Site under development)

Sunday, August 24, 2008

Teaching Science? Where does your school stand?

Here's a video done by children for adults:

So, what can you do about it?
Teachers, please note, you can teach science and math at the same time, or, science and literature at the same time., or, science and history at the same time. You can teach science on the playground or when you go for a walk.

There are grants you can get to get equipment for your school.

Parents, please note, you can have an after school homework club where a group of kids are supervised by one or two different parents every day. You can check your child's homework. You can volunteer at school. You can take your children to museums, botanic gardens, zoological gardens and observatories. You can go for a walk at a national park. You can volunteer at school. You can talk with your chil and his or her teacher(s).

Youth, you can study. You can find something you are interested in and study science standards through that subject area.

You can all write to your polititions.

You can use resources in the left hand column of this blog.

Saturday, August 23, 2008


Dr. J's mother died peacefully during her after lunch nap around 3:00 on August 20, 2008.

It is not necessary, but, anyone wishing to, may make donations of any amount in memory of Marie Shipman to your choice of charities including any listed below, or donor's choice:

Smile Train

The Audobon Society

Emily Dickinson Foundation

The Northeast Square Dancer

St Joseph’s School, Middletown, NY 113 Cottage Street Middletown, New York 10940
(845) 343-3139

Dumont High School, 101 New Milford Ave Dumont, NJ 07628

Orange County Community College

SUNY New Paltz 75 S. Mannheim Blvd., Suite 9, New Paltz, New York 12561
(845) 257-3244

William Paterson University

The Statue of Liberty- Ellis Island Foundation
The Statue of Liberty-Ellis Island Foundation, Inc. Attention: Donor Services
17 Battery Place #210, New York, NY 10004-3507 (212) 561-4588

The Botanical Society of America

Recent Visitors have been from many Parts of the World. Thank you.

Num Perc. Country Name
drill down35678.24%United StatesUnited States
drill down4910.77%CanadaCanada
drill down204.40%Unknown-
drill down40.88%JapanJapan
drill down40.88%United KingdomUnited Kingdom
drill down30.66%MauritiusMauritius
drill down30.66%IndiaIndia
drill down30.66%AustraliaAustralia
drill down20.44%SerbiaSerbia
drill down20.44%IrelandIreland
drill down20.44%PhilippinesPhilippines
drill down10.22%SwedenSweden
drill down10.22%ThailandThailand
drill down10.22%IsraelIsrael
drill down10.22%New ZealandNew Zealand
drill down10.22%BelgiumBelgium
drill down10.22%NetherlandsNetherlands
drill down10.22%South AfricaSouth Africa

Source August 23, 2008

Mark your Calendars

International Botanical Congress

Field Trip up Mount Fuji

"I had a good excursion to halfway up or 5th step
(2,400m above sea level) of Mt. Fuji (3,700m above
sea level) in order to watch alpine wild flowers
together with 16 members of the society of KATSURA
on August 21, 2008 by bus. you can see a photograph
of them in an attached file.

"We had very fine weather around Mt.Fuji on August
21, 2008. You can see photographs of far Mt. Fuji
and close Mt. Fuji in the attached files [Please click links below.].

"We watched 30 species of alpine wild flowers.
Especially, I will show you the photograph
of Monotropa hypopithys L in an attached file[Please click links below. ]."


Far Mt. Fuji

Close Mt.Fuji

Members of KATSURA

Respectfully submitted,

The Society of Practical Education in Biology
Saitoh Institute for Biology Education

Wednesday, August 20, 2008

Ever since Ozmonty ...Australian things are popping up. Here are some genetics ideas...

Wild virus attacks rabbits, your teacher says...Myxomatosis...Hmmm! It's a mystery because the virus no longer kills the rabbits. Why do they want to kill the rabbits. It must come down to money. What did the poor rabbit do to them? Ruined the human food supply? What? Are you kidding? How can we find out about it. Well, let's search the net and see what we come up with. Here are some leads.

First, you should do some research. Skim through these and find some points you can use. Be sure to site them with website and date accessed, according to the style manual your school or teacher uses (probably MLA, but, perhaps in science, CBE)

Here's the wiki site. It is helpful, but, a lot of schools are snobby about it, So, don't use only wiki. Still, it is a good starting point and can bridge you up to journal articles:

Here's a site that is biased in favor of humane treatment of rabbits:

Here's an abstract from a journal article. If you go to one of the colleges, the librarian can help you get a copy of the whole article. This is the level of reading that you should start to be introduced to on the high school level (so you are not shocked when you get to college and they expect you to find and read them on your own without being told...). Try to find more articles on this level:

Great, we've got some basic material. What do we need next? A plan. That's it, we need a plan. Just like a video game strategy, we need a Rabbit Population Mystery Strategy.

Time for the H.O.T. Skills Wheel(TM).
So Knowledge...Hmm, we can read and take notes on the articles we found. We can also find more articles. We could cut out some newspaper articles or find some pictures, perhaps.
Can you paraphrase what the articles said? That means, can you say them in your own words.
How can you use this information? Can you suggest public policies from it?
Can you critique the journal articles you found? Can you reanalyse some of the data you read about? Can you analyze data you collected? Do you know whether to use statistics or not? What statistics to use if you do need to use it?

Synthesis or evaluation
(The highest two thinking levels are sometimes switched)

What can you create? Build? Design? Can you design an experiment to test a new hypothesis you have made based on your analysis of the information you gathered from material you read?
Can you evaluate the results of your experiment and library research? Can you suggest public policy? Should a rabbit law be made? What should it say? Why?

Sunday, August 17, 2008

Organisms that cause Plant Disease

Click here for fact sheets fungi related to plant quarantines and you can learn how to prevent spread of plant disease

Mycologists Fight Plant Disease and Save the Food Supply

Mycologists all over the world cooperate to prevent devastation of food crops. In this way, they help to prevent famine. It is great that people internationally cooperate to solve world problems...Global solutions. I like that! Below is a mission statement and the related link in the USA that is used to fight plant disease. Places like this are found all over the world and countries cooperate so that people the world over can eat well especially when we use resources wisely.

"The mission of the Systematic Mycology and Microbiology Laboratory is to increase the knowledge and application of the systematics of fungi essential to solving problems in sustainable and conventional agriculture. Research emphasis is on organisms important as pathogens that threaten the production of a safe and abundant food supply and biological control agents of insects and diseases in order to reduce the need for chemical inputs in agriculture. On-line information about plant-associated fungi is provided to users through Internet access to electronic databases. The U. S. National Fungus Collections and databases about fungi serve as unique reference resources developed for use by customers throughout the world."

"Amy Y. Rossman, Research Leader
Rm. 304, Bldg. 011A, BARC-West
10300 Baltimore Ave.
Beltsville, MD 20705
(301) 504-5364"


One kingdom of organisms that not many people think of as beneficial is the Kingdom Fungi. But fungi provide many more benefits than just gourmet mushrooms. Reflect on all the benefits of organisms in the Fungal Kingdom. You might want to try cultivating mushrooms.

To get you started in the wonderful world of fungi, here is a link to the International Mycology Association <> Find events on their calendar.

More information can be found at this link to the Mycological Society of America,

Find the African Mycological Association at, and,

the British Mycological Society is located at

and, h
ere is a link to Fungi Perfecti (Registered trademark of Fungi Perfecti LLC PO Box 7634 • Olympia, WA 98507 • USA (US & Canada): 800 780 9126 Phone: 360 426 9292 • Fax: 360 426 9377 email:

Cultivation Tools
Mushroom Cultivation

Tools for Hobbyists
& Professionals

If you are aware of other great links on fungi and mushroom cultivation, please add them in the comments section. Feel free to post your reflections, too, by clicking comments.

Saturday, August 16, 2008


Horses are the focus but what else do you see in this film? Think of all the kingdoms of organisms and write about what you see.

Much of science is about observation. Sometimes we do not see all the organisms, but only those of the animal kingdom, or, sometimes only ourselves, Homo sapiens. Reflect on your position as one of the organisms among all the kingdoms of organisms.

Friday, August 15, 2008

Marshes and Tidal Flats: Spartina and Saltwater Survival

Plants and the Circle of Life

Spartina alterniflora, and related topics mentioned in the video, can be studied at various levels of higher order thinking. The video is packed with information. What knowledge can you gain from it? Take notes Cornell Style while you watch the video. You might want to add definitions, for example , for, producer, photosynthesis, and others that you feel are important. Note-taking and defining words are part of the "knowledge" level of higher order thinking.

Making a summary of the video or paraphrasing its key points is moving up to comprehension. How about application? Can what you heard be applied? How?

As you continue using H.O.T. Skills (higher order thinking skills), you might want to learn more. I've added some references on Spartina alterniflora to assist you. These include journal articles and web sites and references to journal articles. Feel confident and use "Reach reading," to attack them. There might be a lot of words you don't know. But, just like when you learned to walk or climb stairs, you can learn the skills necessary to read these articles and absorb them. It might take time, but, you can become and expert after three to five articles. But, even if you only get the gist of one of them, you are still increasing your reading ability and should congratulate yourself. (Remember, science fair winners usually use journal articles.)

Reading research on the marsh grass can increase the knowledge base and make easier higher order thinking like analysis, synthesis, and evaluation. You might use your new knowledge to solve world problems in energy, or, hunger, for example. Good luck and happy discovery!

Additional reading for your pleasure:

Photosynthesis and Nitrogen Fixation in Marsh Grass

Photosynthesis and root growth in Spartina alterniflora in relation to root zone aeration Pezeshki S.R. 1 Photosynthetica, Volume 34, Number 1, 1997 , pp. 107-114(8) Springer

Biomass Production

Animate your Science Ideas

Sometimes students learn by drawing, or, they focus that way. There notebooks are full of sketches. Channeling that artistic energy and simultaneously teaching something new in both art and science can be done through animation.

Students (and teacher/mentors) can pick a science standard from what you are learning during the year, and, then animate a film about it. There are some websites about animation to give you an idea of how animation is done. But, you can do animation with a flip book if you don't have computer access for everyone. Clay has also been used, as presented in "Botany Beat," linked here.

A website for animation concepts using stick figures is:

Some reference information can be found at:



Amino Acids

Cell Surface Receptors

DNA and Chromosomes

Gene expression for Deacetylation

Metaphase Histones (DNA Proteins)

A website for adults who want an idea of what is possible with computer animation (but, check it out first, parents may not want this for all ages of children. It is a showcase of animation from Algonquin College):

Another website, an advertisement for a school, also requiring parent or guardian checking, can be found by googling: Very Cool 3D Medical Animation. Some medical images are not suitable for all ages, however, this video can point to a career for some.

Happy animating!

Thursday, August 14, 2008

Plants have Mitochondria

Why is the headline, "Plants have Mitochondria?" Because, so often students remember that plants do photosynthesis but they forget that plants also do cellular respiration.

Review the basic biology of cells. Think about eukaryotes and prokaryotes. Think about your cells. What kinds of cells do you have? Think about kingdoms of organisms? What types of cells does each kingdom have?

Review the organelles in plant, animal, fungal, protistal, and, bacterial cells.

Edited 10-20-09:
The following article might be of interest to readers of this post.
Connecting photosynthesis and cellular respiration: Preservice teachers' conceptions
Mary H. Brown, Reneè S. Schwartz

15400 - Science Department.
The link is:
Lansing Community College, P.O. Box 40010, Lansing, Michigan 48901-7210
and Department of Biological Sciences, Mallinson Institute for Science Education, Western Michigan University, Kalamazoo, Michigan.

Mary H. Brown
Mary H. Brown
5400 - Science Department
Lansing Community College
P.O. Box 40010
Lansing, Michigan 48901-7210.

Tuesday, August 12, 2008

Scientists meet...

When scientists meet, many ideas are exchanged. People get excited and bring home new research ideas.

You can hold a small scientific meeting with your friends. Get together and present the research you have done since you last met. Have 10 minute formal presentations. Then, take a break, have a snack, and discuss the research. See if you get new ideas for more experiments.

Write an experimental design and submit it to your parents or other supervisors and see if you can do your experiment or another similar one. Remember, those in charge have many things to think about: the budget, time constraints, safety, among others, so, you might not be able to do your experiment, however, designing the experiment itself is fun. Try it.

Tuesday, August 5, 2008

What do you think about organic farming? Can it save energy and water? Here are some videos on this topic. Make up your own mind about what you think. Remember to evaluate if there is bias in any information you read or see on this topic, including these videos. Checking for bias is an important higher order thinking skill.

under development

Journal of Practical Education in Biology No.27 to No.48

"You are able to read the journal of practical
education in biology No.27 to No.48 [on] the following



Nitrogen fixing bacteria:

Research on the cellular level (with Ted Cocking):

Legumes: (under development)

What do you think about how nitrogen fits into your life?

Monday, August 4, 2008

Experiment Ideas: Plant Pigments Link (USA to Japan to USA again...)

An excellent way to learn science is by being a scientist as you learn. That means participating in the process of science. People are moving away from the idea of "scientific method" because (to some) the idea didn't convey well enough that the method consists of several processes and that these processes are exciting. Whatever skills you have, the process of science can use, music, attention to detail, observation, writing, perseverance, ...many, many skills lead to well done science. The idea is to try some experiments. Plant pigments provide an opportunity for such investigation.

I clicked on the link in the left hand column for the Japanese-based Society for Practical Education in Biology (, which you can find on this blog, and landed here: back in the USA at Berkeley. That activity is what led to this exercise in the study of plant pigments. The internet can be an aid to your research, but, you still need to think deeply about what you find. For example, the Berkeley site gives a lot of information and is a great starting place. Let's see what you can do to become a self-directed learner from there. Pick out ways of learning that support your developing an interest in your studies. As you learn, step up to higher order thinking, which will keep you motivated and interested. Use
your talents. For example, if you are a theater buff, use the plant pigments to suggest colorful costumes, or, create a play about plant pigments. A math whiz? What do wave lengths of light have to do with the pigments. Maybe you just love science labs. How could you extract the plant pigments? Could you use them for another chemical process? Art? Help convey the results you get in a beautiful way. Let's get started.

Take a look at the information on
plant pigments and see what questions come to mind. What experiments does it make you think about? Post a comment if you have any questions.

Much of the information is
definitions. Can you describe the words? Do you recall them when you close your eyes? Could you label chemical structures of the pigments with the right name? Great. These are Knowledge-based skills...Skills of remembering. You might also gather information you didn't know before:
The development of the most brilliant red coloring of
autumn is commonly ascribed to the action of frost.
This explanation is probably incorrect, for careful
observation indicates that the color is most intense
when a moderately low temperature is accompanied by
bright sunshine. In warm, cloudy autumns the colors
are more likely to be dull, with the yellows predominant.
In other seasons, when cold weather is delayed, autumn
coloration may be brilliant and near its climax before
the first frost occurs. That sunlight is important in
the development of the red pigment in many plants may
be shown also by an examination of a leaf that has been
closely shaded by another. The pigment stops so abruptly
where the shade begins that a perfect print of the upper-
most leaf results. An abundance of nitrogen in the soil
prevents anthocyan[an] formation in some plants. This
fact may explain in part the greater brilliancy of colors
seen on hillsides and river bluffs than on adjoining
Edited by John W. Ritchie
Accessed 10-29-08 See also:
Can you paraphrase the definitions? (The word paraphrase means to say, or write the information in your own words.) Paraphrasing shows comprehension or understanding. Other skills that show comprehension or understanding include: matching, giving examples, interpreting, summarizing, classifying, illustrating and explaining. Inferring, rewriting, and distinguishing are other ways of thinking about plant pigments that show comprehension. Can you organize information that you read so you can remember it?

Application (Applying) is another step up the thinking skills ladder. If you are using the HOT Skills Wheel TM, you can see that you've moved to another section. When you can apply the knowledge that you've learned, you can dramatize it, use it, solve with it, and, produce with it, for example.

Analysis is another form of higher order thinking that you can apply to your study of plant pigments. Compare, analyze, distinguish, infer, analyze, classify, differentiate, point out, subdivide, survey. Think more deeply! What can you infer from the colors of leaves and fruits? Can you differentiate among different plant pigments? How? (Add your own questions and responses. Keep track in your lab book or journal.).

Synthesis, or "creating" includes verbs like: compose, design, produce, organize, originate, combine, plan, hypothesize, role play, create, develop, construct, invent. Can you make a hypothesis and design an experiment to test out your ideas on plant pigments? If so, you are thinking well. Congratulate yourself. If not, learn by doing: try to create a hypothesis to test and then, after checking with an adult and having supervision, do the experiment. You need to check for safety reasons and for budget. Just like real scientists (which you are), you will have safety, space and budget constraints. But don't worry, you can come up with other ideas that fit the constraints and challenges you run in to. Meeting such challenges makes science fun.

Analyze your data and then, evaluate
it. Judge whether your experimental design was good as you did it, or , if you would like to modify and repeat your experiment. Do your experimental results support community policies? Can you summarize your experiment into an abstract? Have you considered various ways of looking at the data you collected? Did you critique your own experimental design and experiment? Evaluation is a type of higher order thinking. Again, congratulations.

As you reflect on plant pigments, go back and re-use any of the higher order thinking skills. Use these skills again, as needed to achieve your goals.

Try communicating with other scientists, such as Philipp Simon, or, me, about your questions. You can find some results of Philipp Simon's experiments at:

Try out the Berkeley link. Do some experiments and then publish the results here or in a journal. Let us know where you have published.
Good luck, good science, and,
great thinking!

Additional reading:
Aluminum/aluminium and plant pigments
Autumn leaves and pigments
Blueberry pigments used to make solar panels
(c) 2008 J. S. Shipman