Category: Natural World

Humans, 90% bacteria + 10% us

90% of the cells in your body are bacteria and other provocative facts about the Domain Bacteria are the subject of a great but long article by Valarie Brown.

[R]esearchers have also discovered unique populations adapted to the inside of the elbow and the back of the knee. Even the left and right hands have their own distinct biota, and the microbiomes of men and women differ. The import of this distribution of microorganisms is unclear, but its existence reinforces the notion that humans should start thinking of themselves as ecosystems, rather than discrete individuals.
—Brown (2010), in Miller-McCune.

The article makes for great reading during this cycle’s work on classification systems and evolution. One choice paragraph summarizes the fundamental differences between the domains of life:

There’s such ferment afoot in microbiology today that even the classification of the primary domains of life and the relationships among those domains are subjects of disagreement. For the purposes of this article, we’ll focus on the fundamental difference between two major types of life-forms: those that have a cell wall but few or no internal subdivisions, and those that possess cells containing a nucleus, mitochondria, chloroplasts and other smaller substructures, or organelles. The former life-forms — often termed prokaryotes — include bacteria and the most ancient of Earth’s life-forms, the archaea. (Until the 1970s, archaea and bacteria were classed together, but the chemistry of archaean cell walls and other features are quite different from bacteria, enabling them to live in extreme environments such as Yellowstone’s mud pots and hyperacidic mine tailings.) Everything but archaea and bacteria, from plants and animals to fungi and malaria parasites, is classified as a eukaryote.
—Brown (2010).

Bacteria are prokaryotes. Image by Mariana Ruiz Villarreal.

Brown also gets into a discussion of if bacteria think:

[B]acteria that have antibiotic-resistance genes advertise the fact, attracting other bacteria shopping for those genes; the latter then emit pheromones to signal their willingness to close the deal. These phenomena, Herbert Levine’s group argues, reveal a capacity for language long considered unique to humans.
—Brown (2010).

Trimming this article down would probably make it a good source reading for a Socratic Dialogue.

Bacteria are the sine qua non for life, and the architects of the complexity humans claim for a throne. The grand story of human exceptionalism — the idea that humans are separate from and superior to everything else in the biosphere — has taken a terminal blow from the new knowledge about bacteria. Whether humanity decides to sanctify them in some way or merely admire them and learn what they’re really doing, there’s no going back.
—Brown (2010).

Erosion as diffusion

Landforms in the sandbox before and after the rain.

We left the sandbox uncovered under last week’s heavy rain, and the result was a new perspective on erosion, sedimentation and the evolution of landforms.

Nice, sharp, hand-sculpted valleys were smoothed out by the raindrop splatters. The beautifully steep sided fjord on the lower left, in particular, eroded into the gentler slopes of a fluvial surface.

This process is diffusional. Sand moves from high peaks to fill in the low valley floors, evolving toward a softer, flatter land surface in the same way dye in pan diffuses from the high concentration droplet to a more uniform distribution.

There was enough rain that water pooled, for a little while, at the lower end of the sandbox. This allowed the formation of a beautiful little delta from the main river, which was most remarkable to observe while it was raining because the channel bifurcated at its mouth with running water to the left and right of the depositional landform.

Island bluffs surrounded by sandy beaches.

The standing water in the “ocean” also caused the islands to partially erode at the edges to create steep bluffs overlooking sandy beaches.

And finally, if you looked carefully at the sides of the river channel you could see where the water was beginning to cut into the banks, a little offset on either side, to start the formation of meanders.

Annotated sandbox features.

Tree of life

One of the easiest and most elegant ways of explaining the classification of organisms, the history of life on Earth, and the relationships between different organisms is to construct a phylogenetic tree. I have a great exercise I like that takes just some bits of colored paper, string, a poster board and some thumbtacks.

To start, each student writes the Latin domain, kingdom, phylum, class, order, family, genus and species names on separate pieces of colored paper. I hand out paper in stacks and give them strict instructions not to rearrange the order of the colors. Wikipedia is actually a great resource for this because they tend to be quite reliable on this if they have the specie you’re looking for (and they have quite a bit).

Students then tape the pieces of paper together on a string, species at the bottom, domain at the top, and, one by one, tack them to the poster board. As each student attaches their string to the board they say the common name of their organism and then recite the phylogeny.

When I did the exercise on Monday, I asked the students to use the organisms they’re working on for their independent research projects so everything started with the domain Eukaria. Interestingly enough, the Wikipedia pages don’t have the domain classification, probably because they think it’s too obvious, but I had a number of kids spend quite a bit of time trying to figure it out; they probably benefited from doing so I didn’t mind at all.

Constructing the phylogenetic tree.

Classifications that are the same are tacked one on top of the other, Eukaria on top of Eukaria, Mammalia on top of Mammalia and so on, so that, as students add their parts of the phylogeny, you begin to see the phylogenetic tree. We had insects, mammals, plants and reptiles, so there was quite a nice variety represented.

After about half a dozen lineages were on the board, the procedure began to get a bit repetitive, so I started to ask students to guess, based on the common name, where the next species to go on would diverge from the rest of the emerging tree. Students seemed to like this part of it. I had started with homo sapiens when I demonstrated the procedure so it was salutary for them to see how much the other organisms differed from humans.

When everything is tacked on, you end up with a cute picture of a the tree of life that makes a cute, but awfully real looking, phylogenetic tree. Students tack their pieces of paper on the string at different distances, some much closer together than others. As a result, the final tree is looks as though it shows the genetic divergence between the different groups. It a fake, but lends a sense of verisimilitude non the less.

What’s the difference between humans and animals?

In the field of cognition, the march towards continuity between human and animal has been inexorable — one misconduct case won’t make a difference. True, humanity never runs out of claims of what sets it apart, but it is a rare uniqueness claim that holds up for over a decade. This is why we don’t hear anymore that only humans make tools, imitate, think ahead, have culture, are self-aware, or adopt another’s point of view. – Frans De Waal (2010).

My students studied the question, what is life, last cycle, and through their readings and Socratic dialogue I’ve been trying to approach the question of what is sentience and what distinguishes humanity from other organisms (or robots for that matter).

We’ve found that the lines between us and them are very hard to draw.

Pushing the discussion into questions of morality, primatologist Frans De Waal has a wonderful post on where it comes from, and if there is any clear distinction between humans and other animals. He argues that morality is innate, a product of evolution, and there aren’t clear distinctions.

The full article is a worthy read, with good writing and well constructed arguments. It’s a bit too long for a Socratic Dialogue but might be of interest to the more advanced student, particularly those going through religious, coming-of-age, rites of passage, like preparations for confirmations and Bar Mitzvahs. While De Waal’s evolutionary reasoning has been used to argue against religion, he takes a much more subtle approach:

Our societies are steeped in it: everything we have accomplished over the centuries, even science, developed either hand in hand with or in opposition to religion, but never separately. It is impossible to know what morality would look like without religion. It would require a visit to a human culture that is not now and never was religious. That such cultures do not exist should give us pause. – Frans De Waal (2010).

Science of Cooking at the Exploratorium.

The Science of Cooking from the Exploratorium. (© The Exploratorium, www.exploratorium.edu)

The San Francisco Exploratorium has a wonderful website on the science of cooking.

They have a very nice bread science page that explains what happens with the yeast and gluten as you mix, kneed and bake bread. There is a set of recipes, including sourdough and Ethiopian Injera, that my students might want to try. They even have a great links page to pretty much everything you might want to know about the science of bread and how to manipulate it.

Checking eggs for cracks. (© The Exploratorium, www.exploratorium.edu)

I was also very interested in their pages on eggs, with the virtual tour of an organic egg farm, science of cooking, beating and mixing eggs, and a wonderful set of activities including removing the eggshell while keeping the membrane intact and demonstrating osmosis through the egg membrane.

And I haven’t even gotten into the pickles, meat and seasoning sections yet.

Salt on vegetables= Osmosis

Water droplets extracted from slices of squash by a sprinkling of salt.

This year we have a lot of food in the curriculum. My objective is to make sure everything is edible and add as much more as I can.

Sprinkling salt on slices of squash creates the concentration gradient necessary for osmosis to suck the liquid out of the squash cells, creating little water droplets.

Now we batter them and fry them up to make tempura.

The effects of placing freshwater plant cells (Egeria densa) in salt water solution.

For comparison, the image adjacent shows what happens to the cells of a plant when the water leaves (osmosis under the microscope).

Mitosis dance

Anaphase.

One way to represent the process of mitosis is through dance. One of my students suggested they do an interpretive dance for their natural world personal project. I think they were mostly kidding, but with a fair bit of encouragement they did end up doing it.

The dance is much more literal than it probably needs to be since I helped a bit with the final product. I still think it’s pretty useful though because it’s abstract enough that you have to know the mitosis process to figure out what’s going on. So much so, I had them perform it twice at the end of our synthesis discussion. The second time through I narrated it so the steps would be clear to everyone.

I think it might make for a good “spark the imagination” lesson if one was needed.

Right now the dance needs four people, two for the chromosomes and two for the centrioles, but it would be really neat if the entire class participated by representing the cell membrane.

The diagram with the steps is: mitosis.svg. The instructions are below.

Steps

  1. The DNA (DNA 1 and DNA 2) stand facing the audience with DNA 2 hidden behind DNA 1 since the DNA have not yet duplicated.
    • The centrioles (C1 and C2) just stand there with C2 pretending not to be there.
    • DNA 1 mimes touching the nucleus walls while DNA 2 pretends not to be there.
    • DNA 1 dances the DNA helix, which probably involves lots of hand motions and spinning around taking 23 steps to represent the number of chromosomes in humans.
  2. Replicating: DNA 2 steps forward while C 2 moves around the two DNA to get to the other side
  3. The DNA join hands and spin around (because it’s fun to do, apparently)
  4. The DNA line up next to each other and lock elbows while the centrioles start extending their threads, which probably involves some type of waving hand motion.
  5. The centrioles move in, with their threads, and grab the open elbows.
  6. The centrioles pull the DNA apart.
  7. The two DNA act out the reforming of their nuclear membranes.
  8. The DNA-centriole pairs wave each other goodbye as they become separate cells. (This is where having the rest of the group as the cell membrane would be nice.)
Steps to the mitosis dance.

The Edible Schoolyard

Alice Waters has been in the news a lot recently with the recent evaluation of the Berkley School Lunch Initiative (full report).

Waters instituted a program that:

… offered cooking and garden classes integrated with selected classroom lessons along with improvements in school food and the dining environment. – Rauzon et al. (2010)

The report, which followed 5th and 6th graders into middles school, found that they knew more about nutrition and had greater preferences for fresh fruit and vegetables than students in comparable schools.

The researchers did not go into all of the ancillary benefits of gardening and cooking in the school, because the lessons tie into science and social studies curricula. Of course these benefits should be familiar to the Montessori community since Montessori advocated the erdkinder farm school for adolescents.

Diagram of squash flowers.
Diagram of squash flowers.

The Hershey Montessori School seems to be a good example of what Montessori was aiming for (as is the glimpses we get of child rearing in Mirable). We do a lot ourselves in our little program. I’ve noted before how our greenhouse and bread baking tie into math, science, social studies and art.

I sometimes think that the progression of education traces the evolution of culture and technology over the course of human history much in the way that embryonic development was supposed to recapitulate the evolutionary history of the species.

Ontology does not recapitulates phylogeny, and my observations are probably just about as accurate, but the psychosocial development of early adolescents, who are just discovering who they are and realizing their place in society and history, parallels the fundamental reorganization of human societies brought about by the emergence of agriculture.