Cells and extending perception: some tools of biology

 Two items need to be added to our list of what constitutes life for biology 

All life that we know about is carbon based and all living things are composed of cells. In essence, living things are composed of little bags of chemicals.

1. All living things that we know about are composed of cells.

2. The cell is the smallest thing that we know that can perform all the functions we recognize as life. As such, the cell is the smallest unit of life.

3. All cells come from pre-existing cells.

 But I'm getting ahead of myself. Cells exist on the order of micrometers. A micrometer is a thousandth of a millimeter and that's way too small to observe with just my eyes. I need help with that so let's talk about microscopes first.

When we moved from Denver to Roswell, we moved lightly. Most of our stuff, we left behind, so I've been replacing some things and reorganizing since the move. In a way, that's good because I was collecting way too much stuff. This blog is about experiencing the world out there and that means inexpensively and portably.

There is also the issue of me dumping my phone into the washing machine. Now I have a new phone. Beside the expense, moving and destroying my phone was a good thing and, to some degree, enjoyable. It let me evaluate what I have, what I need, and what I want. I've spent some time reorganizing and getting to know my set-up.

So now I have two clip-on microscopes to try out. I have my old clip-on that I brought with me. It's not terribly powerful but very portable. I keep it in the phone wallet I carry on my belt on technical hikes. The other is the much more powerful clip-on from ScienceWiz. It's a little more fiddly but the magnification is considerably more. It's still not strong enough to show a lot of very important cell structures but it's fine for field observations.

The top left is my old clip-on. The magnification wasn't expressed when I bought it and I'm still not sure how powerful it is. The other photos are of my new ScienceWiz. It's a replacement. The magnification for that microscope was expressed in the package insert and on the website. It's a fascinating piece of technology that I will discuss later in the blog.

Of course, the best thing about both in my case is that imaging is done through my smartphone so that all the functions of the phone are available, including my blog editor.

The differences between the scopes are important 

The old clip-on is a reflection microscope. It shines a light onto the specimen which returns it's image to the scope to be magnified. It uses the back camera with its better magnification and resolution. 

The rear camera actually has two cameras. One has a resolution of 50 megapixels and the other has a resolution of 8 megapixels. The front camera (selfies and mirror) has a resolution of 32 megapixels.

Resolution is an important limit which I will explain (and demonstrate) later. It is the total number of pixels that the camera captures in a single picture.

The main camera has an aperture of f/1.8. f stops are related to the size of the opening. In general, the smaller the number, the larger the opening, the more light is gathered, the sharper (and closer) the focus, and the shallower the depth of field, (the subject is in sharp focus but the background is more out of focus.) f/1.8 is about as low as it gets for digital cameras. Electronically, higher f stops can be simulated. T

he pixels for the primary camera are 0.61 micrometers across. That provides for decent resolution (it can resolve details in the tens of micrometers). A micrometer is a thousandth of a millimeter.

The secondary camera has an aperture of f/2.2 and a pixel size of 1.12 micrometers. It's intended for macrophotography.

The front camera is located at the top of my camera screen as a 4 millimeter wide black dot. It's used by the ScienceWiz microscope and the image is right there on the phone screen beneath the microscope. That camera has a f/2.4 aperture with 1 micrometer pixels.

It may have struck you that, maybe, the better rear cameras could be used by the stronger microscope, but then the screen would be face down. That would be practical with an add-on monitor, which is available for phones. I may consider it later. The ScienceWiz clamp-on is illuminated from above so that what you see is light after it has passed through the subject. That makes the other microscope better for opaque subjects.

The cameras on my phone (I have several) will provide up to 4x magnification. That may sound good but that is where resolution comes in. You can improve the size of an image but resolution caps clarity and detail. Optical magnification can give you sharper images. Digital magnification can not.

So, the ScienceWiz microscope provides from 200 to 400 X magnification according to the phone optics. With 4x zoom, that expands to 800 to 1600 X power. Again, zooming (digital magnification) doesn't improve resolution.

Above is a slide with a print of the letter "e" on a slide. The other two images used my old clip-on microscope. This shows the forte of this clip-on. The magnification isn't great but I can focus on small things, even opaque things like minerals or small flowers. 

To get rid of the walls of the microscope shown in the bottom left, I can zoom in. The zoomed image in the lower right shows the color dots that make up the image.

As for the magnification power....

The two lines above are two millimeters apart on the ruler. In the left photo, the lines are four millimeters apart, indicating a magnification of 2x. The zoomed image makes the lines 24 millimeters apart indicating a magnification of 12x.

The top photo was taken through my old microscope. The center left is zoomed twelve times. It's a splinter carved off an old stump in the front yard. The other two images were taken with the ScienceWiz microscope and is probably similar to what Robert Hooke saw when he named cells "cells".

Several folks were said to have invented the microscope including the inventor of the telescope, Hans Lippershey, around 1600. When Robert Hooke named cells, he wasn't looking at anything alive. His specimen was a fragment of cork, which is the dead outer layer of the bark of a cork tree (a species of oak).Being dead, the cells were not doing anything and were, in fact, empty and they looked to Hooke like the cells (private rooms) of a monastery.

I have mentioned that I have several camera apps and they all have strengths and weaknesses. The one used here, the standard camera for Motorola phones will not zoom with the front camera. I have since found that a couple of my other phones will, so I'm still learning.

The resolution problem that I have repeatedly mentioned is a problem and should be kept in mind, but it's perhaps not as much of a problem as I've indicated because the phone itself has algorithms to clean up blurry photos, to an extent, and photo apps such as cameras and Google Photos give you tools to clean up and modify photos. The edges of the image in the large photo at the bottom has been sharpened.

This is my second try at a stained slide since biology labs back in the 70s. The first was bad....

These are all a classic first slide, onion skin stained with iodine. The bottom photo was made using my old microscope so it didn't surprise me that I couldn't see cells.

Cells are tiny objects in the micrometer (micron) range. Even the more powerful microscope would be hard put to see much of cells but the two photos above are a good try. The left was stained with pH indicator and, for the right, I used Betadine. Iodine stains starch blue or black and cell walls brown 

If you want to try, strip the fine onion skin out from between two layers of an onion (I was frying onions and peppers for hotdogs that night). Put a drop of water on a microscope slide and place the onion skin in the drop. Add a drop of stain (food color will work, too). Slowly lay a cover slip over the specimen and if fluid seeps out, lay a piece of paper towel or tissue paper along side of the cover slip to draw the excess out.

Although you can't see the detail within the cells, you can see how the cells are lined up in rows.

There is another classic "first slide", the cheek epithelium scraping slide.

To create that, place a drop of saline on a slide (animal cells without rigid cell walls are more vulnerable to bloating than plant cells). The saline can be mixed by dissolving  1/4 teaspoon (1.5 grams) salt in 166 milliliters water. Using a toothpick, scrape the inside of your cheek repeatedly and then rub the toothpick into the saline drop. Add a drop of stain (I used blue and red food coloring for the microphotographs below.) Gently lay a cover slip over the drop 

The top left photo is not zoomed. Unlike the Android camera, my other camera apps will zoom the front camera, so the second one is zoomed  The blue food color worked well and I'm pleased that the nuclei showed up clearly. The other photos were zoomed about 3x. The left center, right center, and lower left photos include the red dye. The lower right photo shows what happens at maximum zoom 

Optical magnification exposes detail in a photo microgram but digital zooming does not add detail. It just makes the image larger. The result is blurring.

Phone cameras have algorithms to conserve details in zoomed photos. For instance, they can take several images and layer them, sharpening edges. But even the tricks that digital cameras use can only deal with so much zoom  4x is about the limit and anything above 6x is currently useless.

With the equipment I use to keep cost low (the ScienceWiz microscope is outstanding at less than $50) and portability high, I won't be able to delve too deeply into the inner workings of the cell.

The microscope is special because it uses a spherical lens with a short focal length to augment the cell phone's camera lenses. This design has been used to provide third world countries with inexpensive, accessible, 3d printable medical equipment 

For deep explorations of cell biology, I use cell models and there are three exceptional ones that I keep around:

The 3d tour of the cell video at ScienceWiz

https://sciencewiz.com/portals/cells/tour-inside-the-cell/a-tour-of-the-cell-more-advanced/

Tour of the Cell

The Cell Biology Wikibook

https://en.wikibooks.org/wiki/Cell_Biology

And Kahn Academy's College and AP biology sections 

Those will carry you as deeply as you could want to go into cell biology.

Some people suggest that you look at a cell like a city. I've worked in a lot of factories, so I prefer seeing a cell as a factory, a very automated factory 

The walls of the factory is a membrane made of fat and phosphate that likes to align itself with the phosphate heads pointing outward into the watery environment, and the fatty tails pointing inward. It's a phospholipid bilayer because both the outer and inner environments are watery. In other words, the walls of the cell factory are fluid with things stuck in and through them (like doors and windows that only let certain things through.) Plant cells have more sturdy cell walls around the membranes that are made of stuff like cellulose. Fungus cell walls gave chitin, similar to the stuff that makes up insect bodies  Bacteria can have some strange stuff.

The control center is the nucleus in eukaryotic cells. In prokaryotic cells like bacteria, everything just pretty much floats around  The cell's business is programmed on long tapes (actually spirals or helixes with two outer rails that the program units are arranged between.) A complex mechanism unzips the two parts of the tape, composed of desoxyrhibonucleic acid (DNA) and use one as a template for instructions to be carried out to the rest of the cell. The mechanism has to be complex because errors in the instruction can be disastrous. The process is called "transcription". The result is a strand of ribonucleic acid (RNA) that makes it's way out of the nucleus through pores in the nuclear membrane into a series of corridors called the "endoplasmic reticulum".

What the DNA codes for is proteins. The endoplasmic reticulum, specifically the part called the rough endoplasmic reticulum, is studded with machines called ribosomes (there are also ribosomes floating around free in the gooey cell center, called the cytoplasm). Ribosomes read the RNA instructions and create proteins. Those are carried down the hall to an organelle called the Golgi Apparatus. It looks like a stack of pancakes, but the pancakes are hollow. They check the big molecules to makes sure there are no errors and then package them into neat bundles called "vacuoles" that are sent down fibers (like little railways or monorails) to their destination. That can either be to places in the cell to help produce chemicals other than proteins or to break down sugar for energy, or they can be sent outside the cell where they might act as hormones......messengers to other parts of the body.

That breaking down sugars....... that's how the cell gets energy to do things and it takes place in organelles called "mitochondria". There are complicated chains of chemical reactions that break down sugar to water and carbon dioxide and in the process add phosphate groups to ADP (adenosine diphosphate) to form adenosine triphosphate.

The machines in cells don't use electricity to operate

 When a phosphate group break off ATP it releases a jolt of energy and that's what cells use for power. It's a lot safer in tiny machines than electricity or fire 

Plant cells have installed an extra source of energy. They don't need to transport sugar into the cell for energy. They create their own in organelles called "chloroplasts". That's what makes plant cells green because chloroplasts use a green pigment, chlorophyll, to combine carbon dioxide and water to create sugar.

I've read that microbes can form cysts that can last in soil for a long time, so I wanted to check that out. I collected some of our desert soil in a test tube, added water, and let it sit over night. Then I took some microphotographs.

Nothing was moving but I circled some suspects. They definitely have nuclei so they're eukaryotes. That would indicate that they're protozoans but the images are too small to identify. The upper right photo shows the same scene stained differently without the marks  most of the small dots are dirt particles.

I wanted to see if I could catch some of the fast division and growth of yeast cells. After 45 minutes (1 tablespoon sugar and a package of active baker's yeast in warm water) it looked like this:

But I think I waited too long. Division had slowed down. Here's a video of the action 

Yeast

There is some motion but it's primarily due to gravity. The slide was slanted.

But what I primarily wanted to see was if polarized light could be used as a "stain" and I was pleased at how it brought the chromosomal materials out in the cells 

For those slides, I placed a polarizing filter under the microscope stage, between the lens and the front camera. Most of the cells are in interphase and the chromatids are not visible, but some of the cells are getting ready to divide and you can see the chromosomes.

Later, when I look at cell division and reproduction, I'll try this again but catch the cells earlier.

Even though I absolutely recommend that you play around with making your own slides if you're going to study biology......

Pretty pictures caught when I zoomed out and saw what the glass slide was doing with the polarized light 

but you're not stuck with homebrew. Many suppliers of lab equipments also sell prepared slides. Both Home Science Tools and ScienceWiz sell sets of prepared slides. These are from the ScienceWiz animal slides collection.

And there are several sites online that provide microscopic images, including Wikimedia.

And, of course, if you want to study biology, you'll need some sources. I'm working through the Khan Academy biology sections and reading the Wikibooks in their biology section. I am very impressed with both!

But the bottomline is that there are two kinds of cells.

A prokaryotic cell is a bag of chemicals in a gelatinous goo.

A eukaryotic cell is a bag of bags of chemicals in gelatinous goo.

If you're reading this blog, you are composed of eukaryotic cells.

You might want to learn how to take care of those cells 

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Life

Top left clockwise: lichen on rock, hawk on street light, autumnal trees, grasses, plants, cheeky squirrel 

Top left clockwise: chipmunk (also cheeky), moose, duck, the same hawk, milkweed

Most people would consider all those things to be living things, but what do they have in common that makes them "living" and how do they differ from these things

Top left counterclockwise: minerals at the School of Mines in Golden, Colorado, cabbage rolls, fire (too close to my fingers), water worn arcose sandstone pebble, water from our tap

 things that people consider non-living like rocks and fire and tornadoes and steaks and (and this is a really tough one), viruses.

Animals are animated....they move around under their own volition. It's no coincidence that the two word, "animal" and "animated" are similar. In classical Greek thought, the soul (animus) is what animated animals. An animist is a person who believes that everything possesses soul (or spirit, those two words tend to be rather nebulous in meaning, sometimes interchangeable, sometimes not) but they don't usually require motion, just some kind of self recognition. The closely related panpsychic is a person that believes that everything has consciousness.

Animation might be regarded as a characteristic of living things. Even plants move in relation to light. But a lot of things move. Air and water move, generally in response to gravity, but plants and animals also move in response to other things. Fire spreads. Maybe movement isn't a good choice for something that's fundamental to life.

These problematic things that I listed above: rocks, fire, tornadoes, steaks and viruses......maybe they have to display a set of characteristics to qualify as "living", what Wittgenstein called a "family resemblance.

Not long ago, most people who even thought of such things were vitalists. They believed that living things were living because they possessed a mysterious energy that animated them, but the more people studied living things, they first found that the chemicals that percolated through living bodies, organic chemicals, could be produced from inorganic chemicals through regular chemical changes, and that life seemed to emerge from chemical reactions.

Over time, scientists came up with a list of characteristics that qualified things as "living". Here they are:

1. Living things grow. They take materials out of their environment and make it part of themselves.

2. Living things reproduce. They create similar things to themselves with important modifications  

3.  Living things respond to their environment.

4. Living things use and emit energy using chemical reactions called "metabolism.

5.  Living things maintain their internal state within tolerable limits. That's called "homeostasis".

6. Living things evolve. When they make copies of themselves, they do so to adapt their kind to their environment. They tend to create offspring that work better than themselves 

The mineral crystals grew into the form they display in the School of Mines museum, but any internal change of state is driven by outside influences. 

The cabbage roles used to be alive but they can't create other cabbage roles by themselves. They'll never produce seeds like the cabbages they once were . If they're hot, it's because the air around them heated them. They can't maintain a constant body temperature.

The fire uses fuel to transform chemicals into heat and it grows and can even split into more fires, consuming as they go. But they can't maintain an internal state that allows them to just keep going.

The rock and the water are at the mercy of their environment. They can't protect themselves.

These are the things I'll be looking at in the future. 

Go outside and look around. Do you see all the living things? Are you missing anything? Did you notice the fungi in the soil beneath you? What about yourself? You carry a world of living things around with you.....tiny mites that clean your skin and hair of microorganisms, bacteria in your gut that help you digest your food.....Did you look under the rocks? Look closer.

Meanwhile...

Obituaries are a thing.

America is an odd culture. We avoid the topic of death like a plague yet the Internet is packed with discussions of people who read the newspapers (and Internet) obituaries everyday of their lives and why they do it. A cursory examination of Google Scholar did not turn up any studies, nor could I find any data, on people who read obituaries.

There are many citations on Google Scholar about obituaries, though...how to read them, how to write them, how and why to research them, what they tell us about the people they discuss, what they tell us about society in general.

It's interesting reading. You might take some days to study obituaries.

Why am I talking about them? 

Well, it's a lead in to my excuse for my absence from this blog for a couple of months.

First, a very close friend died. Learning can be…somber, but it's always potentially edifying. I learned that, as you get older and old friends die off, it gets easier to shrug it off. Bereavement is about loss, not pity for the deceased. After you loose enough, you get used to it and life teaches you that everything isn't necessarily about us. The world goes on.

When you know you are dying, you can either say, "I'm dying," or "I'm going to live until I die." Mike showed that it is entirely possible to do the latter with all the determination of a 20-something with nothing but life ahead of them. Another person I knew who "died well" was my father. You can learn a lot from folks like that.

A week later, I went to church and couldn't sing. The next day, my annual episode of bronchitis was in full swing. I have learned to expect it every year. Some truths are just nasty. So, for a month, I sat around hacking my brains out and wearing myself down.

A close friend and college math professor was scheduled to attend a mathematics conference in town and I had said that I would go with him. It was the week after my hacking cough had let up and I was flat worn out but I keep my word, and I really did want to go since I'm an amateur mathematician and it would give me something to blog about. I had the opportunity to go as his guest, which meant a 95% discount. On my pension, it was an offer I could not refuse.

Of course, it was mostly sitting through lectures and strolling around math art exhibits and vendors (I bought gifts for folks). There was a surprising lot about my own, not so deep interests - math education and statistics. So, at least I enjoyed further abrading my life force. And I got some close-ups of the big blue bear.

At least, between bear and horse, the more personable one is the more accessible.

Finally, I'm on the mend and I've even knocked out another terminal hike (that leaves three to go) and that will be the subject of my next blog.

I recommend not avoiding mental adventures like community lectures and conferences because you think they will be boring. It's all mindset. Things that you expect to be boring usually are.

Shake out the obituary section of a newspaper. Look at some obits online. Do they have a consistent structure? Do you know an obituary reader? If so, why do they enjoy reading obituaries? What do obituaries tell us about our attitudes toward death? What do obituaries tell us about our attitudes toward life?

--- Notes on life and death ---

We call such things as life and death "opposites," but this is not altogether a satisfactory name.... In fact life and death are not opposed but complementary, being two essential factors of a greater life that is made up of living and  dying just as melody is produced by the sounding and silencing of individual notes.

Alan Watts

It doesn't feel like philosophy to me. We know, without doubt, that we die - that death punctuates a life. What we do with that knowledge - how we interpret it, determines how we approach death. It's a personal decision.

What happens after death? Philosophy needs evidence if not facts. If a person has the evidence, they can't communicate it in any persuasive fashion. If they have no evidence, then they approach the end without certainty. But we're not talking about afterlife here.

When my father died, he died a good death - he taught me to die a good death. He didn't say, "I'm going to a better place," although he might well have had reason to believe so. What he said was, "this body doesn't work right anymore. I'm tired and old and ready to go."

Alan Watts was a Zen Buddhist. He believed in reincarnation but whether he believed that persons continued after death with their essence isn't certain to me. In the quote above, he says nothing about what happens after the song. Yet, again, he doesn't approach death as a bad thing.

So, the experience of death - the adventure of death - that's what I'll talk about here. Americans seem to avoid the topic vigorously. If it bothers you, just skip this blog. That's a good thing about blogs - you can skip the ones you don't like. But for completeness sake I should at least give the nod in it's direction.

And how timely! An intimation of death doesn't have to be a near death experience - it just needs to be something to remind you that you will, one day, die. Many say it's a valuable experience. As for Horace, Robert Herrick, and many other poets, it reminds you to make the most of life while you have it. It underlies my two tenants for life.

Fill your life with things that matter (value density) and for me that would be my relationships and active lifelong learning.

Live so as to minimize the number of regrets at the end.

As you get older, intimations of mortality come more frequently. There are many opportunities to revisit old familiar illnesses, but much more often, there are new concerns and each one makes you think - is this the one?

December 7, I took buses to Broomfield for an eye doctor appointment. It was a very cold and dry day and I arrived early enough to eat lunch. Generally, I like cold and dry and the short walk invigorated me, but it also triggered my immune system and a serious bronchitis. That would not have been so bad - I was quite familiar with bronchitis, a lifelong acquaintance - but there was something else, a very profound fatigue. I didn't understand that and, two days later, checked myself into the local hospital to see what was going on.

I wasn't dying. But a visit to my general practitioner placed me on bed rest until a next appointment and there I am now. I haven't been very active on the blog lately - here is the explanation and the excuse. Did I ever think I was dying? I don't think so, but I have certainly been reminded that I'm closer to death now than I ever have been before. I do look forward to washing dishes again and returning to the trail.  This one isn't going to stop me.

My father came out of the depression and went into the Army. He was a mortar Sergeant and one of the first wave of American military in the Philippines during World War II. I never realized how some of his personality was associated with "Sarge" until much later in life.

He survived the war and came home with a, then, lethal dose of amoebic dysentery. Luckily, his home town doctor knew about research being done in Atlanta, Georgia that would save his life.

After that, he supported a family, meaning he followed the jobs. My take on macho in his generation, and my take away was:

A man does what a man has to do.

And watching my mother, I came to the conclusion that the exact same rule applied to "real women."

Between us, I think my father and I have done most kinds of jobs. Neither of us have walked on the moon, but he has walked on an amphibious lander with bombs exploding around him, and I have walked on a lay barge with the sea exploding around me. I can see some similarity. In both cases, a wrong step can get you killed and there are some situations where you really don't have much choice in the matter.

My father was known as a person who would give you the shirt off his back, literally. If he knew of some one who needed something he had, he would give it to them. He knew that he would come through it anyway and he knew that they might not. My take away - I'm responsible for others well-being, and I can get through anything - confidence and philanthropy I learned from my father.

My brother was with my father when his doctor told him that he had lung cancer. I am told that the initial reaction was very transient. After that, he said that he was ready - he was tired and his body didn't work well any more. I saw very little change in his daily life style. We did a lot of the things that he enjoyed - gem and gold hunting - and he continued working with his hand. In my memory, he didn't stop (barely even slowed down) until a couple of weeks before his death.

He became close to one of the orderlies while he was in the hospital. The orderly told him that he would be transferred to a Hospice facility the next day and he said, "Don't worry about it. I won't be alive tomorrow." And, sure enough, he died five minutes before midnight. I was holding his right hand and my brother was holding his left. At the very end, the cancer took his voice. It didn't seem that bad - maybe it really wasn't to him.

Even his funeral was amazing. It was supposed to rain all that week. An hour before the funeral, the sun came out and stayed out until an hour after the funeral - and then the weather took up it's regular programming.

He gave me his name - Payton Bailey VanZant. He lived well and he died well. I hope he gave me that also.

                       V

 When I die, I'll die the proud death.
 To this I will commit myself
 And graciously I will concede
 My body to the earth.
 I will not fear death.

 But as I live on this earth
 I will neither fear life.
 And will search it for it's best
 And live to my extent.

 On the low plains with the wild and free
 On the high plains with my God.
 By this I will live my life
 Until death sets me free.

From The Werewolf
(Confessions and Dreams of a Functional Werewolf)
by Wolf VanZandt
January 16, 1977