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 

.

Biology resources

There have been many changes in science curricula since I was in school. Most of the stuff back then was descriptive. Physics was more structural mechanics. Now there's a lot more subatomic stuff and cosmology. Chemistry was more about how the elements and their compounds looked and behaved. Now, there's a lot more mathematics....calculating yields and such, and more about what happens at the atomic level.

Biology.....they used to talk about cells, organization of bodies, cell division, and the tree of life (organization of species) but now the tree of life is a different tree. It used to be based on observable similarities between different plants and animals ( and there were only two kingdoms.....plants and animals) but now it's based on similarities between their DNA which reflects how living things are related through evolutionary development.

I'm watching the lectures from the MIT introductory course in biology. They start with molecular chemistry then briefly touch on cellular organization. Then they spend a lot of time on how genetic materials translate into proteins. They end up with considerable amounts of medical biology....stem cells, immunology, cancer...

If you want a deep introduction, the MIT course is at https://ocw.mit.edu/courses/7-016-introductory-biology-fall-2018 .

As usual, there's a lot out there. Let's see. What's in my tool chest? It's nice to have all my tools in one place so I try to consolidate as much as I can on my phone. Beside the general purpose apps I've been using (the calculators, sensor apps, and general purpose tools) there are some useful programs specifically oriented toward biology.

A major emphasis on biology is imaging. Biological entities range from submicroscopic viruses (we won't be looking at them since it would take some very expensive and very non-portable equipment, like electron microscopes. We might do some Internet safaris, though ) to whole forests of Aspen trees (an Aspen Grove may well be a single organism.) The parts of organisms are important also, from the molecules that power them (again, too small for us to actually see) to individual cells, to whole ecosystems.

I walked down to Dry Creek Park the other day to take some pictures. I was a bit disappointed. We're in a period of cooling and frequent storms and everything was quiet......no birds or squirrels in sight. The creek was flowing so that microorganisms are washing downstream.....no stagnant water there to play with and the cold water encourages them to go dormant. Still, I got a few pictures.

This ash tree was still green. The grass in my lawn looks like it's getting ready for fall but the trees haven't quite caught on yet 

I have some identification books stored in my phone but I used Google Lens to check my identification. Once you have an image in Google Pictures, a poke at the Lens button  will search the Internet for a similar image. There are similar apps available for different phones and computers.

I can zoom in with my phone camera to about eight times (8x) but notice that, in the photos of an ash leaf above, the more I zoom, the blurrier the picture is. In an electronic camera, the number of light sensitive elements (pixels) there are in the CCD (charge-coupled device chip...the part of the electronic camera that replaced the film in older cameras and changes patterns of light into electrical signals)  is constant. Since the picture resolution is determined by the number of pixels available, that's constant, too. Resolution is usually specified as the number of pixels on the CCD. In my phone, the front camera ( the one on the same side as the user....the "selfie camera") has 16 mega pixels ("mega"="million") and the back camera (the one I usually use) has 50 megapixels. My phone actually has three lenses that focus the light on different sections of the CCD.

Imaging is important in biology because there is so much detail that matters that is hard or impossible to see. You probably got to use laboratory microscopes in school that magnified to over a thousand times. Field microscopes are usually lower powered for a couple of reasons. Portability is an obvious virtue in a microscope that will be in the field. Often, though, samples are brought back to the laboratory for examination. Most laboratory microscopes used to look at field samples trade resolution for field of view. They're usually bulkier than laboratory microscopes and have two eyepieces ("stereoscopic microscopes") to enhance the dimensionality of the image.

I determined the optical characteristics of my camera here:

http://adventuringbcc.blogspot.com/2021/05/i-am-camera.html

I have a very portable clip-on microscope for my phone that is quite serviceable in the field. It's rated at 60x magnification with more magnification possible with zoom.

That's sorta an advertising misinformation. You can get larger pictures with electronic zoom but the resolution remains the same so a zoomed picture will be blurry. Still, you have to zoom to get rid of the "tunnel" effect in the top picture above. I can get a fairly reasonable image at around 80 or 90x. The maximum around 120x is pretty poor.

There are ways to improve a blurry image. Most phone cameras have editing features that allow you to play around with a photo image. "Sharpen" is one that can improve an enlarged image. It senses borders in the image and averages the values of the pixels around the border, replacing the pixels on the border with the averages. It's an illusory improvement that can miss some important details, but with some skill, a photographer can get some decent photomicrographs like that. There are also "magnifying glass" apps that have the sharpen feature built in.

The bottom line is that if you want really good photomicrographs, use optical magnification instead of electronic (zoom) magnification.

I also have a clip-on front camera microscope that has a stage like laboratory microscopes and uses transmitted light (my other clip-on has a built in light that reflects light off the sample). Actually, I got that microscope with the "Cells" Science Wiz kit. 

Here is some stuff I found in Little Dry Creek. It's not very impressive since the water flow was pretty high and the water was cold. All the little beasties were hiding for the autumn. The magnification is about the same - around 60x.

Big things and distance views are important in biology field work also. My Carson telephoto lens will give me a moderate field, zoomable, magnification of six times. That's about perfect for wildlife photography. You want to be far enough from wildlife to avoid spooking them or from being mauled or trampled by them.

At telephoto distances, tiny movements of the camera can blur the image so a camera tripod with a phone adapter is necessary. For wildlife photography the tripod needs to be set up in a location that's as obsured as possible and a portable blind is useful. On the day I was taking photos for this blog, everyone was at home asleep. Winter does that sometimes. Anyway ....leaves.

And, of course, phone cameras usually have a video mode that lets you take movies of, say, wildlife behavior.

Microscopy requires things like stains, slides, droppers, knives to slice samples. There are good kits that aren't expensive. I have a couple from Home Science Tools and the Cells kit from Science Wiz.

A particularly useful tool is a microtome that lets you make very thin slices of materials to put on microscope slides. You can pay as much as you want for one. Mine:

an economy model, cost less than $20 and came with a razor blade. It's basically a flat plate with a screw piston that pushes the sample by tiny increments up through the center of the plate so it can be sliced off. Table models can run to four figures but you don't want a table models in your backpack, anyway.

I won't be doing any high powered microscopy but it can be pretty fascinating. You can equip yourself for considerably less than a thousand dollars (or more) and a good source is American Science and Surplus. Avoid the cheap kiddie microscopes. The affordable ones have poor, plastic optics and are not worth the savings. A good option, around $100 is the Celestron line of digital microscopes. 

There's life out there (even in the winter.) so go out and study it!

A Snowy Interlude

We haven't had a lot of snow this winter in the Denver area. A lot of places in the U.S. have had a lot more than they're used to.

Snow is a part of geology, too. It packs pockets in the mountains to form glaciers. The seasonal freezing and thawing allows water to sleep into cracks in rocks and wedge them apart. Earth science includes the study of the solid, liquid and gaseous parts of our planet and they all cooperate to make Earth what it is.

This time, I did a common science hobby activity that I've never done before. I tried first on February 1, when the snow was first packing in, but it was a very fine dust with very little crystal development. On the second day, there were big flakes and I got these photographs.

I took them with a clip-on microscope lens for a smartphone. It has a built-in LED illuminator, which explains the glare. After cropping and sharpening the images, I ended up with these images.

To get the photographs, I caught the flakes on a slide that I had left in our freezer overnight and used the smartphone camera with microscope lens, hand-held, to capture the images. It was quick and sloppy work but easy.

The flakes themselves were from a single sample. Had I spent a lot more time catching more I could have likely come up with better examples, but these are quite good enough to show the varied hexagonal nature of ice.

When taking pictures of snowflakes, the surface you use (in this case, a plastic microscope slide) must be below freezing or the flakes will melt as soon as they land on it. Also, don't use a hot light source like a hot incandescent lamp to illuminate the slide, and don't breathe on the flakes.

Of course, an actual microscope would give you better results, but the scope should also be chilled, perhaps by leaving it for an hour in the place where you will be photographing, and in humid environments, protect the instrument from condensation (cover it and use an eyepiece cap until you're ready to shoot). 

If you use a smartphone camera, you might be able to use a gooseneck camera holder and phone clamp to steady the phone.