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There’s an immense world of tiny stuff within us and around us—but how do we know about it? In this episode of Crash Course Biology, we’ll discover how we see what we can’t see, thanks to the help of centuries-old tools and more recent technology. Along the way, we’ll learn about the major types of microscopes and how to use a typical light microscope.

Discovering Bacteria 0:00
Methods for Observing Molecules 1:36
Microscopy 2:25
Types of Microscopes 3:30
Cryo-Electron Microscopy 7:54
How Light Microscopes Work 8:38
Review & Credits 11:34

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CC Kids:
In 1683, Antonie van Leeuwenhoek stumbled on a vast, never-before-seen world… in his own mouth.

And as a kid, lil’ Sammy was low-key obsessed with how he did it! While playing around with making microscopes in his spare time, he scraped some plaque from his teeth and plopped it under a lens to see what it looked like close up.

He was astonished to see tiny living things. Some spinning like a top, others swimming through his spit like a fish. Many doubted his findings, but the discovery filled Leeuwenhoek with a sense of awe and wonder.

He called the tiny organisms “animalcules.” Get it, like animal…molecule? The name didn’t stick, but his discovery did. Because he leaned into the sheer quirkiness of his curiosity, Leeuwenhoek was the first person to ever observe what we now know as bacteria.

He had seen the unseeable, with just a single lens. And since then, microscopes have gotten way more powerful – and more accessible – allowing everyday people like you and me to see further into the microcosmos than Leeuwenhoek could have ever imagined. Hi, I’m Dr.

Sammy, your friendly neighborhood entomologist, and this is Crash Course Biology. Hey guys, serious question. Can we look at my mouthgoo? ‘Cause why are we letting Leeuwenhoek have all the fun here?

Come on camera crew, get in there! You gon’ learn today! Ahh -- uh huh -- ahh [THEME MUSIC] When you consider that every organism is made up of teeny-tiny cells, it makes sense that a lot of biological processes happen on a microscopic scale.

In fact, most bacteria, like the ones Leeuwenhoek observed, are even smaller than animal cells. Proteins, your body’s super diverse tool kit for keeping everything running smoothly, are even smaller still. There are several ways that scientists get up close and personal with tiny biological bits.

With chromatography, for example, we can separate chemical compounds —which all living things are made of— and figure out what’s in the mix. We can also identify unknown molecules in organisms or in air, water, or soil through mass spectrometry. This technique reveals a molecule’s identity by showing exactly how much it weighs.

Spectroscopy, on the other  hand, identifies molecules  based on the wavelengths of light they absorb. Today, we’re focusing on the same tool that Leeuwenhoek used to investigate the inner workings of his mouth —the microscope. Thanks to advances in microscopy, or the scientific field that involves observation using microscopes, we’ve gone from barely being able to see a cell, to being able to peek at individual atoms: among the tiniest units of matter.

To be fair, we can’t see those atoms in super great detail yet. The best picture we’ve got basically looks like a bunch of blurry Milk Duds. But microscopes have come a long way since Leeuwenhoek’s time.

They’re better at magnification— making bigger images of tiny stuff. They have better resolution, meaning that you can more clearly make out the fine details, and distinguish between objects even when they’re really close together, like with pixels in a JPEG. And with new ways of enhancing contrast— or, making light and dark parts stand out— we can distinguish between  the most miniscule parts.

And those advances help us better understand a whole range of things: like the arrangement of atoms in molecules, the inner workings of our cells, and the viruses that make us sick. Now, the old faithful of microscopes is the light microscope, also known as an optical microscope, which goes back at least to the year 1600. Biologists, and other scientists, still use light microscopes today.

But before we can unpack how a light microscope works, it’s helpful to think about  how human vision works. Basically, as waves of light hit objects, the objects reflect some of that light. The reflected light reaches our pupils, and then other amazing parts of our eyes help us see the object in focus.

Our brains translate these stimuli into what we discern as images. So, a light microscope works by modifying that light before it reaches the eye. It shines a light through, or at, the thing you want to see, also typically known in biology as a specimen.

The light bounces off the specimen and passes through special lenses that bend it. This bending of light makes the image projected into your eye seem bigger than the original, actual thing. This is similar to how eyeglasses work for near-sightedness.

The lenses in the glasses bend visible light  to magnify the image before  it reaches your pupils. So a bunch of blurry squiggles become letters on an eye chart, or that tall attractive gentleman over there becomes… a coat rack? Sammy, bro, do you need glasses??

Right, so, the most powerful light microscopes can make a subject appear over two thousand times its actual size. But the more magnified things get, the less clear the resolution. Using a light microscope on the tiniest molecules is sort of like taking a camera phone from the turn of the century bird watching.

This fuzzy blob was a fluffy-backed  tit babbler, trust me. So for what light microscopes can’t clarify, we’ve got electron microscopes. First invented in the early 1930s, these tools work by focusing beams of electrons on a specimen instead of light.

You see, light travels in relatively large waves, so it doesn’t always interact much with very small specimens. The wave might travel above, or below it, rather than through it. But the negatively charged particles that circle around the nucleus of an atom — yeah we’re shooting actual electrons — they also travel in waves.

Much smaller waves. And because of their charge, we can use magnets to direct the path of those waves to focus on the specimen. With that power, electron microscopes can capture really detailed images of stuff that’s even smaller than cells.

Modern electron microscopes can make specimens look more than 100 thousand times their actual size, with resolution about 100 times sharper than a standard light microscope. Another type of microscope, invented in the early 1980s, is the scanning probe, which doesn’t use light or electrons at all. Instead, it has sharp probes that pass over the thing you want to see.

Kind of like those pin-impression toys you used as a kid to make a mold of your hand …or your whole face. [apprehensive noises] Nah... Except a scanning probe runs over the surface of the specimen, gathers a bunch of information, and then mashes it together to make a detailed enlarged image. We’re talking up to 100 million times the size of the original specimen.

Yeah, stuff just got real! Even with all these technological advances, there’s no one-size-fits-all microscope. Each type has a range of  sizes they can help us see,  and they’re all useful for different reasons.

Like, good news: electron microscopes can capture more detailed images than a light microscope. But bad news: preparing a specimen for an electron microscope usually kills the cells. So it can’t help us look at living stuff like a light microscope can.

Also, electrons are pretty energetic and focusing  a beam on a specimen for too  long can burn a hole in it. That’s a mistake I’ve made more times than I’d like to admit. There are also various techniques that can be used in conjunction with these types of microscopes.

Like, through special dyes, biologists can label tiny parts of living cells, so the view looks like it’s marked up with mini highlighters. Then, by shining particular wavelengths of light on the dyed molecules, we can begin to create a map that helps us fill in the gaps of what we can’t see with a standard light microscope. And because the structures within cells are constantly in conversation with each other, lighting them up with fluorescence lets us watch their interactions in real-time.

Sort of like a full-color silent movie. And if we want to slow that movie down, well, we’ve got a technique for that, too. One that works with electron microscopes: cryo-electron microscopy, which involves freezing samples below negative 160 degrees Celsius.

That’s almost twice as cold as the lowest temperature ever recorded in Antarctica! This makes rambunctious Earth molecules hold still long enough for a photoshoot thousands of pictures long. Those can be combined into a super-detailed 3-D image.

Some of those molecules include proteins – which run chemical reactions, hold our cells together, and keep us from getting sick. Being able to see these complex molecules gives us a better idea of how they work, including their functions in our bodies, what happens when they don’t work correctly, and how to fight disease with targeted medicine. This is exciting stuff—but it’s likely that a cryo-electron microscope won’t be the first one you lay eyes on.

Instead, you’ll probably start out with the light microscope. That tried and true tool that has worked for Renaissance scientists and 21st-century biologists alike. To take a closer look at how a light microscope works, we need to go on a quick field trip to Hammy’s Used Microscope and Magnifying Glass Emporium.

Here’s Hammy now! Come on down! Come on down!

We’ve got ‘em new, we’ve got ‘em used, and we’ve got ‘em ready for you to take for a test drive. This one’s a 2010 model: sleek, well-maintained, it’ll last for miles. The kind of microscope I learned to science with.

Up top is the ocular lens:  the part you look through. Now, some light microscopes have just one—but this beauty? It’s got two of ‘em.

Just one look through these crystal-clear goggles, and whatever’s on your slide is going to look ten times bigger. Now, this model comes with a full set of objective lenses, which you can flip through to make an image look a little bigger, a lot bigger, or somewhere in between. Below that is the stage: spacious seating for your specimen to slide in and get ready for its big moment in the spotlight.

You can pick your lighting with this here iris diaphragm, which opens and closes to let a wider or narrower beam of light through. And the light adjustment knob amps up the lamp’s brightness or tones it down. With easy-access knobs on the side, you can customize the view that’s right for you.

The big one, the coarse adjustment knob, lets you smoothly lift the stage up or down. The smaller one, the fine adjustment knob, brings your specimen into focus. Now, every visitor to our  emporium gets a free lesson.

My assistant, Yeasty the 255th, will help us out. And I want you to remember three things: Start low. Center and focus.

And it’s fine at the top. When you get your first microscope, I know it’s tempting to rush into the  magnifying part right away. But ya gotta slow down and start low.

Before anything else, lower the stage as low as it can go. Then you flip your objective lenses, so they’re on the lowest power possible. Next, center and focus.

You want to make sure your specimen is securely strapped right in the middle of the stage. Get Yeasty centered and  focused on that lowest power. Only then should you bring  him in for his close-up.

Twist the coarse adjustment  knob to raise the stage. And lower those higher-power objective lenses, one by one, dialing the fine adjustment knob each time until everything’s in clear view. And lastly, and this is important, once you’re using the highest-power objective lens you’ve got, don’t raise the stage up any further… or you’ll risk shattering a lens and hurting little Yeasty here.

Remember, it’s fine at the top, so fine adjustments only. And there you have it! Happy microscoping, everyone.

Here’s my card. Thanks, Hammy! Anyway, when you get a chance to try a microscope yourself, it’s kind of amazing to remember it’s a tool that’s been used for centuries —since before we even knew bacteria were a thing.

And microscopes are still rocking our world. In fact, these days they’re  more accessible than ever. You can become a community scientist with nothing more than your cell phone and a detachable microscope adapter.

And while there’s no perfect tool for seeing all the imperceptible bits that make up life on Earth, new tools and techniques continue to push our understanding of life forward, helping us visualize molecules  and cells in new ways, and opening new windows on that immense, tiny world around us. In our next episode, we’ll take a tour of the cell —and learn how the power of microscopes helps us  understand the inner workings  of life’s building blocks. Peace.

This series was produced in collaboration with HHMI BioInteractive. If you’re an educator, visit for classroom resources and professional development related to the topics covered in this course. Thanks for watching this episode of Crash Course Biology which was filmed at our studio in Indianapolis, Indiana, and was made with the help of all these nice people.

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