Microbes Don’t Actually Look Like Anything

This is a ciliate, just a eukaryotic microbe
waving its cilia around under our microscope. And this is the same ciliate. And yup, here it is again… …and again. But as you’re probably noticing, while the
rough outline of this organism seems the same from shot to shot, the ciliate itself and
the world around it clearly look very different. Colors change, details are more apparent. In one case the organism seems to be lit from
within. On this channel, we’re constantly flipping between different ways of capturing images of organisms. So which one of them is what they actually
look like? Well…none of them. Anything you see through a microscope is an
image, which in our case, means that everything we show you on this channel, every frame,
is not the microbial world itself. It’s an interpretation of the life on the
other side of our objective, translated through the lens into details, and shapes, and colors—all
affected by the way we light up the life we want to see. Light is amazing, it’s also very weird. It travels in waves, and as it interacts with
particles and materials, it scatters and shifts. Even if we can’t actually see those light
waves in motion, so much of what we observe in the world around us is rooted in the physical
properties that define those waves—like how we can observe certain frequencies of
light as colors. But waves have far more to them than just
their frequency, and microscopy has combined the resourcefulness of many different sciences
to use light to give us different ways to peer into the microbial world. So let’s start simple. Good old fashioned white light. Early microscopists used oil lamps and sunlight
to see through their microscopes, and while the technology has changed, the simplicity
of this has endured into the modern technique of brightfield microscopy. It all starts with a source of light, though
modern microscopes have their lamps built in, set up underneath the stage that holds
our sample. Light travels from the source through a condenser, which works to focus the light onto the sample above it. This focused light travels through the sample
towards the objective lens, which takes in an image and magnifies it into these bright
backgrounds with organisms, sometimes rendered transparent by the intensity of the light. You might say that this is as close as we
get to seeing what the microcosmos actually looks like, but that would be like taking
a 2000 watt light bulb into your living room and saying, “this is what my home looks like.” Light affects things, and we’re not even
shining light on these organisms, we’re shining light through them. Now, Brightfield might seem relatively simple,
but that simplicity has been incredibly powerful in allowing scientists old and new to wade
through microscopic waters. Still, there are limitations to consider with
any scientific technique, and one of the major challenges for brightfield microscopy, particularly
when looking at microbes, is contrast. Pigmented organisms are easy to visualize
against the bright background, but in cases where the organism has been rendered transparent,
it can be harder to distinguish their bodies from the rest of the world they inhabit. Scientists can navigate these challenges using
stains that make certain structures more visible, but for our purposes, we like to avoid stains
because they can affect the microbes themselves. There are other ways though to contend with
this challenge, one of which is built on one of those simple-yet-strange properties of
our world: you don’t always need to shine light directly onto an object to see it. This technique is called darkfield microscopy,
which sounds like it must be almost the opposite of brightfield microscopy. It’s not. The two techniques are actually very similar:
light travels from a source through a condenser, goes through the sample, and then it travels
into the objective lens, producing the image we see. But what we want in darkfield microscopy is
for the beam of light to hit the sample, but not our eye. So, in darkfield microscopy, a circular disk
is placed inside the condenser, blocking the central part of the light from shining through
the sample and into our eye..or, our camera.. This means that when there is no sample on
the slide, all you see is black. But the disk doesn’t block all of the light:
there is still a hollow cone of light that travels around the disk, unable to reach the
objective or our eyes, but that still hits the sample. When it does, those microscopic, transparent
bodies scatter those hidden rays into our view. And as they do, an image of their bodies forms
against a dark background, providing us with this almost cinematic footage. Another method to get better contrast than
brightfield microscopy is called phase contrast microscopy, and it’s built on working with
a property of light that we can’t actually directly experience. Microbes , or really anything, that is easily
visually observed with brightfield microscopy are called amplitude objects because as light
passes through them, the amplitude of the light wave changes, which we see as changes
in light intensity. But there is another class of specimens: these
are called phase objects. As light passes through these objects, the
waves slow down and shift slightly in phase compared to the unaffected light around it. And if you’re wondering what that means
in terms of what we can see, that’s the issue: our eyes don’t process these differences
in phase. And so in the final image, these objects (or
in our case, organisms) are very difficult to see. Well, in the 1930s, a physicist named Frits
Zernike developed a method to shift the direct light just slightly enough so that these changes
in phase could actually be translated into changes in amplitude, producing an image of
these formerly hard-to-see phase objects by essentially treating them as amplitude objects. There is a lot of physics in this that we
are not going to get into, but the result was so important that it would eventually
win Zernike the Nobel Prize in Physics. And of course, selfishly, we here appreciate
his work because it lets us see more of our more hidden microbial friends. And for the last type of microscopy we’ll
go over today, we’re going to be getting into another property of light that we can’t
directly see, and this one can make the microcosmos glow. Most of the light we see has an electrical
field that vibrates in all sorts of planes relative to the direction the light is traveling in. But that vibration can be restricted to just
one plane, and when that happens, the light is said to be polarized. We can’t see the difference between polarized
and unpolarized light. Now you might see the difference in how the
world looks when you’re wearing polarized sunglasses, but these changes are brought
about by changes in color or intensity, not the polarization of the light itself. So when does polarized light help microscopy? Well, a lot of materials stay the same optically-speaking,
no matter what direction you shoot light at them from. But there are certain materials where specific
properties, like how fast light travels through them, can vary depending on which way the
light is striking them. These materials called optically anisotropic,
can also take in a ray of light and divide it into two separate beams. By aiming polarized light at our sample and
then reconstructing an image based on how the various parts of the organism interacts
with that restricted light, particularly by how it might cause that light to split, we
can see more of these optically anisotropic materials in action. In our case, it often takes the form of shiny
internal crystals. So we’ve given you the big overview of what
these different techniques can do, let’s go back and look at what that means for that
original ciliate we started with. Here it is under brightfield microscopy. The background is bright, the image produced
by changes in light amplitude that allow us to see the overall shape. But some of the detail is hard to make out. Under darkfield though, the contrast increases
and some of these details become more obvious, displaying compartments and cilia in greater
detail that are also apparent under phase contrast. And then under polarized light, the crystals
that blended in with the organism previously are now visible and vibrant. Now, of course, there are many other microscopy
techniques that use light in many different ways, but we think it’s incredible that
with just these four, the world of the microcosmos looks almost like different universes, wrapped
up into one invisible world around us. The journey, it seems, is not just about what
you see, but also how you see it. And ultimately, none of these views are what
the microcosmos actually looks like, either that, or all of them are. Our brains play tricks on us to make us believe
that the world looks one way, but the world looks different at night than in the day,
and both of those things have more to do with the physiology of our eyes and our brains
than with objective reality. Asking what a microbe actually looks like
is, to some extent, forcing our own experience onto something that is beyond it. Which is not something I ever would have thought
of if it weren’t for this little youtube channel. This is the last episode of our first season
of Journey to the Microcosmos. It’s been really wonderful, and don’t
worry, we’re just going to take a week off and then we will be back with our second season,
featuring more of our microbial buddies and their various antics. Thank you for coming on this journey with us as we explore the unseen world that surrounds us. And a special thank you to all of these people, our patrons on Patreon. Who make it possible for us to take such a deep and interested look at this wonderful world. Thank you everybody for being a part of that. If you want to see more from our Master of Microbes, James, you can check out Jam and Germs on Instagram. And if you want to be here and ready for next season, go to YouTube.com/microcosmos


  1. WARM WARM LOVE AND GRATITUDE to everyone on the JtoM team!!! I have been so happy with the first season 🙂 I look forward to the day I can get on board with the Paetron 🙂

  2. Hm, so lighting and the perception of it is relative, but what about how that light impacts the microbes themselves? Like, if there was a galaxy-sized life form that was observing us, we'd likely get sunburned and be running around screaming as our insides boil, but since the giant can't see us without lots of light due to the inverse square law, our panic would be seen as baseline normal behavior since we can't be observed in our natural ambient lighting. Sure, the giant might try some other wavelengths, like x-ray, which wouldn't sunburn us, but we'd still be affected in another way (in this case, it would seem normal for us to get cancer like crazy from excessive x-ray exposure). I guess there's a bit of an "if a tree falls in a forest but nobody's there to hear it, does it make a sound" issue. In that way, wouldn't our macro forms, which shouldn't be subject to the Schrodinger's Cat concept, be just like the subatomic particles' superposition state? To the giant, we could be both sunburnt and riddled with cancer, but they'd only be able to determine (and we'd only become as such) upon observation. Hm! Perhaps particles have an unobservable base state but we're only able to detect the modified states (sunburnt/cancerous) when we affect them through our observation methods? Ack! My head hurts!

  3. Thankyou for making this series. It's educational, relaxing, aesthetically and aurally pleasing. Enjoy your break. Looking forward to series 2.

  4. Could you please get Jam to do a video on how to find and care for these little guys, the amount of microbes you get in one frame is astounding and it’d be really interesting to see how you do it.

  5. This is one of my fav episodes yet! I was always curious why things look the way they do under the scope, this channel has been such a soothing source of something so interesting and informative! Can't wait for more to come!

  6. Thanks for explaning all of that Hank. It is truly amazing how those different light fields render clarity & color to all of those interesting microbes. Great work & have a nice week off……………… 👍👍

  7. The macro world doesn't really look like anything either. I remember looking out over a nighttime landscape when sheet lightning came. For one second it was daytime, perhaps even brighter. Then it was night again.

  8. A question for next season: What senses do these microbes have and can they feel the bright light passing through them?

  9. Found this one a bit difficult to follow, I think I needed some diagrams of how the light works! (Or maybe I just can't deal with physics when distracted by pretty cells)

  10. After watching several episodes, I get a small thrill every time i'm able to identify a microorganism before I read what they're called. Thanks Hank and Jams Germs for giving me knowledge while i'm being entertained. 🙂

  11. 8:22 While we cannot see polarization all willynilly, we can usually perceive light polarization experienced under optimal conditions; many people don't even realize it and filter out the brush without even thinking about it.
    If you look at a white screen and tilt your head repeatedly on an LCD, you will see a yellow-blue structure in the center of your vision.

  12. Journey To The Microcosmos is such an exquisitely beautiful look into an entirely alien zoo of animals, plants and things neither and both that live all around, in and on us, normally invisible to our eyes, and easily one of the finest productions ever to grace the internet. Thank you so very much for every single episode, from music to narration, to the wondrous vistas you show to us. I look forward to every new entry, and feel sad when each episode is over, eager for the next.

    Season One was a triumph, and pure fascination. I cannot wait for Season Two. Thank you utterly for the best damn show on YouTube.

  13. When I was a casual non-focused kid with my toy microscope in the Fifties, I was only interested in the live specimens I brought in from puddles and ponds. I did this in Washington State, Tennessee, Okinawa, and Colorado. I couldn't understand the very few adult adult books I found about the subject. In Florida I tried as hard as I could to see salt-water luminescent organisms: zero results. I discovered some of these techniques accidentally. I often struggled to bring them back, sometimes successfully. This show, with its quiet narration, is a perfect recall of the quiet intimate tantalizing solitude of me and my microscope. It's very nostalgic for me. I thank you for it.

  14. What a wonderful first season, what a lovely way to bring it to a close…and it's going to be mildly like torture to wait for the next season! I am so very glad you won't leave us quite yet. This channel has been such a pleasure to watch and to listen to; I've learned a lot and I've also treasured each little slice of meditative peace every week. I don't know which I value more, right now, the knowledge or the chance to just breathe and exist. The synergy of image and voice and music makes for an experience that's very zen.

  15. Really love this series. I think this episode in particular could have used a diagram on the side for each of the different lighting techniques so that we can better understand your explanation. Keep up the good work!!!

  16. Wow! So much of this video went waay over my head. I didn't realize how much I didn't know about microscopes. This is a great episode. My curiosity is peaked. Thank you all

  17. This is easily one of the best YouTube channels in its history. Highly sophisticated and educational, yet simple and beautiful. All that being made by individual creators, not some company.
    I'm truly grateful for every episode I see, dumbstruck every time. You're making this website's (and medium in general) history.

  18. I love how fractal the universe is. That is, our microcosmos shares similarities to our larger cosmos, out in space. Because as you describe the forms of light we use to see the microcosmos, and how none of them are really THE ONE objective way to understand their existence, I think of nebulas and how we see an interpretation of the light they shine at us. If we were able to travel into distance space toward them, we would not see the colorful plumes of gas and cosmic matter that the Hubble telescope images showed us. Pretty cool to think of the similarities between the two “worlds”.

  19. Hello, what are the very green and fast animals that i saw in the video and are quite round elongated shape? I have the same animals in my aquarium and they move very fast and are green usually making circles. I can spot them with a usb glass

  20. Curious if anyone's ever overlayed multiple techniques at the same time🤔 these images are breathtaking, another world all around us

  21. I got so excited when it got to the polarized light microscopy. Learning the optics of those types of microscopes was a huge part of my Optical Mineralogy and Igneous and Metamorphic Petrology classes, The labs were tedious but fulfilling since it involved looking at pretty colors and shapes from rock thin sections and learning to recognize the different minerals. For some reason it never occurred to me that this optical method could be useful in microbiology. I learned me a thing today 😃

  22. Thank you guy's so much for these videos. The way in which you present the microcosm is engrossing and I can't get enough. I hope there are many sessions to come!!

  23. When you guys showed the polarized light example, it instantly reminded me of Swamp Thing #34 (of all things). I totally have to get a replacement for my missing copy…

  24. I’m questioning my own sanity at this point but, isn’t it micro-scopy and not micros-copy??

    The way he says it just seems odd to me.

  25. Could you add the microscopic type visible, phase, dark, polarized as was discussed in this video along with the 10x 100x 200x… in header of the video.

  26. What is that called at 3:10?? It;s strange looking and haven't seen anything like it before
    Very much enjoyed your video and gave it a Thumbs Up

  27. Yeeeeah just as i was wondering this, te video comes out
    I also would like to know what's up with the Bacillaria colony, What's that?

    And never noticed the music is by Andrew Huang lol

  28. Have you guys done any episode on viruses and viral infections, or any episode on human or animal cells? I think you’d do an amazing job! I love this channel! And the science show too! Your videos make my day!

  29. ok that little half second hold after you said last was cruel.

    my jaw dropped and I froze for a second till you finished with season. and let my poor heart off the hook.
    when i was a kid YEARS ago I always wanted a microscope but never had one.
    I love this channel. so we dont need no LASTS.

  30. This video is full of great information and beautiful footage, but what will stick with me most is that apparently my eyes cannot perceive everything about visible light. That is just super weird and unsettling and I'd had no idea. I've never even heard of light phases before.

  31. Love this episode soooo much. I'm a materials engineer so I've always used these techniques on inorganic substances. But when I have kids I'll buy a microscope and hunt for micro-organisms with them to inspire the next generation of me to look at organic creatures because oh my god is it not the most phenomenal thing we can even observe.

  32. I so love this channel. Honestly it's probably my favorite. You make learning all this so easy. Wish I had this channel when taking biology in college, it would have made things much easier.

  33. Could you give us an entire video of just microbes under polarized light? Like, just that – no narration, just sparkly microbes and chill music.

  34. Nothing actually looks like anything because vision is a subjective experience, so if you can see it somehow, that's how it looks. And the microbes in this video look great and you can't tell me otherwise.

  35. I would be interested in seeing more feeding, and escaping clips, as well as looking inside of the cells, and trying to explore what's going on in there. Can we see any changes in them, that appear to be caused by their environment?

  36. I'm going to be honest here, I have a hard time keeping up and understanding most the things you guys talk about here. Though I still find these animals both beautiful and fascinating.

  37. My family and I absolutely LOVE this channel! We often watch it, and other educational YouTube channels, together via our living room TV. Thanks to EVERYONE associated with this wonderful channel. You all make the world a better place. Love, The Rodgers Family

  38. I think this is my favourite YouTube channel. Great work!
    Anything with Hank in it always ends up being super good but this is my fav.

  39. I feel the exact same way when doing astronomy and astrophotography. It's easy to think that the way we see, the way we percieve, is "What things really look like." But that's incredibly shirt sighted and self centered. These tools and techniques allow us to witness what would be totally imperceptible otherwise. That's what science is for. It broadens our understanding of the universe. We evolved to percieve the world in a particular way, but some people can't help but feel that means the world was designed to been seen through their own two eyes.

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