CornBursts
A few of the people above me seem to have forgotten about things like particle accelerators. That or they are interpreting your question to include only optical wavelengths heheh.
Electron microscopes do not use optical wavelengths, that usually refers to visible light and has a rather low resolution power compared to using things with much smaller wavelengths. However, when referring to "directly observed", that usually refers to our ability to resolve an object, hence we're sticking to ways to "see" atoms, not simply prove/support their existence. The OP was confused as to the importance of "seeing" an atom, but to me, that's unimportant.
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Anyway my point is that atoms, like cells, have such a ridiculously large amount of evidence for their existence that it would be silly to claim either are not proven too exist despite the fact that atoms are typically not resolved in the optical (what humans see) wavelength. (Though cells CAN and have recently been resolved in the optical wavelength).
Like I said, the most powerful microscope on the planet does not have the resolution capability to resolve an atom, it's not "typically", it's fundamentally impossible to do so with optical light. Why? The diffraction limit... because given that the lowest wavelength you can use is still 450nm, in practice it's damn hard to get an optical microscope that can resolve 200nm or smaller. That's 2x10^-7, to resolve an atom, like I said, you need to be able to resolve on the fm scale, about 8 orders of magnitude away.
It's not just "typically not resolved optically", it's fundamentally impossible, the wavelength of optical light is simply too large.
... Cells, by the way, have been resolved for quite some time... Robert Hooke did so in the 1600s. He only had an optical microscope.
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In particle accelerators we can detect very precisely the presence of electrons, anti-electrons (positrons), protons and neutrons (the particles in the atomic nucleus) and more and distinguish them all from one another.
Perhaps for our less informed readers you might want to elaborate on the workings of particle colliders. You are aware the mechanisms for detecting fundamental particles in colliders is VASTLY different from the entire process of "viewing" or "seeing" a particle, right? Lemmy give you a hint, on the ATLAS experiment there is a reason they have more than one calorimeter.
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We can even detect particles made up of only 2 quarks emerging from colliding nuclei.
I think you're talking about Mesons, but I'm gonna be technical and correct you, they're made up of a quark and an antiquark, just in case it isn't obvious to the readers. I don't believe I've ever heard of a plain 2 quark particle, but, this isn't my field of expertise so I'd be happy if morbie or lost correct me ^^;
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Protons and neutrons are made up of 3 quarks. Single quarks are a little more tricky but I believe within the past year we have found them a couple times. I may remember incorrectly but I can find the link to that article if you like.
It's not difficult to detect quarks either, we've got 6 different "flavors", and we see them a lot more often than a few every year. up, down, top, bottom, strange and charm. The Top quark I believe was the most recently detected, it was found over 10 years ago thanks to the Tevatron. (Lost Iguana can fill in a lot more details on this I'm sure)
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So not only can we detect atoms, but we can detect many of their constituent parts and have been doing so for decades. =)
I hope this helps!
I hope you now understand there is a difference between "detect" and "see". Just because you can detect a particle does not mean you can see it, we're still well off from being able to resolve things on the fm scale.