18 - Methods to See Really Small Things (w/ Neela Yennawar!)
18. Methods to See Really Small Things
Invasive species challenge the natural environment of many places they once did not call home. Why are invasive species dangerous? What are invasive species contributions to ecology, geomorphology, the economy, human health, or biodiversity? Let’s learn to be scientifically conversational.
General Learning Concepts
1) What are some things that are small and of interest to scientists?
a. Units of small things: To be able to measure small objects reliably, the scientific community required having the right units for labeling.
i. Millimeters: Coffee bean, grain of rice, sesame seed.
ii. Micrometers: Amoeba (500 um), human egg (130 um), skin cell (30 um), bacteria like E. coli (1 um)
iii. Nanometers: Viruses like influenza (130 – 150 nm, episode 3), phage (200 nm), common cold virus rhinovirus (30 nm), a single phospholipid (1 – 3 nm)
iv. Picometers: Glucose (900 pm), a carbon atom (340 pm), water molecules (275 pm)
v. Femtometers: The approximate size of a proton
b. Microbiology: We have previously discussed invention of the microscope in episode 15, biofilms. It’s simply important to remember that there were microbiological processes and diseases that were interesting in the 17th century. Antony Van Leeuwenhoek popularized the use of microscopes by developing superior lenses that achieved magnification of 270X. These microscopes were used to see bacteria, yeast, blood cells, and other single celled organisms.
c. Physics: Although we use particles like electrons to be able to resolve many small materials and specimens of interest, physics still has a need to be able to characterize their particles and subatomic particles. This is often difficult because of the immensely small size of relevant physical particles.
d. Material Sciences: Although by technicality material science is as old as the stone age, using bone and clay, moving through bronze and other metallurgy, the modern field of material science was born in the 1940’s and 50’s looking for new materials for advances in space and military technology, moving from a name like “metallurgy” to material sciences. Nowadays, many material sciences use similar techniques to biologists and chemists to be able to characterize their work.
2) Microscopes and energy sources
a. Light microscopy: Popularized by Leeuwenhoek. Capable of seeing things (with a powerful enough light microscope) down to the size of the wavelength of light (about 0.275 uM wide). Beyond this, objects would become blurred and obscured.
b. Electron microscope: Invented in 1931 by two German scientists, Max Knott and Ernst Ruska. Beams of electrons are focused onto some type of sample and scatter. Scatter patterns allow for visualization of small objects like viruses, DNA, circuits on computers, metals, etc.
c. Scanning probe microscopy: Uses a physical probe to scan back and forth over a sample that is translated into an image from a computer gathering those data. Resolutions from these devices can came to be a nanometer by use of a probe mounted tip that can be as fine as a single atom.
d. X-rays: A wave of high energy that has a short wavelength that allows for the wave to pass through materials that may not allow through visible light. Humans often use X-rays for medical imaging because they’re able to pass through the human body. However, the x-rays are absorbed by different tissues at different rates (bones have calcium which absorb x-rays at higher rates, leaving high contrast for x-ray detectors).
3) Crystallography
a. What is a crystal? Matter formed into a specifically ordered 3D arrangement of atoms, molecules, ions, etc. This can be as simple as salt to as complicated as gemstones (snowflakes are also crystals!). Crystals can be arranged in a certain number of shapes that help determine what the shape of the crystal identity later.
b. What is crystallography? The ability to use some type of diffraction (the use of a beam of light which spreads as a result of passing through an aperture or a slit) technique to identify and characterize solid materials. This diffraction could use X-rays, neutrons, or electrons as an energy source. The diffraction reflects off of the crystal and is detected by a detector that is capable of recognizing those energy sources.
c. What is the result of crystallography? A 3D atomic or molecular structure from a crystal. Those crystals may be small molecules or large complexes, like the biological machines that are called proteins. Because the appearance of these small to large molecules can give ideas to the function of their actions, scientists often find crystallography to be essential for full understanding of biochemical activity.
4) Fun Tidbits
a. X-rays can be harmful: Over-exposure to high energy X-rays can damage DNA in the body and cause thymine-dimers. Yet medical professionals will use radiation therapy to kill tumors by damaging their DNA! The radiation dosage is much higher than what is used for common imaging.
b. Nobel Prizes: As a science, crystallography has produced 28 Nobel Prizes, more than any other scientific field.
c. Describe an X-ray crystallography machine:
5) Solicited Naïve Questions
a. Why do you need crystals for crystallography? Making crystals can be challenging as the methods for making crystals varies widely. Sometimes, it can take so long and be so challenging that researchers will call some molecules “crystallizable”. The crystals are necessary for allowing for diffraction. Researchers have come up with work-arounds, for example using a porous metal complex that absorbs and orients small molecules for crystallography. Still, this technique didn’t work for large molecules, water soluble molecules, or highly flexible molecules.