Science Fail Monday: How a dead salmon taught us about statistics

Posted on December 9, 2018 by Kasey Skinner

Any scientist knows the importance of a good negative control. A negative control in an experiment is a group of samples or subjects in which no response is expected to an experimental treatment. The experimental group can then be compared to the control group. Such negative controls are gold standards in science and are supposed to provide confidence in experimental results. However, occasionally, a negative control gives unexpected and hilarious results worth of an Ig-Nobel Prize, the highest honor for scientists who publish the silliest research. Such was the case in an experiment involving fMRI, human emotions, and an Atlantic salmon.

https://commons.wikimedia.org/wiki/File:FMRI_scan_during_working_memory_tasks.jpg

An example of an fMRI scan in a human. The red spots have higher brain activity when subjects are performing a memory task.

fMRI stands for functional magnetic resonance imaging. If you’ve ever had a knee injury or a concussion, you have likely experienced a normal MRI scan, which uses radio waves and a magnet to take a structural picture of the organ of interest. The “functional” in fMRI means that researchers can use MRI images to measure brain activity and take a snapshot of changes over time. When a strong magnet is turned on over the brain, the hydrogen atoms in all of the water molecules in the blood point in the same direction, like a compass needle next to a refrigerator magnet. When the magnet is turned off, the hydrogen atoms relax back to their original positions, which releases a signal. This signal changes based on how much oxygen is in the blood, so the end result is a picture of the brain with information about which regions have more oxygenated blood. Regions needing more oxygen are generally assumed to be more active. Researchers can even have study participants perform a task during an fMRI scan, such as viewing particular images or listening to music, and use the fMRI data to determine which areas of the brain are active during the task. These types of studies can tell us a lot about which brain regions are involved in everything from social situations to processing fear.

In the Ig-Nobel Prize-worthy experiment, researchers wanted to use fMRI to determine which parts of the brain were active in response to seeing human faces displaying different emotions. However, they needed a negative control for their human subjects just to make sure that any brain activity they saw in response to the faces wasn’t just due to chance. The ideal candidate for such a negative control? A four-pound Atlantic salmon, purchased by one of the researchers at the local fish market.

https://commons.wikimedia.org/wiki/File:Salmo_salar-Atlantic_Salmon-Atlanterhavsparken_Norway_(cropped).JPG

The authors of the IgNobel prize study used an Atlantic salmon like this one as their negative control.

The researchers put the dead salmon in their fMRI scanner and, for the sake of science, asked it what emotions it thought the humans were displaying in pictures flashed up on the screen in the scanner. The authors do not comment on the salmon’s responses, but it can be assumed that the salmon was not a model experimental participant and did not comply with the study directions. Expecting to see nothing, the authors analyzed the fMRI signal in the salmon’s brain before and after the salmon “saw” the photos of the faces. Imagine the shock in the room when a few spots in the salmon’s itty-bitty brain lit up like a Christmas tree, suggesting that it was thinking about the faces it saw. Duh duh duuuuuhh….zombie salmon?

Obviously, the salmon was not alive, nor was it thinking about the emotional state of humans. Luckily for the field of fMRI, instead of publishing a paper telling everyone they should use dead salmon to study human response to the emotions of others, the authors of this study delved deeper into why they were seeing “brain activity” in this very dead fish. In their original data, the researchers failed to correct for multiple comparisons: basically, because you are comparing so many brain regions to so many other brain regions, you’re much more likely to find a spot with significant activity in fMRI purely by chance (for more info on multiple comparisons, click here). The authors applied the appropriate statistical corrections to their data, and voila, no more zombie salmon. And then, because scientists have a funny sense of humor, they wrote up and published these results as a lesson to all on the importance of having a good statistician.

Peer edited by Claire Gyorke.

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Understanding Sea Turtle Navigation with Laser-based Imaging

Posted on November 13, 2018 by Jessie Barrick

If you’ve ever been lost in an unfamiliar city or tried to walk around in the dark, then you may have found yourself wishing you had the eyes of a cat or the echolocation abilities of a bat. But have you ever wished for the navigation abilities of a sea turtle? While many animals are known for their superb sensory perception which make them better navigators than humans, it may surprise you to hear that sea turtles are among the elite navigators of the animal kingdom. Sea turtles are able to cross entire ocean basins (covering distances of thousands of miles) surrounded by seemingly featureless, dark water in order to return years later to their original nesting grounds. This behavior is as perplexing as it is impressive: while we know that sea turtle navigation has something to do with sensing Earth’s magnetic field, the mechanism which enables them to sense and interpret magnetic fields has not yet been identified.

To compare, humans have five senses. Each of these senses is linked to some kind of receptor which converts the environmental stimulus into a signal which our brains can interpret as either an image, a sound, a taste, a texture or a smell. For example, our eyes contain photoreceptors which convert light into electrical signals that travel to our brains and are interpreted as images. Sea turtles have another sense: they are able to sense magnetic fields. This means they must have some magnetic receptor which converts the magnetic field into a signal which is interpreted by the animal’s brain. However, scientists don’t know what these magnetic receptors are or where they are located within the body of a sea turtle. This is a crucial step on the path to understanding the impressive navigation abilities of sea turtles.

Working in collaboration with biologists who study sea turtle navigation, my research project is to design and build a special imaging system which is able to locate these magnetic receptors in sea turtles. This project can be broken down into three parts: design the imaging system, develop a method for detecting magnetic particles, then build and test the hardware.

Designing an Imaging System

You may wonder why it’s so hard to find these magnetic receptors if we know they must exist. It’s difficult because these magnetic receptors are extremely tiny, thought to be smaller than the size of a single cell, and they may be located anywhere inside the body of the sea turtle. The smallest species of sea turtle is roughly the same size and weight as a Labrador, with some species being several times larger, making the search for a cell-sized particle challenging. For an imaging system to detect these magnetic receptors, we need the following conditions:

High resolution- Because these receptors may be very small, we need high resolution to locate where they reside within the tissue.
High magnetic sensitivity- If we want to detect very small magnetic particles, then our system has to be very sensitive to small amounts of magnetic material.
Fast- Because we have to search through large volumes of tissue, we need a fast imaging system to do this in a reasonable amount of time.
Non-destructive- Many existing imaging methods require the addition of dyes and other contrast agents which irreversibly alter the tissue. We would like to avoid this because sea turtles are endangered and finding dead sea turtle tissue to image can be challenging.

So why can’t we use an imaging system that already exists? Although there are several imaging systems which are able to detect magnetic particles, none of them meet all four of our requirements. For example, magnetic resonance imaging (MRI) is very sensitive to magnetic material, but the resolution is not high enough for our aim. A microscope has really good resolution, but it can only image a very small section of tissue at one time, so the overall imaging speed is slow.

In order to meet all four imaging system requirements, we use a relatively new optical imaging system called Optical Coherence Tomography (OCT). OCT is very similar to an ultrasound, the same technology used to produce fetal sonograms. Rather than using sound waves to form an image as in ultrasound, OCT uses light waves from a laser to create an image. By using light instead of sound, we shrink the scale of the imaging down so that our resolution is much better than that of MRI or ultrasound. By its nature, OCT is also non-destructive.

OCT works by illuminating the sample we want to image with light waves. When the light hits the sample, it can either pass through the sample or it can bounce away (we call this scattering). OCT captures the light that is scattered back in the direction from which it came. We record this light on a camera along with light that was reflected from a stationary mirror in a process called interferometry. By comparing the light reflected from the mirror and the light back-scattered from the sample, we can tell how far the light travelled after it was scattered from the sample. This allows us to create 2D images of the sample.

Developing a Method for Magnetic Particle Detection

To get the desired magnetic sensitivity, I designed and built an electromagnet which can produce a sufficiently high magnetic force. We place this magnet over the tissue we want to image. By applying a current with a sinusoidally varying amplitude to the electromagnet, we create a magnetic field with a sinusoidally varying amplitude. This variation in the magnetic field strength causes the magnetic force felt by a magnetic particle to vary sinusoidally as well. Therefore, any tiny magnetic receptors in the sea turtle tissue we are imaging will oscillate up and down in sync with the applied magnetic force. As the magnetic particles oscillate up and down, they will cause the surrounding tissue to deform. This deformation causes a measurable change in the back-scattered light. We record a series of images while applying the oscillating magnetic force. We can then compare consecutive frames to identify any pixels whose intensity is varying in sync with the applied magnetic force and by doing so, locate the magnetic receptors (see Fig. 2). An OCT system combined with this method of magnetic particle detection is called magnetomotive OCT.

https://users.physics.unc.edu/~aold/MethodsMMimaging.htm

Fig. 2 Schematic Diagram showing that when the magnetic receptors (black spheres) feel the oscillating magnetic force, they oscillate up and down creating a measurable change in the light reflected from the surrounding tissue.

Testing the Magnetomotive OCT System

After designing and building the magnetomotive OCT system, we first had to test the system to ensure it met our requirements for resolution, speed, and magnetic sensitivity. We measured the resolution by imaging small, highly scattering particles and confirmed that we achieved our desired resolution. To test the imaging speed, we imaged human bronchial epithelial cells. These are the cells lining our airways which contain cilia and secrete mucus. The mucus layer acts like a shield preventing the bacteria we breathe in from entering our bloodstream. The cilia beat to propel the mucus (containing all those trapped bacteria) out of our airways and are a vital component of a healthy immune system. Therefore, the ability to image living, beating cilia is helpful to doctors who study respiratory diseases such as Cystic Fibrosis. Our collaborators in the Cystic Fibrosis Center at UNC provided us with a sample of these cells, and we were able to image the beating cilia. This was a very exciting result. Not only did we confirm that our OCT system has a fast imaging speed, but we also discovered that this novel imaging system may be useful for helping to diagnose and research respiratory diseases.

Future Research: Turtles and Beyond

Our imaging speed experiment using epithelial cells demonstrates a vital point in the scientific process: often, by setting out to answer one question, you may open avenues of investigation you had never considered. We demonstrated with this experiment that our OCT system has the best combination of high resolution and high-speed of any OCT system to date. We will next measure the magnetic sensitivity of our system by imaging tissue phantoms, silicone-based samples which mimic the light-scattering properties of biological tissue, containing increasingly small concentrations of magnetic particles. Once we are sure that our system has the desired magnetic sensitivity, we can begin imaging animal tissue. If we are able to locate the magnetic receptors, it would be a huge breakthrough in the study of sea turtle navigation. If we are able to find these receptors, biologists can study them to understand exactly how they are used to sense magnetic fields and how the turtles use that information to navigate. Building this novel imaging system is just one step toward finally understanding sea turtle navigation. In addition, we have also discovered that our technology may have other uses, as our preliminary work with the cilia suggest. We will continue toward our goal of detecting magnetic receptors in sea turtle tissue while also investigating the system’s applications in respiratory disease research.

Peer edited by Allison Lacko and Laetitia Meyrueix.

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Uncovering Ancient Mysteries with Cosmic Rays

Posted on December 3, 2017 by Jessie Barrick

https://en.wikipedia.org/wiki/Giza_pyramid_complex

The Giza pyramids. The center pyramid (tallest) is the pyramid for King Khufu.

You probably don’t usually think of particle physics and the Great Pyramid of Giza as having much in common. In some ways, the two seem diametrically opposed: the Giza Pyramid is the pinnacle of past achievement while particle physics relies on cutting-edge technology. The Great Pyramid of Giza is the only one of the seven wonders of the ancient world that is still standing. It is the tomb built over 4,500 years ago as a monument to Pharaoh Khufu. Little is known about how such a massive structure was built so long ago or what the internal structure looks like. Historians and archaeologists have been trying to uncover these mysteries for centuries. On the other hand, particle physics is often portrayed in movies and TV as a futuristic discipline in which scientists develop futuristic weapons. As a result, when an article was published in Nature on November 2 with the title “Discovery of a big void in Khufu’s Pyramid by observation of cosmic-ray muons,” there was a media frenzy.

What are cosmic rays?

Though we sometimes think of science as a means to developing a more technological future, it is also importantly a means to understanding the secrets of the past. Much of the information we have about the origins of the universe and the evolution of galaxies has come from studying the fundamental building blocks of matter. For example, some particle physicists study the atomic nuclei falling toward Earth’s surface in cosmic rays. Studying this material provides insight into how galaxies are formed and how they evolved chemically.

When the protons and other nuclei in cosmic rays collide with nuclei in Earth’s atmosphere, pions are created. Pions then quickly decay and form muons. Muons have a negative charge like an electron but 207 times greater mass. The Earth’s atmosphere slows down all of the particles in the cosmic ray showers that are constantly raining down on the Earth. Because of their relatively large mass, muons are actually able to reach the surface of the Earth, unlike lighter particles. Detectors on or near the Earth’s surface can then detect these particles. In order to eliminate background noise from measurements, some particle detectors are placed deep underground in mines and caves. Learn more about what it is like to conduct scientific research in an underground laboratory in Underground Science at SNOLAB.

Using muon detection as an imaging technique

As early as 1955, physicists have taken advantage of the ability of muons to penetrate through rock by measuring the thickness of rock formations using muon flux (the amount of muons passing through an area of a detector). The concept of these measurements is similar to x-ray imaging. An x-ray is a high-energy form of electromagnetic radiation. Due to their high energy, x-rays are not readily absorbed by soft tissue such as skin and organs but are absorbed by denser structures like bone. If an x-ray source is aimed at a human arm and a film is placed on the other side of the arm, an image of the bones will be formed by the relatively low number of x-rays that reach the film behind the bones. Similarly, physicists working with cosmic rays realized that they could image large structures by taking advantage of the the fact that higher-density materials (such as stone) will absorb more muons than areas of lower density (such as air).

Muon detection is a promising method for studying the pyramids because we can infer information about the internal structure without having to destroy it or to open up sealed sections. In 1970, researchers first attempted to use muon flux to search for cavities in the Giza pyramid. By placing detectors in the subterranean chamber (label 5 in the schematic diagram below), they were able to image a region of the pyramid occupying approximately 19% of the pyramid’s total volume. No new chambers were discovered in this region. Since then, detector technology has become more sensitive to smaller amounts of muon flux. In 2015, a team comprised of researchers from universities in Japan, France, and Egypt tried once again to use muon detection to search for cavities within the great stone structure. They tried three methods of muon detection, and this time they were successful.

https://commons.wikimedia.org/wiki/File:Cheops-Pyramid.svg

Cross-sectional schematic diagram of the Great Pyramid of Giza. 1) Original entrance 2) Forced entrance 3) Granite blocks which blocked off passage 4) Descending passage 5) Subterranean chamber 6) Ascending chamber 7) Queen’s chamber. 8) Horizontal passage 9) the Great Gallery, above which the void was detected. 10) King’s chamber & air shafts 11) Antechamber 12) Well shaft

Detection of the new void

First, they placed detectors inside the Queen’s chamber and in the corridor outside. These measurements were taken over the course of several months so that a relatively high number of muons would be recorded, making the measurements more accurate. The measured muon signals were compared with the signals they would expect based on what was previously known about the structure of the pyramid. From this method, they detected an unexpected excess of muons coming from the region above the Great Gallery. From this excess, the researchers inferred that there was an unexpected region of air inside the pyramid. The excess of muons is about the same as the excess of muons that pass through the Great Gallery, meaning the the newly detected void is approximately the same size as the Great Gallery. In order to verify their findings, the researchers used two additional muon-detection methods over the course of the next two years with detectors placed in different locations. Signals from all three methods pointed to the same conclusion: there exists a void in the stone structure above and parallel to the grand gallery.

While this information doesn’t directly tell us why or how the pyramid was built the way that it was, it adds to our knowledge about the structure and may help archaeologists infer something about the design. Although, since the publication of the article, there has been some controversy over whether or not this is actually new information, this research still clearly demonstrates that cosmic rays may be useful for understanding not only events that happened billions of years ago but also events that happened much closer to home. And importantly, this shows that science and the humanities have something to offer each other. As scientific advances continue to shape the political and cultural landscape of our future, we will also understand more and more about our past.

Peer edited by Mimi Huang and Jon Meyers.

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The Excellent Journey of Bob Bagnell

Posted on October 27, 2015 by Chris Givens

As I enter the Microscopy Services Laboratory (MSL), a soft southern accent greets me: “Come in- want a cucumber? Help yourself!”

Dr. Bob Bagnell, the faculty director of the MSL, is an institution at UNC. Over the course of thirty years, he has developed the MSL from a set of electron microscopes in the Pathology Department to a full-featured microscopy core, offering numerous light and electron microscopy services in the basement of the Brinkhous-Bullitt building. Bob is an expert at microscopy, a natural teacher who never hesitates to help his patrons whether they are newbies or experienced users. His good nature combines with acumen for troubleshooting in such a way that even if your slides are worthless, leaving the MSL in a bad mood is difficult. You know how to fix your experiment, and almost feel joy from your failure, because you learned from Bob. His frequent offers of fresh bread also help. Continue reading →

The Pillars of Creation and Destruction

Posted on September 4, 2015 by JoEllen McBride

We like to think of the Universe as static. Our time is very short compared to the age of the Universe. But there are processes in space that happen on the time scales we inhabit. The variation in brightness of certain types of stars allow astronomers to measure the distances from the Earth to the galaxies where they reside. By taking images at different times over the course of a few years, the trajectories of stars orbiting the supermassive black hole at the center of our galaxy can be followed. And, using instruments like Hubble Space Telescope, we can see the destruction of large structures such as the Pillars of Creation.

Image courtesy of the National Science Foundation’s 0.9-meter telescope on Kitt Peak using the NOAO Mosaic CCD camera.

The Pillars of Creation are a small part of the Eagle Nebula (pictured above), a huge expanse of gas (mostly hydrogen) and dust where stars are created. The entire structure is estimated to be 5 million years old. The Nebula is 38 quadrillion miles from Earth in the constellation Serpens and is approximately 400 trillion miles at its widest point. The Eagle Nebula is so far away that when viewed from Earth, it would barely span the thickest part of the crescent Moon on the sky. In Hubble Telescope image shown below, we are zoomed in on a small part of the Eagle Nebula, highlighted in a yellow box in top most image. At 23 trillion miles in length, the leftmost pillar would stretch from the Sun to our closest stellar neighbor, Alpha Centauri.

The Pillars get their shape from a group of young, hot stars that were recently created. We can imagine that at one time the Eagle Nebula was a vast expanse of gas and dust with some regions having higher density than others. Gravity works quickly in these situations and the denser portions of the nebula begin to condense further, pulling in more of the surrounding material. Eventually, the densely packed gas ignites and a star is born. These newly formed stars blast away at the remaining gas, heating up and dissipating everything in their path.

Hubble Space Telescope image of the Pillars of Creation taken in 2014.

The Hubble images are a bit deceiving, although the pillars appear to be straight up and down, they are actually angled towards the young, hot stars that are illuminating their structure. As viewed from Earth the leftmost pillar is behind the young stars and angled towards them, causing it to appear brighter than the rest of the structure. The remaining pillars are in front of the young stars and angled towards them and appear darker. At the top of each pillar resides a thicker, denser pocket of gas which shields the remaining gas from the intense stellar radiation. This is why the gas formed ‘pillars’ instead of completely dissipating.

1995 and more recent Hubble images for comparison.

In 1995, five years after its launch, Hubble snapped the first highly detailed image of the Pillars. Twenty years later, for Hubble’s 25th anniversary, an even more detailed picture has been released by NASA. After just 19 years, there are visible differences between the two images, revealing how quickly the gas is being blown away. According to some astronomers, the Pillars should last another 3 million years, possibly dissipating into space before the group of young, hot stars run out of fuel and explode as supernovae. There are a few astronomers that believe the Pillars have already been eradicated by a supernova explosion, the light of which has yet to reach us. Whether or not they still exist, the Pillars of Creation are being destroyed right before our very eyes, but they will not passively disappear into space. Instead, they will live on through the stars they are creating within their dense insides, leaving behind a beacon to their once impressive existence.

Peer edited by Chelsea Boyd & Christina Lee

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This article was co-published on the TIBBS Bioscience Blog and on Jo’s blog AstroPunkin.

Canis lupus familiaris gestation and postnatal development

Posted on July 8, 2015 by Bailey Peck

Puppies are cute. We don’t often get to see them in utero, but now we can, thanks to this sweet radiograph courtesy of my mom, a Labradoodle breeder at Red Rock Doodles. Can you guess the number of puppies by counting the heads and tails? How many do you see?

I think puppies are fabulous, but our Content Editor, Chris Givens, told me I couldn’t just post pictures of puppies and other baby animals on The Pipettepen. He said we were better than that and that our posts must have scientific merit and meaning. So here it is:

5 Scientific facts about puppies and other baby animals:

Continue reading →