Saturday, December 23, 2017

The genetics of the calico cat

In an earlier post, I detailed the life and work of Nettie Maria Stevens, the namesake of our new calico cat. Nettie Stevens is known for her discovery of the X and Y chromosomes as the basis for sex determination. While researching the post, I found myself in another internet rabbit hole and I wanted to share some of the things I learned about cat genetics because, it turns out, calico cats are an excellent lesson in genetics.

The genetics of cat fur color (like the genetics of human hair color) are rather complex. There are many different genes that create the spectrum of coat colors and patterns found in domestic cats. In other mammals, white fur color alone has been linked to at least six genes (MITF, EDN3, EDNRB, PAX3, SOX10, and SNAI2). For this discussion, I will focus only on the gene loci that create the calico pattern: agouti (A), orange (O), and spotted (S). Based on the combined expression of these genes, some cats are tortoiseshell, a mix of black and orange and some cats are calico, a mix of black, orange, and white. Because the Orange gene is on the X chromosome, most torties and calico cats are female. There are rare cases of male cats with Klinefelter syndrome (XXY) that can have these fur color variants.
Figure 1 Schmidt-Kuntzel, et al., 2009
Agouti (gene name ASIP) encodes a protein that inactivates the melanocortin receptor and thus controls the distribution and amount of pigment cells (melanocytes) in the hair. The Orange gene has not yet been identified, but its position on the X chromosome has been mapped. Interestingly, the MC1R gene, which has been linked to red hair in humans and other mammals, is not involved in the coloring of calico cats because it isn't on the X chromosome. A recent study of the Syrian hamster, which shows sex-linked inheritance of yellow fur color, described the sex-linked yellow gene (Sly) as being independent of MC1R function and not likely homologous to the Orange gene in cats. However, recessive versions of the MC1R allele create orange/amber fur color in Norwegian forest cats. The gene for white spotting (S) has been linked to the KIT locus; more recent publications have shown that a retroviral insertion in the KIT oncogene caused white spotting, with a full insertion leading to the recessive all white mutation.

The genetics of the tortoiseshell/calico cat
If fur color followed the rules of Mendelian genetics, you would expect cats to be only black and white or orange and white, not two or three colors at once. The patterns observed in calico and tortoiseshell cats can be explained by a phenomenon called X chromosome inactivation. Somatic chromosomes come in even pairs, but the sex chromosomes are not created equal. The Y chromosome is rather small and does not encode many genes. In contrast, the X chromosome contains lots of protein-encoding genes. If an XX individual expressed all the genes on both X chromosomes, they would have a huge imbalance in protein expression in comparison with someone with XY. Organisms have different ways to level the compensate for these differences. In mammals, this involves silencing one of the X chromosomes in each cell with the XX genotype. In organisms like the fruit fly, the XY males just double the expression of the genes on the X chromosome.

The specifics of how this happens is actually pretty amazing. (For further details of the process, check out my post on Nessa Carey's book Junk DNA.) In short, a long non-coding RNA known as Xist (X-inactive specific transcript) turns off one copy of the X chromosome in each cell; on the opposite strand of DNA, a gene called Tsix is found. Xist and Tsix have mutually exclusive expression, which ensures that only one X chromosome is inactivated in each cell. X chromosome inactivation occurs at the 8 cell stage of the embryo. Different cells inactivate different copies of the X chromosome, which means some cells express alleles for orange and white and other cells express black and white alleles. These 8 cells then divide and produce the millions of cells that make up a cat. This random pattern of gene inactivation leads to the pattern observed in Nettie and other calicos.

Carbon copy (left) is a clone of Rainbow (right)
Importantly, because these traits are not strictly inherited by classic Mendelian patterns, it makes cloning cats a bit trickier than other animals. As highlighted in the book Frankenstein's Cat, scientists were disappointed when the cloned cat Carbon Copy ended up looking quite different from its clone mother. Had they thought more carefully about the genetics of calico cats, they might have picked a different breed for their experiment!
maneki-neko calico cat figurines are
thought to bring good luck

Calico cats like our Nettie offer excellent lessons in genetics as they higlight X-linked genes and dosage compensation. After all this reading, I think I will take advantage of cat genome sequencing to discover the specific mutations in our cat. I learned more than expected about cat genetics and hope to share these lessons with you soon. For now, if you want to learn more about the genetics of cats, you should check out Herding Hemingway's Cats by Kat Arney.

Wednesday, December 13, 2017

Caesar's Last Breath: Sam Kean brings his keen eye for storytelling to explore the air around us

I just finished reading Sam Kean's new book Caesar's Last Breath: Decoding the secrets of the air around us. I wasn't planning to write a review, but when I realized my blog has covered every other book by Sam Kean (including Dueling Neurosurgeons and The Violinist's Thumb), I felt like it deserved some attention.

The theme of the book is understanding the molecules that make up our air. Each chapter is devoted to a component or two that is found in the air we breathe. This approach means there is some overlap with Kean's brilliant debut, The Disappearing Spoon. Luckily, the overlap seems only to include the best stories in the history of chemistry and Kean is able to explore the stories further. For example, we get more background on the German chemist Fritz Haber inventor of the process to make ammonia from nitrogen and hydrogen, thus spurring the development of agriculture and chemical weapons. I don't want to spoil it, but if you want a taste, you can check out Kean discussing the story on Radiolab.

Not all of the stories are as serious as Haber's. For example, Kean's chapter on methane allows a moment of silliness in the details of the life of the French performer Le Pétomane, a man who trained himself to fart at will. At his peak, he was the highest paid performer in France, bringing bigger crowds to the Moulin Rouge than even Sarah Bernhardt. 

It is difficult to choose a favorite among the chapters, but if I had to pick just one, it would probably be "Controlled Chaos", which focuses on water and its role in the Industrial Revolution, through the work of James Watt and others to develop steam power and the work of Alfred Nobel to make explosives. Nobel's legacy now is pretty securely tied to the prizes bearing his name. However, during his life time, Nobel's work cost many lives and left him in poor health, guilty and haunted by his reputation as a merchant of death. In fact, this guilt was the impetus for his starting the Nobel prize, much to the chagrin of his family who fought to inherit the wealth.

Because I read so many science books, I often have a sense of déjà vu when reading. However, Caesar's Last Breath included lots of new and interesting tidbits, like the surprising connection between Albert Einstein and refrigerators and the strange history of the manipulation of the weather. Perhaps my only complaint with the book would concern the final chapter on the air on other planets, which felt a bit disconnected both in subject and style.

I highly recommend Caesar's Last Breath for people interested in chemistry or the periodic table as well as those interested in the history of science.

Monday, December 4, 2017

How to Tame a Fox (and Build a Dog): a long term experiment and a story of perseverance and hope

The story of Dmitry Belaraev's long-term experiment in fox domestication was beautifully covered by Scientific American and The Discover Blogs as well as on Radiolab. I found the story and the science behind it fascinating, but I wasn't sure a book was needed to delve further in the story. After I read How to Tame a Fox (and Build a Dog), I learned how wrong I was.

Lee Alan Dugatkin co-authored the book with one of the original researchers, Lyudmila Trut. The authors are able to tell the story of Belaraev's seemingly Quixotic plan to tame foxes in a way that is compelling, even when I knew the major plot points.

The project's hypothesis was simple: continuous breeding of the tamest/gentlest foxes would lead to foxes that behaved like dogs. I found it amazing that they were so committed to scientific rigor that they ran a parallel experiment where they chose the most aggressive foxes. At the time, Belaraev faced obstacles from the ruling Communist party. Today, scientists would also question funding such a long-term experiment. Most geneticists use animals with short lifespans (e.g. fruit flies, C. elegans, yeast) so they can get results quickly and at lower costs. The experiment started producing results far earlier than even the principal investigators would have guessed. Even after a few generations, they found that the foxes showed more dog-like traits (floppy ears, tails, and other classic signs of neotony.) After 10 generations, they found that females went into estrus earlier and some male pups showed changes in fur color.

These changes were all predicted by Belaraev, who had a pretty revolutionary idea at the time, which he called "destabilizing selection". He suggested that the changes that occur in the course of domestication aren't simply due to the accumulation of mutations, but rather changes in the expression of existing genes.

Graphical Abstract from Parker et al Cell Reports 2017
Once genome sequencing arrived on the scene, the domesticated foxes were soon the subject of several studies. The first approach was to compare 700 genetic markers that had been used in the initial dog genome sequence with both the wild and domesticated foxes.  The researchers found several cases of convergence between the two domestication events, which included genetics variations that would ultimately lead to changes in the appearance and behavior of the tame animals. In 2010, a paper in Nature reported the genomic changes that accompanied the domestication of dogs from wolves.  Of course, the research is still in progress. One recent paper in Science suggests that dogs were domesticated in Eurasia and Eastern Asia from 14000 to 6000 years ago. The most recent data (published in my journal Cell Reports) suggest that different breeds of dogs had origins in different geographical locations. Importantly, the work published so far suggests that Belaraev was right: changes in gene expression not just mutations were key to domestication.

Perhaps the most fascinating parts of the book were the details concerning the barriers to science in Soviet-era Russia. These included the domination of genetics by a non-scientist named Trofim Lysenko, who was staunchly opposed to the ideas of Darwin and Mendel; these ideas were gaining acceptance at the time in the West. Lysenko even convinced Lenin that putting seeds in the cold would make crops grow better at low temperatures (they don't). Lysenko fabricated data to support his ideas and those of the party, which devastated Soviet agriculture for decades. Lysenko was celebrated by the Communist party simply for being a peasant and for going against "bourgeois Western science".  Interestingly, Khrushchev's daughter Rada, a journalist who trained as a biologist, argued against Lysenkoism and fought to protect science and the work of Belaraev. I think this serves as another example of why it's best to keep politics out of science (but not science out of politics!) The stories of the suppression of science in the height of soviet Russia are evocative of current anti-science rhetoric in these United States.

One of the reasons that Belaraev was able to persevere in the face of such odds was his enthusiasm and charisma. Belaraev was a social chameleon, who could easily adapt to his audience. These traits made people gravitate towards him and helped him argue for the benefits of the fox experiment to the powers that be. Officially, the rationale of the experiment was to breed foxes that would have more variety in their colors, which would help fetch higher prices for their fur. The domestication experiment was funded despite the crackdown on work in genetics. This isolationism crippled Russian scientists, who were cut off from the science in the rest of the world.

In the late 1980s the fox experiment was 30 years old. The farm started to have some trouble with funding and the researchers had to scale back the experiment. The situation was made worse in 1998 when the Russian economy collapsed. The scientists started sacrificing some of the foxes and selling their pelts. Shortly after this, they contacted a few select media outlets to cover the story, which helped them secure some funding for the project. Today, the experiment has been going on for 60 years, which is a long time for a laboratory experiment, but a short time frame for evolution.

How to Tame a Fox (and Build a Dog) was a fascinating and ultimately hopeful story. Even in such a difficult political climate, this scientist and his visionary experiment were able to persevere with some patience and ingenuity, a message that I think will resonate with scientists that are struggling to stay afloat in 2017.

Sunday, November 5, 2017

Exploring the world through the mind of an octopus: review of Sy Montgomery's book

Coming off some recent books about neuroscience and animal cognition, I found The Soul of an Octopus by nature writer Sy Montgomery in the local library. I thought it fit my reading theme nicely, so I decided to give it a try.

Overall, the book is interesting and easy to read. Unlike the books I normally read, the organization is not centered around the scientific themes, but rather towards the author's experience of the wonders of the octopus. The book focuses on the author's visits to the New England Aquarium here in Boston as well as to a few other aquariums around the country (notably the Seattle aquarium, which hosts an octopus blind date on Valentine's Day). She also visits the cephalopod laboratory at Middlebury College, where researchers study octopus cognition using an array of mazes and puzzles.

Octopuses (one thing I learned is that this is the correct form of octopus as it is a Greek derivative, like hippopotamus) are incredibly developed in their cognition. Their nervous system is on par with mammals like dogs in terms of the numbers of neurons. This complexity makes them expert problem solvers  they can use tools to help them catch prey and they can figure out how to remove food from puzzle boxes. They are natural escape artists, which makes it difficult for aquarium staff to keep them caged. YouTube has lots of examples of daring octopus escapes.

I did want to point out a few of the interesting facts I learned from the book. Octopus taste receptors, which are on their suction cups, can pick up taste signals from at least 30 yards. This gives them an excellent sense of changes in their environment. They also have a powerful camouflaging ability, which allows them to change colors very quickly. In the wild, they use this in a variety of predator-prey interactions. In the aquarium setting, the color changes are an indicator of the octopus' mood.

Perhaps the most amazing thing I learned was about octopus ink, which is a complex mixture of molecules. Of course, the list includes melanin, which gives ink its characteristic color; it also contains molecules like tyrosinase, which can irritate the eyes and gills of the surrounding sea life. More surprisingly, tyrosinase has been reported to have effects on oxytocin and vasopressin levels, suggesting that octopus ink could calm the squirted prey. Ink also includes dopamine, a neurotransmitter often called the reward hormone. These features of ink suggest that ink isn't just for defensive purposes, but it may also be used to help them capture prey. This has been observed in some species of squid, but not in octopus.

The book spurred me to look into recent publications on cephalopod neural complexity. One notable paper in Cell shows that cephalopods like the octopus have an unusually high rate of RNA editing. The process is unique to the branch of cephalopods called the coleoids, which are behaviorally complex (some might label them as "smart"). In addition, the sites of genome editing occur most frequently in genes associated with the nervous system. These correlations suggest that the ability to edit their genome is what gives them their complexity. Surprisingly, these changes at the RNA level can be inherited. Of course, this ability has its price. While these cephalopods have greater plasticity of the proteins made by RNA, they have a decreased mutation rate in the protein coding regions of DNA, which is the more traditional fodder for evolutionary variation. For more information on this surprising ability, check out the coverage in The Atlantic and New Scientist.

These stories left me wondering what other sorts of mysteries can be found in the octopus, an organism that is often compared to an alien due to its ability to camouflage rapidly, its knack for squeezing into tight spaces, its unusual defense mechanisms, and its uncanny problem solving. I will be heading soon to the New England aquarium to catch a glimpse of one of the octopuses that the author describes and will keep an eye out for more primary research that explains the mysteries of this amazing creature.

Saturday, October 7, 2017

She's a brainiac: taming my amygdala's response to neuroscience

Cerebellar neurons by Ramón y Cajal
The study of the brain has always seemed so inaccessible to me. There is something so meta about it that, frankly, it seems to me that only super advanced beings could think about how our thoughts are formed. I felt comfortable in my single cell universe of cell biology, and I felt like neuroscience was far too intricate and complicated for my brain to handle.

Last year, I started working at Cell Reports, which is a broad science, open access journal. We get submissions from every field of biology. I am a cell biologist by training, so my comfort zone is there, but by new journal has really pushed me to read even more broadly than my previous experience at BBA.

For me, neuroscience papers are harder to access, especially because I have a hard time distinguishing my lateral habenula from my amygdala. To solve this shortcoming, I decided it was time to do some immersion therapy. I've read a few popular science books about the brain beforemost memorably Sam Kean's Dueling Neurosurgeons. More recently, I read The Genius of Birds, which taught me a lot about how scientists are approaching experiments with the brain and behavior. These experimental designs are ingenious (more evidence that neuroscientists are just smarter beings), but they can seem a bit funny at times (e.g., mouse behind the wheel). Recently, using high resolution brain imaging like fMRI has allowed researchers to map changes in the brain as people think about people or listen to different types of music or are under the effects of LSD.

To continue my immersion therapy, I have been trying to find good popular science books about the brain. Browsing my local book store, I came across The Brain: The Story of You, by David Eagleman, a neuroscientist and adjunct professor at Stanford University. The book, which is also a PBS series, includes some new research as well as some classic experiments in neuroscience. These classical approaches, which were very well cataloged in The Dueling Neurosurgeons, is to rely on patients that are missing part of their brain and see what sort of behaviors they exhibit. This is certainly a noninvasive approach, which could be considered as a physiologically relevant organ-specific knock out. The problem is that the brain is incredible plastic (that word means something very different in neuroscience) and so it can adapt to the limitations of a missing piece. The other problem is that there are a limited number of people with missing parts to their brains!

Luckily, advances in neuro-imaging and the advent of techniques like optogenetics, have allowed neuroscientists to stray from these classic experimental models. Of course, that doesn't keep Eagleman from telling the crazy stories reminiscent of Oliver Sacks and his contributions to Radiolab. For example, he tells the case of the man who lost his sight at 3 years old and had a stem cell therapy to restore his vision in middle age. The therapy restored the ability of his eyes to receive visual stimuli, but his brain needed to be re-trained to interpret the messages from the eyes. Another fascinating bit was about proprioception, which could be considered the sixth sense that controls your body position. You might not know you have it- until you lose it, but this is what allows us to have fluid movements like walking or biking. There are rare cases of people who have lost this sense and the affected individual has to think carefully when moving and must train themselves to be able to move with some degree of fluidity.

While The Brain probably isn't the best book on the subject, it is very accessible and fun to read and certainly has helped in my immersion therapy. While I can now remember what the amygdala does, I'm still shaky about the lateral habenula or the nucleus accumbens, suggesting that my immersion therapy should continue.

Sunday, September 24, 2017

I Contain Multitudes: Ed Yong walks us through the wonders of the microbial world

Science stories about the microbiome seem to be as ubiquitous as microbes themselves. There's good reason: it is fascinating to consider that we are home to a completely invisible zoo of microbes, some of which help us to digest our dinner and some of which change our behavior. This intense curiosity has caused some over-hyping of the power that the microbiome can have and the effects that we can exert upon it.

In his first book, I Contain Multitudes, Ed Yong navigates the complexity of the microbiome with his characteristic writing, which deftly combines the nuts and bolts of the science with the wow and wonder at the diversity of the natural world. He discusses some of the amazingly weird microbial relationships that occur in nature as well as those that happen on and in the human body. He seems to hit all the high points of the microbial world, including the ubiquitous symbiont Wolbachia, which scientists are just starting to exploit in insect populations to fight Dengue and Zika, and the amazing research into the human microbiome, which included the awesome roller derby study.

A major theme of the book is the evolving view of our relationship with microbes. The publication of the first microscopic images of microbes by Antonie van Leeuwenhoek (1673) led to an appreciation that there was more to life than what meets the naked eye. Once germ theory started to take hold in the time of Pasteur (ca. 1850), we started thinking that the microbial world was all bad and needed to be eradicated. As the theory of symbiogenesis started to come into favor, our thinking about microbes changed again, leading us to see that there could be "good" and "bad" microbial interactions. As I discussed in my recent post on symbiotic theory, many scientists placed symbiosis/cooperation in opposition to Darwinism. However, as scientists explore these relationships more deeply, it becomes clear that these relationships are much more complex. Yong writes that symbiosis is conflict; conflict that can never be totally resolved. Thus, it may be time to re-evaluate the language we use to describe these relationships and consider adding new terms to capture the complexity of these interactions.

Ed Yong has a knack for finding unusual stories, thus there is no shortage of fascinating tidbits here
all clearly explained and well researched. Two in particular captured my imagination: Sodalis and the mealybug; both of these were adapted for his column in The Atlantic, so you can read these to get a sense of the style of the book. Sodalis is a microbe that has been found as both a free living and a symbiotic organism, so it appears to capture the beginnings of a symbiotic relationship! Mealybugs are insects that form a sort of Russian nesting doll of symbiotic interactions (it's bacteria all the way down!). The mealybug has acquired multiple microbes to solve different metabolic problems. In evolutionary terms, Yong reminds us, this is a smart move. Bacteria are quick to adapt and they are legion, so if you have a problem that needs solving, there are likely microbes that have already found a solution. Biotechnologists and synthetic biologists are just starting to exploit the diversity of microbial functions that have evolved over billions of years of natural selection; they are starting to put existing organisms to work at new tasks, like cleaning up oil spills or radioactive waste, or to design and build completely new organisms to do these things or so many more.

We are really just at the beginning of understanding the microbes around us. Most of the recently published human microbiome studies are little more than inventory lists, with some studies attempting to make correlations for differences in why certain populations are associated with certain microbes sometimes with conflicting conclusions. Yong explains that we simply do not have large enough samples yet to trust the conclusions; for example, if you sampled ten people off the street where 5 were wearing blue and 5 were wearing green, you could find a few striking differences if you ask them enough questions. This means we need to be careful with the conclusions from microbiome studies until we have more data!

Ernst Haeckel's diatoms
I hope you will forgive me, but I need to take a moment to talk about poop. (According to Yong, anyone who studies the microbiome should prepare themselves to have blenders of animal droppings on their lab bench.) The first time I heard about the microbiome, it was in the context of fecal transplants. Here, Ed Yong describes the history of the FMT (fecal matter transplant) and its success in treating antibiotic- resistant C. diff infections. At this point, FMT is not an exact science and thus it has had mixed results. The ultimate goal here is a stool substitute, a "sham-poo" if you will. In this way, each patient can be treated precisely according to their needs and can be treated with the microbe(s) that can help address each problem. This is a long way off, but it is amazing to consider.

Frankly, I enjoyed reading this book immensely. Yong is an incredibly talented writer and reading his work in long form reminded me how far I still have to go as a writer. I remind myself that he has honed his craft for many years and try to use that as an incentive to keep writing!

Tuesday, September 19, 2017

The Genius of Birds teaches us that "bird brained" is a misnomer

Shortly after discovering the Great Backyard Bird Count last year, I started to realize what a perfect hobby birding could be for me. There is something in the process that appeals to meboth as a biologist and as a lover of lists. Unfortunately, I have not had as much time to develop my skills as a birder as I would like. Instead, I take a multi-tasking approach to the hobby as I look for birds on my runs or bike rides or from the comfort of my front porch. My newfound interest also inspired me to expand my reading list from the typical molecular and cell biology.

Enter The Genius of Birds by Jennifer Ackerman. The book explores the wonders of bird behaviors and cognition (a more scientific and less nebulous term for intelligence) and explores the latest research to understand how birds accomplish their unique feats of memory and critical thinking. Just as Lab Girl gave me a new appreciation for trees, The Genius of Birds gave me a new perspective on the birds around us.

Ackerman convinced me that "bird brained" is truly a misnomer. While birds do have small brains, they are densely packed with neurons and neural connections. Some birds are smarter than others. Corvids, the family that include crows, ravens, and parrots, are on the Einstein end of the spectrum, while quails, ostriches, and turkeys are on the Cletus the Slack-jawed yokel end. (Ackerman is always quite generous when writing of the simpler birds and would never be so pejorative with her subjects. She suggests that we just haven't observed the brilliance of these birds yet.) Crows have been considered smart since the time of Aesop, whose fable The Crow and the Pitcher highlights the type of problem solving that scientists enjoy exploring with these animals. The internet is filled with the fun stories about corvids and their feats of genius, like collecting gifts for people who feed them and even using tools. This genus has developed a reputation for clever and innovative behavior. Neuroscientists even use corvids as a model organism to better understand human cognition.

Aves is a large and diverse class of animals and each member has a unique set of skills, which Ackerman deftly and comprehensively illustrates. While corvids excel at problem solving, parrots and mockingbirds have exceptional skills in language. Bower birds have a strong artistic eye: the male constructs elaborate nests to entice females, who are able to discern even subtle differences in these ornate bowers. Other birds are expert navigators and map makers.

Even the common sparrow is a star in terms of its ability to adapt to humans and use our presence to further its species. The house sparrow is present on every continent except Antarctica, and is thought to have expanded its ecological range in parallel with humans. Surprisingly, the sparrow has gotten to be the bird with the largest range not simply due to its introduction in different habitats. It is the adaptability and flexibility of this bird that has made it so successful. Sparrows are inventive in how they forage for food (they are willing to explore food sources before other birds) and even in how they build their nests (in cities sparrow nests can be found with cigarette butts, which help repel parasites). I admit that this chapter gave me a bit more respect for the bird that always seem to monopolize the seed in my bird feeders. Now I can appreciate why!
Pigeon brain via Wikimedia Commons
I also enjoyed learning more about how researchers figure out how bird brains work. (Hint: it isn't just about dissecting them!) My favorite chapter involved understanding the navigational systems of birds. Thanks to experiments with birds that are superstars for their ability to navigate, including homing pigeons and an array of migratory birds, scientists have learned that birds use a two step "map-and-compass strategy. Like so much of neuroscience, they figured this out by knocking out one sense and seeing if homing pigeons could still get home. The compass seems to rely on magnetoreceptors near the beak, but the map strategy is not as clear. The theory now goes that birds create extensive maps of where they have stored caches of food or where they need to return to nest.
Birds that excel at navigation have a larger hippocampus, the region of the brain that stores maps and memories; what's more this brain region can get bigger just by using it more. This correlation was also observed in a study of London cab drivers, where drivers with a longer work history have a correspondingly bigger hippocampus.

As you can tell, the book is filled with tons of interesting examples of bird behavior and neuroscience. One high point was the fascinating history of the homing pigeon, which has been used by Julius Caesar, Allied troops in North Africa, and modern day Cuban military officials. (I can't believe this hasn't been its own book.) In short, I recommend The Genius of Birds, especially if you you have an interest in birds, animal behavior, or the brain.

Wednesday, June 21, 2017

The Vaccine Race: The Limits of Leonard Hayflick and the WI-38 Cell Line.

I have been anxiously awaiting the release of Meredith Wadman's book, The Vaccine Race: Science, Politics, and the Human Costs of Defeating Disease, which does a deep dive into the early history of cell culture and the development of vaccines for polio, rubella, and rabies. Wadman started researching this story for a piece in Nature in 2013 (I liked it so much that it is near the top of my list of great science blog posts.) Thus, the book is a well-researched and scientifically detailed account of how many lives have been saved and improved by these scientific advances. It also describes, with unflinching honesty, the sometimes questionable practices of researchers and doctors in the time before informed consent and clinical trial review boards. Like Rebecca Skloot's The Immortal Life of Henrietta Lacks, it is an important look at the history of medical ethics. The Vaccine Race also emphasizes why we need funding for basic research and details the beginning of intellectual property law in biomedical research.

While the book focuses on the scientific development of vaccines, Leonard Hayflick is still at the center of the action. Hayflick, an early practitioner of tissue culture, was interested in developing a normal diploid human cell line. Other cell lines in use at the time were either non-human or from cancer cells. The source of his cell lines were human fetuses obtained from legal abortions. In developing the normal diploid cell lines, he observed that the cells could not grow and replicate forever, but typically replicated only 40-60 times.This result contradicted the famous experiment of Alexis Carrel, whose normal chicken heart cells were continuously cultivated in the lab for 34 years. The Carrel result was considered dogma and so Hayflick's findings were initially met with skepticism and suggestions that Hayflick must not be culturing the cells properly. After increasingly careful repetitions with the same result, he performed a co-culture experiment using young cells from a female and old cells from a male, which showed that the cells died after 40-60 replications no matter when they were added to the culture. He finally convincing the scientific community of the existence of the Hayflick limit. Carrel's result was then called into question. Many years later, Carrel's former lab technician confirmed that the method of preparing the fresh culture media was constantly adding new, young cells to the supposedly elderly cells, allowing them to appear to grow immortally.

Images of WI-38 cells from ATCC; listed as diploid human fetal lung fibroblasts.
After 38 attempts, he found success with a cell line named WI-38 (WI for Wistar Institute), which could proliferate without problem and be infected with virus and continue to replicate. Once he had a reliable cell line, Hayflick then had to convince others of its efficacy and safety for vaccine development. The cell line was eventually used to develop vaccines for adenovirus, MMR, and chickenpox. (Of course, when the source of the cells became known, there was a backlash from religious groups who thought that there was no excuse for using fetal cells.)

The other major battle that Hayflick fought was with the NIH, who had given him a contract to distribute the cells to researchers working on certain NIH grants. When he left the Wistar Institute in 1968, he took the cells with him to his new lab at Stanford. Over the next 8 years, he distributed the WI-38 cells, first at prices similar to those of commercial distributors (like ATCC) and then at increasingly high prices, charging even more for young cells at low passage numbers. In 1974, Hayflick  interviewed for a position as director of the Institute of Aging; this spurred an investigation of his management and practices of the cell line. Eventually, Hayflick resigned from Stanford and hired a young lawyer whose expertise was intellectual copyright; this lawyer later represented many of Silicon Valley's biggest players, like Apple and Facebook. Hayflick was fighting a battle with the NIH that had little precedent. Wadman uses the WI-38 case to describe the advent of intellectual property and biological patent law and how these helped spurred the success of the biotech industry. These chapters were among the most interesting. 

Leonard Hayflick proudly displays his cell line.
The book includes some pretty harrowing details of clinical trials with early vaccines that were given to patients in mental wards, babies born in public hospitals where the majority of patients were African American, inmates in prisons whose release was tied to their participation, members of the US military, and terminal cancer patients all without informed consent. In most cases, the vaccines behaved as expected and side effects were minimal or nonexistent, but there were exceptions. These cases led Henry Beecher (an anesthesia specialist at Harvard Medical School) to publish an article in the New England Journal of Medicine entitled "Ethics and Clinical Research" which detailed the specifics of the questionable human experiments. After Beecher's article, the tide started to change.

Overall, The Vaccine Race is an excellent read, particularly for its coverage of the history of science and medical ethics. If I had one complaint it would be that it was not as detailed about the science of viruses and vaccines, but Wadman does end on a strong, scientific note as she describes the Nobel-prize winning discovery of the enzyme telomerase, which explains the mechanistic basis of the phenomenon observed by Leonard Hayflick. 

Wednesday, June 7, 2017

The impact of Nettie Stevens on genetics, chromosome theory, and the naming of cats in our house

We recently welcomed a new member to our family: a beautiful calico cat! We were struggling to find a suitable name for this feisty one. Because I have had so few female cats, I wasn't really sure where to start. As a woman of science, I decided to use female scientists for inspiration.

Then I remembered the work of Nettie Stevens. I stumbled upon Dr. Stevens' work when I was researching Thomas Hunt Morgan for my two posts on the movie The Fly Room. Stevens was most famous for identifying the chromosomal basis of sex inheritance-she found that males are XY and females are XX. Calico cats are almost always female because the genes that control fur color are on the X chromosome, so we decided to name the cat Nettie. What I learned in my reading suggested that Nettie Stevens, like so many female scientists, was pretty amazing and definitely underappreciated for her impact on genetics, chromosome theory, and the use of model organisms in cell biology.

Nettie Stevens (1861-1912) was born in Vermont and grew up in Westford, MA as a fifth generation New Englander and the daughter of a carpenter. Her love of biology was likely spurred by summer science courses on Martha’s Vineyard. She taught high school zoology and physiology for many years, eventually saving up enough to attend Stanford (then Leland Stanford University) at the age of 35. Interestingly, Stanford was about 40% women at the time of Stevens’ matriculation in 1896. According to a Stanford newsletter about Nettie Stevens, they aren't really sure what attracted East Coasters and women in record numbers to their institution at that time. They speculate that it might have been the lower cost of tuition compared with the more established East Coast school.  

Stevens started her doctorate at Bryn Mawr in 1900; at that time the university was home to Thomas Hunt Morgan and Edmund Beecher Wilson, who were both leaders in the burgeoning field of cell biology (then called cytology). Stevens started her PhD in Morgan’s lab at a critical moment in the history of genetics: Gregor Mendel’s work had recently been rediscovered. The big question at that time: what is the biological basis for Mendel’s law of heredity? These ideas were causing excitement in parts of the scientific community. However, Thomas Hunt Morgan was initially not very interested in the Mendel revival. Instead, Morgan focused on the processes of regeneration (admittedly a very cool topic as I have covered in my post on axolotl), which is why Stevens started her PhD studying regeneration in various marine models, including the planaria.

Stevens received a fellowship to fund her travel to Germany to study in the lab of Theodor Boveri. At that time, Boveri was deeply involved in the Mendel revival. Using sea urchins, Boveri had shown that all the chromosomes had to be present for embryonic development to take place. He published these results in 1903 in parallel with Walter Sutton, who showed the same results in grasshoppers during his PhD work in the lab of E.B. Wilson. Wilson later termed this the Boveri-Sutton chromosome theory (notably Sutton, a derelict PhD student, was able to get the recognition that eluded Nettie Stevens.)   

Image courtesy of Rachel Ignotofsky 
Stevens returned from her time in the Boveri lab with a strong interest in the idea of inheritance through chromosomes. Morgan allowed her to work independently on this project, which was uniquely part of the culture in the Morgan lab; as the project progressed, Morgan became interested in the idea as well. For me, this story points out how Stevens was at the leading edge of the Mendel resurgence and brought this interest to the Morgan lab.

In 1903, Stevens completed her PhD at Bryn Mawr, but found it difficult to find a permanent research position. In her application to the Carnegie Institute requesting funding for her research, she stated, “College positions for women in Biology this year seem to be very few.” In her proposal, she planned to study the connection between chromosomes and sex determination, which was controversial at the time. While C. E. McClung had proposed that the “accessory chromosome” could be involved in sex determination, most researchers, including Morgan and Wilson, believed that sex was determined by environmental conditions.

To address this question, Stevens started looking at the full set of chromosomes of many different organisms. In 1905, while observing cell division in the mealworm Tenebrio molitor, she noted that females had 20 large chromosomes, while males had 19 large and 1 small chromosome. She suggested that the sperm determined the sex of the offspring, based on whether it carried the small or the large chromosome. This was in contrast to the results obtained by Wilson, who found that males had one fewer chromosome than females; in his case this was because the organism he studied was XO and XX. In the fall of 1905, Stevens published her work entitled "Studies in Spermatogenesis" just two months after Wilson's work was published. Her conclusions did not gain acceptance, but when Wilson published his next paper confirming the XX/XY inheritance model, the scientific community accepted the results as true. 

Stevens also examined the role of sex chromosomes in a variety of insects and marine organisms, which led her to conclude that the XX/XY inheritance was generalizable. (In contrast, Wilson’s XO males were relatively rare.) Thus, Nettie Stevens was at the vanguard of utilizing different organisms for research in cell biology. In her experimentation with different organisms, she even worked with the fruit fly, Drosophila melanogaster and introduced the model to Morgan's lab.
On July 7, 2016, a Google Doodle celebrated what would have been Dr. Stevens' 155th birthday. This brought her name out of obscurity. Like so many female scientists, perhaps most famously Rosalind Franklin, she had virtually been erased from scientific history. Why did she not get credit for her work? Was it the lack of a permanent position and lab of her own? Or was it a case of sexual discrimination? Some argue that Wilson was given credit not due to primacy of results, but the substance of his entire body of research. While it can't correct this historical oversight, we will acknowledge the contributions of Nettie Stevens in our house.

Further Reading

This post by Cristy Gelling is highly recommended; she details more about the sexism and Morgan's obituary of "Miss Stevens".

This podcast from Babes of Science was fun and filled with facts about Nettie Stevens that I hadn't read elsewhere.