Sunday, December 1, 2013

The Wandering Gene: BRCA1 mutations and population genetics

For some time I have been searching for a book similar to Rebecca Skloot's book about Henrietta Lacks. After some searching on Amazon, I found The Wandering Gene and the Indian Princess: Race, Religion, and DNA, which a number of review suggested was just as good. Because it was on the shelves of my local library, I picked it up immediately. Jeff Wheelwright's book examines the population genetics of a particular BRCA1 mutation. The BRCA1 and BRCA2 (breast cancer 1 and 2) genes were first linked to heritable breast and ovarian cancer (HBOC) in the early nineties. Since the initial discovery of the genes, scientists have identified many mutations in BRCA1 and 2 that are linked with HBOC as well as other cancers.

When functioning properly, the BRCA tumor suppressor genes produce proteins (breast cancer type 1/2 susceptibility protein) that are primarily involved in DNA repair. These proteins ensure that cells with errors in their DNA sequence either fix the mistakes or are destroyed. When a BRCA mutation is present, there is still a wild type ("normal") copy of the BRCA gene on the matching chromosome. Thus, the presence of a BRCA mutation is not necessarily an assurance of getting cancer (cancer risk rates for BRCA mutation carriers range from 35-80%, depending on the study and the type of cancer). If something occurs to alter the function of the wild type copy of the gene, then the cell is left with no functional BRCA1 or 2. Thus, DNA errors become more prevalent, which makes it more likely that a healthy cell will become a cancer cell. BRCA mutations account for only 10% of breast cancers; the majority of cancers are sporadic, caused by random rather than inherited mutations.  

The Wandering Gene focuses on the BRCA1 185delAG mutation; this mutation is due to the deletion (del) of two DNA residues (A and G, or adenine and guanine) at position 185, which results in a frame shift (or misreading) in the DNA sequence and ultimately the sequence of the protein that the DNA encodes**. This particular BRCA1 mutation has been linked to Ashkenazi or Eastern European Jews. Here, the author meets the Medinas, an Hispano family from New Mexico, as they receive genetic counseling and testing for the 185delAG mutation. The family is descendants of Native Americans and Spanish Catholics; thus, they were surprised to learn that they carry a mutation that has been linked to Ashkenazim. Geneticists and historians think that the 185delAG mutation in this group likely arose from a population of Jews from Spain, who were persecuted during the inquisition, converted to Catholicism, and then established themselves in the Americas.




The most interesting element of the book examines where the 185delAG mutation arose and how it became fixed in one particular population. There is evidence that a 2500-year-old Jewish founder could be the source of the mutation. Two particular characteristics of Jewish history (the cultural isolation and the large losses of population, such as from pogroms, forced relocation, and mass murders) led to frequent genetic bottlenecks. Bottlenecks occur due to the loss of genetic variability in a population; dramatic losses of population size can cause deleterious mutations (such as the BRCA1 mutation) to become fixed in a group. The founder effect can also explain the presence of other heritable diseases that are linked to the Jewish population, such as Tay-Sachs disease (carried by one in 25 Ashkenazim) and more than forty other genetic disorders.  It is important to note here that Jews are not more susceptible to genetic mutations; it is simply that, for a variety of reasons, they have been studied more thoroughly than other population groups. There are other examples of founder effects in small, isolated populations, including the Amish and fundamentalist Mormons.

The book also discusses the rise in genetic screening in certain populations where BRCA mutations are more common. Interestingly, such large-scale screening programs began in an effort to control Tay-Sachs disease as early as the 1980s. A group called Dor Yeshorim  screens Orthodox Jews for the most common genetic disorders and informs couples looking to wed whether or not they are a good genetic match. This approach has decreased the incidence of Tay-Sachs disease. The blood samples from Dor Yeshorim were useful for determining the prevalence of the 185delAG mutation in the Jewish population (1%). A recent story in the New York Times highlights the efforts in Israel, where one in 40 women carry a mutation in BRCA (compared to one in 100 women in the population as a whole), to begin universal screening for the mutations. The June 2013 Supreme Court decision, which ruled that naturally occurring human genes and mutations cannot be patented, should decrease the cost of the test in the United States. Prior to that decision, Myriad Genetics held patents on BRCA1 and 2, which led to high costs (more than $3000) for the test.

The subtitle of the book is definitely a good representation of what is inside; each of these topics seemed to get equal treatment. When the focus was on the DNA or race, the book held my interest. However, when the focus was more on religion, I found myself skipping pages. I didn't see how the history and beliefs of the Jehovah's witnesses helped the reader understand the genetics of this mutation. There were some surface similarities with Rebecca Skloot's book, as both have a very strong human angle. The book was a quick read, it taught me some new things about population genetics and BRCA mutations, and it served as an excellent jumping-off point for me to learn more.


**Footnote: If you imagine DNA as a sequence of three letter words, the phrase "The fat cat has the hat" becomes a very different sentence if two letters (at of cat) are eliminated and the spacing stays the same: "The fat cha sth eha t".

Sunday, November 17, 2013

Oh, the places I go! Another reason I love being a Scientific Editor

My job as a Scientific Editor gives me the opportunity to read much more broadly than I did when I worked in the lab. While researching manuscripts for suitability for the journal or while trying to find reviewers, I sometimes end up in very unexpected places. I discussed this briefly in my post about the book Elephants on Acid and Other Bizarre Experiments. I often find myself reading abstracts for papers that sound like fodder for Seriously, Science (formerly known as NCBI ROFL). The premise of this site is simple: post abstracts from PubMed with a simple description of the work. Of course, they tend to choose papers that sound pretty ridiculous on the surface. These are typically the types of papers that would garner criticisms about why such research should be funded. Here are some recent examples: "Study proves 'old person smell' is real"; "Curvy vs. straight - which glass ups your drinking rate?"


As a graduate student I studied the motility of the sperm from Ascaris, an intestinal parasite from pigs; we affectionately called our system "worm sperm". Thus, I understand the appeals and perils of working with an offbeat system. These unusual systems actually have important applications (otherwise they would not likely be funded). For example, worm sperm has a novel machinery for cell motility (more specifically, it uses a completely unique protein to power the movement of its amoeboid sperm), which could help us understand how more traditional cells crawl. Studying simple cells to understand more complex ones is a common approach in cell biology. The idea is that there should be conserved elements that should be comparable between the different cell types; such an approach can allow scientists to generate a minimal parts lists for a cellular process of interest. Thus, brewer's yeast can be used as a model system for a surprising number of cellular processes, even neurodegenerative diseases like Huntington's and Parkinson's.

A few weeks ago, I was looking for reviewers for a paper about protein stability during cryopreservation of heart tissues (now available in BBA - Proteins and Proteomics). The work could eventually have an impact on how tissues are stored prior to tissue transplants.  I found myself reading title after title about the stability of proteins after cryopreservation of semen of various types, especially boar and horse semen. The funny thing was -  I was not surprised to stumble upon these papers because I had seen them before. On the previous occasion, I was researching a paper on the proteomics of horse semen. These areas of research might elicit some giggles even from the seasoned scientist, but the work could have important implications for animal husbandry.

I recently evaluated a paper that described the protein in Venus fly traps responsible for digesting arthropods. Interestingly, it is a chitinase, an enzyme that can break down the chitinous exoskeleton of the fly trap's lunch (now published in BBA- Proteins and Proteomics). While searching for reviewers, I found a plethora of interesting papers, such as the mechanics of the opening and closing of Venus fly traps and proteomics to identify the components involved in digestion in a variety of carnivorous plants. I also see a lot of papers about insect venom. For example, we recently received a paper about the proteomics of fishing spider venom. As I learned in the book Wicked Bugs, insects and spiders have some pretty amazing (and terrifying) ways of attacking their prey. Some recently published papers demonstrate that understanding how the venom works can be useful for developing new pain killers as well as novel pesticides.

Every week I seem to find a new and strange corner of PubMed to explore. Sure, I still have some knee-jerk reactions and giggle when I read some of the titles. Generally, though, once I dig deeper to understand what the long-term goal of the work is, I tend to be amazed at the boundlessness of scientific curiosity and the ingenuity of scientists for finding new ways of solving problems.

Monday, October 14, 2013

The Poisoner's Handbook and my idea for a new tv show

I just finished reading The Poisoner's Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York. Similar to Sam Kean's book about the periodic table (The Disappearing Spoon), this book focuses on stories about some rather dangerous and fascinating chemistry. Here, author Deborah Blum culls stories from the Prohibition Era in New York City. Before that time, New York City's police department was poorly run. Then in 1918, Charles Norris was appointed as chief medical examiner (M.E.); Norris was the first M.E. who actually had suitable credentials for the position. Once in the department, Norris brought toxicologist Frank Gettler on board. Together, they helped to establish the role of forensic medicine in the investigation of crimes. Both Gettler and Norris worked countless hours in the laboratory to establish tests for the lethal doses of various poisons; they also investigated some of the more notorious crimes of the Prohibition Era.

Each chapter is focused on a different poison (e.g., radium, methyl alcohol). Blum chooses stories that are all linked to Gettler and Norris and the development of forensic medicine. A few of the chapters focus on what are likely seen as standard poisons, cyanide and arsenic. These poisons were readily available at pharmacies and hardware stores; thus, murders by these methods were almost commonplace. The work of Norris and Gettler established tests to help police convict poisoners who decided to use rat poison to get rid of an irksome husband or mother-in-law.

Of course, because the book focuses on the Prohibition Era, many stories described the effects of methyl alcohol and ethyl alcohol. When alcohol was outlawed in the US, the government decreed that industrial alcohol should increase the percentage of methyl alcohol. This was intended to decrease the chance that the alcohol would be imbibed. Instead, there was a sharp increase in the number of alcohol-related fatalities; these were mostly poor folks who couldn't afford safer alcohol. Blum discusses the chemists who were involved in bootlegging during this time period, which gave me an excellent idea for a new show: Breaking Bad meets Boardwalk Empire. Imagine the mild-mannered chemists like Walter White who found themselves in league with the unscrupulous bootleggers like Nucky Thompson!



from Wikipedia
The poor policy decisions behind prohibition were responsible for an increasing number of deaths; in addition, the lack of federal oversight of industry was also proving dangerous. For example, one company sold hair depilatories that included thallium; while the product did fulfill its promise of removing unsightly hair, it often made the users blind and eventually killed them. Another heart-breaking story, which I first read about in Radioactive, was that of the radium dial painters. In 1917, the Radium Corporation in Orange, New Jersey employed several young women to paint the faces of watches and other radium-dial instruments for the military. The employees shaped the tips of the paintbrush with their lips to produce the fine point necessary to make the small numbers on the dials. None of the employees found this behavior risky because radium was a popular panacea, which was present in a number of health tonics and spa treatments. Unfortunately, the women all became very ill; by 1924, nine of the dial painters died. The medical examiner in New Jersey (Harrison Martland) consulted with the NYC M.E.s to investigate these illnesses. They found that the living dial painters, called the "Radium Girls" by the press, were exhaling radon gas. The bones of the deceased dial painters were radioactive enough to generate an image on X-ray film and set off a radiation detector. The data gathered by the two groups of medical examiners were critical for the case brought by five of the Radium Girls, who were asking for a settlement from their former employer to help pay their medical bills. In the end, the women received a very small settlement ($10,000 in cash and complete medical care); while it was much less than they originally sought, they were happy to have any money while they were still living. Interestingly, the dial painters all died of aplastic anemia, which was also the cause of Marie Curie's death in 1934. 

Despite the amount of press that the case of the Radium Girls received, products containing radium were still on the market. It wasn't until the death of millionaire Eben Byers in 1931 that the safety of these products was called into question. On the advice of a physician, Byers was regularly drinking a product called "Radithor" for the treatment of an arm pain. The state of Byers' body was similar to those of the Radium Girls. Shortly after Norris and Gettler released the results of their autopsy, the government issued a warning regarding the safety of drugs like Radithor. In 1932, the products were officially banned by the government.

In the final analysis, The Poisoner's Handbook was interesting and included lots of off-beat stories from a strange time. However, its focus is more on history and forensics than chemistry. Thus, I slightly preferred The Disappearing Spoon.  

Monday, August 26, 2013

Henrietta Lacks' Immortal Cells

This month brought some progress to the family of Henrietta Lacks, whose cells were collected more than fifty years ago while Lacks suffered from cervical cancer. The resulting HeLa cell line has been critical for the development of cell culture, the generation of the Polio vaccine and many other important scientific discoveries. Recently, the genome sequence of HeLa cells was published online, a development that concerned Lacks' family members. As of this writing, the NIH has agreed to include two members of the Lacks family in the decision making process for the future use of the cells (check here and here for coverage of varying depth). The agreement does not result in any remuneration for the family. While this agreement is a clear step forward, this is still an isolated case and has not set a standard for consent about the use and sharing of genomic data.

I wanted to write something about this event because it brings the excellent book by Rebecca Skloot back into my mind. The Immortal Life of Henrietta Lacks is definitely on my top five list for best science books; this list includes books by Stephen Jay Gould and Carl Sagan. Skloot has received many accolades, and with good reason. The book does an amazing job of laying out the history of a complex story in an easy, digestible way and she makes the story compelling. The book was written in such a way that you feel the thrill of the investigation, as well as an emotional connection to the Lacks family. Skloot was careful not to place blame on the scientists involved. Rather, she presents the issues surrounding the case with the professionalism and rigor of a journalist, rather than someone trying to sensationalize the case, which is certainly easy to do in a situation like this, where the patient was a poor, African-American woman whose cells were taken without permission (at the time, there was no standard for informed consent).

Henrietta Lacks was infected with both human papillomavirus (HPV) and syphilis (probably by her husband), which were likely the cause of and a contributing factor to the aggressiveness of her cervical cancer. Now, several groups of researchers are sequencing the genome from HeLa cells to pinpoint what made HeLa cells grow so robustly. In a paper published in the August 8 edition of Nature, Adey and colleagues report that the HeLa genome is hypertriploid (meaning that the cells had just over three sets of chromosomes, whereas healthy cells would have two copies; aneuploidy or abnormal chromosome numbers is a hallmark of cancer cells), has a surprisingly low rate of point mutations during the course of normal cell culture, and has had a fairly stable chromosome count since the initial isolation of the cells. Most interestingly, the study describes the insertion of the HPV genome at a fragile site on one copy of chromosome 8. Only two thirds of the HPV genome was observed at chromosome 8; importantly, copies of the E6 and E7 oncogenes of the HPV genome were integrated. These oncogenes have been linked to cervical cancer progression, malignancy, and cell immortalization. Notably, the sequence for E2, the inhibitor of E6 and E7, was absent. Finally, the site of HPV integration was 500 kilobases from MYC, a canonical proto-oncogene; MYC showed very high expression, but only from the copy of chromosome 8 that included the HPV genome. Essentially, the oncogenes from HPV were hyper-activated, as was the MYC oncogene from the HeLa genome and this was directly caused by the insertion of HPV near the MYC oncogene. Thus, the research suggests that the interaction between the HPV DNA and the HeLa DNA may underlie the robust growth characteristics of the HeLa cell line. These results are exciting and suggest that we still have a lot to learn about HeLa cells. 






Sunday, August 11, 2013

Amy Stewart's Wicked Bugs, Lyme disease, and me (or my lousy summer has really ticked me off)

I had Lyme disease this summer. I was very lucky to catch it early, so the treatment was effective and the issues resolved quickly. The symptoms that I had were different each day and included the standard flu-like presentation as well as some very violent thoughts that nearly provoked me to punch someone on the subway. In my defense, the person probably was talking too loudly on the phone or taking up several seats. (It is a testament to how sick I was that I was riding the subway to work rather than biking.) Needless to say, it was a strange trip. Once the antibiotics started to work and the misery started to fade, I became more interested in the bug, as well as the bacteria, that caused all the trouble in the first place. 


Thus, I picked up Wicked Bugs by Amy Stewart. Two aesthetic things that I really liked about the book: the design of the cover and the illustrations. This is Stewart's second book in the Wicked series and both books have the same pocket size and general cover design. The unusual size of the book makes me wonder the intention (if any) of the book design. The illustrations, such as the one of a deer tick on the right, are so detailed and lovely; it makes you forget some of the more ick-inducing details about the bugs in question.

The book covered a large variety of interesting bugs. My only complaint was that there was not more narrative. Instead, the book read like a compendium of interesting factoids about bugs. Surprisingly, this made it very easy to read in small bites. The louse mentioned in the subtitle of the book (The Louse That Conquered Napoleon's Army) was actually one of the less interesting stories in the book. It seems that Napoleon's army was decimated by typhus caused by body lice; in addition, Napoleon also had scabies for a good portion of his life.

According to Stewart, termites were an important factor is the destruction of New Orleans in the wake of hurricane Katrina (more information can be found here). Both the foundations of buildings in the city and the levees themselves were affected by the bugs, which compromise structural stability with their webs of tunnels through wood. The seams of the flood walls were sealed with bagasse, which is the pulp of the sugarcane leftover after the extraction of sugar. As you can imagine, bugs love that. Thus, termites may have played a role in the failure of the levees. In the aftermath of the storm, the mass exodus of residents meant that fewer people were keeping up with pest control, which led to increases in the populations of termites and further damage to the buildings, which were already ravaged by the storm. To my surprise, she doesn't mention the most interesting thing about termites: termites rely on a symbiotic bacteria in their gut to digest the cellulose. Those bacteria, in turn, rely on another symbiont to produce some of the digestive enzymes required for this process.

Like many of the insects covered in this book, deer ticks have a strange life cycle, which can involve three hosts. The larvae feed on rats, mice, or birds; as nymphs, they feed on small rodents or humans; and as adults that feed on deer. Sometimes, at the larval stage, ticks are infected by the bacteria that causes Lyme disease, a spirochete called Borrelia burgdorferi. Interestingly, Lyme disease was noted in medical writings dating as far back as 1550 BC, when it was called the "tick fever". In the northeast United States, cases have shown continual increases over the past decade. Climate change and loss of predators are thought to be the cause of these increases.

A chapter entitled "Zombies" focused on some other curious life cycles in insects. This section is certainly not for the squeamish. In fact, some of these stories make my skin crawl. Generally, these insects all seem to have a similar M.O.: they sting another insect and take control of it, typically to lays their eggs inside the poor victim. In the case of the emerald cockroach wasp, the wasps deliver a sting directly into its victim's (a cockroach) brain. At this point, the wasp can have total control of the cockroach. The cockroach will serve as a nest, a source of food, and eventually a cocoon for the wasp's offspring. The adult wasp will emerge from the cockroach, leaving only a shell of the former insect behind. These stories are all so unusual. How would something this devious evolve? What is inside that sting that can be such a powerful paralytic? These are some follow up questions I will have to research. One thing is certain, these stories make me hope that reincarnation is not real.

While Wicked Bugs wasn't the best book I read this year, I will be adding Wicked Plants to my reading list.

Enjoy this video from the author, Amy Stewart.




Wednesday, July 24, 2013

Another great read from Sam Kean - The Violinist's Thumb

Because I enjoyed Sam Kean's Disappearing Spoon, I was excited to start the Violinist's Thumb. This book did not disappoint. I have to admit that I finished this book some time ago and now it is really overdue at the library. Thus, I present some rather unconnected thoughts.

Much like The Disappearing Spoon, this book has lots of fascinating stories. There were several parts of the book that really stuck with me. By far, my favorite was the history of the discovery of DNA. Kean discusses the story of Watson and Crick and all the good stuff (e.g., infighting, competition, and other assorted nastiness) you may have read or seen in The Double Helix, but the book also delves into some other very interesting characters that had major roles in unraveling the function and structure of DNA. One of the many things I loved about being in the lab was the plethora of unusual people that are attracted to that particular line of work. The lab of Thomas Hunt Morgan at Columbia around 1907 certainly attracted its fair share. The so-called "Fly Room" was a very small space with many large personalities that bred fruit flies as well as revolutionary science. Eventually, Morgan's lab lead to major contributions towards our understanding about mutations and heredity as well as sex-linked traits. Of course, his other contribution was the introduction of the fruit fly as a model organism.

The book also focuses on several other important scientists who were integral to our understanding to DNA and inheritance. These scientists included Sister Miriam Michael Stimson, who (like Gregor Mendel) performed science while in service to the church, Lynn Margulis and Barbara McClintock. This chapter, entitled "DNA Vindication", was centered on the important findings that each of these women made. This chapter was also very character-driven; each of these scientists was very much about going against the grain. In the end, I found these stories to be insightful not just about the results, but also about the restrictions on and expectations of women in science. I was glad that not only Rosalind Franklin (the Sylvia Plath of molecular biology) got coverage here!   

Sam Kean has talked about several of the stories in this book on the Radiolab podcast. In the episode entitled Double Blasted, we hear the story of a man who was present in both Hiroshima and Nagasaki when the atomic bombs were dropped. In the episode Inheritance, he discusses some spurious results with midwife toads that led to the downfall of the scientist behind the work, Paul Kammerer. In the same episode, they discuss some really interesting stories about epigenetic modifications, which has completely changed the way we look at genetics. Now it is no longer simply what genes you are passing down to your child. Rather, it can also be about the environmental effects that your ancestors experienced generations ago.

Here are some other highlights:
  • The titular story concerns the violinist Paganini, who was allegedly blessed/cursed with a rare joint disease that allowed him to have much great flexibility in this fingers. This allowed him to accomplish feats that other violinists would deem impossible. 
  • The chapter about post-mortem diagnosis of historical figures is quite good. There were lots of great stories about the possible genetic disorders of Toulouse-Lautrec, King Tut, and Abraham Lincoln. I had never heard before that John F. Kennedy had Addison's Disease, a condition of the adrenal glands that depletes the body of cortisol. One common side effect of Addison's is the bronze skin, which served JFK well in his debate against the pasty Dick Nixon in 1960.  
Of course, there were lots of these interesting tidbits peppered throughout the book. Overall, the book was organized in an interesting and logical way. I like that Kean is about telling the story of science with the scientists being the main characters and the results being the major plot points. 

Wednesday, March 6, 2013

My year away from the bench

It has now been one year since I left the lab. In May 2012, I found a full time position as a Scientific Editor for BBA with Elsevier in Cambridge. It is an excellent job for me: I get to read other people's science all day. Plus, it has been an exciting change of pace. In the first few months, it was tough to get used to the relaxed atmosphere; suddenly, there was much less pressure to produce results. I have since adapted to the vagaries of scientific publishing. The best part of this normal schedule: I have a more balanced life again. For me, this has included reading more books, watching movies, and running more regularly. 

I have also started to develop my skills as a baker. Anyone who has tried my brownies knows that I am familiar with the power of combining eggs, butter, and flour. However, in the past few months I have started to take this to a new level. About six year ago, I stumbled upon Cook's Illustrated/America's Test Kitchen. If you are unfamiliar, they have an amazingly scientific approach to developing a recipe; essentially, they make 100 batches of chocolate chip cookies so you don't have to (by the way, their chocolate chip cookies are amazing and are worth every extra step). I started to think about my baking differently. I have been reading more about the science of cooking, specifically the chemistry of the ingredients and how changes in the ratios of the components can lead to predictable changes in the resulting product. 

I decided to work on one of my standard recipes: the oatmeal raisin cookie. In the past, I have done a little bit of experimenting with my recipes, but I have never been very methodical. For this new undertaking, I invested in two new tools: a scale and a notebook. After a few batches, I think I have a successful recipe, which has consistently (N = 3)  achieved the desired outcome: a cookie with a good combination of chewy and crunchy with a lot of molasses and oatmeal flavor. 

I suppose this means that I miss the lab more than I had anticipated. Of course, in contrast to experiments in the lab, a bad result in baking is still a good outcome: treats to enjoy! 

   

   

Saturday, February 23, 2013

Packing for Mars by Mary Roach

I have a pretty broad interest in science. However, space and astronomy were never at the top of the list. Even in middle school, my interest in attending space camp (spurred by watching that Joaquin [nee Leaf] Phoenix film)  was fairly short-lived. Instead, I dreamed of working as a trainer at Sea World. Thus, I was surprised to find Packing for Mars by Mary Roach on my reading list. I had previously read Roach's book Stiff: The Curious Life of Human Cadavers. I read that shortly after the end of the series Six Feet Under, so I was searching for something to fill that morbid void in my life. Stiff definitely fit the bill.  I remember enjoying the gory details.

However, Packing for Mars was more of a mixed bag. Some chapters were quite good, packed with little scientific tidbits, while others seemed to be more for the shock value. For example, there was an entire chapter devoted to motion sickness and another very long entry about crash testing with corpses (the latter was common fodder for Stiff). Two other chapters seemingly geared toward a middle school audience focused on space hygiene, specifically how smelly do astronauts get after a few weeks with minimal washing and how astronauts deal with going to the bathroom in zero gravity.

Of course, there were some interesting elements. The central theme of the book is to examine how space programs have addressed the problems that are encountered with an increasingly complex series of space missions, from orbiting the Earth to landing on the moon and current work on the International Space Station (ISS) and a future mission to Mars. Each mission poses a new set of problems, such as how people interact for long periods of time in isolation and how the human body reacts to long periods of zero gravity.

To address the first question, which has been a major issue for astronauts on the ISS, space programs have developed some interesting methods for screening candidates for ISS missions. To investigate the second question, NASA has been performing experiments on bed rest to determine how bone loss can be limited. According to Roach, you can make some good money by participating in these studies. I know I have seen the ads on the subway here in Boston. The trouble is you have to stay in bed for three months, doing very very little. Of course, scientists are also examining the physiology of black bears to understand how they cope with extended periods of inactivity during hibernation. Interestingly, there are some studies to examine whether parathyroid hormone from black bear (thankfully synthesized) can lessen bone loss in rats. These experiments have obvious implications for the treatment of osteoporosis, as well as the relevance for astronauts going to Mars.

The idea that there may be a manned mission to Mars by 2030 still sounds pretty fantastic. After reading this book,it seems that the biggest obstacle may not be in the science or the logistics, but in the finances. Hopefully, the recent landing of the Mars rover Curiosity has renewed interest and enthusiasm in the project.

Wednesday, January 30, 2013

Sam Kean's Disappearing Spoon and my renewed excitement about the periodic table

The Disappearing Spoon by Sam Kean explores the periodic table and the stories behind a variety of elements.  It made me realize how much I had forgotten from my chemistry classes. Of course, it also made me think about how I learned about chemistry in the first place. My high school chemistry teacher, Ms. Simms, was excellent. She had a number of great illustrative methods to think about things like orbitals and electrons. However, despite her superb teaching, I really struggled with chemistry at the time.

My graduate classes in biology always included lots of narratives of the scientific process and how the scientists reached their discoveries. This is a great way to learn about how to think about a problem and how to design experiments properly. It is also an excellent way to learn about science. This book taught me far more about chemistry than I had originally intended.

The story of how the periodic table developed and evolved is a fascinating one. (As an aside, the Radiolab podcast Yellow Fluff did a great story on this as and it serves as a nice complement to sections of this book.) In fact, one of the most interesting stories in The Disappearing Spoon was the biography of Dmitri Mendeleev. Chapter 3 discusses Mendeleev's personal story; my favorite part is how his widowed mother "bundled him on horseback and rode 1200 miles across  the snowy Ural mountains to an elite university in Moscow". While that university did not accept Dmitri, he later found a spot at a university in St. Petersburg. Sadly, his mother died shortly after he was enrolled. Mendeleev excelled in school and worked in lots of different chemistry labs. Using this knowledge, he started to organize the elements; the story goes that Mendeleev used to play a sort of chemical solitaire with the elements written on index cards. 

Periodic table according to relative abundance (from io9)
The story surrounding Midas and his golden touch was also examined (Chapter 13- Elements as Money). It seems that Midas' golden touch may have been more of a brass touch. The king's metallurgists thought they were making bronze, an alloy of tin and copper, but in fact were making brass, an alloy of copper and zinc. Thus, the brass had more of a golden tone to it. Indeed, the soil in the area of Asia where Midas once ruled is indeed rich in zinc and present day metallurgists have shown this hypothesis to be a likely explanation for the myth. 

The book explores other topics including how elements are used in times of war. In Chapter 5, Kean talks about the importance of molybdenum (wolfram, W) in the development of Germany's weapons, which were spiked with wolfram to withstand higher heat, in World War I. This chapter also tells the story of Fritz Haber (another great Radiolab episode) as well as the elements that have fueled the conflict in Congo -- tantalum and niobium, which are commonly used in cell phones and other electronics. 

In the end, The Disappearing Spoon, much like Walter White in Breaking Bad, has renewed my appreciation for the periodic table and  helped me understand better some of the things I probably learned 20 years ago. 


A few related links:


For your viewing/listening pleasure, I present They Might be Giants, Meet the Elements.

The dynamic periodic table. I wish they had this kind of thing when I was in school.