I love post-collapse science fiction in any form, so it is no surprise that I have been binging on the genre of late. Most recently, I finished Children of Men, the basis for an excellent movie, and Margaret Atwood's MaddAddam, the final book in the eponymous trilogy that includes Oryx and Crake and Year of the Flood. MaddAddam struck me with some of the details and descriptions of the post-collapse environment. It reminded me of The World Without Us by Alan Weisman, which I decided to re-visit due to my recent obsession with apocalyptic fiction. The book is something of a thought experiment to address the question of how the world would look without humans; it is definitely on my great science reads list.
I am Legend's image of New York City without us
My original vision of a post-collapse world was a paradise where plants and animals take over the newly vacated cities. The traces of our civilization would be quickly covered in kudzu and dust, as seen in The Walking Dead or I am Legend. However, Weisman's book changed this view; his book suggests that while some vestiges of our existence would disappear rather quickly, other elements would persist long after we are gone.
A crumbling Brooklyn Bridge five years after us (K. Brown)
My favorite chapter is "The City Without Us". The author spoke with a variety of experts (e.g., engineers, chemists, geologists) to discover how New York City would change after humans disappear. During the development of Manhattan, various environmental engineering projects transformed the island from a tidal
500 years after humans: New York City becomes a forest
marsh filled with rivers and streams to the metropolis we know today. All of this water, currently trickling unseen under the city, would be a major force for change after humans are gone. The subway tunnels would fill with water only a few days after the power turns off. As the water seeps through the subway system, it would cause weaknesses in the roads and sidewalks. In combination with seasonal changes in temperature, bridges and roads would collapse quite quickly. Without people around to maintain the infrastructure, roads and bridges would likely be crumbling after just five years. In about 500 years, Weisman predicts that the city would be a forest, with a unexpected array of animals, including deer, moose, bears, and coyotes. The images on the right are from the author's website, where you can find more amazing visions of New York City without humans.
Abandoned bumper cars in Pripyat, Ukraine, the site of Chernobyl
Within days of our disappearance, power plants
would go offline, causing meltdowns at nuclear plants. Chemical and
industrial plants would catch fire without maintenance, making the initial landscape rather hellish. While the fires would eventually extinguish, the chemical and nuclear wastes would persist. These pollutants
would then become a force for adaptive change. The city of Pripyat, the site of the 1986 Chernobyl meltdown, can serve as an example of how the landscape changes without us. The fallout from the disaster is estimated to irradiate the environment nearby until at least 2135. The Exclusion Zone (a 30 km radius evacuated around the plant) has highlighted how adaptable
nature can be. Weisman discusses how the biodiversity in the Exclusion Zone has improved; in fact, the zone has become home to an increasing number of animals (e.g., moose, voles, rabbits, birds). Surprisingly, it is unclear whether these animals are experiencing an increased mutation rate (primary article with coverage on ScienceBlogs). The inner reactor core has proven to be a unique niche for evolution: scientists discovered a radiotrophic fungi as a black
slime on the inner reactor core; this fungus converts gamma rays into energy for growth. Other published articles have described how plants have adapted in the highly radioactive environment.
One vestige of human existence that would persist without us: plastics. Weisman thoroughly discusses the issue of plastics pollution, including the North Pacific Subtropical Gyre, more commonly known as the Pacific garbage patch. Like the four other oceanic gyres, this area of the ocean has become a sink for plastics in varying states of decay; plastic debris is reduced to smaller and smaller sizes by the action of waves and the sun. The majority of the plastic wastes in these gyres is in the form of microplastics. Because plastics have only been in use for about 60 years, scientists are only starting to understand the ramifications and possible outcomes of the life cycle of plastics. Likewise, this relatively short time frame means that microbes have not yet evolved to degrade them. Despite the gloomy information in this chapter, the author keeps a positive tone, suggesting that while we do not know how long it will take for plastics to degrade, there is hope on the geological timescale: "Like trees buried in bogs a long time ago....were changed into oil and coal," maybe plastics will degrade when microbes evolve to degrade them or when something else changes them altogether (p. 128). This geological view from the book's website may also help keep things in perspective.
The World Without Us informs the reader of the knowns and spurs the imagination of the unknowns. In this way, it captures the things about post-collapse fiction that I find appealing: that initial sadness at the loss of our humanity, the imaginings of what kind of place the world will become without us, and the hope that the world could be better.
More links:
* The author also discusses the Mannahatta project, which has done extensive research to chronicle what Manhattan looked like before Henry Hudson landed. I am adding the book about the project to my ever-growing book list.
* To get some ideas for this post, I read a lot of opinions on why human
are so obsessed with the apocalypse. I did not find a really satisfying
answer, but this piece was the best of the relevant articles.
Here is a running list of my favorite science reads (in no particular order), which I will attempt to keep updated. I have included links to the Amazon page as well as the related post from my blog.
Genome - The Autobiography of a Species in 23 Chapters by Matt Ridley came highly recommended on Amazon. Despite the fact that the book was published in 2000, I decided to read it. The
structure of the book is rather clever: each chapter focuses on one
chromosome. This format
allows Ridley to expand the metaphor that the human genome is a book:
each chromosome is a chapter; the genes are the sentences; the codons
(the three letter DNA sequences that the cellular machinery reads) are
the words; and the DNA nucleotides are the letters. This kind of metaphor can help non-scientists visualize and remember the
organization of the genome. Unfortunately, Ridley eschews the proper scientific
terminology, calling codons "words" and
nucleotides "letters". Science writing should
teach people more about the subject matter; to eliminate the use of fundamental terminology seems a folly.
In each chapter, the author highlights one gene of interest on the
chromosome. For example, the chapter on chromosome 13 introduces BRCA2. Like
the Jeff Wheelwright book I reviewed previously, Ridley discusses the population genetics of BRCA2. In some chapters, he writes about genetic lessons
from a particular chromosome. In some cases, the conceit works brilliantly (e.g., the chapter on the X and Y chromosomes examines sexually antagonistic genes), but other times, it was not as successful. Ridley uses
Chapter 21 to discuss eugenics. While the history of the topic is interesting,
the connection to chromosome 21 seems a bit tenuous. Parents are increasingly using
prenatal screening to detect chromosomal abnormalities, the most common of
which is Down syndrome, which is caused by an extra copy of chromosome 21. I
found the book worked best when there was an obvious candidate gene to discuss
on the chromosome.
It is amazing to consider how much the field of genomics has changed since the publication of Ridley's book (February 2000). In June of that year, the initial rough draft of the human genome was published. When the sequence was officially completed in April 2003, the final cost was estimated to be $2.7 billion; the project took more than a decade. Today, we are approaching the benchmark of the $1000 genome (discussed here and here). The next step is to improve the speed and portability of sequencing equipment as well as the ability to process and analyze the data.
The human genome project has been considered a success in terms of yields for basic research. However, there has been some disappointment that the completion of the project hasn't led to more clinical applications (for more specifics, see these editorials from Francis Collins and Craig Venter, the heads of the Human Genome Project). One problem is that very few diseases are caused by a single gene. Another confounding factor is that there is 1-3% difference between any two individuals' genome sequences. These variations can complicate genomic analyses. To perform a genomic study of a population with a genetic
condition, knowing the differences that are normally present in the
genome can help narrow down the possible regions that are linked to the
condition of interest. Thus, having more complete sequences available will allow scientists to connect DNA sequences with genetic conditions. The 1000 Genomes Project plans to identify all the genetic variations present in the human population. The initial phase of this project was completed in just over four years with the publication of 1,092 complete human genome sequences from 14 populations across the globe. In the coming years, the project plans to complete a total of 2,500 genome sequences to improve the representation of various human populations across the globe.
Another major change in the genomic landscape is the advent of personal genomics, such as 23andme. These companies offer DNA analysis service that supplies information on your possible ancestry as well as information about other genetic markers. These markers include both the innocuous ones, like whether you can detect a terrible smell in your urine after eating asparagus, and genes linked to possible health risks (e.g., BRCA, Huntington's disease). After intervention by the FDA, the service is now limited solely to ancestry. Scientific American had a fascinating piece about why we should really be concerned about companies like 23andme (TLDR: they are collecting and storing your most personal data – your DNA).
I would not recommend this book to a non-scientist. If you want to learn more about the human genome and DNA, look elsewhere. I highly recommend The Violinist's Thumb by Sam Kean; the recently updated Double Helix by James Watson and the newest book from Craig Venter are likely to be good reads.
Want read more? * The Human Genome at 10 Special Issue in Nature covers the changes in the genomics landscape with editorials and articles by a number of major players in the field. * There is also abundant information on other "big science" approaches to genomics, such as the HapMap, the ENCODE project, and The Cancer Genome Atlas [TCGA]. I have not explored these for the sake of brevity.
I
love a good cocktail. The rise in the popularity of cocktail culture and craft
cocktails has made me very happy. As with professional chefs, I find it
amazing that people can still come up with unique creations. Our last dinner out included the Nasturtium
(citrus vodka, St. Germain, and aperol - served down) for me and an Algonquin
(rosemary-infused rye, fresh pineapple, dolin dry vermouth, and orange
bitters - served up) for my husband. I admit that I rarely know much about the
particulars of these beverages that have become an integral element of
dining out. Thinking that it might be fun to learn more about the
components that create these little glasses of deliciousness, I picked up The
Drunken Botanist: The Plants That Create the World's Great Drinks from
my local library.
Like Wicked
Bugs, The Drunken Botanist is written as a compendium of
sorts with accompanying pen and ink illustrations of
the plants described. Here, Stewart focuses on the plants that people
have used throughout history to create alcoholic beverages. There is good
coverage of both the classic ingredients (e.g., rye,
wheat, hops, and grapes) and the plants used for the
mixers and garnishes that are essential to create the perfect
cocktail. In the spirit of the book, here is a litany of things that
I learned:
The invention of the Moscow Mule highlights the kind of story I love. The drink was first created in 1941 through the collaboration of a vodka distributor, who hoped to introduce Americans to vodka, and a bartender, who had extra ginger beer in stock. Because the bartender's girlfriend owned a company that manufactured copper mugs, these became an element in the recipe. A recent rise in the cocktail's popularity has led to an increase in thefts of the distinctive copper mugs. (In the course of my research, I noticed that Wikipedia has a slightly different version of the story of the invention of the drink, which is to be expected.)
The distinctive smell of the dentist office is caused by the use of clove extract as a dental anesthetic.
The
fragrance of jasmine flowers is due to several compounds,
including phenyl-acetic acid. Based on genetic differences, some
people find that jasmine flowers smell like honey, while others
compare the scent to urine. This is similar to the small genetic differences that cause some people to perceive a horrible smell in urine after eating asparagus or
to find that cilantro
tastes like soap (Julia Child and I share that one).
Some figs
must be pollinated by a wasp in order to reproduce. The wasp then lays its
eggs inside the fig and dies there. Those figs would contain little bits
of wasp carcass. Most figs in use today can bear fruit without
pollination. This tidbit makes me love figs just a little bit more.
I was
surprised by the number of stories about the link between alcoholic beverages and
scurvy. For example, in the 1500s, the British navy included beer in their fleet's rations, both because water would spoil at sea and to keep the sailors happy. Unfortunately, beer also went bad on longer voyages, which led to the use of grog (rum
mixed with water, lime juice, and sugar). The lime juice was initially added to
make the drink palatable, but it had the indirect result
of improving the sailors' health. In some cases, the vitamin C
deficiency was combated with spruce beer; spruce trees produce
ascorbic acid to help them survive the cold. Spanish explorers used bitter orange as a treatment for scurvy. In the course of their travels, they left seeds on an island called Curaçao, where the bitter oranges are the ingredient in the eponymous liqueur.
Initial
attempts to make wine from grapes grown in America were abject
failures; both native and imported vines were unsuccessful. One problem was an aphid called phylloxera; the American grapevines were resistant to the pest, but European vines were not.
Unfortunately, Americans sent infected grapevines to France, where
the aphids quickly devastated the wine industry there. The solution: grafting American vines onto old European vines. The second problem was that the American grapes had undergone
natural selection by birds, while the European vines had been subjected to hundreds of years of artificial selection by humans. Even today,
researchers are working on making palatable wines from the grape vines native to America.
There were numerous mentions of the Dogfish Brewery, who are resurrecting old approaches to making beer. In collaboration with a molecular archeologist, they have recreated several ancient beers based on the discoveries at dig sites.
There
are probably other fascinating stories that I am missing, but I think I
need to go make a cocktail.
Growing up in Florida, my interest in science was spurred by my love of the ocean. I decided I wanted to be a marine biologist at a very young age. Later, I thought that becoming a trainer at SeaWorld would be the perfect job. My subsequent interest in animal rights and environmentalism made me lose my fondness for SeaWorld.
My dolphin encounter.
When I visited my family in Florida in 2012, my mother suggested that we go to SeaWorld. I figured it was a good compromise as I certainly did not want to go to Disney and I did feel some obligation to let my son experience the place that once brought me such joy. We had a nice day in the park. I touched a dolphin for the first time and got so excited that I flashed back to my younger self. At the end of the day, we went to see the orca show. In past visits, this was always my favorite part, but it had been the better part of 20 years since my last trip to SeaWorld. During the show, I started crying; I eventually realized that I was crying for these poor whales, who were stuck inside this relatively small tank in an overly warm tourist attraction. After that experience, I concluded that I would probably not come back to Sea World. Last week I watched Blackfish on Netflix, which solidified my opinion. The documentary explores the story of the killer whale Tilikum, who has been linked to the deaths of three individuals during his time in captivity. The documentary is based primarily on interviews with former SeaWorld trainers as well as killer whale experts. The main complaint against SeaWorld Orlando (SWO) in the film is that they did not accurately represent the threat that Tilikum, who had killed one trainer before arriving in Orlando in 1992, might pose to the trainers there. According to the trainers interviewed in the film, SWO never made that history or the incidents that may have precipitated that event known to the trainers. Later, Tilikum was involved in the strange death of a tourist who allegedly wandered into the tank. SWO claimed that hypothermia killed the man, rather than by an attack by the killer whale. In February 2010, trainer Dawn Brancheau was killed by Tilikum. SWO claims that Brancheau's death was due to trainer error.
The other trainers in the film argue that this was not the case. A lawsuit by OSHA eventually forced SeaWorld to remove the trainers from the tanks with the animals. SWO isolated Tilikum and kept him from performing, as least until until 2011. However, Tilikum is not likely to leave the park as he has been incredibly profitable as a breeder: the bull orca has sired 21 offspring during his time in captivity. According to the film, Tilikum is frequently found nearly immobile for hours at a time in his tank. They speculate that his large size and his treatment while in the Sealand park in British Columbia may be the reason for his erratic behavior.
In addition, the film charges that SeaWorld does not accurately present
scientific facts about killer whales. Science education and species
preservation has always been a strong defensive point for the park.
However, comparing the talking points of the former and current trainers
and tour guides with the facts, it seems that teaching
people the science of killer whales is not a priority for the park,
especially if the facts can make the organization look bad. For example, whales in captivity frequently have a dorsal fin that is flopped
over. SeaWorld claims that this is common in the wild as well. However, the
killer whale expert interviewed states that this is only
observed in about 1% of whales in the wild. The park also claims that the
whales in captivity have a similar lifespan to those in the wild; in
fact, captive whales live 30-50 years while those in the wild live 50-90
years. In the end, the film confirmed my view that SeaWorld is just another theme park, which puts its own interests above both those of its animals and its workers. The film ends with a powerful scene, as the former trainers go on a whale watching cruise; they all seem emotional as they observe a pod of killer whales in their natural habitat, jumping and swimming in the open ocean with their family intact. The film succeeded in making its case against the capture and captivity of whales. It convinced me that I should never go back to SeaWorld. Now I just have to break the news to my mom.
For some timeI 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. Agroup 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 2013Supreme 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 readerunderstand 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".
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.
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I love post-collapse science fiction in any form, so it is no surprise that I have been binging on the genre of late. Most recently, I finished Children of Men, the basis for an excellent movie, and Margaret Atwood's MaddAddam, the final book in the eponymous trilogy that includes Oryx and Crake and Year of the Flood. MaddAddam struck me with some of the details and descriptions of the post-collapse environment. It reminded me of The World Without Us by Alan Weisman, which I decided to re-visit due to my recent obsession with apocalyptic fiction. The book is something of a thought experiment to address the question of how the world would look without humans; it is definitely on my great science reads list.
