Voyage of the Beagle (Non-fiction fan fiction)

11/11/15

It’s #NaNoWriMo – National Novel Writing Month. In honor, and because I had the day off work and am procrastinating from other tasks, I spent the morning artistically imagining The Voyage of the Beagle by Charles Darwin* for a young audience.

Voyage of the Beagle

Preface

     Have you ever dreamed of having a truly grand adventure? Then this story is for you. But you must be prepared. You will sail across oceans, climb to the tops of mountains, come face to face with wild creatures, and have only the stars to guide you on the darkest of dark nights. Each day will have challenges and rewards. You will conquer your fears. You will make discoveries. This is the life of an explorer. Are you ready?

Chapter 1

     It was the wish of Captain Fitz-Roy to have a dog on board Her Majesty’s ship, a ten-gun brig, scheduled to sail from Devonport on the 27th of December, 1831, on a journey around the world. You see, dogs, especially hounds, were quite useful on expeditions such as this. Hounds are known for their friendship and steady assistance, as well as their keen sense of smell. The Captain did not himself own a dog, so it was through the kindness of the hydrographer, Captain Beaufort, who had recently acquired a young beagle that a dog was gotten for the voyage. Captain Beaufort had purchased the hound for his niece whose mother had died and who was under the care of her father. An offer was made by Beaufort of giving up part of his own accommodations so that the dog could accompany the Captains on their expedition, and this was sanctioned by the Lords of the Admirality. It was not, however, sanctioned by Henrietta, Captain Beaufort’s niece.

You see, though it had been but 10 days since the dog was gifted to Etty, the two had formed a substantial bond. The girl’s uncle did not doubt the strength of this connection, due to the aforementioned friendship so characteristic of such hounds and the child’s recent loss. The death of Etty’s mother one month prior certainly dictated that another loss in the child’s life would be a misfortune and could do harm. For this reason, Captain Beaufort requested that the child be granted permission to join him and the dog on the upcoming voyage.

You will not be surprised to learn that Etty’s father did not approve of this request. He included in a letter to Captain Beaufort the following list of concerns:

September XX, 1831

  1. It will be disreputable to my character as a father hereafter to allow a young girl to take part in such a wild scheme.
  2. To allow a young child on such a journey it must be a useless undertaking.
  3. The accommodations would be most uncomfortable for a child.
  4. I would consider it a distraction from Henrietta’s studies.
  5. Furthermore, a ten-gun brig is no place for a dog.

The same day, the Captain replied to the letter with what occurred to him upon reading each of the objections.

September XX, 1831

  1. I should not think it will be in any way disreputable to your character as a father, as I, the child’s uncle shall be responsible for her care and well-being on this expedition.
  2. Looking upon the child as a girl of enlarged curiosity, it affords her the opportunity of seeing people and things as happens to few.
  3. If sanctioned by the Admirality, we have a claim to be as well accommodated as the vessel will allow.
  4. The child would have definite objects on which to engage herself, and might acquire and strengthen habits of thought, and I should think would be as likely to do so as in any way in which she is likely to learn in the next two years at home. I can assure you her pursuit of knowledge in the expedition would be in the same track as she would have to follow otherwise.
  5. It is at the request of Captain Fitz-Roy that a young hound of the finest quality and character accompany the expedition and lend assistance, by its loyal tendencies and advanced nature of olfaction, to the Naturalist, one Mr. Charles Darwin.

*Note – Much of this text is taken directly from The Voyage and from The Autobiography of Charles Darwin (Barlow, 1958). I did not seek, nor have I received, reproduction permission for the adopted text, so I do not claim this as original writing, though the creative imagining is an original idea (including the characters of Henrietta, her father, and the hound). Since I do not claim that all of these words are my own, you should not attribute all of them to me. Any original text is copyrighted to the owner of this blog (C.M.S.) and may not be reproduced without permission.


Lucy in the sky…and on Nature Knowledge Project

I am pleased to share that a peer-reviewed article I wrote for the Nature Education Knowledge Project about the fossil human ancestor, Lucy, has been published online.

This article is tailored for high school classes and introductory-level undergraduate courses.

I am grateful to a number of people at Nature and to Dr. Holly Dunsworth for their determination to get this article and others in the Human Fossil Record room published; the Scitable resources are an excellent way for educators to incorporate into their curricula high quality, peer reviewed written materials.

You may reproduce the Lucy article, without modifications, in print or electronic form for your personal, non-commercial purposes or for non-commercial use in an educational environment.

Full URL: http://www.nature.com/scitable/knowledge/library/lucy-a-marvelous-specimen-135716086


Evolutionary Genomic Medicine: New approaches and challenges to understanding human health

The December, 2014, issue of Current Opinion in Genetics and Development (Vol 29) comprises a collection of review articles dedicated to the theme of “genetics of human origin.” The article by Rodríguez, Marigorta and Navarro[1] discusses the integration of genomic data and evolutionary medicine, a relatively new approach to the study of human health.

What is evolutionary medicine?

In the burgeoning field of evolutionary medicine[2] the principles and habits of mind of evolutionary biology are considered foundations for and are integrated with traditional research, education, training, and practices of medical and health professionals. One goal of evolutionary medicine is to use the concepts of evolutionary biology (i.e., adaptation, maladaptation, population genetics) to explore the etiology and presentation of human disease, vulnerability to disease, and anatomical and physiological correlates of genetic and environmental influences on human health.

What is medical genomics?

Rodríguez, et al. (2014:97) explain that “the field of medical genomics focuses on immediate questions about how diseases appear and how they advance within an organism.” To understand medical genomics, it is helpful to review what is meant by “the human genome.” Nearly all of your cells contain DNA[3]. DNA has a “double helix” structure – think of a ladder that has been twisted around its long-axis. The “rungs” of the DNA ladder are molecules called bases. There are four bases—A, T, C and G—and they pair up in a specific way: A pairs with T and C pairs with G. A typical human’s DNA is composed of approximately 3,000,000,000 base pairs packaged in 23 pairs of chromosomes (in each cell!). Among those 3 billion base pairs are very specific sequences of bases that are functional, meaning they play a role in the body’s physiological processes.

DNA double helix

DNA double helix structure

Most functional sequences within the DNA are referred to as genes. Many genes contain the instructions (via the order of the As, Ts, Cs and Gs) that tell the body what proteins to manufacture[4]. Human nuclear DNA[5] contains tens of thousands of functional DNA sequences, and the sum total of all the genes in human DNA is considered the human genome. The study of the human genome is called human genomics.

There are some clear associations between disease and mutated genes; the most familiar may be that of breast and ovarian cancer and the genes called BRCA1 and BRCA2. Mutations in the BRCA genes can prevent the body from producing proteins that suppress tumor growth. Rodríguez, et al. (2014:97) point out that in the 1960s and 1970s, “prior to the genomics era,” certain human leukocyte antigen (HLA) genes were associated with specific autoimmune conditions. Over the last decade, genome-wide association studies (GWAS) have sought to explore the complete human genome to identify the genetic loci[6] most frequently associated with a particular phenotype[7]. For example, GWAS have identified correlations between celiac disease, an autoimmune disorder, and mutations in genes called HLA-DQ2 and HLA-DQ8.  But how can genotype-phenotype associations such as these be evaluated or conducted in an evolutionary context to better understand and predict not only who is susceptible, but why certain people are susceptible to particular diseases? And what is the role of evolutionary genomic medicine (EGM) in improving diagnosis and treatment?

Integrating medical genomics and evolutionary medicine

In an age of companies like 23andMe[8], more people are aware of connections between genotype[9] and phenotype; however, the general public may not realize just how much is yet to be understood by researchers about the full extent of genotype-phenotype relationships, particularly with regard to disease susceptibility and/or adaptation. In their review article, Rodríguez, et al. explain why EGM is still a nascent discipline and requires novel approaches to more fully develop as a field of research.

As Rodríguez, et al. discuss, there have been successful cases in evolutionary genomic medicine – for example, the research and discoveries regarding sickle-cell anemia and lactose tolerance. So, why is it not common sense and commonplace strategy to interface genomics, evolution and medicine to study and better understand human diseases? Rodríguez, et al. (2014:98) discuss two “glaring gaps in our knowledge: the twin dissociations between health and fitness and between genotypes and phenotypes.” Fitness refers to reproductive fitness—the primary measure of success in the world of living organisms. An individual is “fit” if he or she has offspring and those offspring can also have offspring (more healthy, viable offspring equates to greater fitness). Hence, “survival of the fittest” refers to survival of those members of a population who successfully reproduce, thereby passing on their genes to future generations. The authors point out that fitness may or may not be affected by health and disease in some circumstances; so, adaptive (or maladaptive) explanations for diseased states can be difficult to identify or test. Additionally, what we now consider diseased states—those that are detrimental to health and/or fitness in some or all modern human populations—may have been adaptive phenotypes or evolutionary trade-offs in the past (i.e., the Pleistocene).

A deeper awareness of the relationships between genotype and phenotype and between health and fitness are needed to further advances in EGM, but there are steps that can be taken today to elucidate the etiology, estimated occurrence, diagnosis, and treatment of human disease in light of evolutionary biology.

 

[1] DOI: 10.1016/j.gde.2014.08.009

[2] See Nesse, R. http://www.randolphnesse.com/articles/darwinian-medicine for a list of useful articles and books about evolutionary medicine.

[3] Some cells, in particular red blood cells, which lack a nucleus, do not contain chromosomal DNA.

[4] Genes can also turn on and off, or regulate, other genes.

[5] Organelles called mitochondria also contain DNA, referred to as mtDNA.

[6] A genetic locus is a specific location in the DNA; loci are typically distinguished by letters and numbers that identify their position on a chromosome.

[7] Phenotype refers to the form or function of an organism’s body systems (e.g., eye color or whether or not a person exhibits the symptoms of a disease).

[8] 23andMe.com is a DNA analysis service now required by the U.S. Food and Drug Administration to report only on ancestry; prior to this regulation, the company also provided genetic information related health and disease susceptibility.

[9] A person’s genotype is determined by which versions, or alleles, of genes the person possesses.


Why Dwarfism? Celebrating #Hobbit10

For an updated version of this bit of writing, please see my 2016 blog post at SAPIENS.org: http://www.sapiens.org/blog/animalia/island-dwarfism

 


An Open Bar Graph to the Supreme Court

In May, 2009, a USA Today survey conducted by the Gallup Organization*asked 608 U.S. adults age 50 and over if marriages between same-sex couples should or should not be recognized by the law as valid, with the same rights as traditional marriages.

Of those 608 U.S. adults age 50 and over, 35% responded that same-sex marriage should be recognized by the law as valid.

62.7% of them responded that same-sex marriage should NOT be recognized by the law as valid.

In the Fall semester, 2010, and Spring semester, 2011, I obtained the following responses to an anonymous online survey of 468 U.S. adults age 18-22.

Same sex marriage

Survey results based on 486 anonymous online questionnaire responses. Sample: U.S. adults, ages 18-22 inclusive, enrolled in at least one course at a large state university, who graduated from a public high school in the U.S.

Bar Chart Citation: Schrein, C.M. (2013) Unpublished data. paleophile.wordpress.com (Access date).

*Acknowledgement: The survey results reported here were obtained from searches of the iPOLL Databank and other resources provided by the Roper Center for Public Opinion Research, University of Connecticut. Citation: Gallup/USA Today Poll, May, 2009. Retrieved Mar-27-2013 from the iPOLL Databank, The Roper Center for Public Opinion Research, University of Connecticut. http://www.ropercenter.uconn.edu.proxygw.wrlc.org/data_access/ipoll/ipoll.html


What is evolution?

Evolution is a phenomenon.

A phenomenon is an occurrence, a circumstance, or a fact that is perceptible by the senses (Source: http://dictionary.reference.com/browse/phenomenon, accessed Sept. 17, 2012).

What humans perceive is that populations of living organisms have changed and are changing over time.

“The theory of evolution” is shorthand for the set of explanations that seek to explain the phenomenon of evolution. Sometimes “the theory of evolution” is also called “evolution,” and this can be confusing.

Really, the theory is “the theory of evolution BY natural selection, genetic drift, gene flow and mutation.” In science, a theory is a set of well-tested hypotheses and repeatable experiments that together provide an explanation for a phenomenon.

Again, evolution is the phenomenon.

Scientists have demonstrated that the processes, or mechanisms, of natural selection, genetic drift, gene flow and mutation, together explain WHY and HOW the phenomenon of evolution occurs.

If you want to be clear, you should use “evolution” to refer to the perceivable fact and “the theory of evolution” to refer to the scientific explanation for why and how evolution occurs.

To be even clearer, you should say, “TTOEBNSGDGFAM” for “the theory of evolution by natural selection, genetic drift, gene flow and mutation.” Pronounce that any way you like, I suppose.

There are not currently any scientific alternatives to TTOEBNSGDGFAM.

So, any legislation that states that public school teachers should be able to teach alternatives to TTOEBNSGDGFAM in their science classrooms is bad legislation that is not based on valid science.

Public school science teachers who state in their classroom that evolution is not a real phenomenon and/or promote (or denigrate) non-scientific views regarding the origins and diversity of life on Earth are at risk of violating the Establishment Clause of the First Amendment of the Constitution (i.e., breaking the law).

p.s. The theory of gravity seeks to explain the phenomenon of gravitation.


Why Intro Bio Should Blow Your Mind…and Why It Probably Doesn’t.

Hey, Mom and Dad,

Classes are going ok, I guess. I dunno. I thought I liked biology, but I really don’t. Now I’m not sure what I’m going to major in. Sigh. It’s not that it’s hard, really, I just don’t get all these stupid experiments we’re doing because we go so fast and just follow all the stupid steps in the lab manual and I don’t even learn anything. And the professor goes so fast and the lectures and the labs don’t match up with each other. I feel like I’m in high school biology again, but there’s just 100x more stuff to know. Whatever. I like that art class I’m taking. Maybe I’ll major in that. Maybe if the other kids in my bio class actually cared about what we’re learning, it would help, but they don’t. And the teacher is always so grouchy. She’s a grad student or something (you went to grad school, right, Mom?) and always seems tired. I thought I wanted to do the cancer research thing, but it just seems so unrealistic now. Grr…can’t wait to come home for my birthday.

Love,

me

vs.

Hey, Mom and Dad,

Classes are going really well. I can’t believe I’m saying this, but I actually think biology is my favorite class. Who knows, maybe I can be a doctor or something one day! I have a pretty good teacher and the lab is really fun. You’re not gonna believe this. Last week we learned how to extract DNA from our own cheek cells!! It was awesome. My group made a few mistakes, but by the third try we got it and we were even able to compare our DNA on this thing called a gel that used electricity to move the DNA. It was really cool. This week we learned how to put DNA from one organism into the cells of another organism! It’s like I’m a bioengineer! Next week, we’re going to take the DNA from jellyfish that glow green under a black light and put their DNA into bacteria cells (the bacteria are E. coli, but don’t worry, I won’t get sick from it!) and then the bacteria will glow green, too, if we do it right! (Remember the green glowing bunny on that episode of Sherlock on PBS!? It’s just like that!) But first we have to figure out how to do it. That’s the best part — figuring it out. My group is pretty good and messes up a lot, but we usually get it right before the other kids in the class, which appeals to my competitive side! I can’t believe how much better this class is than I thought it would be. It helps that the lab instructor is really enthusiastic and takes her time to explain stuff to us. Some of my other teachers aren’t like that. And the best part is, she explains why this is important. We’re not just doing stuff for the sake of doing it. She’s a grad student and she actually uses this stuff in her Ph.D. research. I mean, she said one day I could probably work in a lab doing cancer research or something! Wouldn’t that be awesome? I could cure cancer! Woo! Gotta run. Lots of laundry to do.

Love ya!

me