[T]wo subjects which moved my Father perhaps more deeply than any others were cruelty to animals & slavery – his detestation of both was intense, and his indignation was overwhelming in case of any levity or want of feeling on these matters.  – William Darwin

The trick to finishing books this year is getting up early, apparently.  I managed to get through the last four chapters of Darwin’s Sacred Cause this weekend while the baby slept. In the process, I’ve had to come to terms with  the disquieting beginnings of my own discipline and the bloody and violent antecedents of the town I’ve called home for the past dozen years.

Charles Darwin and Abraham Lincoln share a birthday, but they also share a tumultuous period in history. I’ve always been struck by the realization that Origin of Species was published just a few short years before the Civil War. After reading Darwin’s Sacred Cause, I get the idea that it was not coincidental.  Yes, Darwin sat on his big idea for 20 years, publishing travel journals, works on geology, and a four-volume monograph on barnacles. Why barnacles?  First, to document the amount of variation present in species, which natural selection requires to operate; and second, to establish himself as a knowledgeable naturalist in the eyes of the Royal Society, and provide the credentials needed to discuss his theory. In addition, describing the complete lineage of these marine arthropods provided an example of common descent. Barnacles were a proxy for a much more controversial topic – human variation.

Not science

Human variation is what I study as a biological (or physical) anthropologist. Physical anthropology has its roots, at least in part according to the authors, in phrenology. That’s the pseudo-science of determining temperament from the shape of the skull.  Not surprisingly, given that phrenology developed in Europe, Europeans were said to have the most refined skulls, and phrenological findings were used to justify slavery, something Darwin’s entire family was against.  Darwin would not have been impressed with the physical anthropologists of his day, especially in America, where differences in skull morphology were seen as “proof” of a polygenic origin of humans. According to the polygenists, each human “race” had its own pair of progenitors and were separately created, an idea used to justify all sorts of atrocities, since non-Europeans were seen as less than human. Darwin held the monogenist view, and saw all peoples as descended from a common ancestor, meaning they were all worthy of being treated with dignity and respect, and slavery was unjustified.  Actually, he took it farther than that, and saw a common ancestor for all living things.

It is absurd to talk of one animal being higher than another.–We consider those, where the cerebral structure/intellectual faculties most developed, as highest.–A bee doubtless would when the instincts were. – Charles Darwin

He spent a number of years studying pigeons, just to demonstrate that all the fancy breeds (“races”) descended from a common ancestor. Another proxy for human variation.

Darwin’s Pigeons – from Variation in Animals and Plants under Domestication (1868), with the common ancestor, the rock dove, in the center.

The tension between these two worldviews played out in my hometown, before the Civil War even started. In 1856, Sheriff Samuel Jones led a pro-slavery posse into Lawrence, Kansas, which had been established by abolitionist settlers two years before, sacked the town, burned the Free State Hotel, smashed the presses, and killed an antislavery supporter.

The ruins of the Free State Hotel

Darwin’s mentor and friend, geologist Charles Lyell, who encouraged him to publish his ideas on natural selection, was a Southern sympathizer. The Anthropological Society of London was founded in 1863, in the midst of the Civil War, with three Confederate agents on the council, whose sole purpose was to push a pro-slavery agenda.

Plaque marking the site of the Free State Hotel, downtown Lawrence.

That’s what Darwin was up against.  Not just other naturalists, but Victorian society. No wonder he waited two decades to publish.

My discipline has come a long way since Darwin’s day.  The American Anthropological Association’s “Statement on Race and Intelligence” states in part:

WHEREAS all human beings are members of one species, Homo sapiens, and

WHEREAS, differentiating species into biologically defined “races” has proven meaningless and unscientific as a way of explaining variation (whether in intelligence or other traits),

THEREFORE, the American Anthropological Association urges the academy, our political leaders and our communities to affirm, without distraction by mistaken claims of racially determined intelligence, the common stake in assuring equal opportunity, in respecting diversity and in securing a harmonious quality of life for all people.

And the American Association of Physical Anthropologists has their own “Statement on Biological Aspects of Race,” which says:

Physical, cultural and social environments influence the behavioral differences among individuals in society. Although heredity influences the behavioral variability of individuals within a given population, it does not affect the ability of any such population to function in a given social setting. The genetic capacity for intellectual development is one of the biological traits of our species essential for its survival. This genetic capacity is known to differ among individuals. The peoples of the world today appear to possess equal biological potential for assimilating any human culture. Racist political doctrines find no foundation in scientific knowledge concerning modern or past human populations.

–

Image Credits:

Ryan Somma’s flickr stream

Wikimedia Commons

Dr. Steven M. Carr’s website

The potential grad student explained that she was concerned about waiting until she finished her degree, as her grandmother had two children late in life with Down Syndrome, and she didn’t want to run the risk of a complicated pregnancy by waiting too long.  The current grad replied, “If you want a complicated pregnancy, try having a kid while in graduate school.”

I can see her side, she has three kids ages 5-1, was teaching during all three of her pregnancies, and took at most 6 weeks off (with no paid maternity leave). As Dr. Isis and Arlenna have lamented, campus childcare here is something you should sign up for about 2 years before you plan to conceive, so the chances of being able to have your infant on campus with you are slim.  On the other hand, your schedule as a grad student, even if you are teaching, is generally more flexible than a 9-5 job, and allows for tag-team parenting.

In the case of this particular student, she’s graduating in May, getting married over the summer, and moving to a new state to start grad school in the fall, where she’s planning to get a Master’s degree and then go to another institution for her PhD.  My advice to her would be to wait, maybe until she gets her Master’s, before having kids.  She’s young, there really is no rush. My husband and I were married for four years (and together for nine) before my oldest was born the summer before our last year of undergrad.  Taking the time to establish our identities, both as students and as a married couple, helped us be better parents, I think. And if the women in our lab are any indication, waiting a little while doesn’t guarantee a risky pregnancy (despite the “advanced maternal age” code on my OB chart). Five of those fourteen babies were born when their moms were over 35.

Including this one.

]]> http://freethinkersasylum.com/2010/03/reproducing-in-grad-school/feed/ 5 http://freethinkersasylum.com/2010/03/freethinkers-2010-bookclub-update/ http://freethinkersasylum.com/2010/03/freethinkers-2010-bookclub-update/#comments Mon, 01 Mar 2010 06:52:08 +0000 Kris http://freethinkersasylum.com/?p=631 So we’re coming to the end of February, and I’m still reading Darwin’s Sacred Cause, having rechecked it from the library – twice.  Not able to get as much pleasure reading done as I had planned, especially this semester.  I’m taking three classes (Epidemiology, Biostats II, and Grant Writing), plus developing my own research projects and participating in a faculty development program.  I’m also in the process of prepping for two conferences this Spring, and writing up portions of my dissertation for publication (looks like 4 articles). All great things that I’m thoroughly enjoying, but I still have a couple of chapters to go on January’s book.

Not that I haven’t gotten any reading done.  I have a bit of a commute, so I’ve tapped into the audiobook offerings at my local library, and this month I listened to Emma by Jane Austen, and Full House by Steven Jay Gould.  I wish more of the books for this year’s book club were available in audio format, as it would make better use of my time.

Going forward, I think what I’ll do (at least until summer) is choose two books for the month, and pick one to read.

The picks for March are:

Remarkable Creatures: Epic Adventures in the Search for the Origin of Species

Lives in Science: How Institutions Affect Academic Careers

***

Speaking of Spring conferences, the first one is coming up next week.  I’ll be tweeting from the Interdisciplinary Exploration of Migration (#kumigration).

• The sequence analysis was conducted from a sample of human hair that was recovered from permafrost, and the DNA was recovered from the hair shaft, not the root. This opens a whole new avenue of paleogenomic research.
• SNP analysis shows that the hair belonged to an individual who carried a number of traits frequently found in modern Asian populations, including shovel-shaped incisors and dry ear wax.
• 85-87% of the genome was sequenced – phenomenal coverage given the age of the sample.

Chukchi women (seated front right), circa 1906

• Population genetic analysis (principle component analysis of genetic distances) revealed the closest relationship between the Greenland genome and the Chukchi, a population in northern Siberia, suggesting a recent migration (in the last ~5,000 years) from Siberia across the Arctic to Greenland. This would be in addition to the three migrations (Amerind, Na-Dene, and Eskimo-Aleut) traditionally hypothesized for the peopling of the New World.

Rasmussen et al. (2010) Figure 3b. PCA of populations - Saqqaq genome indicated by star.

I was disappointed that more North American samples weren’t included in the analysis.  With the exception of populations from West and East Greenland, Na-Dene in western Canada, and Aleuts, the only other Native American groups are from Central and South America. But overall, this study demonstrates how ancient DNA analysis can help answer historical questions.

–

Disclaimer: One of the co-authors (Michael Crawford) was my graduate mentor. Which, for me, makes this study even more awesome.

Image credit: Wikimedia Commons

Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M., Wang, Y., Raghavan, M., Campos, P., Kamp, H., Wilson, A., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, E., Binladen, J., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T., Grønnow, B., Meldgaard, M., Andreasen, C., Fedorova, S., Osipova, L., Higham, T., Ramsey, C., Hansen, T., Nielsen, F., Crawford, M., Brunak, S., Sicheritz-Pontén, T., Villems, R., Nielsen, R., Krogh, A., Wang, J., & Willerslev, E. (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo Nature, 463 (7282), 757-762 DOI: 10.1038/nature08835

The best advice? Just do it. If that’s what your passion is, go for it.

When I was a very little girl, I remember my father coming to pick me up from daycare one day. I was in tears, and when he asked me what was wrong, I told him that my teacher had asked all of us to tell what we wanted to be when we grew up. When I said that I wanted to be an astronaut, my teacher said I couldn’t because I was a girl (this was pre-Sally Ride). My father confronted the teacher, and informed her that his daughter could be anything she wanted to be. Knowing that a trusted adult believed in me gave me the confidence to pursue my dreams. Just one of the reasons I adore my dad.

Sally Ride - First American Woman in Space

My high school biology class turned my attention from outer space to DNA. After those Punnett squares, I never looked back. But that confidence in my abilities never wavered.

***

Also, the National Postdoctoral Association posted their 6 Core Competencies for postdocs:

to offer guidance to individual postdoctoral scholars who must seek out relevant training experiences, in collaboration with mentors, institutions, and other advisors who provide this training…These competencies are meant to serve primarily as: (1) a basis for self-evaluation by postdoctoral scholars and (2) a basis for developing training opportunities that can be evaluated by mentors, institutions, and other advisors.

Postdocs can use the checklist to identify areas for future development, and as a springboard for discussion with their mentors.

***

Finally, an article from Science Careers – Reaching gender equity in science: The importance of role models and mentors.

One of the factors that has inspired more women to pursue scientific careers has been having examples of successful women who have done the same.

I feel very fortunate to have a team of mentors, one of whom is a very prolific and successful scientist, woman, and mother.  When I started graduate school, my concern was mostly with the academics. Completing my courses, making sure I had enough time in the lab to get my research done, writing.  I hadn’t really considered the importance of mentoring in establishing my career. I can see now that it is essential, and especially beneficial to have a group of senior researchers interested in your professional development, even if their advice seems sometimes contradictory.  And while this may not be the case for some postdocs, I know that they all genuinely have my best interests in mind.  I’m beginning to see my graduate training, and by extension my postdoc, as an apprenticeship.  A position where I learn how to be a scientist, with all the core competencies that entails.

Click here to view the embedded video.

• Scitable – “a free science library and personal learning tool” from Nature. The current focus is genetics (my favorite topic).
• Women in Science – from the Smithsonian Institution Archives, a collection of “images documenting women scientists and engineers from around the world, most of whom were pioneers in their respective fields, or were the first women to receive advanced graduate degrees in their discipline.” The photo below is of Dr. Mary N. Crawford, who discovered the rare Lutheran a-b- blood type.
  

  Mary N. Crawford

  The entire photo collection is an inspiration to women in science.

• Lifeworks E-Mentoring – from the National Institutes of Health Office of Science Education, “a free e-mentoring program that helps high school and college students who are interested in behavioral and social science, biomedical science, dental, and healthcare careers find a mentor.” Sounds like a great place to volunteer if you’re so inclined. What better way to improve science literacy than to help mentor the next generation of scientists?

***

Speaking of science literacy: On the book club front, I’m about 2/3 of the way through January’s book.  It’s interesting but dense reading, and I haven’t had as much time to read while nursing as I thought. Baby keeps grabbing the book.  It’s easier to read while pumping, but that gives me roughly 30 minutes a day. I have had a couple of long waits at the car shop over the last week, so I’m making good progress.  Maybe I’ll be finished by this weekend.

The 19 million citations and abstracts covered by the US National Library of Medicine’s PubMed search engine include nearly 830,000 articles published in 2009, up from some 814,000 in 2008 and around 772,000 in 2007. That growth rate shows no signs of abating, especially as emerging countries such as China and Brazil continue to ratchet up their research.

With that amount of data overload, how is an established researcher going to keep up with relevant work in their field? Nevermind how a new investigator can a handle on establishing a research focus, or a midcareer scientist switch tracks.  That’s where literature mining comes in.  There are several start-up services on the web to help scientists find relevant research, make connections, and generate hypotheses. A few of these are discussed in Lok’s article, but there are many others.

PubMed – My default search engine for research papers, this is the first stop for many scientists.  So let’s try a little experiment.  Searching “alcoholism” generates the following – Results: 1 to 20 of 66827. PubMed does have tools to help you narrow your search.  Say I’m interested in the genetics of alcoholism. Searching “alcoholism genetics” returns – Results: 1 to 20 of 5940. A lot of research to go through. Restricting that search to only publications in the last 5 years, in English, and about humans gives Results: 1 to 20 of 1283. Still a lot of literature, even if you’re only reading the abstracts.

That’s where literature mining can really make a difference.

Scientific Literature Mining Services

• pubget – One of the most time consuming tasks in research is going through the literature and trying to stay current. Add to that most institution’s clunky access to online resources, and the process can be painfully slow.  I can search for articles from my library homepage, but have to go through several extra steps to actually get my hands on the pdf. The “find full text” function in the newest version of EndNote has been a tremendous help in accessing content, but for those researchers at institutions that don’t provide that service (and even those that do but want an additional resource), pubget is a handy tool.  When you create an account, pubget signs in to your institution and allows you to search the subscribed resources. When you find a reference you want, just click the pdf icon and there it is. No clicking through to content provider websites. You can tag references as “keepers” to come back to them later, or search for the newest articles from a particular journal. Unfortunately, it doesn’t allow you to annotate the pdfs. Not yet anyway.

Click here to view the embedded video.

• GoPubMed – A search engine where “your keywords are submitted to PubMed and the resulting abstracts are classified using Gene Ontology and Medical Subject Headings (MeSH).” So using our example search “alcoholism genetics” pulls 5,940 abstracts from PubMed. What’s different about GoPubMed’s results is the navigation panel.

GoPubMed top terms

You can click the check boxes next to the relevant terms. Restricting the search to “genetic predisposition to disease” gives 720 references. Under the Knowledge Base > Named Groups category, you could restrict it further to only studies using adult subjects, or to exclude studies in children. GoPubMed provides additional information on your search topic as well, including top authors (who’s doing the research) and top journals (who’s publishing the research). There’s even a network of top authors, so you can see how they collaborate on your search topic.

Author network for genetic predisposition to alcoholism.

Philanthropologist might recognize a name toward the top of that network. A useful tool for finding potential collaborators.

• NextBio – A freemium service (basic is free, pro is subscription) that allows researchers to set up a profile, but also has a database for lit mining.  Searching for “alcoholism” in NextBio brings up several relevant sources, including associated genes, literature, researchers, news, even clinical trials.
  

  NextBio genes associated with alcoholism

• EbiMed – analyzes PubMed results “to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species.” Searching “alcoholism” here turns up a table of links to various sources, including proteins, genes, and biological processes related to the search term.
• PubGene – specifically for finding genes, PubGene draws a network of genes associated with a particular keyword.
  

  PubGene network for alcoholism

This network is searchable. Clicking on a gene allows you to browse the literature associated with that gene, in addition to highlighting associations with other genes.  As a geneticist, this tool has considerable utility.

• PubAnatomy – “integrates [the] Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data.” A keyword search for “alcoholism” lights up regions on the brain map associated with the disease.

PubAnatomy brain map

And clicking one of those highlighted regions displays the relevant references for that brain structure, as well as genes that are active in that region.

• Neuroscience Information Framework – “An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Information Framework advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.” This tool can search the full text of articles (at least those that are open source), rather than just the abstract. But it does much more.

Second from the bottom, NIF diplays grants related to your search. You can read the abstract, see who is doing research on your topic, and which granting agencies are funding that research. Useful info when preparing your own proposals.

All of these tools help scientists sip from that firehose, giving different ways to access and interact with the data. What an exciting time to be starting a career in science.

–

Lok, C. (2010). Literature mining: Speed reading Nature, 463 (7280), 416-418 DOI: 10.1038/463416a

The researchers compared STR variance for this haplotype in several European populations and three Turkish groups, and found a significant correlation (R² = 0.358; p = 0.004) between that variance and the longitude of the population (i.e., how far east the population was located).

Balaresque et al. Figure 1C. Distribution of haplogroup R1b1b STR variance

From the plot, the greatest variance (indicated by the most intense color) within haplogroup R1b1b2 is found in Turkey. They also calculated the time to most recent common ancestor (TMRCA) using STR variance, and found that the oldest lineages, dated between 7,000-7,989 years, are also in Turkey.  The youngest lineage is in Cornwall, dating from 5,460 years ago. The researchers inferred that R1b1b2 originated in Anatolia and spread rapidly into Europe with the spread of agriculture.

Balaresque et al. Figure 1B. Frequency distribution of Haplogroup R1b1b2. More intense color indicate higher frequency.

A couple of things strike me about this study. 1) Haplogroup R1b1b2 reaches it’s highest frequencies in Western Europe, up to 85% of Y-chromosomes in Ireland belong to this haplogroup (Figure 1B). And there are two populations, one in Germany (GE1) and one on the northwest coast of France (FR2), with TMRCA dates in the range of the Turkish dates (7,282 and 7,384 years, respectively). 2) The Turkish data come from Cinnioglu et al. (2004), and consist of samples collected in 90 cities from blood banks, paternity clinics, and university students classified into geographical areas by self-reported “paternal residential heritage” (128).   There is the possibility of introducing error into the sample from this self-reported residence. It’s also possible that the high variance present in the Turkish R1b1b2 lineages reflects more recent immigration.  In addition, TMRCA applies to the molecule, not the populations in which it is found, so while a particular lineage may be 7,000 years old it does not mean that the population has been in that particular location for that length of time. And the authors note, in the supplemental information, “…there is a tendency for TMRCA to be underestimated when single-haplogroup data are considered.”

It’s an interesting hypothesis, though, and I’m curious to see what analyses with additional populations will show.

–
Balaresque P, Bowden GR, Adams SM, Leung HY, King TE, Rosser ZH, Goodwin J, Moisan JP, Richard C, Millward A, Demaine AG, Barbujani G, Previderè C, Wilson IJ, Tyler-Smith C, & Jobling MA (2010). A predominantly neolithic origin for European paternal lineages. PLoS biology, 8 (1) PMID: 20087410

Cinnioğlu C, King R, Kivisild T, Kalfoğlu E, Atasoy S, Cavalleri GL, Lillie AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O, Cavalli-Sforza LL, & Underhill PA (2004). Excavating Y-chromosome haplotype strata in Anatolia. Human genetics, 114 (2), 127-48 PMID: 14586639