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

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

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

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

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

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

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

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

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

Cerebellar neurons by Ramón y Cajal

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

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

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


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


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

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

Resources for finding a career away from the bench

If you are a graduate student or postdoc in the sciences, you are likely aware of the "PhD problem"*, the academic bottleneck caused by an increasing number of PhDs with a concomitant decrease in the number of tenure track positions. Unfortunately, the statistics suggest that the problem is not likely to get better any time soon. In fact, the issue has gotten so bad that even the mainstream media has picked up the story. The default pathway is no longer PhD to postdoc to tenure track; this great infographic from ASCB  (see below) suggests that the tenure track is the real alternative career. While the statistics may seem grim, I think there is some good news: the academy is starting to wake up to the harsh reality**. In the past, postdocs and grad students complained that PIs were only capable of training them to become a PI. Increasingly, PIs and universities are aware of the prospects for their trainees and they are starting to find ways to help guide them for a number of careers.

ASCB.org infographic

As a Scientific Editor, I often get questions from graduate students, post docs, and PIs about my transition away from the bench. After a recent chat with a grad student at a meeting, I decided it was time to put together a post of useful resources for finding a career away from the bench. Because I am in publishing, my links tend to focus on that path, but all of the websites I list below have articles about other career paths as well. 

The first two places you should be looking for a job in science are Nature Jobs and Science Careers. Both websites have listings for a variety of careers paths as well as an array of great content for helping you navigate your job search. Whether you are just starting to think about your future directions or preparing for an interview and negotiating your salary, there are relevant articles for you.

Nature Jobs has a very well-organized site. I recommend spending some time there to explore their content, especially their blog and their career toolkit. This article from their blog gives a great general overview of the types of jobs available to people with a PhD in the sciences. Be sure to check out The Postdoc Series for articles aimed at post docs at different stages of their careers. Nature Jobs also hosts a career expo, which I have read good things about.

On the Science Careers website, check out the tips and tools and explore the articles in the Career Magazine; they have more than 10 years of content available. By far the most valuable resources I found when I was searching for my current job were this collection of articles about science writing and editing and this 2002 article "Careers in Science Editing". These give a very general idea of what different types of scientific editing jobs entail. This informative article from Cell Press' Debbie Sweet describes the specifics of working for a reviews journal or a primary journal. Once you find something of interest, the related article feature (which seems to be available for newer articles only) will help you find more to read.

Societies relevant to your field will likely also have career resources available. For cell biology, ASCB's Career Development section has a number of articles available. My favorite among these is the Career Publications, which are free to download as PDFs. The ASBMB also has some useful articles, like these Career Case Studies.

The Chronicle of Higher Education is generally best for searching for a faculty job, but they also have some excellent articles on non-academic jobs, such as "The PhD's Guide to a Non-faculty Job Search".

If you are feeling isolated in your decision to leave the bench, you can find some comfort by reading some "quit lit". It seems many scientists find it cathartic to share their story;  indeed, I have written my own quit lit posts on this blog (here and here). Over the years, I have read many posts in this genre; I particularly enjoy finding updates, which tend to have a happier mood than the original post. Eva Amsen's (Outreach Director for Faculty of 1000) "Five Years Later" was very positive and shared some useful links and tips. Likewise, SciCurious (a science writer in neuroscience) tells her story in "The system failed me. It should have failed me sooner." 

To learn more about a career in science writing, read Ed Yong's collection called "On the Origin of Science Writers" where a variety of working science writers share their journey as well as tips on how to make a living writing about science. The National Association of Science Writers also has some great content in their resources section.

In short, these links should give you some ideas of the paths that are available to you. Hopefully you also have some valuable resources at your institution (e.g, postdoc association or a career development office). If you find other useful links, please share them in the comments. 

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* There are numerous suitable links that describe the problem; I have chosen the one that I first discovered. Nature had a 2011 special issue called The Future of the PhD, which included the great story The PhD factory.  

** The Future of Research symposium has been putting together meetings to find solutions to these problems.

Altmetric Explorer as a complement to your news reader for keeping up with exciting new research

Altmetric is one of several tools currently available to track the usage of published articles via social media, mainstream media, and reference managers. The Almetric score is calculated by giving different weights to each mention of a published article, so that a newspaper story counts more than a blog post, which is worth more than a tweet. The benefit of alternative metrics is that it can give researchers instant feedback on the impact of their article. Alternative metrics can also be used by publishers and editors to help determine what could be the next high impact story. Importantly, it is unclear whether Almetric scores correlate with citation rate. At this time, only 15-25% of papers receive any Almetric score, depending on the field.  

 Altmetric Explorer is a new tool from Altmetric for examining the impact of articles using a variety of search parameters. You can search all mentions of papers to see what the most popular stories may be at any given time. By creating workspaces for individual searches, you can have the results updated by email on a regular basis. You can export all the articles or export the Altmetric data to Excel, allowing you to sort for papers based on an individual metric (e.g., Mendeley or blog posts). Workspaces could include searches of a particular set of journals to see all the high-attention content in one space. Alternatively, a search with a keyword can indicate where the most attention-grabbing stories in a particular area are being published. 

Altmetric Explorer is easy to learn to use and the help desk has been very responsive, giving answers in 24 hours. This is a for-fee service, but as an Elsevier employee, I have free access to a publisher account. I started experimenting with Altmetric Explorer as a tool for content development. While it has not been helpful for that purpose, I have found it to be a nice complement to my news reader/RSS feed for finding new, interesting stories published in the journals that I normally follow.