STEMinist Profile: Christine Clarke, Research Associate, Microbiology

Oct 12 2012 Published by under Uncategorized


Christine Clarke, Research Associate (Microbiology)

Taxon Biosciences

What inspired you to pursue a career in STEM?
Both of my parents are scientifically-minded – my father has a degree in biochemistry and my mother has hers in kinesiology – and they did a good job of instilling my siblings and me with a sense of wonder about the natural world. Not only a sense of wonder, but a sense that there were answers: answers that we were equipped to find ourselves. Equipped with those mental tools, it became irresistible to try and find the answers.

As soon as I took high school biology, everything clicked with me and I knew that was what I had to study. Nothing was more inspiring or more meaningful to me, so I knew it was my calling. Luckily, biology is still as exciting and fulfilling to me today as it was when I was a child.

What is the coolest project you have worked on and why?
The coolest project that I have worked on has been a microbial ecology study. Science has become very interdisciplinary these days, so don’t be surprised when I say that we were using next gen genetic sequencing techniques to study microbes on the community-level (rather than on the individual species level) in order to better understand the geology of the area. Microbes have an ecology going on just like the traditional “a lion eats a zebra” example.

We used the microbial community to sense what was happening in the environment both chemically and geologically, because geology affects microbes while microbes affect geology. Using next gen sequencing, we were able to identify certain core “consortia” of microbes which always seemed to co-occur (they all seemed to need each other to survive).

Using targeted isolation techniques, we were able to find and grow all the species in one such consortium under laboratory conditions, and then study their metabolisms both individually and as a community. We were able to produce a carbon-flow model of what happens in the environment, and how those microbes interacted to produce some of the mineralization we observe and by-products they produce.

The study of biogeochemistry is becoming very important, especially now as we learn more about things like the nitrogen cycle and the methane cycle, both of which are driven by microbes but have global-scale effects.

Role models/heroes:
Melissa Jurica is one of my major role models. She is a brilliant woman who has been able to start a family and stay in academia – no small feat. It is true that in the USA, STEM women tend to leave academia for industry if they want to have a family and/or children because industry is more accommodating towards maternity. This shouldn’t be the case, but it is.

A few more of my heroes include: Dorothy Hodgkin because, really, X-ray crystallography is intense and never fails to impress me; Stephen Jay Gould and Richard Dawkins for their work in evolutionary biology and for helping the public and non-specialists to understand and conceptualize the major points of their field; Margret Sanger for helping forward birth control advocacy and sexual rights; and Betty Dodson for helping women accept and embrace their sexuality.

Why do you love working in STEM?
I love working in STEM because it gives me a chance to explore the world around me and make discoveries about life itself. It is a very gratifying experience to contribute to new data and discoveries, and I think it gives me a healthy sense of self-worth and pride in my abilities.

When months or years of work suddenly starts to fall into place and you start making sense of all your meticulously-collected data: that is the greatest feeling in the world. I also love that it forces me to keep learning new things every day, and that I am always finding new things that amaze me or blow my mind.

Advice for future STEMinists?
If you get bogged down by the day-to-day drudgery of STEM work, take some time to step back and look at the big picture and remind yourself of the big questions you are asking. Sometimes STEM work can feel tedious, especially since there are times when you must focus so much of your brainpower onto a tiny (yet crucial) portion of your work, and that can get both mechanically tedious and mentally exhausting.

If you find yourself in that situation, taking a short break to reflect on these things will give you a better perspective, and instead of feeling stuck you can recognize that your work has not been mundane. Much of the progress in STEM builds up slowly over time, which is why looking back is helpful.

I will also say that you should really work on building a solid foundation in math and computers. This might seem obvious but a lot of people (men and women) shy away from math and computers, especially in some of the biological disciplines. However, those fields actually do use a lot of math and computers on a daily basis, so if you beef up your mathematics, you will stand out as being very valuable in your field. Don’t assume that you won’t need mastery of math or computers for any STEM job you want to pursue.

I can guarantee that no matter which field you want to work in, both skills will help you succeed and advance. For example: yes, an ecologist needs to be very good at ecology, but everybody else working in ecology does amazing ecology work as well – that’s why they’re in that field. But if you’ve also taken a class in programming, are familiar in Linux, and are not scared of using mathematics; you’ve got an edge. You’re valuable.

Favorite website/app:
I have two apps that are very impressive and absolutely indispensable:

Sigma-Aldrich’s “Substructure Search” is invaluable to me, and also free to use (they want it to help you buy chemicals from them). They have brought together MarvinSketch, JME Molecular Editor, and ChemDraw (all amazing) in one applet. You can “sketch” an organic molecule, and then have the applet calculate the IUPAC name for what you have just drawn (and vise-versa). IUPAC naming is a good method of standardization, but it can get tricky.

Common names are easier to remember, but are not standardized (and often result in 10 different names for one molecule). This does lead to trouble sometimes! That’s why we all remember our O-Chem professors giving extra credit problems on our homework with a drawing of a very huge and ugly molecule, with the deceptively simple instructions “Give the IUPAC name for this molecule.”

I use this applet for my work all the time, but I can imagine that if I had this as a child, I would have loved to spend hours drawing the weirdest molecules possible, trying to “stump the program.” I think this is a natural tendency kids have, but in the process they would still learn a lot about molecular naming and be entertained by discovering that this atrocity they have just drawn actually has a name.

The ARB Project is another free program that I could not do without. If you have a Linux computer, you can download it and start making phylogenetic trees (the image on their homepage is a good example) at home. You don’t even need to generate your own genetic data to get started, you can download some reference trees of genetic sequences submitted by other scientists from http://www.arb-silva.de/and then start playing with them in ARB. You learn a lot about taxonomy and phylogeny just by playing around with trees in ARB.

Website and Twitter: My personal Twitter account is @Steenaire, and my personal website is www.certainly-strange.com. I mostly blog about personal things or post silly doodles, but recently I have decided to try my hand at science reporting that is accessible and interesting to non-specialists. After reading far too many “evolutionary narratives” in popular science reporting, I decided that if I really wanted anything to change then I should be contributing.

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STEMinist Profile: Alexandria DeWolfe, MAVEN Science Data Center lead

Oct 10 2012 Published by under Uncategorized

Alex Dewolfe_Steminist Profile
Alexandria DeWolfe, MAVEN Science Data Center Lead

Laboratory for Atmospheric & Space Physics (LASP), University of Colorado

What inspired you to pursue a career in STEM?
I've been interested in science ever since I was little, thanks to my wonderful parents and some excellent teachers. My dad was a very early computer programmer - he taught me BASIC on a home-built Sinclair in 1982 - so it's no surprise that I've found myself in a computing job. When I was in high school I took physics and loved it, and decided to major in astronomy in college. I went to Wellesley College, which is a women's college and a great place to do science.

What is the coolest project you have worked on and why?
MAVEN! It's NASA's next Mars mission, launching in November 2013. Ten months later, it'll go into orbit around Mars to collect data about the current and past state of the Martian atmosphere. I manage the Science Data Center, which is kind of like the centralized data library for the mission, where the entire MAVEN team can get all the latest data for doing science. Needless to say, it involves a lot of computing power: we don't have a huge data volume, but everything has to be carefully backed up, and accessible to the team but secured against unauthorized access.

It's really exciting to work on a planetary mission, especially since I joined the mission a couple years ago and will be able to take the data center from the initial design through implementation to daily operations during the mission. Also, I can't wait to go to Kennedy Space Center and watch the launch! Follow @maven2mars on Twitter for more info.

Role models and heroes:
Ada Lovelace, Elizabeth Cady Stanton, and Sally Ride.

Why do you love working in STEM?
I love working in the space program and feeling like my work is part of something really important and exciting. I actually took a break from STEM work for a few years and went to graduate school to study ancient Middle Eastern languages, which was really interesting, but I'm glad to be back in a field with more job opportunities, and I like being able to work on something completely new and innovative.

Advice for future STEMinists?
Working in science is great! There are so many opportunities out there for you if you study a STEM field.

Favorite website or app:
Goodreads and Ravelry, supporting my hobbies.

Twitter: @rocketshipmom - so named when I asked my then-three-year-old son what he thought my job was and he said "Rocketship girl."

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STEMinist Profile: Jarita C. Holbrook, Researcher

Oct 08 2012 Published by under Uncategorized


Jarita C. Holbrook, Researcher
Women and Gender Studies at UCLA

What inspired you to pursue a career in STEM?
My career is really two stages if not three. I hold degrees in physics, astronomy, and astrophysics through my doctorate. At that point in time, I wanted to be an astrophysicist but by the time I finished my PhD, I had changed my mind.

The next stage of my career has been as a social scientist focused on the links between humans and the night sky: Cultural Astronomy. To make the transition from physical science to social science was not easy! I had to learn a new language and way of approaching and analyzing data.

What is the coolest project you have worked on and why?
The third stage of my career is that I am a filmmaker! When I am making documentary films I focus on minority astronomers and astrophysicists. Being a cultural astronomer takes me to amazing places and I talk about the sky and gather information about the sky from everyone I meet; when I am making a film I follow astronomers to cool places and focus on them and their research.

Role models/heroes:
I have many great mentors but role models is more difficult: Anthony Aveni added respectability to Cultural Astronomy and his work is amazing. I love the work of filmmaker Julie Dash, but I have never met her. Angela Davis is my role model for how to always be gracious no matter how famous.

Anthropologist Brackette Williams taught me how to undermine my opponents because they are predictable. Finally, former dean of the UA business college Ken Smith taught me some tricks to being an effective academic leader. All of them I consider to be my role models.

Why do you love working in STEM?
I like being able to develop a hypothesis, design a research project to test it, and then to look at my results to see if my original hypothesis was correct. This step 1, step 2, step 3 that you can always fall back on. What I absolutely love is when I am looking for one thing and I discover another thing!

Advice for future STEMinists?
Being an interdisciplinary scientist is difficult because the academy is rigid so everyone wants to fit you into somebody else's box. However, I think that the most exciting work is occurring in the spaces between disciplines.

Career-wise, I have had to compromise and occupy places where I do not fit intellectually, however I have always learned things important to my research from my colleagues in every situation. I have occupied history of science, applied anthropology, Africana studies, and now women and gender studies not to forget physics and astronomy, too.

Favorite website/app:
I have always been a movie person so nothing beats IMDB and their app.

Twitter: @astroholbrook

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STEMinist Profile: Mónica I. Feliú-Mójer, Ph.D. Candidate in Neuroscience

Oct 05 2012 Published by under Uncategorized

Mónica I. Feliú-Mójer_Steminist Profile
Mónica I. Feliú-Mójer

Ph.D. candidate in Neuroscience at Harvard Medical School and vice-director of Ciencia Puerto Rico

My Ph.D. program is based at Harvard Medical School and my laboratory is in Massachusetts General Hospital. Ciencia Puerto Rico is the non-profit I co-direct as a volunteer.

What inspired you to pursue a career in STEM?
I grew up in Vega Alta, a small town in northern Puerto Rico, where nature was my playground, so I was always curious about how the world around me worked, what the biological basis for events that surrounded me was. While I never really had a scientific role model as a child, my parents were always very encouraging of my interest in science.

When I was 11 years old, someone very dear to me was diagnosed with a mental disorder and upon seeing how that person's behavior was changed as a result of this affliction, I began to develop an interest in learning how the brain works and how it leads to behavior.

At the beginning I thought I would become a physician, because I didn't think there were any other career options in science, until my General Biology professor (the very first scientist I ever met) encouraged me to try a summer research program. After that first research experience I was hooked, and I knew that was what I wanted to do: be a researcher.

What is the coolest project you have worked on and why?
The coolest project I have ever worked on is Ciencia Puerto Rico, the non-profit I've volunteered for during the last 6+ years. Ciencia Puerto Rico is a resource and expert network for anyone interested in science and Puerto Rico. Through its online collaborative platform, Ciencia Puerto Rico brings together members of the greater Puerto Rican scientific community and leverages their knowledge to give back to Puerto Rico and help advance science, research and science education in the archipelago.

Ciencia Puerto Rico has given me the opportunity to give back to Puerto Rico; to connect with scientists and individuals with shared interests, background and experiences; and to mentor younger students (from grade school to college) interested in STEM. Moreover, this project has helped me realize the impact of science beyond the bench and the importance of public engagement with science.

Role models and heroes:
There are many people that fit in this category. I would say that everyone that has taken the time to mentor me at different steps of my career and my life. The best advice I ever got is to have multiple mentors, figure out what they do best and how they do it, and learn from that. The support and advice from my mentors has helped me achieve my goals, and they are the reason I want to pay it forward by mentoring others.

Amongst these people, I have to give a special mention to my undergraduate research mentors, Carlos Jiménez-Rivera and Rafael Vázquez Torres, who really helped shape my scientific interests, gave me the first opportunity to think independently, and to explore my capabilities as a scientist to the fullest.

They were always demanding, but loving and encouraging, and frankly made me fall in love with scientific discovery. My Ph.D. advisor, Josh Kaplan, has also been very supportive of my academic and non-academic interests, and has allowed me to grow and mature as a graduate student and a scientist.

I also have to single out the Ciencia Puerto Rico volunteer team. They are a group of professionals highly committed to the organization's mission and to each other. They are a great source of advice, ideas and inspiration, both at the personal and professional level. We are like a family to me and working with them is a privilege.

Last but not least, my family. They have been a constant source of inspiration, support and encouragement.

Why do you love working in STEM?
Nothing compares to the thrill of discovery and of contributing to the advancement of knowledge. Working in STEM has encouraged me to be curious and think outside the box, something that is definitely helpful in the lab and in life. Also, being a scientist has allowed me to meet people from diverse backgrounds and expertise, and that diversity has enriched my life.

Advice for future STEMinists?

  1. Be passionate about what you do.
  2. Keep open to new directions and think outside the box.
  3. Be a leader.
  4. Have multiple mentors.
  5. Don't be afraid to network. You'd be amazed at the unexpectedly great opportunities that arise from networking.
  6. Believe in yourself and be confident.
  7. Don't let people say you can't or that it is too hard to do it, particularly because you are woman. I was once part of a panel and someone asked me if I ever felt at disadvantage because I was a double minority in science (a woman and Hispanic). My response: No, because I never let that define me. I've never seen myself as a Hispanic woman scientist; I am a scientist that happens to be a Hispanic woman. The way I see it, being a Hispanic woman is an advantage rather than a disadvantage, because of the diverse set of skills, experiences and knowledge that I can bring to the table.
  8. Work hard.
  9. Don't be afraid to ask for help.
  10. Always be curious.

Favorite website or app:
My email! It is an important tool for work, to stay in touch, network. Twitter is my one-stop for news about science, current affairs and issues that I care about. Facebook allows me to keep in touch with family and friends.

Twitter: @moefeliu
Site: www.cienciapr.org

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STEMinist Profile: Suzie Sheehy, Research Fellow

Oct 02 2012 Published by under Uncategorized

Dr. Suzie Sheehy
Research Fellow

I work in the Intense Beams Group of the Accelerator Science and Technology Centre (ASTeC) based at STFC Rutherford Appleton Laboratory where I am supported by a Royal Commission for the Great Exhibition of 1851 Research Fellowship.

What inspired you to pursue a career in STEM?
I find it hard to narrow it down to one particular moment. Lots of people say "it was my teacher" or "I looked through a telescope for the first time and just knew!" but it isn't like that for me. I don't remember the point when I knew I wanted to pursue a career in STEM, I had a lot of interests when I was younger and I was as interested in musical theatre as I was in science! My careers advisors in high school told me I could do anything I wanted for a career—in a way, that was quite empowering.

My choice of subjects at university (where I started out doing a double degree in both Engineering and Science) was based on what I was good at and what I thought would leave as many doors open as possible. Only in second year Physics did I realise that I might be able to pursue a career in research—I still remember when one day I asked a lecturer a question about what he'd shown us and he said "we don't know, actually—that's my research, I'm trying to figure it out." I had some great lecturers who encouraged me to pursue that curiosity. So I guess it was when I realised that physics doesn't have all the answers that I finally got interested!

What is the coolest project you have worked on and why?
The coolest project I've worked on is called 'EMMA', which stands for the Electron Machine for Many Applications. It's a new type of particle accelerator which I refer to as a 'rock-star accelerator' because the way it is designed breaks a couple of really important rules that accelerator experts like to stick to.

I think it's a cool project because it's the first of this kind in the world and many people in the field doubted it would work. During my PhD I got to control the machine hands-on during experimental shifts (not many people can say they've run a particle accelerator, even a small one!) Oh, and it really does work!

Role models/heroes:
Dame Jocelyn Bell-Burnell is definitely a role model for me, she is one of the most respected physicists of our time and meeting and getting to know her a bit during my PhD in Oxford was really inspiring. I also have to say that a number of the London 2012 athletes are also my role models, Mo Farah, Jess Ennis, and loads of others who have proven that if you put in the hard work and have the right support you will see results.

I'm a runner too and training for my first half marathon earlier this year taught me a lot about hard work and dedication, which is now crossing back over into my life as a scientist. If I'm stuck with a problem I now tell myself "if you can run for over 20km you can do this too!", it's very motivating!

Why do you love working in STEM?
There are so many things to love about it! One of my old high school friends recently summed it up nicely for me when she said "While the rest of us sell people things they don't need or spend our lives doing something which will be easily forgotten, you spend your days pushing back the boundaries of human knowledge. In my job I might make a difference to a few people's lives but imagine the difference you can make—it's practically limitless. You have the most amazing job." I was totally humbled.

Advice for future STEMinists?
Do what inspires you and play to your strengths. If you're anything like me you probably have lots of different interests – so don't forget you can combine them in surprising ways! For example, I'd always had an interest in theatre and as a scientist I use my stage presence and vocal techniques all the time when giving public lectures and science shows for schools.

Also, don't be afraid of doing things differently. I approach my research in a slightly different way to the rest of my research group and it took me ages to realise that it's OK, in fact, it's really valuable to have members of a team with different approaches!

Favorite website/app:
I'm a little bit obsessed with Pinterest at the moment—I've been using it to put together ideas for decorating my new house, finding yummy things to cook and even, occasionally, ideas for science demonstrations or interesting bits and pieces.

I'm also loving RunKeeper—it's where I store all my running data so I can check out the statistics like my pace and heart rate and see my improvement, it keeps me motivated.

Twitter: @suziesheehy
Website: www.suziesheehy.co.uk

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STEMinist Profile: Kim Arcand, Science Outreach Coordinator

Oct 01 2012 Published by under Uncategorized

Kim Arcand_Steminist Profile

Name: Kim Arcand

Occupation/Job Title:
Science outreach and visualization coordinator for high-energy astrophysics
Newbie co-author (“Your Ticket to the Universe” coming out April 2013)

Organization:
NASA's Chandra X-ray Observatory, Smithsonian Astrophysical Observatory

What inspired you to pursue a career in STEM?
When I was little, every year I would pick a new career, and they all had something in common: science. Nurse, doctor, astronaut, environmental scientist, veterinarian, microbiologist. My parents were supportive, and each Christmas there would be some special gift, a chemistry set, a microscope, a stellarium. I loved science, or what I thought of as science: the idea of discovering something new, of figuring out puzzles, of contributing to people's lives in some significant way. That first crush never went away.

What is the coolest project you have worked on and why?
It’s hard to pick just one! Can I have two?  I have to start off with the Chandra X-ray Observatory. It's an engineering and scientific marvel. A sister telescope to Hubble, Chandra orbits the Earth out to about 1/3 of the distance to the Moon. The phenomena it studies are exotic – black holes, exploding stars, huge clusters of galaxies to name just a few. And the incredibly beautiful images and the discoveries they lead to are awe-inspiring[1].

Working for Chandra led me down a new path in scientific outreach. I organized a project called "From Earth to the Universe[2]" that brought astronomical discoveries into unique locations – picture large images of planets, nebulas and galaxies set up in public parks, metro stations, shopping malls, art festivals, and even prisons. My colleagues and I created a framework for organizers around the world to easily adapt the free materials for an exhibit in their desired locale.

We started out hoping for a couple dozen exhibits that would be run during the International Year of Astronomy in 2009. We ended up with about 1,000 different sites all over the world, on every continent except Antarctica and translated in over 40 languages. Some of the exhibits are still ongoing today. We could never have personally disseminated astronomy to so many people, but by enabling others we were able to reach exponentially more people.

Role models and heroes:
My mom. Growing up, I watched her juggle kids and family, going back to school for nursing, and working the late shift as a waitress. I would sit near her as she did her anatomy homework on the dining room table, or go with her to the local community college to buy the mammoth-sized books for her class. She made it seem completely normal and doable. I secretly hope that my own son and daughter might feel even a tenth of that for me some day.

Why do you love working in STEM?
Our collective scientific viewpoint is always changing, as new discoveries are made, old discoveries shift, and cultural frameworks evolve. So we're always learning and adapting to new things. It’s exciting to work in a field that is so dynamic, and that touches everything, everyone, everyday in some way. In my day-to-day work, I am most directly involved in astronomy, of course, but science is so much bigger than one specific field. There are connections everywhere.

My colleagues and I are just about to launch a new project that celebrates that fact.  “Here, There, and Everywhere[1]” will explore the connections that exist between the seemingly incongruous - how are a bumblebee, farmer and starburst galaxy related? Can you think of how a neon sign in Las Vegas, an Aurora in Norway, and an exploding star light years away from us might be somehow connected?  The intent of the program is to help to demonstrate the universality of physical laws and the connections between our everyday world and the Universe as a whole.

[1] http://hte.si.edu (Goes live on August 27, 2012)

Advice for future STEMinists?
Find something you're passionate about. Your passion will help you succeed, even if it's something that's difficult. I don’t know how many people can say that science is an easy subject in college, but it wasn't easy for me. At university, I would breeze through my literature courses (I was and still am a Jane Austen junkie), but struggle in my science classes.

I managed to get through the physics, chemistry, microbiology and anatomy courses, but I can vividly recall getting a D in genetics. I had never gotten a D before, and it made me doubt my abilities and that I should even continue with a degree in science, never mind a career.

But I stuck with the degree in biology, rounded out my skill set in computer science to be safe, and eventually found a niche that I was very comfortable in – communicating science with others, and researching how people respond to certain aspects of science (mostly imagery). I had the background to feel at home in the scientific content, but also an understanding that science can be alienating, or frightening, or just plain boring to some.

And to me that is such an exciting opportunity. How can we help others find their niche in science? I'm interested not only in people who might want to pursue a hobby or career in science. I also want to help foster the larger population's perspective on and awareness of science as a whole.

Favorite website or app:
For science sites, I'm in love with the Encyclopedia of Life and for leisure apps, I’m addicted to Brainium's Spider Solitaire, the 2 suit game.

Twitter: @kimberlykowal
Site: http://yourtickettotheuniverse.com/

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Why does a cow have four legs?

Aug 01 2012 Published by under Uncategorized

I think that I have talked enough in these posts about variational and transformational evolution, and so today I will write something about how phylogenies affect the way biologists work as scientists.  Why is the concept of evolutionary history so important in biology?

In one sense, science is about problem solving. We set out to find the answer to a particular question, and in order to do so we have to solve the puzzle posed by that question. So, a relevant point is this: Is problem solving different in the biological sciences compared to the physical sciences (eg. physics and chemistry)? My answer is "yes and no".

To me, there is a way in which they are all the same, and this involves performing some sort of experiment to test any ideas we have that might solve the puzzle. So, as I noted in an earlier post, we all attempt to explain natural phenomena in terms of other natural phenomena.

However, in another way biology is different from physics. First, in biology we have to deal with the fact that organisms respond to their environment, which other physical objects do not do. If I drop a stone then it falls downward, and it will do so no matter where I am on earth. However, if I release a migrating bird it will adjust its flight depending on where it is released. This complicates the study of biology. Second, organisms pass information between generations, via their genes. There is no equivalent concept of inherited information in physics.

The consequence of these differences is that in biology unique historical events can have effects that last for millions of years. Something that happened to one of my ancestors thousands or millions of years ago can still affect me now, because the information about that event has been passed down to me in the genes that I have inherited from that ancestor. There may be no other evidence of that past event except in my genes. No physicist has to deal with this concept — in physics, those past events that have an effect now do so by leaving observable traces in the environment. The laws of physics that operated back then are still operating now, and we can therefore study them now.

This ultimately means that cause and effect can be separated in biology by a great deal of time. The explanation for the natural phenomena that I see now may be a long time in the past. For example, the cause may no longer be important in the modern world but it was in the past. How do I know about its importance back then? The cause may no longer be apparent in the modern world, so maybe I don't even know about its existence. Under these circumstances, even imagining the cause may be difficult. Perhaps most importantly, the cause may be an historical “accident” — a one-off event that has not happened since. We believe that modern biology is actually the result of a whole series of historically unique accidents!

How do I study natural phenomena under these circumstances? This is where a phylogeny comes into play. We use phylogenies as the framework for studying biodiversity, because they take into account the historical component of biological studies. In biology we use them to describe the natural phenomena, to explain them, and to predict them.

Consider the question posed in the title: Why does a cow have four legs? This is a question about explanation, not description or prediction. So, merely describing the legs of a cow is insufficient to answer it, and predicting how many legs the next cow will have is also irrelevant (although it may be interesting in its own right!).

A physicist might attempt to answer this question in terms of balance and stability, particularly while the cow is moving. The idea is that four legs are stable while allowing the animal to graze, walk or run. This tries to explain the presence of four legs in terms of what we know about the number of legs on other other objects in the modern world, and how stable they are while moving.

For example, we know that a 3-legged object can keep its balance while stationary, but three legs is very awkward for moving. (It is usually suggested that a 3-legged object would have to rotate itself to walk, alternately standing on each of its legs.)

Alternatively, we know that two legs is okay for walking and running, since we do that outselves; and if you are Swedish then you are well aware that at least one cow walks on two legs! We also know that insects have six legs and spiders have eight legs, so these are okay for balanced movement as well.

This is Mamma Mu (on the left) and Kråkan (on the right).

However, a biologist would not approach the question in this way. A biologist knows that a cow has four legs because it inherited that characteristic from its parents, both of whom also had four legs. Furthermore, those parents inherited the characteristic from their parents, and so on. Therefore, to a biologist the explanation for four legs may have little to do with cows in the modern world. The cows have a set of genes inherited from their ancestors, and it is those genes that cause them to have four legs (rather than some other number). There may be no particular relevance to having four legs (as opposed to two or six) in the modern world — modern organisms have characteristics because they inherited them, and not necessarily because they need them.

This starts a search backwards in time, through a series of ancestors in the phylogeny, searching for the one who first acquired four legs. The answer to the question about cows' legs then becomes a question about why that ancestor had four legs when its ancestors did not.

Thus, all cows have four legs, and so we conclude that the common ancestor of their species, Bos taurus, also had four legs. Indeed, all cow-like organisms have four legs, and so the common ancestor of the genus Bos had four legs. Furthermore,  all bovine organisms (cattle, bison, buffalo, yaks, etc) have four legs, and so the common ancestor of the subfamily Bovinae had four legs. Continuing, we work our way backwards through the common ancestors of (respectively) the Ruminantia, Cetartiodactyla, Laurasiatheria and Mammalia, all four of which we conclude had four legs.

Eventually we come to the common ancestor of the superclass Tetrapoda, which also had four legs. (After all, that is what the name says — tetra = four, pod = limb). Not all descendants of this ancestor still retain four legs in the modern world, of course. Primates have modified the front pair of legs into arms, birds and bats have modified them into wings, whales (and dolphins and porpoises) and seals (and sea lions and walruses) have modified their front legs into flippers and greatly reduced their hind legs, manatees and dugongs have front flippers but no hind legs at all, and snakes have lost all four legs almost entirely. Still, the common ancestor of all tetrapods had four legs.

The part of the phylogeny involving the origin of tetrapods is shown in the next diagram. There are four groups of organisms involved.

The part of the phylogeny involving the origin of tetrapods.

The main point about this phylogeny, for our question, is that modern lungfishes and modern tetrapods all have four limbs, while modern coelacanths  and other fish do not. The number of limbs is:

Tetrapod = 4 legs + 1 tail
Lungfish = 4 lobe-fins + unpaired tailfin
Coelacanth = 7 lobe-fins + paired tailfin
Ray-finned fish (most fish) = 7 ray-fins + paired tailfin.

Each fin on a fish is designed to perform a specific function, as shown in the next picture. (NB. MostSome fish also have a small adipose fin behind the dorsal fin, for stability.) Note that pectoral and pelvic fins come in pairs, one on each side of the body. The picture provides the physical explanation for why fish have so many fins,  in terms of balance and stability while moving in water.

So, modern lungfish all have fleshy, paired pectoral and pelvic fins and a single unpaired caudal fin. The other fins of most fishes are absent from lungfish. Modern tetrapods have muscular, paired pectoral and pelvic limbs and a single tail. So, lungfish and tetrapods have the same number of fins/limbs in the same places. We conclude that this arrangement has been inherited from their common ancestor, which is therefore the one we are looking for to answer our question. So, what did the common ancestor of these four-limbed lungfish and tetrapods look like?

We are sometimes incorrectly told that: "Scientists have long known that ancient lungfish species are the ancestors of the tetrapods." This idea is largely discredited today. Lungfish are the closest extant relatives of tetrapods, not their ancestors. That is, they are not primitive — they are well adapted to their natural environment. However, lungfish are one of many relict species of fish that share many ancestral characters.

So, did the common ancestor look something like this?

Tiktaalik.

Or more like this?

Acanthostega.

Probably neither, because we think that both of these fossil species were descendants of the common ancestor in question. But it was presumably more similar to these than to either modern lungfish or modern tetrapods.

So, the initial question about cows' legs becomes: why did the common ancestor of the tetrapods and lungfish reduce their number of fins from seven to four (and no less)? The answer I was given, by the fish biologist W.J.R. (Pim) Lanzing, when I was a student, was that this is the minimum number of fins that can maintain stability and movement in an aquatic environment.

Most of you know roughly how fish move, and how agile they are in water, so I don't need to describe it. However, locomotion of coelacanths is unique to their kind. They have high maneuverability and can orient their bodies in almost any direction in the water. They have apparently been seen doing headstands and swimming belly up. Lungfish, on the other hand, are essentially sedentary. They are reputed to be sluggish and inactive, but still capable of rapid escape movements using their tail. They can can use their paired fins to "walk" underwater, with alternating movements — first one fin moves forward, then the other. They can also use the fins simultaneously to move forward with a lunging action. So, apparently one is not agile in water when one only has four fins, but one can still move around efficiently.

The first tetrapods are thought to have evolved in coastal and brackish marine environments, and in shallow and swampy freshwater habitats. They used their modified, limb-like fins to get around in the water, as do modern lungfish. That is, the origin of legs wasn’t a transformation that happened on land. Limbs were an aquatic innovation that just so happened to be advantageous when tetrapods began to venture out of the water.

So, why does a cow have four legs? Our phylogeny reveals that this is because one of its ancestors (c. 360 million years ago) was aquatic, and four fins is the minimum in liquid. Most descendants have never changed this number, but they did use it to leave the water and live on land. The first part of this answer is a biological one (about ancestry), although the second part is a physical one (about stability and movement).

This is not the sort of answer that can be determined by an experiment. So, scientific problem-solving in this situation is quite different, making biology distinct from physics.

It is sometimes said that physics lies at the heart of science because all explanations ultimately involve physics. That is, the physics explanation lies beyond the biological one — the biological explanation is a proximal one while the physics explanation is the ultimate explanation. This may be so to a physicist, but I do not see why it should be so to anyone else. The biological explanation (in terms of ancestry) is equal to the physical one (in terms of aquatic balance), rather than inferior to it. Moreover, there are explanations beyond the ones that the physicists consider, although that takes us outside science.

In finishing, you might like to try this physics question, instead: Why are tables generally made with four legs and scientific instruments with three?

4 responses so far

If biology is a science, then ...

Jul 24 2012 Published by under Uncategorized

Since the time of Isaac Newton (the 1600s), scientists have tried to explain the natural phenomena around themselves in terms of other observable natural phenomena. They observe something happen, and then play a "what if?" game to see whether they can explain something else in terms of the first one. That is, they try to extrapolate from something they can study to something they cannot study, by the simple expedient of assuming that the "same thing" is occurring in both cases.

Newton, the apple and the moon

For example, Newton (famously) observed an apple fall from a tree, and concluded that there must be some natural explanation for this behaviour. He had previously observed the behaviour of the moon (assumed to orbit around the earth) and the sun (where the earth orbits around the sun). It then occurred to him that these three observations might all be manifestations of the same "thing", which we now call gravity. All he had to do was assume that gravity acts in the same way on the apple that is right next to him as well as on the stars and planets that are millions of miles away. Thus, by studying the behaviour of objects as they fall on earth, where we can freely perform experiments, we can learn something about the behaviour of stars. From this simple approach Newton derived a whole scheme of celestial mechanics, which made him one of the most famous scientists in history. Not bad for a young man.

Charles Lyell did the same thing for geology. We can observe flowing water washing away soil to form ditches next to roads and paths. This natural phenomenon takes relatively little time to happen. But what happens if we have a lot of time, perhaps millions of years? Well, Lyell suggested that we'd end up with the Grand Canyon. So, once again, an observable phenomenon is used to explain another observable phenomenon — all we have to do is assume that the same "thing" happens over very large distances and/or times.

Aerial view of the Grand Canyon

We can't observe those large distances and times, of course, so the "what if?" exercise cannot be tested experimentally. Nevertheless, this is the basis of modern science — observe and experimentally study whatever phenomena you can, and then use this as a basis for explaining those phenomena that can't be subjected to experiment. If the explanations form a coherent set of ideas, and those ideas are capable of predicting as-yet-unobserved phenomena, or they tie together a lot of observable phenomena, then the "what if?" exercise will be considered to be a success.

Some people reject this approach, of course. These people are not scientists, and there is no reason why they should be. They have their own explanations for observable phenomena, and their own opinions about what needs explaining and what does not. We often refer to these explanations as "super natural", because they postulate the existence of things beyond the observable world. If super-natural phenomena exist, of course, then scientists can say nothing more about them than can anyone else, because science is restricted to a study of natural phenomena only.

The point for this blog post is that in biology we take the scientific approach. For example, we accept that we and the plants and animals around us have a genealogical history. I have a father and a grandfather and a great-grandfather. I have personally met the first one (I talked to him on the phone just the other day) but I never met his father. However, I am sure that his father existed, as did his father in turn, because other people did observe these "phenomena". (What a way to talk about your own relatives!) Furthermore, this observable genealogical history involves relatives that all look different and yet somehow also look the same. Indeed, the closer they are as relatives then the more similar they usually look. You cannot put my father and his two brothers together, along with their several sons (see one of them here), and not suspect that they are all closely related. It's almost embarrassing!

Modern biology is based on the idea that this history of relationships proceeds for millions of years into the past and involves all living things. That is, through time the differences and similarities among all individuals and species have arisen through genealogical descent. In one sense, this is no different from geology and the Grand Canyon — small patterns accumulate through time to create big effects.

There is, however, one difference from geology and physics, and it has created enormous difficulties for the study of biology, not just in the modern world but for centuries. The phenomena being observed seem to be much more complex in biology. As Craig Bohren has pointed out: "The prestige of physics originates partly from its success in achieving its aims. This success, however, has been obtained by applying extremely complicated methods to extremely simple systems ... The electrons in copper may describe complicated trajectories but this complexity pales in comparison with that of an earthworm."

Thus, those scientists studying the non-biological world have often failed to grasp the difficulty of the task being undertaken by biologists, and they have frequently looked on biological experimentation with disdain. What is worse, however, is that it is much harder to explain biology to non-biologists. One only has to look at the plethora of books trying to explain biology to the general public to realize that physicists apparently have it much easier — there are far fewer books because the concepts only need to be explained once.

We now refer to biological complexity as "biodiversity", to distinguish it from the much simpler diversity observed in the non-biological world. I do not know why it took until the 1980s to create a word that we had clearly needed for 3000 years!

The concept of biodiversity leads us to the inevitable question: what does genealogical history look like if we extrapolate it over hundreds of millions of years? It is unlikely to be a simple linear sequence, as in geology, or a mathematical extrapolation from falling apples to orbiting planets, as in physics.

The study of long-term genealogy is called phylogenetics, and the genealogy is called a phylogeny. The latter is a term created by Ernst Haeckel in the late 1800s to describe the reconstructions of species histories that occurred in response to Charles Darwin's ideas on biological evolution. But what does a phylogeny look like?

If we take the observed phenomenon of a genealogy, it is often called a "family tree". Historically, these trees show the male lineage descending from some specified ancestral male, as shown in the picture below, which refers to the current Swedish Royal Family. This shows a branching arrangement, rather than a linear sequence, with (usually) several children in each generation. Nevertheless, a linear sequence does exist in the diagram, since the tree follows only the lineage of those people who became monarch.

The family tree of the House of Bernadotte, the current Swedish Royal Family

(It is worth noting here that recently Sweden change the laws of inheritance, so that it is now the oldest child of either sex who becomes monarch, rather than the oldest male. We thus currently have a "crown princess", Victoria, rather than a "crown prince", as would be usual in other monarchies. This did not happen in the previous generation, for example, where Carl Gustaf became monarch, rather than any of his four older sisters.)

However, a family genealogy isn't a tree either, is it? The different lineages inter-connect through reproduction. My own ancestry, for example, can be traced through either my father's family or my mother's; and their ancestry can be traced through either their own mothers or their fathers.

So, a genealogy is a complex thing. Does this make a family tree a good model for a phylogeny? That is, we are extrapolating from something we can observe, a family genealogy covering several generations, to something we cannot observe, a phylogeny of species covering millions of years. We are also jumping from individual organisms (people) to groups of organisms (species). This has turned out to be more complex than extrapolating from an apple to a planet. This issue is something that phylogeneticists have struggled with for a long time, both in communicating with each other and with non-experts.

I shall look at the possible solutions in the next post.

 

2 responses so far

What is Skepticism

Oct 31 2011 Published by under Uncategorized

There seems to be a theme running around the intertubes today... a them about skepticism.  I'm nothing if not unoriginal, so here are my thoughts on the matter.

Skepticism is not saying everything is wrong.  Skepticism is saying that you aren't sure of something without further evidence.

Skepticism is not making up arguments to support your thoughts on the subject (pro or con).  Skepticism is honestly trying to find the information that you need to stop being skeptical.

In that way, skepticism should be about data, logic, and the scientific method.  Every scientist should be a skeptic.   But skepticism does not mean doggedly defending your point of you beyond the realm of rationalism either.

Many people claim to be skeptics.  Some of them even are.  Most are not (about something).  We all have our pet notions.  "If I wear my lucky socks on game day, then the Cowboys will win."

Skeptics can be convinced by sufficient information.  That's one way in which evolution-deniers and climate-deniers are not skeptics.  They cannot be swayed by sufficient information.

Muller is a skeptic.  He thought climate scientists were wrong.  He spent two years looking at the data... not to prove the climate scientists wrong, but to find the correct answer to the question he thought was important.  He got the results of his work and is now convinced that the Earth is warming.  I think he remains skeptical about human causation of the warming trend, but maybe he will continue his research.

Watts is not a skeptic.  He is a denialist.  He said he would change his mind and accept whatever Muller found, but he has not.

I could go on and on.

The point is that a skeptic can change his/her mind to fit the evidence.  Does that mean a skeptic must have every possible answer complete?  No.  If every possible question was answered, then scientists would be out of a job.  It would all just be making license plates from then on.

At what point can a skeptic make a decision one way or another, well, that all depends on the question, the evidence, and the skeptic.  As Carl Sagan said, "extraordinary claims require extraordinary evidence".

For Muller, it was 2 years of heavy data analysis.

 

 

5 responses so far

My Project

Oct 29 2011 Published by under Uncategorized

I am hesitant to discuss much of this as I normally don't talk about my work.  There are good reasons for that.

You see... I'm the enemy.  I am a content specialist for a major producer of standardized tests.  My specialty is (duh) science.

Now, I've been in this industry for 3 years now and let me tell you, it's not what you think it is.  Unless you are in the industry or actively involved as a client, you can't imagine what it's like.  I can share a few things with you.

It takes over 18 months for a question to go from an idea in someone's head to an operational item (that means it's scored and the score counts for whatever the test is for).  Each question, depending on the project requirements, will be seen by 2-3 content specialists (usually each one more than twice), artists, copy editors, fact checkers, clients, client committees, and a bias/sensitivity expert before ever even seeing a test form.  Then there is field testing, data review, final review by the client... then it MIGHT get on a test.

The first thing most people think of when they hear 'standardized testing' is the recently ended No Child Left Behind and maybe Obama's Race to the Top programs.  I will say that it is my opinion that these standardized tests in these contexts are used for entirely incorrect purposes and at incorrect times.  But those are client decisions and "him what pays, says".  But there are a lot of tests that have to be standardized that you might not think about.  Every industry that has some kind of certification exam has standardized tests... nurses, IT techs, aircraft mechanics, etc. etc.  Those are generally used properly.

When I say properly, let me explain.  What is the purpose of a test?  To see if the tester knows something.  Now, a well designed test question will not only tell you if the student knows the information, but can also tell you why the student got it wrong.  That last bit is critically important and why much of the high school testing... isn't properly used.  There's accountability with no chance at improvement. If the tester doesn't learn, then there' s very little point in doing it... if you don't learn, there's very little point in doing anything.

A properly designed test should have a diagnostic component.  Which is a pre-test.  What does the tester know now?  It can identify areas of improvement and even (sometimes) over clues into the misconceptions the tester has so they may be taught correctly.  Any assessment is a tool that students, teachers, parents, state officials can use to see what's going on with education at their level.  Unfortunately, it's not being used this way (mainly because it is expensive).  Again, there's a big difference between public school assessments (which are free for the students to take) and professional certification tests that are not free.

But why a standardized test?  Well, that just means that over a given period or group, all the testers take the same test.  Their are several reasons for this.  One is so that scores can be compared between students, schools, classrooms, socioeconomic groups, gender, ethnicity, ect.  And yes, we do compare every test question in every single one of these ways to check for issues.  Because tests are standardized, they can even be compared year to year.  Usually a group of questions are carried over from one year to the next and these form the basis of some extensive statistical analyses to determine how students compare year over year.  It is truly staggering the amount of information that is developed from these tests.

It can go even further.  A few of you may remember Obama's "Sputnick Moment".  Well that's from another standardized test (PISA) that is given to students all over the world.  The same questions given to students in 70+ countries.  The US didn't do so well in the latest one, hence the "Sputnick Moment".

Another complaint that people often have about standardized testing is that it is too easy to guess.  99% of the time, the questions are 4 option multiple choice.  Well, that is changing.  A number of industry leading companies have a variety of new products out.  Items that are hot spots, where a tester selects one or more portions of an image and the computer tabulates the location of each click to determine a score.  Drag and drop, which is a glorified matching question, but often with some advanced features.  There is even some significant research into computer scored essay questions.  I've seen a demo and it is absolutely stunning.  It is not a word count type of system.  It is a learned relational database.  It can tell the difference between a BS answer with lots of technical terms and one that has the exact same terms, but correct.  I've seen it.  It is truly amazing tech.

Sorry for the digression, but I hope that this has given you some insight into the industry.  Like any industry, there is a lot of proprietary technology, processes, clients, etc.  I can't get into that.  If you have any questions, then I'll try to answer them if I can... the more general the better.

But standardized testing is here to stay.

Now, on to my project that I am epically excited out.  This is really a pinnacle of the career type of thing.  I am responsible for the development of the science standards for a MAJOR client.  This isn't state wide or even national.  We are likely to go multi-national with it.  Now, I'm not doing this by myself.  There is the client, various advisory committees, consultants, consultant groups, and a host of businesses all involved.  But I'm the guy that is actually putting the words on paper.  Which means, a lot of what I say will be incorporated into the science standards.  I've made a number of changes and recommendations and the client seems to pleased.

My trip to New York, next week, will be the first of a series of committee reviews of these standards.

When I think about, which I try not to do, I am excited that I am working on such a major project.  Then I get seriously nervous.  What if I say something wrong, what if I didn't push hard enough to get something vitally important in or get something that ends up a waste of time out?

I actually started another draft document today and that's why I'm thinking about this now.  We're talking about being an influence (however small it might be) on literally hundreds of thousands of students a year.

I can say for certain that evolution will be a major theme.  The client unambiguously agrees with me and a consultation group that I assembled from experts in science education.  We're not going to beat around the bush either.  Common descent, speciation, selection, etc.  will all be fair game.  I am very happy about that.  Even if students don't believe it, they still have to learn it and they will learn what evolution is really about instead of the misinformation that is promoted almost everywhere in the US.

I'm just babbling now... and as usual... I'm not sure where to stop.  So, if I can answer any questions you might have, let me know.

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