Two Science Online 2012 sessions for your consideration


Tomorrow, I head for North Carolina to attend Science Online 2012. I attended last year as an an information sponge and observer who knew no one and experienced some highlights and lowlights. This year, I’m attending as a participant and as a moderator of two sessions. The first session, on Thursday afternoon, is with Deborah Blum, and we’ll be leading a discussion about how and when to include basic science in health and medical writing without distracting the reader. The second session I’m moderating is with Maia Szalavitz, and we’ll be talking about whether or not it’s possible to write in health and medicine as an advocate and still be even-handed. Session descriptions are below, as are the topics that we’ll be tossing around for discussion.


Thursday, 2:45 p.m.: The basic science behind the medical research: Where to find it, how and when to use it. 

Sometimes, a medical story makes no sense without the context of the basic science–the molecules, cells, and processes that led to the medical results. At other times, inclusion of the basic science can simply enhance the story. How can science writers, especially without specific training in science, find, understand, and explain that context? As important, when should they use it? The answers to the second question can depend on publishing context, intent, and word count. This session will involve moderators with experience incorporating basic science information into medically based pieces with their insights into the whens and whys of using it. The session will also include specific examples of what the moderators and audience have found works and doesn’t work from their own writing.

Deborah and I have been talking about some issues we’d like to raise for discussion. The possibilities are expansive. Some highlights:

  • Scientific explanation (and understanding) is the foundation for the best science writing. In fact, if the writer doesn’t understand the science, he or she may miss the most important part of the story. But we worry that pausing to explain can slow a story down or disrupt the flow. In print, writers deal with this by condensing and simplifying explanations and also by trying to make them lively and vivid, such as by use of analogy. But online, we use hotlinks as often if not more often for the same purpose. 
  • Reaching a balance between links and prose can be a difficult task. Another possible pitfall is writing an explanation that’s more about teaching ourselves than it is about informing a reader sufficiently for story comprehension. How many writers run into that problem?
  • On-line the temptation is to do the barest explanation and the link to the fuller account, but that approach has pros and cons. More information is available to the reader and the sourcing is transparent. But how often do readers follow those links – and how often do they return? Issues with links include that they are not necessarily evergreen or can lose reader (can be exit portal), or that the reader may not use them at all, thus losing some of the story’s relevant information.
  • A reader may actually learn more from a print story where there are no built-in escape clauses. So how does the on-line science writer best construct a story that illuminates the subject? Are readers learning as much for our work as they do from a print version? (And there’s that age-old question of, Are we here to teach or to inform?)
  • Are we diminishing our own craft if we use links to let others tell the story for us? If we simply link out rather than working to supply an accessible explanation, negatives could include not pushing ourselves as writers and not expanding our own knowledge base, both essential to our craft.
  • How much do we actually owe our readers here? How much work should we expect them to do?
  • What are some ways to address issues of flow, balance, clarity? One possibility is, of course, expert quotes. Twitter is buzzing with scientists, many of whom likely would be pleased to explain a concept or brainstorm about it. (I’ve helped people who have “crowdsourced” in this way for a story, just providing an understandable, basic explanation for something complex).
  • Deborah and I are considering a challenge for the audience with a couple of basic science descriptives, to define them for a non-expert audience without using typical hackneyed phrases. Ideas for this challenge are welcome.
  • We also will feature some examples from our own work in which we think we bollixed up something in trying to explain it (overexplained or did it more for our own understanding than the reader’s) and examples from our own or others’ work of good accessible writing explaining a basic concept. We particularly want to show some explanations of quite complicated concepts–some that worked, some that didn’t. Suggestions for these are welcome!
  • Finally, when we do use links in our online writing– what consitutes a quality link?
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Saturday, 10:45 a.m.: Advocacy in medical blogging/communication. Can you be an advocate and still be fair?
There is already a session on how reporting facts on controversial topics can lead to accusations of advocacy. But what if you *are* an avowed advocate in a medical context, either as a person with a specific condition (autism, multiple sclerosis, cancer, heart disease) or an ally? How can you, as a self-advocate or ally of an advocate, still retain credibility–and for what audience?

The genesis of this session was my experience in the autism community. I’m an advocate of neurodiversity, the basic premise of which is that people of all neurologies have potential that should be sought, emphasized, and nurtured over their disabilities. Maia, the co-moderator of our session, has her own story of advocacy to tell as a writer about pain, pain medication, mental health, and addiction. 


Either of these topics is controversial, and when you’ve put yourself forward as an advocate, how can you also present as a trustworthy voice on the subject? Maia and I will lead a discussion that will hit, among other things, on the following topics that we hope will lead to a vigorous exchange and input from people whose advocacy is in other arenas:

  • Can stating facts or scientific findings themselves lead to a perception of advocacy? Maia’s experience is, for example, about observing that heroin doesn’t addict everyone who tries it. My example is about noting the facts from research studies that have identified no autism-vaccine link.
  • Any time either of us talks about vaccines or medications for mental health, we’ve run into accusations of being a “Big Pharma tool” or with worse terminology. What response do such accusations require, and what constitutes a conflict of interest here? What is the level of corruption of data that’s linked to pharma involvement? If they are the only possible source of funding for particular studies…do we ignore their data completely?
  • We both agree that having an advocacy bias seems to strengthen our skeptical thinking skills, that it leads us to dig into data with an attitude of looking for facts and going beyond the conventional wisdom in a way that someone less invested might not do. Would audience members agree?
  • In keeping with that, are advocates in fact in some ways more willing to acknowledge complexities and grey areas rather than reducing every situation to black and white?
  • We also want to talk about how the passion of advocacy can lead to a level of expertise that may not be as easily obtained without some bias.
  • That said, another issue that then arises is, How do you grapple with confirmation bias? We argue that you have to consciously be ready to shift angle and conclusions when new information drives you that way–just as a scientist should.
  • One issue that has come to the forefront lately is the idea of false equivalence in reporting. Does being an advocate lead to less introduction of false equivalence?
  • We argue that you may not be objective but that you can still be fair–and welcome discussion about that assertion.
  • And as Deborah and I are doing, we’re planning a couple of challenge questions for discussants to get things moving and to produce some examples of our own when we let our bias interfere too much and when we felt that we remained fair.

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The entire conference agenda looks so delicious, so full of moderators and session leaders whom I admire, people I know will have insights and new viewpoints for me. The sheer expanse of choice has left me as-yet unable to select for myself which sessions I will attend. If you’re in the planning stages and see something you like for either of these sessions, please join us and…bring your discussion ideas! 


See you in NC.

Double Xpression: Debbie Berebichez, PhD Physicist

Deborah is the first Mexican woman to graduate with a physics PhD from Stanford University. She is a physicist, author, and media personality whose initiatives to popularize science have impacted thousands of people around the world. Her passion is to popularize science and motivate young minds to think analytically about the world. This has led her to pioneer learning initiatives in schools and universities in Mexico, Africa, the US and Israel. She is a frequent public speaker and has been recognized by numerous media outlets such as Oprah, CNN, WSJ, TED, DLD, WIRED, Martha Stewart, City of Ideas, Dr. Oz Show, Celebrity Scientist and others. She regularly appears as a science expert on different international TV networks; currently she is the TV host of National Geographic’s “Humanly Impossible” show. And she will appear on the Discovery Channel’s upcoming show ‘You’ve Been Warned.’  You can find Deborah on Twitter, or on her blog, Science With Debbie.  You can also find Deborah telling her story for The Story Collider.



DXS: First, can you give me a quick overview of what your scientific background is and your current connection to science?

I grew up in Mexico City in a fairly conservative community, and as a child, I was discouraged from doing and studying science.  My parents, family, and peers would all ask, “oh, why don’t you study a more feminine career?” Although I was pretty good in school, I wasn’t exactly a math wizard.  I used to say that I loved philosophy and physics – because philosophy was a deep discipline of asking questions about the world.  And physics studied the world itself.   
It was clear when I was born that my personality was was quite different to the one of my mom.  When I was growing up, my mom was scared because she didn’t know what to do with this little girl that was smart and always asking questions.  She is not a naturally curious person, so she kept trying to tame down my curiosity and kept telling me not to tell boys that I was interested in math and science because I would never find a husband.  According to her, the life goal for a girl was to find a husband, have kids, and that’s it.  Women didn’t have to have a career.  (Not that there is anything wrong with not having a career.)  My high school teachers and counselors were not so different and encouraged me to go into philosophy or literature, not into math or physics.  And my friends in school told me I literally had to be an out of the world genius to be able to study physics.      
Given the circumstances, I started studying philosophy in Mexico.  There were some classes with logic, and some with a little bit more math, and those were the ones I just devoured!  And, at the same time – secretly – I was reading the biographies of scientists.  For some bizarre reason, I was hugely attracted to their life stories.  I didn’t have any family members, or anyone else for that matter, that had pursued a career in science, so I didn’t have a mentor or a role model.  I felt an extreme kinship with Tycho Brahe, who in the late 1500’s was locked in a tower, doing all of these calculations for years, hated by everyone in the town.  Go figure! I felt some kinship with these scientists.   But I didn’t have the courage nor the means to switch majors.  I did confess that I wanted to study another area (physics), but in Mexico one cannot study two majors. So, I studied philosophy for two years.

In the middle of it, I felt way too curious about science and I decided to apply to schools in the US.  It was hard at the time because college in Mexico was a lot cheaper than in the states.  At the private school where I was attending, my tuition was about $5,000 per year.  If I were to come to the US, I would be looking at costs exceeding $35,000 per year. I couldn’t really ask my dad to help me with that price tag so I started to apply everywhere and anywhere that had scholarship opportunities.

I ended up getting a letter from Brandeis 

University saying that they would let me take this advanced placement test and write an essay, which, if I did well, would give me a full scholarship.  I received a full Wien Scholarship and was to continue studying philosophy in the US.  This was probably the nicest thing that has ever happened to me because it opened the path of opportunity.

Brandeis transformed me as a person – I saw females doing science!  But, the bravado moment that changed my life was a very general course called Astronomy 101.  The teaching assistant, Roopesh, was a very sweet man from India and he saw that my eyes would just light up when I was in that class – I was much more curious than the random student that was just taking it to fulfill some requirement.   
At the end of that year, Roopesh and I 

were walking around Harvard Square and stopped to sit under a tree.  I started to tell him, with tears in my eyes, that I just don’t want to die without trying.  What I meant by that is I don’t want to die without trying to do physics.  Everyone’s questioning of my decision made me question my actual ability.  Everyone telling me ‘no’ hampered my development.  I mean, I was good at math, but I definitely didn’t have the same background as all the kids coming in with advanced math and physics courses. 
 

I told Roopesh that I don’t even remember how to solve the equation (a+b)2 – even my algebra was rusty!  But, he believed in me and went back to his professor and told him my story.  This professor decided to meet with me and ends up telling me about someone who had done this sort of thing in the past.  His name was Ed Witten and he went on to become the father of string theory.  

He said “Witten had switched from history to physics, and I will let you try too.”  With that, he handed me a book on vector calculus called ‘Div, Grad and Curl’ and told me that If I could master it in three months by the end of the summer, they would let me switch my major to physics and also let me bypass the first two years of course work.  This would allow me to graduate by the time my scholarship ran out.        
I have never in my life experienced the level of scientific passion condensed into such a short amount of time and I am jealous of the person I was that summer.  I had so much perseverance and focus.  I don’t think I can ever reproduce that intensity again.  From the moment I woke up to the moment I went to sleep, and even in my dreams, I only thought about physics. Roopesh, who became my mentor for the summer, taught me.  

I always wanted to pay Roopesh for his tutoring, but he would never accept any money.  He told me that when he was growing up in the mountains of Darjeeling in India, there was this old man who would climb up to his home and teach him and his sisters English, the musical instrument Tabla, and math.  Roopesh’s father always wanted to pay the old man for his tutoring, but the man always declined.  The man said that the only way he could ever pay him back was if Roopesh did the same thing with someone else in the world.  And by mentoring me, Roopesh fulfilled his payment to the old man.  
Out of that, that became a seed for my physics journey and purpose.  It is now my life’s mission to do the same for other people in the world – especially women – who feel attracted to science but feel trapped.  They for some reason, whether it is social, financial, etc., just can’t find the way toward science.  That is the motivation that dictates my actions.
I was able to pull it off and graduated Brandeis Summa Cum Laude with highest honors in physics and philosophy. I went back to Mexico afterwards to figure out what to do next and to spend some time with my family. At the same time, I did a master’s degree in physics at the largest university in Mexico UNAM.  My curiosity for physics didn’t diminish and in 1998, I randomly applied to two physics PhD programs in the US.  I applied very, very late, but, fortunately, I won a merit-based full scholarship from the Mexican government who provided me with funding, which made it easier for me.    


Because I loved biophysics, I did a search on who was doing this line of research.  I came across Steven Chu, who is currently the secretary of energy.  At the time I was applying, he was at Stanford and was one of the first to manipulate a single strand of DNA with his ‘optical tweezers.’  To me, his story was fascinating!  Without really knowing who he was other than what I found on the web, I wrote him an email asking him if I could work in his lab.  Had I known who he was – that he had just won the Nobel prize in 1997 – I would have been too intimidated.  


I was admitted to Stanford and was invited to work with Dr. Chu, but after two years I decided to switch labs.  As expected, it was a very challenging environment and having only studied two years of physics at Brandeis, I wasn’t as prepared as most of the other students.  I struggled for the first two years.  Everyone worked so extremely hard at Stanford and there I was, struggling to be the best, but, in the beginning, I couldn’t even be average.

Fast forward four years.  I had worked my butt off and ended up becoming the first Mexican woman to graduate with a PhD in physics from Stanford.  It was the best day of my life – I kept thinking that I was so blessed to have my parents live to see this!  It was so moving, I was crying so much and I couldn’t believe what had happened.  My friends had flown in from all over the world to be with me.  It was amazing. 

When people hear what I do, they – especially teenage girls – feel intimidated.  But, when they hear the whole story, their tune changes.  I tell them that I know what it is like to not understand something.  I was not the kind of person where comprehension of my science came naturally.  But I did it.  And if I can do it, anyone can do it!  My story can be inspirational to someone who comes from a background completely lacking in science because they, like me, can reach their goal. 
DXS: What ways do you express yourself creatively that may not have a single thing to do with science?

I was always a very curious girl growing up. I had a lot of interests, one of which being theatre.  I wanted to be an actress when I was young, but my father didn’t let me pursue that as a career, which was probably a good idea.  But, during high school, I went to an after school drama program.  I wrote my own plays – three of them – and performed one of them.  I was in heaven when I was on stage. 

In NY, I have tried to do a little bit of that.  Of course, I’ve never done any big roles, but I will be an extra in a film, or if there is a small production being made in Spanish, I will play a part.  It doesn’t matter how big the role is – I just love doing something creative and getting into a character. 

DXS: What types of productions and/or films have you done?

I don’t think I would come up in the credits as an extra, but I did a movie with Simon Pegg, Kirsten Dunst and Megan Fox in the movie “How to lose Friends and Alienate People.” It was a very, very fun film!  In theatre, Jean Genet, who is a French playwright, has a play called The Maids, and I was the madame.   

DXS: Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific?

Debbie talking to the TEDYouth audience about waves.

I have a concept that I call “physics glasses.”  And what I mean by that is, for me, physics is not a subject that you just teach in a complex way in a classroom.  Rather, physics is something that is related to everyday life.  From the moment you wake up, you can just put on your physics glasses.  It is a mode of thinking – it is a way where although reality can be very rich and diverse, physics goes very deep and it abstracts commonalities, general principles that apply to many things.  To give you an example, I asked the kids in the audience of my TEDYouth talk, “what do the sun, the ocean, and a symphony orchestra have in common?”  When just looking at them on the surface, there isn’t much in common.  I mean, they are all beautiful things but they are not obviously related.  But, to a physicist, they are all waves.   You have sound waves, light waves, and water waves and you can interchange many of the concepts in physics to explain all three.



Where most of us see the world with our eyes through light waves, other might see the world differently.  Take, for example, my friend Juan, who is blind.  He “sees” the world with sound waves – he senses sound as it bounces off the objects around him.  Through this, he can bike, play basketball, and do a load of activities using sound as a guide.  This is one of my favorite analogies because, really, physics “infects” the way I see the world. 

Deborah the Physicist model

To give you a more specific example in the creativity realm, when I got to NY, I felt really un-feminine.  When I was studying physics, I felt that if I was even slightly feminine, I wouldn’t be respected.  It didn’t help that some of the other women in the physics program at Stanford were more of a “guys girl,” always wearing a baseball cap and t-shirts.  Now, since I am Latin, I first showed up wearing a skirt to class, but I quickly learned to dress down.  Looking feminine would assure that no one would talk to me in class.



So, when I got to NY, I had an explosion.  I wanted to know what it was like to express myself as a woman and my friend suggested that I do some modeling.  So I did.  It was a brief, lasting about a year.  But during that time, my friend, who was a designer from Mexico, asked me to work with her and I wrote and did some videos about the physics of fashion, which also included the physics of high heels video.  


Some people could consider fashion to be superficial, but not me.  I love fashion and color.  But, other scientists generally looked down upon you for liking this sort of thing.   This fueled my desire to prove to everyone that there actually is science everywhere, including fashion, and that they shouldn’t be snobs about it.  There is complex science in how different materials work, how they interact with the environment and you can prove to the women, like my mother and friends back home who think that science has nothing to do with their everyday lives, that it has EVERYTHING to do with it.   So I talked about a Newtonian theory for color – how to pick the right color for you based on how much light the color would reflect on that day, etc.  

DXS: Like a more sophisticated version of colors based on your “season?”

DB: Exactly! 

I also did pieces on the materials, including some of the newest engineering accomplishments with fabric.  For example, I hooked up with a woman and helped her to design a fashionable and very scientific coat.  It ended up costing $11,000, but it was made up of nano fibers and it had a patch in it that could detect the temperature and the probability of rain.  Based on this probability, it could change permeability of the fabric.  It was a very light coat that was comfortable in nice weather, but when it would rain, it would become impermeable to water once it detected a high probability of rain, transforming into a raincoat.

DXS: That’s incredible!  I wish it wasn’t $11,000!

DB:  Yeah, that’s usually the problems with these technologies.  They are often so novel, but one day I’m sure we can figure out how to make things like this scalable.

Science is very much what guides my thinking when I am being creative and I wish I had more time to do creative things while being influenced by a scientific mindset.

DXS: It is so cool that physics has such an incredible overlap with everyday living.  Like, when we take a shower, I want to know “how is the water getting pumped from the ground or through pipes and make its way out of the showerhead?”  But, as a biochemist, I often find it hard to relate everyday things to biochemistry, but I would like to!

DB: Its funny that you say that.  When I try to teach girls that the worst thing they can do is memorize.  Critical thinking is so important and they shouldn’t take anything at face value, and they should even question teachers and authoritative figures in their lives.  Always ask: what goes into making this?  Why is this here?  Why is it this way and not another?  Constantly ask questions.  That s the gift that physics will give you. 

DXS: Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?

Without saying I am a scientist, I can tell you that people have come up to me and told me that before they even hear me speak, they think I am dumb.  They are usually surprised that I am smart!  I think it is because I am bubbly and friendly and that often makes an impression as being unintelligent.  For them it seems that if a woman is intelligent, she is very cold and distant and serious.  


I’ve met a lot of physicists, and yes, some of them do tend to be that way, often as a reaction to how others treat them.  Or, people would say to me that, because I am Latin, my cultural identity comes across as being warm and the last thing they’d expect me to be into was something as cold as physics.  So yeah, I have definitely been judged so many times!  


It even happens in my current job on Wall Street, especially with my male peers.  When there are off site client meetings, I’m often accompanied by my male sales colleague.  Sales people are generally required to know less about the complexities behind our risk models compared to someone on a more research-oriented role, like me and he will bring me along to these sales meetings in case the potential client has more sophisticated questions that go beyond what he can comfortably answer.  Many times upon meeting the clients for the first time they think that I am the sales person, there to be the smiling face to sell them something, and that he is the risk modeler.  They always direct their mathematical questions to him. 
It came to a point where I became so annoyed that I decided to stop caring.  Now, my sales colleague goes out for drinks with the clients and I know that I am going to be invisible. So I don’t go anymore. I know that I am always going to struggle to get the full intellectual respect in that industry – it will always be a challenge.

DXS: Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?

Yes, absolutely.  For example in Mexico, unlike the US, you absolutely have to do an honors thesis project as an undergrad in science.  Because I had already studied philosophy for four years, I wanted to do a thesis project in philosophy.  But I also wanted to do one in physics.  I recall that back in 1997, when you presented a dissertation in front of the physics community, if you had any power point, forget it.  You would be immediately be called dumb or not a good physicist.  Because, who takes the time to do something fancy!  If you had any color in your presentation, forget it!  


So, literally, the smartest students in physics were people who didn’t really communicate that well, or didn’t really speak English that well, or just didn’t really make an effort.  Their slides were on those overhead projector things with those rolls of plastic sheets, and most of their talks were so confusing and couldn’t be interpreted!  But they were respected!  It was just assumed that if the formula looked complex, they were probably right. 
So what I did was completely different.  I infused my talk with my spiciness and color.  I did an artwork of liquid crystals, which was my research at Brandeis.  Liquid crystals are little cigar-shaped molecules that actually make up the screen of your laptop.  If you pass an electric field through them, they all orient themselves and that is how we can use them for displays in our laptops and TVs. 

I colored these cigar-shaped molecules with purples and reds and greens, and I tried to explain it at the most basic level. This is because of one my philosophy professors in Mexico, who told me that if you cannot explain what you do to your grandmother or 6 year old niece, you don’t understand what you are doing – I loved it!  


And I said to myself that I shouldn’t care what they think.  I pretty much expected to not gain a lot of respect from the physics department, but it had the opposite effect!  I actually had one of the professors from that department come up to me and tell me that he had never really understood what a liquid crystal looked like or what it really was!  He said that “finally I understand [liquid crystals] because of your drawing.  Thank you!”  It was incredible!  


To see the effect on people and from then on, I bounced up in down, I made jokes, I put in creativity.  It doesn’t always have a great effect on very serious audiences, but the younger generation is definitely appreciative.  When it keeps going well, you gain confidence.  And, for me, I even started wearing high heels to the next talk.  When someone commented about my attire, I would counter, hey I have a PhD!

DXS: How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?

This question is deep and a little bit of a struggle at the moment.  This is because I still have that fear – when I arrived in NY, I did that short stint in modeling and I expressed myself and I would dress very creatively – just like my other girlfriends who were not scientists.  But I did feel a little bit of a backlash.  By that I mean that I would post a photo of myself on Facebook or something like that.  They were pretty pictures, not at all seductive or provocative, and my high school mates, usually male, would write me saying: “I always knew you as a serious person and you have achieved so many things – I am just telling you for your own good that this can really damage your image.”  That made me reply with “so you’re telling me that being smart is actually kind of a bummer?”  That actually means that I have to dress very differently from what other women wear for the rest of my life? 

I remember feeling very upset about all of that.  I think that not being taken seriously is still a little bit of a fear of and I think my website has damaged my serious image a little bit.  As a scientist, I was very secluded from the outside world.  I didn’t have a lot of friends when I moved here, but I did know an amazing and powerful woman who happened to be the CEO of Blip TV.  She was insisting that I do videos!  So she invited me to her place and showed me how to do video.  Being the quick woman that she was, she asked me to make up a name for myself on the spot.  When I didn’t answer, she instantly coined “The Science Babe” for me.  I was like, sure, what a cool idea! 

It was kind of a cute name, but because English is not my first language, I don’t always understand some of the cultural connotations associated with some English words.  A few months later, I started to get a few emails from mothers who were upset that I was using my looks.  They would say things like “Are you saying that women have to be in the kitchen or wear short skirts  to be scientists?”  I would answer that no, that was not it at all.  I would further explain that I was trying to change the definition of “babe.”  If you are smart, if you are empowered, you will be a babe no matter how you look.  I am trying to shift what people think of when they think “scientist.”

I don’t feel quite successful with The Science Babe.  It seems like there are quite a few people, especially some from the older generation, who say that they’d love to introduce me to fancy science organizations but are worried that the name “the science babe” will make it difficult.  Also, I had the BBC wanted to talk to me about doing a TV show in NY, and then they said but there’s so much bad stuff out there about you!  And I was like, what do you mean?  They answered “All these things with the “science babe” brand…”

It doesn’t happen all the time, but some people are really critical about the science babe theme, citing that its way too feminine.  Other female scientists that haven’t gone that route have perhaps discounted my seriousness about science.  They assume that what I am doing is not really that important because I do focus on the science everyday life, which is simpler, and it is too much color and too much vivaciousness for our field.  I feel like my femininity has decreased over the last few years because I’ve been too nervous about not being taken seriously.  It s almost like the balance tipped the other way. I feel like perhaps I’ve feminized things to a fault and now I want to appear more serious.  So, I am changing my website to “Science With Debbie” because I really felt the backlash.

It is a struggle to find the balance between being able to express my femininity and presenting myself in a way that people will take me seriously.  In a way, I wish I had a little more courage to not care that much about what people have to say about the science babe but, unfortunately, agents have told me that if I don’t go to the “dumbed down version of femininity” I would get better speaking engagements.  Being feminine has literally affected my career, and it’s because of other people’s perceptions.  I’m never going to be bland, but I will try to change things so I am more serious

DXS: Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?

The fact that I am approachable and pretty down to earth has allowed me to reach corners of society that more distant and fancy scientists would never even consider. For instance, I am going to a small university to give a talk.  Some of my friends ask why I even bother, especially considering that this insitution is not the most renowned university.  But, I feel the opposite – it is these corners that need the influence the most!  Similarly, when I go to Hispanic high schools, many of the mothers have never seen a scientist.  And there I am, a scientist from Mexico, speaking to them and their kids.  It is that powerful combination of being a smart and warm female that can be shocking, which is cool.

In line with this, there was an experiment where women were asked to draw a female scientist.  Most drew a plain, relatively unattractive woman.  Immediately when you break that mold, it has an incredible effect.  People say, “Hey! She kind of looks like me and she dresses like me.  Maybe I can do science too!”  Some girls are afraid that by being smart, boys won’t talk to them.  My femininity allows me to be a voice in a field that has tended to isolate themselves from the public, which is bad. Some of my colleagues have become a little snobbish.  The fact that I have serious credentials (PhD and 2 postdocs) shows that I had to work like crazy – looks and personality can only go so far.  It s hard work that gets you there! Serious science communication has a lot of math and problem solving in order to explain things accurately to the public. So I still feel like I am doing science!

   

   

So What’s the Big Deal About the Higgs Boson, Anyway? A Physics Double Xplainer

The ATLAS detector at the Large Hadron Collider, one of four
detectors to discover a new particle.
By Matthew Francis, physics editor

After decades of searching and many promising results that didn’t pan out, scientists working at the Large Hadron Collider in Europe announced Wednesday they had found a new particle. People got really excited, and for good reason! This discovery is significant no matter how you look at it: If the new particle is the Higgs boson (which it probably is), it provides the missing piece to complete the highly successful Standard Model of particles and interactions. If the new particle isn’t the Higgs boson, well…that’s interesting too.

So what’s the big deal? What is the Higgs boson? What does Wednesday’s announcement really mean? What’s the meaning of life? Without getting too far over my head, let me try to answer at least some of the common questions people have about the Higgs boson, and what the researchers in Europe found. If you’d rather have everything in video form, here’s a great animation by cartoonist Jorge Cham and an elegant explanation by Ian Sample. Ethan Siegel also wrote a picture-laden joyride through Higgs boson physics; you can find a roundup of even more posts and information at Wired and at Boing-Boing. (Disclaimer: my own article about the Higgs is linked both places, so I may be slightly biased.)

Q: What is the Higgs boson?
A: The Higgs boson is a particle predicted by the Standard Model. It’s a manifestation of the “Higgs field”, which explains why some particles have mass and other particles don’t.

Q: Whoa, too fast! What’s a boson?
A: A boson is a large mammal indigenous to North America. No wait, that’s bison. [Ed note: Ha. Ha. Ha.] On the tiniest level, there are two basic types of particles: fermions and bosons. You’re made of fermions: the protons, neutrons, and electrons that are the constituents of atoms are all fermions. On a deeper level, protons and neutrons are built of quarks, which are also fermions. Bosons carry the forces of nature; the most familiar are photons–particles of light–which are manifestations of the electromagnetic force. There are other differences between fermions and bosons, but we don’t need to worry about them for now; if you want more information, I wrote a far longer and more detailed explanation at my personal blog.

Q: What does it mean to be a “manifestation” of a force?
A: The ocean is a huge body of water (duh), but it’s always in motion. You can think of waves as manifestations of the ocean’s motion. The electromagnetic field (which includes stuff like magnets, electric currents, and light) manifests itself in waves, too, but those waves only come in distinct indivisible chunks, which we call photons. The Higgs boson is also a manifestation of a special kind of interaction.

Q: How many kinds of forces are there?
A: There are four fundamental forces of nature: gravity, electromagnetism, and the two nuclear forces, creatively named the weak and strong forces. Gravity and electromagnetism are the forces of our daily lives: Gravity holds us to Earth, and electromagnetism does nearly everything else. If you drop a pencil, gravity makes it fall, but your holding the pencil is electromagnetic, based on how the atoms in your hand interact with the atoms in the pencil. The nuclear forces, on the other hand, are very short-range forces and are involved in (wow!) holding the nuclei of atoms together.

Q: OK, so what does the Higgs boson have to do with the fundamental forces?
A: All the forces of nature have certain things in common, so physicists from Einstein on have tried to describe them all as aspects of a single force. This is called unification, and to this day, nobody has successfully accomplished it. (Sounds like a metaphor for something or other.) However, unification of electromagnetism with the weak force was accomplished, yielding the electroweak theory. Nevertheless, there was a problem in the first version: It simply didn’t work if electrons, quarks, and the like had mass. Because particles obviously do have mass, something was wrong. That’s where the Higgs field and Higgs boson come in. Scottish physicist Peter Higgs and his colleagues figured out that if there was a new kind of field, it could explain both why the electromagnetic force and weak force behave differently and provide mass to the particles.

Q: Wait, I thought mass is fundamental?
A: One of the insights of modern physics is that particles aren’t just single objects: They are defined by interactions. Properties of particles emerge out of their interactions with fields, and mass is one of those properties. (That makes unifying gravity with the other forces challenging, which is a story for another day!) Some particles are more susceptible to interacting with the Higgs. An analogy I read (and apologies for not remembering where I read it) says it’s like different shoes in the snow. A snowshoe corresponds to a low-mass particle: very little snow mass sticks to it. A high-mass particle interacts strongly with the Higgs field, so that’s like hiking boots with big treads: lots of places for the snow to stick. Electrons are snowshoes, but the heaviest quarks are big ol’ hiking boots.

Q: Are there Higgs bosons running around all over the place, just like there are photons everywhere?
A: No, and it’s for the same reason we don’t see the bosons that carry the weak force. Unlike photons, the Higgs boson and the weak force bosons (known as the W and Z bosons — our particle physics friends run out of creative names sometime) are relatively massive. Many massive particles decay quickly into less massive particles, so the Higgs boson is short lived.

Q: So how do you make a Higgs boson?
A: The Higgs field is everywhere (like The Force in Star Wars), but to make a Higgs boson, you have to provide enough energy to make its mass. Einstein’s famous formula E = mc^2 tells us that mass and energy are interchangeable: If you have enough energy (in the right environment), you can make new particles. The Large Hadron Collider (LHC) at CERN in Europe and the Tevatron at Fermilab in the United States are two such environments: Both accelerate particles to close to the speed of light and smash them together. If the collisions are right, they can make a Higgs boson.

Q: Is this new particle actually the Higgs boson then?
A: That’s somewhat tricky. While the Standard Model predicts the existence of a Higgs boson, it doesn’t tell us exactly what the mass should be, which means the energy to make one isn’t certain. However, we have nice limits on the mass the Higgs could have, based on the way it interacts with other particles like the other bosons and quarks. This new particle falls in that range and has other characteristics that say “Higgs.” This is why a lot of physics writers, including me, will say the new particle is probably the Higgs boson, but we’ll hedge our bets until more data come in. The particle is real, though: four different detectors (ATLAS and CMS at CERN, and DZero and CDF at Fermilab) all saw the same particle with the same mass.

Q: But I’m asking you as a friend: Is this the Higgs boson?
A: I admit: a perverse part of me hopes it’s something different. If it isn’t the Higgs boson, it’s something unexpected and may not correspond to anything predicted in any theory! That’s an exciting and intriguing result. However, my bet is that this is the Higgs boson, and many (if not most) of my colleagues would agree.

Q: What’s all this talk about the “God particle”?
A: Physicists HATE it when the Higgs boson is called “the God particle.” Yes, the particle is important, but it’s not godlike. The term came from the title of a book by physicist Leon Lederman; he originally wanted to call it “The Goddamn Particle”, since the Higgs boson was so frustrating to find, but his editor forced a change.

Q: Why should I, as a non-physicist, care about this stuff?
A: While it’s unlikely that the discovery of the Higgs boson will affect you directly, particle colliders like the LHC and Tevatron have spurred development of new technologies. However, that’s not the primary reason to study this. By learning how particles work, we learn about the Universe, including how we fit into it. The search for new particles meshes with cosmology (my own area): It reveals the nature of the Universe we inhabit. I find a profound romance in exploring our Universe, learning about our origins, and discovering things that are far from everyday. If we limit the scope of exploration only to things that have immediate practical use, then we might as well give up on literature, poetry, movies, religion, and the like right now.

Q: If this is the Higgs boson, is that the final piece of the puzzle? Is particle physics done?
A: No, and in fact bigger mysteries remain. The Higgs boson is predicted by the Standard Model, but we know 80% of the mass of the Universe is in the form of dark matter, stuff that doesn’t emit or absorb light. We don’t know exactly what dark matter is, but it’s probably a particle — which means particle colliders may be able to figure it out. Hunting for an unknown particle is harder than looking for one we are pretty sure exists. Finding the Higgs (if I may quote myself) is like The Hobbit: It’s a necessary tale, but the bigger epic of The Lord of the Rings is still to come.

Why being a Nature editor is like riding the Knight Bus

 
Have you seen a picture of our science education editor, Chris Gunter (above)? She looks kinda nice, doesn’t she? Would it surprise you to learn that once upon a time, she was viewed along the lines of the love child between a rock goddess and Darth Vader? Perhaps picture Grace Slick in a long black cape, glaring at you. Like this:
 
Via Wikimedia Commons.
Why was Chris such a badass? Because she was an editor at Nature, science’s toppest-tier journal, for almost seven years, dealing with submissions in the genetics/genomics side of things. You might be surprised to learn, as Chris relates in telling about her experiences at Story Collider, which features compelling stories about science, that what sounds like an intensely precise and technical field generated “mountains of drama.” In telling her tale, Chris likens her experience to riding the Knight Bus in Harry Potter, in which you’re never quite sure who your seat mate will be. She writes, 

People ask me all the time what the job was like. The best analogy I’ve I found is riding the Knight Bus in Harry Potter. The Knight Bus is the magical transport full of crazy people and events, both amazingly good and scarily over the top. Similarly, I felt like I was on this magical transport that went to the wildest places, and every week I’d think, “There is absolutely no way we will get to our destination” of putting out a magazine. Yet, thanks in part to the skillful drivers on the editorial and production teams, every week we did arrive at the publication of an issue, and it was an exhilarating ride.

For more about Chris and her experiences on the Knight Bus … er, at Nature … read on over at Story Collider, where her story has been filed under “Stress.” For good reason.

 

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

Pregnancy 101: On the cervical mucus plug and why I’ve never been more happy to hold something so disgusting in my hand

Like the eye of Sauron drawn to the One Ring, one cannot resist looking at the mucus plug.
June 3rd, 2007 fell on a Sunday. I awoke that morning feeling disappointed that I was still pregnant. My due date had come and gone and, honestly, I was sick of being a human incubator. I had enough of the heartburn, involuntary peeing, and the overall beached-whale feeling. The baby in utero was resting comfortably on my sciatic nerve, and I could barely walk. And perhaps even more important was the fact that I just wanted to finally meet the child I had grown from just a few cells!

Feeling like it would never come to be, I slowly waddled into the bathroom and somehow negotiated the tall edge of the bathtub in order to take a shower. As I stood allowing the hot water to pour down my back, I looked down at the giant watermelon growing from my abdomen and literally began to beg. “Little baby, please please PLEASE make your way out today!” Right at that moment, and I kid you not, my cervix released my mucus plug and deposited it into the palm of my hand.

Video of a mucus plug being poked and prodded with tweezers. Watch at your own risk.
Suddenly, I saw the light at the end of the pregnancy tunnel. I excitedly called for my husband. “Jim! You have to come see this!!” He came running in as he was already on edge, given the circumstances. “My mucus plug came out! Do you want to see it?” As much as he tried to resist looking at something that was potentially grotesque (and it was), instinct overrode logic. His actions did not match the words coming out of his mouth, which were along the lines of “hell no!” and, like Sauron responding to the wearing of the ring, his eyes were slowly drawn down to what was gently wobbling in the palm of my hand.   

The human eye is poised for setting its gaze upon things that are aesthetically pleasing and the mere mention of the word “mucus” could potentially elicit a queasy feeling in one’s gut. However, mucus plays a significant biological role in our bodies. In general, the mucus serves as a physical barrier against microbial invaders (bacteria, fungi, viruses) and small particulate matter (dust, pollen, allergens of all kinds). Protective mucus membranes line a multitude of surfaces in our bodies, including the digestive tract, the respiratory pathway, and, of course, the female reproductive cavity.

But when it comes to matters of ladybusiness, the function of mucus goes beyond that of a microbial defense system. Produced by specialized cells lining the cervix, which is the neck of the uterus and where the uterus and vagina meet, mucus also plays a role in either facilitating or preventing sperm from traveling beyond the vagina and into the upper reproductive tract.

For instance, cervical mucus becomes thinner around the time of ovulation, providing a more suitable conduit for sperm movement and swimming (presumably toward the egg). Furthermore, some components from this so-called “fertile” cervical mucus actually help prolong the life of sperm cells. Conversely, after the ovulation phase, normal hormonal fluctuations cause cervical mucus to become thicker and more gel-like, acting as a barrier to sperm. This response helps to prepare the uterus for pregnancy if  fertilization happens.

During pregnancy, a sustained elevation of a hormone called progesterone causes the mucus-secreting cells in the cervix to produce a much more viscous and elastic mucus, known as the cervical mucus plug. In non-scientific terms, the mucus plug is like the cork that keeps all of the bubbly baby goodness safe from harmful bacteria. It is quite large, often weighing in around 10 g (0.35 oz) and consists mostly of water (>90%) that contains several hundred types of proteins. These proteins do many jobs, including immunological gatekeepers, structural maintenance, regulation of fluid balance, and even cholesterol metabolism (cholesterol is an ever important component of healthy fetal development).
As a woman nears the end of a pregnancy, the cervix releases the mucus plug as it thins out in preparation for birth. Often, the thinning of the cervix can release some blood into the mucus plug, which is why some describe the loss of the mucus plug as a “bloody show.” However, losing the mucus plug is not necessarily an indication that labor is starting. Activities like sex or an internal cervical examination can cause the mucus plug to dislodge. It can fall out hours, days, or even weeks before labor begins. In my case, the loss of my mucus plug was associated with the onset of labor, which is why I have never been so happy to hold something so disgusting in my hand. 


Last week, I told the story of my two births, including the loss of my mucus plug, at an event called The Story Collider. I described the mucus plug as “a big hot gelatinous mess.” I pushed it a bit further by providing the following graphic imagery: “Picture a Jell-O jiggler, but instead of brightly colored sugar, it’s made up of bloody snot.” I was pleased with the audience response, which mostly consisted of animated face smooshing accompanied by grossed-out groans and sighs. For the rest of the evening, I heard people call to me from all over the bar by screaming “MUCUS PLUG!!!” Given the importance of the mucus plug during pregnancy (and mucus in general) combined with its comedic potential, its no wonder that it was a hit. Go mucus!


Jeanne Garbarino, Double X Science biology editor

References

Kamran Moghissi, Otto W. Neuhaus, and Charles S. Stevenson. Composition and properties of human cervical mucus. I. Electrophoretic separation and identification of proteins.. J Clin Invest. 1960 September; 39(9): 1358–1363.

Lee DC, Hassan SS, Romero R, Tarca AL, Bhatti G, Gervasi MT, Caruso JA, Stemmer PM, Kim CJ, Hansen LK, Becher N, Uldbjerg N. Protein profiling underscores immunological functions of uterine cervical mucus plug in human pregnancy. J Proteomics. 2011 May 16;74(6):817-28. Epub 2011 Mar 23.

Ilene K. Gipso. Mucins of the human endocervix. Frontiers in Bioscience 2001 October; 6, d1245-1255.

Merete Hein MD, Erika V. Valore MS, Rikke Bek Helmig MD, PhD, Niels Uldbjerg MD, PhD, Tomas Ganz PhD, MD. Antimicrobial factors in the cervical mucus plug. American Journal of Obstetrics and Gynecology 2002 July Volume 187, Issue 1, 137-144

Naja Becher, Kristina Adams Waldorf, Merete Hein & Niels Uldbjerg. The cervical mucus plug: Structured review of the literature. Acta Obstetricia et Gynecologica. 2009; 88: 502_513

Welcome to the 21st century and welcome to MARS

Parachutes and SKY CRANES!
Image credit: NASA. Woohoo, NASA!
by Emily Willingham, DXS managing editor, who totally stayed up to watch all of this unfold

Update: Check out below what you see in the above graphic, except that it’s a real image of the real rover with its real parachute, heading for the surface of Mars! Image by way of the Bad Astronomer, a.k.a., Phil Plait. 


Via NASA.
Because we are freaky, geeky, and totally tweaky excited about the Mars Curiosity landing (woohoo!), today we bring you a links roundup related to this event. For some perspective–my own–I was born the year before the first people walked on the moon, an event known as the Moon Landing. That day was such a big deal that in a photo book of baby images capturing my first year, six dim Polaroid photos of the moon landing take up the entire last page, fuzzy, blurry images of our ancient Zenith television, including one of an Earth-bound Walter Cronkite (I still miss that man) wiping his face in disbelief. As someone who was born in the mid-20th century and knew and lived with people born in the 1800s, I am in awe of what I’m seeing today in the second decade of the 21st century.

You can relive that moment from 43 years ago in the video below. You might even recognize the real-life versions of some of the characters who featured in Apollo 13, one of my favorite movies. I also am a fan of Janet Armstrong’s hair in this video. The entire clip sequence is typical ’60s news television and features a strikingly young Mike Wallace. Armstrong is on the moon at around 9:39. “One small step for man… “


The moon is a mere 238,900 miles away from us. We could practically fly there on a space plane (assumes this biologist). But Mars? That’s 350 million miles. The rover we just dropped on the planet, using technology with shades of the latest Star Trek movie, will spend a planned two years roving the red planet, sending back data about what it finds. The Great Hope, of course, is that one thing it will find is signs of Life.

Now, enjoy this video of the successful Curiosity landing from the wee hours this morning. “Thumbnails complete! We’ve got thumbnails! Woohooooo!” My favorite quote: “You can see dust particles on the window!” 



Then, visit NASA’s page dedicated to the Rover Curiosity, where NASA’s posting great images from 350 million miles away.  

Our own physics editor, Matthew Francis, has a post up over at his blog, Galileo’s Pendulum, giving a personal perspective on this historic event. He’s also included links to a post by Emily Lakdawalla telling us what comes next for Curiosity and to ArsTechnica’s retrospective overview of Mars missions

The L.A. Times, near ground zero of mission control, has a lengthy piece complete with links to photo essays. Worth exploring and enjoying. 

Finally, just follow Mars Curiosity itself @MarsCuriosity (natch) and follow along at the related hashtags:

A couple of these are currently even trending on Twitter, which gives me hope for science and humanity. In that spirit, I leave you with a screenshot of this tweet from Story Collider’s Ben Lillie:


Science, FTW! We sure have come a long way since 1969, baby.