Everyone wants to be noble

              Science is gathering data and trying to make sense of it.  Just like detectives piecing together clues from a murder mystery, scientists take small hints about a world we cannot see and stitch a story that encompasses all the evidence we’ve gathered.  Our stories are models, which are different than facts.  The motive for murder is a model pulled together along with admissible evidence by detectives and tested in court.  The truth will never be known 100%, but the most probable way to explain what the police do know happened for sure becomes the working model for the lawyers.  Similarly, scientific models are pulled together by experimental evidence and tested in other experiments and in peer-reviewed work.  

                Let’s look at an example of how a model is built.  Facts: Amy spent her day at the park, then had a dinner of steak and mushrooms.  Following her dinner, she developed hives.  She would like a model to explain what caused the hives.  Experiments: The next week after her hives were gone, she went back to the park.  That night, she didn’t have any hives.  The next day, she ate a dinner of steak.  No hives.  Finally, she ate a dinner of mushrooms and that night developed hives.  Experimental Model: All of her experimental evidence suggests that she is allergic to mushrooms.  At this point, it is not proven that Amy is allergic to mushrooms, but it takes the experimental evidence and fits it with the known facts, thus creating a good working model for her: if she doesn’t want hives, then she should not eat mushrooms.  The model might be further amended as she gathers more evidence.  For instance, she might find out that only raw mushrooms give her hives while cooked mushrooms do not.  More evidence has refined her model.  This is very similar to how scientific models are created, reviewed, and updated.

                Models have been developed to explain what an atom looks like, how atoms behave, how atoms form bonds (actually, two models exist for this – some molecules are easily explained by one model and other molecules are easily explained by the other model; strange) and basically everything that happens at the level of atoms, molecules, cells, organs, etc.  

Our topic today deals with molecules and started with an observation about a special group of atoms.  If you look at the periodic table, the furthest right column is called the inert gases or the noble gases (Figure 66.1).  Scientists labeled them as such after they discovered that, no matter how they tried, these gases simply would not form molecules with anything else.  Carbon, oxygen and nitrogen readily jumped to form new molecules like carbon monoxide (CO), carbon dioxide (CO₂) or diatomic nitrogen (N₂), but helium, neon and argon couldn’t have been less interested.  They wanted to stay as neon (Ne), argon (Ar) and helium (He) only.  Why?  

Most people know that atoms are small nuclei comprised of neutrons and protons with electrons whirling around.  The sharing of electrons is also what causes two atoms to form a bond.  (I touched on this in my post What Does Water Look Like?)  Scientists needed a way to explain how these electrons are arranged and came up with a good working model, which I will explain very briefly here.

                Think of a school with two playgrounds.  The first playground is very close to the school building while the second one is a bit further away.  The first graders may only play on the close playground.  The fifth graders can play on either playground, but they mostly choose the further away one because what respectable fifth grader hangs out with six year olds?

                Okay, keep this in mind when we talk about electrons.  Let’s say an atom has six electrons.  Two of these six are like the first graders; they have to stay closest to the school building (nucleus).  The remaining four electrons have their choice of hanging close to the nucleus or being further away; most will be found further away. 

                The two electrons that must stay close to the nucleus are not involved in bonding with other atoms.  They are simply too close to the nucleus and are not interested.  It is the remaining four, which are predominantly found furthest away from the nucleus, that are involved in bonding.  Let’s call the electrons that are predominantly found furthest away the valence electrons.  An atom has room for eight valence electrons.   This particular atom only has four.  It would really really rather have eight.  How can our atom get four more electrons?  Why, by sharing electrons with other atoms!

                Check out Figure 66.2 and the water molecule I showed you in the What Does Water Look Like? post.  Each atom in a molecule or the neon alone has eight electrons around it.  The carbon or oxygen atoms alone have less than eight so they form a molecule such that, after sharing, each atom then has eight. 

                After investigating the electron counts in many different molecules and looking at the electron counts in the noble gases, scientists developed a model for why atoms form molecules.  It is summed up nicely as “Everyone wants to be noble.”  The inert gases have eight valence electrons already.  Atoms that do not have eight valence electrons form bonds (share electrons) with other atoms such that, once the sharing occurs, their valence shells will have eight electrons.  Everyone wants to have eight electrons.  The noble gases already have eight electrons so it is said that all other atoms want to achieve eight electrons to be like the noble gases.  Everyone wants to be noble.

* - Okay, one little thought: the water molecule in What Does Water Look Like? clearly shows that hydrogen only has two electrons around it.  Why doesn’t it have eight?  Well, because scientists realized that hydrogen and helium were different than every other atom.  Instead of wanting eight electrons, both of them are fine with two.  Every other atom follows the octet rule (I want eight electrons!); hydrogen and helium follow the doublet rule (two is cool).

                There are at least eight more posts I could write about electron configurations to fully explain what valence electrons truly are, where they hang out, what an orbital is, how orbitals change in an atom versus a molecule, etc.  However, the sentiment of this post remains true.  Rest assured, so much more could be said on this topic!

REFERENCES

Zumdahl, Steven S. “Chemical Principles, 4^th Edition” (2002) Houghton Mifflin Company, Boston, MA.

A Cry from a Scientist

                 This post is going to be a lot of venting so I apologize in advance.  However, part of science is anger – full-fledged, I want to throw something against the wall (or kick a trashcan across the room) seething rage.  Mine has been building up for close to two years and there are days when I feel like I can’t take it much longer.  Lucky you gets to read it, but at least you can read it knowing that I am not the only scientist with these thoughts or rages.  At one point or another, all professionals reach a point where life has handed them too much.

                I read a lot of message boards about various life topics.  I enjoy being able to escape science every now and then because, let’s be honest, when your experiments aren’t working, you are about two inches away from jumping off a cliff.  Recently, I’ve been reading my fair share of pregnancy and marriage boards because that’s the state of life I’m currently living.  It’s interesting to hear from real people about what happens next.  Unfortunately for me, I’ve read too many vaccine debate threads recently.  They make me want to tear my hair out.  It’s no one’s fault, of course – the internet is littered with horrible websites expounding ideas that are entirely false.  And then, in this celebrity-obsessed culture, we have Jenny McCarthy spewing some of the most inaccurate theories ever that some people are more than willing to lap up, so I want to throttle her.  Plus, we have the media who finds a story and holds onto it obsessively like a dog that has gotten his very first treat.  One paper linked vaccines to autism; tens of papers have since refuted it and all but one of the authors on the original paper has recanted.  Yet, the “debate” rages on. 

Today, an article appeared on CNN.com entitled “Science journal could provide recipe for bioterrorism.”  I cursed too many times to repeat my exact reaction here when I read it.  The best part?  It’s at least a week too late; Nature published one of the two articles in question last week.  I posted about it on both this blog and Dr. Amedeo.  So, if the recipe for bioterrorism is out there (which it really isn’t) then it was leaked seven days ago.  But, you know what really gets me about the article?  It’s inflammatory journalism about a topic that not too many people have the background to understand.  I am in no way saying they are ill educated - I am saying that they need the proper setting to understand why these papers are linked to bioterrorism and to see that they aren't.  CNN.com doesn't provide such context. They just spew out words like “avian flu,” “pandemic,” and “d-e-a-t-h” so people will read it and think that scientists are irresponsible.  The fact that a moratorium was placed on this research months ago and that many major scientific institutions discussed the research before publishing it is inconsequential.  Scientists are out to make a super-duper avian flu, they are unethically publishing this work, bioterrorists are going to read it to kill us all, and we’re definitely covering up that vaccines cause autism.  Oh, and we’re responsible for all the “chemicals” in the world.  What else?

Let me just be one scientist to say: holy god, we are NOT doing any of the above.  Also, don’t get your scientific information from your local news, CNN, FoxNews, a freaking celebrity or anyone other than a real live, honest-to-goodness scientist with a Ph.D. who has done real research that has been published in a peer-reviewed journal.

Let’s also talk about these statements: “All this money given to scientific research and they still don’t have a cure for cancer!” or “How has science not come up with a medication for that yet?”  Believe me – if it’s a subject worthy of research, someone out there is working on it.  Do you know how many labs are working on cancer research?  “Cancer” is also such an all-inclusive word.  Each cancer is different and has its own set of problems.  This isn’t going to be a one-medicine-fits-all cure.  Scientific research is also expensive.  Supplies, ideas, and troubleshooting experiments take time and money.  And don’t think that the scientists doing the research are making money hand over fist here, either.  I could tell you what I made as a graduate student (which is a position in lab just as hard-working as a post doctoral associate or staff scientist), but I don’t want to scare off anyone who might be interested in science.  What I make as a post doc is a matter of public knowledge and can be found on the NIH’swebsite.  Yes, the government determines the worth of my Ph.D. and, let me tell you, they don’t think highly of it.  The scientists who are doing the cutting edge research are not fairly compensated for their time, efforts, and thoughts.  And then, as a thank you for all the work we do, we are slandered in the media, discussed incorrectly by the general public, and generally on the receiving end of all sorts of fear-mongering.

All of this goes back to why I write this blog.  I want people to understand.  I want more people to get it.  I wish everyone understood that we’re in the trenches here, getting little recognition or payment and doing it out of our love for science.  I’m sure every profession has a part of the experience ladder like this.  I am not special or different, but I at least have a platform to vent my frustrations.  I know that my husband could sit down and write an equally impassioned post about how lawyers are thought to be something they aren’t, as well.  He has taught me quite a bit about how the law profession works and removed a lot of my knee-jerk reactions to lawyers.  He should get a blog, too.

Read Science (www.sciencemag.org) or Nature (www.nature.com) for excellent information pertaining to scientific topics.

Controversial Influenza Research

              Two papers were submitted to the journal Nature in August 2011 that dealt with influenza.  One came from the University of Wisconsin-Madison lab of Yoshihiro Kawaoka; the other from a team at the Erasmus Medical Center in Rotterdam, the Netherlands, and was headed by Ron Fouchier.  To say that this research caused a stir would be an understatement.  A “pause” was placed on this research in both countries due to fears from the community about viral release (the original letter and a note about it was found on my other blog, Dr. Amedeo).  Meanwhile, the papers themselves were heavily discussed by Nature editors, the World Health Organization, the general public and the US National Science Advisory Board for Biosecurity (NSABB).  The initial position was that, in the interest of public security, these papers should only be made available to certain people who applied for the information or published without their methods and certain key results hidden.  In a land of peer-reviewed work and government red-tape, these options were not well received.  After much discussion, the NSABB backed off and left Nature to make the final publication decision.  Nearly nine months after the papers were first received, the Kawaoka paper was published in the journal Nature, appearing online ahead of print on May 2^nd, 2012.  The Fouchier group paper will be published in the journal Science in the next few weeks.

                What was the hub-bub all about?  Pandemics.  Bioterrorism.  Freedom of information.

                I covered the influenza virus, and the Spanish influenza in particular, in an earlier series of posts on this blog, which you can find here.  Three key pieces of information from those posts are important to explaining the above papers:  

One. Two proteins exist on the outside of an influenza virus that are very important to viruses being able to bind a cell and then get inside.  They are called hemaglutinin (HA) and neuraminidase (N). Several versions of each protein exist and each version is given its own number.  An influenza virus is named for the versions of HA and N that are found on the outside.  For example, most people remember the H1N1 scare.  That particular strain of influenza had version 1 of HA and version 1 of N.  

Two. Influenza viruses are specific for certain species.  Human influenza viruses exist; avian influenza viruses exist; even swine flus exist.  In each of these viruses, the HA protein is specialized for binding to the cells in that particular animal.  The number 5 in H5 is telling you the version of HA in the influenza, and species specific nature of the virus tells you what cells that particular H5 is specialized to bind.  

Three. The specialization of each HA is not static.  Viruses quickly infect cells, replicate inside, and move on to infecting other cells and replicating again.  This is a lot of DNA replication and virus generation in a short time.  Mutations happen.  Influenza viruses gain mutations (aka evolve) quickly.  Sometimes these mutations allow for a previous version of H5 that could only bind to birds now suddenly being able to bind humans.  When these types of sudden shifts happen, pandemics can result.  The Spanish Influenza was an example of this sudden host change from birds to humans and resulted in a pandemic that swept through World War I America.

                Currently, a form of influenza called H5N1 is circulating in Indonesia, Vietnam, and Egypt among other places.  This virus is able to infect birds and has resulted in the culling of millions of birds.  578 humans have been infected by H5N1 resulting in 340 deaths.  Interestingly, there is little evidence for human to human transmission of the virus.  The virus only infected a human from direct human-bird contact.  The virus gained the ability to infect a human but not to be easily transmitted between humans.  This keeps the H5N1 virus somewhat contained and low risk to the public.  However… what if, just like the Spanish Influenza of the early 20^th century, H5N1 suddenly gained the ability to infect humans and transmit easily between them?  Well, we could possibly have a pandemic on our hands that could result in the deaths of thousands or millions of people throughout the world.  

The labs of Kawaoka and Fouchier wanted to know what changes could occur in the H5 protein that would allow it to reliably infect humans and allow for easy human to human transmission.  The Kawaoka paper highlights two areas of the protein and how they could be mutated to potentially switch H5N1’s ability to easily infect humans.  The Fouchier paper is still unpublished, but I know its focus is similar.  The concern about these papers arose from two things: 1. These labs made viruses that could infect humans.  Did these labs have regulations in place to safeguard escape of the virus from the laboratories?  2. These papers outline, in detail, how to switch the strictly avain H5N1 virus into a potential deadly human weapon.  Should that information be made public?  In the end, it was decided so.  

Kawaoka published an impassioned editorial explaining the reasoning for his research and the importance it holds to staving off future pandemics.  The WHO asked for higher safety standards, with which both labs complied and those standards will be published by the WHO in the coming weeks.  The journals wanted the option for peer-reviewed quality work (something that would not happen if these papers were only released to certain people or without methods).  In a Nature editorial, the reason for publication was outlined as thus:

Having now considered these matters in depth, the editors of this journal have decided that we will not consider either alternative for papers in Nature in the forseeable future.  A paper that omits key results or methods disables subsequent research and peer review.  Furthermore, after much internal and external deliberation, we cannot imagine any mechanism or criterion by which to sensibly judge who should or should not be allowed to see the work.  Nor do we believe that any restricted information distributed to university laboratories would stay confidential long.

If you are curious to the contents of the Kawaoka paper, see my most recent post on Dr. Amedeo.  When the Fouchier paper becomes available, I will post a similar summary there, as well.

REFERENCES:

Kawaoka Editorial: Kawaoka et al. "Flu transmission work is urgent." Nature 

Nature Editorial: "Publishing Risky Research." Nature (2012) 485, pg 5

Kawaoka Paper: Imai et al. "Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets." Nature (2012), published online ahead of print