Monday, July 9, 2018

Is the US Prepared for an Influenza Pandemic?

I am in post-CONvergence 2018 recovery. Thanks to all who came to visit and listen to what I have to say! I was thinking about a post-CVG2018 write-up, but I think discussing pandemics is a great start to the post-CVG2018 life. Why? Because of CONcrud... you know, that head or chest congestion, sore throat, and headache that comes with sub-zero hotel room air and close contact with strangers. It's like watching in mini-pandemic. So, let's talk about pandemics!

It has been 100 years since the great influenza pandemic of 1918, which infected over 500 million people worldwide and killed somewhere between 50 and 100 million people. (Note: The death toll is hard to estimate accurately due to difficulty in tracking deaths in some countries, like India. The most recent estimates suggest that the death toll was closer to 100 million people.) The 1918 flu dropped the life expectancy in the United States by 12 years. In addition, while most influenza deaths occur in young children, older people, and people with compromised immune systems, the 1918 flu caused high death rates in young, healthy people.

This year had a particularly nasty influenza season, you've no doubt seen it on the news. The number of pediatric deaths due to influenza is up compared to previous seasons (See CDC for current epidemiological data) and more people have been hospitalized for influenza related complications. Because of the 100 year anniversary of the 1918 pandemic, experts and planners are looking back to the past and at our current infrastructure to determine if we are prepared for the next pandemic.

We've had 100 years to figure out to do with the next "big" pandemic. (Note: there have been several pandemics since 1918, but nowhere near as devastating.) Science has sped forward and thousands of new treatments for thousands of diseases have been developed. We have a better understanding of how influenza infects, how the human body responds to infections, and how to prevent infection. But, is the US ready for another "big" pandemic?

Short Answer: NO

Long Answer:
This year I was able to attend the ASM BioThreats 2018 meeting (American Society of Microbiology) and from experts in the fields of infectious disease, emergency preparedness, public health, and pharmaceutical (vaccine and antiviral) research, it seems as though we have not made much progress in preparedness since the 1918 influenza pandemic. There are a several reasons that are, in my opinion, indicative of our lack of preparation:
  1.  Lack of an effective universal influenza vaccine. While I hope you all  go out and get your flu shots every year, you may know by now that those vaccines take 6+ months to produce and the strains of influenza targeted by those vaccines is all based on educated guesses by scientists and epidemiologist. While these well-educated professionals do their best, their predictions can be wrong. That was the case this year - the predictions were wrong. What does this mean? It means that the vast majority of people who got the influenza vaccine are still susceptible to getting the most common strain that is causing disease. To better address this issue, many biotech companies and academic labs alike are working on developing a universal influenza vaccine, which would mean it could protect you from most strains of influenza. I am happy to go into the science behind that if you really want to know (post a comment or email me!) Predication is only one of the issues that are causing a problem with the vaccine. The length of time and method for producing the vaccines are based on technology from the 1950s and can cause major issues in people with egg allergies.
  2. Lack of effective antiviral treatment options. You have probably heard of Tamiflu, a medication developed to help treat the symptoms of influenza. It has okay efficacy and can shorted the duration and severity of symptoms when given early on in illness (within 48 hours of symptom onset). However, patients don't often visit their doctor within 48 hours of symptom onset, nor do they know if what they have is influenza or something else. Thus, few patients are able to receive Tamiflu early enough for it to be effective. Ideally, prevention is the best medicine (vaccination, quarantine), but more effective options for influenza treatment after a patient has become ill are needed.
  3. Lack of appropriate training of health-care professionals. We saw it with Ebola, even when people are supposedly trained in appropriate handling/care of infectious patients, most are not trained well enough. If they were, we would not have seen nurses or other caregivers with Ebola exposure. Now, while there is no threat, is the time for hospitals to train and exercise their staff on appropriate protocols. This may include in-class training as well as a walk through of actions needed to take care of infectious patients including donning and doffing personal protective equipment, decontamination techniques, and post-exposure prophylaxis. However, it is expensive to pay people to train and hospitals being in the health care BUSINESS are reluctant to pay staff to work without being able to bill patients for that time and effort. I will stop there because my universal healthcare rant could be its own blog post.
Individuals (read: you) should also be taking protective measures in your daily life before the flu season even begins:
  1. Vaccinate yourself and your loved ones. It's not perfect, but it DOES help reduce the risk of getting influenza as well as reduces the severity of disease if you do get it.
  2. Cut it out with the hugs and handshaking. It sounds impersonal, but this close contact is how influenza spreads. 
  3. Wash your hands and quit touching your face. If you do come in contact with someone who is sick, you will reduce your chance of getting it.
If you're already sick:
  1. STAY HOME. I can't stress this enough. Just. Stay. Home.
  2. If you insist on going out, WEAR A MASK and wash your hands frequently. If you're afraid of looking weird, tough crap, you're a walking cloud of disease like Pigpen.
Don't be this guy (Credit: Wikipedia)


Sadly, until the US and the country's hospitals and clinics are better prepared, your safety is in your hands.

Tuesday, September 12, 2017

Leaving Academia

I want to change pace just a little bit. Many people that I meet when doing outeach activities are young scientists - grad students, undergrads, and even high school students, who are interested in becoming scientists. I thought that being a scientists meant being at the bench and doing research for the rest of my life. It turns out that I was wrong about what path I would take.

About two years ago I had to make the agonizing choice of whether or not to leave academia. They say, once you leave you can't go back. I do want to talk about my decision and how it came about.

In graduate school, I was sure I was going to go for a faculty position. Once I graduated, I went on to a post-doc in a prestigious lab in my field. I found out quickly that my advisor, like so many academic scientists, was having trouble procuring funding for our project. I was on my own T32 grant for three years, which I thought would be enough time for a grant to get funded and I could continue on my progess. It was not. Two years into my post-doc, I jumped ship to another lab to extend my skill-set (from bench science to bioinformatics). Both my new lab and my old lab had no funding for me past my own 3 year grant. It was tough decision time. 

At the time my post-doc was ending, I saw two colleagues get faculty positions: one had been at his post doc for 7 years, the other at hers for 10 years. 10 years... they had both applied for tens of positions for years prior to landing their coveted faculty positions. What could I do as a post-doc without a lab that could house me for another 4-7 years?

The answer was nothing. I may have been able to scramble for a third post-doc position, but by then my resume would have been unappealing to universities (why did she have to do THREE post-docs??) Instead, I went ahead and made the tough descision to leave academia.

My first challenge was to convert my CV into a resume. I could list all of my skills and put it into the proper format, but I forgot to translate so many of my skills to my resume! It's a problem so many PhDs have. We can list all of the assays and experimental procedures we need to do, but that list lacks the depth of knowlege and full skill set we have. A few things I forgot I could do:
  • Write/edit for scientific publications
  • Ability to communicate complex scientific topics for a wider audience
  • Project Manage
  • Mentor junior graduate students and undergrads
  • Problem solve
Once I had a decent resume put together, I had to face the inevitable challenges of the job market. I had full confidence in myself, but I have always had trouble selling myself. I filled out application after application. I tailored my cover letter and resume to each job description, I followed all of the steps I was supposed to take, and I was met with silence.

I know this happens to EVERYONE, not just those looking for jobs in science. But seriously, why not make a digitally generated rejection letter? It's not hard!

When I did land a coveted interview, I had additional personal stuggles to face. For those of us who are not personable (and I have been told a million times that I come off a cold or distant) it means we have to work harder than the average bear. We have to change our personalities in order to play the game. It's tough to do, but I've done it with some success. FYI I come off as cold and distant because I don't volunteer information about myself as much as others do, because I assume everything will think I'm boring (who wants to hear about bagpipes and hula? No one). During interviews I had to mask my true personality with "Dr. Positive" and become bubbly and excited. I'm not entirely sure this is a desired trait in professional women specifically, or if it's necessary for men as well, but it was exhausing. 

Finally, what landed me my job is a friend from graduate school. She fought to get me hired on, saying that I was the type of person she desperately needed on her team. I learned right there that networking was the only way into a job these days. Very few companies seem to hire anyone, even interview them, without and in-house recommendation or something on their resume that the company can exploit for business purposes. It's frustrating for the job applicants, to say the least, but it seems to be the way of the world these days.

Tuesday, August 22, 2017

The Nasty Fate of Scientific Articles in the Media

When I was in graduate school, one of may papers was chosen by the university for a press release. That's when I learned first-hand what happens to science when it passes through the filters of the media. Here's how it went:

Step 1: We sent the paper to the press release office, where someone read it and write the first draft of the press release. We later learned that this was a fairly entry-level position and the person responsible for writing the press release was a communications major with no scientific background.

Step 2: We were able to edit our press release and correct some of the conclusions the press release writer seemed to find. We converted the more sensational language back to more scientific non-committal language. For example, we changed "X does Y!" to "The study shows that X may contribute to Y happening." In otherwords, we made it a lot less exciting again.

Step 3: Repeat steps 1 and 2.

Step 4: The press release goes out! LOOK! WE'RE ON THE INTERNETS ON A WEBSITE! It was exciting, for sure! Then we watched more and more places pick up our press release and summarize it even more.

Step 5: Watch your hard work get further distilled into sensationalist conclusions and inaccuracies.

Step 6: Give up.

PhD Comics did a pretty accurate cartoons about it here. I have to say, ours kind of stopped around step three of the comic's cycle, no one is really that interested in fungi unless they're watching Monsters Inside Me. But I've certainly seen the rest of the cycle happen to other perfectly respectable papers.

Why does this happen? 

  1. It happens because of a lack of scientific acumen in the science reporters of the world. Most of them weren't science majors or have not had rigorous training in scientific reporting. It's a crying shame, because how many of you think we have cured cancer a thousand times? Well, we've discovered certain drugs help reduce the tumor size in certain cancers, but that information got distilled by the science reporting cycle. Someone read "has been shown to reduce tumor size" and translated that into "treats" which later got translated into "cures." Publishers of these articles (including newspapers, popular news websites, etc) could and should hire scientists to be their science reportetd or else spend some money to send their science writers/reporters out to get some education. If a someone writes to the editor to correct errors, the editors shouldn't blow them off, they're trying to help (totally had that happen after I saw a very facutally incorrect news story).
  2. Clickbait is way more exciting than facts. I mean, I get it. I have a tendency to click on certain kinds of clickbait (sorry, I like lists!!) BUT when it comes to SCIENCE, clickbait pretty much undoes everything that we work so hard to do. No scientist thinks that they've "cured" something and no scientists "hate her" because a regular Jane discovered that baking soda cures skin cancer (it doesn't).
How do you know? Read my post Is it fake? Read the original article. Even if you can't, try reading the abstract, which is a summary of the article written by the authors. If all else fails, ask someone! You can certain ask me, or find a friendly neighborhood scientist and ask them. 

Monday, August 7, 2017

Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells

On July 6th, 2017 Science published a brief article titled "How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA." I thought it was an important thing to look at both scientifically and ethically. The general public often hears about intersting or new discoveries and advances in science but don't always fully understand the implications of such news. In the Science article, they describe how a Canadian research team, led by David Evans from the University of Alberta, were able to reconstruct a pox virus that is closely related to smallpox.

Image from http://www.sciencemag.org/news/2017/07/how-canadian-researchers-built-poxvirus-100000-using-mail-order-dna

Why aren't we looking at the primary literature? I need to first point out that this particular article is not primary literature. The scientists have discussed their findings but have not yet published the paper on it. Part of that is because it has been rejected twice - once from Science for not really adding much to the current knowledge we have and the second was by Nature Communications for unknown reasons. There is a debate as to whether or not it is ethical to even publish the data. The risk with publication is that someone can take the materials and methods and create the virus that causes smallpox for bioterror purposes.

What do I need to know before I read the article? Variola virus is the causitive agent of the disease smallpox; horsepox is closely related to variola virus. Smallpox was elimited through a worldwide vaccine program and the last cases of smallpox occured in the late 1970s. On May 8th, 1980, the world was deemed smallpox free. (For additional information on smallpox, see the Centers for Disease Control and Prevention.) Since that declaration, the vaccination of the public ceased, leaving the vast majority of the population susceptible to contracting smallpox. The majority of smallpox samples have been destroyed or are stored in Russia or the US (at the CDC). 

What did Evans et al do? According to the article, which is purposely vague, Evans et al ordered the horsepox genome in multiple sections of DNA. Each section of DNA had a section of overlap that allowed for homologous recombination. Thus, the scientists were able to stitch together a bunch of small pieces of DNA into long pieces that made up the entire horsepox genome. Evans et al then introduced the genome to cells in vitro, which were able to be infected by the naked genome and start producing viable viral particles. It is important to note that there are a number of virus genomes that can be infectious, this is not unique to poxviruses.



The technology used by Evans, et al, was based on a 2002 Proceedings of the National Academy of Science (PNAS) paper by Domi and Moss. The article, "Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells" describes a method for reconstituting vaccinia virus in vitro. Again, this suggests that the technology isn't really novel, but a continuation of previous work. What was novel with what Evans et al did was that it was cheap. The final bill for the work was around US$100,000, making it finanically as well as technically feasible, hence the ethical issues.

The scientific community has faced such controversy previously, one example is when a group of scientists produced a pandemic-flu in the lab (see this article for more information or here for an article by the researchers). There are several things to consider when debating the ethics of such research:

  • Does the research provide useful information? In other words, what are the benefits of the research overall? For some controversial studies, the research gives insight into the evolution of deadly diseases or steps to treatments or vaccines, such as the work by Yoshihiro Kawaoka, the scientist that researched highly-virulent strains of influenza. Other work provides little new knowledge beyond the technical.
  • What are the risks to the general public? It is easy for scientists to sometimes forget that the strides they make in the lab could potentially put the public at risk. Often, their goals are to gain knowledge and insight into biological processes that can lead to helping people in the long run. The hope is that the research they are doing will lead to great strides in their fields and open doors to new treatment options, drug targets, and vaccines. In today's political climate, and post-Bacillus anthracis attacks in the US (B. anthracis is the causitive agent of the disease anthrax) scientists and government agencies need to consider the use of recreated or hypervirulent microbes for bioterror attacks. Thus, there is another layer to the risk taking in letting some knowledge out to the general public through publications where scientists who are more nefarious can take it and create bioweapons.
  • Do the pros outweigh the cons? The scientific community will always debate such controversial studies. It is often up to ethics boards and journal editors to make the tough decisions to publish or not. 
In the end the scientific community, including ethics boards and journals, look at each study on a case by case basis. The Evans et al article has been rejected twice now, it will be interesting to see if any journal will pick it up and publish it. 

Personally, I hesitate to pass judgement unless I have more knowledge of how Evans et al's work is different from previously published studies. I can speculate, but without reading/hearing about the exact experiment, it's hard to judge the level of danger to the general public. I do trust the opinions of journal editors, reviewers, and ethics panels to make the appropriate decision. What do you think? Should they publish it or not? Why? Let me know in the comments!

Wednesday, August 2, 2017

Opinion versus Scientific Conclusion: What's the difference and why is it a big deal?

Climate change, vaccines, cures for cancer, "big pharma"... these are all ideas that are commonplace in the news and someone is always chiming in with their opinion on them. There is, however, a lack of understanding between an opinion and a scientific conclusion. I'd like to clarify the difference here.


A simple Google search shows that an opinion is "a view or judgement formed about something, not necessarily based on fact or knowledge." Everyone has an opinion, and opinions are ok to have. Opinions can be based on the available data (what you've read), or how you feel, or maybe a gut instinct. Opinions can be swayed based on what someone else says and whether or not you believe them. You can integrate your new knowledge into your personal database and your opinion may or may not change.

A scientific conclusion is backed up by data. There must be enough data to support the conclusion and conclusions can change based on the data available. This is why eggs were bad for us, then good, for us, then bad for us again. The scientific community is always producing more data, which can change the conclusion. The key here is that there is always data. Without data, it is not a scientific conclusion but rather it is an opinion.

Scientists can have opinions too, especially when we discuss "models." A scientific model is usually proposed when a scientist has some information about a process but there are holes. They often speculate on what might be happening with the idea that they will create experiements to fill in the holes and can and will change their model once they have additional data.

What is the problem with opinion and a scientific conclusion? Often, the general public gives as much validity to the opinion as they do to the scientific conclusion. In the world of the general public, an opinion weighs just as much as a scientific conclusion when the scientific conclusion should be given more weight.

There is a certain amount of trust in scientists needed for those members of the public that do not read or cannot understand the primary literature. Practice is needed to learn how to think critically about a study or article. THAT'S OK! It take time and practice. If you don't have the time or desire to read primary literature, that's ok too. Take a look at my previous post "Is it Fake" for ways to find good summaries or news articles on scientific studies.

Monday, July 17, 2017

Hitting the Scientific Pay Wall

Hitting a paywall can be incredibly frustrating when you're searching for primary scientific literature. For those of us who are "casual" readers of science - in other words, we're reading it to learn about it for fun and not work or school, there are many options for open access journals where you can peruse full articles.

Image from http://runawaytrader.com/

For a directory of open access journals, check out the DOAJ (Directory of Open Access Journals, of course!) Some of my favorites of the biology based open access journals are the Public Library of Science (PLoS), which I have mentioned in the past, which has a variety of different journals on many scientific topics. Another is mBio, which is relatively new journal published by the American Society for Microbiology that started up within the last five years or so. PubMed is the most commonly used search engine for scientific articles for those in the biological sciences. Many articles that have never been or are no longer behind a paywall can be found linked through PubMed. 

If you're a student (I'm talking university here, unfortunately), you can usually log into or connect to your university library and access most articles, as long as your institution has an scubscription. Once you're logged in, PubMed will show links to the articles that are available through your university. If you do hit a paywall, ask your local librarian if you can borrow the article from another library. They can often get the article (even a PDF) for you from another institution.

High school students might be able to access some journals through their library if the schools have agreements with local universities. It never hurts to ask your friendly locak librarian! 

One other source I think is useful is the Faculty of 1000 (F1000), which has a relatively low subscription rate ($9.95/month) and it will give you article suggestions and summaries of new articles that are written by scientists in the field. In other words, F1000 is where the smart kids go to talk about the work that excites them that's been done by other smart kids.

Being a biologist, I know that I have neglected pretty much every other field out there. I invite anyone who is an expert in any scientific field to chime in with any other suggestions for open access articles! Please comment below.

Monday, July 10, 2017

Is it Fake?

This past weekend, I spent a considerable amount of time at CONvergence in Bloomington, Minnesota. CONvergence is my opportunity to interact with a wide variety of geeks/nerds and talk about a wide variety of subjects.

While I am a huge fan of board games, I spend the vast majority of my time on science panels talking about my work and general cool science stuff. Several of this year's panels focused on how people can tell if a science article is fake or not. My panelists and I (including Doctor V) came up with some excellent criteria.

  1. If they don't cite the original article or study, it's probably no good. Good writers and scientists are taught to cite their sources when possible. When a study comes out, the article should be linked or the source should be cited. For example, if a new study shows that chocolate lowers blood pressure, the article should either have a direct link to the study or say "In this month's issue of Nature, a study by [author(s)] shows that chocolate may lower blood pressure."
  2. If the article has a grandiose declaration, it's likely fake or poorly reported. A lot of websites want to drive traffic to their site. By stating that something "cures cancer" or "cures all diseases," websites can generate more traffic. Unfortunately, if you see these statements it's likely click bait and less likely that the article is truthfully reporting the science.
  3. Check the website. If the site is a known click bait site (Natural News, Info Wars) you are likely reading poorly reported or fake science articles.
I've given you some guidelines on what to look for, but how do you find good sources?
  1. Blogs! That's part of why I wanted to start this one! Look for blogs by reputable scientific journals and scientific societies (we'll talk about that in a second), scientists that are experts in their fields, and groups that publish articles written by the primary scientist who did the work or someone who has a good understanding of the field.
  2. Reputable journals and scientific societies often publish magazines or blogs that summarize (often in layman's terms) and highlight the research in their latest journals. I personally enjoy Microbe Magazine, put out by the American Society for Microbiology. They also have additional blogs written by the scientist who did the research. 
  3. Primary literature. The best way to learn about science is to start reading about the science. Primary literature can often be very difficult to understand at first, and you may have to look up a lot of terms on Wikipedia (usually a good source of general information that cites sources), but once you get a few papers under your belt, they become easier to understand. Many are found behind paywalls, but the Public Library of Science (PLoS) and others have open access journals.
I'm going to try my best to highlight recent scientific articles and talk about the science (the good, the bad, and the ugly) in this blog. I'm happy to take suggestions or answer questions directly as well! You can email me with your questions or articles. 

Is the US Prepared for an Influenza Pandemic?

I am in post-CONvergence 2018 recovery. Thanks to all who came to visit and listen to what I have to say! I was thinking about a post-CVG201...