How to Submit to Abstract 2.0

I’m very glad to finally initiate Abstract 2.0. I hope this resource will be of great help to anyone willing to utilize it.

For now, I have set up a separate website for the submission and archiving of abstracts by those who contribute. The website is

Here is an example of a re-written abstract:

Colleen T. O’Loughlin, Laura C. Miller, Albert Siryaporn, Knut Drescher, Martin F. Semmelhack, and Bonnie L. Bassler (2013) 110:17981–17986, doi:10.1073/pnas.1316981110

 A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation

 Quorum sensing is a way a bacterium communicates to the cells around it to regulate behavior of the community as a whole. This process occurs in harmless bacteria as well as pathogens. One such pathogen, Pseudomonas aeruginosa, uses quorum sensing to attack its host in a concerted effort by all the cells present and to control how the cells ‘stick’ together once infecting the host. In an effort to prevent P. aeruginosa attack and infection, researchers tested synthetic molecules to identify those which block cells from receiving the attack message. One such molecule, meta-bromo-thiolactone (mBTL), succeeded in blocking the message and protected a roundworm model system and human lung cells from dying due to infection. The paper also discusses how mBTL works at the molecular level. The results from this study could help control complications in cystic fibrosis and hospital infections due to contaminated equipment.

Abstract 2.0 Is On: Help Wanted

I have sat on this long enough. It’s not like a have anything else going on right now (except the birth of a son in a  month, syllabus to write, classes to prepare, evaluations to do, data to journal, …). Introducing:

Abstract 2.0

Here are the details presently. I and anyone willing to help will scour the journals of our respective fields and choose those we feel need to be disseminated to the larger public. In a short synopsis (abstract if you will), an overview of the article and why it is important will be written and deposited here. Details will be worked out on how to submit the abstracts in the near future.

Now is the time to act (or later if now is not convenient)!

The Science Bubble

The following link is profound. The current issue of EdgeScience takes a brilliant look at how the current era in science is more about rushing technology to market to benefit society than the underlying universal truths that must first be studied. The consequences have been strikingly similar to the ‘Housing Bubble’ and may not have fully burst yet.

Please take a look:

A STEM Book Explaining Bacteria to Kids: Begging Without the Cardboard Sign

I was recently approached about developing a children’s book to educate about bacteria in hopes of clarifying misconceptions many have about ‘nasty germs’. I must say how amazed and honored by the invitation I am. The company is small without a lot of capital to produce such a book at will. So, I was asked if I had contacts that would graciously sponsor the production of the book. This to me is bittersweet. I would love to be a part of something that would be so helpful for the public regarding the reality of microbes (they tend to get bad press in general). However, I’m not one to ask for money…ever. 

This has sparked questions in my head about the state of educational media production. S.T.E.M. is all the rage these days and rightly so. As our society progresses, the need for a workforce trained for technical and scientific positions is essential. One example…billboard signs. Growing up, I used to get excited and amazed when I saw a person putting up a new billboard sign. Taking the old one off, applying the new one in its place. However, now these signs are replaced by digital billboards. Who is going to change the billboard advertisement? Someone trained to tear down the old and glue the new one on? Someone with a background in electrical engineering? If there is a problem with the billboard, who will fix it? A carpenter or an engineer? This is just one example. 

The STEM push is necessary and welcome in my opinion. However, a quite fitting phrase comes to mind: show me the money. We are throwing money into public school systems that are fueled by bureaucracy and inefficiency. Yet we still have to cut out box tops to support local schools and have several fundraisers a year for a new gym floor. Anyone see the irony?

Put the money where it can be useful. Put it in projects that will encourage our children to pursue a career that will promote curiosity and critical thinking. This has been my soapbox, today sponsored by the letters S, T, E, and M.

Telling the Scientific Method Story

science art, storytelling in science, science in society
The scientific method as a bucket filled with Mother Nature’s water with an ever -changing hue.

The science gap is huge. One of the biggest misconceptions hindering the advancement of scientific literacy in society is also one of the most crucial – the scientific method. And no wonder. Most people would look back at primary and secondary school and cringe when thinking about all the facts and concepts they had to memorize in science classes. I cringe when I think of the public concluding science is static and just the sum of all data gathered through the centuries.

The scientific method is dynamic and so is the collection of accepted scientific knowledge

Nothing in science is certain. In the words of the great Richard Feynman:

We absolutely must leave room for doubt or there is no progress and no learning. There is no learning without having to pose a question. And a question requires doubt. People search for certainty. But there is no certainty. People are terrified — how can you live and not know? It is not odd at all. You only think you know, as a matter of fact. And most of your actions are based on incomplete knowledge…

The idea that scientific knowledge is like a statue is a horrible, infectious disease in society. Consider this…

The scientific method is a bucket. This is not just any bucket; it holds all the scientific knowledge gathered throughout history. The bucket is just a utilitarian tool for collecting knowledge. Luckily, this bucket has a hole in the bottom. The scientific method is a two way street and is objective just like a bucket is just a bucket. At the beginning of it all, the bucket was filled with crystal clear water. Mother Nature had filled it for us but all its contents were a complete unknown. As human inquiry began, discoveries were like drops of color that allowed us to have a glimpse of the contents as it dispersed like food coloring in a glass of water. Each new discovery or observation adds a touch of color to the bucket. Nature’s true color will not be observed in our lifetime or possibly at all. Our curiosity and practice only adds to the hue within the bucket.

Sometimes we don’t know the hue of the water is wrong until new knowledge is obtained and added to the large bucket. With addition of the new color, drops of discolored water pour from the hole in the bucket. Soon the prevailing knowledge is uniform within the bucket. Science never sleeps so this constant increase in knowledge and data get us one step closer to the true color of the universe, or so we think until we find out the hue is all wrong as the hole opens and a novel color drops in.


Science: Solving Mysteries One Clue at a Time

This past Tuesday, something mysterious and amazing happened. My wife noticed a strange deposit into our bank account; a large deposit: $1,400. She asked when I was supposed to be paid for something I was working on and I told her not until later. This deposit piqued both our curiosities. What was it? Why was it in there? Who put it there? I started investigating; researching as much as I could. I was able to find out it was $1,400 cash, which bank branch and what time the money was put in. Paranoid it was some scam perpetrated to clean out our bank account, my wife wanted me to call the bank to inquire. So, Wednesday morning, I called. Long story short, my wife received a call Wednesday afternoon from a bank employee saying someone anonymously deposited money in our account because they thought we should have it. What? To say the least, we were humbled and astonished. The curiosity has not gone away. We are still trying to figure out who this saint(s) is.

This mystery made me think; it is eerily like the field of science. The path to discovery in any science discipline begins with something very simple, an observation. My wife observed a strange deposit into our bank account. Observations lead to curiosity and ultimately yield questions. What was this deposit? Why was it there? Who put it there? Explanations or answers to the questions are developed. These explanations, or hypotheses, have their validity tested through experiment or some action. My wife’s initial explanation was that someone deposited it to somehow gain access to our account to clean it out. My action of calling the bank to report the deposit as not originating from the wife or myself was partly to make sure the deposit was legitimate and not some clever scam. Through experiment or action, facts are gathered to support the explanations or rule them out. The fact a bank employee called to let us know the deposit was from an anonymous ‘Good Samaritan’ ruled out the hypothesis of the scam. Scientific discovery ultimately leads to more observations, curiosity, questions, and hypotheses.

For my wife and I, the discovery that someone thought so highly of us to give us any amount of money has only fueled the mystery. The main question now is, who did it? Unlike any good mystery, or science for that matter, we may never find out.

This post is dedicated to my family’s ‘Good Samaritan’. Thank you…

Storytelling in Science: The Cell as Your Favorite Restaurant Part I

Many say storytelling in science is a great way to describe complex material in an understandable way for the masses. In this post, I will try to use an analogy to illustrate the complexity of a typical motile bacterial cell.

Microbial Physiology through Storytelling

If there is anything Americans know, it’s food. We are a nation obsessed with food and frequent restaurants on a regular basis.

Imagine your favorite restaurant as one huge bacterial cell.

When I travel to another city, I can’t rely on habit to guide me to a restaurant for dinner. I have to search for it while driving down the road. In order to know when I have found the restaurant I am searching for, I must rely on signs telling everyone what the restaurant is. The sign is a way to recognize and identify the building as i) a restaurant and ii) the specific type of restaurant. Bacteria do the same. They have ‘signs’ (proteins and other molecules) attached to the outside of the cell that lets other cells around identify what the cell is. I go into the restaurant through a door that allows patrons to move in and out of the building like bacteria have gates or channels that allow molecules to move in and out of the cell. Almost always, patrons are different leaving than they were when entering the restaurant; filled with yummy food they consumed and perhaps stopping to make a deposit in the waste room before leaving. Many molecules that leave a cell are different than those that enter. The workers of the restaurant have to keep track of the number of patrons entering and leaving the building to efficiently serve the patrons. Each employee has a specific job to do for very specific patrons. The employees have to identify their patrons and serve them as described by the bosses. Bacteria have an array of workers (proteins and protein complexes) that have very specific job descriptions depending on the patrons (substrates and product molecules) present in the cell. The restaurant survives by serving as many patrons as possible efficiently and correctly just as a cell must survive by responding correctly and quickly to everything in its environment.