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.

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Storytelling in science: Metabolic pathways as circus rings

My family and I recently went to a circus. It had one ring, and that was manageable. We have also been to a traditional three ring circus in the past. Personally, I felt there was too much going on at one time to enjoy all three rings at once. Each ring had skillfully trained performers doing their job for the enjoyment of the audience simultaneously. That is how a circus functions. Now imagine if you were able to observe a circus with more than 1000 rings. Imagine the complexity and the majestic choreography unfolding before your eyes. This is essentially what bacteria have been doing f0r millions of years with ease Instead of rings, these little circuses have pathways, a group of proteins/enzymes that all function together to perform a task. Like a circus, these pathways are not in isolation but instead many are performing at the same time. Even the “simplest” bacteria have over 500 pathways. Imagine trying to watch a 500 ring circus and understanding what is going on or being in charge of all 500 rings as they perform. Just because we don’t understand microbes does not make them simple, it makes us naive.

When sequencing a bacterial genome, computers and researchers try to connect all the dots. That is, they try to predict the role each gene/protein plays within that circus. For a bacterial circus with 5000 members (genes), only about one third of those can be assigned to a particular ring (pathway). This means a majority of members from a genome have a role we haven’t observe enough to classify its context. Now, imagine two thirds of KNOWN genes in KNOWN bacteria and the fact we approximately know 1% (or less) of the total number of bacterial species on, or in or above, earth. It doesn’t take long to discover that there is much more to discover in microbiology.

We as humans are beginning to utilize bacteria, or their pathways, to advance our civilization. Whether it is to clean up our polluted, toxic land or to advance medicine through fecal transplants, bacteria will play a much bigger role in the near future. Not bad for such small species. 500 rings or 2000 rings, these circuses are truly the greatest shows on earth!

bacteria, metabolism, pathways, microbiology

A 1500 ring circus from a typical bacterium.

Continuing on the theme that bacteria are Nature’s smallest circus, I want to highlight the most glaring problem with our knowledge of these 2000 ring circuses. We have discussed how proteins encoded by genes within a microbe’s genome often work together to carry out their function, i.e. pathways (or rings). To date, according to the NCBI genome site 4019 bacterial genomes have been sequenced to the point that we know the number of genes and proteins each organism contains. Moreover, this equates to 7,309,205 genes total or roughly 1818 genes per genome. These are astonishing numbers. To show our futility as experts of all things natural, over 30% of these genes are considered hypothetical or uncharacterized. In some genomes, these genes make up 60% of the total genes. These terms are a technical way of saying “hell if we know what they do”. Computers have recognized them as genes or open reading frames, however, the gene itself isn’t similar enough to known or characterized genes for scientists or computers to call it “the same”. If these gene products (proteins) functions are unknown, they cannot be assigned to a ring in the circus therefore making the largest ring by far in any bacterial circus the “unknown” ring.

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

Recap: The restaurant is the bacterial cell, the employees are the proteins/enzymes that serve the patrons which are the compounds/metabolites.

Who are the bosses that determine which, and how many, employees are needed for each type of patron?

The restaurant managers have a very important job to perform. They have to make sure the right number of employees are available to help their respective patron. If the balance between employees and patrons is not well maintained, it could cause disaster for the restaurant itself. In a past post, I tried to describe how bacteria made decisions. One of the predominant ways was the use of two-component systems. For this story, think of the restaurant managers as actually two people who need to work well together. One identifies its respective patrons and the other makes changes to the number of employees for those patrons. It is this balancing act that helps the entire restaurant to work smoothly.

A successful restaurant will open up new locations. The same can be said for bacteria. If conditions are right, the cell will divide into two cells. As with a cell, restaurants have to make sure certain activities are undertaken to ensure the new restaurant will be exactly like the successful one it is copying. The success of this restaurant is based upon the ability to keep the employees happy (by having patrons to serve and not sitting around bored) and keeping the patrons coming in. To duplicate this success, the new restaurant should have a building exactly like the current one so the patrons will easily continue to enter and leave. The new restaurant will also need the exact employee list for the managers to call upon when needed. The employee list is the genome of the cell that encodes the proteins needed for survival. That would make the copy machine that duplicates the employee list the DNA replication machinery. This special restaurant building is state of the art. It can expand until it is roughly double its original size then place a dividing wall down the middle of the large building until the building becomes actually two buildings. Now the restaurant can serve twice the number of patrons with the same efficiency as before. Each new building has the same employee list and rough the same number of employees to start off with. Then the managers start their work identifying the patrons in the restaurant to make sure the employees are there to serve them.

The two buildings shake hands and go their merry way…ready to serve.

In Part III, I will talk about the intercom system that allows major changes to happen to the kind of employees needed for economic downturns.

My Dream for Science Literacy: Abstracts 2.0

I have been wondering for some time: How can I make the biggest impact to science literacy (This was a start). However, I know I can do more.

Science Literacy

I received my weekly email of the Table of Contents for one of my favorite journals PNAS today and read over the titles of the articles. As usual, I’m reading them and saying in my head, blah blah blah because I am looking for certain keywords to identify the article as something I would be interested in (like chemotaxis or second messenger cyclic-di-GMP). Then it occurred to me,

I’m trained to know what these titles mean and which ones would interest me. What about everyone else in America? To them it’s just blah blah blah without the training to know if they would like the research or not. 

A majority of published scientific research is federally funded by taxpayer dollars in the U.S. yet most taxpayers have no idea why the research findings from these funds are important or how they contribute to a better society.

What if the article abstracts, laced with big words and jargon, were rewritten to a level where most people could understand; an abstract 2.o if you will? By reading a short summary of the work, anyone who wanted to know could actually understand the problem studied and the results. Maybe more importantly, the reader would not have to rely on interpretations of the research from popular media sources that have higher priorities than educating the public.

I will have more on this concept in the near future. Please let me know what you think and add comments and suggestions.

Never underestimate clever bacteria: bacterial persistance

If there is anything I try to convey to anyone who will listen: never underestimate the intelligence of bacteria. A new case-in-point was published in the journal Infection and Immunity (Abstract only- Paywall) from researchers in Buffalo, New York to back up my claim. Former knowledge from two pathogens that cause strep throat, ear infections, and colds suggested they did not survive long outside the human body. However, a new study about Streptococcus pyogenes and Streptococcus pneumoniae suggests we were wrong and the bacteria were right.

Previous studies used unnatural conditions; i) cells grown in broth media and ii) free-living cells. These both are not encountered by bacteria which invade a human host. S. pyogenes and S. pneumoniae both infect humans as biofilms; very resistant, closely-connected bacterial communities. The present study used biofilm bacteria to test how long these bacteria could survive outside the body and still infect mice.

To drive the message home, researchers tested a day-care center for S. pyogenes and S. pneumoniae living on surfaces and capable of causing infection. Results indicate these bacteria were found at high levels and viable even after surfaces were cleaned before sampling.

Let me re-iterate: bacteria know survival. Don’t underestimate their ability to evade our most clever defenses and come out on top while we lay in bed recovering.

Who would be on your fantasy #science team? #scio13

Bill Nye the Science Guy at The UP Experience ...
Bill Nye the Science Guy at The UP Experience 2010. Note: this photo is Creative Commons Attribution. You are welcome to use it with “photo by Ed Schipul” (Photo credit: Wikipedia)

In my quest in advocate science education and science literacy, this thought came to me as I was laying in bed last night. There are fantasy everything leagues. I’ve even participated in Fantasy Nascar and Fantasy Golf (don’t tell anyone). My wife has even been in a Fantasy Celebrity League. What about a Fantasy Science League? Who would you want on your team (they must be living)?

I’m going to give away my draft strategy…

I would start with a ringer; someone high profile that does a lot for humanity. Since a majority of Americans can not name a living scientist, this is difficult. I would have to start with Bill Nye. He is a beloved TV personality and advocate for action on climate change and science literacy. Heck, he even has ‘Science’ in his name (The Science Guy).

Second I would go another high profile in Neil Degrasse Tyson. A great director of the Hayden Planetarium in NYC.

Next, I would pick someone probably less known to the masses, Lucy Shapiro,  member of the National Academy, life long researcher who has mentored some of our best scientists including Sean Crosson and Christine Jacobs-Wagner.

Following Lucy would be Derek Lovley. With a great PR department at UMass, Lovley has created a major buzz in the microbial and alternative energy world. Lovley’s work with Geobacter has discovered the potential to create a microbial fuel cell due to extracellular electron transfer. In other words, bacteria conducting electricity as a by-product of cell metabolism.

George Church would be a great addition to any fantasy science team. He recently made headlines due to awful translation. He had pioneered genetic research and to add a cool factor, has appeared on The Colbert Report. He most recent book was ‘translated” onto DNA. 20 million copies of his book were encoded onto DNA and is kept in a small vial.

I think 5 team members is a good start. I may pick up some more scientists off the waiver wire later, but I like my chances to make it to the championship. We’ll see…

Dr. at the November 29, 2005 meeting of the NA...
Dr. at the November 29, 2005 meeting of the NASA Advisory Council, in Washington, D.C. (Photo credit: Wikipedia)