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.

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.

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.

Part 2: Oh the Sad Irony; Thoughts on a Report to President Truman in 1945

The Bush Report as it is known was proposed before the end of World War II so specifics were not the objective of this particular report. This report was more ideological than would be delivered to the White House any other time in history. Here are some more quotes from the report (bold added by me to emphasize important parts).

The Importance of Basic Research

Basic research is performed without thought of practical ends. It results in general knowledge and an understanding of nature and its laws. This general knowledge provides the means of answering a large number of important practical problems, though it may not give a complete specific answer to any one of them. The function of applied research is to provide such complete answers. The scientist doing basic research may not be at all interested in the practical applications of his work, yet the further progress of industrial development would eventually stagnate if basic scientific research were long neglected.

From my time on the inside (assisting DOE’s Office of Science), I know one of the highest priorities of our government is to move the knowledge discovered through basic research into applications that are attractive to industry. The Executive Branch understands that future economic growth is intimately tied to research being conducted today. Any short-sighted moves by the Legislative Branch to make our R&D funding stagnate will have grave consequences for the country in the future when innovations attractive to industry come from overseas.

This is reiterated later in the report section:

A nation which depends upon others for its new basic scientific knowledge will be slow in its industrial progress and weak in its competitive position in world trade, regardless of its mechanical skill.

What are we to do when industry looks to capitalize on innovations from countries such as  India or China? Please don’t make me say I told you so…

A New Blog Series: Time for an American Renaisscience

A major reason Science does not have a more prevalent position in our society and government is the lack of understanding of what Science really is and can do for us. So, I have decided to use this blog as a starting point to hopefully explain some of the crazy, wild, innovative, creative, and science-fictionesque stories coming out about current research. I hope this will get more of the public excited or, at least, interested in what science and health research can accomplish.

Four Reasons to Teach Science Well

I’ve been reading up on K-12 Science teaching recommendations from the National Academy of Sciences. The following is from a 2007 document, Ready, Set, Science!: Putting Research to Work in K-8 Science Classrooms (National Academies Press).

Four Reasons to Teach Science Well

  1. Science is an enterprise that can be harnessed to improve quality of life on a global scale.

  2. Science may provide a foundation for the development of language, logic, and problem-solving skills in the classroom

  3. A democracy demands that its citizens make personal, community-based, and national decisions that involve scientific information.

  4. For some students, science will become a lifelong vocation or avocation.

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p>Another good reference from this publication:

Four Strands of Science Learning

Strand 1: Understanding Scientific Explanations

Strand 2: Generating Scientific Evidence

Strand 3: Reflecting on Scientific Knowledge

Strand 4: Participating Productively in Science

Types of Support Teachers Need to Teach Science Well:

  • High-quality curriculum or supplementary materials
  • Means by which to have their questions answered (texts, colleagues, outside experts)
  • Time and support to work through science tasks as learners
  • Opportunity to explore a variety of materials and experience problems that students might have
  • Time to think about and assess the knowledge their students bring to class