Mother Nature’s Chuckle: The Language of the Universe is not English

Miraculous opportunity for self-reflection.

 

There it is. Our home. To us it seems like such a huge place where we will never meet all our neighbors. A place where we live our daily lives consumed with news and opinions from all directions. We work. We play. We do silly stuff like fight wars or think we are the best at this sport or that.

Now look at the picture. Could you spot ‘us’ without the circle? As the dominant species on our planet, we think we are on top. We can explore our Moon. We can travel to our neighbor planet with robots. It is said the human brain is the most complex piece of matter in the known universe.

All Mother Nature can do is chuckle.

As the above image easily shows, it is all about perspective. Our grandeur is self-inflated. Despite the best efforts and actions of us on Earth, Mother Nature will always have the upper hand. She gives us room to explore. She allows us to make strides, great and small. But inevitably, she always reminds us we can not walk confidently on our journey. Stellar threats are all around; invisible until the time of their death in our black or blue sky. Prehistoric mass extinctions to modern day injuries and destruction in Russia last year.

Mother Nature does not speak any of our earthly language. She only speaks the language of the universe. The language we wish to learn through our research and study. The language we long to understand for it will tell us our true history…from the beginning.

On this International Women’s Day, remember, we are all very important to ourselves. However, our great Mother still laughs at us.

 

 

 

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:

www.scientificexploration.org/edgescience/edgescience_17.pdf.

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.

A Look Back (and not just about science)

I have never been one to look back the past year and reflect. It goes against my ADD personality, but this past year was really the best and worst of times…

The year started in style: the Animal Kingdom Lodge in Orlando on the concierge level in our pajamas dancing to the music in the lobby 6 stories below (we couldn’t sleep if we wanted due to the incredibly loud music). Life was good; I was a Science Writer. Little did I know in graduate school that this would be my dream job. How was I lucky enough to land it right out of the gate? We were rich (by our standards), my wife was preparing to quit her job as an underpaid, under-appreciated kindergarten teacher in the local public school district. Life was good.

For the first time in my life, I felt whole. I was providing for my family, contributing to the dissemination of scientific discovery to all that would listen (or read), and I was happy (especially taking pictures of deer outside my office window almost weekly to show my four year old daughter). I was even finding new creative ways to reach a broader audience through teaching myself 3D graphic/illustration software for the visual learners like me. Showing science was not a book of facts, but instead a beautiful creative glimpse at Mother Nature in all her glory.

The cards fell mid-August when I was told my position was being eliminated (post here). By mid-September, I was an over-qualified (yet under-qualified) stay at home dad with a Ph.D. I was broken and still am. Even though I have found one (maybe two hopefully) part time gigs to bring in some income, but my wife now must suffer through another year of purgatory-resembling bureaucracy teaching kids while pregnant (Yay!). It’s not fair to her or my family.

What a year, 2013. Good riddance.

Thinking of moving operations to Blogger via JustScience.co.vu

I’ve been thinking about this for a long while. I have had a Blogger site up for a while and I think it is time to make the complete transfer. I love the community of WordPress, but I don’t like the restrictions for free users like myself. So, visit JustScience.co.vu and take a look. Please let me know what you think.

Thanks.