A New Home!


I have bitten the bullet and created my own website, Sci of Relief. This site will host my Just Science blog with its science education resources. It will also host the project Abstracts 2.0 which provides scientific journal abstracts summarized for the general public. Take a look, and, please, make comments and suggestions. As always, they are welcome.

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.