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.




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)!

Bacterial Chemotaxis and Human Memory: Pete and Repeat

Many do not place ‘bacteria’ and ‘memory’ in the same sentence. Normal human perception does not connect the two concepts. However, Mother Nature seems to have a more profound perception. The past 50 years or so of scientific investigation has shown how our uniqueness as humans is actually commonplace across all forms of life on Earth. Case in point, how closely associated molecular memory is between bacteria and human.

Bacteria use adaptation to signals as memory

Swimming bacteria do not move randomly in their environment. This behavior would be futile and counterproductive. Instead, bacteria are constantly monitoring their environment in search of food and poisons. Moving towards the former and away from the latter. This observation was first published in the late 19th century. Bacteria, like the famous and infamous E. coli, use molecular antennae to receive these important ‘signals’ as the basis in the decision of which direction to swim. What if the bacteria find a great place to reside with lots of food but still need to receive signals to ensure they remain there? The antennae have sections that can be modified easily and reversibly. These modifications, in the form of methylation, alter the sensitivity of the antenna protein to subsequent signals. Methylation allows these antennae not to receive the number of absolute signals but relative signals. In other words, the antenna protein through fine-tuned methylation detects changes in the number of signals now versus some time in the past. This is the basis of molecular memory.

These antennae are proteins called methyl-accepting chemotaxis proteins, or MCPs. MCPs accept methyl groups from the essential cofactor S-adenosylmethionine (aka SAM or AdoMet). AdoMet is essential to both prokaryotes and eukaryotes like humans. The methyl groups are added by a protein called CheR (pronounced ‘key R’) which transfers the methyl from AdoMet to very specific amino acid side groups of glutamate. The process, called O-methylation adds the methyl group to the single-bonded oxygen on the carboxyl.

O-methylation reaction
O-methylation reaction. Courtesy of www.brenda-enzymes.org.

The length of a bacterium’s molecular memory is very short in comparison to how we perceive memory at only a few seconds. But, to bacteria it is long enough to successfully navigate the environment with similar precision when concentrations of food or poison vary (up to several orders of magnitude, or ~1000x).

Does the basis of molecular memory in humans mimic bacteria?

Eukaryotes, including humans, use a very similar mechanism in signal transduction to bacteria. Phosphorylation (transferring a phosphate group from ATP or GTP to a protein amino acid) is the basis of all signal transduction and cell regulation. Bacteria use histidine kinases and response regulators, as do plants to some degree. However, the majority of regulation through signal transduction in eukaryotes is through two types of proteins, RAS proteins and the heterotrimeric G-proteins. G-proteins interact with membrane receptors that regulate their activity. What determines which surface receptors G-proteins interact with? Isoprenylcysteine methyltransferase, or ICMT, is one of two methyltransferases that regulate signal transduction activity. ICMT is a membrane protein that uses AdoMet to add methyl groups to isoprenylcysteine, a post-translationally modified cysteine residue on both heterotrimeric and RAS-related G proteins. Methylation regulates which receptors the G-proteins interact with, thus playing a major role in connecting the initial signal to downstream regulatory pathways. The carboxyl methylation essentially modulates G-protein signalling globally.

G-protein carboxyl methylation is regulated by GPCR signaling and, as seen above, GPCR signaling is regulated by G-protein carboxyl methylation. This feedback/feed forward loop could be seen as a form of molecular memory stored in methylation patterns. Within the brain, ICMT activity is almost exclusively found in the region controlling coordination of movement. Thus, methylation could be used to modulate certain neuronal signaling pathways which result in learned patterns of sensory-motor skills.

The only other major methyltransferase is from a protein known as PPMT. PPMT interacts with a major enzyme in signal termination, the protein phosphatase PP2A. PPMT adds methyl groups to the backbone carboxyl of a specific leucine in PP2A. This carboxyl methylation helps determine which B subunit PP2A interacts with and where in the cell PP2A can be found. PPMT structurally resembles CheR in bacterial memory. Moreover, the enzyme that removes the methyl group from PP2A, PME, structurally resembles the bacterial enzyme that removes methyls from MCPs, CheB.

PP2A is one of the major regulators of pathway coordination to maintain synaptic plasticity in the brain. Interestingly, methylation defects and PP2A-PME complexes are suggested to play a role in the cause of Alzheimer’s Disease and memory loss. Methylation defects leading to defective phosphatase activity of PP2A leads to accumulation of a phosphorylated subunit of the structural protein microtubule. In this phosphorylated form, the filaments used to keep axons structurally sound collapse and lead to loss of normal synapses. Therefore, molecular memory in the form of methylation plays a vital role in promoting normal brain activity and its disruption can ultimately lead to dementia. 

Chicken, meet egg. Egg, meet chicken.

So, from bacteria to human, carboxyl methylation is necessary for memory. Did these pathways evolve individually in parallel, or did the memory we have today originate in the predominant lifeforms found within us?


Suggested Reading

Li and Stock. (2009) Biol. Chem. 390: 1067-1096. DOI 10.1515/BC.2009.133

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.