I would like to start today with a big sorry to my readers. Sorry for taking a gap and not writing articles. Some of you might know that I am a Ph.D. student. So I was very busy recently. Also, I would like to tell my readers that from now my "Classical Molecular Dynamics series" will be coming out monthly once or so. I will never stop it. But I think steemit has to grow a little bit more for this particular technical article series. I am telling this, based on the feedback I am getting. If you have a different opinion and wants this particular series to come often, please do reply to this article (or you can find me on discord in #steemSTEM group). I will reply and decide based on the response. Thank you.
So let us get into today's topic.
From Wikimedia Commons, License: CC BY-SA 3.0
What do you think about the coordination of a school of fish? If you look into the school of fish inside oceans, it is seen that there is no any kind of central coordinator in this process. But each fish may be trying to mimic the neighbor through its senses. So there is a local information sensing. But overall it is a self-organization which emerges from this local processes. We call this emergent phenomenon! The interplay between information-driven processes and self-organization processes is there in biology at different scales. Today I wanted to focus on molecular level in biology.
"CENTRAL DOGMA OF BIOLOGY" is one of the most important primary lessons we go through in biology. At least that gives you a bigger picture. Let us see what does central dogma says:
Central dogma is about the information flow in biology. It says that the information in DNA is transferred to RNA which is again transferred to proteins to execute tasks. DNA is like a hard disk storage of genetic information in form of nucleic acid sequences. The information in DNA is copied to mRNA (messenger RNA which acts as a template of information to be transferred protein). This process is called transcription. Then the information in mRNA is again used to create the corresponding protein with the aid of molecular machinery called Ribosome. This process is called translation because the "language" of information is changed from nucleic acids(as in DNA and RNA) to amino-acids from which proteins are made. Proteins are the workhorses in cells. To read about central dogma more, maybe you can see:
- The wiki article on central dogma
- @hadji 's articles about central dogma:
-The Central Dogma theory 1: DNA,
-The Central Dogma Theory 2: DNA Replication,
-The Central Dogma Theory 3: RNA, transcription and the genetic codes and
-The central dogma theory 4: reverse transcription and synthesis of proteins
- I will strongly recommend this 4-minute youtube video from Khan Academy if you have never read about it:
Sometimes I see people giving too much importance to players in central-dogma namely nucleic acid chains and proteins. They seldom talk about membranes or sugars. I think INFORMATION-FLOW is really important, but we are overlooking the significance of other players like membranes. Membranes predominantly made up of lipid molecules are very important players in biological processes. Where is the information coded corresponding to membrane actions? There is no such instruction set for the processes behind membrane actions. Here comes the second important concept in sustaining life for any biological creature. But membranes are not lipids alone(they have sugar molecules and proteins in them too), proteins can modulate their actions. So there is of course interplay between the information-driven processes and self-organization driven processes. I would argue that SELF-ORGANIZATION processes work hand in hand with the information flow to sustain life. What do I mean by self-organization? Think the case of processes like lipid bilayer formation. These processes are not directed by any information encoded in any molecules like DNA. They spontaneously occur purely based on the physics. Interested readers may start from the following links:
In short, what I wanted to say is encapsulated in below figures:
Image adapted from Wikimedia Commons: Arduino,DNA, ribosome and protein. License of sources: CC BY-SA 3.0 or 2.0
The above figure illustrates an information-driven process in analogy with a computer code getting executed on an Arduino computer. There is information in the form of DNA sequence information. Now what the ribosome machinery does to the information in form of mRNA is not written as such anywhere. It is not encoded anywhere. But this process is a purely physics-driven process.
We find very important members in Central Dogma like proteins and nucleic acid chains. But I feel sorry for lipids not being part of this Central theory. Yes, of course, central dogma is a very simplified picture of very detailed central biological processes. But in order to carry on these processes, we need many platforms. One of the necessary components for biology to happen is compartments. We need compartments like cells, and sub-compartments like organelles (like mitochondria), nucleus etc to carry out important processes of life. How are these compartments made?
These compartments are a result of self-organized processes like aggregation of lipids to form higher order structures like bilayer-lipids. See a simulation video of lipids here from youtube:
The above figure illustrates a self-organization process. There is no information encoded anywhere to initiate such a process. The phospholipids below transition temperature Tm acts like a gel ordered state and above the Tm, they act as a fluid. Similarly, dimerization of proteins, reaction-diffusion processes etc are in this class of self-organization processes.
So the final message of this article is to see life as a process which incorporates the interplay between INFORMATION-DRIVEN processes and SELF-ORGANIZATION DRIVEN processes.
For further reading :
[1]: Physical Biology of Cell by Rob Philips et al.. [Beautiful book! Love this really]
If you like my content please upvote and resteem it. Below are few of my recent posts, you may find interesting:
- Why is it wrong to equate Shannon Entropy to Disorder?: Visually Explained!
- Evil genius series!: Building a crude EMG circuit
- Gradient, Divergence, and Curl: Visually Explained!
- The history and mystery of Belousov–Zhabotinsky reaction: Did it violated 2nd law of Thermodynamics?
I am currently doing three article series:
- Evil genius!: My experiments with electronics and other DIY stuff!
- Classical Molecular dynamics: Focusing on teaching and setting up a molecular dynamics simulation of atomic systems. (Dormant mode)
- Visually Explained!: Explaining technical concepts visually.
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