How many lines of code

You may have to write and load

To build an aeroplane or a complicated road

That it may have to follow

From its origin to its destination

Tackling terrains over many different nations,

And how complicated are the software languages

How ugly are their passages

How many kinds of them are there

How different are their messages.

How many rules of syntax

How many different compilers

And how many ways to index.

 

Supercomputers spaceships and transistors

Such complex systems designed by their human masters

Or galaxies black holes and clusters

Big bang or any other creation

Supernova explosion

Or any other destruction or disaster.

Complex processes are involved

Many rules may need to be followed and solved.

 

In contrast

The complexity of life

In its simplest form

For it to assemble and to perform

Is immense

Compared to anything else

That has been designed

Found or refined

Or has come into existence.

 

For example

Just to make a molecule that is simple

Such as sugar

The molecular machines that life has to make

And the processes that it has to trigger

With such precision and such coordination

The fidelity is beyond our imagination,

And the whole system to be able to duplicate

So that life can carry on and replicate

Generation after generation,

The chain of events and the fine tuning

The miniaturization and the grooming

Of the aesthetic side

Stand out and supersede

Any other complexity in the universe

That our human mind can see or read

Or can traverse.

 

But when it comes to codifying this complexity

Life has taken a very different approach –

The simplicity

Which is really very elegant

And very pretty.

Language syntax and compiling

And in its execution and styling

Coding of life is universal and unique

And for this

Life has adopted the simplest possible trick.

The sequence of events

The events themselves

And the actors –

All have been deconstructed,

And then they have been written

In the DNA sequence,

Using the simplest possible coding

They have been hidden

And encrypted.

 

Anything other than life

If we humans have to write

Codes for their designs and constructions

We seem to be in a fight

With languages that are messy

And algorithms that create our frustrations.

 

On the other hand

In order to maintain

The simplicity in its coding

Life has been using

Only four letters

Which are then laid down

In various combinations

But only in linear fashion

In the form of long chains

That goes by the name –

DNA.

 

These letters are called A T C G

They are short for small molecules

Adenine Thymine Cytosine and Guanine

Are their names in full.

They are found

As they move around

Inside living cells,

But when many of them combine

In a long line

But only in the right sequence

Then they are able to spell

The creation

Of some functional protein

Which is a molecular machine

That may then be the part of the structure

Or the function

Of that living being.

 

Difference in combination

Is what makes it possible

To code for the creation

Of proteins of different kinds

That we find

Inside any living cell.

 

But this combination

Does not happen in random

As DNA can only be copied

From a preexisting DNA template

From which the replication machinery can read

And build a new DNA chain

Following the rule of base pairing

Where A pairs with T

And G pairs with C

Allowing a new complimentary strand to form,

Life can only come from life

This base pairing is what led to this norm.

 

Protein synthesis

Is the most important reaction

For any species,

This is what life has to do

In order to carry out its actions.

The machineries

And the detailed process

Is fine tuned, coordinated and complex.

 

Proteins are large molecules

They are the kings who make the rules

Of how life will shape and perform.

They are the molecular tools

That directly or indirectly

Carries out all the reactions

With such accuracy and coordination

That the property we call life

Can emerge and survive

As the overall combined effect.

No single reaction

Or limited combination

Can claim this for a fact

That they themselves alone are the architect.

Thus life may seem to appear

As an emergent behavior

Like some other properties in nature

Such as temperature, may be time, and pressure

Where the collective behavior of the aggregate

Looks different than the behavior of its constituents

When they are viewed as separate.

 

Some proteins may act

As regulators and switches

So when they are made

They can dictate

How and when some other proteins should be made,

They may try to modulate,

Or some other proteins they may just activate.

This is how life has chosen

To encode not only the structure of its components

But also the behavior and direction of their movements

In the same linear construct which is the DNA.

So the structure function

Coordination and progression –

How to do all of these – the instruction

Is written in the same linear entity

Using the same basic units

Following the same rules

And in the same exact fashion.

 

The genius and the beauty reside

In the ability to disguise

All such information

In a linear form

Using only four letters

Creating the unique DNA sequences

That ultimately leads to the consequences

Known as ‘life’

Along with all of its wonderful dances!

 

That proteins are so important

Is not hard to understand

As virtually any medicine you are prescribed

Once they are inside

Your system

They try to interfere or stop

The function

Of some protein

So that the reaction

That it controls

Slows down or halts.

 

Aspirin for example

A medicine known to us all

Blocks a protein named cyclooxygenase

Whose action

Produces inflammation and pain

And thus by its blocking

The pain and inflammation

May feel like

A little less shocking.

 

Viruses lack the ability

To carry out this crucial duty

Of synthesizing proteins,

They lack the machinery,

As a result

They have to sneak in

To some cell that is still living

In order to hijack its tools

So that it can make copies of its own

As the host cell it continues to fool,

Damaging or destroying this cell

Eventually out of this they themselves expel

To find their next victim

Which will be another living system.

For this reason

Viruses are not alive

Until they are inside

Of a living cell

And does its things

As just described.

 

For making proteins

Detailed instructions are needed

This is what is seeded

In long molecules that is the DNA.

These long chains behaves

As life’s apps

Where instructions are coded

And then they are copied and loaded

In large molecular machines,

Proteins are the final productions

Made according to these instructions

That were part of the DNA structure

And its function.

 

Proteins are long chains

Of units

Called amino acids

Which are small molecules

Twenty of them exist

Inside the cell’s list.

They have been given

Cool and artistic names

Such as –

Proline, Serine and Arginine

Alanine, Valine and Glycine,

Tyrosine, Cysteine and Histidine

Threonine, Glutamine and Lysine.

 

Taking various combinations

And then laying them down

Again in a linear fashion

Is how proteins are made,

Which amino acids to take

How many and in what order

Is what the code in DNA dictate.

Protein chains,

Also known as polypeptides,

Are of varying lengths –

From tens of amino acids

To thousands.

Human insulin

Is a protein

That has 2 polypeptides –

One with 21 amino acids

And 30 on the other side.

Titin

Also Known as Connectin

Is a giant protein

That behaves

Like a molecular spring

Inside our muscle cells,

Being part of their contractile machinery,

Its polypeptide chain can vary

In length

From 27 thousand amino acids

To more than 30 thousand

It can carry.

Some proteins can come together

To form more complex structures.

Each is called a subunit

And together they are able to complete

Some function

That cannot be done

If anyone of them

Is acting alone.

Hemoglobin,

Which is a complex of proteins,

Carries oxygen

From our lungs to our tissues.

It has 4 subunits

To deal with this issue.

Enzymes are proteins

That carries out reactions.

Others are called structural –

Acting like nuts and bolts

Is how they feel natural.

Collagen, Elastin and Keratin

Are examples of structural proteins

That gives the structure of our skin.

Pepsin, Trypsin and Chymotrypsin

Are enzymes that are found in our gut,

The proteins that we eat

They like to break down and cut.

This is how digestion is done

Making some proteins tear down the others

Is how nature tries to have its fun.

DNA Polymerases are enzymes

That copies DNA from a preexisting template,

This is how any new DNA is made

This is how life is able to replicate.

In DNA

The letters are A T C G

Each three letter combination

Is what is known

As a codon

That codes for one specific amino acid

That the cell’s decoding machine can read.

On top of these

There are 3 combinations

That are called stop codons

That tells the system

When to end this mission.

For example

The DNA sequence ATG

Codes for amino acid Methionine

But TAG is a stop codon

Telling the system to end

The synthesis of that particular protein.

 

A specific part of a DNA

That codes for a specific protein

Is called the gene

For that particular protein.

Some sequences in DNA

Are genes

Coding for proteins.

But others have the goal

To regulate and control,

As in these sequences

Some regulating proteins can bind

And thus can exert their influences –

On some other genes

That may be located in front or behind,

Turning them on sometimes

And shutting them off in other instances.

 

Genes are first copied into mRNA

Which has sequences

That are complimentary to DNA.

Making mRNA through this copying mechanism

Is known as transcription

Which is done by enzymes that are known as

RNA Polymerases.

The process of making a particular protein

Following the information in DNA coding – its gene

Is what is meant by its gene expression,

And the first step for doing this

Is its transcription.

Promoters are sequences in DNA,

Located near various genes,

Where RNA polymerase can bind

And start transcribing.

Regulatory proteins

Through their interactions

With this process of transcriptions

Are able to affect

Various gene expressions,

And so these important actors

Are called transcription factors.

 

Hox genes

Encode a group of proteins

That act as transcription factors,

That regulates the formation

Of body plan

In multicellular organisms

Such as flies and humans.

Mutations in these proteins

Can result in deformities.

For example some mutations

In humans

Result in too many fingers or toes.

And in flies

The way it goes

Is that with some mutations in these genes

What people have seen

Is the formation of legs

Coming out of their heads.

Some proteins control

Cell cycle and cell division,

And their mutations

Can result in uncontrolled proliferation,

Which then can lead to tumors and cancers,

Such details are important

To find treatments and answers.

BRCA1 and BRCA2 are two genes

That encode proteins

Whose functions

Are to repair DNA, control cell cycle and transcriptions,

And with their mutations

Individuals can be more susceptible

To certain forms of cancers,

Breast and ovarian are two

Among some others.

mRNA is loaded into ribosome

A molecular machine

That is the home

Where proteins are made,

It reads the mRNA sequence

Three letters at a time,

As it passes through its gate,

And brings the correct amino acids accordingly

And then combines them simply

One after the another

Until it finds a stop codon

Then it knows that it has finished its mission.

A new protein has just been made

As the cell continues with this parade.

This whole process of making

The polypeptide chain

That takes place in ribosome

Is Known

As Translation.

For a protein to do its function

It has to fold

And conform in the 3 dimension

in a very specific fashion.

This 3 dimensional structure

Is what makes this architecture

A properly functioning machine.

For this to happen

Its amino acids have to be of the right sequence –

They have to be of the right kind and of the right number

And in the right position,

Even a single amino acid being wrong

Sometimes may be enough

For the protein to lose its function.

So randomly generated chains of amino acids

Cells never allow or greet

As they will not be useful at all

And will create nothing but trouble.

There is no gene with such random DNA sequence

Life is precise in this sense

It has no tolerance

For any such nonsense.

One such example

Where a single mutation

Can cause so much trouble

Is the sickle cell disease –

Where replacing a single amino acid

With a wrong one

In a specific position

Can cause this condition.

 

Moreover –

Generating random DNA sequences

And then trying to read

You soon find out that you cannot succeed

In making any functional protein

As you hit

Stop codons

Pretty soon

So what you end up with

Is a junk chain of amino acids

Unable to perform any function

So the cell will decide

To go ahead with its destruction.

These observations

May qualify as valid objections

That goes against any conclusion

Or any suggestion

That life’s creation

Was an event

That was totally random.

Controlling the cell’s internal reactions

Is part of the proteins’ dedicated functions,

But interactions between cells

Are controlled by some other proteins as well.

They usually stick out from the cell’s membrane

Or they may be released in the environment

To reach some other cells that are at a distance.

This is how genes are governing,

Through the actions of their proteins,

The organization of cells

Leading to tissues organs and the systems,

From one cell going to trillions

This is how a big organism comes into existence.

 

Here is the simplified chain of events

Of how life starts proceeds and reaches its end –

Starting always from a pre-existing template

DNA is copied and then passed on

To the next generation.

Then through carefully choreographed

Gene expressions

Different proteins are made

In various successions

Which then set off the cascade

Of various reactions,

And this cycle can carry on

Leading to other cycles and so on

So that cells can form organize and specialize

Leading to tissues systems and the whole organism.

From a simple bacteria to the complex human brain

The fundamental processes of life

Remain the same.

 

The characteristics of life

That are crucial for any form

That is known

Are processes like replication and division

Maturation, maintenance and termination.

All of these seem to be coded in DNA sequence

Although not all the details are known to us humans,

Yet.

 

But the genius and the beauty

Is apparent

When we observe and comprehend

That the most complex system

In its creation –

Not only of its components

But also their coordination and functions,

Including the ability

To self assemble and replicate

With such stability,

Was able to codify all necessary instructions

In such simple and linear structures.

Thus any claim of any superiority

By anything else

It very easily ruptures!

By,

Kris Mojag

Written somewhere in California in a calm and cloudy day in October of 2021.

(Warning: This is a poem, not written as any medical advice, but for entertainment and general informational purposes only)

The Content of this post / poem may be too technical or unfamiliar concepts for non biologists. In that case please consider watching these following videos from my YouTube channel that should clarify things a little better.