How is the communication of molecules possible ?

Future University - HakodateSystem Information Science

Shigeru Sakurazawa

Before the origin of “life” What are differences between the living matter and

the material ?

Molecule 1nm = 10 m-9

T4 Phage100nm = 10 m

-7

Paramecium100m = 10 m-4

Animals, Plants 1m

What is this ?

In fact ・・・

Muscle protein

Muscle

Myosin

Myosinミオシン繊

維

Actin

Globular Protein球状のタンパク質

2 nm

Actinアクチン

Actomyosin system

Myosin.mov

Fluorescent label for actin

Actinアクチン

Fluorescent Molecules

Fluorescent Labeled蛍光標識された

In vitro motility assay

ATPCa2+

The movie of the in vitro motility assay

These are molecules.

Information

First, the moving fiber was recognized as a living matter.

After getting the information of the function of the fiber, the fibers are recognized as just a material.

Important thing: How does the information emerge? Information is emerged in the relationship between two

matters. Interaction and communication

Communication

This is communication. Is it transmission of information using languages?

Transmission of information ?

A BLanguage

In the case of different language

This is also communication. Abstract expressions can be communication skills. Are these skills only for humans who understand

the means of the expression?

Only human?

SignGesturesMusic (Sound)Pictures

EnglishJapanese

In the case between a human and an animal

This is also communication. They can imagine the situation of each other

from each other’s experiences.

HumanAnimal

imagine

Behavior

Communications

Transmission of information between machines is called “communication”.

But it requires communication protocols. The protocols were created by humans who use

this equipment for their communication.

PC PCCommunication

Communication

Particles in Brownian motion

Is this communication ? Usually, we say “No”. It is

interaction by electro static fields.

rFF

20

21

4 r

qqF

-q1 -q2

repulsion

How to use the word “communication”

We tend to use the word “communication” for living things. We never use the word “communication” in physics.

Living ThingsCommunication

Non-Living ThingsInteraction

Physical World

Mental World

In a park

There were many pigeons in a park. They looked so pretty. A man approached the pigeons. The pigeons move away to the

outside of a circle with radius r. The experimenter who observes this

phenomena from outside of the system may explain this as interaction of repulsion.

However, there is no force between the man and the pigeons. The man and the pigeons just act from their free-will.

r

Observation from outside of a system

The experimenter is the observer who observes from outside of the system.

He describes the phenomena as a result of many experiments to cancel differences between individual samples.

The descriptions of the phenomena by the external observer are not required to be concerned with the free-will of the objects.

So, the descriptions confuse free-will with the field of force.

Difference of Recognition Process in Japanese and English

Yasunari Kwabata “Yukiguni” 川端康成　「雪国」 国境の長いトンネルを抜けると雪国であった． THE TRAIN came out of the long tunnel into the snow

country.

View of First Person View of Third Person

In the case of the particles

In the case of humans and pigeons, we can find the mistake of the description. There is no force between human and pigeons.

In the case of the particles, nobody has any question about the existence of this force.

When we accept particle’s behavior based on their own observation, we must think that the particles observe the state of the neighbor particles, which includes a distance and an electric charge.

If the particles can very quickly observe neighbor’s changes like interaction of electrons, the description has no problem.

rFF

20

21

4 r

qqF

-q1 -q2

repulsion

Difference of observation - misunderstands

If the pigeon and the man cannot finish the observation quickly, the following situation is considered.

The man approaches the pigeon with love. However, the pigeon feels danger from the man. The pigeon will make distance from him. If this situation continues, the relation between the man and the pigeon will be broken.

The pigeon will fly away.

Danger ?!Love !

If the relation could have been maintained, ・・・

A kind of synchronization must occur between their groundless predictions.

He may give me food ?!

He may like food ?!

A new semantics has been produced

After the synchronization, even though they have different understanding of the food, there is no problem in their relation.

Here, a new semantics of food is produced.

A new upper layer of the world is produced at this moment.

This seems to be the nature of “communication”.

I love him. I want him to become happy by eating the food. He will love me.

food

foodHe seems that he likes to put food here. Lucky !

Upper layer

present layer

present layer

For establishing communication・・・ Perfect agreement between mutual observations is not

required. The observation needs to take a long time. A short time is merely interaction.

Interaction is simple without conflict. Communication include some conflict and resolution.

We can think that molecules can establish their communication in the process of chemical evolution.

Primitive Earth

Amino acids

Amino acids are the source of proteins. Amino acids were made in electro discharge experiments. It could be said that amino acids were formed in the prebiotic earth.

Peptide bond

Two amino acids form a peptide bond reducing one H O molecule.

In our body, peptide formation is carried by ribosome, which is one kind of protein.

2

Protein

Protein is long peptide with more than 100 amino acids.

Fibrous chain of peptide becomes a globular structure by the rotation of chemical bonds around -carbon.

Chicken and egg problem Here we can find one paradox. Proteins are made from amino acids by ribosome. Ribosome is a kind of protein. So, a protein makes proteins. This is like chicken and egg problem.

How was the first protein made ? S. W. Fox et al. reported in 1950’s that protein-like polymers

were formed by only heating amino acids.

Chicken egg

Thermal Heterocomplex Molecules - Proteinoid

Mix amino acids as powder state. Heat them at 200 ℃ for 3 hours. These molecules are polymerized

randomly. The polymer is thought of a

prototype of proteins. So, it is named proteinoid.

Aspartic acid Proline oven

1 mol : 1 mol 200 3 hours℃

In water

When the polymer is put into water and boiled, it dissolves into the water.

When the solution is cooled, the dissolved polymer aggregate with each other as micro spherical particle and sediment.

Add water, boil cool with ice bath

Microspheres made from DP

The polymer makes many micro spherical particles in aqueous solution.

The particles change their morphology with environmental changes, i.e. temperature, pH, etc.

Long term relaxation in temperature change

The particles dissolve into water at temperature increase, and aggregate again at temperature decrease.

The biggest particle is made at a cooling rate of from 0.01 to 0.1 /℃ min, which corresponds to day cycle.

Thermal hysteresis The vertical axis corresponds to the

amount of aggregated state molecules.

Dissolution and aggregation occur at different temperatures from each other.

This phenomena might induce energy transformation from thermal energy to evolutional energy.

It means that the molecules might have the ability to get energy from environmental fluctuations.

What will happen in pH change ?

The molecules changed their state in temperature change with long time relaxation.

What will happen in pH change ?

These molecules are acidic. So, they dissolve into the water by pH increasing addition of alkaline solution.

In the optimum condition

When the pH is increased in the optimum speed, we can get these capsule-like structures in the solution.

Thickness of the wall of the capsule depends on the speed.

Capsule formation in pH changes

pH increase induces microcapsule formation.

From particles to microcapsules

The capsule was made from the particle by dissolution of inner part.

When the capsule cracks, the alkaline solution flows into the capsule and a second capsule is formed in the first capsule.

Formation process

The first molecules of the surface dissolve into water.

The molecules aggregate again as many nanoscale particles, and attach to the surface.

A microcapsule is formed at the outside of the particle.

The inner particle dissolves slowly, finally, the capsule become empty.

Capsule formation mechanism

The shell structure is not prepared in initial particles. The structure is formed only in optimum dissolve process after pH change.

At last, all structures are dissolved into free molecules at final pH. The capsule formation is a temporary phenomenon.

initial state

fast dissolve

slow dissolvecapsule formation

increase

very slow dissolve through the shell wall

timedi

amet

er

This process is a result of communication of the molecules

We could see that the capsule formation reaction continues for very long time.

The molecules have a long relaxation time for not only temperature change but pH change.

In another words, the molecule change its state very slowly. Additionally, when the molecule on the surface of the particle dissolves into water, it affects neighbors.

So, the mutual observation between molecules is never finish completely.⇒Nature of communication

This capsule formation seems to be the result of communication of molecules.

Summary

To establish the communication Perfect agreement between mutual observations is not required. People never know completely what the faced person is thinking in his/her

blinded mind. If people can maintain their relationship, a kind of local synchronization must

occur between their groundless predictions. Here, a new semantics is created and their world progresses to upper layer. Final their state can have a wide variety.

Long relaxation time If there are some molecules which have long relaxation time due to growth in

chemical evolution, perfect observation between them can not be done. The temporary capsule formation is the expression of the local synchronization. Bifurcation of the final morphology occurs in uniform solution conditions. Molecules start communication due to long relaxation time.

Responses of DPV microspheres for Tris-HClmM 48 91 130 167 286 333 375 500 615

① MS MS Dissolve Dissolve

② MS MS TypeⅠ TypeⅠ③ MS MS MS MS(Ⅰ )

④ MS MS MS MS

pH 6.8 ⑨ MS MS MS MS

⑩ MS MS MS MS

⑫ MS MS MS Dissolve

⑬ MS MS MS TypeⅡ⑭ MS MS MS MS

① MS MS TypeⅡ TypeⅡ Dis/Ⅱ Dis(Ⅱ )

② MS MS TypeⅠ Dissolve Dissolve Dissolve

③ MS MS MS Dissolve Dissolve Dissolve

④ MS MS MS Dissolve Dissolve Dissolve

pH 7.5 ⑨ MS MS MS MS(Ⅰ ) TypeⅠ Dis/ Ⅰ⑩ MS MS MS Dissolve MS/TypeⅠ TypeⅡ⑫ MS MS Dissolve Dissolve Dissolve Dissolve

⑬ MS MS TypeⅡ Dissolve Dissolve Dissolve

⑭ MS MS MS Dis/Ⅱ Dis/ Ⅰ Dissolve

① MS Ⅰ /Ⅱ TypeⅡ TypeⅡ Dissolve Dis/Ⅱ Dis/Ⅱ② MS TypeⅠ Dissolve Dissolve Dissolve Dissolve Dissolve

③ MS MS MS/TypeⅠ Dissolve Dissolve Dissolve Dissolve

④ MS MS MS/TypeⅠ Dissolve Dissolve Dissolve Dissolve

pH 8.0 ⑨ MS/TypeⅠ MS MS/TypeⅠ MS MS Dis/Ⅱ /Ⅰ Dissolve

⑩ MS MS MS MS MS Ⅱ /Ⅰ Ⅰ /Ⅱ⑫ MS MS TypeⅡ TypeⅡ TypeⅡ Dissolve Dissolve

⑬ MS/TypeⅠ TypeⅠ Ⅱ / Ⅰ TypeⅡ Dissolve Dissolve Dissolve

⑭ MS TypeⅠ MS/TypeⅡ TypeⅠ Dissolve Dissolve Dissolve

pH change after the reaction

-1.00

0.00

1.00

2.00

3.00

4.00

5.00

6.00

pH 6.8 167mM

pH 8.0 91mM

pH 7.5 167mM

pH 8.0 167mM

pH 8.0 285mM

Concentration of Tris Buffer

pHの変化

1.0 0.7 0.3： ：1.0 0.9 0.1： ：1.0 3.0 1.0： ：1.0 0.5 0.5： ：1.0 1.0 1.0： ：1.0 2.5 1.5： ：1.0 1.5 1.5： ：1.0 2.0 2.0： ：1.0 1.5 2.5： ：

Type D：PV D：P：V pH 6.8 167mM pH8.0 91mM pH 7.5 167mM pH 8.0 167mM pH 8.0 285mM

A 1：4 1.0：2.0：2.0 MS Dissolve/TypeⅠ TypeⅡ Dissolve/TypeⅡ Dissolve

B 1：4 1.0：1.5：2.5 MS MS Dissolve Dissolve/TypeⅡ Dissolve

1：4 1.0：2.5：1.5 MS MS/TypeⅠ TypeⅡ Dissolve/TypeⅡ Dissolve/TypeⅠ1：4 1.0：3.0：1.0 MS Dissolve/MS MS TypeⅠ Dissolve

1：3 1.0：1.5：1.5 MS TypeⅠ TypeⅠ Dissolve Dissolve

C 1：2 1.0：1.0：1.0 MS MS MS Dissolve/TypeⅠ Dissolve

1：1 1.0：0.5：0.5 MS MS MS Dissolve/TypeⅠ Dissolve

1：1 1.0：0.7：0.3 MS MS/TypeⅠ MS MS Dissolve/TypeⅠ1：1 1.0：0.9：0.1 MS MS MS MS TypeⅡ /TypeⅠ

pH

change