4 Replies Latest reply on Apr 26, 2013 6:51 AM by Mitsuru Yamada

    Are complex biomolecules themselves living?

    Mitsuru Yamada

           This is an amateur physicist.

      I have read various books ranging from general biolgy to biochemistry.

      Especially impressive book was John Taylor Bonner's "Life Cycle".

      When I contacted him, he suggested me to read D.L.White's "Animal Thinking".

           You must not doubt that a dog has his mind.  Just in the same way, you do not doubt a cat has her mind.

      Next, let us move to other species.  Do you believe that a bird or an insect like ant can have their mind?

           They do.  This is my conclusion derived from reading the above quoted two books.

      Let's go down furthermore lower ladder.  Does an amoeba has its mind, that is, can an organism lacking nervous network have a "mind"?

      All of the above listed animals are individuals of "zoo"s which is composed from various cellular oragns,or tissue organs.

      Jumping a gap toward further lower biological level, my story proceeds to the molecular scale.

      Think of an enzyme molecule, e,g, phosphorylase, or nucleic acid chain i.e., the double helix of DNA.

      Do you think they are absolutely mechanically driven when they cause motions?

      To me they look like animate entities.  I imagine that almost of all the heavy molecules called enzyme can detect the target substarates which are roaming distant from the enzyme wanting them, and can very efficiently collect them to do chemical operation on them.  To me, the DAN helices too look like doing computation on their biochemical condition of their envirment e.g., the intensities of activities and concentartions of varoius biological molecules. (For example, imagine the motion of the proton in the hydrogen bonding between the base pairing as "digital computer")

      Thus, my imagination is that the biological chemicals are, in a sense, living, always desiring to function something.

      My further imagination is this.  Such an intricate ability of complex biomolecule must be based on the quantum mechnaics.

      The name of the quatum mechanics compises the word "mechanics", but the entire behavior of the biomolecule are never "mechanistic" though the quantum "mechanics" governs the whole activity of the molecule.  When the biomolecule is regarded as an hugely intricate system of quantum mechanics, the computational results of the biomolecular system can barely anticipated or even vauguely grasped by the quatum mechanical Schroedinger equation solving .  It seems to me that the impossibility of the ordinary periodical clock like  solution must be the very key factor that yields "animateness",or "living state" of the biomolecule, amoeba, ant, bird , cat and dog.

       

      MitsuruYamada

      October 18, 2011.   

        • Re: Are complex biomolecules themselves living?
          Mitsuru Yamada

          Hello, everybody!

           

          Did you see the article "RNA GET EXCITED" published on page 10 of  C&EN October 15, 2012 issue?

          This is really a fresh news!  Untill recently, all of us are shown and taught in textbooks the typical biomolecular structures in their ground state always!  How are we foolish!  As a matter of course, a complex molecule must has an infinite kinds of various quantum mechanical states and conformations and configureations, of course!

           

          Frankly speaking, this article has many ambiguous points for me to understand.  But I believe its content is true.

           

          Anyway, please let me talk about my speculation.

           

          My speculation is this.

          What is the agent or agents that causes the change from gorund state to excited state and vice versa of the RNA fragment?

          I am a dreamer based on quantum mechanics.

          So I do really dream of a possiblity of the interactions between the quantum mechanical waves of the various biomolecules that are there in the biological cell.  And I speculate further that the quantum mechanical waves are viblating like an animal voice, which if possible could by its tone stimulate and get a responce in another biomolecule or could even let and command the target molecules swimm toward the master molecule (RNA in this case.)

           

          The article's figure might be just a one snapshot of the structure of an active biomolecule.

          In actual case in the living cell, the biomolecules are continuously changing their electronic state and nuclear configuration and conformation, and as its result, are affecting the sourrounding biomolecules through the "voice of wave function".

           

          How do you speculate about this article, Sirs?

           

          My name is PSY(x1,y1,z1,x2,y2,z2,(keep counting up by yourself until),x10,000,y10,000,z10,000)

          October 24, 2012

            • Re: Are complex biomolecules themselves living?
              Mitsuru Yamada

              Good evening, Sirs!

              In Japan it is 21:30, February 4th, 2013 now.

              In Japan the earthquake has become very frequent recently.

              The earth is very dangerous place to live on.  So I think that we humankind should migrate to the Mars where the seismic activity seems calm on someday in future.

               

              Please look at the page 25 on C&EN February 4, 2013 issue.

              Did you read the article "Protein senses high level of salt"?

              The protein, the TMC protein, must be a heavy molecule.

              It must be composed from many, many amoino acids.

              The nuclei and electrons that constitut that molecule might be obeying the classical Maxwell's equation when they move.  But I imagine that the Maxwell's equation cannot give or afford such an extraordinary capability such as to sense the level of salt!  When using the Maxwell's equation, we usually assume the electrons and nuclei to be point charges.  So such an assembly of negative and positive point charges cannot but show only a trivial mechanistic behavior.

              So we should rather replace the research base from classical physics to quantum physics.

              In quatum world, everything changes to strange things.  Everuthings behave very strangely.

              Maybe there must be still many many strange states and behaviors and capabilities of particles awaiting our discovery.

              In biological cell, the fundamental interaction must yet be the long range effective Coulombic interaction.

              But the ellectrons involved in a protein are never regarded a classical simple dull particles.  Instead they are quantum mechanical entities.  Even the mere single electron is difficult to understand its behavior.  The large group of electrons involved in a protein must be much more difficult to know and to predict its behavior.  The only single protein molecule may be able to show an acrobatic performance!  But such a power comes not from classical physics, but comes from unknown quantum physics of a large group of particles!

              In the biological cell, the cytoplasma is sol state, that is, half liquid, so that the all molecules are in state of loose direct contact to enable the quantum mechanical interactions between groups of electron of various biomolecules. By chain of quantum mechanical molecular contacts, a protein might be able to collect information of e.g. the number of salt atoms floating near by at once.  Such a hypothetical mechanism is too complex to be called a mechanics like a device made from simple gears and levers.  It might be better named a "miniature living machine".

              The protein molecule is living!

               

              A man who requires the biologists to solve the time-dependent Schroedinger equation of all boimolecules until tommorow morning

              February 4, 2013

                • Re: Are complex biomolecules themselves living?
                  Mitsuru Yamada

                  Good evening Sirs!

                  It is PM11:00 in Japan now.

                  I must leave home at AM6:30 tommorow morning.

                  I must go to bed in a hurry now, sorry.

                   

                  But did you read an article on page 37 of C&EN April 8, 2013 issue?

                  The article is "Reactions Illuminate Intricate Biochemistry."

                  From that article, I have known a fresh term "bioorthogonal reaction."

                  It is introduced at the begining part of that article as "Reactions that monitor biochemical process without interfering with them, known as bioorthogonal reactions,..."

                   

                  About 27 years ago I indulged in reading a book "Biochemistry" (1975) written by Albert L. Lehninger.

                  In that book, it was emphasized that the free energy difference of a biochemical reaction leads the things that happen in a biological cell, according to my memory.

                   

                  Today I have met the new notion "bioorthogonal reaction."  This has no relation with the notion of free energy!

                  Though the C&EN's article shows the applicational consequence for observation of Taxol's action on microtubules in cancer cells, I myself have conceived an idea of the term of bioorthgonal reaction.

                   

                  Think secondary bioorthogonal reactions, think thirdly bioorthogonal reactions, and so on.

                  There might be many many other biological chemicals that can function bioorthogonal reactions.

                  If this can be true, then there is many many layered cascades of network of bioorthogonal reactions.

                  Then a chemical signal that occured in one place can be transmitted to all place in the cell in one instance!

                  The biologicalk cell is a bag in which a society of biomolecules are interacting with each other, and an information can spread all over the entire cell.  Or it could be said that simultaneously all of a cell-biological information are investigated by all of the constituent molecules of the cell.

                  This chemical processing function is the life itself, is'nt it?

                   

                  A Pithecantropus Japonicus who, in a cave in paleolithic time, is receiving electronic delivery of C&EN from ACS by advanced potential wave

                  April 8, 2013 


                • Re: Are complex biomolecules themselves living?
                  Mitsuru Yamada

                  Good evening Sirs!  It is PM8:00 in our country now.

                  This is a Pithecantropus Japonicus. ( Is my sense of humor so bad?)

                  Recently I have encountered an amazing article which was informed from Prof. 00254851's blog "If the Model Suggests Link between Intelligence and Entropy...."

                  The website is http://physics.aps.org/articles/v6/46

                  Reading the article which was written by science free writer Mr. Don Monroe, I was surprised to know the amazing behavior of simple physical system.

                  It was as if a rigid pedulum or even one wandering particle in a box have their intelligence!

                  At least according to the article, they behave in an amazingly "intelligent" way!

                  Why don't you extend this extraordinary finding to the atomic system or molecular system?

                  Though it seems to me a difficult task, it must yield much more interesting chemical knowledge to us in future.

                  Do you think the above behaviors of the simple physical systems are only a superficial "intelligent", or do you believe they really have true "inteligence", Sirs?

                  There is a lot of more fundamental problems in the field of quantum mechanics.  Think quantum mechanical interpretations on the slit interference experiment. I am also puzzled by the Heisenberg's uncertainty principle.

                  An atom of uranium has 92 electrons.  It is not possible for us to know exactly the quantum mechanical state of the electrons even now.  Possibly even an atom or its electron of hydrogen can behave in an intelligent way.

                  How do you think, Sirs?

                   

                  A pithecantropus Japonicus who is gazing a piece of rock and efforting to communicate with it

                  "Yes, this rock must has his mind and must be thinking something!"

                  April 26, 2013