Suipwksiow:  I think your questions of "why" are beyond the scope of physics and philosophy, and may be pointing to religion.  This is because physics is limited in the scope of science, which only deals with observable and reproducible phenomena.  And philosophy can raise many questions but itself cannot answer them (satisfactorily).  As long as the question of the origin of life is not known in scientific and philosophical terms, the "why" questions will be unanswered for a long long time..........

Hi Suipwksiow, 

This is such a great question! And it is one of my favorites.

First - Ke-Wei is absolutely correct - philosophy is utterly irrelevant to this question. Philosophy refers to the synthesis of knowledge from information extracted from data. That data can come from literature, biological observations, careful  observation of physical phenomena, etc. To understand your own question, its key to understand how all of these things/fields are related. In other words, how is biology related to chemistry, and how is that related to physics? They are all  just ways that we humans have categorized our  study of the same thing - the natural universe - and they are essentially different levels of focus. Here's a completely made up story to illustrate how these fields are related....

The literature PhD studies the words created by other humans, and he is fascinated by how many different versions of the same story there could be. He thinks about it and concludes that all of these minds are similar in composition, but develop down different trajectories giving rise to the different versions of what appear to be relatively similar stories.

The neurobiologist reads a summary of this  work and thinks, fascinating - but if all of these minds are truly similar in composition, then I should be able to observe similar patters across the brain, which my predecessors showed to be comprised of neural cells. So they disect the brain and image brain activity, and measure brain chemicals as best they can to draw conclusions about the similarities between brains. They note that certain regions of the brain exhibit frequent excitation of electrical activity which leads to the release of a variety of chemicals - neurotransmitters. 

The biochemist reads the neurobiologists latest discoveries in a journal over lunch and begins to speak with his good friend the general chemist about the possible structures of these neurotransmitters. Together they use what they learned from the neurobiologist and propose a theory that these chemicals are comprised of a variety of different atoms and have a specific shape, which then bind to proteins on the surface of the neural cells. They are able to define with great precision the interaction between the proteins and the neurotransmitters and determine that their shape is key to the binding process.

The chemist and biochemist go on after this publication to work with a theoretical physicists  to explain how these atoms bind to one another. They develop a theory based on the observations of fellow scientists that these proteins and molecules aren't static, but vibrate with high frequency - causing the proteins to change conformation. They realized that 85% of the time the protein is in confirmation A, while the other 15% of the time it is in confirmation B. Astounding.

The physicist then reads this paper and thinks to themself - my goodness, these molecules behave in such an interesting way! Perhaps I can develop a theory to explain why these molecules vibrate to begin with! He starts to consider the very nature of the constituent parts of the molecules, the atoms themselves. He studies the behaviors of the electrons among all of the elements, and builds a giant magnetized ring to accelerate simple atoms close to the speed of light so that he can smash them together to see what they break apart in to. This work gains traction and before long 1000s of experimental and theoretical physicists are collaborating to understand what the fabric of  matter is and they realize that it is nothing more than intersecting fields produced by subatomic particle waves rippling through the very fabric of space-time.

So all of these scientists elect a spokesperson to condense all of the findings from the  neurobiologist, the chemists, the biochemist, the physicists both experimental and theoretical, to write a review article. The spokesperson brings the review article to the literature PhD and discusses it all over a cup of coffee.

So this is the end of the completely made up story - I hope you've made the connection.

All of these fields are studying different aspects of the same thing. 

If you can learn a little bit from each field, then the reason that macromolecules behave the way they do (for example, why transcription factors bind to DNA) becomes apparent. I'll give you a leading summary, and with this you can start your journey to gaining a broader understanding for yourself.

The physicists and chemists taught us that each atom has a different configuration of atoms.When these atoms bind to one another, we call this a molecule and we know that molecules a huuuuge variety of charge characteristics. Some molecules are polar, some are neutral, some are negative, some are positive, etc. Some are stable,  others are highly unstable, the list goes on. Proteins are just molecules. They are a combination of atoms.

But here is the clincher:

Most atoms when bound together will form an unflexible lattice that is a repeating pattern over and over. Metals and rocks. There is no flexibility to a lattice that is repeating and these molecules either stay in the conformation forever if they are stable, or break down if they are unstable (as is the case of high atomic weight atom lattices). And actually, most of the atoms in the universe are just single proton atoms - hydrogen. However, when stars compress low atomic weight atoms such as hydrogen and helium in their cores (leading to never ending nuclear fusions explosions that make our sun what it is), they form a variety of different atoms now with different numbers of protons and electrons. When these stars go nova, they undergo one final massive compression, fusing together LOTS of atoms, and explode in a ridiculous display call a super nova (if the sun is big enough). These explosions innevitably lead to the create of the most important element (atom) to life. The CARBON atom.

The difference between a protein and piece of metal is that proteins, and all other molecules that form the basis for life, revolve around the all important carbon atom - which provides the atomic property of flexibility. Proteins are structured around the carbon atom and carbon atoms allow a large variety of different types of atoms to come together. There is an entire field dedicated to studying this flexibility and the endless combinations of atoms that revolve around carbon. This field is called 'Organic Chemistry'.

So when it comes to a transcription factor binding to DNA, what is REALLY happening?  Well, DNA is an organic molecule, based around the carbon atom, rich in phosphorous, and therefore exhibiting an overall negative charge. But,the individual nucleotides that are ordered along the phosphate backbone have their own charge domains. So you can think of a piece  of DNA, a transcriptional start site for example, as a unique sequence of charges that are either exposed (homochromatic) or not exposed (homochromatic). Lets not  forget that a transcription factor is a protein, which is also a molecule with its own unique pattern of charges across its surface. What happens when a positive charge and a negative charge come in to contact? They bind. But the charge pattern across the sequence of DNA and the binding domain of the protein have to match in order for them to actually bind.

Its almost as if each molecule was encoding some kind of charge pattern allowing it to bind...

Indeed, this is the very high level essence of the genetic code. This molecule encodes every protein that exists in the cell - transcription factors, cell membrane signaling molecules, hell, even the histone proteins that the DNA wraps itself around are encoded. The entire cell is just a crazy complex combination of encodings that determine which molecules bind with which, when, and where. And its all based on fundamental physical properties of atoms. 

To be absolutely clear, the complexity of these systems arises through a natural evolutionary process. And there is plenty of evidence to show that complex systems absolutely CAN arise from simple beginnings using an evolutionary mechanism. We have demonstrated this both in living systems and computationally. Google for evidence if you are unsure whether or not to believe me.

So, in summary - why do molecules like transcription factors behave the way they do? Philosophically that is an irrelevant question. Scientifically that is THE question that theoretical and experimental physicists are currently trying to answer. Guys like Sheldon from 'The Big Bang Theory', or Stephen Hawkin in real life, guys like Albert Einstein,  etc. How do molecules behave the way they do? Encoded charges spread through the molecule by their fundamental physical properties. Even the behavior of proteins as complex as endonucleases can be deconstructed in to sequences of behaviors that arise from their composition and fundamental physical properties.

Pretty neat, huh?

Molecules choose to do what they do because they imagine that their intention will cause changes that will satisfy their desires and feel good.

Same as us.

Although we live in the third millennium, although people think they know more than they know, we are going to tell them that they do not know enough. People cannot surpass their own limits, their own conventions. They must understand philosophy, the science or the nonscience beyond the definitions offered by the dictionaries, (limited conventions) or beyond their current capacity of understanding, beyond their limits. According to their intuitions, there are certain confusions, as in the case of your questions, but they are either too hurried, anxious to find out the truth and they forget about this truth, or they ignore it, without being aware of it, because they fail to make the essential connections between these elements of knowledge and the unlimited we are and we are part of. If we were to relate the limits of human knowledge, whatever their type, to the unlimited of the Unconventional Entity/Universe/, (E/U)n¡, we will notice that they are zero. Moreover, they are not any scientific zero, (mathematical, physical, biological, chemical, etc.) or nonscientific, (astrology, parapsychology, magic, zodiac or any kind of palmistry, etc.), they are ulimitedly small zero, that is a yero similar to Morgana. The closer we get to this zero, the farther it will be. Nobody and nothing can reach the unlimitedly small or the unlimitedly big zero, because, similar to any horizon, the closer we get to them, the farther they will move. We must understand that the divisions of the mathematical unit are always divisible by the infinite, an infinite that in our extrapolation as Unconventional-Philosophy, (F/N)n¡, towards the unlimited, without any exceptions or limits, we define as unlimited, ©, beyond the symbol convention (infinite ∞) in the sciences or nonsciences. Furthermore, the divisions in their turn are divisible by this unlimited, any type of division is divisible by this unlimited. Consequently, the unlimited exists even if we will never be able to reach it and it must not be mistaken for the mathematical or human infinite, which are limited, relative symbols, or a limited reflection of this unlimited. In this case, where the unlimited and any unit stand for the unlimited, for unlimitedly small sequences and any entity/universe (form of organization) is a mathematical whole or a unit, (which leads to the confusion between the goat and the cabbage, as one is both the goat and the cabbage, which confuses us). It would be absurd to believe that ''the God particles” or the Higgsʼ bosons are the last barrier of the unlimited or of the matter/energy or of knowledge. Unfortunately, as we have already mentioned, people mistake philosophz as essence for its particular limited and conventional versions. According to the definition of philosophy offered by the dictionary,  

“Science made up of an ensemble of solid notions and ideas, that interpret and reflect reality from the general point of view; general conception of the world and life. 2. The totality of the conceptions and methodological principles that lie at the basis of a discipline or science. 3. (Rarely used) Wise attitude in relation to lifeʼs happenings; specific manner of considering lifeʼs issues. 4. (Fam.) Something difficult to carry out. – ngr. philosophia, fr. philosophie.

we will notice that its essence is “the reflection of reality.” We will also observe that it is limitedly considered “science.” Furthermore, we will conclude that it is considered as totality of  “the conceptions and methodological principles that lie at the basis of a discipline or science.” Philosophy is mistaken for the sciences, but the definition excludes the nonsciences. Unfortunately, both sciences and nonsciences represent knowledge as a whole or philosophy, not only sciences. The advice of the old people during the primitive communal system stood for the common representative of sciences, but also nonsciences, in those times when the bulks and the enchanters were popular, and not the researchers or the physicians. To make things clear, we can mention that the main issue is the fact that we do not actually know what reality is, before reflecting it in one way or another. We mistake the world of our ideas for the reality it reflects, which is not reality. According to the definition, there is a reality of ideas, reflected by these ideas. In this case, we must define or understand reality more comprehensively and clearly. Unconventional philosophy, Fn¡, defines an Unconventional reality,  Rn¡, as representation of simultaneity, (neither parallel, nor interdisciplinary) of three realities, Unconventional/Reality/Universe in Itself, (U/R/S)n¡, or of the universe of the unlimitedly small dimensions and any entity/universe, whatever its nature, Unconventional/Reality in Itself, or Reality in Itself (R/S)n¡, or the reality of the nature that exists within and outside ourselves,  Unconventional/Reality/Illusion/Reality, or Illusion/reality (R/U/S)n¡, of the ideas or the spirit belonging to the entities/universe of any kind, as simultaneity of these ideas. Let us not mistake the idea defined by the dictionary, which is limited, for the unconventional one. One is a phenomenon limited to the human psyche, the other one stands for a phenomenon, unlimited as resonance of the energies or indirect effects of any entity/universe. The idea is contained by the matter that sustains it and it is not the result of a direct reflection, but of resonances as as its indirect effect. More precisely, the matter is simultaneous with its ideas, whatever the nature of the matter or its ideas. The atom contains the idea of atom and it is not our reflection that invents the idea of atom. Our conception on the atom is the reflection of the idea contained by the atom, by means of unlimited intermediaries, our senses. The simplest proof is the fact that in the primitive communal system, the idea of atom did not exist. This was due to the nonexistence of their idea on what an atom represented, and not because there were no atoms. We first discover an object, then we form a true notion of it. It always exists both as matter and idea. The Unconventional/Reality/Universe in Itself is the reality of the unlimitedly small sequences (as division of any whole, entity/universe, by the unlimited), that nobody and nothing can ever reach. Reality in Itself represents the nature we are part of and which is reflected by the ideas of any spirit in one form or another. The spirit (simultaneity memory/thinking/senses/feelings/intuitions/instincts) is the representative of these ideas and of the Illusion/Reality specific to each of us or to any entity/universe. All we have to do is to take a close look at ourselves or any entity/universe (atom, molecule or “the God particles, etc.) and we will understand that we are a simultaneity of ideas and a simultaneity of matter/energy particles we are made of, but also a simultaneity of unknown, unlimitedly small divisions, as our division to the unlimited. In this context, your question has three types of answers, according to the realities we try to reflect, one nobody and nothing could ever reach, another that we can only reflect in relation to a certain system of reference, but which becomes relative due to the limited system of reference and a spiritual one, that is concerned with our ideas on the other realities. We have tried to introduce you to another world of philosophy, another way of reflecting things there where philosophy remains the mother of sciences, but also of nonsciences, not only as the reflection of an unclear or ambiguous reality, defined by the dictionary, but of an unlimited extrapolation of our reality Illusion/Reality or virtual reality, towards the unlimited that exists whatever our will or wish. As result of our work, the paper entitled “The Unconventional/Truths” will appear. It is a complex paper in the sense of the Unconventional/Philosophy with applicability in any domain, whether science or nonscience. Sciences remain the particular cases of philosophy, where the condition concerned with the identity of time is mandatory, whereas nonsciences remain the particular cases of philosophy, with the condition of nonidentity of the sequences they make reference at. All of them are reflections of reality, they are not reality itself.  

Part two

In the second part of the paper we will resume the answer of our question, with the specification that any science is relative, similar to the solutions it offers. Furthermore, philosophy offers answers in as far as the directions that it presents are accepted as answer. The infinite, the indefinite, the impossible or the death in Mathematics or in our daily life are answers accepted, without being an answer. It is absurd to believe that solutions such as infinite, indefinite or impossible are solutions. They are solutions only if we conventionally accept them as solutions. Otherwise, they are meaningless, they only prevent us from searching and obtaining information on that direction. There are similar solutions in Biology as well. Death is such a solution, apparently impossible for the spirit that disappears, but logical for the unlimited transformation of any kind of entity/universe. Death is a solution only if we conventionally accept it as solution. Otherwise, it is far from making things clear or satisfying the curiosity of knowledge. The answer to the question has consequently an impossible solution at the level of the unlimited, that nobody can reach. It has a natural solution that we can only reach bz means of intermediaries, more exactly our senses, or he senses of other entities/universe. The last version is represented by our limited conventions as a reflection of nature. The last ones can be extrapolated towards the unlimited, but they will never be nature itself or its unlimited. Things are different in the unlimited, where there are no contraries, limits, or conventions, whatever their nature. There are only unlimitedly small sequences, that accumulate into unlimitedly big sequences represented by us or any entity/universe. Your proteins are such unlimitedly big entities/universe. Let us take a look at the stem cells, the chromosomes or the DNA, that were unique and indivisible, similar to the atom, or “the God particles,” as they are now called. At the same time, we should ask ourselves how is it possible that different, never identical entities/universe take shape out of the same sequences, (particles). The same chromosomes give birth to people or animals, that are never identical, such as the stem cells give birth to different organs. Two teeth that are formed from stem cells are only apparently identical. Within the limits of the  Unconventional/Entity/Universe, there is no identity. Everything is simultaneously identical and non identical, beyond our conventions, as understanding. This similar to figure zero in Mathematics. Zero is positive/negative simultaneously, in relation to the system of reference and not to its limit, that we cannot reach with our conventional reflections. According to Smarandache Florentinʼs neutrosophy, any number r ranges between r-ε and r+ε, which is also valid for zero. This means that however close we get to zero, these sequences are negative, when they are related to the negative and positive when they deal with the positive. We will never reach the perfection of the unlimitedly small zero, where the positive and the negative become one and the same thing. This zero is neuter. It does not exist, but it separates our conventional contraries. The DNA, the molecules, or the stem cells are apparently identical, there is no identity, there is only our incapacity to get in one form or another beyond our limits. Identity is related to our limited systems of reference, that deal with the relative. This is similar to the people that turn into apparently identical points from a distance. Enlarge their dimensions, or reduce the system of reference, (the system of measuring, interpretation or reflection) and zou will find the differences. There is no identity in reality. Mathematics or any other science would disappear in the absence of the sign of equality or identity. Many of us think that two iron atoms or two water molecules are identical, but let us not forget that both the atoms and the molecules, or even apparently immaterial phenomena fail to occupy the same space at the same time. Furthermore, it is absurd to believe that an iron atom in my office is identical with an iron atom present in the pencil you write with. The atoms have a dynamic construction, electrons, protons, fragrances, etc, in a permanent movement. It is only out of neglicence that we can assume that these dynamic phenomena superpose identically. Any entity/universe has both an interior universe, as we have shown above and an exterior one, unlimited, that permanently influences it and nonidentical, due to the position space/time it has. The proteins or the endonucleases that you study are not identical, whatever their nature, which is also valid for the DNA, the same chromosomes, the stem cells, the atoms or the molecules that constitute us. We actually deal with the illusion of their reflection, in relation to our limited and relative systems of reference. Philosophy recommends you to search for two simultaneous directions, one concerned with the nonidentity of these molecules or apparently identical sequences, and the other one with the fact that any entity is defined by its connections, by the energies that make up these connections and not by the matter represented by these energies. Any connection, whatever its nature, deals with the energy, it is not material, as we might think. An entity/universe is well defined by the connections of its material sequences, represented by energies, and not by the material sequences that these energies connect. The energies of both the interior and exterior universe are unlimited. Identity is only a compromise between sciences and reality. Let us not neglect their relative aspect. Everything is relative not because it is relative, but because the systems of reference in relation to which we represent or evaluate an entity/universe are relative. The relative is introduced by the limited system of reference, not by the absolute of the entity/universe that we represent.

Instead of the end

Unconventional/Philosophy represents the ensemble or the simultaneity knowledge/ignorance, where each element is a simultaneity science-nonscience. It is the newest generalization as extrapolation towards the unlimited of our ideas or conventions. However, we should not mistake the ideas for the nature they reflect.  Moreover, we should take into account the fact that any entity/universe, matter/energy contains the idea. It is not reflection that shapes this idea. The idea of object will never exist in our mind in the absence of the object.  

Nice Contribution Frank Landis