Breaking the Universal Speed Limit?

Well, how do you measure the speed of light - and thus check that everything is observing this ‘universal speed limit’? Seven years ago, the closing months of 2011 saw much excitement in sciencey circles with the highly mediatized announcement that researchers at CERN, the world's most expensive physics laboratory, had detected sub-atomic particles apparently travelling faster than the speed of light. This, the papers assured us, was in defiance of Einstein and all the rules of relativity. Yet the plain ‘fact’ of the matter is that the speed of light is not magically ‘out there’ but merely a human convention. In a relativistic universe, how could it be otherwise?

Here the point is put nicely by Burt Jordaan in a blog posting of January 25, 2010. Burt writes:

‘In order to measure any one-way velocity, we essentially need two clocks: one at the start and one at the end. Obviously, the two clocks need to be synchronized and run at the same rate (and to be sure, they must not be moving relative to each other and also be at the same gravitational potential). Yet we reasonably assume that the two clocks run at the same rate, at least close enough for all practical purposes. Now we need to synchronize the two clocks to read the same at the same moment. How is this done?


In his 1905 paper on Special Relativity, Einstein says: “We have not defined a common ‘time’ for A and B, for the latter cannot be defined at all unless we establish by definition that the ‘time’ required by light to travel from A to B equals the ‘time’ it requires to travel from B to A”.

One can reasonably read Einstein's ‘by definition’ as ‘by convention’. 
Using Einstein’s convention to set the distant clock at a known distance, call it ‘D’, in empty space, we send a light signal at (say) time zero and when the distant clock detects the signal, it sets its time to D/c sec (the light travel time), where c is the standard speed of light in vacuum.

Now we can measure the speed of any object moving between the two clocks. We can also use the two clocks to measure the one-way speed of light, but we are obviously guaranteed to always get c. In this sense, we get the speed of any object only relative to c and not absolutely. 
In this way, the one-way speed of light is a convention, depending on the convention for clock synchronization."

Burt concludes by observing that there is a general belief system prevailing in physics that ‘whatever is known exists and rest is non-existent’. It is because of this belief system that scientists tend to fill  these existence-nonexistence gaps by cofficients. Yet there can be much more existent and important entities quite apart from the usual quantitites of space and time which physicist are led to ignore. This attitude is the reason that the existence of Dark Matter was unimaginable for four hundred years. As to the spped of light itslef, Burt says explicitly that he cannot understand why Einstein established a ‘religion of special abilities and qualities’ for light. Specifcally, he objects tha even though there are ways to measure the speed of light, there is no reason to believe that nothing can travel faster.

Our own correspondent, Muneeb Faiq, took up the issue for Pi too. Here he offers a thought experiment which again shows the arbitariness of the ‘speed of light’.

‘In fact, there is a lot of confusion about the harmony between the classical and quantum definitions of speed.If both quantum speed and classical speed mean the same then a very interesting difficulty comes to the front.

Suppose there exists only one body in the universe. Just a single point mass and space. Is it at rest or in motion? If, however, there come out two photons of light moving parallel to each other. What speed are they moving at? If an observor is stationed on the point mass, then both the photons are moving with the velocity of light. Suppose, all of a sudden, the point mass ceases to exist. Now there are two photons moving with same speed parallel to each other. Nothing else exists except space. Are these two photons moving now because they are at same position in relation to each other which will be defined as the state of rest.

It is interesting to note that before the point mass existed, the two photons were moving with the velocity of light. Now since the point mass has ceased to exist but nothing changed about the photons, they are not supposed to be moving now even if they are moving with the same previous speed.’

Q&A On the Status of the Speed of Light

Pi’s New Year Q&A: Is the One-way Speed of Light a Convention?

Martin Cohen and former Pi contributor, Muneeb Faiq explore one of the claimed certainties of physics.

To introduce the issue, here's blogger Burt Jordaan wondering, way back in January 2010, about why the 'speed of light' suddenly became the one true measure of all things scientific.

Burt writes:

'In order to measure any one-way velocity, we essentially need two clocks: one at the start and one at the end. Obviously, the two clocks need to be synchronized and run at the same rate (and to be sure, they must not be moving relative to each other and also be at the same gravitational potential). Let we reasonably assume that the two clocks run at the same rate, at least close enough for all practical purposes. Now we need to synchronize the two clocks to read the same at the same moment. How is this done?'

Recall that Einstein himself clearly admits, in his 1905 paper on Special Relativity, that: "We have not defined a common 'time' for A and B, for the latter cannot be defined at all unless we establish by definition that the 'time' required by light to travel from A to B equals the 'time' it requires to travel from B to A."

Burt says from this that what Einstein terms as being 'by definition' is equally 'by convention'*. Consider: Is the radius of space's curvature related to the speed of light?

The Q&A


Martin: That's a four-guinea question, innit? I believe conventional accounts make space into 'space-time' and the speed of light is allowed to determine things like that, yes.

Muneeb: I don't understand why Einstein established a religion of special abilities and qualities of light. Though there are ways to measure the speed of light but there is no reason to believe that nothing can travel faster. I think a few thought experiments should be propounded to at least break the myth that light owns special physics and light makes nature asymmetric.

There is a lot of confusion about the harmony between the classical and quantum definitions of speed, for example. If both quantum speed and classical speed mean the same then a very interesting difficulty comes to the front. Suppose there exists only one body in the universe. Just a single 'point-mass' and space. Is it at rest or in motion? If, however, there come out two photons of light moving parallel to each other. Now what speed are they moving at? If an observer is stationed on the point-mass, then both the photons are moving with the velocity of light. Yet, suppose, all of a sudden, the point-mass ceases to exist. Now there are only two photons moving with same speed parallel to each other. After all, nothing else exists except space. Before, when the point-mass existed, the two photons were moving with the velocity of light. After, when it has ceased to exist, they seem to not be moving at all! And yet nothing has changed regarding the photons. I hope I have made my point!

Martin: Yes, I get your point... I've wondered about this sort of thing too!

Isn't the usual idea that the universe started with a single point, 'the singularity', and at this time indeed none of the usual laws applied. Then there seems to be a suggestion that the speed of light may not have become 'defined' in the key moments of the first 'explosions'.

Now what this caused me to puzzle a little about, is that if, in fact, the singularity was one particle - as you say, a photon - and if it travels, by definition, at the speed of light, then surely it can be everywhere at the same instant, because of those peculiar Einsteinian laws. In other words, could it be that the universe consists of just one photon, which is everywhere, creating both space and time?

Bear with me! Suppose this is the universe, then why would it matter what speed the photon travelled at, any more than where it was or when? Nothing would be meant by these comparative terms.
What do you think? Can we put our ramblings into a form that would make a suitable webpage? I'd like to try, PI is a good way to organise and explore ideas.

Muneeb: There is an interesting point to note: what are usual laws? Why are they usual? Are the laws of physics really laws in the first place - because if they would really be laws; then they should never fail to explain behaviour of everything that exists. This difficulty hovered around the intellect of many great physicists - including Einstein - and that is why he spent so many years in search of a unified theory that he hoped would explain everything.

Mathematics, theory and philosophy should go hand-in-hand in order to get a further insight into reality. Otherwise we all have to be convinced (like Stephen Hawkings) that there can never be a grand unified theory. But I am afraid in that case, then we have to be convinced that there are no governing laws at all. All physics will melt away.

Instead, let physicists, philosophers and mathematicians come together and work in harmony in an open-hearted, interdisciplinary manner to understand what none of these disciplines will ever be able to get grasp of independently.

Martin:   Well, y'know, this is certainly a good question, but I'm not sure it is quite as clear a distinction as you imply. For example, we might say it is a law of physics that energy can neither be created nor destroyed, no? Without being obliged to throw that principle away just because (eg) some neutrinos evidently don't want to be part of the present theory about cosmic speed limits?

Muneeb:   Yes. You are right. We, of course, can say it is a law of physics that energy can neither be created nor destroyed without being obliged to throw that principle away just because some neutrinos evidently don't want to be part of the present theory about cosmic speed limits. But what is the applicability percentage of these well established laws? If energy and matter can neither be created nor destroyed, then from where did it blast into existence? Shall we then opt for the principle of first cause where these laws fail altogether? No Newtonian law holds good when we discuss atoms and sub-atomic particles. Einstein himself said that quantum mechanics (which is again a set of laws)is not absolute. Furthermore- quantum and classical worlds are composed of same material and, therefore, some basic underlying principles must be obeyed which we have not yet been able to discover. It is not the question of neutrinos only because most of the universe is composed of dark matter and dark energy which was concealed from over imagination for hundreds of years because of the over emphasis paid by physicists on the laws that are collectively described as quantum and classical mechanics.

The portion of the universes that the currently available laws explain is negligible as compared to the great splendour of dark matter and dark energy that fill the universes (previously we concieved only one universe but now we say universes). There may be some "extra-bright matter" and "extra-bright energy" awaiting our discovery. For that, we again have to wait for the failure of currently known laws of physics and those great mathematical equations that terrify all those who are not physicists and mathematicians. Once we fortunately fail, we will be obliged to look for an explanation for the failure and may consequently theorize existence of very weird materials and phenomena faintly conceivable as of now within the delineated perimeters of quantum and classical conditioning. That is why I emphasize on first understanding what makes the universe (what material and quality of materials and types thereof constitute everything), then we need to classify all that material and non material on some sound basis.

We also have to classify on the basis of discovered and not-discovered. Then we have to understand their behaviour. On the basis of the theory generated; we then can develope mathematics which explains things and helps us to imagine what we cant with the help of mere theory. I hope I don't sound insane!

Martin:   Mmmm, absolutely, I do agree that physics is full of 'black holes' to pun little! But I just want us to avoid addressing ill-founded assertions in conventional science with our own ill-founded assertions. For example, the 'dark matter' mystery - is this not a theoretical construct itself, intended to plug an experimental hole in current theory? You speak of it as a discovered reality, but isn't that to fall into the same way of thinking as the people you are critiquing?

Thinking about the 'problem' of where the energy in the universe came from, isn't it perfectly logical to simply say that there is no 'before' to be dealt with or explained?

Over to you, or anyone reading?

Muneeb: Haha! I am caught in a loop.I am not smart enough for arguments. However, though my writing apparently reveals that dark matter is a reality but I don't mean that. That is why I have guessed the existence of extra-bright matter and energy. What I am doing is to use the discoveries of physics to prove the inconsistencies in physics itself.

I should put a caveat here that I am not anti-science or anti physics. Dark matter was discovered by science to plug the black holes (as you say)and may be some other matter and energy will sooner or later be discovered which disproves everything. Does it mean that we should try to adjust our current theories without revising our basic understanding of the universes. Science has made aeroplanes fly etc. but that does not mean science is correct everywhere. Regarding your question of Un-important "before", please allow me to disagree with you because "before" is of great importance.

First question is; what time-point in the evolution of universes is the beginning? Why is a particular scale of past not a "before" and why all of a sudden we think of something as "before"? Cant it be that this "before" may give us inkling into the evolution of the behaviour of everything that apparently exists. What happened before big bang seems to me as important as what happened afterwards. This is because if we come to know the state, status and behaviour of matter, energy, space, time, void etc.before big bang, we will surely get some idea about how matter, space and time evolves to a better extent than if we stop at big bang. Thanks!

Six Problems in Standard Physics

By Muneeb Faiq

Reposted from Pi alpha

Is certainty the proper aim for science – or a misleading vanity?

The human mind seems to have a tendency always to try to understand everything to the level to which comprehension reaches. The natural laws which govern the behavior of everything in universe and the experiences gained by mankind out of the pursuit to understand that behavior summed up and eventually came to be known as Physics.

It is perhaps both the beautiful inquisitive nature of human mind as well as its frailties that paved way for the beauty of theoretical physics. Mind is equipped with faculties of inquisitiveness and understanding but its power of understanding has its own limits to which limitations in our abilities to expalin and communicate must be added in turn.

The dismissive, 'no-no' attitude of much of modern physics towards innovative ideas and the discipline's alienation from pure philosophy has added to this inherent defect. Every intellectual pursuit in physics is a question (or a set of related questions) built upon certain understandings and theoretical explanations. Worse, as the human mind seeks to answer one question, another appears ready to confront and to confound; more complex than the original one and more difficult to address.

Many physicists have made valiant attempts to tackle such questions and solve these ever-growing mysteries but known and unknown factors alike have instead contributed to the great asymmetries that the physics of today suffers from. This problem is made much worse because the world of physics seems to have closed its doors to genuine philosophers and other thinkers who could potentially contribute in much needed domains of this subject.

We are told instead that a physicist’s guess is a great pearl of wisdom while the same guess by someone else is an unworthy idea. This attitude is stalwartly discouraging and may in the long run prove fatal to this beautiful science particularly as many of these 'guesses' are beyond the bounds of conventional logic, thereby making of physics an illogical trade. With such guesses, logical asymmetries cannot but keep on increasing and have now precipitated serious problems in physics - even at the most basic level. The questions arising from the predictions made beyond the boundaries of standard logics need to be answerered.

1. Physics as recursive analysis

Physics is justifiably considered to be one of the most fundamental yet complex sciences but this science proves to be an incomplete description or reality at the fundamental level. In physics, we have been earnestly inquisitive to reach the smaller and smaller sizes of the scale. This has helped us to know and identify a plethora of elementary particles with postulation of many previously unknown forces and interactions. But so far we have not reached the smallest particle despite a lot experimentation and artistic work of fiction build to explain the observed phenomena.

Physics deals with many physical and fundamental quantities but it is interesting to note that a satisfactorily complete definition of any physical quantity has not been identified. This may seem a little weird yet it is true.

Mass is defined as matter and matter is defined as mass. 
Time is defined as period (or something related) and period is defined as time.

Definitions in physical quantities are just verbal synonyms. This is the example of limits of explanation which in a circular manner limits our understanding. It is a typical linguistic problem but precipitates great hitches in physics. Imperfections in understanding lead to miscommunication which creates problems into domains of explanation which in turn lead to further weaknesses in understanding.*

It seems to be a linguistic game but it is not so. The following discussion will reveal that. In order to understand a brick, first one has to understand all the properties mentioned in its definition. In order to find the definition of one property it gives rise to many more terms which in turn are to be understood and process carries on and our idea of understanding a brick becomes complex in consequence. The same is the case with physics or, should we say, throughout the whole of science.

While answering one question many more questions arise which are more difficult to answer and our intention of understanding any scientific point remains stuck at its place and is paralyzed. Our notions in physics to fabricate complete definition of physical quantities are still very far from being practical. The difficulties in our definitions pose as greater hurdles in our understandings and communication which in a “Loop amplificative” manner create more difficulties. These difficulties have grown with time and have concealed the mechanism and exact status of many facts in universe. We are still very eager to know the answer of the question as; how and by what means the present state has been achieved by the universe. Many ideas (some including terrifying mathematics while others complex theoretical basis) have been put forward but even today none is satisfactory to the extent it should have been. And the tradition of plugging the holes with new supporting hypotheses rather than revisiting the previous one has added fuel to the fire.
 
2. Gravity as ungrounded postulates

Newton’s universal law of gravitation is a blazing idea which although doesnt prove but explains why an object when dropped freely falls to earth. Not only this, the law also explains the planetary motion et cetera.

When Newton put forth the idea of gravitation he tried to escape the difficulties by certain postulates which were taken to be true as such and without any argumentation. For example; if gravitation exists and everytime it is attractive then universe should fall to a single point, which doesn’t happen. This thing would have put universal law of gravitation to rejection as soon as it was hypothesized but Newton supported his ideas with other supporting postulates. He escaped this difficulty by saying that for such a fall there should be a centre of gravity where all the stars should fall but there is none and the centre of gravity is uniformly distributed throughout the universe. This postulate is neither true nor false. This is an over complex concept requiring far greater amount of mathematics and comprehension physics has yet reached to. So everyone agreed to universal law of gravitation in the disguise. This additional postulate masked the weaknesses and asymmetries in the universal law of gravitation.

Many properties of gravitation have been theorized as the gravitational force is a long range force; this force is always attractive etc. But one question spoils all the knowledge we have about it. The question is; where from does this force come? What is the origin of this force and what is the mechanism of its generation? Coming back to the origin and mechanism of generation of gravitational force; this problem has not been adequately addressed yet. Of course, the origin of this force i.e. the gravitational force is said to be a particle called graviton but unfortunately graviton is an act of faith and here is an example when science becomes religion. The graviton is a hypothetical particle assumed to be existing but has not been observed to date.

3. The unexplained quantitization of charge

Robert Andrew Milikan has been one of the greatest experimentalists of all time. He is thought to have estimated the fundamental value of charge by his famous oil drop experiment. Many experiments alongwith Milikan’s oil drop experiment revealed that charge cannot have any arbitrary value except the integral multiples of its fundamental value. The fundamental value of charge was found to be 1.6x10-19 coloumbs. This meant that charge is quantized. The concept of quantization of charge is unproblematic but classical as well as the concepts of modern physics have not been able to explain as why is charge quantized. Milikan postulated the granularity of charge on the basis of his experiment but there was always a chance that his experiment was limited with a certain degree of scale for observation beyond which he could not achieve any results.

Smaller quantities of charge were not probably observable by his experimental setup but his findings were never revealing of the postulate that charge cannot have any smaller value. As soon as he observed his charge quantities the multiples of 1.6x10-19 coloumbs, he took no time in postulating that charge cannot have any smaller value. This was a presumptuous hypothesis and we know in the modern day physics that even smaller quanta of charge do exist. Our experimental setups and our power of observation has its limits beyond which we need to be careful in deducing and explaining things.

Maybe we might reach to smaller and smaller quantas of charge but it does not mean that the smallest we observe today is really the smallest. There is room for observation of even smaller quantas. And why quantization at all? Why not a smooth distribution of charge without any granularity? There is another problem other than this “why granularity”; an exception to the concept of quantization of charge has arisen. Assumption of the existence of particles called quarks has violated the symmetry of the concept of quantization itself. The concept of quantization of charge may be bolstered by many phenonema like structure of atom, thermionic and photoelectric emission, Milikan’s oil drop experiment etc. But the existence of quarks makes the concept asymmetric. Now there are two problems with the concept of quantization of charge. One that modern as well as classical physical has not been able to explain why charge is quantized. And second that the same concept is not perfectly symmetric due to the existence of quarks.**

4. Problems with photons

The photoelectric equation described above is unable to tell us whether the photon is a particle or a wave. If the photoelectric effect is instantaneous (which it is) then the incident photon is a particle because the whole bunch of energy hits the electron at once instantaneously and the electron is ejected without any delay. We should, therefore, regard a photon as a particle. But the double slit experiment does not allow us to do that because of the fringes of constructive and destructive interference observed (typical of wave behaviour). The photoelectric effect does not allow us to consider photons as waves while the double slit experiment does not allow us to consider photons as particles.

What exactly are photons? Everytime we go through the concepts and arguments, we see physicists thinking in terms of either particles or waves without realizing that a third possibility is not forbidden. The mind of physics as a whole seems to be closed to a third possibility. Both double slit experiment and photoelectric effect are practical facts but antagonistic to each other. What actually a photon is? This question still remains. This question is a mystery and clearly reveals the asymmetry of both the practical facts both as regarding the photoelectric effect and as regards the double slit experiment. This reveals that somewhere inconsistency lies in our understanding of the nature of existent things in the universe.

We know a great deal about the properties of an electron, say it has particle as well as wave behavior. An electron has resinous i.e. negative charge equal to 1.6x10-19 coloumbs. We also know e/m or specific charge of an electron, we know all the quantum numbers belonging to it etc. Then why can’t we imagine the picture of an electron. As we know all the properties of an electron, we should be able to make a mental picture of the same. Most of the people think of electron as spherical ball having the tendency to attract positive charge. But this is the picture of a localized thing; a spherical ball. In imagining so, we clearly, put a gag on its delocalization property. We can’t even imagine both the properties that is wave and particle, simultaneously because it violates the logic and Heisenberg’s uncertainty principle does not allow us to do so. This argument clearly indicates that somewhere in discovering the properties of say an electron, an imprecise logical deduction clearly lies.

5. Unanswered questions on motion

Motion is one of the most important and significant natural and physical phenomenon. Motion creates everything in the universe which includes even “time”. Newton’s laws of motion give a good insight into the understanding of motion. First law states, “every object in the universe will continue in its state of uniform motion or of rest for ever unless and until disturbed by some external force.” A simple question as; “who has seen ever?” poses a great problem to the integrity of this law. If we take this law as universally true then there is a problem with the existence of universe. What caused the Big Bang? Was it an external force? If yes then we need to reformulate the theories of evolution of universe. If no then Newtonian mechanics needs to be amended. Stephen Hawkings might be happy to discuss this because he seems consider big bang as the beginning saying that there is no significant before (in his book: The Theory of Everything).

The third law of motion, “to every action there is an equal and opposite reaction” says that action and reaction are simultaneous thereby violating the principles of relativity. The third law reveals that force signals travel at infinite speed which relativity does not allow. The antagonistic nature of the third law of motion and relativity reveals the problems in our understanding of the behavior of matter. We are not yet clear what reality actually is? This is one of the strong questions in the world of physics.

Physics (and mathematics) is the study of qualitative as well as quantitative measurements. One of the most fundamental aims of physics is to record the measurements and observations. Many rules have been constructed in order to record measurements. The concept of significant figures has proved to be a boon to scientists. This idea has provided a lot of help to scientists of all times. But there is a difficulty with it; no one in the world of science can record his measurements with hundred percent accuracy. No measurements and records are accurate, some degree of uncertainty lies in the measurements.

Coming back to motion, one of the paradoxes called the Zeno paradox does not allow motion. In the case of motion, an object is shifted from one place to another.

Zeno's aargument seeks to reveal that somewhere in our understanding of time and space the asymmetry has jumped in. Understanding matter, mass, energy, time, space is yet a dream and we are still far away to make this dream a reality. The laws of science allow us to divide a line segment into infinite number of points which makes any motion impossible.

6. On infinity

There is a problem with our understanding of infinity. Maybe the number of points in a line segment (which forms the displacement of an object in motion) are infinite but this infinity is a “limited infinity” [ref] and it obviously has to be a “limited infinity” in order to be true because to cross and complete this infinity (in displacement from one place to another), it is merely a matter of few seconds. The infinite number of points in a length on a few meters can be completed in a few seconds. This means that the infinite points in a length of few meters are finite. Though this is an intellectual confusion but it is true. A similar concept was put forth by a great mathematician (who unfortunately was never recognized and had to spend the last days of life in a mental asylum) named Cantor in his continuum hypothesis in which he says that there are smaller infinities and then there are bigger infinities. This is the time to revisit his continuum hypothesis and adopt insights from his mathematical explanations to understand what infinity means and how can smaller and larger infinities be brought to conceptual and practical use.

Up until now many of the nuclear properties have been discovered and many intranuclear particles like photons, electrons, protons etc. have been observed. Many facts and properties belonging to these elementary particles have been deciphered. For examples photons have mass of zero million electron volts, leptons (including electrons, muons and neutrinos) have charge, spin etc.; mesons including pions and kaons and protons, neutrons, sigma hyperons, omega hyperons are all baryons. We know many properties belonging to above listed elementary particles. In addition to this, physics has 'discovered' many forces like gravitational forces, electrostatic forces, weak forces and nuclear forces and their properties and consequences inside the nucleus. In spite of all these discoveries made, a complete description of the structure of nucleus remains a challenging question.

Many attempts are being made to discover the actual facts involved in physical, chemical or biological phenomena. The origin of universe is still doubtful. The modern society is covered with scientific atmosphere yet science has not made us able to define say matter or mass. I am not anti-physics but I want to reveal the inability of human intellect and the closed attitude of physics towards imbibing inspirations and explanations from other potentially contributive sources. Physics, even in the modern day development still needs a philosophical paradigm and a subject of “philosophical physics” should find its establishment in at least some good universities and/or research centers in the world. Meetings should be organized for “interdisciplinary physics” where non-physicists from many areas will have their contributions and opportunities to comment.

Scientists deserve recognition and acknowledgement and that no one can deny them. But at the same time science should be guarded against becoming an act of faith where present theory is taken as heavenly law. Every theory is subject to revision, particularly if it does not give complete explanation (and how can any theory do that?) irrespective of the authority or brilliance of the scientist who propounded it.

---

Citation
The main and original text for this article is drawn from an essay by Muneeb Faiq. He is currently an ICMR Senior Research Fellow at All India Institute of Medical Sciences, New Delhi.
 

*The term “Loop amplification” has been used for such phenomena. Physics is incapable of defining any physical quantity (of which it boasts to be the complete explanation) unless and until it takes the route of and help from its properties. What is that? An example should work here. For instance, if I ask what a “brick” is; what will be the answer? It seems to be simple that a brick is a somewhat red, cuboidal, hard substance used in construction of houses. The definition seems to be fairly good and has a nice face value but we have invited many questions to our mind by this definition. We have defined brick by only relating its properties to it. The definition mentions its colour but not what it is. The definition says that a brick is cuboidal in shape but still does not make it clear that what a brick is. So the definitions tend to give all the properties of a physical quantity (a brick in this case) but are not able to tell what that physical quantity is.

**In the case of the photoelectric effect (explaining which fetched a Nobel Prize to Einstein) electrons are ejected by the incident photons. The photoelectric equation can be written as:

hν = φ + KE

where “h” is Plank’s constant, “ν” is frequency, “φ” is the work function of the metal and “KE” is the kinetic energy of the ejected electron. Now the question is; if ‘ν’ is the frequency which a quantum object can have and ‘KE’ is the kinetic energy (1/2mass X velocity2) which only a classical object can posses (because it contains mass in its mathematical expression) then how do we relate quantum and classical mechanics.

Special Investigation: Gene Therapy and the Origins of Life

The process of natural selection and survival of the fittest lies at the surface of the great molecular chronicle of gene therapy. This investigation argues  the approach will play a great use in near future- as long as  attention is paid to the very spirit of its conceptualisation.

A Special Pi Investigation into the Biochemical Mechanisms involved in Origins and the Evolution of Life - centred on the role of Gene Shuffling.

by Muneeb Faiq and PI editors

Is gene therapy - or gene shuffling as we might alternatively call it -  a product of human genius or a traditional method employed by evolution for last 3.2 billion years in order to give rise to all forms of life that the planet earth has seen? 

Indisputably, this is a very important question which has escaped attention from theoretical biologists for almost four decades (since gene therapy was conceptualised) and there seems to be almost no literature available on it. Instead, there is a general tendency to think that gene therapy is a very recent phenomenon innovated by human mind to achieve desired functioning of a gene and consequently an organism.

That notion is correct in its own right but when you look at it with a little scrutiny, you have to be drawn to the conclusion that gene therapy has been the modus operandi of the process of evolution for billions of years and it is the process of gene therapy (or gene manipulation for that matter) that has brought about the variety and complexity of life that we witness today.

This philosophical investigation will oppose the self-evident notion that the best survives (which begs the question of what the 'best' means) by emphasising that it is the shuffling, the complexity, of gene manipulations that is the real engine of evolution.




Gene therapy lies at the crux of evolutionary mechanisms and how the manipulation of DNA (the genetic material, DNA, or deoxyribonucleic acid, and I find it is the hereditary material in humans and almost all other organisms) has helped gene therapy to achieve the target of producing millions of different species of plants and animals. But before discussing this further, it is imperative to define the terms first so that it becomes easy to understand the arguments put forth in this investigation. Here is how we go, starting with what I call the Central Dogma of Molecular Biology.


First, the most important thing to explain is that, broadly speaking (there are exceptions), DNA makes up the genetic material. DNA synthesis from DNA (to be passed on to progeny) is called Replication. RNA synthesis from DNA is called Transcription and protein synthesis from RNA is called Translation. This is all that we need to bear in mind in order to make sense of what we are about to discuss.

 

UNDERSTANDING THE CELL

To perform any function, the ultimate goal of a cell is to produce a protein which will bring about the requisite purpose. Proteins are like workhorses of the cells while DNA and RNA molecules are just information carrying molecules. DNA carries information across generations while RNA carries information from DNA to the protein synthesis machinery of cells. Proteins are the part of structures of cells, they are enzymes, they play role in most biochemical transformations, they are signalling molecules, they carry signals to various parts of the cells as well as various cells of the body of a multicellular organism (multicellular simply means an organism comprised of more than one cell).

Proteins also manipulate DNA to produce its copies to bring about that process called Replication. They also regulate which part of the DNA (i.e. which gene) is to be expressed in a particular cell type by forming euchromatic and heterochromatic regions. Proteins also help cells to react to various environmental conditions by carrying information to the DNA and then leading to synthesis of relevant proteins to bring about the pertinent function. The expression of genes (simply understood as stretches of DNA) is also regulated by proteins (as transcription factors etc.).

So, in simple terms, life can be understood as the chemical hodgepodge, pot-pourri and conglomeration of these three types of molecules (viz. DNA, RNA and Proteins), one managing the synthesis and function of the other. This intricate fabric of interconnected and interdependent saga of chemical processes (brought about by these three types of molecules) is essentially life. All cells and multicellular organisms (no exceptions) are the extreme expression of the biochemical transformations brought about by these three important molecule types.

GENE MANIPULATIONS AND EVOLUTION

Now, what is gene therapy? This is an easy question and definitions have well been developed for this process. Before going into that, let us first discuss what genes do and where does gene therapy come from. Living systems have been around on earth no less than 3.2 billion years ago with simpler forms of life evolving first and then evolution bringing about more and more complex forms. We don’t need to get confused about what is simple and what is complex. It is conventional. (There is no need for a philosophical metaphysics of this.)

The earliest living organisms were single celled and did not contain any internal organelles. (An organelle is a minuscule organ inside certain cells called Eukaryotic cells). The DNA of such organisms (recall that life is believed to have started with RNA as the first genetic material) is not bound by histones (proteins that bind to DNA and help in its packing inside the cell and its regulation). So we understand that the earliest living forms were simple and capable of a limited number of functions. Assuming that their genetic material was  RNA,  DNA gradually took over owing to its greater stability. (Even today, RNA serves as genetic material in certain viruses,  but otherwise all living cells have DNA as genetic material). DNA contains genes and genes contain bits of information. These collections of all the genes (the DNA) decide every aspect (structure, function, behavior, lifespan, shape etc.) of a cell. So everything a cell does is in fact an omnibus of the dictums of its genes embedded in the DNA molecule.

You may be wondering how this fits into the definitions of gene therapy. But we were, till now, just discussing the background of the concept of gene therapy and now it is easy to understand gene therapy by definition itself. If any cell has any kind of defect in its gene (or more than one gene), the function related to that gene will be hampered which, as a consequence, will jeopardise the life of the cell. This is what happens in many diseases like phenylketonuria, cystic fibrosis et cetera. In these diseases one of the genes is defective which disturbs the whole cascade of cellular functions and precipitates conditions of metabolic stress inside the cells; thereby generating many metabolic defects (and even death in certain lethal gene defects).

If, however, we have a method by which we could transfer a correct copy of the gene to the DNA of the cells (in place of the defective gene), we will overcome the problem of the lack of function due to defect in the gene in question. This technological method is called gene therapy. So gene therapy can be thought of as a therapeutic use of genetic molecules (genes and RNAs) in order to set right and /or fine-tune the functioning of a living cell. We could, alternatively, define gene therapy as “the therapeutic use of DNA as a pharmaceutical agent”. This can be brought about by a variety of methods like use of viruses, plasmids etc. but I don’t intend to go into the details here because our focus in this investigation is different.

POPULAR CULTURE

Historically speaking, it was in a classic paper by Freidmann and Roblin titled 'Gene Therapy for Human Genetic Disease?' published in Science in 1972 that this technique was conceptualised. But it was not until 1990 that a Food and Drug Administration's approved trial was carried out for a disease called ADA-SCID. As of now, almost 1700 clinical trials of gene therapy have been conducted worldwide using various methods of gene transfer (e.g. adenoviruses, lentiviruses, herpes simplex virus, vaccinia, pox virus, injection of naked DNA, electroporation, sonoporation, magnetofection, lipoplexes, nanoparticles, gene guns etc.). Gene therapy has also been a great topic for science fiction writers and Hollywood including the TV series 'Dark Angel', the video game 'Metal Gear Solid', the  James Bond Movie, Die Another Day, a fiction book titled Next, and so on. The technique has seen considerable success in last two decades with alternating period of ups and downs. But recently the world has once again seen a great hope in this therapeutic domain of technological advancement of human species.

GENE THERAPY: THE HEART OF EVOLUTION

As far as the current literature is reviewed, gene therapy is viewed as a purely human development (artificial in its essence) which has nothing to do with natural processes. Gene therapy has always been thought of technological exploitation of some properties of genes and gene vectors without realising that it might have a much deeper connection with life and its evolution and maintenance. No scientist (so far as the current status of the available literature is concerned) views gene therapy as a process that was going on in nature for billions of years. Gene therapy is rather thought of a very recent concept restricted to last four decades involving a few human technological interventions to manipulate DNA.

It is important to understand that this is not the case. Gene therapy is the means nature has been exercising since the inception of life for development and evolution of life. If a little thought is applied on the biochemical mechanism of evolution, one easily understands that evolution is a process of piecemeal improvement and modulation of genes of an organism. This process initially took place through gene transfer and then gene modification (via mutations and polymorphisms). Development of complex forms of life from simpler ones is just an outcome of the process of natural gene therapy. Though it may not be viewed as therapy per se, but improvement of gene function in order to cope up with environmental challenges is also a therapy and that is what evolution has been doing for billions of years.

The hallmark of evolution is to lead to the formation of organisms better suited to the environments they live in. Development of carnivorous set of teeth in flesh eating animals, flat teeth in herbivores, development of wings in birds, cellulose digesting enzymes in grass eating animals, taste buds on the tongue, most sense organs on the heads and modes of excretion are all decided and developed by the process of evolution.

How does evolution do all that? This is also a very important question and we need to address it in detail. First, recall that initial discussion about the function of three basic molecules of life (DNA, RNA and proteins) where it is explained that almost all cellular processes are carried out by proteins which are directed and dictated ultimately by DNA. So if any process is to be enhanced, improved, modulated, upregulated, downregulated and so on, all that is needed is to alter the genes in DNA. This can be done at protein level but then proteins are not transmitted to the progeny. It is very much sensible to introduce changes in DNA in order to make the change in function (or any other aspect of the cell) to manifest in coming progenies. This is simply what evolution does. Evolution works by altering the DNA sequences (i.e. genes) in order to modulate and improve certain functions of an organism (both unicellular as well as multicellular). Scientists have been using various methods of changing DNA sequences (like we have already mentioned above) in order to bring about the desired function in the organism and they have learnt to introduce genes in the DNA that replace the malfunctioning genes of the organism. This is what gene therapy is and that is what evolution also does (more or less).

A PubMed  search of the word 'gene therapy' (PubMed is the largest database of references and abstracts on life sciences and biomedical topics) returned 139950 entries on 9th August, 2012. In spite of so much of a literature available, the connections of gene therapy with natural process of evolution has not been explored. There are certain reports which discuss gene therapy and the process of evolution but they don’t tend to see the similarities in the two processes. These reports rather consider the effects of conventional gene therapy (a scientific development) on the process of evolution thereby completely ignoring the fact that conventional gene therapy (kind of a process) could well be a part of evolutionary mechanism used by nature to produce the splendour of life.

Let us now come out of the complexities of these terms of molecular biology. Let us put it in very simple words. Evolution is gene modification in order to improve function (a natural process) and gene therapy is gene modification in order to improve function (a scientific method). From this we arrive at a very gay but strong conclusion that gene therapy, though a recently conceptualised technique is a very important concept exploited by nature in order to play evolution for no less than 3.2 billion years and exploited by scientists in order to treat diseases.

At this point, it is necessary to justify the above hypothesis of this investigation by examples. We will be considering a few biological processes ranging from the origins of multicellularity, development of complex forms of life, development of cellular organelles to cellular processes like reproduction and recombination.

GENE THERAPY AND THE ORIGIN OF LIFE

Origin of life itself was (presumably) a process of gene therapy (this may or may not be true, it is just a presumption). Theoretically speaking, primitive cells are minuscule bags of chemicals containing DNA to manipulate these chemicals. So if a bag of such chemicals (we now refer to as cytoplasm/protoplasm) is being subjected to a process of gene therapy (i.e. supplied with a full stretch DNA molecule), in principle, it makes the bag of chemical alive and this bag of chemicals starts behaving as a full-fledged living cell. So a simple process of gene therapy may presumably have brought life into existence at the first place. It should be noted that this concept is not as non-practical as it seems to be.

A recent technique of Somatic Cell Nuclear Transfer (SCNT) exploits this phenomenon (more or less) to create stem cells or to bring fossil DNA molecules to life. SCNT is the technique that was used to create the world’s most famous animal (Dolly the sheep). This discussion gives impetus to the idea that creation of life by putting DNA (or RNA) into a small chemical bag could very well have lead to the formation of primitive forms of life and then the whole process of evolution would have been the improvement and alteration of this DNA molecule inside this chemical bag (we think of a primitive cell) thereafter. Now that the concept of gene therapy has helped us to hypothesise how life presumably could have originated by gene therapy, we will now see how evolution brought about its great orchestra of life using this beautiful process.

 

GENE THERAPY AND THE EVOLUTION OF MITOCHONDRIA AND CHLOROPLASTS

The development of eukaryotic cells (that is cells with internal organelles, nucleus bound in membrane etc.) emerged long back in evolution at about 1.6 to 2.7 billion years ago. Before that cells were relatively simple. Eukaryotic cells are thought to have evolved from simpler forms (Prokaryotic cells). Eukaryotic cells have their own small organs (organelles) to perform various functions. One of the very imperative organelles is the energy providing Mitochondrion (plural mitochondria). Mitochondria evolved by a process called endosymbiosis.

In this process (it is thought) one cell ate (engulfed) a prokaryotic cell; but instead of digesting it, used it as a servant inside its body. It was good for the servant cell also because the servant got readily available food and shelter and provided energy supplies to its master. So the relation turned to be a symbiotic relation rather than a strict Master-servant relation. With the passage of time this servant cell lost some of its functions (efficiently carried by the Master cell for itself and the servant) and vice versa. Utilisation of oxygen (oxidative phosphorylation) was then the duty of the servant celluloid (the cell like creature created out of the servant cell with the passage of time). With the passage of time, this servant cell retained genes necessary for its replication and oxidative phosphorylation, which turned off in the master cell. There was, therefore, a symbiosis established. The servant cell became the mitochondria and the master cell a more complex eukaryotic cell.

This process describing the emergence and evolution of mitochondria is also a typical gene therapy process. The small cell that was engulfed can be thought of a vector with certain genes capable of doing some specialized functions (oxidative phosphorylation in this case). It was just that this gene transfer enhanced the oxidative respiration capacity of the host cell: this is simply what can be referred to as gene therapy. It was a process of transfer of genes (via a bag of chemicals containing a DNA stretch) into a cell in order to improve its bioenergetics. If a little thought is applied in this domain, one is compelled to think that mitochondria are the outcome of the process of gene therapy. Same is the case with chloroplasts (organelles for photosynthesis created out of cynobacteria-the blue-green algae) which also emerged by the same mechanism and lead to the evolution of all the plants on earth.

So gene therapy has paved way for the emergence and evolution of all animals and plants on earth and yet scientists still think of gene therapy as a scientific genius a mere four decades of age.

GENE THERAPY AND EVOLUTION OF MULTICELLULARITY

Development of multicellularity is a very important event in evolution. More than one type of cell in an organism is particularly very useful because it makes every cell well suited to its functions (through division of labour). Sensory neurons in our body carry signals from the peripheral areas to the brain, retinal neurons carry the codes of photons to the brain, beta cells of pancreas secrete insulin, cells on the intestinal villi absorb nutrients, hepatocytes (liver cells) produce bile etc. every cell in a multicellular organism has its special functions. One cell type can do its function at a significantly amplified pace and efficiency but is not able to do many of the other functions. So there are different cells meant for different functions in a multicellular organism.

All these highly specialised, improved and efficiently conceded functions are only possible in a multicellular organism if certain genes are upregulated, some downregulated and others switched off. This means that certain functions need to be improved and others need to be downregulated while a few others completely switched of depending on the cell type. Nature has methods for that. The DNA is packed in the chromosomes and the packing pattern of the DNA decides the expression of particular genes in a particular cell type (though there are other ways also). If we see, this process is also gene therapy by definition. It is the regulation, modification and modulation of the gene function.

 

GENE THERAPY AND REPRODUCTION

Let us now turn our attention towards reproduction. The most important process that takes place in the physiology and biochemistry of reproduction is fertilisation. In this process, the ovum (egg) waits for the sperm and the sperm swims in the genital tract, reaches the egg and then pushes the genetic material into the egg. This initiates a saga of processes of life starting from the formation a zygote followed by formation of morula, then blastula and moving through many embryonic stages to the birth of a new organism.

It is worth noting that before the sperm transfers the DNA into the ovum (egg), no process of embryonic development initiates and no new organism is formed. Once the sperm transfers its DNA to the ovum; the biochemical narrative of life starts, leading to the development of a new organism. What sperm does is just the transfer of DNA into the ovum and start of all the life processes. Let us wait a little and think for ourselves. Isn’t is gene therapy of the ovum? At least in a certain sense that has lead to the embryogenesis and development of a new organism. It is mentionworth that the sperm does not transfer anything other than DNA to the ovum (not even mitochondria or cytoplasm). So the process of fertilization is just meant to transfer DNA to the ovum and from there all the processes of life start; the consequence of which is all variety of plants and animals around us. This is what evolutionary gene therapy has done for us. Moreover, the events referred to as recombination events in cellular division (meiosis) could also be described as some sort of gene therapy.

AND THE MORAL IS?

The process of natural selection and survival of the fittest lies at the surface of the great molecular chronicle of gene therapy. This investigation may find a great use in near future if attention is paid to the very spirit of its conceptualisation. Gene therapy could be improved upon and the technique could find new horizons inspired from evolution (biomimicry). I believe that gene therapy has much greater potential than is currently being spoken of. I would go so far as to say that gene therapy is the hope of  future medicine. But right now, scientists need already to acknowledge that it is a natural process which can and should be utilised - in a considered and  controlled manner - to bring about many of those long sought dreams of therapeutic medicine.


This is an edited version of an essay  by Muneeb Faiq (adapted for Pi), who is ICMR Senior Research Fellow at All India Institute of Medical Sciences, New Delhi.