Religion and Science unification
“I do not wish to judge how far my efforts coincide with those of other philosophers. Indeed, what I have written here makes no claim to novelty in detail, and the reason why I give no sources is that it is a matter of indifference to me whether the thoughts that I have had have been anticipated by someone else” ~ Ludwig Wittgenstein, Tractatus Logico-Philosophicus
Science and Religion are treated by some as contradictory ways of thinking. This is not true. In this section, I will analyze the philosophy underlying both sectors and show that these two ways of thinking are not in conflict, but actually two sides of the same coin. You can never know life fully, unless you see the cosmos in both perspectives.
The existence of God can be proved by both the tools of logic and faith. Religious people are some of the greatest scientists of all times. Science and religion do not always rely on logic and faith respectively. In an era when the new advances of science surprise us every day, religion stays powerful and current. That is not without a reason. No matter how much science advances, there will always be metaphysical questions that their answer can only be found in other ways. Science does not tell us anything about how we feel, about how we taste, about how we can feel sad from hearing a song or joyful from seeing an old friend. Modern science does not have human as part of the picture it tries to create and that makes it even more demanding for all of us to change way of thinking. Why we exist cannot be answered inside a lab… Logic is a scientific tool as much as experimenting is. And there are a lot of interesting conclusions about our life and purpose in life that Logic has led to. It is important to understand that for science and religion to coexist harmonically, not only religion has to be careful not to interfere with the things science investigates. Science must also be very careful not to have philosophical assumptions undermining its work.
Despite the science-religion “war” that some people like Dawkins are trying to make us believe that exists, the truth is much more different, simpler and more “friendly”.
Few people actually realize that the ancient Greeks, who are regarded as the genuine first free thinkers of all time, actually HAD a religion. And we should not forget that Christianity was first willingly adopted by the founders of Logic and true Science, the Greeks.
Let us not also forget that all the Greek manuscripts of Aristotle and Plato, the founders of “free” scientific thinking as regarded today, were saved from the passage of time by the Greek Orthodox Christians in the Byzantine Empire and the Islamists Arabs of the medieval times.
It is characteristic that the “priest” of modern atheism, Richard Dawkins, is a professor at the College of St. Mary!!! So much “war” is going on between religion and science, that religion has created a college for its greatest enemy to teach.
So perhaps there is not only white and black in this discussion, but other intermediate colours as well. The main points of a religion and science unity that exists but still eludes most people are depicted in the pages that follow.
2 Science for “how”, Religion for “why”
The realm of exact sciences (Note: I refer to the physical / exact sciences with the term “science” in this chapter from here on – except when stated differently, for simplicity purposes) is the physical phenomena world. On the other hand, questions like “what is our purpose in life”, “why do we exist” or “what is reality” are out of science’s scope (jump to Conclusions of this chapter for more on that).
Science deals with the “how”, while religion deals with the “why”. Both things are interdependent and supplementary. Even if science finds out how every cell of the human brain functions, it will still haven’t discovered why it works that way! The “first cause”, the beginning of existence is outside of science reach. One could say that science deals with the natural world and the natural phenomena while religion with the supernatural phenomena  . That is why both science and religion are needed for the quest of truth. Religion deals with questions science can never answer as the famous ignoramus et ignorabimus (“We do not know and we will never know”, like the “I only know that I don’t know” of Socrates) of the German physiologist Emil du Bois-Reymond states  (although Hilbert attempted to deny that there are things we will never know, Gödel with his incompleteness theorem proved that Emil du Bois-Reymond was finally right).
I can believe anything, provided that it is quite incredible. ~ Oscar Wilde, The Picture of Dorian Gray, 1891
It is also very important to understand that science and religion are both based on some kind of faith. Science on the faith that an ultimate truth exists and that logic can reveal that ultimate truth and religion on the faith that an ultimate purpose (and, thus, God) exists (what is interesting to note here is that even though Logic has been proved by Gödel that it cannot prove the truth people still believe in it with no questions asked). Throughout science history, science had God as its starting point. The notion of us, humans, being made in the image of God gave scientists like Newton the power and will to try to understand the universe: “if we are made in His image, then we have the ability to understand His creation”, people said from the time of Saint Thomas Aquinas. On the other hand, religion has God as its ending point. It tells us how to behave and act in this world so as to earn a place in the “other” world. Science does not deal with problems of ethics or praxis at all. It may tell you how a nuclear bomb explodes, but it has nothing to say about whether you should use it and how. Science deals with measurable things, while religion with things that cannot be measured. And the latter (things for which we cannot speak scientifically) are the ones which distinguish us from animals…
As Albert Einstein said, “Science without religion is lame, religion without science is blind”. A cold inhumane science which deals only with equations is not what we need as humans today.
3 Logic arguments for metaphysics
Many people are empiricists or materialists and deny the very existence of metaphysics. In this section I have some logical arguments in favor of the existence of things that non-religious people think belong to the world of fairies. My purpose is to show that saying that the universe has a purpose and that there is an initial cause for its existence is something that is based on logic and not only faith. And what we must not forget is that every opinion or philosophical system (both the theistic and the atheistic ones) are based on unproven assumptions and axioms. But everyone should at least try to know them. And once you do, you will understand that the assumptions and axioms required for the belief in the existence of a God are much less in numbers and much less difficult to justify than the assumptions and axioms required to believe in “randomly generated life in a universe which just happened to exist for no particular reason at all”…
3.1 Metaphysics – A definition
(Gr. meta ta Physika – «μετά τα φυσικά») Arbitrary title given by Andronicus of Rhodes, circa 70 B.C. to a certain collection of Aristotelean writings. Traditionally given by the oracular phrase: “The science of being as such”. To be distinguished from the study of being under some particular aspect; hence opposed to such sciences as are concerned with ens mobile, ens quantum,etc. The term, “science”, is here used in its classic sense of “knowledge by causes”, where “knowledge” is contrasted with “opinion” and the term cause has the full signification of the Greek term aitia [«αιτία»]. The “causes” which are the objects of metaphysical cognition are said to be “first” in the natural order (first principles), as being founded in no higher or more complete generalizations available to the human intellect by means of its own natural powers. Secondary and “derivative meanings: (a) Anything concerned with the supra-physical. (b) Any scheme of explanation which transcends the inadequacies or inaccuracies of ordinary thought. 
From that perspective, metaphysical issues are closely related to things existing without any prior cause – look at the “First Cause” argument below for more details and analysis on that.
3.2 “Believe” – A definition
Because the word “believe” has been misunderstood many times, I would like to make a clarification on the way I use it in this chapter. From my point of view, “believe” DOES NOT mean either “know” or “I am certain that this is it”. When I say “I believe” something I use the word with what seems to be the dictionary definition of the word: I have some data to point me towards one conclusion but which are not enough to make me certain (in that case I would say “I know”), so I say “I believe this is it” based on that data and on some logical arguments. I do not use the word “believe” in the religious “bad” version of “censor all other opinions”.
For example, when someone says “I see clouds so I believe it will rain”, he is not promoting any religious ideas. He is just making some (probably) valid conclusions (that may even be called “scientific”), but he uses the word “believe” instead of “I know” because he is not 100% certain.
3.3 A higher purpose exists
I believe (i.e. “my logic dictates that to me after I have examined many facts about the universe” and not “I think so with no supporting logic or evidence”) that there is a higher purpose in life. Since everything we do in life we do it with a purpose in mind , I find it illogical and highly improbable that our life as a whole has no purpose. This is known as the “teleology” argument.
I don’t know what that purpose is. I may never find out! But many things we know and experience indicate that something of “higher essence” is part of our existence – that we are partly made of something more than dust. Luminous beings we are, not this crude matter! Science may never understand why we come to tears when we listen to an old favorite song (even though it may explain thoroughly the chemistry and the mechanism of tears), why we laugh, why we may love someone so much that we may give our life for (and I am not talking about the love a mother has for her child – which may be explained by the theory of evolution since the mother has that love to protect her child – but I refer to all other kinds of love a human may exhibit, like the love a human has for his/hers friend et cetera), why we are good, why we exhibit altruistic behavior by helping people unknown to us while at the same time risking our own lives (and without ever wanting that to be known so as to get a reward of some kind), why human strives for creation, writing, poetry, why we may give our lives for higher ideas like freedom, why people kill themselves (if surviving was the ultimate thing we had in mind like the theory of evolution implies, then we would never even consider killing ourselves) and so on…
3.4 The First Cause argument
The Universe is intelligible and that logically means (at least that is what this meant to Aristotle) that a First Cause [Gr. Πρώτη Αιτία] must exist. Or in other words, an Unmoved Mover must have set the world in motion in the first place.  Science from the beginning of time tries to find the causes of all phenomena, so it is rather ironic that some scientists claim that there is no initial cause. It is not logical to say that every event has a cause, but that the universe itself has not!
After all, when examining an event, e.g. a glass of water that falls on the ground, you try to find the initial cause. If you say that “the glass fell because of the law of gravity” you would have “cheated”. You did not find THE cause, you just stated the first-most immediate cause. For your analysis to be complete, you must find the cause of the law of gravity, the cause of that cause etc. If no initial cause exists (God?), then actually the simple phenomenon of the glass falling has no cause at all! The world would stop from being intelligible…
Moreover, as the “sufficient cause” argument of Leibnitz states, there must be sufficient reason for something to “be”. So, there must be some reason for the entire universe to exist, instead of nothing.
In summary the “First Cause” argument is as follows:
- The cause of existence for something can lie outside of (so we talk for “possible” things) it or inside it (so we talk for “necessary” things). A child is a “possible” thing: it requires an “outside” cause to exist (i.e. its parents). God (as defined by religions) or the ever-existing universe (as described by Heracletus) are “necessary things (i.e. the cause for their existence lies inside them).
- Something can exist or not-exist. Something exists only if there is “sufficient reason” for it to exist. This is the only way that existence can be justified against the possibility of non-existence. A child can exist or not-exist. If it exists, it does so because of a sufficient cause: its parents and their decision to make children.
- (1) + (2) => Universe requires a cause of existence.
- Nothing can be created from nothing. If at some moment (i.e. before the Big Bang) there was nothing, then nothing should exist now either. So the universe either exists for ever or was created at some point.
- If the universe existed for ever, it does not need an “outside” cause for existence – it is “necessary”. Otherwise it requires an “outside” cause for justification of its existence.
- All the things we observe are “possible” (i.e. they require an “outside” cause to exist). For example I exist because of my parents. This text exists because I write it.
- The universe exists and is the sum of all things that exist in it.
- (6) + (7) => Universe is “possible”, so it needs an “outside” cause to exist. This cause, we call “First Cause”.
- Everything has a cause. So, the first cause must also have a cause.
- If the first cause has an outside cause, then we end up with an infinite series of causes => No “first cause” exists.
- The above conclusion (10) is not correct, since it does not agree with conclusion (8).
- (8) + (11) => The first cause does not need an outside cause for existence. The first cause is “necessary”.
No (arrogant) claim of scientists that “we know what caused that phenomenon” can escape dealing with the “first cause”. What we seem to “know” is usually only the first or second most immediate cause of a physical phenomenon and nothing more. However, that means that we do not actually “know” the “true” cause of the phenomenon, i.e. the Initial Cause. Science is an excellent tool to examine reality but unfortunately is has its limits. And these limits seem to pose a solid wall at where the explanation of the essence of our existence lies. If we are to accept that we can understand the universe, then we cannot ignore the implications of that “understanding” that we everyday “feel”…
The First Cause argument is one of the most well-known and well formulated arguments in favor of a God. Atheists (with Hume being one of the examples) in their attempts to discredit it or deny it have reached to the point of denying the very existence of “causality” in the Universe! Some claim that “we are not sure that causality exists, why not have an infinite series of causes?” while probably forgetting that the whole structure of science is based on the very existence of causality! Some others claim that “no causality exists in quantum mechanics, so in the beginning of the universe no causality existed and an infinite series of cause is a valid theory”. These people forget that even for the complicated and still-in-debate field of Quantum Mechanics where more that 10 (!) interpretations exist, most known scientists believe a deterministic (i.e. including the notion of causality) interpretation.    
It is important to remember that the point here is not if causality exists or not, or if the argument can persuade everyone or not. Causality may or may not exist. This is something to be examined by philosophers and scientists. (actually mainly philosophers, science always follows philosophy and fills in the ‘details’) The main point is that there is a logical background in the arguments for the metaphysical realm of God, that the metaphysical can be part of human intellectual.
By the abovementioned argument I do not want to do anything more than just pinpoint that there are good and valid arguments for the existence of a God, as there are some arguments against it. If someone accepts that there is absolutely no causality at all in the universe, it would not change much actually: I would still ask “why is there something instead of nothing?” – a question which is not linked to causality in any way. But if there is no causality, then those who believe in scientism would have much more to explain.
3.5 “A priori” and “a posteriori” knowledge
Empiricists deny the existence of knowledge that does not come from experience (“a posteriori” knowledge = knowledge based on experience). In other words: they deny the existence of any “a priori” knowledge. However, Kant postulated that there can be human “a priori” knowledge. For example, the “1 = 1” syllogism is an a priori knowledge – it is independent of any present, past or future experience. The argument “if A is true and A => B, then B is true” is also an “a priori knowledge”. Another example comes from our experience in science of counting: when we count or measure we use the underlying notion of “quantity”. That notion should be “embedded” in us before we start counting. It is an “a priori” knowledge.  
The sum of “a priori” knowledge is actually knowledge that exists without prior cause – something like the “First Cause” stated in the above sub-chapter. That “a priori” knowledge (e.g. of the notion of “quantity” or the notion of “quality” – according to Kant) is the basis of our own understanding of the Universe. And the very existence of such a kind of knowledge states that “something” gave us that knowledge. That “knowledge with no causes” is what the area of “metaphysics” is all about.
God sits on the sky when a scientist appears and says to Him “God we do not need you anymore. Finally science has managed to create life from nothing. In other words we can do what you did in the Beginning”
“Really? Please tell me!” answers God
“Well, we take dirt and we shape it like You did, then we give life to it like You did and there we have a human”
“Very interesting, show me how…”
Then the scientist takes dirt and starts forming the shape of a human body
“No, no” answers God “take your own dirt!”
The attempt of some empiricists to explain our “a priori” knowledge with terms of evolution fails. In particular, some people claim that what we seem to know before any experience of ours is actually the encoded knowledge of our ancestors in our genome. Again, finding a possible immediate cause does not mean that we know the true (initial) cause of a phenomenon. So the question in this case is simply transferred one “level” back to the question: “how did the first human know how to count if he did not have an a priori sense of the notion of quantity?”…
3.6 Ontological arguments
Many thinkers have attempted to prove the existence of an all-powerful being (like the one religions call “God”). These attempts are interesting not because they prove something beyond the shadow of a doubt (there are indeed logicians who think they are correct, but there are also others who think otherwise), but because the show that logic can be a tool that leads to God. One of the greatest logicians of all times, Gödel, has made such an ontological argument which you can find at the book “Types, Tableaus, and Gödel’s God” .
The argument is as follows.
We first assume the following axiom:
- Axiom 1: It is possible to single out positive properties from among all properties. Gödel defines a positive property rather vaguely: “Positive means positive in the moral aesthetic sense (independently of the accidental structure of the world)… It may also mean pure attribution as opposed to privation (or containing privation)” (Gödel 1995)
We then assume that the following three conditions hold for all positive properties (which can be summarized by saying “the positive properties form an ultrafilter”):
- Axiom 2: If P is positive and P entails Q, then Q is positive.
- Axiom 3: If P1, P2, P3, …, Pn are positive properties, then the property (P1 AND P2 AND P3 … AND Pn) is positive as well.
- Axiom 4: If P is a property, then either P or its negation is positive, but not both.
Finally, we assume:
- Axiom 5: Necessary existence is a positive property (Pos(NE)). This mirrors the key assumption in the respective Anselm’s ontological argument.
Now we define a new property G: if x is an object in some possible world, then G(x) is true if and only if P(x) is true in that same world for all positive properties P. G is called the “God-like” property. An object x that has the God-like property is called God.
With the above reasoning, Gödel argued that in some possible world there exists God. Then he went on proving that since a Godlike object exists in ONE possible world, then it necessarily exists in ALL OTHER possible world (since “necessary existence” is one of its positive properties).
And a small addition by me in the debate, which may solve the issue once and for all: Some people argue that Gödel had defined “positive” too vaguely. “Why should existence be a positive property?”, they ask. Well, to all these people I say: OK! Let’s say that “existence” is a “negative” property. Then all people should stop worrying about dying, since “not existing” is something good! In that way all great philosophical problems of humans will be solved in a strange way. Philosophy works in mysterious ways.
The problem of the existence of God is then solved indirectly: Since non-existence is a good thing, the phrase “God does not exist” takes a weirdly positive effect that could puzzle the greatest of atheists…
All in all, one might disagree with that argument. But the critical point here is that some other logicians agree! So even though this argument has not solved the great mystery of them all, it has given us a great lesson: Logic is not a tool for atheism only, it is a tool for theism as well…
3.7 The Design argument
The Universe seems to be designed. Modern cosmology has discovered that as many as 10 parameters are set to exactly the necessary values so as to have a universe that sustains life. This seems to be indication of a “Design” by many. Modern cosmology is the modern theology… Others of course do not reach to the same conclusion: such a set of fine-tuned parameters could be (according to a very extreme claim) a result of pure luck. A coincidence of cosmic proportions I would say.
The point to note again is not the fact that this is a final argument proving God beyond the shadow of a doubt. Every phenomenon can be interpreted in different ways. Most of times the underlying philosophical stance of the observer is what dictates him/her what to conclude. However, what one should understand from that argument of “Design” is the fact that observations and logical analysis can provide the basis for faith in God’s existence. Whether you agree or not with this logical analysis does not null its value.
3.8 Other arguments
The existence of what we call “free will” can also show the existence of God. Few people have thought about the implications of the existence of “free will”. In a fully “materialistic” (materialism is a dogma believed by many scientists today, who forget that noone has proved or shown that only matter exists in the cosmos) world of universal absolute physical laws that define everything there is no room for free will. The only way to justify the existence of free will is to base that existence on “something” that does not follow the physical laws (which are the ones which make everything predictable in the universe). The foundations of free will must be set on “something” that does not follow the logic “initial conditions” + “physical rules” => predictable behavior. In that way free will opens the path for the only being that could deviate from the path of the physical laws – God (as a “first cause” – see above respective argument).
The fact that many people are willing to commit suicide or sacrifice their lives so as to uphold some “higher” noble ideas (like honor or freedom of speech for example) directly indicates that something “more” than pure matter exists. If we were to seize existing the moment we died, then no one would care to sacrifice his life for a stranger or conduct altruistic actions whatsoever.
I can stand brute force, but brute reason is quite unbearable. There is something unfair about its use. It is hitting below the intellect. […] The way of the paradoxes is the way of truth. When the Verities become acrobats we can judge them. ~ Oscar Wilde
3.9 Philosophy and the “Being”
In conclusion, most philosophy is built on top of the great question that troubled Heidegger so much: what “Being” actually is? That question about what reality actually is, is what triggered the creation of the world of the Ideas of Plato, the “Unmoved Mover” (Gr. Ακίνητο Κινούν) of Aristotle or the ego of Freud. All philosophy is based on that very question. And Heidegger was right in saying that we have forgotten how important it is . All fields of science are failed attempts to get away from the difficulty of that question by breaking it and transforming it to many others. The fact that we have broken down the question of “Being” into many smaller ones, does not mean that we have made any real progress. Instead, we have even forgotten the importance of the question! The “Being” is something we cannot define. Heidegger tried (via an etymological analysis of the way the word “ον” was used in the pre-Socratic time) but failed. However, he did show some of its properties. “Being” is not. The notion of “Being” only appears inside objects which have that property. Thus, “Being” [as a gerund] (ον) cannot exist on its own because if it did, it would be a being [thing that exists]. “Being” entails the notion of not-Being in that way. Even the most thorough analysis of a painting cannot reveal anything about the “Being” of the thing drawn in it. When we see a painting, we see the “Being” of what the painter painted, we do “see” something more than the set of oil and paint on the canvas. In a way the tautology “Being is” (like the Christian phrase “Εγώ ειμί ο ων“) is the best way we have to describe what we feel about that notion that defines all things that “are”. And it is of great importance to note that “Being” is not the same as “Exist”. We humans “are” because we “exist”.  The word “exist” comes from the Greek words εξ-ίσταμαι, which means “to stand outside of”. Humans “are” because they can exist, or in other words because they can stand outside of themselves and question their own existence…
4 Logic and not only faith
Some people counter-argue that all these are “indications” and not scientific proof. This could not be further from the truth. It is a great mistake of the atheists and the agnostics to claim that every argument in favor of the existence of God is “not-logical” or simply “false”, while the reverse arguments are valid. The job of every scientist and open-minded person is to question everything. It is not thus logical to say that “we can and must question everything and we must not be dogmatic” but have exceptions on that rule. If we are to question everything, then the dogma of the modern materialistic age that “Everything was created by chance out of nothing and for no purpose at all” (this is the actual dogma here, the “God does not exist” position is merely a consequence of that) must be questioned as well.
We must also bear in mind that for things that relate to all these metaphysical questions (like the question of what is our purpose in life, what created the universe etc), there is little hard measurable (i.e. not of the type “I watch the universe and calculate the law of gravity based on the planetary movements”) evidence to rely on. At least not in the way scientists expect measurable data to conduct an experiment. Metaphysics is the realm of “non-measurable” things which are by definition outside the scope of science. Although one could have some hard data about the universe’s structure and way of working, we have to also rely on what I call “soft” (i.e. not “hard”, mathematical, measurable) evidence and logic to make the analysis required in order to explain things in the metaphysical world.
This does not make the arguments in favor of God wrong or inadequate. They are still based on logic and evidence, just not in the same type of logic we use when writing a paper on conductive polymers and their use in the PCB industry. Regarding the creation of the universe for example, we still have evidence (we see the universe existing, we see that all things in the universe have a cause etc) and we still use logic (induction) to reach a conclusion on the First Cause (see above). It is just that we do so without equations or experimental apparatus per se. This does not mean anything regarding their validity. Or it may even mean that such arguments are even more valid than any mathematical arguments, which anyway also start from arbitrarily chosen points (a.k.a. axioms). Modern AI has great issues in dealing with everyday life and the field of fuzzy logic is a very promising field of research, even today. This is not without a good reason. The structured logic of computers does not allow them to cope with the ‘simple’ (and, thus, more difficult) tasks we face when going out for a simple walk.
And we must also note that at least the ones that argue that there is a purpose in life (or that something/ someone created the cosmos) have some indications to base their arguments on – while the ones that claim there is absolutely no purpose in life (or that everything was created out of nothing by chance) do not even have indications, they just have speculations.
For example, the theory of evolution is based on some fossil. And it really explains well some things in micro-level: how some species evolve and change over time. I admit that the theory of evolution really works well up to a point and within the scope of biology (this is almost a tautology and we should not even discuss about it, but I am afraid it is necessary in today’s dark era or scientism).
However, explaining how fish evolved and went to the land, doesn’t mean that we have explained there is no purpose in life or that there God doesn’t exist! This is a huge logic leap that isn’t at all explained by the ones that favor the theory of evolution and use it as an argument for their irrelevant philosophical beliefs. Most importantly: the theory of evolution explained the “how” up to a point (the “up to a point” phrase is really important and that is why I keep repeating it), not “why”. Even if everything is one day explained by the theory of evolution, we still wouldn’t have answered the question why do all species follow the laws of that theory. Maybe because of another law that says that all species must follow the rules of evolution? And why that another law exists? And the questions move on and on, until we reach the “beginning”.
At the end, it all comes down to what someone thinks about that beginning. Do not let anyone fool you that he is ‘objective’ which you are not, when debating the existence of e.g. a First Cause. All debates about the above-mentioned issues are based on different views on the basic philosophical dogmas on which we have founded our line of thinking. We must all accept the fact that humanity has so little knowledge about our existence (so little that we don’t even know how flu works or how to fight it!) that is really funny for someone to argue that he has found the purpose of our life or that we have no purpose in life!
I am a scientist and my logic tells me that something of higher essence exists in the cosmos. All the indications together with my common logic say that to me. My conclusions are based not only on faith but on (soft and sometimes hard) evidence and (common) logic as well. Faith is anyway required to make the final step from the “it is possible” to “I believe this is it”, but this is something common for all people and all things. There is no absolute knowledge; even scientists must have faith in something to draw a “final” conclusion. (to the axioms they use, to begin with) Faith it is not the only component of the things I say. (if that was true, then we would be talking about blind faith and that is indeed something bad) And we must note that these indications also say the same thing to other scientists as well. Being a scientist does not necessarily mean that you do not believe in God or in a higher purpose in life. Of course, this just is my logic; the logic of someone else may reach to different results based on the same data.
The logic of Aristotle told him that a “First Cause” existed. And no one can accuse him of being blinded by Christian dogmatism, right? The logic of Gödel (the most important logician after Aristotle) said that God exists, and he even formulated a logical proof for that . The logic of the scientist that led the project for decoding the human DNA for the first time (Dr. Francis Collins, the director of the Human Genome Project), also told him that God existed. Most of greatest scientists who won a Nobel prize were religious. According to 100 Years of Nobel Prize (2005), a review of Nobel prizes awarded between 1901 and 2000, 65.4% of Nobel Prize Laureates, have identified Christianity in its various forms as their religious preference.  There is no indication that a person’s logic or level of education means anything regarding his logic reaching to pro-God conclusions (actually there might be evidence to the opposite, but this goes beyond the scope of this short book).
It is true that I believe First Cause (you can call it God or ‘chair’ if you so wish) exists (faith), but I have also some strong indications to argue in favor of my opinion (logic, evidence). On the other hand, the ones who argue that the universe was created by chance out of nothing (and, thus, there is no God) also believe (have faith) many things which are not yet proved: That nothing can create something, that chance can be a source of order (even though we know that random movements in a system only creates more entropy), and so on and so forth. Some of them also argue that even though the current theories (e.g. the theory of evolution) do not explain everything right now, they believe that one day they will! To them I say: OK. When they do, I will re-evaluate what I write in this book – no problem! In summary, these people have no proof for claiming extreme position, only a well rooted BELIEF that the universe can exist by accident, that the cosmos can exist for no reason, that the physical laws are there by chance, that we are able to understand the cosmos just… because. How many of these people would write a scientific paper claiming that the cause of a phenomenon is chance?
Last but not least, humans have many and diverse tools to reach for the truth. (if such a thing as an objective truth even exists, philosophy is not yet sure about that) We have our feelings and our intuition. And my feelings and intuition tell me that something “higher” than us exists. If someone has the feeling that we – humans (or some alien species we have not yet discovered) – are the highest level of spirit in the universe it is ok by me, but he has as much “hard proof” as I have. We do not know whether our logic or our feeling and intuition are better guides for the truth. Some of the greatest mathematicians have used their intuition to formulate theorems that every mathematician believes today as true, even though they are still unproved.
Science and religion, religion and science should work together to fill in the pieces of the puzzle of human existence. Until we have some better clues, we have to rely on the indications we have and not to believe we have the correct answer to everything.
5 About Faith
Most people have come to think religion as related to faith, while science as something based on evidence we see. It is true that most of us think of mathematics and physics as the realm of logic and hard evidence. What I will show here is that the abovementioned belief is not correct: “faith” is a basic and integral element not only of religion but of science and everyday life too.
As Socrates, the great Greek philosopher, said “you must know what you talk about before you talk about it”. That means that we must first define the term “faith” in order to analyze it. That being said, we use the term “faith” in this chapter with the following definition in mind: Faith is a belief in the trustworthiness of an idea that has not been proven beyond the shadow of a doubt. However, this does not mean that faith in something is based on completely nothing else than imagination. I will show that faith in the truth of a syllogism (e.g. that there is a First Cause) can be based on both evidence and logic.
6 Faith in science
Scientists use logic to reach conclusions, based on data from observations. These conclusions are based on a series of very subtle underlying beliefs. They are often called axioms or principles. And most of the time, they are shrouded in a cloak of authority that no one dares question. I have already analyzed those beliefs in the “The Limits of Science” chapter, so I will only indicatively refer to some of them here:
- All that exists in Universe is matter and the physical laws. We must not forget that materialism is an underlying dogma of most of today’s scientists.
- Belief that “Logic” works correctly: This belief is used mainly in physics, since in mathematics it has been proved that logic has flaws and inconsistencies (see Russell paradox and Gödel’s Incompleteness Theorem).
- Belief that all physical laws apply to the whole universe: For example, we can see that gravity applies to our solar system and we believe that the same gravity applies also to galaxies we have not yet even observed).
- Belief that logic induction leads to correct conclusions: This is another rule of our logic and the basis of most modern physics. When we observe a physical phenomenon and then verify that the same phenomenon takes place in a second and a third and a fourth experiment, we conclude that the same phenomenon will occur also in the next experiment. But we cannot be sure about that. It is highly possible that we have observed the three exceptions to the rule and that all the other experiments we will conduct will result in something different.
- Belief that our senses work correctly: This is of the uttermost importance, but we insist on forgetting it. Our whole perception for the world is based on our senses. We do not know how close is what we feel via our senses to “reality”. Take for example the color red. We see red, so we conclude that it exists. However, we forget that most animals do not see red. So what is the “real” thing after all? Does red “exist”?
- Belief in the fellow human: This may sound weird, but it is the basis of our scientific society. When a scientist publishes a conclusion all other scientists believe him just be trusting his word. If a paper is published on a scientific journal with prestige, then it “must” be true. However, we have seen many times scientists tampering with their data and posting fake “groundbreaking” conclusions. And let us not forget that the problem of reproducibility  is one of the greatest problems in the fields of exact sciences today.
- Belief that all things are measurable and that all phenomena can be reproduced in a laboratory.
- Belief that the axioms on which we base our theories are “true”. As mentioned in the beginning of this section, this is the most important faith of them all. We must never forget that ALL theories are based on axioms (some of them mentioned in this list) and that not axiom is proved. Change the axioms at will and you will end up with a different theory. Simple and, thus a but intimidating. But this is science. Do you believe you can draw one parallel line to an existing one?
The abovementioned beliefs are not bad per se, but they tend to transform to dogmas when we forget that we are using them. When we forget that our conclusions are based on such beliefs that we cannot be sure they are true, then we become dogmatic and stop being true scientists. We must acknowledge our limitations and move on by embracing them, not by ignoring them. This is what makes good scientists.
7 Misuse of Science
Many modern-day atheists (or atheists hidden under the cloak of ‘agnosticism’, i.e. people answering ‘I do not know’ in every question that might result in unsettling conclusions, even though they have strong opinions on many other things which they also ‘do not know’ with certainty) use science to serve their own purposes. No better example of that can be found but in the case of the Theory of Evolution. Those people (with Richard Dawkins standing in the first line) try to establish the idea of a “War” going on between science and religion, something which is simply not true.
7.1 New scientific findings
New findings in science point towards a different look to our world. Teleology (existence of a purpose) seems to find its way through physics. No scientific theory indicates that the cause must always exist before the result. Quantum mechanics experiments (e.g. the double slit experiment) show that an electron may “decide” whether it behaves like a particle or like a wave during its course only after a human have watched it. And it “decides” for the whole length of its existence – not only after it has been recorded in a particle detector but even before that! (see Human Consciousness and the end of Materialism chapter) Moreover, the laws of physics seem to have limits. The universe has a specific amount of processing power (if you look at every particle as a bit of information, then the universe is like a giant computer – according the theory of information nowadays) and this means that it (the universe) can calculate for example the position of planets up to a specific decimal point. Higher accuracy has its limits even for the cosmos itself. The world laws of physics are not so platonic and perfect as once we thought they were. That, along with the fact that the human watching the experiment helps the electron determine its existence, creates more room for teleology. The gap left from the imperfect laws of the cosmos, might be filled in with what we have blatantly ignored so far: our self. If the human observer decides for the electron, maybe he decides for the universe laws as an observer of these as well (or, in other words, the planets move the way they move so as to obey their “purpose” of behaving in the way the human observer wants them to)? Like the electron that its whole existence is determined by its goal (purpose) to look like a particle or wave at a certain point of time, the human life may be the way it is because of a higher purpose we have in the universe, or because of a higher purpose the universe has for us. Maybe the universe has the higher purpose to be explained by us and we have the higher purpose to reach the higher mental level and connect to the universe itself (theosis, “θέωση” in Greek). We still do not know, but the window for the truth is open.
7.2 Evolution as an accident…
The best example of science misuse is the attempt to apply the theory of evolution to philosophy, so as to show that there is no purpose of First Cause. If there is not purpose in life, then we should accept the sayings of the theory of evolution, which claims that we are an accident of nature, that we exist because we just happened to exist. And why do we exist? For no particular reason. This is in every way illogical: by saying that we exist with no purpose in life, you null the value of human life, you tell everyone that being a human or a banana is exactly the same. And you choose to ignore all the indications I mentioned above: if there is no purpose in life and if man is so completely stripped off anything of “higher value”, then why do we everyday strive to get out of our body and grow spiritually?
7.2.1 Problems with the theory of evolution
Furthermore, some things for the theory of evolution are yet unanswered: How does a system evolves in something more functional over time? We know from physics that every system’s entropy (quantitative measure of the disorder of a system) increases over time (law of thermodynamics). How species then evolve by pure luck? Scientific experiments with flies and other insects have shown random mutations over time, but none of these mutations has led to a better species.
In other words, the modern Theory of Evolution has showed that it can be used as a great tool to analyze biodiversity, but not as a tool to find the ultimate truth about everything concerning life.
The problem of ethics is another major problem that cannot be addressed by the theory of evolution. Please refer to the Evolution and Intelligent Design chapter for more on the theory of evolution and its philosophical misuse.
7.2.2 Evolution theory is not falsifiable
According to Carl Popper, all proper scientific theories must be falsifiable: i.e. if you are to compile a new scientific theory, you should state in what way or in which case your theory will be proved wrong. For example, a theory stating “all frogs are green” is proven wrong when a black frog is discovered. However, the theory of evolution cannot be proven wrong in any way: after you see a species alive and well, you name / baptize it as ‘fit for survival’. If you see a species extinct, you name it (again after you observe it) as ‘not fit to survive’. No matter what you observe in nature, the theory of evolutions works after the observation and not before it in a way that makes the theory unfalsifiable.
The most notorious example of that is the case of the fish coelacanth (Latimeria chalumnae). That fish was thought to be extinct from the Cretaceous period, so the evolution biologists claimed that it was not fit for survival, thus it was extinct. However, on 1938 the fish was discovered to be alive! One could think that this would lead to the conclusion that the theory of evolution was wrong about coelacanth. But No! After the fish was found alive and well, the evolution biologists simply said that “the fish was fit for survival and, thus, it survived”! As simple as that! And life goes on…
7.3 Medicine is “inhumane”
The best argument many people find for science is medicine. However, the exactly opposite is true: medicine has become so inhumane today that it offers the perfect argument against science!
First of all, medicine is not a science with the proper definition of the term! Science is about creating models for the prediction of systems’ behavior in the future via theories. Medicine does not formulate theories in the same way physics do. Medicine is based on observations and, surprise surprise (!), more observations. But making observations and deducing conclusions is not Science in the exact (and perhaps more idealistic) sense of the word. If it was, then baboons “watching” coconuts falling on each other and breaking apart would also be making “science”. Too much? I don’t think so.
Secondly, medicine must not be confused with technology. “Seeing something in the ultrasound equipment” is not “science”. And surely “Seeing something in the ultrasound equipment” is not medicine. Medicine is many things and an indication on the iU22 xMATRIX screen is in the bottom of that list.
As I stress in the “Why Medicine is NOT a pro-Science argument!” article in Harmonia Philosophica web portal , medicine is all about love, it is all about care and compassion, it is about faith. Things which are now forgotten by our “modern”, “scientific” medicine. And when we try to analyze the connection of medicine with these notions we may be startled to discover that medicine can be more “unscientific” and more “irrational” than its believers would like to admit.
Empirical observations do help, but again what do they help us about anyway? If we see ourselves as machines then it is surely good that we will live 10, 20, 30 years more. But why would we want to live more? Why should we even care about that? Philosophy has not found ANY reason why health is better than sickness (see Harmonia Philosophica – Main Thesis for such irrational ideas ) and we surely do not know if life is better than death in the first place.
Sticking into the materialistic mechanistic view of humans will help us treat patients up to a point. Patients though need other things as well. We are all going to die. Trying to make everyone live longer and longer without ever wandering what life is, or without realizing that death is also part of life, is plainly wrong.
The topic is not an easy one. There are many parameters to take into account and this short book is not the place to do so. My goal is just to create the spark which could ignite something inside you, my dear reader. And hopefully, this will lead to a paradigm shift in medicine in the years to come. When doctors get diagnosed with cancer, they tend not to use the treatments given to patients, so as to die peacefully. . Maybe the know something more? When doctors go on strike, mortality rates stay the same or, more often, decrease. [23, 24, 25, 26] I believe it is time for science to reunite with philosophy and start questioning some basic axioms in modern medicine. This is the only way to make medicine humane again.
If we are machines, I do not know why we should even care that we die. Dogmas turn us dead long before we die…
7.3.1 Do not let dogmas into science
All of the above teach us an important lesson: We should not let our dogmas (i.e. “materialism”, “theism”, “atheism” et cetera) lead our scientific findings. Let us think freely without any axioms in mind. Or at least, speak freely about the underlying dogmas of our theories so that other people can judge them properly…
Unfortunately, the Theory of Evolution is a playground of materialistic dogma spreading around the world these days. And people should be extra careful when dealing with dogmatism, no matter where it comes from.
8 Science is driven away from humans
The most important thing to say about today’s science is that Science has stopped to have human life as its primary focus for a long time now. In its effort to explain everything, it has forgotten that its main purpose is to serve human and improve our lives. By telling people that we are nothing more than dust and water certainly doesn’t help in that direction (although it will certainly grant some people a good funding to go on researching why people are so similar to bananas…). If you axiomatically think the world is consisted only of particles and physical laws that govern their behavior, then no wander you cannot find any evidence of spirituality in the universe. If you axiomatically think that there is no purpose in our existence, then it is more than logical that you cannot find any proof for the existence of purpose in the cosmos.
Let us not fall into the trap of some atheists who wish to have a “war” between science and other ways of reaching the truth, like philosophy or religion. Logic is as much a good tool as intuition and instinct. Many atheists today have tried to make a hero out of Galileo Galilei by distorting the facts around his trial and his general behavior. As philosopher Paul K. Feyerabend says, the case of Galileo was a minor and not-at-all important episode of the life at that time. Galileo had made a promise and he had attempted to hide behind lies. He wanted to reach a compromise and he finally did. Modern scientist, in a look for a “hero”, managed to change the story of a frightened “con” to the story of the clash between “giants”.   
Science must re-unite with philosophy and religion and – as in the times of Aristotle and Plato – try to reach truth with a more holistic way of thinking. Science must understand that the dogmas on which it relies are wrong. Science must understand that not all things are measurable (like moral, emotions, love) and that there are things we will never know via science (see Gödel “incompleteness theorem” for that).
9 Post-Modern Philosophy
Wittgenstein – a pioneer post-modern philosopher – thought that all philosophical problems are actually misunderstandings caused by the limitations of our language. For example, the phrase “the pig hereres” is neither true nor false. That phrase is nonsense: the words used have no meaning. Thus, we cannot claim anything about its truthfulness. In the same way, the phrase “God exists” cannot be true or false either. In that phrase we use the word “God” without knowing what “God exactly is and the word “exists” without having defined exactly what “existing” means. So, that phrase is nonsense too.
The teachings of Wittgenstein were wrongly used by many atheists to claim that no God exists. The Vienna Circle attempted to make such a misuse and that is why Wittgenstein did not go to their meetings. The reality is quite different. Wittgenstein in his work Tractatus Logico-Philosophicus was clear on one thing: the things that are of real importance in life are the ones for which we cannot speak about! We may not be able to answer the question “does God exist?”, but that does not mean anything about God’s actual existence! And that question – in spite of what many agnostics “believe” – is indeed one of the most important ones: knowing who we are and how we came to being is knowledge we must all have! As Heidegger  said, we may not know what “is” is, but the search for its meaning is what makes us humans…
As the Interacademy Panel (IAP – Global network of Science Academies) stated on an announcement it made for the theory of evolution on 21 June 2006: “Human understanding of value and purpose are outside of natural science’s scope. However, a number of components – scientific, social, philosophical, religious, cultural and political – contribute to it. These different fields owe each other mutual consideration, while being fully aware of their own areas of action and their limitations. While acknowledging current limitations, science is open ended, and subject to correction and expansion as new theoretical and empirical understanding emerges”.
It is also very important to note that when Edward J. Larson of the University of Georgia in USA attempted in 1997 to repeat an older study conducted in 1916 (by the noted psychologist James Leuba) concerning the percentage of scientists believing in God, he was surprised to find out that the percentage remained the same despite the great advances of science! A very stable 40% of the scientists surveyed (biologists, mathematicians, physicists and astronomers included) answered that they believed in the existence of a God, despite all the astounding scientific breakthroughs in the years that have elapsed  ! What is more, a 2005 survey of scientists at top research universities found that more than 48% had a religious affiliation and more than 75% believe that religions convey important truths . What is more, in the Global Values Survey that is conducted since 1981) it is shown that the higher the educational level of a person the more possible it is that this person will be religious.  So being religious is not incompatible to being a scientist as some people are trying to make us think.
People are tired of dogma (religious or scientific) and of cold science as well. As a final conclusion one could say that we must stay humble in front of the wisdom of nature, search like a scientist, believe in human and its higher value like a theologist and work all together to discover the truth! Asking the right questions is sometimes more important than knowing the answers…
- Science and religion: Reconcilable differences, Berkeley, retrieved from http://undsci.berkeley.edu/article/ science_religion on 01/09/2001.
- Dagobert D. Runes, The Dictionary of Philosophy, Philosophical Library, USA, New York
- Mary Midgley, Purpose, Meaning & Darwinism, Philosophy Now, 2009, retrieved from http://www.philosophynow.org/ issue71/71midgley.htm on 01/09/2011.
- Aristotelian view of God, Wikipedia article, retrieved from http://en.wikipedia.org/wiki/Aristotelian_view_of_God on 01/09/2011.
- Interpretation of quantum mechanics, Wikipedia article, retrieved from http://en.wikipedia.org/wiki/Interpretation_ of_quantum_mechanics on 01/09/2011.
- David T. Pegg, Causality in Quantum Mechanics, Physics Letters A 349 (2006), Elsevier, retrieved from http://www.qcaustralia.org/Publications/2006/Pegg.pdf on 01/09/2011.
- William R. Wharton, Causation with Quantum Mechanics, Physics Department, Wheaton College, Wheaton, Illinois 60187, submitted to American Journal of Physics, Nov. 1, 2005, retrieved from http://www.wheaton.edu/physics/ faculty/wharton/causation_with_qm.pdf on 01/09/2011.
- Mauricio Suarez, Causal Inference in Quantum Mechanics: A Reassessment, Universidad Complutense de Madrid, retrieved from http://philsci-archive.pitt.edu/archive/00003229/01/ SuarezCausalInference.pdf on 01/09/2011.
- A priori and a posteriori, Internet Encyclopedia of Philosophy, retrieved from http://www.iep.utm.edu/a/apriori.htm on 01/09/2011.
- A priori and a posteriori, Wikipedia article, retrieved from https://en.wikipedia.org/wiki/A_priori_and_a_posteriori on 01/09/2011.
- Types, Tableaus, and Gödel’s God, Springer, Series: Trends in Logic , Vol. 12, Fitting, M., 2002, 196 p., Hardcover, ISBN: 978-1-4020-0604-3
- Martin Heidegger, Sein und Zeit, Heidegger’s Gesamtausgabe, volume 2, ed. F.-W. von Herrmann, 1977, XIV, 586p.
- George Steiner, Heidegger, Fontana Press, 1978.
- Philosophy of Mathematics, Stanford Encyclopedia of Philosophy, retrieved from http://plato.stanford.edu/entries/ philosophy-mathematics/ on 01/09/2011
- J. Davis and R. Hersh, The Mathematical Experience, Birkhauser, 1980.
- Martin Heidegger, Wikipedia article, retrieved from http://en.wikipedia.org/wiki/Martin_Heidegger on 01/09/2011.
- Paul K. Feyerabend, Farewell to Reason, 1987, ISBN 0-86091-184-5, ISBN 0-86091-896-3.
- Johnston, George Sim, The Galileo Affair, Princeton, NJ: Scepter Press, retrieved from https://www.catholiceducation. org/en/controversy/common-misconceptions/the-galileo-affair.html on 01/09/2011.
- Some Lies and Errors of History by the Rev. Reuben Parsons, D.D.; Notre Dame, Indiana: The Ave Maria; 7th edition; 1893; pp. 95-122, retrieved from http://elfinspell.com/Liesand ErrorsGalileo.html on 01/09/2011.
- Vic Biorseth, The Galileo Inquisition, retrieved from https://www.catholicamericanthinker.com/the-galileo-inquisition.html on 01/09/2011.
- Getting the story straight: Galileo and the church, retrieved from https://timpanogos.wordpress.com/2008/01/31/ getting-the-story-straight-galileo-and-the-church/ on 01/09/2011.
- World Values Survey Portal : Cross-reference “Importance of Religion” with “Highest education level attained”, Years 2000-2004 [http://www.worldvaluessurvey.org/].
- Cunningham SA, Mitchell K, Narayan KM, Yusuf S, Doctors’ strikes and mortality: a review, Social Science & Medicine (1982) [10 Oct 2008, 67(11):1784-1788], retrieved from http://europepmc.org/abstract/MED/18849101/reload=0;jsessionid=qOxjEVJ2JGcWLXe5RyBQ.12 on 01/09/2011.
- Dr Raj Persaud, Dr Peter Bruggen, When Doctors Go On Strike Patients Stop Dying, 14/05/2012, retrieved from http://www.huffingtonpost.co.uk/dr-raj-persaud/when-doctors-go-on-strike_b_1513689.html on 15/05/2012.
- Dr John Briffa, Some potentially good news for UK patients: doctors may go out on strike, 19 January 2012, Food and Medical Politics, retrieved from http://www.drbriffa.com/ 2012/01/19/some-potentially-good-news-for-uk-patients-doctors-may-go-out-on-strike/ on 01/09/2011.
- Will fewer people die if doctors strike?, Full Fact article, retrieved from https://fullfact.org/health/will-fewer-people-die-if-doctors-strike/ on 01/09/2011.
- Spyridon Kakos, How doctors choose to die, Harmonia Philosophica, retrieved from http://harmoniaphilosophica. wordpress.com/2012/05/31/how-doctors-choose-to-die/ on 01/09/2011.
- Spyridon Kakos, Why medicine is not a pro-science argument, Harmonia Philosophica, retrieved from https://harmoniaphilosophica.com/2011/12/26/why-medicine-is-not-a-pro-science-argument/ on 01/09/2011.
- Spyridon Kakos, Harmonia Philosophica (Main Thesis), Harmonia Philosophica, retrieved from https://harmoniaphilosophica.com/harmonia-philosophica-antithesis-synthesis/ on 01/09/2011.
- List of Christian Nobel laureates, Wikipedia article, retrieved from https://en.wikipedia.org/wiki/List_of_Christian_ Nobel_laureates on 01/09/2011.
- Schooler, J. W. (2014). “Metascience could rescue the ‘replication crisis’, Nature. 515 (7525): 9. Bibcode: 2014Natur.515….9S. doi:10.1038/515009a. PMID 25373639.
APPENDIX I – The fake heroes…
Many modern blind followers of scientism (not “science”) use the example of Galileo to prove there is indeed a war going on between religion and science. The case of Galileo does not prove something like that. Many atheists today have tried to make a hero out of Galileo Galilei by distorting the facts around his trial and his general behavior. As philosopher Paul K. Feyerabend says (see his book “Farewell to Reason”), the case of Galileo was a minor and not-at-all important episode of the life at that time. Galileo had made a promise and he had attempted to hide behind lies. He wanted to reach a compromise and he finally did. Modern scientists, in a look for a “hero”, managed to change the story of a frightened “con” to the story of the clash between “giants”.
The case of Galileo can be summarized in the following:
1. There were many people advocating the Copernical views many years before Galileo’s case. The Catholic authorities of Galileo’s day had little trouble with heliocentrism per se. Many of the leading Catholic scientists were actually Copernicans. Copernicus’s treatise on heliocentrism had been in print for seventy years prior to Galileo’s conflict with the Church. The Church, especially, recognized no significant dividing lines between theology and science; it was all philosophy, or the quest for ultimate truth. And so, for some, if Aristotelian thought was wrong, then that might make Christianity wrong, which was unthinkable. Galileo challenged church and caused such reactions mainly because he arrogantly claimed to know the truth about “reality” and not because of his opinion.
2. The main reasons behind the church’s reaction were the fact that Galileo claimed that Copernican theory was a “fact” rather than an unproved theory (while contradicting the then much better established Aristotelian physics) and the fact that Galileo claimed to be in a place to interpret Holy Scripture in a time of unrest in church matters (Reformation). The use of the Bible as a “final frontier” was not as absolute as many people think: Bellarmine said that in case the Earth is finally proved to be revolving around the Sun, then the church should be very careful with the interpretation of the Holy Bible and maybe think that they have interpreted it falsely. The fact that the church was reluctant in denouncing a very succesful and proven theory like the physics of Aristotle is not something weird: scientists today are also reluctant to change existing theories not too much evidence against it exist. Surely theories that existed and produced predictions for 1,700 years were not an easy prey for unproved theories (Galileo’s telescope observations were antiphatic and not reproducable – those who did actually reperformed them, i.e. Kepler, could not draw the same exactly conclusions). A modern physicist could try to teach new alternative ways of medicine to see how “free” he is today to try new methods. Or a modern chemist could try to revolutionize the human nutrition theories and see if he finds any opposition from the established “scientific” dogmas. Or a modern biologist could try to teach anything else than the established Theory of Evolution and see if he survives one day at work… (at least the church then stated its ruling clearly and accepted the possibility of changing views) 
3. The reason behind the final punishment of Galileo was the fact that he did not hold the promise he had given to the Pope and not the scientific controversy between the heliocentric and the earthcentric systems. As simple as that. No science-religion war, no conspiracy there…
In more details:
Galileo expressed scientific views supporting Copernicus, and also his related biblical views, in a 1615 letter to the Grand Duchess of Tuscany. Although it was a private letter never intended for publication, the references to Scripture contained in it were focused upon, and became the basis of his first examination, trial and censure. This was the first of two trials of the Galileo inquisition.
Pope Paul V ordered Cardinal Bellarmine to summon Galileo to appear at his palace, and to promise “not to teach, defend or discuss his doctrine or opinions”. He submitted at once, and as a result the decree made no mention either of his name or of his writings. This delicacy on the part of the Roman authorities is not relished by Galileo’s opponents, so they spread a false report that he had been forced to abjure his opinions, and had been given a penance. In a written statement Cardinal Bellarmine branded both these statements as false.
As a result of this censure Galileo promised, under pain of further punishment, to not hold or publish Copernican theory as scientific fact, but only as unproven theory or hypothesis. As a matter of pure science, at that time, the theory was indeed unproven, by Galileo or by anyone, and was very much up in the air.
Not only were the two competing theories under hot debate in scientific circles, but the timing of events was crucial to the importance given the whole matter by the Church. Add to Galileo’s letter the building list of “forbidden literature” born of Martin Luther’s (1483-1546 A.D.) renunciation of Church authority and new Scripture interpretations, among the many others (all born of the Reformation) and you get the picture. The Church forbade Catholics access to this heretical literature, which included any and all literature challenging orthodox Scripture interpretation. The Reformation was introducing all sorts of new “revelations” born of non-authoritative group and even individual new interpretations of Scripture. In the midst of identifying and challenging new and heretical Scripture interpretations, along comes the Galileo inquisition and an apparent Scriptural re-interpretation by a layman, who was also challenging the established science of the day, sometimes with not-so-strong or valid arguments. For example Galileo said that the phases of Venus he discovered “proved” that the heliocentric model was correct, however as Kepler also noted back then, a heliocentric model would indeed leas to phases of Venus but the phases of Venus did not imply anything as per the validity of the heliocentric model. Galileo also used the tides as an argument for Earths rotation around the Sun. However we know today that the tides are irrelevant to that phenomenon: it is the Moon’s rotation around Earth which is causing them. Galileo finally also tried to use the existence of stellar parallax as an argument for the movement of Earth. With one minor detail: That his observations did not find any stellar parallax. (even though now we know such thing exists, however Galileo could not and should not have used this as an argument back then – if he was indeed honest.
That’s what originally lit the whole fire.
Galileo’s friend Cardinal Barberini was elected Pope on August 6, 1623, under the name of Urban VIII. From that moment Galileo fondly hoped that he would obtain a reversal of the decree. He wrote his II Saggiatore (The Assayor) in answer to an attack by the Jesuit, Horace Grassi, and dedicated it to the Pope who read it with pleasure. It was a skillfully veiled defense of the Copernican theory, but Galileo managed to hide this fact from the Pope and the censor, Riccardi, who gave him an imprimatur. He declared that as the Copernican theory had been condemned by the ecclesiastical authorities and the Ptolemaic theory was contrary to reason, scholars were bound to look for a new theory. In 1624 Galileo made another visit to Rome. The Pope gave him six long audiences, promised a yearly pension to his son, and presented him with a gold and a silver medal. He also wrote to Ferdinand of Tuscany praising Galileo for his scientific genius and his ardent piety.
Had Galileo possessed a modicum of common sense, he would have been content to let matters rest. But his head was turned by the Pope’s great kindliness, and his mind embittered by the many accusations of heresy made against him. He forgot that Pope Urban in a private audience had assured him that he would never accept the Copernican theory; he forgot his promise to Cardinal Bellarmine.
And to be honest, Galileo not only did he not have common sense, but he had the logic of a fraud. In his life he managed to claim for himself dozens of discoveries others made (including but not limited to the telescope previously invented by Hans Lippershey, the Sun spots previously discovered even by ancient Greeks and more recently previously analyzed by Christoph Scheiner, the four moons of Jupiter previously discovered by Simon Mayr, the parable trajectories of projectiles discovered by Cavalieri etc – see “Discover Newton” by William Rankin). He also managed to even ridicule correct ideas of others (e.g. the planets’ elliptical orbits or the tides created by the effect of the Moon on Earth discovered by Kepler, the existence of comets discovered by Tycho Brahe etc), while postulating his wrong ideas as correct. This case was not different. He just wanted to make himself known to the world, but without even having to prove what he said. Note that the stars’ parallax was not known back then. And since Galileo could not prove his theory, he even reversed things by asking the Church to prove her position! (see “The Galileo Case”, Mario D’ Addio, p. 79 and “Discover Newton” by William Rankin) His final refuge was sophistry.
In 1632 he published a clean-cut defense of the Copernican theory in his famous Dialogo dei due massimi sistemi del mondo. Two of his friends, Sagredo of Venice and Salviati of Florence, take the part of interlocutors in the book defending Galileo’s views, while an imaginary philosopher, Simplicio (imbecile) defends the Ptolemaic theory in a manner to make it appear absurd. Galileo put in the mouth of Simplicio faulty arguments of low quality, but that was not the end of story. It is not certain why Galileo did that, but he actually used some of the arguments the Pope himself had used in the mouth of Simplicio and that certainly did not help…
That is what resulted in Galileo’s conviction on suspicion of heresy resulting in a lifetime house arrest. The issue at hand, and for which he was ultimately sentenced was not Galileo’s science; it was the violation of his earlier agreement with the Church, which appeared to be an open public challenge of their authority. Something to bear in mind when talking about that case.
No scholar today believes the fable that Galileo at this meeting stamped his feet in anger, and cried out: “E pur si muove”—”but it does move.” The records of the trial prove that he was submissive throughout, and most anxious to curry favor with his judges. This ridiculous statement was first ascribed to Galileo by the unreliable, gossipy Abbe Irailh in the third volume of his Querelles Litteraires (Paris, 1761).     
(similar comments of history misinterpretation can be made for the case of Ypatia as well, who was not killed for her philosophical views – these actually entailed God as well – but because of her political relationship with the imperial prefect Orestis in the middle of a political power game – see “Hypatia of Alexandria, Harvard University Press, Cambridge, Massachusetts, 1995” by Maria Dzielska or OODE)