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Just a Theory

“You know Evolution is just a theory”

Ok, I’m going to ignore that Atheism and evolution are actually two completely different subjects. If you want, look up Directed Panspermia and the Realians, those are examples of atheists who don’t buy the concept of human evolution.

Anyway, I wanted to tackle this “It’s just a theory” (emphasis on “Just”) thing.

What is a theory?

A scientific theory is many things such as

1)      A predictive model

  1. It is a way to predict what the natural world will do under well-defined circumstances

2)      A falsifiable explanation of observable phenomenon

  1. In other words, it explains what we can observe and can be tested and, perhaps not “proven” right, at least be able to be proven wrong if an experiment were to give certain results

3)      A collection of facts

  1. This is true, but it’s more accurate to say it’s the end result of the collection of facts

4)      Constantly in flux

  1. Theories must be tested, retested and reevaluated and, on occasion, modified to conform to new data

5)      The best explanation for all the data available

  1. Is it the only? No. But it’s one the accounts for all observable evidence and has the fewest assumptions possible. If it doesn’t, then go back to point 4.

A theory has also, by definition, gone through scientific peer review and has been tested and tested and retested over and over and over again until it can actually be called a “theory”. That’s part of the scientific process.

Hypothesis VS Theory

What people really mean when they say “it’s just a theory” is “hypothesis” which is a possible explanation of a set of facts. A hypothesis is also, by definition, something which has not gone through peer review, been tested and refined or seen as a reliable predictive model. You can think of it as a precursor to a theory in the same way that the Model T was a precursor to a Mustang. The Model T was a good start but it needed to be refined and reworked before it was readily accepted by the public at large. They have things in common, but, the end result is always a work in progress too and is usually very different than the starting point.

What is a Law?

A scientific law is something completely different from both a theory and a hypothesis. A law is a principle that holds true in all cases and has been proven to do so using logic or mathematics. As a result, the only scientific laws in existence are ones which can be expressed solely in terms of mathematics or logic.

Evolution is a theory because it’s biological in nature and can’t really be expressed in terms of mathematics. Even though we can observe it in action (and we have) it’s not a law because we would have to show that it’s true in all cases and that, because of the sheer amount of resources it would take, is impossible for humans to ever do.

It’s a Theory… and a Fact

Yeah, sure, it’s a theory and unless we come up with some kind of mathematical representation for it, it will always be a theory. But, at the same time, it’s also a fact.

It’s a fact in the sense that we can see it happen and demonstrate its existence. We’ve seen it happen in the lab and in the wild. We know it works. We’ve used it to predict actual phenomenon. It’s there just as much as gravity is – there are alternate explanations for both but the scientific theories are the only ones which account for all observable data and contain the fewest assumptions. How else would you define a “fact”?

Other Things which are “Just Theories”

In case you were wondering:
Cell Theory in Biology
Einstein’s Theory of Relativity
Newton’s Theory of Gravity
Kepler’s Theory of Planetary Motion
The Big Bang Theory
String Theory
Atomic Theory
Plate Tectonic Theory
Meteorological Theory
Stellar Theory
Global Warming
Germ Theory
Music Theory
Acoustic Theory
Color Theory
Kinetic Theory of Gases
Helio-Centric Theory
Get the idea? Almost everything in science and even other fields of studies are “just theories”

So, yeah, Evolution is “just a theory”. We really do science a disfavor by calling anything a “theory” because the public’s idea of what is a theory is completely different from the nuanced scientific definition. They tend to think a theory is what Columbo spouts off at a trial or during an investigation – that it’s just someone’s “best guess” to what’s going on. It’s not anywhere near that.

So, for any creationists out there who want to use the “It’s just a theory” argument, my advice is this: Stop. Just stop. Stop before you hurt yourself. It will only end badly for you.


Misconceptions About Atheism part 3

A few of these misconceptions I thought about making into their own posts, but they were just too short. So I’ve just listed 5 of them in one. I think I might stick to this.

“You don’t believe in God because you hate Him.”

oh really? So, you don’t believe in Santa because you hate him as well? Or the Easter Bunny? Now, I’m sorry if comparing your deity to those fairy tales is insulting – I honestly didn’t mean to do that. I only meant that these, too, were things I once believed in but don’t anymore. I don’t hate God because I can’t hate something which I don’t believe in. I didn’t stop believing in God because of hate or anger, either. The reasons that I had before just fell flat under scrutiny.

“You don’t believe in anything, then?”

No, that’s not quite right. Atheism, by definition, is the lack of belief in a God. It says nothing about what I do believe, only about what I DON’T. I can believe anything I want but as long as I lack a belief in God’s existence, then I’m still an atheist.

“Well, you were never really a Christian in the first place, then”

This is the “No True Scotsman” fallacy. Look it up.

“You just want to sin/you have no morals”

I suppose that depends on how you define sin and morality.

If, by sin, you mean “I wish to live without God”, then you’re assuming God’s existence. I’m not so that sort of sin never really comes into play or is even really a concept. It simply doesn’t exist.

As for sin and morality within atheism, every moral code is based on altruism and empathy including an atheistic or secular one or even a theistic one. There’s been several recent studies on group selection theory and how it relates to altruism and empathy. There’s a very good naturalistic explanation to those traits and they have advantages to society as a whole so it’s beneficial for me and others, in this physical existence if nothing else, to adhere to those ideas. There’s nothing supernatural about them and you don’t need a belief in God to have them or live by them.

“So, you believe nothing happens when you die?”

You got it.

ok, gang, that’s 5. Till next time.

Misconceptions About Atheism part 2

“So, you believe God doesn’t exist, then?”

Yeah, I get this one a lot. It’s easy to understand why, though. For starters, there are atheists who assert that there is, indeed, no God at all. But this is a subset of atheists similar to how Baptists are a subset of Christians but not all Christians are Baptists or hold Baptist beliefs.

Another reason this myth persists is that it’s easy for people to divide everything into two groups. Us or Them. Black and White. Chocolate or Vanilla. Atheist or Theist. Edward or Jacob. Republican or Democrat. This mentality is a lowest common denominator – it’s the simplest to understand – so its pervasiveness should come as no surprise. It’s also particularly advantageous to preachers and clergy because of how conducive that rhetoric is to cohesiveness within a congregation. “Stay with us or go with them”. This not only encourages the group to stick together but also separates it from any outside influences. The implied threat of ostracism also does not and should not go unnoticed.

To put it in the form of an analogy let’s say you woke up in an empty room with nothing, no doors, windows or anything, but a computer monitor there for you to see. Let’s forget how weird this is and just continue, shall we?

Now, if the screen started printing out a message such as “In this building there is a room. In this room there is a box. In this box there is an object. This object is an apple”, would you believe it? Well, why would you? You have no reason to believe the room you are in is in a building, that the building has any more rooms than the one you’re in, that one of the rooms has a box or that the box in the room which you can’t see has anything in it at all, let alone an apple.

But, on the other hand, you could not say for certain that there is no room in that building which has a box in it which contains an apple. Logically you must exist in such a state where you can neither assert or deny the existence of the box or the contents in it. You can, however, assert what is not in the box which is a subject for another discussion.

Simply put, atheism is by definition the absence of a belief in God but not necessarily a belief in the absence of God.

Just because you refuse to reject a positive claim does not mean you accept the negative by default.

Misconceptions About Atheism part 1

I’m not sure about the rest of you but when I was growing up, the word “atheist” was nearly a four letter word. Somehow on the same level of despise as communism or facism.

Most of these ideas arrise out of two things. Ignorance of what atheism really is or just plain, old fashioned misrepresentstion.

So, my next series of posts will be about dispelling some of the more common misconceptions theists have about atheists and atheism. Stick around. Should be fun.

Reduce This… part 2

Bacteria are a remarkable life form. Truly. They are quite possibly the most resilient forms of life on this or other planets. I say other planets because of this article:

Fascinating stuff, really. It implies a lot of just mind blowing things but I won’t get into that right now. Right now we’re going to talk about one of the most ingenious little devices which bacteria have created for themselves: the bacteria flagellum.

First, let’s start with what the bacteria flagellum is. Below is a diagram I grabbed right off of Wikipedia. Sorry, I didn’t have the time nor the energy to make my own up this time.


Take a good look at it. Now, if you’ve taken a shop class at some point, it should immediately look familiar. It is, and there is no other way to say this, a motor. Really, check it out. It’s got a shaft, a rotator, etc. It’s a motor. Indeed, the flagellum is used almost exclusively in just that manor – for locomotion in the bacteria’s environment.  It really is a machine and I challenge any of you to find a better way to describe it.

Now, according to Irreducible Complexity, we should not be able to do two things:

1)      Remove any part or parts of this flagellum and get anything functional

2)      Find functions for the individual components when not in use as a flagellum

As for point one, the flagellum is broken into about 40 or 50 different genes. I won’t bore you with those details. Each gene maps to a protein which makes up one component of the flagellum. So, if we were to deactivate or just plain remove a chunk of them we should have something completely unusable, correct? Lets say, 30 or 40 of the genes which make up basically the tail of the flagellum were removed. Don’t ask how or why, the point right now is to remove them and show that the result is unusable. Here’s something we might get:


Yeah, that doesn’t look like mu…. WWWAAAAIT a minute. That’s a type-3 secretory system. Heh, yeah, I know, not really obvious, but that’s really what it is. Even the proteins are the same. The type-3 secretory system is another ingenious little device bacteria use in a similar manor that you might use a syringe – it injects proteins and other things into cells for multiple reasons. Reproduction, defense or to create an environment suitable for the bacteria by inducing certain auto-immune responses. Kinda cool, huh? Well, maybe not. That last one is how the bubonic plague works.

OK, so I found a use for it. So what? How did we get all the other parts?

Well, the proteins I removed are found everywhere in the bacteria’s DNA. It’s not hard to imagine how they can get swapped from one part to another. It’s a type of mutation called gene duplication. Happens all the time, including in humans. On top of that, intermediate forms of the bacteria flagellum are found throughout the animal kingdom but they each have different uses. The trick, it seems, is to not assume that an intermediate form has the same function as the current one.

So, here’s what we started with:

1)      We assumed the bacteria flagellum was irreducibly complex.

2)      The definition of irreducible complexity is such that

         2.a) None of the sub-components are useful on their own

  1.               2.ab) If you remove any part or group of parts from the mechanism, it would break

3)      But, removing a few genes from the bacteria will produce a type-3 secretory system instead of a flagellum – something used in several bacteria species

4)      Also, the proteins and genes we removed are duplicated elsewhere in the genome of most bacteria species.

5)      We’ve disproven 2.a and 2.b so our initial assumption must be incorrect.

Proof by contradiction.

And there you have it. Part 2 of “Reduce This”. Irreducible complexity… bullocks.

Most of the information I got was from this presentation by a great biologist named Dr. Ken Miller. He was actually part of the defense in the Dover’s trial and argued against the Intelligent Design proponents.

Anyway, next I’m not sure what I’ll be tackling. For the few of you who read this, send some stuff along. I’ll see what I can do.

Reduce this… Part 1

Irreducible Complexity is the idea that a biological component or system can be so complex that were you to remove one part or “reduce” it the component would cease to function. Common examples of this are the eye and the bacteria flagellum, among others.

Intelligent Design proponents and Creationists like to tout this assertion as an argument for their side. “How can something irreducibly complex ever evolve without a designer”, they postulate? Right off the bat, that should be a red flag to anyone. It’s basically saying “I can’t think of a way for this to evolve, therefore, it didn’t”. It’s an argument from ignorance, at its root. Just because we can’t think of it, doesn’t mean the explanation doesn’t exist. It just means we or, more specifically, the ID or Creationist proponents haven’t thought of it yet.

When you break the argument down it has two basic assertions:

1)      Things which are “irreducibly complex” could not have evolved because intermediate forms are useless.

2)      That taking parts out of something which is “irreducibly complex” renders it completely useless.

I’ll tackle these two arguments by using the same two examples I gave above – the eye and the bacteria flagellum. In this post, I’ll only cover the eye. I’ll cover the bacteria flagellum in a later post.

The Eye

For the eye, I will show how it’s possible that intermediate forms can exist and have an evolutionary and naturally selective advantage and how natural variation within a population will lead to the eventual evolution of an eye.

Step 1

Remember, we’re working forwards, not starting with a fully formed eye and working backwards. So, first, let’s start with a photosensitive skin cell. Most animals have these but they are too few and spread out to be of any real use. I read somewhere that humans do as well but I can’t substantiate that claim at the moment. They aren’t of any use to us now because we have an evolved eye which is much more efficient. But, you can imagine that, were we blind, we might become more sensitive to these cells as time and generations passed.

Step 2

Imagine a whole population of individuals with no eyes and these photosensitive skin cells around their body. It would be within natural variation that some of these individuals would have more cells than others and, thus, be more sensitive to light. If you’re more sensitive to the light then you’re more likely to know if it’s night and day. You could track prey more easily if and detect if you’re under some kind of shelter. It’s clear these individuals would have a slightly better chance of survival. Over several generations, most of the population would have a higher number of these photosensitive cells.

Step 3

Now take this population of the same species and you can imagine, due to natural variation within a population, some of these individuals would have patches of skin where more of these cells are than others. We have similar patterns within our species, don’t we? Some individuals have patches of skin which contain more melanin than other patches. It’s not hard to imagine that some individuals within the population of this unnamed species. So, now, these individuals would be able to get their light sensitivity from one or two specific places on their bodies rather than all over. They could also be more sensitive to the light and be able to point whatever body part happens to have these patches towards something to figure out if it’s emitting light or not. It’s clear these individuals would have more advantages than others at detecting light and, therefore, would survive longer and, thus, reproduce more. It’s easy to imagine that, over several generations, this population might be filled with individuals who have similar photosensitive patches.

Step 4

It would be within natural variation in this species that some parts of their skin may not be perfectly smooth. Take a close look at your skin and you’ll notice there are peaks and valleys all over. It’s not perfect. Some of these imperfections are acquired but many are inherited. Now, what if one of these valleys happens to fall on one of these patches of photosensitive skin? Take a look at the figure below to see a cross section of what this would look like.


Yeah, it’s overly simplistic, I get that. But notice that, were light to be shown at an angle with this arrangement, some of the cells would be illuminated and some would not. We now have directional capabilities for these skin patches because of the way light would be angled! Granted not very good directional ability but, before, we had none at all. Clearly, these individuals have a selective advantage and would survive longer to pass down their genes for this.

Step 5

Moving on, imagine if a thin layer of transparent skin cells are put over the patch. It isn’t really too hard to imagine since our own epidermis is transparent. Now this patch of skin cells is protected and now we can use our primitive eye longer without it getting damaged. Again, these individuals would survive better than others and these genes would be passed down.

Step 6

From here, some of the transparent skin cells will be thicker than others. Now, if the variation of thickness is relatively evenly spread, that’s not going to do anything. But, you can imagine that some individuals will, by sheer statistics, have a thicker layer near the center than on the outside – again within normal variation of a species. Now what will happen? Well, what happens to light as it passes through a lens of a similar shape? I’m sure you’ve seen a magnifying glass before – it focuses the light. Now, on top of having much better directionality, we have a clearer picture of what we’re looking at.

I’ll stop here since this is essentially all we need for an eye. Look back and see where we started. We started with an entirely blind species and went from no eyes to at least something that serves the function of an eye. Current archeological evidence suggests that the eye itself actually evolved in parallel several times so “our” eye is not the quintessential eye. Indeed, it should be noted that this is not our eye. Actually, this is precisely the evolution of the eyes of a specific family of marine animals – mollusks. Jelly fish would be the first step – just a random dispersal of photosensitive cells. Octopi and squid happen to have the most sophisticated eyes, even better than our own, of the group. All throughout their phylogenetic tree you can see each of these stages of an eye. And, keep in mind; we did all of this using only the natural variation within a single species. There’s even one deep ocean species that has a version of an eye inside a transparent skull.

Are there other “examples” of irreducible complexity? Sure. But they all fall into the same pattern that I just laid out. The whole idea that the eye has to be fully formed in its current state to be useful ignores the actual evolutionary pattern of the eye. In short, this form of irreducible complexity arises from an ignorance of the process of natural selection and natural variation within a species.

Next up – The Bacteria Flagellum.

Wanna bet?

Most of you are familiar with Pascal’s Wager even if you don’t know it by name. Blaise Pascal was a 17th century Mathematician and philosopher. He’s the guy who created Pascal’s Triangle which, if you don’t know, has to do with binomial coefficients along with tons of other very useful mathematical concepts which we still use. I know, riveting right?

Anyway, I’m not going to talk about his Math. I’m here to talk about his Wager.

Pascal’s Wager goes like this: You can either choose to believe or not believe and God either exists or does not exist. If you do not believe and God does not exist, you neither lose nor gain anything but if God does exist, you lose everything. However, if you believe and God does exist you gain everything and if God does not you neither lose nor gain anything. So, bet fully on belief since it’s the only possible outcome where you can come out ahead.

It’s based, in part, on the idea that there is no empirical evidence for God otherwise there would be no need for a wager or even belief. It would be like “believing” that the sun comes up in the east – sure, you can but, strictly speaking, you don’t need to. You can see that it does, measure it and quantify the phenomenon and even show it mathematically using some of Kepler and Newton’s laws of planetary motion. Belief never has to enter the picture. Since there is no evidence for a God that means there are an infinite number of possibilities and each one is just as likely as the next so why not bet on the one with, seemingly, the only possibility for reward?

On the surface this seems sound and tempting. But there are a few problems with it. I’ll go through the ones I can think of just off the top of my head.

1)      It’s not an argument for the existence of God. Only the belief in God

This is the one that gets me. The wager doesn’t do anything to prove or disprove the existence of God but offers as its sole basis for belief some kind of system of punishment and reward. I find this rather insulting that the only reason I would believe in something is if I was rewarded for doing it and punished for not. I’m not a dog and I have no master named Pavlov. That whole paradigm stopped working when I was 12 when I realized there are better reasons to do or not do anything than my own selfish desires.

2)      You might believe, but you might end up believing in the wrong God

It’s entirely possible that there is a God but hasn’t been discovered yet or has been but the faith itself was wiped out somehow or that it still exists but not many people are exposed to it. Pascal made the critical error of having an Abrahamic-centric view on Deities. He ignored all other possibilities and, when dealing with the infinite, you simply cannot afford to do that. In this instance, sure, you might have one case where you get rewarded but, since this is infinite, you have an infinite number of cases where you do not or even get punished.

3)      God may not care one way or another

Deists believe in a “clock maker” God. A God that set up all the laws of physics, let go and quietly retired never to be seen or heard from again. This God has no interest in human affairs, if He’s even aware of them, but it’s entirely possible that this is reality. In this case there is no case for reward or punishment. This is effectively as though there is no God though, so I suppose you could lump this in with that.

4)      God might reward based on works rather than faith

Pascal’s Wager is also based on the idea that God rewards Faith. What if He rewards works instead? If there is a personal God out there, one that interferes with the affairs on this lonely little backwater planet, it seems to me that he would care more about how we treat each other than what we believe in.

5)      There might be more than one God

There’s no evidence to suggest there isn’t more than one. True polytheistic religions are rarer now-a-days (Hindu’s, depending on the sect, are actually monotheistic) probably because the practice of monotheistic religion is just simpler and easier to grasp than all the rules and regulations for several Gods. But, that doesn’t mean they aren’t possible. In this case, there are multiple God and Goddesses to believe in, not simply one.

6)      God might punish everyone no matter what

Several belief systems say this. The Egyptians come to mind. In this case, belief doesn’t matter.

7)      God might reward everyone no matter what

Several belief systems say this as well. In this case, too, belief doesn’t matter. It’s similar to point 6 but the reward and punishment is switched.

8)      God might reward honest skepticism over blind faith

Why not? Say you die and you get to the pearly gates. Why wouldn’t God say “OK, you believed in me without question but this other guy used the brain I gave him. Sure, he came to the wrong conclusion but he was honest about it and gave it his best shot. He can come in. You? You get to sit out here and think for a few more millennia”. That makes sense to me. At least you’ll have some company. In this case, a God could exist but might reward disbelief (atheism or agnosticism) instead of faith. And wouldn’t God see through this? Believing just to get a reward rather than an honest belief?

9)      That there is no difference in a life lived believing in God than a life lived not believing

Pascal’s wager does not take into account your time on earth and how it can be affected by your beliefs. Surely there are other things to do on a Sunday (or Saturday if you’re Jewish or Friday if you’re Muslim or… whatever else). You won’t be wracked with guilt when the next time you see an attractive individual your mind immediately turns to what it’s biologically predisposed to turn to and you won’t feel as though you’re being watched all the time. It can be reasoned that, while on earth, you can live a more enriching life, free from the bonds of guilt and oppression, by rejecting the belief in a supernatural power and turning to secularism, empathy and altruism as a source of morality.

Phew! OK, that’s all I can think of. I’m sure there are others.

When you really sit down to think about it, Pascal’s Wager isn’t a wager at all. It’s a threat. It basically says “believe in God, or else”! And it doesn’t even go a good job at that because it requires far too many assumptions that simply have no basis.

In short, it’s riddled with holes, makes no sense even in its own context, it has an extremely ethnocentric view of the supernatural and fails to stand up to even the most basic of criticisms. This is why, as an argument for Theism, I threw Pascal’s Wager out.

Anyway, next up – irreducible complexity…