Thursday, December 16, 2010

Time for prayer again

“@time: Science acknowledges the medicinal power of prayer | (via @TIMEHealthland)”

There are so many things wrong with this I don't know where to start.

For starters the study and the title Time gave this article have almost nothing in common. It was a sociology study of 62 women victims of domestic violence. And it has to do with the emotional aspects of abuse, not medicinal power. That is a dishonesty level I find unacceptable.

And it suggests:

"prayer can be…a way for victimized women to learn to forgive their abusers,"

Why must an abused person forgive their abuser? That is a disgustingly immoral suggestion to me. Yes I will heal, and be happy, but how dare they suggest that I have to forgive them. If you feel it helps you to forgive, that is up to you of course. But don't assume this is necessarily a good thing. In fact, it continues:

"he finds that it can also keep some women from getting out of violent situations."

Exactly. And does the study say that prayer is even the best way for women to get out of abusive relationships? Nope, it sure doesn't.

What the study essentially says is that prayer can be used as a coping method (like children often use an imaginary friend).

Real scientific studies into prayer show no medical effect as my blog post on prayer discusses.

Tuesday, December 14, 2010

Atoms, They DO Exist!

Seeing something directly with our eyes is not required for scientific evidence to support a theory (empirical evidence can come in many forms) but looking at images that are built up from electron scanning can often give us an even better view.

To that end, researchers in Japan led by Yuichi Ikuhara have imaged some Hydrogen atoms for our viewing pleasure using a scanning transmission electron microscope technique:

Mathematical Miracles

Fractals and Strange Attractors are mathematical equations (some quite simple) that can demonstrate Infinite complexity (the Mandelbrot set is an example of infinite complexity from the equation z -> z^2 + c iterated over the complex plane) and emergent order through a process of iteration. Furthermore, these equations model exactly the type of signals and structure we observe in the universe.

Another type of computational model is that of the cellular automata. Two special types of behavior that can be observed to emerge from even simple cellular automata is that of Self-Replication and Universal Computation, which means that simple cellular automata can be setup to perform arbitrarily complex calculations, including all of mathematics.

These blindingly simple cellular automata can contain self-replicating structures which are subject to mutation and selection pressures and can therefore evolve over time into more complex structures that (given enough processing power) could express intelligence and such constructs would give the appearance of design where non-existed.

And this doesn't require a stochastic (random) process at all, the mutational factors are built into the structure, operating according to the exact same laws.

There need not be anything 'random' about 'random' mutation either. Indeed, even in our world we label things as 'random' merely because they are beyond our ability to predict. Not for reasons that they cannot be predicted (with the possible exception of Quantum Mechanical processes but it is not demonstrated that Quantum Mechanics is purely random!)

That such beautiful order and complexity emerge from such simple, rigid, deterministic computational processes is one of the many reasons that I believe the universe is NOT a place filled with agency constantly violating the otherwise natural processes.

One might be inclined to ponder, "but who created this order" but that in turn would beg the question of who created the creator. At some point, the buck has to stop and I firmly believe that Thomas Aquinas made some wonderful arguments for the 13th century but they are just that. Ideas limited by the 13th century understanding of the universe, before we had knowledge about fractals, and chemistry, and DNA, and cosmology, and abiogenesis, and evolution, and computers, and quantum mechanics (and the inherit limits it places on the world).

To grant this extra-agency all the power strips it away from where it belongs, with the Universe itself - whatever that ultimately is.

On Agnosticism

Agnosticism is a term that is bandied about by many, but is often misunderstood if not completely misused (at least from my perspective as a long-time Agnostic). There has certainly evolved a generic usage of the term 'agnostic' as an adjective which means to consider a proposition as unknown or unknowable. But I don't think it's reasonable for someone to claim this as their position on the question of God (hint, it's an adjective).

But as a proper noun, the -ism was coined by Thomas Huxley with a very specific definition as Michael Martin writes in "Atheism: A Philosophical Justification":
Putting aside the current popular sense of the term, "Agnosticism" was coined by T. H. Huxley in 1869. According to Huxley, Agnosticism is not a creed but a method, the essence of which lies in the vigorous application of a single principle. Positively the principle may be expressed as, in matters of intellect, follow your reason as far as it can carry you without other considerations. And negatively, in matters of the intellect, do not pretend conclusions are certain that are not demonstrated or demonstrable. It is wrong for a man to say he is certain of the objective truth of a proposition unless he can produce evidence which logically justifies that certainty.

As you can see from this definition Agnosticism is not just a statement about knowledge whereas atheism is a statement about belief (but the two positions can still be compatible). Agnosticism, properly understood is a Positive belief in what we might call science or skepticism. In this sense it is a very different thing from the common form of atheism today (which is a rejection of theistic beliefs, or more accurately "a lack of belief in a god or god(s)").

I personally believe that even Positive Atheism is a fairly well supportable position these days. 100% absolutely certainty is NOT the point of belief - you can reasonably believe something when it is not contradicted by the evidence and has reasonable supporting facts. For example, scientists generally believe that there are Black Holes even though they are far from absolutely proven to exist (as described by relativity) and there are many open questions.

In his paper "Am I An Atheist Or An Agnostic?" Bertrand Russell wrote:
Here there comes a practical question which has often troubled me. Whenever I go into a foreign country or a prison or any similar place they always ask me what is my religion.

I never know whether I should say "Agnostic" or whether I should say "Atheist". It is a very difficult question and I daresay that some of you have been troubled by it. As a philosopher, if I were speaking to a purely philosophic audience I should say that I ought to describe myself as an Agnostic, because I do not think that there is a conclusive argument by which one prove that there is not a God.

On the other hand, if I am to convey the right impression to the ordinary man in the street I think I ought to say that I am an Atheist, because when I say that I cannot prove that there is not a God, I ought to add equally that I cannot prove that there are not the Homeric gods.

None of us would seriously consider the possibility that all the gods of homer really exist, and yet if you were to set to work to give a logical demonstration that Zeus, Hera, Poseidon, and the rest of them did not exist you would find it an awful job. You could not get such proof.

Therefore, in regard to the Olympic gods, speaking to a purely philosophical audience, I would say that I am an Agnostic. But speaking popularly, I think that all of us would say in regard to those gods that we were Atheists. In regard to the Christian God, I should, I think, take exactly the same line.

From this, I think that in Russell's day a more positive atheism was the prevailing brand of atheism whereas today the majority base their position on the lack of evidence for theism.
I generally identify myself as Huxley-Agnostic these days but I do not believe in any gods and therefore I am, in that sense, atheistic and will sometimes use that term when discussing with less discerning company. But I have always disliked the idea of defining my position in opposition to theism as I don't place that much importance on it.

Certainly Agnostics (and many others) have pondered if we can even ask questions like "does god exist" or "what is the origin of the universe". Such things might be truly unknowable -- but I would want that claim to be demonstrated before I accept it as fact!

Monday, December 13, 2010

How Slow Can You Go (Light)?

It is a common misconception that light speed itself changes in a medium, what changes is the rate of PROPAGATION. It is not the photon that is slowed, it is only the propagation of information that is slowed (the photon is absorbed and re-emitted).

One way to understand the implication of relativity is to understand that spacetime is one thing and you have a constant velocity vector through this spacetime. And the absolute value of every velocity vector, in spacetime, is constant = 1.

So everything is always moving through spacetime at "the speed of light". But what happens is the direction of the velocity vector can be tilted more towards space dimensions or more in the time dimension.

An object at "rest" in space moves through time at a unit rate of 1 (consider units where c = 1). As the object starts to move through space the velocity vector is tilted slightly causing the object to move less through time and more through space.

There are other effects as well but that's a good summary that can help people understand the effects in a more natural way. It also explains why you can't go faster than light-you already are moving at 'lightspeed' through spacetime.


This is a purely speculative post, I just wanted to put some ideas down on 'paper' when I wrote this. A bit of brainstorming if you will. A possible flow-chart on how we move from observable, sensory data towards a model that represents knowledge.

Observation > Analysis > Categorization > Correlation > Inference > Elimination > Synthesis > Deduction > Confirmation > Knowledge

First, we make observations. These can come from external or internal sources (we can hear , feel , or think about something).

Our brain then analyzes the data, breaking it up into chunks and ultimately categorizes it (that is a cat, that is a dog, that is the word 'brain'). There are probably many layers of categorization, e.g., visual processing, language processing, etc.

We then make correlations with the data against previous data, looking for patterns which we draw inferences about. Many of those inferences will be wrong which begins the pruning process where we Eliminate as many fallacious and false inferences as possible.

Synthesis begins the process of putting things together from the inferences, thus creating hypotheses to be tested using more deductive forms of reasoning. This is, I suspect, the first time we reach the level of conscious thought in the process.

We then seek out Confirmation of our conclusions and when we get Confirmation we store that bit of information away as knowledge.

flagellum flagellum

Intelligent Design proponents originally claimed that the flagellum was "irreducibly complex". But there are, in fact, a vast array of flagellum and flagellum pre-cursors evident in nature so it is clearly not irreducibly complex. This claim is one of the best examples of the flaw in the entire approach of Intelligent Design which would ask that you stop looking any further for a natural explanation when in fact, there is a tremendous amount of knowledge hiding behind understanding the TRUE origin of the flagellum.

The flagellum of E. coli contains 40 proteins but only 23 of these proteins are common to other bacterial flagella. Furthermore, many of these proteins server other functions in the cell. For example: the hole used by the flagellum existed prior to use by the flagellum as a protein export portal.

Evolution: Reducible Complexity — The Case for Bacterial Flagella" is just one of many scientific papers on the resolution to this question.

See also, 24 Evolution Myths and Misconceptions

Thursday, December 9, 2010

Abiogenesis, Part I

Abiogenesis, Part I

This is more of a brain dump of what I have learned than anything else, so apologies if I ramble a bit.

I do not claim that science has all the answers here (this is an active area of research). But much like the early Church's stance on the Earth being the center of the universe, abiogenesis research has broken claim after claim made by the creationists about how it "must be" and what science has been able to piece together is a compelling series of events. It takes absolutely no faith to see the incredible progress that has been made in this field over the past 55 years (that is, IF the person bothers to actually investigate this field of study).

The original timescale involved was ~0.7B years in a lab the size of the entire Earth (possibly the solar system) so we have a lot of catching up to do in understanding the most likely pathways that the early Earth could have taken in creating the first organic "life" (some chemical structure capable of self-replication, mutation, and natural selection).

If creationists want to prove that abiogenesis is impossible then only need to find some specific STEP that absolutely cannot have happened naturally. Not a fallacious statistical argument saying that it's just too improbable to believe. An actual chemical combination that cannot possibly happen in nature and the specific, scientific reasons why.

So, what evidence do we have in support of a natural abiogenesis?

Here is a good review for starters: How life began on Earth: a status report

Remember that the DNA/RNA genetic system we have today is just what things have evolved into, don't assume they are required to kick start the process. What scientists generally believe happened was that there was a boot strapping process leading up to that first strand of self-replicating material (be it RNA/DNA or something else).

Peptide chains are simply "shorter" chains of amino acids (aka proteins). These naturally formed chains can perform functions, they can "store information", they change over time, and they can reproduce (e.g., see prion research). Those are all the things required for "evolutionary" processes to work over time.

(1) First of all, Jeffrey Bada's experiment showed once again that a wealth of organic chemistry and amino acids are generated naturally in the early Earth environment. There is also the later Miller experiment about organic chemistry in icy conditions (so it could be that an ebbing between warmer and colder conditions are required). The original Miller-Urey experiment was validly criticised for an inaccurate starting mixture, but even later versions of that experiment had corrected those problems.

(2) We are now also aware of a large number of exogenous sources of organic precursors (IDPs, Meteorites, Asteroids, Comets)

Murchison meteorite: 14,000 specific compounds, including 70 amino acids, were identified...tip of the iceberg

(3) This soup can include shorter fatty-acid chains (created in geothermal vents on the clay walls) which under certain Ph conditions naturally form into protective vesicles, these vesicles can also divide under mechanical conditions AND they tend to combine with smaller vesicles into larger ones such that the contents are merged as well -- but tend to only grow so large before undergoing mechanical division.

(4) Unlike modern cell walls, these primitive vesicles are porous which allows building blocks in, which combine with other components and then are too large to escape

(5) Eventually, some of the peptide chains prove beneficial to the fatty-acid vesicle structures.

(6) We know that some peptide chains are self-replicating -- by setting up even a simple peptide chain which can self-replicate we set the stage for evolutionary processes over time to work. And we know that some single RNA strands have been found to be capable of replication as well.

(7) We also know that the Qb virus can reproduce without a cell if the chemical environment is available.

See The Fifth Miracle by Paul Davies (excerpt)

(8) Finally, we're just now at the stage where we can start building complex life from scratch directly in the lab:

There are, of course, many open questions, nobody is denying that -- but they are just questions and there is absolutely no indication that any of these problems are intractable (including ribose and chirality). Try Google Scholar: abiogenesis ribose

There are 100's of more research papers on the subject, this is just barely scratching the surface.

One of the big problems with religious belief structures which claim revelatory knowledge from God is that it blocks people from even attempting to understand what is true. Where in the bible does it explain the mechanism that God supposedly used to create the universe and to create life? If it doesn't speak to the how, then how do you claim to know that organic life could not have happened as part of the natural course of the universal laws which ultimately drive everything?

You should investigate further: Dr M Reza Ghadiri and Dr Jack Szostak

How do you get to RNA without the mechanisms in place today to create it?

That is now at least a half-solved problem, See Dr. Sutherland's research:

the chemicals naturally formed a compound that is half-sugar and half-base. When another half-sugar and half-base are added, the RNA nucleotide called ribocytidine phosphate emerges. A second nucleotide is created if ultraviolet light is shined on the mixture. Dr. Sutherland said he had not yet found natural ways to generate the other two types of nucleotides found in RNA molecules, but synthesis of the first two was thought to be harder to achieve. If all four nucleotides formed naturally, they would zip together easily to form an RNA molecule with a backbone of alternating sugar and phosphate groups.

More resources to read:


Tuesday, December 7, 2010

Intercessory Prayer

Long-Awaited Medical Study Questions the Power of Prayer: If you know you're being prayed for you sometimes do worse.

The studies on Intercessory prayer (the type of prayer where you asking for your 'higher power' to intercede with human affairs on your behalf) have been fairly inconclusive in the past but as better testing methodology is brought to bear on the question the studies tend to actually show negative effects when the person is aware that others are praying for them. The hypothesis is that their failure to get better causes some depression and possibly a weakening of the natural immune system.

This is a surprising result which pretty strongly shows that, not only is intercessory prayer ineffective, but that the wrong kinds of wishful thinking are actually harmful as well.

I think that understanding this aspect of the failure of prayer is an important step in coming to grips with reality and rejecting millennia old superstitions.

The second stage of understanding comes when you can stop seeing every good thing that happens as a result of God's actions while ignoring every bad thing that happens. The Chilean miners are a perfect result of this blindness in action. Yes, it is wonderful that the Chilean miners were able to be pulled out, but what about the dozens of other people in the mining profession that died in the line of duty during that same process? And why trap them in the first place?

If you look more closely you can see that in every single one of these cases there is always a natural explanation (and in future articles I will discuss why natural explanations do not give credit to a theistic, personal God -- as we already see is the case of intercessory prayer).

Scientific Literature: neurobiological origins of primitive religion

One of the things I hope to do in this blog is expose people to more of the scientific literature.

For starters, I offer "The neurobiological origins of primitive religion: Implications for comparative mythology" by Steve Farmer, Ph.D. There is a tremendous bibliography at the end of the paper with many hours of reading for interested persons but I will be discussing some of the finer points in more detail in the future. Please at least try to give a read, you'll probably be surprised at how much you can at least get the gist of, even if you don't understand every point. And that's ok -- learning is a life long process.

One of things I hope that readers new to scientific literature will do is stop and think for a moment about just how many scientific papers there are (literally millions of them) and what a herculean task it would be to truly become an expert in just one field of inquiry. There is so much knowledge and information out there, it is not reasonable to expect any one person to understand all of it, indeed, it takes about 6 billion of us to understand only a good fraction of it. This is why arguments from ignorance are just not acceptable (and no, making an argument from ignorance doesn't mean that YOU are ignorant, it means that you are basing your viewpoint on an absence of knowledge and evidence).

Think about that when you ponder how it all began and how life started, especially if you are tempted to think "There just MUST be a God, all this couldn't just happen". Just because you don't understand something, and even if no person in the entire world understands it, that doesn't mean that there has to be a supernatural explanation for it! And also remember that by proposing a supernatural God as the explanation for how our Universe began you ponder the existence of something infinitely more complex "just" existing than our Universe.

And there is absolutely much that science does not yet understand about the subatomic world, our world, and the cosmos. But while we may not know some things with certainty, we do have many clues, hints, and hypotheses.

Think about all the things we have learned over the years about our universe. We used to believe the stars were fixed into the "firmament" of the heavens, we had no idea that they were stars much like our own Sun and we had no idea that some of those stars were ENTIRE galaxies of stars. And we had no idea that there was a vast and rich structure to the universe. And we have also learned much about the extremely tiny. First discovering molecules and then the elements that compose them, and then breaking into the details of the Atom and now even far deep into the structures of the subatomic world. We've learned much about Chemistry, especially organic Chemistry. We've learned about how simple gases and liquids (with the addition of some energy from sun, lightening, volcanoes, thermal vents, and even chemical sources) can drive those elements into complex organic molecules. We even know now how almost every single molecule that is important for the beginning of what we call life (which seems to require some kind of self-replicating structure at a very minimum; although we now struggle to draw any sharp line between life and so-called non-life -- we have many strange forms which fall in the gap in between).

So I ask that you suspend belief in a supernatural God for a moment and ponder just how amazing and wondrous the ACTUAL Universe that we experience every day is. It is both breathtaking and terrifying. It has created animals and Humans with the capacity for love and sacrifice but it is also cruel beyond measure and unmoved by Human emotions (unless WE take action). The authors of the Bible were certainly correct to express the idea that we should be thankful for each and every day because every moment could truly be our last - and I think that they were more acutely aware of that than we tend to be today.

To save the world requires faith and courage: faith in reason, and courage to proclaim what reason shows to be true. ~ Bertrand Russell

Some research tools you may not be aware of:

What is Millenarian Iconoclasm?

An Introduction

Millenarianism is the belief in a coming major transformation of society (usually on a 1000 year cycle but not exclusively). Christianity is a millenarian belief structure that is, in theory, looking for the return of Christ. They have, at times, believed this so strongly that they were willing to put others to torture and even death in order to "save them" before this return. That kind of extremism is obviously exceedingly harmful to society. And I somewhat apologize for the Christian focus that will undoubtedly unfold - but it is the counter force that I know the best. But fear not, dear Reader, for my comments generally apply to all the major and minor religions of the world. Please do not take my words to apply only to Christian beliefs, where applicable please also take similar offense if you belong to some other religion.

Iconoclasm on the other hand is the destruction of the icons of religion. In this case I mean it STRICTLY in the realm of IDEAS. I absolutely reject ANY attempt to outlaw religion. I absolutely reject ANY attempt to physically harm religious people OR property.

So, my goal is to tear down some of these millenarian ideas that lead to false beliefs and I hope the reader will comment and further my own education in such matters. I plan for this to be a far ranging blog as this subject touches on every aspect of our lives in some way or another. I will be rude, out-spoken, rambling and even wrong at times. I will have typos and grammatical errors (in my defense my brain is just not wired for English, I have always struggled with it, but feel free to extract amusement where you can find it). But hopefully I can be articulate enough to get my points across.

I do not hide the fact that I am fairly liberal-minded (I suppose I have the "novelty" seeking gene) although I subscribe to no specific ideology outside of Thomas Huxley's brand of Agnosticism (which means to say that I value Reason and Evidence). I reject the wishy-washy alternative brands of agnosticism that sloshed around after Huxley's passing. But I am not a Democrat nor am I a Republican. I am a thinking human being capable of making my own judgments based on the things I value.

I will attempt to be extremely clear on where I place value so that you can assess not just my ideas on any given subject but perhaps better understand the motivations behind them. I have a hope that liberals and conservatives alike place fairly similar values on most things but we just disagree on a path that will get us there (which I believe are due to differences in Secondary values, not primary values). I am a strong constitutionalist. I am FOR small government (especially when it comes to someones Personal life). But I am also for the right solutions for the right problems. One approach does not work for all types of problems, ideologists seem to forget that.

I hope that we all want life, liberty and the pursuit of happiness.

Agnosticism will be a recurring theme because I feel that many people who call themselves an Agnostic (noun) really mean that they are agnostic (adjective) in their beliefs. These are two Vastly different positions and I will attempt to distinguish them and support my position on Agnosticism as a Positive belief in Reason and Evidence.

I am not afraid of the term atheist and, similar to Bertrand Russell, I tend to identify myself as an Atheist outside of certain groups (those who have read something on Philosophy, Huxley, Russell, etc) and can make the finer distinction between being an Atheist because you don't believe in a god and being Agnostic because you believe in Reason and Evidence. I don't want to define myself relative to something I don't accept as an ontologically valid position. I don't call myself an aTeapotist either. There are indeed an infinite number positions that I lack, so, to me, it is better to list ones I value (Reason + Evidence) than the ones I do not.

So count me among those that lack a belief in any theistic god.

Please set aside your preconceived notions of Agnosticism for the moment and try to understand what I mean by the term:

Agnosticism, in fact, is not a creed, but a method, the essence of which lies in the rigorous application of a single principle. That principle is of great antiquity; it is as old as Socrates; as old as the writer who said, "Try all things, hold fast by that which is good" it is the foundation of the Reformation, which simply illustrated the axiom that every man should be able to give a reason for the faith that is in him; it is the great principle of Descartes; it is the fundamental axiom of modern science.

Positively the principle may be expressed: In matters of the intellect, follow your reason as far as it will take you, without regard to any other consideration. And negatively: In matters of the intellect do not pretend that conclusions are certain which are not demonstrated or demonstrable. That I take to be the agnostic faith, which if a man keep whole and undefiled, he shall not be ashamed to look the universe in the face, whatever the future may have in store for him.

Huxley coined a word for his position: "agnostic." Although this word is sometimes defined (as in the Oxford English Dictionary) as relating to the Unknowable, Huxley denied having that as source of the word.