What would constitute evidence for God?

As a so-called New Atheist, one of the cornerstones of my worldview is that evidence is absolutely key in coming to any sort of important conclusion. To believe otherwise is to believe dangerously, at least when it comes to anything important. (Our belief that, for instance, a bridge isn’t going to collapse beneath us is an assumption, and so I exclude such beliefs when I use the word “important”.) That is, to believe something without evidence is to believe on faith. And, of course, that is entirely random; faith is not a method of belief by any means, but rather an arbitrary basis that can lead a person to absolutely any conclusion, including abortion clinic bombings, giving a homeless person a dollar, and committing war atrocities. In short, faith is the worst thing the world has ever seen.

So all that said, I reject faith fully. This is why I call myself an atheist: I am without any form of theism because there is no evidence in its favor. Indeed, there is no good evidence in favor of even deism. (I’m also an anti-theist, but for different reasons.) But I’ve often wondered, what sort of evidence would I accept as pointing towards a knowing, intervening creator? I recall Jerry Coyne and PZ Myers having a back and forth prior towards everyone in the New Atheist movement, including Coyne, shunning Myers for various reasons, so it was a civil exchange, but I don’t recall the details. All I remember now is that Coyne said there is possible evidence whereas Myers took the faith-based position in saying that no evidence could convince him. I won’t bother finding those posts since they aren’t especially relevant here. What is relevant is this B-level Onion article:

Researchers at Harvard University announced today that they have found what appears to be a message from God written inside the human genome.

In a little-explored section of non-coding DNA, a team of top geneticists discovered a 22-word snippet of ancient Aramaic in which God confirms his existence and his role in creating life on Earth.

The stunning finding represents nearly irrefutable evidence of God’s existence and his role in creating the process of evolution by natural selection.

The message was discovered when researchers noticed strange mathematical patterns appearing within a certain section of the genome.

“Hello my children. This is Yahweh, the one true Lord. You have found creation’s secret. Now share it peacefully with the world.

Again, this is an article in the style of TheOnion, a tongue-in-cheek piece meant to be funny. It comes from The Daily Currant, which has had some success in fooling people with its articles (not that that was their intention), but I’m not a big fan.

At any rate, this is a perfect example of what it would take to show me evidence God exists. It isn’t that if we find there are no hidden messages in our DNA we’ve falsified the God hypothesis. No, rather it’s that something like this would be strong evidence for the existence of a creator, I think. The odds that natural selection would, by chance, produce something so precise as this is very, very small.

Of course, let me take this moment to point out that natural selection is not actually a chance process. I only describe it as such in the above instance because natural selection acts to increase an organism’s ability to survive – it does not act to produce linguistic codes that translate into multiple sentences in order to form a coherent message. That is, natural selection is not a chance process, but for it to produce a lengthy message would be insanely freak chance since no part of its regular process leads to anything like messages. That old creationist chestnut about a tornado producing a 747 would actually have some applicability here.

So there we have it. There certainly is possible evidence for the existence of God, and I think this brings us to an important conclusion: God is a refutable hypothesis that can be subjected to the rigors of science just like anything else postulated to exist and/or have an affect on the Universe. The problem for theists is that they’ve never been able to present a test their particular, cultural god could pass.

More on the destruction of the Fourth Amendment

In case you missed it: The Supreme Court has ruled that the police can take a DNA sample from a person without probable cause, without a warrant, and without a conviction. So long as a person has been arrested for a felony, he is subject to an intrusion upon his body. It’s an overt violation of the Fourth Amendment that, given the specific arguments of the Court, will undoubtedly lead to DNA sampling for absolutely any crime for which one may be arrested, including jaywalking or running a red light.

There are incredible problems with all this. First, unlike with fingerprinting, the point of DNA sampling is not to identify a suspect. The sole point is to solve other crimes. This is the explicit intent of the state legislatures that have passed such laws. It is exactly the same as if a state legislature declared that a person’s home was automatically subject to being searched upon that person’s arrest. The police are now allowed to go on horseshit fishing expeditions.

Second, while there are often restrictions placed upon what the police are allowed to do with your DNA, that can be changed on a whim by a given state’s governing body. Moreover, do you trust the government to keep its blinders on? If you had a 100 page journal and a judge told the prosecution that it could read it but it had to stick to pages 14-17, do you really think that would happen? Of course not. Pages 1-13 and 18-100 would be absolutely scoured, regardless whether or not the information found therein could be used directly against you.

The only civil liberties decisions of the past 100 years more important than this one are Brown v Board of Education and Loving v Virginia. Every American is forever subject to suspicionless searches and seizures, less the states pass a sorely needed amendment to the constitution.

Greatest Scientific Events of the 20th Century

I’ve recently been kicking around my personal list of what might constitute the greatest scientific achievements of the 20th century. There are so many things to consider and the list is necessarily so subjective that I’m not going to pretend to be giving a highly considered, thoroughly vetted list. I have put thought into this, but there will surely be dozens of examples I could easily find myself reconsidering if brought to my attention.

5) The Expanding Universe

In 1929 Edwin Hubble made the discovery that the Universe is actually expanding. This had direct implications throughout physics and astronomy. It was the reason Einstein called his cosmological constant “the biggest blunder” of his life.

Hubble used Cepheids, commonly known as “standard candles”, to get the relative distances of various galaxies. He then plotted this against their known redshifts. What he discovered was that these redshifts increased as a linear function of distance. That is, the Universe was uniformly expanding. In 1998 it would be discovered that this expansion was actually increasing in speed, contrary to expectations.

4) Cosmic Microwave Background Radiation

In the early 60′s, Robert Dickie was searching for the radiation that should have been left over if the Big Bang model was correct. He had assembled a team to look for what science had predicted, but he was beaten to the punch by Arno Penzias and Robert Wilson. And they weren’t even looking for the CMB.

Using a Dickie radiometer (designed by Dickie himself), Penzias and Wilson happened upon an interfering sort of fuzz while doing other research in 1965. They assumed it was coming from some nearby source, perhaps New York. After ruling out all the obvious possibilities (including pigeons), they were unable to conclude precisely what it was. They published a paper describing their results, which Dickie then used to correctly interpret as the discovery of the CMB. Penzias and Wilson won Nobel Prizes in 1978.

3) The Structure of DNA

There’s the saying that nothing in biology makes sense except in the light of evolution. This is crucially true, but the essence of the saying can be broaden to another area in biology: nothing in biology makes sense except in the light of the structure of DNA as discovered by James Watson and Francis Crick in 1953. I dare say, aside from Darwin’s discovery of how evolution happens, the discovery of the molecular shape of DNA has been the most significant event in all of biology. Interestingly, it shouldn’t have happened the way it did. Watson and Crick were one of several teams studying the structure. One member of another team, Rosalind Franklin, had actually produced accurate images of the molecule on her own, but determined she wasn’t ready to present her findings quite yet. Her teammate, Maurice Wilkins, would have none of that and decided to show her images – covertly – to Watson and Crick. They almost immediately recognized its significance (and to an extent Franklin hadn’t quite grasped): DNA formed as a double-helix with a uniform width all the way up its length.

Franklin’s work has unfortunately been drowned in history because of Wilkins’ betrayal, not to mention the fact that she is a woman in science – and that’s no easy task (especially in 1953).

Watson, Crick, and Wilkins received their Nobel Prizes in 1962 – Franklin got nothing.

2) General Theory of Relativity

Albert Einstein described his general theory of relativity in 1915, updating Newton’s ideas on gravity. He presented one of the most brilliant ideas man has ever had, fundamentally changing our understanding of how the Universe works. His science knocked down the notion of absolutes within spacetime, indeed, even helping to define the term. (Credit does not go directly to him, but his theory of special relativity was key in the development of the concept, and general relativity is an expansion of special relativity.)

Einstein received his Nobel Prize in 1922 (for 1921). (It was given for work as it specifically pertained to his special theory of relativity, not his theory of general relativity.)

1) Life on Mars

For the life of me, I don’t understand why no one seems to care about this. NASA recently announced it had reexamined a meteorite discovered in 1984 and confirmed that it contained within it microbial life which did not originate on Earth. While that may seem unfitting for a post about 20th century discoveries and events, the meteorite was originally described in 1996 to much fanfare. Over time a quiet consensus grew that the shapes in the rock could be formed via geological processes. The recent analysis blew those concerns out of the water.

RNAi

RNAi is an arrestingly interesting little mechanism for protecting the health of cells. The “i” stands for interference, and with good reason. RNAi is made up of a series of molecules which work to detect and destroy possible viruses and RNA which could be viruses.

It was first detected in 1986 when an attempt was made to make a really, really purple flower. The reason was purely for aesthetics, but it would prove to be far more important.

Knowing the gene which coded for purple pigmentation in petunias, geneticists made the logical conclusion and figured adding a bunch of those genes to the flowers would increase the depth of purple coloring in them. But as it turned out, they were wrong. In fact, they were remarkably wrong. Instead of deep purple flowers, they produced white flowers. Not a hint of purple anywhere.

No one had an answer to why would be. It took 12 years until researchers came up with the answer (and another 8 until they were awarded a Nobel Prize).

When viruses invade a cell, they ‘seek’ to make copies of themselves by utilizing the available DNA source. Post-transcription, this comes out with a funny shape due to the RNA making a mirror image of itself. The RNAi then recognizes this strange shape and destroys it with dicers. But it doesn’t stop there. Any sequence which comes out of the nucleus thereafter is also destroyed. This prevents any of the viruses (hopefully) from being translated and replicating (thus exploding out of the cell and infecting other cells).

Something similar happened when the geneticists tried making the super purple flowers. There wasn’t a mirror-image RNA sequence, but there was a funny sort of shape created by all the extra purple pigmentation genes. The RNAi recognized this as a potential virus and began destroying it. All of it. This meant there were no genes for purple getting translated into proteins.

Example petunia plants in which genes for pigmentation are silenced by RNAi. (http://en.wikipedia.org/wiki/Rnai)

Example petunia plants in which genes for pigmentation are silenced by RNAi. (http://en.wikipedia.org/wiki/Rnai)

So far this is pretty exciting stuff. It’s a post-transcriptional defense mechanism against viruses no one ever knew existed. But it has so much more potential than just as a passing curiosity.

Think about it. If RNAi can essentially turn off genes by destroying them through a sort of sequence-detection, then what stops it from curing diseases? This discovery has the serious potential to cure all the major ailments facing the world today: AIDS, cancer, Alzheimer’s. There has already been success in treating macular degeneration. This is a disease where too many blood vessels are growing in the eye. It damages the retina over time and makes vision majorly cloudy and blurry. There are simply too many genes for blood vessels being produced. But one way to stop this disease is to stop that blood vessel growth. To achieve this, a patient is given an injection which contains a copy of the gene with its mirror image (two mirror strands of DNA). The RNAi detects this misshape and destroys it. It then destroys all other likewise sequences. The same principle could be applied to any number of diseases.

There is an excellent NOVA video on RNAi which can be viewed here. It’s certainly worth watching (and only 15 minutes long).

New information

I’ve posted about “new information” in the past, but I recently wrote this for some friends and figured it may as well go up here, too.

~~~~~
This is from a YouTube video by some dishonest creationists who poorly edited a video to make it look like Richard Dawkins couldn’t answer a question. It doesn’t deserve to be linked.

“[Is there] an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome?”

The answer is yes. But I won’t get to the heart of the question right away. It needs explaining.

A definition of “information” is drastically needed here. It’s a term that doesn’t really mean anything in the given context. However, we can ascribe it some definition which is useful. My best proposition is that it can mean DNA itself (nucleic acids), amino acids, or genes. I’ll tackle DNA first.

Our genetic code consists of four ‘letters’, A, C, T, and G (or adenine, cytosine, thymine, and guanine). These four letters are mixed in a huge number of ways in order to form amino acids. It is amino acids which compose our genes. But let’s slow down.

An amino acid is composed of 3 letters. Let’s say we have CGU. That makes arginine. If we replace that final letter with, say, another “C”, we have CGC. As it happens, that still gives us arginine. Different letter combinations can make the same amino acid. When a mutation occurs which does this, it’s called a silent mutation. It’s neutral and natural selection is blind to it.

Now let’s say we change that middle “G” to an “A”.That gives us CAC, or histidine. This is a completely different amino acid. It’s presence in a given gene in place of arginine can have potentially huge consequences. This single letter substitution is called a missense mutation. (It is also called a point mutation because just one letter was changed; the same applies to the arginine example.)

So as should be clear, single letters of DNA can be considered information because they can have profound effects on genes, which in turn affect how proteins are made. However, we have another avenue.

An amino acid can be considered information because it is more directly responsible for the changes to how a protein operates than a simple letter. Personally, I prefer this option the least, but I digress.

Genes are composed of chains of amino acids. Some can be quite short while others range into the hundreds, even thousands. Recall how an amino acid is composed of a series of 3 letters of DNA. That means those letters go back to back to back to back to etc…, each set of 3 making an amino acid. After one triplet, there’s another. And another. Each “another” is an amino acid. (Eventually, a gene can be defined, at least one way, by identifying where the stop codons are – triplets which tell the gene that it is at its end, thus releasing the amino acid chain.)

But if we’re going to call amino acids information, we may as well go a step further and just say genes. And this gets more to the heart of the question. Genes essentially determine what protein will be made (epigenetic or environmental factors are important, but there’s no need for those here). A mutated gene is mutated information, at least in a sense. So how can an evolutionary process be seen to increase the information in a given genome?

It’s actually pretty simple. DNA is far from perfect. It has incredibly high fidelity, meaning it makes few copying errors, but it isn’t perfect. That’s one way we get mutations. Another thing we can get is extra copies of genes. There are a myriad of ways this can occur which I will not discuss here. But it does occur all the time. In one recent text, I read of 12 copies of a gene for seeing green in relation to eyesight.

So what does it mean to have too many copies of a gene? Sometimes it can mean a lot. A lot of the time, though, it doesn’t have to mean too much, such as with the aforementioned case. But what happens to all those extra copies in the next generation, especially if they have no real world (phenotypic) results? They are not subject to the pressures of natural selection. They are free to mutate in whatever way they ‘please’. This gives these genes a huge range to become useful in other ways. In this case, they may affect vision acuity or color sharpness and that may be an advantage.

This is, for all intents and purposes, new information.

A gene gets duplicated. It mutates. It becomes useful, by chance, in some other way. It is subject to the pressures of natural selection. For that reason, it is maintained in the gene pool. Those with this gene have increased the size of the ‘information’ in their genomes.

How inviting

I have been cordially invited to attend a viewing of Expelled at the University of Maine at Augusta campus on Tuesday, April 7 at 5:30 p.m. until 8:00 p.m. (You must be logged into Facebook to view.) Here is the event description.

We will be watching “Expelled: No Intelligence Allowed”

The debate over evolution is confusing and to some, bewildering: “Wasn’t this all settled years ago?” The answer to that question is equally troubling: “Yes…and no.”

The truth is that a staggering amount of new scientific evidence has emerged since Darwin’s 150-year-old theory of life’s origins. Darwin had no concept of DNA, microbiology, The Big Bang, Einstein’s Theory of Relativity or of the human genome.

Then after we will be hanging out and discussing it

For more information on this move check out http://www.expelledthemovie.com/aboutthemovie.php

Amazing. First, they still think evolution is up for debate. Creationist ignorance check point one. Next, they call it a theory of “life’s origins”. How does evolution imply that at all? Creationist ignorance check point two. Then, of course, we get unrelated theories in physics. That’s three. And they could have hit so many more. Where’s the second law of thermodynamics? The ‘natural selection if a tautology’ bs? Come on! Amateurs!

I’m rather undecided about attending this. I am certainly not going to see the movie. I saw it once and that was torture enough, but I will be on campus around the time they will be having their discussion (and by this I mean ‘spreading of disinformation’). Perhaps I can lend my voice to be sure they don’t think this somehow supports intelligent design. Yes, that’s right. The person with whom I originally saw the movie (a young creationist minister) said he “loved that there was a lot of great science”. Of course, there is no science behind intelligent design, but the movie doesn’t even make an attempt to discuss science. It’s wholly about how there’s a big, mean conspiracy to keep intelligent design advocates down and out because “Big Science” is so evil. Oh, and evolution caused the holocaust. Can’t forget that gem.

I’ll keep you updated.

Origins

It’s only a matter of time until something very much like life is created in the lab. Until then, scientists are still working on how it happened, nearly 4 billion years ago. The research is promising.

With the aid of a straightforward experiment, researchers have provided some clues to one of biology’s most complex questions: how ancient organic molecules came together to form the basis of life.

Specifically, this study demonstrated how ancient RNA joined together to reach a biologically relevant length.

RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn’t have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other).

Ernesto Di Mauro and colleagues examined if there was some mechanism to overcome this thermodynamic barrier, by incubating short RNA fragments in water of different temperatures and pH.

They found that under favorable conditions (acidic environment and temperature lower than 70 degrees Celsius), pieces ranging from 10-24 in length could naturally fuse into larger fragments, generally within 14 hours.

The RNA fragments came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size (larger is better, though efficiency drops again after reaching around 100) and the similarity of the fragment sequences.

The researchers note that this spontaneous fusing, or ligation, would [be] a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes.

Enzymes basically make things go faster. That means that reactions that are caused by a particular protein (say, lactase breaking down lactose into its constituents – if you can’t do this or do it poorly, you’re lactose intolerant) can happen anyway, but they will happen far more slowly. In some instances, they essentially will not happen except by tremendous stroke of luck (though, again, the potential is always there).

What’s particularly interesting to note here is that it is very difficult to say what the pH balance of different bodies of water would be on an early Earth. It is entirely plausible that acidic levels would be higher, leading to the ability of these RNA molecules to form 3D shapes. And, of course, because biology is very much dependent on shape, these formations could act as proteins, if not plainly be defined as such. By doing this, a rudimentary evolution could begin to take place. We may not define these replicators as being life, but they would hold many of its characteristics – taking in energy and out, being subject to at least a form of natural selection.

Eyespots

History recently aired a series called “Evolve” which focused upon various aspects of evolution: wings, sex, guts, etc. But the most interesting episode was probably the one on eyes. It’s pretty clear they started out with eyes because of all the hub-bub made by creationists who find this organ to be too complex to have evolved by blind chance (what about the brain?). Natural selection is not chance (though it is blind – half credit), but such a misconception is one of the reasons eyes needed to be a starting point.

What History didn’t do, however, was get down to the cellular level of eye evolution. They may have touched upon photoreceptive cells, and that’s technically the cellular level, I suppose, but it overlooks an important aspect of evolution: everything which evolved today began its evolution (eventually) at the cellular level. So it is to my delight that I came across a Wikipedia article on eyespots.

Eyespot apparatus of euglena

Eyespots are a lot like they sound they are. They’re photoreceptive areas found in some plants cells (algae) and even in single celled organisms such as the euglena featured above. These are simply areas which cause a reaction to light – it becomes too bright, you may be too close to the surface. Swim away.

The advantage should be quite clear. The ability to detect light – not shape, size, dimension, or detail – gives an organism a lot of information about its environment. Specifically, History did address the eyespots of certain squids. These squids, only having nervous systems (no brains), would simply go into a sort of lull when coming near a certain wave length of light. As it not-so-coincidentally happens, that wave length corresponds with the wave length common near the food source of these squids.

Here’s the interesting kicker for which I think everyone should perk up: the origin of these eyespots works upon signal transduction, which is initiated by enzymes. This is what happens in every cell everywhere. Enzymes catalyze various things within cells. Lactase, for example, catalyzes lactose into galactose and glucose monomers – you drink milk, proteins (lactase) in your body will break it down into its constituents. It’s basic biology.

So how do new enzymes arise that can cause the formation of eyespots? This is a matter of a mutation within the DNA of a cell. Some “letter” of DNA is changed through some sort of error in copying. It happens all the time. You have 50-100 mutations in you right now (most, if not all, are probably neutral). DNA replication isn’t perfect. So a simply mutation can quite easily code for a new enzyme, which can cause the formation of an eyespot – the beginning of the eye. A slow, cumulative building through, perhaps, further mutation combined with the non-random action of natural selection can (and has separately over 40 times) evolve a complex eye worthy of fighting on the evolutionary stage of life.

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