Wait...what?

Where do I even begin with this one?



You know what? I'm just going to let this picture do the talking.

Gee, why didn't I think of that?

Courtesy of theologian extraordinaire Agonaces of Susa from fundie megasite christianforums.com:

"According to mainstream scientists and chronologists, based on uranium-lead series radiometric dating of moon rocks the Earth is only 4.6 billion years old therefore years did not exist before that because the Earth wasn't orbiting the Sun." [emphasis added]

  I really wish I had a witty retort here, but I'm dumbstruck at the sheer ignorance.

Nephy's Nylonase Nonsense

Oh, Nephilimfree, you've done it again. You went and dragged genetics through the mud again, and I won't stand for it.

At this point, having dedicated a few posts to his inane ramblings, debunking Nephy's claims is beginning to feel like picking on the fat kid at the playground. He's a slow, lumbering target, and all the other kids on the playground keep picking on him because he's easy prey. But Nephy is so ripe with nonsense, so overflowing with vacuous crap like a bountiful cornucopia of bullshit, that it's hard to resist tearing his arguments apart when I'm looking for something to write about. And his silly website [Edit: 06/11/11: Looks like Nephy has let his registration of his domain lapse, so that link doesn't work any more. I tried to find an archived version, but had no luck] has no shortage of fodder for a creationist asskicking.

This week, I took a look at this article he wrote about the enzyme nylonase. You've probably heard about nylonase before, as it is often given as a great example of an evolutionary adaptation that has occurred in recent history. In 1975, a team of researchers from Osaka University in Japan got the idea to try and culture sludge obtained from the waste water outside of nylon factories¹. The samples they collected were used as inocula, and added to cultures which contained a form of nylon (6-aminohexanoic acid cyclic dimer) as the sole carbon and nitrogen source. Any bacteria that grew would have to rely on metabolizing nylon to survive. And grow they did. They designated the strain as KI72, and after isolating the bacteria, they identified it as a strain of Achromobacter guttatus, although later work by the same team reclassified the species as a strain of Flavobacterium². A few years later, the researchers identified two novel enzymes which allow the bacterium to metabolize nylon: 6-aminohexanoic acid cyclic dimer hydrolase and 6-aminohexanoixc linear oligomer hydrolase (6-AHA CDH and 6-AHA LOH, respectively)^3,4. Since nylon production began in the 1930s, these enzymes had to have originated in the time since then. After all, it doesn't make much sense for a bacterium to  have produced enzymes to specifically degrade nylon before nylon itself was invented. These genes, then, represent an example of a novel adaptation arising outside of the lab and within the past century.

But Nephy disagrees. He states, 

"Because the bacteria encountered nylon and developed an ability to digest it does not provide evidence of any kind of evolutionary change. This ability does not effect the form and structure (morphology) of the bacteria by introducing any new structural feature, nor does it transform any existing structural feature of the bacteria into a new kind of structure with a new physiological function."

Two paragraphs in, and he's already run into a major problem. He seems to have this odd idea that unless a change results in gross morphological alterations, it cannot be an evolutionary change. He simply discredits novel biochemical adaptation out of hand without any sort of justification. He simply wishes to define evolution as changes in "form and structure" and ONLY changes in "form and structure" - any other kind of change he refuses to acknowledge as evolutionary change. In essence, he's defining evolution in his own incredibly narrow terms, so that any actual evolutionary change can be shrugged off as "not evolution". If we were to narrowly define creationism as "the spontaneous formation of aardvarks from forest detritus", it would be pretty easy to discredit, too.

But beyond that, it is simply silly to only accept large changes in morphology as the only kind of evolutionary change. Morphological alterations cannot occur all at once. Any modification to an organism's body plan would require many not-so-obvious biochemical changes to occur first - the very type of changes that Nephy does not accept as "evolution". Evolution can only work with what it has available. No organism is going to mutate and grow wings de novo all in one shot, even if it would be advantageous. Such changes would require modifying the existing body plan, and this would require extensive biochemical changes to happen first.

Nevertheless, the discovery of novel nylon-degrading enzymes is indisputable. Musing over the origins of these enzymes, Nephy declares that these proteins, or any protein, could not have simply evolved. No, he says, statistical analysis says otherwise:

"The field of sicence [sic] called Statistical Ananlysis [sic] which is employed to determine probability in various fields of science, has determined that the formation of proteins by random molecular interactions is on the order of 10^950, which is 1 to a number for which no name exists; a number greater than all of the paticles [sic] of matter in the speculated universe. In other words, according to science itself, the chance of a single, medium-sized protien [sic] arising by purely materialistic molecular interactions is considered impossible to science because it is considered impossible times impossible times impossible. The evolutionist would have you believe that random mutation is capable of producing novel protiens [sic] which have specific function, but this is not only unfounded but exceedingly irrational."

This is a typical creationist talking point: whipping out statistics to churn out large numbers and proclaim "See! It's statistically impossible for evolution to occur!"  It is also typical, as Nephy demonstrates quite well, for creationists not to cite the source of these statistical calculations. The problem with Nephy's argument is that he does not take into account the process of selection during evolution. Forming a protein "randomly" and all at once is incredibly unlikely (though not entirely impossible), but if you factor selection into the equation, it becomes an incredibly likely phenomenon. Richard Dawkins illustrates this beautifully in his book The Blind Watchmaker, where he likens evolution to monkeys banging away at typewriters. If you were to wait for a monkey to type out the sentence "Methinks it is like a weasel", you'd be waiting for eons for it to "randomly" happen. But suppose you were to use cumulative selection to pick and keep the letters that work. Dawkins wrote a computer program to do just this (as computer programs are much cheaper and easier to work with than hordes of monkeys). Starting with a string of gibberish and then changing one letter per generation, the computer program "evolved" the correct sentence is about 40 generations⁵. It took only a few minutes for the computer program to complete this task, whereas single-step selection (waiting for the correct sentence to happen randomly, and all at once) would have taken the computer "a million million million million million years"⁶. Obviously, selection gets past the staggering statistical improbability that creationists argue.

But Nephy continues. He tells us that it was discovered that the nylonase genes originated from a frameshift mutation, resulting in an alternate reading frame which produced a novel enzyme⁷. This may be true, but recent work by Negoro et al indicates that the origin of the genes might be due to base substitutions after an ancestral gene duplication⁸. Nephy proceeds to tell us that there are only two ways that such a frameshift can occur: a random mutation or by a "Programmed Translational Frameshift Mutation".

At last, we come to the crux of Nehpy's argument. According to him, random frameshift mutations are invariably bad and the idea of a random frameshift mutation is a cop-out employed by "evolutionists" to ignore the reality of intelligent design. The origin of nylonase must be due to "Programmed Translational Frameshift Mutation", a process, he claims, is divinely inspired..

At this point I feel I should clear something up. Nephy, I hope you're reading. There is no such thing as "Programmed Translational Frameshift Mutation". Programmed Translational Frameshift (PTF) is a very real process, but it is not a mutation. PTF actually describes a variety of complex, but similar, processes. The essence of the idea is this: under normal circumstances, a protein is produced when a ribosome translates a strand of mRNA. Usually, the ribosome translates in a linear fashion, starting at the 5' end of the strand and reading the length of the strand until it comes to a stop codon at the 3' end. But in certain cases, the ribosome can be induced to "skip" or "hop" over a number of nucleotides in the sequence. The result is that the ribosome is shifted out of frame, and the resulting gene product is unlike the original⁹. With PTF, one gene sequence can produce multiple gene products: the original, unshifted, product and the second, shifted, gene product. This process is not a mutation. Mutations are changes to the genetic sequence itself, and such changes do not occur during PTF.

Perhaps Nephy's mistake stems from him being unable to comprehend the scientific literature. In his article, he describes PTF as "the modification of the arrangement of amino acids in a chain caused by information in the DNA which programs the event to occur", which is inaccurate, to say the least. This is further evidenced by the fact that he chooses to illustrate PTF with a diagram of alternative splicing, which is an entirely different process altogether! These errors would indicate that he simply did not understand what PTF is. I get the feeling that Nephy just skims through paper abstracts, pulling out words to form misshapen ideas, rather than taking the time to actually read any scientific papers.

But, regardless of whether or not PTF counts as mutation, Nephy's argument that nylonase originated due to PTF, rather than a simple frameshift mutation, doesn't hold much water. What we know about nylonase - the gene's sequence, how it is regulated, etc - would indicate that PTF is NOT at play here. As mentioned above, PTF occurs when a single transcript is read in two different reading frames, resulting in two different gene products. But in the case of nylonase, there is only ONE reading frame. It is always read by the ribosome in the same fashion. At no point is the ribosome prompted to switch to a new reading frame during translation - a hallmark of PTF. In many cases, this switch is induced by particular sequence elements, but the nylonase gene does not contain any such sequence elements. All evidence points to an ancestral gene that underwent a frameshift mutation that permanently altered it's reading frame, rather than two different and active reading frames from a single sequence. The original frameshift alteration was likely transcriptional in nature rather than translational.

Nephy's claim that random frameshift mutations are always harmful is nonsense as well.  In any case where a mutation is deleterious, creationists are quick to say "See! Random mutations are bad!"; any case where a mutation proves to be beneficial, they shout "That didn't count! That was Intelligent Design!". This amounts to little more than special pleading. Nephy does not see it this way. He states 

"The problem for evolutionists is that we have discovered that random frameshift mutations produce novel proteins which do not have a function in the cell, and when produced in great numbers, are causes of diseases such as Alzheimers and Tay-Sachs."

But how are deleterious mutations and non-functional proteins a problem for evolution? On the contrary, they are a huge problem for Creationists! After all, why would God allow for non-functional proteins to cause deadly conditions? Why would God allow for mutations to begin with? Pretty sloppy work for a Creator who is supposedly "perfect".

Another issue with his argument is how he ascribes PTF as an "intelligent design process". What evidence does he have that PTF is not a naturally occurring process? Why does he call it intelligent design? He gives no reason. He simply slaps the ID label on and announces "Hah! PTF proves intelligent design!" with no justification whatsoever. One could just as easily label espresso brewing "intelligent design" and proclaim that Starbucks baristas are evidence of divine creation. It is nonsensical. 

Nephy proceeds with a few paragraphs of rambling spew about DNA being a "computer code". I have already talked at length about why DNA is not a code, so I will not go into it here. Needless to say, it makes little sense.

So what it all comes down to is this: the nylonase gene is a product of a frameshift mutation and not programmed translational frameshift; programmed translational frameshift is not a mutation, nor is it evidence of Intelligent Design; biochemical adaptations do count as evolution; and nylonase still illustrates a wonderful example of evolution occurring within recent memory.  Once again, Nephilimfree abuses genetics to form a murky mire of distorted truth, and once again, his claims do not stand up to the scrutiny of critical thought.

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1. Kinoshita, S.; Kageyama, S., Iba, K., Yamada, Y. and Okada, H. (1975). "Utilization of a cyclic dimer and linear oligomers of e-aminocaproic acid by Achromobacter guttatus". Agricultural & Biological Chemistry 39(6): 1219−23

2. Negoro, S.; Shinagawa, H.; Nakata, A.; Kinoshita, s.; Hatozaki, T. and Okada, H. (1980). "Plasmid control of 6-aminohexanoic acid cyclic dimer degradation enzymes of Flavobacterium sp. KI72".  Journal of Bacteriology 43(1): 238-245

3. Kinoshita, S.; Negoro, S.; Murayama, M.; Bisaria, V. S.; Sawada, S. amd Okada, H. (1977). "6-aminohexanoic acid cyclic dimer hydrolase . A new cyclic amide hydrolase produced by Achronobacter guttatus KI72" European Journal of Biochemistry. 80: 489-495.

4.  Kinoshita, S.; Terada, T.; Taniguchi, T.; Takene, Y.; Masuda, S.; Matsunaga, N. and Okada, H. (1981). "Purification and characterization of 6-aminohexanoic-acid-oligimer hydrolase of Flavobacterium sp. KI72". European Journal of Biochemistry. 116(3): 547-551

5. Dawkins, R. (1986). The Blind Watchmaker, p. 48

6. Ibid. p. 49

7. Ohno, S. (1984). "Birth of a unique enzyme from an alternate reading frame of the preexisted, internally repititious coding sequence".  Proceedings of the National Academy of Sciences. 81: 2421-2425

8. Negoro, S.; Ohki, T.; Shibata, N.; Sasa, K.; Hayashi, H.; Nakano, H.; Yasuhira, K.; Kato, D; Takeo, M. and Higuchi, Y. (2007). "Nylon-oligomer degrading enzyme/substrate complex: catalytic mechanism of 6-aminohexanoate-dimer hydrolase". Journal of Molecular Biology. 370: 142-156

9. Farabaugh, P. (1996) "Programmed Translational Frameshifting". Microbiological Reviews. 60(1): 103-134 

A lame argument about laminin.

It would seem that debunking Youtube creationists has become a hobby of mine. This week, I present a fellow by the name of MyGhettoGospel (I guess Jesus was into gangsta rap), who, for the sake of brevity, I'll refer to as MGG henceforth. MGG believes that biology can prove that the Bible is true, and presents his argument in the video below.



His argument is as follows: the Bible tells us that God "holds everything together"¹. If it were not for God, he claims, everything would simply fall apart and the universe would be devoid of any sort of structure - and this includes people. Luckily for us, MGG says, biology provides evidence that this is indeed the case. The cells in our bodies are held together by adhesion molecules. One class of these molecules are laminins (or 'laminin's' as MGG seems to prefer). And, Great Scott, these molecules look like crosses. MGG has a picture and everything! What else could this be but the indelible mark of the Creator? A sound theological argument. Too bad it isnt reality.

MGG's argument falls apart for a variety of reasons. The first, and probably the biggest flaw in his argument is that laminin  doesn't actually look like a cross. In his video, MGG states "If you look up laminins in any scientific medical piece of literature, this [the cross shape] is what you will see'. Well, I called MGG's bluff on this one and took a brief perusal through the literature. Here is an image taken from Denzer et al (1998)²:

 

Look much like a cross to you? Maybe, if it were constructed by a carpenter in a drunken stupor.  How about this image from Beck, Hunter and Engel (1990)³:

Nope, still not a cross. I guess the literature does not support MGG's argument as strongly as he thinks.   His error is in mistaking diagrams of laminin, like the one he presents, for the molecule's actual physical appearance. Diagrams of any molecular structure are stylistic representations. They are always drawn in a way that makes it easy to understand the basic structure of  a molecule - where the domains are in relation to one another, how many peptide chains comprise the molecule and how they are linked together, for instance. They are not meant to be taken as representing precisely what the molecule looks like. There is always some creative liberty taken when designing a diagram. Laminin does not have a rigid cruciform structure. It resembles a cross only vaguely.

This vague cross-like shape shouldn't be in any way surprising to start with. A cross shape is very simple; it's just two lines running perpendicular to one another. Given the number of different types of proteins in the body and the variety of conformations that they can take on, it would be incredible if there weren't any proteins that resembled crosses. It can easily occur naturally and randomly. Imagine tossing toothpicks across a table. Given enough toothpicks, you're bound to find some that fall to form a cross. Would anyone argue that God had a role in this? I guess Divine Toothpicks aren't marketable.

But even if laminin did take on a rigid shape, who is to say that it depicts a cross? It could look like many things. Rotate it 90° and it looks like a dagger. I think you'd be hard pressed to find anyone who would claim this is a molecular representation of a Sikh's kirpan, and therefore Sikhism is the one true religion. The cross argument is equally absurd.

Another reason why MGG's argument is bunk is that it takes for granted the shape of Jesus' execution device as a cross. The shape of the cross has been branded into the public conscience for centuries but there is little historical reason for this. Implements for crucifixion took a variety of shapes. Writing 75 CE, the Roman historian Josephus commented that crucifixion was done in a variety of ways⁴. Indeed, crucifixion was sometimes done using wooden devices shaped like a T, like a Y or even like an X, as well as using the familiar cross shape. Is there any reason to believe that Jesus was crucified on a cross? Surprisingly, no. The word used in the Bible to describe Jesus' execution implement, in the original Greek, was "σταυρός" (stauros). This is translated as "upright stake" or "wooden post", indicating that he was nailed to a simple, single upright beam (known as a crux simplex). Plutarch and Lucian describe the stauros as having the form of the Greek letter Tau, or T. Neither of these interpretations can be taken as meaning a cross. So if Jesus being crucified on a cross is of dubious nature, so too is the laminin argument. If Jesus actually died on a simple wooden pole, then a cruciform molecule has no significance.

MGG's argument is also problematic theologically. The structure of laminin predates the supposed crucifixion of Christ by many millions of years. Even by Creationist standards, the crucifixion did not occur until thousands of years after Creation. Why would God decide to use a design based on the cross, then? Did he have foreknowledge that Jesus was to be crucified? This would indicate that Jesus was destined to die on the cross for mans' sins. And if Jesus was destined to die on the cross, then mankind was destined to sin. This sort of deterministic implication is at odds with the rest of theology, which claims that God gave man free will and that sin is a choice. MGG's argument implicates the opposite. Which is it, MGG? You can't have it both ways.

In essence, MGG's argument fails. Not only does laminin not resemble a cross, but even if it did, it wouldn't make any sense to interpret it as as sign from a Creator. Creationists, please stop polluting molecular biology with your nonsense. Besides, we all know who really holds us all together.

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1. "The Son is the image of the invisible God, the firstborn over all creation.  For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him.  He is before all things, and in him all things hold together" Collosians 1:15-17

2. Alain J. Denzer et al. Electron microscopic structure of agrin and mapping of its binding site in laminin-1 . The EMBO Journal (1998) 17, 335–343, doi:10.1093/emboj/17.2.335

3. Konrad Beck, Irene Hunter, and Jürgen Engel . Structure and function of laminin: anatomy of a multidomain glycoprotein . The FASEB Journal . 4(2), 2148-2160

4. Josephus, Wars of The Jews, 5.11.1

DNA and the Case of the Bad Metaphor: Now with 100% more Creationist Smackdown!

I love DNA. It is a wonderfully complex molecule and the mechanisms whereby genetic information is stored and accessed is fascinating; and yet, at the same time, the basic premise by which is works - the "central dogma" of molecular biology - is beautifully simple. There is little wonder why DNA has caught the eye of the public in a way that few other biological compounds have. This fascination with DNA has necessitated trying to explain the concepts underlying genetics to the public. Therein lies a problem for scientists and science journalists: how to convey the intricate and often confusing workings of science in a way that is both interesting and easy to understand for the layperson. The one tool brandished about the most is the metaphor. Unfortunately, the metaphor can be dangerous, and there is no better example of this than those metaphors used to explain DNA. Two unfortunate metaphors for DNA have been devised: the idea that DNA functions as a "blueprint" and the idea that DNA functions like a "computer code".

The 'blueprint' metaphor is especially poor. Consider what a blueprint is, exactly. It is a scale schematic used to represent a structure. If you have a blueprint of a hotel, you have a schematic of how to build that hotel. The blueprint tells you everything you need to know - how high the ceilings are, how long each wall is, how many steps are in each flight of stairs. Furthermore, you know that 1 inch on the blueprint represents, say, 1 meter in the actual hotel. From the blueprints, you can precisely construct the hotel. But there is more to a blueprint than this. The information conveyed in a blueprint works both ways - you can use a blueprint to construct a hotel, and from a fully constructed hotel, you can derive a blueprint. If a wall in the hotel is 3m in length, you can draw a wall on the blueprint 3 inches long. The information is reversible. You can go from blueprint to structure and from structure to blueprint.

This is where the analogy with DNA fails. DNA does not work as a blueprint because the information is not reversible. DNA does contain information necessary to construct an organism, but if you examine a fully formed organism, you cannot reconstruct the original DNA sequence. You cannot measure the length of a nose or determine the colour of an eye, and then write out the specific sequence needed to create these features. This is a very important aspect of a blueprint, and DNA does not meet this requirement. Rather, DNA acts more like a recipe. A recipe tells you what ingredients you need and in what manner to combine them in order to create a pie. But if you have a pie, you cannot examine it, even in the most minute of detail, and work out the exact recipe that was used. The information contained in a recipe is not reversible, just as the information spelled out by our genes is not reversible.

The 'computer code' metaphor is also a poor one, for multiple reasons (this particular analogy was popularized by Discovery Institute lackey Stephen C. Meyer). The way a computer code works is that the exact sequence of the code - the precise order of the binary 1s and 0s - spells out exactly what operations the computer must perform. But in genetics, the sequence is only part of the picture. Just as important are genetic regulatory networks - which genes are turned on at what times and in combination with which other genes. Phenotypes are not simply the result of particular gene sequences but the result of specific gene-gene (or gene network-gene network) interactions.

But DNA bears little relation to a "code" in a more fundamental way. Consider exactly what a "code" is. A code is a system of arbitrary symbols used to represent  ideas and objects. In a sense, language itself is a "code"; the symbol "dog" represents that furry tetrapod with a waggly tail, for example. In a code, the symbols themselves have no inherent meaning. The letter "d" is meaningless by itself, as are the letters "o" and "g". It is only in combination that they derive meaning, and their meaning is derived from the idea that they represent. Furthermore, they only have meaning because we give them meaning. "Dog" is merely the label we apply to Fido; in a universe without sentient beings, "dog" would be meaningless. DNA does not fit this description at all. DNA is not arbitrary in any way; each letter of the genetic "code" is an actual biological compound. ACCGTCGA might be the gene for determining how long your toe hair is, but unlike a code, A, C, T and G each have their own non-arbitrary meaning. And this meaning exists independently of human sentience - the sequence of nucleotides does not have meaning only because we give it meaning. It would have meaning even if humans didn't exist at all.

What DNA is, is a polymeric chemical that follows a dynamic chemical process, governed by universal physical rules. It is only a "code" in the same sense that nuclear fusion is a "code" for how stars produce light

So why am I taking the time to mention these things? The reason is because both these weak metaphors have been abused time and time again by creationists (and particularly the Intellignent Design IDiots). Just recently, the video below was posted to Youtube by Nephilimfree, who you may recall from my last blog post (to which he made no attempt to refute, despite having been made aware of my critique - something that should probably come as no surprise to anyone, given the tendency for creationists to retreat with tail planted firmly between their legs when presented with cold, hard, scientific fact). This latest video does not appear to be made by Nephy himself (though he gives no credit to the video's creator), but is nonetheless filled to the brim with that Nephy-brand distortion of science. While it is significantly shorter than his last few 14-minute diatribes, it might still result in significant impairment to your mental faculties, so watch at your own risk.



The video wastes no time in misleading the viewer, tossing out the "blueprint" metaphor 39 seconds in: "DNA contains the blueprint of all life and is by far the densest information storage mechanism known in the universe".  For reasons stated above, we know this metaphor is misleading at best and deceptive at worst. But it continues: "The program code and design of such an incredible system indicated a supremely intelligent designer".

Now, a claim like that one is pretty bold, and would require pretty strong evidence to rationally accept it as fact. So what kind of evidence does the video provide? The answer, really, is "none". It immediately cuts to clips of creationist talking heads (Ken Ham, Dave Hunt, and the like) who reiterate one point: "DNA is a code, and codes are information, which only comes from intelligence". Yet, at no point do they present one shred of evidence for why this is the case. They expect the viewer to simply take what they say as being true. Here we have a major distinction between science and creationism - any scientific claim will be backed up by evidence and cite sources explaining why the claim is true, whereas creationism makes assertions which they simply expect you to believe.

The video proceeds to give some details of DNA - it is self-replicating, has error-correction mechanisms ("there are special proteins called enzymes...making repairs" announces Frank Sherwin - a statement that could only be more generic had he said "there are chemicals that do stuff"), etc. But throughout, a unifying theme is repeated - "these things are complex and only God can produce complexity". But again, they provide no reason why we should believe this is true. Perhaps it is left up to our imagination.

What the video boils down to is that creationists make two claims about DNA: 1) that DNA is a "code", and 2) information/complexity (via the genetic code) can only come from an intelligent designer. Both these claims are really nonsense.

Calling DNA a "code", as explained above, is simply incorrect. DNA is not a code in any sense of the word. But let's assume for a moment, that DNA is a code written by God. If this were the case, then God could definitely benefit from taking an introductory computer programming course. God seems to be an awful coder. DNA is very error prone, and the code is regularly mistranslated and copied incorrectly. Different organisms have similar functions, but use different coding sequences. Some organisms contain the code for functions they don't even use, and the majority of code in any given organism is completely non-coding! For an all powerful supreme being, his code is awfully amateurish.

The argument that "information and complexity can only come from intelligence" is also absurd. To begin with, whenever creationists fling around the term "information" they never define what it is they mean by the term. "Information" can mean different things in different contexts. To a creationist, information is some amorphous concept, never, or only vaguely, defined. The idea that "information" cannot be arranged by nature is also silly. Consider the following situation. A friend says to you, "The sun has to have been created by an intelligent creator. There is no other way to explain sunlight." "Don't be silly," you retort. "The sun is a burning ball of hydrogen which emits energy with wavelengths in the visible spectrum." Unfazed, your friend replies, "That is nonsense. Consider the sources of light we have here on Earth. We only ever see light from light bulbs. Light bulbs do not arise naturally! They are the produce of man made design. We never see light occurring naturally. The sun has to have been intelligently designed. Chemicals cannot just come together and "randomly" create light!". Such an argument is not unlike that creationists use to explain genetic information. They claim that genetic information has to have been designed because information does not arise spontaneously; but the claim that information does not arise spontaneously assumes that genetic information was designed! Once again, a creationist argument is little more than tautology.

In the end, the argument presented in Nephy's little video can basically be paraphrased as "Look at DNA! Look at it! Isn't it complex?! And look at cells! They are soooooo complex!", and then baselessly ascribing that complexity to God. This is, of course, patently untrue. There are many examples of complexity arising through completely naturalistic mechanisms. Snowflakes are a perfect example of this. Do creationists really think that their God spends time making each individual snowflake? What about crystals? Pour some sugar into hot water and suspend a string in it, and before long, you have beautiful and complex crystalline growth. This is an entirely natural process - complexity without the intelligence.

Complexity is not the hallmark of design. DNA is not a blueprint nor is it a computer code. And once again, Nephilimfree is not correct.

Another creationist doesn't understand science. Who knew?!

Nephilimfree, Youtube creationist extraordinaire and posterboy for the giant headphone lobby, has posted a new video entitled "Overlapping and Embedded Genes". Unfortunately for him, I am a lover of any and all things genetic. Also unfortunately for him, he doesn't have a clue what he's talking about. Fortunately for me, this provides me an opportunity to tear his video to shreds.

A little background may be necessary. Nephilimfree (who I will henceforth refer to as "Nephy", as I am an avid believer of making infuriatingly inane things tolerable by giving them cute names) made this video in response to a conversation he had with Sofiarune. He does not mention it, but I was also involved, as I am Sofiarune's go-to guy for molecular biology. I guess you can say I have a personal interest in this video, but I'd pick apart Nephy's claims in any event since they are, as usual, stupid on a Goats On Fire level.

First, the video. Be warned, it is rather long, running at just over 14 minutes. If you don't have the time (or the patience) to watch the whole thing, I'll give you the tl;dr (...or is that tl;dw...) version below. Go grab some coffee, because this post is gonna be a long one.



Nephy's argument is basically this: (i) the existence of overlapping genes is an obstacle to evolution because a single mutation will be deleterious to multiple genes and (ii) these gene pairs could not have possibly evolved and are thus evidence that they have been created. As we will see below, both of these points are patently false, and they demonstrate the extent to which Nephy is ignorant of both evolution and genetics.

Nephy starts the video off by mentioning his discussion with Sofiarune, and his insistence that genes overlap and that this is somehow proof that evolution isn't true. He states that "being the evolutionist that she is, she said 'No, no, no. Genes are read linear and they are not embedded'." Nephy is only telling a half truth here. In their original conversation, he presented "overlapping genes" in a very different manner than he does in this video, as the figure below demonstrates:

 

So Nephy broached the subject with a cryptic sentence about overlapping sequences "causing entropy" to "the code". Understandably, Sofia asked for clarification. In response, he talked about overlapping sequences in shotgun sequencing. This is entirely different. Overlapping sequences in shotgun sequencing and overlapping genes in the genome are not the same thing - one is a bioinformatic technique used to align sequence data in the proper order and the other is the idea that sequences can have multiple open reading frames (ORFs) coding for different gene products. He followed this up with a link to an article [not shown] which further obfuscated what he had meant. It talked about how, in the early days of molecular biology, there was debate over how the genetic code was read; were sequences read in one long linear manner, or were all three possible reading frames of a sequence read at once, resulting in overlapping sequences? It was determined early on that the correct answer was the former - codons were read one at a time in a linear fashion. In this context, Sofia was entirely justified in saying that genes did not overlap. Nephy seemed to have gotten all these concepts confused, but in his video, he presents it as if he gave Sofia a concrete definition of "overlapping genes". Leave it to a creationist to be vague, only to misrepresent your response.

Nevertheless, Nephy now has a concrete definition: overlapping genes are multiple coding ORFs contained within a sequence. Such overlapping genes do exist, primarily in RNA viruses. A study done by Chirico et al¹ (which I will go into some detail below) found that 75%  of the 2000 or so known species of virus have some extent of gene overlap. This does not mean that it is a widespread phenomenon as Nephy seems to believe. He points to an article entitled Mammalian Overlapping Genes: The Comparative Perspective² and is seemingly impressed by the numbers. It shows a total of 774 total overlapping genes in the human genome, and this might be impressive to Nephy, but it isn't to anyone who actually took the time to read the paper. This 774 is out of the 34,604 annotated gene sequences posted to the NCBI human genome assembly (build 33). That's a whopping 2.2% of genes.  So overlapping genes in humans are more the exception than they are the rule. This is the same for pretty much all eukaryotic organisms; overlapping gene sequences do exist, but they are pretty rare. They are mostly seen in viruses (indeed, overlapping sequences were first discovered in he late 1970s by researchers working with the phage φX174). Nephy talks about overlapping genes as if they are as numerous as the grains of sand on the beach, but they are actually quite infrequent. 

But Nephy isn't only concerned with the existence of overlapping genes. He claims that overlapping genes are a problem to evolutionists. He thinks this is because a mutation in the overlapping sequence would be deleterious to both genes and evolution could never favour such a situation. This is demonstrably false, and the evolution of overlapping genetic sequences can, and has, been explained. A paper by Rancurel et al.³ (2009) did just that. According to the authors, there are two characteristics of overlapping genes that alleviate evolutionary constraints on them: (i) overlapping proteins are full of amino acids with a high level of codon degeneracy and (ii) the regions of proteins encoded by overlapping sequences have a tendency towards structural disorder. It is worth going into some detail about these.

(i) To understand what the first point means, you will need to understand what is meant by "codon degeneracy". There are 64 different codons which can be constructed from the four nucleotides, but only 20 main amino acids which comprise any polypeptide. This means that there will be some amino acids that are encoded by multiple codons. Arginine, for example, has 6 different codons - CGU, CGC, CGA, CGG, AGA, and AGG. You'll notice that these codons are pretty similar to each other, and that is pretty handy for the cell. If, for instance, a mutation changes a CGU codon into CGC, CGG or CGA, it will still encode for arginine. The sequence has changed, but the output of the sequence remains the same. The mutation will have no effect on the protein sequence. This is what is meant by codon degeneracy. Amino acids with codon degeneracy will be able to tolerate some degree of mutation. This is important to overlapping genes, because the proteins produced by overlapping genes are high in amino acids that have codon degeneracy. What this means is that mutations to the sequence can be tolerated and won't have a deleterious effect. This is quite the opposite of what Nephy claims. He feels that a mutation will be doubly deleterious to overlapping genes, and he would be right if it weren't for the high frequency of codon degeneracy found in these proteins. In many cases, a mutation will have no effect at all on either protein in the pair.

ii) Structural disorder describes the extent to which the 3D structure of a protein is defined. Those proteins with a high degree of order have a strictly defined 3D secondary structure, while those with a high degree of structural disorder do not. They tend to rapidly change from one structural form to another - their secondary structure is not strictly defined. Since it is the amino acid sequence of a polypeptide that largely determines it's 3D shape and thus function, those with a high degree of structural disorder can tolerate some degree of mutation. Mutations will not affect the protein's 3D shape much because it doesn't have a definite shape to begin with. As the authors put it, "[d]isordered proteins are generally subject to less structural constraint than ordered ones". It should not be surprising, then, that the regions of proteins which are encoded by overlapping sequences tend to be structurally disordered. Those parts do not have a rigid secondary structure, so mutations will have less of a deleterious effect on these overlapping regions. Again, this is antithetical to Nephy's claim that mutations in overlapping genes are a death sentence for a cell.

As an aside, this point about structural disorder raises an interesting theological question: if overlapping genes were created by God as Nephy believes, then why did God decide to create proteins which have regions of structural disorder? If he created these proteins for a particular reason, then would he not have designed them all to have a definite 3D structure that belies their function? Did God just get lazy and figure "Eh, I'll just make some of these proteins structurally ambiguous. No one's gonna notice"? From a design perspective, it doesn't make sense, especially when the designer is perfect and all powerful. Why would he even design overlapping genes to begin with? Wouldn't he just stick to the good old "one gene = one gene product" plan? It's much simpler. It's a hallmark of poor design when things are more complicated than they need to be. How can a perfect God have an imperfect design, anyway?

So Rancurel and co. have thoroughly shown Nephy's point on mutation to be bunk. But they also give his claim that overlapping genes could not have evolved a thrashing. In fact, they do this in the very first paragraph of their paper! They state:

"Among several mechanisms, they [overlapping gene pairs] can be created by a process called "overprinting", in which a DNA sequence originally coding only one protein undergoes a genetic modification leading to the expression of a second reading frame in addition to the first one...The resulting overlap encodes and ancestral "overprinted" protein region and a protein region created de novo (i.e., not by duplication) called an "overprinting" or "novel" region" [See figure below, click to embiggen].

In other words, overlapping gene pairs can be explained easily by a natural process. Two genes exist with reading frames shifted relative to one another, with one upstream from the other. The loss of a stop codon in the upstream gene results in this gene being extended into the region of the second gene where it ends at a stop codon. The result, then, is two genes which share a region of sequence. This has an important evolutionary consequence. The novel region is free to take on novel cellular functions. For the reasons stated above, the novel region is under fewer constraints. In fact, the creation of proteins de novo in this manner has likely played a very important part in viral evolution⁴. In many viruses, the novel protein in overlapping protein pairs are virulence factors or encode enzymes that allow the virus to escape host defence mechanisms. De novo creation of novel proteins by overlapping genes represents another mechanism by which novel "information" is added to the genome, something creationists love to deny is possible. 

But not only can we explain how overlapping proteins pairs have evolved but we also have some good ideas why they would evolve. Chirico et al give four possible reasons why overlapping gene sequences may have evolved in viruses.

1.  Mutation rates: given the high mutation rates seen in viruses, it makes sense that there is pressure on viruses to keep their genomes short. Longer genomes will accrue more mutations than shorter ones. Overlapping genes are a way for a virus to expand its repertoire of genes without extending its genome.
2. Capsid size: some viruses have capsids of limited size. Increasing the size of these capsids to accommodate increased genome sizes is quite the undertaking and is likely to have a fitness cost. Thus it would be advantageous for the virus to have genes which overlap, since this takes up less space within the capsid. 
3. Gene length: larger genomes tend to have less overlap than smaller genomes. This might be because there is more room in larger genomes for the genes. Viruses may have overlapping genes simply because they have small genomes and cannot fit all the genes linearly.
4. Expression regulation: it is possible that overlapping genes evolved so that the genes in a gene pair can be regulated together.

The authors studied the sequence data from 62 different virus families to see which of the four possibilities best matched. They determined the likely cause for the evolution of overlapping genes in viruses was the constraint caused by capsid size. Nonetheless, it is entirely possible that any of the other three may have occurred in certain cases.

The reason I bring this up is because science has at least made an attempt to explain why overlapping genes exist at all. Nephy and his creationist brethren are content to claim that God created overlapping genes but they don't say a word about why he would have done so. The naturalistic explanation offered by evolution not only explains how but also why. The explanatory power of evolution is massive, while creationism offers little more than just-so stories and ad hoc justifications.

But despite all this, Nephy talks for 9 minutes about how overlapping genes are evolutionarily impossible, while saying absurd things like "Geneticists today are shying away from the use of the word 'gene' because it really doesn't describe what we observe in the genome of life. The preferred term is 'sequences' because it is difficult to say what code ends where and starts where in some cases". As someone with a degree in molecular genetics, this took me by surprise. No one sent me that memo! This statement makes little sense; genes and sequences are not equivalent, and it's actually pretty easy to determine where one sequence starts and one sequence ends. We've even been able to develop computer software that can predict such things in a matter of milliseconds. Given that Nephy has little scientific background and is definitely not part of the geneticist community, I'd like to know just where he got the idea that the term "gene" was passé. It's still very much a useful term and is used constantly in the scientific literature. 

He finishes off his video with a five minute snippet of a talk given by Hubert Yockey. I find it amusing that Nephy introduces this clip by saying "And now a few select moments from a lecture by a geneticist", followed immediately by a screen declaring "Biophysicist Hubert Yockey". Nephy, a biophysicist and a geneticist are not the same thing. Not even close. And Yockey isn't even a biophysicist to begin with; he's a physicist. He did some work on information theory and how it applies to biology, but this does not make him a biophysicist. I know these are big words for you, but do try to understand the distinction between them before you toss them around again. I won't actually go through the claims made by Yockey in the video (to be honest, I didn't even watch that part) because really, a physicist's claims about biology are about as meaningful as a butcher's claims about nuclear physics.

So once again, Nephilimfree has demonstrated that he has no idea what he is talking about. Overlapping gene sequences are NOT evidence of Divine creation - they make no sense if one assumes they were created, and they make perfect sense when interpreted in the light of evolution. We have a perfectly naturalistic explanation of their origin which conforms to experimental observation. Furthermore, mutations within overlapping genes are not always a bad thing, and have likely contributed to the evolution of pathogenicity in many species of virus. His claim that mutations in overlapping genes are always deleterious is patently nonsense. In fact, at one point in the video he claims that "all genetic mutations cause degretory[sic] effects to the genome's code", a claim that literally thousands of examples can disprove. He says that he has told evolutionists this for a long time and they "refuse to listen". There's a simple reason for that, Nephy - it's because you're flat out wrong.

Consider this a challenge, Nephy. Show me how what I have written is incorrect. Show me why the authors I have quoted are wrong - critique their work. Give me evidence taken from peer-reviewed scientific literature that backs up your claims, and not just idle speculation on your part. Give me a thorough refutation, thoroughly sourced. Because until you do your claims will be little more than verbal diarrhea.

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1. Nicola Chirico, Alberto Vianelli and Robert Belshaw. Why genes overlap in viruses. Proceedings of The Royal Society Biological Sciences . 2010 . 277: 3809-3817

2. Vamsi Veeramachaneni et al. Mammalian overlapping genes: the comperative perspective . Genome Research . 2004 . 14:280-286

3. Corinne Rancurel et al. Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation . Journal of Virology . 2009 . 83(20): 10719-10736

4. F. Li and S. W. Ding . Virus counterdefence: diverse strageties for evading the RNA-silencing immunity. 2006 . Annual Review of Microbiology . 60:503-531

Not exactly the type of thing I thought I'd be associated with.

Going over my blog stats today I noticed something odd. I wrote a post two years ago about the interesting discovery of a virus that uses another virus as it's host. This actually seems to be the most popular thing I've written on my blog - it has about twice as many views as the next most viewed piece. In the last two days it has had quite a few views, and this is not odd, but I did notice that someone had found it by googling "cwgk.blogspot.com/2008/08". Kinda weird. I was curious what kind of search results that would turn up, so I tried it myself, and I found only four results: three were from my blog (expected) and one more from a forum called RevivalSermons.org.

Ok, so some Bible lover linked to my virus post on a religious forum. That in itself is kinda strange. But not as strange as what I found when I clicked on the link...

"Virus > could viruses and prions be Satan's attempts to create the building blocks of life - unsucessfully [sic] - or just a Satanic weapon ?" 

This was followed by four links to different sites that talked about the virus dead/alive debate, mine being the first. I have no idea how my blog post supports the poster's idea that viruses are some kind of satanic weapon. To be honest, I'm kinda creeped out.

Theistic Evolution, a Case of Special Pleading and a Case of Denying Evidence

Not much in the way of science in this post, just something I had been musing about for a while.

Among people of the religious persuasion, there seem to be three main camps of people when it comes to attitudes towards evolution. There are those who outright deny evolution is possible - the Ken Hams and Ray Comforts of the world - and a large chunk of time is often dedicated to debunking the asinine claims of these nutjobs. There are those creationists who will accept "microevolution" but deny "macroevolution" (whatever such a distinction means, if anything) - individuals who will accept what they see as "just" adaptation within populations but are still diehard creationists at heart. And then there are the "theistic evolutionists" - people who will accept that evolution is completely true but nonetheless insist that life was originally started by God; they posit that God acted as a sort of kickstart for evolution. In a sense, they are still a form of creationist, albeit a "weak creationist", since they still believe that life was created by a supernatural force and evolution proceeded from there. But there is another form of creationist, one that falls in between the last two categories. These are the individuals who will accept evolution in all cases except as it applies to humans. They believe humans to be God's "chosen" species (though, given the plethora of ailments we humans often suffer from, one might begin to wonder what benefit being chosen has, if any), and we were created in cutis by God as mentioned in the Bible and have remained the same ever since. This is a weaker form of theistic evolution (which itself is a weak form of creationism¹!), and quite obviously, a case of special pleading.

All of these positions are untenable for a variety of reasons but it is the problems with this last position - that of the "evolution for all but humans" proponents (which I'll refer to as Humans-Only Creationism, or HOC, for simplification) - that I wish to focus on.

Being that those who hold such a view are accepting of the evidence for evolution in all cases except that pertaining to the evolutionary history of hominids, it is perhaps unexpected that evolutionary evidence of the hominid lineage would raise issues for this view point. Let us assume for a moment that humans are a special case - that they were created as is by God, and have remained unchanged since their genesis. What, then, would we make of the other hominid fossils that have been found? Since HOC makes the claim that humans have not evolved, then these fossils could only possibly be either fully "human" or fully "non-human" (or "fully ape", most creationists would claim), as any gradient between the two would indicate evolution. But this is problematic. Firstly, how would one determine which category any particular fossil specimen belonged to? Many fossils have traits that are "human-like" and also other traits that may be described as "ape-like". No one specimen has characteristics of only one or the other - they are an amalgamation of traits both human- and ape-like. Secondly, the record of hominid fossils does show a gradient from more "ape-like" to more "human-like" in many characteristics, and to claim that such a gradient does not exist is to outright deny observable fact.

Also, the "ape-like" hominids create problems for HOC. If they are not hominids, then what, exactly, are they? They are obviously more like humans than any extant primate. Are they supposed to be Gods "failed attempts" at creating humans? But if God is supposedly omnipotent, then how could this be? How could a perfect being create an imperfect creation? He would surely have gotten it correct on the first attempt. Anyone who subscribes to HOC has no choice to claim that God created them for a specific purpose. Why, then, did he create them so similar to humans?

HOC proponents are also guilty of doublethink. They freely admit to accepting evolution for all other species based on the overwhelming evidence in its favour. But in the same breath, they dismiss with a wave of the hand the idea that humans evolved - an idea which is based on the very same sort of evidence that they accept for other species! How one can hold these two beliefs at once and not succumb to crippling cognitive dissonance is beyond me.

When the evidence is examined, of course, the reality shows though - humans, like every other animal in existence, is the product of countless years of evolution.
-----------------------------------------------------------------------
1) Perhaps we should call this idea "doubleweak creationism".

Dawkins' Answers Some Questions

His answers are interesting enough, but the best part starts at 11:42, when he reads out some of his hate mail.

The Food Network caves to Big Prayer™

The Food Network is not a television station that I watch alot (mainly because it makes me very hungry whenever I do), but earlier today I was watching a show about using liquid nitrogen in the kitchen. During one of the commercial breaks, an ad caught my attention. It featured a man, on the street, lamenting about the world's economic situation (try as I might, I can't seem to find the ad on Youtube). What piqued my interest was that the man began saying how he began praying that things would get better...but it didn't seem that prayer made any difference. He went on to say how he was beginning to question if prayer actually did anything. "Alright," I said to myself, "an ad supporting critical thinking and rationality!" That's when the ad turned a different direction: the answer, the man said, was because he simply wasn't praying big enough.

The ad, it turns out, was for a book called Pray Big. There wasn't really any information about the book, but it gave a website to check out: praybig.ca. So I did.

Pray Big, sponsored by "Crossroad Christian Communications" (the folks responsible for spewing out 100 Huntley Street) is written by Will Davis Jr., a guy who resembles a wimpy Al Bundy. He likes to point out that his official title is Dr. Will Davis Jr., despite the fact that his CV consists of a BA in History from Baylor University and a Masters in divinity and a "doctorate in ministry", whatever the hell that is, from Southwestern Baptist Theological Seminary (try getting a PhD from a real University before calling yourself a doctor next time, Davis).

The website claims:

"Will Davis Jr. offers straightforward guidance on how you can pray with focus and confidence for big things, small details, other people and, yes, even yourself. He teaches you how to pray and includes one hundred pinpoint prayers based on the Bible."

Davis supposedly teaches the idea of "big, pinpoint prayers". In other words, he thinks that prayers work better if they are specific and for big things (ignoring the fact, of course, that prayer of any kind doesn't work at all). He claims that when people pray they typically "underask" for things from God. The problem with prayer, he says, is that people should ask for MORE.

To be honest, I'm not surprised by this at all. The whole idea of prayer is inherently a selfish one. Christians believe that God put humans on the planet for the sole purpose of worshiping him, and nevertheless, they expect that their God should give them whatever they demand, just as long as they put their hands together, close their eyes and whisper some words off into the aether. Davis simply takes the egotistic concept of prayer and stretches it to the next level: don't ask for wimpy things, ask for BIG things!

But the bigger issue here is: why is the Food Network airing ads for this Christian hogwash? They are a private company, so I suppose they are allowed to air whatever ads they wish, but what do you think the chances are of airing an ad supporting a secular or humanist view? What do you suppose their excuse would be rejecting such an ad?

My take on accomodationism.

Lately the science blogosphere has been abuzz with discussion about accomodationism. It all started off with a piece by Jerry Coyne for New Republic on the subject, which has since stirred the pot and prompted Chris Mooney, Jason Rosenhouse, Ken Miller and P.Z. Myers to give their two cents on the issue (a chronological list of postings and replies [as of June 12th] can be found here). There is alot to read about accomodationism but it all revolves around one question: is there room in science for religion - that is, can science and religion get along, or are they diametrically opposed?

And if you ask me, no, they can't and yes, they are.

The simple reason why is because science deals with the observable, the empirical, the testable; while religion deals with the metaphysical, the unobservable, the untestable. To be a scientist requires, then, a certain mindset - one that forsakes reliance in the intangible and deals wholly with physical reality. For one to have this scientific mindset and still hold a belief in religion requires a measure of doublethink in the true Orwellian fashion.

Much of the accomidationism discussion has talked about Gould's Non-Overlapping Magisteria (NOMA). In his 1999 book, The Rock of Ages, Gould proposed that science and religion attempt to explain different aspects of life: science attempting to explain how the world works and religion attempting to explain how we should act. If kept separate, then, the two magisteria should never conflict with one another. Accomidationists tend to use NOMA to suggest how science and religion can co-exist: if people keep them separate then there should be no problem with believing in both. Unfortunately, there is a big problem with using NOMA to justify accomodationism: the two magisteria DO NOT stay separate. Religion constantly makes an attempt to explain how the world works - take creationism for an example. Religion makes many claims about the physical world, which is supposedly science's realm. And many times, what religion claims and what science posits conflicts. To believe BOTH means you have to twist one to fit the other - usually twisting religion to fit science. The usual way is to claim that certain Biblical statements are just "symbolism". This poses a question: how do you decide which aspects to take "for real", and which are just "symbolism" (the answer is, of course, there is no criteria for deciding this). And if ANY of the Bible is symbolic, then what reason do you have to believe that any of it is real?

But there lies a bigger problem with accepting NOMA as a basis for accomodationism. If one is able to keep the magisteria separate, the very fact that one accepts the religious magisterium means that one accepts the idea that there are intangible, untestable entities and processes in existence. As a scientist, how could you ever divorce that idea from explaining the observable world? What keeps you from invoking the metaphysical to explain the physical? Again, there is no defined criteria for this judgement. One is resigned to proposing that there might be some unknown, intangible - in other words, unscientific - entity/process behind the physical world. And at that point, one ceases to be a proper scientist.

Now, I want feel I should say that this does not mean you cannot be a good scientist and be religious, or that being religious necessarily makes one a bad scientist. What matters is whether or not you incorporate your religious beliefs into your scientific activities. Once you try mixing the two, you cross the line from "good scientist" to "poor scientist". This is what separates the Ken Millers from the Michael Behes; Miller, while openly Christian, leaves his religion out of his science, and Behe, also openly Christian, insists on mixing the two. The problem lies, as I said above, in that to do this requires a measure of doublethink. You have to ignore (or attempt to explain away) the areas where science and religion are in disagreement, and you have to use the metaphysical for religious purposes and the physical for the scientific despite having no clear reason why they should be kept separate in the first place.

No doubt the accomodationism debate will continue. One wonders if it will ever be settled.

On Assumptions and Conclusions

One of the things that creationists often say that really annoys me is that evolution and creationism are not all that different in that they both rely on the same facts and observations, but come to different conclusions because they use different starting assumptions. Biologists, they claim, begin with the assumption that natural selection, common descent and descent with modification are all real phenomena, while creationists begin with the assumption that the Bible is the inerrant word of God. They posit that, because the two groups use different starting assumptions, they interpret the data differently, in a way which confirms their preconceived views; when a biologist looks at a giraffe, she sees the byproduct of billions of years of evolution, whereas a creationist sees obvious design.

This claim is absolute rubbish. Anyone who makes such a claim is exposing their incredible ignorance of the scientific method. In fact, such statements run completely contrary to the way the scientific method is supposed to work!

Generally, the scientific method works like this: you gather observations and empirical data, and from analysing the observations and data, you draw out general conclusions which explain all of the data. In other words, science does not start with any unfounded assumptions; it begins with the data, and from the data determines general principals on how the world works. Scientists do not begin by assuming the nonexistance of God - God doesn't even factor into the equation for the most part. In the case of evolution, biologists do not begin with assuming God does not exist and then interpret the data in a secular manner; instead, biologists determine from the data that species arise from a purely naturalistic process, and God's non-involvement follows as a natural conclusion.

Creationists, on the other hand, follow such counter-scientific principals to the tee. They start with their supposed conclusions - goddidit - and then ask "What facts can we find that support our conclusion?" To creationists, facts follow conclusions and not the other way around. They begin by assuming that the Bible is the inerrant word of a supernatural entity, and then stretch, skew and distort any facts they find to try and make them fit into their biblical beliefs.

The idea that science and religion simply begin by making different starting assumptions is antithetical to science. This is a big part of the reason why "creation science" is such a huge joke.

New Answers in Genesis Ad: Godless Heathens will Kill You / We Kill Godless Heathens

Answers In Genesis, the very same group of know-nothings that brought you The Creation Museum and the pitiful attempt at "real science" known as the Answers Research Journal, are starting to branch out with new advertising. Check out their new ad below:



Their little slogan makes me wonder: "If you don't matter to God, you don't matter to anyone", said while a wife-beater clad youth points and cocks a gun at the camera.

This can be taken in two different ways:

1) "If you think that God does not exist - that you don't matter to Him - then you don't think life has any meaning. To atheists, your life and the lives of others don't matter. Godless atheists will have no moral qualms about killing you (and probably will)."

or

2) "If you think that God doesn't exist, then you don't matter to anyone. Especially not us Christians. So don't be surprised when we start shooting you atheists, because you just don't matter."

I wonder which message they were trying to send. Either way, it's absolutely appalling, not to mention completely untrue. Just because one does not believe in a bearded man in the clouds does not mean one cannot be a compassionate individual who cares for the lives of others. To suggest otherwise is a complete non sequiter. There is no link between belief in a deity and compassion for your fellow man. Once again, Answers in Genesis glows like a big, shiny beacon of ignorance.

Perhaps the Virgin Mary made her do it?

The small French town of Lourdes is perhaps best known for its masses of pilgrims who go there to seek the supposedly holy waters of a small grotto in search of miraculous healing. Of course, of the hundreds of millions of people who have visited Lourdes (9 million last year alone), there have only been a handful of "confirmed miracles", meaning if Lourdes' history were thought of as a drug trial, the FDA would have condemned miracles long ago.

But now, Lourdes is beginning to get a new reputation. One for a completely different kind of crazy than the usual delusional flocks of faithful: a woman in Lourdes, who thought she was possessed by the devil, stabbed her mother to death using a crucifix (the crucifix scene from The Exorcist comes to mind...).

She apparently told police "I had visions in a dream. I saw that I was the devil, that I was evil," and proceeded to beat her mother senseless with anything within reach before murdering her with a crucifix. She was promptly carted away to the loony bin.

This is what I don't get. Lourdes is filled to the brim with Catholic pilgrims every year. Ask any random assortment of pilgrims, and at least some are sure to tell you that "God has spoken to them" or that their faith is strong because "God had revealed himself" to them. Lourdes itself is a place that became famous after a teenage girl claimed to have seen the Virgin Mary herself. Yet, none of these people are put though psychiatric assessment.

Why is it that when someone claims to see or hear God or Jesus, it's taken as a divine event. Yet when someone claims to hear or see the devil, they're labelled as crazy and institutionalized? It's a complete double standard. Both are controlled by the same psychological phenomena: they're both simply delusions of an imaginary being.

One might make the claim that, as in the case above, those who think themselves under the control of the devil commit violent acts, but that would be ignoring the multitude of times throughout history that masses of people were murdered after some leader believed he had been told by God himself that it was a good idea. (George Bush and Iraq, anyone?)

It's time to stop treating Godly visitations as being sane.

Arkansas and 5 Other States Still in the Dark Ages.

I think it's really funny when Christians cry out that they're being persecuted. Christians can hold public office in any state in America. There are no laws against god-believers in the public service. Too bad the same cannot be said for atheists in Arkansas and a handful of other states:

"Arkansas is one of half a dozen states that still exclude non-believers from public office. Article 19 Section 1 of the 1874 Arkansas Constitution states that "No person who denies the being of a God shall hold any office in the civil departments of this State, nor be competent to testify as a witness in any court."

If you don't believe in God, you are legally barred from public office, and you're not even legally allowed to testify in court. I'm literally appalled that such a law exists, despite the fact that such laws were deemed unconstitutional by the American Supreme Court in the 1960s.

So next time you hear a Christian spouting their persecution complex, remind them that at least they're not legally second-class citizens in half a dozen states.

EDIT: Seems this has also been covered by P.Z; might want to head over there for a more comprehensice writeup.

Move over Banana, the Chicken is Ray Comfort's New "Atheist's Nightmare"

...except that it's every bit as bird brained as his first argument.
Ray thinks that the classic conundrum of the chicken and the egg is a stumper to evolutionists, but is cut and dry to those who take Genesis as fact:

"So which came first, the chicken or the egg? For those who believe the Bible, it was the chicken, and the first egg came some time later. However, it’s not so simple among the Genesis-less generation. Did the first chicken come from the first egg, or was it the chicken that first laid the first egg?"

He quotes Aristotle as posing this question himself, dumbfounded by the dilemma:

"Long ago, even Aristotle (384-322 BC) spoke of the egg dilemma. He philosophized: "For there could not have been a first egg to give a beginning to birds, or there should have been a first bird which gave a beginning to eggs; for a bird comes from an egg.""

Too bad for Ray that Aristotle lived some 2100 years before Darwin, and the idea of evolution had never even crossed his mind. (I also find it funny that he quotes Aristotle, when most classic theologians decried Aristotle's writings [and those of Plato and others] as being the works of heathens). Aristotle was a smart guy. If he had been chatting with Darwin, he would have easily seen an answer to his question.

Evolution is not stumped by this question. Quite to the contrary, evolution provides a very satisfying answer to it: the egg, of course, came first. Evolution would predict that, before there was a chicken, there was an ancestor to the chicken (let's call this ancestor a "protochicken"). The protochicken would have been very much like the chicken indeed, perhaps even phenotypically identical but genotypically distinct from the modern chicken. (This is a vast simplification of course, since there is no one type of chicken that can be called a "modern chicken"; all chickens are genotypically different at some level). A population of protochickens were subject to evolutionary pressure of some sort, certain aberrant traits were selected for, and one day, a protochicken or two (or likely, many) laid an egg, and out hatched a chicken. Evolution posits a firm solution to the chicken-or-the-egg question.

But Ray doesn't seem to get this very simple explanation:

"Let’s say evolution was responsible for the beginning, and let’s say the egg was the first to evolve (before the chicken). Why did it do that? Why would there be nothing, and over millions of years, nothing became simple organisms, then these organisms became an egg? I can understand that a fish evolved legs and lungs over millions of years--because he (and his necessary female help mate) wanted to breathe, and to walk on dry land. But why would a thoughtless egg appear first and then want to become a chicken?"

Ray shows here something that I see in creationist arguments somewhat often - the idea that organisms want to evolve. They seem to think that, for evolution to work, organisms have to want to evolve some particular trait. They suppose that evolutionary theory dictates that a giraffe evolved a long neck because it wanted to reach the leaves high up in the trees, or, as in Ray's example above, fish evolved legs and lungs because they wanted to breathe and walk on dry land. In other words, Ray is stuck behind the idea of Lamarckian evolution - that "needed" or "wanted" traits were acquired and passed on to progeny. Perhaps Ray did not get the memo, but Lamarck's ideas on evolution have been discredited for pretty much the last century or more.

There is no want in evolution. There is no thought out goal. What evolves is not product of an organism's needs or wants, but rather a product of the organism's environment. Eggs evolved shells, for instance, because those few with shells survived the rigors of the environment better than those without. It's really that simple.

Ray continues with more questions:

"If the egg was shaped with a rounded point at each end for ease-of-laying (a square egg would be painful), how did evolution know to make it that shape if there were never any chickens in the first place to know that an egg is made to be laid? Another small dilemma. How did the first egg get fertilized to become the first chicken? What or who fertilized it, and why did he fertilize it and sit on it until it hatched? How did the fertilizing creature evolve and have the ability to fertilize an egg that he found. How did he get the seed into the egg to fertilize it? And why did the (rooster) evolve as a bird? Unless he was an egg first, and if so, we have the above questions to deal with, because his egg would also need to be fertilized. Who did the fertilizing?"

Again, evolution did not "know" anything. Evolution is a blind process. It tries out many different things, and those that work best get passed on. How did the first egg get fertilized to become the first chicken? It was fertilized by a protochicken before it. Evolution is a slow, incremental process. The process to create an egg did not just come together all at once; it was the result of millions of years of tiny steps, one step an improvement on the step before it. All of the questions he asks can be explained through a basic understanding of evolutionary principals; asking such questions, then, shows Ray Comfort lacks such an understanding. (He also asked how the seed got into the egg to fertilize it. Perhaps he should Google "how a chicken egg is formed", and learn that the shell is not formed until after the egg has been fertilized. This is grade school stuff).

As with most creationist arguments against evolution, Ray displays a lack of understanding of how evolution is supposed to work. It makes me wonder if he's ever actually tried to learn about evolution aside from trying to find faults with it. I'd love to challenge him to take an exam on basic principals of evolution to see how he'd do, because from what I can tell, he doesn't have a clue.

They'll believe just about anything...

Taken from Yahoo! Answers, a seemingly popular, vacuous intellectual void loved by Creationists:

"THE CITY OF GOD ? IS IT TRUE THEY FOUND IT?

my sister told me that my brother [hes christian ] told her that somewhere outer space they found like city but gravity didn't let the camera get closer and that the city was really Bright and they could see a figure like a castle so does any one know this story or have any footage of this ?"

They'll believe this crap, yet somehow find evolution to be unbelievable beyond comprehension. Sigh.

It's Darwin's Birthday: Edmontonians Show their Ignorance (Part II)

Continuing from my last post, we have a letter from one Peggy Heather of Edmonton:

"Re: “Evolution, creationism debate still simmers; Iconic naturalist would be amazed at the controversy over his ideas,” The Journal, Feb. 7.

Religious beliefs aside, one would be hard pressed to believe in evolution. The fossil record does not support it and the mathematical improbabilities of us evolving out of nothing are staggering.

Chris Eckert, an evolutionary biologist at Queen's University, is correct in saying that there are numerous species, but that in itself does not point to evolution. That’s happened thanks to the marvellous DNA in all living things, which allows for numerous variations, as any dog breeder can testify. This can be called microevolution. However, a dog will still only produce a dog, no matter how you tweak it. If you really stop to think about it, if for example birds evolved from dinosaurs, how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either? He’d be a sitting duck for predators.

Apes can mimic a few words taught by trainers in response to rewards, but lack the throat and brain structure necessary for speech, vocabulary and grammar. One can go on and on why macroevolution is impossible, but evolutionists keep insisting on reviving a dead horse.

Peggy Heather, Edmonton"

While not nearly as long as Hendrickson's nigh-on-incoherent babbling, Peggy no less piles on the stupid.

First of all, the fossil record DOES support evolution. In every way, shape, and form does the fossil record support evolution. To doubt this shows you know nothing of evolution nor the fossil record. What does the fossil record show? It shows us the gradual progression of life from simple organisms to more complex organisms over the period of millions upon millions upon millions of years. It shows us early forms of body patterns familiar to us and it shows these patterns changing over time to become what we see today. It shows the beginning of different families of organisms and the ends of other families. All of these things are predicted by evolution. There is not a single aspect of the fossil record that does not support evolution, and if you claim otherwise, then you are either ignorant or lying.

Secondly, the mathematical improbabilities of us evolving "out of nothing" matter very little. The improbability of winning the lottery is staggering, yet someone always wins. Improbable does not imply impossible. Even if the chances of life evolving were one in one hundred billion trillion, the fact is, it happened. A lot of these arguments about the probability of life evolving are terribly fallacious: they scrape together large numbers they assign arbitrarily and output a large number that generally means nothing. People look at the large number and think "wow, that number is too large for me to grasp. I cannot argue against such a big number. I guess the conclusions drawn from this big number must be right." Dangle a few dozen zeros after the 1 in front of people and you're bound to get someone who believes you, no matter how asinine your argument.

Peggy follows this up by outright accepting microevolution. But what keeps her from accepting macroevolution? What is the barrier that prevent macroevolution while allowing microevolution? She doesn't say! Perhaps this is because there simply ISN'T one. Macroevolution is what happens when microevolution continues for long periods of time. Sure, a dog still produces a dog over the course of a few centuries, but give it a few million years of microevolution and what you're left is not going to be anything like a dog. She asks regarding the dinosaur-to-bird transition: "how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either?" What makes her think that legs became useless once wings began to evolve? I wonder how she explains the birds perching on the branch outside her window if she thinks having wings means legs are now useless. She obviously does not understand how evolution works in the least.

She then talks about apes lacking the necessary anatomy and brain functions for proper speech, yet can mimic words taught by trainers in response for rewards. What better evidence is there for evolution? Other primates cannot speak like us, yet still have the capacity to learn speech. How else could one explain this except in light of evolution?

I think that someone should tell Peggy that "macroevolution" is not a dead hose by any means. Evolution is stronger than ever before. Every day that goes by, we find more and more evidence for evolution. There is no single scientific principal that is more strongly supported than evolution.

Hopefully tomorrow's edition of the Journal will contain some pro-Darwin rebuttals to today's display of idiocy, but I wouldn't hold my breath.