Friday, 30 January 2009

The God that Time Forgot

It is a somewhat common claim by creationists that the concept of time is a huge problem to atheists. Just days ago, for instance, Kirk Durston used this same argument in his debate with P.Z. Meyers. The "Argument from Time" may have different varriations. Durston's argument went something like this.
"When did time start? What created time? In order for time to start/be created, there had to be a time prior, which was 'timeless'. The prime cause/creator, then had to be timeless"
Ray Comfort makes a similar claim about the "timelessness" of God:
"Time is a dimension God created, to which He subjected man. With God there is no time. He dwells in "eternity," a dimension of which we have no comprehension. You will go into eternity when you "pass on" from the earth."

However, the way I see it, time creates a bigger problem for Creationists than for us atheists.

Consider how we measure time. Surely we can count the seconds ticking away on the face of a clock, but our ability to measure time goes deeper than that. As conscious beings, we can measure time in our head. That is to say, we have the ability to "feel" the passage of time. You might not know exactly how much time has passed since you got up this morning without checking your watch, but you have the intrinsic knowledge that it's in the realm of "past". You know that it happened prior to the current instant without refering to a clock. Our minds have the abiliy to sense the passage of time, however inaccurate timepieces they may be.

Now let us consider God. God is supposedly omnipotent. There is supposedly no limit to God's abilities or capibilities. Argubly, God is a concious entity (it is claimed that we cannot know the "mind" of God, after all), and his omnipotence, then, applies to his cognitive prowess as much as it does to his other aspects. It follows that we cannot posess a cognitive ability that God does not, him being omnipotent and all. God, then, should be able to sense the passage of time, just as well - if not better - than we can.

Creationists like Ray and Durston claim that God existed "before time", in an era of "timelessness". It was during this "timeless" era that God decided to create the universe, giving birth to energy, matter and time itself. Being a conscious entity, the creation had to have been a conscious effort on God's behalf. If God was conscious before he created time, then he would have been able to measure the passage of time in his Godly mind before he had even created time. This is an obvious logical contradiction.

"But time didn't exist, so he was unable to measure it in his mind!" the Creationists will cry. But that is unallowable if God is conscious and creation was a conscious act. For example, imagine God thought to himself "Gee, it's awfuly boring sitting in this vast nothingness. I think I'll create the universe for some entertainment." If God was conscious - and he would have to be to think such a thing - then in his mind, he would know that a certain amount of time elapsed between him fist muttering "Gee" and ending with "entertainment".

The bottom line is if God is conscious and the creation a conscious act at all, God could not have existed in a "timeless" era. There are two ways Creationists could ratify this problem. One is to change their mind about the nature of time: that it has no beginning or end, that it exists independently of God or Nature - in which case it ceases to be a problem for anybody. The second, more likely way a creationist would try to dodge the logical hurdle they ran themselves into is to say that the genesis of the universe was NOT a conscious act, and that (at least prior to creation) God himself was not conscious.
But if this is the case, why need God? With an unconscious Creator/creation you can claim no theistic or deistic explanation for the origin of the universe. The best you could get away with is a pantheistic explanation - that the universe IS God, however it came to be.

Time, then, is far more of a problem for Creationists than it is for atheists. Claiming God created time leads to a logical contradiction, and trying to avoid this contradiction gives no support to the idea that a theistic/deistic God exists in the first place. Quite to the contrary, it supports the idea of His nonexistance.

Friday, 23 January 2009

Addition of Genetic Information Made Simple

A common argument among creationist types is that evolution is impossible because it requires an addition of genetic information to a genome, which, they say, never happens. Instead they posit that genetic information is only ever lost through mutation A mutation in a gene encoding for alcohol dehydrogenase, for instance, results in the loss of the ability to metabolize alcohol. This represents a loss of genetic information. Further, they claim that beneficial mutations are exceedingly rare (or impossible) - a claim that is incredibly fallacious - and because of this, evolution is impossible. Some creationists have even claimed that this question stumped Richard Dawkins himself, however this has been shown to be an outright hoax.

The most obvious problem with this claim is that what is meant by "information" is never actually defined by creationists. Do they mean new genetic "instructions" - new and different genes being added to a genome? Do they mean new physical DNA being added to expand a genome? "Information" is quite a vague term, and can mean a multitude of things.

I would assume, however, in most cases, "information" refers to new genes being "added" to a genome, since genes ultimately supply the "information" or "instructions" an organism needs for body plan organization, carrying out metabolic processes, growth and development. And if the claim really is that there are never new genes added to a genome, then the claim is blatantly false.

Adding new "information" to the genome is actually quite simple and very common in the natural world (that is, outside the laboratory). It's a little process called gene duplication.

I won't get into all the nitty gritty details about the various ways that gene duplication occurs, because they're not all that relevant to the topic at hand, but common causes of gene duplication are homologous recombination, retrotransposition, or simply errors in DNA replication (the DNA Polymerase slipping back along the DNA strand, for instance). In either instance, the result is an extra copy of a gene is present in the genome.

A great example of gene duplication are the human globin genes. We do not simply have one gene for "hemoglobin"; rather, humans have a variety of hemoglobin genes: α-hemoglobin, and β-hemoglobin are the two expressed the most in adults, with ε- and ζ-hemoglobin expressed in the embryo, and γ-hemoglobin expressed during all stages of development. It should be of no surprise that all of the hemoglobin genes, despite being expressed at different times during the human life cycle and having slightly different functions, are all very related. The various forms of hemoglobin have arisen through gene duplications. According to Ross Hardison1,
"In the distant past, some ancestral - probably single-celled - organism had one hemoglobin gene, and therefore one kind of hemoglobin protein. But at some point, this gene was duplicated, so that each of the resulting daughter cells carried two identical copies of the ancestral hemoglobin gene. Gradually, during successive cell divisions, small variations in the sequence of nucleotides - the subunits that make up a gene - started to appear. In this way, the two genes that started out identical acquired sequence differences and later, functional differences. It is quite likely that additional hemoglobin genes were acquired the same way, by gene duplication followed by modifications in the nucleotide sequence."

I can already hear the cries of the creationists. "But," they proclaim, "this doesn't show evolution at all, for the different hemoglobin genes are still all the same kind!" (Oh how I hate that dreaded "kind" word). This is where gene duplications can get interesting. Once a gene duplication occurs, you have an extra copy of whatever gene that's been duplicated in your genome. This essentially works like a "backup" copy of the gene. Since a lot of mutations are deleterious (but not most mutations, as the creationists would have you believe), then having this backup copy gives a clear advantage - one copy is free to be mutated without the organism encountering any deleterious effects. These duplicated genes gain mutations at a faster rather than other genes, since potentially disastrous mutations in them won't kill the organism, allowing them to be passed on to future generations and sustain even more mutations (compared to a non-duplicated gene, where a disastrous mutation kills the organism, so neutrally and unmutated copies are what get passed on to future generations).

What does this mean? It means that the gene now has the potential to take on new functions, different regulation, etc. In essence, the duplicated copy has the potential to become an entirely new gene - one that gives an entirely new function - such as being able to metabolise a new food substrate, break down toxic compounds or grow larger and more quickly. New genetic "information" has been added to the genome.

It amazes me that the "no new genetic info" claim is still such a common one among creationists. Gene duplication as a major player driving evolution has been accepted by the scientific community for the better part of the last 100 years2. Indeed, Susumu Ohno had claimed back in 1967 that gene duplication is the single most important factor in evolution3. The reality is that new genetic "information" is added to genomes - yours, mine, every living organism's - quite easily and quite commonly.

EDIT: And it can get even easier. Prokaryotic organisms, like bacteria (and even some eukaryotes like amoeba) can take up bits of exogenous DNA (that is, DNA that is simply floating around in their environment), adding "new information" to their repertoire almost instantly!

EDIT #2: Looks as if some simple multicellular organisms like bdelloid rotifers are also able to take up foreign DNA from their environment.

1. Hardison, R. (1999) . "The Evolution of Hemoglobin" American Scientist 87.2: p126
2. Taylor, JS. & Raes, J. (2004). "Duplication and Divergence: The Evolution of New Genes and Old Ideas" Annual Review of Genetics 9: 615-643
3. Ohno S. 1967. Sex Chromosomes and Sex-linked Genes. Berlin: Springler-Verlag. 192 pp.

Thursday, 22 January 2009

Fancy new Header

I made a shiny new header for my blog. It's more eye-catching than the standard one that Blogger adds to your blog, but I still think it could be fancier. Think of it more as a pretty placeholder until I really whip out my Photoshop skills.

I was sure I swore more than this...

Seems my Cuss-O-Meter is registering as low. Only 1.7% of my pages contain cursing? I have a little more than 100 posts, meaning I've only swore in about two of them? I'm much more foul mouthed than that in real life...

Now to try and find a Blaspheme-o-Meter. That one'll probably have a thermonuclear meltdown analyzing my blog...

The Blog-O-Cuss Meter - Do you cuss a lot in your blog or website?

Saturday, 17 January 2009

A Quick Primer to Kantian Philosophy

Immanuel Kant is a pretty important philosopher, but to laymen, his ideas aren't all that easy to understand. So here's a quick primer to his work that I swiped from Ron's Philosophy Page entitled Kant's Ethics: The Short Version:

  • How would you like it if everybody did that?
  • If you do something because you're a dick, but then it works out okay anyway, you're still a dick.
And that's pretty much it. Kantian morality is based around two ideas. First, the principal of universalization ("Act only according to maxims which you can will also to be universal laws", according to Kant). What this means is "only do things that work out well if everybody did them". Being honest works well if everyone does it, so according to Kant, being honest is moral. On the contrary, stealing doesn't work well if everyone does it, nor does lying. So according to Kant, these are not moral things to do.

Secondly, Kant believes that you should not use people as a means to achieve an end. In other words, if you do something immoral, even if the end result is something good, then it was still an immoral act.

If you'd like to learn more about Kant's views on ethics, I suggest picking up The Great Philosophers, by Stephen Law. It does a good job at exploring Kantian ethics in some detail, without getting too technical (as well as explain the philosophies of 49 other great thinkers). Highly recommended book!

Tuesday, 13 January 2009

Ann Coulter: Still Running off at the mouth, still doesn't have a clue.

I really hate Ann Coulter.
She has a long history of being a complete moron, including thinking Canada supported the US in Vietnam, claiming that Jews want to be "perfected", and storming out of an interview when she doesn't get her way.

I have yet to read any of her books (and for good reason, I would rather my brain not spontaneously combust), but this excerpt from her book Godless: The Church of Liberalism, is enough to prove that it's complete drivel. This is her take on the theory of evolution:

"Throw in enough words like imagine, perhaps, and might have -- and you've got yourself a scientific theory! How about this: Imagine a giant raccoon passed gas and perhaps the resulting gas might have created the vast variety of life we see on Earth. And if you don't accept the giant raccoon flatulence theory for the origin of life, you must be a fundamentalist Christian nut who believes the Earth is flat. That's basically how the argument for evolution goes."

No, Ann. That's basically how the argument for creationism goes. There is no definitive proof of a creator, much less of the Christian god; no proof of instantaneous creation of even a speck of dust, much less all the matter and energy in the universe; and no proof that any of the Biblical tale of creation is true. We are left to imagine that God exists, and decided on a whim that perhaps he should create a vast, mostly empty universe to house his most important creation - mankind - on a rock in the middle of galactic nowhere, and he might have done it by sneezing into a mud puddle.

While there are uncertainties in how life began (that's abiogenesis, Ann, not evolution), the theory of evolution is not just some story scientists came up with one day over tea and crumpets. It's the end product of two centuries (and indeed, even longer) of scientific work. Sure, there are things we don't know yet, but there is no imagining involved. We are lead to evolution by considering the evidence, and what the evidence presents to us factual.

I would imagine that perhaps Coulter should shut her skeletal maw, because she's so dense, her brain might have become a singularity. That's much more plausible than creationism, anyway.

Saturday, 10 January 2009

Gene of the Week: FOXP2

The Gene of the Week is a new feature that I've decided to bring to my blog. Each weekend I'll (try to) write a bit about a gene and it's related gene product that I think is pretty cool.

This week's gene is FOXP2, a gene that has been implicated as having a role in the development of language skills, and is likely to have played a major role in shaping the early evolution of Homo sapiens.

FOXP2 is a member of the Forkhead Box gene family (called "forkhead" after the prominent helix-turn-helix motif that resembles a forked head). It's located (in humans) on the q-arm of chromosome 7, and has a 2285bp transcript. It's gene product, the FOX P2 protein, is fairly large, at 715 amino acids in length. The gene is required for the proper development of the brain and the lungs, but where the gene shines is it's involvement with speech and related processes.

The history of the gene is actually quite interesting. Around 1990, a family known simply as the KE family, caught the scientific community's attention. The family was of particular interest because, over the previous three generations, around half of the family members developed severe problems with speaking - to a point that their speech was quite incomprehensible and they had to rely on sign language to communicate - as well as other physical and mental handicaps. A pedigree of the family and the disorder showed a pattern of inheritance suggestive of a mutation in a single, autosomal dominant gene.

It was not until 1998, when Fisher et al.1 did a linkage study and narrowed the location of the gene to a small region of chromosome 7 (7q31), and named the hypothetical gene SPCH1. Three years later, in 2001, Lai et al.2 made an interesting discovery. Working with a patient that exhibited a similar to that of the KE family, they discovered that the patient had a chromosomeal translocation affecting chromosome 7. In fact, the break point of the translocation was in the very region that Fisher and colleagues pinpointed in 1998. Going back to the KE family, the team found that the same gene that was broken in their patient had a point mutation in all of the affected members of the KE family and was not found in any of the unaffected members or control groups. In effect, they had found the gene that was causing the disorder in the KE family. The popular media caught wind of this discovery and, unsurprisingly, overexaggerated the finding with claims of a "gene for language", implying that this was a gene unique to humans that allowed us to talk - a claim that was blatantly false.

The gene that Lai and fellows found was a member of the FOX gene family - FOXP2.

Since then, lots of work has been done on the FOXP2 gene. It's been shown to affect vocalization in mice pups, song learning in finches, and even in the development of echo-location in bats. It has also been found that the gene is widely conserved, from fish to alligators to humans. However, what makes the gene particularly interesting from an evolutionary standpoint is that the human form of the gene is a bit different from the rest: it differs from the form of the gene found in other primates by two amino acids. It is speculated by some researchers that this difference is what lead to the development of language in humans, though a mechanism for this is yet unknown. Other researchers are of a different mind, claiming that the two amino acid difference is unlikely to have resulted in the development of language, but rather, a difference in gene regulation - when and where the human form of FOXP2 is expressed - is a more likely origin.

Much work remains to be done on FOXP2. It is a known transcription factor, but the genes it regulated are still unknown. Investigations into its role in evolution will undoubtedly continue. Be sure to keep your eye out for developments in this gene; it's bound to shed some light on the recent evolution of our species.

1. Fisher et al, Nat Genet 18, 168 –170 (1998)
Lai et al, 'A forkhead-domain gene is mutated in a severe speech and language disorder' Nature 413, 519 - 523 (2001)

For further reading and more details, see: