21 May, 2009

Axioms and Absolute Truth

Have you ever found yourself drawn into a debate with a presuppositionalist? If not, count yourself lucky. It is surely one of the most painful experiences known to man. It is basically the adult equivalent of a child repeatedly asking 'but why?'.

What happens in a debate is the presupper will sooner or later get to the question 'how do you know X?'. You might answer 'I know X because of Y', but the crafty presupper will ask 'how do you know Y?. You might answer 'I know Y because of Z', but the crafty presupper will ask.......well you get it......it could go on for ever.

What eventually happens is that you get to a stage in the debate where you need something as a foundation for your knowledge, e.g. if Z is self-evidently true then it is perfectly fine for you to declare that you know Y and X. The presupper would not be able to question this because your answer for 'how do you know Z?' would be 'Z is axiomatic and so is self-evidently true'. This axiom is God as far as the presupper is concerned, and based on this they will claim that they have an avenue to certainty. On hearing this, you might feel the need to provide your own axiom. The question is what are possible axioms for the non-presupper?

Well, Ryk has provided a nice list of axioms to be used in a debate with a presupper. The list is a more reader-friendly version of the techniques Darrin uses over at Skeptical Studies (check the link for a jargon-heavy but thorough pasting of presupper Sye). It includes concepts that are self-evident, such as perception and consciousness. The proof of the existence of these things is that any proof of their non-existence would necessarily require perception from a conscious being in order to interpret the proof as valid. Thus, perception and consciousness are self-evident and can be considered axiomatic. In addition, logic is self-evident since logic would be needed to disprove logic.

Another way to put this is in terms of certainty or truth. We are all certain of specific things but a presupper will insist that certainty or truth mean nothing unless is it 'absolute' certainty or 'absolute' truth. They will ask what your source of absolute truth is. They are banking on you answering that there is no absolute truth because they will then counter this by asking:

"Is it absolutely true that there is no such thing as absolute truth"

At first glance, it may seem that you are cornered. If you answer yes, then you have just confirmed an absolute truth. If you answer no, you are conceding that absolute truth does exist. As the presupper considers God to be absolute truth, this effectively is their way of proving his existence.


The strategy to use here is not to just explain that there is no such thing as absolute truth, but to also state that there is only truth or not truth, i.e. something is either true or not true and so the terms absolutely true or absolutely false become redundant. When asked:

"Is it absolutely true that there is no such thing as absolute truth"

the answer is simply

"Your question makes no sense, however it is true that there is no such thing as absolute truth"

Unless your opponent can point out a difference between truth and absolute truth then this approach holds. But how can there be a difference between truth and absolute truth? One might be tempted to say that absolute truth is somehow more true than truth. But that's ridiculous. If something is true, it is already 100% true. If something is termed absolutely true, it is still only 100% true. The word 'absolutely' cannot add anymore truth to an already true statement. In fact, Ryk has argued that stating something as 'absolutely true' as opposed to 'true' renders the statement false:

Call true T and absolutely A. and a Statement S. S=T describes a true statement describing a statement as absolutely true would be S=T+A for this to be true A=0 if a has no value it is a non valid qualifier if A>0 then you have a contradiction T+A does not =T so you have a false statement.

To sum if A=0 then there is no reason to call something absolutely true, so therefore a statement can not be absolutely true it can only be true or false.

If A>0, for instance if if the term absolute adds meaning then an absolutely true statement is false because the qualifier absolute makes it non true. So again in this instance a statement is not absolutely true it is simply true.

So does truth exist? Yes, of course. This is self-evident as any disproof of truth, if valid, would itself be true.

With the axiomatic quartet of perception, consciousness, logic and truth, non-presuppers have a solid foundation for their arguments against presuppositionalists. It's a pity most presuppers don't have a good grasp of the latter two...


20 May, 2009

Are men going extinct?

I'm going to a lecture tonight by Prof Jennifer Graves of the Australian National University entitled 'The Decline and Fall of the Y Chromosome and the Future of Men'. Should be interesting. I'll update tomorrow. Here is the ad:

'The Decline and Fall of the Y Chromosome and the Future of Men'

Delivered by

Professor Jennifer Graves

(PhD, FAA Director, ARC Centre of Excellence for Kangaroo Genomics Head, Comparative Genomics Research Group Research School of Biological Sciences The Australian National University Canberra, ACT 2601, AUSTRALIA)

On Wednesday 20th May 2009

at 7pm

To celebrate Charles Darwin's 200th year anniversary, the 2009 Public Lecture Series will focus on the theme Evolution featuring renowned leader in the Australian and international cell biology, genetics and genomics communities Professor Jennifer Graves. Jenny is particularly well known for her theories of the origin and evolution of human sex chromosomes and sex determining genes, and her dire prediction that the Y chromosome will disappear! the topic of this current lecture. We are delighted and privileged to welcome Professor Jennifer A. Marshall Graves to our college.


Well it was very interesting...

She started the lecture by explaining the origin of the Y chromosome. It was originally identical to the X chromosome, but a mutation in a gene called SOX3 led to the emergence of a new gene called sex-determining region Y (SRY), which encodes a protein with the ability to promote the development of the testis, and hence controls male development. Following the emergence of this gene, other male-specific genes (e.g. controlling sperm production) emerged and were selected for in the same region. Over time, this resulted in difficulties to recombine between the X and Y chromosomes and the Y chromosome became highly susceptible to mutation, leading to the inactivation of many of it's genes. In fact, the Y chromosome has degraded and shrunk so much that of the 1300+ genes it once had, it now is mostly junk and contains a measly 45 active genes. At this point in the lecture, we had the first indication of the overall theme - if it continues to degrade and shrink, who is to say that it won't eventually disappear?

Next Prof Graves explained how they have studied the sex-determining mechanisms in other animals. In marsupials (she is Australian after all!) there are similar X and Y chromosomes to humans, suggesting that this mechanism is as old as the marsupial/placental spilt. However, when you look in the platypus, the sex-determining mechanism is more similar to the ZW system in birds (in this case the sex-determining gene promotes female development). What this tells us is that the X and Y chromosomes are a maximum of 166 million years old, as this is when the last common ancestor between humans and the platypuses is thought to have existed. So it seems that the Y chromosome has lost over 1300 genes in about 166 million years. Based on this, Prof Graves predicts that the Y chromosome only has about 6 million years left before it will disappear.

So what does that mean for the future of men?

Well......not much. Prof Graves speculated that a new sex-determining gene is likely to evolve, providing a new mechanism. This is where the talk got a bit fuzzy, and she didn't really go into much detail (she admitted as much in the Q&A), but there is one intriguing possibility that directly follows from her hypothesis...

If a new sex determining gene was to evolve, and the mechanism switched so that this gene promoted female development instead of male (as is the case in birds), this would eventually result in two populations, one with the SRY male-promoting gene and one with the new possibly female-promoting gene. What would happen if a member of each population mated? The offspring would have signals promoting both maleness and femaleness during their development. Prof Graves speculated that this could result in humans consisting of males, females and a third male-female hybrid! In fact she suggested that this scenario may have happened in the past, and that it would inevitably be a driving force for speciation.

Prof Graves is an excellent speaker and she has a proven track record in this area. Read an interview with her here. I'm not sure if I buy into all of her ideas about the future but it is certainly an interesting topic.

As an aside, she is a staunch defender of science and evolution and has had a few run-ins with the Discovery Institute; they have tried to use her research as evidence for intelligent design in the past (she mentioned this in her talk but I can't find a link). Because of this she is currently setting up a Dumb Design website (again, no link as yet), which will catalogue biological examples of bad design as evidence against an intelligent deity.


14 May, 2009

Nature review: Origin of 'RNA world'

OK this is cool. Really cool. But I suck at chemistry so I'm gonna keep it real simple...

It's a given that life somehow emerged at least once on this planet about 4-4.5 billion years ago. Understanding how this amazing event happened is a major challenge though. There are a multitude of theories out there but problems tend to arise in trying to reproduce the origin of life event in the lab. One theory is that prior to DNA and protein-based life there was an exclusively RNA-based world. Indeed, this theory is probably widely accepted as the most plausible, if not the only possible, scenario.

As I said, each theory has it's own problems, and the RNA-world theory is no different. The main difficulty is how to combine the three elements of an RNA molecule, i.e. the nucleobase, the ribose and the phosphate. In particular, attempts to join together the nucleobase and the ribose have always been met with failure, casting doubt on the likelihood of these molecules spontaneously combining in Earth's early atmosphere...

That is until now.

Researchers Powner et al (1) have published results in Nature showing that a nucleobase and a ribose can combine in plausible early Earth conditions. They achieved this by using a totally different approach to previous attempts. It had long been assumed that the nucleobase and the ribose must have first formed independently and then joined together in a secondary reaction (See FigA). Instead, Powner and colleagues have now shown that the combined nucleobase-ribose molecule can emerge from a precursor molecule, side-stepping the need for both to first form independently (FigB). Specifically, "activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates"

Figure taken from article by Jack Szostak (2)

So this work gives a plausible mechanism for the origin of the 'RNA world'. Pretty cool, isn't it?

Well yes, but I've saved the best part till last.....

The catalyst for this series of reactions that combine a nucleobase and a ribose is........wait for it......


That's right. The third component of RNA is needed for the precursor molecules to form the activated pyrimidine ribonucleotides. Phosphate controls several steps in the reaction. Specifically, it "controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer". Following completion of it's job as a catalyst, phosphate is then incorporated into the molecule at a later stage, thus completing the RNA synthesis. The beauty of this system is incredible, and is described perfectly by Szostak:

Phosphate continues to have several essential roles in the remaining steps of Powner and colleagues' pathway, in one case causing depletion of an undesired by-product, and in another saving a critical intermediate from degradation. The penultimate reaction of the sequence, in which the phosphate is attached to the nucleoside, is another beautiful example of the influence of systems chemistry in this set of interlinked reactions. The phosphorylation is facilitated by the presence of urea; the urea comes from the phosphate-catalysed hydrolysis of a by-product from an earlier reaction in the sequence.

This work represents a major breakthrough in our understanding of how life might have emerged as it has provided an elegant mechanism for the spontaneous generation of RNA. As always, more research needs to be done, but we now have an exciting new perspective on an age-old problem.

(1) Powner et al. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239-242 (14 May 2009)

(2) Jack W. Szostak. Origins of life: Systems chemistry on early Earth. Nature 459, 171-172 (14 May 2009)


13 May, 2009

Did someone ask for transitional fossils?

A common claim by creationists is that there are 'no transitional fossils', despite advice from their own people to stop using this argument. These claims are often made in a blog or forum comment section rather than on an official website, since it is clearly a ludicrous statement. They also crop up a lot in comments on YouTube videos alongside such gems as 'If we evolved from monkeys, why are there still monkeys?'. (The mindset of the claimant is usually clear enough due to the accompanying derogatory statements about Barack Obama and/or homosexuals.)

Anyway back to my point, transitional fossils. This is one of my favourite photos:

Skull A is that of a modern day chimpanzee, the closest living relative to humans, which are represented by Skull N (Edit: For those who claim there is no proof of the relationship between humans and chimps, see here - prepare to be pwned). Since evolutionary theory predicts that humans and chimps share a common ancestor, there necessarily must have been hominid-like organisms in the past with intermediate morphologies between the two modern day species. Now look at all the other skulls. Pretty convincing evidence if you ask me. Here is a list of the species for each skull and the given dates for their ages:

(A) Pan troglodytes, chimpanzee, modern
(B) Australopithecus africanus, STS 5, 2.6 My
(C) Australopithecus africanus, STS 71, 2.5 My
(D) Homo habilis, KNM-ER 1813, 1.9 My
(E) Homo habilis, OH24, 1.8 My
(F) Homo rudolfensis, KNM-ER 1470, 1.8 My
(G) Homo erectus, Dmanisi cranium D2700, 1.75 My
(H) Homo ergaster (early H. erectus), KNM-ER 3733, 1.75 My
(I) Homo heidelbergensis, "Rhodesia man," 300,000 - 125,000 y
(J) Homo sapiens neanderthalensis, La Ferrassie 1, 70,000 y
(K) Homo sapiens neanderthalensis, La Chappelle-aux-Saints, 60,000 y
(L) Homo sapiens neanderthalensis, Le Moustier, 45,000 y
(M) Homo sapiens sapiens, Cro-Magnon I, 30,000 y
(N) Homo sapiens sapiens, modern

Now the photo is slightly misleading in that it suggests a steady progression from chimps to humans. This is not how evolution happened. The chimp and human lineages split about 5-7 million years ago and so predate the above photo. The chimp skull is just there for reference. The comparisons should really be studied from B-N, that is from Australopithecus to humans. A similar diagram could be made tracking the evolution to the modern day chimp, but the differences may be less obvious. In fact, at a glance, the modern chimp skull is actually quite similar to Australopithecus (although there are many differences, look at the eye sockets).

Another thing to point out is that these particular skulls may not have belonged to individuals that were direct ancestors of modern humans, they may well have been on other branches on the hominid evolutionary tree (see picture below). This is not really a problem though, as it is simply like comparing similarities between aunts, uncles and cousins, instead of directly comparing parents and offspring. The point being that comparisons can still be informative and a range of transitional features from modern day chimps to modern day humans is evident, indicative of common ancestry. Of course, the fact still remains that many of the species above could have belonged to populations that were direct ancestors of modern day humans.

Hominid evolution (including Kent Hovind, proponent of the 'no transitional fossil' argument)

Tracking the changes in the skull between Australopithecus and humans, we can notice gradual changes which would be considered transitional. Notice how the palate (roof of the mouth) retracts over time, indicating that less strength was needed to chew food. Although not visible on the above photo, the lower jawlines of these early hominid skulls are even more pronounced and follow a similar pattern of change.

This is most likely a direct result of the use of fire, as cooked food is much easier to breakdown and chew than raw meat and plants. It is thought that Homo habilis invented the use of fire for cooking, and accordingly it is the Homo habilis skull (Skull E) which first shows a reduced size in the palate.

Also, notice how the brain size increases massively in a steady progression from Australopithecus to humans. One hypothesis actually links these two morphological changes. Is is thought that a mutation in a protein called MYH16, a chief component of the powerful jaw muscles, resulted in a reduction in the size of the chewing apparatus. This may have reduced the physical restraints on the rest of the skull, allowing it to grow and accommodate the increasing size of the brain.

All fascinating stuff!

Now how on earth can a creationist look at these skulls and claim that there are no transitional fossils? Well some claim that this is just evidence of 'variation within kinds' or that transitional fossils must be direct ancestors and not from other branches. These claims are weak. Firstly, if it only represents 'variation within kinds' then these creationists are still conceding that chimps and humans are the same 'kind', in direct contradiction to their faith. Secondly, no evolutionist claims that transitional fossils must be from direct ancestors, merely that they show transition between the morphology of a particular feature in two distinct specimens. These changes show that features have evolved in populations over time. It is not necessary to show the change in these features in a direct ancestral line.

Look at it like this...

Imagine you were trying to find and catalogue a photo of each of your direct male relatives, father, grandfather, great-grandfather, etc, in order to compare a particular feature, say nose size. You have photos that span 10 generations (unlikely, but humour me) but you are missing one photo, lets say the 7th generation. As luck would have it, you do have a photo of the brother of your missing direct male relative. Of course you would prefer to have the actual direct relative, but in the absence of this photo, the photo of the brother can still act as a good substitute. It is likely that the brother had similar features to your direct relative and so his nose size is still informative. In fact you could look at photos of siblings for a few of the generations and not really lose any informational power. This is why transitional fossils, or features, do not need to come from a direct ancestor.

Anyway, the demands of creationists in this respect are ludicrous. Even if there were fossils in a direct ancestral line in front of them, they would simply say that there still isn't enough evidence. They would ask for the fossils that show transition from each specimen to the next (i.e. imagine a photo with twice as many skulls). If you could provide them, they would ask for the next set of intermediate fossils, and again, and again...

More fossils to a creationist doesn't mean more evidence, it means more gaps! It seems like the only way to satisfy them would be to produce fossils from every organism that has ever lived on this planet.



Edit: Below is the chart showing that although creationists are adamant that none of these are transitional and all are either apes or humans, they are not able to agree on which are which.

Evolutionists also disagree on how fossils should be classified, which species they belong to, etc. True enough. But according to evolutionary thinking, these fossils come from a number of closely related species intermediate between apes and humans. If this is so, we would expect to find that some of them are hard to classify, and we do. Creationists, on the other hand, assert that apes and humans are separated by a wide gap. If this is true, deciding on which side of that gap individual fossils lie should be trivially easy. Clearly, that is not the case.

Uploaded with ImageShack.us

Hat tip to BathTub


11 May, 2009

The Dan Brown Code

Wanna know how to write a best seller and guarantee a movie deal?

Easy. Use the Dan Brown code:

Ageing Harvard professor
+ Attractive young female
- Murdered father who is brilliant scientist
+ European city
+ Famous landmarks
+ Trail of clues
+ Catholic church (great for pre-release controversy)
+ Secret society
+ Ruthless assassin working for mystery employers
- Loyalty from said mystery employers
+ Knowledgeable old disabled man
+ Race against time
+ Irrelevant romantic ending

= Cha-ching!! Several hundred million dollar profit

Class dismissed.


05 May, 2009

Nature review: Type I interferons and AIDS

Viruses have evolved highly effective mechanisms to manipulate the host immune response and facilitate replication. Following HIV infection in humans or simian immunodeficiency virus (SIV) infection in rhesus macaques, a chronic activation of the innate immune system is observed. This immune response is triggered by the recognition of viral RNA and DNA by members of the Toll-like receptor (TLR) family, specifically TLR7 and TLR9 on plasmacytoid dendritic cells (pDCs). These cells are also known as interferon (IFN)-producing cells due to the massive quantities of IFNa secreted following stimulation. One outcome of this chronic inflammation is a reduction in the regenerative ability of CD4+ T cells. This effect results in significant T cell depletion and is a major contributor to immunodeficiency associated with AIDS.

However, it now appears that divergent host immune responses can also result in different outcomes to the same virus. For example, in contrast to rhesus macaques, sooty mangabeys do not progress to AIDS following SIV infection, but instead act as a reservoir host for the virus. A recent paper in Nature Medicine by Mandl et al (1) examined the differences in the immune response to SIV in both sooty mangabeys and rhesus macaques in order to understand the mechanisms contributing to AIDS progression. Although viral replication was comparable in both species, minimal T cell and NK cell proliferation was observed in the sooty mangabeys following SIV infection, as opposed to high cell proliferation and expansion in the rhesus macaques. In addition, pDC activation was increased in the rhesus macaques but not in the sooty mangabeys, as measured by expression of the chemokine receptor CCR7, a reliable marker of pDC migration to lymph nodes (1). These results show a significant attenuation of the immune response to SIV infection in the sooty mangabeys, suggesting that the lack of AIDS progression in this species is a result of specific immune response mechanisms, as opposed to properties inherent to the virus itself.

Figure from O'Connell and Siliciano (2).

The authors next investigated TLR7 and TLR9 responses to SIV in peripheral blood mononuclear cells (PBMCs) from humans, rhesus macaques and sooty mangabeys. Despite high IFNa production in humans and rhesus macaques, they found much lower secretion of IFNa from sooty mangabeys (1). However, this effect was not limited to SIV infection, as reduced IFNa production was also observed when PBMCs from sooty mangabeys were stimulated with a panel of TLR7 and TLR9 ligands. Interestingly, the ability of sooty mangabey PBMCs to produce the proinflammatory cytokines TNFa and IL-12 was not diminished, implying that TLR7 and TLR9 recognition of SIV is normal in these cells, but that there is a deficiency in the downstream pathways leading to type I IFN production (1). The researchers suggest that this deficiency may lie at the level of interferon regulatory factor 7 (IRF7), the critical transcription factor for type I IFN production. They come to this conclusion following sequence analysis of genes encoding prominent members (including TLR7, TLR9, MyD88, IRF7 and several type I IFN promoters) of the TLR7 and TLR9 pathways in humans, rhesus macaques and sooty mangabeys. Whilst most genes were highly conserved, several polymorphisms were found in the sooty mangabey IRF7 coding sequence. The authors speculate that these polymorphisms, which cause amino acid substitutions in the transactivation domain of IRF7, may be responsible for the deficiency in type I IFN signaling, and consequently the protection against AIDS.

This study has provided an interesting new insight into the immune mechanisms contributing to the progression of AIDS. Specifically, it appears that IRF7 polymorphisms resulting in the attenuation of the type I IFN response in sooty mangabeys protects against the development of AIDS. These mutations have been preserved in sooty mangabeys as they offer an evolutionary advantage, namely a reduced susceptibility to immunodeficiency disease. This implies that the pathogenesis of AIDS in susceptible species may be a combination of both viral replication and prolonged immune activation. Based on this research, a potential therapeutic strategy to combat AIDS would involve inhibiting virus binding to CD4 on pDCs, thus attenuating cell proliferation. In addition, the inhibition of excessive type I IFN release by pDCs may prove to be beneficial, either through the use neutralising IFNa antibodies or by specifically targeting IRF7. However, these potential strategies are not without limitations, as an inhibition of type I IFN production would leave a patient dangerously immunocompromised. Instead, more research into the contribution of innate immune mechanisms to AIDS progression may result in the use of specific inhibitors as part of a combinatorial therapeutic approach.

(1) Mandl et al. Divergent TLR7 and TLR9 signaling and type I interferon production distinguish pathogenic and nonpathogenic AIDS virus infections. Nat Med. 2008 Oct;14(10):1077-87.

(2) O'Connell and Siliciano. Immune alteration fends off AIDS. Nat Med. 2008 Oct;14(10):1016-8.


01 May, 2009

Stupid Goddam Blasphemy Law

This is beyond ridiculous.

Dermot Ahern and the rest of the Fianna Fail bozos are actually considering bringing in a blasphemy law. If it's passed, a fine of up to €100,000 will be imposed on blasphemers.

This can't possibly be happening, can it? I mean, Jaysus, like, what's the problem...?