genomics, epidemiology, and the complexity of help

Here’s an interesting quote from a recent paper on using genomics in the study of the spread of disease. It may be an example of the complexity of dealing with disasters in non-industrialised nations; basically, the world is broken and stuff is complicated. I just found it striking; a really sad irony (if the purported origin of the disease is correct).

Global datasets can also be used to inform local epidemiology. Following an outbreak of disease, investigators frequently wish to know where it originated. Comparisons of outbreak genomes with others that have already been sequenced can shed light on this, but such comparisons require a larger sample so that the outbreak can be placed in context. Following the cholera epidemic that arose in Haiti following the 2010 earthquake [27], rumours suggested that peacekeepers from Nepal, a region of endemic cholera transmission, travelling as part of the United Nations relief operation could have inadvertently introduced the outbreak strain. Genome sequencing confirmed a close relationship between the Haiti outbreak strain and recent V. cholerae isolates from Nepal, consistent with this hypothesis. It should be noted that existing samples of diversity are not such that we can definitively link the outbreak to Nepal through sequence data alone—although strong evidence supports a South Asian origin, closely related genomes have also been sampled from Cameroon. However, the combination of traditional and genomic epidemiology suggests a probable Nepalese origin.

Croucher et al. Bacterial genomes in epidemiology–present and future. Phil. Trans. R. Soc. B. 2013. p. 368


DNA: Celebrate the unknowns

There’s a very very interesting article with the title of this post, on the topic of molecular genetics and molecular evolution, published in the most recent edition of “Nature” by London science writer Philip Ball. I intend to cite it, or at least some of the articles it references, in my thesis. Well worth a read if you’re into this stuff (perhaps noone who reads this blog is though) and have access via a university library or such.

Amongst other things, he dares to highlight the fact that there is debate over the capacities of natural selection to explain molecular evolution – he notes neutral evolutionary processes as another option, but that it is all generally unclear. For what it’s worth, I’m inclined to think that there is yet more going on.

“On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level, suggests Philip Ball.”

“In short, the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess. That should not be a criticism, but rather a vote of confidence in the healthy, dynamic state of molecular and evolutionary biology.”

“Barely a whisper of this vibrant debate [[on the nature of the gene]] reaches the public. Take evolutionary biologist Richard Dawkins’ description in Prospect magazine last year of the gene as a replicator with “its own unique status as a unit of Darwinian selection”. It conjures up the decades-old picture of a little, autonomous stretch of DNA intent on getting itself copied, with no hint that selection operates at all levels of the biological hierarchy, including at the supraorganismal level2, or that the very idea of ‘gene’ has become problematic.” [[It’s no big secret that Dawkins is overly simplistic (at best) in his science, as well as in his philosophy]]

phylogenetic tree image from

Update: earlier this month, in the Proceedings of the National Academy of Sciences (PNAS), another interesting paper was published (at least one!). This one argues that the concept of junk DNA must be retained. There are various interesting issues concerning function and the wide range of ‘DNA elements’ which this paper raises and which I hope to ponder more, but here is one quote that raises interesting teleological possibilities (I’m over-using the word ‘interesting’, I know):
If the human genome is junk-free, then it must be very luckily poised at some sort of minimal size for organisms of human complexity. We may no longer think that mankind is at the center of the universe, but we still consider our species’ genome to be unique, first among many in having made such full and efficient use of all of its millions of SINES and LINES (retrotransposable elements) and introns to encode the multitudes of lncRNAs and house the millions of enhancers necessary to make us the uniquely complex creatures that we believe ourselves to be. …” – from “Is junk DNA bunk? A critique of ENCODE” by W Ford Doolittle.

another quote: “it cannot in general be the case that selection operating at the level of fitness of individuals within a species can favor the origin or maintenance of traits that incurs selective cost at that level, while offering only the remotest hope of future benefit to the individual and its descendants.” [the author then goes on to discuss mechanisms outside of ‘selection at the organismal level’]

Another interesting point: gene duplication can help facilitate expression which is specific to a particular cell type or tissue.

Church v State – and we all lose

“Keep the Church separate from the State – it’s best for both of them!” is complete crock. Well, at least partial crock anyway. Hear me out on this.

I actually need to do more reading, to work out the subtle distinctions between ‘religious motivation’ and ‘religious reasoning’. But in a broad sense, I see no reason to deny religious reasons in the public square – and I see some clear and relatively non-controversial examples to include them.

1) promoting compassion. Often Christians who lean left in their policy preferences will argue for things like higher taxes and greater government support of minorities. (I personally think such things need to be assessed on a case-by-case basis; I don’t have a huge ideological bias either way, just generally want to see greater government involvement well justified when it happens, but this is beside the point for now.) Let’s accept that it will best promote human flourishing to pursue a particular ‘compassionate’ policy. Such policies will often be argued for by religious people acting on their religiously-based values – and who (other than greedy selfish godless capitalists) could possibly object to that? But, if that’s okay, why aren’t we uncomfortable with the religious reasoning involved? (Note, whether the full reasoning is publicly stated or occurs only behind closed doors seems fairly irrelevant to me.)

2) preventing severe injustice. I think of the development of some prominent totalitarian state systems in the 20th century (I don’t need to name them). Unfortunately, many Christians went along with or only very weakly objected to the gross violations of human rights which were occurring. It is probable that many people were told in no uncertain terms to keep their faith out of their politics – and the world was far worse off as a result. (I’m reading Eric Metaxas’s book “Bonhoeffer”, which is causing me to ponder such things. It’ll be available to borrow soon if anyone wants.)

Bonhoeffer on a retreat with students from a confirmation class, in 1932 (image from Wikipedia)

escape from reason

I’m reading through ‘escape from Reason’, a small book by Francis Schaeffer that’s been sitting on my shelf for a few months. I’m surprised at how readable and insightful it is – no doubt there’s some dubious historical scholarship in there, but plenty of gems too.

e.g. p.35:
“when a man says that thinking in terms of an antithesis is wrong, what he is really doing is using the concept of antithesis to deny antithesis. That is the way God has made us and there is no other way to think.”

and another one which strikes me as profoundly insightful, p. 77:
“If we think we are escaping some of the pressures of the modern debate by playing down propositional Scripture and simply putting the word ‘Jesus’ or ‘experience’ upstairs [[in the realm of the non-verifiable/non-rational]], we must face this question: What difference is there between doing this and doing what the secular world has done in its semantic mysticism, or what the New Theology has done? At the very least the door has been opened for man to think it is the same thing. Certainly men in the next generation will tend to make it the same thing.
If what is placed upstairs is separated from rationality, if the Scriptures are not discussed as open to verification where they touch the cosmos and history, why should one then accept the evangelical upstairs any more than the upstairs of the modern radical theology? …”

religious reasoning – relegated to the dustbin of history?

The debate over same-sex marriage is more or less over in the realm of civic politics in NZ – proponents of SSM overwhelmingly won the final vote in parliament. The opinion ‘on the ground’ where the real people are in NZ is probably rather different (more like a 50-50 split, by most representative polls that I am aware of), but be that as it may, there are interesting issues in the background of the debate.

One is the place of religious reasoning in public policy discussion.

In the final speech of the debate in parliament, I was intrigued to hear Moana Mackey say something like “it’s not the role of the State to uphold one group’s religious beliefs over another’s”.  This sounds nice – good ol’ church-state separation and all that. But, the difficulty is that tonight one group’s religious beliefs concerning the nature of marriage and human flourishing were effectively rejected by the State.

It’s not clear that the State can be entirely neutral on matters of religion, given religion’s pervasive claims over all of life!

what excites you?

This excites me – it gives me a thrill, but also challenges and provokes and troubles me; it gives me reason to praise God and reason to plead with Him.

News of university missions in secular Europe: [here] “The Fellowship of Evangelists in the Universities of Europe (FEUER) is proclaiming the gospel to thousands of students all over the continent as part of an evangelistic campaign to hold 25 university missions in 25 major cities in 25 countries in 25 months.”

I’ve heard people I know fairly well say that I never seem excited about anything. For this I profusely apologise, and beg to differ a little. They need to talk to me more about this kind of thing; perhaps I need to talk to them more about it too! Presenting the gospel persuasively, and impacting cultures in this way is something that seems to me to be worth living for; actually, worth throwing one’s life away for. 

The name “FEUER” is appealing – it means ‘fire’ in German. Germany is at the heart of secular Europe, and we can only pray for ‘Pentecost-like’ occurrences there, following on from the preaching of the Word as was the case at Pentecost, that may impact the rest of Europe. Or vice versa – however God acts!

Fire. I wonder if the ‘fire tetrahedron’ depicted here has spiritual analogies.