best. intro. ever.

Quite often I enjoy reading papers for my research project, for varying values of ‘enjoy’. Seldom are they worth sharing for non-biologists though (I don’t think any biologists working in the field of evolutionary microbiology are likely to read this blog particularly often), but this one is hard to beat:

“The capacity of current sequencing technologies has revolutionized fields such as microbial ecology and evolution. Research projects and entire careers have been invented. For example, it has now become respectable, indeed fashionable, to sequence poop. Mouse poop, human poop: it is officially a cottage industry. Why? …”

The authors later go on to coin (perhaps someone else came up with it earlier though) the term “poop-omics”, which would be loved by skeptics of the ‘omics’ revolution. I’m personally not sure what to think of this revolution in biology (few tangible benefits have yet come out of it), but it is very interesting and gives me something to do each day (and if I’m lucky a scholarship for the next couple of years, but we’ll see), so I can’t really complain. 🙂


on the work of the Holy Spirit

Stuff I’ve been thinking about a little, and will perhaps think on more.

“People often cry out for the work of the Holy Spirit and yet forget that when the Holy Spirit works, there is always tremendous cost to the people of God-weariness and tears and battles.” Francis Schaeffer.

From here [link].

I want to learn more about the Holy Spirit and His work. There are plenty of ideas out there, and whatever our background I think we need to be careful not to let cultural things and stories we’ve been told overly influence us away from taking account of the broader Christian witness on the topic.

this one will go viral

Here’s a fun, old-school (or, actually quite new) molecular biology fact – the proportion of our genome comprised of Endogenous Retroviruses (8%) is larger than the proportion which encodes proteins. When you start to think about it, it’s nuts, but it is a scientific fact (assuming the identification of ERVs is correct; I haven’t looked into it for a while).

I knew ERVs were important, but didn’t realise quite how much so… Most interesting for me are the cases where ERVs are known to have positive effects; I’d like to look into this more. More on that later, perhaps.

a joke for ewe

An engineer, an economist, and a philosopher are hiking through the hills of Scotland. On the top of a hill they see a black sheep. “What do you know,” the engineer remarks. “The sheep in Scotland are black.” “No, no”, protests the economist. “At least one of the sheep in Scotland is black.” The philosopher considers this a moment. “That’s not quite right. There’s at least one sheep which is black from one side.”

You can replace engineer with ‘scientist’. I like this, as it’s the only joke that I’ve heard (with a bit of adjustment) combining the things I studied in undergrad, and it’s about the problem of induction too.

From here:

reducing the claims of physics

I found this, quoted in an article I’m reading for background ideas for my thesis, quite nicely ironic:

‘just when physics is moving away from mechanism, biology and psychology are moving closer to it. If this trend continues it may well be that scientists will be regarding living and intelligent beings as mechanical, while they suppose that inanimate matter is too complex and subtle to fit into the limited categories of mechanism’
David Bohm (physicist), 1969.

‘the day my Pikachu turned into a Raichu’, or ‘reflections on genomes’

“Just as there is an added dimension of pleasure in enjoying the creative work of someone you know, so there is an added pleasure in studying the world if you know the creator.” Andrew Briggs, physicist, Oxford.

I study evolution, occurring in real time in baker’s yeast (Saccharomyces cerevisiae). It doesn’t crop up too much on this blog or what I like to talk about in my limited hours of spare time, but it’s true – contrary to common belief I’m not doing a masters in theology or philosophy, but in the bioinformatic analysis of microbial experimental evolution. As it turns out, philosophy is (though I’m making slow progress here) not highly regarded in the lab/office environment where I spend most of my time, and theology if it were ever mentioned would probably verge on being a term of abuse – jesuschrist is a casual swear word in any case – but, perhaps more on that another time. I manage to bluff my way through science through the day, and spend any extra hours on other stuff.

the more evolved form

While there is room for improvement in science eduction to overcome the tendency towards scientism, it’s a real privilege to be able to study the natural world, and in particular to try to contribute to the literature on the molecular basis of evolutionary trade-offs. Reading ‘Darwin’s Black Box’ [here – although not the most friendly overview] perhaps 7 years ago, I could not have imagined being in this place now, with the opportunity to talk with distinguished evolutionary biologists about my own project in the field, and through my reading, thinking, speaking and writing to shape their views on these topics a little.

It’s been a hard and not entirely successful slog this year learning techniques in microbiology and bioinformatics and theory in population genetics, molecular and experimental evolution (200+ articles in my reference list, and counting), while doing various unrelated things, but contrary to my expectations at many points this year it’s starting to pay off in being able to coax results out of the craptonne of data derived from whole genome sequencing of yeast populations. Things are looking promising, after quite a remarkable turn-around over the past week, and I’m now hoping to eventually submit both a biology and a philosophy paper written with my supervisor over summer.

‘The day my pikachu evolved’ never actually happened, but something kind of similar did yesterday. I observed that evolution through gene duplication (technically copy-number increase) had happened across multiple independent replicate lines evolved in a sugar-limited environment. In other words, convergent evolution in response to selection, clearly demonstrated. This is the kind of thing that could’ve been big news a few years ago, and while it’s much easier to find now, it’s still quite cool. The only site obviously affected by this kind of duplication beautifully aligns with one of the two genes (sugar transporters) that we would have predicted from first principles and previous work to undergo duplication. It may not look like much, but the following image was absolutely thrilling to observe, after having checked here [link] for the gene present at the site. The large peak in the middle of the 1st and 3rd rows shows the addition of perhaps 3 copies of the gene in the entirety of these populations, or else more copies in a subset. Being a cynic, I had assumed that gene duplications would be impossible to find in the noisyness of whole population sequencing data (compared to the standard of sequencing individuals), but I was happily wrong.

a beautiful transformation

Less easy to visualise but more technically interesting, a similar kind of convergent result, with a different kind of adaptation, was found in populations evolved in a high salt and nitrogen-limited environment (I am using populations evolved in the lab by a predecessor). A subset of genes involved in response to that environment were hit with mutations across multiple separate populations – working out the implications of the kind of mutation involved here will I think be fruitful in developing theory in this area. I’ve kept the details of all of this vague, for more I guess you’ll have to wait for the articles to come out!

The more I study the genomes of ‘simple’ cells of bakers yeast, the more I am amazed with the combination of adaptability and high functional integration which they exhibit. That we live in a world which works together so well at the molecular level and at many higher levels too I think testifies to the creator’s care and creativity. While I am a science student, I am more fundamentally a Christian who wants to know the truth, and as such very open to and interested in explaining why I think the crazy things that I mention here, and to hearing why you agree or disagree 🙂

A fun fact – as I was googling to check what Pikachus turn into, I discovered that one of the recommended searches was “what do Pikachus taste like?” I assume the answer is something like a chubby electric hamster.

my Dad made all of this

Picture this conversation between children.

Adam: “my Dad’s a builder. He’s creating a huge house for a millionaire right now!”

Bruce: “my Dad is a millionaire. We have a boat, and when he’s not working, I’m learning to go sailing”

Carl: “my Dad’s a firefighter, he’s saved like over 100 cats, and quite a few people!”

Jesus: “my Dad made the universe by speaking. As a small token of this, I can walk on water and calm large storms by asking. Through my death, billions of people will be saved from eternal destruction, and my return from the dead in a glorified body will inaugurate the new creation my Dad has planned.”

Bragging is less fun with Jesus around.

I thought of this while considering the massive privilege of knowing the creator of the universe personally, and the relationship of this to daily study of the natural world.