Replication

© Artyom Korotkov, freeimages.com

The scale of the universe is truly mind-boggling, and it’s worth dwelling on. But it’s important to keep looking in other directions. Every day your body produces millions of new cells without you even thinking about it. Each of your cells contains the same set of DNA instructions*. Your cellular DNA quota (genome) is an incredibly thin chemical chain with about 6 billion links called nucleotides, and is approximately 2 metres long** (don’t test this at home!) Each time a new cell is produced, that DNA has to be copied to an extremely high level of accuracy.  It was the same for all 50 trillion cells in your body – it all started with DNA replication.

When a cell is about to divide, a number of proteins recognise and bind to the DNA at specific points. Geneticist John Bryant has said that it’s harder to begin DNA replication than it is to start a nuclear war – the process is that tightly controlled. At least forty different proteins have to be in position before replication can begin.

DNA replication, Madprime, 2007. Creative Commons Attribution-Share Alike 3.0 Unported license

Once initiated, DNA replication happens relatively quickly. The clue to how this works is in the iconic DNA double helix image that is represented in art and architecture the world over. DNA consists of two complementary strands twined together: one is a mirror image of the other. This helix is unwound, and each chain is used as a template to build a new complementary strand of DNA.

When you were conceived, you received a copy of each of your parents’ DNA. Making DNA is like writing: without proper editing mistakes will undoubtedly slip in. For DNA replication, multiple layers of proofreading ensure a high level of accuracy. So out of your 6 billion inherited DNA chain-links, only 30-70 of the links are wrongly copied. That’s a maximum of one mistake in every 100,000,000***. If I could do anything that accurately I’d be very happy! And this is all happening at great speed: 6 billion chemical reactions often in less than 24 hours.

I remember writing about DNA replication in great detail during an exam at university. At the end of my essay I waxed lyrical about how this process was happening incredibly fast, at such a high level of accuracy, and without any conscious effort on our part. I’m not sure what the person marking my exam thought about my reverie, but I was impressed!

I often find that looking in detail at the universe – even just standing outside on a dark night – gives me a feeling of smallness. Staring at the stars, or studying cosmology in depth, has given some people an awareness that there might be a God out there after all. What does looking at the very small and complex make people think? Tiny packages like cells or atoms can contain surprisingly complex systems, and immense power. Nothing is as simple as it seems. Perhaps as biology proceeds over the next few decades we’ll hit up against similar philosophical questions to those raised by the older sciences of physics and astronomy.

 
*Apart from the lenses in your eyes and your red blood cells, in which the DNA is broken down to make way for crystallins and haemoglobin, respectively.
** This 2m of DNA is not a single unbroken strand but comes in 46 chunks, packaged into chromosomes.
*** The vast majority of those mistakes don’t cause any problems, mostly thanks to the large proportion of noncoding DNA (which is often more flexible in terms of nucleotide sequence than sections of the DNA that code for proteins) in our genome. There is also redundancy in the genetic code, so that mutations in ‘coding’ DNA are not always destructive.
 
References for the exceptionally keen
DNA replication:
http://www.ncbi.nlm.nih.gov/books/NBK21113/
Human mutation rates:
http://www.nature.com/nrg/journal/v13/n4/full/nrg3206.html
http://www.nature.com/ng/journal/v43/n7/full/ng.862.html
http://www.nature.com/news/2009/090827/full/news.2009.864.html
http://www.ncbi.nlm.nih.gov/pubmed/22345605

The Research Scientist’s Psalm

Image courtesy of NASA

Psalm 111 is often called the ‘research scientist’s psalm’.

Great are the works of the Lord, studied by all who delight in them. Psalm 111: 2

I’ve already told the story of how the second verse of this psalm came to be on the door of both the old and new Cavendish laboratories in Cambridge. James Clark Maxwell’s successor as Cavendish Professor of Experimental Physics was the Nobel Prize-winning Lord Rayleigh. Rayleigh was also a Christian, and he had the famous verse printed on the front of each volume of his collected papers. Geneticist R.J. Berry writes in the journal Science & Christian Belief that Psalm 111 demonstrates wisdom rooted in the study of reality. If verse two is the scientists (and artist’s) charter, it needs to be balanced by verse ten.

The fear of the Lord is the beginning of wisdom; all those who practice it have a good understanding. Psalm 111: 10

God’s provision comes on God’s terms. In other words, the correct response to a study of nature is ‘reverence mingled with delight, gratitude and trust’. This psalm also demonstrates that wisdom is best shared in community: scientists should communicate their findings so that others can ‘delight in them’ too.

I will give thanks to the Lord with my whole heart, in the company of the upright, in the congregation.

Psalm 111: 1

Finally, there is a seamless relationship between history and science. God’s creation, his generous provision and his interaction with us are all part of the same story. As Berry has said:

We are here for God’s purposes, on God’s terms and in (and for) his world. For Christians, science should be both a religious activity and an intellectual discipline.

R.J. Berry, The Research Scientist’s Psalm, S&CB (2008) 20, 147-161

Johannes Kepler may have had Psalm 111 in mind when he wrote his now famous prayer, which came at the end of one of his scientific works:

If I have been enticed into brashness by the wonderful beauty of your works, or if I have loved my own glory among men, while advancing in work destined for your glory, gently and mercifully pardon me; and finally, deign graciously to cause that these demonstrations may lead to your glory and to the salvation of souls, and nowhere be an obstacle to that. Amen.

(The Harmony of the World (1619), end of Book)

The Magnitude of God

E. coli

Another talk that I heard at the ASA meeting a couple of weeks ago was on ‘The Magnitude of God’ by Pamela Bryant. The whole talk was an attempt to comprehend the scale of the universe, from the very large to the very small, along the lines of the video ‘Powers of ten’. The slides are here (60 MB…), complete with references, and are well worth a look.

It often seems that in our search for knowledge we are only limited by the power of our imaginations. Nano scale research and applications are the perfect example of scientists playing with technology that many people in the world use without having a clue how it works. You can buy a 32 Gigabyte micro SD card a few millimetres long that holds  720 hours of movies, but compared to what is already out there our technology looks very clunky indeed. The bacteria E. coli are ten times smaller than the average micro SD card and they compute about a thousand times faster, their memory density is a hundred million times higher and they need only a hundred millionth of the power to operate.

There are some fun details in there too. If you took all the people alive in the world today and removed all the empty space from all the atoms in their bodies, they would fit into a space the size of an apple (originally posted on John Topley’s blog – has anyone checked!?)

Pamela also told some of her story – she is from Texas originally, where she studied chemistry and became a high school teacher. 20 years later she moved back into the lab, completed a PhD in chemistry, and found herself as a postdoc at MIT, doing work on nanomaterials that she said was beyond her wildest dreams. After some time as a postdoc she returned to Howard Payne University in Texas, to give something of her experience back to her students. And Pamela’s own reaction to the torrent of scientific information she delivered in her talk?

‘Humility, wonder and a sober understanding of God’s magnitude.’