h2g2 The Hitchhiker's Guide to the Galaxy: Earth Edition

What, exactly, is the relationship between the information in our DNA and our physical reality?

What I mean by this is that often DNA is referred to as the blue print for the organism. Yet I don't see how our DNA can contain the information on each and every cell in our body, where it goes and what it connects to (and how it connects).

So whilst I can see that DNA contains the relevant information on how to build the types of cells involved, what tells the cell what sort of cell it is going to be?

A very good explanation is contained within Richard Dawkin's "The Blind Watchmaker", where he outlines an analogy of how DNA works by developing computer generated models.

It's a kind of recursive algorithm. The DNA code does not actually contain the blue-print for the finished article, just the code for the cell under construction, but as the process recurs and recurs millions of times a final organism is arrived at. If there is any change in the initial DNA composition, a different end-organism is arrived at.

Or something like that. There are a few evolutionary biologists here so I'll defer to their expertise..

Yeah, that's a good book and one of the ones that first got me thinking!

What you highlight is about where my understanding gets to, although not as lucidly put as you did!

What I'm trying to work out is what says that the current cell being worked on that it is going to be a neuron. Or a skin cell or a muscle cell or whatever. I'm guessing there is some communication between the cells as they develop.

The computer models in TBW (as I recall, so I may be wrong) are simple a-life models where OK the shape changes but the individual components of the picture are all the same.

You can apparently take a immature cells from one part of a foetus, and make it into a different kind of cell by placing it in another part of the foetus.

Leroi talks about it in his book Mutants. Something to do with a lot of hormones overriding each other and stuff.

It's a long time since I studied embryology (and I was lousy at it at the time...) but as far as I remember it's all to do (at least in the early stages) with the cell's position in the embryo. To start with, the embryo has one cell, then two, then four, and so on. Initially, they're all pretty much the same. But eventually, some cells will find themselves on the outside of the organism, in contact with only a few other cells, while others find themselves on the inside, completely surrounded by other cells. Each cell produces growth factors and other signalling molecules - the amounts of signal that each cell is exposed to depends on where they are in the developing organism. So, cells in different positions start to develop slightly differently (ie, different genes are transcribed depending on the environment). As they develop, they start to secrete different growth factors, which affects the cells around them, and so on and so on...

If that didn't make any sense, I'll try again!

HOX genes. Their discovery won the Nobel prize for medicine about 15 years ago I think.

They were discovered in the evolutionary biologists most oft used organism drosophila fruit flies.

Basically they discovered a set of 12(ish?) gene which they temed homeotic box genes (The 'box' is a repeated nucleotide sequence shared by them all) that caused specific effects on growing embryos.
They were named according to the effect they had on the embryo so they have strange names like Wingless and Hedgehog.

Anyway, these same genes have been found in almost identical form in all organisms looked at and they are sort of master genes for cell differentiation.

Basically in a growing embryo gravity or another factor will cause accumulation of hormones which will switch on certain HOX genes and these will turn on a cascade of downstream repsonses which will turn the cell into say a neuron or a muscle cell etc.

Sonic Hedghog protein (the gene product and yes, the name, I know) which is the human equivalent of drosophila hedgehog will turn susceptible cells into neurons for example.
It has been the subject of intense research as a possible cure for Parkinson's and Alzheimer's disease as a result (with notable failure so far I would add).

>which they temed homeotic box <<
termed! hence HOX, Homeotic bOX

orcus! I'd heard of HOX genes but not followed up on it.
So it is a self organising principle, and it seems environmental factors play into our development, may even be essential to our development, from the offset?

Is this theorised then to perhaps cause oddities if the development occured in zero-G?


btw, I heard they're trying to rename a load of these genes since they now feel that PhD. Student humour is perhaps not the best method for naming them

Well I got the gravity bit from how seed develop, knowing which way is up, my guess is that it would be more hormonal in higher organisms.

The theory that HOX genes discovery went hand in hand with is the Collinearity theory I think. The collinearity theory went along the lines of that organism exhibited a kind of linear symmetry. head at one end, tail at the other and legs either side of the axis, one eye each side and so on. The collinearity theory was such that it was predicted that the genes responsible for this embryo development would be similarly lined up along the chromosome. The HOX genes it turned out are indeed, as predicted, lined up according to the collinearity theory.

I think there names are actually derived from the effect that knocking them out has on the embryo in fact.

Shouldn't PhD level humour be of a fairly advanced and sophisticated variety?

It´s when the HOX genes get screwed up that you get cows with legs where their horns should be and such.

"I think there names are actually derived from the effect that knocking them out has on the embryo in fact."
That's what I heard, but, erm, there's ways and ways again of naming things after the effect it has. Some are perhaps little more crude and non-pc than might be required! Plus I think some of the dinosaurs are narked they ain;t in latin

Well renaming them will probably happen, can't say I'm bothered really other than a slight pang at the loss of Tiggywinkle Hedghog (my personal favourite) from the scientific vernacular.

One of my profs at med school back in the medevial days (according to my offspring anyway) claimed that the hedgehog to blame is Sonic http://www.sega.com/sonic/content.php

which wouldn't surprise me at all... far too many grad students spend too much computer time doing anything but science...



PS Hootoo is much more amuzing than protein gene product 9.5

"What, exactly, is the relationship between the information in our DNA and our physical reality?"

Good question - it's one of the biggies.

Answer: don't really know yet because it's dead hard. We know what the blueprint (the genome) looks like - however, we don't know how the blueprint builds itself into an organism.

One of the major challenges of biology is trying to figure out how the "genotype" (the particular genetic make-up of an individual) becomes the "phenotype" (the physical traits that come about from the expression of the genotype). Since we have just got a handful of full genome sequences we are just starting out on that path.

Once we know how so-called "complex traits" are controlled genetically we'll be able to fix a lot of human disease such as Alzheimer's, Cancer, Aging, Parkinson's, etc., etc., etc. The genetic diseases we're working to fix now are simple, single gene defects such as cystic fibrosis.

We are starting to work out the complex gene interaction networks that regulate and build the body, and Evo-Devo (AKA evolutionary development) is starting to work out how the genes of different species work to put those species together in their particular way, giving us insights into their function.

It's all very exciting and new and potentially highly beneficial to mankind.


Ste

PS. Genes are traditionally named after what the organism looks like once the gene is mutated (especially in Drosophila genetics).