“GENETIC INFORMATION ARISES NOT FROM DNA ALONE BUT THROUGH ITS ESSENTIAL COLLABORATION WITH PROTEIN ENZYMES” – No, it arises initially from DNA. Enzymes, which are also synthesized from DNA, hack up and re-piece together in different ways the mRNA that is transcribed from the DNA until it becomes the strand of mRNA that they translate into a protein.

Of course, this is a gross generalization.

The problem is we need a new metaphor. Here’s mine:

Imagine you have a machine shop, and a big library full of blueprints on microfiche. Some of the blueprints include all the information the machine shop needs to make a microfiche reader.

The library includes blueprints for most of the tools in the machine shop. And also for various consumer products that the machine shop can produce to exchange for everything else it needs. And the library includes a business plan to tell it what to produce and when.

This business plan has evolved by repeating whatever has worked well in the past. So the shop makes swim gear in the late spring and skis in the late fall. But how does it know when spring comes? The library can’t tell it. The business plan has evolved to use whatever signals it happened to find useful in the past. So it might tell spring by subtle changes in wood, that it evolved to measure for some other purpose. Or sensors it developed for another purpose might track the difference between the ratio of UV versus red light at noon. Or it could measure temperature patterns. Or even use a clock. Each method has problems. Different parts of the business plan might use different measures to track the seasons.

There might be multiple business plans, and something signals when to switch from one to another.

The system has to track lots of things, not just seasons. Like temperature. Some machine parts are affected by temperature, they don’t work correctly when it’s too hot or too cold. The library may have blueprints for variations that work right then. And a temperature shift can signal which version to make. How does the system measure temperature to decide which parts of the library to read? There are lots of ways and different processes will vary. One way is to design particular machine parts which are particularly sensitive to temperature, which provide the signal by their failure.

And if you get an unusual sequence of events, that call forth an unusual collection of machine parts that are not usually all present at once, anything can happen. Because there has been little natural selection to prepare for that rare circumstance.

It’s possible to look at this and say “The library is in control because every machine part has its blueprint in the library.”. That’s true in a way.

Or you could say “The library is in control because every scrap of the business plan gets copied out and read to decide what to do next.”. That’s also true in a way.

Or you could say “The library is in control because there are parts of it that determine which other parts can be read, by themselves getting changed, even though they don’t actually produce anything themselves.” And that can be sort of true too.

All that was useful when it was becoming known. But nowadays it kind of misses the point. Now the point is, we have lots of feedback loops that were evolved by whatever accidental controls happened to work at the time.

And if there’s any immediate practical result from this, it’s that — to the extent you want your body to work as it was evolved to — you should try to live in an environment that provides the same cures that your ancestors got from the environments they lived in.

Note that he didn’t exactly make that generalization. He invited YOU to make that generalization and tell him what you thought the group was doing. And you sensibly did not.

Here was Edith Heard ‘s comment:

It is amazing to see how epigenetics has been propelled into the headlines over the past decade. On the one hand, it has been hailed as an explanation for inter- and intra-individual diversity, and on the other, as a purveyor of hidden information — beyond genes — that can be influenced by intrinsic and extrinsic fluctuations. The ‘hype’ surrounding epigenetics may partly be due to the fact that, since the human genome was sequenced 10 years ago, we have been confronted with the reality, and perhaps inevitability, of our genetic constitution. Epigenetics may provide hope that we are more than just the sequence of our genes — and that our destiny and that of our children can be shaped, to some extent, by our lifestyle and environment. The recent groundbreaking discoveries on induced pluripotency have also brought the reversible nature of epigenetic states to the forefront. Such reversibility brings much hope for treating diseases such as cancer, which have not just a genetic but also an epigenetic basis, for which ‘epidrugs’ can be used to reverse aberrant epigenetic changes (epimutations).”
(Heard et al. 2010. Ten years of genetics and genomics: what have we achieved and where are we heading?)

There clearly is an ideological Lysenkoisian aspect to the promotion of epigenetic.

Then why don’t they call the DNA that’s transcribed from a gene?

Limiting epigenetic manifestations by cellular level is a temporary stupidity. The problem is that the physical carrier of the epigenetic control system is yet unknown.

See my introductory article in our book “LIFE and MIND – in Search of the Physical Basis” 2007 available at http://www.misaha.com – BOOK

Savely Savva

Nope, it turns out a shockingly large (don’t have the number at hand) amount of intergenic DNA is transcribed sometimes, but it’s just (probably) noise.

http://topsy.com/twitter/razibkhan

and a link from MR.

again, a testament to the broad appeal of epigenetics?

I see a lot of articles that are ‘O HAY WE FOUND THIS GENE THAT AFFECTS THIS IF YOU MUTATE IT’ and some of them don’t actually say what that gene makes.