DNA or RNA - which would you choose?

So you're in the market for an information storage molecule. You'd like something functional and compact, runs on regular gas, and doesn't cause cancer in rats.

A quick scan down the options, what is there out there that you could base a species on?

DNA

At the top of the popularity list is DNA. No one ever got fired for choosing DNA, DNA is a the choice of the masses. Its used by 99.9999% or so of all known organisms. Its the safe choice, its the sensible choice, its the boring choice.

RNA

However, maybe you aren't one to follow the pack, maybe you like to dabble a little in stuff thats not run of the mill. RNA at number two in the list might suit you. Its not the popular choice, but other organisms have made a go of it, so maybe you can too.

Others

If your really into the exotic, you can go with untried and untested types, PNA, GNA, TNA might work for you, but you can't get them off the shelf, you'll have to make those yourself.

Choosing RNA

So - how about choosing RNA as your hereditary molecule? Its got a lot going for it. It can replicate, its already used to make proteins, its got any number of jobs around the cell. Its also pretty fast - only one strand to replicate, and the base it uses U is probably less expensive to make than the regular T.

However, RNA has its down sides too. Sure, its cheap to make, and allows you to live life in the fast lane, but its not very stable - too much wild living. When its not busy doing other things, or involved with other molecules, it likes to attack itself.
Its also a little shoddy when it comes to replication. It figures close is good enough. It mostly copies itself ok, but it slips up now and again, perhaps a little more frequently than you'd like.

Choosing DNA

DNA may be the old codger, but there is a reason most organisms go for DNA when looking for something to encode their lifes work. So its not as fast and loose as RNA, but at least it tends to keep what it started off as. Sure it may take a little longer to copy, but thats partly because it keeps checking itself to see if its doing it right. It will also stand back, and compare its second strand with the newly copied strand - just to check things are going on ok.

DNA requires a whole load of support infrastructure though, so you are probably going to need a package deal. You'll probably need to buy the copying, repairing and checking bits separately if they are not included in the main package - check the small print.

How to dry your hands.

I talked about how when you really understand something, the possibilities for lateral thinking really emerge.

Drying hands.

So there I am one day, in a motorway service station, having been to the toilet and washed my hands. I step over to the dryer, and put my hands under it and feel the warm air blow over them.

I've done this many times in my life, but this time I stopped and thought about it. What was I trying to do? I was trying to get my hands dry.

OK - that's the simplistic question, now lets see if I can refine it a bit more, what am I trying to do? I'm trying to get the water that is on my hands to evaporate into the air.

Evaporation is the key.

Now how does that come about? Well lets think about it a bit. The water on my hands is a collection of H₂O molecules that are attracted together by weak forces. On average, if you add up all the energy of the molecules and divide by the number, you get a value for the average energy, which is what we call heat. Some molecules have this energy, some have more, some have less.

Now and again, these forces are weak enough that a molecule near the surface which happens to have more than the average amount of energy breaks away from the pack and flys free. Once it is free, it gets to wander around in the air. As a result, the average energy drops a tiny bit, and so therefore does the heat. That's why wet hands feel cold.

Escape to freedom?

However there is a reasonable chance that any given escaping molecule may bounce off some other air molecules, and end up back in the bit of water its just left. It may not, but if might. You can reduce this by moving the air around just above the water - a hand dryer does this - OK so that's good.

Encouraging the leap

How can I encourage water molecules to make the leap from liquid to gas? Well its all down to their energy. If they have enough, and they're near the surface there is a good chance they'll break free. Give them more energy and the chances will increase. I supply them with energy already. My body heat supplies the water molecules vibrational energy.

I can't do much about my body temperature. Evolution has worked long and hard to give me a body that maintains a constant temperature. However, I can get more heat into the water from the hot air coming out of the drier. So holding my hands under the warm air is going to give more energy to the water molecules.

Making the leap easier.

OK - well I was already doing that. Is there anything else I could do?
Yes there is. These evaporating high speed molecules can only get out if they are near the surface of the water. If they're not, chances are they'll bounce into some other molecule on the way out and never make it. So if I can make the surface bigger, and the layer of water thinner, I should be able to dry my hands quicker.

How can I do this? Well smearing the water out into thin layers is the easiest. A sphere of water has the least surface area for its volume, and a 1 atom thick film of water the most. So therefore the ideal way to dry my hands is to rub them together, so smearing out any drops of water, whilst holding them under the warm moving air. I need to balance the moving warm air getting into contact with the water with the shielding effect of my rubbing hands. So a vigorous action that keeps allowing the air to get at the water is best.

Result!

What do you know - that's just what it says on the dryer! However I feel so much more superior having worked it out for myself! Try it for yourself some day. Try just holding your hands under the dryer, and compare that to vigorously squashing the water flat by rubbing your hands together. See if you can spot the difference.

The learning experience

Learning... what is learning?

I've come to the conclusion, that for me at least, there are three stages to learning and understanding something.


Stage 1.

I know nothing. This is how we all start of course.

Pick a topic, like say playing a musical instrument, cooking or the electromagnetic-spectrum. You start off knowing nothing about it, at least at one stage in your life you do. You are an outsider at this point. Maybe you can watch others perform music, cook a meal, or predict the warming effect of a beam of light.

However to you, its all just a form of magic. You know there is nothing magic about these people, but they just have some sort of gift that you don't possess. I've been in all of these places.

Stage 2.

You learn how to do something. You decide you've come this far, and really its time you knew how to cook. How do you go about fixing it so you can cook? Well there are the obvious ways. You can take a course, you can read a how-to book, you can ask someone who can cook to show you. Gradually you'll get into the zone where you can cook. Cooking in this way is a wrote mechanism. You want to bake a cake, you take down the recipe book, turn to the page, and follow the recipe. You're passingly familiar with the notation. You know what eggs are, and what cups/grams/teaspoons mean as measures. You can cook now. Or at least you can cook if you have a recipe. You also need the ingredients, and if you don't have the balsamic vinegar the recipe requires, you move onto a recipe you have all the stuff for. If you have a recipe that calls for a technique you're not familiar with, you move on until you are back in the familiar.

The same with musical instruments. You learn the musical notation, you press the keys, cover the holes, or depress the strings and with practice slowly you can make music. I have to admit this is as far as I got with my musical studies. To go further, you need enthusiasm, which is probably one of the rarest commodities around - and easily removed by careless remarks.

If you remain at stage 2, you can solve a certain class of problems, and this can be fine for some things. You probably know how to do long multiplication in this way. You take two numbers - you follow a learnt procedure and you get a result. That's good enough for most people, after all, you're mostly interested in the result, not the method.

Stage 3.

This is where things start to happen. To get to stage 3 you need either a natural inclination for the subject, or sufficient enthusiasm to get you to the stage. A good teacher helps too of course.

At stage 3, you sort of transcend the topic. Its where you get to what Robert Heinlein defined, in one of his novels "Stranger in a strange land", to "Grok" the subject.

Its a great feeling when you get to that level, and its difficult to describe what it feels like, but you must have come across it in one discipline or other. A musician who really understands his/her subject, is no longer confined to the notes on the page. They begin to understand the underlying rules to what makes a good performance, and that really the notes are only a guide. Jazz is one form of this.

The same with cooking - OK the recipe demands demerera sugar, but you can see really what is required here is sweetening - and that white sugar will also work, though maybe not as well. Honey, or treacle is also an option here. Yes it says two eggs, but at a pinch one will probably do, if you make up with a little liquid, and perhaps a little raising agent if one is all you have.

Breakthrough

When it happens, a breakthrough to learning can be the most wonderful feeling. Its an epiphany of understanding, and suddenly the murky waters clear, and all that stuff you've been struggling with drops into context. Its not the end of the road by any means, but its suddenly the case you can see what it all means.

I can still recall the day the electromagnetic spectrum broke through for me. I'd been studying physics at school for some years, and I understood that light was made up of colours. I understood you could take pictures of peoples bodies with X-rays. I knew that you could put together electronics in a way that would pick up radio waves. I'd probably even been told these were all part of the same thing. But you can be told, and you can understand! I remember it happening, quite vividly - getting out of the car after my mum had driven me home from school, and there in the driveway of our house, the E-M spectrum suddenly revealed itself to me! It clicked together in my head. Radio waves were just kind of slowed down light waves, and X-rays were just speeded up light waves. Well not really, it was just a difference in energy, but it was a way of visualising it. Now, I could see it made no sense really to say at what frequency do radio waves begin and end - they're all the same thing. Radio waves are just an arbitrary human division. The E-M spectrum had clicked, and looking back, I couldn't for the life of me see why it never had before. It is sooooo obvious.

To really learn something, you need to do it, teach it, or simulate it.

This is where being a good teacher is hard. You can see now how it all works, but can you remember what it was like before it clicked? What makes it click for you, may not make it click for someone else. This is also why you need a deep understanding of a subject to teach it. You need to be able to explain the concept in different ways. You're standing at the top of the mountain, and you can see the path you got there via. However others will stumble and fall on this path, but there are paths all around the mountain. One of these will probably work for someone else. If you only know the path you got there with, you probably can't explain it to others.

Doing it obviously helps in understanding, but I don't think it always allows you to make the jump to stage 3. When teaching, you need to be prepared to look at alternate strategies, which leads you into deeper understanding.

Computer (or other) simulation is almost as good - as the program asks questions you need to know the answer to. OK - what happens when the program gets into this state? What should happen?


Wrap up

Stage 3 - the groking level, is the one to aim for - because it not only allows you to understand and solve problems - but extrapolate it to other similar problems. Stage 2 will get you by if you need to do something, but you're missing out. Stage 1 is ignorance, and life is short so you have to pick what you're willing to be ignorant on, as you can't do all things.

Day 1

So here I am, wondering if I have the enthusiasm to maintain a blog about the fascinating world of science. I'm interested in nearly all aspects of science, though I tend to drift across areas from time to time. As I drift in and out of disciplines, I discover all manner of things that make me think WOW, or hmm - thats interesting.

So - I'm wondering if its worth writing some of this down to share, and whether anyone else would find it interesting. At the same time - do I have the discipline to keep writing, and will I keep discovering interesting stuff fast enough!

Time will tell...