Not about everything

March 17, 2007

Camping gardening

Filed under: idea,travel — takaita @ 10:31
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2006. On holiday in Spain. On a camping. Man, is it dry out there. I live in the Netherlands, and that is full of water. Spain is hot and dry. Of course that was one of the reasons to go there, looking for a change. But I could not stand the dryness of the camping ground, I pitied the brown grass, it looked all dead. I decided to do something about it. And I hope that I will start a new trend among visitors of campings. Help your camping be more green. Help nature and learn about nature. Join the new project: Camping Gardening.

Here’s a report of my first (and so far only) camping gardening project.

Camping gardening, step 1
The first step was to select a piece of camping ground to garden on. I did this my grabbing a few stones and putting them on the borders of an area of about one square meter. With another stone I draw the borders in the ground.

Camping gardening, step 2Camping gardening, step 2
The second step in this case was to take a big bottle, fill it up with water in the toilet building on the camping and pour the water over the selected area. Repeat that until the water no longer is soaked up by the dry ground. The pouring has to be done carefully when the ground is very dry, otherwise the water the water will run out of the selected area. It took quite some patience in this case, but it was rewarding to notice that about 20 liters of water could be poured on the selected square meter.

In fact that was all what was needed in this case. I did not want to plant roses or any other beautiful flowers, because, as you can see in the first photo, the selected area located on a spot where others could later (after I left the camping) place their tent. In the case of roses, it would not be good for the tent, in other cases it would not be good for the flowers.

So I repeated the procedure of pouring water over me camping garden every day, until I left the camping. I’ll show some results below. But first this. My girlfriend – we were together on holiday – got also interested in my project, and while I was away, probably doing one of the other important things a person does while on holiday, she carefully relocated a flowering plant to my piece of ground. It is visible as a pink spot on the next photo in the lower left corner of the square. Of course at my return to the camping, I recognized it immediately as an unnatural feature and remembered that the same flower had been growing a few meters away. But our relationship is such that I just needed to smile to her after pointing with my eyes to the flower, and we completely understood each other.

Camping gardening, the secretly planted flower

And now for the result. I’ll limit this part to posting some photos. They are resp. from 9, 11 and 13 August. I’ll leave it to you, dear readers, to see how much my project had visible results in such a few days.

Camping gardening, August 9 August 9.

Camping gardening, August 11 August 11.

Camping gardening, August 13 August 13.

March 10, 2007

The beneficial prion, evolution and the origin of life

Filed under: biology,idea — takaita @ 23:01
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This article is speculating about evolution of species which is not based on changes in DNA.

Horizontal Gene Transfer
Currently, evolution is seen as DNA-based, because DNA is regarded as the only part of organisms that is inherited. DNA is the blueprint for an organism in the next generation. Richard Dawkins, in his book “The Selfish Gene” even shifted the focus of natural selection from complete genomes (species) to single genes. There is recently some unrest about Horizontal Gene Transfer (HTG, also called Lateral Gene Transfer). HTG is troubling, because it impacts our view of the tree of life. If genes are tranfered from one species to another, then the Tree of Life no longer has only branches (where species split of), but also knots (where the genome of different species are mixed to produce a new species).

Horizontal Gene Transfer is however not the only reason that the Tree of Life might have knots. There are researched cases of new species developed from hybridization of two other species, for example in the butterfly genus Heliconius and cichlids in Lake Tanganyika (fishes in East Africa).

The beneficial prion
A prion is an infectious protein. Some diseases are caused by prions, such as the Mad Cow Disease. A protein is a long chain of amino acids. Proteins can carry out their function in a cell because they have a special three-dimensional shape. Some proteins can be folded in different shapes. When such a protein has been folded differently, it will no longer be able to carry out the function it used to do. Prions are proteins that are shaped differently and also have the ability to refold other proteins into their own shape. The latter makes prions infectious. Once a single prion comes into a cell, it folds another protein. After finishing the job, there are two differently shaped proteins which each can fold another protein into their own shape. Then there are four, eight, sixteen etc of them.

It is interesting to notice that prions are self replicators. They require a very specific substrate which is only found in certain living cells.

Prions are usually a disease. They disturb the normal functionality of proteins and replace it with another (or no) functionality. That is what they have in common with mutations in the DNA, a change in a gene produces will produce a changed protein and only very rarely this protein has a beneficial effect on the organism. However these rare beneficial mutations in DNA are assumed to drive evolution.

Are there any beneficial prions? It is thinkable, and in fact there is an example of it. In yeast, a prion has been identified which in certain circumstances is beneficial, see for example Prions act as stepping stones in evolution. The remarkable thing is that the effect can be passed on to the offspring.

Inheritance of prions
It is important to notice that reproduction of organisms does not only involve the passing of DNA. Sexual reproduction involves an egg and a sperm cell. A sperm cell is assumed to be just DNA, encapsulated in machinery to transport the DNA into an egg. The egg however contains the complete machinery of a living cell: organels, proteins, ribosomes. That is needed because DNA on its own can not replicate, DNA on its own isn’t alive. DNA needs the machinery of a cell for reproduction.

A female who has acquired a beneficial prion might be able to pass this prion on to her offspring through the egg. And the offspring will then also pass this prion to the next generation. The prion is inherited.

There it is: a non-DNA-based mutation which is inherited.

Co-evolution of self-replicating systems
Continuing to speculate, I would like to consider living organisms not as just a machinery to replicate genes. This latter view, which has been promoted by Richard Dawkins in his book The Selfish Gene, seems too limited. There is more to an organism then just the manifestion of the information stored in the DNA. There is more inherited then just DNA.

There are several theories about the origin of life (I wish to ignore the creationist theories). They all agree on one point: it started with something able to self-replicate. In some theories that first thing is RNA. In other theories it is metabolism-first.

I like to think about the origin of life in terms of co-evolving self-replicating systems. There was RNA, there were bubbles of lipids, there were reaction chains (metabolism) and they all were self-replicating independently. RNA and reaction chains which would get into a bubble of lipids formed a self-replicating system and they co-evolved to living cells. The self-replication of each element became heavily dependent on the self-replication of the other elements. In the safety of the cell, RNA has partly been replaced by DNA.

A beneficial prion is a inheritable mutation in the metabolism-system, but not in the DNA-system. The different self-replicating subsystems of a living cell still have the possibility to evolve. Of course the DNA-based evolution is the most obvious. The blueprint model is the easiest to understand. It is the subsystem which has been subject to research when it comes to evolution.

What to research
I admit that there is a lot of speculation in the above. It needs research. And here are a few ideas for that. The trouble is that all living organisms are supposed to have evolved from a single common ancestor which already had evolved considerably. This Last Universal Common Ancestor (LUCA) must already have been pretty good at self-reproduction, because it outcompeted all rivals at the time. It must have had a well-developed integration of the different subsystems. What we should be looking for is examples of differences between species in the integration of the subsystems. Because we are facing the situation that all living organisms stem from this well-integrated LUCA, it is probably impossible to find a totally different way of integration. Although there is an exception: viruses. Viruses are not considered to be part of the LUCA ancestry. The origin of viruses is speculative.

The proteins of a metabolism-chain are currently seen as the result of DNA-based evolution. If they are the result of co-evolution between DNA and the metabolism-chains, then the metabolism-chains might have adapted to the DNA. As DNA (indirectly) produces proteins, some metabolism-chains might have changed to use available proteins. This opens the possibility that related metabolism-chains in different species rely on totally different genes. Are there any examples of this?

Are there more beneficial prions then the one found in yeast. Are there any proteins that act like prions, but are so beneficial that every member of a species has this prion.

Can viruses be considered as a different result of co-evolution of subsystems?

March 3, 2007

Man digs hole and needs help getting out

Filed under: photography — takaita @ 10:19
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Vespacar near a hole in the streetA college owns a Vespacar, because it does not need a drivers license to drive it, and it does not need any money to park it (it isn’t a car officially).The street it was placed on needed some digging, and someone asked if they were going to bury the Vespacar. That was a funny enough reason to take some photos of what was going on. So there I went. With my camera.
While at the scene I witnessed something that surprised me. The hole was apparently made using a machine, but it needed some tweaking, and one of the men had stepped into the hole to do that. The hole was quite deep, and it wasn’t easy to get out with grace. The solution was easy, and well known to the men, but new to me. Another man stepped in the machine (while urging me to photograph the funny plate inside, it says: “your village called, they want their fool back”). The machine can function as a lift.
Man in a hole in the street Other man gets in machine
Machine goes to help man in the hole Machine lifts man out of the hole

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