Not about everything

December 16, 2012

Documenting my own life

Finally I have found what I have been looking for: a virtual machine with mediawiki installed,  it is here.

As many of us, I have boxes full of unsorted photos from before digital photography, I have boxes full of handwritten letters from before email (yes I am old) and generally I have lots of memories which I think are worthwhile remembering. Well, maybe my children won’t care very much about my memories. But maybe one day they, or their children’s children get interested in genealogy. I did. And I very much would like to have some more information about my great grandparents personal life. Something more then just their date of birth, marriage and death. I wished they left some more documents. But they could hardly write and photography was for a different class in those days.

Maybe someday someone will be lightly interested in my life. Not as much as I am of course. To me – I have to admit –  my life is of quite some importance. And I have done some efforts to materialize my memories. A directory on my computer devoted to my life, a dozen of annotated photo books on the shelf.

So I have been looking for a way to document my life that would be easy for me, easy for others and sort of permanent. Permanent in the sense that in 30 or 100 years people should still have software to open it.  My guess is that HTML is the most permanent format. There is so much  information in HTML available now already, that it will be and remain worthwhile to have programs understanding HTML.

Easy for me means, that is it is easy to expand and easy to change and wikipedia came to my mind. I know that editing in wikipedia isn’t immediately easy, but I have done enough wikipedia edits to be familiar with it. The outcome is HTML. So anyone can easily consume it.  It is not very hard to learn to edit it.  So,  as a benefit, I could allow my wife and children to have an account and also add articles and edit stuff.

Running it in a Virtual Machine is great, because it is easy to duplicate (“fork”),  so every child of mine could get his own copy and share it with his own children. Even in the long run, I think that virtual machines will make sense. Maybe  in 50 years, to run my current vm, it needs a vm in a vm in a vm.  But it sounds like it will be possible. Or maybe people will just have everything in a cloud. Who can predict the future?

I am aware that I might drop a precious idea here. Wouldn’t it be nice to have an online project based on our personal lives, our personal stories and histories that we can write ourselves. We could give relatives and friend permissions to view or even edit certain articles, as they would give to us.  It would result in a vast  network of personal history. Nothing like the neutrality of the wikipedia (nothing against that). Just our own stories and the stories of those who matter(ed) to us.

Anyway, I expect that the wikiproject that I just started will live on for some centuries – given that my “line” doesn’t die out.

So at the end: a big cheerio for the people from BitNami, for providing a virtual machine with MediaWiki pre installed. Because I am simply too lazy (or rather too busy with other things) to make such a thing myself.


September 29, 2007

Your own robot on the moon?

Filed under: idea,internet — takaita @ 07:56
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Doesn’t it sound like a very cool thing to be able to sit behind your computer and control the actions of your very own robot on the moon? I recently read about this idea, which originally is from the Dutch Nobel prize winner Gerard ‘t Hooft. I am not totally sure where he first launched this idea, but it might be in his book ‘Planetenbiljart’, published in 2006 (not sure if it has been translated, the title translates as ‘Billiards of the Planets’). The idea is based on the much older idea of colonizing space with the use of robots, it only democratizes it: each of us will have our own robot on the moon and we can use it to build a civilization there. Very much like Second Life, but for real this time.

In one of the articles I found while trying to Google the idea, I read that a US company has developed plans to have your robot on the moon, but I haven’t been able to figure out which company that is. Suggestions are welcome.

September 7, 2007

A greeting to future historians

Filed under: history,idea,world wide web — takaita @ 22:53
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Link rot, web archive, copyleft to preserve content for the future, the digital dark age. I was in a discussion on the interweb about this. The current diarrhea of weblogs and myspace stuff and photos, the highly praised content of web 2.0, created by the average user about his or her average life and average opinion. It should all be preserved. Future historians want to know all about us.

Yes, I gladly join. This is my content. Mediocre as can be.

For the occasion, a special greeting to future historians. Let me keep it simple. One word. “Hi

Mikulov - Jewish cemetery

As always it needs a photo. What is more appropriate then a photo taken on a graveyard.

June 18, 2007

Idea: a new HTML attribute on the IMG tag for zoomable images

Filed under: idea,photography,world wide web — takaita @ 06:52
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Often is stated that more megapixels on the web is not so useful. Computer screens are not big enough to display all those pixels. Of course screens get bigger in time. But the size of computer screens does not increase very fast. It will also have a reasononable limit. Most people would not want to sit at screen of several square meters.

10 million megapixel camera
10 million megapixel? This must have been a mistake.

But what about zoomable images? We have them all over already with maps that are made available by big companies like Google and Yahoo. What about a new attribute to the <img> tag, that will automatically add zoom functionality to the image displayed. Wouldn’t that be great?

Something like <img src=”myphoto.jpg” width=”300″ height=”200″ zoom=”yes”>. Then when the actual photo is 3000 x 2000 pixels this automatically displays a zoom bar on the photo which allows step-by-step zooming in to the actual pixels. The area in which the image is displayed does not grow bigger while zooming in. But it should be possible to move the zoomed-in photo around in that area with the mouse. Exactly like the different map-applications work.

Of course this effect can be created now too, but it requires lots of (javascript) coding and it requires that for each zoom level a new resized image is created and placed on the server. That’s not really easy.

May 10, 2007

I took my camera and shot back

Filed under: idea,internet,photography — takaita @ 19:14
Tags: , , , , ,

Finally I had the nerve to do it after thinking about it for months. My response to the violation of my privacy. The interweb is getting everywhere, it’s logging all that I do, based on anti-terrorism laws. Yes, I am a suspect, I need to be controlled because I might be dangerous just like anyone. Who knows what I search for on the interweb, what I post, about what I discuss, which nick names I use, what my real name is, what my number is, where I live, who I love, what I do for a living and how I spend my money, where I post my photos (with EXIF-data and preferably geo-tagged), what I think and of course what my garden looks like. Yes, that is right. I looked up my house on Google Earth and I clearly saw the two garden chairs which I own, standing in my garden. I must have been lucky that I wasn’t there when the Google satellite passed by. But who knows when i comes along next time. I can no longer sit quietly in my garden, because every moment that satellite might fly over and photograph ME. They’ll know what I am drinking, what I read and in a while the satellite might even monitor what I think.

I am just sitting in my garden.

What can I do? How can I hide? Can I hide at all? I just want to be by myself and with the people I chose to be with. Not with some spying satellite around that will post me and my garden on the interweb.

So slowly my plan took form. It took me weeks to think about my little revenge. Then I started planning, the weather must be just fine, the colors of the sky just right. And I had to overcome my fear. What if….What if that satellite just was there. Or what if it just wasn’t there. I needed luck. The satellite should have to be there, but it should photograph something else, not my garden.

Then one day I dared. I took my camera and shot back.

I took my camera and shot back

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?

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