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# Duda Jarek

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1. ## Data correction methods resistant to pessimistic cases

You mean encoding polynomial coefficients by values in more than degree number of points? I agree that it's great method but still pessimistic local arrangement of errors destroys whole block. Besides is very slow in decoding... This standard approach takes some blocks of the data and enlarge it to protect against some specific set of errors. We loose whole block if we get out of this set. I want to show that it's not the only way - that we can use not a small block to locate errors inside, but be able to use potentially all succeeding bits. So even if errors creates some pessimistic pattern, like clustering around a point, investing a large amount of time we could still be able to repair it.
2. ## Data correction methods resistant to pessimistic cases

Standard data correction methods, has some maximal number of errors they can correct. For example Hamming (7,4) uses 3 additional checksum bits for 4 bits of information - it works fine when there is at most 1 error per block of 7 bits. We use quite large redundancy, but is it safe now? The problem is with pessimistic cases - if expected error rate is 1/100 bits, still quite often it can happen that we have 2 errors in some of 7 bit blocks. I would like to propose some statistical approach to data correction, which allow to protect against such pessimistic cases. Thanks of this we can for example reduce redundancy to achieve similar safeness. The trick is to use a very precise coding - such that any error would make that the following decoded sequence should be completely random 0/1 sequence (p(0)=p(1)=1/2). For example a block ciphers, which uses previous block to calculate the following one, but there is much better coding for it I will say later about. Now - add to the information some easily recognizable redundancy - for example insert '1' between each digit. If while decoding it occurs that there is '0' in one of these places - that means we had some error before. Knowing statistical characteristics of expected errors, we can make list of most possible errors in such cases, ordered by their possibility - on the top of this list there should be 'switched previous bit', ... after a while there can appear 'switched two bits:...'. This list can be very large. Now if we know that there (nearby) appeared some error, we take this list position by position, correct as it was really this case (switch some bits) and try to decode further fixed number of bits (a few dozens). If everything is ok - we get only '1' on selected positions - we can assume that it was this error. If not - try the next one from the list. This list can be generated online - using large amount of time we could repair even badly damaged transmission. While creating the list, we have to remember that errors can appear also in succeeding bits. Using block ciphers is a bit nasty - slow, we have large blocks to find errors ... There is new coding just ideal for above purpose - Asymmetric Numeral Systems (ANS) - new entropy coder, which has very nice properties for cryptography ... and data correction - it's much faster than block ciphers and uses small blocks of various length. Here for example is demonstration about it: http://demonstrations.wolfram.com/DataCompressionUsingAsymmetricNumeralSystems/ What do You think about it?
3. ## Immunity by incompatibility – hope in chiral life

SF writer, Greg Bear (http://www.gregbear.com/blog/display.cfm?id=982), pointed me out that we need viruses - the point is that we use some parts (eg capsid) of REV (retrovirus which is in our DNA) in some essential mechanisms, so we can't replace it to something neutral. But over this millions of years, this capsids have been optimized for our purposes. Maybe it's good point for viruses to begin evolution, but there is still a long way, counted in thousands-millions of years. Viruses for evolution requires friendly environment - cells. Ours has quite good protection, much better then when viruses evolved last time. We can also think about transforming only eg human, and use original bacterial flora, which could be compatible (after teaching the immune system)? I've received a long letter from Steve Winter. One of many things he mentioned was that " there was a study where a group fed some bacteria chiral food, and it eventually evolved the ability to eat the food". It's large problem, but I think they should have much more problems with evolution of interactions (like aggressiveness) with chiral organism, and in supported by us chiral ecosystem, they should be dominated... And they usually die with the carrier. But the largest benefit from chiral life are viruses - let's say that we can manage with microorganisms, but elimination of viruses looks hopeless http://virology.wordpress.com/ And the lack of them should slow down the evolution of bacterias, making the creation of stable ecosystem easier. What are the costs of such project? The most of the cost is to transform a few cells of each needed specie - I think that required technology should be standard in a few dozens of years. Then we have to replace seeds for a few fields, clone some cattle ... and humans for adoption... The replacement process can be very slow. And the income ... HEALTH ... crop production ... pests ... maybe to be or not to be for natural Martian life until terraforming
4. ## Immunity by incompatibility – hope in chiral life

How to make such prokaryote? Huge problem is to create chiral enzymes, I will sketch in a moment how how I imagine that. Now take a solution of phospholipids, it will automatically create a bubble, fill the membrane with proteins, pump DNA, ... , ATP ... and voilla About the other parts of it... The cell should 'live' in specyfic, precise conditions, without most of them. Then it should try to stabilise itself, rebuild what's needed (like the wall). This would give us time to do something to allow it to reproduce. Having this small factories, synthesis of elements will be simple. But the real problem is with eukaryote. I think we could use the original cell and just replace/add what we need... Most of the proteins work with symmetric molecues, the other we could block or do nothing with them - if we place the cell in good conditions, feed it (even artifically with eg ATP), it should be stable while 'slowly' adding chiral molecues, replacing DNA ... and after some time/generations it will replace everything itself. Here is a sketch of production the (chiral) string of protein(/DNA): Prepare a surface with with oriented lattice of something that can adhere amino acids and that they can be easly released (by light, electric current, pH, temperature...). Then 'just' print (like ink printer) or litograph (use different solutions of aminoacids and light specyfic pattern to adhere) given patterns of strings of amino acids... Then use some catalysis to join neighbours. We would have maaany copies full of errors at one time. For selection process, we can use something the correct ones would adhere to. Now we can slowly recreate bottom-up customized ecosystem... But how to do it more effective and stable? Maybe we need viruses? I have a discussion about it on http://www.scienceforums.net/forum/showthread.php?t=27078
5. ## Harmony-the way to increase effectiveness of ecosystem

We can use normal cell too, especially to transform eukaryote. Most of the proteins work with symmetric molecues, the other we could block or do nothing with them - if we place the cell in good conditions, feed it (even artifically with eg ATP), it should be stable while 'slowly' adding chiral molecues, replacing DNA ... and after some time/generations it will replace everything itself.
6. ## Harmony-the way to increase effectiveness of ecosystem

I think I have a sketch of production the (chiral) string of protein(/DNA): Prepare a surface with with oriented lattice of something that can adhere amino acids and that they can be easly released (by light, electric current, pH, temperature...). Then 'just' print (like ink printer) or litograph (use different solutions of aminoacids and light specyfic pattern to adhere) given patterns of strings of amino acids... Then use some catalysis to join neighbours. We would have maaany copies full of errors at one time. For selection process, we can use something the correct ones would adhere to. About the other parts of prokaryote... The cell should 'live' in specyfic, precise conditions, without most of them. Then it should try to stabilise itself, rebuild what's needed (like the wall). This would give us time to do something to allow it to reproduce.
7. ## Harmony-the way to increase effectiveness of ecosystem

How someone from a few hundrets years ago wolud react to our world... When the nature gives us the possibility - sooner or later someone will use it... This is a kind of discussion to see such possibility, dangers and prepare for them - find a good solution. And don't You think that it's better to realise such possibility now then in 50 years, when required technology should be generally availible...? Science is unstopable and maybe leads to autodestruction - maybe it's the reason why we don't see other civilisations... or maybe matured civilsations has some other motivations ...
8. ## Harmony-the way to increase effectiveness of ecosystem

I really do know that it isn't easy... We are just entering to this scale of control. But in hundreds of years, I think we will try to construct our own 'better' life. What is the whole talking about nanorobots? One of the first steps should be copying of the nature - chiral ecoli. Just to show our power. Will we copy more? How to make such prokaryote? Huge problem is to create chiral enzymes. We have to fasten it somehow and add amino acids one by one. Analogically with DNA... Then we will be able to copy nature's mechanisms... Now take a solution of phospholipids, it will automatically create a bubble, fill the membrane with proteins, pump DNA, ... , ATP ... and voilla Having this small factories, synthesis of elements will be simple. But the real problem is with eukaryote. But maybe we could use the original membranes and just replace what we need... Now we can slowly recreate bottom-up customized ecosystem... Human won't be on the beginning - don't worry, he will have what to eat In this thread I'm asking what to select in this customisation...
9. ## Harmony-the way to increase effectiveness of ecosystem

In my opinion creative thinking is something that avers us from animials... But on the other hand, how would world built of individuals look like... We've lost the point ... Sport is good example of stress that requires extra energy, but improves immune system, gives health ... and can be overdosed. About energy effectivenes - food generally isn't now required, how it will look like in 50 years? It's very difficult to stop populationg growth, especially in poor country... The other thing is that natural energy resources, even nuclear power, is predicted (if we replace to closed fuel cycle too late) to run out even in this century... Maybe this chemical energy, converted form solar, is one of our hope? We should think about more effective use of it, then just burning... Eg many mitochondria and large membranes that uses natural pomps to create pH gradient, which can be converted into electicity... What do You think about chiral life? Create simple, closed, sterile ecosystems?
10. ## Harmony-the way to increase effectiveness of ecosystem

About stress... Living long with good health isn't priority for evolution. It is a process that favorates organisms which can use availible energy statistically most effective to breed as many as possible. It's why we are lazy - we need motivation to use energy. Stress is a kind of such motivation - to spend extra energy for immune system, to repair something... You cannot say that it is generally 'so bad'. It is damaging, when exceeding some limit, below it is positive - it's kind of motivation, which require extra energy in the given moment, but gives long-term benefits, like sports, learning, etc... Thinking about us - humans, energy isn't the priority, it's 'good:)' that we allow stress stay on opimal level on many aspects of life. About points - I agree that only 1 is essential. Is it possible to create stable, more effective ecosystem, eg crops, while removing some parasites? And if would remove some more organisms? How to make it to stable increase effectiveness, using organism we know or artifically weaken?
11. ## Harmony-the way to increase effectiveness of ecosystem

To do it we have to use tons of pesticides, etc... http://en.wikipedia.org/wiki/Pesticide. They are no neutral for us/them/enviroment, not perfect, expensive, not killing every parasite... In fact they only reduce number of them, and plants can defence themselves, but this defence costs too. But they cannot do anything with viruses - I imagine that there should a constant level of them, which influence the effectiveness... Replacing damaged cells wasn't high priority in evolution - it costs energy and give significal benefits rather for older humans then taken under consideration by evolution - that had prodigy (mainly let say 15-30 years). Small amounts of stress stimulate organism to spend extra energy - hormosis. http://en.wikipedia.org/wiki/Hormesis We should learn how to use optimally this mechanisms, but I can agree that infections aren't the best way of stress - we can throw out 3 from my list?
12. ## Harmony-the way to increase effectiveness of ecosystem

ok, short question Assume that we can completely remove all viruses, do You think it would result more crop prodution per hectar? The same question with crop/food animal parasites? One another - how You explain positve effects of small amount of radiation? Cell division can produce errors, but when it had to replace damaged one...
13. ## Harmony-the way to increase effectiveness of ecosystem

The required tool should be available in a few dozens of years (chiral life) Let's focus on a possibility of eliminating some parasite... What would it result in? Here is the list of general parasites positive effect, I can think of... Please expand it and discuss... 1. Population control - when the density of some organisms is growing, it's easier for its parasites to expand - this factor influence stability of the ecosystem. The question is if without it, some specie could dominate its ecological niche? Maybe it could be set that it would be automatically controlled by concurrency, food access,...? Maybe such domination wouldn't be so bad? Maybe without this control factor, ecosystem would achieve different point, which would be stable? 2. Stress increase - the elimination of weak organisms. It improve selection, required to evolution. But after a few billions of years, a few thousand shouldn't be so important... If it would be planned well, evolution shouldn't throw it out from the stable point... Removing of weak organisms, makes place for new too, which probable would have positive influence on the effectiveness of ecosystem, but needs some energy to grow earlier. So the removing of the parasite should make the population older, but I think that it wouldn't affect the effectiveness much...? 3. Stress increase - elimination of weak cells Small amount of radiation can have positive results, perhaps because it helps to remove damaged (weaken) cells, thanks of what there should be smaller probability of cancer... Summarizing - cells are being more frequent replaced - it's energetic cost, but thanks of it, organism should be more healthy and live longer... So reduction of this stress among animals looks positive from our point of view (it increase selection of organisms too), but about people - energy isn't a priority - we should choose it as optimal as possible... There should be many ways of replacing stress from infections. We could eg use radiation - I think we should study this technique precisely. I was thinking about using our immune system - teach him a very delicate autoimmune reaction, but it could be very dangerous. Anyway we would have to give immune system something to do - living in the sterile environment can lead to autoimmune diseases (hygiene hypothesis).
14. ## Harmony-the way to increase effectiveness of ecosystem

I have to add that I thought mainly about eliminating (micro mainly) organisms that practically only parasitize, not contributing anything positive into the ecosystem, like eg viruses, locust ... We couldn't restrict to system plants + us... soil have to be fertilized, fragments has to be decomposed, some reactions has to be made, plants has to be pollinate, etc, etc ... We need trees too (oxygen), we have different environments, specifications of places... Whereas most of the higher organisms in this moment, instead of farm animals, are rather keepsake of nature, they rather don't influence on our ecosystem... The question eg is, if we can manage with that viruses helps control some populations...
15. ## Immunity by incompatibility – hope in chiral life

There is a problem - for example we have human endogenous retroviruses (HERVs) in our DNA. Before transforming organisms, we should identify any dangerous parts in our introns, virus's capsids, and replace them with something neutral. If not - they can be used as a good start for evolution... I was thinking about projecting ecosystem based on harmony - there are maaaany problems to take under consideration - I've decided to start new thred. Generally - let's say we can manage with most of microorganism, there are some concetps for viruses too, http://virology.wordpress.com/ but they looks a bit hopeless for me...
16. ## Harmony-the way to increase effectiveness of ecosystem

If we look at our ecosystem - it's one huge domestic war - organisms uses most of energy on competition, fight... It's mainly energy from the cleanest, never ending source - the sun. In the times of threat of energy crisis, overpopulation, one of our hope could be increasing the effectiveness of this changing solar energy into needed sugars, proteins. The other thing is that we are geting closer to the concept of creating completely new ecosystems, like on Mars, where this effectiveness of development of ecosystem is essential for the whole project. I would like to initiate a discussion about the possibility of such increase of effectiveness: is it possible and how much we could increase it? One way I see to do it, is by selection of organisms - to create a very precise ecosystem, in which organisms almost haven't opposite interests. We could replace some organisms with handicapped ones by eg removing sequences coding some proteins too(evolution couldn't repair it quickly) . The tool we could use to remove some organisms, could be chiral life, I've presented in different thread. Let say, we have this Noe's ark to select, modify ... Let's think if it would be possible to such a stable, more effective ecosystem? How to make it make it, so the proportion of organisms would be automatically keep on the appropriate levels? So that evolution, climate differences wouldn't spoil everything...?
17. ## Immunity by incompatibility – hope in chiral life

why with chiral? Becouse there has been everything made ... a few billions years of evolution, just take what you need... Of course there is possible much more 'perfect' life, in devalopment of which we will make huge steps, not possible while evolution, like exchanging neurons with something based on conductors - with much higher speeds ... But devalopment of it, is unimaginary difficult ... much easier, for the beginning, is to copy (reflect) the nature About overpopulating, population becaming older ... it's already inaviodable social problem... In this way You can say to go back a few hundreds years... Science can give tools to make life easier, longer ... but what do people do with it...? About effectiveness... Look at the ecosystem - it's neverending domestic war, most of energy is 'waste' on competition, fights... And we would like to change it into something closer to harmony, by removing some organisms, so the energy (solar) would be mainly used to production of proteins, sugars and reproduction ...
18. ## Immunity by incompatibility – hope in chiral life

To create a stable ecosystem, we would have to transform a large part of ours. We would do it to reduce maximally competitiveness, aggressiveness - to maximize its effectiveness by harmony. Of course there will be many empty, profitable ecological niches and organisms would want to evolve to use them. But... 1. I cannot imagine that viruses would be needed - they wouldn't be transformed at all - they would have to evolve from zero, like free DNA. But last time it evolved pararelly with its victims, now organisms have very advanced specific/non-specyfic defensive systems ... 2. We would need many kinds of microorganisms. Symbiotic ones rather wouldn't need have aggressive mechanisms - they would have evolve them from zero. The problem would be with eg. saprotroph, but without viruses, evolution should be much slower and we humans can make it much more difficult for them. 3. Higher organism would need enormous large time to evolve... And if we would have new large problem, we can reverse again. There are some problems with living in sterile environment. There is the hygiene hypothesis that it can lead to autoimmune diseases. We would have to weaken the immune system or give it something else to do, learn it good responses. The other thing is that small amounts of stress (like radiation or infections) is positive - it eg. helps to get rid of damaged - weak cells. But I think we will understand better this mechanisms and learn to use them more effective artificially. Maybe transformation of our ecosytem would be to expensive, but in some time we would need to create completly new ecosystem eg. on Mars, and its effectiveness will be veeery important...
19. ## Immunity by incompatibility – hope in chiral life

About finding the way by pathogens... Evolution is a process of finding local fitness maximum by small steps... Let say that a virus get into chiral cell ... what next? Bacterias would eg need normal sugars... Chiral enviroment would be hostile for them, there is no way that eg virus could just transform naturally into chiral form. They would have to evolve from zero. Or by sabotage... but then we could easier controll their population, and they couldn't reach actual level. The danger I've found is that eg unicell which is able to photosynthesis wouldn't have many natural enemies ... it could evolve...dominate our enviroment. Very important priniple for the beginning would be: from chlorophyll organisms we can transform only plants which population can be controlled! About problems of sterile life... there is quite sensful 'hygiene hypothesis', that it would increase susceptibility to allergic diseases. But I think we would be able to manage with it...? About symbiotic organisms... Of course finally it would be needed to transform large part of our enviroment. We could start with eg ecoli and use them as a factories on the beginnig. Plants... and finally maybe human... Question if such chiral cell would function normally? I've found an article arxiv.org/ftp/cond-mat/papers/0507/0507347.pdf which says in abstract that corrections for P-symmetry would be 10^-17(...?). I could'n find more pricise formulation, but this number suggests that it would be many orders of magnitude smaller than thermal noise. It could be essential in symmetry breaking, but not in funtioning. We humans like to show our power and it's rather unavoidable that some day, we would be able to create a new life (what is the whole talking about nanorobots?) ... I think we will start with chiral... They could give us not only health, but I think they could allow us to increase efficiency of our ecosystems, of the most clean and powerful source of energy - sun.
20. ## Immunity by incompatibility – hope in chiral life

A while ago I thought about some concept, which should which should allow us, to get rid of all unwanted life. This is – by becoming incompatible. Previously I thought that we could do it by changing the language which encodes nucleotide triples into amino acids (be replacing eg tRNA), but it could result in enormous number of problems with gene regulation. I’ve just found the “safe” way – take mirror reflection! If we replace left-handed amino acids with right-handed, we would get mirror reflections of natural proteins. Analogically we could get chiral DNA, sugars, etc. on which new enzymes would work perfectly. Finally we would get normally functioning mirror reflection of natural organism, on which natural viruses couldn’t interact. We know, that there is a small violation of such symmetry (P), but it shouldn’t change the biochemistry. Such organism would have to be feed with reflected food, produced eg by reflected plants, which use to production symmetric (not chiral) molecules and unpolarized light. In such world natural hostile organisms, if wouldn’t be translated by a terrorist organization, wouldn’t have chance to transform into chiral versions. They could evolve from zero, but we would have many thousands years of peace. How to make it? We can imagine synthesis of every molecule, such reflected zygote is made of. The problem is to create the correct structure of membranes with specific concentrations … fill it with life… What with actual trends in nano-engineering should become possible in at most 50 years, I think. Then we could slowly transform our ecosystems. In that way we could get rid of any plagues. But if in such sterile environment, we would have perfect health? Maybe stresses created by small infections can, like small amounts of radiation, have positive long term influence…? What do You think about this concept?
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