ivanov_petrov: Загадочное объяснение

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shkrobius@lj
2006-06-08 22:10 (ссылка)

If you are interested in my professional opinion, and I know quite a bit about this problem, all existing theories of prebiotic evolution are total crap. Yours is only one of 10,000 concerns that can be raised with this dubious concept. If one separates fact from wishful thinking, no progress towards the solution has been made over the last 70 years. I, for one, refuse to believe that Life originated on this planet, with fully functional phototrophs popping out of nowhere in 300 Myrs after solidification of Earth's crust. There were no "untold millions of years" for this evolution. The story of a randomly assembled RNA molecule that originated all Life as we know it has the same currency as the more familiar story of Adam and Eve.

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	ivanov_petrov@lj 2006-06-09 02:28 (ссылка)
	Да, примерно так я понял, прочитав еще и современные публикации. Тональность высказываний разная, но примерно так (Ответить) (Уровень выше)

If you are interested in my professional opinion

e2pii1@lj
2006-06-09 03:59 (ссылка)

Скажите, имеет ли событие of a randomly assembled RNA molecule that originated all Life в бульоне из органических веществ, который вполне возможно существовал тогда на земле, при условии действия известных физических и химических законов, положительную вероятность (пусть даже крайне малую) или же вероятность нуль ?

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Re: If you are interested in my professional opinion

shkrobius@lj
2006-06-09 10:16 (ссылка)

It is 0. For starters, there was no "soup of organics." You do not call a dilute solution of a few picomole/L a soup. Furthermore, recent re-evaluations of terrestrial atmosphere composition in the early Archaean suggests the existence of primordial oxygen. Once you have oxygen, Urey-Miller mechanism for synthesis of N-rich organics completely breaks down: everything is reoxidized back to elements. Actually, there is no geochemical evidence for the existence of "organic soup" anywhere on this planet. Even if such a molecule would mysteriosly appear, it would not replicate because the building blocks would be exremely scarce, whereas chemical (photo)degradation is fast. Besides, the difference between RNA and a cell is greater than that between a pebble and a skyscraper. Forget it. By your probability argument, there is a finite probability that the first cell or - what the hell - the first kangaroo - appeared whole as a random permutation of atoms. Then you do not need RNA.

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Re: If you are interested in my professional opinion

e2pii1@lj
2006-06-09 10:57 (ссылка)

"
recent re-evaluations of terrestrial atmosphere composition in the early Archaean suggests the existence of primordial oxygen
"

Насколько надежны данные о составе атмосферы несколько миллиардов лет назад ?

"
it would not replicate because the building blocks would be exremely scarce
"

Почему современные организмы находят достаточно материалов для питания, а тогда были трудности ?
Ведь химические элементы никуда не делись и не возникли из ниоткуда.

"
the difference between RNA and a cell is greater than that between a pebble and a skyscraper
there is a finite probability that the first cell appeared whole as a random permutation of atoms
"

Полагаю, если уж как-то появилась простейшая молекула способная к само-дублированию, вероятность случайного возникновения клетки пренебрежимо мала по сравнению с вероятностью эволюции этой молекулы до клетки путем естественного отбора.

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Re: If you are interested in my professional opinion

shkrobius@lj
2006-06-09 12:01 (ссылка)

1) not too reliable, but certainly better than 50 years ago when Miller's experiment was first suggested.

2) they do not, without a fight. 95% of the organics are made through photosynthesis. You are recycling photosynthetic carbon. Availability of fixed N is the main limiting factor for Life in the ocean. It is still very tough on us. Chemical "elements" are neither here nor there. You cannot subsist om air (that has N and O) and a lump of coal (that has C). Life does not thrive on "elements."

3) you are hung up on self-replication. What is it about it? I am a man, I cannot self(!)-replicate. Yet I am alive. If all other people but me suddenly die, I am still alive. There are sediment bacteria that live for millions of years and divide once in 100,000 years. They are alive. On the other hand many things that self-replicate (e.g., crystals) are not. You think that "replicating" oneself is the property of extremely complex organic molecules. That is not so. Consider H2 gas in the radiation field of a star whose UV light dissociates H2 into H + H. The remaining H2 molecules would serve as the third body in a H+H+H2->2H2 reaction, thus "replicating" themselves. And so what? Your "simplest molecule capable of self-replication" is, well, the simplest molecule. What does that have to do with Life?

Finally, even the most ardent believers in prebiotic evolution do not claim that the latter has been driven by "natural selection." The concept of differential survival presumes the quality of being alive. Some popular definitions of "Life" specifically call alive all things that evolve by "natural selection." You are entitled to your beliefs about which one of the improbable events is more likely. I have no idea how to estimate their likelihood, and so is anyone else. Perhaps we are very fortunate that it was an RNA molecule. Could have been a TV set or a vacuum cleaner...

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Re: If you are interested in my professional opinion
(Анонимно)
2006-06-09 13:52 (ссылка)

recent re-evaluations of terrestrial atmosphere composition in the early Archaean suggests the existence of primordial oxygen.

В современной атмосфере Земли 21% кислорода, что не мешает всему объему воды в Черном Море, за исключением нескольких десятков метров приповерхностного слоя, быть восстановительным из-за растворенного сероводорода.

Even if such a molecule would mysteriosly appear, it would not replicate because the building blocks would be exremely scarce

Концентрация урана в земной коре в среднем 3-4 части на миллион; это не помешало возникновению самоподдерживающейся цепной реакции в залежи урановой руды в Окло. Существует масса механизмов приводящих локально к возрастанию коцентрации чего угодно на много порядков; для возникновения жизни не требуется, чтобы bottleneck был преодолен одновременно во всем объеме Мирового Океана, достаточно окрестности одного подводного горячего источника.

- http://lj.rossia.org/users/p_k

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Re: If you are interested in my professional opinion

shkrobius@lj
2006-06-09 15:27 (ссылка)

1) It is news to me that anoxic deep waters of the Black Sea are teeming with life.
2) Why do not you do some reading about the source of U pitchblende before suggesting me this argument? You'd learn that UO3 is a satellite of iron/copper ores all of which have biogenic origin, mainly forming during the oxygenation of the ocean by in the mid Archaean. The mechanism for concentration of the U was via processing of seawater by marine life and subsequent metamorphization in the sediment (sandstone). Such ores are tale tell indicators for Life. There are, actually very few mechanisms for concentrating trace ions in seawater that are not biogenic, directly or indirectly. Think again.
3) the popular "hydrothermal vent" story has absolutely no factual support. The earliest evidence for life comes from 3.45 Gyr old Strelley Pool Cherts, a carbonate bed and a shallow marine environment completely devoid of any hydrothermal activity. 'Nature' just published a review on these Archaean stromatolites which you might find interesting
http://www.nature.com/nature/journal/v441/n7094/full/441700a.html
These are built by calcifying cyanobacteria, your basic phototrophs. Frankly, the hydrothermal idea never made much sense. Most of the bacteria that live there are HS- oxidizers that use oxygen to make sulfite. No oxygen, no Life. We have thriving communities near these vents in our deeps because those are already oxic, due to the billions of years of photosynthesis. W/o that, you get your reqular Black Sea depths, brackish and dead. All these tales of 'once upon a hydrothermal vent' are just so stories and impotent hand waving.

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Re: If you are interested in my professional opinion
(Анонимно)
2006-06-10 04:15 (ссылка)

It is news to me that anoxic deep waters of the Black Sea are teeming with life.

Большого разнообразия жизни в сероводородной зоне не встретить, но и совсем стерильной она тоже не является. Более того, там живут довольно интересные организмы, с весьма необычным метаболизмом (источник энергии - окисление метана и восстановление S^{+6}):

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12169733&dopt=Abstract

UO3 is a satellite of iron/copper ores all of which have biogenic origin

Согласен, пример с урановой рудой неудачный; точно такое же возражение можно выдвинуть и к любому другому примеру из геологии - к сожалению, чистого эксперимента не получится, на Земле жизнь уже есть, а других планет с заметным присутствием воды мы не знаем. Однако утверждение об отсутсвии абиогенных механизмов концентрации (кстати, концентрировать надо не редкие ионы, а органические молекулы) слишком сильное, на мой взгляд. Например, любое выпадение осадка приводит к возрастанию концентрации примесей, ушедших в осадок, на много порядков; вымораживание увеличивает концентрацию растворенных веществ и т.п.

the popular "hydrothermal vent" story has absolutely no factual support.

Отсутствие прямых (ископаемых) свидетельств зарождения жизни вблизи подводных источников совершенно не удивительно. Океанская кора очень молода (<180 млн. лет), то, что было этой корой 4 млрд. лет назад, давно переплавилось в зонах субдукции. Существуют, однако, сильные косвенные аргументы в пользу гипотезы о гидротермальных источниках - например, филогенетические, согласно которым гипертермофилы принадлежат к очень рано отколовшейся ветви живого.

No oxygen, no Life.

См. выше пример с циклом окисления метана.

- http://lj.rossia.org/usres/p_k

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Re: If you are interested in my professional opinion

shkrobius@lj
2006-06-10 18:41 (ссылка)

Thanks for the reference; it is very interesting. A symbiosis of Archaea with eubacteria (in this case, sulfate reducers) is very uncommon (I cannot think of any other example off the top of my head). Sulfate reducers, of course, are very common; I just came recently across a few less usual ones
http://shkrobius.livejournal.com/49484.html
Sulfate reducers are almost always symbiotic: you have to find a way to close the electron chain.

In shoert, I am well aware that there are anaerobes, the point was that the present thriving hydrothermal ecosystems are based on aerobic respiration. For methane reduction, they did not need, specifically, a vent: there was plenty of methane in the Archaen atmosphere. Then, why should we look for such vents? Your own Black Sea example shows how tough is the going in the absence of redox gradients in the environment: you need a symbiosis of two completely different metabolisms just to keep alive. In short, we are talking about a very advanced metabolical design -- and that is supposed to be the point of the departure?

Surely there are some abiogenic mechanisms for concenrating the organics; however, what is needed is nothing short of a miracle. Concentrating the organics that one needs to make the RNA is only the beginning. You have to get the phosphates, pick out the right sugar stereomers out of the racemic mixture, phosphorilate them in the right way, and somehow add to those water-insoluble N-rich heterocycles. You can shake those in a test tube for 300 Myrs without getting anywhere. You have to make self-replicating stereoregular ribozymes and provide enough building blocks for them so that they can replicate for millions of years (in that mysterious locale). Again, the story

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Continued

shkrobius@lj
2006-06-10 18:45 (ссылка)

Again, the story of Adam and Eve looks more convincing than that.

As for your point that the thermophiles are basal to all Life, at present this is unsupported hypothesis. Molecular clocks do not work that far back, and the argument is weak at best. Some thermophiles (eg Thermus) and their relatives do not seem to be related to anything. My favorite is this one
http://shkrobius.livejournal.com/26418.html

It is far easier for me to imagine something like D. radiodurans or its friends hithching a ride on a grain of dust and becoming the LCA than all of these forced RNA world scenarios. Young Earth was not the right kind of environment for this type of chemical experiments. One has to pile one improbablility atop of another. We have not began here, and there is nothing random in that beginning.

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avrukinesku@lj
2006-06-09 04:16 (ссылка)

Согласно Вашему профессиональному мнению, ходячие теории возникновения жизни из нежизни - мусор. Вы отказываетесь верить (и далее по тексту). Но остается тот же вопрос, ведь где-то жизни пришлось возникнуть. Есть ли у Вас гипотеза, что заставило (толкнуло, вынудило, соблазнило) мертвечину пуститься на такой шаг?

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shkrobius@lj
2006-06-09 10:43 (ссылка)

I do not think yours is the correct question. The correct question is, What is Life? If you know the answer to that question, then you'll answer this derivative question in a flash. Alas, nobody knows the answer to that more important question. Some of these answers render your question nearly meaningless. Eg, according to the Gayan hypothesis what we call "Life" is the way in which planets stabilize their geochemistry. The whole Earth is alive, from its birth. Another possibility is that we call many things that are alive "dead." Why is the cell alive but the Galaxy is not? Try to answer this question honestly and you'll see how forced your arguments rapidly become. Perhaps Life did not 'originate' at all. It might be the inherent property of the Universe (like in Bergson's cosmogony). It has always been around, assuming different forms in different places on different scales. Alternatively, one of these forms did have a far greater chance of appearing randomly than the one that we have around and, after much evolution, engendered all others (just like we are trying to do with our machines). The one that we have, speculations aside, cannot appear "randomly" at all. What we have is someone's advanced chemical technology; perhaps it has no other purpose than keeping this planet in a good shape for further use. In short, the answer is a minor corollary to a more pertinent question, to which there is no answer.

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