Thermodynamically destined to exist.

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Thermodynamically destined to exist.

From the article

 

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There are exactly 20 standard amino acids — complex molecules that combine to form proteins, which carry out instructions specified by RNA and DNA, its double-stranded and self-replicating descendant.

Ten were synthesized in the famous 1953 Miller-Urey experiments, which modeled conditions believed to exist in Earth's early atmosphere and volcano-heated pools. Those 10 amino acids have also been found in meteorites, prompting debate over their role in sparking life on Earth and, perhaps, elsewhere.

Pudritz's analysis, co-authored with McMaster University biophysicist Paul Higgs and published Monday on arXiv, doesn't settle the former debate, but it does suggest that basic amino acids are even more common than thought, requiring little more than a relatively warm meteorite of sufficient size to form. And that's just the start.

If the observed patterns of amino acid formation — simple acids require low levels of energy to coalesce, and complex acids need more energy — indeed follow thermodynamic laws, then the basic narrative of life's emergence could be universal.

"Thermodynamics is fundamental," said Pudritz. "It must hold through all points of the universe. If you can show there are certain frequencies that fall in a natural way like this, there is an implied universality. It has to be tested, but it seems to make a lot of sense."

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Interesting. This

Interesting. This dovetails nicely with my speculation (which I doubt is original with me but whatever) that chemical processes should tend to occur in the places that are favorable for them to occur. Then, the universe being isotropic, it seems unlikely that there is not other life out there.

 

A couple of additional points:

 

There are at least 90 amino acids that have been found in meteorites. This suggests that whatever the process that formed them is more complicated than the conditions on the early earth. Probably the 20 that we do have here are the ones that are favored by our specific environment. I am probably guilty of overspeculating here but there may well be other environments where conditions favor some of those other amino acids. So at least as a principal, there could be viable biospheres elsewhere that have different atmospheric temperature and pressure than we can live in.

 

Also, about a year or so ago, someone found several previously untouched samples from one of the later runs of the Miller Urey experiment that was supposed to simulate conditions in a volcano. With modern lab equipment, they found 22 amino acids.

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I think the transcendental

I think the transcendental argument for god (TAG) fits in nicely here. Or at least, an alternate, naturalistic view of the TAG fits in nicely.

If we truly base our maths and logic on properties of the universe, it seems to follow that maths and logic would express themselves in natural formations -- and indeed they do, from the creation of heavier atoms from hydrogen and helium in the fusion reactors that are stars, to the regular orbits of the planets, right down to the odd and yet regular chemical properties of atoms and molecules.

The various chemical properties of atoms seems to make them ideal for self-constructing things like water and amino acids. The fact that amino acids are themselves ideally suited to be building blocks of other nifty molecules is mathematically inevitable, I think.

I've always thought that the mathematical properties of chemistry indicated life was inevitable. It's good to see some research in that direction.

Holy cow. I just realized that, if this line of reasoning is correct, life itself is a refutation of the necessity of god.

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Unfortunately, I think

Unfortunately, I think Theists can argue it both ways:

If science seemed to show that the chemistry of life was extremely unlikely to arise naturally, they will say that proves God must exist to 'create' life.

If the properties of matter naturally lead to chemicals that are suitable for constructing molecules that can self-replicate, and so on, they will say that proves God designed the properties of matter and the laws of physics to make that so....

 

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Well Bob, that will

Well Bob, that will happen when one side uses multiple open ended arguments that don't actually go anywhere. As long as there is a gap in our knowledge big enough for god to hide in, that is where god will be found.

 

The irony at this stage in the game is that we are giving the theists the best tools to promote themselves. A thousand years ago, they could make their own arguments from pretty much everything. Today, they have to turn to the fruits of science for their tools because we have already dealt with the easiest arguments.

 

So a year or so ago, they were arguing that the bacterial flagella somehow proved something beyond the fact that certain bacteria have them. That did not work out so well for them and in a couple of years, I will expect them to come back, again with something from the world of scientific inquiry. Possibly they will try some variation of the anthropic principal and the fine tuned universe.

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BobSpence1

BobSpence1 wrote:

Unfortunately, I think Theists can argue it both ways:

If science seemed to show that the chemistry of life was extremely unlikely to arise naturally, they will say that proves God must exist to 'create' life.

If the properties of matter naturally lead to chemicals that are suitable for constructing molecules that can self-replicate, and so on, they will say that proves God designed the properties of matter and the laws of physics to make that so....

 

Dawkins refers to the anthropic principle as a refutation of theism.  If "god" is a magical, supernatural entity, what need is there of physical laws that support life?

 

 

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todangst wrote:Dawkins

todangst wrote:

Dawkins refers to the anthropic principle as a refutation of theism.  If "god" is a magical, supernatural entity, what need is there of physical laws that support life?

Hey! That's just what I said!

Dawkins had better quit copying me.

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todangst wrote:BobSpence1

todangst wrote:

BobSpence1 wrote:

Unfortunately, I think Theists can argue it both ways:

If science seemed to show that the chemistry of life was extremely unlikely to arise naturally, they will say that proves God must exist to 'create' life.

If the properties of matter naturally lead to chemicals that are suitable for constructing molecules that can self-replicate, and so on, they will say that proves God designed the properties of matter and the laws of physics to make that so....

 

Dawkins refers to the anthropic principle as a refutation of theism.  If "god" is a magical, supernatural entity, what need is there of physical laws that support life?

 I agree.

I was basically pointing out that whatever science seems to show, they will find a way to make it consistent with their belief.

It really reinforces the fact that 'God' is such an ill-defined concept that it can 'explain' anything, which means it is not a real explanation of anything.

 

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todangst wrote:  

todangst wrote:

 

BobSpence1 wrote:
Unfortunately, I think Theists can argue it both ways:

 

If science seemed to show that the chemistry of life was extremely unlikely to arise naturally, they will say that proves God must exist to 'create' life.

 

If the properties of matter naturally lead to chemicals that are suitable for constructing molecules that can self-replicate, and so on, they will say that proves God designed the properties of matter and the laws of physics to make that so....

 

Dawkins refers to the anthropic principle as a refutation of theism. If "god" is a magical, supernatural entity, what need is there of physical laws that support life?

 

Well, I can certainly run with that. Remember however, if you put three theists in a field with a fence running down the middle, it is only a matter of time before they figure out how to stand on all four sides of the fence at the same time.

 

As far as the anthropic principal goes, remember that it can be stated vaguely enough to drive a mack truck through it. For example, consider the age of the universe. If the universe was half as old as it really is, there would not be enough population 1 stars for complex chemistry to work out favorably for the evolution of complex life. If the universe was twice as old as it really is, there would not be very many main sequence stars for complex life to evolve around.

 

Stated that way, it could be twisted in such a way as to be a problem for the Copernican principal. Except for the fact that it really doesn't say anything about our location in the universe (apart from a very broad location in time). The universe just doesn't change that much over the much broader scale of, say, a hundred million years. Nor does it say anything about god. Occam's razor alone is enough to dispel that.

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I've been pulling out the

I've been pulling out the new results to this experiment in debate in a number of circles for close to a year now, and so far none of the opponents has had anything to say on the subject after this was presented to them. Granted, I've probably mostly been running into the hit & run type, but it works more often than not. Maybe 50-0 and counting.

Of course, they usually switch subjects at that point, so it only goes so far.

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Vastet wrote:I've been

Vastet wrote:

I've been pulling out the new results to this experiment in debate in a number of circles for close to a year now, and so far none of the opponents has had anything to say on the subject after this was presented to them. Granted, I've probably mostly been running into the hit & run type, but it works more often than not. Maybe 50-0 and counting.

Of course, they usually switch subjects at that point, so it only goes so far.

I don't understand which part of the article you find such a potent argument? 


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OrdinaryClay wrote:Vastet

OrdinaryClay wrote:

Vastet wrote:

I've been pulling out the new results to this experiment in debate in a number of circles for close to a year now, and so far none of the opponents has had anything to say on the subject after this was presented to them. Granted, I've probably mostly been running into the hit & run type, but it works more often than not. Maybe 50-0 and counting.

Of course, they usually switch subjects at that point, so it only goes so far.

I don't understand which part of the article you find such a potent argument? 

 

Well I can't speak for Vastet, but I presume the same part of the argument that the rest of us find interesting; the fact that amino acids can form by themselves under relatively mild conditions without the requirement for any sort of intervention.  An argument is often put forward that abiogenesis could not occur because the building blocks of life couldn't have self-assembled under the conditions of a primordial earth (or whatever other scenario you choose), which this research goes a long way to refute.

 

M

 

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MichaelMcF

MichaelMcF wrote:

OrdinaryClay wrote:

Vastet wrote:

I've been pulling out the new results to this experiment in debate in a number of circles for close to a year now, and so far none of the opponents has had anything to say on the subject after this was presented to them. Granted, I've probably mostly been running into the hit & run type, but it works more often than not. Maybe 50-0 and counting.

Of course, they usually switch subjects at that point, so it only goes so far.

I don't understand which part of the article you find such a potent argument? 

Well I can't speak for Vastet, but I presume the same part of the argument that the rest of us find interesting; the fact that amino acids can form by themselves under relatively mild conditions without the requirement for any sort of intervention.  An argument is often put forward that abiogenesis could not occur because the building blocks of life couldn't have self-assembled under the conditions of a primordial earth (or whatever other scenario you choose), which this research goes a long way to refute.

M

 

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

 


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OrdinaryClay

OrdinaryClay wrote:

MichaelMcF wrote:

OrdinaryClay wrote:

Vastet wrote:

I've been pulling out the new results to this experiment in debate in a number of circles for close to a year now, and so far none of the opponents has had anything to say on the subject after this was presented to them. Granted, I've probably mostly been running into the hit & run type, but it works more often than not. Maybe 50-0 and counting.

Of course, they usually switch subjects at that point, so it only goes so far.

I don't understand which part of the article you find such a potent argument? 

Well I can't speak for Vastet, but I presume the same part of the argument that the rest of us find interesting; the fact that amino acids can form by themselves under relatively mild conditions without the requirement for any sort of intervention.  An argument is often put forward that abiogenesis could not occur because the building blocks of life couldn't have self-assembled under the conditions of a primordial earth (or whatever other scenario you choose), which this research goes a long way to refute.

M

 

 

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

 

The experiment does definitely advance our understanding of the chemistry involved in the possible ways in which life emerged from the 'pre-biotic' environment. If you had really understood the article, you would know that it was not just about the particular pathway by which amino acids and peptides can be produced. It showed that these compounds are much more likely to form spontaneously than had been thought, therefore there would be many more of these molecules around in any suitable environment, therefore making it far more likely that the next steps in pre-biotic chemical 'evolution' could take place.

In any complex mix of compounds, the relative thermodynamic 'cost' of any particular process is what determines which of the many possible compounds will form in significant quantities.

This is very significant.

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OrdinaryClay wrote: I don't

OrdinaryClay wrote:

 

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

 

The experiment pretty much confirmed that the building blocks of life are probably common throughout the universe. This has been confirmed. Finding amino acids in meteorites and so on indicates that the spontaneous assembly of organic compounds is a common event.

However you look at it, this is a tremendous blow to the typical creationist stance that life couldn't spontaneously assemble. Yes, there are still complexities to overcome in our understanding of how it did spontaneously assemble, but both the Milliken experiment, and the discovery of amino acids in space, are excellent experimental confirmation that it is possible. After all, the hypothesis of the spontaneous origin of life predicts that the precursors of life can assemble without life.

Of course, we can show that these amino acids can form self-replicating chains, and still creationists wouldn't be satisfied. They'd just move the goalposts again, just like Behe does with his "irreducible complexity" argument. That's the way most creationist "science" works: make predictions based on a creationist understanding of the universe, and when the evidence turns against you, simply claim that it didn't. Double points if you can say, "This evidence further supports god's design."

Anyway, the cool thing about discovering amino acids in space shows that not only can amino acids spontaneously form, but the do spontaneously form. That is a great thing, as it supports the scientific assumption that life formed spontaneously.

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OrdinaryClay wrote:I don't

OrdinaryClay wrote:

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

 

 

Bob and Nigel have pretty much made my response redundant but here goes.

 

The point is not "Oh look, chemical reactions can form amino acids and peptides".  I'm a chemist - admittedly a bad synthetic chemist - and I could have told you that when I turned 13.  The point is that amino acids can form without the need for anyone to be involved.  No deliberate push or pull.  Thermodynamics predicts percentage chances of formation and what do you know?  Those percentages match (within a degree of error) the proportions we find in asteroids.  So we know the building blocks of life can spontaneously form without any design.  There are many theories out there that easily explain the steps from here to cellular to multi-cellular life.

 

What does it mean for us?   These reactions can happen pretty much anywhere in the universe.  Earth does not sit in a perfect crucible.  Life can (and probably will) evolve anywhere.  The published paper confirms this.  It's an astounding piece of science that gives heft to the idea of extraterrestrial life.

 

I'd also like to point out that it opens up the potential of freaky alien sex Eye-wink

 

M

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MichaelMcF wrote:

OrdinaryClay wrote:

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

Bob and Nigel have pretty much made my response redundant but here goes.

The point is not "Oh look, chemical reactions can form amino acids and peptides".  I'm a chemist - admittedly a bad synthetic chemist - and I could have told you that when I turned 13.  The point is that amino acids can form without the need for anyone to be involved.  No deliberate push or pull.  Thermodynamics predicts percentage chances of formation and what do you know?  Those percentages match (within a degree of error) the proportions we find in asteroids.  So we know the building blocks of life can spontaneously form without any design.  There are many theories out there that easily explain the steps from here to cellular to multi-cellular life.

What does it mean for us?   These reactions can happen pretty much anywhere in the universe.  Earth does not sit in a perfect crucible.  Life can (and probably will) evolve anywhere.  The published paper confirms this.  It's an astounding piece of science that gives heft to the idea of extraterrestrial life.

I'd also like to point out that it opens up the potential of freaky alien sex Eye-wink

M

 

No offense guys but you are all pretty much saying the same thing, and since M is a chemist it will be more fruitful I hope to engage him in this discussion.

Ya, okay we have a proverbial cesspool of organics bubbling and in thermodynamic heaven, so now explain how life pops out? There is a noble prize just waiting for whoever can connect the final dots. There has been for decades. Why can we not connect those last dots? We don't need multibillion dollar colliders. We don't need profound new mathematics. We have, and have had, the tools to do this chemistry experiment for decades, but we just can't seem to make those last few steps. Why?

So where are the aliens? I know the holy grail of atheism is alien discovery, but why no evidence of any form. Okay interstellar travel is bullshit we can all agree on that, but why no electromagnetic signals of any kind whatsoever. We can detect the background radiation of the big bang but not a scintilla of evidence for intelligent life. If you look at us as an example, once we became sentient we rocketed to the point of being able to leak signals into space. Either sentient life is rare as hell or it blips out almost as fast as it becomes sentient. Both cases I find fascinating.

 

 


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OrdinaryClay

OrdinaryClay wrote:

MichaelMcF wrote:

OrdinaryClay wrote:

I don't know anyone who denies organic chemistry. Finding that chemistry produced amino acids or even short peptides leaves a very large gap to life. Our understanding is pretty much the same as it has been for a very long time, but I guess by writing another article it becomes re-interesting.

Bob and Nigel have pretty much made my response redundant but here goes.

The point is not "Oh look, chemical reactions can form amino acids and peptides".  I'm a chemist - admittedly a bad synthetic chemist - and I could have told you that when I turned 13.  The point is that amino acids can form without the need for anyone to be involved.  No deliberate push or pull.  Thermodynamics predicts percentage chances of formation and what do you know?  Those percentages match (within a degree of error) the proportions we find in asteroids.  So we know the building blocks of life can spontaneously form without any design.  There are many theories out there that easily explain the steps from here to cellular to multi-cellular life.

What does it mean for us?   These reactions can happen pretty much anywhere in the universe.  Earth does not sit in a perfect crucible.  Life can (and probably will) evolve anywhere.  The published paper confirms this.  It's an astounding piece of science that gives heft to the idea of extraterrestrial life.

I'd also like to point out that it opens up the potential of freaky alien sex Eye-wink

M

 

No offense guys but you are all pretty much saying the same thing, and since M is a chemist it will be more fruitful I hope to engage him in this discussion.

Ya, okay we have a proverbial cesspool of organics bubbling and in thermodynamic heaven, so now explain how life pops out? There is a noble prize just waiting for whoever can connect the final dots. There has been for decades. Why can we not connect those last dots? We don't need multibillion dollar colliders. We don't need profound new mathematics. We have, and have had, the tools to do this chemistry experiment for decades, but we just can't seem to make those last few steps. Why?

So where are the aliens? I know the holy grail of atheism is alien discovery, but why no evidence of any form. Okay interstellar travel is bullshit we can all agree on that, but why no electromagnetic signals of any kind whatsoever. We can detect the background radiation of the big bang but not a scintilla of evidence for intelligent life. If you look at us as an example, once we became sentient we rocketed to the point of being able to leak signals into space. Either sentient life is rare as hell or it blips out almost as fast as it becomes sentient. Both cases I find fascinating.

 

The emergence of life is not a trivial problem, its a forensic task where the 'crime' happened a few billion years ago. This study is part of a continuing process of piecing the story together, a significant piece. There is no indication that we have come to a total block, this report itself is evidence that progress continues.

You might as well ask why it took 400 years or so to come up with the Big Bang theory once Galileo had discovered the true nature of the Solar System...

Regarding SETI, we have not listened to signals from more than a tiny fraction of potential sites for life with sufficiently sensitive equipment, coupled to sufficiently sophisticated analysis software, that might stand a realistic chance of detecting signals that might indicate advanced civilizations, to be able to say anything conclusive about this, even for the tiny fraction of the Universe within range of such equipment.

Even if there are millions of such civilizations scattered across the Universe, the chances of even one being close enough for us to detect, on the slight chance they are directing some transmission in our direction, is vanishingly small. The results so far merely indicate that such civilizations do not appear to be common in our immediate vicinity.

Noone seriously expects intelligent life to be common, but even if there was only a one in million chance of intelligent life arising at least once in a whole galaxy, that still allows the possibility of hundreds in the observable universe, but all way too far away for contact, according to our current knowledge.

 

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Quote:Ya, okay we have a

Quote:

Ya, okay we have a proverbial cesspool of organics bubbling and in thermodynamic heaven, so now explain how life pops out?

That's molecular and cellular biology. That's my discipline. I thus present you with the following:

The Third Revolution

Once you are finished with that, and therefore have an appreciable understanding of biology in chemical terms, then it is crucial you read the following before proceeding:

Chemical Evolution

The latter articles details a scenario of what is still an open question, namely the means by which the first cell lines were established. As you can see from the two articles of mine I provided, the definition of biological can extend to chemical systems far more primitive then the ones that must obey the cell doctrine. As I detailed in the second link, which gives the scenario of the earliest history of life on Earth which is best in line with the evidence we have from studying ribozymes for the last 27 years, a modern cell, which is a membrane-enclosed chemical system with a distinct physical boundary, which obeys the fundamental dogma of molecular biology (that is, information can only move from nucleotides to polypeptides, never the other way around), operates on a system where the replication of DNA and the division of the cell are both extensive processes which require the duplication and control by, polypeptides. But during the early history of life on Earth, chemical systems which employed DNA as the central replicative polymer and polypeptides as the main product encoded by the sequences they contained did not exist. What did exist were systems of ribozymes which were free to diffuse throughout various populations of ribozymes, in which a central process of this evolution was the formation of enclosed membrane-bound compartments that were topologically distinct from each other. That process is also detailed in the link above. During the earliest history of life on Earth, the replication of the ribozymes (as indicated in the article above) would have been independant. Ribozymes which were capable of catalyzing the formation of the phosphodiester bond that links nucleotide monomers together would have diffused through a pool of ribozymes. This is believed to be the highly primitive origin of cellular life. Only when the existence of compartments allowing the sequestering and confinement of ribozymes to certain regions would have allowed for the development of RNA-based systems of sufficient complexity we could coherently speak of a discrete membrane-enclosed chemical system, the contents of which could duplicate. In other words, once RNA-based systems reached sufficiently complexity allowed the system of phospholipid-based membranes, would we see the emergence of "cells". These very primitive precursors to modern cells, which employ DNA and polypeptides for functions that primitive cells would have used RNA for, would be the first chemical systems we could speak of to obey the cell doctrine.

Quote:

but we just can't seem to make those last few steps. Why?

Surely you must realize the utterly monumentous problems facing anyone studying the earliest history of life on Earth? You're talking about reassembling events that began over three and half billion years ago and that occured over a period which spanned more than 600 million years! Of course the process will be fraught with immense difficulty, not just of assembling the pieces of the early history of life on Earth, but also of trying to understand the conditions that would have been present.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

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(Excuse me if I pass over

(Excuse me if I pass over your abiogenesis comments. Seems deludedgod is the man to talk to on this subject.)

BobSpence1 wrote:

Regarding SETI, we have not listened to signals from more than a tiny fraction of potential sites for life with sufficiently sensitive equipment, coupled to sufficiently sophisticated analysis software, that might stand a realistic chance of detecting signals that might indicate advanced civilizations, to be able to say anything conclusive about this, even for the tiny fraction of the Universe within range of such equipment.

Even if there are millions of such civilizations scattered across the Universe, the chances of even one being close enough for us to detect, on the slight chance they are directing some transmission in our direction, is vanishingly small. The results so far merely indicate that such civilizations do not appear to be common in our immediate vicinity.

Considering I'm a Christian, and you know I'm a Christian, you should read the skeptics view http://www.csicop.org/si/2006-03/seti.html 

I assume the SETI guys are not just randomly searching the universe. That would be pretty dumb. I assume they are using a heuristic of some type. Based on this I assume they would target stars similar to ours. Considering the sensitivity of life to high energy particles I would also assume they would target the areas of our galaxy that are the same or less energetic then our local area. In other words they should be targeting areas with highest likelihood of life. Yes, I know obvious, it is important though because it  strengthens the negative evidentiary value of not finding anything. 

The duration of our search is irrelevant since by any measure it is only a point in time. What matters is the duration of transmission. We know for sure once life becomes sentient it will discover electromagnetic communication pretty darn quick. Would I be too optimistic if I assumed it survives 100,000 years, longer given the purported power of technology? Remember the galaxy diameter is about 100,000 light years. So if you are a believer in Bayesian probabilities this continually accruing evidence would increase our belief that either 1) life is rarer then we fantasize about or 2) it blips out pretty darn fast. Again, both are fascinating from my perspective. I suspect the very fleeting thought that we are alone in the universe bugs the shit out of atheists.

 

BobSpence1 wrote:

Noone seriously expects intelligent life to be common, but even if there was only a one in million chance of intelligent life arising at least once in a whole galaxy, that still allows the possibility of hundreds in the observable universe, but all way too far away for contact, according to our current knowledge.

I always enjoy when SETI believers start talking probabilities. Based on what? It seems it is a gut feeling about the law of large numbers I guess. That somehow because we exist the population mean of existing life containing planets is something very promising. Its does not work that way. If you arbitrarily pick the probability to be "hundreds in the observable universe" I can with as much justification reduce the probability to a number sufficiently small that we are the only life in the entire universe.

I would remind you that improbable events do not get more probable with the sample size. The purpose of sampling is to estimate population parameters. From a frequentist standpoint our sample of one says nothing about the population. If you are Bayesian then okay, so you start with some hopelessly optimistic prior and go from there. The problem is the evidence we are gathering as time goes on reduces the likelihood of life. It does not increase it. The faith that other life exists is an extreme inference based on very, very little substance. Yet, people get all giddy about it. SETI is kind of like a shrine for the faithful or something. Eye-wink

 

 


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deludedgod wrote:That's

deludedgod wrote:

That's molecular and cellular biology. That's my discipline. I thus present you with the following:

Good. Can you provide any of your peer reviewed publications. I respect your privacy if you wish not to provide.

 

deludedgod wrote:

Once you are finished with that, ... 

I read both your essays.  

 

deludedgod wrote:

The latter articles details a scenario of what is still an open question, ...

We have had for a long time evidence of amino acid and simple peptide formation in the "primordial" wild. We have a clear gap from there to the "RNA world hypothesis". Do have an hypothesis for this gap.

Let's grant the faith to accept the above gap is filled. What evidence do we have that the "RNA world hypothesis" is actually the correct one? 

In the "RNA world hypothesis" do we have any lab evidence of how such a system survived in the "primordial" wild?

Do we have any physical examples of RNA based "organisms". By which I mean an RNA "machine" that catalyzes and replicates using RNA(I don't mean our own Ribozymes)? The assumption is that these are very primitive.

What was the energy source for our RNA "creatures"(yes, I'm using creatures very very loosely I realize, but you should no what I mean).

One of the most stunning things about biological science is the incredible evolutionary diagram we have laid out before us. I don't mean fossilized. I mean the extant living organisms. We have life from the most simple to the extremely complex. (You have to admit biologists were the lucky scientists. No one else got such a big cheat sheet. Smiling As exobiologists love to point out we have primitive prokaryotes that have adapted to extracting energy from all sorts of chemical bonds far more flexible then our dependence on the Krebs Cycle. Despite the unbelievable diversity. Despite the unbelievable ability for life to adapt. The common thread is always the same DNA/RNA/Protein dependence. You would think that there would be some niche somewhere where this pre DNA chemistry is able to eke out an existence. Speculations?

 

deludedgod wrote:

Surely you must realize the utterly monumentous problems facing anyone studying the earliest history of life on Earth? You're talking about reassembling events that began over three and half billion years ago and that occured over a period which spanned more than 600 million years! Of course the process will be fraught with immense difficulty, not just of assembling the pieces of the early history of life on Earth, but also of trying to understand the conditions that would have been present.

You must agree that our understanding of RNA and organic chemistry is stunning and pretty mature. Your essays demonstrate this. Chemistry is the same today as it was 3.5 billion years ago. Our understanding of the conditions that were present is pretty well understood as well. The possible set of early earth conditions is not that large. If you combine our deep understanding of current biochemical processes and a reasonably good understanding of early earth it would seem we could do better - at least in the lab.

So no, I don't appreciate the difficulty. Perhaps you could explain. Be as esoteric as you like. To be honest I don't really accept "it was a long time ago", or it took a long time as legitimate answers. Maybe you disagree so please explain why time is a factor in the chemistry of early life. Note, I'm not asking how time is a factor in an evolutionary process. I understand that. I'm asking what time has to do with the chemical reactions that produced the first RNA "creatures".

 

 


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OrdinaryClay wrote:(Excuse

OrdinaryClay wrote:

(Excuse me if I pass over your abiogenesis comments. Seems deludedgod is the man to talk to on this subject.)

BobSpence1 wrote:

Regarding SETI, we have not listened to signals from more than a tiny fraction of potential sites for life with sufficiently sensitive equipment, coupled to sufficiently sophisticated analysis software, that might stand a realistic chance of detecting signals that might indicate advanced civilizations, to be able to say anything conclusive about this, even for the tiny fraction of the Universe within range of such equipment.

Even if there are millions of such civilizations scattered across the Universe, the chances of even one being close enough for us to detect, on the slight chance they are directing some transmission in our direction, is vanishingly small. The results so far merely indicate that such civilizations do not appear to be common in our immediate vicinity.

Considering I'm a Christian, and you know I'm a Christian, you should read the skeptics view http://www.csicop.org/si/2006-03/seti.html 

I assume the SETI guys are not just randomly searching the universe. That would be pretty dumb. I assume they are using a heuristic of some type. Based on this I assume they would target stars similar to ours. Considering the sensitivity of life to high energy particles I would also assume they would target the areas of our galaxy that are the same or less energetic then our local area. In other words they should be targeting areas with highest likelihood of life. Yes, I know obvious, it is important though because it  strengthens the negative evidentiary value of not finding anything. 

As a regular listener to the 'Are We Alone?" podcast I can assure you those guys are fully aware of all these considerations.

Quote:

The duration of our search is irrelevant since by any measure it is only a point in time. What matters is the duration of transmission. We know for sure once life becomes sentient it will discover electromagnetic communication pretty darn quick. Would I be too optimistic if I assumed it survives 100,000 years, longer given the purported power of technology? Remember the galaxy diameter is about 100,000 light years. So if you are a believer in Bayesian probabilities this continually accruing evidence would increase our belief that either 1) life is rarer then we fantasize about or 2) it blips out pretty darn fast. Again, both are fascinating from my perspective. I suspect the very fleeting thought that we are alone in the universe bugs the shit out of atheists.

The duration of search is entirely relevant, no matter how short it is - as is duration of transmission. I considered mentioning that in my response but I was trying not to go on too long, and I had already mentioned enough factors to make the point that the failure to detect anything yet was not remotely an indication that there was nothing 'out there'. Itdoes allow us to set bounds on the probabilities.

I can assure you from personal knowledge and discussion both personal and listened to, that your last thought is simply not the case. It simply demonstrates something that you would like to think was true. 

Quote:

BobSpence1 wrote:

Noone seriously expects intelligent life to be common, but even if there was only a one in million chance of intelligent life arising at least once in a whole galaxy, that still allows the possibility of hundreds in the observable universe, but all way too far away for contact, according to our current knowledge.

I always enjoy when SETI believers start talking probabilities. Based on what? It seems it is a gut feeling about the law of large numbers I guess. That somehow because we exist the population mean of existing life containing planets is something very promising. Its does not work that way. If you arbitrarily pick the probability to be "hundreds in the observable universe" I can with as much justification reduce the probability to a number sufficiently small that we are the only life in the entire universe.

I would remind you that improbable events do not get more probable with the sample size. The purpose of sampling is to estimate population parameters. From a frequentist standpoint our sample of one says nothing about the population. If you are Bayesian then okay, so you start with some hopelessly optimistic prior and go from there. The problem is the evidence we are gathering as time goes on reduces the likelihood of life. It does not increase it. The faith that other life exists is an extreme inference based on very, very little substance. Yet, people get all giddy about it. SETI is kind of like a shrine for the faithful or something. Eye-wink

Just what is your point here? We are not assigning probabilities, just the implications of various assumptions, given the latest estimates on the number of likely candidate planets.

EDIT: I picked the value of "one in million" not because I was assuming that that might be anywhere near the actual figure, but specifically to make the point that, because of the size of the Universe, there could well be many other advanced civilizations in the Universe, yet we would still have negligible chance of detecting them, even with vastly more sensitive equipment than currently available. So whatever your opinion of the SETI program, negative results there are never going to prove we are alone.

A sample of one allows us at least to start with the reasonable assumption that the probability of life emerging is not zero. It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common. The accumulating evidence that likely planets are probably much more common that once thought, and that the basic chemical 'building blocks' of life are present 'out there', and that the probability of them forming more complex precursor molecules that are on the path to life-as-we-know-it has been shown to be higher than the default assumption, ups the chances of other life being 'out there'.

SETI does not start with "hopelessly optimistic prior" assumption. They just search, with all the considerations you mentioned in mind, and many more. You are correct that we really have little to base a 'solid' estimate on, which taken seriously and without pre-conceptions, means that we cannot ignore the possibility that there may be life detectable by our current or the next generation of equipment, so it would be crazy not to spend some moderate amount of effort on the search, given the significance of a positive result.

I hope you are not starting with the assumption that the probability of detecting life in range of our instruments is vanishingly small, with the implication they are wasting their time on a fantasy based on faith - we can leave the fantasy world of faith to people who take the nonsense concept of infinite super creator beings seriously.

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Quote:Good. Can you provide

Quote:

Good. Can you provide any of your peer reviewed publications. I respect your privacy if you wish not to provide.

I do not do research into the early history of life on Earth.

Quote:

We have had for a long time evidence of amino acid and simple peptide formation in the "primordial" wild. We have a clear gap from there to the "RNA world hypothesis". Do have an hypothesis for this gap.

The problem with supposing that peptide fragments are the fundametal chemical basis for the early history of life on Earth is that polypeptides cannot encode the template of their own replication, unlike nucleic acids. It is therefore not possible that the earliest life forms on Earth could have been polypeptide based, since any system which relies on the physical structure of polypeptides to perform central cellular functions requires a system of translation and protein synthesis to be read off from strings of nucleic acids.

The means by which RNA-based systems began to employ peptide fragments, and the eventual superseding of the catalytic functions of ribozymes by polypeptides, is hypothesized in the second article. A hypothesis of transcription is also presented, but the origins of translation are still very much shrouded in mystery.

Quote:

Let's grant the faith to accept the above gap is filled. What evidence do we have that the "RNA world hypothesis" is actually the correct one?

The RNA World is best in line with the evidence we have from studying RNA, and from studying the way modern cells work. The study of ribozymes revolves around a technique called elution chromtaography. Randomly generated RNA sequences with certain properties (like the ability to catalyze a phosphorylation reaction) will elute much more slowly in specific column chromatograms and will bind to the column. The technique is called SELEX. We begin with a randomly generated sequence of nucleic acids of fixed length (so of course, with four bases and n monomers, we get 4n possibilities). The column is then saturated with target molecules in order to select ribozymes with certain properties (researchers are particularly interested in those which can catalyze the formation of the phosphodiester bond). The RNA left on the column are put through amplification (and invariably mutation). Then we do it again. And again. It was by the SELEX techniques that we derived in vitro the various ribozymes mentioned in the second link.

Cells themselves give clues that they are descended from primitive RNA based counterparts. Not all features have been superseded by polypeptides. Within the mechanisms of modern cells there are still steps and mechanisms that would appear redundant or unusually primitive such as SSI (Self-splicing introns). Even the process of transcription is technically redundant, although it is now so firmly established in modern cellular machinary that it cannot be removed. I say "redundant" because protein biosynthesis is a process with many steps and which consumes tremendous amounts of energy. On the face of it, therefore, transcription (which is very energy costly) would seem a strange intermediate. This is especially true in bacteria, where the ribozyme actually follows directly behind the RNA polymerase. In other words, the ribosome actually starts to process the nascent mRNA while it is still being made. At first sight, this is extremely bizarre. Somewhat like that Futurama episode where Hermes recieves a letter from the Center of Beauracracy. That letter in turn informs him that he is about to receive a letter from the Center of Beauracracy.

Biologists now suspect that much of the RNA intermediacy, not just in transcription, but also in ribozymes, and other RNA-protein complexes, and primitive mechanisms which still rely on RNA such as SSI, reflect the fact that RNA came first, and that it originally served both purposes of catalysis and encoding. In effect, the evolution of modern cellular life has been built around RNA.

Quote:

Do we have any physical examples of RNA based "organisms". By which I mean an RNA "machine" that catalyzes and replicates using RNA(I don't mean our own Ribozymes)? The assumption is that these are very primitive.

There are still numerous ribozymes that operate in modern cells. Unsuprisingly, nearly all of them are complexed with polypeptides (like ribozymes, and snoRNP and snRNP) but as for organisms which are based on RNA? Unless you count viruses, no. And that's not suprising, because DNA is better as the central hereditary molecule. To base an organism off RNA limits the biological complexity it could achieve (because very long RNA polymers break much more easily, a consequence of having ribose instead of deoxyribose).

Quote:

What was the energy source for our RNA "creatures"(yes, I'm using creatures very very loosely I realize, but you should no what I mean).

All energy in modern cells is derived from processes which exploit pairs of molecules or atoms or ions which have high redox potential difference in order to extract electrochemical work from the movement of the electrons from the reducing agent to the oxidizing agent. In modern cells, this is done indirectly to power ATP synthase.  The last step is oxidative phosphorylation at the end of whatever process allowed the otherwise thermodynamically unfavorable formation of ATP from ADP. It is thought that during the early history of life on Earth, inorganic oxidizing agents like iron were very plentiful. I would suspect that the earliest cells (and indeed, lithotropes which can survive deep in the hydrothermal vents of the Earth employ something similar) would extract energy from the transfer of electrons from Fe 2+ to Fe 3+. That has a redox potential of +0.77V. In other words, it is thermodynamically favorable. It is however, much smaller than the redox potentials that occur in modern cells. This is not suprising, because primitive cells could not have employed conjugate redox pairs with a very high pd, because they had not yet developed long stepwise pathways of oxidation, and the release of that much energy in one or a few steps would destroy the cell.

Quote:

Perhaps you could explain.

These hypothetical organisms that we are discussing no longer exist. They have been outphased entirely, and they have been outphased for so long, that we have to backtrack through all the evolution that has occured in the last 3.5 billion years. It is a great deal easier to understand early DNA based organisms, because we know that evolution is a very conservative process, and that the process of genetic innovation is based largely on recombining old structures in new ways, as opposed to forming structures de novo. So while we have many explanations that are very reasonable (although we don't have any that are complete) the information we have to rely on is what exists in modern cells, in order to see what features are derived from the most ancient forms of life. These inferences are made difficult by the fact that these cells have had 3.5 billion years to evolve, become very complex, and much of the primitive mechanisms that early cells relied on have been outphased entirely by more sophisticated mechanisms. Like anything else in evolution, the trail gets murkier the farther back we go, because the sequences have had longer to diverge (by the principle of the molecular clock),and  homologies can become almost impossible to detect unless the sequence under consideration is extremely well conserved.

Quote:

I'm asking what time has to do with the chemical reactions that produced the first RNA "creatures".

Time is a factor because once short sequences of RNA molecules existed, the process of evolution by natural selection could act upon them. Evolution is very gradual. As for the formation of those RNA molecules themselves, we suspect that they in turn are actually molecules which outphased even more primitive nucleic acid sequences based on PNA. But beyond that, we really have no idea. Like I said, this is hypothetical.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

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The comment that I made that

The comment that I made that was responded to was answered better by others than it probably would have been by myself, so I'll leave that alone.

OrdinaryClay wrote:

I always enjoy when SETI believers start talking probabilities.

And I always LOVE it when creationists start doing the same, because all of their probabilities are fundamentally flawed on multiple levels, and it's fun to point it out to them.

OrdinaryClay wrote:
 Based on what?

The universe.

OrdinaryClay wrote:
 It seems it is a gut feeling about the law of large numbers I guess.

That's incorrect.

OrdinaryClay wrote:
 That somehow because we exist the population mean of existing life containing planets is something very promising. Its does not work that way.

Yes it does, because of how we exist. We exist because of natural chemical and electrical processes, amongst other things, that are not unique to the Earth and its solar system alone. Therefore it is certain that these processes have occurred elsewhere, elsewhen, in a similar or completely different fashion, leading to life in some form or another.

OrdinaryClay wrote:
If you arbitrarily pick the probability to be "hundreds in the observable universe" I can with as much justification reduce the probability to a number sufficiently small that we are the only life in the entire universe.

We can justify our probabilities, you cannot justify your own.

OrdinaryClay wrote:

I would remind you that improbable events do not get more probable with the sample size.

On the contrary. You have a 1 in 6 chance of rolling a six with one die. You have a 6 x 1/6 chance of rolling a six with six dice. It is simple math, and simple logic, that you should have learned before attending preschool.

OrdinaryClay wrote:
 The purpose of sampling is to estimate population parameters. From a frequentist standpoint our sample of one says nothing about the population. If you are Bayesian then okay, so you start with some hopelessly optimistic prior and go from there. The problem is the evidence we are gathering as time goes on reduces the likelihood of life. It does not increase it.

You're looking at some pretty ridiculously blatantly false evidence to be able to suggest this. How about you provide it so we can show you how wrong you are in your interpretting of it. 

OrdinaryClay wrote:
The faith that other life exists is an extreme inference based on very, very little substance.

Quite the opposite. That life exists elsewhere in the universe is a certainty. Even if your god exists, the only way life wouldn't form elsewhere is if it took an active hand in its prevention.

It is the nature of nature to be natural, and life is natural.

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BobSpence1

BobSpence1 wrote:

Unfortunately, I think Theists can argue it both ways:

If science seemed to show that the chemistry of life was extremely unlikely to arise naturally, they will say that proves God must exist to 'create' life.

If the properties of matter naturally lead to chemicals that are suitable for constructing molecules that can self-replicate, and so on, they will say that proves God designed the properties of matter and the laws of physics to make that so....

 

How convenient. It would take a miracle(or at least a better drug than religion) to convince most theists God does not need to exist.

 

“Religion is regarded by the common people as true, by the wise as false, and by the rulers as useful.” Seneca


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OrdinaryClay wrote:I would

OrdinaryClay wrote:

I would remind you that improbable events do not get more probable with the sample size.

Clearly, the probability of the event occurring in a single test does not increase, but if you perform more tests, the probability of a specific scenario occurring always increases. For example, if I flip a coin, the chance of me not getting tails is 50%. If I flip the coin again, the probability of not getting tails is still 50%. This is indisputable (hopefully). However, if I take both tests into account at the same time, I can see that the possible results include:

1) H, H

2) H, T

3) T, H

4) T, T

So if you flip the coin twice, the probability of not getting tails in those two tests would be one/fourth or 25%. If we do this again:

1) H, H, H

2) H, H, T

3) H, T, H

4) H, T, T

5) T, H, H

6) T, H, T

7) T, T, H

Cool T, T, T

Now, the chance of not getting tails at all is 1/8. Each coin flip has two possible outcomes. When we performed two tests, we had four possible outcomes. When we performed three tests, we had eight possible outcomes. So the number of possible outcomes equals two (possible outcomes for each tests) to the number of tests power, or, 2^tests. In all, there can always only be one outcome with no tails.

Ergo, four tests > 2^4. 16 outcomes. 1/16 probability of no tails. Five tests > 2^5. 32 outcomes. 1/32 probability of no tails.

This argument works brilliantly for the existence of life on other planets, as well as against many design arguments. 

Quote:
The problem is the evidence we are gathering as time goes on reduces the likelihood of life.

How?

Our revels now are ended. These our actors, | As I foretold you, were all spirits, and | Are melted into air, into thin air; | And, like the baseless fabric of this vision, | The cloud-capped towers, the gorgeous palaces, | The solemn temples, the great globe itself, - Yea, all which it inherit, shall dissolve, | And, like this insubstantial pageant faded, | Leave not a rack behind. We are such stuff | As dreams are made on, and our little life | Is rounded with a sleep. - Shakespeare


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To be fair, the argument

To be fair, the argument about the number of throws of the dice increasing the probability of a particular result was not what was meant by 'sample size'. As I have previously argued, the number of throws is equivalent to the actual number of planets 'out there', so the more planets, the greater the chance that life will emerge on at least one planet somewhere in the universe.

'Sample size' refers to the number of these planets we have been able examine - the more we can examine, the more confidence we can have that the observed percentage of hits is a good estimate of the actual rate. Since until we find at least one other example of intelligent life, the observed sample hit rate is 1/(number in sample), so as the number sampled rises, the hit-rate will fall until we start getting some more hits in addition to ourselves.

My point was that since the sample size is so tiny, the uncertainty attached to the hit-rate is so large, that we cannot say with any real confidence what the actual likelihood of other intelligence is, based purely on that hit-rate. This uncertainty goes both ways, so it doesn't allow us to say anything meaningful about the likelihood of at least one other example of intelligent life in the universe, whether zero or millions.

This is another point about sample size that OrdinaryClay did not refer to, namely that the lower the number of hits we are testing for, the bigger the sample has to be before we can say that the observed hit rate has a particular likelihood of accurately reflecting that actual rate. So to have any confidence that there are no other intelligences in the whole universe, we would have to 'sample' close to the whole universe. By the same logic, we would have to 'sample' almost our whole galaxy to be able to say with any confidence that one intelligence per galaxy was statistically likely to be the rate in the whole universe, assuming that the chances were similar for all galaxies.

IOW the sample size has to be big enough that there is better than even chance of getting a hit for any given hit-rate, before we can say that the actual total proportion of inhabited planets is likely to match our sample hit-rate.

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BobSpence1 wrote:

 Itdoes allow us to set bounds on the probabilities.

What are these bounds?

 

BobSpence1 wrote:

Just what is your point here? 

The point was that many who talk lightly about the possibility of life rarely base their comments on actual reason. It is most often a giddy sense of excitement or a lacs reliance on an intuitive sense of confidence. Below we have Vastet declaring with certainty.

 
BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common.

Agreed. That is why I believe our friend Carl Sagan, and many many others, were acting out of faith when peddling the common life scenario.

 

BobSpence1 wrote:

The accumulating evidence that likely planets are probably much more common that once thought, and that the basic chemical 'building blocks' of life are present 'out there', ...

The accumulating evidence? We have always been uber optimistic about likely planets. What the evidence is showing is that this optimism may not be justified. Because we find a similar mass body around a likely star hardly is "new evidence". What astronomer in their right mind would have ever suggested otherwise. New? No. On the contrary the accumulating evidence is reducing the likelihood.

 
BobSpence1 wrote:

 

I hope you are not starting with the assumption that the probability of detecting life in range of our instruments is vanishingly small, with the implication they are wasting their time on a fantasy based on faith - ...

I support what SETI does. I would rather a very minimal amount of public funds be spent on SETI, though. I would much rather see it go toward robotic exploration of our own solar system.

 

 


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deludedgod wrote:I do not do

deludedgod wrote:

I do not do research into the early history of life on Earth.

Are you in research?

 

deludedgod wrote:

The problem with supposing that peptide fragments are the fundametal chemical basis for the early history of life on Earth is that polypeptides cannot encode the template of their own replication, unlike nucleic acids. 

So why do abiogenesis researchers make such a big deal about finding amino acids? We need nucleotides for the RNA world view. No?

 

deludedgod wrote:

The RNA World is best in line with the evidence we have from studying RNA, and from studying the way modern cells work. The study of ribozymes revolves around a technique called elution chromtaography.

Does this help us much when it comes to early earth conditions? This is hardly a wild environment. Have we been able to demonstrate thermodynamic conditions that could have produced such things in the wild?

 
deludedgod wrote:

Cells themselves give clues that they are descended from primitive RNA based counterparts. Not all features have been superseded by polypeptides. Within the mechanisms of modern cells there are still steps and mechanisms that would appear redundant or unusually primitive such as SSI (Self-splicing introns). Even the process of transcription is technically redundant, although it is now so firmly established in modern cellular machinary that it cannot be removed. I say "redundant" because protein biosynthesis is a process with many steps and which consumes tremendous amounts of energy. On the face of it, therefore, transcription (which is very energy costly) would seem a strange intermediate. This is especially true in bacteria, where the ribozyme actually follows directly behind the RNA polymerase. In other words, the ribosome actually starts to process the nascent mRNA while it is still being made. At first sight, this is extremely bizarre. Somewhat like that Futurama episode where Hermes recieves a letter from the Center of Beauracracy. That letter in turn informs him that he is about to receive a letter from the Center of Beauracracy.

If they are less then optimal why would these not have disappeared through selective pressure? It would seem if there were a more energy efficient method then that would have large selective pressure.

 
deludedgod wrote:

There are still numerous ribozymes that operate in modern cells. Unsuprisingly, nearly all of them are complexed with polypeptides (like ribozymes, and snoRNP and snRNP) but as for organisms which are based on RNA? Unless you count viruses, no. And that's not suprising, because DNA is better as the central hereditary molecule. To base an organism off RNA limits the biological complexity it could achieve (because very long RNA polymers break much more easily, a consequence of having ribose instead of deoxyribose).

I was not asking why DNA based organisms dominate. I was asking why we would not see any vestige niche containing such "organisms". The assumption must be that some RNA soup or maybe RNA vesicles existed in the wild. If the chemical conditions were found in some exotic place on earth one would think it possible that we could still find them. The argument that DNA was better at heredity and thus wiped out by RNA universally assumes there is no energy niche where a very simple RNA based soup could not be found today.

 

deludedgod wrote:

All energy in modern cells is derived from processes which exploit pairs of molecules or atoms or ions which have high redox potential difference in order to extract electrochemical work from the movement of the electrons from the reducing agent to the oxidizing agent. In modern cells, this is done indirectly to power ATP synthase.  The last step is oxidative phosphorylation at the end of whatever process allowed the otherwise thermodynamically unfavorable formation of ATP from ADP. It is thought that during the early history of life on Earth, inorganic oxidizing agents like iron were very plentiful. I would suspect that the earliest cells (and indeed, lithotropes which can survive deep in the hydrothermal vents of the Earth employ something similar) would extract energy from the transfer of electrons from Fe 2+ to Fe 3+. That has a redox potential of +0.77V. In other words, it is thermodynamically favorable. It is however, much smaller than the redox potentials that occur in modern cells. This is not suprising, because primitive cells could not have employed conjugate redox pairs with a very high pd, because they had not yet developed long stepwise pathways of oxidation, and the release of that much energy in one or a few steps would destroy the cell.

Modern Lithotrops use complex "chemical pathways"(from your essay) so I don't understand how this gives us any evidence about how inorganics were used as energy sources in our RNA World View.

 

deludedgod wrote:

These hypothetical organisms that we are discussing no longer exist. They have been outphased entirely, and they have been outphased for so long, that we have to backtrack through all the evolution that has occured in the last 3.5 billion years. It is a great deal easier to understand early DNA based organisms, because we know that evolution is a very conservative process, and that the process of genetic innovation is based largely on recombining old structures in new ways, as opposed to forming structures de novo. So while we have many explanations that are very reasonable (although we don't have any that are complete) the information we have to rely on is what exists in modern cells, in order to see what features are derived from the most ancient forms of life. These inferences are made difficult by the fact that these cells have had 3.5 billion years to evolve, become very complex, and much of the primitive mechanisms that early cells relied on have been outphased entirely by more sophisticated mechanisms. Like anything else in evolution, the trail gets murkier the farther back we go, because the sequences have had longer to diverge (by the principle of the molecular clock),and  homologies can become almost impossible to detect unless the sequence under consideration is extremely well conserved.

We have more then just a cellular trackback. We have our understanding of modern chemistry. Both combined is more then either separately.

 

deludedgod wrote:
 

Time is a factor because once short sequences of RNA molecules existed, the process of evolution by natural selection could act upon them. Evolution is very gradual. As for the formation of those RNA molecules themselves, we suspect that they in turn are actually molecules which outphased even more primitive nucleic acid sequences based on PNA. But beyond that, we really have no idea. Like I said, this is hypothetical.

I understand how time plays a role in an evolutionary environment. It is stochastic with natural selection picking the winners and losers. Got it. The problems is it was not a stochastic process prior to obtaining the RNA sequences , or anything that can be acted on through natural selection. It is a chemical process. We understand chemistry very well. Why is it we can not even conjecture on a wild stage that allows for these RNA soups to pop into existence? Nobody is asking to see a prokaryote produced from nothing in the lab, but why can we not reproduce the conditions that bring about whatever it is we believe were the first set of organics that were subject to evolution? That is the gap.

 

It seems pretty obvious that what we have is still a massive gap from nothing to DNA/RNA/Protein based life. Even if you subscribe to the RNA World view, there is still zero evidence for how such a nascent ecosystem popped into existence. 

 

 


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Vastet wrote:The comment

Vastet wrote:

The comment that I made that was responded to was answered better by others than it probably would have been by myself, so I'll leave that alone.

I guess you're off the hook.

 

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common. 

Vastet wrote:

That life exists elsewhere in the universe is a certainty. 

Looks like you have faith. Congratulations.

 

 

 


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butterbattle wrote:

OrdinaryClay wrote:

I would remind you that improbable events do not get more probable with the sample size.

Clearly, the probability of the event occurring in a single test does not increase, but if you perform more tests, the probability of a specific scenario occurring always increases. For example, if I flip a coin, the chance of me not getting tails is 50%. If I flip the coin again, the probability of not getting tails is still 50%. This is indisputable (hopefully). However, if I take both tests into account at the same time, I can see that the possible results include:

You are missing the point. Sampling (assuming replacement, which is obviously the case here) does not effect the population probabilities. They are what they are. In your case you know a priori the population probability function. This is powerful knowledge. It allows you to make big assertions. In the case of the population of planets with life we do not know this information. Sampling allows you to try and estimate these values. The fact that we exist does not effect the population probability whatever it is. 

 
butterbattle wrote:

Quote:
The problem is the evidence we are gathering as time goes on reduces the likelihood of life.

How?

We are reasoning under uncertainty. We are not flipping coins. The best way to reason under uncertainty is Bayesian. Bayesian learning updates our outlook based on new evidence. Negative evidence can reduce the values you end up with in your posterior probability.

 

 


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OrdinaryClay wrote:

BobSpence1 wrote:

 Itdoes allow us to set bounds on the probabilities.

What are these bounds?

In this case, upper bounds on the probability of life under the assumption that that probability is similar across the Universe for any randomly chosen planet.

Actually I will cover this in a response to my next post where I considered this aspect more thoroughly.

Quote:
 

BobSpence1 wrote:

Just what is your point here? 

The point was that many who talk lightly about the possibility of life rarely base their comments on actual reason. It is most often a giddy sense of excitement or a lacs reliance on an intuitive sense of confidence. Below we have Vastet declaring with certainty.

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common.

Agreed. That is why I believe our friend Carl Sagan, and many many others, were acting out of faith when peddling the common life scenario.

Not really. It is more a matter of what parts of the available scientific evidence you gave more weight, which is to an extent subjective, but more evidence-based than 'faith' would imply, more a matter of individual assessment of admittedly inconclusive data.

Quote:

BobSpence1 wrote:

The accumulating evidence that likely planets are probably much more common that once thought, and that the basic chemical 'building blocks' of life are present 'out there', ...

The accumulating evidence? We have always been uber optimistic about likely planets. What the evidence is showing is that this optimism may not be justified. Because we find a similar mass body around a likely star hardly is "new evidence". What astronomer in their right mind would have ever suggested otherwise. New? No. On the contrary the accumulating evidence is reducing the likelihood.

Now this is where you are just plain wrong.

In terms of actual science, not speculation, I think the earliest hypotheses on the origin of the solar system implied that planet formation was due to very unlikely events, such as the close approach of another star dragging out a plume of matter from the Sun which then condensed into the planets. 

So it is utterly wrong to assert that those actually studying the topic have "always been uber optimistic about likely planets".

As we were able to study other nearby stars and their environment in more detail, it became apparent that the most likely path of star formation was by collapse and condensation of a localized concentration of gas and dust into a central star surrounded by the remnants of the original cloud, which in turn condensed into more-or-less solid bodies of all sizes, which after a period of relatively chaotic orbital motion around the sun settled into a few major chunks (the planets) and a whole hierarchy of lesser bodies, in more stable orbits.

This suggested planets were much more likely to be formed in association with a broad range of classes of star, so the probabaility of planets was assessed as much higher than previously assumed.

Now we have actual observation of hundreds of planets going around nearby stars, justifying even higher estimates on more solid data.

Even if you want to assert that scientists were always making estimates very much on the high side of what the available data suggested, the actual estimates would have still been rising, because new and more accurate observation have justified much higher estimates.

To then suggest that "accumulating evidence is reducing the likelihood" is utterly and demonstrably incorrect.

Quote:

 
BobSpence1 wrote:
 

I hope you are not starting with the assumption that the probability of detecting life in range of our instruments is vanishingly small, with the implication they are wasting their time on a fantasy based on faith - ...

I support what SETI does. I would rather a very minimal amount of public funds be spent on SETI, though. I would much rather see it go toward robotic exploration of our own solar system.

Thankfully they have managed to get enough private funds to build a dedicated radio telescope array, so it will be interesting to follow their progress. They do 'spin off' a lot of interesting work as part of developing the science and technology required to support their quest, including, not surprisingly, a lot of stuff directly relevant to the exploration of own system.

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OrdinaryClay wrote:

BobSpence1 wrote:

My point was that since the sample size is so tiny, the uncertainty attached to the hit-rate is so large, that we cannot say with any real confidence what the actual likelihood of other intelligence is, based purely on that hit-rate. This uncertainty goes both ways, so it doesn't allow us to say anything meaningful about the likelihood of at least one other example of intelligent life in the universe, whether zero or millions.

This is correct except with Bayesian methods you can reduce the probability with negative evidence. Not discovering something is still information. You can use this information to refine your , albeit uncertain, estimates. 

Yes of course, but the evidence has not been negative except with respect to the assumption that intelligent life was very common, like of the order of 1% or higher on any given star system.

Quote:

BobSpence1 wrote:

This is another point about sample size that OrdinaryClay did not refer to, namely that the lower the number of hits we are testing for, the bigger the sample has to be before we can say that the observed hit rate has a particular likelihood of accurately reflecting that actual rate. So to have any confidence that there are no other intelligences in the whole universe, we would have to 'sample' close to the whole universe. By the same logic, we would have to 'sample' almost our whole galaxy to be able to say with any confidence that one intelligence per galaxy was statistically likely to be the rate in the whole universe, assuming that the chances were similar for all galaxies.

If you start with very low priors and you attach less meaning to the evidence then low and behold the gathering of evidence has less of an effect. But so what. This is just admiting you have no idea about the actual population. In the end you are still less certain. In one case you calculated it, and in the other case you assumed it.

In all cases negative evidence is still negative evidence. It does reduce the liklihood.

See my previous comment - yes it does reduce the likelihood of very high densities, but in the context of much lower densities estimates the reduction is very small.

Quote:

BobSpence1 wrote:

IOW the sample size has to be big enough that there is better than even chance of getting a hit for any given hit-rate, before we can say that the actual total proportion of inhabited planets is likely to match our sample hit-rate.

 

A small random sample of a large population can still have some predictive ability. You seem to like the idea of "even". You use it a lot. Why do we need an "even chance of getting a hit"?

 

In this case it is a simple informal expression of the math - the term 'likely', unqualified, implies 'more likely than not', which is just what 'better than even chance' means. What is your problem, dude??

Quote:
 

An important point to remember most life predictions are not based on our SETI sampling. Hardly, most are based on conditional probabilities of our guess of available planets for life. We have no way of sampling these except for a very, very rough guess using mass and location of "observed" planets. The majority of life factors are not detectible.

EDIT: Obviously, until SETI scores a hit, it can only set some rough upper bound. 

But we are improving our ability to detect them all the time. We are just beginning to be able to detect atmospheric composition of the observed planets in useful detail, and expect to be able to test for water and methane, both extremely significant here.

Why so persisently negative, way more negative that a realistic assessment of the actual current state of research in this area, could possibly justify? The assertion of the current data decreasing the likelihood of ETI is just so off-the-planet mistaken that it points to a deep unwilliness to accept that ETI is plausible or likely.

 

 

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Quote:Are you in

Quote:

Are you in research?

Yes.

Quote:

So why do abiogenesis researchers make such a big deal about finding amino acids? We need nucleotides for the RNA world view. No?

The in vitro synthesis of polynucleotides (short ones) by randomly generated pools of RNA to which SELEX was applied (and consequently ribozymes with the ability to catalyze the phosphodiester bond formation) is something that has long since been accomplished in the laboratory. The next major step in the process of chemical evolution after the development of compartments for the sequestering of metabolites, monomers and ribozymes was the formation of short peptide fragments. This process was the precursor to the outphasing of ribozymal catalysis by polypeptides. That is why it is a big deal.

Although, perhaps as indicated with this experiment, perhaps short oligopeptides could have been formed without the sequestering of amino acid monomers by RNA based systems. That raises the interesting possibility that there already existed pools of oligopeptides which could give selective advantages to RNA-based systems which captured them. If more experimentation was done on this idea, it might help to clear a major hurdle in our understanding of the transfer from RNA to polypeptide dominated systems.

Quote:

If they are less then optimal why would these not have disappeared through selective pressure? It would seem if there were a more energy efficient method then that would have large selective pressure.

Well, as per the principle of coevolution, the formation of oligopeptides and polypeptide fragments would have relaxed selective pressure on ribozymes, and consequently the need for RNA based catalysis but not on the sequences themselves because those were what encoded the amino acids which constituted the sequence of polypeptides. Remember, evolution has no foresight. It isn't a designer which decides to do certain things. That (as an aside) is what people who are proponents of irreducible complexity fail to understand, that systems with mutual dependancy can be established from the components of systems which were not mutually dependant to start with. Because of this, certain sequences and systems are permanent. They cannot be outphased because another component of the system depends on them. Transcription is thought to be an example of this. The most primitive genomes would have had to be formed by templated polymerization of DNA monomers on the pre-existing sequences of RNA which performed major functions or encoded polypeptides with major functions, in the cell. So while the need to store all the information of the cell in long RNA nucleic acids (which is a disadvantage) would have been taken away by the formation of DNA-based nucleic acids, the need for polypeptides to be synthesized off of RNA chains remained. Much like the modern mitochondria descendants of the original endosymbiotic processes, transcription is an irreversible part of biology.

Quote:

Modern Lithotrops use complex "chemical pathways"(from your essay) so I don't understand how this gives us any evidence about how inorganics were used as energy sources in our RNA World View.

Sorry, I made a mistake above. That should say the transfer of electrons from Fe3+ to form Fe2+ (obviously, the other way around doesn't even make sense). I wasn't using lithotropes as evidence for the origins of metabolics in early life, but as an illustration of how organisms can use inorganic metabolites. Obviously, the system employed by lithotropes has had a long time to evolve. I was just illustrating a hypothetical. The origin of metabolics in the RNA world is still an open question. There is another hypothesis called the iron-sulfer world hypothesis which gives an account of the formation of metabolic pathways originating from inorganic homogenous catalysis on the adsorption surfaces of transition metals such as Va and Ni. The RNA world does not postulate that metabolics came before oligonucleotides, however. The formation of the first RNA chains (see below) would not have needed specific metabolic pathways because the change in energy is so low. The need for sophisticated metabolic systems developed alongside the formation of more complex systems of ribozymes sequestered in vesicles. The fundamental process in all metabolic systems is the transfer of electrons from a reducing to an oxidizing agent. This process is thermodynamically favorable and thus releases energy. In modern cells, the electron transport is driven by the electric potential between molecular oxygen and NADH. The oxidation of NADH is very favorable. The electrons occupy a very high energy state. The problem is forcing NAD+ to accept them in the first place and that, in effect, is what sources of energy for the first stages modern metabolic pathways do. But when the Earth was still very young, inorganic molecules which held high energy electrons were readily available. That was why I presented the scenario I did. It's simply the most logical to suppose that early life exploited this ready availability of energy rich electrons to extract energy from an electrochemical gradient. Better details emerge for what happened around 3 billion years ago, when cyanobacteria began proliferating extensively due to the evolution of photochemical reactions.

Quote:

Does this help us much when it comes to early earth conditions? This is hardly a wild environment.

We don't suspect that the original environment in which the first RNA based systems emerged was particularly "wild" although we do postulate that it was certainly quite different to the one that we are in now (see below) as the Earth has undergone several major atmospheric, chemical and geological changes over the course of the history of life on Earth. These changes are consequences of biological life itself, such as the oxygen catastrophe. In vitro selection in SELEX is a reasonable approximation to what we suspect are conditions that the earliest RNA would have found themselves in (the tube is saturated with free nucleotides, and for particular eluants, sometimes particular metabolites are fixed to the column so that researchers can see if in vitro selection can produce ribozymes which can sequester particular transition metals or catalyze central metabolic processes like phosphorylation. They can).

Quote:

I was asking why we would not see any vestige niche containing such "organisms".

For the same reason that there is no trace of the vast majority of organisms which have existed and proliferated over the course of the history of life on Earth. Even if RNA-based organisms had managed to eke out a little niche of their own after the superseding of them by DNA, their lack of sophistication (biological sophistication of RNA based organisms being limited by their inability to retain long strings of nucleic acids due to the tendency of the ester link to break) would have ensured that any major change in the conditions of the Earth (I'm thinking specifically of the oxygen catastrophe) would have almost certainly wiped them out, owing to difficulty in their adaption to conditions that were different to those in which they evolved.

Quote:

Why is it we can not even conjecture on a wild stage that allows for these RNA soups to pop into existence?

We can. The RNA world hypothesis holds that prior to the formation of biological life on a large scale, the early seas (the "primordial soup, although I hate that phrase) was saturated with free-floating nucleotides. Biochemists who subscribe to the RNA world hypothesis (which is a large number, it is a major contender for chemical evolution) differ on what they postulate to be the most likely scenario that led from free floating nucleotides to short RNA sequences (that is, some biochemists suspect that the RNA world was preceded by an more primitive world in which oligonucleotides formed out of more rudimentary monomers like PNA, although the evidence for this is far from conclusive). The RNA world is divided into several stages. The first and most primordial stage is the formation of short RNA fragments in what is essentially a randomized process. The formation of very large strings (i.e billions of base pairs long) with very high fidelity on the basis of templated polymerization (as occurs in modern cells) is very thermodynamically unfavorable and consequently requires a highly developed and regulated metabolic system. But the formation of short RNA sequences from free floating nucleotides has a low change in energy of state (and consequently a low binding equilibrium constant). The RNA world hypothesis holds that certain short sequences (which were essentially randomly formed) had very primitive catalytic abilities that allowed them to lower the activation energy (do not confuse activation energy with enthalpy change) required for nucleotides that would collide with the chain to bond with the nucleotides on the end. Consequently, the binding energy equilibrium constant would go up, and such chains would grow faster than they would shrink.

After that is where the essay already linked starts, as it begins with short RNA fragments and traces out the RNA world hypothesis from those fragments up to more sophisticated systems which incorporate DNA and polypeptides.

Quote:

It seems pretty obvious that what we have is still a massive gap from nothing to DNA/RNA/Protein based life

We aren't moving from nothing to DNA/RNA/Protein based life. We are moving from nucleotides to primitive RNA catalysts to RNA-selection to RNA-based vesicle systems  to RNA/protein based life to DNA/RNA/Protein based life.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

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OrdinaryClay wrote:You are

OrdinaryClay wrote:

You are missing the point. Sampling (assuming replacement, which is obviously the case here) does not effect the population probabilities. They are what they are. In your case you know a priori the population probability function. This is powerful knowledge. It allows you to make big assertions. In the case of the population of planets with life we do not know this information. Sampling allows you to try and estimate these values. The fact that we exist does not effect the population probability whatever it is.

Ah, I see. My post was pointless then.

 

 

Our revels now are ended. These our actors, | As I foretold you, were all spirits, and | Are melted into air, into thin air; | And, like the baseless fabric of this vision, | The cloud-capped towers, the gorgeous palaces, | The solemn temples, the great globe itself, - Yea, all which it inherit, shall dissolve, | And, like this insubstantial pageant faded, | Leave not a rack behind. We are such stuff | As dreams are made on, and our little life | Is rounded with a sleep. - Shakespeare


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 Our existence does set a

 Our existence does set a lower bound of one per Universe. It means it isn't zero.

The SETI sampling sets an upper bound.

EDIT:

This very small sample that SETI has been able to make so far means that that it has only effectively eliminated eliminated the very high end of possible density of ETI's per star, on the assumption of roughly uniform probability of intelligent life per suitable planet.

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OrdinaryClay wrote:Vastet

OrdinaryClay wrote:

Vastet wrote:

The comment that I made that was responded to was answered better by others than it probably would have been by myself, so I'll leave that alone.

I guess you're off the hook.

That would imply there was something to be hooked on, while there wasn't. My response was perfectly defended by others who were not refuted by yourself, therefore my points stand unmitigated.

OrdinaryClay wrote:

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common. 

Vastet wrote:

That life exists elsewhere in the universe is a certainty. 

Looks like you have faith. Congratulations.

Never said I didn't have faith. I have plenty of faith in things that have a very high likelyhood to occur or exist; such as the idea that the sun is mostly made up of hydrogen; despite the fact that I can't go into the sun and see for myself.

Your god doesn't qualify.

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BobSpence1 wrote:

OrdinaryClay wrote:

BobSpence1 wrote:

 Itdoes allow us to set bounds on the probabilities.

What are these bounds?

In this case, upper bounds on the probability of life under the assumption that that probability is similar across the Universe for any randomly chosen planet.

Actually I will cover this in a response to my next post where I considered this aspect more thoroughly.

I did not see any justification for bounds determination. The only bound I have seen you determine was that because we exist the probability is greater the 0. This is only a lower bound, and it is very uninformative at that. I stated before based on this observation alone I can arbitrarily pick a probability that is small enough so as to make us the only life in the universe.

 

Quote:

Quote:
 

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common.

Agreed. That is why I believe our friend Carl Sagan, and many many others, were acting out of faith when peddling the common life scenario.

Not really. It is more a matter of what parts of the available scientific evidence you gave more weight, which is to an extent subjective, but more evidence-based than 'faith' would imply, more a matter of individual assessment of admittedly inconclusive data.

You contradicted yourself. Faith by any other name is still faith.

 

Quote:

So it is utterly wrong to assert that those actually studying the topic have "always been uber optimistic about likely planets".

...

Now we have actual observation of hundreds of planets going around nearby stars, justifying even higher estimates on more solid data.

Drake believed 50% of all new stars formed planets. If the belief is higher now I'm sure it is not by much. So what is the current estimate?

 

Quote:

Even if you want to assert that scientists were always making estimates very much on the high side of what the available data suggested, the actual estimates would have still been rising, because new and more accurate observation have justified much higher estimates.

This is a non sequitur. An early, and high esitmate, could just be confirmed by new evidence.

 

Quote:

To then suggest that "accumulating evidence is reducing the likelihood" is utterly and demonstrably incorrect.

Please demonstrate this then. Just saying that we now believe there are more planets is a very, very weak argument for increasing evidence. Obviously, there are many, many more factors then having a planet form. I don't understand why you have such an unwarranted optimism. Does this particular optimism hold some special place in your belief system?

The trend is that life is more difficult to achieve then first thought. The probability for life is a complex joint probability. Some factors are independent and some dependent on each other, but the scientific community is definitely learning that it is a *lot* more then getting a planet near a similar sun.

 


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BobSpence1 wrote:Yes of

BobSpence1 wrote:

Yes of course, but the evidence has not been negative except with respect to the assumption that intelligent life was very common, like of the order of 1% or higher on any given star system.

...

See my previous comment - yes it does reduce the likelihood of very high densities, but in the context of much lower densities estimates the reduction is very small.

The reduction still exists. As I said, whether, you calculate it or assume it, low densities reduce your overall optimism for life. Even if the reduction is non-linear it is still a reduction. If intelligent life is rare then there is no reason to believe that any life is more common in a long run. Once we formed life there was an inexorable march to more complexity. This is negative evidence.

Our understanding of the collection of conditions needed for life has increased as well. To say that having planets significantly increase odds for life is very simplistic. That is almost tantamount to saying, having matter in the universe greatly increases the likelihood for life. Conditions for life are cumulative. This creates a conditional probability. It is no coincidence that we exist in a paper thin layer on our planet. I think people have a tendency to underestimate the fragility of biological life in the context of the universe we have discovered to exist over the last 100 years. We pretend that life is robust, when in fact it is, and has been, on the lip of extinction. Fascinating.
 

Quote:

Quote:
 

A small random sample of a large population can still have some predictive ability. You seem to like the idea of "even". You use it a lot. Why do we need an "even chance of getting a hit"?

 

In this case it is a simple informal expression of the math - the term 'likely', unqualified, implies 'more likely than not', which is just what 'better than even chance' means. What is your problem, dude??

I understand what likely means both formally and informally. I was hoping you would justify your math in  - why do we need an "even chance of getting a hit"? Even if stated informally you must be able to base this on math. I hardly consider this having a problem, dude??
 

Quote:
 

EDIT: Obviously, until SETI scores a hit, it can only set some rough upper bound. 

What is this rough upper bound?

 

Quote:
 

 

Why so persisently negative, way more negative that a realistic assessment of the actual current state of research in this area, could possibly justify? The assertion of the current data decreasing the likelihood of ETI is just so off-the-planet mistaken that it points to a deep unwilliness to accept that ETI is plausible or likely.

Apparently you did not read this http://www.csicop.org/si/2006-03/seti.html I just don't feel an emotional need to be unreasonably optimistic. Being alone does not scare me.

 


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deludedgod wrote:The in

deludedgod wrote:

The in vitro synthesis of polynucleotides (short ones) by randomly generated pools of RNA to which SELEX was applied (and consequently ribozymes with the ability to catalyze the phosphodiester bond formation) is something that has long since been accomplished in the laboratory.

Where did the nucleotides come from in the wild?  I'm not looking for hypotheticals. I'm looking for evidence that the early earth environment produced and maintained the conditions that allowed simple RNA chains to form.

 

Quote:

Although, perhaps as indicated with this experiment, perhaps short oligopeptides could have been formed without the sequestering of amino acid monomers by RNA based systems. That raises the interesting possibility that there already existed pools of oligopeptides which could give selective advantages to RNA-based systems which captured them. If more experimentation was done on this idea, it might help to clear a major hurdle in our understanding of the transfer from RNA to polypeptide dominated systems.

Of course, it could also be a simple coincidence that amino acids happen to be an organic compound that finds available the thermodynamically favorable conditions in nature, and it has nothing to do with abiogenesis. The mere existence of amino acids in nature supports my hypothesis just as much as any other.

 

Quote:

Well, as per the principle of coevolution, the formation of oligopeptides and polypeptide fragments would have relaxed selective pressure on ribozymes, and consequently the need for RNA based catalysis but not on the sequences themselves because those were what encoded the amino acids which constituted the sequence of polypeptides. Remember, evolution has no foresight. It isn't a designer which decides to do certain things. ... Because of this, certain sequences and systems are permanent. They cannot be outphased because another component of the system depends on them.

They can be outphased if another mechanism achieving the same purpose is produced and selected for. If a better, from an energy perspective, strategy is found there would be heavy selective pressure to utilize this strategy. You can not a prior assume these are paelo-processes that have some how been sheltered because of coevolution. In other words, coevolution does not prevent more stable strategies from being achieved. Our vantage point is such that we may not be able to conceive of the dynamic that produced evolutionarily stable strategies we see at the biochemical level today.

 

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The origin of metabolics in the RNA world is still an open question. There is another hypothesis called the iron-sulfer world hypothesis which gives an account of the formation of metabolic pathways originating from inorganic homogenous catalysis on the adsorption surfaces of transition metals such as Va and Ni. The RNA world does not postulate that metabolics came before oligonucleotides, however. The formation of the first RNA chains (see below) would not have needed specific metabolic pathways because the change in energy is so low. ... t's simply the most logical to suppose that early life exploited this ready availability of energy rich electrons to extract energy from an electrochemical gradient.

Then the postulate is that there were thermodynamically favorable conditions. We have no evidence for this. Can we do this in the lab? Do we have evidence that any early earth conditions were chemically favorable to the production and survival of RNA chains with no metabolic pathway.

 

Quote:

In vitro selection in SELEX is a reasonable approximation to what we suspect are conditions that the earliest RNA would have found themselves in ...

Interesting claim. Can you please provide a citation, which should be very easy for you, no? Note: What I'm looking for is not that SELEX has been done. I'm looking for a paper that provides some evidence that SELEX reasonably approximates an early earth environment.

 

Quote:

For the same reason that there is no trace of the vast majority of organisms which have existed and proliferated over the course of the history of life on Earth. Even if RNA-based organisms had managed to eke out a little niche of their own after the superseding of them by DNA, their lack of sophistication (biological sophistication of RNA based organisms being limited by their inability to retain long strings of nucleic acids due to the tendency of the ester link to break) would have ensured that any major change in the conditions of the Earth (I'm thinking specifically of the oxygen catastrophe) would have almost certainly wiped them out, owing to difficulty in their adaption to conditions that were different to those in which they evolved.

Saying that the earth conditions have changed due to life itself is a given, but still we have all kinds of micro environments where organisms that can not survive in oxygen rich environments survive. If the RNA soup was so robust to survive millions if not billions of years then it seems plausible that there would be some microenvironemnt hat had the thermodynamic conditions for some remnant evidence of its existence. We have nothing. It is very, very fishy that we do not have any evidence in the lab or in the wild that such a thing can exist on its own.

 

Quote:

The RNA world hypothesis holds that certain short sequences (which were essentially randomly formed) had very primitive catalytic abilities that allowed them to lower the activation energy (do not confuse activation energy with enthalpy change) required for nucleotides that would collide with the chain to bond with the nucleotides on the end. Consequently, the binding energy equilibrium constant would go up, and such chains would grow faster than they would shrink.

 

Then we should be able to reproduce this in the lab. We have not.

 

Quote:

We aren't moving from nothing to DNA/RNA/Protein based life. We are moving from nucleotides to primitive RNA catalysts to RNA-selection to RNA-based vesicle systems  to RNA/protein based life to DNA/RNA/Protein based life.

If an hypothesis has no evidence to bridge parts of its reasoning then these are assumptions based on nothing. The chain is simple organics - gap based on nothing - Primitive RNA World based on very limited evidence - RNA Selection (which allows hand waiving because it is a stochastic mechanism and long time periods can be invoked as magic).

 

The bottom line is that if this hypothesis were correct there is no reason why we could not in the lab create the favorable thermodynamic conditions that produced an RNA World which was then available for selective process. Then given this there is also no reason that we could not produce a live experiment that let this RNA World evolve. Simple organisms evolve extremely rapidly and we could see some very interesting results. Still all we have are some simple chemistry experiments that show very little.

 

 


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BobSpence1 wrote: Our

BobSpence1 wrote:

 Our existence does set a lower bound of one per Universe. It means it isn't zero.

The SETI sampling sets an upper bound.

These bounds are so loosely defined as to be meaningless.

Judging from your extremely loose definition of "suitable" planet I don't think our current evidence is very potent, in fact, almost impotent.
 


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Vastet wrote:OrdinaryClay

Vastet wrote:

OrdinaryClay wrote:

Vastet wrote:

The comment that I made that was responded to was answered better by others than it probably would have been by myself, so I'll leave that alone.

I guess you're off the hook.

That would imply there was something to be hooked on, while there wasn't. My response was perfectly defended by others who were not refuted by yourself, therefore my points stand unmitigated.

You seemed to be confused by the metaphor. Your admission that someone answered in your stead implied that you no longer felt a need to answer. This is what is meant by "off the hook".
 

Quote:

OrdinaryClay wrote:

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common. 

Vastet wrote:

That life exists elsewhere in the universe is a certainty. 

Looks like you have faith. Congratulations.

Never said I didn't have faith. I have plenty of faith in things that have a very high likelyhood to occur or exist; such as the idea that the sun is mostly made up of hydrogen; despite the fact that I can't go into the sun and see for myself.

Your god doesn't qualify.

Revising your belief from certainty to "high likelihood" no longer qualifies your belief as faith, but please, by all means, calculate this "high likelihood".
 


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And yet it seems that not

And yet it seems that not being alone does scare you, since the probabilities work infinitely more towards not being alone than they do towards being alone, and here you are defending a highly unlikely scenario for an undetermined purpose in the face of evidence to the contrary.

And that is merely when calculating the probability of life elsewhere in the galaxy. The fact of the matter is that repeated impacts have thrown life that developed on Earth into space. So even if life did not develop on its own elsewhere, it will or has due to life expelled from Earth which can survive the rigours of space, life which we know can survive the rigours of space, as we have seen it do so.

It is therefore a fact that life is not peculiar to Earth, since the existence of life on Earth has guaranteed that life would extend through the universe. The only questions are in the details.

Although it is still ridiculously likely that life formed elsewhere, since the reactions and chemicals which lead to it here exist in perpetuity across known existence, and there are no known factors to prevent it ocurring as it did here.

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OrdinaryClay wrote:Vastet

OrdinaryClay wrote:

Vastet wrote:

OrdinaryClay wrote:

Vastet wrote:

The comment that I made that was responded to was answered better by others than it probably would have been by myself, so I'll leave that alone.

I guess you're off the hook.

That would imply there was something to be hooked on, while there wasn't. My response was perfectly defended by others who were not refuted by yourself, therefore my points stand unmitigated.

You seemed to be confused by the metaphor. Your admission that someone answered in your stead implied that you no longer felt a need to answer. This is what is meant by "off the hook".
 

Quote:

OrdinaryClay wrote:

BobSpence1 wrote:

It is as much an act of faith to assume that there is no life elsewhere in the universe as to assume it is is common. 

Vastet wrote:

That life exists elsewhere in the universe is a certainty. 

Looks like you have faith. Congratulations.

Never said I didn't have faith. I have plenty of faith in things that have a very high likelyhood to occur or exist; such as the idea that the sun is mostly made up of hydrogen; despite the fact that I can't go into the sun and see for myself.

Your god doesn't qualify.

Revising your belief from certainty to "high likelihood" no longer qualifies your belief as faith, but please, by all means, calculate this "high likelihood".
 

I didn't revise anything, I merely quantified it for your benefit.

And before I present any calculations showing the reality, I'll ask for your calculations that show the opposite. They will be necessary to run a comparison anyway, but we won't have to since I'll be showing you how your equations are flawed and irrelevant to your argument.

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Vastet wrote:And yet it

Vastet wrote:

And yet it seems that not being alone does scare you, since the probabilities work infinitely more towards not being alone than they do towards being alone, and here you are defending a highly unlikely scenario for an undetermined purpose in the face of evidence to the contrary.

Since you seemed to have missed my previous invitation, I'll ask again, please provide us all with your calculation of the probability of life? You are a logic based atheist I assume you understand how strong this would make your argument.

 

Quote:

And that is merely when calculating the probability of life elsewhere in the galaxy. The fact of the matter is that repeated impacts have thrown life that developed on Earth into space. So even if life did not develop on its own elsewhere, it will or has due to life expelled from Earth which can survive the rigours of space, life which we know can survive the rigours of space, as we have seen it do so.

You are claiming that life could survive in ejecta debri, please by all means justify this belief. I think you are also implying it could survive reentry and collision with another planet. Again, I would love to hear your evidence for this. Remember life is more then amino acids, so finding amino acids in meteorites does not count as "life".

 

Quote:

It is therefore a fact that life is not peculiar to Earth, since the existence of life on Earth has guaranteed that life would extend through the universe.

No offense, but I think you have been watching too many movies.


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Vastet wrote:And before I

Vastet wrote:

And before I present any calculations showing the reality, I'll ask for your calculations that show the opposite. They will be necessary to run a comparison anyway, but we won't have to since I'll be showing you how your equations are flawed and irrelevant to your argument.

Thanks for the update, Apparently you have not been following the thread, as I have not claimed I could calculate the probabilities. No one can. We can guess (see the drake equation), but these have been hoplessly optimistic as has become evident over time (see the article I posted). 

Of course, it seems you have some unique insight into life in the universe so please enlighten us all with these calculations.

 


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OrdinaryClay wrote:Vastet

OrdinaryClay wrote:

Vastet wrote:

And yet it seems that not being alone does scare you, since the probabilities work infinitely more towards not being alone than they do towards being alone, and here you are defending a highly unlikely scenario for an undetermined purpose in the face of evidence to the contrary.

Since you seemed to have missed my previous invitation, I'll ask again, please provide us all with your calculation of the probability of life? You are a logic based atheist I assume you understand how strong this would make your argument.

Since you seemed to have missed my previous invitation, I'll ask again, please provide us all with your calculations of the probability of life forming. You are claiming to be a logic based theist, so I assume you understand how strong this would make your argument.

And yes, the mockery was intentional. I even fixed a grammer error or two for you.

OrdinaryClay wrote:

Quote:

And that is merely when calculating the probability of life elsewhere in the galaxy. The fact of the matter is that repeated impacts have thrown life that developed on Earth into space. So even if life did not develop on its own elsewhere, it will or has due to life expelled from Earth which can survive the rigours of space, life which we know can survive the rigours of space, as we have seen it do so.

You are claiming that life could survive in ejecta debri, please by all means justify this belief.

http://en.wikipedia.org/wiki/Extremophile

OrdinaryClay wrote:

I think you are also implying it could survive reentry and collision with another planet. Again, I would love to hear your evidence for this.

 http://en.wikipedia.org/wiki/Extremophile

OrdinaryClay wrote:
Remember life is more then amino acids, so finding amino acids in meteorites does not count as "life".

Define life, so I can show you how your definition of life is insufficient to account for life and non-life, thereby reducing your argument on amino acids to irrelevancy.

OrdinaryClay wrote:

No offense, but I think you have been watching too many movies.

Also no offense, but I think you've been reading too many bibles.

Proud Canadian, Enlightened Atheist, Gaming God.


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OrdinaryClay wrote:Vastet

OrdinaryClay wrote:

Vastet wrote:

And before I present any calculations showing the reality, I'll ask for your calculations that show the opposite. They will be necessary to run a comparison anyway, but we won't have to since I'll be showing you how your equations are flawed and irrelevant to your argument.

Thanks for the update, Apparently you have not been following the thread, as I have not claimed I could calculate the probabilities. No one can.

Then how do you justify your position that Earth is the only place in all of the universe where life has arisen? I've seen your previous comments regarding signals, but that is easily ignorable due to the logistics of distance and time. We don't see a single star, not even our own, as it currently exists by looking at it. We see the star as minutes ago for our own, years or centuries or millenia or eons for stars further away. The light took that long to get here, yet you are making the assumption that a signal would traverse the laws of physics and magically appear to us despite the logistical unlikelyhood of such occurring. You also force the preposition that this life must be intelligent, where it is not required to be intelligent to qualify as life.

OrdinaryClay wrote:
We can guess (see the drake equation), but these have been hoplessly optimistic as has become evident over time (see the article I posted). 

Of course, it seems you have some unique insight into life in the universe so please enlighten us all with these calculations. 

On the contrary. Everything we learn about life increases its diversity and capabilities. We have never once learned something that reduces the capabilities of life.

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Vastet wrote:OrdinaryClay

Vastet wrote:

OrdinaryClay wrote:

Vastet wrote:

And yet it seems that not being alone does scare you, since the probabilities work infinitely more towards not being alone than they do towards being alone, and here you are defending a highly unlikely scenario for an undetermined purpose in the face of evidence to the contrary.

Since you seemed to have missed my previous invitation, I'll ask again, please provide us all with your calculation of the probability of life? You are a logic based atheist I assume you understand how strong this would make your argument.

Since you seemed to have missed my previous invitation, I'll ask again, please provide us all with your calculations of the probability of life forming. You are claiming to be a logic based theist, so I assume you understand how strong this would make your argument.

And yes, the mockery was intentional. I even fixed a grammer error or two for you.

OrdinaryClay wrote:

Quote:

And that is merely when calculating the probability of life elsewhere in the galaxy. The fact of the matter is that repeated impacts have thrown life that developed on Earth into space. So even if life did not develop on its own elsewhere, it will or has due to life expelled from Earth which can survive the rigours of space, life which we know can survive the rigours of space, as we have seen it do so.

You are claiming that life could survive in ejecta debri, please by all means justify this belief.

http://en.wikipedia.org/wiki/Extremophile

OrdinaryClay wrote:

I think you are also implying it could survive reentry and collision with another planet. Again, I would love to hear your evidence for this.

 http://en.wikipedia.org/wiki/Extremophile

OrdinaryClay wrote:
Remember life is more then amino acids, so finding amino acids in meteorites does not count as "life".

Define life, so I can show you how your definition of life is insufficient to account for life and non-life, thereby reducing your argument on amino acids to irrelevancy.

OrdinaryClay wrote:

No offense, but I think you have been watching too many movies.

Also no offense, but I think you've been reading too many bibles.

I would really like to know which extremophile you suppose is the one that can survive a collision large enough to eject debri into the solar system. You see again, I hate to burst your high hopes, but astrobiologists are interested in extremophiles not because of their ability to "seed the galaxy", but rather as examples of life that could develop in inhospitable environments.

Again no offense but your version of nana-nana boo-boo is boring.
 


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Introducing life capable of

Introducing life capable of surviving at extremes was merely the tip of the iceberg. Life doesn't have to directly survive a collision and reentry. It could be sealed within a rock which will provide it more than adequate defense against such conditions.

The fact that you think I'm just "nana-nana boo-booing" is amusing, since you are the one repeatedly failing to back up your arguments and assertions with evidence and data, making you the one who is "nana-nana boo-booing".

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OrdinaryClay wrote:You

OrdinaryClay wrote:

You contradicted yourself. Faith by any other name is still faith.

Not quite.  Hopefully the Oxford English Dictionary will suffice?

http://dictionary.oed.com/cgi/entry/50081813?query_type=word&queryword=faith&first=1&max_to_show=10&sort_type=alpha&result_place=2&search_id=z8eP-oxPGU4-8897&hilite=50081813

Definition 1:  I. Belief, trust, confidence.   1. a. Confidence, reliance, trust (in the ability, goodness, etc., of a person; in the efficacy or worth of a thing; or in the truth of a statement or doctrine). Const. in of. In early use, only with reference to religious objects; this is still the prevalent application, and often colours the wider use.   b. Belief proceeding from reliance on testimony or authority.

Definition 3:  3. Theol. in various specific applications.    a. Belief in the truths of religion; belief in the authenticity of divine revelation (whether viewed as contained in Holy Scripture or in the teaching of the Church), and acceptance of the revealed doctrines.    b. That kind of faith (distinctively called saving or justifying faith) by which, in the teaching of the N.T., a sinner is justified in the sight of God. This is very variously defined by theologians (see quots.), but there is general agreement in regarding it as a conviction practically operative on the character and will, and thus opposed to the mere intellectual assent to religious truth (sometimes called speculative faith).    c. The spiritual apprehension of divine truths, or of realities beyond the reach of sensible experience or logical proof. By Christian writers often identified with the preceding; but not exclusively confined to Christian use. Often viewed as the exercise of a special faculty in the soul of man, or as the result of supernatural illumination.

Read more if you'd like, but I think those two bits demonstrate the point.  There are two distinct types of faith.  The first is the belief/trust/confidence/reliance part.  If I've known someone for decades, I might say I have faith that he's a good person.  If I'm a boss and need to delegate a task, I might say I have faith in the person I'm assigning the job to because he's done well in the past.  This is faith based upon past evidence.  I do not know for a fact that my friend is a good fellow or my subordinate will do the job well, but based upon what I have seen in the past, I have confidence in him, I believe in him, I trust him, etc.

The second is religious faith, and the primary objection to this type of faith is that it promotes faith as a source of knowledge.  That because you believe in something religious, it holds as much or more weight than an empirical observation.  That you blindly trust this faith over every other thing, and don't you dare be a "Doubting Thomas."

So faith is not quite always faith.  For example, if I was to insult you, I could either be calling you a name, or I could be hitting you with a metal pipe.  Hopefully you'd agree those two meanings are quite different,