Wednesday, March 09, 2011

A Scientific American article on the impasse in origin of life research

Scientists, according to this article, have no clue as to how life began. But the author thinks this doesn't support a theistic account, because theists can't answer the question "Who made God?"

61 comments:

Steven said...

The only way the theistic hypothesis is relevantly different from the panspermist hypothesis is if the God posited by the theists is a necessarily existent living being, something that is living but does not need any explanation of its own existence.

Unfortunately, this goes well-beyond what the phenomenon of the existence of organic life suggests to us.

The existence of organic life can be explained within the theistic framework, but it cannot give much evidence itself for the whole of the theistic framework.

Tony Hoffman said...

The question of low life began seems a little to me like the question of what was the first thought. In other words, I'm not sure why it's considered a vital scientific question.

Btw, I do think that most scientists are in agreement about how life began: chance.

Boz said...

Victor said: Scientists, according to this article, have no clue as to how life began. But the author thinks this doesn't support a theistic account.

are you implying that this does support a theistic hypothesis for he origin of life?

William said...

Questions of life's ultimate origin have no real place in biology, any more than the questions of where water comes from are relevant to oceanography.

Such questions might belong in chemistry, though, since it is chemistry that might tell us whether spontaneous generation is actually possible and how it might occur.

Victor Reppert said...

If all the atheist can come up with is the "Who made God" objection, then I think we should consider the possibility that there is an argument for theism here. But I don't know if things are that bad in origin of life research.

Do scientists believe that life began by chance because they have looked at the evidence and have a good chance-explanation?

David B Marshall said...

Nick Lane gave it a pretty good whirl in Life Ascending. He thinks life arose in a certain kind of underwater vent, and makes his scenario sound plausible. His account was suspiciously chipper, though -- one hesitates to look under the carpet.

BenYachov said...

>Btw, I do think that most scientists are in agreement about how life began: chance.

What if I was an Atheist who believes the Universe is governed by Quantum Super Determinism? I won't believe in God but I wouldn't believe in chance either. Chance like free will would be a mere illusion.

OTOH Aquinas a Theist, believed in Chance and natural processes.

Anonymous said...

Btw, I do think that most scientists are in agreement about how life began: chance.

A shame that opinion is non-scientific in the only sense that could matter in this conversation. Chance is not an explanation, just as it is not a cause.

In this case, scientists don't even know how to get life to start from non-life even when eliminating chance and pursuing the tasks themselves. And if someday they do manage to develop life from non-life, that will be evidence for design on the spot.

RD Miksa said...

Hello Steven,

Your comment:

"The only way the theistic hypothesis is relevantly different from the panspermist hypothesis is if the God posited by the theists is a necessarily existent living being, something that is living but does not need any explanation of its own existence."

I would have to disagree here and say that this is actually incorrect.

The fact is, the origin of life problem does support the theistic hypothesis a great deal more than the panspermist one. The reason for this is quite simple. In essence (and I obviously do not present this idea formally here...just a rough sketch), because all our current knowledge shows that life would have extreme difficulty (and this is an understatement) in arising naturally, then we, as human beings, have good and rational reasons to believe, at our present state of knowledge, that life anywhere in the universe would have extreme difficult in arising naturally. But since the panspermist hypothesis requires that life arose naturally somewhere in the universe, then we have good and rational reasons to either reject this hypothesis or give it less weight then other options. By contrast, the theist hypothesis does not suffer from this weakness, since, as we are positing a theistic deity, we are positing a Being both quite capable of creating life and simultaneously wishing to be interactive with his creation, thus making the creation of life not unexpected or improbable. Therefore, from this fact alone, and in the sense of an inference to the best explanation, the origin-of-life problem supports theism over other hypothesis. And because it is simply an inference to the best explanation, we can still accept it even if we do not have the answer to the question "Who/What made God?" (Assuming that we actually consider this a valid question in the first place.) For we do not need to answer this question in order to accept a theistic deity as the best explanation to our original origin-of-life problem. We can just leave it unanswered for the moment, and still be rational in beleiving in the existence of a theistic deity.

Take care,

RD Miksa
rdmiksa.blogspot.com

Tony Hoffman said...

"Chance is not an explanation, just as it is not a cause."

I don't agree. What is the reason that the holder of last night's winning lottery ticket was chosen?

Al Moritz said...

We just discussed this recently here:

http://dangerousidea.blogspot.com/2009/06/mcgrath-on-what-augustine-would-say.html

I am a Christian, but I find an origin of life by natural causes now extremely likely. For an overview of recent research, see my article on the evolution website Talkorigins.org:

http://www.talkorigins.org/faqs/abioprob/originoflife.html

I would have agreed with the article in Scientific American 10 years ago though. But the research on the topic since then has just been spectacular, in my view.

Bottom line, the article is dated.

And yes, in this case chance *is* an explanation because the odds are far less astronomical than in cosmological fine-tuning (where playing the chance card without invoking a multiverse is ludicrous -- cosmologists, also atheistic ones, agree on that). Let's say that the chances are 1 in a million years that a genetic molecule, enclosed in a fatty acid cell membrane (the enclosing step is piece of cake, by the way) acquires the ability to replicate and undergo Darwinian evolution from there (that's all that's needed as I point out in my article). What does it matter in terms of geological deep-time if life started 3.802 or 3.803 billion years ago?

Anonymous said...

I don't agree. What is the reason that the holder of last night's winning lottery ticket was chosen?

Because a series of events took place which involved (hopefully) obscuring the answer to humans until the moment the selection was made? What do you think happened - that Eris descended from on high, reached into the basket of tickets, and selected a winner using the power of acausality?

As for Al, the state of OoL research does not hinge on his personal credulity. Google for "Psst, don't tell the creationists, but scientists don't have a clue how life began." That's (not exactly theist-friendly) John Horgan as of around a couple weeks ago, summing up the status of Origin of Life research. Be sure to read his link to the NYT article on same as well.

Incidentally, I'm calling 1 in 3 odds Al will respond to this post with hand-waving, snorting at dissenters, and assuring everyone that - despite the laundry list of outstanding problems in OoL research - everything is essentially figured out, because he feels in his heart of hearts it is. Is chance an explanation for his response? ;)

BenYachov said...

I did google this:

"Nobody understands the origin of life. If they say they do, they are probably trying to fool you." — Ken Nealson, 2002

In principle it's doesn't matter to me if someone finds a naturalistic explanation for the origin of life.

Aquinas believed Spontaneous Generation was a natural process not a supernatural one.

But I maintain a healthy skepticism on the matter in light of Oderberg's arguments that seem to say Metaphysically we might not be able to account for the origin of life naturalistically.

Al Moritz said...

As for Al, the state of OoL research does not hinge on his personal credulity.

No, it hinges on the data. Read my article.

Bilbo said...

Yes, Vic, things are that bad in the origin of life research.

Anonymous said...

No, it hinges on the data. Read my article.

The data is the reason *I* believe the OoL is far away from being solved. Your article mostly appeals to imagination: what maybe is possible, if you fill in considerable amounts of the problems with hopeful speculation. It's an interesting replacement for science.

And, does chance explain your response? I did give 1 in 3 odds. ;)

Al Moritz said...

The data is the reason *I* believe the OoL is far away from being solved.

Of course the issue is not yet solved. However, conceptually there are far fewer and less serious roadblocks than just a decade ago.

Your article mostly appeals to imagination: what maybe is possible, if you fill in considerable amounts of the problems with hopeful speculation. It's an interesting replacement for science.

Erm, that is how science is done. Hypotheses are formed, and then tested (and many hypotheses have been tested successfully in that field of research). Science is not just the finished data.

BenYachov said...

One thing that I do wonder regarding the Origin of Life.

If it is a natural process how come it hasn't repeated itself on our planet?

(Not that I believe there are no natural processes that can or might happen only once mind you.)

Anonymous said...

Of course the issue is not yet solved. However, conceptually there are far fewer and less serious roadblocks than just a decade ago.

Along the lines of how there are fewer and less serious roadblocks now than just a decade ago when we consider directed panspermia. You may as well be saying Craig Venter's work just highlighted the viability of the ID hypothesis.

Erm, that is how science is done.

If mere imagination about what maybe is possible is science, the bhagavad gita can be considered a science textbook.

Anonymous said...

If it is a natural process how come it hasn't repeated itself on our planet?

Because then common descent wouldn't be true.

Tony Hoffman said...

Me: "What is the reason that the holder of last night's winning lottery ticket was chosen?"

Anonymous: "Because a series of events took place which involved (hopefully) obscuring the answer to humans until the moment the selection was made?"

Is than an answer to my question? If it is meant to be answer, does that mean that choosing a winning lottery ticket is not determined by chance? 

Anonymous said...

Is than an answer to my question? If it is meant to be answer, does that mean that choosing a winning lottery ticket is not determined by chance?

It's determined by the mechanics of the lottery process and the processes and intervening forces, if any, that underwrite them. Are you seriously suggesting that something called "chance" reaches down and selects a winner? That chance thinks to itself "Okay, I determined the winner. I'll let everyone know tomorrow."?

Matteo said...

It's determined by the mechanics of the lottery process and the processes and intervening forces, if any, that underwrite them.

Not to mention that the lottery, by design, has good enough odds that winners occur at a reasonable rate. If anyone ran a lottery that had a probability of winning that was, say, 1 in 10^150, there'd be few takers.

For this reason, lotteries are a very poor analogy for saying "See, nature could spontaneously generate life, because people win the lottery all the time!"

Yes, they do. By design.

Tony Hoffman said...

Anon: "It's determined by the mechanics of the lottery process and the processes and intervening forces, if any, that underwrite them. Are you seriously suggesting that something called "chance" reaches down and selects a winner?"

No on 2. So, how do you imagine that your first sentence differs from the common definition of chance? Because it sounds like you're objecting to my using the term "chance" to mean approximately what you define in your first sentence.

Anonymous said...

So, how do you imagine that your first sentence differs from the common definition of chance? Because it sounds like you're objecting to my using the term "chance" to mean approximately what you define in your first sentence.

If the common definition of chance assigns chance a causal role, as if there is this thing called chance that acts on nature, the common definition is bullocks.

"Chance" is not an entity acting on the world. Unless you have some kind of odd Erisian idea of chance in mind. You're the one who's been speaking of chance as a force, a thing that actively works and determines. Not myself.

unkleE said...

Al Moritz:

Hi! I appreciated your paper which you linked to, thanks very much. (I recommend it to all.) I especially appreciated this paragraph:

"Upon considering this self-organization of material structures in the realm of philosophy, one may conclude that it happens either because the underlying laws of nature, which have to be exceedingly special to allow for it (Rees 2001, Smolin 1999, Susskind 2006), simply are the way they are (possibly in the context of a multiverse) or because they were designed by God for this purpose. Since we know that the laws of nature are so self-sufficient that, based on them, the complexity of the entire physical universe evolved from fundamental particles, and further, complex life forms from simpler ones during biological evolution, we can reasonably extrapolate that they would also allow life itself to originate spontaneously, by chemical evolution of suitable structures – regardless if we believe these laws are designed or undesigned. Therefore, we should expect an origin of life by natural causes from both theistic and atheistic philosophical perspectives."

If militant atheists and militant creationists truly understood this paragraph, I think we could see a lot more light in discussion of God and science. Thanks again.

David B Marshall said...

The problem with that philosophy is that, both from a Christian and an empirical POV, it isn't true. Miracles do seem to happen. The resurrection is just a special instance. Therefore the unfolding (evolution) of history is not continuous: events are sometimes fed into it from "outside," if God be so perceieved.

The laws of nature may or may not be "self-sufficient," but we know (historically) that that is not the whole story. Therefore, the origin of life, and all the fits and starts in evolution that tax even the imagination (still more rigorous forms of scientific inquiry), cannot be solved by waving this particular, or any other, philosophical wand.

Having said that, it MAY be that the origin of life can be explained naturally -- we'll see.

BenYachov said...

>The problem with that philosophy is that, both from a Christian and an empirical POV, it isn't true. Miracles do seem to happen.

How do you define a Miracle? Is it a suspension of an alleged law of nature (i.e. the post Enlightenment view)?

Or do you define it according to the Classical view? In the Classical View God continuously sustains the existence of the Universe in a top down causation terminating with him. A miracle is nothing more than a potency God who is Pure Actuality actualizes directly rather than threw secondary causes in the top down causal chain.

It makes a difference which you believe.

Tony Hoffman said...

Anon: "You're the one who's been speaking of chance as a force, a thing that actively works and determines."

I don't recall doing this. Can you show me where I spoke of chance as a force that actively determines?

Tony Hoffman said...

Mattero: “If anyone ran a lottery that had a probability of winning that was, say, 1 in 10^150, there'd be few takers.
For this reason, lotteries are a very poor analogy for saying "See, nature could spontaneously generate life, because people win the lottery all the time!" Yes they do, by design.“

I think you are asking too much of the lottery analogy. The purpose of the analogy, I think, isn’t to show that it must be probable that we would purchase the winning lottery ticket; it’s meant to show that given a certain number of lottery tickets printed and a certain subset purchased, someone is likely to hold a winning ticket. This has nothing to do with design; it’s probability based on how we observe that natural events occur.

To say that life could only occur by design is to mistake the winning lottery ticket for something with intrinsic value; I think the winning lottery ticket has instrumental value, and selecting a winner in that event does not require design. (Usually all it takes is one of those clear boxes with the numbered ping pong balls.)

Ana said...

Ben said:

If it is a natural process how come it hasn't repeated itself on our planet?

and Anon said:

In this case, scientists don't even know how to get life to start from non-life even when eliminating chance and pursuing the tasks themselves. And if someday they do manage to develop life from non-life, that will be evidence for design on the spot.

Interestingly, when I point out similar things to the above, to naturalists, they don't seem to get it at first. I'll say we have yet to observe, in nature, abiotic material self-assemble and integrate into a fully functioning [basic] living unicellular organism . And yet usually, the response I get is an example of RNA synthesis in the lab, or en example of scientists re-engineering a cell. But that doesn't help build the case of a naturalistic origin of life.

We should be able to currently find examples of life emerging out of the abiotic environment –- self-design of life –- in nature, by nature.

Ah, but then the thing they'll say is, that modern earth conditions are not congenial to natural origins of life (but that the early earth with its chemically well-supplied oceans swishing around, would have inevitably given rise to life).

I guess my simple question is, is abiogenesis falsifiable and if so, how?

Blue Devil Knight said...

Not an article, but a blog post. By a journalist, not a scientist. The quip about god is a throwaway line at the end.

In other words, levity not gravity is needed for this one.

Anonymous said...

In other words, levity not gravity is needed for this one.

He made reference to the state of the OoL field given by an expert, and was airing his views bluntly.

And who cares what your recipe for an answer is? You're not even in the same field. Speak up when the topic is neurology or chess, otherwise kindly hush like a good lil' boy.

Ahh, arguments from credentials. Gotta love 'em.

Tony Hoffman said...

Anon: "Ahh, arguments from credentials. Gotta love 'em."

Ahh, insults from obscurity. Gotta admire 'em.

Blue Devil Knight said...

Anonymous: I was talking about Horgan's god comment, a throwaway quip from someone that typically writes with levity and bravado. It wasn't the produce of any argument. It was a throwaway line on a blog by a science journalist who likes to be provocative, not a considered opinion. Describing it as an impasse is tendentious, and not reflective of the NYT article which was much more catholic and ecumenical.

In other words, there are a couple of layers of levity operators to be applied to Horgan's commentary.

Or you can blow it all up out of proportion and start attacking people and be all serious and put on your gansta scowl LOL have fun with that...it's like watching Tony dance around stage in the West Side Story.

Blue Devil Knight said...

Incidentally, I was thinking about this research at dinner, and implications for my atheism. Frankly, if science can never explain the origins of life, and this could be proven (say there were five scenarios, equally plausible, but we could not decide amont them without having a time machine to collect some crucial bit of evidence). That wouldn't rattle me at all as an atheist. There are things that happened in the past that we will never explain. Historical sciences are incredibly difficult.

The reason I focus on consciousness is because it doesn't have that excuse. It is something that is happening now, in billions of animals all over the planet, and we still don't understand it. A complex sequence of chemical reactions that happened 2 billion years or so ago? I would be surprised if science could piece it together without gaps.

I'm impressed at how good the origins of life research is, given that we are talking about quite specific events deep in geological time.

That said, if there were a proof that no natural sequence of events could have given rise to life, that would of course sway me. But mere ignorance or gaps? Not even close, it's exactly what I'd predict (and this prediction is admittedly from a state of ignorance of the details of geochemistry which are crucial so I don't put a whole lot of trust in these predictions).

Blue Devil Knight said...

Ana asks:
I guess my simple question is, is abiogenesis falsifiable and if so, how?

This is a great question, and for reasons I spelled out in my previous post, it isn't clear that it is falsifiable. We could falsify particular theories (e.g., theory X requires an atmosphere rich in oxygen, but this wasn't available so it can't be what happened).


But to falsify abiogenesis tout court? Likely impossible since any individual datum or experiment will not be enough to take down such a huge and unruly class of theories, many of which contradict each other in the details (e.g., metabolism (protein) first versus nucleotides (RNA) first versus both at the same time (RNA that acts as an enzyme)).

It strikes me as asking whether geology is falsifiable. It's a huge sprawling field with tonds of great individual discoveries, and many individually falsifiable theories, but the field as a whole falsifiable? Falsifiability rarely applies on such a scale.

I think when we hit this scale it is better to ask things in a more Lakatosian vein. Is it a degenerate or progressive research programme?

SteveK said...

Tony,
>> I don't agree. What is the reason that the holder of last night's winning lottery ticket was chosen?

Randomness can't create things out of whole cloth. There must first exist potential.

The potential for winning the lottery existed before the random number picking got started. The same thing can be said about life. The potential for life - rational life - had to exist from the very beginning.

What would that "beginning" have to entail in order for that potential to exist? It seems to me it must entail much, much more than matter, energy, space and time.

Bilbo said...

BDK,

There are no plausible theories of the origin of life. All of them are extremely implausible. Crick's statement from his book, Life Itself, is as applicable today as it was when he wrote it in 1981:

"An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going."

The difference is that we know even more how applicable it is.

Blue Devil Knight said...

Bilbo you seem to have a very strong opinion on this, and I know people who have equally strong opinions that the research is promising and on the right track. People who know a hell of a lot more than I do about the topic.

So much of these argments about life's origns depend on deep ignorance we have of the conditions back then, it is really hard for me to get motivated.

"Hey here is this complex chemical event that happened 2 billion years ago, and people seem to have a lot of trouble reconstructing exaclty how it happened."

You can see why I might be underwhelmed.

On the other hand, in the meantime, feel free to fill that knowledge gap with god: by all means I can't prove you are wrong. I can only say that is a really weak reason to believe, and I hope you have others.

Blue Devil Knight said...

Bilbo, I'm curious what you think of this article. Also, have you read Al's excellent piece, and have criticisms of it? He knows a lot more than me, but perhaps you are in the loop more than both of us on this research. I don't pretend to have the expertise in geochemistry required to be able to see possibilities (e.g., this reaction could do that, and this organic synthesis reaction could easily be done in subtrate X, givine us needed product Y). It has been years since I studied organic chemistry.


Hell, it would be hard enough to reconstruct the events if the were happening right now, if we went back in a time machine and collected samples of water right were abiogenesis were happening, how many years before researchers were able to get it right? So what do we expect given that we don't have that luxury?

If the difficulties in such research were someone's sole reason for believing in god, they'd be sillyheaded.

Tony Hoffman said...

"What would that "beginning" have to entail in order for that potential to exist? It seems to me it must entail much, much more than matter, energy, space and time."

Yawn. But it doesn't seem that way to me. And that's why argument from intuitions is boring. And it's why discussions with those who idolize Aristotle are so predictably dull.

Tony Hoffman said...

I have to say that smug statements about the state of OOL research have no truck with me. If none of our explanations for the OOL seem reasonable, God of the gaps! If we find a reasonable explanation, then God designed the universe that way!

I look around, do a self check, and yup, looks like life can occur naturally. There are more pressing areas of scientific study that I'm curious about.

Now if a theist wanted to show how liffe can about supernaturally, then I'm all ears.

Anyone? Anyone...

SteveK said...

Tony,
>>Yawn. But it doesn't seem that way to me. And that's why argument from intuitions is boring. And it's why discussions with those who idolize Aristotle are so predictably dull.

You have your interests, and I have mine, Tony.

I'm more interested in why the potential for lottery winners existed before the mechanism was turned on. You're more interested in how the mechanism goes about producing winners.

Bilbo said...

Hi BDK,

Shapiro rejects Sutherland's work here.

The RNA-first hypothesis depends upon a prebiotic soup, which Moran rejects here.

But Shapiro's and Moran's metabolism-first hypothesis is refuted here.

And Orgel characterized all research as depending upon if pigs could fly scenarios.

But if all we had were gaps, that wouldn't be much of an argument for design. Design arguments depend upon (1)gaps, and (2)resemblance to design. The more resemblance, the more confident our inference of design. Thus when Venter said, "This is as much a philosophical as a technological advance. The notion that this is possible means bacterial cells are software-driven biological machines," one's suspicion of design should rise sharply.

Blue Devil Knight said...

Thanks Bilbo will take a look if I have time. You didn't say whether you agreed with the criticisms. Citing scientists disagreeing with each other isn't particularly convincing in any direction. That's how science works, after all, and one of them might be right, all might be wrong, all may have their finger in a partial truth. It isn't really clear where you stand, how much you have studied the requisite chemistry and such to have such a strong opinion as you do. I personally have a not very strong opinion on specific scenarios, because this stuff takes some heavy-duty knowledge of organic chemistry synthesis reactions that I am very rusty on.

Again, I'm not very worried that it is hard to reconstruct a very complicated series of chemical reactions that happened over 2 billion years ago.

Blue Devil Knight said...

One thing I like is the scientific creativity of these studies, the discovery of cool functions of RNA, even the beauty of Miller's old experiments. Such things wouldn't happen if they had just seen the gap in our knowledge and thrown up their hands. Gaps are the engine of scientific creativity, experiments, and progress. The relentless, stubborn, creative attack of such gaps by scientists is an inspiration to me personally. It is easy to say it is doomed. That's what the vitalists said about development, they would make fun of the "mechanistic" philosophers' attempts to find "atoms" of inheritance and development. There were dozens of "failures" in these experimental/theoretical attacks of the problem of heredity/development. Which "failure" was most important in leading to success, I wonder? It cannot be predicted.

Al Moritz said...

Unklee:

If militant atheists and militant creationists truly understood this paragraph, I think we could see a lot more light in discussion of God and science. Thanks again.

Thanks Unklee for that comment. Related to that is what I later say in the article, in chapter 7:

In fact, creationists should seriously ask themselves if their concept of God is not a belittling one: the Intelligent Designer as "tinkerer" who is forced to break his own created laws of nature once in a while because they are insufficient to achieve certain stages in the development of the material world. From a theistic philosophical perspective, the actual findings of science suggest a much grander idea of God: the Designer who laid out an elegant and self-sufficient set of laws of nature that accomplish the unfolding of his creation by inducing self-organization of the material world. This idea is easily compatible with the concept of God of many mainstream religions, including most Christian ones.

I might add: I prefer to believe in a God who performs miracles when He *wants* to, not when He *has* to.

Al Moritz said...

Ana:

Interestingly, when I point out similar things to the above, to naturalists, they don't seem to get it at first. I'll say we have yet to observe, in nature, abiotic material self-assemble and integrate into a fully functioning [basic] living unicellular organism . And yet usually, the response I get is an example of RNA synthesis in the lab, or en example of scientists re-engineering a cell. But that doesn't help build the case of a naturalistic origin of life.

It does. Not the re-engineering of a cell, but showing in the lab that a simple protocell (much simpler than the simplest modern bacteria) with characteristics of life can be made, yes that will help. You can never show precisely which sequence of events did take place 4 billion years ago, that is 'forensically' impossible. However, once you can show experimentally how life may have started, you are done. You have shown that conceptually an origin of life by natural causes is possible and even likely (I think this also is partially an answer to BDK's points).

Prebiotic chemistry tries to establish what may have happened under realistic prebiotic conditions in nature. For example, the recent breakthrough in prebiotic RNA synthesis (see my article, link above) was not about synthesis of RNA per se, which is trivial in the modern laboratory, but how nature may have self-assembled RNA nucleotides on the ancient Earth. Once that is shown, the concept is proven that this may have been one of the essential parts for life to have gotten started.

We should be able to currently find examples of life emerging out of the abiotic environment –- self-design of life –- in nature, by nature.

Ah, but then the thing they'll say is, that modern earth conditions are not congenial to natural origins of life (but that the early earth with its chemically well-supplied oceans swishing around, would have inevitably given rise to life).


That is correct. Life could only have arisen under the reducing, or at least neutral, atmosphere of the early Earth. The oxidizing atmosphere of the current Earth, which is prohibitive for prebiotic chemistry, was exactly *created* by life over 2 billion years after it had gotten started. So we cannot expect life to arise under current conditions. Also, the chances for life arising cannot be that great, since then life on Earth would not have a common ancestor. If we are talking about chances of once in millions of years (the bottleneck is the molecule that by chance has precisely the sequence required for self-replication), spontaneous generation of life should *not* currently be observed (apart from the fact that the necessary atmospheric conditions are not there anymore, as I just pointed out).

Al Moritz said...

Bilbo:

Shapiro rejects Sutherland's work here.

Shapiro criticized that one of the components necesary for synthesis, cyanoacetylene, would have been far too unstable to be present in sufficient amounts. Sutherland countered that it would be used immediately after generation. Shapiro was the only one in the field who made that objection. The reaction to Sutherland's findings among his colleagues, many of whom have made far more significant contributions to the field than Shapiro in recent years, has been overwhelmingly enthusiastic.

The RNA-first hypothesis depends upon a prebiotic soup, which Moran rejects here.

I don't think anyone currently believes that life originated in a prebiotic soup out in the open ocean. By its very nature, the origin of life must have been a localized event. Puddles with repeated wet-dry cycles to concentrate components would be a better candidate. An even far more powerful alternative would be thermal gradients in mineral pores (as found in deep-sea vents, but also in more shallow-water vents), which can concentrate components up to 100-million fold. This has been recently shown both for RNA molecules and for lipids that could encapsulate them, see my article. Your information is lagging behind the most recent data.

(cont.)

Al Moritz said...

(cont.)


And Orgel characterized all research as depending upon if pigs could fly scenarios.

This is not true. Orgel only dismissed metabolic cycles, as specified in the link, but not "all research" as you suggest. He very much embraced the gene-first scenario and the RNA World hypothesis. In fact, it was a review by Orgel that, in 2006, finally convinced me of an origin of life by natural causes, a conviction strengthened by further study and by the most recent research developments after 2006.

(cont.)

(Sorry to snip my post, the badly designed blogger system does not accept my full-length post.)

Al Moritz said...

But Shapiro's and Moran's metabolism-first hypothesis is refuted here.

And yet, while I do not quite subscribe to the metabolism-first secenario, on metabolic cycles a lot of unexpected progress has been recently made by the group of Martin at Harvard University.

Bilbo, you appear to have an immense confirmation bias on the issue, but rather limited knowledge of the actual research -- certainly in no healthy proportion to the magnitude of your confirmation bias.

I agree with BDK when he says:
If the difficulties in such research were someone's sole reason for believing in god, they'd be sillyheaded.

if you make your belief in God dependent on this, you will be in for a truly nasty shock one day. There are far better and more powerful reasons to believe in God.

Blue Devil Knight said...

Al, thanks for taking the time to respond to Bilbo. It all seemed a bit quick and easy to refute these people who are obviously creative scientists battling in the treches. But I still haven't read through the stuff, and am a mere dilettante with origins of life research.

Al Moritz said...

BDK,

you're welcome. And thanks for the compliment above and for your contributions to this thread, which have been valuable.

Bilbo said...

Al: "Shapiro criticized that one of the components necesary for synthesis, cyanoacetylene, would have been far too unstable to be present in sufficient amounts."

Shapiro's main criticism, here, is that

"The flaw with this kind of research is not in the chemistry. The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth."

Or as Stephen Meyer put it,

" the reaction that Sutherland used to produce ribonucleotides involved numerous separate chemical steps. At each intermediate stage in his multi-step reaction sequence, Sutherland himself intervened to purify the chemical by-products of the previous step by removing undesirable side products. In so doing, he prevented—by his own will, intellect and experimental technique—the occurrence of interfering cross-reactions, the scourge of the pre-biotic chemist.

Third, in order to produce the desired chemical product—ribonucleotides—Sutherland followed a very precise “recipe” or procedure in which he carefully selected the reagents and choreographed the order in which they were introduced into the reaction series, just as he also selected which side products to be removed and when. Such recipes, and the actions of chemists who follow them, represent what the late Hungarian physical chemist Michael Polanyi called “profoundly informative intervention[s].” Information is being added to the chemical system as the result of the deliberative actions—the intelligent design—of the chemist himself.
"

More later.

Blue Devil Knight said...

Bilbo that is great, the Meyer quote is a lot like the quotes I see from the 19th century vitalists I've been reading.

"Sure you can make urea in a test tube, but there is no reason to think this is how it is done in living cells."

It turns out that the synthesis of urea was extremely important existence proof, an experimental isonali that led to an avalange of further work filling in a vacuum created by the dogma that the vital processes in living things cannot be produced by ordinary chemicals outside of living things.

That line from Shapiro, frankly, comes off as sour grapes in the context of the amazing discovery by Sutherland. I love the Sutherland response:
"They're perfectly entitled to disagree with us. But having got experimental results, we are on the high ground."

Theory, meet experiment.

Al Moritz said...

Bilbo,

undesirable side-products are taken care of to a good extent by the reaction conditions themselves. Have you read the primary scientific article in Nature? You should read it.

In his Scientific American article on the issue,

http://snipurl.com/vo5jg

Szostak explains that a central intermediary molecule to the synthesis, 2-aminooxazole, may be purified automatically before undergoing further reactions:

A complex web of reactions—with phosphate acting as a crucial catalyst at several steps along the way—produced a small molecule called 2-aminooxazole, which can be viewed as a fragment of a sugar joined to a piece of a nucleobase. A crucial feature of this small, stable molecule is that it is very volatile. Perhaps small amounts of 2-aminooxazole formed together with a mixture of other chemicals in a pond on the early earth; once the water evaporated, the 2-aminooxazole vaporized, only to condense elsewhere, in a purified form. There it would accumulate as a reservoir of material, ready for further chemical reactions that would form a full sugar and nucleobase attached to each other.

Furthermore, Szostak points out that UV irradiation destroys unwanted side-products (as also discussed extensively in the primary scientific article in Nature by the Sutherland group):

Another important and satisfying aspect of this chain of reactions is that some of the earlystage by-products facilitate transformations at later stages in of the process. Elegant as it is, the pathway does not generate exclusively the “correct” nucleotides: in some cases, the sugar and nucleobase are not joined in the proper spatial arrangement. But amazingly, exposure to ultraviolet light—intense solar UV rays hit shallow waters on the early earth—destroys the “incorrect” nucleotides and leaves behind the “correct” ones. The end result is a remarkably clean route to the C and U nucleotides.

Also, Sutherland is well aware that a one-pot reaction would be desirable. From the original research article:

Although the issue of temporally separated supplies of glycolaldehyde and glyceraldehyde remains a problem, a number of situations could have arisen that would result in the conditions of
heating and progressive dehydration followed by cooling, rehydration and ultraviolet irradiation.


And a one-pot reaction is exactly what Sutherland and Szostak performed in the next article, published less than a month ago. It is not perfect yet, but it comes 'dangerously' close to the final goal:

http://www.ncbi.nlm.nih.gov/pubmed/21043502

***

It is clear that the God of the Gaps is becoming smaller and smaller when it comes to the origin of life. In fact, on this issue God will become so small that in the end He will become a dwarf. I doubt that God would appreciate such belittling by you and other creationists. The God of the Gaps is lousy and dangerous theology, and not worthy of an intelligent believer. As I said before, if you base (some of) your belief in God on the origin of life, you will be in for a nasty shock someday.

Al Moritz said...

BDK says:
That line from Shapiro, frankly, comes off as sour grapes in the context of the amazing discovery by Sutherland.

Precisely. Scientists are just human beings, after all. It seems envy, plain and simple.

Bilbo said...

Hi Al,

I appreciate your showing me how theologically committed you are against ID. Personally, it wouldn't matter to me how God brought about life in this universe. I figure He's in charge and has the right to do it however he wishes.

I'll be curious to see Shapiro's reaction to the "one pot" scenario. Meanwhile, I finally found Shapiro's
Scientific American article from a few years ago. I think he would say his criticisms still apply.

By the way, how does one get UV radiation down to deep sea thermal vents?

Al Moritz said...

Bilbo:

Personally, it wouldn't matter to me how God brought about life in this universe. I figure He's in charge and has the right to do it however he wishes.

I am glad you think that way.

Meanwhile, I finally found Shapiro's
Scientific American article from a few years ago. I think he would say his criticisms still apply.


Well, let's take one example: his criticism of the production of cytosine is probably justified, but cytosine is sidestepped altogether in Sutherland's synthesis of cytidine nucleotides.

By the way, how does one get UV radiation down to deep sea thermal vents?

One does not. Szostak talks about shallow waters. Hydrothermal vents are in shallow waters too, surrounding volcanoes, but RNA synthesis may have taken place there, or it may not have.

Bilbo said...

Well I'm a month late, but we can cross off hydorthermal vents now.