Origins and Science

[FSHWILDFIRE]

The debate on origins is a very interesting topic. It is true that evolution and origins are different. However as Dawkins points out there had to be some sort of evolution present during this time. A form of chemical evolution and Natural selection. Aside from that, I was just wondering where do you stand on the Origins debate? i.e. ID, Panspermia, ocean vent theory, chemical affinity etc... and why. It is a very satisfying field. The Paleontology courses on top of my biochem courses I had to take made me realize how important this topic is and that there should be more scientists in this field. Something we should all talk about in the big conversation of life! Lets hear your side!

 

[ApocryphaNow]

There will be more scientists in the field. However, they are all going to be Asian or Indian. Americans are simply too apathetic and willingly ignorant to enforce a strong scientific education. "Science is too hard! I'm going to major in business instead!"

Anyway, I support whatever ideology that has legs in the laboratory. Not all professions require a complete understanding of evolution. Chemists, arguably, do not need to know much about this, as their work is on functionality and synthesis and not historicity. A chemist can be a creationist and get away with it (as long as they keep their mouth shut when it comes to philosophy).

Biochemistists, however, do require at least some small idea of what is going on because living beings are dynamic systems. If they do not understand at least the basics of natural selection, they clearly do not even know what they are doing in the lab on a daily basis "Oh crap! I lost my expression plasmid in my BL21 strains! God stole it!" The work of a biochemist, like their chemist brethren, is biological structure and function. Biochemists can get away with the intelligent design trend. In fact, my experience with them indicates they are pretty superstitious people in general.

Finally, molecular biologists need to have a firm grasp of evolution or they are useless wastes of lab space. Homology, mutation, gene transmission, reproductive constraints, selective constraints, probability, and a whole much of other junk I can't think of right now are all required to understand genetic systems. Molecular biologists need to understand where things came, not just what they do. Genetic information does not just appear in a vacuum. Though I think these people have poor math, chemical, and verbal skills, I have to agree that critical analysis is a must.

It should be noted that there is much interplay between these three disciplines. For example, I consider myself a little bit of all three. There are some biochemists who lean more towards chemistry. There as some molecular biologist who spend a lot of time doing biochemical research. In this case, one must understand all the scientific concepts required.

I don't blame people who aren't molecular biologists for not buying evolution. They don't need it in their daily life, so why should I expect some lazy American to pick up a textbook and read? I do, however, get annoyed when people try to pass off their religion as if it were serious science. Totally lame.

 

[FSHWILDFIRE]

I would still like to hear some more people and their take on the Origins debate and what theory they hold too.

 

[funyun]

I personally think the "iron-sulfur hypothesis", or a related metabolism-first theory is the most promising current framework to scientifically pursue the origin of life.

I also agree with ApocryphaNow that there seems (from my point of view) to be too little scientific research in this field, and that's why I plan on studying biochemistry and molecular biology in college.

 

[HairlessSimian]

I'm an organic chemist and all the organic chemists I know are atheists or at least atheistic on the issue of the origin of Life.

I firmly believe that, one day in the distant future, we will have a strong and experimentally based notion of how life could have arisen. I agree that there is too little research in the area, and for a number of good reasons.* Even once we have a workable hypothesis that can take us from small molecules to a crude system that can be called a lifeform, we will never know for sure how it actually happened in our case, and there will always be doubters/naysayers. Nevertheless, we will be able to invoke Occam's Razor and claim that "no special creation is needed and here's proof". At the moment, we can't give that proof. However appealing and important this is, it's somehow less satisfying than, say, finding the cure for cancer.

In the meantime, I think we can already refute arguments against abiogenesis based on improbabilities. Here's a story.
I'm not up on origin-of-life research, but I've read a few things. I personally prefer a scenario I've not yet seen published, but which could already be in the literature. It involves random peptide/protein synthesis which becomes auto-catalytic and obviously requires a pool of amino acids. An enormous number of sequences can be prepared in very tiny quantities in this way, even if very slowly and inefficiently. A great many proteins will be functional, if unoptimized, enzymes. Some of these will break down some of the protein and recycle the amino acids. Some of these will make lipids which will encircle some of the reaction mixture into micelles. Some will make sugars. Some will make heteroaromatics. Some will form an early TCA cycle, although it need not yet employ ATP. And so on. When the lipid coat and the innards get to be big enough, they can split into two smaller micelles. Reproduction. And so on, until we have basically micelles making micelles, each a machine making molecules for no reason or purpose. At this point, there is no genetic material (none is needed so long as the protein-making machinery keeps pumping out proteins). I'm a little obscure about details (I don't spend a lot of time thinking about this) but at some point, a self-replicating system needs to develop. I suspect some of the proteins will be able to catalyze their own assembly, but it needs to be more complicated than that. In any event, protein-making machines would eventually hit the right combination of molecules for a crude genetic storage-translation-protein synthesis system. From there, natural selection takes over and the rest is history.
These "experimental" chemical machines can involve a few molecules operating very slowly, but the "experiments" can be going on in the trillions per gram of medium, and in trillions of locations all over the earth over hundreds of millions of years.
All we need is one successful cell (weighing a nanogram or less) in one location. Natural selection will ensure that the successful cell will rapidly monopolize the resources of its local environment and so kill off other "experiments". In fact, there may have been many such "successes" in life's history. Only one survived.

*Why is there not more research?
(a) Whatever the conclusions, there will be no certainty as to historicity.
(b) Funding opportunities and priorities apparently lie elsewhere.
(c) It's high-risk business, and it's easier and more fruitful to do something else.
(d) The ultimate experiment, the creation of new life de novo, will take a very long time. And will be an ethical quagmire.
(e) Someone needs to make a fundamental discovery that will inspire others to join the fray.

 

[Arik Soong]

I'm an organic chemist and all the organic chemists I know are atheists or at least atheistic on the issue of the origin of Life.

I firmly believe that, one day in the distant future, we will have a strong and experimentally based notion of how life could have arisen. I agree that there is too little research in the area, and for a number of good reasons.* Even once we have a workable hypothesis that can take us from small molecules to a crude system that can be called a lifeform, we will never know for sure how it actually happened in our case, and there will always be doubters/naysayers. Nevertheless, we will be able to invoke Occam's Razor and claim that "no special creation is needed and here's proof". At the moment, we can't give that proof. However appealing and important this is, it's somehow less satisfying than, say, finding the cure for cancer.

In the meantime, I think we can already refute arguments against abiogenesis based on improbabilities. Here's a story.
I'm not up on origin-of-life research, but I've read a few things. I personally prefer a scenario I've not yet seen published, but which could already be in the literature. It involves random peptide/protein synthesis which becomes auto-catalytic and obviously requires a pool of amino acids. An enormous number of sequences can be prepared in very tiny quantities in this way, even if very slowly and inefficiently. A great many proteins will be functional, if unoptimized, enzymes. Some of these will break down some of the protein and recycle the amino acids. Some of these will make lipids which will encircle some of the reaction mixture into micelles. Some will make sugars. Some will make heteroaromatics. Some will form an early TCA cycle, although it need not yet employ ATP. And so on. When the lipid coat and the innards get to be big enough, they can split into two smaller micelles. Reproduction. And so on, until we have basically micelles making micelles, each a machine making molecules for no reason or purpose. At this point, there is no genetic material (none is needed so long as the protein-making machinery keeps pumping out proteins). I'm a little obscure about details (I don't spend a lot of time thinking about this) but at some point, a self-replicating system needs to develop. I suspect some of the proteins will be able to catalyze their own assembly, but it needs to be more complicated than that. In any event, protein-making machines would eventually hit the right combination of molecules for a crude genetic storage-translation-protein synthesis system. From there, natural selection takes over and the rest is history.
These "experimental" chemical machines can involve a few molecules operating very slowly, but the "experiments" can be going on in the trillions per gram of medium, and in trillions of locations all over the earth over hundreds of millions of years.
All we need is one successful cell (weighing a nanogram or less) in one location. Natural selection will ensure that the successful cell will rapidly monopolize the resources of its local environment and so kill off other "experiments". In fact, there may have been many such "successes" in life's history. Only one survived.

*Why is there not more research?
(a) Whatever the conclusions, there will be no certainty as to historicity.
(b) Funding opportunities and priorities apparently lie elsewhere.
(c) It's high-risk business, and it's easier and more fruitful to do something else.
(d) The ultimate experiment, the creation of new life de novo, will take a very long time. And will be an ethical quagmire.
(e) Someone needs to make a fundamental discovery that will inspire others to join the fray.

Hmmm... advocating a metabolism-first scenario. As you have said, you are an organic chemist so you are probably aware that water is a poor medium for polymerization so to avoid this problem, you advocate metabolism-first. So you believe that a version of the Krebs cycle would form sponetaneously? Orgel said that there is no reason to believe that a mineral surface or the intermediates of the cycle (e.g. citrate, isocitrate, acontate, alpha ketoglutarmate, fumarate, malate, oxaloacetate) would catalyze all of the necessary reactions. Surely one mineral might catalyze one reaction of the citric acid cycle (or the reductive version of it) but I doubt that a mineral could catalyze all of the reactions necessary of the citric acid cycle. Well, if I sound inelegant let Leslie Orgel explain: http://www.pnas.org/cgi/content/full/97/23/12503

I heard you said amino acids could do it... how would they replicate without the information being stored on a nucleic acid. The RNA World scenario provides an answer to this but one must believe in the notion of RNA could act as an efficent polymerase and this has not yet been demonstrated despite numerous valient attempts by David Bartel and coworkers. Also, lets not forget about the difficulties inheritant in prebiotic nucleotide synthesis. One difficulty is attaching the correct nitrogen atom of the base (9') to the correct carbon atom to the sugar (1'). If it attached to one, it must be in its furnanose (5 vertice ringed form) instead of the pyranose (6 vertice ring.) If it is attached to the 1' carbon of ribose, it must be in its beta anomer not the alpha anomer.

 

[funyun]

So Hairless, you would agree that it is more, for lack of a better word, economical, to have metabolism come first, rather than genetics?

 

[Arik Soong]

So Hairless, you would agree that it is more, for lack of a better word, economical, to have metabolism come first, rather than genetics?

So I see you will have no problem using Robert Shapiro's publications (who is adamently opposed to a nucleic acid first scenario) to bash the views of James Ferris and David Bartel who are both RNA world proponents. Shapiro argued against the plausiblity of cytosine and ribose being prebiotic and he also critically analyzed adenine's prebiotic role (I did not read his publication about adenine though.) So without these components of the nucleotides, then the RNA World has no foundation. For example, deny Ferris of his ribonucleotides, then his montmorillonite clays would have nothing to catalyze. Even with his nucleotides, he could only get 90% of the desired 3'-5' phosphodiester linkages (using adenine deriviates as the activating group since nucleotides without an activating group will not polymerize) with the polynucleotides he synthesized. Do not believe my statistic then here: http://www.mbl.edu/CASSLS/FERRIS.ABS.html.

 

[ImmortalTechnique]

in the end, though, arik... you're still arguing a god of the gaps scenario... that's all ID can really ever be... it might be true, but it could never be shown scientifically (at least not by anything put forth so far, I would welcome a way that could demonstrate the existence of a designer)


and abiogenesis research is NOT inherently atheistic or anti-ID... saying so is like saying that (if there had indeed been a world flood) it would be atheistic to study the weather patterns that brought it about... abiogenesis happened (unless you claim that god is biological life) and there was some process that happened... whether it happened on its own or as the result of some outside intelligence is a question that science, it appears, simply cannot answer

 

[Arik Soong]

in the end, though, arik... you're still arguing a god of the gaps scenario... that's all ID can really ever be... it might be true, but it could never be shown scientifically (at least not by anything put forth so far, I would welcome a way that could demonstrate the existence of a designer)


and abiogenesis research is NOT inherently atheistic or anti-ID... saying so is like saying that (if there had indeed been a world flood) it would be atheistic to study the weather patterns that brought it about... abiogenesis happened (unless you claim that god is biological life) and there was some process that happened... whether it happened on its own or as the result of some outside intelligence is a question that science, it appears, simply cannot answer

Whatever! Maybe I am using be arguing a god-of-the-gaps argument but I was merely pointing the flaws in some origin of life scenarios. Also where did I say origin of life research is atheistic. I have no theological objection to ribozyme engineering experiments so I do not think that RNA World proponents are worshiping the devil or whatever.

 

[funyun]

So I see you will have no problem using Robert Shapiro's publications (who is adamently opposed to a nucleic acid first scenario) to bash the views of James Ferris and David Bartel who are both RNA world proponents. Shapiro argued against the plausiblity of cytosine and ribose being prebiotic and he also critically analyzed adenine's prebiotic role (I did not read his publication about adenine though.) So without these components of the nucleotides, then the RNA World has no foundation. For example, deny Ferris of his ribonucleotides, then his montmorillonite clays would have nothing to catalyze. Even with his nucleotides, he could only get 90% of the desired 3'-5' phosphodiester linkages (using adenine deriviates as the activating group since nucleotides without an activating group will not polymerize) with the polynucleotides he synthesized. Do not believe my statistic then here: http://www.mbl.edu/CASSLS/FERRIS.ABS.html.

I'm sorry, who is bashing who again?

 

[Arik Soong]

I'm sorry, who is bashing who again?

Well, since you are advocates of metabolism first, I doubt you would like Bartel's and Ferris' views on the origin of life.

If I notice one thing in the origin of life community...it is that adherents of one scenario usually attack another origin of life scenario. For example, Leslie Orgel attacked Gunter Wachterhauser and Harold Morowitz hypothesis for believing life started as a non enzymatic cyclic metabolic reaction i.e. reductive citric acid cycle. Morowitz and Wachterhauser are well aware of the difficulites of a nucleic acid first scenario. I will also add so is Dr. Orgel, yet his continues to research hoping for a breakthrough that will vindicate the nucleic acid first paradigm.

Another example is A.G. Cairns-Smith. He was a critic of the RNA World too which was evident in his book Genetic Takeover and the Mineral Origins of Life. He listed nineteen difficulites of nucleic acid synthesis but he also advocated his clay mineral hypothesis. Those who are adherents of the RNA world countered by saying his hypothesis had no evidence.

 

[USincognito]

I was just wondering where do you stand on the Origins debate? i.e. ID, Panspermia, ocean vent theory, chemical affinity etc... and why.

I myself don't sweat the small stuff since we really don't have enough data to formulate a solid biogenetic theory. I agree the research is interesting, and one of the possilbilities I find least likely (Panspermia) has found the most interesting support (Opportunity on Mars, Comets, Spectral analyses of distant stars).

I think until we can get some more solid information, or the IDers come up with some viable arguments/evidence for a designer, I just avoid the topic in the gesthalt of C&E debate. In fact I'll take a page from the ID playbook and say my position is "abiogenesis" without speculating what the abiogenetic process was.

 

[Arik Soong]

I myself don't sweat the small stuff since we really don't have enough data to formulate a solid biogenetic theory. I agree the research is interesting, and one of the possilbilities I find least likely (Panspermia) has found the most interesting support (Opportunity on Mars, Comets, Spectral analyses of distant stars).

I think until we can get some more solid information, or the IDers come up with some viable arguments/evidence for a designer, I just avoid the topic in the gesthalt of C&E debate. In fact I'll take a page from the ID playbook and say my position is "abiogenesis" without speculating what the abiogenetic process was.

Space? How does one find polycyclic aromatic carbons or formic acid in space support the idea of a naturalistic origin of life. I would be more impressed if nucleotides or polypeptides are found in space. About nucleotides Orgel wrote this

The inevitable conclusion of this survey of nucleotide synthesis is that there is at present no convincing, prebiotic total synthesis of any of the nucleotides. Many individual steps that might have contributed to the formation of nucleotides on the primitive Earth have been demonstrated, but few of the reactions give high yields of products, and those that do tend to produce complex mixtures of products. It should also be realized that any prebiotic synthesis of a nucleotide would yield a racemic product, not the biologically important D-nucleotide. Recent publications, particularly those of Zubay and his coworkers (cited above), suggest that the search for a convincing prebiotic synthesis of the nucleotides is not hopeless. However, the difficulties remain so severe that alternatives to the de novo appearance of RNA on the primitive Earth deserve serious consideration. The succeeding sections of this review, in addition to discussing possible routes to RNA from a hypothetical source of prebiotic nucleotides, will also consider other ways in which the RNA World could have appeared.

Source: http://66.102.7.104/search?q=cache:...a.com/news/stories/2/2004/07/23/story101.html
Unfortunately for myself, they only presented part of the paper and I am unable to get more than the abstract from other sources. If you do not believe Leslie Orgel wrote it, here http://www.crbmb.com/cgi/content/abstract/39/2/99. I could not get the article there because I have to subscribe and subscription is not free.

Also about Mars, I do not understand how the idea of water = life works.

If one cannot answer some sixteen year old kid who has some doubts on a naturalistic origin of life, then how could one call the arguments of ID ineffective. So if you cannot deal with this, consider how you will deal with others with more tricks up their sleeve (e.g. Mike Gene and Krauze). And one cannot deal with them by simply labeling them as creationists as they are not. Also one cannot use their religion against them as Krauze is an agnostic and Mike Gene's religious preference is an enigma.

 

[Tomk80]

Space? How does one find polycyclic aromatic carbons or formic acid in space support the idea of a naturalistic origin of life. I would be more impressed if nucleotides or polypeptides are found in space. About nucleotides Orgel wrote this

http://www.universetoday.com/am/publish/milkyway_chemistry.html?27122005

From the article: "A planet forming disk located about 375 light-years from Earth has been found to contain some of the building blocks of life: acetylene and hydrogen cyanide. The chemicals were discovered around "IRS 46" using NASA's infrared Spitzer Space Telescope. When mixed with water in a laboratory, these chemicals create a soup of organic compounds, including amino acids and a DNA base called adenine."

Source: http://66.102.7.104/search?q=cache:NXHa1czHKD4J:www.rednova.com/news/stories/2/2004/07/23/story101.html
Unfortunately for myself, they only presented part of the paper and I am unable to get more than the abstract from other sources. If you do not believe Leslie Orgel wrote it, here http://www.crbmb.com/cgi/content/abstract/39/2/99. I could not get the article there because I have to subscribe and subscription is not free.

Also about Mars, I do not understand how the idea of water = life works.

If one cannot answer some sixteen year old kid who has some doubts on a naturalistic origin of life, then how could one call the arguments of ID ineffective. So if you cannot deal with this, consider how you will deal with others with more tricks up their sleeve (e.g. Mike Gene and Krauze). And one cannot deal with them by simply labeling them as creationists as they are not. Also one cannot use their religion against them as Krauze is an agnostic and Mike Gene's religious preference is an enigma.

Nobody said all answers regarding abiogenesis have been answered. Nobody said that current theories of abiogenesis are complete and do not have their problems. All current theories of abiogenesis have problems, and only the future will tell whether these problems will be solved. That does not mean that we can't say that some models may seem more likely currently than others.

But problems with one theory are not support for another. That is why arguments of ID are ineffective, because they have no support on their own. They only point out problems with other theories. But even if we discover that all current lines of research regarding abiogenesis are incorrect, this still forms no argument that ID is correct. It only tells us that we still don't know how life came into existence.

 

[Arik Soong]

http://www.universetoday.com/am/publish/milkyway_chemistry.html?27122005

From the article: "A planet forming disk located about 375 light-years from Earth has been found to contain some of the building blocks of life: acetylene and hydrogen cyanide. The chemicals were discovered around "IRS 46" using NASA's infrared Spitzer Space Telescope. When mixed with water in a laboratory, these chemicals create a soup of organic compounds, including amino acids and a DNA base called adenine."

Whatever, adenine is not a nucleotide. It is not linked to the 1' carbon of ribose to even form a nucleoside. Well, if you read what Orgel wrote, he spoke of the difficulties of fusing adenine to ribose as the proper form of the nucleoside was only produced in 3% yield.

 

[Tomk80]

Whatever, adenine is not a nucleotide. It is not linked to the 1' carbon of ribose to even form a nucleoside. Well, if you read what Orgel wrote, he spoke of the difficulties of fusing adenine to ribose as the proper form of the nucleoside was only produced in 3% yield.

It does show that the substances needed to form life are present in space. A small yield in itself may not be too much of a problem, if their is a mechanism that can concentrate this yield. But I really don't know enough of abiogenesis theories to make a choice between one or the other. I just gave the link to indicate that current research does support a galactic origin of some of the necessary elements.

Could you please respond to the second part of my post, because that was, in my opinion, the really important part.

 

[USincognito]

Also about Mars, I do not understand how the idea of water = life works.

If one cannot answer some sixteen year old kid who has some doubts on a naturalistic origin of life, then how could one call the arguments of ID ineffective.

When the sum total of ID arguments consist of Behe retreads of the flagellum and blood clotting I don't see any problem with my rejecting the premise out of hand until it, to paraphrase Clara Peller (you do know who she is right?) they show me "where's the beef?"

As far as the naturalistic origins of life, I guess I should have elucidated further. It really does not matter to me one whit with regards to whether evolution on Earth has occured via special creation, abiogenesis, Panspermia or as the senior project for a class of hyperdimensional High School students - the evidence that evolution has occured cannot be denied.

I personally, based upon a general acceptance of naturalistic origins skew towards an abiogenetic explanation, but whether that's true or not doesn't effect whether evolution has occured since the biogenetic event - whatever it was. At this point, since semantics is apparently as important a topic around here as paleontology and chemistry, I remain empirically agnostic regarding the advent of life on Earth.

I'll try and look up the Spirt/Opportunity discoveries I cited above and put them into the context of this thread when I'm again on broadband... Look for them within the next 36 hours.

 

[funyun]

Well, since you are advocates of metabolism first, I doubt you would like Bartel's and Ferris' views on the origin of life.

And how does disagreement (not even disgareement, because I am just as open to an alternative possibility) equal "bashing"?

If I notice one thing in the origin of life community...it is that adherents of one scenario usually attack another origin of life scenario.

I have never seen that. From what I have observed, people tend to be open to the opinions of others as well as alternate explanations.

For example, Leslie Orgel attacked Gunter Wachterhauser and Harold Morowitz hypothesis for believing life started as a non enzymatic cyclic metabolic reaction i.e. reductive citric acid cycle. Morowitz and Wachterhauser are well aware of the difficulites of a nucleic acid first scenario. I will also add so is Dr. Orgel, yet his continues to research hoping for a breakthrough that will vindicate the nucleic acid first paradigm.

What, to you constitutes an "attack"? Apparently, from what I've seen, all someone has to do to "attack" someone else is disagree with them.

Another example is A.G. Cairns-Smith. He was a critic of the RNA World too which was evident in his book Genetic Takeover and the Mineral Origins of Life. He listed nineteen difficulites of nucleic acid synthesis but he also advocated his clay mineral hypothesis. Those who are adherents of the RNA world countered by saying his hypothesis had no evidence.

Once again, that sounds unlike an attack and more like an objective analysis by fellow scientists.

 

[Arik Soong]

And how does disagreement (not even disgareement, because I am just as open to an alternative possibility) equal "bashing"?



I have never seen that. From what I have observed, people tend to be open to the opinions of others as well as alternate explanations.



What, to you constitutes an "attack"? Apparently, from what I've seen, all someone has to do to "attack" someone else is disagree with them.



Once again, that sounds unlike an attack and more like an objective analysis by fellow scientists.

Fine, I am sorry I used words like "attack" instead of "critical analysis." Robert Shapiro uses "a critical analysis" in the title of some of his origin of life publications.