The Origin of Life

[Jose]

The abiogenesis story nonetheless follows the same rules as the rest of science. We gather information--data, observations, etc--from the world. We then develop models to explain the observations. The rules are that we can't invent things for which there are no data. ... If we stick with facts--hard evidence from geochemistry and from experimental chemistry--we're kinda stuck with current ideas for the origin of life. We may be dissatisfied that we don't have a complete story yet, but that doesn't justify the response that so many people have: throw out everything we know, in favor of magical stories that emerged in a pre-scientific age.

But abiogenesis does exactly that. It invents a mechanism that explains the creation of life to fit with the theory of cosmogenesis even though there is absolutely no data to support it and ignores the masses of data that debunk it. ... Hard evidence from intensive experimentation suggests that life does not originate in this way at all. There is no evidence that biological/living processes can evolve from non-living self replicating molecules and all the data suggests that they do not. By all means believe it if you must but it isn't science.

The above exchange illustrates the basic issue. The Origin-of-Life researchers have lots of data and lots of ideas, but no absolute proof of a particular mechanism by which life certainly arose from plain old chemistry. The anti-evolution folks insist that the physical origin of life (as opposed to special creation) is hogwash, a flight of fancy for which there are no facts. They use this to claim that evolution is impossible, although "evolution" is what life does after it exists, not before.

Questions for Debate

1. Are there data and ideas? Are they valid? What is the current status of Origin-of-Life research?
2. What, if anything, has been debunked?
3. Is it valid to pretend that a chemical origin of life is impossible until it's been re-constructed in the lab, with a complete description of every step? We don't require this level of certainty for medical research; why require it for this?

__________________
Use a small broom for the corners.

[Jose]

Hello and welcome, FinalEnigma!

Your points are entirely valid. We have no evidence that life was, or was not planted here by space aliens. So, while we cannot say that is how life arose, we also cannot rule it out. It has often been said that this hypothesis is much more scientific than creation by one or more gods, since it is theoretically testable. All we'd have to do is find the aliens and look at their historical records. Gods, on the other hand, tend to hide, as you so astutely observed.

We should also keep your calculation in mind. Indeed, Michael Behe should have made such a calculation before using his probability arguments against evolution in Kitzmiller v Dover. His anti-evolution calculation, when examined in the courtroom, turned out to show that his "virtually impossible" event was not only possible and probable, but actually very likely.

We should be wary of probability calculations, and examine their assumptions and constraints before we accept their implications.
_____________________

I appreciate your honesty Jose. I would not use the word "pretend" myself, because it is too loaded with implicit meanings which imply intentions other than an honest examination of the facts in a search for truth.

That is precisely why I used "pretend." All of those implicit meanings, juxtaposed against the search for truth, raise the eyebrow of irony. By contrast, it is far sneakier to paint a veneer of neutrality over one's writing by using supposedly unloaded words, and then conclulde by summarizing others' careful considerations as "idle speculation." Of course, it might be worth noting that I applied the term "pretend" to the acceptance of a pre-determined conclusion without even looking at the data. Drawing such a conclusion would, indeed, be "imagination, if not blind faith."

Alas, it is true that I did not use phrases such as "which is by no means certain," or "as yet, no data to support." But then, we had not yet come to the opportunity to do so. We have yet to reach the point of discussing data, or the interpretation thereof. Indeed, there are Banded Iron Formations (the BIF's to which your quote refers), and indeed, they appear to signal a shift from anoxic to oxygen-containing atmosphere. As I undertand it, this used to be taken as evidence for photosynthetic oxygen production, but that additional data and additional thought have raised the question about the reduction-capacity of the atmosphere. Perhaps the BIFs signal the decline in reducing power more than they signal the rise in microbial photosynthesis. In any event, the BIFs indicate only the oxygenation of the atmosphere; by themselves, they tell us little of the origin of the oxygen.

[Rob]

Since this historical [Miller-Urey] experiment, the field has veritably exploded. In the last three decades, the origin of life has been the subject of dozens of books, scores of essays, thousands of articles, relating an enormous amount of experimental and theoretical work. Periodicals devoted exclusively to the subject have been founded. Textbooks dedicate whole chapters to it. The reason for this upsurge of interest is simple. As I have attempted to show ..., we have come to know enough about life to draw the basic blueprint according to which all extant living organisms are constructed. Scientists faced with the blueprint (or, rather, with their own version of the blueprint, because they tend to see life through different glasses, depending on their fields of specialization) find the problem of how the plan materialized almost inescapable. This turned out to be my case as well. (110)

But I must add a warning. If not considered totally outlandish any more, the field still remains largely confined to speculation. When it comes to events that happened several billion years ago, hard data are scarce and, perforce, are supplemented by reasoning and imagination, if not blind faith. Yet, life did start somewhere, sometime, somehow. Trying to reconstruct the events that led to its birth holds almost irresistable fascination, especially now that we have available so much new knowledge on the nature of life and so many new tools for digging into the past and approaching the problem. (110)

The tale is told in simple historical style, without any of the probability weighings, plausibility assessments, and other precautionary periphrases that it requires.[2] (112-113)

[2] The readers' attention is called to this point, lest they be misled by the apparently dogmatic style of the script. All statements should be read as conditional and hypothetical. (112)

-- de Duve, Christian (Nobel Laureate) Blueprint for a Cell: The Nature and Origin of Life. Neil Patterson Publishers. 1991.

Alas, it is true that I did not use phrases such as "which is by no means certain," or "as yet, no data to support." But then, we had not yet come to the opportunity to do so. We have yet to reach the point of discussing data, or the interpretation thereof.

Nobel Laureate de Duve seems to think it important (for the sake of integrity) to add his "warning" (frank admissions) at the point such claims are being made. If one is aware of these qualifications, which you imply you are Jose, why then did you not do the same? Your statement below, after all, is hardly representative of the facts in their full context, but more of polemics for the sake of winning an argument, as is clearly indicated in your omission of the simple truth noted by de Duve above and your silly statement "This isn't what you'd expect of an intelligent designer, unless, perhaps, he wasn't so intelligent after all," a statement that says more about you than the honest truth of the facts under discussion.

Geochemical evidence is that there were "things we don't understand" that led to geochemical signatures that plain old chemistry doesn't do, and that current life doesn't do. These look like signatures of early life that was chemically different from what eventually out-competed it. The data, in other words, point to various kinds of chemistry in self-organizing systems, with eventually one kind of chemistry becoming common. This isn't what you'd expect of an intelligent designer, unless, perhaps, he wasn't so intelligent after all.

Your own polemical statement above belies your attempt to sneak in this claim that "geochemical evidence is there [that]... geochemical signatures [exist] that plain old chemistry doesn't do." This is little more than polemics and not an honest search for truth. Well, such an unqualified dogma for polemical purposes isn't what one would expect from an intelligent and informed scientists either, and that is why phrases such as "which is by no means certain" and "as yet, no data support" such a claim are always juxtaposed to such claims on the spot by intelligent world class scientists as Nobel Laureate de Duve, Sapp, and Franklin M. Harold (Emeritus Professor of Biochemistry and Molecular Biology), and Sarkar (Professor of Intergrative Biology, MIT), and others. Just for the record, I have no problem with the existence of such so-called "geochemical signatures," just the fact that less than the full and honest scientific context is being expressed in Jose's claim above. If Jose knows the full context, why not then paint the picture in its full context?

It is far sneakier to paint a veneer of neutrality over one's writing by using supposedly unloaded words, and then conclulde by summarizing others' careful considerations as "idle speculation."

Ironicly, Jose characterizes Nobel Laureate de Duve, Sarkar, Franklin, and Sapp, et. al. as "sneaky," for they all to the man and many more to boot characterize these assertions you have been making as "idle speculation." But then, they are often writing to or speaking in symposiums of fellow scientists and cannot get away with half the story (their fellow scientists would call them on it) in a context in which a high standard of integrity is expected. The only "veneer of neutrality" being presented here Jose is your so-called presentation of the facts. The truth is Jose, and you know it full well, no honest person with any passion and intelligent questioning mind is "neutral" towards the great questions in life, such as "Is organic evolution a fact?" or "Does God exist?" or "Is organic evolution a chance and random accident or part of a larger divine plan?" Some questions belong to the domain of science, some to philosophy, and some to theology and personal religious experience. But long ago the myth of neutrality in the domain of science was shattered by scholars such as Thomas S. Kuhn and his work " The Structure of Scientific Revolutions."

The real question Jose is whether or not the scienific facts are being honestly presented in their full context as the worlds most renowned scientists actually present them? After all, if science really is the pursuit of truth (which I belive it is), at least the truth as best we can ascertain it at any point in our search, than of supreme value is the fullness of the current context, warts, doubts, speculations, hard facts and all; for we owe it (science) more than cheep polemics and half-truths devoid of context for little more than argumentative gains.

Honest scientists with integrity make it a duty, a point, to present the caveats when engaging in discussions about the current state of science, for anything less is misleading and little more than the weaving of modern myths called scientism. And in the end, scientism undermines the very core values of the scientific enterprise itself, in that it replaces the honest search for truth and fact with platitudes and dogma.

In the beginning was the Word; so says the gospel of Saint John. Goethe's Faust, the prototypic modern man and scientist, thought otherwise: in the beginning was the Deed. Rephrased just a little, scholars still divide into those who seek the origin of life in information and those who look to energetics. Those who believe, a I do, that living organisms are autopoietic systems capable of evolution by variation and natural selection, must keep a foot in both camps and risk being scorned by both. But the definition really sharpens the issue: the question is not only how life arose on earth, but how nature generates organized material systems to which terms such as adaptation, function and purpose can be applied. Readers will have noted that this is still a free-wheeling inquiry, in which the few solid facts need not seriously impede the imagination; let me take advantage of what, sadly, become a very rare privilege. (Harold 2001: 249-250)

Granted that, as de Duve says, we are compelled by our calling to insist at all times on strictly naturalistic explanations; life must, therefore, have emerged from chemistry. Granted also that simple organic molecules were present at the beginning, in uncertain locations, diversity and abundance. Leave room for contingency, some rare chemical fluctuation that may have played a seminal role in the inception of living systems; and remember that you may be mistaken. With all that, I still cannot bring myself to believe that rudimentary organisms of any kind came about by the association of prefabricated organic molecules, born of purely chemical processes in their environment. Did life begin as a molecular collage? To my taste, that idea smacks of the reconstitution of life as we know it rather than its genesis ab initio. It overestimates what Harold Morowitz called the munificence of nature, her generosity in providing building blocks for free. It makes cellular organization an afterthought to molecular structure, and offers no foothold to autopoiesis. And it largely omits what I believe to be the ultimate wellspring of life, the thermodynamic drive of energy dissipation, creating mounting levels of structural order for natural selection to winnow. If it is true that life resides in organization rather than in substance, than what is left out of account is the heart of the mystery: the origin of biological order. (Harold 2001: 250)

Scientists formulate hypotheses, not just at the conclusion of an inquiry but from its very outset. Karl Popper and Thomus Kuhn both taught that, absent a preconception of some sort, we do not know what questions to ask or even what facts to observe. The downside is that we will cling to an outworn hypothesis, well aware of its shortcomings, until a more credible alternative comes to hand. This, I suspect, is where the study of biopoiesis now stands: the past unburied, the future not yet born. I will also venture an opinion about where we should look. The hurdle is to understand, not the origin of organic molecules, but of systems that progressively come to display the characteristics of organisms: boundaries, metabolism, energy transduction, growth, heredity and evolution. This is hardly a startling or even original proposition, but its unapologetic holism makes it a minority view. (Harold 2001: 250-251)

I hold, then that cellular organization was not a codicil to the true origin of life, but part and parcel of it. That implies compartmentation of some kind (not necessarily lipid membranes) from the beginning. Biological order is dynamic, created and sustained by a continuous stream of energy, and that also must have been true all along. Therefore, a credible biopoietic theory will be one that generates mounting levels of complexity naturally, by providing the means to convert the flux of energy into organization. But energy dissipation can only carry life over the first jump; evolution is hamstrung until the emerging "functions" within the developing system have been codified in a "text" of some kind that can be transmitted, executed, altered, and put to the test of utility again and again. Nucleic acids or their precursors must have come on stage early, if not when the curtain rose. No satisfying scheme of this kind is presently on the books, and I have none to offer, I have only the strong hunch that there is much more to this mystery than is dreamt of in molecular philosophy. (Harold 2001: 251)

It would be agreeable to conclude this book with a cheery fanfare about science closing in, slowly but surely, on the ultimate mystery; but the time for rosy rhetoric is not yet at hand. The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication. Even the principles of biopoiesis still elude us, for reasons that are as much conceptual as technical. The physical sciences have been exceedingly successful in formulating universal laws on the basis of reproducible experiments, accurate measurements, and theories explicitly designed to be falsifiable. These commendable practices cannot be fully extrapolated to any historical subject, in which general laws constrain what is possible but do not determine the outcome. Here knowledge must be drawn from observation of what actually happened, and seldom can theory be directly confronted with reality. The origin of life is where these two ways of knowing collide. The approach from hard science starts with the supposition that physical laws exercise strong constraints on what was historically possible; therefore, even though one can never exclude the intervention of some unlikely but crucial happenstance, one should be able to arrive at a plausible account of how it could have happened. This, however, is not how matters have turned out. The range of permissible options is to broad, the constraints so loose, that few scenarios can be firmly rejected; and when neither theory nor experiment set effective boundaries, hard science is stymied. The tools of "soft," historical science unfortunately offer no recourse: the trail is too cold, the traces too faint. (Harold 2001: 251-252)

They tell a story of Max Delbrück, one of the pioneers of molecular genetics and the ironic inventor of DNA, whom I was privileged to meet during his later years at the California Institute of Technology. He had stopped reading papers on the origin of life, Max once observed; he would wait for someone to produce a recipe for the fabrication of life. So are we all waiting, not necessarily for a recipe but for new techniques of apprehending the utterly remote past. Without such a breakthrough, we can continue to reason, speculate and argue, but we cannot know. Unless we acquire novel and powerful methods of historical inquiry, science will effectively have reached a limit. (Harold 2001: 252)

[Franklin M. Harold is Emeritus Professor of Biochemistry and Molecular Biology at Colorado State Univeristy.]

-- Harold, Franklin M. The Way of the Cell: Molecules, Organisms and the Order of Life. New York: Oxford University Press; 2001; pp. 249-252.

Many influential contemporary discussions of the origin of life have concentrated on the origin of information, in which information is construed simply to be nucleic acid sequences (e.g., Eigen 1992). Implicit in these discussions is the assumption that nucleic acid sequences ultimately encode all that is necessary for the genesis of living forms and, therefore, that a solution to the problem of the initial generation of these sequences will solve the problem of the origin of life. The move away from sequences [reductionism] would put these efforts in proper perspective: to explain the possible origin of persistent segments of DNA [which we can only speculate about at this time] does not suffice as an explanation of the origin of living cells. However, I do not wish to harp on this point since, quite justifiably, most molecular biologists think that such discussions of the origin of life are little other than idle speculation. (Sahotra 2005: 246)

-- Sarkar, Sahotra (2005) Molecular Models of Life. The MIT Press.

[Sahotra Sarkar is Professor of Integrative Biology and Philosophy at the University of Texas, Austin.]

Millers classic experiments -- as historically important for the field as they are -- are not the solution (or even a valuable starting point) to understanding the origin of life on Earth. An intellectually honest and well-informed science educator (they are usually the former but only more rarely the latter) should therefore point to the amount of [so-called] progress that has been in this field, describe some of the ongoing research, and stop far short of saying that the promblem has been solved.

-- Pigliucci, Massimo (2002) Denying Evolution: Creationism, Scientism, and the Nature of Science. Sinauer Press. p. 242.

Refute the falsehoods of creationism; but to replace them with the equally false claims of scientism would accomplish little, and leave us no more enlightened, in that we will have replaced one myth with another.

[Jose]

Thank you for your words of wisdom, Rob.

I might note that there are a huge number of verbal traditions in science, all aimed at distinguishing findings from interpretation, and interpretation from extrapolation and speculation. One need not use the same phrases over and over; to do so creates tiresome prose. To one not used to the use of language in a specific field, or to one who chooses to paint anothers' interpretation as a claim of fact, these verbal traditions may not be evident. Making it even more difficult to parse the language, is the fact that different fields have evolved different verbal traditions.

Consider, for example, the statement with which you have taken issue:

Geochemical evidence is that there were "things we don't understand" that led to geochemical signatures that plain old chemistry doesn't do, and that current life doesn't do. These look like signatures of early life that was chemically different from what eventually out-competed it. The data, in other words, point to various kinds of chemistry in self-organizing systems, with eventually one kind of chemistry becoming common. This isn't what you'd expect of an intelligent designer, unless, perhaps, he wasn't so intelligent after all.

I note the following phrases:

• things we don't understand--this looks pretty honest to me, and doesn't sound like the polemical scientism you claim it is.
• geochemical signatures that plain old chemistry doesn't do--I've summarized in too-short a space a seminar by a geologist; if you'd like to take issue with his analysis, perhaps we can try to dig it up
• these look like signatures of early life--this does not say these are early life, or that they are the chemistry of early life; it merely says they look like them
• life that was chemically different--if the chemical analysis indicates something that current life wouldn't do, then it seems reasonable to suggest that it's different; again, however, this is merely what the data "look like."
• the data point to--obviously, data can point to one thing, but actually be the result of something else; this does not say "the data prove" something
• what you'd expect--perhaps I should have said "what I'd expect," if in fact it actually is what you would expect. Personally, I'd expect an intelligent designer to design the thing he's designing intelligently, and get it right the first time. The geologist whose work I recalled here suggested that there were a number of different types of chemistry going on, as different types of early proto-life. Such a scenario indicates a life-generating system that doesn't know what it's doing, and that doesn't get it right the first time. I suppose an intelligent designer could start out with no knowledge but with infinite capacity to learn, and we are seeing the footprints of his learning curve; at a minimum, however, stumbling around and making alternate, not-very-good proto-life systems indicates that the intelligent designer is not as omniscient as some of the theological models suggest.

Needless to say, discussion of the data and interpretation of the data requires appropriate qualifiers. If de Duve wants to say "which is by no means certain," he may. Usually, people make such statements when referring to the work of others; de Duve may have the confidence to cast doubt on his own interpretations this way, but not many scientists raise such flags in their papers. Rather, they tend to offer their interpretations of their data, and qualify them to be "indications" or "suggestions" or "inferences." These serve the same purpose of indicating that the author knows that the conclusions are not Absolute Truth, but have the tentative nature of all scientfic conclusions.

The real question Jose is whether or not the scienific facts are being honestly presented in their full context as the worlds most renowned scientists actually present them? After all, if science really is the pursuit of truth (which I belive it is), at least the truth as best we can ascertain it at any point in our search, than of supreme value is the fullness of the current context, warts, doubts, speculations, hard facts and all; for we owe it (science) more than cheep polemics and half-truths devoid of context for little more than argumentative gains.

A most excellent point. We should, indeed, present the scientific facts in their full context, and skip the polemics. In this vein, I would urge us all to present the data for us to examine, so we can develop our own interpretations. It is pointless to argue over the interpretations of others, or about the personal bias of those who have drawn one interpretation or another. Intepretations are not facts. Let us, indeed, stick to the scientific facts--the data.

[Rob]

Geochemical evidence is that there were "things we don't understand" that led to geochemical signatures that plain old chemistry doesn't do, and that current life doesn't do. These look like signatures of early life that was chemically different from what eventually out-competed it. The data, in other words, point to various kinds of chemistry in self-organizing systems, with eventually one kind of chemistry becoming common. This isn't what you'd expect of an intelligent designer, unless, perhaps, he wasn't so intelligent after all.

A number of data are presented that raise serious doubts on the cynobacterial origin of the traces and, even, on their biological origin. (fn. 3, p. 314)

-- de Duve, Christian. Life Evolving: Molecules, Mind, and Meaning. Oxford: Oxford University Press; 2002: 314.

[Winner of the Nobel Prize in Physiology or Medicine]

There are, as yet, no data to support that BIF precipitation was linked directly to microbial activity

-- Klein, Cornelis. Some Precambrian banded iron-formations (BIFs) from around the world: their age, geologic setting, mineralogy, metamorphism, geochemistry, and origin. American Mineralogist. 2005 Oct; 90(10):1473(27).

If the oxygen in those ancient BIFs is of biological origin, which is by no means certain, then oxygenic photosynthesis must have been in place at that time.

-- Sapp, Jan, Editor. Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Norton; 2005: 66-67.

But I must add a warning. If not considered totally outlandish any more, the field still remains largely confined to speculation. When it comes to events that happened several billion years ago, hard data are scarce and, perforce, are supplemented by reasoning and imagination, if not blind faith. Yet, life did start somewhere, sometime, somehow. Trying to reconstruct the events that led to its birth holds almost irresistable fascination, especially now that we have available so much new knowledge on the nature of life and so many new tools for digging into the past and approaching the problem. (110)

The tale is told in simple historical style, without any of the probability weighings, plausibility assessments, and other precautionary periphrases that it requires.[2] (112-113)

[2] The readers' attention is called to this point, lest they be misled by the apparently dogmatic style of the script. All statements should be read as conditional and hypothetical. (112)

-- de Duve, Christian (Nobel Laureate) Blueprint for a Cell: The Nature and Origin of Life. Neil Patterson Publishers. 1991.

Many influential contemporary discussions of the origin of life have concentrated on the origin of information, in which information is construed simply to be nucleic acid sequences (e.g., Eigen 1992). Implicit in these discussions is the assumption that nucleic acid sequences ultimately encode all that is necessary for the genesis of living forms and, therefore, that a solution to the problem of the initial generation of these sequences will solve the problem of the origin of life. The move away from sequences [reductionism] would put these efforts in proper perspective: to explain the possible origin of persistent segments of DNA [which we can only speculate about at this time] does not suffice as an explanation of the origin of living cells. However, I do not wish to harp on this point since, quite justifiably, most molecular biologists think that such discussions of the origin of life are little other than idle speculation. (Sahotra 2005: 246)

-- Sarkar, Sahotra (2005) Molecular Models of Life. The MIT Press.

[Sahotra Sarkar is Professor of Integrative Biology and Philosophy at the University of Texas, Austin.]

Alas, it is true that I did not use phrases such as "which is by no means certain," or "as yet, no data to support." But then, we had not yet come to the opportunity to do so.

I might note that there are a huge number of verbal traditions in science, all aimed at distinguishing findings from interpretation, and interpretation from extrapolation and speculation. One need not use the same phrases over and over; to do so creates tiresome prose. To one not used to the use of language in a specific field, or to one who chooses to paint anothers' interpretation as a claim of fact, these verbal traditions may not be evident. Making it even more difficult to parse the language, is the fact that different fields have evolved different verbal traditions.

We have here now two reasons for not using "phrases such as 'which is by no means certain,' or 'as yet, no data to support'" such a claim as is made as a matter of fact above. On the one hand, because "we had not yet come to the opportunity to do so," and on the other hand, the more emotive (and therefore, revealing) excuse that "One need not use the same phrases over and over, to do so creates tiresome prose." Imagine that, statements of scientific truth in context being characterized as "tiresome prose," and from an educator to boot

It all reminds me of the following:

[L]ike the Bellman's "Rule of Three" in "The Hunting of the Snark":

"Just the place for a Snark! I have said it twice;
That alone should encourage the crew [students].
Just the place for a Snark! I have said it thrice:
What I tell you three times is true."

Martin Gardner, commenting on the "Rule of Three", points out that the cyberneticist Norbert Weiner who had written that a computer's effectiveness may be checked by asking it the same question serveral times, or asking the question of serveral other computers, had speculated that the human brain might have a simlar checking mechanism, and noted the similarity with Bellman's rule of three. J.B.S. Haldane also confessed to Bellmanship:

"I give annual ... lecture courses. I introduce an idea with such words as 'A possible explanation of these facts is ...' Next year this becomes 'the most probable explanation ...', and after I have said it three times it becomes 'the explanation'. What is worse, when I write a text book I use this last phrase. I fear that a good many scientific theories originate in this way."

-- Reid, Robert G.B. (1985) Evolutionary Synthesis: The Unfinished Synthesis. p. 163.

Perhaps the "Rule of Three" is invoked when speaking the full truth in context seems a bit tedious and therefore can be dispensed with as "tiresome prose." Perhaps the "Rule of Three" is one of those "verbal traditions of science" (more accurately, human tendencies) which we should remain aware of less we confuse fact with fiction (half-truth) and end up unable to distinguish between the factual findings in context and truncated and distorted interpretations of only half the story because the other half is deemed tedious "tiresome prose."

But this is not the first time Jose has attempted to pass off speculative Snarks thrice times said, as scientific fact, for he was long ago on this site made aware of the statements made by de Duve et. al.

And now, added to the statements of those eminent scientists cited above, we can add Jose's rephrased satire (perhaps he ought to take some "prose" lessons from his fellow scientists above, for they managed to say essentially the same in far fewer words and with far greater prose!), which is in my view, closer to the truth than perhaps either of us likes to admit:

Geochemical evidence for which the interpretation is by no means certain is that things occurred in the past, the nature of which is by no means certain. These events led, by a mechanism that is by no means certain, to geochemical signatures that it is by no means certain that plain old chemistry is capable of doing, and that it is by no means certain that current life is capable of. Although it is by no means certain what these signatures represent, They look like signatures of early life, the nature of which is by no means certain. The data, in other words, are unambiguous proof that there was ancient chemistry the nature of which is by no means certain. Although it is by no means certain what these chemical systems were, and it is by no means certain why such systems have not been seen in current investigations, the fact remains that the chemistry of living things is common among living things. Although it is by no means certain what to expect of an intelligent designer, and although it is by no means certain that intelligent designers might even exist, given that there are no data that speak to the by no means certain nature of the by no means certain designer, the path by which chemistry became self-organized enough to call life, which is by no means certain, was by no means certain enough to warrant any but the most idle speculation that the by no means certain designer had a certain design at the outset, which is by no means certain. Most scientists would consider discussions of such supernatural beings to be nothing but the most idle speculation.

[Jose]

I'm afraid you've lost me once again, Rob.

You seem to want me to say that a particular conclusion is by no means certain, yet to make this statement, it is necessary to evaluate the data upon which the statement is based. It's hard to evaluate the data when no data have been mentioned. If you'd like to discuss the strength of conclusions, then give us the data so we can evaluate it. The OP indicates that the topic of this thread is the data and the interpretations thereof, not the summations of others.

You seem uncomfortable with the idea of using equivalent phrasing for undertainty, and you consider it unscientific to think about the prose becoming tiresome. OK...I'll rephrase the offending statement:

Geochemical evidence for which the interpretation is by no means certain is that things occurred in the past, the nature of which is by no means certain. These events led, by a mechanism that is by no means certain, to geochemical signatures that it is by no means certain that plain old chemistry is capable of doing, and that it is by no means certain that current life is capable of. Although it is by no means certain what these signatures represent, They look like signatures of early life, the nature of which is by no means certain. The data, in other words, are unambiguous proof that there was ancient chemistry the nature of which is by no means certain. Although it is by no means certain what these chemical systems were, and it is by no means certain why such systems have not been seen in current investigations, the fact remains that the chemistry of living things is common among living things. Although it is by no means certain what to expect of an intelligent designer, and although it is by no means certain that intelligent designers might even exist, given that there are no data that speak to the by no means certain nature of the by no means certain designer, the path by which chemistry became self-organized enough to call life, which is by no means certain, was by no means certain enough to warrant any but the most idle speculation that the by no means certain designer had a certain design at the outset, which is by no means certain. Most scientists would consider discussions of such supernatural beings to be nothing but the most idle speculation.

[achilles12604]

QED-

You are so embroiled with the mincing of words with Sleepy that you have not yet examined the numbers I have put forth.

For example the rate of mutation between generations being .002.

*sigh* OK...0.002 what in what time frame? For mammals, it's 0.2 base changes per million bases per year. That comes out to about 264 mutations per person per generation.


Having said all this, I'd like to suggest that we look back at the OP. The idea is to look at what is known, and what has actually been suggested. What we think based on our own views of common sense is irrelevant. I may think that 150 million years is "long enough," and achilles may think that it's "too short," but without any data our gut-level feelings about it don't count.

Sorry. As I said in my prior mentioning of this number it is .002 mutations per generation. Sorry I didn't give all the information the second time.

I get your point on Mutations. However, when I read things like this, . . .

http://www.ornl.gov/sci/techresources/H ... prim1.html

Each time a cell divides into two daughter cells, its full genome is duplicated; for humans and other complex organisms, this duplication occurs in the nucleus. During cell division the DNA molecule unwinds and the weak bonds between the base pairs break, allowing the strands to separate. Each strand directs the synthesis of a complementary new strand, with free nucleotides matching up with their complementary bases on each of the separated strands. Strict base- pairing rules are adhered to adenine will pair only with thymine (an A- T pair) and cytosine with guanine (a C- G pair). Each daughter cell receives one old and one new DNA strand (Figs. 1 and 4: DNA Replication). The cells adherence to these base- pairing rules ensures that the new strand is an exact copy of the old one. This minimizes the incidence of errors (mutations) that may greatly affect the resulting organism or its offspring.

I understand that Mutations happen. I am not saying they don't. But it seems to me, that genetics seems to avoid mutations. It is almost as though our body's attempt to keep all the DNA exactly the same.

With this resistance to change, doesn't this logically imply that the numbers of mutations would have been small?

[Grumpy]

achilles12604

I understand that Mutations happen. I am not saying they don't. But it seems to me, that genetics seems to avoid mutations. It is almost as though our body's attempt to keep all the DNA exactly the same.

With this resistance to change, doesn't this logically imply that the numbers of mutations would have been small?

The cell has EVOLVED resistence to mutation, it would not have had that level of capacity in earlier times. Even with that resistence each person will experience hundreds of mutations in their lifetimes. Most are benign, some are harmful(cancers, etc), some are advantageous. If a population of 5 billion people has several hundred mutations per person, that works out to roughly a trillion mutations of genes per generation over the whole Earth(among humans only, we don't want to get to the huge numbers involved with the simplest bacteria). If those mutations occured in the sexual gametes(as a portion do) they can be passed to the next generation, causing disease, defects and, occasionaly, an improvement. If that improvement means better survival chances for the person and their offspring(smarter, faster stronger, etc) they may produce more offspring over the generations and may replace their competitors.

For the first chemical/biological systems, without the self repair mechanisms of modern cells and given the likelyhood of higher energy flux the mutation rates would have been astronomical, leading to many different genesets to be tested by natural selection. I think it likely that early chemical/biological systems were as diverse as we see today in nature, all of them in cutthroat competition with each other. Finally R/DNA based systems came along and were so superior they outcompeted all others. All life we know today is R/DNA based, but there is every reason to think that was not always the case.

Grumpy

As in all science, the views expressed by this poster are not carved in stone and are subject to revision, given new evidence

[achilles12604]

achilles12604

I understand that Mutations happen. I am not saying they don't. But it seems to me, that genetics seems to avoid mutations. It is almost as though our body's attempt to keep all the DNA exactly the same.

With this resistance to change, doesn't this logically imply that the numbers of mutations would have been small?

The cell has EVOLVED resistence to mutation, it would not have had that level of capacity in earlier times. Even with that resistence each person will experience hundreds of mutations in their lifetimes. Most are benign, some are harmful(cancers, etc), some are advantageous. If a population of 5 billion people has several hundred mutations per person, that works out to roughly a trillion mutations of genes per generation over the whole Earth(among humans only, we don't want to get to the huge numbers involved with the simplest bacteria). If those mutations occured in the sexual gametes(as a portion do) they can be passed to the next generation, causing disease, defects and, occasionaly, an improvement. If that improvement means better survival chances for the person and their offspring(smarter, faster stronger, etc) they may produce more offspring over the generations and may replace their competitors.

For the first chemical/biological systems, without the self repair mechanisms of modern cells and given the likelyhood of higher energy flux the mutation rates would have been astronomical, leading to many different genesets to be tested by natural selection. I think it likely that early chemical/biological systems were as diverse as we see today in nature, all of them in cutthroat competition with each other. Finally R/DNA based systems came along and were so superior they outcompeted all others. All life we know today is R/DNA based, but there is every reason to think that was not always the case.

Grumpy

As in all science, the views expressed by this poster are not carved in stone and are subject to revision, given new evidence

The cell has EVOLVED resistence to mutation, it would not have had that level of capacity in earlier times.

This would mean that resistence to mutation was part of the DNA strands. But if mutations occur within that strand then the resistence to mutation would change? Also, the first DNA/RNA should have mutated every single time it reproduced if mutations are only limited by a mutation in the DNA which causes them to be limited.

This is a bit of a streach. How about a much simpler explaination that mutations occur very very slowly and not very often simply because DNA replication attempts to reproduce itself exactly and every once in a while it is wrong in a place or two? This would fit more with the scientific view wouldn't it?

If a population of 5 billion people has several hundred mutations per person, that works out to roughly a trillion mutations of genes per generation over the whole Earth(among humans only, we don't want to get to the huge numbers involved with the simplest bacteria).

True. But the rate of mutation has been figured out to .002 per generation.


Here are a few numbers and facts I found about mutation . . .

http://www-personal.k-state.edu/~bethmont/mutdes.html

mutation-- a change in the genetic material (ie. DNA)

Let's further define mutation as a heritable change in the genetic material. This point becomes important in multicellular organisms where we must distinguish between changes in gametes (germline mutations) and changes in body cells (somatic mutations). The former are passed on to one's offspring; the latter are not but we will see they can be very important in causing cancer.

In detection of germline mutations in humans and measurement of human mutation rates we have the problem of diploidy. Most forward mutations (normal gene to mutant form) are recessive and so won't be detected unless a zygote gets two copies of the mutant allele. [Reversion or reverse mutation (mutant back to normal) is generally much less frequent because there are a lot more ways to "break" a gene than there are to reverse an existing mutation.]

One study detected seven infants born with sporadic achondroplasia in one year among 242,257 total births recorded. So the rate (actually a frequency but we won't be concerned about the difference for the purposes of thinking about rates in this course) is 7/242,257 x 1/2 (2 alleles per zygote) = 1.4 x 10e-5.

This rate is roughly in the middle of the range reported for various human genes: those with high mutation rates like NF1 (neurofibromatosis type 1) and DMD (Duchenne muscular dystrophy) (ca. 1 x 10e-4) and those with low rates of new mutation like the Huntington's Disease gene (1 x 10e-6). This hundred-fold range shows that mutation rates per gene can be intrinsically different.

While this is on humans, these numbers are REALLY small. .0001 or .000001. This is much smaller than I read before.

Probably because Bacteria reproduce much faster than humans. Hence I got .002 per generation.

Notice this is a LOOOOOONG way from a

trillion mutations of genes per generation over the whole Earth

As in all science, the views expressed by this poster are not carved in stone and are subject to revision, given new evidence

May everyone be as openminded.

[Grumpy]

achilles12604

While this is on humans, these numbers are REALLY small. .0001 or .000001. This is much smaller than I read before.

Probably because Bacteria reproduce much faster than humans. Hence I got .002 per generation.

Notice this is a LOOOOOONG way from a Quote:

trillion mutations of genes per generation over the whole Earth

This .002 number is per base pair per generation. Humans have

a rate of 1 x 10e-6 mutations/gene x 5 x 10e4 genes/haploid genome = 5 x 10e-2 mutations per gamete (=5/100 or 1/20). 1/20 x 2 gametes per zygote = 1/10 chance that each zygote carries a new mutation somewhere in the genome.

1 in ten chance for each zygote(read fertilized egg) to carry a mutation. And if that child grows up to be an airline pilot, the chances of his/her child carrying a mutation in their gamete(sex cell) roughly doubles(1 in 5) due to gamma ray radiation. Astronauts are even higher(they are actually discouraged from reproduction, except through stored sperm/eggs, it's just one of the hazards). Even Astronomers are discouraged from spending too much time on top of high mountains.

This is in humans, within their sexual gametes(egg/sperm). Bacteria ARE their own sexual cells, their mutation rate is very much higher.

By the way, I got my numbers from the source you quoted, taking a few minutes to actually try to understand the numbers I am quoting.

trillion mutations of genes per generation over the whole Earth

That is taking into account the FACT that each human recieves enough radiation/ chemicals/ faulty replication to accumulate several hundred(I have read 200-300) mutations in their WHOLE BODY, not just their gametes, in their lifetimes. Skin cancer is probably the worst example(in terms of outcome). 200 times 5 billion(number of people on Earth) is = 1 trillion mutations per lifetime over the whole Earth. I should not have used generation, it was a slip.

So the rate of mutation in humans is quite high, imagine what it would be in primative cells without a self correcting system and subjected to even higher energy(IE gamma radiation, radioactivity, etc)fluxes. The rate of mutation(and thus diversity) would be astronomical, as I said.

Disclaimer: What is written here may be poo, if information is found to discredit all of scientific knowledge.

Grumpy

[Goat]

I understand that Mutations happen. I am not saying they don't. But it seems to me, that genetics seems to avoid mutations. It is almost as though our body's attempt to keep all the DNA exactly the same.

With this resistance to change, doesn't this logically imply that the numbers of mutations would have been small?

Well, there is a filter that goes on. That filter is known as 'survivial'. If a mutation shows up that would cause fantality in formation, that mutation is not passed on.

Were you aware that 70% of all human pregnancies end up in miscarrage, mostly before the first month? What percentage of themdo you think could be caused by a mutation of a critical function?