Before Darwin

Even as political rhetoric and court battles reflect a public struggle over Darwin's theory of evolution as an explanation for the origin of humans, a different struggle is unfolding within science about the adequacy of evolution as a theoretical foundation for biology. On the surface, the two debates seem to have little to do with one another, but in a subtle way both reflect the need for a richer theoretical biology. The perception of evolution among the wider public might even be improved by better communication of scientific concerns about the limitations of evolutionary theory, and how those concerns are being addressed.

A sympathetic reading of public distrust over evolution would be that a simple theory of change seems too bare to account for the richness of structure we see in the world around us, and for how that structure first came to form. This certainly indicates a failure to appreciate the complex origins of order, and most popular science writing on evolution has been devoted to explaining the surprising and delightful origins of eyes, wings, or peacock's tails. But besides this, an intuitive discomfort that a theory of change cannot adequately account for genuine novelty has a scientific counterpart. The original emergence of life from a lifeless geosphere is one of the most striking such cases.

While they share a certain level of unease, the public and scientific debates diverge sharply on how to overcome the limitations of evolutionary theory. Public rejections of Darwinian ideas are bound up with a wish to introduce something more complicated than undirected variation and brute selection: a creator or designer responsible for novelty and innovation. In science, we recognize that while evolutionary theory is limited, some of the limits concern its connection to simpler - not more complicated - scientific principles than those introduced by Darwin. The remarkable story that is emerging about the origin of life is that these simpler principles may account for aspects of the biosphere that are older even than the evolutionary era itself, and which tie life at its core to the geochemistry of the earth.

To understand the role and also the limitations of evolutionary thinking in biology, it is helpful to recall a little history. Biology as a unified science did not even exist until well into the 20th century. Before that time, only application domains were recognized: systematics, botany, morphology, ecology, paleontology, physiology, medicine, and so forth. Each of these fields had its own domain-specific knowledge and even some elements of theory. However, the possibility of an overarching theory for all of life was not central to any of them. When this situation changed, the change was not a result of new ideas, but rather of ideas that had already been current for nearly a century, and had gone unrecognized as a foundation for theoretical unity.

The two ideas that we now think of together as the "theory of evolution" were Gregor Mendel's conception of the gene, and Charles Darwin's model of natural selection. Mendel had argued ¹ in 1865 that traits do not mix like paint when they are handed down from parents to offspring, but rather are shuffled like cards. The concept of the unmixable source of a trait (say, whether peas would be smooth or wrinkled) was given the name gene, and Mendel's important observation was that the particular forms of genes usually did not change as they were passed from parents to offspring. This kind of faithful inheritance of traits, and shuffling instead of mixing of genes, allows populations to preserve diversity, instead of washing all traits out to some average form.

Darwin contemporaneously (1859) ² had argued that the infrequent variations that do occur as traits are passed from parent to offspring need not be directed in order to enable adaptation. The greater reproductive success of individuals with better-adapted traits would be sufficient to establish the favorable forms. Darwin called this process natural selection as a reference to the selection exercised deliberately by human breeders, and he recognized that variation is necessary to give either breeders or nature the raw material from which to create changes in form.

Mendel's heredity and Darwin's selection were not theoretically central to the many particular life sciences, and were not even linked to each other until they were brought together by several researchers in the 1930s and 1940s, into what Julian Huxley called the Modern Synthesis of evolutionary biology. ³ The key observation of the Modern Synthesis (as it is now known) was that Mendelian heredity preserves the diversity of forms available in a population, while Darwinian selection changes their frequency of occurrence. Together the ideas link variation on the short-term to change in average properties on the long term. This synthesis did not replace the domain-specific theory in many life sciences, and in many cases it did not significantly change how it was used. The Modern Synthesis proposed a way in which random variations, with no foresight, could systematically lead to population changes in a manner that made sense in each of these fields.

This theory of evolution is really a framework for thinking about change in the living world. It provides no specific guesses for the kinds of traits that may exist, no strong requirements or prohibitions on how they may interact to make a complex organism or ecosystem, and no commitments to how innovation can occur. Even the problem of how a differentiated population ultimately divides into two distinct species (posed in the title of Darwin's seminal work) ² remains a major technical problem in evolutionary biology.

There is no reason to view Mendel's and Darwin's ideas as self-contained or complete for biology, in the sense that all needed principles of organization can be generated from these two ideas alone. What they provide is a new class of dynamics that is different from what had previously been considered in physics, chemistry, or engineering. While these ideas seem particularly suited to answering questions about life, they have also found their way into thinking about such diverse fields as economics and Internet security, so they are certainly not uniquely biological.

Darwin's ideas were controversial as soon as they were introduced, because he and his contemporaries appreciated (and he intended) that they separated the concept of "good design" (called adaptation in evolution) from a need for a designer. In the enthusiasm for this one point, many other equally important points about the principles of evolution have been glossed over, and their omission is starting to be felt in practical problems in biology. Both Darwin and Mendel, working more than 150 years ago, took as self-evident what constituted an individual organism, and with a little more care, which similar organisms constituted a species. They recognized that individuals reproduced similar types of individuals, apart from minor changes, and that birth and death of individuals marked the change of generations.

Today, as we consider more life forms and their interactions, and especially as we consider the origin of life from a lifeless geosphere, the situation is more complicated. When multiple strains of virus "mate" by coinfecting a host, many different notions of individual become blurred even within a single infected cell: the two viral strains that might insert genes into the host genome; the viral and host genomes that are both struggling to control the same cell's metabolism; and the host cell's participation in a larger organism. We have learned that quite distinct strains of bacteria and archaea routinely exchange genes, and they probably did so much more promiscuously in the earliest stages of cellular life than they do today. Thus, the genetic and metabolic notions of individuality become even more loosely bound, and the concept of species becomes extremely problematic. These examples, and many others as well, illustrate that the concepts that Mendel and Darwin took as the starting points for their science may not apply to all biological situations. Indeed, even when they do apply, they must be explained within the context of a larger science.

We can identify four assumptions that must be made for evolutionary ideas to be even expressible, and we can then ask what science must be done to justify these assumptions, in particular for the first emergence of life.

Traditionally in physics and chemistry, preparing an experiment in the same way twice was expected to lead to the same outcome, as a criterion for asking well-posed questions. A feature that makes biology a fundamentally new science is that "replaying the tape" of life would, in many important respects, not lead to the animals and plants we see in the world today. ⁴ If the nature of life did not permit such variation, it would not have been possible for Mendel's peas to take either smooth or wrinkled forms, while remaining parts of viable pea plants. The fact that smooth or wrinkled variants could be passed down through heredity, without quickly reverting to a single form, meant that the form of each new generation was contingent on the form of its parents; that is, random variations in the past potentially could be preserved in populations for long stretches of time. Evolution can occur only when variations can arise and be preserved in this way.

Of course, heredity requires not only the possibility for variants to persist; it also requires a way that the features of the parent can be remembered and passed down, and this is the role of DNA and RNA, the carriers of Mendel's genetic information. The memory of life works so spectacularly well that it is often forgotten in biology just how difficult it is to produce a material that can remember anything, let alone remember it for billions of years as life has remembered many details of cellular structure and function. Yet the material of cells is not different from the material of the nonliving world except in its arrangement, and it is well understood in physics that arrangements constantly decay due to thermal jittering and other shocks. Some of the most sophisticated ideas in the field of condensed-matter physics concern the making of materials such as magnets, whose order is self-reinforcing over long times, allowing them to form memory devices.

Memory alone is not enough for evolution to occur. Unless different genomes could reliably create different kinds of organisms and ways of life, the remembered variations could not be submitted to natural selection for comparison and judgment. But any controller, including a genome, must first have autonomy from the thing controlled (the definition of control is that instructions mostly flow in one direction), leaving the controller somewhat detached from feedback about the consequences of its actions. When the components of the controller themselves fluctuate, wear out, or fail, it becomes capable of unfettered mistakes, and all human-designed control systems ultimately rely on intervention from the human world to repair and re-align them. Yet within life, control mechanisms have not only spontaneously emerged; they are self-sustaining within the enclosed system of the biosphere.

The reason it is possible for Mendelian heredity to preserve variation, and for Darwinian selection to act on it, is that traits do not mix continuously like colors of paint. At the same time, traits are not inherited independently. The many variable features of an organism are reproduced as a package if the organism successfully reproduces, and they are lost as a package when it dies. The granular nature of both traits and the individuals in which they are aggregated make selection a very complex mathematical process. Moreover, as we saw above, many different ways of collecting traits together in individuals exist, each with different dynamics. Yet at the same time, new forms of individuality are rare, suggesting that there are stark limits to how traits may be bound together in an organism while preserving in it the ability to evolve. ⁵

In physics and chemistry, none of these four features is a common occurrence, and yet evolution presupposes all of them. If life began in a physical world where none of them was present, we must first understand how and why they came into existence, before we can apply evolutionary ideas to study their subsequent change and refinement. Some modern studies of the origin of life ⁶ are addressing these older problems of emergence and looking for mechanisms that were predominant before Mendelian/Darwinian evolution was possible. The possibility that these mechanisms were simpler than evolutionary mechanisms also suggests that they are more robust, and that the order they initiated may still be observable in the organization of the biosphere today.

How does such a change in theoretical perspective lead us to reexamine the order in the biosphere? For one thing, if we do not assume the primacy of individuals, we notice that the strongest regularities of modern life cannot be seen in individual traits, but only at an ecological level of organization. ⁶ Here we find a common set of reactions for the synthesis of biological molecules that is universal throughout the biosphere and across the whole history of life. The stability and invariance of metabolic pathways gives them the appearance of features of the geosphere rather than of anything that depends on memory or control by individuals.

One of the most primitive functions life must perform lies at the very core of metabolism: It is the capture of carbon from environmental carbon dioxide (CO ₂), which was abundant in the prebiotic era, and its synthesis into the backbones from which the rest of biomolecules are made. An amazing, small cycle of only 11 simple molecules, known as the reductive citric acid cycle, is capable of performing this feat. Some version of the reactions in this cycle is the foundation for biosynthesis in every kind of ecosystem on earth.

The cycle's basic function is to access otherwise inert CO ₂, combine the carbon with electrons, and make molecules capable of repeating this reaction. The reaction sequence has the remarkable property that any molecule in the cycle, by accreting CO ₂ to become longer and then splitting into two, reproduces a second copy of the same molecule while returning the first copy. Thus, like compound interest, it grows and draws diffuse carbon into a very specific pathway. The mathematics of energy and carbon that flow through this cycle resembles the mathematics that drive a hurricane to become the major transporter of moisture and energy over the oceans where it forms (see Figure below).

Carbon fixation is one of the most conserved reactions throughout the biosphere. It suggests that a bridge between geochemistry and life may be found in the mechanisms of metabolism and the principles of ecology, not in compartments or memory molecules, which could have come later. A metabolic organization capable of serving as such a bridge, however, could not have come from just any old network of organic chemical reactions. It would need to have been: 1) sparse within the network of possible reactions so that a few molecules were created in large supply, rather than a huge diversity of one-off molecules arising happenstance (which could not be assembled into anything); 2) particular, in that the pathways observed should be necessary and predictable, rather than accidents (which would depend on later memory mechanisms to be preserved), and 3) robust under jittering of the components, to permit later molecular memory systems to emerge using them as foundations. These principles can be used to find other primal reactions.

If the biosphere emerged through the self-organization of a metabolic system, like the citric acid cycle, the later formation of individuals would be understandable as solving a different problem of packaging. Distinct species can make up an ecosystem by partitioning metabolic tasks to become complementary specialists, but only if they solve the complex problems of obtaining the resources they do not make and settling into a balanced flow of resources among all the members of the ecosystem.

This view of the origins of life changes our understanding of the biosphere today in two ways. First, ecological principles become the foundations for the rest of biology, rather than merely secondary consequences of relations among individuals. Second, we should be warned that when we act as engineers in the living world, imagining that we can manipulate properties of individuals but remain ignorant of principles of ecology, we should expect the biosphere's response to be complex and not necessarily in accordance with our designs. The rapidly rising cost of industrial agriculture, and its fragility to shocks in energy supply, to pests, and to weather, is directly tied to the loss of natural ecological sources of stability in industrially managed agricultural systems.

When we consider what would be required for metabolism to have self-organized without supervision, we realize there is a rich, hierarchical, modular structure of the extant metabolism of the biosphere that looks far from accidental. The functions that particular chemicals fulfill, in the context of both the network and the constraints of the geochemical environment, suggest that the presence of these chemicals as a foundation for life may be required from first principles.

Many of the biological amino acids have simple and perhaps inevitable synthetic pathways starting from citric acid cycle backbones. Phosphorus, the element responsible for the assembly of large biomolecules by polymerization of small ones, naturally leads through a range of intermediate-sized compounds (technically termed cofactors, but we know many of them as the vitamins), which are central to molecular assembly and catalysis throughout metabolism. Even the genetic code, a master instruction set for the translation of RNA memory into protein control, has regularities that may be of precellular chemical origin. ⁷

Perhaps the most important feature of a chemical logic for metabolism on the early earth is that such a logic would not have become irrelevant when memory and control arose. More likely, it determined easy paths for biosynthesis, and gave fitness advantages to organisms that used them, over organisms that attempted to deviate too strongly. Thus we should not be surprised that modern life continues to respect an organization that first came about in the geosphere⁶.

The observations turned up in this way of asking about origins are ordinary enough, but they suggest a conceptual framework for biology that extends well beyond the classical theory of evolution, not only for the origin of life, but for its organization at all times. By drawing inputs from the many theoretical sciences that bear on the transition from lifeless to living matter, and in the process embedding biology more thoroughly in the framework of the other natural sciences, we learn that the required other origins of order may be simpler than the Darwinian paradigm, not more complex.

If public discontent with classical evolution as an inclusive theory stems partly from an intuitive appreciation of its limits, perhaps we as scientists can accomplish more by discussing how these limits are considered scientifically than by downplaying them.

Eric Smith is a professor at the Santa Fe Institute.

One could not agree more with Eric that biology is way too young of a science for an overabouondance of rigorous theory. It was only 231 years ago when the term "biology" was coined.

"Thus, the mathematical rigor that has characterized physics for over two millennia since Aristotle (ca. 400 B.C.) could not be hastily enforced on unripe subjects ? who were, moreover, for a long time somewhat unready and occasionally unwilling" - I wrote in the paper "The Principle of Recursive Genome Function" that just went Online by Springer. (A free full archived copy can be easily Googled on the junkdna domain).

It may be noteworthy (also cited in the paper) that great thinkers of the last Century, e.g. "Schr￶dinger?s 'What is Life?', von Neumann?s 'The Computer and the Brain', and Szilard?s 'A theory of aging' argued in unison that information-theoretic aspects would become key to a future understanding of biology".

A strong case is Genomics - since even Richard Dawkins admitted that it "became a branch of information science" (see junkdna domain).

Geometrization of biology; neuroscience and now genomics used to be particularly difficult because professional informatics specialists for too long were considered "intruders".

Times changed since the ENCODE results' first release a year ago - another Anniversary that largely went unnoticed. Two outdated axioms (the "Central dogma" and "Junk DNA" misnomer) could be reversed to yield the principle of recursion of genome function, and since the DNA-RNA-PROTEIN-DNA-RNA (etc) recursion is not a closed system (e.g. through the protein-to-protein interaction it is open to the environment) - fundamental theoretical flaws of one-and-a-half-century-old tenets of biology are rapidly replaced by geometrical algorithms of genome informatics.

pellionisz_at_junkdna.com

Interesting article (and responses) but agree with one of the comments regarding the 'intelligent' artwork of Michele David. Discovered her website via this article, www.micheledavid.co.uk and was very impressed. More use of artwork like this please!

There is no argument within science about whether evolution has taken place, or about the essential correctness of Darwin's idea about natural selection. To pretend otherwise is to obfuscate the overwhelming amount of evidence that has been amassed. Certainly there are unanswered questions, but the basic one is not among them.

I must say that I was a little surprised that at the end of this medium-long article there was little worthy of an original take-home message.
Christian DeDuve has written whole books over the last twenty years which more and more concentrate on how we might imagine the metabolic developments which would be consistent with early emergence of complexity from prebiotic soups. I think a re-cap of what was said there would have been a more suitable introduction to this article than a discussion of what people believe or don't believe about what we can imply from what Darwin said or wrote.
This is of course an area open to conjecture and always will be. Whatever happened, a system which lacked one of the cardinal features of sustainability, feed-back control, and memory (heritable within certain constraints) and inherent mutability, while perhaps being a flash in the pan in its day, certainly didn't contribute much to what we conjecture to have been the first life form. When I say that, of course it is embedded in the belief that there was a first life form (and something similar, but unripe, just before, from which everything else evolved.. and Darwin and most of the rest of us are assuming just that, and supported daily as new evidence for evolutionary pathways flows in.
Referring to a lot of the comments which the article invoked: I would like to put the question to the laypeople and ask them what they have to offer that would change our perspective on this. Saying "I don't understand you" is just too lame to demand an answer.


Bye the way, for those of you that read my suggestion that we should look more closely at rotifers to find out how they managed to evolve for many millions of years without sexual reproduction, the answer is out: see Gladyshev, E.A. et al. 30 MAY 2008, 320, 1210 SCIENCE www.sciencemag.org; they increase their variability by picking up their genes from all over the place, from other organisms. Since apparently Coenorhabditis elegans does this too, now we can ask why does it go to all the trouble of having sexual reproduction as well?

Huh?

While it is great to see an evolutionist admitting to a problem in the theory I think a major issue is still being avoided. Evolution ought to be a general process so one can reasonably ask whether intelligent life on another planet might come up with a theory of evolution and whether it would be the same as Darwinism. The answer to the last question is clearly no - an examination of Darwinian principles shows that there are at least four points in the exposition in which there is a reference, usually implicit, to characteristics and interests of the species homo sapiens of planet Earth. If you doubt this try the simplest case - define 'natural' as in "natural selection" without any reference to humans (for a warm up try 'selection'). It is, of course, possible to rewrite the theory to avoid such references but then the definitions are just that bit different and a gaping hole appears in the logic. A little bit of statistics reveals that the vast majority of novel species arived via the logic hole - making some of the Darwinian ideas somewhat irrelevant to the question of the origin of species (however you define that term). The real problem with evolution is that the theory has the same fatal flaw that Ptolemaic astronomy had - fundamental principles flawed by unacknowledged homocentric assumptions. It is not particularly difficult to identify and eliminate these assumptions but I have yet to encounter any writer on evolution who is prepared to abandon the priveleged position of their species.

The reason we seperate science and religion is so we introduce as few biases as possible when we conduct experiments. It helps us get along. To claim that science and religion are based on different modes of thought, however, is false.

Religion is an experiment. What happens if I pray every day? What happens if I keep the law of chastity? If you look around you and the experiment produces positive results you try another experiment based on the theory of the gospel.

Do I know why God lets misery continue in the world? Do I know why Jesus had to die? Nope, but I would love to let science explain what a photon is, what the path of an electron is inside it's orbit and what gravity is.

When it comes down to it, we are both acting on limited knoledge trying to figure out what the nature of the universe is. The difference is whether we find religious or scientific experiments to more accurately explain the truth.

Eric Smith?s article is refreshing and thought provocative. For far too long scientists have worked under the premise that Darwin was right. Yet what Darwin described was not the end-all answer to life on Earth (and the Universe for that matter). And how many times has scientific convention been turned on its head when confronted with a new way of looking at the same data. Write or wrong, enlightened or misguided, Mr. Smith?s article has caused a stir. A wealth of knowledge, decades of singled-minded science, and careers hinged on one-man?s idea generated over 150 years ago is no reason to ignore new and emerging principles.

This argument is both confused and naive. Natural selection is not, and never was, intended to explain the origin of life. The author has little or no understanding of the way metabolic pathways or even single enzymes interact with their control mechanisms, if any, and how that can easily occur by mutation and natural selection. A critique of everything wrong with this article from sloppy illogical analysis, inability to separate concepts and facts into appropriate classes, supposing that something is difficult to do because people have a hard time designing it, claiming that simpler systems are more robust when what the author is trying to do is compare a single reaction to a biological system, would be ten times longer than the article. I assume that the author is new to biology and that, because of his weak understanding of entropy, ha has not migrated from physics. It is really rather shocking that this was published in The Scientist.

It is just too bad that such a rich and significant topic is presented in a confusing and "trackless" way. Similarly the neglect of a diverse fossil and biochemical record edging back to almost 4 billion years now (in a 4.5 billion year old world), and paleoenvironments which add significance to the question, is indeed the life laboratory of this planet. To neglect that record is to overly "mystify" and dilute the question.

Donald Wolberg
Socorro, New Mexico

Eric Smith has, earlier this year, outlined with stunning detail his paradigms in: Thermodynamics of natural selection I-III. Jour. Theoretical Biology 252(2):185-220.
His research is also to be found in 2006: Chemical Carnot cycles, Landauer's principle, and the thermodynamics of natural selection. Santa Fe Institute Working Paper 06-03-11 [24 pages].
Those here who insist they don't understand Eric's thoughts (if one can read Steve Gould's 2002 panoramic survey of evolutionary thought, then Eric is easily accessible), don't seem to understand how to creatively think.

Dearly departed Stephen Jay Gould taught me all I know about evolution by explaining it in nearly common English. If the author of the story cannot write down to us hoi polloi, perhaps he can suggest an author who can. I enjoyed reading his article, but it was more confusing than enlightening. If he could recast it as a lecture for incoming freshmen, perhaps I could get it.

Chemical reactions depend on free energy and the availability of a low energy state. Sufficient mixing must occur for an opportunity for change to become available and a ?nested position? must exist for the lower energy state to become occupied. Life could be considered as a dynamic balance between Gibbs free energy and the second law of thermodynamics. Or life might be the break in the symmetry of the reversibility of the Gibbs condition due to the presence of catalytic reaction products. Sometimes the energy derived from entropy into the lower state can be sufficient to drive a reaction in a sustained way.

Flame and rust both have the ability to catalytically produce more of the same, yet we do not regard them as life. Still, such recurrent self perpetuating patterns in nature seem to be the precursors of the complex fermentation process that we call life.

It is relatively easy for us to work on topics within well defined fields and simply avoid the larger questions. It is even easier to criticize those that attempt to formulate views on these matters without providing substantial input ourselves. Or we might want to marginalize and entire realm of pursuit by calling it metaphysics, religion, or poor science. There is certainly safety and security, but less progress, if we only consider specific embodiments and ignore the driving principles.

There is a lot of work in this area. I would expect someone writing this kind of article to have seen some of it. The writer seems off in an abstract world somewhere.

Just a couple of examples beyond those mentioned - It would take about 60 million years for complex organics to form in the Oort cloud. We know they exist in comets. Earth was bombarded by comets for a long time.

RNA has been shown to have interesting characteristics in water ice. It's not static. Long periods of time went by with water ice coexisting with liquid.

Most people, and it seems perhaps this author, have trouble comprehending what 1 billion years or even million means. It is an incredible span of time.

A brave thing to try to venture an opinion on, but Robin's reaction is closest to mine: pretty disappointing (though I think I'll have to read this again just to be sure). Love to hear more from Robin on that nano thing! I can't help thinking that if something like the citric acid cycle is key, then something is inherent in matter itself for that to happen.

My favorite line is "Even the genetic code, ..., has regularities that may be of precellular chemical origin." I'm wondering what else other than chemistry would anything precellular have to draw on, anyway?

Modern understanding on the origin and change of life has been dominated by the Darwinian views. The two most important cornerstones for the Darwinian theories are: (1) all life forms are derived from a common origin; and (2) life form changes due to natural selection on the fittest forms randomly generated. However, many evidences indicate that life on Earth could not all originated from a single common ancestor and the evolutionary process for life is not random at all. Natural selection as a proposed force for evolution is an abstract concept that cannot be measured in any definable way. Fitness as a proposed ultimate goal for evolution is an obscure term that means nothing for predicting the direction of evolution. Furthermore, Darwinian theories ignore the contribution of previous abiotic evolution on subsequent biotic evolution and basically separate the underlying abiotic evolution from the upper level biotic evolution. A new evolution theory is proposed here which integrates all useful information into a cohesive framework. This new framework shows a historical link between abiotic and biotic evolution and highlights a simultaneous contribution of both abiotic and biotic factors into the origins and changes of life forms. By emphasizing this organic link between the abiotic and the biotic aspects of life formation and change it is hoped that complex and enigmatic biotic phenomena will be subjected to precise physico-chemical studies and thus be understood in simple and clear terms.
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More can be read at "Evolution: An Integrated Theory − Criticisms on Darwinism − Fifteen Years Ago" (LINK
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Or Contact SVL@logibio.com

The author is apparently unaware of a large body of work conducted from the 1940's until fairly recently on the origin of life. Arguments are offered that make enormous leaps of complexity and fail to cover the progression from the simplest systems into complex systems as if this was all very mystical. Scientific experiments have demonstrated many of these simpler steps without which a cell could not have evolved into a complex cellular structure. I find this argument to be more traditional and naive than informative. The issues of intelligent design are religious issues, not scientific and have no place in science, despite many efforts to the contrary. People simply don't like not knowing, so they must have something to embrace. As science has not collected its many postulates and theories into coherent laws of science, the average person is confused and uncomfortable.

I found the article disappointing. What use is it to use so many words to say so little about such an interesting topic? The author avoids considering core aspects of the subject, such as that all life on this planet is based on the same highly functional, highly mechanical nano technology that works from at least the sub-atomic level up, and that that, in itself is curious - why arenﾴt there more variations in core cellular mechanisms? Life is built on a highly shared molecular library, running off the same cellular "operating system" (DNA-coded protein replication, etc.), and a key question is, perhaps, why evolution hasnﾴt generated a variety of core cellular systems? Explaining to the public how "accidental" evolution can develop incredibly complex and highly functional organisms when mankindﾴs most deliberate efforts canﾴt even develop a "half intelligent" computer is not an easy task, and unless we can address the main issues with clarity, what hope is there to convince the general public? Almost every month we read of new discoveries that only make the understanding of evolution even more difficult, and perhaps we need to reconsider our view of evolution from first principles.

While the art accompanying the "Before Darwin" article is intelligent, placing it behind the opening text obscures that text and is an example of faulty design.

While Waechtershaueser (1) made an argument from the retrodiction of metabolic pathways that the reverse TCA cycle is similar to the first metabolic pathway to evolve, carbon dioxide fixation hardly is ?one of the most conserved reactions throughout the biosphere?. To the contrary, a variety of pathways, reactions, and enzymes are being discovered that are used to fix CO2 (see (2) for a recent overview):

RubisCO in the traditional Calvin cycle found in plants and many proteobacteria.
(PEP carboxylase in C4 plants, but this really is more of a pre-fixation)

The Reverse Krebs cycle (or reverse tricarboxylic acid - or reverse TCA cycle).

The Reductive acetyl CoA Pathway in methanogenes

The 3-Hydroxypropionate Pathway

The 3-hydroxypropionate/4-hydroxybutyrate cycle.

1. Wachtershauser, G. (1990) Evolution of the first metabolic cycles. Proc Natl Acad Sci U S A, 87, 200-204.
2. Thauer, R.K. (2007) Microbiology. A fifth pathway of carbon fixation. Science, 318, 1732-1733.

It's a catchy title..and maybe I'm naive, but weren't Darwin's book and theory about the origin of species (variation) rather than the origin of life (genesis)?

Just curious........

Bryan

Eric Smith begins "Evolution's Real Problem" with a guarded acknowledgement of the disparity between professional and amateur perceptions of Darwinian evolutionary theory. Then he says ?The perception of evolution among the wider public might even be improved by better communication of scientific concerns about the limitations of evolutionary theory?? How about improving the perception of limitations of evolutionary theory among academics by them paying attention to what amateurs in their field are saying, instead of sticking their fingers in their ears and saying very loud ?You?re a creationist, you?re a creationist, I can?t hear you??

I studied biochemistry at University College London and went on to become a professional medical writer. I proudly declare myself to be an amateur evolutionist. I am not a creationist, I am a card-carrying humanist. My book "Save Our Selves from Science Gone Wrong" (see evolvedself.com) has back cover blurbs by Mary Midgely, John Horgan author of "The End of Science," and Robert G. B. Reid, Emeritus Professor of Biology at the University of Victoria, British Columbia and author of "Evolutionary Theory: The Unfinished Synthesis." Yet here?s how one of Darwin?s bulldogs reviews my book on Amazon:

"Worthless tripe! ?his scurrying away like a cockroach when confronted with real scientific questions reveals his real purpose - to make a quick buck?. He feels that scientific qualifications, experience, knowledge, the scientific method and the peer review process are all unnecessary when a layman such as he has the gift of insight. Actually, he doesn't even offer that much. There's not a grain of originality, much less real science. He's counting on there being enough gullible, scientifically ignorant people out there, who will buy this trash, to make a quick killing. He knows they exist because look how much money charlatans like Michael Behe, Philip E. Johnson and William Dempski make with the same, fraudulent claims. At least they're desperate and cunning enough to be original? In summary, you're going to read the work of con artists, you might as well go the deceitful source where this "science gone wrong" crap originated - the Discovery Institute!"

We had exchanged posts on an Amazon bulletin board. Following my departure he and the other participants congratulated each other on having silenced me and driven me away.

Should professional scientists care how amateurs in their field are treated? Even having to raise the question is ironic since Darwin and Wallace were both amateurs when they came up with the theory of natural selection. Would Darwin be proud to know that self-appointed bulldogs were crushing dissent in his name, with the silent acquiescence of professional evolutionists?