What critics of critics of neo-creationists get wrong: a reply to Gordy Slack

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Note: this turned into kind of a rough draft of an essay, and I think the part about the origin of life and complexity of the cell would be publishable in perhaps an education journal. So I welcome any comments on the argument, supporting or undermining points, etc. I don’t have my references folders handy at the moment but I have references in mind for all of the factual assertions, although more are always welcome. I’m very happy to acknowledge commentators if this does get published, or even have a coauthor if someone else is interested in working on this. Thanks!

I have not been able to blog much lately, due to minor distractions like grad school and actually having a social life for once (don’t everyone gasp at once an suck all of the air out of the room). But now it is summer and I am in a coffee shop, and I am feeling frisky. I just came across blogs by Jeff Shallit and PZ Myers responding to an essay in The Scientist entitled “What neo-creationists get right” by Gordy Slack, journalist and author of an excellent book on the Dover trial, The Battle Over the Meaning of Everything: Evolution, Intelligent Design, and a School Board in Dover, PA. (And Slack’s reply to PZ and PZ’s surreply.) Slack argued that part of the reason for the persistence of creationism is that evolutionists often react with “ridicule and self-righteous rage” on some issues where creationists might have a point, or are at least not so clearly wrong.

I consider both Slack and his critics friends and colleagues, and both sides make some valid points. But I think many of the arguments that both Slack and his critics make in this particular instance don’t work.

Origin of Life (OOL)

Slack lists a “few worthy points” creationists make. Here is the first:

First, I have to agree with the ID crowd that there are some very big (and frankly exciting) questions that should keep evolutionists humble. While there is important work going on in the area of biogenesis, for instance, I think it’s fair to say that science is still in the dark about this fundamental question.

Minor point first: Shallit points out that “biogenesis” means production of life from life, whereas Slack is talking about the origin of life (OOL). Oops.

Major points: PZ says that sure, big exciting unanswered questions like the origin of life exist in science, but scientists said this first, and furthermore consider them research opportunities, not flaws. Shallit separates OOL from evolution, specifying that evolution is what occurs after you have life; Shallit does this in the face of Slack asserting that this response is disingenuous. Shallit also argues a little over whether or not we’ve made only “little progress” in understanding the OOL, but says even if we’ve only made a little progress, it’s better than ID.

This mini-debate points out what I think, and have often said in conversations, is a major flaw in how we respond to creationists. All too often, when the OOL comes up in popular discussions (reporters, online debates, etc.), the anti-creationist will reply with some variation of “sure, it’s a tough unsolved problem, but we’re working on it”, or the wizened statement “actually, the OOL is outside of the domain of evolutionary biology”, or finally, “we’re pretty much in the dark about the OOL, but at least what we have is better than the creationists giving up and saying a miracle occurred.”

My take: It is high time all of these statements be discarded or highly modified. They are basically lazy, all-too-easy responses relying on hair-splitting technicalities or nearly philosophical assertions of the “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” variety. And the worst part is that these sorts of statements mis-describe the actual state of the science among the people who work in the field. It is simply not true that we, the scientific community, know almost nothing about the OOL (what an individual who spent a career working on fossils or fruit flies or speciation might know personally is a different question).

Here is a short list of things we have discovered or confirmed in the last 50 years or so pertaining to the origin of life. In my opinion all of these points have reached high enough confidence that they are unlikely to change much with future discoveries, and our confidence in them does not depend in uncertainties in the remaining unanswered questions.

OOL Discovery #1. All known life can be traced back to a single common ancestor which, compared to what most people think of as present-day life (i.e. plants and animals), was relatively simple – microscopic, single-celled, perhaps as complex as an average bacterium or perhaps somewhat less so.

Because a lot of creationists, and sometimes others, are a bit thick in the head on correctly understanding this point, let me bash away at some common misconceptions. The phrase “single common ancestor” does not, and never has for people who were paying close attention, referred to a literal single individual organism. Think about a phylogenetic tree with humans and chimps on the branches. When you trace the tree back to the “common ancestor” of chimps and humans, does that node represent a literal single individual? No, of course not! Everyone (well, everyone paying attention) realizes that that ancestral node represents a species or population sharing genes in a gene pool. Ditto for all of the other ancestral nodes in a phylogenetic tree, including the Last Common Ancestor of known life.

With this understood, the debate initiated by Ford Doolittle and others over the precise nature of the Last Common Ancestor – they argue that it was a population of unicells that were rampantly trading genes – can be put in the correct context. It’s basically a debate about how wide or narrow the bottleneck the Last Common Ancestor represents, and whether (for example) modern life might contain some genes derived by lateral transfer from pre-LCA lineages that are now extinct. These debates are fascinating and highly technical, but they don’t undermine at all Point #1. Somewhat ironically and counterintuitively, those who say that there was rampant lateral transfer – this is supposed to be the “radical” position that “uproots the Tree of Life” when its proponents get their blood up – are actually pushing the LCA to something more and more like a traditional gene pool, i.e. species, i.e. what every other node in a phylogenetic tree represents.

Any way you slice it, all known life (with minor derived exceptions, and excepting viruses) shares a suite of protein and RNA genes, a DNA-RNA-protein system and a mostly standard genetic code (again with minor derived exceptions), etc. Even if various other bits of modern life came from other ancestral lineages (unlikely for most features in my opinion but there may be some exceptions), this shared system indicates that all known life, i.e. all the stuff that’s not extinct, descends from a pretty good bottleneck where these features were fixed in the “population.” And this reconstructed ancestor is maybe as complex as a typical bacterium and probably less so. It could be that in the last 50 years science discovered that known life had for-real multiple origins, or that at the root of the tree was a complex multicellular organism with 30,000 genes and huge, elaborately regulated, genome, but instead we get a unicell with a relatively small & simple genome. Various caveats, important to scientists but irrelevant to beginner-level education and dealing with creationists (e.g., somewhat more genes may have been passed through the bottleneck in some but not all organisms if the LCA was more of a gene-trading community) should not be allowed to distract from the Main Point: science has confirmed the hypothesis, going back at least to Darwin, that the ancestor of modern life was much less complex than life today.

OOL Discovery #2. The Last Common Ancestor itself was the product of evolution from an even simpler ancestor. The simplest piece of evidence for this is that a number of the genes found in the Last Common Ancestor are homologous, thus derived from a single common ancestor by duplication and modification. An example is the F1Fo-ATPase of bacteria, which interconverts proton gradients (or sometimes sodium ion gradients, which are chemically very similar) and ATP, the main energy currency of cells. It has relatives in all branches of life: the V1Vo-ATPases in eukaryotes (and some prokaryotes), and the A1Ao-ATPases of archaea, and phylogenetic analysis indicates that this membrane-embedded system was found in the LCA (this also confirms that the LCA had membranes, which is useful although already very likely on multiple grounds).

Anyway, the bit of the V/F/A-ATPases that deals with ATP is a heterohexamer, i.e. complex of six proteins (that’s the “hexamer” bit) of two different types (thus “hetero”), cleverly named alpha and beta. The alphas and betas alternate in the six-protein ring, and the betas interact with ATP. The key point here is that the alpha and beta subunits share statistically strong sequence similarity. The simple explanation is that the heterohexamer was descended from a homohexamer made up of six identical proteins forming a ring. Thus we know – as strongly as we know that two people are related by ancestry based on DNA sequence similarity – that long before the last common ancestor of life there was a cellular organism that had something like the F1Fo-ATPase, but a simpler version with a homohexameric ATPase complex instead of a heterohexamer.

This may seem like a trivial point by itself but it is just an example; there are dozens, perhaps hundreds, of others. The evolution of ATPases can be traced much further back: the next closest relative is a homohexamer found in, of all things, the core of the bacterial flagellum and the nonflagellar type 3 secretion systems. Thus the V/F/A-ATPases and the flagellar/nonflagellar type 3 secretion systems can be traced back to an ancestral membrane-associated complex with multiple shared proteins (because the V/F/A-ATPases and type 3 secretion systems shared not just the ATPase protein but also an associated external stalk protein, FliH/Fo-b, which by the way is something I pretty much predicted in 2003 in the Big Flagellum Essay and which Mark Pallen and colleagues nailed down for real in the peer-reviewed literature in 2006).

Even more distant relatives are known: the homohexameric rho (involved in bacterial RNA processing) and homohexameric RecA (DNA processing). And there are even more distant hexameric sister groups; the whole related set of proteins is known as the AAA ATPases if you want to look them up. And if memory serves there are yet more distant non-hexameric relatives.

In other words, the Last Common Ancestor had a suite of ATPase proteins which had already evolved from a single protein ancestor by duplication and divergence events which are still strongly statistically detectable in the present day. And there are a number of other genes for which the same can be said, and undoubtedly many others which occurred but are not statistically detectable billions of years later due to the decay of the signal.

So far we’ve established that anyone, creationist, evolutionist, or whomever, who says that the scientific understanding of the origin-of-life is chemicals –> mystery –> modern-complexity life doesn’t know the first thing about what they’re yapping about. At the very least we’ve got chemicals –> mystery –> quite simple precursor to the LCA –> LCA –> modern life. But there is yet more that we know

OOL Discovery #3. DNA/RNA/protein-based life was preceded by something even simpler, an RNA world or at least an RNA-heavy world.

The RNA world has gotten better press attention than OOL Discoveries #1 and #2 so I will spend less time on it. Read the wikipedia page for an introduction and particularly the EvoWiki page for some of the main supporting evidence.

There are two points worth making about the RNA world that should be made every time this issue is discussed in popular or remedial creationism-related discussions. First: there was a time, not too long ago, when the fact that DNA coded for proteins, and proteins were necessary for making DNA, seemed like the ultimate intrinsically unsolvable problem in the study of the origin of life. It’s the ultimate chicken-and-egg problem, or, if you like, the ultimate “irreducible complexity” problem. And yet, scientists worked on it for a few decades and discovered a workable, surprisingly simple solution.

Second, surprisingly enough (well, surprising to creationists or the naive), this solution, the RNA world, hasn’t just sat around as a purely theoretical just-so story. A highly productive research program has been built on the RNA World concept. Areas that have experienced substantial success in the last decade or two include: the discovery of increasingly diverse catalytic capabilities of RNA; the evolution new capabilities in replicating, evolving RNAs; the evolution of the genetic code which translates DNA to RNA to protein; and the prebiotic origin of RNA components.

Each of these areas has developed into a subfield which has experienced major research discoveries in recent years. For example, on the origin of the genetic code, this paper assembles dozens of indicators on the order in which amino acids were added, step-by-step, to the genetic code and shows that the evidence strongly supports a fairly specific scenario (which shares many similarities with early, more speculative scenarios built on the basis of just a few lines of evidence).

Ergo, we don’t just know that the Last Common Ancestor of Life was simple, and that it’s ancestor was simpler, and that it’s ancestor was an even simpler RNA-dominated critter; we even have a decent idea about the order of the steps by which the genetic code itself evolved.

OOL Discovery #4. The increasingly simple ancestors of modern life weren’t made out of just anything, they were made out of chemicals that just happen to be generated by plausible abiotic mechanisms found in early solar systems. This area is also better known, but many, both creationists and scientists and journalists who haven’t thought about it enough, tend to think of prebiotic chemistry as the beginning and ending of origin-of-life studies, and for some extremely foolish reason which I can’t fashion, probably simple carelessness, tend to think that until chemists pop life out of a test tube then we “know nothing” about the origin of life.

Here’s a short list of discoveries about prebiotic chemistry, all of which increase our confidence in the idea that the origin of life was a gradual process, from abiotic chemicals to simple replicators to the simple ancestors of modern life which were discovered above. I’ll include some subtleties that I’ve seen lead people astray on occasion.

* Water is one of the most common compounds in the universe, and was/is common in the solar system (subtlety: most of it is frozen, but remember that on any planet with hot stuff inside and cold frozen stuff outside will have a just-right region in-between where water will be liquid)

* Earthlike planets are likely reasonably common (subtlety: we haven’t discovered them directly yet, but this is isn’t because they aren’t there, it’s because our instruments are at present only sensitive enough to detect big, close-in planets around other stars. Nevertheless, the distribution of the stuff we can detect strongly indicates that there are plenty of earthlike planets in earthlike orbits which will be discoverable in the near future. That’s a prediction, scientists will test it, that’s science for you. Remember that back in the 1990s, ID proponent William Dembski was skeptical of the whole idea of extrasolar planets. Whoops!)

* Amino acids are easy to generate by a variety of processes, and this is not only supported by experiment, but by observation of amino acids in meteorites and other extra-terrestrial material. (Subtlety: There is a body of serious scientific thought which suggests that the Earth’s early atmosphere was more neutral and less reducing than was thought a few decades ago, but (1) this isn’t for sure, the redox chemistry of the Earth’s rocks and atmosphere is a complex business (and I wonder if the impact which produced the moon, removing much of the mantle but leaving the Earth enriched in heavy iron might have made the Earth’s atmosphere more reducing, at least early on – comments?); (2) even in a neutral atmosphere/ocean system there will be locally reducing conditions – heck, there are local reducing conditions here on earth right now even with our heavily oxidized crust and atmosphere; (3) as it turns out, even neutral atmospheres can produce amino acids in respectable yields anyway; and (4) this whole sub-debate is somewhat moot since we have direct evidence of amino acids forming in the solar system e.g. in meteorites.)

* RNA precursors are somewhat tougher, but there has been progress in that area also, and anyway there is no requirement that the first replicator must have been RNA; various other simpler “worlds” have been suggested and are being explored (PNA, peptide nucleic acids; other NAs of various sorts; and lipid worlds, which have the distinct charm of instant replication ability and statistical inheritance, with daughter bubbes containing a subsample of the chemicals making up the mother bubbles, and growth occuring by incorporation of lipids from the environment and other bubbles; so maybe the first “replicators” were even simpler than some have thought).

* The main energy source of present life is ATP and other energized phosphate molecules. So, what was the prebiotic source of those? It turns out that inorganic polyphosphates (chains like phosphate-phosphate-phosphate-phosphate) have energetic bonds very similar to those of ATP (which is adenine-phosphate-phosphate-phosphate), and yet can be formed by the simple heating of certain rocks.

* Less well-known is the fact that prebiotic origins of many cofactors and other universal small biotic compounds have also been reconstructed

What is actually being worked on. The above should convince you that the idea that we know nothing or very little about the OOL is just uninformed foolishness. The field has made major progress. There are some famous puzzles remaining, but they do not add up to “we know nothing about the origin of life.” Furthermore, some of the puzzles that creationists, and sometimes others, consider to be major hangups, are not necessarily so. For example:

* The origin of chirality (the left-handedness of amino acids). This is a major puzzle if you make the extremely foolish and unthinking assume (like creationists do, but sometimes others) that the first use of amino acids in early life was supposed to be in long amino acid chains made up of 100+ amino acids randomly assembled from an even mixture of 20+ different amino acids with an even mixture of right- and left-handed amino acids. But over here in the real world, where the origin of the genetic code has been reconstructed in some detail, we know the following: the first primitive genetic code used just one or a few amino acids, and one of the first was glycine, which is the simplest amino acid, the most common amino acid produced in prebiotic experiments, and which is achiral (no left-hand/right-hand difference) to boot. If, as has been proposed, the first use of amino acids was as something relatively prosaic, i.e. a short chain of hydrophobic residues to insert into an early membrane, then (a) the odds of getting 10 or so amino acids at once that were either left-handed or glycine were not small at all, and (b) it wouldn’t have mattered much if the occasional right-handed amino acid was incorporated, because the crude chemical property of hydrophobicity is all that is really important, and (c) therefore the origin of a preferred chirality could have been more or less random. There is some very interesting work indicating that nature has various processes which might increase the proportion of left-handed amino acids, but it’s not at all clear that these will be necessary to explain chirality.

* The origin of the first replicator. This really is the big cahuna of the OOL discussion, and where the big and contentious debates are still occurring within science, but again I find that many discussants operate with very crude and naive assumptions about what early replicators “should” have been like and what prebiotic experiments “should” be able to produce to “solve” this problem. It’s a mini-version of the “produce a modern cell in a test tube for me or you haven’t solved the OOL” silliness, i.e., “produce a self replicating RNA World, with duplicating ‘informational genetic sequences’ in the test tube, and until you do you can’t say we know anything about the origin of replicators.”

Again, over here in reality-land the distinctions between replicators and nonreplicators are not so clear. I have already mentioned “lipid-world” ideas and the concept of “statistical inheritance”, where overall chemical properties are transmitted or accumulated, without the need for exact inheritance of a sequence. Similar concepts have been applied by OOL workers to amino acid and nucleic acid “sequences”, where before exact inheritance of sequence is acheived, there might have been a stage where inexact incorporation of a range of chemically similar bases was occurring.

Another subtlety is the difference between “self-replication” and processes where prebiotic compounds go through a series of chemical processes, and differences in chemical kinetics increase the frequency of compounds that have more rapid kinetics; if these compounds are auto-catalytic, they can begin a feedback system where chemicals with higher kinetics take over in a proto-selection system. Strangely, although everyone who takes college chemistry learns that the product of chemical reactions is a combination of thermodynamics and kinetics, many discussions of the OOL from scientists, and all of the derivative critiques by creationists, have focused on thermodynamics. This is particularly odd since self-replication is the ultimate example of kinetics overwhelming thermodynamics.

What’s the point of this sub-discussion? Well, if it is the case that the origin of the first “replicator” was, like everything else we’ve discovered in the study of OOL, a slow, gradual (meaning step-by-step), cumulative process, then it is pretty foolish to have in our heads the idea that OOL experiments should produce full-on replicators in one go to be successful experiments. This is basically a strawman expectation that expresses conceptual confusion about what an evolutionary origin of life “should” look like.

(As an aside, I think biology education would be a lot better off if the above points were consistently made in science curricula and textbooks at the high school and college level. Teaching OOL as a story from simple to complex, rather than a detective story from complex to simple, is probably a mistake if the goal is to get students to understand why scientists think the way they do about these issues.)

The Main Point

Now that we’ve briefly reviewed the OOL field and discussed the major discoveries and some of the common misconceptions, let’s return to the statements I quoted at the beginning. Is it really true that “science is still in the dark” on the OOL, as Slack said? Not a chance. If we lived in a world where it actually looked like the first living things were as complex or more complex than life today, or where the last common ancestor contained absolutely no evidence of an evolutionary history, or where big obvious puzzles like the interdependency of DNA/RNA/protein had no hint of solution, or where the building blocks of life were completely unrelated to those produced in prebiotic experiments – all of these things would be true, say, on a robotic planet without microscopic life, where robots were replicated by macroscopic assembly performed by other robots, and powered by hooking up to a grid of fusion-fueled power plants – then we could say “science is still in the dark” on the origin of this robotic biosphere. But instead, we have numerous lines of evidence all pointing towards the notion that current life descends from a relatively simple ancestor, and that ancestor descends from a series of even simpler ancestors. Why should any of this evidence exist, if life was poofed into existence all in one step, which is what the creationists/IDers think happened even when they won’t admit it, because they are not brave enough to defend what they actually think? Additionally, why should the remaining puzzles, particularly about the origin of the first replicator, cause any unusual amount of discomfort for scientists? Whether or not that puzzle is solved, the gap between prebiotic experiments and the first replicators (or better yet, pseudoreplicators with statistical inheritance) is a drastically reduced vestige of a gap compared to what the gap looked like in, say, 1950. When you think about it, the creationists’ attempt to insert miraculous divine intervention into this tight little gap which is left is actually pitiful, and a pretty sad commentary on the state that creationism/ID has been reduced to. The verse “And God said, let the NA precursors link together into a short noncoding kinetically favored chain and pseudoreplicate approximately statistically after their kind” just doesn’t have the same ring to it.

Similarly, if my characterization of the state of the science is accurate, then it is highly irresponsible for scientists to address creationist arguments about the origin of life with statements like, “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” or “actually, the OOL is outside of the domain of evolutionary biology.” The first statement surrenders without argument a favorite bogus creationist talking point, and so confirms and passes on their misinformation, even if the evolution “wins” the argument in his own head on some broader philosophical point. Instead of putting the creationist back on his heels with a wave of contradictory evidence, that sort of response, even if the philosophical point is valid, leaves the creationist and any of his sympathetic readers irate that the empirical point is not being addressed, and that the creationist/ID position is being excluded by the rules of the game. The fact that this sort of response is a lot easier and faster to put together does not make it the best one.

The second statement, splitting the OOL from evolutionary theory, is only technically correct in a sort of legalistic, hairsplitting way. Sure, it’s true that technically, “evolution” only happens once you have life, or at least replicators, but getting from replicators to the last common ancestor is most of what most people think about when they’re thinking about the origin of life, i.e., “where did the evolutionary ancestor of all life today come from?” and all of that is evolution all the way. Furthermore, even the origin of the first classical “replicator” was itself very likely an evolutionary process, in that it occurred in stepwise fashion and not all-at-once, and that the first replicator was likely preceded by various sorts of pseudoreplication, statistical inheritance and kinetic biases. If you remove evolution from your thinking about the origin of the first replicator then it is very likely you will never understand how it happened, or what the current research on the question is about. Finally, even apart from these detailed considerations, “evolution” reasonably has a broader meaning – the evolution of the universe, the solar system, the planet, and the planet’s geochemistry, and the origin of life and the origin of the first replicator must be understood as part of that larger evolutionary history.

One other telling point is that the statement “but the OOL is outside of evolutionary theory” response also has the problem of simply dodging the hard work of describing the discoveries and work of modern science, a problem I have already described. In conclusion, if it were up to me, I would completely scrap this statement from the rhetorical toolkit of evolution defenders.

The OOL topic turned into an essay on its own, but we still have another few of Slack’s points to address.

Slack’s second point: the cell is more complex than Darwin could have imagined

Slack highlights another area where he suggests that creationists/IDists might have a point:

“Second, IDers also argue that the cell is far more complex than Darwin could have imagined 149 years ago when he published On the Origin of Species.”

Shallit responds with a “Darwin got some things wrong 150 years ago, so what?”-type of response, and PZ says that “Scientists say” that cells are more complex than they seemed to Darwin and that creationists have just copied them. However, both of them do point to some evidence that Darwin’s understanding of the cell was not as primitive as the talking point suggests.

The problem with both sides of this discussion is that it’s basically all ahistorical bunkum. I am pretty well convinced that if any actual historian of science ever actually did a serious historical study of what Darwin and other serious people who had studied microbiology and genetics in the 1800s thought about the complexity of the cell (such as study has not been conducted, or at least I’ve never seen either scientists or creationists cite such a study when they repeat this legend), they would find that the complexity of the system was well-appreciated from early on. A quote of recent NAS president Bruce Alberts which creationists/IDists like to cite notes that cells seem way more complex now than they did in the 1950s and 1960s when the main method of study was to grind them up and study the reaction rates of the various chemicals and enzymes in them, but this says nothing in particular about what Darwin thought.

To get an idea of that, let’s read some Darwin. This from near the end of Darwin’s 1868 book on the mechanisms of inheritance, The variation of animals and plants under domestication, page 404. Darwin proposed the idea of “pangenesis”, which was that heredity worked by each part of the body sending “gemmules” to the reproductive organs. This idea was wrong in detail but was an important step towards the eventual discovery of “genes” (so named after pangenesis). At any rate, Darwin thought a bit about what his hypothesis of heredity, or any similar hypothesis, said about the complexity of life:

Finally, the power of propagation possessed by each separate cell, using the term in its largest sense, determines the reproduction, the variability, the development and renovation of each living organism. No other attempt, as far as I am aware, has been made, imperfect as this confessedly is, to connect under one point of view these several grand classes of facts. We cannot fathom the marvellous complexity of an organic being; but on the hypothesis here advanced this complexity is much increased. Each living creature must be looked at as a microcosm – a little universe, formed of a host of self-propagating organisms, inconceivably minute and as numerous as the stars in heaven.

Bam. It appears that everyone was wrong – scientists who sometimes made a minor offhand remark saying people used to think the cell was simple, and creationists who made a major talking point of this, and Slack who heard it so many times from creationists/IDists, without prominent contradiction from scientists that he believed it himself. Like various dubious statement about the OOL which I discussed above, the “Darwin thought the cell was simple” statement became an unquestioned factoid merely through creationist repetition and flawed assumptions from the critics of creationists – it seemed reasonable, nothing crucial hung on it for scientists so they didn’t bother to double check in a serious way, and besides it is a lot easier to agree with your opponent and declare on other grounds that their point is irrelevant to the fundamental issues, than to do a serious analysis. It might be true that a creationists’ point is irrelevant to the bigger issues, but it lets the creationists get away with something that should not be gotten away with, and through an accumulation of such points the creationists build up a body of claims that even sincere, intelligent, creationist-skeptical, reasonably well-informed people like Gordy Slack find reasonable. Then you get essays like the one Slack produced, and irate responses that shed heat rather than light, and encouragement for the creationist leaders to feel like they’re on the right track.

The moral of the story is, as Wes Elsberry once told me, when a creationist says the sky is blue, go outside and check. I am sensitive to this particularly subtle issue because there have been similar problems in the past. Many of the early responses to Jonathan Wells’s Icons of Evolution, which asserts on its face that many biology textbooks have errors, and asserts in the semi-subtext that all of the common evidence for evolution is fraudulent, were weak-kneed and conceded too much to Wells. An all-too-easy response was to say, “well, everyone knows textbooks have errors, this doesn’t effect the fundamental scientific case for evolution.” Perhaps true in the abstract, but in practice it gave the creationists confidence in their attack on the textbooks, and left teachers and others without a direct rebuttal. As I pointed out several years ago, this sort of response fell into Wells’s trap.

The history of creationism is another example. Everyone critical of ID “knew” that ID was just creationism in a cheap tuxedo, but strangely enough, precisely because this was well-known, there was little serious attempt to enquire into the actual origins of intelligent design, which occurred pre-Discovery Institute and pre-Phillip Johnson. Once the Kitzmiller case prompted such an investigation, the dividends were substantial.

There are some other points where I disagree with Slack and his critics, primarily dealing with the motivations of creationists. You are not really understanding them if you call them dishonest liars (e.g. Shallit), because they mostly do believe what they say. What they say is a product of wishful thinking and ignorance and ideology, but that is different than lying. Similarly, I doubt the allegedly arrogant attitude of scientists or atheists is really a fundamental cause of the persisence of creationism; if these features weren’t found at all the scientific community, they would be (and in some cases have been) invented. It would help a bit if the war-between-religion-and-science rhetoric was not so common but I doubt it’s a determinative factor either way. What is really going on involves whether or not someone views the Bible as inerrant and the theology and worldview attached to that, and the then-bizarre interaction that occurs when creationists try to bring science in to defend this worldview. But that is a large and complex discussion for another time.

5 TrackBacks

I have often been frustrated by creationists claiming that evolution can’t explain the origins of life, but even more irritated when evolution’s defenders try to halt the discussion by saying that “Evolution doesn’t address abio... Read More

Origin of Life from frankhagan.com on July 3, 2008 12:26 PM

One of the historical arguments against the existence of God was that something cannot come from nothing, and the idea of God creating living matter from non-living matter (”dust of the earth”) was “illogical”. The problem with... Read More

Nick Matzke has a fine summary of progress in research into abiogenesis. He chastises those people who try to argue that abiogenesis is independent of evolution, or that you can get out of trying to answer the question of where... Read More

So earlier this week I posted about PZ Meyers accusing some of us of puntingon the question of the origin of life when it comes up in a conversation about evolution. I posted about how I disagreed because I thought that while abiogenesis is related the... Read More

Origin of Life from A Blog Around The Clock on July 12, 2008 9:10 PM

Nick Matzke wrote an excellent update on what we know about the Origin of Life: Here is a short list of things we have discovered or confirmed in the last 50 years or so pertaining to the origin of life.... Read More

233 Comments

Yeah, yeah, that’s all well and good, but what’s her name??

LOL that’s the most hilarious PT comment ever.

Well, you did a much better job than I did on Slack, but I have to admit being a little puzzled by some of your complaints about my brief blog post.

1. You characterize my response to Slack’s point about abiogenesis as “I’m too busy to back it up right now”; yet I cited this paper right in my text.

2. You fail to note that my distinction between abiogenesis and evolution was not a “hair-splitting technicality”, but a response to Slack’s analogy to the Big Bang in physics. I say explicitly that abiogenesis is relevant for biology. The crucial line in my post was “Slack compares the Big Bang to physics, but then he doesn’t compare the origin of life to biology, but rather to evolution. Isn’t it clear that the analogy is faulty?”

3. After Dover, you of all people say that dishonesty is not a significant problem in creationist/ID circles? Bill Buckingham? cdesign proponentsists? (I also dislike your phrasing “if you call them dishonest liars (e.g. Shallit)” because a quick read might suggest it is me you are calling a liar.) I agree with you that not all ID proponents are liars, but the movement is shot through with dishonesty of various kinds.

This is a brilliant essay (I wish that I had written it myself!) and I look forward to reading more (there will be more, right?).

Essentially, the point is that while creationists’ points range from irrelevant to wrong to “not even wrong”, they should all be addressed. In science, many questions are irrelevant, but in education, there are no topical but irrelevant questions (even if there may indeed be stupid ones). Scientists must give no quarter: creationists need to be corrected every time that they spout anything wrong.

Of course, this turns even the shortest creationist paragraph into a “Gish Gallop”, so rife is all that they say with wrongness. The job is not easy. It is a massive failure of the American education system that this situation could arise in the first place, and a serious challenge to correct. That does not mean that it should not be done.

Finally, I would like to point out that, at least for all of the points that Nick presents here, PZ is still correct: everything that Slack concedes to creationists is done unnecessarily and incorrectly, and will impede the reception of the points that scientists are trying so hard to make. The points that Nick makes do not seriously contradict the points that PZ makes. A creationist is an opportunity for education (at least, if they are willing to listen), and while it would be nice to find something useful that they bring to the table, the fact is that it has yet to be done. This is a frustrating thing in science, to be sure. But we are not talking about science here so much as science education, and there, that fact is irrelevant. Education demands patience and attention, on both parts, and on the teacher’s part that means not saying “that’s not important” when an interesting question is asked.

Thanks, Nick. I have been puzzling over why defenders of evolution make a clear separation between abiogenesis and evolution for some time, but I could never clearly articulate my objection to the distinction. This helps heaps.

Welcome back Nick. Hope you can keep blogging as long as it’s not a drain on your studies or social life.

I just skimmed the post (I’ll read it fully later today), and forgive me if I missed it, but whenever an anti-evolutionist brings up OOL in the presence of an audience, the most important thing IMO is to ask them when the blessed event(s) occurred. While classic YECs and OECs have no problem with the audience learning that there are irreconcilable differences among anti-evolutionists on such a basic question, as you know, the “don’t ask, don’t tell” IDers want to avoid that. Granted, the most seriously compartmentalized rank and file creationists in the audience will tune it out anyway, but I think they can be dragged out of their comfort zone if the topic is emphasized enough.

The anti-evolutionists on PT and Talk.Origins may not be representative of the professionals or the rank and file, but I have noticed a very curious habit that most or all of them share. That is, whenever I ask the age of life, the ~70% that don’t refuse to answer give me their opinion of the age of earth instead. Getting the anti-evolutionists to show how they evade, or bait-and-switch, key questions might make at least the non-hopeless evolution-doubters in the audience take notice.

Correction: ~70% do refuse to answer. And the ~30% that do answer are often so vague that it’s almost a refusal to answer. The last one only said that she disagreed with Behe (and said “earth” when I clearly asked for the age of “life”), not committing to “older” or “younger.” The follow-up question was ignored.

Note: this turned into kind of a rough draft of an essay, and I think the part about the origin of life and complexity of the cell would be publishable in perhaps an education journal.

I happen to know of such a journal. There is currently a policy of not publishing anything that has already been released (including online), BUT I think a community-authored paper that develops online and is then refined offline by the lead author would be a cool concept. How to deal with arguments that we don’t know how life started therefore evolution didn’t occur is of considerable importance, since that seems to be the new default position to which anti-evolutionists have moved.

Good article. As a more or less permanent lurker who was originally sympathetic to ID and continues to consider these origins of life issues, I thought this particular essay was well done. I think more of this type of thinking and less polarizing writing could foster further learning and educational opportunities for all.

It is simply not true that we, the scientific community, know almost nothing about the OOL (what an individual who spent a career working on fossils or fruit flies or speciation might know personally is a different question).

I think your point is valid that evolutionary principles apply to periods earlier than the first complex cellular life. As a result, the origin of life issue is not strictly outside evolutionary biology. There also, of course, is continuity between origin of life research and subsequent evolution as there is no magic moment when we would say it suddenly switches from chemistry to biology. Moreover, most biologists probably expect that a solution to the question exists, even if we never sort it out entirely – though I suspect that there is reasonable optimism that we *will* figure it out. However the point remains that until then, the origin of life question has little bearing on our understanding of evolution *after* cells evolved. Note, as you say, that people studying evolution from neontological or paleontological perspectives – i.e., most of evolutionary biology – need not know much about origins work to carry out their studies. So, it’s not exactly a cop-out to say “it doesn’t matter how life started for us to understand what happened afterward”. The influence is one-way (and the opposite of the anti-evolution claim): the evidence for evolution and the mechanisms thereof is independent of the origin of life, but it can be important for discussing how life originated.

Just as an addendum to what Prof. Gregory said: in my post I said, “Evolution is, by definition, what happens after there is a replicator to replicate.” There’s probably a long distance from the first replicator (which was almost certainly not a cell) to “complex cellular life” and all of this domain and history is fair game for evolution. But before the first replicator is, I think, not within the domain of evolutionary biology. It’s certainly of great relevance to biology, however.

I freely concede that these distinctions may seem more important to someone with mathematical training, and seem like hairsplitting to everyone else.

Just as an aside, I do find it strategically helpful sometimes in discussions with average creationists (not the professional conmen) to sometimes postpone the discussion of OOL by defining it as a separate issue form evolution/common descent per se. This is because it gives the creationist an “out”… common descent seems less threatening if there remains this “not fully understood” gap at the origin. Unsatisfactory as a scientific position and as a long-term position, but I have had considerable success with fundamentalist teaching colleagues using this as my “wedge” to getting them to become more accepting of evolution in this way. It takes time, and sustained interpersonal effort, that is only feasible in circumstances like mine, ie teaching with creationists at my school.

Having said that, I learned a lot form your post. Thanks.

After Dover, you of all people say that dishonesty is not a significant problem in creationist/ID circles? Bill Buckingham? cdesign proponentsists?

At the risk of splitting hairs, I think you are both correct. The underlying faith seems entirely honest, even though it is based on childhood indoctrination, emotional needs and fears, and the resulting urgency to deny reality. However, the political implementation of this faith clearly requires deliberate misrepresentation. To paraphrase Martin Luther, if lying for Jesus is the best way to save souls, then it is not dishonest, because the end justifies the tactic.

Think of, I don’t know, breaking the speed limit by an ordinarly unconscionable amount, to rush a dying person to the emergency room. Are you breaking the law? Well, yes. SHOULD you be breaking the law? Well, yes! Are you a criminal? Nick says no. I’d tend to agree.

Flint said: … Think of, I don’t know, breaking the speed limit by an ordinarly unconscionable amount, to rush a dying person to the emergency room. Are you breaking the law? Well, yes. SHOULD you be breaking the law? Well, yes! Are you a criminal? Nick says no. I’d tend to agree.

Yes, but if a cop stops you and asks you why you were speeding, if you say “to get this dying person to the hospital” that’s one thing. The cop might even help you get there.

But if you say “I wasn’t speeding” when you both KNOW you were, then you are going to get a lecture and a ticket.

It reminds me of the scene in Young Frankenstein where Igor answers the doctor’s offer of help with his deformity by saying “What hump?”

That kind of answer from creationists just sends the entire communication process off on a tangent.

Hi Jeff – you make good points, I am leaving the internets for the weekend so I can’t make edits right away, but at some points I was at cross purposes mixing the specific (e.g. your comments) with my assertions/comments about “things I often here people say” which were not identical.

But if you say “I wasn’t speeding” when you both KNOW you were, then you are going to get a lecture and a ticket.

And this is exactly where the issue with creationist honesty arises. If you are saving a life (or a soul), then there is no such thing as speeding. You do whatever it takes. The nominal rules simply don’t apply because they are trumped by the urgency of the goal.

However, a cop who places a higher value on abiding by speed limits than on saving lives (because he doesn’t believe you’re doing so) is going to regard you as a criminal. Which is exactly why creationists are fighting to control the means of civil law and enforcement.

Nice post, but I have some major disagreements.

Now that we’ve briefly reviewed the OOL field and discussed the major discoveries and some of the common misconceptions,

This part of the post was excellent. I strongly agreed with the paragraph that followed, of course, which continued the argument that we have evidence for a natural origin of early life.

Here’s where I have problems, though.

Similarly, if my characterization of the state of the science is accurate, then it is highly irresponsible for scientists to address creationist arguments about the origin of life with statements like, “even if thecreationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” or “actually, the OOL is outside of the domain of evolutionary biology.”

The first statement is an imaginary straw man argument placed in the mouth of an imaginary “poorly arguing scientist” of your own invention, so I won’t waste time on it, but let’s talk about that SECOND statement.

The second statement, splitting the OOL from evolutionary theory, is only technically correct in a sort of legalistic, hairsplitting way.

This is absolutely not true, unless by “legalistic” and “hairsplitting” you mean “absolutely critical”. Despite the exciting work in the fields related to abiogenesis, none of it approaches the definitive level of our knowledge of molecular biology, genetics, and natural selection in modern cellular life and viruses.

It is a critical point that, not only do we have quite a lot of good work on abiogenesis, not only is it almost certain that basic evolutionary processes predate modern cellular life and viruses, but EVEN IF we did not have any knowledge of abiogenesis whatsoever, evolution would STILL be an observable characteristic of all cellular life and viruses, an observable charactersitic explained by the theory of evolution.

You seem to concede the false, illogical creationist argument that “evolution don’t not work because we ain’t 100% sure how them there cells originated”. (The poor grammar is used to emphasize the illogical nature of the creationist argument; no ridicule of anyone’s informal local dialect is intended, and I’d be ridiculing plenty of my own ancestors and relatives if it were.) But we should NOT concede this false argument.

A good analogy someone once made is that, yes, we can study the moon, even though the origin of the moon is not necessarily 100% settled. We have good ideas about the origin of the moon, too, but we don’t need to wait until we are utterly certain of how it originated to study its current behavior. We know with great precision how the present moon orbits and affects the present earth, and by extension, how it has behaved since it was the moon. An exact idea of how it originated will be wonderful, but its lack does not negate the knowledge we do have.

Sure, it’s true that technically, “evolution” only happens once you have life, or at least replicators, but getting from replicators to the last common ancestor is most of what most people think about when they’re thinking about the origin of life, i.e., “where did the evolutionary ancestor of all life today come from?”

This paragraph seems odd to me. “Getting from replicators to last common ancestor” is what ALL people should think of if they’re thinking about the natural “origin of life”, at least if your implicit distinction between “last replicators” as non-life and non-ancestor, and “first ancestor” as life, is to be drawn.

It not correct to imply that this is what “MOST” creationist literature disputes. Creationists spend far more time arguing against the evolution of cellular life, especially the evolution of humans from hominid ancestors. Vertebrate evolution is particular is their top focus. Their second major focus seems to be bacterial evolution; presumably because science so easily observes it.

In sum, there is no reason to fail to make BOTH correct replies to false creationist statements about “the origin of life”…

1) Actually, we do have some excellent ideas about the origin of life

AND

2) We also have definitive evidence of the evolution of cellular life and viruses even without it.

harold said:

2) We also have definitive evidence of the evolution of cellular life and viruses even without it.

Absolutely on board. EVEN IF WE KNEW ABSOLUTELY NOTHING ABOUT ABIOGENESIS there is not a single thing in neo-Darwinian evolutionary theory that would change in the slightest.

Evolutionary theory is a book on computer programming. Abiogenesis is a book on computer design. Considering that’s what I got my BSEE in, I can state with a clean conscience the two are, if closely related, not at all the same thing.

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Nick Matzke said: All known life can be traced back to a single common ancestor…

The Earth has 200 million square miles of surface, with water depths and atmosphere heights yielding a mixing bowl of about a billion cubic miles. Stir that pot for a billion years or more of assorted abiotic chemical activity, with occasional energy inputs from sunlight (visible+IR+UV), lightning, vulcanism, meteor/comet strikes, interstellar travelers and time travelers, naturally-occurring ionizing radiation and passing cosmic rays (not to mention the occasional neighborhood novae/supernovae)…

Who is to say there was only a single common ancestor? There were probably fragments of different kinds of life or near-life floating around for many millions of years before the first “ancestor” finally came together.

Who is to say there was only a single common ancestor? There were probably fragments of different kinds of life or near-life floating around for many millions of years before the first “ancestor” finally came together.

The definition of an ancestor gets hazy here. From what I’ve read, there are things about life as we know it that are (1) pretty arbitrary (like chirality), but (2) would necessarily prohibit any sort of merger with life that by chance went the other way. So I can most easily envision a very early competition among inherently incompatible groups of replicators, and the common ancestor of all subsequent life arose from the group that survived.

Sure love to see a tight version of this as an oped piece in the New York Times

Flint wrote

So I can most easily envision a very early competition among inherently incompatible groups of replicators, and the common ancestor of all subsequent life arose from the group that survived.

In fact, I can envision ‘life’ (in the sense of chemical replicators with heritable variation) emerging right through the history of the earth up to today, but being regularly eaten for lunch by the already existing voracious forms that won the earlier competition. Once the dominant forms become as ubiquitous as they are it’d be real tough for something new to wedge its way into the system.

Paul Burnett Wrote:

Who is to say there was only a single common ancestor?

You may have noticed that well-coached IDers tend to preface “common descent (or ancestry)” with the word “universal.” That is, when they address it at all instead of their preferred “macroevolution” or the catch-all “Darwinism.”

Dembski all but spelled out the bait-and-switch when, in the same article he contrasted Behe’s acceptance of common descent with Carl Woese’s “denial.”

I think y’all are missing something important. “The Scientist” has a history of naivete in finding a compromise between science education and religious fundamentalists. I’m guessing the editors found something they like in Slack’s book, so they invited him to write an article for them to prod discussion along. Editor Richard Gallagher has previously written of his belief that “critical analysis” and “evidence against evolution” could be incorporated into biology instruction. He wasn’t stating that he believed that the second law of thermodynamics disproved evolution, or anything specific for that matter, he just took the naive position that there was an obvious political compromise that would make everyone happy. It would seem that the naivete continues.

There seems to be a continuum here from Myers’ crusading atheist takin’ no prisoners, to relying on the ACLU and the 1st amendment, to Nesbit framing of science education, to Gallagher critical analysis, to the teacher that gives an optional Behe book assignment in the belief that its harmless. We need to nudge “The Scientist”, and whatever discussion they’re generating, more towards Nesbit. Remember, this is politics being fought here, not science.

I will be teaching basic biology to adults next semester, including a significant portion on evolution. I had already decided to stress that non-life to life is a continuum, something I expect will be difficult for them. This post will be a useful resource for me as I have not been following OOL research - thanks.

Nick Matzke Wrote:

Strangely, although everyone who takes college chemistry learns that the product of chemical reactions is a combination of thermodynamics and kinetics, many discussions of the OOL from scientists, and all of the derivative critiques by creationists, have focused on thermodynamics. This is particularly odd since self-replication is the ultimate example of kinetics overwhelming thermodynamics.

Emphasis added.

I realize that the thermodynamics issue has been dealt with multiple times, but the misconceptions about thermodynamics still keep popping up; in fact, they have occurred recently on this blog. And the misconceptions surrounding concepts in thermodynamics (entropy in particular) are genetically the same misconceptions that are propagated into “information” and “design” to cause confusion and give the impression of “impossibility” of highly complex and organized systems.

Thermodynamics is not a “barrier” to be “overcome or overwhelmed”. There is nothing in thermodynamics that is “obstacle” to something happening. There are no “mechanisms” in thermodynamics that operate to impede or forbid processes from occurring. At the very bottom of thermodynamics (and entropy in particular) is simply a process of enumeration, i.e., counting available energy states, totaling up where energy comes from and where it goes.

When physicists and chemists use terminology like “forbidden by thermodynamics”, they actually mean something else. They are simply eluding to proposed physical mechanisms in which the laws of thermodynamics wouldn’t hold (in other words, the mechanism(s) are not consistent with our known physical universe in which all energy can, in principle, be accounted for).

Another problem is to confound the spatial locations and arrangements of matter with the number of available energy states. For example, saying that an ordered arrangement of molecules in a snowflake has “lower entropy” than when the molecules are knocking about randomly is a misuse of entropy. Entropy is about the multiplicity of energy states. Thus, even when atoms or molecules congregate into patterns based on their electromagnetic interactions and the rules of quantum mechanics, they can only do so if energy is released from the system and is carried off to infinity by some means such as phonons or photons.

I suspect that the misconceptions surrounding thermodynamics, entropy and information are also lurking in the background when dealing with the “Origins of Life” issue. Nick is hitting pretty close to the issue by bring up the statistical nature of replication followed by selection.

Organization and replication are far more common features in this universe than many people realize. These processes are “built in” because of the underlying rules of quantum mechanics at the atomic and molecular level and by quantum-like rules (eigenstates) that often apply to emergent phenomena at the classical level. Certainly most physicists are not “overwhelmed” by the idea of a “first replicator” of biological systems. There is nothing in the laws of physics that “forbids” such a thing. It is just a matter of time before we stumble onto it, and it may turn out to be more obvious than we thought once we find it (or them).

And the laws of thermodynamics will still be true.

Nick,

Well done and much appreciated. It’s oftentimes difficult to stay up on the latest in OOL research, so I always appreciate it when someone summarizes where we’re at.

One question though. You stated:

Each of these areas has developed into a subfield which has experienced major research discoveries in recent years. For example, on the origin of the genetic code, this paper assembles dozens of indicators on the order in which amino acids were added, step-by-step, to the genetic code and shows that the evidence strongly supports a fairly specific scenario (which shares many similarities with early, more speculative scenarios built on the basis of just a few lines of evidence).

When you said, “this paper…” what paper were you referring to? If there’s supposed to be a link embeded there, I would really like to have it so I could keep it in my own personal library.

Thanks.

I have posted this OOL outline various places;

Here is all that Darwin had to say about the origin of life in his Origin of Species.

“ I believe that animals are descended from at most only four or five progenitors, and plants from an equal or lessor number.

Analogy would lead me one step farther, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide. Nevertheless all living things have much in common, in their chemical composition, their cellular structure, their laws of growth, and their liability to injurious influences. … Therefore, on the principle of natural selection with the divergence of character, it does not seem incredible that, from some such low and intermediate form, both animals and plants may have been developed; and, if we admit this, we must likewise admit that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy, and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants.”

And, from the book’s last sentence;

“There is grander in this point of view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one ; .…”

So I note that Darwin was consistent in his opinion that there were few first life forms, and merely a possibly that there could have been only one. Also note that Darwin is little interested in the issue using well under one page of text from a 450 page book.

From the 6th edition, http://www.literature.org/authors/darwin-charles/

Charles R. Darwin, in a letter to the botanist Joseph Hooker (1871) wrote, “It is often said that all the conditions for the first production of a living organism are present, which could ever have been present. But if (and Oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed. “

Later in the same letter, he observed,

“It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter.”

The theory of evolution is an explanation of the diversity and distributions of life forms, not the initial origin of life. This is an active area of research called “abiogenesis,” “astrobiology,” or simply origin of life (OOL). It is obviously part of the larger scientific project to understand the universe, but is not fundamental to evolutionary theory.

“The Emergence of Life on Earth: A Historical and Scientific Overview” by Iris Fry, (2000 Rutgers University Press), is still the best general reader book available on the topic. A second edition is warrented to bring her presentation up to date.

There are quite a list of specifics that go into origin of life research, and very few research groups go far with more than a few. Just to list the key areas as I see them:

1) Composition of the Hadean/early Archean atmosphere.

The key references here are:

Feng Tian, Owen B. Toon, Alexander A. Pavlov, and H. De Sterck 2005 “Hydrogen-Rich Early Earth Atmosphere” Science 13 May 2005; 308: 1014-1017; published online 7 April

Genda, Hidenori & Abe, Yutaka 2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical aspects” Icarus 164, 149-162 (2003).

Holland, Heinrich D. 1984 The Chemical Evolution of the Atmoshphere and Oceans, Princeton Series in Geochemistry Princeton University Press

Holland, Heinrich D. 1999 “When did the Earth’s atmosphere become oxic? A Reply.” The Geochemical News #100: 20-22 (see Ohmoto 1997 )

Kasting, J. F., J. L. Siefert, 2002 “Life and the Evolution of Earth’s Atmosphere” Science 296:1066

Pepin, R. O. 1997 “Evolution of Earth’s Noble Gases: Consequences of Assuming Hydrodynamic Loss Driven by Giant Impact” Icarus 126, 148-156 (1997).

There are others, but anyone reading those above will get the basics. The result is that there was a reducing atmosphere, and ocean system with highly reducing oases. A recent paper:

Rosing, Minik T. and Robert Frei 2003 U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis” Earth and Planetary Science Letters, online 6 December 03

presents data that suggest there were very early oxygenic life forms in marine basins that most likely (to me anyway) were wiped out.

So, with a reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, “cold” sun, we can ask the next question which is,

2) What was the source for “organic” molecules?

The classic paper was of course Stanley Miller’s 1953 paper

Miller, Stanley L., 1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions” Science vol. 117:528-529

With a bit more information included in:

Miller, Stanley, Harold C. Urey 1959 “Organic Compound Synthesis on the Primitive Earth” Science vol 139 Num 3370: 254-251

Miller showed that a very simple set up that mimicked some key asspects of the early Earth could rapidly produce amino acids, among other things.

This result has been one of the most often repeated (and confirmed) experiments I have ever encountered. In spite of this, creationists regularly claim that it is invalid. Jonathan Wells, a fellow of the creationist “Discovery Institute” claims to have refuted the Miller/Urey experiment (and all of what he called Darwinist “icons.” Wells himself has been exposed as a very shallow thinker.

But, the atmosphere is not the only synthesis location. For example

Amend, J. P. , E. L. Shock 1998 “Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems” Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans 2001 “Experimental shock chemistry of aqueous amino acid solutions and the cometary delivery of prebiotic compounds” Origins of Life and Evolution of the Biosphere 31(1-2):15-51, Feb-Apr

Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan 1990 “Cometary Delivery of Organic Molecules to the Early Earth” Science Vol. 249:366-373

Engel, Michael H., Bartholomew Nagy, 1982 “Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite”, Nature , 296, April 29, , p. 838.

Matthews CN. 1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br. Interplanet Soc. 45(1):43-8

Schoonen, Martin A. A., Yong Xu 2001 “Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the Prebiotic Synthesis of C-H-O-N Compounds” Astrobiology 1:133-142

So amino acids are easy and plentiful on a pre-life (abiotic) Earth.

But, we need more than just amino acids- sugars, nucleic acids, and lipids are also needed. I’ll take those next.

Let’s see.. I guess this is

2a) amino acids 2.b) sugars

Why do we need sugars? Well, the biggest reason is that without five carbon sugar our building life form can’t make a “memory” like RNA or DNA. I’ll get to the details later. First, where are the sugars?

Weber AL. 1997 Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. Origins of Life and Evolution of the Biosphere 28: 259-270.

{I know the title says “amino acid” but sugar is in there. Hint: formose is a kind of sugar. }

Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel 2001 Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth Nature 414, 879 - 883 (20 Dec 2001) Letters to Nature

Cody, George D., Nabil Z. Boctor, Timothy R. Filley, Robert M. Hazen, James H. Scott, Anurag Sharma, Hatten S. Yoder Jr. 2000 “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate” Science v.289 : 1337-1340

Sephton, Mark A. 2001 Meteoritics: Life’s sweet beginnings? Nature 414, 857 - 858 (20 Dec ) News and Views

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. 2004 “Borate Minerals Stabilize Ribose” Science January 9; 303: 196 (in Brevia)

Stanley Miller, and collegues suggested an earlier substitute for sugar in :

Lazcano, Antonio, Stanley L. Miller 1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time” Cell vol 85:793-798

Nelson, K. E., M. Levy, S. L. Miller 2000 “Peptide nucleic acids rather than RNA may have been the first genetic molecule” PNAS-USA v.97, 3868-3871

There are many more articles, but the bottom line reads “We got sugar.”

OK, I’ll do nucleic acid bases next. There aren’t many that are used on Earth, just four.

There are a large number of creationist’s books and web sites that claim there is some huge stability problem with nucleic acid base synthesis. This is a nice demonstration of how creationists copy eachother, since there are only a handfull of creationists with the education to even understand what this means. None that I know of have actually done research in the directly relevant area. Their claims generally can be traced back to a legit scientist, Robert Shapiro. Two of his representitive publications are:

Shapiro, Robert 1986 “Origins: A Skeptics Guide to the Creation of Life on Earth” New York: Summit Books

Shapiro, Robert 1999 Prebiotic Cytosine Synthesis: A Critical Analysis and Implications for the Origin of Life. Proceedings of the National Academy of Science 96 (8): 4396 *Side reactions make cytosine synthesis unlikely, but see Nelson et al (2001)

The 1986 book is very out of date, and very popular with creationists.

The 1999 Shapiro paper has also been answered. Levy and Miller raise a question of their own in:

Levy, M and Miller, S.L., 1998 The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38,

But, like superior scientists, they answer the questions they raise.

The following are a selections of research articles that address the pre-biotic origin of nucleic acid bases:

For our fans following along at home, there are aspects of nucleoside synthesis in the earlier referenced papers as well.

So, we got plenty of nucleic acid bases.

2c) lipids.

Lipids are the stuff of membranes, they are what keeps inside in, and outside out. Today they are made by simple cells and moved up the food chain. So where did they come from 3.7 billion years (or so) ago?

One probable source seems to be from meteors.

Deamer, D. W. 1985. Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792-794.

Deamer, D. W., and Pashley, R. M. 1989. Amphiphilic components of carbonaceous meteorites. Orig. Life Evol. Biosphere 19:21-33.

Krishnamurthy, R., Pitsch, S. & Arrhenius, G. 1999 Mineral induced formation of pentose-2,4-bisphosphates. Origins Life Evol. Biosph. 29, 139-152 ().

Dworkin, Jason P., David W. Deamer, Scott A. Sandford, and Louis J. Allamandola 2001 “Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices” PNAS 98: 815-819

Pizzarello, Sandra, Yongsong Huang, Luann Becker, Robert J. Poreda, Ronald A. Nieman, George Cooper, Michael Williams 2001 “The Organic Content of the Tagish Lake Meteorite” Science, Vol. 293, Issue 5538, 2236-2239, September 21, 2001

Segre’ D., Ben-Eli D. Deamer D. and Lancet D. 2001 “The Lipid World” Origins Life Evol. Biosphere 31, 119-145.

So now that we got ‘em, what do they do once they are on Earth?

They make things.

Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak 2003 Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division Science October 24; 302: 618-622. (in Reports)

D.W. Deamer 1997 “The First Living Systems - A Bioenergetic Perspective”, ; Microbiology and Molecular Biology Reviews, 61(2): 239; June

Chakrabarti, A.C., R.R. Breaker, G.F. Joyce, & D.W. Deamer 1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 ( December)

Khvorova A, Kwak YG, Tamkun M, Majerfeld I, Yarus M. 1999. RNAs that bind and change the permeability of phospholipid membranes. Proceedings of the National Academy of the Sciences USA 96:10649-10654.

Yarus M. 1999. Boundaries for an RNA world. Current Opinion in Chemical Biology 3:260-267.

Walter P, Keenan R, Scmitz U. 2000. SRP-Where the RNA and membrane worlds meet. Science 287:1212-1213.

So far, we have amino acids, riobose and/or other 5 carbon sugar substitutes (pentoses), we have lipid membranes which encapsulate mineral particles and “organic” molecules. This is without any needed “interventions” and is purely the result of ordinary chemistry.

But, there are more things that need to happen before there is life on Earth.

Point 3) formation of complex systems

3a) Chirility

Pastuer discovered that most amino acids came in two forms which can be identified by how they refract light. We label theses L- (for levo or left) adn D- (for dextro, or right). The interesting thing is that life on Earth uses the L form of amino acids, and hardly ever uses the D- form. A solution of just one form is called “chiral” and a mix of forms about 50/50 is called racimic. The kinds (L or D) are called enantomers.

The nucleic acid bases I mentioned earlier are also found in L- and D- forms, only in this case life on Earth only uses the D- form.

Creationists like to present this as a profound mystery that is supposed to “prove” that they are correct. I want to mention a neat instance where both left and right amino acids are used in a living thing. It is very rare, but it does happen. Next time a creationist claims to be an “expert” and that amino acid chirility “proves” something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an “adult beverage” that all proteins are exclucive L- amino acids.

Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called “racimization” becuse eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attatched to one another, or better yet, if they are also attatched to a mineral, racimization can be very slow. Very, very slow.

This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form. The advantage comes from a surprising direction: outer space.

Cronin, J. R. & Pizzarello, S., 1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances in Space Research 23(2): 293-299.

Service, RF, 1999. Does life’s handedness come from within? Science 286: 1282-1283.

Antonio Chrysostomou, T. M. Gledhill,1 François Ménard, J. H. Hough, Motohide Tamura and Jeremy Bailey 2000 “Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1” Monthly Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February

Michael H. Engel and Bartholomew Nagy, 1982 “Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite”, Nature , 296, April 29, , p. 838.

Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart Clark, François Ménard, and Motohide Tamura 1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular Homochirality Science 1998 July 31; 281: 672-674. (in Reports)

Chyba, Christopher F. 1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997)

Engel, M. H., S. A. Macko 1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature

That should do for that. The next question is can the advantage of L- amino acids be conserved in the formation of more complex molecules called “peptides?” Yep.

Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross-inhibition in the synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K, Ghadiri MR, 2001”A chiroselective peptide replicator”, Nature 409: 797-51, Feb

Singleton, D A,& Vo, L K, 2002 “Enantioselective Synthsis without Discrete Optically Active Additives” J. Am. Chem. Soc. 124, 10010-10011

Yao Shao, Ghosh I, Zutshi R, Chmielewski J. 1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature. Dec 3;396(6710):447-50.

And there seems to be other L- selction advantages as well. For example:

Hazen, R.M., T.R. Filley, and G.A. Goodfriend. 2001. Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proceedings of the National Academy of Sciences 98(May 8):5487.

So chirility doesn’t seem to be a big problem. This is far different from the way creationists present this. They cite a few out of date reports and then falsely claim that chiral life is impossible by natural means.

But what about the nucleic acid bases? A new paper has just laid out the next step:

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. 2004 “Borate Minerals Stabilize Ribose” Science January 9; 303: 196 (in Brevia)

Pizzarello, Sandra, Arthur L. Weber 2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661: 1151, 20 February 2004

It turns out that the selective advatage of L- amino acids will force the selection of D- nucleic acids, and the whole reaction can proceed under common, natural conditions. And a final note is that the origin of life was most certainly not chiral. We have two very strong pieces of evidence for this. The first is that life is not chiral even today! You will be able to win several drinks at the next conference you attend by betting with most biologists that life is not chiral. The give them the example of Gramacidin A, a racemic transmembrane peptide. And then hit them with the large number of racemases that are used to generate D aa. For example; Zhengyu Feng and Raúl G. Barletta 2003 “Roles of Mycobacterium smegmatis D-Alanine:D-Alanine Ligase and D-Alanine Racemase in the Mechanisms of Action of and Resistance to the Peptidoglycan Inhibitor D-Cycloserine” Antimicrobial Agents and Chemotherapy, January 2003, p. 283-291, Vol. 47, No. 1

Well, we have all the pieces. Our planet was formed from massive collisions of planetoids that had undergone independent evolution and weathering which retained much of their atmospheres to add to the growing planet Earth. We have amino acids, sugars, nucleic acid bases, lipids and minerals under an anoxic to reducing atmosphere and ocean with a thin hot crust and a UV rich cold Sun. Plus, remember that the Moon is closer and orbiting faster producing massive tidal flows compared to modern times.

Will these combine to make any thing?

Yep, they sure will:

Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis of long prebiotic oligomers on mineral surfaces [see comments] Nature, 381, 59-61.

Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR. 1996 “A self-replicating peptide.” Nature Aug 8;382(6591):525-8

A.C. Chakrabarti, R.R. Breaker, G.F. Joyce, & D.W. Deamer 1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 (1994 December)

Smith, J.V. Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars Proceedings of the National Academy of Sciences of the United States of America 95(7): 3370-3375; March 31, 1998

Smith, J.V., Arnold, F.P., Parsons, I., Lee, M.R. Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal- hemical modeling, formation of first cells, and geological clues Proceedings of the National Academy of Sciences of the United States of America 96(7): 3479-3485; March 30, 1999

Blochl, Elisabeth, Martin Keller, Gunter Wächtershäuser , Karl Otto Stetter 1992 “Reactions depending on iron sulfide and linking geochemistry with biochemistry” PNAS-USA v.89: 8117-8120

Dyall, Sabrina D., Patricia J. Johnson 2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.” Current Opinion in Microbiology 3:404-411

Huber, Claudia, Gunter Wächtershäuser 1998 “Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life” Science v.281: 670-672

Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K. 1999 “Elongation of oligopeptides in a simulated submarine hydrothermal system“ Science 283(5403):831–833.

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, 1997 Emergence of symbiosis in peptide self- replication through a hypercyclic network. Nature, 390: 591-4

Trifonov (2004) confirmed two ideas, that the earliest amino acids were the easiest to form abiotically, that codons and aa’s organized contemporaniously to form short ogliomers (what he didn’t cite was the notion that oligomers can form spontaniously, are “selected” merely by being stable, and that RNAs (or Lacanzo and Miller’s PNAs) imprint and replicate “successful” short peptides.) “The amino-acid chronology itself is a quintessence of natural simplicity and opportunism: use first those amino acids that are available. When done with all codons, take from those amino acids that have too many.”

The fact that there are a growing list of short proteins with D- aa’s, (most of the ones I know of are bacterial membrane components but there are also examples from yeasts to humans). That most bacteria have evolved enzymes that convert L-aa’s to D-aa’s for the same Miller/prebiotic amino acids.

Argument: 1) ancient first cells were using L- and D- aa’s because they were readily available, 2) biological and biochemical events reduced the availability of D- aa’s, 3) bacteria evolved racemases to maintain/sustain their existing metabolic pathways. Ergo: The chirality “problem” in OOL isn’t a problem.

Trifonov, Edward N. 2004 “The Triplet Code From First Principles” Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1,

JasonF, the above Trifonov 2004 paper is a likely candidate for the one Nick was referring to. There is much more at Trifonov’s site:

There are some truly important facts concerning the Origin of Life that many biologists ignore completely. I read a ridiculous statement by a biologist that said “We obviously have difficulty understanding biology because we cannot even understand something simple like physics!”

This statement clearly demonstrated that the person making it was totally clueless as to the nature of matter itself, and the complexities of understanding it.

Similarly ridiculous statements are constantly appearing in biological literature about how modern developments in atomic and molecular physics do not obtain to biology because biological molecules are too large for these developments to apply!

We have on one hand the Creationists claiming that a Magician God pulls living organisms out of a divine hat, and on the other claims that molecules that are being treated in biological papers with 19th century chemical understanding with an equal degree of magic, by accident fall together. The magic word “Darwin” is constantly muttered to have rocks begin evolving into aardvarks and zebras with the same piety as the Creationists calling upon a Magician God!

We know a lot about how mutations occur that can make genetic code produce errors. We (if we be honest about it) know little about how series of mutations can occur to produce dramatically different genetic information that does something dramatically different than the code that was changed! Almost always all of the intermediate forms would have no survival value at all, and dramatically many changes are required for any meaningful change.

Unless science be careful, it risks becoming a religious faith in itself. Science must not use Darwin as an incantation! Science is NOT religious faith, and creating the Darwin incantation is doing just that! It is only once step away from lighting candles and incense.

Darwin was just one scientist among many - he just happened to put things together a few years or decades before those ideas would have become obvious to most biologists anyway.

Henry

Robert Pavlis said:

Almost always all of the intermediate forms would have no survival value at all, and dramatically many changes are required for any meaningful change.

Again we see the problem of the dated creationist playbook. The Lenski study, much talked about here, demonstrated that the many needed genetic changes need not contribute survival value. That argument is as dead as Darwin.

Robert Pavlis said:

We (if we be honest about it) know little about how series of mutations can occur to produce dramatically different genetic information that does something dramatically different than the code that was changed!

Actually we know quite a bit about it. Every time a gene duplicates it adds information to the genome. Of course, the Beheian knee-jerk response is that it is not impressive enough, or dramatic enough, but “impressedness” and “dramaticness” are not scientifically useful terms. They serve only to allow the creationists to weasel away from any and all evidence that contradicts their position.

Robert Pavlis babbled:

We have on one hand the Creationists claiming that a Magician God pulls living organisms out of a divine hat, and on the other claims that molecules that are being treated in biological papers with 19th century chemical understanding with an equal degree of magic, by accident fall together. The magic word “Darwin” is constantly muttered to have rocks begin evolving into aardvarks and zebras with the same piety as the Creationists calling upon a Magician God!

Please provide us with a specific quote of an actual scientist who claims that aardvarks and zebras evolved from rocks due to accidental falling together and magic, or stop making a babbling idiot of yourself.

Hi Gary,

I’m going to spend the next few months studying origin of life research. According to you, things have changed a lot in the last 6 years or so, and I’m going to need some time to evaluate all of the latest articles against the materials I currently own/have access to (almost all of which indicate a neutral early atmosphere e.g. J. Schopf’s 2002 “Life’s Origin”). Maybe I’ll post some more then, if this site is still active. If not, then take care.

Jeff

Jeff L said: e.g. J. Schopf’s 2002 “Life’s Origin”).

Personally, I think that Iris Fry, 2000 “The Emergence of Life on Earth: A Historical and Scientific Overview” Rutgers University Press

is still the best single text available. She needs to write a second edition.

Hi Nick, you may remember me as the guy who submitted corrections and additions to the “evolution of the immune system” bibliography a few months back.

I’ve been reading a lot on OOL issues lately, so I thought this might be a good place to data-dump reviews of various books.

Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life

One has to admire Yockey for his early recognition that information theory had a lot to say about biology, but he is a bit of an oddball. He accepts that, after the first cell, evolution is the only reasonable explanation for the origin of all known species. At the same time, he is a semi-creationist in that he believes that the first life was too complex to arise naturally and therefore must have been created by God, though in this book he only argues that the origin of life is fundamentally unknowable.

In the same way, this book is a bit of an oddball. It contains good historical surveys e.g. of the deciphering of the genetic code. But it also contains whopping errors like “any substance composed of only one optical isomer must have come from life”. Even Pasteur knew better than that, and in fact Yockey describes the very experiment where Pasteur manually selected synthetic tartrate crystals by shape to get pure optically active isomers.

Yockey is highly competent with math and statistics, but sometimes blunders in assumptions. His analysis of whether the genetic code could have evolved (chapter 7) assumes that it must always have coded for all the amino acids that it does today, which gives a very high improbability. But current theories lean towards the idea that it originally coded for only a few amino acids, perhaps even only glycine, leading to a very different result. On the other hand, I found his analysis suggesting that Lysine was added to the genetic code later than Arginine quite penetrating. (Our Most Assiduous Reader will have noted that these 2 analyses contradict each other.) He is also quite clear and precise in demonstrating that gene duplications do add information.

Chapters 8-11 cover OOL. Yockey is skeptical in his review of existing theories, particularly shredding Haeckel’s Urschleim and the entire class of “protein first” theories. While I think some of his conclusions are questionable, they are all carefully argued and cannot be dismissed lightly. For example, he uses the mathematical impossibility of distinguishing truly random sequences from sequences produced by sufficiently-highly-organized deterministic mechanisms to argue that we will never be able to prove that the origin of life was NOT directed by something, so that, while he expects that a plausible purely mechanistic explanation can be constructed, we will never know whether it is correct or not. It took me a while to see that this only holds if the Director is trying very hard to imitate pure randomness.

In chapter 12 he quickly disposes of Intelligent Design (spending e.g. less than a page on Behe). “… once life has appeared, Shannon’s Channel Capacity Theorem … assures us that genetic messages will not fade away and can indeed survive for 3.85 billion years without assistance from an Intelligent Designer.”

In summary, a good book with a lot of technical meat, but one which needs to be read carefully because of occasional errors.

Tibor Ganti, The Principles of Life

Ganti attempts to construct a minimum chemical model of what can be considered alive, called a chemoton. It is somewhat abstract, but can be (and has been) fleshed out into a more detailed model. Basically, it consists of 3 interlocking chemical cycles: one for basic metabolism, one for building cell membrane, and one for replicating the information-carrying (“genetic”) component that directs the whole process. These are linked stoichiometrically, so that all components of the system are doubled in the same time period.

The strength of this model is that, like life, it is chemical. It is more concerned with what chemical reactions are happening than it is with how these are guided; catalysis is seen mainly a matter of speeding things up. A weakness is that it is somewhat vague about how the “genes” control anything.

There is a lot of good OOL material in here, including a section on abiotic formation of loop-RNA (such as tRNA structures). Highly recommended.

Manfred Eigen, Steps Towards Life

I didn’t find Steps Towards Life nearly as useful as Eigen’s scientific publications (e.g. on the Hypercycle). It’s aimed at too general an audience, and rarely gives pointers for further reading. Some sections are worth reading, particularly the explanation of quasispecies. But I think he overvalues his own contributions (e.g. spending a long time on hypercycles without even mentioning Ganti’s chemotons), which leaves the book feeling a bit narrow-minded.

Eigen and Winkler, Laws of the Game: How the Principles of nature Govern Chance

Laws of the Game is a different beast entirely, a wide-ranging philosophical speculation covering random cellular automata, games, music, and many other topics. Most of it is not really applicable to OOL.

Werner Loewenstein, The Touchstone of Life

A general coverage of information in biology. A few parts are relevant to OOL and evolution, but it suffers from the drawback of most purely informational approaches, which is that it fails to deal with the issue of metabolism.

Freeman Dyson, Origins of Life 2nd Ed.

Dyson boldly takes the opposite tack, by assuming that protein-based metabolizers must have come first, and that informational replicators like RNA must have been later obligatory parasites on them.

The original contribution of this book is a toy model of metabolism which is simple enough to be directly solved. In the solution, a functioning metabolism appears through a kind of “phase transition” from a non-functioning one. Dyson has to make a lot of simplifying assumption to get to his model, so it’s unclear how realistic it is, but some of the assumptions could be removed at the cost of more computational work. I think the key message to take away is that complex dynamic systems can make transitions to qualitatively different states, but that there may be constraints on their size or structure for that to happen. For example, in Dyson’s model the number of monomer types is ideally 8-10; fewer than that and the organized state doesn’t exist, more than that and the probability of getting to it becomes too low.

Miklos Farkas, Dynamical Models in Biology

Section 4.3 talks about OOL models, mainly Eigen’s Hypercycle.

Hermann Haken, Information and Self-Organization

A heavily mathematical book centered on analyzing complex systems and their properties. I don’t think I can summarize, but topics include “Self-Creation of Meaning”, “Fokker-Planck Equation”, “The Maximum Information Principle”, “Landau Theory of Phase Transitions”, “The Slaving Principle”, “The S-Theorem of Klimontovich”, and these are applied to problems such as convection instability, lasers, pattern recognition in the presence of noise, and the psychology of hand movements. There isn’t much direct OOL analysis, but a lot of this math is applicable to the general idea of spontaneous increase of information or organization in OOL or evolution.

John Avery, Information Theory and Evolution

This clear little book delivers a nice overview of its topic. I particularly admire chapter 4, “Statistical Mechanics and Information”, which is the best explanation of the connection between information and thermodynamics I have ever seen. For example he shows that temperature has dimension energy/bit:

1 degree K = 0.95697*10^-23 joule/bit

gives a graph of the entropy of ammonia (NH3) in bits per molecule, and so on. Anyone who is confused about information and entropy should read this chapter (and Tom Schneider’s online primer) to get straightened out.

John Maynard Smith and Eors Szathmary, The Major Transitions in Evolution and The Origins of Life

These are essentially the same book. Major Transitions was earlier and more technical; Origins is later and contains new material, but is aimed at a broader audience. There is also a 1-hour lecture by Maynard Smith (on YouTube as 6 10-minute chunks) that covers some of the same topics.

The basic idea is that there were certain points in the history of life where the rules of the game changed. These are the major transitions, such as origin of replicators or the beginning of the genetic code or the first multicellular organisms. After each of them, many things become possible which were not possible before.

For the genetic code, Szathmary realized that in an RNA world, it would be really useful for a ribozyme to grab onto an amino acid and use it as a coenzyme. Proteins are much more effective at catalysis than is RNA. So he hypothesizes that RNAs learned how to hold aminos acids first, and only later began hooking them together in specific ways. While this is still sketchy, it does give a plausible pathway from an RNA world to a primitive genetic code, and it has some support from the structures of tRNAs and ribosomes.

Anyway, I’d recommend either book for a big-picture overview of critical problems in evolutionary theory.

One curious thing is that many of the transitions involve cooperation. Merging of individual genes into chromosomes; combining of chromosomes into cells; multicellularity; endosymbiosis; in each case, things that were previously reproducing and evolving (and competing) separately switched over to reproducing and evolving as a group. This will come as a shock to those who view evolution as always being a brutal, dog-eat-dog process. Often, the “fittest” is the one best able to cooperate and form healthy productive alliances. Just ask any honeybee.

Torbjörn Larsson,

“- You can, in principle, have a perfect replicator without variation, so no selection within the population. (Selection between different types of populations, of course.) “

But that doesn’t fit the definition. Which was:

“Brian Macker’s Definition Of Life: A lifeform is anything that evolves by decent with modification within it’s natural environment, or any other suitable environment. “

Your example has no decent with modification.

harold said:

Thus viruses are life, computer viruses are life, etc. Doesn’t matter if it has a metabolism or not. Doesn’t matter if it’s a producer, a saprophyte, a virus, or a symbiote. So what if the non-scientist doesn’t get it. It’s a scientific definition.

I thought the link was very good but I don’t agree with this one part.

Actually, this is a purely semantic definition, and not a scientific one at all.

How so? I don’t think your following statements support this view and therefore see it as a mere assertion.

There’s really no need for a universal scientific definition of “life”.

Not sure that makes sense in a discussion of abiogenisis, or biology. If you want to make universal statements (that’s part of what science is about) then how are you going to do that without universal definitions? If your definition of life is wishy-washy then it just isn’t going to cut it at the boundaries.

Some things are clearly alive, others are clearly not, but the boundary between the states is not necessarily clearly defined.

I guess by this you mean that the boundary is not sharp. However that is the case with most definitions even in science. What is a human? How far back does the definition go? What is a crystal? What’s the smallest collection that can be called a crystal?

“The author wants to include biological viruses as “life”, and so, makes up an excessively broad definition of life, in order to be sure that biological viruses are included.

Actually I don’t “desire” it, however if they fit the definition then they are in fact alive. Turns out that I know of no existing virus that fits the definition. Doesn’t mean that one couldn’t be developed however.

He ends up at the absurd conclusion that the type of software code referred to, purely by analogy, as “computer viruses”, is “alive”.

Those types of virus are indeed merely analogous because they don’t, in fact, fit the definition. There is no “modification with decent”. The have no natural capacity to generate variation.

That does not however mean that computer viruses couldn’t develop that would reach the standard, in which case they would be lifeforms.

Think more like Dawkins in “The Extended Phenotype” and you will get my drift. Beaver dams are in reality part of the beavers phenotype. People think of fingernails as part of living things but they certainly don’t think of beaver dams as such. In this regard they are actually wrong, and thinking them wrong is scientifically useful.

Sure the boundary is going to be fuzzy no matter where you draw it but I think we draw it too closely to ourselves. We are bigots in that regard. If decent with modification operates within a population that something is a member of then it is a lifeform in relation to it’s own environment. The human environment is not the only perspective.

I said “I know of no existing virus” meaning computer virus only.

Jeff L said: {clipped} I’m going to need some time to evaluate all of the latest articles against the materials I currently own/have access to (almost all of which indicate a neutral early atmosphere e.g. J. Schopf’s 2002 “Life’s Origin”). Maybe I’ll post some more then, if this site is still active. If not, then take care.

Jeff

I took a few hours to read “Life’s Origin” edited by J. William Schopf. There are only a few of the contributed chapters that even mention the early atmosphere/oceans, and only two with serious discussions. None of the authors “indicate a neutral early atmosphere” as is claimed by Jeff L. in his earlier post. They most they would say is that the issue is “still controversial.” Further, only one contributer is a geologist (Schopf) the rest being biochemists. None of the authors had ever contributed to the primary literature on the Hadean/Archean redox of the earth. And, as much as I liked this book, there was not even references to the major articles on Hadean/Archean redox published since the early 1990s.

This last observation is both the appeal and weakness of this book; The appeal is that all of the contributers are the senior most scientists of a particular (hetrotrophic) OOL model; Or‘o, Miller, Lazcano, Ferris, Orgel, Schopf and the rest have been close associates for over 40 years. Their interests and perspecives are quite fixed. They are (were) the living experts (and largely the originators) of their school of thought, and its best presenters. The weakness is that competing proposals are given short shrift, and the resources are somewhat dated. For example, the references used by Schwartz and Chang for Hadean/Archean redox are from the 1980s except for a single book of reviews published in 2000. This was the most thorough of the discussions in “Life’s Origin.”

Gary said:

I took a few hours to read “Life’s Origin” edited by J. William Schopf. There are only a few of the contributed chapters that even mention the early atmosphere/oceans, and only two with serious discussions. None of the authors “indicate a neutral early atmosphere” as is claimed by Jeff L. in his earlier post. They most they would say is that the issue is “still controversial.”

Reply:

Ammonia, methane, hydrogen, and water were the four components in Miller’s reducing atmosphere. Ammonia and methane break down in sunlight (particularly in the strong UV of the early sun). No plausible source of ammonia to replenish it in the early atmosphere is known, and it is unclear whether outgassing could generate enough methane to overcome photodecomposition (Schopf 2002, 66-67). Hydrogen escapes from Earth’s gravitational field. The exact rate may be debatable, but it seems clear that hydrogen was not anywhere near as abundant on the early Earth as in Miller’s reducing atmosphere, which required at least a 1 to 1 ratio of hydrogen to carbon for satisfactory results. It is also suggested on 66 that the moon-creating impact may have blown away any early hydrogen rich (from the solar nebula) atmosphere.

“[C]arbon dioxide seems certainly to have been the dominant carbon-containing gas released by volcanism and hydrothermal activity on the ancient planet” They go on to say that carbon monoxide and carbon dioxide are the dominant gases produced in vaporization of impacts and geologic processes. Also on 67, “In contrast with this picture of a carbon-dioxide rich atmosphere, most scenarios for chemical evolution call for a highly reducing atmosphere.”

In other words, the “picture” formed by available evidence is that the early atmosphere, post moon-forming impact, was most likely neutral, containing water (from outgassing and impacts), carbon dioxide (eruptions and impacts), nitrogen (outgassing), small amounts of methane (solar, outgassing, limited by UV), small amounts of H2, trace amounts of ammonia (limited by UV, no plausible source), and other trace gases.

On page 90, “[A]tmospheric scientists tend to favor neutral (nonreducing) compositions, whereas specialists in prebiotic chemistry favor a more reducing makeup…

In other words, scientific consensus of atmospheric experts leans towards neutral, unless you specialize in the origin of life, in which case you hope and assume the atmosphere was more reducing. My textbooks and other various articles all led me to believe that most geologists, geochemists, and atmospheric scientists feel the evidence, uncertain as it is, weighs in on a neutral atmosphere (this being through the 90’s into early 2000’s). This consensus is what led researchers over the past few decades to begin serious study of hydrothermal vents and extraterrestrial origins of life. If there wasn’t any problem with the old picture of a reducing atmosphere, these other venues would have no need of exploration. By the way, I’ve read a few of the articles you’ve posted about, and so far the only one that actually discusses Earth’s early prebiotic atmosphere is the NASA article. But I am going to continue reading.

Jeff

Gary,

A quick look at a recent perspective article in Science magazine (“Rethinking Earth’s Early Atmosphere”, page 962, May 13, 2005) confirms exactly what I am saying. For the last few decades, the consensus has been a neutral atmosphere. Notice:

“However, by the 1960s, the validity of hydrogen-rich (and hence reducing) model atmospheres for early Earth, such as the CH4- NH3 atmosphere used by Miller and Urey, was under attack (3). Since the 1970s, carbon dioxide (CO2)–rich atmospheres have been favored (4)”

or

“Now a 30-year, albeit shaky, consensus on the nature of the early atmosphere may have to be reexamined…”

So, the consensus has been a carbon dioxide-rich atmosphere. Now, as you have pointed out, this is being challenged. Which is why I said I need to read up on the latest articles. How could you have missed the consensus (“albeit shaky”) of the last thirty years?

Anyways, we seem to largely talk past each other, each seeing things in articles that are apparently invisible to the other. Which is why I haven’t engaged in online discussions in years. You, a far better qualified scientist compared to me (a high school teacher), argue and argue with me about what I had known and read and taught for years. How can we have a valuable discussion when you deny a well-known (I thought, anyways) trend in science?

Jeff L, I don’t know if we are talking past each other or not. I presented the data (in the form of references) for a reducing atmosphere in the Hadean and early Archean, or minimally a “an early neutral to reducing atmosphere, with highly reduced oases.” These are the conditions I have been consistently presenting (see my comment from the 17th of July).

I have already observed that the articles in “Life’s Origin” edited by J. William Schopf (2002) are largely from organic chemists. They have only referenced older, secondary literature on the early redox state of the earth. Many of these early papers assume that the atmosphere was the result of mantle out-gassing. This assumption had been shown to be wrong.

So, the point is not that there had been a “shaky consensus,” but that the consensus was wrong. If you want to read about how the consensus was achieved and its strongest presentation, I recommend

Holland, Heinrich D. 1984 “The Chemical Evolution of the Atmosphere and Oceans,” Princeton Series in Geochemistry Princeton University Press.

This is a very good introduction for anyone with adequate chemistry and geology background. It was the most cited reference I saw for a decade following its publication. However, always bear in mind while reading it that a mildly oxic atmosphere and hydrosphere in the early Archean was a wrong idea. There is no better literary evidence for this than Holland’s argument against an early oxic environment presented in 1999 “When did the Earth’s atmosphere become oxic? A Reply.” The Geochemical News 100: 20-22 (see Ohmoto 1997, “When Did the Earth’s Atmosphere Become Oxic?” The Geochemical News, 93: 12-13, 26-27.)

There is much better physical evidence, and this is what I have been trying to present. I have hardly “missed the consensus” but it was wrong. What can be stated clearly and confidently is that at the relevant time period, the earth had neutral to reducing atmosphere, with highly reduced oases. I am persuaded by the data available that the earth’s atmosphere and hydrosphere were reduced with possible neutral oases, rather like the opposite of today.

Your selective reading of Chyba (2005 “Rethinking Earth’s Early Atmosphere” Science 13 May 2005 308: 962-963) is unfortunate. He was commenting on the article by Tian et al (2005 “A Hydrogen-Rich Early Earth Atmosphere” Science 13 May; 308: 1014-1017), and took no position for or against their result. As such it was not germane to the discussion. I have already suggested that you read Tian et al, and the critical reply by David Catling (2006 “Comment on ‘‘A Hydrogen-Rich Early Earth Atmosphere’’ SCIENCE VOL 311 pg. 38a) as well as the response.

Regarding ammonia, NH3, in the early atmosphere I recommended an earlier paper by Sagan and Chyba, 1997 “The Early Faint Sun Paradox: Organic Shielding of Ultraviolet-Labile Greenhouse Gases” (Science v. 276 (5316): 1217-1221) and the perspective by James Kasting, “Planetary Atmospheres: Warming Early Earth and Mars” pp. 1213 – 1215. I would also point you to JAY A. BRANDES, NABIL Z. BOCTOR, GEORGE D. CODY, BENJAMIN A. COOPER, ROBERT M. HAZEN & HATTEN S. YODER JR 1998 “Abiotic nitrogen reduction on the early Earth” Nature 395, 365 – 367.

Much of the confusion over the early redox state was from dating and analytical errors from the 1960s and ‘70s. It also was thought that life originated much later than we currently know it to have been. There is direct evidence for oxygenic photosynthesis as early as 3.7 Ga, in two papers, T. Minik Rosing, 1999 “13C-Depleated Carbon Microparticles in >3700-Ma Sea-Floor Sedimentary rocks from West Greenland.” Science 283 (5402): 674, and Minik T. Rosing, and Robert Frei (2004) U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis” Earth and Planetary Science Letters, 217: 237-244. Further, these papers give a compelling argument for a complex surface and submarine geology with segregated oxic and reduced components in which life already florished.

Let’s take a wider perspective. Too much of the discussion of the physical conditions of the early earth makes an unwarranted assumption of global uniformity. Ozone everywhere or nowhere, either highly reduced or oxic oceans everywhere if anywhere. There is aquatic life in hot hypersaline lagoons, boiling or cold alkaline to acidic, or organically starved alpine waters. There is also life in freeze dried rock, and the hottest deserts. Even today there are highly reduced, neutral, and oxic environments. And there is life in all of them. The earliest planetary organic chemistry we know of was reduced. The earliest forms of biochemistry we know of are reducing.

I belatedly noticed that Nick had asked for specific comment about the Giant Impact and the formation of the earth moon system. I wrote a short article on creationism and the origin of the earth/moon system a few years ago, “Oard’s Moonbeam”

The physical data to test various models is mostly from analysis of the noble gas isotopes found in marine basalts. This is a large literature. I am swayed by two arguments found in;

Genda, Hidenori & Abe, Yutaka 2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical aspects”, Icarus 164, 149-162 (2003).

Gerasimov, M. V., Yu. P. Dikov, F. Wlotzka 1998 “Is There An Alternative For The Huge Impact-Generated Atmosphere?”, abstract from Origin of the Earth and Moon Conference, Monterey, Dec.

that the earth’s atmosphere, and eventually the hydrosphere, were the product of the moon forming impact, and then augmented with later infall of volatile rich comets. Hydrodynamic escape arguments by R. O. Pepin;

1991 “On the origin and early evolution of terrestrial planet atmospheres and meteoritic volatiles” Icarus 92, 2-79 1997 Evolution of Earth’s Noble Gases: Consequences of Assuming Hydrodynamic Loss Driven by Giant Impact Icarus 126, 148-156 (1997).

require the assumption that the bulk of the earth’s atmosphere was from mantle outgassing which does not appear to be the case.

Life intervened, but finally returning to old threads FWIW:

Howard A. Landman said:

While this is still sketchy, it does give a plausible pathway from an RNA world to a primitive genetic code, and it has some support from the structures of tRNAs and ribosomes.

Interesting. I just saw some papers such as this, that suggest that the phylogeny of tRNA split genomes (and their coding) in some Archaea is best explained by a combination of two genes, one binding to AA and one to DNA.

Brian Macker said:

Your example has no decent with modification.

Exactly; I wasn’t discussing observations that was consistent with a definition of what is currently observed, but possible observations of what could happen.

As an example of how fast the abiogenesis literature is growing, here are two articles from the Aug 15, 2008 issue of Science that are both of interest.

The first is on the late Archean redox state of the oceans:

Donald E. Canfield, Simon W. Poulton, Andrew H. Knoll, Guy M. Narbonne, Gerry Ross, Tatiana Goldberg, and Harald Strauss 2008 “Ferruginous Conditions Dominated Later Neoproterozoic Deep-Water Chemistry” Science 15 August 2008: 949-952.

“Low sulfur input caused the deeper ocean to become anoxic and rich in ferrous iron 750 million years ago, a reversal from the more oxidizing conditions of the previous 1 billion years.”

Now this might not seem related to OOL research, but it is an intersting set of observations about the stratification of the oceans which will lead to better measurement of the deep ocean redox and sulfur/iron economies. This is of great significance to OOL.

The other article is;

T. R. Kulp, S. E. Hoeft, M. Asao, M. T. Madigan, J. T. Hollibaugh, J. C. Fisher, J. F. Stolz, C. W. Culbertson, L. G. Miller, and R. S. Oremland 2008 “Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California” Science 15 August 2008: 967-970.

“A primitive form of photosynthesis in which arsenic is the electron donor occurs in purple bacteria in a California lake, perhaps a relic of early life forms.”

This is of more direct OOL interest, suggesting a new anoxic metabolism pathway.

I’m a creationist and sceptical of abiogenesis. I’ve read the four lines of evidence carefully, here’s my response.

As usual it abounds both in confidence for a complex life out of a messy organic gunge and a prescribed dose of ad hominem scorn for creationists, but not much to persuade a sceptic.

I summaries the four incontrovertible lines of ‘evidence’ for abiogenesis.

1 A shared suite of protein and RNA genes, a DNA-RNA-protein system and a mostly standard genetic code

Hardly an earth shattering confirmation of evolution, essentially it reiterates homology arguments - it’s no proof of ancestry, especially given the nature of distribution of the aa differences in proteins and base differences in DNA between species.

2 The last common ancestor (LCA) must have been simpler, because, for example, of a hexamer composed of two similar proteins with sequence similarity. Therefore the precursor must have had a hexameric complex with identical units. Evidence for this huge leap of speculative reasoning please!

Let me offer a mirror argument for a moment to show how dangerous this leap can be.

Myoglobin and haemoglobin are structural support molecules for haem an iron complex that allows light and reversible binding with oxygen. According to Stryer a standard text their complex 3 D structural is extremely similar. Therefore the two must come from a common ancestor. WRONG! They have almost completely different amino acid sequences (from memory of 146 aas less than 10 are the same in the same site) so it’s exceedingly unlikely, they evolved similar tertiary structure s via a common ancestor gene.

Their function dictates their configuration not a putative common ontogeny.

3 Lots of interesting RNA research demonstrates RNA must have been how early life began.

Two simple questions then, one where did the ribose come from - sugars are notoriously difficult to synthesise and to my knowledge early earth (Urey Miller) conditions have never come close to creating them. Two, one example of an RNA self replicator please? All example I know of parasitise other organisms’ DNA.

4 Water, planets, amino acids in locally reducing circumstances, and phosphate polymers abound and we’re working on nucleic acid precursors (but not ribose) so it’s not all so impossible.

The last is hardly worthy of much comment - so how far do these take you out of a messy organic gunge toward a self replicating and repairing nano-device, Nick? Still sounds more like wishful thinking than hard science to me.

Charles says:

I’m a creationist and sceptical of abiogenesis. I’ve read the four lines of evidence carefully, here’s my response.

Obviously, Charles, you understand the biology in some reasonable depth, which is good. I’m really tired of trying to talk to people like Jobby who neither have, nor will bother to get, a clue about how the machine works.

But I’m curious; how you reconcile your belief that life was created (intelligently, I assume) with the obvious lack of any visible design artifacts?

It seems fairly obvious that entire groups of modern animals were adapted from a couple of master plans. For instance, humans, bats, giraffes, and whales seem to have the same basic bone structure.

Why did the creator build bat wings and whale flippers by modifying fingers, rather than just, well, designing wings?

The eponymous “Panda’s Thumb” isn’t a thumb. It’s a modified palm bone, pressed into service as a grasping tool (the bone that forms our thumb is used elsewhere).

Why didn’t the creator just make a thumb? After all, he did it for primates and rodents?

It seems that imagining a designer who doesn’t seem to actually design anything and just makes it look like stuff evolved in long line of subtle changes is vastly more problematic than imagining it actually, well, did so.

stevaroni, thanks, although I’m not doing research nowadays, so I don’t regard myself as being at the coalface any longer.

I don’t think it’s for me to justify the pentadactyl plan or other examples of homology, although I agree it’s intriguing - but the very fact you don’t see design features when faced with a system of bewildering complexity and interdependence reveals a basic presuppositional problem. One frankly I shared till my late teens and wrestled over hard at med school.

Let me put it this way, if you saw intricate self replicating machines made from materials you’d never met before - would you safely assume they had self assembled? Why then do natural machines blind us to the statistically negligible possibility of their random arrangement by the incredibly crude process of abiogenesis.

Let me put another question to you, why do evolutionists so blythely assume that virtually identical structures evolved convergently - when they don’t fit in with their supposed descent? (The invertebrate eye being the classic example.) Doesn’t that suggest a paradigm problem to you?

charles said:

Let me put another question to you, why do evolutionists so blythely assume that virtually identical structures evolved convergently - when they don’t fit in with their supposed descent? (The invertebrate eye being the classic example.) Doesn’t that suggest a paradigm problem to you?

If the structures are identical in two or more different species, then, according to evolutionary biology, it is strongly assumed that the structure in question was present in the latest ancestor. If the structures are not identical in two or more different species, then it is apparent that each lineage developed their own version of the structure. So, no this does not suggest a paradigm problem to us.

On the other hand, Intelligent Design proponents, such as yourself, evade all questions about the logic of why an Intelligent Designer would make so many extremely different versions of particular structures, be they eyes, fins, wings, flagella, or anything else, rather than use a standardized form for each structure.

Furthermore, please explain why you think that the eye of decapod cephalopods is identical to the eye of vertebrates, even though the nerves and blood vessels of the decapod cephalopod eye enter from the outside, and whose retina can not detach, while the nerves and blood vessels of the vertebrate eye enters from one location from the inside, thereby causing a blind spot, as well as making the retina vulnerable to detachment?

Also, please explain why you think that the compound eye of arthropods are identical to both the decapod cephalopod and vertebrate eyes.

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This page contains a single entry by Nick Matzke published on July 3, 2008 12:22 AM.

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