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.
233 Comments
RBH · 3 July 2008
Yeah, yeah, that's all well and good, but what's her name??
Nick (Matzke) · 3 July 2008
LOL that's the most hilarious PT comment ever.
Jeffrey Shallit · 3 July 2008
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.
Opisthokont · 3 July 2008
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.
Mike Haubrich, FCD · 3 July 2008
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.
Frank J · 3 July 2008
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.
Frank J · 3 July 2008
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.
TR Gregory · 3 July 2008
Joshuabgood · 3 July 2008
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.
TR Gregory · 3 July 2008
Jeffrey Shallit · 3 July 2008
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.
Sylvilagus · 3 July 2008
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.
Flint · 3 July 2008
chuck · 3 July 2008
Nick (Matzke) · 3 July 2008
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.
Flint · 3 July 2008
harold · 3 July 2008
iml8 · 3 July 2008
Paul Burnett · 3 July 2008
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.Flint · 3 July 2008
Tailspin · 3 July 2008
Sure love to see a tight version of this as an oped piece in the New York Times
RBH · 3 July 2008
Frank J · 3 July 2008
Mike · 3 July 2008
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.
Richard Simons · 3 July 2008
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.
Mike Elzinga · 3 July 2008
Jason F. · 3 July 2008
Gary Hurd · 3 July 2008
Gary Hurd · 3 July 2008
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,
JohnK · 3 July 2008
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:
Ryan Cunningham · 3 July 2008
You should be VERY careful about asserting things as fact that are still being researched. If we make discoveries later that invalidate something stated above, creationists are going to have a field day. It's better to own up to our uncertainty in the beginning.
The point that we've made interesting inroads on this problem is well made, though.
iml8 · 3 July 2008
Gary Hurd · 3 July 2008
Mike Elzinga · 3 July 2008
Henry J · 3 July 2008
Flint · 3 July 2008
Henry J · 3 July 2008
iml8 · 3 July 2008
Reed · 3 July 2008
I think one reason the "evolution doesn't explain OOL" argument is so often made is that creationists like to say "You can't explain OOL, therefore everything evolution claims follows is false or at least suspect"
This is of course is fallacious, and pointing out the problems is worthwhile.
The point of the argument is that regardless of the parts of OOL that we don't understand, we know that from a first cell or first replicator, we can get everything else: e. coli, cats, you, me. The process works regardless of how we got to the starting point. If God poofed the first cell into existence, or a passing alien sneezed in the primordial ocean, it doesn't invalidate the rest of the evolutionary process. Since what the creationists are (generally) arguing about is that the complexity and diversity of life can't be explained by evolution, this is an important point. The creationists generally haven't been driven back to the OOL gap (i.e. claiming God poofed the first cell and evolution did the rest), they are just using OOL as a red herring. Rather than go into the (extremely interesting) details of OOL research, it may be more productive to just point out the red herring.
It might be better to say that the validity of evolutionary theory doesn't depend on any particular OOL. That doesn't mean we don't know or care about OOL, or that OOL isn't deeply intertwined with evolution. On the contrary, your excellent essay shows that it is an exciting, productive area of research and clearly involves evolutionary processes. And FWIW, that part of your essay was a really enjoyable and fascinating read.
Torbjörn Larsson, OM · 3 July 2008
Torbjörn Larsson, OM · 3 July 2008
Torbjörn Larsson, OM · 3 July 2008
Mike Elzinga · 3 July 2008
Paul Burnett · 3 July 2008
Mike Elzinga · 3 July 2008
Gary Hurd · 3 July 2008
Gary Hurd · 3 July 2008
Holy Cowabunga, Torbjörn Larsson!
Your link to: "D-Amino Acids: A New Frontier in Amino Acid and Protein Research - Practical Methods and Protocols"
is great. That would have wiped my project. There is no second place in science (only administration).
afarensis, FCD · 3 July 2008
Since others have responded to the OOL portion, I would like to respond to the part about Darwin and the complexity of the cell. Darwin was actually a first rate microscopist with a talent for slide preparation, see here for example, and he used the microscope in a lot of his work. A number of his pictures in his book on insectivorous plants and in some of his papers, indicates that he was aware that there is more to the cell than a blob of protoplasm (see here for some pictures). I agree with Nick, this would make an excellent research project for someone.
John Kwok · 3 July 2008
AnswersInGenitals · 3 July 2008
Whenever a creationist or ID proponent insists that our not knowing exactly how and when life began invalidates the theory of evolution, I totally agree with them and then point out that our lack of knowledge of exactly when and by whom several books of the bible were written totally invalidates the entire bible.
They usually think about this for a few moments, and then run around their houses tearing all their bibles to shreds and then spend all their free time on atheist blogs.
Frank J · 3 July 2008
iml8 · 3 July 2008
Shebardigan · 3 July 2008
Henry J · 3 July 2008
Henry J · 3 July 2008
Paul Burnett · 4 July 2008
iml8 · 4 July 2008
Dan · 4 July 2008
Torbjörn Larsson, OM · 4 July 2008
Frank B · 4 July 2008
Fundamentalists have problems with everyone who is not a fundamentalist, and so fundamentalists think it their duty to give them problems. Creationists are fundamentalists with a particular hobby. Would you blame a gay person for being combative with a fundamentalist? Would you blame a person in a common law marriage who stands up for his/herself. Fundamentalists not only choose to be anti-science, they go out of their way to make problems.
Judge Jones and others have been surprised at the reaction they have received from fundamentalists. We don't blame Jews for battling Nazism, don't blame scientists for battling Fundies.
Rolf · 4 July 2008
bigbang · 4 July 2008
Mike Elzinga asks: “Can God make two adjacent black holes so gravitationally intense that he can’t hold them apart?”
.
The more relevant question is can God create a singularity having the inexplicably low entropy that the singularity, from which our universe evolved, had----unlike the singularities that are black holes and that have enormously high entropy.
Of course the infinite, eternal multiverse resolves this problem, where not only are all universes possible, including ours, they’re inevitable.
harold · 4 July 2008
harold · 4 July 2008
I could google this, but here's an OOL question...
A critical difference between individual between replicators and a cell is that a cell is surrounded by a continuous lipid membrane, and can regulate the intracellular environment relative to the extracellular environment. This is true of both prokaryotes and eukaryotes.
Does anyone have anything to say about how the membrane could have originated? I'm not talking about how lipids got to earth or the fact that detergents form mycelles, but how it happened the replicators got consistently associated with a unique membrane per replicator set.
Bigbang, I already know your answer is "it was done by magic by the designer"; I'm looking for something more satisfying.
harold · 4 July 2008
Timothy Sandefur has another "no comments allowed" post.
And it consists of an approving link to the well-known and controversial right wing site "little green footballs". http://en.wikipedia.org/wiki/Little_Green_Footballs
The piece in question is pro-science, but has little to add.
Sandefur could have written an intelligent post on the fact that some right wingers support science, if that's his point, and opened it up to immediate and uncensored feedback. That's what a person with a shred of intellectual honesty or courage would do.
Instead, he embarrasses PT by putting up a juvenile, adulatory link to a right wing hate site, a link with NO READER COMMENTS ALLOWED.
Do you see the difference between that and open discussion? It should be obvious to anyone that this creates the outrageous implication that PT, or biologists in general, endorse or approve of "little green footballs".
Political extremists of many stripes don't deny evolution, and can put a boilerplate "support of science" post from time to time. Will PT be including links with reader comments disallowed to all political sites that do so? Or is it fair to say that when someone has deliberately made themselves known as a controversial political extremist, links to their sites should be qualified, and reader feedback should be not merely allowed, but encouraged?
I put Sandefur in the same league as Mark Hausam. Simply accepting part of scientific reality is not enough. Sandefur clearly craves expressing some type of offensive views, but doesn't dare to do it openly, nor to allow feedback.
Sandefur's "contributions" to this site are ludicrous and 100% negative. All he does is show up once every few months and make a creepy attempt to sneak barely relevent far right political content on, with comments disallowed.
He is very clearly exploiting some sort of personal relationship in an attempt to trick PT into seeming to endorse his extremist political views.
Any honest person of any political persuasion should be disgusted by this.
At this point, I feel that it is silly for Sandefur to be allowed to contribute. If his nepotistic connections are so strong that he cannot be gotten rid of, at least make him allow free, immediate, honest feedback and deal with it.
And let's not forget the details. For extra creepiness, this was snuck in on the Fourth of July, under cover of darkness, so to speak. To bad for Sandefur that I'm working on a project at my computer this weekend. Also, to the best of my knowledge, LGF is itself a comment restricted site
Seriously, enough is enough.
iml8 · 4 July 2008
tomh · 4 July 2008
Henry J · 4 July 2008
iml8 · 4 July 2008
Torbjörn Larsson, OM · 4 July 2008
OT, but speaking of creationists:
Catching up on my reading I note that Swedish Engineers magazine features an article on US creationism. (They are interested in science and education, and why it can go bad - and of course anything that decreases other nations competitiveness.)
The Chris Comer/Barbara Forrest case is described and it's connection to Bush, Joshua Rosenau and NCSE get to tell the story on US and Texas education (and Florida and the brother Bush connection), and NAS third book on creationism Science, Evolution, and Creationism is mentioned. No creationist gets to tell "the controversy" and Josh gets final comment. Refreshing!
Torbjörn Larsson, OM · 4 July 2008
Torbjörn Larsson, OM · 4 July 2008
Sorry about the running sentence - but so am I. Dance night. Ta!
harold · 4 July 2008
harold · 4 July 2008
TL and Frank J -
Thanks for the comments and links on membrane origin.
For now I will just comment that the membrane is exactly as important as replication or translation for the origin of life. Without the membrane, a unique set of replicating/translating molecules would have no obvious way of being associated within physical boundaries, or modifying conditions within their immediate environment.
One could say that it is the membrane which is precious close to whatever makes something "alive". Naked nucleic acids can replicate with ease in a test tube, but to be part of an "organism", a unique and relatively complete set of them must be enclosed in a membrane.
iml8 · 4 July 2008
tomh · 4 July 2008
Karl Lembke · 4 July 2008
Little Green Footballs restricts commenting to registered users. Registration is closed some 99% of the time. It is thrown open for an hour or two at a time, and closed again after a hundred or so new members have signed up. The new members are then observed to see what sort of comments they leave. (For some reason, the site attracts people who want Israel destroyed, and accuse anyone who doesn't similarly hate Israel of being in the pocket of the Grand Zionist Conspiracy. He still sometimes refers to examples of hate mail he receives.)
That more controversial posts routinely get hundreds of comments, and that a hundred new members will register during the brief unannounced times when new members are accepted tells me this sort of gate-keeping is not just a paranoid affectation.
Gary Hurd · 4 July 2008
Re membranes
Did I forget to post:
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)
Martin, W., and M.J. Russell.
2003 "On the origin of cells: A hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" Philosophical Transactions of the Royal Society B 358(Jan. 29):59-85.
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
Deamer, D. W., and Barchfeld, G. L.
1982 "Encapsulation of macromolecules by lipid vesicles under simulated prebiotic conditions" J. Mol. Evol. 18:203-206.
And then I would list a dozen articles with Deamer as co-author. I have not read these recently, but they should give a good start to the literature.
My ideas reduced to the bare minimum are:
Phospholipids a la Deamer form vesicles, crashing waves mechanically replicate many trillions of vesicles a day with pores derived from short (less than 20 aa), racemic polymers made from Miller aa's, which encapsulate minerals which act as catalysts, racemic PNA (mediated/augmented by iron sulfides, calcite and montmorillonite), replacement of PNA by RNA then DNA.
Crash waves onto hot rocks and there is concentration by evaporation plus additional energy inputs and incorporation of minerals. Natural selection is at first merely durability. Pore formation facilitates vesicle durability as easily as changing internal water pressure (see Gramicidin A), but energy production from proton harvesting might be possible. Later developments include "stealing" genes by "eating" other vesicles or "harvesting" them when gene containing vesicles are broken mechanically, or chemically (this is a variant of Wose's "lateral transfer" and leads to Lynn Margulis' endosymbiosis). Slight advantages of large molecules which are more easily formed chirally, added to minor biases of L- aa's and D- sugars from extraterrestrial sources trend toward homochiral systems. Racemase enzymes evolve to maintain production of critical small peptides which continue to be racemic.
Hazen's "central mystery" now becomes a question of how minor advantages become dominant features which is after all merely Darwinian gradualism.
Ichthyic · 5 July 2008
The piece in question is pro-science, but has little to add.
actually, having read a couple hundred of the comments in that thread, the commenters don't add anything either.
It's like a bunch of random noise.
Of all the places Sandefur could have linked to on that day, I rather think he chose the one site that pretty much had the least interesting commentary.
The only thing of note was the link to Harun Yoyo. An old and well known link under the Circus Big-Top the creobots have created for themselves (dating back before the Kansas Kangaroo Kourt), and last I checked, the leader of that group (Adnan Oktar, who writes under the psuedonym Harun Yahya, and also calls his group that) had been sentenced to 3 years in prison for crimes (a veritable laundry list) dating back to 1999.
I've read back page newspaper articles with more journalistic interest.
btw, I recall hearing something about a challenge to Oktar's sentence, but never heard any followup.
Please tell me this lackwit is still behind bars?
D P Robin · 5 July 2008
Frank J · 5 July 2008
cmo · 5 July 2008
i think your just underestimating what god can do. how come he cant cause evolution, just because its not in the bible. there are many things we know to be true that weren't mentioned in the bible.
http://sensicology.wordpress.com/2008/07/03/what-a-surprise-fisheries-are-to-blame-4-fish-decline/
harold · 5 July 2008
harold · 5 July 2008
Gary Hurd -
Many thanks for expanding. That is exceptionally cool stuff.
Any model that could get a fairly unique set of replicating/translating molecules inside a membrane, such that they could get resources across the membrane in a sustainable way, and reproduce and then split themselves into two approximately equal sets, each with a membrane, would strike me as a very powerful model of how abiogenesis could have occurred.
Of course, we both seem to be assuming, and this is certainly correct for me, that viruses evolved from cells. Since there is no example of any virus that reproduces independently or can harvest any type of energy from the environment except through parasitic relationship with a cell, I think this is a fair assumption.
Gary Hurd · 5 July 2008
I think the current concensus is that viruses evolved from cells. Prions might be left overs. I don't know ...
trrll · 5 July 2008
Nick Gotts · 5 July 2008
Thanks very much Nick (and Gary Hurd for the list of OOL references) - I've saved the page and (as an interested non-biologist who often debates creationists) I'm sure will refer to it often in future.
Troy Britain · 5 July 2008
Harold said what I would have said, and probably much better.
I have also run into may a creationist who wants the OOL tied to evolution and who believe that if we don't have the OOL down pat then everything that follows is meaningless. Why play into their hand?
Do both. Point out that we are not completely in the dark and that we are making progress on the OOL, but also point out that whatever lack of knowledge and certainty we may still have about the OOL it has no effect whatsoever on our knowledge and certainty about the evolution of life after it originated by whatever means.
Anyone have three cents change for a nickle?
iml8 · 5 July 2008
Sharmuta · 5 July 2008
Hutch · 5 July 2008
Debate, outrage, indignation:
Beats the heck out of working.
harold · 5 July 2008
iml8 · 5 July 2008
Richard Simons · 5 July 2008
Rock the Casbah · 5 July 2008
tomh · 5 July 2008
Science Avenger · 6 July 2008
Atheist · 6 July 2008
Harold is correct. LGF censored me simply for arguing that Freshwater should not have been crucified.
All of which seems to prove Slack's point of arrogance, self-righteousness, and intolerance among anti-creationists, doesn't it?
As an atheist, I find all religious myths absurd. But then, I also find the term "rap music" just as absurd, an oxymoron. Self-righteous intolerance (verging upon hatred) is no more appropriate an approach to religion and creationism, than it is to rap music.
Rock the Casbah · 6 July 2008
harold · 6 July 2008
Rock the Casbah · 6 July 2008
Rock the Casbah · 6 July 2008
Sharmuta · 6 July 2008
Sharmuta · 6 July 2008
harold · 6 July 2008
Sharmuta · 6 July 2008
Gary Hurd · 6 July 2008
I think there is more graffitti for the bathroom wall.
harold · 6 July 2008
Sharmuta · 6 July 2008
Sharmuta · 6 July 2008
Science Avenger · 6 July 2008
Torbjörn Larsson, OM · 6 July 2008
Gary Hurd · 6 July 2008
Mike Elzinga · 6 July 2008
Gary Hurd · 6 July 2008
Torbjörn Larsson, OM · 6 July 2008
Sharmuta · 6 July 2008
Torbjörn Larsson, OM · 6 July 2008
Gary Hurd · 6 July 2008
Hazen is vastly taken with the chirality problem (his central mystery) because (I cynically suspect) he thinks the solution is found in the chiral binding to mineral surfaces, particularly calcite. This happens to be the focus of much of his reasearch:
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.
Calcite is obviously very important to OOL, as it is to life today. I think it was fitting and poetic that the last publication of Stanley Miller was,
Cleaves, H. James, John H. Chalmers, Antonio Lazcano, Stanley L. Miller, Jeffrey L. Bada
2008 “A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres” Orig Life Evol Biosph (2008) 38:105–115
For a generation, critics have belittled his key paper in 1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions” Science vol. 117:528-529. They attacked low yields, the reducing conditions, and the large percentage of carbon in "tars" These are all eliminated by the addition any of a few minerals including calcite.
Gary Hurd · 6 July 2008
harold · 6 July 2008
harold · 6 July 2008
Gary Hurd and Tobjorn -
You both put a lot of effort into communicating some very interesting stuff about OOL, and membranes in particular, and I really enjoyed that part of the thread and am still checking things out.
I also felt it was important to deal with some other issues at the same time. That's the internet for you. Thanks again for your contributions to the enjoyable part of the thread.
Sharmuta · 6 July 2008
Harold- so Panda's Thumb can engage in conduct such as "flushing comments" in order to uphold what they feel is the integrity of this site, but Charles Johnson at LGF can't?
My views at LGF are not protected- they stand up to criticisms by other members or they do not. It has become crystal clear to me you have no idea what you are talking about when it comes to LGF. I believe you have allowed your personal scientific views to become so politicized that you would refuse the assistance of some who agree with you scientifically simply because they disagree with you politically, and I think that's a detriment to science.
I won't respond to you again either, because I now feel uncomfortable discussing this highly off topic matter. It was not my intent to disrupt the conversation, only to set the record straight on LGF when other people were the ones who broached the subject.
Torbjörn Larsson, OM · 6 July 2008
Torbjörn Larsson, OM · 6 July 2008
harold · 6 July 2008
Gary Hurd · 6 July 2008
Here is the link to the Bathroom Wall. Go there.
It is not censorship. Some people like to hang out in bathrooms - even conservatives - even elected conservatives in airports, and consecrated conservatives on meth.
The Bathroom Wall isn't like that. You'll like it. Flame all you like. If harold wants to ratshit Tim, or Ed, I'll help.
Michael · 6 July 2008
Eric Finn · 6 July 2008
David Stanton · 6 July 2008
Micheal wrote:
"How does one explain why a non-thinking process would always evolve forward, and not lets say evolve backwards?"
One doesn't have to explain it because it isn't true. Lots of things "evolve backwards". Cetaceans returned to the sea after evolving from ancestors who had colonized the terrestrial environment. Humans lost the ability to synthesize vitamin C which had evolved in their ancestors. Ths list goes on and on. In fact, many creationists claim that this is all tha evolution can do.
A "miindless" process will evolve forms both more and less comkplex, depending on the selecticve constraints in the environment. What a "non-thinking proicess" cannot do is anticipate ways in which the environment will change and prepare for them. Of course, ther are no example of that, so evolutionary theory is sound.
harold · 6 July 2008
Stanton · 6 July 2008
Gary Hurd · 6 July 2008
Nigel D · 7 July 2008
Thanks, Nick, for providing much food for thought.
Yum!
Nigel D · 7 July 2008
Nigel D · 7 July 2008
Nick (Matzke) · 7 July 2008
Nick (Matzke) · 7 July 2008
Nick (Matzke) · 7 July 2008
Thanks for all your references and comments Gary!
Re: cleaning up thread -- I will try to get to that but not this morning.
Torbjörn Larsson, OM · 7 July 2008
Torbjörn Larsson, OM · 7 July 2008
Torbjörn Larsson, OM · 7 July 2008
Torbjörn Larsson, OM · 7 July 2008
Henry J · 7 July 2008
Larry Boy · 7 July 2008
Nigel D · 7 July 2008
harold · 7 July 2008
Larry Boy -
In fact, neoplasia in general essentially happens when a cell that was part of a multicellular organism evolves into what amounts to a population of unicellular parasites. The parasite population is then selected for at the expense of the host. However, typical neoplastic cells don't spread from host to host easily. (They sometimes do get to this, for example if they are injected into an immunodeficient mouse.)
The example you give could even suggest that some viruses evolved from this kind of entity - neoplastic cells of multicellular eukaryotes. The superficial similarity between the effects CTVT cells and human papillomaviruses is pretty striking.
Nigel D · 7 July 2008
Brian Macker · 8 July 2008
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.
Once you understand that an environment consists of all it's particulars, like other organisms and other chemicals then you will get it. Obviously something that evolves by decent with modification is a replicator in this definition.
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.
Then natural selection covers all these evolving things organic or not. It also covers the evolution that occurred before metabolisms were evolved. All the way back to when the first replicator(s) arose.
Abiogenisis then becomes about how the first replicator arose from non-replicators.
Nigel D · 8 July 2008
Brian, that's an interesting take, and one I have not seen before.
However, while it does shift the abiogenesis question back to the origin of the first replicators, it does not change the fact that there are many interesting questions to answer between first replicator and LCA (last common ancestor). As Nick has shown, the LCA was itself the result of evolutionary processes acting on the ancestors of the LCA.
However, I think that, as exciting as the research is, all concerned must acknowledge that it may never be possible to firmly elucidate the exact pathway from first replicator to LCA. The required evidence may no longer exist. Having said that, of course, I am sure that we all hope that it is possible. At the very least, we should eventually be in a position to propose a "most plausible" route from first replicator to LCA.
Matt · 8 July 2008
I think it's important that the details of other Scientific fields of research not be entirely glossed over here, heh. While no Earthlike planets have been found yet, it's not -entirely- due to the sensitivity of our instruments. We have, in fact, found planets -much- smaller than earth orbiting pulsars: http://blogs.discovermagazine.com/badastronomy/2008/04/10/no-its-not-the-smallest-exoplanet-found/
It's just a matter of time before we discover a planet very similar to Earth (and not one that masses 5 times as much, although 5 times is pretty good when you consider it's a rocky body whose radius is only 50% greater than our own!)
SteveG · 8 July 2008
Creationists are not dishonest liars (the ones that are - which is an awful lot of them because an attitude of dishonesty is pervasive in creationist attitudes) because they don't believe what they say when they say it. They are dishonest liars when they deliberately ignore the factual information you present to them showing them that some particular claim or argument they have made is wrong, and then they defiantly continue to promote their erroneous argument regardless of the facts. It is this deliberate, defiant refusal to correct their errors by which they demonstrate their fundamental dishonesty. Indeed, it is this very attitude of deliberately ignoring contrary information and defiantly promoting erroneous information that has made creationism what it is today. You don't have creationism (of the "scientific" creationism form) without this basic attitude of fundamental dishonesty.
Tom English · 8 July 2008
Nick,
I had wanted very much to know the current state of OOL research, and was having trouble finding a good source for someone like me. Thanks so much.
My view of evolution is abstract, and it seems to me that certain principles of evolution apply when you have discrete self-replicators in a bounded arena, and not before. That is, I doubt that the way to get a good model is to lump what happens before and after, no matter that you can apply the term "evolution" throughout.
Daniel Smith · 8 July 2008
My only question is "Why?"
Why did life first form?
What power continuously propelled life's precursors forward towards more organization and complexity?
And why?
GuyeFaux · 8 July 2008
Mike Elzinga · 8 July 2008
Science Avenger · 8 July 2008
harold · 8 July 2008
Stanton · 8 July 2008
Nigel D · 9 July 2008
Larry Boy · 9 July 2008
harold · 9 July 2008
Nigel D -
Very nice answer. I took the "why" questions to be philosophical, as in "was there any greater plan?" (which in itself is not offensive, at least to me), but was also quite suspicious that they barely disguised some insinuations, as my reply plainly shows.
There's always a lot of semantic debate about the handy but overly simplistic "science explains how but not why" formula. It's technically not true, given the general use of the word "why". Certainly we say that the earth's rotation is "why" the sun rises in the east.
Still, I tend to stick with the "how but not why" formulation, more or less, since science can answer "how" unambiguously, but ambiguity can be claimed if a straightforward natural explanation is given for a "why" question. The questioner can say they meant "why" in the sense of hidden purpose or meaning from some supernatural force. From the position of "theistic evolution" and like attitudes, which I personally don't hold but have no problem with, a physical explanation doesn't rule out a "deeper" explanation.
We'll see what this particular questioner meant if he returns and responds to the replies he got.
If he never responds, that is, sadly, weak evidence for the correctness of my suspicions.
Gary Hurd · 9 July 2008
Torbjörn Larsson, OM · 9 July 2008
Torbjörn Larsson, OM · 9 July 2008
harold · 9 July 2008
harold · 9 July 2008
Oops - I meant to say that real viruses have some features in common with cellular life.
Jim Harrison · 9 July 2008
The universe is pretty much dark and empty, and natural processes almost never produce anything complicated at all. If there was a creator who foresaw the consequences of the natural laws he ordained, it very much looks as if his intention was not to produce life or intelligence at all. Sentient beings are apparently a rare impurity that the divine chemist couldn't quite avoid as he devised natural processes. Why is there something rather than nothing? Nobody's perfect.
Mike Elzinga · 9 July 2008
CJO · 9 July 2008
Jim Harrison · 9 July 2008
Mike Elzinga · 9 July 2008
Dave Luckett · 9 July 2008
There is the old chestnut about the Philosophy Final exam that had only one question: "Why?"
Those who wrote "Because!" received a C.
Those who wrote "Why not?" received a B.
Those who wrote "Why, indeed?" received an A.
All others failed, except for one student who wrote, "Fish" and received the Dean's Award.
Torbjörn Larsson, OM · 10 July 2008
Torbjörn Larsson, OM · 10 July 2008
Torbjörn Larsson, OM · 10 July 2008
Stuart Weinstein · 10 July 2008
Stuart Weinstein · 10 July 2008
Jim Harrison · 11 July 2008
The most recent estimate I've seen suggests that the average density of the universe is about one hydrogen atom per cubic meter. Great news if you've got claustrophobia. Lotsa closet space.
The old metaphysics used to appeal to what was called the principle of plenitude. Life would be everywhere in the cosmos because of the infinite creativity of God. People seriously expected to find Mercurians on Mercury, Venusians on Venus, Martians on Mars, even Solarians on the sun. Now I myself would bet that life occurs on quite a few planets across the galaxy; but on the evidence, the universe as a whole seems more like what Pascal ("These infinite spaces frighten me.") or Democritus expected. Atoms and void, with a lot more void than atoms.
Stanton · 11 July 2008
Jim Harrison · 11 July 2008
So why do you think I'm a pessimist? I'm simply pointing out that conducting philosophy or theology on an inductive basis doesn't result in anything like traditional theism.
Stanton · 11 July 2008
Jim Harrison · 11 July 2008
And what is particularly "optimistic" about making false claims? Biological processes do mostly produce corpses or, to be more accurate, they don't usually get that far. The universe is mostly void. Or do you have information to the contrary?
Once again, I'm not sure why being matter-of-fact about matters of fact should be perceived as pessimistic. Let us have the courage to live cheerfully in the real world, which is, so far as I know, rather more the place I describe than the place you apparently imagine. Every human being, however humble or miserable, came up with the winning ticket in the lottery by virtue of simply getting born. Indeed, since the history of everybody's lineage is three or four billion years worth of hairbreadth escapes and lucky chances, let us celebrate our splendid improbability.
Stanton · 11 July 2008
Firri_Triah · 11 July 2008
Getting back to the original article . . . I personally feel that trying to explain the state of research into OOL to creationists is probably a waste of time. Despite the advances made, the clarity and solidity of the data describing OOL compared to that supporting standard evolutionary theory is very weak. Until a simple, self replicating cell is made completely artificially, the arguments over OOL will continue. And even then people will debate whether such a thing is possible in nature. We may never find (or at least be able to prove) the specific process by which life originally formed, because of course we don't even have the original life form(S) to work with.
Do scientists really want to spend their time defending RNA world and the origin of the genetic code, when we can't even get a fair number of people to accept the very basic, and extremely well demonstrated principles of evolution?
I don't see anything wrong with leaving OOL as something of a black box, since even the advances described in the article, which are intriguing and suggestive, are far from solid evidence and well described processes. Creationists are going to go after what they perceive as the weakest link and it seems like the debate should be kept, as much as possible, on the more solid ground of evolution and common descent.
Torbjörn Larsson, OM · 11 July 2008
Jim Harrison · 11 July 2008
I'm reminded of the common argument against atheism that it can't be true because it would be depressing.
I'm not interested in pessimism or optimism. I want to understand the nature of things and coming to understanding sometimes involves a change of perspective from the usual edifying take on the world. For example, one important fact about living things and their evolution is that an immense amount of waste is required to produce any yield at all. Indeed, just to maintain viability in the face of the inevitability of copying errors, a huge number of individuals have to eliminated in each generation and that's true even for long-lived, k-selected species like our own, at least in the haploid generation. There is simply no other way of getting around the xerox problem, i.e. the build up error in copies of copies of copies. That's just how things are.
Torbjörn Larsson, OM · 11 July 2008
Torbjörn Larsson, OM · 11 July 2008
Torbjörn Larsson, OM · 11 July 2008
Nigel D · 11 July 2008
Steviepinhead · 11 July 2008
Cheers, Nick, both for this article and your personal and professional developments!
Recognizing that this is a first draft of sorts ("fashion" ==> "fathom," etc.), I'm still going to link to it in several differnt ongoing discussions in several evolutionary fora, and will look forward with deep interest to such refined and reference-replete redrafts as you may find time to turn out.
This is really what I was hoping for when I spent good money for Hazen's Gen-e-sis, but instead got more of his personal ruminations and a rather haphazard (and overly author-centric) review of the "current" research: not just a review of where science stands, but what it means in the big OOL picture, and what's left to do, and who's working on it, and how are they doing (like, yesterday, not four years ago!), and -- most importantly for anti-creo, pro-science purposes -- how incredibly wrong they are, with the last delivered with truly crushing force!
I'm wondering if this shouldn't become its own "page" or something somewhere permanent on the Interwebs -- TO or the NCSE site? -- so that it can be kept as up to date as possible (if not by time-constrained Nick, then perhaps by a community of individuals who have good reason to follow relevant aspects of the literature)...
I'm not as interested in the specific pro- or anti-Slack aspects of things, though I'm appreciative that the squabble motivated Nick to produce this at a time when he HAD the time to do so.
In fact, it might make some sense to break this post into two separate posts: the where OOL REALLY stands part, and the "framing" part that deals more directly with the debate that instigated the OOL review.
Again, Nick, thanks! That's at least three fairly major coups the reality-based community owes ya (Dover, flagella, and OOL), and I've probably overlooked several others!
Steviepinhead · 11 July 2008
Now what the frick good is a message like that, when the comments box gives no line count?
Bah, frickin' bah!
--and here I had all kinds of nice things to say about Nick...
Steviepinhead · 11 July 2008
On top of which, the comment that had the "supposedly" (since I looked for it repeatedly, despite the lack of meaningful direction) mismatched tag got eaten...
Grrr!
Wes, c'mon! What's the point of this broken tag system anyway? Why not let the comment -- OR AT LEAST THE PREVIEW?!?! -- post up, so the commenter can SEE what worked and what didn't, and then give them an edit option?
Dumb and dumber.
Robin · 11 July 2008
Steviepinhead · 11 July 2008
Anyway (he said, more calmly, staying far, far away from any HTML tags)I have gone on to say admiring things about Nick's post today at such places as TalkRational and Internet Infidels.
That's at least three biggies the reality community owes to Nick, including Dover, flagella, and this very thought-provoking OOL post, which should certainly be developed into published form or some other form of "permanent" resource!
Jeff L · 16 July 2008
Gary Hurd's comments back on page one about "how much we know" about the OOL has at least one major error. I checked "Life and Evolution of Earth's atmosphere" in Science magazine, as it was supposed to support the idea of a reducing atmosphere on the early Earth. Turns out it only talks about how microorganisms could have contributed to a warm, reducing, atmosphere early in Earth's history. Obviously if we are interested in the origin of life we need to find sources of a reducing atmosphere that do not depend on life to create it. Oops.
Gary Hurd · 16 July 2008
Gary Hurd · 16 July 2008
No spelling flame?
Atheist · 17 July 2008
Atheist · 17 July 2008
Jeff L · 17 July 2008
Gary commented:
What do you suppose the conditions were before the evolution of oxygenic photosynthesis? As in before an oxygenated atmosphere? As in, "Can you say reduced? Sure you can." When you read the paper with a little bit more care, you will learn that Kasting and Siefert said the opposite of what you thought they said, and why I encluded it in my outline.
Actually I just reread the article, and it says nothing whatsoever about the atmosphere before the arrival of microorganisms. The entire paper is about how microorganisms have influenced Earth's atmosphere. At first microorganisms could have contributed significant amounts of methane, and later contributed oxygen. The paper very literally has nothing to do with the origin of life or the atmosphere before life arose. Most atmospheric scientists and geochemists think Earth's early atmosphere was neutral, not reducing. Just because an atmosphere has little to no oxygen does not necessarily entail a reducing atmosphere.
Jeff L · 17 July 2008
Don't know what happened there.
I'll repeat my comment.
Gary Hurd insists the article is somehow relevant to the OOL or the supposition of a reducing atmosphere that helped lead to the OOL.
Actually I just reread the article, and it only discusses the influence of microorganisms on Earth's atmosphere. Earlier the microorganisms could have contributed significant amounts of methane, and later contributed oxygen. The paper very literally has nothing to do with the OOL or the atmosphere before life arose. Most atmospheric scientists and geochemists feel that the Earth's early atmosphere was neutral, not reducing. Simply having little to no oxygen does not entail a reducing atmosphere.
H. H. · 17 July 2008
Gary Hurd · 17 July 2008
Jeff L · 17 July 2008
Gary Hurd said:
It is hardly a "supposition" that the Hadean and early Archean saw a chemically reducing environment. Rather, it is the considered result of many independent lines of evidence. The Kasting&Siefert article that seems to have you befuddled mentioned methanogenic as well as oxygenic bacteria. Is that the problem? The reason that they did was two fold; they are addressing the "weak sun / snowball Earth" question, and also the oxidation of the earth via the "Hydrogen escape after CH4 photolysis, therefore, causes a net gain of oxygen (Catling et al)" The direct measurement of this can be found in the mass-independent fractionation of sulfur (Farquhar et al).
Reply:
I was not "befuddled" by the article. I understand the snowball Earth question and the role methane is thought to have played in preventing it. I also understand perfectly well the various mechanisms thought to have contributed to the oxidation of Earth's atmosphere. All I disagreed with was your conclusion that because of the above therefore the pre-biotic Earth had a reducing atmosphere. There are plenty of modern sources that would argue for a neutral atmosphere. Is there some data I am unaware of that makes the current models of oxidation of the Earth's atmosphere incompatible with the early Earth's atmosphere being neutral?
Gary Hurd said:
I gave a number of references that demonstate an early neutral to reducing atmosphere, with highly reduced oases. I included one article out of many which showed that the oxidation of the earth was a late event, much later than to origin of life. I thought the implication was obvious.
Catling, David C., Kevin J. Zahnle, Christopher P. McKay
2001 “Biogenic Methane, Hydrogen Escape, and the Irreversible Oxidation of Early Earth” Science 293 (5531): 839
Reply:
It seems to me that these articles suggest that after life arose, organisms first helped make the Earth's atmosphere more reducing, and then hundreds of millions years later oxygenation somehow overtook reduction. Exactly why still eludes us, for in the words of Catling et al. "all current hypotheses are problematic." They go on to suggest a mechanism by which oxygenation occurred, but unless I missed it (a real possibility) they did not suggest why it took so long. I certainly understand your argument: a reducing atmosphere would take a long time to oxidize. If it were as simple as that, why did not Catling et al. simply say that? Why say "all current hypotheses are problematic"? Again, plenty of modern sources suggest the evidence points to a largely neutral atmosphere due to hydrogen escape (though the exact rate is arguable, as evidenced by the article you cited earlier and comments on the article) and volcanic outgassing. None of this specifically suggests to me that the early Earth's atmosphere was reducing to the degree needed for the late (I just found out) Stanley Miller's original experiments.
Gary Hurd said:
What is rather silly about your protest about my "supposition" of a reduced atmosphere is that the last paper co-authored by Stanley Miller rendered the question of the redox state of the earth vis-a-vis OOL irrelevant:
Reply:
Then why all the fuss to show that the early atmosphere was reducing! After reading the article, I have to say, while interesting, it hardly solves the problem of generating amino acids in a neutral atmosphere. A few problems: they sped up the process for the sake of convenience (understandable) but in nature the long exposure to water and further energy would simply degrade any amino acids formed. Also, the electric discharge used most likely has no analog in nature. Back in the original Miller experiment a "lightning type" charge was used, found to be a dead end and not investigated further. In addition they used, in their own words, "an unlikely prebiotic antioxidant" to facilitate production of amino acids. Sounds a little problematic to me. They then suggest sulfides or metal ions could play a similar role; other studies I have read (e.g. Cohn et al. 2004. RNA decomposition by pyrite-induced radicals and possible role of lipids during the formation of life. Earth and Planetary Science Letters, 271-278) suggest that the organic molecules themselves could be destroyed by at least some sulfides. In any case the experiment needs to be done using the sulfides and ions instead of ascorbic acid. Sorry if my quibbles sound petty, but I hear sweeping claims about the origin of life all the time, and when I look into them I am usually suprised by how little the studies actually move toward any final solution. I have no problem with small progress; I have problems with small or negligible progress being dressed up as some sort of final solution (e.g. "now the atmosphere doesn't even need to be reducing for life to have emerged!" and this after a rather modest, speculative paper that merely suggests a possible pathway to organic molecules in a neutral atmosphere but does not demonstrate it in plausible prebiotic conditions).
Jeff
Gary Hurd · 19 July 2008
Gary Hurd · 22 July 2008
Jeff L · 22 July 2008
Hi Gary,
I haven't left, I've just been busy. More comments soon (I know you can't wait).
Gary Hurd · 24 July 2008
Robert Pavlis · 26 July 2008
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.
Henry J · 26 July 2008
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
Science Avenger · 26 July 2008
Science Avenger · 26 July 2008
Stanton · 26 July 2008
Jeff L · 28 July 2008
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
Gary Hurd · 29 July 2008
Howard A. Landman · 2 August 2008
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.
Brian Macker · 2 August 2008
Brian Macker · 2 August 2008
Brian Macker · 2 August 2008
I said "I know of no existing virus" meaning computer virus only.
Gary Hurd · 3 August 2008
Jeff L · 3 August 2008
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
Jeff L · 3 August 2008
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?
Gary Hurd · 4 August 2008
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.
Gary Hurd · 7 August 2008
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.
Torbjörn Larsson, OM · 15 August 2008
Torbjörn Larsson, OM · 15 August 2008
Gary Hurd · 24 August 2008
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.
charles · 26 September 2008
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.
stevaroni · 26 September 2008
charles · 26 September 2008
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?
Stanton · 26 September 2008