Lynn Margulis: “Definitely a Darwinist”

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Various ID proponents have ‘argued’ that Margulis doubts ‘Darwinian theory’:

Dembski Wrote:

“And yet, Harold continued, ““But we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”

James Shapiro, Stuart Kauffman, and Lynn Margulis have raised similar doubts” Source Unintelligent Evolution

Let’s explore these arguments in more depth. Is Margulis anti-Darwinian, anti-Neo-Darwinian? And if lack of details is such a problem for a scientific theory then how come ID has no details to offer at all? What does this say about the nature of Intelligent Design?

It has been well documented how ID proponents quote people and papers as somehow supporting intelligent design or as evidence of people disagreeing with Darwinian theory. In case of Margulis however we find an unambiguous statement that she considers herself a Darwinist

Michod’s talk was the perfect lead-in for the penultimate lecture of the conference by the acknowledged star of the weekend, Lynn Margulis, famous for her pioneering research on symbiogenesis. Margulis began graciously by acknowledging the conference hosts and saying, “This is the most wonderful conference I’ve ever been to, and I’ve been to a lot of conferences.” She then got to work, pronouncing the death of neo-Darwinism. Echoing Darwin, she said “It was like confessing a murder when I discovered I was not a neo-Darwinist.” But, she quickly added, “I am definitely a Darwinist though. I think we are missing important information about the origins of variation. I differ from the neo-Darwinian bullies on this point.” She then outlined the basis of her theory of the origin of the cell nucleus as a fusion between archaebacteria (thermoplasma) and Eubacteria (Spirochaeta). “We live on a bacterial planet,” she reflected. “The cell is the fundamental unit of life. A minimal cell has DNA, mRNA, tRNA, rRNA, amino acylating enzymes, polymerases, sources of energy and electrons, lipoprotein membranes, and ion channels, all contained within a cell wall, and is an autopoietic (self-regulating feedback) system.” The biggest break in life, she explained, was between the prokaryotes (cells with nucleoids: monera, prokaryota; archaebacteria, eubacteria) and eukaryotes (cells with nuclei: protoctista, fungi, plantae, animalia).

In this framework, Margulis continued, all of life’s history can be divided into three major eons: Archean (3,500 to 2,500 million years ago), Proterozoic (2,500 to 540 mya), and Phanerozoic (540 to 0 mya). “Most evolutionary biologists deal with the Phanerozoic, which is like saying that history began in 1909 when the Ford Motor Company opened shop in Dearborn, Mich,” Margulis quipped. The major steps in evolution involved symbiogenesis, which Margulis described succinctly as “the inheritance of acquired genomes” and more formally in its relationship to symbiosis, “the long-term physical association between members of different types (species).” The problem with neo-Darwinism, Margulis concluded, is that “Random changes in DNA alone do not lead to speciation. Symbiogenesis–the appearance of new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction–is the major source of evolutionary novelty in eukaryotes–animals, plants, and fungi.”

There were no direct challenges to Margulis in the discussion period that followed, so I once again queried a number of the experts in this area after the lecture. The overall impression I received was that Margulis goes too far in her rejection of neo-Darwinism, but because she was right about the role of symbiogenesis in the origin of the first eukaryote cells, they are taking a wait-and-see approach. One scientist added that since Margulis was to receive an honorary doctorate that afternoon, it seemed inappropriate to challenge her in this venue.

Source: Michael Shermer, The Woodstock of evolution, Scientific American June 27, 2005

ID-C literature is full of such references

Dembski Wrote:

In fact, it would tell students more about Darwinian evolution than Darwinists typically want them to hear, notably about the theory’s problems and weaknesses (and we don’t even need to cite ourselves here; critics within evolutionary biology’s own ranks, like the late Stephen Jay Gould and now Lynn Margulis with her theory of symbiogenesis, have saved us the trouble).

Source: William Demsbki Becoming a Disciplined Science: Prospects, Pitfalls, and Reality Check for ID

It should have been a reality check indeed…

Dembski Wrote:

Right now, the basal biology textbooks from which most people in the English-speaking world receive their first serious exposure to evolutionary theory explain the origination of biological forms in terms of the neo-Darwinian mechanism of natural selection ad random genetic errors. This mechanism, however, is now increasingly seen as inadequate to explain the diversity of biological forms, and not just by design theorists. For instance, Lynn Margulis (2002, 103), a biologist who is a member of the National Academy of Sciences, criticizes the neo-Darwinian theory as follows: “Like a sugary snack that temporarily satisfies our appetite but deprives us of more nutritious foods, neo-Darwinism sates intellectual curiosity with abstractions bereft of actual details—whether metabolic, biochemical, ecological, or of natural history.”

Source: William Dembski In defense of intelligent design

Or see how the SciAm article is presented at ARN by Fernando Castro-Chavez

Barham presented the following testimony at the Topeka hearing on May 7, 2005.

It is interesting than recently an increasing number of scientists have been willing to abandon the false comfort of Darwinism and to begin the search for a more adequate metaphysical worldview. Here are some characteristic quotes. All of them are from reputable—in some cases, highly distinguished—scientists, none of whom has a religious axe to grind:

And continues to quote Lynn Margulis. Despite his claim of ‘false comfort of Darwinism’, Margulis considers herself a Darwinist. Quote Mining at its best or worst?

Margulis at Wikipedia describes Margulis’s perspective

“She is best known for her theory of symbiogenesis, which challenges a central tenet of neodarwinism. She argues that inherited variation, significant in evolution, does not come mainly from random mutations. Rather new tissues, organs, and even new species evolve primarily through the long-lasting intimacy of strangers. The fusion of genomes in symbioses followed by natural selection, she suggests, leads to increasingly complex levels of individuality.”

In other words: Variation and selection.

Margulis homepage

A review of Margulis can be found at the excellent site of Gert Korthof

Summary

* Lynn Margulis’ symbiosis theory is a proven theory in biology. * The claim in Acquiring Genomes that symbiosis is the main mechanism for creating new species in evolution is an unjustified extrapolation from a number of well-documented cases to all domains of life. * The claim that the accumulation of mutations do not lead to anything useful is refuted by the facts of molecular and evolutionary genetics. * Margulis unambiguously rejects creationism, despite her criticism of the fundamental neo-Darwinistic mechanisms, and her alternative theory is a fully naturalistic evolutionary theory.

Korthof provides us with a quote from Margulis which indicates that she is by no standard a supporter of Intelligent Design

“Anthropocentric writers with a proclivity for the miraculous and a commitment to divine intervention tend to attribute historical appearances like eyes, wings, and speech to “irreducible complexity” (as, for example, Michael Behe does in his book, Darwin’s Black Box) or “ingenious design” (in the tradition of William Paley who used the functional organs of animals as proof for the existence of God). Here we feel no need for supernatural hypotheses. Rather, we insist that today, more than ever, it is the growing scientific understanding of how new traits appear, ones even as complex as the vertebrate eye, that has triumphed. What is the news?” (quote from the book, page 202).

In Endosymbiosis, cell evolution, and speciation Kutschera et al argue that:

The currently popular book of Margulis and Sagan (2002), which is quoted by many anti-evolutionists around the world, delivers the basic message that genomic variation and natural selection are of subordinate importance in the process of speciation. This erroneous conclusion is not based on solid empirical evidence and it has provided cannon fodder to an anti-Darwinian ideology that has no place in modern science.

PS: AG Evolutionsbiologie im Verband deutscher Biologen is a German website focused on evolutionary theory with some excellent links to literature

It seems clear to me that Margulis is not Anti-Darwinian as she considers herself a Darwinist. She considers herself an anti-Neo-Darwinist but that position seems to be harder to support.

Margulis’s main objections seem to be that evolutionary theory is incomplete and focuses on the wrong aspects.

“What excites Margulis is the remarkable incompleteness of general Darwinian theory. Darwinism is wrong by what it omits and by what it incorrectly emphasizes. A number of microbiologists, geneticists, theoretical biologists, mathematicians, and computer scientists are saying there is more to life than Darwinism. They do not reject Darwin’s contribution; they simply want to move beyond it. I call them the ‘postdarwinians.’” (Kelly, Kevin [Executive Editor of Wired], “Out of Control: The New Biology of Machines,” [1994], Fourth Estate: London, 1995, reprint, pp470-471. Emphasis in original)

It’s not so much that Margulis doubts (neo-)Darwinian theory but rather believes that the source of variation is not provided solely by ‘random mutations’. In other words, Margulis’s comments are about failings of mechanisms not about the failings of the theory of evolution.

Concepts such as cooperation and competion need to be more carefully addressed and evolutionary science has come a long way in this area. Having recently watched “A beautiful Mind”, I would like to mention the work by John Nash.

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Fascinating, I’ve never heard of this symbiogenesis theory, but it seems plausible enough in the case of the nuclear envelope. From my perspective (molecular microbiology), it just seems like another, albeit important, case of lateral gene transfer. I don’t think it is such a challenge to “neo-Darwinism”, as we have known that LGT events occur for a long time, and nobody is trying to claim that they didn’t… However, the claim that symbiogenesis is “the major source of novelty” in Eukaryotes strikes me as extremely presumptuous. I can see bacteria being extremely conspicuous about donating DNA in various ways, but Eukaryotes don’t seem nearly as prolific about it. If that were the case, the available sequence data should indicate it relatively quickly and easily. More sequence availability and analysis will certainly address this concept soon. It should be noted however, that when someone challenges evolutionary dogma with actual data and reason, the establishment does listen. IDists, with their delusions of persecution, should take note of this.

Symbiogenesis—the appearance of new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction—is the major source of evolutionary novelty in eukaryotes—animals, plants, and fungi.”

Could someone please explain this in terms accessible to amateurs?

I have a fuzzy grip on how this mechanism is supposed to have given rise to complex single-cell organisms, aka eukaryotes, but can’t see how it could produce, say, new organs in an existing species of multi-cellular animal. It would seem to require both horizontal gene transfer & a huge saltation, but I don’t think even a honorary doctorate ceremony would stop a roomful of scientists from jumping on something that egregious.

Pierce R. Butler asked: “Could someone please explain this in terms accessible to amateurs?”

I’ll give it a quick try - haven’t got time for depth.

“Symbiogenesis” would be two organisms merging into one. They have a symbiotic relationship, like bees do with certain flowers, and then one day the bee becomes part of the flower (or the flower part of the bee). In the case mitochondria, the cells’ power plants, they have their own DNA and the mitochondria are probably a different organism living in our cells in a symbiotic relationship.

The problem with the bee becoming a reproductive organ of the flower is getting bee and flower DNA to combine into a single genome for a species.

“…the appearance of new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction—is the major source of evolutionary novelty in eukaryotes—animals, plants, and fungi.”

Do you know anything about the genetic algorithm or evolutionary programming? In the genetic algorithm strings of code are mutated randomy. In a Margulian algorithm you would take other strings of code and give them a gentle run through a blender and recombine the parts and use standard selectionism on that.

Is anyone experimenting with Margulian algorithms? I don’t know.

“I have a fuzzy grip on how this mechanism is supposed to have given rise to complex single-cell organisms, aka eukaryotes, but can’t see how it could produce, say, new organs in an existing species of multi-cellular animal.”

You’ve got a point, it takes two different cell types to start symbiosis, so you’d need Darwinian processes to get to the point where you have symbiosis going on.

“It would seem to require both horizontal gene transfer…”

Yes. Maybe you should explain it to me.

“… & a huge saltation, but I don’t think even a honorary doctorate ceremony would stop a roomful of scientists from jumping on something that egregious.”

They might if they were, like us, to confused to jump at this time.

Stuart Kauffman is also “definitely a Darwinist.” I was at a luncheon with him where he told a particular ID supporter, in no uncertain terms, that there was good science in evolutionary biology, that ID could never suffice as science because it rested on the premise that all possible evolutionary pathways had been exhausted, and that he did not support ID. He also made mention of Bill Dembksi, stating that his arrogance in thinking that Kauffman was agreeing with him when he was not, was astounding. He’s made numerous mentions of how he treated the IDists too kindly, which has made them follow him around like puppies who think he’s got a biscuit for them (my analogy).

This, and the way in which IDists have misrepresented many scientific works before at least one state legislature (I’m thinking of Ohio–they probably did that in Kansas too?), really says something about the faith that IDists have in their own movement.

normdoering wrote

Do you know anything about the genetic algorithm or evolutionary programming? In the genetic algorithm strings of code are mutated randomy. In a Margulian algorithm you would take other strings of code and give them a gentle run through a blender and recombine the parts and use standard selectionism on that.

Is anyone experimenting with Margulian algorithms? I don’t know.

In earlier versions of Avida (e.g. ver 1.3) there was provision for a form of interaction unappetizingly called “necrophilia” in which a reproducing digital critter could incorporate pieces of the code of the critter it was killing off to replace. That was a rough analogue of lateral gene transfer. One thing it does in Avida runs is jack up the speed of evolution of complex features in a varied selective environment. In more recent versions there is provision for an operation called “injection” which generates a kind of parasitism:

In Avida, a parasite exists directly inside of its host, and makes use of the CPU cycles that would otherwise belong to the host, thereby slowing down the host’s replication rate. Depending on the type of parasite, it can either take all of the host’s CPU cycles (thereby killing the host) and use them for replicating and spreading the infection, or else spread more slowly by using only a portion of the hosts CPU cycles (sickening it), but reducing the probability of driving the hosts, and hence itself, into extinction.

That’s clearly not a “Margulian algorithm”, though. It’s interesting to think about such an algorithm. Hmmmmmmmm.

RBH

The simulated organisms appear to increase in complexity, in violation of the Law of Conservation of Information. Evolution is just a theory and a Law trumps a theory, obviously. Obviously Avida is a sham then. I bet it secretly communicates with Wikipedia, and downloads information. Then algorithms transmogrify the wikipedia information into simulated biology information.

I really don’t get why Dembski would be trying to quote Margulis to support him. Doesn’t the entire concept of symbiogenesis pretty much demolish the idea of “irreducible complexity?” I mean, Margulis showed that a complex organism, a eukaryotic cell in which very different organelles with very different properties are required to work together, was actually a symbiotic combination of earlier prokaryotic cells which came together to evolve into something more complex. She showed how a very complex system could be reduced to less complex parts through a then-novel form of evolution.

Besides, something tells me that the entire idea of endosymbiosis, that prokaryotic cells originated 3.5 billion years ago, and combined in an endosymbiotic event to evolve into eukaryotes ~1.5 billion years ago, would be complete anathema to the various pseudocreationist groups.

Do the supporters of pseudoscientific “theories” actually read the science that they claim supports their claims? I mean, I cannot imagine how you guys deal with this in your field. At least in politics, even the hardcore capitalists have read Marx and the hardcore communists have read Smith, the authoritarians have read Locke and the libertarians have read Hobbes. You rarely see people trying to quote Locke, for instance, as having supported police states or some other trash like that. Then again, this is not to say that we don’t have incompetence in our field, but wow, even the dumb ones usually know who they’re quoting.

We’re all aware that the popular understanding of the science barely improves from century to century, but the middlebrow concept of biology doesn’t move much faster. A tremendous amount of thinking and research has taken place since the heyday of the new evolutionary synthesis in the 30s and 40s. For that matter, cell biology and molecular genetics are very different now then they were in the late 70s, though the last thirty years of work are barely reflected in the boilerplate accounts of how DNA works that accompany newspaper articles on scientific subjects. Under the circumstances, throwing rocks at Mayr or Dohbzansky is pointless since it isn’t just Margulis who thinks of things differently than they did. Everybody does because of cladistics, the symbiotic origin of organelles, the discovery of the crucial role of small RNA molecules, the human genome program, punk ek, niche construction, evo-devo, hox genes, artificial life research, archaea, etc.

The science keeps moving on. Thing is, though, it keeps moving further and further away from the quaint 18th Century natural theology of the ID folks.

Comment #46684

Posted by Hyperion on September 6, 2005 12:48 AM (e) (s)

I really don’t get why Dembski would be trying to quote Margulis to support him.

Why not? The point is to generate ‘scientific’-looking discussion, pretend there’s a controversy, and demand recognition. How do misleading statements by Dembski interfere with that? If normal scientists complain, that’s just par for the course. Who else will complain? Do you imagine Salvador will wake up and confront him? Not likely. Sal is a Young Earth Creationist, which means you can put anything past him, with the right religious spin. And Dembski would just ban him if he did wake up. He works at a bible college, he can walk out his door and find 5000 Salvador Cordovas.

At last, absloute confirmation Dembski is nuts, he has declared biology dead, not just evolutionary biology but biology full stop, comparing it to soft sciences like economics, sociology and psychology and stating that it’s high time the public stops respecting it. He’s nuts. I am trying to think of some way to interpret it with the principle of charity, but I can find none, Dembski explictly blocks all more liberal interpretations of his thesis by affirming that it’s biology, not evolutionary biology, which is a soft science, if a science at all. obiter dicta, I find it odd that someone with a degree in psychology could declare it dead, but maybe that’s just me.

One wonders what he thinks of modern medecine for example, or even the mapping of the genome, none of the soft sciences he mentions have equivelant discoveries. At the same time he invokes popular support for his postion, describing, in pathlogical depth, those evil ivory tower dwelling biologists whose “Soft pampered life styles” are only made possible by the general public. One wonders whether he is aware of the fact that without vaccines devolped by biologists there’s a very, very good chance he wouldn’t be alive.

I suspect all the fawning mail he get’s from fans on his blog has finally pushed him over the edge into meglomania.

Says Intelligent Design Theorist Timmy :

Evolution is just a theory and a Law trumps a theory, obviously.

Not really. For example Newton drew up the famous law of gravity involving the Universal gravitational Constant . Note the grandiose name: “The Universal Law of Gravitation “. Along came Einstein with his General Theory of Relativity, and blew Newton’s law out of the water. We now go with Einstein’s theory on the large scale, and the quantum theory of gravity on the small scale.

Remember:

It’s not about trying to better understand the world and making it a better place.

It’s not about “doing” science.

It’s not about following the standards and protocols of a profession.

It’s about power, authority, money, and most of all, rolling back the Enlightenment to those good ol’ dark ages when everyone “knew” their place.

What is at stake is the human freedom to think unfettered by an Index of Forbidden Books, or governments (re: Lysenko), or superstitious nonsense.

Sorry. Got carried away.

I know this is off the subject but I’d like to ask paulp a question. What is the scientific theory of quantum gravity and how is it tested using the scientific method? What is the proposed mechanism of action? Has anybody actually detected the proposed graviton and what are its properties?

If I were Lynn Margulis I’d sue for libel and/or defamation of character. A claim that she rejects evolution (in general) could seriously harm her reputation.

Keep in mind that atomic theory preceded the detection of atoms, and in fact many thought that atoms were “mere” theoretical constructs and not “real” entities (I’ll leave it to others to try to figure out what might be meant by such ontological distinctions). But it provided a predictive model that explained many observed phenomena. Quantum gravity theories do the same, with varying degrees of success. “what it is” is a fairly rigorously defined mathematical model that unifies quantum theory and general relativity in the sense of being consistent with the observations at both levels, whereas those theories are inconsistent with each other. It certainly isn’t anything like “the notion that God plays billiards and gravitons are his billiard balls” – i.e., it’s not like ID. However, quantum gravity theories, while active research programs (again, unlike ID), have not reached any sort of scientific consensus, and may or may not get there – much like Steady State theory and Big Bang theory, one did and one didn’t.

No one has detected gravitons, and likely never will. As for properties, gravitons are spin 2 bosons with a rest mass of zero.

If you want to know more, spend more than that three minutes I did googling the subject.

P.S. paulp: There’s a rumor that I D T Timmy is a parody, though he’ll vehemently deny it. The point is, he already knew that.

Some people ask: What is Symbiogenesis?

1. Lynn Margulis is all about microbes: http://www.bio.umass.edu/faculty/bi[…]argulis.html

2. The serial endosymbiotic theory is standard biology I textbook material. Margulis is far from the only one who has done research confirming the idea. In a standard Bio I text one learns: the eukaryotic cell is a chimera of prokaryotic ancestors. In particular, chloroplasts and mitochondria have DNA and are descendants of bacteria that were engulfed or otherwise learned to live inside other cells. Beyond that, some algae evolved through further endosymbiosis, taking in another eukaryote! Again, this is standard Bio I material. Look in a text book – or perhaps someone will provide a good illustrated link.

Comment #46682

Posted by Intelligent Design Theorist Timmy on September 6, 2005 12:20 AM

The simulated organisms appear to increase in complexity, in violation of the Law of Conservation of Information. Evolution is just a theory and a Law trumps a theory, obviously. Obviously Avida is a sham then. I bet it secretly communicates with Wikipedia, and downloads information. Then algorithms transmogrify the wikipedia information into simulated biology information.

A scientific law must be true for every time and place in the universe. Reality that tends to support this law is wrong:

aneuploidy (“not/good/fold”): a condition in which the chromosome number of an individual is not an exact multiple of the typical haploid set for the species. chromosome duplication : single chromosome duplication, instead of a whole genome duplication.

allopolyploid : polyploids created by hybridization between different species (homeologous chromosomes)

allotetraploid: an organism that is diploid for two genomes, each from a different species. (???) allopolyploids are generated by hybridization between two related species. the hybrid is sterile. however, sometimes chromosomal doubling occurs, restoring fertility. if the two parental species are diploid, the resulting allopolyploid is called allotetraploid.

amphidiploid: same as allotetraploid

autopolyploid : polyploids created by chromosome duplication within a species

basic chromosome number (monoploid number): the number of different chromosomes that make up a single complete (chromosome) set.

chimera: an individual composed of a mixture of genetically different cells. (difference from mosaic: different cells in a mosaic are derived from the same zygote, where for chimera, they are not.)

genetic drift: the random fluctuations of gene frequencies due to sampling errors.

haploid number : number of chromosomes in the gametes (note: wheat is a hexaploid with 42 chromosomes; its haploid number is 21, but its basic chromosome number (monoploid number) is 7)

lineage: a linear evolutionary sequence from an ancestral species through all intermediate species to a particular descendant species orthologous locus: a gene that has evolved directly from an ancestral locus. homologous genes: genes that share a common evolutionary ancestor.

paralogous locus: a gene that originated by duplication and then diverged from the parent copy by mutation and selectin or drift. ploidy : number of basic chromosome sets

polyploidy (“many/fold”): the situation where the number of chromosome sets is greater than two.

synteny: a pair of genomes in which at least some of the genes are located at similar map positions.

tetraploid (“4/fold”): having four haploid sets of chromosomes in the nucleus

vertical evolution (phylogenetic evolution): a gradual transformation of one species into another without branching.

http://www.nslij-genetics.org/duplication/

Which also references about 230 papers, 2 textbooks and a dozen or so science-oriented web pages.

And you have? A philosopher, a mathmatician and a lawyer… And a paper that got someone fired and the paper retracted because it was bogus and deliberately side-stepped editorial and peer-review requirements.

Comment #46708

Posted by ts (not Tim) on September 6, 2005 06:59 AM (e) (s)

P.S. paulp: There’s a rumor that I D T Timmy is a parody, though he’ll vehemently deny it. The point is, he already knew that.

Oh yeah, well, your momma’s a parody.

No, IDTheorist Timmy, a law does not “trump” a theory. Theory includes laws.

Here, go see the National Academy of Science’s handy-dandy book on teaching evolution, and get the definition of “theory” from the introduction: http://books.nap.edu/html/creationi[…]duction.html

“Theory: In science, a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.”

If you want to get pedantic about it, evolution has better pedants. Survival of the most fit, you know.

Lynn Margulis is too deep in science to notice what a mathematics-minded philosopher at a Bible seminary says about evolution. Dembski knows that and understands it. The chances that Margulis would respond are almost nil, and Dembski will be able to get away with mis-stating Margulis’ position for a long time. It’s a sure bet that few, if any, members of any state board of education have read Margulis, or know who she is or what her contribution is. Their only context will be what Dembski or the Discovery Institute claims.

Incidentally, that is also why ID advocates so scrupulously avoid meetings of scientific societies. They might run into some of the people they misquote there, and that would be embarrassing to them both.

And don’t get me started on why ID advocates don’t apply for federal grants.

“Intelligent Design Theorist Timmy” is “Creationist Timmy” in a cheap tuxedo. (In other words, he’s a parody, not to be taken seriously, and a really stale joke by now.)

ID Theorist Timmy: Law of Conservation of Information .… This statement is sufficient to see it comes from someone having little knowledge of what he is talking about. There is no such law - it was a meaningless invention by Dembski ignored in the professional literature on information theory. Information is not a commodity which can be conserved. The alleged “law” itself in Dembski’s formulation contradicts the 2nd law of thermodynamics. Hard to decide - is it more laughable or more sad that nonsense emanated from Dembski’s production finds followers ready to parrot any drivel he spews.

Timmy is not a joke so much as an experiment. The point is to see if a creationist’s line of argumentation, taken to its most absurd and unreasonable limit, can be distinguished from what creationists routinely say. Apparently it can’t. I’ve tried. Comment #46682 is maximal lunacy. Timmy’s been doing this for a year. He’s always had my email address (which until recently was visible). And the name’s obviously a reference to the retarded kid on South Park. But reasonable people on this blog mistake him for an actual creationist with regularity.

After a year, I conclude that you can’t distinguish absolute lunacy, from Salvador Cordova, who, honestly, I thought was a parody until his picture was in Nature.

Comment #46733

Posted by steve on September 6, 2005 10:50 AM (e) (s)

Timmy is not a joke so much as an experiment. The point is to see if a creationist’s line of argumentation, taken to its most absurd and unreasonable limit, can be distinguished from what creationists routinely say. Apparently it can’t.

I was never sure, and I’m pretty skeptical. It looked like a parody, especially the “Timmy” part of the name which is an affect I use when I’m using parody.

But the problem is that all of ID and creationism is a parody in-and-of-itself. Thus, there was no “reality” base-line to compare it too. It’d be like Monty Python lampooning Monty Python.

Lynn Margulis is definitely a naturalistic evolutionist, and while I believe she certainly overstates the importance of symbiogenesis, I believe she has made some very important contributions and is correct in pointing out that symbiogenesis plays a very important role in the evolutionary process.

With regard to mitochondria and chloroplasts, she argued as far back as the 1960s that they were bacterial in origin. Only recently we discovered that they have their own DNA, and moreover, that their DNA is circular – as is the case with nearly all bacterial DNA. (Ours and that of other eukaryotes is linear, implying that it has ends, which are then capped by telomeres.) And as it turns out, the closest known extant non-endosymbiotic relative of mitochondria is the Rickettsia bacteria responsible for typhoid. Likewise, the closest known extant non-endosymbiotic relative of chloroplasts would be a species of cyanobacteria, colonies of which are known as blue-green algae.

Lynn Margulis also argues that the eukaryotic flagella was originally a species of spirochette. However, spirochettes have the wrong mode of motility – and it appears that a gradualistic approach may be best with this organelle.

However, what may be one of the more important roles played by endosymbiogenesis (as far as the process of evolution is concerned) is something which Lynn Margulis was initially rather opposed to: symbiosis involving viruses, such as endogenous retroviruses. For example, it appears that at least three species of endogenous retroviruses are responsible for creating a barrier to the mother’s immune system in the placenta, thus protecting the embryo and making possible larger mammalian brains, and that a number of endogenous retroviruses are expressed in much of normal embryonic tissue development. Likewise, in a broad sense, lateral gene transfer may be viewed as resulting in a form of symbiosis. And if (as appears to be the case) retroelements (such as retrotransposons) are generally the relics of past retroviral infections, then it would appear that endosymbiosis plays an important direct role in evolution, its plays an equally important albeit indirect role through retrotransposition. Likewise, transposons are most likely the relics of viral infection – specifically, by single-stranded DNA viruses. Along these lines, two books which may be of interest are “Viruses and the Evolution of Life” and “Retroviruses and Primate Evolution.”

It should be admitted that Lynn Margulis’ rhetoric has been at times somewhat extreme. In part, this is understandable, as she has faced a great deal of opposition in the past, and has found it necessary to present her case quite forcefully. But in part, it is due to her work having been influenced by Marxist intellectual currents to a fair extent, including Marxist dialectics. However, setting aside politics, one could argue that even her dialectics is in certain respects a useful corrective. Much of twentieth century evolutionary theory was decidedly reductive, and with her more dialectically informed approach, she stresses integration – seeing how parts are related to one-another, how they form wholes.

Unfortunately, the rhetoric of people such as Margulis and Gould will sometimes unintentionally play into the hands of Intelligent Design proponents. But at the same time, their work is properly seen as an extension of the Darwinian paradigm – and as proof against the ID argument that evolutionists are dogmatic, that evolutionary theory is closed to new ideas, or that evolutionary science is in any sense dying or dead. It is in fact very much alive and quite vibrant.

normdoering: thanks for your answer, but I’m still profoundly confused.

“Symbiogenesis” would be two organisms merging into one. They have a symbiotic relationship, like bees do with certain flowers, and then one day the bee becomes part of the flower (or the flower part of the bee).

My momma didn’t mention anything about this in her talk about the birds & the bees, and I don’t remember anyone else explaining it either.

In a Margulian algorithm you would take other strings of code and give them a gentle run through a blender and recombine the parts and use standard selectionism on that.

Still sounds like a lot more lateral gene transfer than anyone else has reported between multicellular organisms: viral railroads hauling whole chromosomes around. The concept has promise for a science-fiction story about bewildered ecologists on Planet X, but why is a widely respected biologist pushing it?

…if they were, like us, to[o] confused to jump…

So I’m not the only one who thinks something crucial has fallen between the cracks here? (I’m also a bit perplexed about why everybody else seems to be happily playing the usual game of bash-the-creationists while dancing around this elephant in the living room…) Either a major evolutionary biologist has fallen out of her intellectual tree, or is propounding a significant hypothesis in ways as yet untranslated to dabblers like myself. Odds favor the latter, in which case more detailed exegesis should be expected any minute now.

I was never sure, and I’m pretty skeptical. It looked like a parody, especially the “Timmy” part of the name which is an affect I use when I’m using parody

Every time I wrote a Timmy comment, I attempted to start with a creationist claim which was made above in the comments, and, by applying that logic, arrive at something so profoundly dumb that even the initial creationist couldn’t abide it. Turns out, that is beyond my creative abilities.

Pierce:

Do you at least understand the concept of a symbiotic relationship? (asking in all sincerity)

Because that would most likely be the first step in getting the concept of sybiogenesis.

Lynn Margulis is too deep in science to notice what a mathematics-minded philosopher at a Bible seminary says about evolution. Dembski knows that and understands it. The chances that Margulis would respond are almost nil, and Dembski will be able to get away with mis-stating Margulis’ position for a long time. It’s a sure bet that few, if any, members of any state board of education have read Margulis, or know who she is or what her contribution is. Their only context will be what Dembski or the Discovery Institute claims.

Well, if she’s as concerned about science as she appears to be, then perhaps she could make some sort of public statement categorically rejecting ID, or turn up at one of these school board hearings in support of evolution or something.

We’re getting past the stage where high-profile biologists will be able to safely continue to ignore this stuff, especially when they’re being misquoted in support of the other side.

Either a major evolutionary biologist has fallen out of her intellectual tree, or is propounding a significant hypothesis in ways as yet untranslated to dabblers like myself. Odds favor the latter, in which case more detailed exegesis should be expected any minute now.

Symbiogenesis is legitimate stuff, and fairly mainstream now. Sequence comparisons of organelle genes are very supportive. For example, cytoplasmic malate dehydrogenase and mitochondrial malate dehydrogenase show different affinities in similarity charts. Then there’s the slight variation in the mitochondrial genetic code. I’m sure someone who actually knows what they are talking about could cite more evidence than me.

I agree, it is similar in concept to horizontal gene transfer, but perhaps takes it to another level (ours goes to 11).

Also, I don’t see it as a violation of either common descent or natural selection, since the merging entities all presumably share ancestry, and all their components underwent natural selection in their original setting.

If only ALL mothers were that loving. :o)

Russell,

I did some digging regarding an “airborne HIV.” The article which I had thought mentioned it did not, although it did mention a murine leukemia virus – undoubtedly my memory of that article and another became combined. Digging around some more, I found the following – which suggests that there isn’t much to worry about at least along these lines:

http://www.aegis.com/news/ads/1990/AD900519.html

“Altering the AIDS Virus”

Discover (06/90) Vol. 11, No. 6, P. 14

——————————————————————————– Abstract: A recent article in the journal Science contained a “note of caution concerning…biosafety measures” when culturing HIV. The note, from Robert Gallo, suggested that lab experiments might create airborne viral variants. The note caused widespread concern because it described an AIDS virus altered by coinfection with a mouse leukemia virus. The hybrid had the ability to infect immune system cells not ordinarily susceptible to HIV. Gallo himself, however, downplays the airborne transmission possibility. Although influenza, cold, and Epstein-Barr viruses can spread through the air, “it would be a onetime risk,” Gallo said, because the viruses are not genetically altered and cannot pass the superficial changes on to offspring. Other researchers discount the possibility even more. Mixed viruses have been around for two decades, and “there’s no evidence that they’ve ever traveled through the air,” said Howard Temin, Nobel Prize winning virologist. “The enemy we know is bad enough without worrying about hobgoblins.”

Side Note: More on Ebola Reston

It should also be noted that while Ebola Reston could be efficiently transmitted by means of an airborne vector in green monkeys, it was much less efficient in being transmitted to humans, resulting in only pneumonia-like symptoms as it was unable to breach the barrier between the lungs and the bloodstream when transmitted in this fashion to humans.

This story was mentioned a little earlier…

Grasshoppers brainwashed into suicide by a worm 10 September 2005

THE trick by which a parasitic worm brainwashes its host into killing itself has been revealed.

The nematomorph hairworm (Spinochordodes tellinii) develops inside land-dwelling grasshoppers and crickets until the time comes for the worm to transform into an aquatic adult. At that point it somehow persuades the insect to jump into water, allowing the adult worm to swim away.

David Biron and his colleagues at the Institute for Development Research in Montpellier, France, have found the worms produce proteins that mimic some of the grasshoppers’ own (Proceedings of the Royal Society B, DOI: 10.1098/rspb.2005.3213). Some of the proteins affect neurotransmitter activity and response to gravity.

http://www.newscientist.com/channel[…]18725164.600

I might be a little late to the conversation here, but the most of this boils down to semantics. Evolution is a very complex topic, but it looks simple from the outside. Part of the problem is that the easiest way to explain evolution is selective pressure on (mutational) genetic variations.

And while definitely fundamental, that’s clearly not the sole source of innovative changes. Increasingly so, it is becoming clear that the major revolutions are the consequence of pairing multiple distinct functions in a novel way. That provides a basis for rapid incremental change. In this sense, LGT/HGT, endosymbiosis, and mutualism are all related (though on distinct mechanistic scales).

As an analogy: personal computers were useful before the advent of significant networking; separately, the ARPAnet and early incarnations of the Internet were useful before cheap, widespread access was available. They both came into existence and “evolved” due to entirely different and independent selective pressures. The merger of personal computing and widespread Internet access had an entirely novel consequence. Independent of each other, they were useful; combined, they revolutionized communication and commerce (ie. this entire discussion became even remotely feasible in the span of a few years in the mid-90’s).

Similarly with biological evolution, the “Margulian” theory is that most of the truly revolutionary progressions happened not as a result of incremental mutation (neo-Darwinian) but because of break-through mergers of previously discrete functions (symbiogenesis, mutualism).

In common terminology, neo-Darwinian is evolutionary, but mutualism is revolutionary. And much of the “arguments from personal incredubility” are based on those revolutionary “leaps”.

For what it is worth, my doctoral thesis is somewhat related to this idea. Specifically, my theory implies that these revolutionary pairings are often driven (rather than purely chance) based on functional couplings in an instable environment. Which, if true, also eliminates a great deal of the “random” argument, as it shifts things towards the necessity side in that fundamental “chance or necessity” question.

If anyone particularly cares, I can outline a fairly thorough description of the origin of life up to the LUCA population precursors. There are lots of question marks, but the process is not quite as controversial as one might think.

Which really explains my problems with creationists (whether of the OEC, YEC, or ID variety): if they would only read up on modern (ie. >= 1850) literature, they would surely see that they are wrong (barring fundamental cognitive dissonance). Of course, I’ve sat in a room of five people, one of which was Behe, and found myself occassionaly speechless at his ignorance of modern results and publications… They live in their own special little world, I suppose.

justin Wrote:

Specifically, my theory implies that these revolutionary pairings are often driven (rather than purely chance) based on functional couplings in an instable environment.

Driven??? Doesn’t that imply purpose or intent?

I think I would like to hear more of this theory.

Actually, I’d rather get a better understanding of the above quote.

Justin: …the “Margulian” theory is that most of the truly revolutionary progressions happened not as a result of incremental mutation (neo-Darwinian) but because of break-through mergers of previously discrete functions (symbiogenesis, mutualism).

Please correct me if I’m wrong, but does the “Margulian” view also hold that “most of the truly revolutionary progressions” were on the unicellular level, or did any of these mergers occur among us Phanerozoic newcomers hauling around “tissues, organs, organ systems”, etc?

And, if the latter, how?

…I can outline a fairly thorough description of the origin of life…

Sooner or later, somebody’s got to call you on that one, so it might as well be me…

[crikets chirping]

Miah Wrote:

Driven??? Doesn’t that imply purpose or intent?

No, it doesn’t. Natural processes can drive systems: currents, oscillations, gradients, etc. There is no intent, but there is a specific response.

Biological evolution is driven by the environment. One can think of evolution as a process of accumulating control systems to deal with instability and uncertainty in the environment. The source of an organism’s complexity is the complexity of the environment it develops in.

But can you take that idea and apply it to systems without the baggage of *biological* evolution (ie. informational polymers and replication machinery)? How can a chemical system evolve in an analogous way? Or more generically, a system of simple, non-intelligent agents?

I’ve recently been calling the process “adaptive self-organization”, but I don’t know if that’s terribly helpful. Again, the basic idea is that significant complexity will require a system to be adaptively tied to the environment.

Pierce R. Butler Wrote:

Please correct me if I’m wrong, but does the “Margulian” view also hold that “most of the truly revolutionary progressions” were on the unicellular level, or did any of these mergers occur among us Phanerozoic newcomers hauling around “tissues, organs, organ systems”, etc?

I think most of the specific examples are of the unicellular variety, but the idea is that it applies to more complex systems as well. The specific mechanisms will change, of course. LGT and endosymbiosis on one end, and ecological co-adaptation on the other. And many other things in between.

If I may, I think this is basically just a conceptual argument, trying to overcome the tryanny of DNA in our thinking about evolution. Worrying about specific genetic mechanisms can distract us from more important, higher-level mechanisms. In other words, we need to think about individual organisms, and even cells and cellular processes, as “ecological systems” rather than gene products.

As for tissues et al, I don’t know that anyone has a specific mechanism in mind. One guess is that multicellular organisms (and the various tissues composing them) probably began as symbiotic interactions of several different cell lineages. Over time, the potential for differentiation developed and the genes necessary for the different types of tissues began merging into a single cell line.

But how (and even whether) the genetics “merge” is besides the point. The interesting question is how the multi-tissue organism evolved to begin with. Consolidation of the genetics is “mundane” clean up. Well, it’s not really mundane – actually it’s a fascinating question – but it’s not really relevant to the *origin* of this multi-tissue organism.

Another way of saying this: biology is hindered by the prevailing “structure (DNA) defines function” view, but the reverse “function defines structure” is important, as well. Perhaps even more important. Function-first doesn’t necessarily have to directly alter the genes, it can simply constrain the viable genetic variation.

Pierce R. Butler Wrote:

Sooner or later, somebody’s got to call you on that one [description of origin of life], so it might as well be me…

This is an assembly of a variety of work into a single, semi-coherent hypothesis. There are numerous experimentally testable predictions, however, and certainly many things are wrong or incomplete. But my point was that it’s not the big black box that some seem to think it is.

1. Formation of simple organic compounds: The leading candidates for this are Miller-Urey type reaction in an early reducing atmosphere, organic compounds in meteorites, and reactions near deep sea vents which provided a reducing environment. I favor the Miller-Urey mechanism. The reducing nature of the early atmosphere has been debated, but recent work supports the premise.

2. Development of a primitive metabolic infrastructure: Prior to the advent of enzymes or even ribozymes, significant metabolic networks developed using a combination of organic compounds, simple inorganic molecules, and inorganic catalytic surfaces (such as clays and minerals). A variety of mechanisms probably contributed to this development, including charge-based recruitment to surfaces, self-catalytic networks, differential degradation based on function, functionally-coupled association, and self-sustaining environment modification. This likely all happened in a spatially discretized support (porous clays and/or surface adsorption).

2a. Production of peptide and RNA monomers from the primitive metabolism: These molecules were likely involved in the early metabolism as well, though not generally in the modern polymer form.

3. Production of RNA polymers: In addition to potential catalytic processes derived from the myriad metabolic products, certain clays also catalyze RNA polymerization. Templated copying of RNA polymers would also begin, catalyzed by similar processes.

3a. Origin of simple ribozymes: Some of the RNA polymers would have useful catalytic function, and due to templated copying, these particular sequences would become more prevalent – an early form of information polymer-based evolution.

4. Origin of the primitive ribosome: Interactions between RNA oligomers and amino acids catalyzed the formation of simple peptides. Although they probably used a “mRNA” support, the produced peptides were random as the primitive tRNAs were not specific.

4a. Random, non-catalytic, molten-globule proteins provided a support for ribozymes and other small catalytic compounds, increasing their catalytic efficency and range.

5. Increasing amino acid specificity in the primitive tRNAs: The genetic code began to form based on the sequence of common RNA polymers, rather than RNA sequences adapting to the “genetic code”.

3-5. Enclosure of metabolic “sites” into vesicles and mechanical reproduction of these primitive cells: Again, certain clays catalyze vesicle formation from micelles. And in particular montmorillonite clay also catalyzes RNA polymerization. Interesting coincidence. Also, basic vesicles can grow spontaneously through micelle inclusion and split when forced (by current, for example) through constrained pores. This particular process was likely ongoing through several of the previous steps (thus the 3-5 numbering). However, due to the utility of innovation exchange at this point, the encapsulation of the LUCA population ancestors probably occured relatively late.

3-5a: Origin of membrane-bound receptors: Although many of the early, useful molecules were likely permeable, certain external resources were necessary, and incorporation of those compounds into the “cell” interior were necessary. Perhaps initially simple compounds embedded into the cell wall or modifications to the phospho-lipids that composed the cell wall. As initially many of the useful external resources would be ribozymes, this might explain the relatively common existence of LGT – exchange of genetic information was originally dependent on the exchange of catalytic nucleic acids.

6. Origin of forward and reverse transcriptases: A largely templating reaction, this would likely not have been terribly difficult, and the obvious benefits of having a “backup” of the useful RNA is pretty straightfoward. The useful RNA was highly interactive with various catalytic processes, and thus likely to be easily “damaged”.

7. Origin of amino acid based enzymes: Again, this was likely a subtle transition from simple structural support, to more specific support, to primitive catalyic function. As the original use (structure) became more refined, the particular catalytic utility became more prevalent.

7a. Enzyme catalysis displaced primitive metabolic processes: The greater efficiency and specificity of enzymes would replace the crude forms of simple organic chemistry underpinning the system.

8. Origin of internal cell structure: As the catalytic efficincy grew, cells became larger (more phospho-lipid production). Peptides (originally structure-oriented) provided a primitive skeleton for resource migration.

8a. Origin of motor proteins: Certain proteins were capable of faster movement on the cell skeleton, and developed to carry arbitrary loads (other proteins/resources).

9. Origin of replication: making use of the skeleton and motor proteins, the cell was capable of inducing the mechanical strain necessary for cell-splitting (previously it was just a random occurence). The benefit of parallel development and limitation on cell size caused this innovation to proliferate.

10. LUCA population.

Justin -

Thanks for spelling out your OoL scenario - if, unavoidably, in terms too technical for me to feel great confidence in understanding. Perhaps others here will be able to offer adequate critiques; I’ll just say that I’m glad you offer multiple hypotheses without dogmatic assertions, which I had somewhat suspected from your previous brashness.

Your earlier statement that

…trying to overcome the tryanny of DNA in our thinking about evolution. Worrying about specific genetic mechanisms can distract us from more important, higher-level mechanisms. In other words, we need to think about individual organisms, and even cells and cellular processes, as “ecological systems” rather than gene products.

definitely sounds like you’ve been studying “Margulian” theory in depth. Though I agree that (judging by discussion on evo blogs, anyhow) it seems that ecological considerations aren’t getting the attention they need, this approach as worded sounds like you’re trying to ignore that each & every generation has to pass through the bottleneck of gametic DNA. The current excitement in genetic research does tend to influence thinking more than perhaps it should, but the known limitations do have to be taken into account.

I’d bloviate ignorantly on this a little more, but the average American moves once every two years, so other average Americans have to help friends move even more often than that, and today it’s my turn.

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This page contains a single entry by PvM published on September 5, 2005 9:00 PM.

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