PvM posted Entry 1446 on September 5, 2005 09:00 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/1442

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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Comment #46674

Posted by sanjait on September 5, 2005 10:46 PM (e)

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.

Comment #46675

Posted by Pierce R. Butler on September 5, 2005 10:51 PM (e)

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.

Comment #46678

Posted by normdoering on September 5, 2005 11:30 PM (e)

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.

Comment #46679

Posted by Dave Cerutti on September 5, 2005 11:31 PM (e)

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.

Comment #46680

Posted by RBH on September 5, 2005 11:46 PM (e)

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

Comment #46682

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

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.

Comment #46684

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

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.

Comment #46687

Posted by Jim Harrison on September 6, 2005 1:39 AM (e)

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 #46690

Posted by steve on September 6, 2005 2:10 AM (e)

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.

Comment #46693

Posted by IamnotwhatIam on September 6, 2005 3:12 AM (e)

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.

Comment #46699

Posted by paulp on September 6, 2005 4:45 AM (e)

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.

Comment #46701

Posted by a maine yankee on September 6, 2005 5:24 AM (e)

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.

Comment #46702

Posted by the pro from dover on September 6, 2005 5:49 AM (e)

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?

Comment #46704

Posted by markfiend on September 6, 2005 6:38 AM (e)

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.

Comment #46708

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

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.

Comment #46714

Posted by Pete Dunkelberg on September 6, 2005 8:06 AM (e)

Some people ask: What is Symbiogenesis?

1. Lynn Margulis is all about microbes:
http://www.bio.umass.edu/faculty/biog/margulis.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 #46720

Posted by Moses on September 6, 2005 8:39 AM (e)

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 #46724

Posted by Intelligent Design Theorist Timmy on September 6, 2005 9:20 AM (e)

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.

Comment #46726

Posted by Ed Darrell on September 6, 2005 9:59 AM (e)

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/creationism/introduction.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.

Comment #46728

Posted by Ed Darrell on September 6, 2005 10:11 AM (e)

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.

Comment #46731

Posted by Jim Anderson on September 6, 2005 10:23 AM (e)

“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.)

Comment #46732

Posted by ag on September 6, 2005 10:32 AM (e)

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.

Comment #46733

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

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 #46734

Posted by Moses on September 6, 2005 10:59 AM (e)

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.

Comment #46737

Posted by Timothy Chase on September 6, 2005 11:14 AM (e)

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.

Comment #46738

Posted by Pierce R. Butler on September 6, 2005 11:16 AM (e)

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.

Comment #46740

Posted by steve on September 6, 2005 11:22 AM (e)

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.

Comment #46744

Posted by Miah on September 6, 2005 12:06 PM (e)

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.

Comment #46745

Posted by Albion on September 6, 2005 12:06 PM (e)

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.

Comment #46746

Posted by Bayesian Bouffant, FCD on September 6, 2005 12:13 PM (e)

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.

Comment #46749

Posted by Bayesian Bouffant, FCD on September 6, 2005 12:21 PM (e)

Wikipedia says about symbiogenesis

The idea originated with Konstantin Mereschkowsky in his 1926 book Symbiogenesis and the Origin of Species, who proposed that chloroplasts originated from cyanobacteria captured by a protozoan….

Merezhkovsky

Konstantin Sergivich Merezhkovsky (1855-1921) (also transliterated Konstantin Sergeevich Merezhkovsky, Constantin Sergeevič Mérejkovski, Constantin Sergejewicz Mereschcowsky, Konstantin Sergejewicz Mereschkovsky and Konstantin Sergejewicz Mereschkowsky) was a prominent Russian biologist and botanist active mainly around Kazan, whose research on lichens led him to propose the theory of symbiogenesis - that larger, more complex cells evolved from the symbiotic relationship between less complex ones. He presented this theory in the 1926 book Symbiogenesis and the Origin of Species. However, he had used the term as early as 1909, and the fundamentals of the idea had appeared in his 1905 work, The nature and Origins of Chromatophores in the Plant Kingdom.

I had no idea the idea went back that far, and Mereschkowsky certainly didn’t have gene sequence data to rely on.

I am also amazed that Merezhkovsky was apparently able to publish one of his key works 5 years after his death. Wikipedia is amazing.

Comment #46758

Posted by Russell on September 6, 2005 1:41 PM (e)

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.

Lynn Margulis has been actively associated with NCSE since before I even knew the organization existed. I don’t think she “ignores this stuff”.

Comment #46759

Posted by normdoering on September 6, 2005 1:56 PM (e)

Pierce R. Butler on September 6, 2005 wrote:

“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.”

Your momma didn’t tell you about how when two organisms fall in symbiotic love that a stork, (meaning a virus or plasmid), carries gentic information between them?

“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?”

There would have to be a mechanism, like viruses or plasmids.

The tree of life wouldn’t be a tree any more, it would be a net. Those genes would get scattered around to radically different species and you couldn’t trace inheritance directly.

“I’m not the only one who thinks something crucial has fallen between the cracks here?”

Yea, it’s falling between the cracks of my understanding too.

Comment #46766

Posted by Timothy Chase on September 6, 2005 2:51 PM (e)

normdoering wrote,

“The tree of life wouldn’t be a tree any more, it would be a net. Those genes would get scattered around to radically different species and you couldn’t trace inheritance directly.”

Actually, both Luis P. Villarreal and Salvador Lauria would argue that it is not a net, but a Mexican “arbo de a vida,” or “tree of life.” It is a tree, but with a fine web between the branches. As Luis P. Villarreal states,

It therefore appears that virus and virus-like systems may be contributing in a most profound way to evolution of their host. An early view from Salvador Lauria had envisioned a similar conclusion. When considering the issue of how a virus might contribute to the host, he wrote “… may we not feel that in the virus, in their merging with the cellular genome and their re-emerging from them, we observe the units and process which, in the course of evolution, have created the successful genetic patterns that underlie all living cells?” Thus we may wish to reconsider the architecture of the tree of life. Rather then thinking of it as a tree with the usual structure of unconnected tips from a common branch perhaps a structure more reminiscent of that done by Mexican artisans rendering of the “arbol de a vida” in which horizontal elements, bearing images of both life and death, are connecting the tips may better account for the contributions of viral agents to host evolution.

Here is an article by Villarreal which may be of interest – from 1997.

The viruses that make us: a role for endogenous retrovirus in the evolution of placental species
by Luis P. Villarreal
http://darwin.bio.uci.edu/~faculty/villarreal/new1/erv-placental.html

Comment #46768

Posted by Miah on September 6, 2005 3:01 PM (e)

Let me ask a question here on the basis of ignorance and possible sci-fi to see if there is any resemblace to the current “tree of life (with webs)” idea.

In the movie Outbreak there was a scene where the “nasty” virus had before only been able to infect through direct contact, and then they found out that it became “airborne”.

I believe I have heard of other viruses becoming “airborne”. My question is this, would it be possible that a virus (such as described above) infecting a body could acquire the genetic “material” say from a influenza virus and in turn become airborne.

Would this fall in line with LGT? Or am I simplifying the process too much?

Any help would be greatful.

Thanks!

Comment #46772

Posted by Ron Taylor on September 6, 2005 3:10 PM (e)

Everyone knows atoms were cooked up by those conspiring atheist/communist/feminist Bohrists who want to teach our children that they are nothing but a clump of mindless material particles, no different than a rock or a pile of dirt. Therefore we should behave like rocks and just sit around doing nothing forever. Think about it, if the theory of atoms is true I can do whatever I want to any person and it doesn’t matter. Therefore, atoms don’t exist.

Comment #46774

Posted by Ed Darrell on September 6, 2005 3:20 PM (e)

Albion, the big folks do what they can. But real science moves in different circles than ID does. Kansas’s State Board of Education doesn’t send notices to Harvard asking for testimony before approving textbooks – nor should they. In the normal course of affairs, publishers with a few dozens of hard-working editors and writers, under the direction of a few world-class scientists as authors, create books that accurately reflect the state of science based on what is known and published in the science literature. Margulis and other thinkers and researchers are out on the frontier making that science.

Discovery Institute, to pick the obvious example, is a political group. They monitor state education board calendars and, when time is opportune for them, zip in a Ph.D.’d ringer to claim that he represents all of science or a significant portion thereof, and that “science” has changed its mind.

Unless one’s intent is to skew this process, why would a working scientist bother to do such stuff?

And of course, that’s the answer both ways: Discovery Institute has time to do the political stuff because they don’t do the science stuff.

Here in Texas, NCSE was instrumental in persuading our corps of Nobel winners (mostly in physiology and medicine, the biology area) to speak up at opportune times and places to get good textbooks. But they were not in on the process early, and I suspect they hoped sanity would strike the Texas SBOE before they had to put aside the life-saving science they were working on to deal with such a bizarre situation.

Real scientists do real scientist. Politicians do politics. Intelligent design is politics. With luck, the two worlds rarely intersect, and when they do, politicians listen to scientists about science. Intelligent design is about getting politicians to turn a deaf ear to science.

It’s a struggle.

Comment #46775

Posted by Steve on September 6, 2005 3:27 PM (e)

IamnotwhatIam wrote:

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.

Well of course. Dembski believes that evolutionary theory is basically impossible. Look at the paper “Searching Large Spaces for Small Targets”. The target he selected was an arbitrary protein of length 100. Since the protein was arbitrary the argument applies to all proteins of length 100 and greater. Hence the evolution of proteins is impossible without guidance by an intelligence. So for Dembski to declare biology dead is not a big deal, IMO. Anybody with sense should have seen that Dembski was a crank long before this point.

Comment #46781

Posted by Timothy Chase on September 6, 2005 5:01 PM (e)

Miah wrote:

Let me ask a question here on the basis of ignorance and possible sci-fi to see if there is any resemblace to the current “tree of life (with webs)” idea.

In the movie Outbreak there was a scene where the “nasty” virus had before only been able to infect through direct contact, and then they found out that it became “airborne”.

I believe I have heard of other viruses becoming “airborne”. My question is this, would it be possible that a virus (such as described above) infecting a body could acquire the genetic “material” say from a influenza virus and in turn become airborne.

Would this fall in line with LGT? Or am I simplifying the process too much?

Any help would be greatful.

Thanks!

What matters is whether or not the virus is able to integrate itself into the genome of the gamete (i.e., reproductive cell). Hope you don’t mind, but I will post a little from a previous post of mine here and Panda’s Thumb. It contains links to more recent articles…

With regard to lateral (”horizontal”) gene transfer in the human-chimpanzee clade, there has been plenty of it — in the form of retroviruses. During an epidemic of some exogenous retrovirus, retroviruses may be able to enter the germline, lose their ability to be transmitted through infection, and become fully endogenous — being preserved from generation to generation in the genome in proviral (DNA) form. Thus, for example, there exist roughly 50 copies of the human endogenous retrovirus HERV-K in the current day human haploid (gamete) genome, which have entered the genome at various points in the past 4-30 MYA. But this is just one example. In fact, there exist approximately 30,000 endogenous retroviruses in the human haploid genome.

Endogenous retroviruses can be particularly useful for evolutionary biologists. For example, just by tracking the presence of a few endogenous retroviruses and their mutations, it is possible to construct a fairly complete phylogenetic tree for the old world monkeys. Likewise, endogenous retroviruses made possible the identification of the hippo as the closest extant land mammal to which whales are related.

However, they can also be particularly useful as far as the host is concerned. For example, it appears that endogenous retroviruses are responsible for creating a barrier to the mother’s immune system in the placenta which protects the embryo in eutherian mammals. This made possible later encephalization which reached two pinnacles in primates (and particularly, humans) and cetacea. Moreover, a number of endogenous retroviruses are expressed in embryonic tissue development in the kidneys, testes, lungs, nervous system, and other organs. Much if not all of the retroelements in the host genomes are retroviral in origin, and play a very significant role in the consequent evolution of the host. For example, retrotransposons are responsible for gene duplication. (Similarly, transposons (which are responsible for transposition) are generally thought to have originated as sDNA (single stranded DNA) viruses.) One current hypothesis is that the ancestors of retroviruses may have been responsible for the transition from the RNA World to the DNA World.

Periodic Explosive Expansion of Human retroelements Associated with the Evolution of the Hominoid Primate
Tae-Min Kim, Seung-Jin Hong, Mun-Gan Rhyu

“Five retroelement families, L1 and L2 (long interspersed nuclear element, LINE), Alu and MIR (short interspersed nuclear element, SINE), and LTR (long terminal repeat), comprise almost half of the human genome….”

J Korean Med Sci 2004; 19: 177-85
http://jkms.kams.or.kr/2004/pdf/04177.pdf

Periodic Explosive Expansion of Human retroelements Associated with the Evolution of the Hominoid Primate
Tae-Min Kim, Seung-Jin Hong, Mun-Gan Rhyu
J Korean Med Sci 2004; 19: 177-85
http://jkms.kams.or.kr/2004/pdf/04177.pdf

Constructing primate phylogenies from ancient retrovirus sequences
Welkin E. Johnson and John M. Coffin
Proc. Natl. Acad. Sci.
Vol. 96, pp. 10254-10260, August 1999
http://www.pnas.org/cgi/content/abstract/96/18/10254

Phylogenetic relationships among cetartiodactyls based on insertions of short and long interersed elements: Hippopotamuses are the closest extant relatives of whales
Masato Nikaido, Alejandro P. Rooney, and Norihiro Okada
Proc. Natl. Acad. Sci.
Vol. 96 pp. 10261-10266, August 1999
http://www.pnas.org/cgi/content/abstract/96/18/10261

Human endogenous retroviruses in health and disease: a symbiotic perspective
Frank P. Ryan
J R Soc Med 2004; 97:560-565
December 2004
http://www.rsm.ac.uk/new/pdfs/j_art_dec04.pdf

Expressions and Functions of Human Endogenous Retroviruses in the Placenta: An Update
A. Muir, A. Lever and A. Moffet
Placenta (2004), 25, Supplement A, Trophoblast Research, Vol. 18 S16-S25
Accepted 5 January 2004

Comment #46784

Posted by 'Rev Dr' Lenny Flank on September 6, 2005 5:48 PM (e)

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.

The problem with parodying creationists is that there is NOTHING you can say that is so lunatic and so nutty that some number of creationists somewhere (perhaps even most of them) don’t seriously propose it.

Witness the whole “tuba-playing Neandertals” thingie in Discover Magazine.

Comment #46786

Posted by 'Rev Dr' Lenny Flank on September 6, 2005 5:52 PM (e)

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

Because IDers haven’t done anything original, and instead are reduced to reproducing all of the arguments and tactics used thirty years ago by the creation ‘scientists’ in their (losing) battle. Creation “scientists” were particularly fond of quote-minign people like Patterson, Gould and others.

ID is just more of the same.

Comment #46795

Posted by Pierce R. Butler on September 6, 2005 6:19 PM (e)

Do you at least understand the concept of a symbiotic relationship?

Symbiosis to me means a mutually advantageous relationship between two different species, such as shark-&-remora, human-&-intestinal bacteria, legume-&-mycorrhizae, hippopotamus-&-those birds that clean hippos’ teeth, etc. That implies co-evolution, possibly to the point where the two species couldn’t survive without each other, but not genetic amalgamation.

So far as I could follow Bayesian Bouffant’s example, it dealt with unicellular organisms, which seems to be both a well-settled case of symbiogenesis and distinct from anything similar in us multicellulars.

Again: just how do we get to “new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction”?

Comment #46799

Posted by Jeff McKee on September 6, 2005 8:45 PM (e)

Please note that NOBODY in modern science is a “Darwinist.” Not Margulis, not Kauffman, and not me, although I’m a fan of Thomas Huxley, who coined the term. The term fit back in the 1860s and 1870s. But we’ve come way too far to let anti-science cults, such as the DI, label us as merely “Darwinian”, when evolutionary biology is mainstream science, and important to all of science.

JKM

Comment #46808

Posted by normdoering on September 6, 2005 9:29 PM (e)

Jeff McKee on September 6, 2005 wrote:
“… NOBODY in modern science is a ‘Darwinist.’”

I suspect the term “Darwinism” means nothing more than “metaphysical naturalism” and “atheism” to ID people. It’s hard to communicate when words don’t mean the same thing.

Comment #46810

Posted by Timothy Chase on September 6, 2005 10:26 PM (e)

Pierce R. Butler wrote:

Again: just how do we get to “new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction”?

“Again:”? I didn’t see your previous request.

However, behavior is partly learned, partly genetic. We know this, for example, from birds which are raised without the benefit of hearing the song of their species – they will know the basic melody, but little beyond that. So how does behavior change? Incrementally, for the most part. And that which is learned (although perhaps not simply by means of repitition, but within new contexts where the new behavior is more easily learned) may at some point become hard-wired.

New tissues? Here is one article you might want to check regarding muscle tissue:

Phylogenetic Relationship of Muscle Tissues Deduced from Superimposition of Gene Trees
http://www.umbi.umd.edu/~collins/myoinformatics/muscle-evolution.pdf

Well, hopefully you have some background on the evolution of the eye. For some background on the genetic basis for its evolution, you might try the following for starters:

Development of pigment-cup eyes in the polychaete Platynereis dumerilii and evolutionary conservation of larval eyes in Bilateria
http://dev.biologists.org/cgi/content/full/129/5/1143/

Physiologies?

If by this, you mean body plans, at least during the Cambrian period, this was more likely polyploidy which duplicated HOX genes. I will let you look that up.

Species? Easy – in much the same way as much of the above in terms of mutation (other than that which resulted from polyploidy) if the mutation involved either transposition (brought about by transposons which most likely originated from sDNA viruses) or retrotransposition (brought about by retrotransposons which duplicate genes which may then be subfunctionalized or neofunctionalized) where the population in which such mutations are spreading is small or at least relatively isolated from a larger population.

Of course, there may be other ways. You might want to look up the literature – no doubt evolutionary biologists are putting out a great deal of it.

Alternatively, you may want to check out the relevant literature by some Intelligent Design theorist, such as Dembski.

Here it is:

“As for your example, I’m not going to take the bait. You’re asking me to play a game: ‘Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.’ ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.”

William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002
http://www.pandasthumb.org/archives/their_own_words/index.html

Don’t like that one? How about:

“Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’-but, as yet, no general theory of biological design.”

Paul Nelson, Touchstone Magazine 7/8 (2004): pp 64 ? 65.
http://www.pandasthumb.org/archives/their_own_words/index.html

Still not happy? Try this:

“Intelligent design itself does not have any content.” - George Gilder

EDITORIAL DESK | August 28, 2005, Sunday
Show Me the Science
By DANIEL C. DENNETT (NYT) Op-Ed 2512 words
Late Edition - Final , Section 4 , Page 11 , Column 1
http://query.nytimes.com/gst/abstract.html?res=F20912FB345A0C7B8EDDA10894DD404482

If that doesn’t satisfy you, try this:

“This (the intelligent design movement) isn’t really, and never has been, a debate about science, it’s about religion and philosophy.” - Phillip Johnson, World Magazine, 30
November 1996

If that is still not satisfactory, you might try joining:

“Debunk Creation”
http://groups.yahoo.com/group/DebunkCreation/

Comment #46812

Posted by Timothy Chase on September 7, 2005 4:02 AM (e)

Pierce R. Butler wrote:

Again: just how do we get to “new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction”?

I am sorry – I had mistaken you for an IDer, but beginning from the top, I belatedly realized that your question was with respect to Lynn Margulis’ theory.

Her theory appears to be that persistent bacterial or viral infections may become endosymbiotic, thus modifying tissues and organs. Once one gets beyond the bacterial origin of the mitochondria and chloroplasts, this view is controversial to say the least, and it is not something which I myself agree with. At the same time, there are certain limited contexts in which it makes sense outside of organelles. For example, the gut requires an ecological system of bacteria for proper digestion. Likewise, termites rely upon specific bacteria and eukaryotes for the digestion of cellulose. And we have identified some viruses which to some extent control the behavior of the host. In addition, Lynn Margulis has built a great deal upon the her theory that the eukaryotic flagella originated as spirochettes, taking the view that they are responsible for sensation and motility. As I have stated previously, this theory appears to be false, and given our current understanding, it appears that a gradualistic explanation of the origin of the eukaryotic flagella is the correct one.

My own view is that the role played by infection is typically far more indirect, although perhaps no less important. Some viruses contribute some material to the genome of their host, but far more importantly, contribute the machinery by which the genome is modified over time. Thus, for example, retrotransposons have their origin in retroviruses, and currently it appears that transposons have their origin in single-stranded DNA viruses. Likewise, I suspect that sexual reproduction had its origin in endosymbiosis. (At the same time, there appears to be very little if any lateral gene transfer between bacteria and their host – and almost no mechanism by which such lateral gene tranfer could take place.) But then I am inclined towards Punk Eek, at least with respect to species which reproduce by strictly sexual means. However, an essentially gradualistic approach should be applicable during periods of non-stasis which will occur principally in small populations. Then, I would recognize along with Margulis the roles of endosymbiosis and exosymbiosis in driving much of the evolution of species, and yet of course would also recognize the great importance of the predator/prey-relationship in driving much of evolution – all of which would fall under the rubric of coevolution. And likewise, I recognize the existence and importance of a hierarchy of ecological systems – but the recognition of such a hierarchy is not particular to Margulis: for example, it plays an important part in the theory of Niles Eldredge.

In any case, my apologies, once again, for the misunderstanding.

Comment #46813

Posted by Timothy Chase on September 7, 2005 4:10 AM (e)

[CORRECTION]

Pierce R. Butler wrote:

Again: just how do we get to “new behaviors, tissues, organs, organ systems, physiologies, or species as a result of symbiont interaction”?

I am sorry – I had mistaken you for an IDer, but beginning from the top, I belatedly realized that your question was with respect to Lynn Margulis’ theory.

Lynn Margulis’ theory appears to be that persistent bacterial or viral infections may become endosymbiotic, thus modifying tissues and organs. Once one gets beyond the bacterial origin of the mitochondria and chloroplasts, this view is controversial to say the least, and it is NOT something which I myself generally agree with. At the same time, there are certain limited contexts in which it makes sense outside of organelles. For example, the gut requires an ecological system of bacteria for proper digestion. Likewise, termites rely upon specific bacteria and eukaryotes for the digestion of cellulose. And we have identified some viruses which to some extent control the behavior of the host. In addition, Lynn Margulis has built a great deal upon the her theory that the eukaryotic flagella originated as spirochettes, taking the view that they are responsible for sensation and motility. As I have stated previously, this theory appears to be false, and given our current understanding, it appears that a gradualistic explanation of the origin of the eukaryotic flagella is the correct one.

My own view is that the role played by infection is typically far more indirect, although perhaps no less important. Some viruses contribute some material to the genome of their host, but far more importantly, contribute the machinery by which the genome is modified over time. Thus, for example, retrotransposons have their origin in retroviruses, and currently it appears that transposons have their origin in single-stranded DNA viruses. Likewise, I suspect that sexual reproduction had its origin in endosymbiosis. But then I am inclined towards Punk Eek, at least with respect to species which reproduce by strictly sexual means. However, an essentially gradualistic approach should be applicable during periods of non-stasis which will occur principally in small populations. Then, I would recognize along with Margulis the roles of endosymbiosis and exosymbiosis in driving the evolution of species, and yet of course would also recognize the great importance of the predator/prey-relationship in driving much of evolution – all of which would fall under the rubric of coevolution. Likewise, I recognize the existence and importance of a hierarchy of ecological systems – but the recognition of such a hierarchy is not particular to Margulis: for example, it plays an important part in the theory of Niles Eldredge.

In any case, my apologies, once again, for the misunderstanding.

Comment #46823

Posted by Chip Poirot on September 7, 2005 6:53 AM (e)

Jeff McKee,

Whenever anybody starts out with a statement like “I’m not a Darwinist…” I immediately think of Keynes’ statement that those who claimed to be immune from the influence of economists, are usually citing the ruminations of some defunct economist.

While there is much about Kuhn and the application of his paradigm concept that I dislike and find inaccurate, the basic premise that scientists work in “paradigms” or “research programs” or “research traditions” is a perfectly valid and useful observation. Why deny one has a paradigm?

There is nothing wrong or suspect about this as long as people are open to ammending or revising their paradigm when confronted with fresh empirical evidence or conceptual advances.

Darwinism, or Neo-Darwinism provides a set of basic postulates that guides research. Some scientists are more conscious of it than others. Being unconscious of it (working in a paradigm) does not make it not so.

The interesting question is whether or not Lynn Margulis’ work fundamentally challenges core postulates of Neo-Darwinism thus requiring revision of the research program. My own point of view is that she does challenge the standard assumption that random, minor genetic mutations provide the primary or exclusive source of variation on which natural selection works.

In another sense she challenges some of the strong operating assumptions about explanatory methods employed by some Neo-Darwinists like Dawkins and Dennett who consciously view Neo-Darwinism as both philosophy and research program. On the other hand, she strikes me as being closer to the emergentist emphasis by Mayr and Dobzhansky.

Comment #46828

Posted by Miah on September 7, 2005 8:36 AM (e)

Timothy Chase wrote:

What matters is whether or not the virus is able to integrate itself into the genome of the gamete (i.e., reproductive cell).

First of all Timothy, I appreciate the explaination, I am looking into the references you provided for me.

So per my post on this, as long as the virus integrates inself, then what I purposed is possible? In essence you could have an airborne AIDS virus if LGT between an AIDS virus and an airborne virus.

Don’t think I’d like that kind of evolutionary prediction.

Timothy Chase wrote:

Her theory appears to be that persistent bacterial or viral infections may become endosymbiotic, thus modifying tissues and organs.

Isn’t that what we see happening with tumors and cancerous cells. I know it hasn’t been linked directly to a virus, but seems that mutation in the genetic reproduction of a cell which causes tumors and cancer. Would it be beyond causes from viruses that have yet to be identified?

It seems that you have a wonderful knowledge base with regards to Genetics…I ask in all sincerity…Timothy, do you have a degree in Genetics, or is this something with wich you are extremely interrested in and well read up on?

Comment #46829

Posted by Miah on September 7, 2005 8:44 AM (e)

Timothy Chase wrote:

At the same time, there are certain limited contexts in which it makes sense outside of organelles. For example, the gut requires an ecological system of bacteria for proper digestion.

I was aware of this at a very younge age. And it had always facinated me that there were “bugs” inside my stomatch helping me eat my food.

A couple of questions that I started having soon after I had some introduction to genetics in high school but never found anyone to ask was this:

Where do these bacteria come from? Does a fetus have them?

Any references would be great!

I mean if a fetus has them, how would that be possible? Would there be, at a certain time in developement, a transferr of these symbiotic friends through the umbilical cord? Or is it possible that the DNA from the unity of sperm & egg with all of those “junk” DNA actually blueprints for these biological “playground” in our stomach?

Any help on clearing this up would be wonderful too!

Comment #46830

Posted by Timothy Chase on September 7, 2005 9:06 AM (e)

First of all Timothy, I appreciate the explaination, I am looking into the references you provided for me.

So per my post on this, as long as the virus integrates inself, then what I purposed is possible? In essence you could have an airborne AIDS virus if LGT between an AIDS virus and an airborne virus.

Don’t think I’d like that kind of evolutionary prediction.

Actually it already happened. They were using mice at one point to test the effectiveness of HIV vaccines, and didn’t realize they were infected with an airborne retrovirus. I believe it may have been Mouse Mammary Tumour Virus, but that is one detail I don’t have. In anycase, they deliberately infected the mice with HIV, and the coinfection lead to a hybrid. Fortunately the virus didn’t get out.

Isn’t that what we see happening with tumors and cancerous cells. I know it hasn’t been linked directly to a virus, but seems that mutation in the genetic reproduction of a cell which causes tumors and cancer. Would it be beyond causes from viruses that have yet to be identified?

It seems that you have a wonderful knowledge base with regards to Genetics…I ask in all sincerity…Timothy, do you have a degree in Genetics, or is this something with wich you are extremely interrested in and well read up on?

Honestly, I know very little, but I know more than I did a few months ago. Just something I am interested in and hope to learn more about.

Comment #46832

Posted by Russell on September 7, 2005 9:25 AM (e)

Actually it already happened. They were using mice at one point to test the effectiveness of HIV vaccines, and didn’t realize they were infected with an airborne retrovirus

This virologist is not so sure about that, and would like to see references.

I can’t think of any retroviruses that are readily spread via the airborne route. Various mouse strains are riddled with various retroviruses that are transmitted both through the germline and otherwise (In the case of mammary tumor virus, through milk). But none of them are very good at spreading like flu or cold viruses. Like everything else, viruses have been honed by natural selection, and it’s not easy to back out of a niche you’ve spent millions/billions of generations perfecting.

Also, you can take some comfort in knowing that any virus that is really efficient at killing its host will be weeded out by natural selection - at least in the long run!

Comment #46835

Posted by Pierce R. Butler on September 7, 2005 9:31 AM (e)

Timothy Chase: ‘sallright, no bones broken. ;-)

Lynn Margulis’ theory appears to be that persistent bacterial or viral infections may become endosymbiotic, thus modifying tissues and organs.

“Appears to be” - so Dr. M. has not explicitly written this up in a detailed paper?

How often do such infections incorporate themselves into germ cells (the only way they could become genetically significant, right?)?

For example, the gut requires an ecological system of bacteria for proper digestion.

Are these bacteria inherited (in a strict sense) or acquired in utero or postpartum?

And we have identified some viruses which to some extent control the behavior of the host.

Do I recall correctly that a connection has been recently identified between AIDS & increased libido?

…Margulis has built a great deal upon the her theory that the eukaryotic flagella originated as spirochettes…

Has she been subjected to quote mining from Behe & his fellow ID, um, flagellators?

…I suspect that sexual reproduction had its origin in endosymbiosis.

Said “origin” occurring in a unicellular or multicellular organism? If the former, this would support Margulis’s earlier work on eukaryotes; if the latter, it would support her later(?) ideas in question here (and provoke more questions from me).

…I would recognize along with Margulis the roles of endosymbiosis and exosymbiosis in driving the evolution of species…

In this context, this role would seem to be part of what’s meant by “environment” in the classic version of natural selection, not the radically different mechanism of symbiogenesis (in multicellular organisms) which Margulis seems to be proposing & I’m failing to comprehend - or am I also slipping on a banana peel in trying to follow your explanation?

…the existence and importance of a hierarchy of ecological systems…

Another fascinating set of ideas, elegantly described in a book title, The Ecological Theater, The Evolutionary Play - but perhaps a bit off-topic at present.

Thanks to you, normdoering, Miah, et al, for your attempts to clarify deep issues to a shallow dabbler!

Comment #46838

Posted by Miah on September 7, 2005 9:52 AM (e)

Pierce, I wouldn’t consider you a shallow dabbler. You have presented some intense questions that I am very much looking forward to be answered.

Maybe you’re more of a “provocative” dabbler?!?

Pierce wrote:

Are these bacteria inherited (in a strict sense) or acquired in utero or postpartum?

That is the same question I am asking. I just didn’t put it so…so….eloquently.

Russell wrote:

This virologist is not so sure about that, and would like to see references.

I’m not a virologist, but I would like to see a reference regarding this as well.

Russell wrote:

Also, you can take some comfort in knowing that any virus that is really efficient at killing its host will be weeded out by natural selection - at least in the long run!

I don’t know if I share in your sentiment regarding this. Seems that the more we throw at these viruses and bacteria, the more resistant they become. Evolution at it’s finest! Will there be a day when there is a virus that cannot be wiped out due to it’s exreme resilliance. Remember evolution does not pick sides, if a species cannot adapt to it’s environment, or if the species cannot adapt it’s enviroment to provide for survival, then that species runs the risk of becomming extinct. It has happened many times.

Am I remembering correctly when I heard the AIDS virus also called the Doomsday virus? Or did I just make that up?

Hey Russell, is there a website dedicated to the latest findings on AIDS and the fight against it, or possible cures. I figure askin a virologist would be the best way to go.

Comment #46840

Posted by Pastor Bentonit on September 7, 2005 10:06 AM (e)

miah wrote:

I was aware of this at a very younge age. And it had always facinated me that there were “bugs” inside my stomatch helping me eat my food.

A couple of questions that I started having soon after I had some introduction to genetics in high school but never found anyone to ask was this:

Where do these bacteria come from? Does a fetus have them?

Start here and go through the references if you can access them. In short, the fetus/unborn baby should be sterile (germ-free) in the womb and becomes colonized by skin and intestinal bacterial flora from the mother at birth. Further development of the intestinal flora depends (naturally) on food intake. Breast milk is surely also sterile until it is “delivered”, at this moment skin bacteria will contaminate it.

/The Rev.

Comment #46844

Posted by Timothy Chase on September 7, 2005 10:50 AM (e)

This virologist is not so sure about that, and would like to see references.

I can’t think of any retroviruses that are readily spread via the airborne route. Various mouse strains are riddled with various retroviruses that are transmitted both through the germline and otherwise (In the case of mammary tumor virus, through milk). But none of them are very good at spreading like flu or cold viruses. Like everything else, viruses have been honed by natural selection, and it’s not easy to back out of a niche you’ve spent millions/billions of generations perfecting.

Also, you can take some comfort in knowing that any virus that is really efficient at killing its host will be weeded out by natural selection - at least in the long run!

I don’t believe I have the article immediately available. However, I remember the main subject of the paper was the discussion of the theory that HIV spread to humans by means of the polio vaccine – and the paper detailed some of the refutation of this theory, while admiting that at least one previous vaccine had inadvertently infected humans with a new virus. But as I understand it, essentially, what HIV would require is the appropriate protein envelope to prevent it from drying out. Wouldn’t be that different from the airborne form of ebola which spreads between green monkeys – indeed, the two viruses appear to be closely related.

Incidentally, even an airborne HIV wouldn’t wipe out the human species: from what I understand, about 10% of europeans are immune. (I believe they are primarily of scandinavian descent.) Evidentally they were exposed to virus which made use of the same receptors over an extended period of time, and their immunity to that virus inadvertently resulted in an immunity to HIV. At the same time, any nonsense which gets in the way of good science – as Intelligent Design threatens to do – diminishes our ability to combat possible viral threats to humanity in the future.

Anyway – I will do a little looking around. Just starting work, but I can take a little time out. Might have the article back at the house, though.

Comment #46847

Posted by Miah on September 7, 2005 11:10 AM (e)

Thanks Pastor Bentonit for that reference and article. I am reading it now.

I find it very facinating.

Timothy, I’ll be looking forward to getting some references from you regarding that “airborne HIV” virus and per your most rescent post…the ability of immunity of europeans of Scandinavian descent.

Timothy Chase wrote:

At the same time, any nonsense which gets in the way of good science — as Intelligent Design threatens to do — diminishes our ability to combat possible viral threats to humanity in the future.

Touche!

Right on

Ramen, brother!

Comment #46848

Posted by Russell on September 7, 2005 11:13 AM (e)

I don’t know if I share in your sentiment regarding [how viruses too lethal to their hosts die out].

Well, it’s true in the long run. Hosts can survive without parasites, but parasites need their hosts. (And, of course, as is the subject of this whole thread, hosts can evolve to take advantage of, depend on, or even “adopt” their parasites.) In the short run, you have things like Ebola virus outbreaks.

Seems that the more we throw at these viruses and bacteria, the more resistant they become. Evolution at it’s finest!

Fortunately, the creationists have exempted the study of such phenomena from their “critical analyses” under the “microevolution” clause.

Will there be a day when there is a virus that cannot be wiped out due to it’s exreme resilliance.

Wake up and smell the coffee! (if you don’t have one of those un-wipe-outable respiratory viruses that disables your sense of smell)

Am I remembering correctly when I heard the AIDS virus also called the Doomsday virus?

Oh, probably. But I think that might be a little overdramatic. Then again, if I lived in southern Africa, I might not think so.

is there a website dedicated to the latest findings on AIDS and the fight against it, or possible cures.

That’s a good question. I know of several misinformation sites, like Phil “godfather of ID” Johnson’s. And there’s this general information site. But the latest breaking reliable research news is generally vetted in technical journals before it shows up as “the word on the street”. (Though, of course, there are some who feel that high school health classes should “teach the controversy”, that HIV doesn’t cause AIDS, for instance).

I’ll see if I can find a sort of HIV/AIDS equivalent to Panda’s Thumb.

Comment #46853

Posted by Russell on September 7, 2005 11:31 AM (e)

…the theory that HIV spread to humans by means of the polio vaccine — and the paper detailed some of the refutation of this theory

There was a book several years ago called “The River”, in which the author advanced this hypothesis. I believe it’s been pretty convincingly disproved, but the refutation is very boring compared with a good conspiracy theory.

at least one previous vaccine had inadvertently infected humans with a new virus.

One of the preparations of the Salk polio vaccine turned out to have a so-called tumor virus (“SV40”) contaminant. Definitely a mistake, but I don’t know of any documented disease traced to it.

… what HIV would require is the appropriate protein envelope to prevent it from drying out.

Fortunately, there’s quite a bit more to it than that, and it’s a really daunting challenge. That’s why you generally don’t see viruses that spread by one means suddenly - efficiently - adopting another.

Wouldn’t be that different from the airborne form of ebola which spreads between green monkeys — indeed, the two viruses appear to be closely related.

Actually, no, they’re completely unrelated in an evolutionary sense, though they’re both RNA-genome viruses with a lipid envelope.

Comment #46858

Posted by Timothy Chase on September 7, 2005 11:43 AM (e)

Pierce R. Butler wrote:

“Appears to be” - so Dr. M. has not explicitly written this up in a detailed paper?

I honestly wouldn’t know. I was going off articles I found on the web – and they weren’t particularly technical. (In all honesty, I am more interested in the work of Frank Ryan, Luis P. Villarreal and others – where I am far more likely to look into the technical research.)

How often do such infections incorporate themselves into germ cells (the only way they could become genetically significant, right?)?

You would certainly think. Of course, this would still leave us with the question of how bacteria get into the gut – and below you suggest a number of possibilities which seem quite reasonable.

However, I myself do not believe that her view with regard to this matter makes much of any sense.

Do I recall correctly that a connection has been recently identified between AIDS & increased libido?

I personally haven’t heard anything along those lines. The possibility of a venereal disease which increases libido is an interesting one, something I have toyed with in my own imagination, but as far as I know, it is just science fiction – although it wouldn’t surprise me in the least if a hate group incorporated a fiction along these lines in their literature as fact. But it is well-known that many parasites (including viruses) manipulate host behavior in ways that will increase the likelyhood of their horizontal transmission. Rabies, for example, increases agressive, biting behavior.

Has she been subjected to quote mining from Behe & his fellow ID, um, flagellators?

Certainly. If you write about evolution and offer a solution to what you perceive as a problem with the mainstream approach, you might as well submit your articles to the Discovery Institute for the express purpose of being misquoted. But moreover, her rhetoric (like Stephen J. Gould’s) has lent itself to being misquoted. Any time you argue against “Darwinism” or “Neo-Darwinism” per se, you are setting yourself up for this – as both are synonyms for evolutionary theory in popular literature and the understanding of the general public.

Said “origin” [of sexual reproduction] occurring in a unicellular or multicellular organism? If the former, this would support Margulis’s earlier work on eukaryotes; if the latter, it would support her later(?) ideas in question here (and provoke more questions from me).

Unicellular. I don’t know of any suggestion on her part regarding sexual reproduction at the multicellular level.

In this context, this role would seem to be part of what’s meant by “environment” in the classic version of natural selection, not the radically different mechanism of symbiogenesis (in multicellular organisms) which Margulis seems to be proposing & I’m failing to comprehend - or am I also slipping on a banana peel in trying to follow your explanation?

Agreed – it is part of the environment. But from what I understand, the role of symbiosis in evolution was largely downplayed for a long time by mainstream evolutionists.

As I state, “Lynn Margulis’ theory appears to be that persistent bacterial or viral infections may become endosymbiotic, thus modifying tissues and organs. Once one gets beyond the bacterial origin of the mitochondria and chloroplasts, this view is controversial to say the least, and it is NOT something which I myself generally agree with….

“My own view is that the role played by infection is typically far more indirect, although perhaps no less important. Some viruses contribute some material to the genome of their host, but far more importantly, contribute the machinery by which the genome is modified over time. Thus, for example, retrotransposons have their origin in retroviruses, and currently it appears that transposons have their origin in single-stranded DNA viruses.”

Another fascinating set of ideas [i.e., the hierarchy of ecological systems], elegantly described in a book title, The Ecological Theater, The Evolutionary Play - but perhaps a bit off-topic at present.

I will have to look it up.

Thanks to you, normdoering, Miah, et al, for your attempts to clarify deep issues to a shallow dabbler!

You definitely seem to be on the ball!

Take care, and once again my apologies for the earlier misunderstanding.

Comment #46861

Posted by Russell on September 7, 2005 11:59 AM (e)

… a connection … between AIDS & increased libido?

I haven’t heard of that either, but it doesn’t seem too far-fetched relative to this story in yesterday’s NY Times:

Only in science fiction do people’s minds get possessed by alien beings. For grasshoppers, zombification is an everyday hazard, and it obliges them to end their lives in a bizarre manner….
[A] parasite, known as a hairworm, lives and breeds in fresh water. But it spends the early part of its life cycle eating away the innards of the grasshoppers and crickets it infects.

When it is fully grown, it faces a difficult problem, that of returning to water. So it has evolved a clever way of influencing its host to deliver just one further service - the stricken grasshopper looks for water and dives in….
“We found the parasite produces and injects proteins into the brain of its host,”

The article cites, incidentally, the more familiar case of rabies virus, which influences its host’s behavior in a way that promotes its transmission.

Comment #46867

Posted by Miah on September 7, 2005 12:45 PM (e)

Whoa!!! That is a crazy article Russell. Totally blew my mind.

So this parasite injects proteins into it’s host as a form of mind controll?

Russell wrote:

Hosts can survive without parasites, but parasites need their hosts.

Aren’t parasites a bit different than symbiotic entities.

A symbiotic relationship requires the host to remain alive to a mutual benefit. Whereas a parasite can accept the destruction of their host and lie dormant until another “host” comes along.

Of course it would seem that since I was talking about viruses and such, I would see why you’d divert over to parasites. I guess I should fault myself for seeing a relationship with viruses as symbiotic, when it truth it is more parasitic. My apologies.

I guess a good question might be the relationship of a viruses ability to survive outside it’s host, versus it ability to become dormant.

Russell wrote:

Wake up and smell the coffee! (if you don’t have one of those un-wipe-outable respiratory viruses that disables your sense of smell)

Sorry, my sarcasm/humor detector and decypherer must be not working. Can you elaborate what you meant by this. Thanks.

Comment #46868

Posted by SEF on September 7, 2005 12:53 PM (e)

Symbiosis can become pretty obligate, even for reproduction. I was trying to find something online on the orchid-fungus example. This site may not be the best but it has some other items too.

Ah, on preview I see more posts. In that case, on the freaky side there are also the infected snails with brightly coloured swirling eyestalks who are driven to make themselves visible to birds so that the parasite can get transferred.

Comment #46872

Posted by Russell on September 7, 2005 1:17 PM (e)

Aren’t parasites a bit different than symbiotic entities.

[different from, Miah, not different than, but that’s a whole other topic…]
I would suggest that the organisms in question don’t spend too much time on the semantic differences between “symbiont” and “parasite”. Generally speaking, viruses all appear to be “parasites”, but there’s one retrovirus, for instance, without which a human could not make a functional placenta. You tell me: “parasite” or symbiont”? Likewise, I don’t think the ancestral eukaryotic (nuclear) host and the ancestral mitochondrion signed a prenuptual agreement before hooking up. I suspect what started out parasitic, evolved into symbiotic.

….a good question might be the relationship of a viruses ability to survive outside it’s host, versus it ability to become dormant.

Viruses vary all over the map on this one. You could probably catch polio from an Egyptian tomb, for instance, but HIV or hepatitis B viruses have to be pretty much continuously bathed in body fluid.

Wake up and smell the coffee! (if you don’t have one of those un-wipe-outable respiratory viruses that disables your sense of smell)

Sorry, my sarcasm/humor detector and decypherer must be not working. Can you elaborate what you meant by this. Thanks.

Sorry. I’m really not trying to be sarcastic - just amusing. The point I was trying to make was that there are very few viruses we can even think about eradicating. For most of them - unlike bacteria - we have no drugs at all. (HIV and a couple of herpes viruses would be among the exceptions). I guess the “good news” is we don’t have to worry about their gaining resistance to our (nonexistent) antiviral drugs!

Comment #46876

Posted by Timothy Chase on September 7, 2005 1:47 PM (e)

Fortunately, there’s quite a bit more to it than that, and it’s a really daunting challenge. That’s why you generally don’t see viruses that spread by one means suddenly - efficiently - adopting another.

Yes – anytime a virus leaps from one species to another, it is inefficient in doing so. Likewise, anytime a virus develops a new vector for infection, it will be inefficient. In fact, one of the theories regarding how HIV was able to establish itself in the human population is that dirty needles were used a great deal in Africa, spreading HIV long enough so that it could adapt to sexual transmission in humans. Of course, what I find particularly interesting is the tendency towards a lack of pathogency in the natural host. In the longrun, viruses often tend towards a persistent, asympotomatic infection.

Actually, no, they’re completely unrelated in an evolutionary sense, though they’re both RNA-genome viruses with a lipid envelope.

I realize of course that both Ebola and Marburg are filoviruses whereas HIV is a lentivirus – and that there are some important differences between these clades. However, there is accumulating evidence that even more distant viruses are related:

AEGiS-Reuters: Measles, HIV, Ebola May All Be Related
http://www.aegis.com/news/re/1999/RE990316.html

Moreover, there are other mechanisms in common between HIV-1 and Ebola which would suggest that they are more closely related than we have thought in the past:

TSG101: An Antiviral Target with a Murky Past
http://www.unmc.edu/wagnerlab/publications/papers/The_Scientist_January_2004.pdf
“… Certain killer viruses, including HIV, Ebola, and Marburg, hijack this transport system using TSG101 protein to cloak themselves in membranous escape pods.”

Retrovirus and filovirus “immunosuppressive motif” and the evolution of virus pathogenicity in HIV-1, HIV-2, and Ebola viruses.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8828145&dopt=Abstract

Timothy, I’ll be looking forward to getting some references from you regarding that “airborne HIV” virus and per your most rescent post…the ability of immunity of europeans of Scandinavian descent.

My apologies, but the “airborne HIV” may have to wait until I get home – I am having as much difficulty locating that article as the last time (which I believe may have resulted in my saving the pdf at home when I finally succeeded in finding it).

However, as for the Europeans, you may want to check:

Biologists discover why 10% of Europeans are safe from HIV infection
http://www.news-medical.net/?id=8335

Comment #46878

Posted by steve on September 7, 2005 1:49 PM (e)

by the way, I’m digging on this new nested comment capability

Comment #46884

Posted by Pierce R. Butler on September 7, 2005 2:09 PM (e)

Note: the following comments were written as a single item, and accepted as such by the PT preview option, but were “denied for questionable content” after attempts to post. Therefore, I’m posting them piece by piece in hopes of identifying the “questionable” parts (and in further hopes of encouraging the PT software gurus to either incorporate the posting nannyware functions into the preview mechanism, or maybe even to explicitly identify the screens used here).

…I myself do not believe that her view with regard to this matter makes much of any sense.

Me neither - and that’s what I was afraid of.

Comment #46885

Posted by Pierce R. Butler on September 7, 2005 2:13 PM (e)

…a connection…between AIDS & increased libido?

I think I saw this at newscientist.com - but their server seems to be out of whack at the moment, so I can’t search there to check on it.

Comment #46886

Posted by Pierce R. Butler on September 7, 2005 2:16 PM (e)

Aha! The “questionable content” was my link to the newscientist.com site - not any of the vocabulary I was frantically trying to prune…

I don’t know of any suggestion on her part regarding sexual reproduction at the multicellular level.

Margulis (above): “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.”

Hmmm - could she mean unicellular “animals, plants, and fungi”? Maybe that’s the basis of my confusion, as I read it to mean multicellular organisms…

…from what I understand, the role of symbiosis in evolution was largely downplayed for a long time by mainstream evolutionists.

As was the role of cooperation short of symbiosis, despite attempts to draw attention to it by Kropotkin & others for many decades. SFAIK, the earlier emphasis on competition was driven by individualist/capitalist cultural imperatives, and the “correction” came from the “sixties” communalist/feminist backlash; whether we’re closer to equilibrium now only future historians can say.

Some viruses contribute some material to the genome of their host, but far more importantly, contribute the machinery by which the genome is modified over time. Thus, for example, retrotransposons have their origin in retroviruses…

Perhaps analogous to a student who gets more value from scribbling on the blank backsides of lecture handouts than from the text on the front?

….The Ecological Theater, The Evolutionary Play

I will have to look it up…

Warning: this book seemed rather dated when I encountered it in the ’70s, though I still greatly admire the title.

You definitely seem to be on the ball!

Only in the sense in which you might visualize a circus clown act of that description…

Comment #46887

Posted by Steviepinhead on September 7, 2005 2:23 PM (e)

While I’ve been composing, other commentators have been posting, elaborating on some of this, but I’ll take my whack as well:

To understand the contention that an initially “inimical” parasite-host relationship may–at least in some cases–tend to evolve toward a less-inimical, more “symbiotic” relationship, we can use HIV as an example.

As we know all too well, HIV is a very recent human parasite, and its effects are highly deleterious. Yet, the homologous SIV viruses in our primate relatives seem not to have nearly as detrimental an effect. We hypothesize that the parasite and host have “learned” to live with one another over some longer period of time. Why?

We first need to know something about the lifestyle of our primate brethren: we learn that green monkeys, for example, live in small bands which interact only infrequently with other small bands, in an overall pattern of a sparse and widely-spread population. Because interactions among distinct bands of primates are relatively rare, the parasite will be “hurting itself” if it kills off all the locally-infected primates before it can become established in a new band.

Thus, the virus will more likely survive over the long term if (a) the impact of infection on the local host is relatively mild (not quickly lethal), but if (b)–on the rare occasions when it has an “opportunity” to infect an out-group primate–its mode of transmission is relatively efficient.

The impact of infection (a) and the effectiveness of transmission (b) will tend to seesaw back and forth until they reach some sort of equilibrium–strains of the virus having a milder effect will tend to survive longer in relatively-isolated populations, as will strains that may not be quite so mild, but which take very effective advantage of the available modes of inter-band transmission.

Given the small, sparsely-spread monkey bands, and the manner in which these bands interact–or don’t–with one another, one can see now begin to see how airborne transmission might not be very effective, but blood and body-fluid transmission might be much more effective.

We can also begin to see why, over time, the monkey host and the virus parasite would evolve toward a tolerable, if not precisely comfortable, co-existence.

A parasite that has recently “found” a new host is in a different situation. However HIV first “acquired” human hosts–perhaps through increasing human population and increading penetration of the deep forests, along with such practices as the opportunistic exploitation of “bush meat” for food, you wind up with a virus infecting a host that has not had a chance to evolve defenses.

As a consequence, the virus may have a much more deleterious impact on the “new” human host than on the former green monkey host. Counterintuitively, perhaps, this may have a deleterious impact on the “new” parasite, as well. Despite its initially-successful “conquest” of a new niche, the virus may promptly die out, because the previously “mild” impact of infection on the old, well-defended monkey host turns out to be quickly lethal to the new, defenseless human host–who dies before the virus can be transmitted.

The virus may die out again and again until the right combination of dense population and variation in the virus strain allows at least some of the human hosts to live long enough to share food or sex with other humans, who live long enough, etc. We now have HIV instead of SIV, and we now have an epidemic instead of a tolerable nuisance-level infection.

Of course, something similar may have happened early on in the SIV-green monkey relationship, and it may be possible to find evidence in the monkey genome of the evolution of defenses against a more-virulent ancestral virus.

None of this is any guarantee that HIV will tend to evolve toward a more “benign” relationship with humans, since–unlike our free-living primate cousins–we now live in highly-populous, fluidly-overlapping, and densely-interacting “bands.” A virulent, highly-transmissible, and fast-mutating virus may survive for quite some time without running out of available hosts…

So, the more-virulent to more-benign, parasite-to-symbiote scenario may make sense some of the time, but not all of the time.

And, note that–while the above scenario has elements of a “Just-So Story”–one can also see how, if both it and our current grasp of evolutionary principles are correct, testible predictions can be generated. One would expect to find given things in the monkey genome and immune responses, in the genomes and immune responses of populaces that have lived near the green monkeys–and perhaps been repeatedly-infected at low levels by previous strains of SIV > HIV, and so forth.

What ID would “predict” about any of this, or what other useful things it may tell us about the past history and future cure for HIV/AIDS–

–well, I expect that’s another particularly sad instance of [crickets chirping]

Comment #46889

Posted by Steviepinhead on September 7, 2005 2:37 PM (e)

With regard to an HIV-increased libido “connection”:

It would seem unlikely that HIV has had enough time to “get to know” our behavioral triggers that intimately.

However, the early highly-publicized “vectors” of the disease are likely to have been individuals who happened to indulge in a libidinous or, to employ the politico-religious code phrase, “promiscuous” lifestyle.

And I expect human psychology may play a part–varying from attempts to unjustly “punish” innocent others for one’s own unjust suffering to some sort of a live-for-the-moment, tomorrow-I-die attitude.

I would be greatly surpised if we now know something about the mechanics of the viral interaction with the host that would allow us to generalize from these rather extreme behaviors of isolated individuals under severe pressure. But I’d better go check out newscientist before I saw off that particular limb.

Comment #46892

Posted by Timothy Chase on September 7, 2005 2:44 PM (e)

Steviepinhead wrote:

While I’ve been composing, other commentators have been posting, elaborating on some of this, but I’ll take my whack as well: …

All of this appears to be right on target to me, Lenny.

Comment #46895

Posted by Steviepinhead on September 7, 2005 2:52 PM (e)

Timothy Chase said:

All of this appears to be right on target to me, Lenny.

Eh? I’ll admit to occasionally posting as Lenny’s Pizza Boy (though I’m not the only one), but never as the iminitable Rev. Dr. himself…

I couldn’t hold a candle to his style, even if I were foolish enough to try.

Comment #46896

Posted by Steviepinhead on September 7, 2005 2:54 PM (e)

Heck, I can’t even spell “inimitable,” much less complicated words like Wedge or Ahmanson…

Comment #46904

Posted by Pierce R. Butler on September 7, 2005 3:23 PM (e)

Further aha!

My “questionable content” flag was apparently raised by using an “a href” link instead of a “url href” link to New Scientist.

And the not-so-recent HIV/libido link story can be found, not there, but at http://www.rense.com/general2/hivnt.htm -

HIV May Increase Sexual Desire, Study Finds
http://dailynews.yahoo.com/h/nm/20000712/sc/aids_desire_dc_1.html

DURBAN, South Africa (Reuters) - Infection with the AIDS virus could make men more amorous, which could make them more likely to pass on the virus, U.S. researchers said on Wednesday.

A team at the University of California, Berkeley, said they were checking out one of the basic premises behind natural selection – that organisms that happen to create conditions favorable to themselves will out-compete other organisms and thus become more numerous.

“From an evolutionary perspective, HIV would benefit by influencing its human host to increase sexual activity,” they said in a presentation to the 13th International AIDS Conference in Durban.

Philip Starks and colleagues checked studies that measured testosterone levels in male and female HIV patients. The hormone affects sex drive in both men and women.

“Although testosterone levels generally decrease during later stages of the disease, testosterone levels appear to be elevated in early stages of infection for HIV positive males,” they said.

They did not find the same effect in women, but men needed to be told about the risk.

“Males at risk, or in early stages of infection, should be counseled that HIV infection may increase sexual desire.”

Comment #46905

Posted by Timothy Chase on September 7, 2005 3:26 PM (e)

I don’t know of any suggestion on her part regarding sexual reproduction at the multicellular level.

Margulis (above): “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.”

Hmmm - could she mean unicellular “animals, plants, and fungi”? Maybe that’s the basis of my confusion, as I read it to mean multicellular organisms…

In the earlier part of her career, she focused on symbiosis between single-celled organisms. As I remember, she explained sexual reproduction in that context. The most plausible theory I am aware of is that sex originally would have involved a case of indigestion or infection. But obviously it has since developed into a very well-tuned mechanism for reproduction.

Of course, if you are talking tissues or organs, then you are speaking of a multi-cellular host and most likely bacteria or a virus – but this is later in her career.

As was the role of cooperation short of symbiosis, despite attempts to draw attention to it by Kropotkin & others for many decades. SFAIK, the earlier emphasis on competition was driven by individualist/capitalist cultural imperatives, and the “correction” came from the “sixties” communalist/feminist backlash; whether we’re closer to equilibrium now only future historians can say.

That is how the Marxist in her would explain it – science as the product of an economic ideology. There may or may not be some truth in this, but I personally do not know enough to say. What is important to me is simply recognizing the insights no matter what school they come from, recognizing the limitations of those insights, and then attempting to develop an integrated understanding which incorporates those insights. (Then again, this may just be a bad habit I picked up from Aristotle.)

Some viruses contribute some material to the genome of their host, but far more importantly, contribute the machinery by which the genome is modified over time. Thus, for example, retrotransposons have their origin in retroviruses…

Perhaps analogous to a student who gets more value from scribbling on the blank backsides of lecture handouts than from the text on the front?

Well, the debt that we owe to retroviruses (or perhaps their ancestors) probably runs pretty deep. I have suggested as much with respect to the placenta. But if an RNA-World preceded a DNA-World, retroviruses were probably there at the transition. Moreover, as eukaryotic multicellular organisms have linear chromosomes, they necessarily have telomeres which become shorter during mitosis as part of the aging process. But in the gametes (and a few other places), telomeres are lengthened by telomerase (found in chromosome 5 in humans). But telomerase itself is homologous to the reverse transcriptase of retroviruses – and probably descended from it.

Warning: this book seemed rather dated when I encountered it in the ’70s, though I still greatly admire the title.

I will keep that in mind…

Comment #46906

Posted by Miah on September 7, 2005 3:27 PM (e)

Russell wrote:

The point I was trying to make was that there are very few viruses we can even think about eradicating. For most of them - unlike bacteria - we have no drugs at all.

Gosh…brain fart on my part. Of course, I don’t know why I was trying to imply eradication of viruses…shees! I need a V8!

Sorry for not catching that sooner. Boy is my face red.

I sincerely appreciate you clarifying that though. Even in the amusing way you put it.

Timothy:

Thanks for that interresting read. I enjoyed it much.

Steviepinhead:

Excellent read as well. I am sure there is other factors that can play an important prediction in the evolutionary role of HIV, from a seemingly parasitic virus to a symbiotic one. But I am definately facinated by what you wrote here on it.

Steviepinhead wrote:

What ID would “predict” about any of this, or what other useful things it may tell us about the past history and future cure for HIV/AIDS—

I think we should ask one of them.

YUP - still hear crickets chirping.

Steviepinhead wrote:

with one another, one can see now begin to see how airborne transmission might not be very effective, but blood and body-fluid transmission might be much more effective.

With regards to your “bush-meat” theory. I would have to say that I wouldn’t rule that out. And help my confusion here, but I was under the impression that viruses cannot survive in our stomachs…let alone after being cooked. Now, if you are implying that as a result of the hunt and blood splatter causing the infection, then I understand and would retract my previous statement.

With regards to the quote above: would it be safe to predict a straind of SIV that could have been “airborne”? Say in it’s past? Of course if it wasn’t as effective then natural selection would have singled that out for extinction? I mean one would have to find the right genetic “stuff” to confirm this…right?

Comment #46908

Posted by Steviepinhead on September 7, 2005 3:38 PM (e)

Miah, re “bush meat,” that’s just one hypothesis that I’ve read. But one can certainly picture hunters, transporters, or purveyors of live meat getting bitten, or being exposed to blood, body fluids, etc., in various ways that are not too hard to imagine at various stages of hunting, butchering, transporting, even eating (perhaps certain organs are eaten raw; cooking may not always be thorough; there could be cuts or sores on the hands or in the oral tract; etc.).

Whether ancestral SIV might have been airborne, I just don’t know. I won’t have the time to read the interesting references to relationships among the viruses today, so you’ll probably be well ahead of me…!

Comment #46913

Posted by mike syvanen on September 7, 2005 4:53 PM (e)

pete wrote:

“Margulis is far from the only one who has done research confirming the idea.”

Actually she did not confirm the idea. Woese did. She was simply its most prominant advocate after the death of Mereschovsky about 50 years ealier.

Comment #46919

Posted by Timothy Chase on September 7, 2005 5:21 PM (e)

Pierce R. Butler wrote:

…a connection…between AIDS & increased libido?

I think I saw this at newscientist.com - but their server seems to be out of whack at the moment, so I can’t search there to check on it.

Yes!! It really does work that way!

Hey, wait a second… :-(

Oh Sh*t!!!

In truth, this shouldn’t seem that surprising as HIV clearly mutates very rapidly, and even against the best minds which humanity has to offer, it is still playing one wicked game of chess.

Additionally, it has had plenty of time to learn about other primates, and as far as a virus is concerned, there isn’t that much of a difference between between humans and other old world primates – heck, there isn’t that much of a difference between humans and rodents, as far as they are concerned. Particularly in that part of the brain responsible for libido (which is presumably the amygdala), I would suspect.

At the same time, steviepinhead is correct regarding some of the other causal factors.

Thank you for the link…

Me neither - and that’s what I was afraid of.

Agreed – yet there are things which trouble me more – in particular, the connection with NAM. Hopefully having received some general recognition for her achievements will lessen the tendency towards this. But in the long run it probably won’t matter.

Comment #46925

Posted by Pierce R. Butler on September 7, 2005 6:09 PM (e)

The most plausible theory I am aware of is that sex originally would have involved a case of indigestion or infection.

Oooh, what a terrific straight line…

…if you are talking tissues or organs, then you are speaking of a multi-cellular host…

Which is precisely why all this talk of symbiogenesis & evolution got me so confused.

…science as the product of an economic ideology. There may or may not be some truth in this…

I’d say “science as influenced by sociocultural dominants”, but I think we’re in basic agreement here.

…the debt that we owe to retroviruses (or perhaps their ancestors) probably runs pretty deep… telomerase (found in chromosome 5 in humans)… itself is homologous to the reverse transcriptase of retroviruses — and probably descended from it.

So it may be possible, at least in theory, to assess how much of our DNA is derived from viruses and how much from bacteria? Cool (not least because of how it would send the fundies into spasms!)…

Comment #46928

Posted by Pierce R. Butler on September 7, 2005 6:18 PM (e)

…there are things which trouble me more — in particular, the connection with NAM.

There just aren’t enough acronyms to go around. What does Lynn Margulis have to do with either the New American Movement or the National Association of Manufacturers (and why does this trouble you)?

Comment #46932

Posted by 'Rev Dr' Lenny Flank on September 7, 2005 6:32 PM (e)

Where do these bacteria come from? Does a fetus have them?

Can’t speak to humans, but I do know that hatchling iguanas, who never even see their mothers, get their gut bacteria by “coprophagy”. To avoid triggering all the Net Nanny software, I think I’ll let everyone figure out for themselves what that means …. ;>

Captive iguanas who are raised alone, of course, don’t have access to the, uh, droppings of older iguanas, so they can’t get their little microbes that way. Apparently they get ‘em by swallowing them in their environment (in food, water, soil, etc etc etc). I’d imagine, though, that the process isn’t as efficient as the wild iguanas, happily munching their older compatriot’s, uh, poop.

Comment #46933

Posted by 'Rev Dr' Lenny Flank on September 7, 2005 6:37 PM (e)

Steviepinhead wrote:

While I’ve been composing, other commentators have been posting, elaborating on some of this, but I’ll take my whack as well: …

All of this appears to be right on target to me, Lenny.

Um, thanks, but this wasn’t me. :>

Comment #46961

Posted by Pastor Bentonit on September 7, 2005 11:26 PM (e)

Lenny wrote:

Can’t speak to humans, but I do know that hatchling iguanas, who never even see their mothers, get their gut bacteria by “coprophagy”. To avoid triggering all the Net Nanny software, I think I’ll let everyone figure out for themselves what that means.

Hey, I bet that means that baby iguanas are good little Dembski acolytes then?

(Sorry, could absolutely not resist, and apologies to the iguanas).

Comment #46976

Posted by Harald Korneliussen on September 8, 2005 4:18 AM (e)

Everyone who has had a cat with kittens know what the mother cat does to transfer gut bacteria to their offspring. Yeeech!

Comment #46991

Posted by Miah on September 8, 2005 8:07 AM (e)

Steviepinhead:

I can see what you mean now with regards to the “bush meat” theory. Undercooking the meat, as well as possible organs that were eaten raw.

Hmmm…I wonder if transmission could have also occured if they made “tools” out of the monkey’s stomach (you know like was done with the buffalow…in that they used it for a drinking bottle)?

So it may be possible, at least in theory, to assess how much of our DNA is derived from viruses and how much from bacteria? Cool (not least because of how it would send the fundies into spasms!)…

LMAO!!! That is great!

I wonder if at any time in our ancestrial past the children ate, uh…well…poop.

Harold wrote:

Everyone who has had a cat with kittens know what the mother cat does to transfer gut bacteria to their offspring.

If you are referring to “transmission through ingestion of excrement”, I don’t follow. I have had cats (well not birthed by me) who gave birth, and I’ve only seen the mother cat feed on the excrement of her babies…same with dogs. But I don’t ever recall a time when the roll was reversed.

Could you elaborate for me about that Harold?
Thanks!

Comment #47002

Posted by Russell on September 8, 2005 9:51 AM (e)

With regard to “bush meat”:

First of all, bleccchhhh!

(Sorry. Had to get that out of my system. I know, different cultures and yadda, yadda, yadda… But still.)

Anyway, you’ll recall the SARS outbreak was linked to commerce in civet cat meat in southeast Asia. Same kind of dynamics, I would imagine, with HIV and “bush meat”.

Also - someone suggested that viruses can’t survive the digestive tract. That’s undoubtedly true for a lot of viruses (flu and HIV, for instance). But there are, as I’m sure we’ve all experienced, viruses that specialize in exactly that route, polio and rotaviruses being among the more notorious.

Comment #47006

Posted by Miah on September 8, 2005 10:21 AM (e)

Yeah, Russell, that was me that suggested that. It was more of an request for definate info, and not so much a true suggestion. Since I wasn’t convinced that my info was accurate and all.

As I always have told my kids; for every rule there is an exception.

As I tell other people I meet; I’ll try anything once, and if I like it…I’ll do it again.

Comment #47010

Posted by Joseph O'Donnell on September 8, 2005 10:55 AM (e)

If you are referring to “transmission through ingestion of excrement”, I don’t follow. I have had cats (well not birthed by me) who gave birth, and I’ve only seen the mother cat feed on the excrement of her babies…same with dogs. But I don’t ever recall a time when the roll was reversed.

The reason the mother cat eats the excrement is actually a fairly simple one. By eating the kittens poo she exposes her immune system to any bacteria or viruses the kittens may have picked up. This allows her to make antibodies to those pathogens, which then pass through her milk to the kittens passively immunising them.

The kittens get their flora within moments of birth mostly from the mothers licking, poop and other sources.

Comment #47016

Posted by Miah on September 8, 2005 11:30 AM (e)

If only ALL mothers were that loving. :o)

Comment #47018

Posted by Timothy Chase on September 8, 2005 11:36 AM (e)

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.”

Comment #47020

Posted by Timothy Chase on September 8, 2005 11:52 AM (e)

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.

Comment #47023

Posted by Timothy Chase on September 8, 2005 12:04 PM (e)

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/life/mg18725164.600

Comment #47115

Posted by justin on September 9, 2005 1:22 AM (e)

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.

Comment #47135

Posted by Miah on September 9, 2005 7:57 AM (e)

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.

Comment #47145

Posted by Pierce R. Butler on September 9, 2005 9:40 AM (e)

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…

Comment #47169

Posted by Miah on September 9, 2005 11:53 AM (e)

[crikets chirping]

Comment #47222

Posted by justin on September 9, 2005 5:08 PM (e)

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.

Comment #47278

Posted by Pierce R. Butler on September 10, 2005 9:19 AM (e)

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.