Yet another reason Paul Nelson is extremely silly

| 148 Comments | 1 TrackBack

Over on UD, Paul Nelson claims that he is representing the “Darwinian tree of life” position correctly when he asserts that the tree must trace to a single cell, not just a single species:

Recently, PZ Myers accused me of lying about the views of molecular evolutionist W. Ford Doolittle in a debate on Canadian public television. Before I respond to PZ’s baseless charge, let’s see what mental image the following proposition generates:

All organisms on Earth have descended from a single common ancestor.

I’ll bet “single common ancestor” caused you to picture a discrete cell. And if you opened a college biology textbook, to the diagram depicting Darwin’s Tree of Life, you’d find that same image.

Moreover, if someone asked you to summarize the arguments for the single-Tree topology, you’d say (for instance) that multiple independent originations of the same basic biochemistry — e.g., the 64 trinucleotide genetic code — are too unlikely. It’s far more parsimonious to postulate a single cell as the universal ancestor of life.

That’s the historical topology Jerry Coyne described for Canadian television viewers, which he accepts, and which W. Ford Doolittle does not.

Now, one may equivocate, and say that by “single common ancestor” Doolittle actually means an indefinitely large population of organisms, but such word-jigging is shameful.

Hey Paul – Do yourself a favor and take a look a few phylogenetic trees. For example, this one:

Ask yourself:

a) How many nodes (branching points) are in that tree above the root? (I count about 30)

b) How many of them would, to evolutionary biologists, represent a single organism?

c) How many would represent a species?

d) What? They would all represent a species – thousands or millions of individual organisms or more – and not a single individual?

e) Why, then, would anyone who had thought about it for a moment (I know creationists don’t usually do this, but bear with me for a second) think that the root of the tree represents a single physical cell instead of a “species” (or whatever approximation of a species you want to apply to prokaryotes).

f) Finally, does a picture of a dinosaur in a phylogeny indicate that the authors of the diagram think that there was one single ancestral dinosaur organism for the lineage in question?

And while you’re at it:

g) Now consider this ancestral species, the Last Common Ancestor (LCA). Would evolutionary biologists say that it is the same thing as the very first replicator? Or would they say that the LCA was itself the product of a long evolutionary history?

h) Does WF Doolittle think that the standard genetic code evolved independently several times?

i) WF Doolittle actually does accept universal common ancestry for known extant life in a pretty strong way, doesn’t he?

You had better figure these sorts of things out at some point, considering that you have written a creationism textbook, “Explore Evolution”, which you and the Discovery Institute are clearly aiming at the public schools, which makes this Doolittle-based argument, and which is clearly designed for a lawsuit where you will presumably try to defend this stuff. I’m just saying.

1 TrackBack

And they say evolution isn’t predictable. Ever since ID went down in flames in the Kitzmiller v. Dover case, creationism watchers have predicted that creationism would evolve yet again, this time into something called “critical analysis of... Read More

148 Comments

Maybe I’m confused, but isn’t it likely that for a strictly asexual species, that living members of that species would have a common ancestral individual? (Granted that wouldn’t apply to sexual species.)

Henry

Well see, you envisioned a single cell during your pathetic science training (Paul projects, though it’s probably true for many elementary schoolkids), and thus it must be a single cell (gee Paul, what about all the scenarios which have life pre-existing the first cell?). Learn what science really says? Surely you jest.

Of course there’s another aspect to it. Paul is the opposite of a scientist, he insists upon top-down explanations while working from what is accessible (that is, evidence) is subject to negation from his top-down beliefs.

So like most or all metaphysicians, you have to begin with the simple and the single, or more or less, God. The single cell is what he conceives our God to be (how can anyone think without thinking God?), for it is at least relatively simple (as we suppose the first cell to be) and it is single. What, viruses, DNA exchanges, cells appearing from non-cells? No, it has to be his hierarchy, simple, unscientific, and quasi-religious. He thinks in terms of one source, and if it isn’t really One like his three gods, well, then he can disregard the evidence and all science based on that evidence.

Evolution fails to live up to his preconceptions. Thus he has a mandate to rid the world of it, for how is the world to contradict his beliefs?

Glen D http://geocities.com/interelectromagnetic

But, Henry. Wouldn’t that founding individual–even assuming that we might agree there was only one–itself have been, during its lifetime, just one of a bunch of critters descended in turn from another, earlier such individual.

And so on, and so on…

PZ has a discussion of this same misconception over on Pharyngula (odd that it doesn’t show up below as a TrackBack…) which probably expresses the idea better than me.

Even if we go all the way back to a (hypothetical, and I don’t mean to confine the as-yet-unconstrained possibilites by picking this example) solution of self-catalyzing chemical reactants/products cycling around, just on the verge of becoming the first “replicator,” isn’t it more likely than not–even if there’s only one such fortuitous pocket of reactants-on-the-cusp-of-replicating on the whole planet?–that the emergent replicator is something more like a gradient of interacting molecules–a “population” of sorts–than anything that could be called a single cell or entity?

Put less elliptically, and admitting that the image is probably now a simplistic one, I’ve never thought of a “soup” as a singleton.

Henry, just because genes aren’t recombined during asexual reproduction, doesn’t mean such organisms never exchange genetic information. Genes were likely bouncing all over the place between cells in a manner not linked to reproduction (think of bacterial plasmids, for instance). So our genetic legacy still traces back to a diverse population.

I second the notion to read PZ’s take (link).

Maybe I’m confused, but isn’t it likely that for a strictly asexual species, that living members of that species would have a common ancestral individual? (Granted that wouldn’t apply to sexual species.)

Most/all prokaryotes AFAIK have something equivalent to conjugation, so basically there is some kind of gene pool regardless of whether “major” lateral gene transfer occurred between “distinct” lineages. The difference between this and “lateral gene transfer” gets pretty fuzzy. If two bacteria are nonidentical, but are highly similar and from the same strain, engage in conjugation, is that LGT, or is it just something approximating sex within a species and therefore utterly unremarkable?

It’s all a matter of degree IMHO. Any way you slice it though, known extant life forms share numerous features with each other that indicate one or more fairly tight bottlenecks back at the LCA or before.

Now, one may equivocate, and say that by “single common ancestor” Doolittle actually means an indefinitely large population of organisms, but such word-jigging is shameful.

The word jigging is all Nelson’s, or would be if not for Nick’s interjection that unfortunately misses the point that PZ makes quite clearly. Nelson claimed that Doolittle rejects common descent, which is absurd. Yes there is a dispute about whether all organisms on Earth have descended from, to use PZ’s language and emphasis, “a single common ancestor” or “a large population where species distinctions were greatly blurred”, but there’s no dispute between Doolittle and other evolutionary biologists about common descent, and Doolittle’s disagreement does not in any way challenge or undermine the ToE or support any of Paul Nelson’s medieval and ignorant beliefs.

Woese, Carl 1998 “The universal ancestor” PNAS Vol. 95, Issue 12, 6854-6859, June 9

Woese, Carl 2002 “On the evolution of Cells” PNAS Vol. 99 13:8742-8747, June 25

These two articles should be always referenced when this sort of stupidity is presented by creationists. Basic version, there were extremely high exchanges of genetic material (of what ever kind) following the quite probable multiple origins of life. This alone makes it impossible to disentangle existing genomes to discover the “original” common ancestor. The selective environment was diverse and the organisms were promiscuous.

The notion of “frustrated” origins of life have actually gained some geochemical support in, Rosing, Minik T. and Robert Frei 2004 “U-rich Archaean sea-floor sediments from Greenland — indications of >3700 Ma oxygenic photosynthesis” Earth and Planetary Science Letters, 217 237-244 (online 6 December 03. Incidently, this is also additional evidence against the creationist’s farce of an oxygenated early earth still promoted by J. Wells.

Recently, PZ Myers accused me of lying

Ironically, that itself is a lie. PZ accused Nelson of quotemining and gross misrepresentation, not lying. It is quite possible that Paul Nelson is too stupid to comprehend how his claim that Coyne and Doolittle differ over “the historical topology” is a misrepresentation.

Now, one may equivocate, and say that by “single common ancestor” Doolittle actually means an indefinitely large population of organisms, but such word-jigging is shameful.

But PZ didn’t equivocate; he wrote (emph added) “Doolittle argues that there was a large pool of organisms down near the root of the tree of life that liberally swapped genes among one another, so that you can’t trace life back to a single common ancestor — you can trace it back to a large population where species distinctions were greatly blurred.” It is Nelson who plays a stupid and dishonest game of semantics, insisting that, because Coyne accepts “a single common ancestor” and because that phrase implies a single organism whereas Doolittle argues that it wasn’t a single organism, that Coyne and Doolittle must disagree about “the historical topology”. But unlike theologicians, scientists give primacy to the underlying facts that words refer to, not the words themselves, and Coyne could simply look at Doolittle’s argument and say “yeah, sure, ok, a single common ancestral population, then”, and this disagreement disappears in a puff of smoke, with no effect on “the historical topology” that Coyne and Doolittle agree on. And here is where Nick’s contribution helps – substituting a slightly blurry dot for a tiny crisp dot doesn’t change topology. Paul Nelson should consult a reference work other than the bible before using such big words.

These two articles should be always referenced when this sort of stupidity is presented by creationists. Basic version, there were extremely high exchanges of genetic material (of what ever kind) following the quite probable multiple origins of life.

So just to be sure, what you’re describing here is the same thing is horizontal gene transfer, right?

Well see, you envisioned a single cell during your pathetic science training

Creationists believe their own strawman – that the ToE asserts that a cell magically arose from a random conglomeration of molecules, much like a 747 in a junkyard, and that was the beginning of life.

gee Paul, what about all the scenarios which have life pre-existing the first cell?

“chirp”

Ha Sa Moke Um Boom Di Yea!! Hi Sa Moke Um Boom!! A Ling Ting Tong Trying To sing This Song Singing Ha Sa Moke Um Boon Di Yea!! Hi Sa Moke Um Boom!!

Nick asks:

Why, then, would anyone who had thought about it for a moment (I know creationists don’t usually do this, but bear with me for a second) think that the root of the tree represents a single physical cell instead of a “species” (or whatever approximation of a species you want to apply to prokaryotes).

Well here is what your Uncle Chuck said:

the first creature, the progenitor of innumerable extinct and living descendants, was created.

Charles Darwin

One Creature, Nick! One Creature!

Not to mention the PNAS article by Doolitle characterized (or shall we say caricatured) Darwin’s silly idea in technical language as an “inclusive hierarchy”.

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic

Unique hierarchy combined with first creature implies, one single organism at the root of the tree from which all descended. There were no multiple-ultimate-roots.

Nick asks:

Why, then, would anyone who had thought about it for a moment (I know creationists don’t usually do this, but bear with me for a second) think that the root of the tree represents a single physical cell

I agree. Darwin had stupid ideas. No question.

Somewhere,Beyond the Sea. Somewhere Watching For Me, My Lover Stands On golden Sands and Watches The Ships That Go Sailing.

Somewhere,Beyond the Sea. She’s There Waiting For Me. If I Could Fly Like Birds on High, Then Straight To Her Arms I’ll Go Sailing.

It’s Far,Beyond the Stars, It’s Near Beyond the Moon, I Know Beyond A Doubt, My Heart Will Lead Me There Soon.

We’ll Meet,I Know We’ll Meet, Beyond the Shore. We’ll Kiss Just as Before. Happy we’ll Be Beyond the Sea, And Never Again I’ll Go Sailing.

So Long sailing. Bye Bye Sailing. Au Revior Captain. So Long Ensign. Bye Bye Sailing.

“Beyond the Sea”.Performed by The Late;Great;Still alive Somewhere Bobby Darin. Born Robert Walden Cassotto,1936. Died 1973.

I Think That We’ll all Be A Lot Better Off If We Only Would Pour Ourselves a Snifter of Brandy, Fire Up A Good Dominican or Hondutran Cigar, Put Ray Charles’”Goergia on My Mind” or Bobby darin’s”Beyond the Sea”on The Stereo, Then Sit Back;Relax and Get Jiggy With it!!

Nick asked:

Why, then, would anyone who had thought about it for a moment (I know creationists don’t usually do this, but bear with me for a second) think that the root of the tree represents a single physical cell instead of a “species” (or whatever approximation of a species you want to apply to prokaryotes).

Imagine a population of 1000 cells, all with character X. (It doesn’t matter what character X is for the sake of the thought experiment.) Now, what’s the history of X in the population?

Two possibilities exist:

1. Character X evolved once, i.e., in a particular cell (call it Ur-X), early in the history of the population. Any other cell possessing X must therefore have descended from Ur-X. In this case, the population stems from a single physical cell.

2. Character X evolved more than once: n + 1 times, independently. No single physical cell can be implicated as the progenitor organism, at least for character X.

If (2) is the case, however, character X is phylogenetically unreliable, and we can’t say whether the population shares common ancestry or not. Common descent may, or may not, be true.

Suppose we want to say that LUCA was a population of cells, not a particular (distinguishably unique) cell. If those cells possessed any shared characters, we must infer a common ancestor for them – which would make LUCA a particular unique cell – or show that the characters could have arisen independently, which entails the possible falsity of common descent for that population.

In either case, however, LUCA cannot be a population.

BTW, Nick, do you consider the phylogenetic diagram you reproduced above to be biologically accurate?

In fact Darwin stated that there may be one or several common ancestors. Let’s not be confused by Sal’s quote mining.

My (non-biologist) understanding is that prokyrotes oft transmit genetic materials to other prokyrotes, when these happen to meet.

So characteristic X might be transmitted this way.

(By the way, prokyrote isn’t in the spell-checker. Hope I spelled it right.)

David,

If character X is horizonally transmitted, it will be phylogenetically unreliable for the history of the population of cells as cells. Horizontal transmission of genes greatly complicates inferences to common ancestry.

That’s why I left horizontal or lateral transfer out of my little thought experiment. It only complicates matters, and does not solve the fundamental phylogenetic conundrum about the origin of characters used to infer organismal common ancestry.

Paul,

1. Read about “coalescence” and combine this with the existence of sex-like mechanisms in unicells. Your assumptions in your comment are wrong. Even in an old-fashioned “Neo-Darwinian” model there is no reason to think a common ancestral species had to derive from one single cell.

2. Yes, the tree is accurate to a high degree of precision. No measurement in science is perfect of course. If you have data that gives an alternative tree, you had darn well better give the tree similarity statistics while you’re at it, or you’re just another foolish creationist who thinks that a few discrepant measurements trump a strong signal supported by thousands of them.

I suppose one could argue that endosymbiosis is not explicitly depicted or that snakes have lost the digits that their ancestor had, but these sorts of things are a well-accepted part of modern evolutionary theory. And remember, this is a species tree.

3. Since I nicely answered your questions, please answer mine.

If character X is horizonally transmitted, it will be phylogenetically unreliable for the history of the population of cells as cells. Horizontal transmission of genes greatly complicates inferences to common ancestry.

That’s pretty hilarious, considering that sex has been known to biologists and phylogeneticists, for, I don’t know, FOREVER.

Suppose we want to say that LUCA was a population of cells, not a particular (distinguishably unique) cell. If those cells possessed any shared characters, we must infer a common ancestor for them — which would make LUCA a particular unique cell — or show that the characters could have arisen independently, which entails the possible falsity of common descent for that population.

In either case, however, LUCA cannot be a population.

Oh Lord, have you never heard that it is populations that evolve, not individuals? It’s a little more tricky with asexual organisms (presumably the case with LUCA), but still not all that difficult.

The truth is that LUCA could be a single cell—with conditions. One cannot say that there will be no bits and pieces of DNA transferred to this LUCA, nor that large transfers of DNA are impossible (in the latter case the matter of terminology becomes more arbitrary). Coyne’s scenario for a LUCA remains viable, then (as long as Paul doesn’t insist on unscientific conditions). But what has this to do with Doolittle?

There is absolutely no problem posed by promiscuous recombination of DNA and a LUCA, for LUCA may come well after this condition ended. So then you have a single tree of life stemming from LUCA, but not a tree prior to that. Where is the problem, Paul?

As to the earlier “problem” that Paul brings up, he still seems not to understand lateral transfer. With lateral transfers, shared characteristics which are unlikely to arise more than once in a population may very well have, yes, arisen only once, yet the population need not have a single common ancestor who had that trait. It’s like when antibiotic resistance is transferred into bacterial lines which have diverged at some point in the past, this resistance may have occurred only once, yet the populations of conjugating bacteria which now share resistance cannot be said to have resistance through a common ancestor (common ancestors do account for ease of lateral transference, but that is a different matter).

Because Paul seems not to understand lateral transference at all, he cannot understand how it is that common ancestry need not be the basis for a common (especially a strongly selected) trait that bacteria transfer to each other. He does not understand how traits can have common ancestry without there being a common ancestor incorporating all of the traits shared by a given population, which goes back to his basic inability to understand evolutionary recombination and emergence of traits in a population through recombination.

It’s as if he couldn’t understand that resistance to a disease could not come from outside of a given human population. Let’s say that malarial resistance arose only once, and in Africa among black-skinned folk. By his “reasoning”, white people in France who ended up with that resistance must have a recent single black ancestral pair, since to share the trait of malarial resistance means that these white folk must have derived all of their traits from a single ancestor (if perhaps with subsequent modification), or in this case, a single ancestal pair. He can’t imagine populations having a trait spreading through them without the rest of the traits of the “original source” of that trait also being passed through this population, for he only imagines vertical transmission of traits in evolution.

Meaning that he’s never understood Doolittle’s point as Doolittle intends.

Glen D http://geocities.com/interelectromagnetic

If character X is horizonally transmitted, it will be phylogenetically unreliable for the history of the population of cells as cells. Horizontal transmission of genes greatly complicates inferences to common ancestry.

That’s why you so badly understand evolution. You think in terms of evolution of the individual, not the population.

However, horizontal transmission of genes in bacteria indeed greatly complicates inferences to common ancestry. This is well understood and noted in the literature.

What do you think is Doolittle’s point, anyway? He’s saying that with rampant lateral transference, a single tree of life makes no sense. Without rampant lateral transference outside of the species, the norm in eukaryotes, a single tree of life makes as much sense as we’ve always said it does. You don’t get rid of the fact that a robust tree of life indeed exists just because it may not extend back through all of the history of life.

That’s why I left horizontal or lateral transfer out of my little thought experiment. It only complicates matters, and does not solve the fundamental phylogenetic conundrum about the origin of characters used to infer organismal common ancestry.

Which is why you constantly fail to do credit to what Doolittle writes.

Glen D http://geocities.com/interelectromagnetic

Henry J on July 12, 2007 4:35 PM (e)

Maybe I’m confused, but isn’t it likely that for a strictly asexual species, that living members of that species would have a common ancestral individual? (Granted that wouldn’t apply to sexual species.)

Henry, bacteria exchange genes constantly and the whole concept of species is blurry because horizontal transfer can come from seemingly unrelated bacteria. There are at least 3 genetic mechanism and back in the dark ages I did all of them a few times. Transformation by naked DNA, virus mediated transduction, sexual type conjugation between “male” to “female” bacteria. Some of these aren’t too efficient but when you have billions of cells/ml and short generation times, minutes, hours, days at most, even very rare events will occur. We see antibiotic resistance arise in one pathogen, get packaged up into transposons, which jump to self transmissible plasmids and end up everywhere.

Sexual recombination is so important that few organism don’t do it. Most asexual lineages particularly in metazoans are thought to be dead ends and short lived. The reason for it is thought to be Mullers ratchet. Basically without recombination deleterious mutations build up without a broom function and fitness declines until extinction.

One Creature, Nick! One Creature!

Sal, you magnificent hack, you. Also from the first edition:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one

And it is clear throughout the Origin that Darwin often uses a singular (“form”, “progenitor”, etc.) to refer to a singular species rather than individual organism.

Nick wrote:

Even in an old-fashioned “Neo-Darwinian” model there is no reason to think common ancestral species had to derive from one single cell.

Species are defined by characters. Let’s take character X, from my thought experiment: it is shared (diagnostically) by every member of LUCA, if we take LUCA to be a population.

So, did X originate once, or more than once?

I’m unsure which of your questions are genuine, and which rhetorical. I’ll try to answer the former.

Now consider this ancestral species, the Last Common Ancestor (LCA). Would evolutionary biologists say that it is the same thing as the very first replicator? Or would they say that the LCA was itself the product of a long evolutionary history?

A very long history. But I don’t see how that’s relevant. As a matter of logic – set theory, really – either all organisms on Earth share a common ancestor that was itself an organism, or they don’t.

h) Does WF Doolittle think that the standard genetic code evolved independently several times?

I don’t know. You might ask him: I’d be very interested in his view.

i) WF Doolittle actually does accept universal common ancestry for known extant life in a pretty strong way, doesn’t he?

No. See his paper with Eric Bapteste, “Pattern pluralism,” etc., recently in PNAS. Have you read the paper?

In the Theobald phylogeny, which you reproduced above, the character “organs” appears. What clade or group does this character define?

I’m also wondering about the character “nervous and vascular systems.” Are these features homologous among (or across) all the groups stemming from that node?

Paul – you missed my main question. Do evolutionary biologists think that the nodes in that tree represent an individual organism or a species?

And by the way, Paul, primarily lateral (the vertical is almost always a part of it in metazoans) transfer of traits is very well understood in vertebrates, including in humans. Do you think that the spread of lactose tolerance in human populations meant replacement of those populations?

Yet there isn’t the slightest bit of trouble posed by this to human phylogenetic determinations. It is simply a positively selected trait which spread through those populations, becoming part of the history of life and of the human genome. Indeed, it is simply marked as a positively selected trait when the genome is studied.

I know it’s pointless, but I’ll still say that it behooves Paul to for once study evolution in order to understand it (not to accept, but to actually understand for once), and not to mine it for (usually pathetic) criticisms of same.

Glen D http://geocities.com/interelectromagnetic

Without rampant lateral transference outside of the species, the norm in eukaryotes, a single tree of life makes as much sense as we’ve always said it does. You don’t get rid of the fact that a robust tree of life indeed exists just because it may not extend back through all of the history of life.

I should have said, either a robust tree of life exists, or robust trees of life exist. There may not be a LUCA as such, even as a species (maybe as a population, but it strains the term “LUCA” to suppose that a highly divergent population crossing what we’d call “phyla” is “LUCA”). Makes no difference to the fact that there is a definite tree of vertebrate life.

Glen D http://geocities.com/interelectromagnetic

Nick asked:

Paul — you missed my main question. Do evolutionary biologists think that the nodes in that tree represent an individual organism or a species?

No, I answered it, in my thought experiment, although perhaps too obliquely.

Nodes are defined by characters. Characters arise in species; but they first appear in particular organisms within those species, as unique spatiotemporal events. The first chordate (for instance) was not a species; it was a particular, distinguishably unique organism.

Errm, no, it wasn’t.

There was no discrete character that suddenly marks the appearance of a new species. There is an accumulation of a constellation of genetic traits in a whole population of animals. There was no first chordate, not as an individual. There was a population of prechordate animals that contained certain alleles in the gene pool, and the distribution of those alleles shifted over time, and the suite of chordate characters emerged gradually over many generation and many individuals.

What you are promoting is a naive version of the hopeful monster idea.

So you *do* think that those nodes represent individual organisms! Incredible!

Here’s a thought experiment for you. Take a species. Divide into two subpopulations via some catastrophe in the middle. In the first subpopulation, molecular character 1 arises on gene A. In the second population, molecular character 2 arises on gene B. Each character spreads to a high frequency in its respective subpopulation. Then, migration or environmental recovery brings the two subpopulations back together. Mating/conjugation occurs and suddenly 20% or so of the population now has characters 1+2, but without anyone ever having inherited 1+2 from an single individual organism with 1+2.

In other words, a single character can trace back to a single organism, but the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.

Back from my meeting.

Nick wrote:

Paul, I would be happy to have us point out the flaws in your new textbook on the exploreevolution.com website in an unmoderated discussion. Given the past history of discussions on DI-run blogs etc., I won’t get my hopes up for this actually happening.

I’ll be in Seattle this upcoming week for a couple of days, and will do whatever I can to set up a moderation-free discussion at the EE webpage, debate section.

Popper’s Ghost wrote:

X arose once, Y arose once, Z arose once. But neither Ur-X, Ur-Y, nor Ur-Z counts as the common ancestor of all descendants, since not all of the traits of the descendants can be traced back to any of them. But all of the traits can be traced back to the population containing Ur-X, Ur-Y, and Ur-Z.

Right – three cells (physically distinct objects), Ur-X, Ur-Y, Ur-Z. Now, do the three Urs share a common ancestor that was itself a cell, or not?

We have two options:

1. Yes. Then LUCA is a cell, not a population.

2. No. Then we still have three cells, the three Urs, without a common celluar (unique) progenitor.

If LUCA is a population – a “species” – its members must have acquired their traits either from a common cellular ancestor (in which case, we’re back to option 1), or not, meaning the traits or characters came to be from distinct spatiotemporal events, not by templating from a single object. If (2) is possible, however, the received post-Origin definition of homology [i.e., similarity caused by common ancestry from an organism, via templating from a single object (replicator)] must shift fundamentally. Ford Doolittle and Woese realize this.

Darwin himself was well aware of the problem. There is a logical puzzle at the root of the tree of life, which Darwin solved by positing an act of divine creation for the origin of the first organism:

…therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.

(Origin, p. 484; “by the Creator” added in the 2nd edition)

Post-Darwinian biologists can’t appeal to creation. Most have argued therefore that the origin of the characters defining the first cell was so improbable as to be an unique event (see Monod, Mayr, Dawkins, et al), with LUCA as a single physical cell. Others have argued that abiogenesis was more probable than not (>.5), but return to LUCA as a single cell by having all the other prebio-to-bio lineages go extinct; in effect achieving the same practically-indistinguishable-from-zero probability inferred by Monod et al.

The problem with “LUCA as a population,” therefore, concerns the logical structure of phylogenetic inference, where those modes of historical reasoning come into contact with the boundary between the biotic and prebiotic realms. If you picture LUCA as a population – a “species” of some form – bear in mind that the members of that species will by necessity share traits, whose origin require causal explanation.

Either those traits arose from unique spatiotemporal events, with the probabilities of singleton occurrences, or they did not (with associated higher probabilties). If the latter is the case, the tree of life comes apart from the bottom up.

I … will do whatever I can to set up a moderation-free discussion at the EE webpage, debate section

You’re already participating in exactly that. Why does your every appearance here involve you trying to move the conversation to another venue, i.e. one where you have control? I mean, why would you even have to specify that the discussion you want to set up at EE would be “moderation-free”, unless you are acknowledging that the default attitude there would otherwise be one of intrusive moderation? And given that, why should anyone believe you that it would truly be moderation-free?

Nobody is censoring or manipulating anything you or anyone else has to say here. As you well know, that’s much more a hallmark of the leading lights of your side of the debate. You can talk about whatever you want here without pretending that some special venue needs be set up just to do it. So why do you feel the need to constantly refer to some other potential conversation instead of simply holding up your end of this one?

Also, I’m still hoping to get a link or something to your scientific theory of the origin of biological diversity. That is what you’re here to talk about, right? The science? Maybe you can find a second to provide that among all the hours you’re spending here playing semantic games and nitpicking evolution stuff you obviously don’t understand.

Either those traits arose from unique spatiotemporal events, with the probabilities of singleton occurrences, or they did not (with associated higher probabilties). If the latter is the case, the tree of life comes apart from the bottom up.

No wonder your much touted book has not been published, your logic is one of strawman fallacies. Now I understand that as a philosopher you may find it easier to make up ‘logical puzzles’ than to understand scientific theory.

Exploring Evilution, or Purple Pandas Redeux, is ripe for the shredding.

Even a “lively, open and honest” exchange between EE’s authors and the scientific denizens of the internet would be unprecedented on a creationist website.

Paul will report back that there are technical issues that will prevent an unmoderated discussion thread, not enough bandwidth, higher priority work for the web master to do, against policy or any trumped-up excuse one may imagine, but one thing will be clear: it won’t be Paul’s fault; he tried.

Paul wrote: “Either those traits arose from unique spatiotemporal events, with the probabilities of singleton occurrences, or they did not (with associated higher probabilties). If the latter is the case, the tree of life comes apart from the bottom up.”

I have ancestors that are fish. Whatever we find out about the series of events that resulted in the first cell forming on earth, and whatever we find out about the structure of the first “life” on earth, I realize that I have ancestors that are fish. Here is a link to some of the kinds of information that has enabled some people to determine that I have ancestors that are fish:

http://www.talkorigins.org/faqs/comdesc/

It is reasonable to believe that one cell that formed on earth bout 3.8 billion years ago is the ancestor of every other organism that has lived on earth. A second possibility is that other cells formed subsequently to the first cell, and that the other cells did not leave descendants as complex as plants. A third possibility is that the first life was self-replicating RNA rather than something cellular in structure. Finally, perhaps a number of life forms formed at the very same moment in time, each life form physically touching at least one other life form. And perhaps this cluster of entities is the ancestral population of all the organisms that are alive today. But whichever of those events occurred, or whether some other event occurred, I have ancestors that are fish and so do you. And that is very important.

Moreover, if a number of simple life forms formed at the very same moment in time, each of the forms touching at least one other form, it is not the case that one life form in this cluster evolved into humans while another evolved into fish. The whole cluster together would have evolved into all the complex organisms that have lived on earth, first evolving into fish, then into amphibians, then into reptiles and then into mammals. Here is a link to some of the kinds of information that has enabled some people to determine this:

http://www.talkorigins.org/faqs/comdesc/

ben, in addition to wanting the “discussion” at a venue that he can control, Paul also wants it at a venue where the “Amen chorus” of UD sycophants will post. That would give an innocent bystander the impression that there really is a “controversy”, because there would be all these people debating the book, some on one side, some on the other. For him, it’s all about style, since there is no substance.

Paul said:

Either those traits arose from unique spatiotemporal events, with the probabilities of singleton occurrences, or they did not (with associated higher probabilties). If the latter is the case, the tree of life comes apart from the bottom up.

Back in 200 someone much more articulate than me said:

Some biologists find these notions confusing and discouraging. It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life. But in fact, our science is working just as it should. An attractive hypothesis or model (the single tree) suggested experiments, in this ase the collection of gene sequences and their analysis with the methods of molecular phylogeny. The data show the model to be too simple. Now new hypotheses, having final forms we cannot yet guess, are called for.

Folks are coming up with new hypotheses and new ways to test their hypotheses. Experiments lead to new ideas and new hypotheses all building on the old data and incorporating new data. It certainly won’t involve stepping backwards and putting blinders over our eyes and complaining about the state of affairs. If your new model as alluded to in the last sentence is so earth shattering, trot it out.

Delta Pi Gamma (Scientia et Fermentum)

Paul Nelson wrote:

If you picture LUCA as a population — a “species” of some form — bear in mind that the members of that species will by necessity share traits, whose origin require causal explanation.

You still don’t seem to get it. I’m no expert, but even I can follow the simple arguments here. Yes, LUCA was probably a “species”. Yes, the members of that population shared traits. But, most members also had relatively unique traits, traits shared by only a few members of the “species”.

But keep in mind that the “naturalistic” argument, even of abiogenisis, is one of gradualism. Very gradual gradualism. No scientist is seriously suggesting that all of a sudden, *poof*, there was the first cell. No strong contender has emerged yet, but there is good evidence for possible non-biotic replicators. Gradually, these replicators became better and more efficient at replication. The population of replicators evolved, as better replicators were able to make more copies of themselves than earlier replicators. Slowly, eventually the pool of replicators began to look more and more like the first thing we would recognize today as an early “cell”.

Was there a single pre-biotic replicator that acquired just one single mutation that finally turned it into a true “cell”? Possibly. Presumably such an entity would be dramatically better at using the local resources as the non-biotic replicators, and so would drive all other non-biotic replicators to “extinction”.

But probably not. The line between pre-biotic and biotic replicators is probably a wide and fuzzy one, just like the line between species is a wide and fuzzy one. That’s the whole point of this thread (or one of the main points). Just as there was no single event that separated one species from another, there was probably no single event that separated pre-biotic from biotic replicators. The entire “population” evolved together slowly, gradually. In fact, it’s possible that population of replicators wandered over the biotic “boundary” *and back again* several times.

Second, invoking Darwin’s ignorance to “prove” that God created life is laughable. My meager understanding is that Darwing had no inkling of DNA or molecular mechanisms for replication. Our knowledge has grown a lot since then. We now know that non-biotic replicators are possible. We’ve demonstrated such. Today, it is not such a stretch to leap the gap from a non-biotic replicator to a biotic one. In Darwin’s day, such a leap was not possible. The gap was too large.

Finally, you seem to think that Darwin’s Origin of Species is the “Bible” of Biology. Just as people believe a literal, never-changing interpretation of the Bible, so you seem to think that scientists hold a literal, never-changing interpretation of whatever Darwin wrote. So, Darwin (as a trained theologian) invoked the Creator for something he could not explain. What does that prove? What significance do you think that has for Science today? Why do you think Darwin’s belief (even if it was a literal statement of his beliefs and not merely a metaphor for “the process that brought about the first cell”) is the last word in abiogenis?

Popper's Ghost Wrote:

Glen wrote “billions of H. sapiens ancestors (though many are counted more than once)”, but only a foolish quibbler who had nothing worthwhile to contribute would treat that as something needing correcting.

Quite.

Benson at his usual abysmal self Wrote:

But I do need to correct both you and Glen D. Here goes:

Without the parenthetical caveat I would have been technically wrong. Which is why I included it, dolt. As usual you assert what you cannot argue nor for which you can provide evidence.

If either incorygible or Glen D find that apologies are due, then I freely extent my apologies in advance, assuming my problem is my reading entirely and their writing not at all.

What an apology. Nothing new in your attempt to claim righteousness when you’ve been shown to be wrong. Your stupid quote of a dictionary definition certainly changes nothing, because it only applies before I carved out the host of repeated counts in my parenthetical statement. In other words, it’s more sheer cussed-mindedness and false accusation on your part.

Glen D http://geocities.com/interelectromagnetic

You know, Paul, I asked the following, and many many other things, and you didn’t answer them. But just to demonstrate how generous I am, I’ll repeat this post which I wrote a week or so ago, so that you can show up my sarcasm with some good straightforward answers:

Hey Paul, as long as you’re avoiding all of the questions you can’t answer, which is about all of them, I’d like to ask you how anyone would know if humans are related to each other. I mean, apparently you’re willing to think that it’s just a coincidence that humans and chimps share 95% + of the same DNA, or that for some unfathomable reason your creator decided to design in a way that would look like evolution occurred.

Now all humans share 99.5 to 99.8 percent of the same genetic information, but I don’t see why we should expect common inheritance to account for this fact if the similarities between chimps and humans aren’t supposed to stem from common inheritance. So will you bite the bullet and admit that it may very well be that humans in South America are not actually related to humans in Australia? As you asked previously (and obtusely), if the similarities are supposed to mean common descent, what are the differences supposed to mean?

And please give us a sound scientific epistemology based upon your inconsistent view of things. See, I don’t know how to tell if chimps are related to humans, if Australian aborigenes are related to Eskimos, or if I’m related to my (purported) Mom (note that I didn’t witness my own birth [or for the pedants out here, I didn’t coherently witness it, nor remember it—this is a later addiction], and if there are similarites, then what of the differences? Come on Paul, you try to pretend that you have answers, cough them up). Inform us about pattern recognition, relationships, and the cause-effect expectations from your design model.

If you don’t answer again I just might have to suspect that you have nothing legitimate to say. Huh, imagine that conclusion.

Glen D http://geocities.com/interelectromagnetic

Ever waiting for your science, your good coherent methods to replace our “commitment to naturalism” (or whatever the clack is now),

Glen

Glen D — While with the parenthetical comment, I suppose your wording can be interpreted in a correct manner, there may be some who would not do so, thinking something like “Kind David is my ancestor 25,000 times over,” whatever they might mean by that.

Proper application of reason begins with careful definitions and attempts to proceed from there. Given the readership here, it is possible that at least one reader needed, after that four-way exchange, to actually see the definition.

Finally, I must wonder about the state of mind of somebody who would post that comment regarding what amounts to a tempest in a teapot. Hmmm…

Proper application of reason begins with careful definitions and attempts to proceed from there.

And a pedant is one who insists on exacting wording at every turn.

Given the readership here, it is possible that at least one reader needed, after that four-way exchange, to actually see the definition.

And who needed the dishonesty that you produced?

Finally, I must wonder about the state of mind of somebody who would post that comment regarding what amounts to a tempest in a teapot. Hmmm…

Yes, I wonder what drives someone like yourself to make wildly inaccurate statements over something so trivial. But that is what you do.

Glen D http://www.geocities.com/interelectromagnetic

Glen D #187986 Wrote:

And a pedant is one who insists on exact wording at every turn.

Given how you mangled the definition of the noun lie in comment #187981 on another thread, some pedantry appears to be necessary. Now the non-pejorative portion of the definition of a pedant in my copyright 1947 desk dictionary reads:

a formalist or precisionist in teaching or scholarship.

Sounds to me to be good traits for, at least, mathematicians and computer scientists. (Not that motivation, intuition, humor and empathy are not also desirable traits, amongst others.)

Given that PT has now enjoyed more than a half-million site visits, I’ll stick by the claim that readers should be misled as little as possible. So on the rare occasions I notice (what I believe to be) mistakes or simply phrasings which might lead readers to confused or wrong conclusions, I’ll continue to point these out.

Given how you mangled the definition of the noun lie in comment #187981 on another thread,

You even acknowledged that my meaning is in most “larger” dictionaries, though accompanied by your mean-spirited, bigoted, and stupid swipe at American English. Apparently because you have “standards” other than the actual meaning of words, you think you have cause to fault someone for telling the truth about those standards as they actually exist.

some pedantry appears to be necessary.

No, none of your lies are appropriate.

Now the non-pejorative portion of the definition of a pedant in my copyright 1947 desk dictionary reads:

a formalist or precisionist in teaching or scholarship.

Oh look, little Davey pulls out his 1947 desk dictionary again.

I know what a pedant is, fool, both pejoratively and non-pejoratively.

And if I may step into the role of pedant for a little while, let’s point out what a non-sequitur (ad hominem attack) your ridiculous “reasoning” is, aside from the fact that I am right about the meaning of “lie” and you are wrong.

Sounds to me to be good traits for, at least, mathematicians and computer scientists. (Not that motivation, intuition, humor and empathy are not also desirable traits, amongst others.)

And you are twisting the meaning of my words by resorting to a strict non-pejorative definition. Is there no end to your dishonesty?

Given that PT has now enjoyed more than a half-million site visits, I’ll stick by the claim that readers should be misled as little as possible. So on the rare occasions I notice (what I believe to be) mistakes or simply phrasings which might lead readers to confused or wrong conclusions, I’ll continue to point these out.

Again the twist, the lie. I didn’t object to your pedantry, I objected to this nonsense: “But I do need to correct both you and Glen D. Here goes:”. If you felt the need to explain further, then you should say that, not the dishonest statement that I needed to be corrected.

I can be pedantic where this is indicated. The difference is that I don’t go around accusing people of being wrong just because they understand the meaning of the word “lie” or loosely refer to what brings a “formal count” down (which was my polite way of correcting the ambiguity, unlike your impolite tactics). That is to say, I understand context, and do not try to make mean-spirited points based on misunderstandings as the egregious Benson does.

Glen D http://geocities.com/interelectromagnetic

David B. Benson #188004 Wrote:

more than a half million site visits

Oops. More than five million site visits.

Glad I could correct this before Glen D gets all huffy about that and starts accusing me of lying about it…

Comment #187372

Posted by Henry J on July 12, 2007 4:35 PM (e)

Maybe I’m confused, but isn’t it likely that for a strictly asexual species, that living members of that species would have a common ancestral individual? (Granted that wouldn’t apply to sexual species.)

Henry

Horizontal gene transfer seems to be a mechanism that would show the “same single ancestor” is a position that could have some pitfalls. For example, the E. Coli bacteria that live in your gut only has one gene from mutation different than Samonella. However, it’s picked up 32 additional genes from other bacteria. Going back billions of years ago, it’s quite possible that there were multiple emergent lines that lead to our current diversity. Yet many of those lines simply died out, save for the transference of some of their genes, in different proportions to different populations.

Also, I’ve read that anaerobic bacteria may have been a completely different life tree. I don’t remember if it was speculation, or presented as fact, so I don’t stand behind it.

Paul Nelson Wrote:

Right — three cells (physically distinct objects), Ur-X, Ur-Y, Ur-Z. Now, do the three Urs share a common ancestor that was itself a cell, or not?

I see that you didn’t address any of my points or acknowledge any of the errors I pointed out, you dishonest piece of garbage.

We have two options:

1. Yes. Then LUCA is a cell, not a population.

The L in LUCA stands for “last”, you pathetic stupid idiotic cretinous moron.

Proper application of reason begins with careful definitions and attempts to proceed from there.

No, proper application of reason begins with the sort of intellectual honesty that would prevent one from writing such a transparently ad hoc piece of sophistry.

P.S.

Paul, you ignorant git:

Right — three cells (physically distinct objects), Ur-X, Ur-Y, Ur-Z. Now, do the three Urs share a common ancestor that was itself a cell, or not?

X, Y, and Z were mutations, so no common ancestor of Ur-X, Ur-Y, or Ur-Z had trait X, Y, or Z. Your original discussion was about tracing all organisms back to a single cell, Ur-X – no ancestor of Ur-X is relevant; that’s the whole point – your point – about calling it Ur-X. I pointed out that this argument falls apart as soon as you consider another trait, Y – by your own argument, now both Ur-X and Ur-Y are the “single physical cell” from which the population stems – which is a contradiction. That’s a formal logical refutation, you dumbkopf. Neither Ur-X nor Ur-Y nor any of their ancestors can be, as Nick wrote, “the root of the tree”. The only candidate for that is the population that they were a part of – a single population sharing a single genetic code. QED, you stupid creationist, you.

While with the parenthetical comment, I suppose your wording can be interpreted in a correct manner, there may be some who would not do so, thinking something like “Kind David is my ancestor 25,000 times over,” whatever they might mean by that.

Ah, it’s not that someone might think that Glen is claiming that the number of ancestors grows exponentially as one moves back in time, eventually exceeding the bounds of the planet with their huge throng. Oh no, the problem is that even though Benson supposes that one could be sane and reasonable, someone may interpret Glen’s words in a way that even Benson can’t make any sense of. But the silly pseudo-pedant can’t even discern that the pedantically literal interpretation of Glen’s words is “King David is many of my ancestors”. Yeah, that’s really something to we need to guard against. Thank God we have David Benson to correct us so we don’t lead people so far astray.

If you picture LUCA as a population — a “species” of some form — bear in mind that the members of that species will by necessity share traits, whose origin require causal explanation.

The LUCA shares a set of traits, moron. The traits are laterally transferred, moron. The causal explanation for individual traits is mutation, moron.

Either those traits arose from unique spatiotemporal events, with the probabilities of singleton occurrences

The a posteriori probability of single random occurrences is nearly 1, moron. Think lottery winner, moron.

or they did not (with associated higher probabilties).

Unspecified causes do not have higher probabilities than specified causes, moron. Ockham’s Razor is now a theorem in information theory, moron.

If the latter is the case, the tree of life comes apart from the bottom up.

Aside from the latter not being the case, moron, your metaphor is moronic, moron. An actual tree has a branching root system, but it still has a trunk, moron.

the boundary between the biotic and prebiotic realms

Moronic vitalist crap. It’s organic molecules all the way down to methane; there is no “boundary”, any more than there’s a boundary between the number of chin hairs that can be considered a beard and the number that can’t.

Have Paul Nelson or any of the ID-Creos ever heard of “emergence” and complexity from simplicity? Well may be the only emergence they know of is the one they call POOF! What a bunch of malicious spreaders of ignorance to suit their own preconceptions and desires these people are.

Oh Paul, I just had to ask another question of you, because I don’t see why the embarrassing stream of questions you can’t answer should end just because you ignore them.

Why do you suppose that the patterns of evolution differ significantly between eukaryotes which essentially breed “within species”, and prokaryotes which share DNA “across species”? I mean, evolution predicts that the patterns would differ, based on the differing mechanisms, while “design” would predict, well, what?

And of course, what is so obvious, the fact that there is no actual break between “macroevolution” and “microevolution” (the scare quotes are because of the abuse IDists make of those terms) is not true simply of eukaryotes, it is true of prokaryotes as well. That is to say, your “designer” happens to “design” prokaryotes as if they had evolved according to known prokaryotic mechanisms of recombination, and your “designer” also “designs” eukaryotes as if they had evolved according to eukaryotic mechanisms of recombination.

My my, isn’t that another tremendous miracle that you can sock away into your list of miracles? I mean, of course evolution isn’t possible (you know, due to souls and other theological reasons), but miraculous coincidence of design with what would be expected from evolution, those are dime a dozen.

Poof, poof, and more poof. We asked for “proof”, but “poof” is even better, isn’t it? And you can even predict God’s miracles, just use evolutionary theory to make the predictions, and you know that God will follow it’s dictates.

But then, is God really God, or is he somehow some little slave of evolutionary predictions? See how nice I am, Paul, I’m giving you some good material to work into your previous fantasies. Maybe you can discover some even greater God, the one that orders your silly little God (and note, I’m not calling all theists’ gods silly, just these ridiculous IDC/creo “designers”) to follow the dictates of evolution.

Glen D http://geocities.com/interelectromagnetic

That Sal.

Unlike the rest of us, who can claim to have benefitted from at least the occasional fortunate accident along the way, in Sal’s case it’s not “from the goo to you”–

–it’s just “from the goo to goo.”

Slime all the way down.

ordova: “I agree. Darwin had stupid ideas. No question.”

Well, Cordova, you would be the person to go to when discussing stupid ideas, that much is certain. How can evolution explain the fusing of ribs to the sternum, right Sal? Why, this would require a reorganization of the abdominal viscera!

LOL!

Laughing AT you.…

Hi Larry

hey Nick, greetings from the library. I like my pc much better than this ine but mine was stolen. So I lost all my files - a couple years worth of emails, downloads and lots of photos and etc etc. The box was missing the side panel so that the circuit boards are visible also missing the front panel that is just for looks. So it may be hard to pawn (but not the nice monitor)so it may become someone’s personal computer – neighbiors are suspect but no evidence. so the crew won’t hear from me fopr a while. Jeeze what a lousy screen I am working on. For some reason speloling errors are not marked and the screen is a bit hard to read. there is an interesting paper in nature on inferring the evolutionary history of protein folding if I got it right on a quick look. One Eric Smith in The Scientist writes something about Evolution’s ““real problem”” meaning OOL. Seems to be a complexity enthusiast but he concludes that life started from something simpler than what it now is - duh.

In Barnes and Nobel I have not seen Behe DBB or othe rbook on the shelves recrerntly – two days ago I saw dbb remeindered.

About this Entry

This page contains a single entry by Nick Matzke published on July 12, 2007 3:05 PM.

Nova’s “Judgment Day” Coming November 13 on PBS was the previous entry in this blog.

Don’t say I didn’t warn you… is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.381

Site Meter