Nick Matzke posted Entry 3237 on July 12, 2007 03:05 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3226

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.

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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

Comment #187383

Posted by Glen Davidson on July 12, 2007 5:12 PM (e)

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

Comment #187384

Posted by Steviepinhead on July 12, 2007 5:19 PM (e)

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.

Comment #187389

Posted by Aaron on July 12, 2007 5:34 PM (e)

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).

Comment #187390

Posted by Nick (Matzke) on July 12, 2007 5:38 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.)

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.

Comment #187393

Posted by Popper' Ghost on July 12, 2007 5:50 PM (e)

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.

Comment #187394

Posted by Gary Hurd on July 12, 2007 5:52 PM (e)

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.

Comment #187398

Posted by Popper' Ghost on July 12, 2007 6:17 PM (e)

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.

Comment #187399

Posted by Coin on July 12, 2007 6:21 PM (e)

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?

Comment #187401

Posted by Popper' Ghost on July 12, 2007 6:28 PM (e)

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”

Comment #187412

Posted by ShanghaiJohnnyP on July 12, 2007 7:53 PM (e)

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!!

Comment #187414

Posted by Salvador T. Cordova on July 12, 2007 8:01 PM (e)

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.

Comment #187415

Posted by ShanghaiJohnnyP on July 12, 2007 8:03 PM (e)

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!!

Comment #187418

Posted by Paul Nelson on July 12, 2007 8:20 PM (e)

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?

Comment #187421

Posted by PvM on July 12, 2007 8:32 PM (e)

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

Comment #187425

Posted by David B. Benson on July 12, 2007 8:43 PM (e)

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.)

Comment #187427

Posted by Paul Nelson on July 12, 2007 8:51 PM (e)

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.

Comment #187428

Posted by Nick (Matzke) on July 12, 2007 9:01 PM (e)

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.

Comment #187430

Posted by Nick (Matzke) on July 12, 2007 9:06 PM (e)

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.

Comment #187432

Posted by Glen Davidson on July 12, 2007 9:15 PM (e)

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

Comment #187434

Posted by Glen Davidson on July 12, 2007 9:21 PM (e)

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

Comment #187436

Posted by raven on July 12, 2007 9:25 PM (e)

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.

Comment #187437

Posted by Nick (Matzke) on July 12, 2007 9:25 PM (e)

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.

Comment #187438

Posted by Paul Nelson on July 12, 2007 9:29 PM (e)

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?

Comment #187439

Posted by Nick (Matzke) on July 12, 2007 9:32 PM (e)

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

Comment #187441

Posted by Glen Davidson on July 12, 2007 9:32 PM (e)

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

Comment #187442

Posted by Glen D on July 12, 2007 9:47 PM (e)

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

Comment #187443

Posted by Paul Nelson on July 12, 2007 9:52 PM (e)

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.

Comment #187445

Posted by PZ Myers on July 12, 2007 10:09 PM (e)

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.

Comment #187446

Posted by Nick (Matzke) on July 12, 2007 10:15 PM (e)

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.

Comment #187449

Posted by Longhorn on July 12, 2007 10:29 PM (e)

Paul Nelson, I have ancestors that are fish. So do you. I have ancestors that are bacteria. So do you. I have ancestors that are rodent-like mammals. So do you. I share common ancestors with dolphins. I share common ancestors with all the animals and plants that are alive today. So do you. If you trace my ancestry way way back, you will find that some of my ancestors are bacteria.

Comment #187450

Posted by Longhorn on July 12, 2007 10:50 PM (e)

Paul Nelson wrote:

“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.”

I’m not sure if I see your point. But here is what happened: I share common ancestors with all the fish that are alive today. It is not as if a cell got started 1 billion years ago, and it evolved into all fish. And then another cell got started 500,000 years ago, and it evolved into all humans. All the fish alive today share common ancestors with all the humans that are alive today. The most recent common ancestor that I share with the goldfish that are alive today live over 500 million years ago.

Now I don’t know whether a discrete single cell is the common ancestor of all the organisms that are alive today or whether it is hard to talk about a single cell that is the common ancestor of all the organisms that are alive today. But all the humans, cats, dogs, dolphins, monkeys, flowering plants and bacteria that are alive today share common ancestors.

Comment #187451

Posted by RBH on July 12, 2007 11:00 PM (e)

Paul Nelson wrote

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.

Isn’t that “chordate kind“? Fun to watch the typological mindset at work.

Comment #187454

Posted by Art on July 12, 2007 11:03 PM (e)

Paul Nelson wrote:

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.

Um, they don’t. But they all share a common ancestry.

Comment #187455

Posted by David Stanton on July 12, 2007 11:04 PM (e)

Paul,

Take a closer look at the tree. In cladistics, synapomorphies define clades not nodes. Some of the nodes as labeled as “hypothetical common ancestors” but not one node is labeled as the place where a new character arose.

Nick and PZ are correct. The nodes represent reproductive isolation and branching due to genetic divergence following reproductive isolation. This may occur in the absence of any initial morphological or even genetic differences.

And by the way, lateral gene transfer and introgression of mitochondrial genomes, etc. can pose significant problems for phylogenetic reconstruction. That is why multiple independent data sets are desirable.

Comment #187456

Posted by Incorygible on July 12, 2007 11:07 PM (e)

A recent popular biology book I read (can’t remember which) made the obvious but important point – especially relevant to this argument – that the number of ancestors one actually has increases exponentially with the number of generations removed. This is important to bear in mind, since staring at phylogenetic trees tends to trick our brains into envisioning the reverse. The book was discussing the mitochondrial ‘Eve’, and how it did not imply that all humans were descended from this one woman in the same fashion as her Biblical namesake would suggest. Rather, when we all trace our lineages back far enough – to the point where each of us actually has thousands of human ancestors whose genetic material would eventually, in some fashion, end up in us – she is one of them.

Paul, from which single common human ancestor are you and your siblings derived? Let’s make this easy and restrict the discussion to your last common ancestor living on or about the year 1900. Or do you think that perhaps around that time there was a pool of humans, themselves largely unrelated (one would hope), who unknowingly, unwittingly – and perhaps unwillingly (if only they could have known!) – were the ancestral gene pool of one Paul Nelson and his real or imagined siblings? Is it not conceivable that some heritable trait (a difficulty discerning symbols from that which they represent, perhaps?) originated in just one of those 4, 8 or 16 ancestors, and is now shared by you and your immediate family? However, what if by some stroke of genetic ‘luck’ that trait is not shared by your first cousin’s family? If we agree that one common ancestor produced the trait in all descendants who share it, is that one individual the sole common ancestor of note – the lone progenitor of all descendants in the Nelson clan? For that matter, is he/she not also a common ancestor of your first cousin’s family , which nevertheless lacks the trait? Do you see how there might be many, many individuals with messy relationships portrayed by simple lines, nodes and pretty pictures? If not, perhaps you might wish to explore it some more.

Comment #187462

Posted by Gary Hurd on July 12, 2007 11:30 PM (e)

Syntax Error: mismatched tag 'blockquot'

Comment #187464

Posted by Gary Hurd on July 12, 2007 11:32 PM (e)

It is hard to get far enough away from Sal, but he is always an easy target for correction. Here is all that Darwin had to say about the origin of life in his Origin of Species.

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

Analogy would lead me one step farther, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide. Nevertheless all living things have much in common, in their chemical composition, their cellular structure, their laws of growth, and their liability to injurious influences….

Therefore, on the principle of natural selection with the divergence of character, it does not seem incredible that, from some such low and intermediate form, both animals and plants may have been developed; and, if we admit this, we must likewise admit that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy, and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants.”

And, from the book’s last sentence;

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

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

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

.

Comment #187469

Posted by Incorygible on July 12, 2007 11:50 PM (e)

To make what I’m getting at exceedingly simple – though it is intuitively obvious to most everyone who has really ‘explored evolution’ – imagine that the hypothetical Nelson trait I describe becomes a defining feature of a diverse branch of life existing on this planet a million years from now (*shudder*). For example, let it take the place of “mitochondria, nucleus” in the blue dot at the base of Nick’s tree. There is most certainly one ‘Ur-Nelson’ individual back to which all derived descendants can trace the origin of that trait. But we’re talking about the LUCA. Is the actual LUCA of those descendants a single individual or a population of more than one individual? (Here the mitochondrial Eve and the y-chromosome ‘Adam’ provide good analogs, by the way.) In other words, if we were to gather up all the DNA existing in Nelson descendants a million years from now, could we find one ancestral individual – a single LUCA – that contained it all (even if we were to ignore mutations that had occurred subsequent to the LUCA)? The Ur-Nelson doesn’t fit that bill in the slightest. For humans, it takes two to tango, so the answer is obvious (think the biblical Adam and Eve if you’re unclear about that one). Now if bacteria have even more intricate and messy choreography when it comes to gene transfer, and if the swapping of genetic material for the proto-life on this planet was probably more messy and complicated still, odds are the entire ancestral basis for existing life on this planet was probably never localized within anything we might call a single cell.

Comment #187471

Posted by Gary Hurd on July 12, 2007 11:54 PM (e)

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?

Yeah. Woese basically argues that the first primitive cells engaged in promiscuous (non-selective) exchange of genes.

I view genes as a later development of life altogether, favoring a metabolism first origin. This follows directly from the work of Deamer. If you like to start at the earlier literature, I suggest

Hargreaves, W. R., and Deamer, D. W. 1978. Liposomes from ionic single-chain
amphiphiles. Biochemistry 17:3759-3768.

Deamer, D. W., and Barchfeld, G. L. 1982. “Encapsulation of macromolecules by lipid vesicles under simulated prebiotic conditions” J. Mol. Evol. 18:203-206.

A bit more recent is

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

Comment #187473

Posted by RBH on July 13, 2007 12:14 AM (e)

From Gary’s quotation of Darwin:

But analogy may be a deceitful guide.

Wouldn’t it be nice if ID creationists took that to heart?

Comment #187475

Posted by Popper's Ghost on July 13, 2007 12:22 AM (e)

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.

Paul, you are incredibly stupid. Imagine two characters, X and Y, each of which evolved once, in two different cells Ur-X and Ur-Y. Which of these two single physical cells must the population have stemmed from?

Comment #187477

Posted by Popper's Ghost on July 13, 2007 12:32 AM (e)

Well here is what your Uncle Chuck said:

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

Sorry, Sal, but sentences start with capital letters. And I know that it’s really hard to get this through that religion-addled head of yours, we don’t take what Charles Darwin said as Gospel.

I agree. Darwin had stupid ideas. No question.

Yes, he did have some. So what, moron?

Comment #187498

Posted by Sir_Toejam on July 13, 2007 3:01 AM (e)

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.

that’s a very nice and succinct way of explaining the difference between what is meant by common ancestry and A common ancestor.

Comment #187500

Posted by hoary puccoon on July 13, 2007 3:07 AM (e)

Aside from Popper’s Ghost’s use of stupid and moron (with which I have some sympathy. How many times, now, has Sal been told that biologists don’t worship Darwin?) this thread is a wonderful example of discussing a scientific issue, not just slamming creationists. It would be good to remember when creationists complain that these threads are only profanity and griping.
Of course, it would help a lot if Paul Nelson would read Popper’s Ghost’s entry #187475 and acknowledge his point. That’s the way science works. Researchers correct their mistakes and move on. If that’s not the way ID works, then it simply isn’t science.

Comment #187502

Posted by Nick (Matzke) on July 13, 2007 3:17 AM (e)

What’s really a shame is that Paul didn’t realize the error he was making until after he put it into his creationist textbook Explore Evolution, which the Discovery Institute is now going to push into the public schools.

Comment #187503

Posted by Sir_Toejam on July 13, 2007 3:23 AM (e)

Of course, it would help a lot if Paul Nelson would read Popper’s Ghost’s entry #187475 and acknowledge his point.

nope. Paul is looking for validation, not challenges.

I’ve actually NEVER seen him take a challenge to one of his inane notions head on. Not in all the years he has been a public figure.

and Sal is just pathetic. no need to even attempt to engage, he’s just a quivering mass in the corner, thinking you just want to eat his ice cream bar and not realizing it’s really just a bar of soap (sorry, only Ren and Stimpy fans will likely get that reference).

Comment #187525

Posted by Frank J on July 13, 2007 5:17 AM (e)

Glen Davidson wrote:

That’s why you so badly understand evolution.

I can’t prove it, and he certainly will not utter the words that would support my claim, but I think that he understands evolution quite well. It’s just that he can’t bear the possibility of non-biologists and potential sympathizers of ID/creationism understanding it. Unless they play along, of course.

Comment #187532

Posted by Popper's Ghost on July 13, 2007 6:01 AM (e)

I can’t prove it, and he certainly will not utter the words that would support my claim, but I think that he understands evolution quite well.

Ahem. It’s very low behavior to contradict someone while removing the basis they provided for their claim. This thread (like many others before it) demonstrates (again) that Nelson doesn’t understand evolution, in just the way that you so brazenly snipped from Glen’s statement, as so well demonstrated by Nick and others.

Comment #187537

Posted by Popper's Ghost on July 13, 2007 6:20 AM (e)

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.

The fundamental failure (of imagination, intelligence, logic, understanding …) here is that Nelson takes being a chordate to be a single “character” that arose in a single organism. But there was no single “chordate” mutation that resulted in a chordate offspring from non-chordate parents – that’s a sorites fallacy, which even Paul Nelson must have learned about in his philosophy courses. But perhaps he misunderstood the lesson and thought he was being taught to employ them rather than to avoid them.

Comment #187538

Posted by Rolf Aalberg on July 13, 2007 6:35 AM (e)

It remains to be seen whether Sal or Paul will respond to the responses they got to their somewhat less-than-intelligently designed comments. But here’s to:

Sal, for his proficiency in that age-old creationist exercise of quote mining, and making relevant remarks:

I agree. Darwin had stupid ideas. No question.

Paley beats Darwin, eh?

Pathetic, beating a dead horse won’t make it run.

Paul for, unless I am an idiot, not having understood even first things about evolutionary theory. I know I would have been ashamed of myself if I had expressed a corresponding lack of knowledge/understanding, and would have done everything I could to apologize for my error and beg to be forgiven. And I don’t even pretend to be anything but just another layman WRT to evolutionary theory.

And this guy into the seventh (or eight?) year of producing his book “On Common Descent”?

Could it be more pathetic?

Our problem is that these guys are convinced to the bottom of their soul that evolution must be false. Therefore they don’t even bother to learn, and believe any old argument will do.

Comment #187546

Posted by Marek 14 on July 13, 2007 7:45 AM (e)

Incorygible: Wasn’t that book Dawkins’s “The Ancestor’s Tale”? I remember that he discussed these things in there.

Might be the best popular book dealing with ancestors I read.

Comment #187553

Posted by Paul Nelson on July 13, 2007 8:30 AM (e)

Replies to various:

Nick wrote:

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.

This is Ford Doolittle’s argument exactly:

Perhaps in almost the same way that sexually reproducing species speciate, giving rise to daughter species whose gene pools are initially similar to those of the parent species and contain very many more different alleles than are borne by any one genome. (What is crucially not the same is that the genomes of the progenote population — like those of different modern prokaryotes — bore many different genes, not just different alleles.) Thus, there is no more reason to imagine only a single first kind of cell as the progenitor of all contemporary life than there is to imagine only Adam and Eve as progenitors of the human species.

W.F. Doolittle, “The nature of the universal ancestor and the evolution of the proteome,” Current Opinion in Structural Biology 10 (2000):355-358; p. 357; emphasis added.

In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false. The first populations of cells on Earth contained many organisms which did not share common ancestry from any single cell. Thus, there never was a universal common ancestor, if that means a particular discrete organism.

This is exactly what Doolittle and Woese have been arguing vigorously for nearly a decade. As you put it, “the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.”

Or, as Incorygible writes:

[…] odds are the entire ancestral basis for existing life on this planet was probably never localized within anything we might call a single cell.

Art, I think this is your point as well.

Popper’s Ghost wrote:

Imagine two characters, X and Y, each of which evolved once, in two different cells Ur-X and Ur-Y. Which of these two single physical cells must the population have stemmed from?

I think you’re making the same argument as Nick (I take your point to be that if traits X and Y are combined in the same organism by sexual reproduction, etc., then those traits may have had separate organismal lineages), in which case my reply to Nick extends to you.

PZ wrote:

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.

Let’s take the specific character “notochord.” In some population, notochords first appeared as anatomical features during ontogeny. How? In one organism? More than one? Nick writes that “a single character can trace back to a single organism.” Do you agree? (Popper’s Ghost, you’re interested in this question as well.)

Nick, I’m still wondering what group [taxon] the character “organs” defines, and if the vascular and nervous systems of the various groups (taxa), included under that node in the cladogram above, are homologous.

Since Nick has tied this discussion to the publication of Explore Evolution, I propose we take the whole conversation over to the Debate section of the Explore Evolution webpage.

I have to attend a meeting at the Hilton O’Hare, but I’ll be back later tonight. When the Discovery Institute webmaster is available, I’ll find out what needs to be done to set up moderation-free discussion threads at the Explore Evolution webpage.

Comment #187559

Posted by PZ Myers on July 13, 2007 9:07 AM (e)

Paul Nelson wrote:

if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false.

It doesn’t. That’s what we’re telling you.

Paul Nelson wrote:

Let’s take the specific character “notochord.” In some population, notochords first appeared as anatomical features during ontogeny. How? In one organism? More than one? Nick writes that “a single character can trace back to a single organism.” Do you agree?

I disagree with Nick on that point. A single character, such as a notochord, is not the product of a single genetic event, in most cases. What part of the notochord is the important one? Its inductive role in early development? And which of the several inductive events matters? Its structural role?

Look at the hemichordate stomochord. Is it a notochord or not? I think it’s obvious that many of these characters are not so discrete as simplistic black-and-white creationist thinking would have you believe. There are gradual transitions and ambiguities in even the most concrete characters we use to classify clades – and that means their evolution would have involved many generations and many contributing individuals. There was not one individual who lacked a notochord that gave birth to an individual that had one.

Comment #187563

Posted by Popper's Ghost on July 13, 2007 9:17 AM (e)

In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false.

Since you’ve been told numerous times in this thread that it doesn’t mean that, then you haven’t falsified it. Ding! A ling!

I think you’re making the same argument as Nick

No, what I made was a refutation of your ridiculous argument: “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.”

You see, X there is what is technically known as an “unbound variable” – it could apply to any trait. So, unknowingly, you have argued that your “population of 1000 cells” have simultaneously stemmed from numerous “single physical cell”s, since the population has more than one trait and each of those traits could have originated in a different cell. In other words, your population of 1000 cells stemmed from an ancestral population, not necessarily from a single cell. Which does not refute the theory of common descent, as you have been told over and over and over …

Comment #187564

Posted by Popper's Ghost on July 13, 2007 9:23 AM (e)

Nick writes that “a single character can trace back to a single organism.” Do you agree?

I disagree with Nick on that point.

No, no, no, no, no … you’ve been suckered by Nelson. Nick says that it can – that doesn’t mean that it necessarily does. Here’s the quote:

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.

So no, you don’t disagree, and Nelson is a liar or retarded or both.

Comment #187567

Posted by Popper's Ghost on July 13, 2007 9:28 AM (e)

There was not one individual who lacked a notochord that gave birth to an individual that had one.

As I just noted in my post preceding Nelson’s:

there was no single “chordate” mutation that resulted in a chordate offspring from non-chordate parents — that’s a sorites fallacy, which even Paul Nelson must have learned about in his philosophy courses. But perhaps he misunderstood the lesson and thought he was being taught to employ them rather than to avoid them.

So, Paul, are you retarded, or pathetically dishonest, or both?

Comment #187568

Posted by Popper's Ghost on July 13, 2007 9:33 AM (e)

W.F. Doolittle, “The nature of the universal ancestor and the evolution of the proteome,” Current Opinion in Structural Biology 10 (2000):355-358; p. 357; emphasis added.

Here’s some emphasis for you, bozo:

And it should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import.

That’s got your name all over it, Nelson.

Comment #187569

Posted by Raging Bee on July 13, 2007 9:34 AM (e)

Hello, Sal. Are you going to apologize for equating my words with the (alleged) surgical mutilation of innocent children? If not, why should we take you seriously as anything but a hateful scapegoating liar?

Paul: as long as you’re posting here with impunity (again), why do you feel the need to move a proposed discussion onto a forum we all know to be much less tolerant of us than we are of you?

Comment #187570

Posted by Paul Nelson on July 13, 2007 9:34 AM (e)

PZ wrote (in bold) replying to me (in italics):

if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false.

It doesn’t. That’s what we’re telling you.

Yes, but then – to my surprise – the commenters here largely, if not indeed unanimously (thus far), agree with Ford Doolittle. Universally-shared molecular characters do not indicate common ancestry from a single (discrete) progenitor cell, but could have arisen multiple times independently in a common prebiotic milieu.

As Nick put it, “the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.”

PZ also wrote:

I think it’s obvious that many of these characters are not so discrete as simplistic black-and-white creationist thinking would have you believe.

I’m trying to understand origin of the characters in Doug Theobald’s cladogram, above. You write:

There are gradual transitions and ambiguities in even the most concrete characters we use to classify clades — and that means their evolution would have involved many generations and many contributing individuals.

So could “vertebrae,” another of Doug’s diagnostic characters, have evolved in multiple independent lineages?

Comment #187572

Posted by Incorygible on July 13, 2007 9:34 AM (e)

Okay, Paul. I have an idea. Why don’t you make it VERY clear to EVERYONE in the ID “Big Tent” that a cursory understanding of genetics and phylogeny demonstrates that living organisms on this planet cannot possibly trace their lineage back to a single individual. For example, the genetic material contained within existing humans could NEVER have been contained within one lone Ur-Human (perhaps we could give him a certain proper name?). That’s likely to shake a few of your erstwhile supporters, methinks. In the meantime, we and all those woefully inaccurate evolution books (including the Ancestor’s Tale – thanks Marek, that was probably the one) will be there waiting for the people who might be up to exploring the concepts underlying all those pretty pictures. I would wager a good number of them might actually be able to grasp something analogous to a simple family tree. For example, they might understand the fact that although my brother and I do not share a single individual LUCA, we are nevertheless the products of obvious common descent.

Comment #187573

Posted by Longhorn on July 13, 2007 9:35 AM (e)

Paul Nelson wrote:

“In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false. The first populations of cells on Earth contained many organisms which did not share common ancestry from any single cell. Thus, there never was a universal common ancestor, if that means a particular discrete organism.

This is exactly what Doolittle and Woese have been arguing vigorously for nearly a decade. As you put it, ‘the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.’”
————

Here is an important question: Was there a specific cell on earth about 3.8 billion years ago that is the common ancestor of every other organism to live on earth? First, some people believe that there were subsequent cells on earth that didn’t leave descendants that are as complex as plants. In other words, different cells formed on different parts of the planet at different times and some of those cells did not leave descendants that are at all complex. Here is a quote from Ernst Mayr in which he addresses the issue of whether life may have originated repeatedly:

“Astronomical and geophysical evidence indicate that the Earth originated about 4.6 billion years ago. At first the young Earth was not suitable for life, owing to the heat and exposure to radiation. Astronomers estimate that it became liveable about 3.8 billion years ago, and life apparently originated about that time, but we do not know what the first life looked like. Undoubtedly, it consisted of aggregates of macromolecules able to derive substance and energy from surrounding inanimate molecules and from the sun’s energy. Life may well have originated repeatedly at this early stage, but we know nothing about this. If there have been several origins of life, the other forms have since become extinct. Life as it now exists on Earth, including the simplest bacteria, was obviously derived from a single origin. This is indicated by the genetic code, which is the same for all organisms, including the simplest ones, as well as by many aspects of cells, including microbial cells. The earliest fossil life was found in strata about 3.5 billion years old. These earliest fossils are bacterialike, indeed they are remarkably similar to some blue-green bacteria and other bacteria that are still living” (p. 40).

However, for the sake of argument, let’s assume that life did not originate repeatedly on earth. Let’s assume that there was one and only origination of life. In other words, in a single square foot on earth the self-replicators changed into life, and said life is the ancestor of every other organism to have lived on earth. Here is the question: What did this original life look like? Was it a single cell? I don’t know. AT this moment in time, no person knows exactly which series of events resulted in the first cell forming on earth. It is an important question, and we should keep working on it.

But, Paul, it is important to understand that regardless of the structure of the first life on earth, I share common ancestors with all the daisies that are alive today, and I have ancestors that are fish and amphibians. You seem to be suggesting that this is not the case. It is the case. And it is very important.

Of course, some people believe that an intelligent super being turned inert matter directly into the first human that lived on earth. In other words, at time T there were no humans on earth. And then a super being used a power and turned some of the dust on earth —- poof! —- directly into the first human so that at time T + .2 seconds there was one human on earth. And then the super being removed a rib from this human, and from this rib the super being made the second human. But this didn’t happen. People who believe this are wrong. All the humans descended from ape-like organisms. In fact, all the humans that have lived on earth have ancestors that are fish and bacteria.

Finally, I think it reasonable to believe that a single cell is the ancestor of all the organisms that are alive today. Because before you have two cells you need one cell. But another possibility is that multiple cells formed in close proximity to each other, and that they then came close together and formed into something more singular. And a third possibility is that there was life before a cell evolved. Maybe self-replicating RNA wasn’t really cellular in nature, but we should call that RNA “life.”

Comment #187577

Posted by Popper's Ghost on July 13, 2007 9:47 AM (e)

Yes, but then — to my surprise —

You’re surprised because you’re stupid and ignorant.

the commenters here largely, if not indeed unanimously (thus far), agree with Ford Doolittle. Universally-shared molecular characters do not indicate common ancestry from a single (discrete) progenitor cell, but could have arisen multiple times independently in a common prebiotic milieu.

No, you dolt, the “multiple times” does not follow.

Comment #187578

Posted by harold on July 13, 2007 9:49 AM (e)

Paul Nelson -

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.

One of the very peculiar features of the creationist brain is that they fantasize that some obvious point or two exists that can devastate modern science, and that not one single scientist has ever thought of these points.

First of all, once again, you’re trying to object to the theory of evolution, which deals with cellular and post-cellular life, by objecting to abiogenesis.

You’re clearly motivated to argue that different lineages of modern life don’t share common ancestry. You’re clearly hoping ultimately to claim that humans, for example, were poofed magically into existence, and don’t share common ancestry with other primates. Rather than make that ridiculous claim openly, though, and face a barrage of evidence to the contrary, you resort to what you mistakenly perceive as a clever argument about the origins of life itself.

All existing life is clearly descended from the same or very similar original ancestors. We don’t yet know what those pre- or proto-celluar ancestors were, nor how they came into existence. You can believe it was magic if you like, for now, but that doesn’t change the fact that you’re closely related to chimpanzees.

Whether the ultimate common ancestor shared by all modern life was ever something that could be described as a physically “single” “organism”, or whether a population of highly similar structures came into being roughly contempraneously and more than one such structure contributed to what eventually became modern life, is an interesting question indeed, but not one that impacts on the validity of the theory of evolution.

Comment #187579

Posted by Popper's Ghost on July 13, 2007 9:50 AM (e)

There are gradual transitions and ambiguities in even the most concrete characters we use to classify clades — and that means their evolution would have involved many generations and many contributing individuals.

So could “vertebrae,” another of Doug’s diagnostic characters, have evolved in multiple independent lineages?

No one said anything about “multiple independent lineages”. It’s really hard to believe that your thickness isn’t a put on.

Comment #187581

Posted by Popper's Ghost on July 13, 2007 9:55 AM (e)

For example, they might understand the fact that although my brother and I do not share a single individual LUCA, we are nevertheless the products of obvious common descent.

Paul apparently thinks that, because some of your traits came from your father and some came from your mother, that you must have “arisen multiple times independently”.

Comment #187582

Posted by nickmatzke on July 13, 2007 10:00 AM (e)

Paul Nelson wrote:

In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false.

Woosh. Watch Paul change lanes. My point was that COMMON DESCENT DOES NOT MEAN that all organisms trace their ancestry to a single physical cell. This is based on UTTERLY STANDARD, OLD-FASHIONED, NEO-DARWINIAN, POPULATION-GENETICS THINKING. Therefore Paul Nelson, here and in Explore Evolution, has used the cheap old creationist tactic of setting up a strawman. In his attempt to make it seem like special creation is something more than fundamentalist theology, he portrays as revolutionary and contradictory a conclusion (“no single organism was the ancestor”) that in fact is a completely standard and prosaic result of utterly standard neo-Darwinian theory.

There is a real difference between the real “old-fashioned position” (lineal descent from a common ancestral species) and Doolittle’s view (horizontal descent early in evolution until lineal descent becomes marginally dominant with the three domains and clearly dominant with eukaryotes), but it is far less radical than Paul Nelson thinks. It is basically a question of degree in terms of lateral transfer. If there really was a truly huge amount, then we get something that looks an awful lot like an old-fashioned species.

(PS: I agree with PZ that something like a notochord is not a single character, viewed genetically. But we were talking about molecular/genetic “characters.”)

Comment #187583

Posted by Incorygible on July 13, 2007 10:02 AM (e)

Yes, but then — to my surprise — the commenters here largely, if not indeed unanimously (thus far), agree with Ford Doolittle. Universally-shared molecular characters do not indicate common ancestry from a single (discrete) progenitor cell, but could have arisen multiple times independently in a common prebiotic milieu.

As Nick put it, “the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.”

Paul, Nick’s statement does not imply the multiple appearance of molecular characters via mutation, etc. You’re (deliberately?) misunderstanding/conflating the meaning of “ALL shared characters”, which refers here to the set of shared characters comprising an existing entity as opposed to the origin of each of those characters. For example, humans cannot trace “ALL shared characters” (the suite of genetic material shared by extant humans) to a single individual, but we can, for example, trace our mitochondrial haplotype or our y-chromosome back to their respective single hypothetical-yet-described LUCA individuals. Molecular taits need only arise once in singular individuals/events (although traits like the notochord certainly arose in a long series of such events). Recombination can make those traits shared in the descendants, though they were never shared in the ancestors.

There really is a certain delicious irony in Paul accusing ‘evolutionists’ of postulating the genesis of life’s diversity from individual progenitors. We happen to have a much bigger Ark.

Comment #187585

Posted by drakvl on July 13, 2007 10:07 AM (e)

Paul: Your original objection seems to be the use of “ancestor,” as in “last universal common ancestor,” to describe a population. I can understand; this is not the common usage of the word. However, scientists are rather infamous for using a nonscientific word differently in a scientific context – especially physicists, but biologists do it, too. Ever hear the story of how the cell got its name? A guy was looking through a microscope at cork, which appeared to be divided up into tiny compartments, resembling cells in a monastery.

Similarly, biologists have this huge ongoing metaphor with evolution and its terminology. The whole evolutionary tree – looks a lot like a family tree, doesn’t it? And yet family trees describe relationships between individuals, and the evolutionary tree describes relationships between populations. They’re fundamentally different objects describing different relationships, yet there’s just enough similarity that the evolutionary tree is a useful intellectual tool for simplifying a bunch of information into a smaller set of information, making the data more easily handled. Biologists, understanding full well the scientific context, can afford to relax a bit, and use language which would be confusing to the layperson – such as describing a population as being an “ancestor.” But they know the difference just as well as physicists know that gluons (“glue-ons”) aren’t manufactured by Elmer’s.

Comment #187590

Posted by demallien on July 13, 2007 10:22 AM (e)

I imagine that Paul Nelson still gets all hot and bothered trying to work out which came first, the chicken or the egg…

Comment #187591

Posted by Popper's Ghost on July 13, 2007 10:22 AM (e)

(PS: I agree with PZ that something like a notochord is not a single character, viewed genetically. But we were talking about molecular/genetic “characters.”)

Nelson deliberately uses the vague word “character” so that he can pretend that when you say something about a molecular/genetic trait, you are actually saying it about an arbitrarily large cluster of traits like “having a notochord”.

Comment #187592

Posted by Popper's Ghost on July 13, 2007 10:25 AM (e)

I imagine that Paul Nelson still gets all hot and bothered trying to work out which came first, the chicken or the egg…

Of course; we know that chickens are hatched from chicken eggs and chicken eggs are layed by chickens, so macroevolution is impossible.

Comment #187593

Posted by Paul Nelson on July 13, 2007 10:27 AM (e)

Popper’s Ghost wrote:

So, unknowingly, you have argued that your “population of 1000 cells” have simultaneously stemmed from numerous “single physical cell”s, since the population has more than one trait and each of those traits could have originated in a different cell. In other words, your population of 1000 cells stemmed from an ancestral population, not necessarily from a single cell.

Yes, I noted that explicitly, above. It’s option 2 in my original thought experiment.

Let’s say traits X, Y, and Z are shared universally across terrestrial (Earth) life. These traits either stem (1) from a single cell, or (2) from multiple cells. If (2) is the case, Woese and Doolittle are right, and the cellular state arose polyphyletically (multiple times independently) in Earth history.

Woese argues that this happened three times: “Extant life on Earth is descended not from one, but from three distinctly different cell types” (2002, p. 8746). His paper is freely available here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubm…

Nick wrote:

[…] he portrays as revolutionary and contradictory a conclusion (“no single organism was the ancestor”) that in fact is a completely standard and prosaic result of utterly standard neo-Darwinian theory.

Well, no. Ford Doolittle grasps the implications of his position for (to take an instance) the concept of homology. See the 2000 Structural Opinion paper I cited.

More later. I’m serious about setting up a moderation-free discussion at the Explore Evolution website.

Comment #187596

Posted by fnxtr on July 13, 2007 10:32 AM (e)

Okay, this layman still doesn’t get it.

Mr. Nelson:

If Explore Evolution really isn’t just religious prosletysing, why is it so important to you that it be used as a teaching aid to young, impressionable students, especially since most of the mainstream scientific community thinks it’s a bunch of crap? I’ve never heard of this happening with any other ‘controversial’ idea.

Please explain. Thank you.

Comment #187598

Posted by Salvador T. Cordova on July 13, 2007 10:34 AM (e)

Rolf Aalberg

Hey, is this the same Rolf Aalberg who started the greatest and longest thread in ARN history?

Comment #187599

Posted by Salvador T. Cordova on July 13, 2007 10:39 AM (e)

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.

Actually Nick, Darwin’s work had several incoherencies. Perhaps owing to the possibility he plagiarized ideas and maybe had others help ghost write his book. I merely pointed out there were parts of his book that would lead one to presume a one
organism beginning.

And if you are suggesting Darwin argued for multiple first creations, then you’ve just made Darwin a poly-phyletic creationist of sorts. Well done, Nick.

Comment #187600

Posted by Incorygible on July 13, 2007 10:40 AM (e)

Let’s say traits X, Y, and Z are shared universally across terrestrial (Earth) life. These traits either stem (1) from a single cell, or (2) from multiple cells. If (2) is the case, Woese and Doolittle are right, and the cellular state arose polyphyletically (multiple times independently) in Earth history.

That’s quite the equivocation/non-sequitur there, Paul. We go from talking about the origins of traits X, Y, Z to the supposed polyphyletic origin of “the cellular state”?! Nice try. What if we have a single (monophyletic) origin of “the cellular state”, which produces lots of descendant cells, three of which eventually independently arise X, Y, and Z, which get recombined to form XYZ-shared individuals, who happen to be the remaining terrestrial individuals? Um…no multiple independent origins of “the cellular state” there. Or what if we have X, Y, and Z floating around in DDNA in some non-cellular state, which happens to get absorbed in some fashion, known or unknown, into the progenitor of the cellular state? That works, too, and again – only one genesis of the “cellular state” trait that you tried to slip in there as if that’s what you were talking about. Even your own strawmen are taking a whack at you now.

Comment #187601

Posted by Popper's Ghost on July 13, 2007 10:42 AM (e)

Yes, I noted that explicitly, above. It’s option 2 in my original thought experiment.

No, it isn’t. Option 2 is “ Character X evolved more than once: n + 1 times, independently”. That has nothing to do with what I wrote, which was about different characters, X and Y, each evolving ONCE. You are incredibly stupid or you are an incredibly foul dishonest person pretending to be incredibly stupid – which is it?

Let’s say traits X, Y, and Z are shared universally across terrestrial (Earth) life. These traits either stem (1) from a single cell, or (2) from multiple cells.

Let’s say from multiple cells, once each. X from Ur-X, Y from Ur-Y, Z from Ur-Z.

If (2) is the case, Woese and Doolittle are right, and the cellular state arose polyphyletically (multiple times independently) in Earth history.

No, nothing arose multiple times independently, you git. 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. That’s one population, arising once.

Comment #187603

Posted by Popper's Ghost on July 13, 2007 10:45 AM (e)

Actually Nick, Darwin’s work had several incoherencies.

We don’t care, asshole.

And if you are suggesting Darwin argued for multiple first creations, then you’ve just made Darwin a poly-phyletic creationist of sorts. Well done, Nick.

So what if he was?

Cretin.

Comment #187604

Posted by Wesley R. Elsberry on July 13, 2007 10:48 AM (e)

I’ve actually NEVER seen him take a challenge to one of his inane notions head on. Not in all the years he has been a public figure.

The DI has been angling for a court case for years now. If they get one over “Explore Evolution”, you can bet that any competent opposing legal team will call every single author as a hostile witness and relentlessly make them confront those notions head-on, just as they did for Behe and Minnich in the last one, and were prepared to do for Meyer, Campbell, and Dembski before those worthies were withdrawn. Nick already gave a hint in the close of his post.

Well, Moneymaker might get a pass. Illustrators are presumed to present content prepared by others. But his earlier IDC advocacy might mean that he would get the full treatment, just to establish that all of the authors have a narrow religious viewpoint to push, and have been doing just that for years before deciding to produce “Explore Evolution”.

Comment #187606

Posted by Popper's Ghost on July 13, 2007 10:55 AM (e)

That’s quite the equivocation/non-sequitur there, Paul.

It’s so blatant that it’s hard to imagine that he isn’t just pretending to be stupid. Take three virtually identical cells from a population. Each gets hit with a cosmic ray, producing three different mutations, call them Larry, Moe, and Curly. They mix it up, and billions of years later the planet is populated by their descendants, each of whom has a little bit of Larry, Moe, and Curly in them. Three traits, single origin of cellular state, but not a single cell, three different cells.

Comment #187607

Posted by drakvl on July 13, 2007 10:57 AM (e)

Sal: What are you talking about? Of course Darwin may have said things which were wrong. That’s why it’s called scientific progress – it doesn’t start in a perfect state! All that matters is how good Darwin’s basic arguments are, and how well they extend to other circumstances. I mean, every groundbreaking theory has holes. Newton didn’t anticipate the speed of light being constant in all reference frames; Einstein’s field equations don’t make good predictions on the quantum level. Even Euclid is considered to be woefully lacking according to modern standards of mathematical rigor. It seems you expect the first to be the greatest, which is having it totally backwards.

Comment #187608

Posted by Wesley R. Elsberry on July 13, 2007 11:13 AM (e)

I should note that being called as a hostile witness is something that I’ve given some consideration to, myself. I’ve published on the topic and have been a pretty high-profile critic. I recall the questioning I got on my first outing with ID back in 1997, so I’m taking that as a guide to where the hostile questions would come from and be about. I think I’m ready.

Comment #187609

Posted by Popper's Ghost on July 13, 2007 11:16 AM (e)

Woese argues that this happened three times: “Extant life on Earth is descended not from one, but from three distinctly different cell types” (2002, p. 8746).

Three different cell types no more contradicts common descent than three different body plans. The critical word that you throw in is “independently”, but Woese doesn’t claim that, just the opposite:

A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the “Darwinian Threshold” for the reasons given.

Comment #187610

Posted by PvM on July 13, 2007 11:17 AM (e)

Sal, once again, evolution’s best defender…

Comment #187614

Posted by Glen Davidson on July 13, 2007 11:32 AM (e)

Actually Nick, Darwin’s work had several incoherencies. Perhaps owing to the possibility he plagiarized ideas and maybe had others help ghost write his book. I merely pointed out there were parts of his book that would lead one to presume a one
organism beginning.

And if you are suggesting Darwin argued for multiple first creations, then you’ve just made Darwin a poly-phyletic creationist of sorts. Well done, Nick.

What’s the deal, Sal, do you get so tired of repeating your drivel that evolution is a religion and/or dogma, that you come in here and point out that the very opposite is the case?

We know that Darwin isn’t dogma to us. What we don’t know is why you can’t grasp what science is and how irrelevant your stupid “revelations” are to anyone with a chordate nervous system.

This isn’t UD, you know, where only sycophants who applaud every fart you and your masters make are allowed in. We’re mostly intelligent folk, while you either are not, or your dogma has made you incapable of using whatever intelligence you have.

Glen D
http://geocities.com/interelectromagnetic

Comment #187623

Posted by Glen Davidson on July 13, 2007 11:59 AM (e)

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.

Really? Considering that it was a sexual organism, did it have anything with which it could mate?

If not, it certainly wasn’t “the first chordate” in any sense we’re discussing, for it couldn’t leave descendants.

If so, was its mate a chordate? By your standards, no it was not. So a chordate and a non-chordate mated in this scenario, producing what? Chordate descendants, non-chordate descendants, something in-between? And if there can be something in-between as a descendant, why couldn’t the two who mated also be “in-between”.

The fact is that you just have a lot of typological concepts that anyone who’s had a decent science education can see through at once. And you can’t, or won’t, learn, probably a bit of both.

From a different Nelson post:

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?

Species are not defined by characters, ignoramus. There are various means of defining species, the most meaningful one being a set of organisms that would normally interbreed successfully (this does not work for extinct organisms, nor for asexual organisms (secondarily asexual organisms can fit this definition more or less via proxies)).

It appears that the fact that you don’t know how a species is defined most “naturally” is one reason why you can’t understand Doolittle or any other biologist when they’re discussing evolution.

A species may, by convenience, be defined by one or more characteristics which have become fixed into that species, but it is the species which evolves. The “first chordate” is a meaningless term, because we define this extinct type after the fact according to characters which became fixed within a species (simple version) and which we recognize as being “chordate”. That species took time to mutate, recombine, and select the characters that we know after the fact as what we recognize as being “chordate”.

Paul is mistaking the categories that we all, including evolutionists, use for our convenience, with the process of evolution which (essentially by definition) breaks those categories during the time that characters appear and are selected by the environment.

Perhaps Paul doesn’t understand the concept that he has billions of H. sapiens ancestors (though many are counted more than once), and that he is the result of selection during the various matings of those ancestors. Come to think of it, the “perhaps” was superfluous.

Glen D
http://geocities.com/interelectromagnetic

Comment #187627

Posted by Glen Davidson on July 13, 2007 12:18 PM (e)

Yes, but then — to my surprise — the commenters here largely, if not indeed unanimously (thus far), agree with Ford Doolittle.

Wow, and all you needed to do was to read the literature, ask a few competent “evolutionists,” or in fact read what we (I, certainly) have written at PT in the past specifically in response to your troglodyte claims, and you could have known that Doolittle’s proposition isn’t unsettling to us. Just some decency and understanding, and you wouldn’t have to make a fool of yourself repeatedly.

Universally-shared molecular characters do not indicate common ancestry from a single (discrete) progenitor cell, but could have arisen multiple times independently in a common prebiotic milieu.

Oh quit twisting the point to your misconceptions yet again. Universally shared characters may or may not be capable of independently arising multiple times. It depends on the chances of their arising in a context in the first place.

For instance, the present genetic code could not have arisen multiple times, for it is complex, arbitrary in its “choices” (not necessarily completely arbitrary), and thus the product of contingencies which could not reasonably be expected to be duplicated on earth.

However, simpler molecular characters would be expected to arise multiple times, and to be selected for or against by interactions with our environment. The fact that all life utilizes water during active phases should be considered to be a result of our environment (I’m one who doubts that any kind of life at all must depend on water), not diagnostic of a common origin. Lipid membranes surrounding cells also ought not be considered to necessarily be the result of essentially unrepeatable contingencies (though it looks from other evidence like they may all derive from a common origins).

As Nick put it, “the inference that ALL shared characters therefore trace back to the SAME single organism is wrong, wrong, wrong.”

I think we’ve reached the stage where it’s proper to tell Paul about sex. It’s time he knows.

Glen D
http://geocities.com/interelectromagnetic

Comment #187633

Posted by Nick (Matzke) on July 13, 2007 1:01 PM (e)

What Incorygible said.

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.

Comment #187634

Posted by Frank J on July 13, 2007 1:02 PM (e)

Popper's Ghost wrote:

This thread (like many others before it) demonstrates (again) that Nelson doesn’t understand evolution, in just the way that you so brazenly snipped from Glen’s statement, as so well demonstrated by Nick and others.

If Glen’s statement were not on this page I would have provided a link.

I can say that “NaOH is a strong acid.” Does that mean that I don’t understand chemistry? Not necessarily, especially if I had a reason to misrepresent it as such.

Often, a true, honest lack of understanding is accompanied by a willingness to update previous positions in light of corrections, and even occasionally concede those corrections. Anti-evolution activists show no signs of any willingess to do that, or do anything but grossly misrepresnting evolution to those who don’t care how the activists appear to misunderstand it. And the activists certainly don’t care what their critics think.

But like I admitted, I could be wrong.

Comment #187640

Posted by Glen Davidson on July 13, 2007 1:32 PM (e)

I can say that “NaOH is a strong acid.” Does that mean that I don’t understand chemistry? Not necessarily, especially if I had a reason to misrepresent it as such.

It tends to be indicative of that conclusion, yes.

We know that knowledgeable liars will misrepresent matters, but the ones who do understand what they’re misrepresenting typically don’t say “Sodium hydroxide is a strong acid” or:

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.

Paul really isn’t very convincing to anyone who knows biology, yet he comes in here with the most ridiculous mistakes. It is difficult to believe that he knows better but is trying to convince us with patently stupid misconceptions.

On UD matters are otherwise. I really don’t know to what extent Dembski knows better but writes BS that he knows will play well to his sycophants. You don’t have to be intelligent to tell convincing lies to the people who are still allowed to post at UD (with some exceptions), nor do you have to know that what you’re saying is correct. So I really don’t know if Dembski believes the nonsense he writes or if he doesn’t.

Often, a true, honest lack of understanding is accompanied by a willingness to update previous positions in light of corrections, and even occasionally concede those corrections. Anti-evolution activists show no signs of any willingess to do that, or do anything but grossly misrepresnting evolution to those who don’t care how the activists appear to misunderstand it. And the activists certainly don’t care what their critics think.

You’re mentioning one causal direction, but not the other one. Anti-evolutionists typically have no willingness to learn anything except what they think can be used against their opponents, thus they remain ignorant.

One can think of potential exceptions like Jonathan Wells, who at least learned the basics. Yet despite his impressive credentials, he regularly makes rather basic mistakes regarding fairly fundamental biological knowledge. I don’t think that Wells is personally or intellectually honest, and it appears that he deliberately spreads untruths that he knows have been refuted to all competent minds. Nonetheless, even his much greater knowledge of biology isn’t good enough to really spin convincing falsehoods (except to his targeted audience), partly because his “learning” of biology is strongly filtered by his preconceptions.

I do think that Paul Nelson is relatively more personally honest than Wells is, though his evident lack of intellectual honesty cannot be divorced from the rest of him (and so he is not completely personally honest, since personal honesty in discussing evolution with us entails intellectual honesty).

But like I admitted, I could be wrong.

Either way, you should have made a case instead of merely stating a belief that you have about Nelson. I really don’t want to make too much of this, but PG’s right that I did make a case and you did not. At best that’s not very good form.

Glen D
http://geocities.com/interelectromagnetic

Comment #187645

Posted by Raging Bee on July 13, 2007 1:39 PM (e)

Paul Nelson pretends thusly:

I’m serious about setting up a moderation-free discussion at the Explore Evolution website.

I’ll ask you again: why not have that discussion HERE? You know as well as we do that there’s no moderation, and no censorship.

Comment #187663

Posted by Gary Hurd on July 13, 2007 2:52 PM (e)

Actually Nick, Darwin’s work had several incoherencies. Perhaps owing to the possibility he plagiarized ideas and maybe had others help ghost write his book. I merely pointed out there were parts of his book that would lead one to presume a one organism beginning.

Well Sal, here is you big chance to demonstrate the calculation of the Insanitary Filter. Come on big guy! Or is this just more typical creationist ad hom?

And if you are suggesting Darwin argued for multiple first creations, then you’ve just made Darwin a poly-phyletic creationist of sorts. Well done, Nick.

Actually people with average reading ability would have understood that Darwin cautioned that the extreme extension of common descent to a single ancestor could be misleading. Try sounding out all the letters, “Analogy would lead me one step farther, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide.”

With creationist heroes like you and Paul Nelson, evolutionary science is secure.

Comment #187669

Posted by Popper's Ghost on July 13, 2007 3:11 PM (e)

If Glen’s statement were not on this page I would have provided a link.

Your counterfactual is no answer to what I wrote.

I can say that “NaOH is a strong acid.” Does that mean that I don’t understand chemistry? Not necessarily, especially if I had a reason to misrepresent it as such.

“not necessarily” is the weakest argument as one can make. Seriously, it’s not worthy of response.

But like I admitted, I could be wrong.

And that is the weakest admission one can make.

Comment #187673

Posted by Popper's Ghost on July 13, 2007 3:33 PM (e)

Often, a true, honest lack of understanding is accompanied by a willingness to update previous positions in light of corrections, and even occasionally concede those corrections. Anti-evolution activists show no signs of any willingess to do that, or do anything but grossly misrepresnting evolution to those who don’t care how the activists appear to misunderstand it. And the activists certainly don’t care what their critics think.

Your argument here seems to be that never admitting an error implies that the person understands the material thoroughly. Your logic is even worse than Nelson’s.

I have stated repeatedly that Nelson is either an idiot or he is pretending to be. But that someone pretends to be an idiot doesn’t imply that he’s a genius. There’s good reason to think that Nelson does understand things that he pretends not to – but the role of populations in the theory of evolution does not appear to be among them.

Comment #187676

Posted by Popper's Ghost on July 13, 2007 3:40 PM (e)

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

Apparently Nelson doesn’t know what the L in LUCA stands for, or doesn’t grasp the meaning of the word. I I find it difficult to discern the purpose of feigning that level of stupidity.

Comment #187679

Posted by Wesley R. Elsberry on July 13, 2007 3:44 PM (e)

We’ve got a dedicated thread for the “Explore Evolution” discussion at AtBC.

I’ve put up the press release on AtBC in response to someone wondering how to request a review copy, something that they said they couldn’t find on the DI’s website. Probably ought to have the web guru in DI-land fix that oversight.

Comment #187681

Posted by Popper's Ghost on July 13, 2007 4:05 PM (e)

PG’s right that I did make a case and you did not

My point was actually that he removed your case from sight, freeing himself of any need to consider it as he naysayed you – a point that is not at all met by his irrelevant assertion that he would have linked to your statement if on a different page, which would still have left it out of sight and mind. It won’t do for him to simply disagree with you that Nelson so badly understands evolution, as if that’s all you had said; he needs to respond to your specific charge that Nelson “think[s] in terms of evolution of the individual, not the population”, which has been the whole point of this thread.

Comment #187687

Posted by David B. Benson on July 13, 2007 4:35 PM (e)

I noticed, many comments ago on this thread, a misconception which I can correct. The issue is the number of ancestors, as a function of reverse time. So, I have two parents and they had two parents each, so I had four grandparents, etc. We have the geometric series

1 2 4 8 16 32 …

which gives rise to the temptation that this continues indefinitely. Not so. Eventually the erstwhile number of ancestors exceeds the population size at some time depth. This is made a bit simpler by assuming a fixed population size, say 2048 individuals. Then at eleven generations back everybody was one of my ancestors and I never had any more than everybody at twelve generations back.

Comment #187702

Posted by Popper's Ghost on July 13, 2007 5:38 PM (e)

a misconception which I can correct

A misconception by whom? In any case it’s already been “corrected” by Glen who wrote “Perhaps Paul doesn’t understand the concept that he has billions of H. sapiens ancestors (though many are counted more than once)”.

Comment #187705

Posted by David B. Benson on July 13, 2007 5:45 PM (e)

Popper’s Ghost — It wasn’t Paul nor a regular here.

But you are welcome to read the entire thread yourself to find out the poster’s handle…

Comment #187711

Posted by Frank J on July 13, 2007 5:57 PM (e)

Glen Davidson wrote:

Either way, you should have made a case instead of merely stating a belief that you have about Nelson.

I admit that I can’t make that case, because of my usual caveat that we can never really know what another truly believes. That’s why I constantly refer to what anti-evolution activists promote instead of what they believe or know. And he certainly acts like he misunderstands it.

Popper's Ghost wrote:

I have stated repeatedly that Nelson is either an idiot or he is pretending to be. But that someone pretends to be an idiot doesn’t imply that he’s a genius.

Excellent. I wish everyone would qualify it with “or pretending to be.” And I never meant to imply that he was a genius, or even as evolution-literate as half of his critics. I just can’t imagine him privately understanding less about evolution than I do. And I’m just a chemist with a side interest in the subject, not one who “eats, drinks and sleeps” it like he does. Or has a reason to misrepresent it.

As for Nelson “think[ing] in terms of evolution of the individual, not the population”, of course he does, because that helps him misrepresent evolution to his target audience that is conditioned to think that way. Years ago, when I first heard “individuals don’t evolve, populations do” it was a “d’Oh” moment. Again, I could be dead wrong, and Nelson could be suffering from a severe case of Morton’s Demon, but it’s hard to believe that he doesn’t get such a simple concept.

Comment #187716

Posted by Popper's Ghost on July 13, 2007 6:18 PM (e)

But you are welcome to read the entire thread yourself to find out the poster’s handle…

And you’re “welcome” to be an ass.

Comment #187718

Posted by Incorygible on July 13, 2007 6:38 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #187719

Posted by Incorygible on July 13, 2007 6:41 PM (e)

I noticed, many comments ago on this thread, a misconception which I can correct. The issue is the number of ancestors, as a function of reverse time. So, I have two parents and they had two parents each, so I had four grandparents, etc. We have the geometric series

1 2 4 8 16 32 …

which gives rise to the temptation that this continues indefinitely. Not so. Eventually the erstwhile number of ancestors exceeds the population size at some time depth. This is made a bit simpler by assuming a fixed population size, say 2048 individuals. Then at eleven generations back everybody was one of my ancestors and I never had any more than everybody at twelve generations back.

No misconception – merely simplification/omission. You’ll notice that I described the number of human ancestors each of us has as “thousands” (reached in less than a dozen generations in the geometric series) as opposed to “billions”, “trillions”, etc. Yes, for many (and eventually all) ancestors, you can “get there from here” by many, many paths, so the same individual is counted thousands of times (as Glen pointed out). This fact does not change the point that was made, which was merely that phylogenetic (and family) trees can tend to fool us into thinking the number of ancestors we have DECREASES as we go back in time (i.e., as we zero in on a particular ancestor), when the reverse is true.

Comment #187720

Posted by Popper's Ghost on July 13, 2007 6:50 PM (e)

I admit that I can’t make that case, because of my usual caveat that we can never really know what another truly believes.

How is that different from never really knowing how the flagellum evolved? It’s a cop-out, the same one the creationists use when they say “no one was there”. Cases aren’t airtight, they’re inferential.

Comment #187721

Posted by Popper's Ghost on July 13, 2007 6:55 PM (e)

No misconception — merely simplification/omission

Yes, that was pretty obvious, which is why I asked Benson to be explicit. His inference that you suffered from a misconception is irrational. According to him in another thread, that makes him mentally ill. I do hope he gets treatment.

Comment #187728

Posted by rimpal on July 13, 2007 7:26 PM (e)

Posted by Paul Nelson on July 13, 2007 8:30 AM (e)
I have to attend a meeting at the Hilton O’Hare…When the Discovery Institute webmaster is available…what needs to be done to set up moderation-free discussion threads at the Explore Evolution webpage.

Translation
Eeeeks! Bruce, Bill, Jack, Phil…I gabbed without thinking over at the ‘Thumb. And the guys over there have me by the short-hairs!!! Help!!!

Posted by Paul Nelson on July 13, 2007 9:34 AM (e)
I’m trying to understand origin of the characters in Doug Theobald’s cladogram

Translation Hulloooo! The guys are taking the mickey out of me. And please, I asked for help not for that flunkey Sal wasssissname. He’s a mess.

Posted by Paul Nelson on July 13, 2007 10:27 AM(e) Guys! Are you serious or what. I can’t come up with another excuse. No one is buying that O’Hare thing

The DI folks in Seattle are up to their wazoo in it; is very busy. They’ve skipped lunch. They’re going to be eating their words about the Colorado caper, now that the kook responsible has been tracked down.

Comment #187730

Posted by David B. Benson on July 13, 2007 7:45 PM (e)

incorygible — Thanks for the prompt reply. I should have been more careful to scribe apparent misconception. And I certainly wasn’t disagreeing with your main point.

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

ancestor, n. 1. One from whom a person is descended, esp. at a distance of time; a forefather.

Note this is a binary relationship; either King David is an ancestor of Jesus of Nazareth or he is not. The number of paths possible between descendant and remote ancestor does not matter. Thus in counting ancestors one has to be more careful than either you, or Glen D, or I have been, if one wants accuracy.

So I should revise my earlier comment to state that at the eleventh generation back, one has between 2 and 2048 ancestors, inclusive.

I suppose this is quite a small matter given the subject of this thread.

Comment #187738

Posted by Popper' Ghost on July 13, 2007 8:24 PM (e)

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

Despite Incorygible not having made a mistake. If, say, one enumerates one’s great grandparents, one may end up counting the same person more than once, especially if one is a hillbilly. The same person gets counted more than once, as he said. Which reduces the number of ancestors, as he said. 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.

Comment #187741

Posted by Dave Carlson on July 13, 2007 8:43 PM (e)

Paul Nelson and Sal Cordova are no longer with us. - D. Carlson

Oh wait, I’m sorry. I forgot which site this is.

Comment #187745

Posted by David B. Benson on July 13, 2007 9:11 PM (e)

Popper’s Ghost — Then why didn’t you just ignore it?

I don’t find it a quibble.

The maximum likelyhood time estimate, based on genetics, (see Alex Templeton’s recent papers), is that H. sapiens sapiens left Africa for Southwest Asia and the rest of the world about 135,000 years ago. Assume that date is exact. Assume 20 years per generation is correct.

Do I really have 2 raised to the 6750 power ancestors at that remove? No, probably five hundred to a few thousand.

While I suppose most who post here on PT understand this, it is a point easily misunderstood, or misinterpreted, and perhaps needs greater care than is ordinarily given.

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.

Comment #187761

Posted by Sir_Toejam on July 13, 2007 11:20 PM (e)

I disagree with Nick on that point. A single character, such as a notochord, is not the product of a single genetic event, in most cases. What part of the notochord is the important one? Its inductive role in early development? And which of the several inductive events matters? Its structural role?

then the issue is not that you disagree with what Nick was pointing at but rather that he used insufficiently specific terminology to express it.

If a trait WERE the result of a single genetic event, and some probably are, then his example works just fine. just take the answer to one of your rhetorical questions and plug it in, then you’re on the same page.

so, don’t take Paul’s word for what Nick said, read the post yourself. it was clear to me at least what he meant.

Comment #187763

Posted by Sir_Toejam on July 13, 2007 11:24 PM (e)

here is that Nelson takes being a chordate to be a single “character” that arose in a single organism. But there was no single “chordate” mutation that resulted in a chordate offspring from non-chordate parents — that’s a sorites fallacy

ah, yeah I see PG was onto this long before the exchange between PZ and Paul took place.

Comment #187765

Posted by Sir_Toejam on July 13, 2007 11:28 PM (e)

In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, that theory is false.

here, let me reword that more correctly for you Paul:

In other words, if the theory of common descent means that all organisms trace their ancestry to a single physical cell, then that is a strawman of of the actual theory of common descent.

there, that would be more honest of you.

Comment #187767

Posted by Sir_Toejam on July 13, 2007 11:32 PM (e)

Actually Nick, Darwin’s work had several incoherencies[sic].

and Sal, if nothing else, is an expert on being incoherent.

Comment #187769

Posted by PvM on July 13, 2007 11:39 PM (e)

Let’s not trouble Sal with asking him to do real science or research.

Comment #187770

Posted by Sir_Toejam on July 13, 2007 11:43 PM (e)

The DI has been angling for a court case for years now.

I suspect that just as with Behe, even when they get “what they want” and are utterly annihilated by it as they only can be, it likely won’t do much to reduce their delusions of grandeur.

In fact, whether they suffer from pure denial and are completely insane (Sal?), or whether they are just a bunch of political hacks trying to do a bit of social engineering, or if they are purely in it for the cash (provided by the likes of ill folk like Ahmanson), it matters not if they lose in any arena nameable. So long as they can continue to sell the snake oil to the rubes, there is no advantage in admitting defeat of any kind.

Comment #187808

Posted by _Arthur on July 14, 2007 8:25 AM (e)

I wasn’t familiar with the term “Muller’s Ratchet”, so here it is:

http://en.wikipedia.org/wiki/Mullers_ratchet

My own favorite asexual organism, (not a pop singer) is the dandelion.
There are papers that claim that dandelions sometimes reverse their apomixis, and revert to sexual reproduction, allowing to fix charachters. Dandelions aggregate species is well-adapted to lawns.

Comment #187868

Posted by Scott on July 14, 2007 5:20 PM (e)

Thanks to all the PT regulars for this discussion. As an interested layman and sometime lurker, it’s actually quite enlightening. While it’s great to learn a linear narrative of a subject (in this case, individual vs population, and the true “fuzziness” of the apparently “sharp” junctures in a cladogram), it also helps to learn how a subject can be misunderstood, what points were missed, and so avoid those misunderstandings.

While it seems that education is wasted on creationists, it sure helps the rest of us.

Thanks! :-)

P.S. The word “cladogram” is not in your spell checker’s dictionary.

Comment #187941

Posted by Paul Nelson on July 15, 2007 10:49 AM (e)

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.

Comment #187944

Posted by ben on July 15, 2007 11:29 AM (e)

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.

Comment #187945

Posted by PvM on July 15, 2007 11:30 AM (e)

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.

Comment #187948

Posted by Doc Bill on July 15, 2007 12:36 PM (e)

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.

Comment #187949

Posted by Longhorn on July 15, 2007 12:46 PM (e)

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/

Comment #187950

Posted by Laser on July 15, 2007 12:59 PM (e)

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.

Comment #187964

Posted by Bruce Thompson GQ on July 15, 2007 2:54 PM (e)

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)

Comment #187970

Posted by Scott on July 15, 2007 3:17 PM (e)

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?

Comment #187983

Posted by Glen Davidson on July 15, 2007 4:41 PM (e)

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

Comment #187984

Posted by Glen Davidson on July 15, 2007 4:59 PM (e)

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

Comment #187985

Posted by David B. Benson on July 15, 2007 5:17 PM (e)

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…

Comment #187986

Posted by Glen D on July 15, 2007 5:25 PM (e)

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

Comment #188004

Posted by David B. Benson on July 15, 2007 6:51 PM (e)

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.

Comment #188008

Posted by Glen Davidson on July 15, 2007 7:05 PM (e)

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

Comment #188012

Posted by David B. Benson on July 15, 2007 7:11 PM (e)

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 #188015

Posted by Moses on July 15, 2007 7:29 PM (e)

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.

Comment #188452

Posted by Popper's Ghost on July 17, 2007 10:03 AM (e)

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.

Comment #188453

Posted by Popper's Ghost on July 17, 2007 10:13 AM (e)

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.

Comment #188458

Posted by Popper's Ghost on July 17, 2007 10:26 AM (e)

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.

Comment #188470

Posted by Popper's Ghost on July 17, 2007 10:54 AM (e)

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.

Comment #188478

Posted by Popper's Ghost on July 17, 2007 11:10 AM (e)

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.

Comment #188481

Posted by Popper's Ghost on July 17, 2007 11:36 AM (e)

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.

Comment #188494

Posted by Tyrannosaurus on July 17, 2007 1:17 PM (e)

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.

Comment #188545

Posted by Glen Davidson on July 17, 2007 5:44 PM (e)

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

Comment #188575

Posted by Steviepinhead on July 17, 2007 8:16 PM (e)

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.

Comment #189133

Posted by slpage on July 21, 2007 8:42 AM (e)

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….

Trackback: Don't say I didn't warn you...

Posted by The Panda's Thumb on July 13, 2007 3:10 AM

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...