At last?
Back in 2007, I predicted that the idea of “Intelligent Design” would soon fade into obscurity. I wrote:
My initial assessment of ID in my earliest encounter with an ID proponent* was that ID would be forgotten within five years, and that now looks to me an over-generous estimate.
*August, 2005
I was wrong. Whilst the interest in “Intelligent Design” (ID) as a fruitful line of scientific enquiry has declined from the heady days of 2005 (or perhaps was never really there) there remain diehard enthusiasts who maintain the claim that ID has merit and is simply being held back by the dark forces of scientism. William Dembski; the “high priest” of ID has largely withdrawn from the fray but his ideas have been promoted and developed by Robert Marks and Winston Ewert. In 2017 (with Dembski as a co-author) they published Introduction to Evolutionary Informatics, which was heralded as a new development in the ID blogosphere. However, the claim that this represents progress has been met with scepticism.
But the issue of whether ID was ever really scientific has remained as the major complaint of those who dismiss it. Even ID proponents have admitted this to be a problem. Paul Nelson, a prominent (among ID proponents) advocate of ID famously declared in 2004:
Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’ – but, as yet, no general theory of biological design.
Whilst some ID proponents – Ann Gauger, Douglas Axe are perhaps most prominent among them – have tried to develop ID as science, the general scientific community and the wider world have remained unimpressed.
Then a new young vigorous player appears on the field. Step forward, Eric Holloway! Dr Holloway has produced a number of articles published at Mind Matters – a blog sponsored by the Discovery Institute (the paymasters of ID) on artificial and “natural” intelligence. He has also been quite active here and elsewhere defending ID and I have had to admire his persistence in arguing his case for ID, especially as the whole concept is, in my view, indefensible.
But! Do I see cracks appearing? I happened to glance at the blog site formerly run by William Dembski, Uncommon Descent, and noticed an exchange of comments on a thread entitled Once More from the Top on “Mechanism” The post author is Barry Arrington, current owner of UD and a lawyer by trade, usually too busy to produce a thoughtful or incisive piece (and this is no different). However, the comments get interesting when Dr Holloway joins in at comment 48. He writes:
If we can never be sure we account for all chance hypotheses, then how can we be sure we do not err when making the design inference? And even if absolute certainty is not our goal, but only probability, how can we be confident in the probability we derive?
Eric continues with a few more remarks that seem to raise concern among the remaining regulars. ( ” Geeze you are one confused little pup EricMH.” “Has a troll taken over Eric’s account?) and later comments:
But since then, ID has lost its way and become enamored of creationism vs evolution, apologetics and the culture wars, and lost the actual scientific aspect it originally had. So, ID has failed to follow through, and is riding on the cultural momentum of the original claims without making progress.
Dr Holloway continues to deliver home truths:
I would most like to be wrong, and believe that I am, but the ID movement, with one or two notable exceptions, has not generated much positive science. It seems to have turned into an anti-Darwin and culture war/apologetics movement. If that’s what the Discovery Institute wants to be, that is fine, but they should not promote themselves as providing a new scientific paradigm.
I invite those still following the fortunes of ID to read on, though I recommend scrolling past comments by ET and BA77. Has Dr Holloway had a road-to-Damascus moment? Is the jig finally up for ID? I report – you decide!
ETA link
Alan only sees more sealions
Guided or unguided?
Here is the whole Weiss article that Nelson quote-mined
“To understand the baboon,” Evolutionary Anthropology 21 (2012):131-135.
Go ahead and show us in the article anywhere Weiss is doubting evolutionary theory or UCD. All I see are passages like
“Evolution unites our recognition of both pattern and its evolution, because history preserves functional and nonfunctional parts of DNA, but at different overall rates. And what is most telling in this regard is the remarkable fact that even though each specific functional element has its own unique history of descent and adaptation, the generic connection between history and pattern remains.”
and
“The Rubaiyat of Omar Khayyam is a poem about love, as nature’s Paradise. It’s true: from a Darwinian point of view, the wine, the bread, and the lover are all related. Their DNAs have orderly patterns of similarity that make more sense in evolutionary terms than by any other known criterion”
Actually the more I read the whole article the more dishonest Nelson’s disgusting quote-mining seems.
So you agree evolution cannot account for the 2000 protein families we see. We both know microevolutionary changes can get to a nearby function by small changes. Misrepresentation is poor argument. Do you really think this goes unnoticed?
Are you claiming your magic wand works before new function arrives? Do you understand the irreducibly complexity problem natural selection faces?
I see you completely ignored the entire textbook on evolution through gene duplication I showed you.
Bill when you reach the bottom of the stupidity pit you really need to quit digging.
Adapa,
There is evidence of simple adaption through gene duplication. It happened 1 time over 35 years of e coli evolution in the Lenski experiment. There is also evidence that small mutations in enzymes can enable other small molecules to change. We have common ground that evolution can create simple adaptions.
It’s evolution producing new information and new function. It’s empirically observed Bill. There are no known barriers to the amount of new information or new function which can be accumulated.*
You’re still digging your hole in the stupidity pit deeper and deeper.
*Not including the constraints on biological materials imposed by the laws of physics, i.e. you won’t see a bird flying at Mach 2.
Adapa,
You are claiming that there are no known barriers. Functional information greater than 500 bits may be a barrier especially if it is required to get from the current state to new function. This is certainly possible in more than one transition during evolutionary history.
Like I said, there are no known barriers to the amount of new information or new function which can be accumulated. ID-Creationist unsupported bullshit about an imaginary “500 bits” limit isn’t a barrier to physical reality.
Keep digging that hole deeper Bill.
The only barrier would be if there was not enough energy flow for such amount of bits to accumulate Bill. The amount of energy flow that goes across our planet accounts for much more than needed for a humungous amount of information to accumulate across much more than the life forms known to exist and for evolution to continue happening. We have that thing called “Sun’ right there, which is the main source of the necessary energy. Five hundred bits is ridiculously tiny for that energy flow Bill.
Sorry, but natural phenomena do not owe us the possibility for strong and accurate predictions.
Joe just gave you an explanation about phylogenetic trees and probabilities. That should give you a hint that evolutionary biologists do not expect to produce perfectly resolved phylogenetic trees. So, for example, if you find “unexpected” character distributions in a tree, It might be a good idea to check if you’re looking at poorly resolved branches.
It also depends on which character distributions you might be talking about. For example, some characters are situation dependent and thus might mask/confound evolutionary relationships if it is not known that some phenotype is only displayed if, say, the organisms grows under dry conditions. There’s a few steps between genotype and phenotype that has to be accounted for before deciding that some character is phylogenetically informative.
Which law of physics is that?
Even if it was coherent, how to establish that a pattern is the product of libertarian free will? Let’s politely ask shall we?
Are you talking about libertarian free will? If so, could you elaborate about how one goes about testing that, please?
My gut feeling tells me this is not possible without wading into deep philosophical marshland. Not the best place to start a positive scientific case for ID rejuvenated.
Our conversation seems to be on hold. Here at TSZ there is the thread where you presented a model of what I took to be population genetics using the genome of a single organism represented as a binary string. For me, the issues here are the need to model populations, not single organisms, and the need to appropriately model the environment when you apply Levin’s results.
I’m also unclear on why you think human intelligence cannot be simulated by a Turing machine, eg why you seem to think that it could solve the halting problem. That disagreement came up at PS.
And we seem to have a basic disagreement on the nature of how the math used in explanatory models is justified in empirical science. I emphasize that scientists choose the math structures that work for explaining, controlling, predicting the world being studied by a domain of science.
Joe F and others have their own concerns with your work and the work of your ID colleagues, but the above are where I think we diverge regarding your work.
On J. Swamidass, if your concern on disproving math relates to the thread on MI and cancer cells, I have the impression that you and he were talking about different MIs. I cannot be sure since JS was relying on Venn diagrams, not formalisms, in that thread.
Sorry Paul but your quotes here do not support the claim you make in your talk. You say in your talk that it was initially predicted by the UCD hypothesis that there should be no incongruent phylogenies. But that is just not correct, and your quotes about the extent to which incongruencies would blur out the tree of life do not support it either.
One needs only read the 1965 paper by Pauling and Zuckerkandl to see that, even before the very first molecular phylogenies were made, biologists knew and understood that you would, at least occasionally, expect incongruencies.
“”It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.”
Evolutionary divergence and convergence in proteins
E Zuckerkandl, L Pauling – Evolving genes and proteins, 1965.
Mostly in agreement implies the authors are already aware that incongruencies will some times occur, even between morphological and molecular data. And of course I’d be very surprised to hear that taxonomists constructing phylogenies on the basis morphology have never run into the problem of conflicting trees based on different subsets of morphological characters.
I take stochastic to mean there is a probability distribution invoked with the explanation. See, for example, Joe F’s reply.
Deterministic would be the special case where the distribution is that the probability of one event in the sample space is 1 and the probability for any other is 0. For example, a loaded coin which always came up heads. This is a special case of a degenerate distribution
https://en.wikipedia.org/wiki/Degenerate_distribution
Admittedly, this approach to the meaning of deterministic is something that might only occur to a mathematician, but I think it is reasonable.
Given this, I don’t have an issue with Eric’s claim that scientific explanations under MN involve stochastic processes or laws. I am taking an explanation to be a math equation or a model, or some combination. Math equations capture either laws, like GR, or the evolution of a system, like Schrodinger’s equation. Models could be something more general, such as those used in population genetics.
I don’t have a problem with you subsuming deterministic processes under stochastic ones.
But randomness can be misinterpreted. In the context of a stochastic scientific explanation, it cannot mean simply irregular and unpredictable in principle. That would be no explanation at all. Instead, the explanation has to involve a way of providing a probability distribution (or class of them parameterized in some way).
Of course, we can statistically show that a given (class of) distributions fails to model the data. But if we are doing science, that just means we have the wrong model.
There is a related idea called Knightian uncertainty, which is roughly the idea that we cannot even specify a probability distribution or even some class of them. For me, if we are in that state with regard to a field of study, then we need to do more exploratory work before we can advance a scientific explanation:
https://en.wikipedia.org/wiki/Knightian_uncertainty
LOL. Shame on you, Nelson.
This too is quite misleading Paul.
It has never been a prediction of the theory of universal common ancestry that all genes should be universally shared, or that new genes could not ever evolve in and be isolated to some clade or taxon. Nothing is swelling up to include stuff that was previously disallowed.
Rumraket, to Paul Nelson:
Paul’s reasoning seems to be:
1. Weiss accepts UCD.
2. Weiss was surprised by orphan genes.
3. Therefore, UCD must have predicted that there would be no orphan genes.
4. Therefore, a prediction of UCD was falsified.
5. Therefore, the ‘sphere of UCD’ had to ‘swell’ in order to take in orphan genes.
If it isn’t obvious, the trouble starts in step 3.
Eric,
Add me to the list of folks wondering how you would test a process to determine whether it is non-stochastic (by your definition).
colewd,
Junkyard tornado reasoning. Ignores selection.
Both are colewd specialties.
Well put. We can pretty much just put Weiss aside and try to consider the theory of UCD by itself. What does that theory say, in essence? That all organisms share genealogical lines of descent that meet in common ancestors. That’s it.
It should be pretty obvious that UCD makes no predictions about how many genes should or should not share descent, and no predictions about when or if or how many new genes should evolve.
Weiss may have been right to be surprised to see how many new orfan genes were discovered given some prior assumptions or theories about how frequently that should occur. Perhaps Weiss was working within some framework of biochemistry or molecular evolution that says orfan genes should be extremely rare. But then it is that framework that makes predictions about orfan gene frequencies, it is not the mere fact of common ancestry.
The same problem undergirds Paul’s invocation of the propensity for incongruencies between different gene phylogenies. Again common descent does not predict that there should not ever be any incongruent phylogenies(why would it predict that? What assumption would you have to make for UCD to predict that?). That would require (for example) something like some weird assumptions about the impossibility of convergence in character states in different lineages. But then that would be an assumption about how character states change, not a prediction that follows from the mere fact that those species share common ancestry.
I find his characterization of these different issues simplistic and misleading.
keiths,
Its your burden to show there is something to select. Otherwise you are invoking the selection as a magic wand. Selection does not occur until you have additional function that is beneficial. The tornado in a junkyard is valid as you do not have selection until you have reliable self replication.
Rumraket,
What exactly does it predict? Assertion “like energy flows generate plenty of linear functional information” is not theory.
Paul’s point and I share is where are the cases of falsification that give the theory meat. If you find an exception and re label it a feature all you are left with is dogma.
Why would we expect orphan genes from reproduction alone?
Oh come ON. Nowhere in my talk did I say that Weiss doubted UCD. (Show me the time marker at YouTube if you think I did.) I said he was “having to grapple with the implications” of orphans, which is obviously true, and well-supported by the article I cited. OF COURSE he offers a Darwinian profession of faith, to reassure the reader.
The next year (2013), Weiss returned to orphans — again, grappling with their existence and what they entailed for current theories of evolution and gene origin. Take careful note of the last two sentences of this passage (my emphasis):
This is grappling with the implications of a discovery. It is NOT bailing out of UCD (the remainder of this 2013 article speculates about new evolutionary processes to explain the origin of orphans). I never said Weiss had dropped UCD — again, show me the time marker at YouTube — but it is manifestly the case that orphans are making him re-think his views on a range of evolutionary questions.
Which IS exactly what I said. Get real.
Citation: Kenneth M. Weiss, “Little Orphan’s Nanny,” Evolutionary Anthropology 22 (2013):4-8; p. 4.
Phylogenetic signal is falsifiable by statistical testing, as you have been shown multiple times.
I am still flummoxed why you think orphan genes are a problem for the theory of evolution. Can you explain this? The first thing you need to explain is why orphan genes are lineage specific. Why don’t we find the same identical orphan gene in one primate species and one fish species, and nowhere else?
Can you point to a single genetic difference between humans and chimps that could not have been produced by known mechanisms of mutation? If not, I really don’t understand what you are arguing against. You must know that mutations occur.
Guided or unguided by what?
T_aquaticus,
Does this phylogenetic signal include the maximum number of orphan genes we would expect from reproduction?
Can you point to a single genetic difference between humans and chimps that is not a “simple adaptation”.
Again, asking me to prove a negative. If you make the common ancestor claim its your burden to show known mechanisms can produce the feature. How can an advanced language capability be produced by mutation? Maybe this can be answered in your lifetime.
T_aquaticus, to Paul:
That would violate the Designer’s sense of tidiness. It’s so inelegant to reuse orphan genes outside of taxonomically restricted groups. Sort of like mixing plaids with stripes.
Rum,
I have a conference call today which requires a lot of prep, so this will have to be brief. You call my analysis “simplistic and misleading,” but the worries I raise won’t go away because I’m just another crazy ID person with known bad motives (or something like that). Here’s the problem. You say that UCD allows for plenty of noise (incongruence), and indeed, we should expect as much, given evolutionary processes. Nonetheless, the signal (congruence) which supports UCD makes it through the noise in the end, and thus we can confidently assert that all organisms share common ancestry.
But unless one has a way to predict noise versus signal, this move renders UCD untestable.
Because signal + noise = all the observations. WHATEVER one observes, the outcome will be consistent with UCD. Non-orthologous gene displacement? Consistent with UCD. Just noise. Incongruent phylogenies? Consistent with UCD — noise again. Developmental systems drift? (Do a PubMed search using that term, the data are mind-blowing.) More noise, not to worry.
Hey, somewhere on YouTube (don’t have time to find the link right now), there is a clip of Richard Dawkins saying that the best evidence for evolution (by which he means UCD) is the perfect congruence of molecular and morphological phylogenies. Whatever data one examines, he says, the cladograms are identical.
Paul Nelson,
Sorry, but this whole discussion seems to be off-topic to me. As I see it, ID theory is fully compatible with common descent and the nested hierarchy, even if orphan genes were inserted in the genome by the Designer, so why bring it up?
Also I fail to see how this is going to provide a positive argument for ID, unless you somehow will be able to demonstrate that orphan genes have a supernatural origin (without resorting to “evolution can’t do it”).
It is predictable, from my limited understanding. My expertise is more on the practical side of molecular biology, but having been a part of these debates for quite a few years you pick up a few things.
For example, we would expect ILS to produce more noise when comparing the chimp/human branch to the gorilla branch than it would when comparing the chimp/human branch to the orangutan branch. That is exactly what we see. We would also expect the deepest branches to be the hardest to resolve because of noise, and that is what we see. We would expect homoplasy to produce more noise in DNA sequences saturated with mutations, and that is what we see.
Signal and noise are a part of every single scientific model. I don’t know of a single theory in science that produces perfect correlations. This is why statistics is almost ubiquitous in science.
I have a hypothesis that smoking increases the risk of lung cancer. You point out that there are people who have smoked their entire lives and died in their 90’s without ever having developed lung cancer. Have you disproven my hypothesis?
You have had this explained to you before many times. It’s in Theobald’s 29+ evidences for macroevolution article. Go read it there.
I have no idea what you’re blathering about here but it’s not related to the predictions of UCD.
Good, then that this is not actually what is happening.
Who the fuck says we “would expect orphan genes from reproduction alone”?
There are explanations for different types of orphan genes(how there can come to be orphan genes), but those explanations are not contingent on universal common descent being true.
Bill, go do something else with your time you’re blathering.
It only demonstrates that you can’t detect design in genomes.
That’s not what phylogenetic signal measures.
https://www.ncbi.nlm.nih.gov/pubmed/14740209
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6523144/
The second paper (2019) is open access.
Corneel,
An IDer might not care, but Paul is a creationist. He wants UCD to be falsified.
Well, it’s certainly time-consuming. I’m out until tomorrow AM. Day job.
Best to all.
T_aquaticus,
Why is it relevant?
keiths,
If an assertions main claim cannot be tested in any reasonable way how can it be falsified?
Phylogenetic signal is relevant because it is an objective way of testing hypotheses about common ancestry and evolution based on shared derived characteristics and DNA. I would suggest starting at the link below to learn about phylogenetics:
http://www.talkorigins.org/faqs/comdesc/phylo.html#phylogenetics
29+ tests for common descent:
http://www.talkorigins.org/faqs/comdesc/
One way is to see if the process converges. The Law of Large Numbers says all stochastic processes converge.
If it does not converge, then it is not a stochastic process.
T_aquaticus,
Thanks for this. I have read this explanation before but am struggling to see how it is testing the universal common descent claim. I agree that common descent explains some of the signal but what is the evidence it explains all of the signal? Similarities alone can be the product of design.