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 William Dembski; the “high priest” of ID has largely withdrawn from the fray but his ideas have been promoted and developed by Robert Marks and Winston Ewert.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
Do you accept common descent between vertebrates, but shy away from common descent between bacteria and vertebrates? I would agree that UCD would involve deep nodes that would be difficult to test using phylogenetic methods, but you seem to be giving away more than you realize.
Some concrete examples would probably be helpful here.
Paul,
So if it doesn’t offend the Designer’s sense of tidiness, then why aren’t there more examples of it? Why no examples involving, say, baleen whales and mountain goats?
In other words, why is the Designer so determined to make common descent appear to be true?
keiths,
I took Paul to be agreeing with you about the importance of the Designers’ sense of tidiness: he provided a great example of cellulose synthesis being entirely restricted to the tunicates.
It’s extremely tidy.
I may have misconstrued his point, however.
T_aquaticus,
I agree there is some common descent in the signal. I have no idea where the line of demarkation is and don’t know how to test for it other than compare it to the data where we know common descent has been observed.
EricMH:
You have it backwards. Given your claim…
…we’re looking for you to fill in the blank:
If it is a non-stochastic process, then ______________.
Perhaps you could ask questions to get clarification from people with expertise in these fields if there’s something you don’t understand then?
I’ve done so myself in cases where there’s something I didn’t understand. It is no secret I don’t do this kind of work professionally so there’s all sorts of things I did not initially understand, which when I read it, I still didn’t, so I had to ask people if they would bother to try to explain it to me.
How do different algorithms work? Why do I get these results? How do different rooting methods work? What’s a bootstrap and what does it tell me? How does it work? How are ancestor states inferred? Etc. etc.
If you come to people asking for nothing more than clarification, I find that people are often times happy to give you the benefit of doubt and take some time to explain.
keiths,
And at the same time making common descent look false 🙂
http://www.sci-news.com/genetics/article01036.html
Theobald actually explains how you could do that in his 29+ Evidences article. http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy.
Scroll down to “Potential falsification” and read the section about Consistency Index. And also about consilience of independent phylogenies.
That doesn’t make it look false.
DNA_Jock,
He was actually disagreeing with me. Cellulose synthesis is restricted to the tunicates among animal species, but it appears all over the place in plant, algal, and bacterial species.
Two separate taxonomically restricted groups.
Rumraket, two years ago:
Answer: Not yet.
How does that make common descent look false?
T_aquaticus,
This is how badly he misinterpreted that diagram two years ago:
He never got it.
BruceS,
Mathematicians may (or may not, I don’t know) see deterministic processes as special cases of stochastic processes, but elsewhere in science and engineering these things are usually considered opposites, not varieties of the same.
If stochastic includes deterministic, what term would describe a process with multiple possible outcomes rather than just one?
Well, Eric is a mathematician or engineer with info math background, I think, so that may explain his usage. Perhaps the Wiki authors that wrote the article I linked are too.
As to your example, if there is a probability distribution associated with the multiple outcomes, then it is stochastic. (If the explanation uses outcomes that are without any distribution even in principle, I would say it is not a scientific explanation.)
Measurement in QM is an example of stochastic in that sense, and it is possibly the only example where the probabilities may not simply be reflections of our limited knowledge. In other words, for Laplacean demons everything is deterministic, ignoring QM. Even for QM, there are popular interpretations which are deterministic in principle.
This is all semantics, as the math result Eric uses for his proof that evolution requires intelligence allows for both deterministic and stochastic (in your sense) processes. ETA: I believe the result has nothing to do with convergence of distributions either but I don’t know the details of the proof of Levin’s result, so perhaps it does. Eric likely knows; definitely Tom E. does.
The problem, in my view, is that his math model does not capture the biological reality that evolution applies to.
There are scientific models that take the form
observation = deterministic equation PLUS stochastic error term with mean 0
What would you call them?
Another one of those claims that sounds just weird to a natural scientist (Earth sciences).
Take plate tectonics. Given the all too real limitations of our detailed knowledge and modelling capabilities, this is clearly a stochastic process.
What does it converge on, and why?
Realistic?
If a model or a process allows us to predict each and every outcome with no or only some quite negligible error, we are justified in calling it deterministic. If we can only predict the outcomes with a degree of probability, we call it stochastic. If we can’t predict it at all, we should conclude that we don’t understand it at a basic level.
Subsuming deterministic under stochastic makes many conversations about actual natural processes and how to model them needlessly confusing. Have Newton’s Laws suddenly become stochastic?
This usage is really quite peculiar, and if the ID’ers are interested in clarity they ought to come up with a term that comprises both stochastic and what is commonly meant by deterministic. I can’t think of anything, apart from ‘natural’. Is that what they mean? Then they should say so.
It is the same “ladder instead of tree” thinking that pervades most of ID/creationism. Also, I wouldn’t be surprised if an ID/creationist used that graph to make the argument that there are only 4 species on Earth.
T_aquaticus,
Keiths is making an argument that the designer is trying to fool us into thinking the data supports common descent. This shows He is doing a poor job of what Keiths is claiming.
This is noise in the data that has not been explained except for gene loss in selective lineages. As you mentioned looking at more parts of the tree may explain this but so far no one has explained how genes appear in species separated by 400 million years are missing is species with only 60 million years of separation.
This problem also surfaced in Winston Ewert’s data. Where chimps and rats shared 100 genes not found in mice and humans. More noise for Paul to play with.
keiths,
I saw Harshman wave his hands about 250 times. 🙂
They didn’t need those genes.
How do we know they didn’t need them? They don’t have them. They live, without having them. So clearly they’re not necessary for them to live. It’s rather obvious if you allow yourself a second’s thought.
There are other parts of explanation here too. One is the teleost whole genome duplication which inflated the number of orthologous genes in fish. The other is that gene-annotation in the chicken genome is still seeing significant improvements between different versions. In one recent study, over 4000 previously unannotated genes were added to the chicken genome. It is entirely possible that a significant portion of those that were counted as missing from chickens in the zebrafish genome paper, have recently been added to public databases.
So those are three contributing factors of explanation for what we see in the patterns of shared genes between these species.
In any case, you didn’t answer T_’s question. How does this conflict with common descent?
Rumraket,
Let’s try for some common ground. Do you think it can be labeled as noise in the data? In other words this is not what we would expect or predict from reproduction alone.
You are trying to explain it with random activity in the genome. As such I believe you are conceding this is noise in the data. Common descent when we observe it is a very predictable process.
See what I mean? Bill still doesn’t get it.
But he does appear to have made some progress. He’s no longer talking about the return of lost genes.
Bill, then:
Bill, now:
Nothing about genes being lost and then regained. That’s progress!
This is still hopeless, however:
Maybe in another two years he’ll get it.
ETA: Clarification.
keiths,
Do you believe this is noise in the data? How would you predict this?
Bill,
Nothing about UCD specifically, or evolution generally, predicts that genes can’t be lost.
There is no conflict.
No actually you saw Harshman try to explain things to Sal Cordova and you in the 5000-comment thread multiple times and both of you took turns drooling incoherently in response. And I’ve seen similar things happen multiple times since.
keiths,
This is a nothing claim that UCD does not predict that genes cannot be lost. Whats interesting is what it predicts about gene loss.
The issue is can gene loss be predicted? If not it is the noise in the data that Paul is talking about.
faded_Glory:
I agree. It’s much clearer to separate ‘deterministic’ from ‘stochastic’ than to make the former a special case of the latter.
Bill,
We’ve told you a million times that common descent is about relatedness, not about mechanisms. It doesn’t predict gene gain or gene loss. It just predicts that the gains and losses, when they occur, will fall into the same nested hierarchy pattern as everything else.
Rumraket,
Thanks for citing this. So Harshman does predict Gene gain from the diagram. More noise for Paul to play with. What John did not do is find where the changes were really happening. As Sal mentioned in the later post there was no mechanistic explanation as you have tried on this post.
Let’s try again. Do you believe that these gene trees represent noise in the data?
colewd,
Of course. What the diagram doesn’t show is the loss of genes that are later regained. That was your mistake.
keiths,
You guys appear to agree with Paul. There is signal and noise and you cannot separate them. The noise is unpredictable. There is no model for how the diversity is occurring.
What you’re calling noise isn’t noise. There is nothing in that diagram to suggest that comment descent is not true.
keiths,
If they can be shown to be lost twice then I was wrong. So far this is an assertion.
Then
Handily demonstrating TAq’s point.
How many gene families does that represent, Bill? [10] Could you provide a listing of those genes so that we can review it, and rule out inadequate annotation as an explanation? Thanks in advance.
colewd,
Um, no.
keiths,
Noise is stuff that common descent cannot predict. This is a problem as scientific hypothesis are generally around predicting how nature will behave. The noise we are observing is based on unpredictable events such as mutation and gene loss/gain. We saw these events in the Lenski experiment.
The statement that there is nothing in the diagram to suggest that common descent is not true is interesting. There is obvious noise in the data. Noise reduces confidence levels in results.
This is not even wrong.
Gene loss cannot be “predicted”, in the sense that we can predict tabula rasa which genes will be lost in an unexplored taxon. Gene loss can be predicted, in the sense that if multiple close relatives of species X have lost gene Y then chances are species X has lost gene Y. And this gene loss is PART OF THE SIGNAL.
Bill, you need to be much more specific about what you are referring to when you speak of “noise” and “signal” and “predictions”. Right now, your comments resemble word salad.
I cannot characterize Paul Nelson’s contributions in this thread, since he ought to know better. OTOH he also ought to be able to provide the listing of the chimp&rat¬-human¬-mouse gene set.
Hope springs eternal.
DNA_Jock,
This has already been reviewed at PS.
DNA_Jock,
I agree with you that common descent would predict that apparent “gene loss” would be passed to other species. All that being said the gene loss event is noise as common descent does not predict it. Common descent as we observe it predicts reliable copying and recombination of genes from generation to generation.
Add ‘signal’ and ‘noise’ to the list of concepts that Bill doesn’t understand.
I’ve dealt with a lot of thick-headed Creationists in my day but I’ve never seen anyone work harder at misunderstanding simple scientific concepts than Bill Cole.
LOL! If figures a Creationist would try to explain away a deliberately dishonest quote-mining of a scientist by quote-mining yet another paper. 😀
How about you get real. You dishonestly quote-mined Weiss to paint a false picture of Weiss having serious doubts about evolution when the exact opposite is true. Then you turn around and do it again, posting just the introductory “framing” section of an article and ignoring the rest where the framing question is explained.
Maybe where you come from such out-of context quote mining is considered a valid argument but to virtually all others it’s simply a form of lying by omission. But the end justifies the mean with Creationists, right? There’s a reason the term “Liars For Jesus” was coined.
Adapa,
This post is in blatant violation of the rules. Moderators are you around?
Why is that Bill? Every word in there is true and can be easily confirmed by reading the thread and watching Nelson’s video.
I’m not the only one who noted the deliberate misinformation and misdirection either.
Adapa,
You could make the argument he mis represented Weiss and show why. I don’t think he did as you or Rum has not shown that he has. You guys are very sensitive when evolutionary skeptics point to problems surfaced by evolutionists.
If you can pull a quote where Paul claims that Weiss does not support evolution then I will stand corrected. So far I have not seen any claim like this. If not then you need to apologize to Paul.
I did. Try reading for comprehension instead of knee-jerk defending everything to do with Creationism.
Adapa,
I gave you a chance to support your claim and you failed. You need to apologize to Paul.
I gave you a chance to review the evidence and you failed miserably. You and Nelson need to apologize for choosing to push your religious beliefs over honesty.