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 William Dembski; the “high priest” of ID has largely withdrawn from the fray but his ideas have been promoted and developed by Robert Marks and Winston Ewert.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
I followed the thread at PS where this gets discussed to death. As I said here at TSZ in a Gregory thread on MN, I think MN can accommodate sciences of the mind, like psychology or sociology or anthropology. These sciences need not have any explanations which are incompatible with physics.
I agree with the people who disagreed with you at PS, but I am not interested in re-opening that discussion here at TSZ. So this comment is it for me on mind and mechanism.
https://discourse.peacefulscience.org/t/is-functional-information-functional/7887/
The term “mechanism” gets bandied about, with many people taking to to mean what Descartes and his contemporaries took it to mean. There is a more modern view in philosophy of science, which I think is better.
https://plato.stanford.edu/entries/science-mechanisms/
Did we discuss this mechanism’confusion already?
Joe describes the transition-transversion ratio observed in nucleic acid sequences thought to be related by common descent.
So let’s take his variant of my thought experiment, and tell it a bit differently; this is, in fact, how I would present it to my students:
Take any chimp protein-coding DNA sequence, and, using the frequencies expected under the transition-transversion ratio, predict the homologous human sequence (which, to make the experiment work, of course, you haven’t seen yet).
Given common descent (CD), should those sequences:
A. Be identical?
B. Differ? (If so, which nucleotides?)
C. Can’t say
Now CD is in the driver’s seat, where it belongs, and not post-hoc rationalizing whatever we observe. “Can’t say” is nescience, so it doesn’t count; the question is whether options A or B could possibly test CD.
Because, as Joe explains it, either outcome — indeed, any outcome — would be consistent with CD.
Joe Felsenstein,
I think it means in the case of coin toss the ratio approaches 1. In the case of a process output with a mean and SD it means data points form the shape of a bell curve.
When he says non stochastic process I believe he means the unique capability of a mind ie halting oracle.
To all,
Lively discussion, but must run for today. I’ll check in again tomorrow AM.
Not what he said. Anyway data points from coin tossing do not look more and more like a bell curve. They are still H’s and T’s, which are letters. None of the letters in the alphabet look like little bell curves. (OK, I am messing with you).
Joe Felsenstein,
🙂
BruceS,
Thanks for the citing and I took a brief look at it. To me mechanism is a cause that can be assigned to an effect we are observing. This is basic science. In the case of gravity the major cause is mass as that can be defined as the causal mechanism. At this point we don’t know how mass “curves space-time” but we can model its effects and test the models.
I the same vein I see mind as the causal mechanism of biology. I also am starting to see evidence it is the causal mechanism of mass as physics papers are starting to hypothesize information inside atoms.
Did you finally understand why this doesn’t make common ancestry false?
1. The figure is very hard to build because orthodox relationships can be hard to determine. Note, for example, that the authors talk about after-separation polyploidy (Onhologs), which is but one problem. Other problems arise from copies being fragmented, recombined, lost, etc. It would require exhaustive work to tell how many of the apparent inconsistencies are artifacts, rather than true things that were eliminated in mice, but not humans, etc.
2. Eukaryotic genomes are fragmentary due to their messy nature. They have lots of repetitive and semi-repetitive elements that cause havoc when we try and put them together from the fragments that sequencers produce. Their messy nature is also responsible for difficulties in finding which regions correspond to genes, since genes are discontinuous. The messy nature alone should give away their unmusical origin, but the point here is: with fragmentary and genomes, with hard to detect genes, it is necessary to be cautious about declaring a missing gene a truly missing gene.
3. Note that regardless of whether we can tell artifacts apart, those apparent inconsistencies occur in ways that do not break the evolutionary relative positions of the organisms involved as inferred from other methods. In other words, if you take all the numbers in the Venn diagram, shared, non-shared, etc, and try and built a maximum parsimony hierarchy, you’ll find it to be consistent with an evolutionarily sensible tree.
4. Gene losses do occur and nothing in evolutionary biology demands that gene losses cannot occur in different lineages and leave these kinds of apparent “inconsistencies” behind.
I’m not sure that’s a complete list of things that result in apparently “inconsistent” patterns, but I hope that helps you understand why no scientist would be impressed by your claim that the figure makes evolution look false.
The main problem seems to be that you’re demanding perfection from phenomena that could not even be aware of the concept of perfection. Evolution is not intelligent design Bill. It just happens.
Entropy,
You changed the word “look” to “make”. Any noise in the data puts some doubt into the claim. Keiths was showing a positive example of the appearance of common descent and I was just raising a counter example to challenge his claim that the designer was trying to deceive us by making the data look so much like common descent.
The discussion here is really about testing common descent and if possible developing a predictive model. Is there too much noise in the data to do this?
EricMH,
Let’s be clear, simply admitting “it doesn’t matter” to EricMH, that something still might matter to most human beings. It’s both a presumptuous and ignorant condescending chair to sit on there saying: “I don’t know, so I’ll guess”, EricMH! = P
Instead, I would argue it *does* matter very much (to the shame of Thaxton, Johnson, Meyer, Behe, et al.) that those fields ALREADY use ‘design’ & ‘intelligence’ because it means IDism has a linguistic competitor that it must contend with. Indeed, many of us see the term ‘design’ as having been forcibly high-jacked & stained by the admittedly well-meaning naive IDists who gathered around Phillip Johnson in 1993 -> got funding for the CRSC -> CSC together for agitprop. We don’t like what the DI & IDM has done and is doing with the term, ‘design’ & we are speaking out against it, much to the chagrin of IDists themselves who think all Abrahamic monotheists should adopt the restrictive vocabulary of their reactionary ideology. It’s funny, though, EricMH has repeatedly run away from acknowledging the competition (except for from atheists & agnostics) & instead just dismisses or avoids it. & that’s a major problem for the DI’s particular brand of ‘design theory’.
What if IDism itself is “just a buzzword”, EricMH? Have you never considered that? If so, constructing a worldview & launching a personal crusade with ‘fellow travellers’ around “just a buzzword” doesn’t seem that wise.
The entire IDM is indeed foisted on an imbalanced proposition that certain fields & the scholars/scientists in them are those that are going to ‘save’ knowledge, information, even wisdom herself, from atheism & anti-theism. They have got that badly wrong from the start to the present, continue to push in the wrong direction, & don’t seem to understand why their wrongly-directed pushing rubs people the wrong way and offends their intelligence and integrity as people, often theist & non-theist alike.
The fundamental problem here, EricMH, graduate of the DI’s summer program, just like I am, is actually the ideology of IDism itself. Would you pause, stop & think about that in a moment of quiet, & return to discuss that problem rationally with me or would you rather avoid or distort the fact that ideological IDism is actually what we are dealing with here? Johnson made this clear in his black&white writings against ideological naturalism, so it is nothing new or surprising to be faced with his monumental contribution to the rise of the movement EricMH currently participates in.
It’s time to show some more courage & go further than you did at UD, EricMH. It’s really about much, much more than asking such poorly-oriented questions as, “how can we be sure we do not err when making the design inference?” No, just flip a switch away from that ‘inference’ because it requires duplicity to embrace & an Abrahamic monotheist should not go that route. Turn back if you find yourself doing so, step away from IDism to advance your work for a better cause than the DI’s ‘revolutionistic’ tribalism & revivalist posturing.
Agreed. (But it should be ‘creationism vs. evolutionism’ for a level discussion.)
Again, agreed. I arrived at that realisation about 16 years ago, EricMH. That was even before attending the DI’s Summer Program, which only further demonstrated the point. It seems to have taken a long time for you to realise this. Why? What held you back from this realisation in the past?
The real question, bigger than what you’ve asked so far as a card-carrying, paid member of the IDM, is what do you do after you’ve seen through ideological IDism, accepted the advice of the top devoutly religious natural scientists (which you are not) that you know and which goes anti- & post-IDism, and decided to move on? What’s the next step then? One thing’s for sure, pretty much guaranteed that you’ll stop flipping coins as a way of ‘human argumentation’ for an ideology pretty quickly! = P
This might be because, 1) you’re not looking, 2) you’ve been blinded by the DI’s IDism from seriously looking at those “other disciplines”, or, 3) because you’ve concluded before even doing the work thinking that “other disciplines” simply cannot address what you consider “this big question” (not explicitly framed as a coherent question, no surprise), even while other people are able to do it just fine & without the controversy IDists heap upon themselves in joining the IDM voluntarily, so you believe there is no point in looking, a rather defeatist attitude in the end.
We can’t predict when a radioactive element will decay. So, according to you and your retarded logic, radioactivity is bunk.
DNA_Jock asks
colewd replies
Awesome! So it should be easy for you to provide a link.
All I could find was T_Aq’s comment
to which Joshua replied
Perhaps there is something more recent that you could link to? Has Ewert bothered to look at the sequences yet? Thanks.
Can human minds create proteins? Sure, but only because human minds are embodied and encultured, and so can manipulate the world with tools. Human minds are realized in/depend on /supervene on their bodies and in some sense their environment as well.
Sociology, psychology, biology, biochemistry, physics can all (ETA: in principle) describe this one type of interaction to build proteins, each using explanations particular to their domains, none of which contravene physics.
And that’s the last this embodied mind will type about that.
BruceS,
Yes, as an ideological naturalist yourself, you presumed that MNism is a standard feature of human-social fields, when it need not be, and I have provided a suitable alternative in ‘methodological humanism’ to discuss, which you’ve largely avoided. This is because it means you must defend the ‘secular humanism’ from your worldview, rather than accepting that religious humanism is an acceptable position for scholars in SSH. Yet even so-called ‘religious naturalism’ isn’t on your radar, because pushing away from religion and a divine Creator dictates a significant part of your communications agenda here at TSZ.
When you say “MN can accommodate”, this is an example of slippery, ungrounded philosophistry. Ideological MNism is not needed or welcome by spiritually-oriented or even just by spiritually-sensitive people, among which, sadly, BruceS seems not to count as one as he himself never addresses it.
DNA_Jock,
I emailed Winston and he is side tracked now. Will let you know when he re engages.
BruceS,
We have common ground here. I stipulate the typical objections to this hypothesis but it does gives an explanation of what we are observing in Darwins black box 🙂
colewd,
The words “make” or “look” doesn’t change the point Bill. It doesn’t make it look false. It just shows that there’s imperfections in the data and phenomena. So what? Well, imperfections make clear sense under a naturalistic model. Not so much under the already incoherent ID “proposal.”
DNA_Jock,
These are claims of people who don’t look at the details of the data. I just aligned tubulin from humans to frogs and the outlier on sequence was chimps. Probably simply noise in the data but the sequence data does not always follow the tree.
Entropy,
From my perspective being a theist the noise in the data is significant. Not just this case but other cased also. You are a hard core naturalist and from that perspective I understand your position. Let’s just agree to disagree at this point.
CD predicts there is a high probability a chimp sequence picked at random will have a homologous human sequence but since both species are known to have ORFans the match is not guaranteed. Your “test” is as stupid as demanding to know if “6” will come up on the roll of a fair die then claiming probability theory is all wrong if no one can tell you if it will or won’t in advance.
Thanks Paul for another wonderful example of what passes for honesty in the Creationist approach to science.
Ah, Bill’s standard try-to-save-face bailout when he’s getting his ass kicked over science he doesn’t understand. No noise in that signal. 🙂
Nope. I replied to all of that in the thread. So perhaps you can rant about the replies there?
Surely not, but the data (character states) we use in phylogenetic analysis are.
Also free will. Libertarian free will is by definition a non-stochastic process, i.e. neither random nor determined nor combination thereof.
If you are so interested, this MM article expands on the idea a bit more:
EricMH,
Very interested. Thanks Eric 🙂
It should be. As a theist you should wonder why on earth is the data noisy if it was all Intelligently Designed. Why doesn’t it tell a story of Divine Design and instead bears the scars of natural phenomena unaware of perfection. Unaware of our wants. Unaware of what we might think when we looked at it.
There you are. When non-stochastic process takes of its mask it is libertarian free will. Thanks for the link, Eric. That clears some things up.
Could you produce those measurements? The convergence of cross-entropy and regular entropy and the information capacity of, say, the movements of a pollen grain in a drop of water? (or whatever you like, just making a suggestion).
I wouldn’t say the two are coextensive. Libertarian free will must be a non-stochastic process, but not all non-stochastic processes are necessarily free will.
Will think of an example.
Tubulins are large protein families, with many of its members diverging before the separation of each vertebrate lineage. Aligning a few orthologs against a paralog will make it appear as if the chimps are the outliers.
It is true that sequence data, even the appropriate data, doesn’t always follow the tree, but I suspect that you’re aligning the wrong tubulins with the wrong tubulins. Unless you clearly know which ones you’re talking about that might not even be noise. It’s most probably the wrong sequences to align in the first place.
I couldn’t think of any other, but maybe that’s just me. What other candidates do you have?
Looking forward to it, thanks.
You do realize that a definition tells us how we use the words in ordinary speech and writing. It doesn’t actually tell us anything about reality.
In all honesty, that reads like nonsense to me.
Kolmogorov was talking about mathematics. You describe it as if he were talking about reality.
T_Aq’s comment (at PS) was entirely correct. It is you, Bill, who has failed to look at the data. Not only have you failed to comprehend Ewert’s Dependency Graphic paper, you also failed to click through on the link to PS, where Joshua notes that Winston conceded as much. Joshua furthermore links through to where Winston himself confirmed this. It is thus not the “claims of people who don’t look at the details of the data”, but rather an ACKNOWLEDGED FACT.
Need some details of the data here: which tubulin genes? Protein, cDNA, or gDNA alignment? Please be precise: provide accession numbers.
Also, still waiting for a listing of your 100 genes, remember:
Thanks.
Entropy,
I am looking at the exact same protein. The reason I think the output divergence is noise is that between all these animals alignment is 100% expect for chimps at 99plus %. The chimp data may not represent the population.
Have you aligned the genes we are talking about?
What genes? Be specific. Provide links to every single gene from every single species you say you used please.
This is not relevant. The 100 genes between rats and chimps is what is relevant.
The only thing interesting is that tubulin alpha 1A amino acid sequences are 99% aligned among all mammals including rats and mice. Not much substitution going on here. Do I hear Texas sharp shooter fallacy or maybe you need another label so you try and spin the Irish yarn again. :-). Best technical spin master on the blogs.
Rumraket,
If there are links I don’t know where maybe jock does as he would need to to make the claim he did.
(facepalm) It was YOUR claim Bill you made at PS here.
Were you as usual just regurgitating Ewert’s numbers with no idea how to actually check or verify them?
BruceS,
As usual, you seem to count a half-reply as adequate. I don’t count it so.
When you started diverting the conversation & with KN splitting it up into multiple ‘naturalisms’, perfectly loose discussion space for your philosophistry to unwind & sprawl in, that’s when I departed.
The MNism argument is really not a difficult one. de Vries didn’t realize what he did, this little linguistic black box he opened up with that ‘neologism’, but to his defense, most people have misread it continuing on in their ‘scientism’, which is actually ‘natural scientism’. So problems be damned, or just naturalized, according to such thinking. KN of course, recently admitted he hadn’t read de Vries paper, nor had anyone else here, so there you go. Lots of hot air pretending as educated, without even having read the most important primary source article. Hmm, sound academic or even sincerely concerned about it to you?
Ideological naturalists continue to tilt the playing field their way linguistically. Some unwise, ignorant scientists who are religious theists & should therefore know better, like S. Joshua Swamidass, are tacitly going along with them. So far. This in itself is not that surprising or even that significant. What is troubling is that Swamidass thinks he can bulldoze his way into the ‘hearts & minds’ of unwitting non-mainstream evangelicals & others, while being insensitive to the nuances of discussion in a “multiple competing hypotheses” scenario, & apparently quite unfamiliar with the history of ideologies used in sciences, yet as a way of bringing ‘peace’ to science, philosophy, theology/worldview discourse.
It is not surprising, but will be to no avail, that Swamidass wishes his own ideological influences on his ‘strictly science’ claims would be invisible, rather than embracing how they are both visible & necessarily limiting. Swamidass’ ideologies indeed aren’t invisible to those trained in what to look for & he shouldn’t be so scared to discuss them. Yet going by the way he has treated me in online communication, both public & private, he appears petrified to discuss the impact of his own ideologies on his ‘Peaceful Science’ strategy. That Swamidass is hiding a lot of turmoil behind the niceties, seems obvious so far, especially after the BioLogos scandal.
To be fair to BruceS, Swamidass doesn’t want to talk about humanism either. Neither does the DI. Neither does BioLogos. So when the philosophically superficial claim is made that there is no alternative to naturalism, at that moment when an alternative is indeed shown & presented – an alternative ideology to naturalism for trying to make sense of reality – the success of their actually being an acceptable alternative depends on how many people in the room can switch and speak that rather different language. So far here, very few people are able to do that; mostly ideological naturalists here. It’s likely because ‘secular humanism’ is all that would be defended, & that doesn’t sound like much fun if one can’t go beyond it.
First things first, Bill.
The “100 genes” claim is one that YOU made.
I am waiting for a list of what those genes are, so that I can rule out the “inadequate annotation” explanation.
Thank you for letting us know that your tubulin “analysis” used protein sequences that are ~99% conserved.
What a moronic choice. In addition to the paralog issue that Entropy noted, I can think of two other explanations for your result. Would you like to demonstrate your level of understanding by naming them?
Oh, but it is relevant; OBVIOUSLY so.
Check this out:
(what’s with the chickens?)
Nope, because you haven’t told me which ones they are. Winston Ewert has admitted that he hasn’t aligned them either.
Have you, perhaps?
DNA_Jock,
Thanks for providing the above data. Let’s try again they are not listed in his paper. I am not going to delve into this until he is ready to engage again. Now theses genes are shared families. Why do you think any of the claims that were made by Josh or T are relevant to these genes? If they are orphans shared by only two species?
Whats with the chickens spin master?
WTF?
Why is it relevant? Because any annotation error will show up as a taxonomically anomalous module in Ewert’s paper, that’s why.
At first reading, I think Ewert has found an overly complicated way of spotting annotation errors.
He didn’t align any sequences; this much he admitted to Joshua.
Again I ask, WTF?
Heh. Once again Bill gets called on his regurgitated ID-Creationist bluster and can’t back it up, makes his usual lame excuses and pulls the ripcord. 😀
DNA_Jock,
What was the method he used to judge genes were in the same family?
DNA_Jock,
Looks like TUBA 1A is more highly preserved across the board then TUBA 3E.
Adapa,
You think exploring genes shared between chimps and rats that are not in humans and and mice is good for your religion. I love your optimism 🙂
I think you regurgitating unsubstantiated Creationist bullshit about shared genes because evolution threatens your religious beliefs is both hilarious and pathetic. I love your desperation 🙂