Over at UD, KF has started a new thread criticizing Toronto. He had earlier started a thread criticizing Petrushka.
It would have been nicer if KF had joined here to launch his criticism, instead of taking pot shots from UD where it is my understanding that both Toronto and Petrushka have been banned.
In any case, this is where the two accused can set the record straight by explaining what they actually meant. Others can join in. I may add something later.
Let’s keep it polite. No character attacks. Let’s stick to clear explanations of positions that KF might have misunderstood. And let’s remember the rules of The Skeptical Zone and keep it civil.
Open for discussion.
KF writes:
Obviously, T has failed to do basic homework and does not know that Dawkins has admitted that Weasel is a pre-loaded targetted search. Cf here.
Weasel just shows that selection works it is a child’s toy compared to what can be and has been done with genetic algorithms. If you want an example of a toy algorithm that uses Markov selection and is a notch more interesting than Weasel, try this:
http://itatsi.com click the Start button.
It has no goal and no target. Just a sparse functional landscape in which the drunk can walk in any direction and arrive at any destination. It does not claim to be a model of evolution, but it is a demonstration that functionality (in this case, long words) can be reached by a drunkard’s walk.
There are around four billion possible ten letter strings and just a few thousand ten letter words, and yet these words can be reached by the drunk. Even more interesting to me, the drunk can reach ten letter strings that are not in the dictionary, but look like words, are pronounceable, and sometimes meaningful. In other words, the program invents new words.
But even this is just a toy. It was written to demonstrate that a sparse functional space can be explored without having a target.
I’m too pressed for time to dig it out, but I found a fascinating paper that generated 1.5 million ‘random’ completely synthetic 105-residue peptides based upon a simple rule that ensured that they folded. Several sequences from this library rescued E Coli knockouts, despite having no sequential or structural relation to the deleted protein. This shows a remarkable degree of functional richness in the region of protein space that enzymes actually occupy. It isn’t ‘new’ function, but does give a rough guide to the extent to which proteins other than the ones we actually have at a particular locus would have done the job. I’ll try and find it when I’ve been for a run.
Then SHOW that a designer is possible.
Let’s say I’m the designer and I want to design a life form that will work 100 years from now at the north pole.
How do I know whether there will still be ice there?
What kind of food would be available in a hundred years?
How do I know if a >500 bit change in the DNA will result in the change I want for an environment that I can’t determine?
If your designer doesn’t have the answers to these questions, the existence of your designer is more unlikely than evolution.
It is your decision to NOT come here because of the way we behave, but you have also decided that you WILL contribute to a site that houses the incivility of Joe.
It’s not Joe that’s the problem, it’s you.
You can’t claim we’re too uncivil for you anymore as you accept Joe’s civility to be good enough for you at UD.
If you cheat on your wife, does she have a right to a free affair?
Bad behaviour on the part of subject A does not justify the same behaviour from subject B.
Ask WJM about morality.
Then tell Barry to clean up his act and start treating fellow debaters with respect.
I understand the desire to correct the nonsense being spewed on UD (SIWOTI!), but this dual-blog exchange just gives the IDCists the attention they want without the need to venture from behind the safety of Barry’s skirts in their echo chamber.
Of course I can’t control anyone else’s behavior, nor would I want to, but I’m choosing to respond only to those with the minimal intellectual courage required to post here.
Good point, and I had every intention of doing that before I started! 🙂
That makes for a lot of empty weeks.
In my view there is an obsession with winning at the expense of communication. I’ve seen this from both sides.
Of course I think the other side is the guiltier. why else would they ban and censor people who don’t violate they written rules?
And speaking of written rules, what sense does it make to have a rule that your core positions are out of bounds? What sense does it make to assert the very claims that are being questioned are already answered?
But I have enjoyed a few moments when the opposition engaged in conversation rather than holy war. Such moments are rare.
Toronto,
It’s a daily struggle. I was clean for Lent, but fell off the wagon a couple of weeks ago. I’m better now.
petrushka,
While this probably violates Lizzie’s site rules, I don’t believe the denizens of UD specifically or the intelligent design creationists more generally are interested in bidirectional communication.
The fact is that there is no scientific theory, or even hypothesis, of intelligent design. It explains no observations and makes no predictions. There is no reasonable doubt after this many years that ID is anything other than a fundamentalist Christian political movement.
The only reason to pay any attention to the IDCists is because of the political power their base wields. It is important to prevent them from destroying science education. If they didn’t pose that threat, they’d be of no more intellectual interest than the flat earthers or Velikovskyites.
So you’re damn right — our focus has to be on winning.
I enjoy a good debate more than most. It would, however, be foolish to ignore the history and clear goals of our interlocutors. These people want their religion in our schools. They must be stopped.
I would like to post an open challenge to KF. Since he wants a thread “for the record,” I would like to go one on one with KF. I would prefer that other posters abstain, but that is not a requirement.
All I ask is that this take place where I can post. I’m willing to do it at UD, even if I am only allowed to post on one thread for a limited time. My only demand is that I will not be censored unless I engage in name-calling or some equivalent infraction. By limited time I mean at least a week.
The topic I suggest is whether ID or evolution is the best explanation for the diversity of life. If the discussion takes place, I will elaborate on this.
So it’s in your court KF. Are you willing to take on one lone evolutionist for a time limited discussion?
Thanks Joe, for posting a link to my challenge. I will allow KF to determine how he wants to present his case. The only limits I request is that the discussion be limited to biological facts and theories and not wander into politics. I don’t mind if KF brings up politics, philosophy and theology, but I don’t intend to respond, because I have no knowledge in these areas.
My desire is to have a conversation, a give and take, rather than a debate. But again, I’m not fussy about how other people characterize it.
Not that I expect kairosfocus to take up your challenge, but if he does I hope that you will post a copy of your comments here or in some other venue not subject to UD control.
I appreciate that there is a political aspect to this, but that is beyond my power to control. My interest is to sharpen my own understanding. I have no personal gut fear of being wrong. I’m not even particularly fearful of having my ignorance — of which there is quite a bit — exposed.
I just enjoy the discussion. I’m not dancing in the streets in pre-celebration. I’m just expressing my interested in having a clean give and take discussion.
I appreciate your calling attention to this, Joe, but I think KF can evaluate the prospects for himself. He is free to define ID any way he pleases, and he is free to correct any definition I might present.
It will presumably be his thread, so he will have the ability to counter anything I say using any argument he chooses.I merely stipulate that I have no training or experience in philosophy or theology. So I may not have any response in those areas.
Petrushka,
I mentioned in a reply upthread that I had a paper illustrating a function-richness in a small area of ‘protein sequence space’ that helps shed some empirical light on the question, preferable to the heat of competing assertions. I had thought about submitting it as a ‘journal club’ post.
here
The authors constructed a library of 1.5 million 102-acid peptides, designed to fold in 4-helix bundles but with no design of function. 27 ‘natural’ genes of considerably greater length and structural complexity in E. Coli were deleted, and the library assayed on the basis of ability to get these mutants growing again.
And of their library of 1.5 million, they found 18 artifical sequences, with no designed homology to the deleted proteins, that were nonetheless able to rescue function in four of the 27 knockouts. Bearing in mind that the search was restricted to functional analogues of just 27 proteins, this is quite an impressive hit rate.
There are 4000 other genes in E. coli. It is highly unlikely that they just struck lucky with the genes they chose. More likely is that this library, a tiny subset of the 20^102 20-acid possibilities, itself a subset of larger proteins, is rich with function, if we could assay the whole of the protein set with the ease we can plate out E. Coli nutritional mutants. And if we could extend the assay to the 10’s of thousands of proteins in millions of other species …
This paper also demonstrates the extensive chemical redundancy of the genetic code – their method of building the helixes exploited this feature. Calculations of the type I just did – 20^102 – are extremely misleading in the huge numbers they yield, and the frequent assertions that 20 acids are some kind of magic number for function are simply biochemically naive.
Design fans will point out that these peptides are not truly ‘random’ – but then, neither are evolved ones. Apart from the dawn of protein synthesis, evolution starts from something that already works: a folded functional catalyst. So excluding random peptides that do not fold is entirely legit. There is, by the same token, no reason to suppose that proteins that fold in this particular way are anything special. Either way, for obvious reasons, you have to do some restriction. There is not enough carbon in the world to make every possibility.
They will also point out that this is not new function – but it nonetheless demonstrates that ‘landing’ on a different function is much more likely, given a function-rich space, than is hoped for in the ID world.
Also worth noting that this work was not aimed at assaying sequence space for function richness, per se, but simply trying to find functional synthetic peptides.
There’s a lot more I’d like to say, but it’s hard to get it all in a blog comment. I can hear the ID enthusiast yelling “red herring nice strawman!” as I type, which is rather distracting!
I’ve seen that. I can’t memorize the details, but they lurk in the back of. My mind. My goal in a discussion is not to win, but to explain clearly why I believe what I do. My fantasy is not to convince anyone, but to arrive at a point where each side can paraphrase the other’s position.
Actually I’m getting a 404 error.
I’m embarassed. Apparently part of KF’s massive reply was aimed at me, and I just didn’t notice it! At one point, after describing other people’s arguments and rejecting them, he says:
KF: JF then goes on to suggest that the origin of two sites worth of information and a hypothetical example are adequate to overturn the observations on the source of FSCO/I and the analysis that shows why 500 bits of de novo information is a reasonable threshold for de novo info from an arbitrary start point being reasonably attributed to intelligence.
Of course, beginning in an existing island of function and moving around a few bits at a time through some form of hill climbing is not relevant to the matter, as it begs the question at stake: how to get to the shores of an island of function across a deep isolational barrier from an arbitrary initial condition. And that basic challenge does not begin from already existing life — a big begged question — but from some warm little pond or the like pre-biotic environment.
He is referring to my comment in this thread on 25 August above, where I am pointing out that William Dembski’s Law of Conservation of Complex Specified Information is both unproven, and in the form in which it is stated, unable to show that one cannot accumulate 500 bits of Complex Specified Information (even if the theorem were proven). In my earlier post (linked in the preceding comment) I showed a simple numerical example of the accumulation of 100 bits of CSI.
KF misunderstands Dembski’s argument. It is not about islands of function, and it is intended to apply to evolution after the Origin Of Life.
KF: This issue is often begged in the context where there is no empirically supported causally adequate chance and necessity mechanism to get us from chemicals in a pond or the like to a functioning, encapsulated and gated, metabolising digital coded information using self replicating form. But, observed cell based life is full of things that in any other context would be immediately recognised as strong and reliable signs of design: digital code, algorithms, organised information processing and cybernetic machinery etc etc etc.
Sorry, Dembski is not talking only about prebiotic evolution, he means his argument to apply to evolution after the OOL. I can only suppose that KF feels Dembski’s argument does not apply for evolution after the OOL. (Would that mean that KF thinks that more than 500 bits of CSI could get into the genome after the OOL?) I have read Dembski very carefully and it is quite clear that he does not restrict his theorem to the OOL.
Fisher et al., De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth, PLoS One 2011.
I posted this further up the thread:
Kairosfocus replies on U.D. The bits in brackets [like this] are my comments on his reply.
I take it the response is “not at this time.”
I think all we should care about is what we teach students.
Our side has a mechanism to offer, yours doesn’t.
We can say, “This is how our theory works”, and you actually refuse to even make an effort to come up with one.
Until you have a mechanism of your own that can replace ours, we are under no obligation to take you seriously.
Actually I’m getting a 404 error.
Oh, dammit to hell! The anchor got the TSZ URL stuck in front of it, God knows how.
here:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364
Full open source here:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364
Hi, Kairosfocus.
Let’s do abductive reasoning.
Life is a chemical phenomenon.
Unintelligent chemical processes are known to create chemical phenomena.
Humans can intelligently design chemical phenomena.
Humans were not present on the early earth when life first appeared.
No other intelligent beings are known to be able to intelligently design chemical phenomena, or to have been present on the early earth.
Therefore, I infer that unintelligent chemical processes are the best explanation for the origin of life.
I hypothesise that chemical reactions and chemical evolution led to the first life form(s).
Kairosfocus hypothesises that non-living intelligent designers created the first life forms.
Chemical reactions and chemical evolution are both directly observed realities.
Non-living intelligent designers have never been observed to scientific knowledge, and are not even known to be possible.
Therefore, there is virtually infinitely more evidence for my hypothesis than K’s. Therefore, it is clearly the best current general explanation for the OOL.
Here’s another example.
Humans write books.
There is no other known source of books.
Therefore, human authorship is the best explanation for any book of unknown authorship, and it is reasonable to infer that all books were authored by humans.
Do you agree that that’s good abductive reasoning, Kairosfocus?
I ask, because it might not be popular at Uncomon Descent if applied to a certain famous ancient book.
In fact, some of your colleagues might not be too fond of abductive reasoning in general.
If our mechanism was as non-existent as yours we would call it, “design by birth”.
Someone not banned at UD should give Dembski an invitation to present his case here.
Thanks to keiths for pointing out this.
There it is, a gain of CSI without intelligence!
kairosfocus and Joe, are you going to correct Dembski?
UD enables Joe.
Are you going to keep posting there regardless?
If CSI is information that necessarily is the result of an intelligence, you would have a much easier time of simulating it than we would an evolutionary model.
Show in your model how you would analyze a future environment before you actually start designing the >500 bit biological change required.
Note that I’m not even asking how to make the biological design change. I’m simply asking how would you identify the “specification” required in the future.
Joe kindly attempts to reason with me on U.D.:
Joe: “Earth to dr who:
What is the evidence that life is ONLY a chemical phenomenon? Oh, that’s right there isn’t any such evidence so your “reasoning” fails at the start.
Also Christians are OK with humans authoring the Bible.
But please keep ignoring that and pressing on anyway. You make my point for me-> that it is a waste of time trying to reason with you.” /Joe
I’ll take that to mean that Joe suspects that my reasoning to the best explanation would be correct on condition that there’s nothing other than chemicals in the basic physical composition of life. Otherwise, he’d have thought of a better objection.
The evidence, Joe, is that’s all we observe when we actually physically examine life. Being a chemical phenomenon doesn’t mean that it can’t have emergent properties, which it certainly does have.
As for the Christians, I’m glad to hear it, and delighted that they’ve all appointed Joe as their spokesperson.
As for time wasting, Joe’s participation is entirely voluntary, and my post wasn’t addressed to him, but I always welcome his contribution as I personally regard him as one of I.D.’s finest thinkers.
Joe still seems to want to try and make the case that life isn’t a chemical phenomenon on two more U.D. posts. I wonder whether he’ll realise that he’s undermining something that Kairosfocus claimed earlier on the same thread.
The consistently foolish are the hobgoblins of little minds.
It strikes me that he is undermining Upright BiPed also. If there’s anything admirable about UBP’s theory, it is its lack of ghosts in the machine. UBP seems to believe that ghosts created the machines, but he has ruled out spooks in the operation.
The existence of a designer is itself an inductive argument.
The designer’s abilities are also an inductive argument.
How did you determine the designer exists?
How did you determine his abilities?
How much truth is there in these premises?
Yes, if Joe had mentioned “information” I was thinking of mentioning that.
So true. Either the ghost is in the machine, or the ghost created the machine. It can’t be both. Or at least you can’t argue rationally that it’s both.
This is one of the easiest ways to see that ID proponents are simply praising the lord, and nothing more. You can’t argue on the one hand that an object is designed because it’s so complex, and then also argue that the object needs miraculous intervention to work. But that’s exactly what ID proponents argue at every level from the atom to the entire universe.
Is it me, or has the whole ID “movement” degenerated into a series of individuals talking past each other?
There seems to be some serious mutual undermining going on, with not one of ’em bothering to try and understand the import of what any of the others are trying to say.
A good design question that asks, where does the designer get the information for the functionality required in a future environment that does not yet exist?
So if design is likely, but a designer with the necessary abilities is not, where does that leave the possibility of ID?
I simply cannot penetrate KFs latest ‘questions’ post. We take a long time to get to any questions – half a post in and we’re still smarting over the very notion that one could say ‘don’t link to porn’ in a lighthearted manner (ask Joe – he appears to have a sense of humour), and lots of old-favourite expressions about distractions and attacks. All of this bluster from KF seems designed to distract from a fundamental lack of substance.
I haven’t seen any attempt to address the apparently significant density of functional packing of protein space on an evolutionary scenario, as per the several papers linked above and elsewhere. Instead, the goalposts have moved yet again, back to the OoL – a process about which we know next to nothing. And KF demands to know how we got ‘information’ out of this unknown process. Since we know nothing about it, we really cannot say whether it was within or outside some arbitrarily-assigned ‘probability bound’. Nor can they say how any designer got round the various problems, come to that (including his existence), rendering this a pointless set of questions – “how do YOU explain something whose parameters and constraints are unknown?”. Dunno.
Now KF and Joe insist that nucleotide translation is NOT a chemical process.
Anyone with a basic grounding in biochemistry would be able to point out how utterly wrong this is. Is it because there is hydrogen bonding involved? Is that not felt to be ‘chemistry’, but instead some form of ‘informatic’ exchange? Is the hydrogen bonding in protein folding ‘informatic’ too, or that which keeps your hair from falling out, or water liquid to 100 degrees?
The distinctive bases distal to the tRNA ACC stem form a particular shape, with vital hairpin motifs and certain essential base pairs, all with a 3D shape. They are bound by hydrogen bonds, not ‘informatic bonds’, in the ‘loading enzyme’. Only the right shape will bind, but this is a property common to all enzymes – chemical catalysts one and all, with substrate recognition by shape, charge density and hydrogen bonding. There is nothing different about the ACC stem in this regard, while the supposedly ‘informatic’ anticodon does not come into tRNA recognition.
ATP is then covalently bonded to the amino acid, which is then esterified to the Acceptor. This is chemistry. The tRNA anticodon hydrogen bonds to mRNA, which physically holds it in place by shape alignment enabling the energy of the amino-tRNA link to be transferred to drive peptide bond formation. Again, all chemistry. But not certain, nor even likely, to be involved in the OoL (about which, you will recall, we know nothing).
No doubt another million words are simmering on the matter of good faith, straw men and oil-soaked red herrings, with noises off – but I would prefer to see some basic knowledge of the chemistry of this process demonstrated by people who attempt to ‘correct’ the field on their understanding.
I’m eagerly awaiting UBP’s take on this, since he has 6000 posts invested in the necessarily physical implementation of information. I expect him to show up any minute. Not.
I hadn’t noticed, either, that I got a couple of passing mentions in KF’s most recent jeremiad. First, there’s this:
I’m assuming this is Johnson:
Personally, I prefer the term naturalism as science, in very simple terms, is the process of trying to understand the nature of things, nature being what makes something itself and not something else.
Materialism is the view that the universe is composed of matter and energy in all their forms and nothing else. It is the most rational position because, regardless of what Johnson and his sympathizers might hope and believe, no one has yet shown there is anything else. For sure, there are many big unanswered questions such as why is there anything at all, where did it all come from and what about all the counter-intuitive weirdness at the quantum level, so there is still the possibility there is something else. But that just means there are gaps, it doesn’t mean they’re plugged with whatever your preferred gap-filler might be.
So, for want of anything better, I can live with materialism.
Down-thread there is this:
I must say I’m curious to know what these ” much despised longstanding presentations” are.
The comment goes on to talk about Dawkins’s WEASEL illustration, which has been dealt with at tedious length elsewhere, and the presence of design.
KF and other IDeologues give the impression that “evo-mats” are somehow denying the existence of design in the universe. Well, we don’t. We know full well there is. It’s us. We do it. What IDeologues have yet to do is show there is anyone or anything else doing it.
Speaking for myself, I’m quite comfortable with the possibility of extra-terrestrial intelligent designers. Maybe the universe is teeming with ETs designing things willy-nilly all over the place. Maybe, they’re wasting vast sums on Einstein-Rosen Bridges to Nowhere. (I’m willing to bet they’ll all be material, too.) The only thing we have to worry about is if any of them start having designs on our little corner of the galaxy. But that’s just the stuff of science-fiction. So far.
And if there are, so what? It doesn’t answer fundamental questions like who, if anyone, designed the designers and why is there anything rather than nothing.
As far as I can see, the existence of extra-terrestrial designers is only poses a problem for Christians since the existence of ETs could knock us off our perch as God’s special creation, His chosen people.
Moved
Joe at UD:
Earth to Joe – how does “the translation of nucleotides into amino acids is not a chemical reaction” stop being ludicrous simply because there is not a direct chemical transformation of triplet into amino acid? Of course there is a physico-chemical connection between them! It is called tRNA. The linkage just happens to occur via a series of intermediates operating on one part of the molecule or the other, and those separate parts do not interact directly during the process. But saying there is none is akin to saying that there is no connection between one end of a stick and the other, or between the slots into which the respective ends fit, because none becomes the other.
The informatic element is imparted by us – we give letters to the bases and the acids, we can look up the relationships in tables, and they occur in strings that we can intone “Shannon” or “Kolmogorov” over. But as far as the interaction is concerned, it is entirely physical, with no more ‘informatic’ quality than the rest of chemistry. Products of one enzyme become substrates for another, and this system is the same. It simply happens that one substrate here is large, and different enzymes act on different parts of this large molecule.
A series of 3 RNA bases – AUG, say – is simply a 3D arrangement of atoms, with which other arrangements of atoms interact. There is nothing about this that distinguishes it from any other biochemical arrangement. Either every molecule is ‘informational’, or none of them are. I could buy that they all are, in the same way that there is ‘information’ in a landscape that one could process by riding a bike across it. But the biochemical interactors of translation are ‘informationally’ distinct from every other? Typical map/territory confusion. We just call it translation.
Kairosfocus responds to my abductive reasoning example with a post on the “For record” thread at U.D. I’m going to try to illustrate what he’s doing with abduction again, not for the purpose of stimulating lots of “righteous” indignation on his part, but in the hope that he might take some of the points on board.
KF clearly wants to make the case that life is intelligently designed.
Imagine I want to make the case that an unknown intelligent designer has designed something, and to do so in a way that seems to involve normal scientific abductive or inductive reasoning. I have only humans and their designs to point to as known examples of high level I.D. (other animals aren’t much use).
So, here’s what I can do. I want to make the case firstly for rivers at a time in human history when we did not understand their formation.
A can be observed to cause B.
For this observation, I don’t want to restrict “A” to “human designers”, because then my “A” won’t cover the unknowns. So I go for the more general “intelligent designers”. I don’t want to restrict “B” to canals, because they’re not rivers, so I go for the more general waterways.
And it appears to work, assuming a GAP in human knowledge on how rivers form.
A is an observed cause of B
We know of no other cause of B.
Therefore, we can infer that the river Nile was intelligently designed.
To support that, I could point out how incredibly improbable it is that nature would have hit the target of a river with the exact specifications of the Nile (exact length, width in all places, depth in all places), and add a Texas Sharpshooter fallacy to support my basic induction.
KF points out, and I agree, that humans might well actually design our own life forms in the future from scratch. However, this doesn’t solve the problem, because we know that we still can’t justifiably broaden “A” from humans to “intelligent designers”. We make actual lakes, and one made by us damming a stream is essentially the same as one made by a landslide doing the same. But the inductive inference to design of lakes does not follow.
So why does this process seem so promising to the likes of KF for the OOL? Simply because it’s a gap in our knowledge, combined with the fact that being designed is obviously personally and emotionally important to them.
So, we’ve got the designer of the gaps. And this shows when “evo-mats” are asked for the details on how life came about naturally, whereas I.D., of course, does not have to deal with such a “pathetic level” of detail, as William Dembski would have it. It is not a mechanistic theory.
I personally see no theory at all, and no established mechanism because living intelligence cannot be responsible for the first life.
Dead intelligence? Extraordinary claims require extraordinary evidence.
And please, KF, don’t reply that expecting naturalistic causes for life is “extraordinary” without providing examples of established instances of supernatural causation of observed phenomena in this world.
This illustrates the most important objection to ID. Not that it is proven wrong but that it short circuits curiosity and diminishes the desire to find natural regularities. The search for regularity is practically synonymous with science.
kairosfocus loses focus:
If “non-living” intelligent designers did NOT create life then it must have been “living” designers that created life.
More circular thinking.
Onlookers will notice that TSZ successfully refuted every claim he made.