Over in the ID Quiz thread at Uncommon Descent, Mark Frank asks;
“Here’s quiz on ID for you ID proponents:
On page 21 of “Specification: The Pattern That Signifies Intelligence” William Dembksi defines the context dependent specified complexity ofgiven
as
Consider the context of the bacterial flagellum.
1. What is
2. What is the function?
3. How is
4. What is
5. How isestimated?
6.is meant to be a probability. Under what conditions might the answer exceed 1?”
given 
as ![-log_2[M\cdot N\cdot \varphi_S(T)\cdot P(T|H)]](http://theskepticalzone.com/wp/wp-content/ql-cache/quicklatex.com-e8afc353618be80af64fbcec7564a345_l3.png "Rendered by QuickLaTeX.com")
?
estimated?
is meant to be a probability. Under what conditions might the answer exceed 1?”This seems a fair question, asking IDists to use their own proposed methodology to detect design, empirically.
But instead of heartily embracing this opportunity to show the power of ID, he is set upon.
Joe moans that
“Really Mark? Then tell us how to determine the probability wrt unguided evolution. If you know the answers to your questions you should be able to do that.”
Sorry Joe, it’s your methodology, do your own work, if you can.
KirosFocus has a length moan from large numbers and incredulity, finishing with;
“We cannot stop such from those tactics but we can expose them and red ring fence off those who insist on such tactics.”
STOP. RIGHT. THERE.
If you can’t employ your own design detection methodology it is no ones fault but your own.
Either the methodology is unusable,
OR non of you are smart enough to use it,
OR you’re all secretly supports of Darwinian evolution and are making ID look as ridiculous as possible.
All Mark Frank has asked is for you to employ your own methodology. You can’t. ID is intellectually bankrupt, and only addressing the required calculations will change that.
[Edit: symbols latexed by Lizzie]
coldcoffee,
You’d need to post references to Axe, but the work I’ve seen is not troubling for conventional theory. In one, he serially substitutes acids on the protein’s exterior. Mutation doesn’t work like that. It hits DNA, and has no information on where its exons are, let alone how the protein is going to fold. And the landscape is multidimensional. It’s a bit like trying to prove the negative. If experimental knockouts don’t work, these may simply represent the pile-up of aborted detrimental mutants in vivo. Success may be rare, but evolution can work on it. You’d have to show NO functional substitutions to disbar small evolutionary steps, or demonstrate a broader barrier to indefinite exploration to constrain it. Adding in gene duplication, you add many more dimensions still.
The other thing not mentioned much in ID circles is that most of the evolution of multi-celled organisms has not required new proteins.
Not to mention new folds. According to conventional knowledge most of foldspace was established long before the cambrian, so I’d really like to see Axe’s reference for the claim that the cambrian explosion required establishing whole new folds never seen before.
Most of post-cambrian evolution is just tweaking programs invented in the previous three billion years. Mostly tweaking development.
But according to gpuccio, the designer drops by approximately every two million years to drop in a new domain. My words, his idea.
Considering that Lenski managed to see a three mutation IC chain in ten years in a small lab population, is it too much to see a new protein every two million years?
I think I may have to study protein folds in some more depth from original Axe paper and some different authors ( might be available online somewhere)
Sounds like a plan.
“Surprisingly a large proportion (71%) of all known enzyme functions are performed by this relatively small set of 276 superfamilies. ”
Well 29% of all know enzyme functions is a big number of new folds.
Side comment. I´m very surprised that darwinist can avoid to see teleology when they state that all the biochemistry was already present in the LUCA.
Why was reproductivly more efficient a LUCA with all that biochemistry than a simpliest one? Do you have an answer?
Make your case, publish, and if your argument is strong enough and well supported then others will be convinced to see the same teleology that you do.
Out of interest, is cancer teleological?
No, quite the opposite. Relatively few domain families catalyze many different reactions.
Not all biochemistry, but the majority of domain families that would later evolve to catalyze most enzymatic reactions.
Look Blas, it’s obvious you don’t understand the terminology employed. That wasn’t meant as a slur, but why do you insist on discussing a subject you obviously aren’t familiar with?
I don’t understand the question, try putting some effort into your grammar.
Why would it NOT be reproductively efficient? What’s the minimum set necessary (or at least likely) to of protein families to allow further evolutionary divergence from that time? What do you think the number is?
I think it’s possible the Designer was a “mad scientist” type trying many many different experiments with OoL and primitive life. I think it’s possible that It inserted a handful of new protein-coding sequences into a primitive cell and waited a few million years to see if anything interesting evolved in the population when it reproduced and spread … then inserted a few more new protein codes into a descendant cell and waited to see what would evolve … and repeated the process until It was satisfied that there were self-replicating organisms with a sufficient repertoire of protein reactions and feedback loops that they would be capable of going on to evolve with no need for further intervention. Then It closed the door to its laboratory and It has never come back, as far as we can tell …
Well, not exactly a scientific theory, but a possible explanation for the known facts — and impossible to disprove. Blas, do you think it might have happened the way I describe?
I believe Blas means something like: why did the LUCA win out in natural selection (that is, why did it have a reproductive advantage) over its possible competitors that were simpler?
IF that’s what Blas means, it’s a serious question, because all else being equal, a more-complex cell is more metabolically expensive. How can you have a reproductive advantage if you have to work twice as hard to grow/maintain twice as many protein-coding genes? Of course, all else is not equal.
Why do we waste money on a defense department? All it does is destroy things.
Why a protein-coding organism might outcompete non-protein-coding organisms … do you really have to ask? Is protein not supposed a marvel of Design? If it’s great stuff, all-hail-the-Designer, it is equally great stuff for aiding in the struggles of Life. A primitive proteinless organism, in a world without protein, may replicate just fine. But if protein significantly improves matters … guess which lineage will survive?
Blas,
LUCA is reaonably supposed to have possessed those functions common to all her descendants. There is no call for teleology – it did not have them in order for its descendants to have them, any more than that’s the reason I have a big nose.
Because you don’t know what the word “stochastic” means in the presence of strongly interacting molecules.
Do you have any idea what the charge-to-mass ratios are in chemistry and during the formation of complex molecules in the presence of other substances such as water?
This is simple high school level stuff.
Atoms and molecules are not inert objects that just fly around in an ideal gas and suddenly have to flash into the “proper configuration” to form a SPECIFIED molecule from scratch.
The complex molecules of life evolved. Do you have any idea what that entails? I don’t think you do.
Please refer to Protein as ‘Protein’ if you mean to refer to protein and not molecule in general. If there is strong interaction, the process is guided by interaction. What do you mean by stochastic in that case? that the bonding is random? If you meant that, it depends on the nature of molecule. Eg, If the molecule is hydrophilic, it will be attracted to water molecule. If it is hydrophobic, it will be repelled by water molecule.
Why are you bringing in charge to mass ratio? You want to calculate the number of electrons that would make up a amino acids, that in turn make up a protein? and then discuss the hydrophobic amino acids found on protein’s inner fold ?
I think it is better to work out total charge and charge density to total mass /mass density instead of working out single electron charges to mass ratio.
Suddenly have to flash? Did I say that anywhere?
Of Course it evolved. ID does support common ancestor and micro evolution.
Mike, what are you driving at ? Evolution is not stochastic ?
It does? What does ID say is the last common ancestor? What does ID say is the mechanisms that cause micro-evolution?
You didn’t know? No wonder you are against ID.
There is no name for last universal common ancestor.It is the same as what evolutionists presume – a single cell organism. Micro-evolution is by mutation.
You should refer to ID FAQ since you seem to think ID is creationism.
Here’s a quote:
Common Questions on ID Check out common questions
Common descent is macroevolution. ID definitely does not support macroevolution, that’s why Stephen Meyer wrote Darwin’s Doubt, to imply major phyla does not share common descent through an evolutionary relationship, but had to be independently “designed”(whatever that means) in the early cambrian.
coldcoffee,
The essence of protein activity is folding, and the essence of folding is a very complex interplay between the nuclei and electrons of the amino acid structure, and those of the medium in which it is folding, including their temperature.
Fundamentally, a folded configuration occurs because it has less energy than the unfolded state. If a system can shed energy, it will. The process is stochastic because there are many different paths by which a peptide chain can shed energy, and minor discrepancies between the conditions of two identical molecules can lead to their adoption of very different configurations. Or, they can take different paths and end up in the same place.
Biologically useful proteins are naturally going to be those that fold in a reasonably consistent manner, and they will be a tiny subset of the possible space of proteins.
Hoyle-style analyses take the size and subunit composition of a modern example of such a stable-folding, active protein, and infer a lower limit on the possibility of both folding and activity to be represented by that.
But what appears to be the case is that longer proteins are better than shorter ones, not that shorter proteins cannot work. Most catalytic proteins appear to be long because there is selection for subtlety of kinetics and control, which takes bits. But the structures are modular. Alpha helices, for example, form from a very simple pattern of hydrophilic and hydrophobic acids. You get one turn for 3 or 4 acids; duplications of such regions will give longer and longer coils, which impart a certain ‘springiness’ … if you look at a long region of alpha helix, and attempt to analyse its probability, you have to take account of the possibility that it arose from duplication of a short, not-at-all-improbable motif, requiring many fewer than 20 amino acids. Extension of the amino acid library allows for substitution of one hydrophobic or hydrophilic acid by another, retaining structure but erasing phylogenetic signal. Such consistently-folding motifs become the raw material for other catalysts.
Then a passing astrophysicist does some back-of-an-envelope calculations and declares protein impossible.
It’s basically another god of the gaps argument. And those whose faith lives by gaps will live to see their faith die.
It would be helpful if you would explain:
When you think the designer acts?
How the designer acts?
What level does the designer act (e.g. create a new bodyplan?) at?
What level of complexity does ID allow to evolve without ID?
At what point is ID required to “push” something to the next level?
In the text you quote it says:
What is the ID non-naturalistic scientific explanation for, say, proteins?
You see, I asked William about the ID explanation for cells and he said “They were designed”.
So this:
also in your quoted text, seems to be simply untrue. All Intelligent Design seems able to offer is “It was designed”.
Shall we throw away the textbooks and replace them with a slip of paper that simply says “It was designed”? I’m sure you can see how absurd that is.
So, if ID offers a better explanation and you believe that then why can’t you provide that explanation? And does that inability leave you wondering if ID is really true after all, or is your faith stronger then that doubt?
True ID doesn’t support macroevolution by random undirected process, but believes the macro evolution is guided by intelligent agent.
Allan Miller,
Thanks for the interesting information
ID is abductive reasoning. We observe the present and hypothesize the cause. Then we look at other explanations for the cause and see which fits our observations better. Origin of universe has many explanation but Big Bang explains many of the observations hence we accept the theory is right. Evolution too is an observation, we have to deduce what caused it. ID is a hypothesis which explains the complexities of macro evolution through ‘intelligent agent’. The agent is not identified – it may be a force, alien or super natural force.Archaeologists sees the pottery and decides that it is designed, he doesn’t know who designed it. He doesn’t have to know the identity of the designer to know that the pottery was designed.
The “laws of chemistry” design evolution.
Whatever works, works. Believe whatever you will about why chemistry works the way it does.
You mean Boyle’s law, charles law, second law of thermodynamics, Henry’s law, Graham’s law etc?
Um, so explain it then?
petrushka: The “laws of chemistry” design evolution.
No, those are all laws of physics. (What is it with ID and ideal gases?)
Try ionic/electrostatic interactions, hydrogen bonds, Keesom, Debye, London dispersion forces and the hydrophobic effect.
To Allan’s lucid description of protein folding, I would add the fact that the ability of proteins to “find” their correct fold is impossible, according to ID-Math(tm), because the number of possible configurations is vast (for a 158-amino acid protein it exceeds the UPB). See “Levinthal’s paradox”.
Why did the designer(s) give RNAse A (and , apparently, cobra venom!) the awesome ability to re-nature that most other proteins lack?
Well, finding the fold isn’t impossible, but it’s hard and takes a supercomputer a long time. But chemistry can do it in a tiny fraction of a second.
So there’s something about mere matter that makes evolution easy and design hard.
http://sandwalk.blogspot.com/2008/04/levinthals-paradox.html?m=1
What is the mechanism used by this unknown intelligent agent to do the guiding? Do you have any evidence of either the agent or the mechanism?
That is not true. An archaeologist who finds a pottery shard always assumes the designer was human based on his previous knowledge of human created pottery. The very next thing done is an attempt to determine which humans, at which time, and by which methods. The identity of the designer is of key importance.
What does ID do that’s analogous to any of that?
ID people gloss over the process of design. When we see pottery we are seeing something made or manufactured. What’s missing from the ID scenario is the millennia of incremental learning that preceded the making.
Intelligent design follows Darwin’s key rule: incremental change steered by selection. Industrial R&D follows this rule. All really new objects evolve through trial and selection.
Well the point is if you have simple a very efficient replicator that is able to uptake the nucleotides from the media will prevent any further evolution as to improve that you need gene duplication and modifications. In that context it would be detrimental mutations because you need more nucleotides to be “reproductivly succesful”.
Just an idea come in my mid reading the cite of petrushka in Wikipedi, where the RNA that “survive” is the smallest one. The one that fits the bonding site of the polimerase.
They can all replicate. The direction evolution takes is determined by the environment, which isn’t always static or friendly.
The Spiegleman molecule isn’t intended to demonstrate the origin of life. It’s just an example of how small a replicator can be. It probably isn’t the smallest or simplest possible.
Blas,
How is evolution prevented in that scenario? If a protein-free orgamism undergoes a mutation to produce a simple peptide, and that peptide constitutes a beneficial change, peptide-producers will better compete against those that don’t make the peptide. That’s the central argument for ALL selective change. No wonder you don’t like evoluton; you don’t seem to have even the most basic grasp of it.
Even if the RNA-only organisms replicate faster, that is not the only means by which lineages compete. It is the net of all the ‘trials of life’ that determines lineage survival, not simply getting genes replicated asap. ‘Darwinists’ are not unduly perturbed by organisms that take years to reproduce, and there is a better reason than ideological blinkers.
That experimental setup placed a premium on minimal length. Other environmental setups need not.
Jayzuz. No wonder normal people think ID means IDiots.
IDists can’t think straight even when they’re writing their own faqs.
They meant “frees FROM being bound”, of course, but they’ve weakened their minds so much that they literally cannot think their way through a subject/object relation in an English sentence.
Yeah, “TO” instead of “FROM” is just a typo but it’s a typo that indicates an intrinsically disordered thought process.
Maybe if they weren’t forced to mumble worthless platitudes to each other to keep everyone in the big tent, they would be able to start thinking straight. Maybe for the first time in their lives …
I’m pretty bad about typos, particularly when posting from a tablet.
I’m more interested in hearing about all the research proposals that ID advocates have waiting in the wings.
Freed from the ungodly constraints of materialism and atheism, what would IDists do? If Doug Axe is any indicator, they’d do useless shit that doesn’t address any proposed evolutionary scenarios and doesn’t produce anything useful such as pharmaceuticals.
Pharmaceutical design requires using lab controlled evolution.
E [+ undetectable god effects] = MC^2 [+ undetectable god effects]
Is this what new, “free”, “unbound” science looks like?
Exactly.
Joe G to the rescue!
http://scienceblogs.com/evolutionblog/2014/02/04/another-round-on-probability-and-evolution/
“ID research project? Easy, find out what else there is to living organisms besides matter and energy”
Details please! I bet it includes ‘information’, which will never really get past being configurations of “matter and energy”, despite the creation of a lot of sciency-sounding acronyms.
Remember this?
DI’s Ann Gauger in front of her fake lab?
http://www.skepticblog.org/wp-content/uploads/discovery_institute_greenscreen-640×355.png
I’m waiting also for Gregory to tell us what an unbounded science could do that isn’t being done.
I not that William made an honest attempt at this. The only problem with proposals to study Psi is that it’s been done and is being done. With a big prize for anyone who captures a wild Psi and wrestles it into a lab.
It’s a good comparison.
Psi is basically margin of error. Until something new happens, it’s not going to be taken seriously. And TBH in a few decades when we’re controlling other things with our minds (via technology) and probably projecting our sense of self into them (rubber arm anyone?) Psi will become like the æther. A quaint idea.
We’ll have the relevant powers anyway so…
However, bell curve and all that, some will never give up on the real thing.
ID is just in that phase of getting to the far tail of the curve. The ID journals seem to tell the story there if nothing else, they only indicate a year on year decline rather then an uptick in publication.
Remember the intelligent design Wiki? I wish I’d taken a copy of that. A place where loads of people can get together and collaborate on Intelligent Design. IIRC it was mainly created by a single person. I guess he just gave up in the end, and realized it’s all cargo cult science. All talk. No trouser.
=> ID MECHANISM: Dembski’s take on ID mechanism
SETI researchers are not invoking a mechanism when they explain a radio transmission from outer space as the result of an extraterrestrial intelligence. To ask for a mechanism to explain the effect of an intelligence (leaving aside derived intentionality) is like Aristotelians asking Newton what it is that keeps bodies in rectilinear motion at a constant velocity (for Aristotle the crucial distinction was between motion and rest; for Newton it was between accelerated and unaccelerated motion). This is simply not a question that arises within Newtonian mechanics. Newtonian mechanics proposes an entirely different problematic from Aristotelian physics. Similarly, intelligent design proposes a far richer problematic than science committed to naturalism. Intelligent design is fully capable of accommodating mechanistic explanations. Intelligent design has no interest in dismissing mechanistic explanations. Such explanations are wonderful as far as they go. But they only go so far, and they are incapable of accounting for specified complexity
The answer to this question:
can also be found in the link given above.
Or it’s about “Who,” not “how.”
Which is why it’s clearly apologetics and not science at all.
Yes, we know he’s not interested in the “forensics” of the matter. Anyone who cares about methods that conform to epistemology, however, is interested in the “forensics” first, and most of all.
Glen Davidson
Blockquote:>…and they are incapable of accounting for specified complexity…
Simply not true. And Demski has never even addressed the math of evolution.
He doesn’t even acknowledge that chemistry embodies a Markov selector, which is functionally equivalent to the weasel selector.
He doesn’t address the fact that evolution doesn’t test the entire phase space, but only the immediately adjacent space. So any given population is not faced with trying 10^500 possibilities, but just a few thousand.
There’s an interesting new paper on protein evolution.
It argues that structure (fold) is conserved, but coding sequence not so much.
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003325
Lots of room for drift.
Or the environment?
coldcoffee:
That’s one of my favorite Dembski articles.
He writes:
Um, because Nelson never finished writing it?
The article also includes Dembski’s hilarious infinite wavelength, zero energy hypothesis: