I just love that “we.” Greet our lovely “Light” for us all.!

PO will be missed, indeed.

The weather is finally clearing up [still windy, power came back late afternoon – a lot of poles were knocked down], and indeed let us pray that we have a milder season than is feared.

GEM of TKI

G-d be with you dealing with Dean. I too am hoping for a storm that either misses land, or softens before it does. (We’re visiting the region in Spet, and are praying for a LACK of hurricanes and hurricane devastation.)

PO, you’ll be missed. Just know there are IDers who are willing to discuss the difficult questions at length without ending dialogue. Hopefully some of us demonstrated that.

restricting oneself to guidelines set forth by evolutionary biologists is akin to what W.D. does and hence limits the rejection region one could consider.

Here is what I was thinking.

The example I gave of the proteins being placed in proximity and waiting for chance to form them into a fallgelum is silly (which PO seems to recognize i.e 500 years etc).

BUT that seems to be what PO is asking that we consider in his chance calculations (tornado in a junkyard and all that).

UNTIL PO says things such as “we need to consider what objections an evolutionary biologist would have to the particular chance hypothesis that Dr D chooses” (cf 170)

Which seems that PO is the one who is then putting limitations on what can be considered including the rejection region.

Now, evolutionary biologists don’t posit proteins randomingly winging themselves together into a flagellum.

They start with a flagellum-less bacterium and say the DNA code is added to it somehow which then directs RNA to make the proper proteins in the proper sequence to give it its flagellum.

Now, granted Dembski’s famous calculation involve proteins lining themselves up by chance (and shows that it is pretty silly to think that they did) but — if memory serves — he also had a probility calculation of the undirected formation of the DNA code specifing such a line up that ended up being the same as the winging the proteins together scenario.

Anyway, I think he conceded that if the code was in the DNA the flagellum was a certainity.

As far as I can tell, the rebuttal against Dembski is that he hasn’t calculated for some unkown natural force that might cause DNA code to expand or change to program for things like a falgellum.

That, of course, is a faith statement.

I said it before, it puts them in the same category as YEC.

First, weather situation M’rat: Seems Dean is cutting into the region just N of Barbados, so so far just wind here, maybe up to 40 – 50 in gusts. (Now my concern is that it may have done a number on the farmers in Dominica and St Lucia. But moreso, projections put it very near Jamaica at Cat 4 Sunday. Let’s hope and pray it does an Ivan if so – ducks away from Jamaica by a mysterious swerve. And onward let’s hope it does not do a Katrina etc.)

On a few notes:

1] Prof PO:

It seems he has been excluded, and from the situation, maybe what was intended as a light hearted remark was taken a little strongly. He expressed appreciation to me and to the blog. As perhaps his most strongly objecting interlocutor, I think his time here was a contribution of value, on balance, and hope that we will be able to hear from him again.

2] PaV, 379: “PaVian Simmerisation”

Chuckle, chuckle, chuckle . . . .

There, you got three whole chuckles!

3] I really would like you to respond to the question of why any other chance hypothesis ‘needs’ to be considered in the Caputo case.

PO is not here, so I will note that in 361, I showed where the Bayesian algebra leads. Taking a ration across alt hyps, if one knows the probabilities of the hyps, one can then infer whether or no evidence supports one over the other. Fine if you have that data and computational power.

But, we need not look there to see that as Stove points out by far and away most subsets of a population are similar to the pop, i.e reflect its average, cf my darts and charts example in 68 above. Thus, very rare patterns as show up in Caputo, are utterly unlikely to be in a sample, raising suspicion of “cooking” the data.

Thence we can see that this is an instance of a search on a configuration space where the islands of functionality are sparse/ isolated; sufficiently so that random walks are unlikely to hit them. Thence tornadoes in junkyards assembling 747s and/or microjets in vats [app 1 always linked point 6] assembled by diffusion as utterly improbable.

I will keep away from the headaches of multinomial distributions, thank you – I ain’t a “statistrician” .

4] Trib: restricting oneself to guidelines set forth by evolutionary biologists is akin to what W.D. does and hence limits the rejection region one could consider.

Could you kindly explain/expand a bit what you mean here?

GEM of TKI

I could have continued this discussion for a little while longer, I think.

PO, if you peek back, restricting oneself to guidelines set forth by evolutionary biologists is akin to what W.D. does and hence limits the rejection region one could consider.

The example I provided was a pure chance one. Well, almost pure chance. I did cheat a little.

P.O. and I communicated on other matters outside of UD since he is a mathematician and I have an interest in math. He expresses his thanks to everyone here for a stimulating exchange. He will not be returning, and he is sorry he won’t be posting here anymore.

He asked me to convey his appreciation for you all.

There’s an article in this week’s Science magazine you’ll want to look up at the University.

Here’s and excerpt:

It’s entitled: “Crystal Structure of an Ancient Protein:…”

They write:

Here we report the empirical structures of an ancient
protein, which we “resurrected” (12) by phylogenetically
determining its maximum likelihood sequence from a large
database of extant sequences, biochemically synthesizing a
gene coding for the inferred ancestral protein, expressing it in
cultured cells, and determining the protein’s structure by xray
crystallography. Specifically, we investigated the
mechanistic basis for the functional evolution of the
glucocorticoid receptor (GR), a hormone-regulated
transcription factor present in all jawed vertebrates (13). GR
and its sister gene, the mineralocorticoid receptor (MR),
descend from the duplication of a single ancient gene, the
ancestral corticoid receptor (AncCR), deep in the vertebrate
lineage ~450 million years ago (Ma) (Fig. 1A) (13).

How timely, no?!

“Before we kill the thread, let’s kill Caputo! I was
talking abot your flagellum calculations and only
meant that your chance hypothesis is similar to
Caputo p=1/2, and asked how you’d rule out other
chance hypotheses (similar to Caputo p=37/38).
I was very unclear, sorry! Shouldn’t have mentioned him at all!”

Frankly, I was working the other way around. That is, I thought it would be better to get some clarification as to how the ‘liklihood’ approach actually works in a simple case before we try to tackle a more complicated one.

So, in using the example of the stock market closing price as the determiner of D’s and R’s, surely a random happening, I was trying to get at what other chance hypotheses might need to be eliminated to satisfy a ‘liklihood’ statistician. IOW, I really would like you to respond to the question of why any other chance hypothesis ‘needs’ to be considered in the Caputo case.

Changing the subject a little bit, and in a way that perhaps anticipates what might come next, I would ask you if you think a multinomial distribution could be used for statistical analysis in the case of proteins. What are your thoughts about that?

I have to rush off. See you all later.

P.S. BTW, kairosfocus, I knew what you were getting at with the “PaVian Simmerisation”; I just thought I’d get a chuckle from you!

Seems there is life yet in this thread that keeps going and going.

Okay, a few observations:

1] David Stove’s point on induction, empirical support to a claim and sampling

On another thread, I ran across the name and followed it up fruitfully – UD is good at stimulating that sort of thing. In taking on Hume, Kuhn, Popper et al, he makes some points that jump off the page at me on the stuff discussed above, and at least for the onlookers I think the ideas he raised are well worth at least an excerpt or two. So, PaVian style, the “simmerised” core stuff [quite relevant tot he underlying context to the above], courtesy that ever so humble and too often biased on ID Wiki (which has onward links that get to whole books online, drop me a line through contacts via my always linked . . .):

[Negative task] Consider a claim such as “All ravens are black”. Hume argued that we don’t know this a priori and that it cannot be entailed from necessary truths. Nor can it be deduced from our observations of ravens . . . . Stove argued that Hume was presuming “deductivism” . . . the view, explicitly or implicitly accepted by many modern philosophers, that the only valid and sound arguments are ones that entail their conclusions. But if we accept that premises can support a conclusion to a greater (or lesser) degree without entailing it, then we have no need to add a premise to the effect that the observed will be like the unobserved – the observational premises themselves can provide strong support for the conclusion, and make it likely to be true. Stove argued that nothing in Hume’s argument shows that this cannot be the case and so Hume’s argument does not go through, unless one can defend deductivism. This argument wasn’t entirely original with Stove but it had never been articulated so well before. Since Stove put it forward some philosophers have come to accept that it defeats Hume’s argument . . . .

So, it comes down to defeatable but credible warrant, where we may know reliably enough for real-world purposes, but only provisionally. [Thus, “all men live by faith; the issue is which one, why?”]

[positive task] it is a statistical truth that the great majority of the possible subsets of specified size (as long as this size is not too small) are similar to the larger population to which they belong. For example, the majority of the subsets which contain 3000 ravens which you can form from the raven population are similar to the population itself (and this applies no matter how large the raven population is, as long as it is not infinite). Consequen[tl]y, Stove argued that if you find yourself with such a subset then the chances are that this subset is one of the ones that are similar to the population, and so you are justified [NB:following Plantinga, I would use “warranted”] in concluding that it is likely that this subset ‘matches’ the population reasonably closely . . .

Thus we see that sampling [esp if random or nearly so] tends to reflect the population’s “average” i.e the same basic point that statistical thermodynamics is premised on, and which is very relevant to – here it comes again – Caputo. Thus too, unless we have a large enough sample, we are unlikely to see the extreme strongly represented, on a chance basis.

Further to this, generalising to a configurational space and the task of searching more or less at random, we are far more likely to see states reflecting clusters of configs that are common, than clusters that are rare; absent feeding in enough probabilistic resources to make it likely to climb Mt Improbable. And, random walks in a space where the criterion of inclusion in the specified set is functionality, are vastly unlikely to ever arrive at a functional state to begin with. This is for reasons as identified in my always linked, App 1, point 6, on the micro-version of Hoyle’s “tornado in a junkyard builds a 747 by chance.”

2] PO, 377: I assumed Kf was just joking about the bacteria in the dish; no evolutionary biologist has to my knowledge claimed that all the proteins were sitting in the bacterium and suddenly assembled by chance

H’mm, if you look back at 360, you will see that the example was set up by Tribune 7 not me. But, too, you will see by comparing the just referenced point in my always linked, that his is essentially the same thing as my microjets example addresses; cf the exchange with Trib at 364 (pt 3) and 366, on the issue of the thermodynamics of diffusion, which is what would dominate.

In a nutshell: the number of scattered microstates – the cells in the locational space would be of order 10^-9 to 10^-8 or so metres [1 cc would have ~ 10^18 10^-8 m scale locational cells in it, and you are here dealing with dozens to hundreds of parts] so overwhelms the clumped much less the functionally configured that we probably will have to wait longer than the observed cosmos exists for even EXISTING, known to be functional, proteins to assemble into a flagellum by chance-dominated processes. [Tornado in a junkyard statistics again.]

And, that is before you get to the issue of forming the functional proteins by chance and co-option, requiring a lot of DNA coding as discussed above, up to 27,000 top 45,000 base pairs worth! (No to mention the underlying issue of forming the life forms in the first place out of prebiotic chemistry in realistic environments.)

3] I promise not to use the C-word unnecessarily

That is where a lot of the trouble on rhetoric started; cf just above to see the force of the Hoylean point hat HM et al picked up, probably because of their thermodynamics training in Chemistry and/or Engineering Sciences.

4] let’s go look for some E coli and get started!

E coli are rather easy to find – being a major life form in sewage. But I think Biological supply houses have all sorts of “pet” strains used in studies. [I think there was a flap about producing and using lab strains that would not thrive in the “wild”; for obvious reasons.]

On the challenges of the expt’s design, cf. Just above. Funding will be a bear, in that light.

GEM of TKI