Pope's astronomer dismisses ID and says Church was "spectacularly wrong" in its treatment of Galileo

[StAnastasia]

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life.
Editor in Chief
Matti Leisola, Enzymology and Enzyme Engineering; Aalto University School of Science and Technology, Finland
​

'So, to sum up: The journal Bio-complexity has only ever published two papers, has 30 members on its editorial board (many of whom are financed by the Discovery Institute), and one of the papers from this journal is a “peer reviewed” science article that Axe uses to prove I am “blowing smoke”. This is rich.

First-tier, peer-reviewed scientific journals that deal with matters like “drug resistances” and “protein structure” can easily be found in the U.S. National Library of Medicine “PubMed” database.

Searching PubMed for the journal Nature, for example, returned 92,139 articles today.
Science returned 157,118 articles and the Journal of Biological Chemistry returned 153,459 articles.

Searches for Bio-complexity (or Biocomplexity and several other permutations) returned:

“No items found.”​

 

[buffalo]

'So, to sum up: The journal Bio-complexity has only ever published two papers, has 30 members on its editorial board (many of whom are financed by the Discovery Institute), and one of the papers from this journal is a “peer reviewed” science article that Axe uses to prove I am “blowing smoke”. This is rich.

First-tier, peer-reviewed scientific journals that deal with matters like “drug resistances” and “protein structure” can easily be found in the U.S. National Library of Medicine “PubMed” database.

Searching PubMed for the journal Nature, for example, returned 92,139 articles today.
Science returned 157,118 articles and the Journal of Biological Chemistry returned 153,459 articles.

Searches for Bio-complexity (or Biocomplexity and several other permutations) returned:

“No items found.”

An argument form popularity.

 

[Touchstone]

I think you’re right on this last point here, and it seems that you’re conceiving IC as I have been suggesting, not as rossum does. Two questions: What would you say about rossum’s ‘IC’ bridge example? Could you succinctly explain the flagellum refutation you refer to here?

The proteins in the bacterial system called the Type III Secretory System are directly homologous to the “motor mount” of the bacterial flagellum. The TTSS doesn’t have all 30+ proteins of the flagellum, but has a large subset that indicates a shared evolutionary pathway, eventually diverging into the TTSS on one branch, and the flagellum on another (along with possibly others). Hence the “reducability” of the flagellum. If it’s not clear, the TTSS is functional on its own, and demonstrates what an incremental step toward the flagellum would like like as a functional system.

Lots more here from Kenneth Miller, who’s been a leading debunker of Behe.

millerandlevine.com/km/evol/design2/article.html

-TS

 

[reggieM]

Bio-complexity

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life.
​

Launched in June, 2010. Another sign that “ID is dead”. ​

 

[rossum]

An argument form popularity.

One article and one review is not impressive.

In science the citation index is important. Seminal papers get cited a lot - have a look at the citations of the Miller-Urey paper for example. Routine papers get cited a little and not very useful papers hardly get cited at all, sometimes only once in a second paper that refutes them.

The Bible gets cited a lot more than the Book of Koresh. Christianity is more important than Koreshanity.

rossum

 

[rossum]

Measuring fCSI …

Functional Sequence Complexity alone provides algorithmic instruction
biomedcentral.com/content/pdf/1742-4682-2-29.pdf

Did you read the paper? The authors explicitly say that they have no way to measure FCS:FSC cannot have individual units of fixed value. Does this
negate the reality of FSC? If so, we have a lot of explaining
to do for fields such as engineering and computer science
that depend squarely upon FSC. Language, rationality,
and the scientific method itself all depend upon FSC, not
RSC or OSC. Science must recognize that there are
legitimate aspects of reality that cannot always be reduced
or quantified.

Your second paper directly contradicts this by proposing Fits (analogous to Bits) to measure FCS. Which paper do you want? One but not the other please since they contradict each other.

rossum

 

[buffalo]

The proteins in the bacterial system called the Type III Secretory System are directly homologous to the “motor mount” of the bacterial flagellum. The TTSS doesn’t have all 30+ proteins of the flagellum, but has a large subset that indicates a shared evolutionary pathway, eventually diverging into the TTSS on one branch, and the flagellum on another (along with possibly others). Hence the “reducability” of the flagellum. If it’s not clear, the TTSS is functional on its own, and demonstrates what an incremental step toward the flagellum would like like as a functional system.

Lots more here from Kenneth Miller, who’s been a leading debunker of Behe.

millerandlevine.com/km/evol/design2/article.html

-TS

Except now we know the flagellum came first.

And common components can indicate common design. The point is if you take away 1 component does the motor function and serve its purpose.

 

[wanstronian]

Launched in June, 2010. Another sign that “ID is dead”.

Underwritten by the Biologic Institute, which in turn is underwritten by the Discovery Institute.

This is merely a sign that creationists don’t want ID to be dead, so they’re inventing “scientific” journals to try and gain credibility. It’s a bit too transparent to get creationism into schools, but it’ll doubtless be appealing to the credulous, and give unjustified feelings of righteousness to those who already believe the superstition of religion.

 

[StAnastasia]

An argument form popularity.

No, an argument from reason.

 

[StAnastasia]

Launched in June, 2010. Another sign that “ID is dead”.

It seems safe to predict that it will be difficult for BIO-Complexity to attain its ostensible goal of serving as “the leading forum for testing the scientific merit of the claim that intelligent design … is a credible explanation for life.” But was that really the point? Unable to convince the scientific establishment of the merits of their views, creationists have long been engaged in the project of constructing a counterestablishment, which mimics — or perhaps the mot juste is “apes” — not only peer-reviewed journals but also professional societies, textbook publishers, media organizations, natural history museums, and graduate programs at accredited universities.

The purpose of the counterestablishment is not necessarily to challenge the scientific establishment or to affect the public’s view of science, although those are certainly accomplishments that would not be despised if they were to come to pass. Instead, the counterestablishment seems primarily to serve to reassure the participants, the supporters, and (perhaps crucially) the funders of the creationist movement that there is a worthwhile project under way. To the extent that BIO-Complexity flourishes, it will not be because it is reporting scientific tests of “intelligent design” but because it is evincing, in the otherwise declining “intelligent design” movement, a few feeble signs of life.

 

[Touchstone]

Except now we know the flagellum came first.

That doesn’t help at all. And you don’t know it, it’s likely. But irrelevant. They likely both are branches from the same evolutionary trunk.

And common components can indicate common design.

Yeah. Anything similar can indicate common design. That’s a perfectly vacuous retort, no better than saying “God could have placed the light from new stars right near the earth to make them look old.” Yeah, and he could have made the world from scratch last Tuesday, and he could have used “common design” for all the homologies and similarities we see…

The point is if you take away 1 component does the motor function and serve its purpose.

No, many times because its purpose requires that 1 component. But what Behe, and I guess you, here, are having trouble with conceptually is that the “minus 1” system can have a slightly different, or even drastically different purpose.

How would an eye work without a lens? It’s IC! Well, you can find examples of more rudimentary eyes that don’t have a lens, and which use a “pinhole” perforation which provides less acuity and detail, but which is still useful and evolutionarily advantageous in its own right. Such eyes are useful without the lens, and yet also amenable to the formation of (precursors) to the lens, which are also not nearly as great as a fully honed lens, but are incrementally advantageous all the same.

Even the more rudimentary eyes that have a pinhole or a slit have more crude prior forms that confer advantage. The organism may have been fantastically successful with the development of a simple patch of skin that was photosensitive, and just able to roughly detect relative differences in light and dark. That’s pretty crude compared to an eagle’s eye, but you only need a little edge to make the cut, often. Nature can reward small improvements handsomely.

If you learn how the TTSS works and how it functions it’s easy to see how a flagellum develops incrementally, step-wise out of that, or some similar precursor.

-TS

 

[tonyrey]

Underwritten by the Biologic Institute, which in turn is underwritten by the Discovery Institute.

This is merely a sign that creationists don’t want ID to be dead, so they’re inventing “scientific” journals to try and gain credibility. It’s a bit too transparent to get creationism into schools, but it’ll doubtless be appealing to the credulous, and give unjustified feelings of righteousness to those who already believe the superstition of religion.

Dogmatic belief in materialism is the crudest form of superstition in that it derives the power of reason - on which materialists rely to reach their conclusions - from processes which lack insight and understanding.

Incidentally it is a mistake to equate belief in Design with Creationism. It is abundantly clear that Design is the most **rational **explanation of the immense value, richness and beauty of life and the universe.

If values are subjective the value of rational arguments is also subjective. In other words they are simply a matter of opinion…

 

[edwest2]

Underwritten by the Biologic Institute, which in turn is underwritten by the Discovery Institute.

This is merely a sign that creationists don’t want ID to be dead, so they’re inventing “scientific” journals to try and gain credibility. It’s a bit too transparent to get creationism into schools, but it’ll doubtless be appealing to the credulous, and give unjustified feelings of righteousness to those who already believe the superstition of religion.

Perhaps you should read this journal before pronouncing on it. We must stop any attempt to “get creationism into schools” is the rallying cry of the anti-theist. Do you suggest student backpacks be searched before entering school buildings in case anyone is carrying ID literature?

After reading Signature in the Cell, I’m convinced by the data and I have no need to join or promote any Institute or individual.

Yes, I read things on the internet all the time that appeal to the credulous.

God bless,
Ed

 

[Betterave]

The proteins in the bacterial system called the Type III Secretory System are directly homologous to the “motor mount” of the bacterial flagellum. The TTSS doesn’t have all 30+ proteins of the flagellum, but has a large subset that indicates a shared evolutionary pathway, eventually diverging into the TTSS on one branch, and the flagellum on another (along with possibly others). Hence the “reducability” of the flagellum. If it’s not clear, the TTSS is functional on its own, and demonstrates what an incremental step toward the flagellum would like like as a functional system.

Lots more here from Kenneth Miller, who’s been a leading debunker of Behe.

millerandlevine.com/km/evol/design2/article.html

-TS

Your argument here isn’t very clear. Could you try to make each step in your reasoning explicit? I’ve read part of Miller’s article and so far it’s certainly clear that he’s grinding an axe. I’ll continue, however. In the meantime, what about my other question? Do you think rossum’s example of an IC system - a bridge made of a log resting on two stones - is a good one? Why or why not?

 

[grannymh]

Incidentally it is a mistake to equate belief in Design with Creationism. It is abundantly clear that Design is the most **rational **explanation of the immense value, richness and beauty of life and the universe.

I have been thinking about that. The immense value, richness and beauty of life, including the human species, is part of an objective grand design. Being an objective concept does not keep human onlookers from messing up that design. Or, more to the truth, human onlookers can choose to ignore what the richness and beauty of life teaches.

 

[Touchstone]

Your argument here isn’t very clear. Could you try to make each step in your reasoning explicit?

Uh, no. You specifically asked for a succinct explanation, and I gave you that, along with a link to a good, meaty article. If you suppose Miller’s just grinding an axe with that, I’d be a fool to spend any more time on this with you – I’m not gonna do better than he does, here. Perhaps many of the concepts and terms he’s using are just unclear, and more background reading on the subject would help?

I’ve read part of Miller’s article and so far it’s certainly clear that he’s grinding an axe. I’ll continue, however. In the meantime, what about my other question? Do you think rossum’s example of an IC system - a bridge made of a log resting on two stones - is a good one? Why or why not?

Rossum’s example was awesome. I’d like to use it myself, going forward, because it’s very simple, yet very clean in demonstrating the princple. And, you can illustrate it in simple ASCII characters (that makes it awesome).

The function of the system is “crossing the creek”. Initially, a set of stones gets put out, one by one. At first, the walker can only get a step or two out into the creek, not even across it. But with each successive stone, more progress, until the creek can be crossed from bank to bank. But a log placed (or fallen) in one step makes some/many of the stones superfluous. They can be washed downstream, or other wise removed, and the creek can still be crossed.

An ID-IC advocate would say “Irreducible Complexity”! The stones in the middle are gone, after all, and removing that key log would leave the subject nowhere! And that’s true, but it’s just painfully brittle in its thinking. The stones stepping across the creek were incremental, and useful at each addition, but became superfluous, unneeded, later as another incremental step provided a better solution. The obsolete parts can wither, or otherwise disappear, but the step-wise history remains just that – step-wise, incremental, non-magical.

So yeah, thumbs up to rossum on that one. That’s high quality – pedagogically powerful, and true to the concept.

I didn’t like the monolith/arch example because a key in this is the component/step-wise nature of the development path, which “erosion” seems to leave out. The stones and log example preserves this nicely. And I can relate it in ASCII, to boot. Cool.

-TS

 

[Betterave]

If we define IC as “a system which cannot evolve” then up to now no IC systems have been -]discovered/-] uncontroversially identified in living organsims. If we define an IC system as:

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning.

– Behe, “Darwin’s Black Box”, 39
Then there are many examples of IC systems in living organisms, some of which have known or at least possible evolutionary pathways. Given such a definition there are also non-living IC systems, shcu as Behe’s mousetrap example, and likewise we have evolutionary pathways for some of those, the mousetrap included.

I’d like to hear more about the mousetrap.

From Kenneth Miller’s paper, linked by TS upthread:
“The great irony of the flagellum’s increasing acceptance as an icon of anti-evolution is that fact that research had demolished its status as an example of irreducible complexity almost at the very moment it was first proclaimed.”

Note that Miller follows my interpretation.

No. Dembski admits that his explanatory filter cannot detect a misleading designer who designs something to look as if it arose by law or by chance. While we can say that we have a law/chance path to a particular system, this does not rule out a Loki/Trickster designer who has set out to fool us. Also, since the Discovery Institute refure to tell us what their designer can and cannot do, we are not in a position to say “the designer(s) cannot make this subsystem”. We could do that with palaeolithic man and the aluminium cylinder block because we have a reasoanble idea of the limits on palaeolithic technology. Since we do not know any limits on the posers of the DI-ID designer(s) we cannot ever say that they “cannot” have done something.

Er, right… That was exactly my point, so still, isn’t the obvious equivalent: “If it could be demonstrated that it is not true for any of the complex organs which exist that they could not possibly have been formed by numerous, successive, slight modifications, ID theory would absolutely break down”? And if it’s not good for the goose, why think it’s good for the gander? If we could never demonstrate the antecedent here (Behe), what makes you think we could demonstrate it there (Darwin)? Isn’t there a symmetry between the two cases?

The word “evolve” can be used in non-biological contexts. For example astronomers use if for the extected changes over time seen in stars: ‘stellar evolution’. In all contexts it means ‘change over time’. In biology it means “change in the genomes of a population over time”. In abiogenesis the word ‘evolve’ is not generally used, though it can be applied to “chemical evolution” which is a reasonably similar process to biological evolution: changes over time in the ratios of different chemicals (usually RNAs or similar). It is in this case where spontaneous organisation can have an impact, for example Cairns-Smith’s suggestion that clay crystals helped organise early organis molecules.

So far the “knockout definition” of ID, which I quoted above, has been shown to be evolvable in at least some cases, so we know that the statement, “Knockout ID cannot evolve,” is false. It may be that some as yet untested particular examples of knockout ID may be unevolvable but it is up to the ID scientists to show this. The general statement has definitely been falsified.

You’ve got some serious category errors here. Definitions are not evolvable (unless you’re switching to a discussion of memetics - which you’re obviously not). As for a “knockout case of ID,” I think we (you, me, Miller, Behe) need to get clear about the conceptual structure of ID before you can make that claim. Miller talks very tendentiously about the flagellum as the “poster child” for ID, but if someone besmirches your poster child, that’s still just one child who happened to get stuck on the poster.

As to Behe’s later “unlikely to evolve” definition:An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.

– ISCID Encyclopedia, Irreducible Complexity
This requires detailed knowledge of the actual pathway, which is why Behe’s 2004 paper only dealt with theoretical probabilities. It is also noticeable that no work has been done by ID scientists on actual pathways. Some work has been done on this by non-ID scientists, for example: Bridgham, Carroll, Thornton: “Evolution of Hormone-Receptor Complexity by Molecular Exploitation”, (2006). The second sentence of the Abstract of this paper is a reference to Behe’s IC, and is an example of why I consider Behe’s IC idea to have been useful. It triggered off a lot of good work on the evolution of complex systems. This paper is just one example.

rossum

I think this notion should be intuitively obvious and was already present in Darwin’s Black Box. Maybe I should read it again. Obviously a case of putative IC must be established in the context of current knowledge of actual pathways. How can that not be obvious? And again, that is why IC claims are falsifiable, as has been demonstrated - which, N.B., does not falsify the general notion of IC.

 

[Betterave]

Uh, no. You specifically asked for a succinct explanation, and I gave you that, along with a link to a good, meaty article. If you suppose Miller’s just grinding an axe with that, I’d be a fool to spend any more time on this with you – I’m not gonna do better than he does, here. Perhaps many of the concepts and terms he’s using are just unclear, and more background reading on the subject would help?

LOL! A succinct explanation still means an explanation that gives all the necessary explanatory steps. Succinct doesn’t mean vague hand-waving. Perhaps you are a fool, not for spending time with me on this though, but for assuming that Miller’s paper is beyond reproach, just because you happen to like it and agree with it. Remember: who’s the easiest person to fool? (You are.)

Also please note my previous thread: Miller appears to agree with my interpretation of IC, not yours and rossums. (Ironic? - yes!)

Rossum’s example was awesome. I’d like to use it myself, going forward, because it’s very simple, yet very clean in demonstrating the princple. And, you can illustrate it in simple ASCII characters (that makes it awesome).
…]
-TS

Awesome? Okay, in that case thanks for the assessment, I disagree, but I think I’ll take that matter up with rossum.

 

[Touchstone]

I think this notion should be intuitively obvious and was already present in Darwin’s Black Box. Maybe I should read it again. Obviously a case of putative IC must be established in the context of current knowledge of actual pathways. How can that not be obvious? And again, that is why IC claims are falsifiable, as has been demonstrated - which, N.B., does not falsify the general notion of IC.

This is true. At one point Behe assumed this stance before moving on to his current “edge of evolution” thing; you can disprove all the putative IC systems I suggest, but no worries. I’ll just go looking for more examples that don’t have known developmental pathways.

That’s a solid tactical advantage. IC as a general idea stands undefeated, unfalsifiable, but the IC proponent can throw out example after example. What about this thing? Ok, how about that? And oh, that over there? A single IDist can keep the whole of biology hopping with his proposals. And the scientists do all the work investigating and describing the plausible pathways for the feature (which, in a way, has been ID’s one good contribution to science, a series of challenges to investigate for incremental pathways).

But to falsify a particular example does not falsify the general concept. If the flagellum is shown to be reducible, there’s always something else to wonder about.

-TS

 

[Betterave]

That is the current problem with String Theory. Their ‘A’ is not currently measurable, though in principle it may be measurable in future. It is for that reason that String Theory gets some flak from its opponents as being currently ‘unfalsifiable’.

Right, but that doesn’t address the issue here.

Science does not work in that way. Because there is so much we do not know the “we don’t know” option can never be eliminated. We certainly do not know enough about biology in general or abiogenesis in particular to be able to say that design in the only alternative to evolution.

I never said nor implied that the “we don’t know” option can be eliminated. The point of any hypothesis in science is not to exclude the possibility of other hypotheses. Again, why do you (and people like Miller) claim that it is in this case (Behe), especially when you claim that it is not in the other (Darwin)? - at least it seems you *need *to claim that that is not the point in the latter case, although you may have a hard time doing so *consistently *given your current assumptions.

Yes they did. The function is to cross the river dry-shod. That is not possible initially without the presence of most of the middle stones; I will allow one of two non-adjacent stones to go while still maintaining function. The required function is maintained at all times through all the changes. Starting from a functional non-IC system we have moved to a functional IC system.

You don’t address my argument at all here. Also the example is bad because the system in question is not intrinsically functional at all. It just so happens that it can be used by an extrinsic locomotive entity to accomplish a particular change of location. That doesn’t even begin to look like an IC system unless you have described how this particular act of river-crossing is an essential biological survival function of the river-crosser.

The possible existence of such islands is not in dispute. The question is whether or not any living organsims are actually on those islands. Finding such organisms would be a great puzzle for evolution. A mammal with feathers, rather than fur, might be an example of an inhabitant of such a DNA island.

If “the possible existence of such islands is not in dispute,” then the possible existence of IC (as Miller and I and quite possibly Behe, when read in context, define it) should not be in dispute. Correct?

If found it would indeed falsify Darwin’s theory. All that is needed is to find an example of something very like symbiosis, where both organisms co-operate, but which gives no advantage to one of the co-operating organisms. Symbiosis and parasitism are both relatively easy to recognise so it should be possible to find an example if such exists.

rossum

It would indeed? That’s not much of an explanation. *Why *would it indeed?