The design inference- in peer-review (HT Evolution News & Views)

Often it is claimed by anti-IDists that ID does not appear in peer-reviewed journals.

IDists counter with articles in peer-review that support the design inference. Articles such as the following:

Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors

and

Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds

Anti-IDists tried to counter that claim by saying the scientist involved does not share the same inference as IDists do. However that counterclaim now stands refuted:

I have in fact confirmed that these papers add to the evidence for ID. I concluded in the 2000 JMB paper that enzymatic catalysis entails "severe sequence constraints". The more severe these constraints are, the less likely it is that they can be met by chance. So, yes, that finding is very relevant to the question of the adequacy of chance, which is very relevant to the case for design. In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design.--Douglas Axe

(for the original Evolution News and Views article go HERE)

Supporting Intelligent Design

For those who choose willfull ignorance over reality I offer just a glimpse of support for ID (including a testable hypothesis): Intelligent Design: The Design Hypothesis Intelligent Design in Biology Textbooks Intelligent Design in Biology Textbooks Continued The Design Inference in Peer-Review And as far as ID = Creation, using the same logic the theory of evolution is a Creation theory:

"There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."--Charles Darwin in "On the Origins of Species..." 6th edition, last sentence of the last chapter

And for ID being different than Creation:

"The differences between Biblical creationism and the IDM should become clear. As an unashamedly Christian/creationist organization, ICR is concerned with the reputation of our God and desires to point all men back to Him. We are not in this work merely to do good science, although this is of great importance to us. We care that students and society are brainwashed away from a relationship with their Creator/Savior. While all creationists necessarily believe in intelligent design, not all ID proponents believe in God. ID is strictly a non-Christian movement, and while ICR values and supports their work, we cannot join them."- John Morris, president of the Institute for Creation Research

See also: Intelligent Design Is Not Creationism Response to "Not (Just) in Kansas Anymore" by Eugenie C. Scott:

Scott refers to me as an intelligent design "creationist," even though I clearly write in my book Darwin's Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God." Where I and others run afoul of Scott and the National Center for Science Education (NCSE) is simply in arguing that intelligent design in biology is not invisible, it is empirically detectable. The biological literature is replete with statements like David DeRosier's in the journal Cell: "More so than other motors, the flagellum resembles a machine designed by a human" (1). Exactly why is it a thought-crime to make the case that such observations may be on to something objectively correct?

Creationism and Propaganda:

The logic of intelligent design tells us that it is not the same as creationism. Many proponents of intelligent design are not creationists. And more and more creationists are distancing themselves from intelligent design. Nevertheless, most critics of ID insist on equating intelligent design with creationism. While I am sure there are many critics who are sincere (although misinformed) when equating intelligent design with creationism, nevertheless, the accusation has many of the hallmarks of propaganda.

IOW when all else fails and to hide the fact that evolutionitwits cannot support their position, they have to lie. The only way any anti-IDist is going to get to post a response is to provide a testable hypothesis for non-telic processes. So the prediction is no anti-IDist will be allowed to post a response.

The Explanatory Filter and Biology- the Ribosome

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Evolutionists say they have seen the explanatory filter used for anything dealing with biology. That must be because they haven't looked.

What is the explanatory filter? It's just a process that forces you to follow science's mandate. See Newton's Four Rules.

(page 13 of No Free Lunch shows the EF flowchart. It can also be found on page 37 of The Design Inference, page 182 of Signs of Intelligence: Understanding Intelligent Design, and page 88 of The Design Revolution)

The flowchart for the EF is set up so that there are 3 decision nodes, each node capable only of a Yes or No decision. As are all filters it is eliminative. It eliminates via consideration/ examination. That is why the design inference cannot be the default.

START
↓
CONTINGENCY? →No → Necessity (regularity/ law)
↓yes

COMPLEXITY? →No → Chance
↓yes

SPECIFICATION? →No → Chance
↓ yes

Design


Take the ribosome:
A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.

There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-(from Bioinformatics, Genomics, and Proteomics: Getting the Big Picture by Ann Finney Batiza, PhD, pg 23

There isn't anything in peer-review that demonstrates any ribosome can evolve via accumulations of/ culled genetic accidents in a population that never had one. With Dr. Lenski's long running E. coli experiment there hasn't even been any new proteins, let alone new multi-protein complexes.

As Jerry Coyne said, these things are true, no math needed. As as Christopher Hitchens said “That which can be asserted without evidence, can be dismissed without evidence.”  The necessity and chance hypotheses are hence dismissed. As if I have to do the work of the evolutionists.

So the first two decision boxes have answered "Yes".

Moving to the third node:

The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ‘ s Black Box: “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

He goes on to say: ” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.”

The bacterial ribosome is both complex and specified. Therefor given our current state of knowledge of cause and effect relationships, ie science, we can say with confidence that the ribosome is designed.

"Thus, Behe concludes on the basis of our knowledge of present cause-and-effect relationships (in accord with the standard uniformitarian method employed in the historical sciences) that the molecular machines and complex systems we observe in cells can be best explained as the result of an intelligent cause.

In brief, molecular motors appear designed because they were designed” Pg. 72 of Darwinism, Design and Public Education

And there you have it.

The Explanatory Filter and Biological Systems- the Bacterial Flagellum

-
Evolutionists say they have seen the explanatory filter used for anything dealing with biology. That must be because they haven't looked.

What is the explanatory filter? It's just a process that forces you to follow science's mandate. See Newton's Four Rules.

(page 13 of No Free Lunch shows the EF flowchart. It can also be found on page 37 of The Design Inference, page 182 of Signs of Intelligence: Understanding Intelligent Design, and page 88 of The Design Revolution)

The flowchart for the EF is set up so that there are 3 decision nodes, each node capable only of a Yes or No decision. As are all filters it is eliminative. It eliminates via consideration/ examination. That is why the design inference cannot be the default.

START
↓
CONTINGENCY? →No → Necessity (regularity/ law)
↓yes

COMPLEXITY? →No → Chance
↓yes

SPECIFICATION? →No → Chance
↓ yes

Design


Take the bacterial flagellum:

There isn't anything in peer-review that demonstrates any bacterial flagellum can evolve via accumulations of/ culled genetic accidents in a population that never had one. With Dr. Lenski's long running E. coli experiment there hasn't even been any new proteins, let alone new multi-protein complexes.

As Jerry Coyne said, these things are true, no math needed. As as Christopher Hitchens said “That which can be asserted without evidence, can be dismissed without evidence.”  The necessity and chance hypotheses are hence dismissed. As if I have to do the work of the evolutionists.

So the first two decision boxes have answered "Yes".

Moving to the third node:

The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ‘ s Black Box: “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

He goes on to say: ” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.”

The bacterial flagellum is both complex and specified. Therefor given our current state of knowledge of cause and effect relationships, ie science, we can say with confidence that the bacterial flagellum is designed.

"Thus, Behe concludes on the basis of our knowledge of present cause-and-effect relationships (in accord with the standard uniformitarian method employed in the historical sciences) that the molecular machines and complex systems we observe in cells can be best explained as the result of an intelligent cause.

In brief, molecular motors appear designed because they were designed” Pg. 72 of Darwinism, Design and Public Education

And there you have it.

The advantage of experience over ignorance- my response to desk jockeys Elsberry and Wilkins

Some time after William Dembski had his “The Design Inference” published, John Wilkins and Wesley R. Elsberry wrote a scathing review of the Explanatory Filter.

Some history is required- The Explanatory filter is a process/ procedure that aids in determining how the object / structure/ event came to be- remember that is one of the three questions that science asks- How did it come to be this way?. See Explaining the Explanatory filter revisited and especially The Explanatory Filter (EF)- Who uses it? . You really don't want to miss that one.

It is a flowchart consisting of three decision nodes. The first asks if X can be explained via laws of nature/ regularity/ necessity.

If not you move to the next node which asks if those processes in step one plus chance can account for what is observed. Think time and erosion processes acting on exposed rock.

Again if not you ask does X have some pattern, some specificity? Does X exhibit work, i.e. counterflow, or some recognizable pattern?

If it does not, then we initially, this is key because the EF is just for initial inferences. And as with all inferences it can be either confirmed or refuted with future knowledge. But that is how science operates- no departure there.

Also the EF is a process YOU can choose to use or not. The “beauty” of the EF is that it is not pre-determined for a design output. It forces you to consider the alternatives first.

So what do these guys have to say?

We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational,

Just how can a process that you can choose to use or not do something like that?

The EF is just if you have a question about how X came to be that way.

They go on to say:

and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly.

As I said that goes for all of science. It is the nature of the beast. And that is why we call them scientific INFERENCES. Notice the title of Dembski’s book is “The Design INFERENCE”.

And I am still in the paper’s ABSTRACT!

From my experience a paper built on faulty premises is doomed to fail. And this paper passed peer-review!!!

Skipping down to the end they have their own flow chart. This one has “Don’t Know”, “regularity” and “chance”. IOW we don’t know but we know it wasn’t via agency involvement. Truly pathetic.

I wonder if these clowns think that all the success people have had using the EF or some reasonable fasimile thereof, is just an illusion?

I also wonder if they have a better process for detecting design without being biased toward that end?


Please stay tuned for more…

Measuring Complex Specified Information with Respect to Biology

-
Once again, I don't know why this is so difficult, but here it is:

Complex specified information is a specified subset of Shannon information. That means that complex specified information is Shannon information of a specified nature, ie with meaning and/ or function, and with a specified complexity.

Shannon's tells us that since there are 4 possible nucleotides, 4 = 2^2 = 2 bits of information per nucleotide. Also there are 64 different coding codons, 64 = 2^6 = 6 bits of information per amino acid, which, is the same as the three nucleotides it was translated from.

Take that and for example a 100 amino acid long functioning protein- a protein that cannot tolerate any variation, which means it is tightly specified and just do the math 100 x 6 + 6 (stop) = 606 bits of specified information- minimum, to get that protein. That means CSI is present and design is strongly supported.

Now if any sequence of those 100 amino acids can produce that protein then it isn't specified. IOW if every possible combo produced the same resulting protein, I would say that would put a hurt on the design inference.

The variational tolerance has to be figured in with the number of bits.

from Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007):

[N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon’s original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that “different molecular structures may be functionally equivalent.” For this reason, Szostak suggested that a new measure of information—functional information—is required.

With text we use 5 bits per character which gives us the 26 letters of the alphabet and 6 other characters. The paper below puts it all together- peer-review. It tells you exactly how to measure the functional information, which is exactly what Dembski and Meyer are talking about wrt CSI. So read the paper it tells how to do exactly what you have been saying no one knows how to do- it isn't pro-ID and the use of AVIDA as evidence of "emergence" is dubious*, but the math is there for you to misunderstand or not comprehend.

Here is a formal way of measuring functional information:

Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak, "Functional information and the emergence of biocomplexity," Proceedings of the National Academy of Sciences, USA, Vol. 104:8574–8581 (May 15, 2007).

See also:

Jack W. Szostak, “Molecular messages,” Nature, Vol. 423:689 (June 12, 2003).




*1- Avida "organisms" are far too simple to be considered anything like a biological organism

2- Avida organisms "evolve" via unreasonable parameters:


The effects of low-impact mutations in digital organisms

Chase W. Nelson and John C. Sanford

Theoretical Biology and Medical Modelling, 2011, 8:9 | doi:10.1186/1742-4682-8-9

Abstract:

Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.

Results:

When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.


Conclusions:

Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.