Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Irreducible complexity » God of the gaps and incredulity,a justified refutation of ID arguments?

God of the gaps and incredulity,a justified refutation of ID arguments?

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God of the gaps and incredulity, a justified refutation of ID arguments?

http://reasonandscience.heavenforum.org/t1983-god-of-the-gaps-and-incredulitya-justified-refutation-of-id-arguments

If the theist were to actually say, ''We don't know what caused 'x', therefore, God.'', their argument could indeed be considered a 'god of the gaps' fallacy. What we say, IMHO, is: ''Based on current knowledge, God is a better explanation than materialistic naturalism."  If one is not arguing from ignorance, but rather reasoning from the available evidence to the best explanation, is it not rather ludicrous to accuse them of launching a 'god of the gaps argument'?

1. You check and find no money in your wallet
2. It's an argument of knowledge to say: I have no money.
3. The same happens in biology. You checked, but coded information and irreducibly complex systems cannot emerge naturally
4. Hence, the argument is from knowledge, not from ignorance.  

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. 

Ironically, when critics make this accusation, they are usually committing a "gaps" fallacy themselves. How so? These very same materialists (1) admit that gaps in the evidence for Darwinian evolution exist, and (2) assume that those gaps can and will be filled by materialist explanations. Otherwise, they wouldn't be attacking ID for purportedly filling those gaps with "god." They can't make a "god of the gaps" accusation without also making a "materialism of the gaps" argument -- one that assumes the truth of their own materialistic outlook.

"Incredulous" basically means "I don't believe it". Well, there's a big difference between "not believing" that an actual animal, plant, phenomenon etc. *exists*, versus believing a certain "just so" story about HOW it came to exist.That is the THING that we are incredulous about - a *certain scenario* (Neo-Darwinism and abiogenesis, and that irreducibly complex  biological systems, and coded, instructed or specified complex information could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, Mutations and  Natural Selection. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things.  ORIGIN is not the same as OPERATION. To study how biology works today is entirely different from giving a *plausible* account of how it came about to be in the first place.

Is God a gap-filler? Nah. Not. Creation Demands a Creator. Beginnings require a Beginner. Design Demands a Designer. Laws come from law-makers. Fine-Tuning requires a Fine-Tuner. Life comes only from life. Information requires a source of information. And so do blueprints. A building requires a builder. Morality requires a Moral-giver. From nothing, nothing comes.

This is one of the most used refutations used by proponents of naturalism when confronted with a sound inference of design based on POSITIVE evidence.  "I don't understand how something could have come about, therefore God!" or "hey, look at this, it's really complex and I can't see how it could have happened naturally" is not the logic of our arguments. God of the gaps is a comfortable way to try to criticize and reject our point and avoid to address actually the issues raised. Opponents of ID resort to it all the time, even when a robust case is made, with clear and detailed science-based observation, prediction, experiment, and logical inference and conclusion.  The evidence for intelligent design has not been shrinking in the last two decades. It’s been growing, while the barriers to explain origins through naturalism have grown.  This is obvious in regard to all relevant issues:  the origin and fine-tuning of the universe, life, and biodiversity.

Strawman arguments of intelligent design
http://reasonandscience.heavenforum.org/t2361-strawman-arguments-of-intelligen-design

Observation: Intelligent agents  act frequently  with an end goal in mind, constructing functional irreducibly complex  multipart-machines, and  make  exquisitely integrated circuits that require a blueprint to build the object. Furthermore, Computers integrate software/hardware and store high levels of instructional complex coded information. In our experience, systems that either a)require or b)store large amounts of specified/instructed complex information such as codes and languages, and which are constructed in an interdependence of hard and software invariably originate from an intelligent source. No exception.

Hypothesis (Prediction): Natural structures will be found that contain many parts arranged in intricate patterns, metabolic pathways similar to electronic circuits, and irreducible structures  that perform  specific functions -- indicating high levels of  Information, irreducible complexity, and interdependence, like hard/software.

Experiment: Experimental investigations of DNA, epigenetic codes, and metabolic circuits indicate that biological molecular machines and factories ( Cells ) are full of information-rich, language-based codes and code/blueprint-based structures. Biologists have performed mutational sensitivity tests in proteins and determined that their amino acid sequences, in order to provide function, require highly instructional complex coded information stored in the Genome.   Additionally, it has been found out, that cells require and use various epigenetic codes, namely  Splicing Codes,  Metabolic Codes,  Signal Transduction Codes,  Signal Integration Codes Histone Codes, Tubulin Codes, Sugar Codes, and The Glycomic Code. Furthermore, all kind of irreducibly complex molecular machines and biosynthesis performing and metabolic pathways have been found, which could not keep their basic functions without a minimum number of parts and complex intertwined and interdependent structures. That indicates these biological machines and pathways had to emerge fully operational, all at once. A stepwise evolutionary manner is not possible. Furthermore, knockout experiments of all components of the flagellum have shown that the flagellum is irreducibly complex.

Conclusion: Unless someone can falsify the prediction, and  point out a non-intelligent source  of  Information as found in the cell, the high levels of instructional complex coded information, irreducible complex and interdependent molecular systems and complex metabolic circuits and biosynthesis pathways, their origin is   best explained by the action of an intelligent agent.

Is ID a "god-of-the-gaps" argument?

http://www.ideacenter.org/contentmgr/showdetails.php/id/1159

(1) Biochemical complexity / Laws of the Universe. High information content machine-like irreducibly complex structures are commonly found. The bacterial flagellum is a prime example. Specified complexity found in the laws of the universe may be another. 
Prediction of Design Met? (Conclusion)Yes.

(2) Fossil Record Biological complexity (i.e. new species) tend to appear in the fossil record suddenly and without any similar precursors. The Cambrian explosion is a prime example. 
Prediction of Design Met? (Conclusion)Yes. 

(3) Distribution of Molecular and Morphological Characteristics Similar parts found in different organisms. Many genes and functional parts not distributed in a manner predicted by ancestry, and are often found in clearly unrelated organisms. The "root" of the tree of life is a prime example. 
Prediction of Design Met? (Conclusion)Yes. 

(4) DNA Biochemical and Biological Functionality Increased knowledge of genetics has created a strong trend towards functionality for "junk-DNA." Examples include recently discovered functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. Examples of DNA of unknown function persist, but discovery of function may be expected (or lack of current function still explainable under a design paradigm). 
Prediction of Design Met? (Conclusion)Yes.



The proponent of natural mechanisms may use words like "incredulity" to make it seem that we are arguing about these things because we can't believe it. But the main point is that it has never been seen to happen. They are talking about speculation, based on .... guess what .... philosophical dogmatic naturalism. To them, there must be a natural explanation, no matter where the evidence points to.

God of the gaps is a comfortable way to try to criticize and reject an argument and avoid to address actually the issues raised. Opponents of ID resort to it all the time, even when a robust case is made, with clear and detailed science-based observation, prediction, experiment, and logical inference and conclusion.  The evidence for intelligent design has not been shrinking in the last two decades. It’s been growing, while the barriers to explain origins through naturalism have grown.  This is obvious in regard to all relevant issues:  the origin and fine-tuning of the universe,  of life, and biodiversity.


A short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45. 

Paul Davies once said;
How did stupid atoms spontaneously write their own software … ? Nobody knows …… there is no known law of physics able to create information from nothing.

Dembsky : We also know from broad and repeated experience that intelligent agents can and do produce information-rich systems: we have positive experience-based knowledge of a cause that is sufficient to generate new instructing complex information, namely, intelligence.  the design inference  does not constitute an argument from ignorance. Instead, it constitutes an "inference to the best explanation" based upon our best available knowledge.  It asserts the superior explanatory power of a proposed cause based upon its proven—its known—causal adequacy and  based upon a lack of demonstrated efficacy among the competing proposed causes.  The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection or luck/chance/probablity could theoretically form a new complex morphological feature like a  leg or a limb with the right size and form, and arrange to find out the right body location to grow them , but it could  also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism.  Nature would have to arrange almost an infinite number of trials and errors until getting a new positive arrangement. Since that would become a highly unlikely event, design is a better explanation. This situation becomes even more acentuated when natural selection is not a possible constrained since evolution depends on replication, which did not exist prior dna replication

Today, Darwinists level the same charge against the contemporary theory of intelligent design (ID). They insist that ID is just an argument from ignorance—plugging God into the gaps of our current scientific understanding. Darwinists have made many thoughtful arguments over the years, but this isn’t one of them. The theory of intelligent design holds that many things in nature carry a clear signature of design. The theory isn’t based on what scientists don’t know about nature but on what they do know. It’s built on a host of scientific discoveries in everything from biology to astronomy, and some of them are very recent discoveries.


If you were asked how much change do you have in your pockets. You can put your hand in your pocket, look to see how many coins are there. If there is no loose change, it is NOT an argument from ignorance to state, “Sorry, I don’t have any spare change.” You didn’t guess. You stuck your hands in your pockets and looked, and deduced the quantity to be zero. The same is true with inferences in regard of biology or biochemistry. After the search has taken place, the prediction that biochemical systems are unable to emerge by natural means is confirmed. Hence, there is no argument from ignorance.

In the design revolution, Dembski writes on page 220: 
So see that the argument from ignorance objection is not a magic wand for silencing intelligent design, let's begin with a reality check. When is the argument from ignorance objection raised against intelligent design, who exactly is being accused of being ignorant? Its natural to think that the ignorance here is on the part of design theorists, who want to attribute intelligent agency to biological systems. If only those poor design theorists understood biology better, those systems would readily submit to mechanistic explanation. Matter of fact IMHO is, that despite decades of research, the scientific community has been desperately and unsuccessfully tried to discover how such systems could have formed, what mechanism exactly was in charge. Who is ignorant here? The Scientific community as a whole. In fact, its safe to say that the biological community is clueless about the emergence of biological complexity. How so?

 Because the material mechanisms to which the biological community looks to explain biological complexity provide no clue for how those systems might realistically have come about. the problem, therefore, is not ignorance or personal incredulity, but global disciplinary failure, and gross theoretical inadequacy of Darwin's theory.  James Shapiro, molecular biologist at the University of Chicago, conceded that system that exhibits specified complexity are likely to be designed. Design theorists, in attributing design to systems that exhibit specified complexity (SC), are simply doing what scientists do generally, which is an attempt to formulate a causally adequate explanation for the phenomenon in question. To attribute specified complexity, and thereby design, to a biological system is to engage in an eliminative induction, a form of reasoning, used throughout the sciences. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false.
 ( Contrast this with Popperian falsification, where propositions are corroborated to the degree that they successfully withstand attempts to falsify them ) Provided the proposition, together with its competitors, form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. As Sherlock Holmes famous dictum says: when you have eliminated the impossible, whatever remains, however improbable, must be the truth. This is the ideal case, in which eliminative inductions, in fact, become deductions. The problem is that in practice we don't have a neat ordering of competitors that can then all be knocked down with a few straightforward and judicious blows. 

If naturalistic explanations of the origin of life are not convincing, why not look somewhere else ? 

http://reasonandscience.heavenforum.org/t1508-will-we-eventually-discover-a-naturalistic-explanation-for-first-life

If a certain line of reasoning is not persuasive or convincing, then why do atheists not change their mind because of it? The more evolution papers are published, the less likely the scenario becomes. Some assertions have even been falsified. We should consider the fact that modern biology may have reached its limits on several subjects of biology. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios,  or in a confession of ignorance.  Fact is  there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some technical details; it is a big conceptual gap.  The reach of the end of the road is evident in the matter of almost all major questions. The major questions of macro change and abiogenesis are very far from being clearly formulated, even understood,  and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be on sight. Isn't that a prima facie of a " evolution of the gap" argument? We don't know yet, therefore evolution and abiogenesis? That way, the God hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else?



ID is not a substitute for ignorance. If we don’t know the cause of something that does not mean it was designed. When we make design inferences—and all of us make them every day—we do so on the basis of evidence; the more evidence, the more reliable the design inference.

From Stephen Meyers book Signature in the cell :

In an explanatory context, arguments from ignorance have the  form:

Premise One: Cause X cannot produce or explain evidence E. Conclusion: Therefore, cause Y produced or explains E.

Critics of intelligent design claim that the argument for intelligent design takes this form as well. As one of my frequent debating partners, Michael Shermer, likes to argue, "Intelligent design argues that life is too specifically complex (complex structures like DNA) to have evolved by natural forces. Therefore, life must have been created by an
intelligent designer."  In short, critics claim that ID proponents argue as follows:

Premise One: Material causes cannot produce or explain specified information.
Conclusion: Therefore, an intelligent cause produced specified biological information.

If proponents of intelligent design were arguing in a preceding manner, they would be guilty of arguing from ignorance. But the argument  takes the following form:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example.  

Or to put it more formally, the case for intelligent design made here has the form:

Premise One: Causes A through X do not produce evidence E. Premise Two: Cause Y can and does produce E.
Conclusion: Y explains E better than A through X.

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. 


William Dembsky:
http://www.discovery.org/a/1256
The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability.Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.


Michael Behe’s testable predictions regarding Irreducible Complexity.
Molecular biologist Jonathan McLatchie wrote : An irreducibly complex system is one that (a) the removal of a protein renders the molecular machine inoperable, and (b) the biochemical structure has no stepwise evolutionary pathway.  Michael Behe further describes the condition:

“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.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March 2002.  Source: http://www.ideacenter.org/contentmgr/showdetails.php/id/840).

In other words, natural selection is not capable of selecting given mutations. But even let's argue that natural selection selects neutral ( not deteriorative mutations ) and fixes them into the population. In the case of the chlorophyll pathway, it had to specify the pathway of 17 intermediate steps, in case of heme 8. Not only had it to select the right highly specific pathway sequence ,  it had to have the enzymes readily available for recruitment, which in our case would not be possible, until the given enzymes had evolved as well with gene duplication , mutation, and natural selection, but if available, the enzymes had to be available all at the same time. Furthermore, the selected parts had all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly, at the time, they are needed. The enzymes must work in a coordinated, just the right way. One enzyme picking up the product of the previous step at the right place. Like in a factory production line, one worker handles the part, builds in or advances its construction by adding or mounting a part, and afterward handles it over to the next craftsman for the next manufacturing step. In order to do so, it must know where to handle it over and do it in a chronological sequenced way. In the case of your biosynthesis pathway,  all this must be previously be programmed in the genome, and happen like in robotics, in an automated way without external intervention, because previously programmed.

On the one side, you have an intelligent agent-based system of irreducible complexity of tight integrated, information-rich functional systems which have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed. And on the other side imagine a golfer, who has played a golf ball through a 12 hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes or rains or storms could produce the same result, given enough time. the chances against it however are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12 hole course.

http://www.ideacenter.org/contentmgr/showdetails.php/id/1181

Evolvability. Evolutionary biology’s preferred research strategy consists in taking distinct biological systems and finding similarities that might be the result of a common evolutionary ancestor. Intelligent design, by contrast, focuses on a different strategy, namely, taking individual biological systems and perturbing them (both intelligently and randomly) to see how much the systems can evolve. Within this latter research strategy, limitations on evolvability by material mechanisms constitute indirect confirmation of design.

The Argument of Ignorance Contention Against Intelligent Design Theory:

https://dennisdjones.wordpress.com/2011/04/06/the-argument-from-incredulity-contention-against-id-theory/

ID Theory makes no appeals to the unobservable, supernatural, paranormal, or anything that is metaphysical or outside the scope of science.
To FALSIFY Irreducible Complexity: Show: 1. The molecular machine still functions upon loss of a protein. OR, 2. The biochemical structure DOES have an evolutionary pathway.

According to the definition of irreducible complexity, the hypothesis can be falsified EITHER way, by (a) demonstrating the biochemical system still performs its original function upon the removal any gene that makes up its parts, or (b) showing that there are missing mutations that were skipped, i.e., there is no stepwise evolutionary pathway or precursor.  Irreducible complexity can still be falsified even if no evolutionary precursor is found because of the functionality qualifier.   In other words, the mere fact that there is no stepwise evolutionary pathway does not automatically mean that the system is irreducibly complex.

Those who object to irreducible complexity often raise the argument that the irreducible complexity hypothesis is based upon there being gaps or negative evidence.   Such critics claim that irreducible complexity is not based upon affirmative evidence, but on a lack of evidence, and as such, irreducible complexity is a gap argument, also known as an argument from ignorance.  However, this assertion that irreducible complexity is nothing other than a gap argument is false.

The reason why the irreducible complexity hypothesis is logically valid is that there is no attempt to base the prediction that certain biochemical molecular machinery are irreducibly complex based upon the absence of evidence.  If this were so, then the critics would be correct.  But, this is not the case.  Instead, the irreducible complexity hypothesis requires research, such as various procedures in molecular biology as (a) gene knockout, (b) reverse engineering, (c) examining homologous systems, and (d) sequencing the genome of the biochemical structure.  The gene knockout procedure was used by Scott Minnich in in 2004-2005 to show that the removal of any of the proteins of a bacterial flagellum will render that bacteria incapable of motility (can’t swim anymore).  Michael Behe also mentions (e) yet another way as to how testing irreducible complexity using gene knockout procedure might falsify the hypothesis here.

When the hypothesis of irreducible complexity is tested in the lab using any of the procedures directly noted above, an obviously thorough investigation is conducted that demonstrates evidence of absence. There is a huge difference between absence of evidence and evidence of absence.  One is a logical fallacy while the other is an empirically generated result, a scientifically valid quantity that is concluded upon a thorough examination.  So, depending upon the analysis, you can prove a negative.

Evidence of Absence

Here’s an excellent example as to why irreducible complexity is a logically valid, and not an argument from ignorance.  If I ask you if you have a change for a dollar, you could say, “Sorry, I don’t have any change.” If you make a diligent search in your pockets to discover there are indeed no coins anywhere to be found on your person, then you have affirmatively proven a negative that your pockets were empty of any loose change. Confirming that you had not changed in your pockets was not an argument from ignorance because you conducted a thorough examination and found it to be an affirmatively true statement.

The term, irreducible complexity, was coined by Michael Behe in his book, “Darwin’s Black Box” (1996).  In that book, Behe predicted that certain biochemical systems would be found to be irreducibly complex.  Those specific systems were (a) the bacterial flagellum, (b) cilium, (c) blood-clotting cascade, and (d) immune system.   It’s not 2013 at the time of writing this essay.  For 17 years, the research has been conducted, and the flagellum has been shown to be irreducibly complex. It’s been thoroughly researched, reverse engineered, and its genome sequenced. It’s is a scientific fact that the flagellum has no precursor. That’s not a guess. It is not stated as ignorance from taking some wild uneducated guess. It’s not a tossing one’s hands up in the air saying, “I give up.” It is a scientific conclusion based upon a thorough examination.

Again, if you were asked how much change do you have in your pockets. You can put your hand in your pocket, look to see how many coins are there. If there is no loose change, it is NOT an argument from ignorance to state, “Sorry, I don’t have any spare change.” You didn’t guess. You stuck your hands in your pockets and looked, and scientifically deduced the quantity to be zero. The same is true with inferences in regard of biology or biochemistry. After the search has taken place, the prediction that biochemical systems are unable to emerge by natural means is confirmed. Hence, there is no argument from ignorance.

The accusation that irreducible complexity is an argument from ignorance essentially suggests a surrender and abandonment of ever attempting to empirically determine whether the prediction is scientifically correct.  It’s absurd for anyone to suggest that ID scientists are not interested in finding Darwinian mechanisms responsible for the evolution of an irreducibly complex biochemical structure. If you lost money in your wallet, it would be ridiculous for someone to accuse you of rejecting any interest in recovering your money. That’s essentially what is being claimed when someone draws the argument from ignorance accusation. The fact is you know you did look (you might have turned your house upside down looking), and know for a fact that the money is missing. It doesn’t mean that you might still find it (the premise is still falsifiable). But, a thorough examination took place, and you determined the money is gone.

The Logic Fallacy Has No Bearing On Falsifiability:

Here’s yet another example as to why irreducible complexity is scientifically falsifiable, and therefore not an argument from ignorance logic fallacy.  If someone was correct in asserting the argument from incredulity fallacy, then they have eliminated all science. Newton’s law of gravity was an argument from ignorance because he didn’t know anything more than what he had discovered. It was later falsified by Einstein. So, according to this flawed logic, Einstein’s theory of relativity is an argument from ignorance because there might be someone in the future who will falsify it with a Theory of Everything.

Whether a hypothesis passes the Argument of Ignorance logic criterion, or not, the argument is an entirely philosophical one, much like how a mathematical argument might be asserted.  If the argument from ignorance were applied in peer-review to all science papers submitted for publication, the science journals would be near empty of any documents to reference.  Science is not based upon philosophical objections and arguments.  Science is based upon the definition of science, which is observation, falsifiable hypothesis, experimentation, results and conclusion. It is the fact that these methodical elements are in place which makes a science indeed empirical science.

Whether a scientific hypothesis is falsifiable is not affected by philosophical arguments based upon logic fallacies.   Irreducible Complexity is very much falsifiable based upon its definition.  The argument from ignorance only attacks the significance of the results and conclusion of research in irreducible complexity; it doesn’t deter irreducible complexity from being falsifiable.  In fact, the argument from ignorance objection actually emphasizes just the opposite, that irreducible complexity might be falsified tomorrow because it inherently argues the optimism that its just a matter of time that an evolutionary pathway will be discovered in future research.  This is not a bad thing; the fact that irreducible complexity is falsifiable is a good thing.  That testability and obtainable goalpost is what you want in a scientific hypothesis.

One of the most common objections of atheists is that arguments provided by theists are based on gaps of knowledge and ignorance. Each of following sentences are based on positive premises. Not ignorance. 

The mind predates matter. Matter cannot produce consciousness
A Bang needs a Banger
The laws of nature require a Law-giver
Fine tuning needs a Fine-tuner
Life can come only from Life
Only intelligence can build complex factories and machines
Coded Information has always a mental origin
Language is always a mental invention
Logic and reason come only from rational minds
Free will can have its origin only in consciousness
Objective morals exist. Therefore there is a Moral-Giver

1) http://intelligentreasoning.blogspot.com.br/2007/10/intelligent-design-design-hypothesis.html



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From Stephen Meyers book Signature in the cell :

Argument from Ignorance?

http://reasonandscience.heavenforum.org/t1983-is-irreducible-complexity-merely-an-argument-from-ignorance?highlight=ignorance

Over the years, I have participated in many debates about the theory of intelligent design at scientific conferences, on university campuses, and on television and radio programs. In nearly every debate, my debate partner has claimed that the case for intelligent design constitutes an argument from ignorance.

Arguments from ignorance occur when evidence against a proposition is offered as the sole (and conclusive) grounds for accepting some alternative proposition.

Critics of intelligent design often assert that the case for intelligent design commits this
fallacy.

1 They claim that design advocates use our present ignorance of any natural or material cause of specified information as the sole basis for inferring an intelligent cause for the origin of biological information. They accuse ID advocates of arguing for intelligent design based only upon evidence against the adequacy of various natural causes. Since we don't yet know how biological information could have arisen, we invoke the mysterious notion of intelligent design. In this view, intelligent design functions not as an explanation, but as a fig leaf for ignorance.

The inference to design as developed here does not commit this fallacy. True, some of the previous chapters of this book do argue that, at present, all types of material causes and mechanisms fail to account for the origin of biological information from a prebiotic state. And clearly this lack of knowledge of any adequate material cause does provide part of the grounds for inferring design from information in the cell, although it is probably more accurate to characterize this supposed "absence of knowledge" as knowledge of absence, since it derives from a thorough search for alternative materialistic causes and a thorough evaluation of the results of numerous experiments performed over several decades.

In any case, the inadequacy of proposed materialistic causes forms only part of the basis of the argument for intelligent design. We also know from broad and repeated experience that intelligent agents can and do produce information-rich systems: we have positive experience-based knowledge of a cause that is sufficient to generate new specified information, namely, intelligence. We are not ignorant of how information arises. We know from experience that conscious intelligent agents can create informational sequences and systems. To quote Quastler again, "The creation of new information is habitually associated with conscious activity."2 Experience teaches that whenever large amounts of specified complexity or information are present in an artifact or entity whose causal story is known, invariably creative intelligence—intelligent design—played a role in the origin of that entity. Thus, when we encounter such information in the large biological molecules needed for life, we may infer—based on our knowledge of

established cause-and-effect relationships—that an intelligent cause operated in the past
to produce the specified information necessary to the origin of life.

For this reason, the design inference defended here does not constitute an argument from ignorance. Instead, it constitutes an "inference to the best explanation" based upon our best available knowledge. To establish an explanation as best, a historical scientist must cite positive evidence for the causal adequacy of a proposed cause. Indeed, unlike an argument from ignorance, an inference to the best explanation does not assert the adequacy of one causal explanation merely on the basis of the inadequacy of some other causal explanation. Instead, it asserts the superior explanatory power of a proposed cause based upon its proven—its known—causal adequacy and
based upon a lack of demonstrated efficacy among the competing proposed causes.


we know from ordinary experience as well as from the results of scientific experiments and computer simulations that intelligent agents do produce large amounts of specified information. Since I had previously shown via a thorough search that no known material process produces this effect, I argued that we can infer design as the best explanation for the origin of information in the cell. The inference to design, therefore, depends on present knowledge of the demonstrated causal powers of material entities and processes (inadequate) and intelligence (adequate). It no more constitutes an argument from ignorance than any other well-grounded inference in geology, archaeology, or paleontology—where present knowledge of cause-and-effect relationships guides the inferences that scientists make about the causes of events in the past.

Formulated as an inference to the best explanation, the argument for design from biological information exemplifies the standard uniformitarian canons of method employed within the historical sciences. The principle of uniformitarianism states that "the present is the key to the past." In particular, it specifies that our knowledge of present cause-and-effect relationships should govern how we assess the plausibility of inferences we make about the cause of events in the remote past. Determining which, among a set of competing explanations, constitutes the best depends on knowledge of the causal powers of the competing explanatory entities, knowledge that we acquire through our repeated observation and experience of the cause-and-effect patterns of the world.4 Such knowledge, not ignorance, undergirds the inference to intelligent design from the specified information in DNA.

Arguments from ignorance make an obvious logical error. They omit a necessary kind of premise, a premise providing positive support for the conclusion, not just negative evidence against an alternative conclusion. The case for intelligent design as an inference to the best explanation does not omit that necessary type of premise. Thus, it does not commit the fallacy.

Let's take a closer look. In an explanatory context, arguments from ignorance have the
form:

Premise One: Cause X cannot produce or explain evidence E. Conclusion: Therefore, cause Y produced or explains E.

Critics of intelligent design claim that the argument for intelligent design takes this form as well. As one of my frequent debating partners, Michael Shermer, likes to argue, "Intelligent design argues that life is too specifically complex (complex structures like DNA) to have evolved by natural forces. Therefore, life must have been created by an
intelligent designer."  In short, critics claim that ID proponents argue as follows:


Premise One: Material causes cannot produce or explain specified information.
Conclusion: Therefore, an intelligent cause produced specified biological information.


If proponents of intelligent design were arguing in the preceding manner, they would be guilty of arguing from ignorance. But the argument  takes the following form:


Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.


Or to put it more formally, the case for intelligent design made here has the form:


Premise One: Causes A through X do not produce evidence E. Premise Two: Cause Y can and does produce E.
Conclusion: Y explains E better than A through X.


In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy of arguing from ignorance. It's really as simple as that.



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Is intelligent design generally, and  irreducible complexity particularly, a mere argument of ignorance ?

http://reasonandscience.heavenforum.org/t1983-is-irreducible-complexity-merely-an-argument-from-ignorance?highlight=ignorance

According to Wiki: Argument from ignorance , also known as appeal to ignorance (in which ignorance stands for "lack of evidence to the contrary"),  asserts that a proposition is true because it has not yet been proven false . According to Rationalwiki The concept of irreducible complexity is based entirely around this idea of personal incredulity. One person (Michael Behe) cannot see how something evolved naturally, therefore it can't possibly evolve naturally. Another example is : You can’t prove that there aren’t Martians living in caves under the surface of Mars, so it is reasonable for me to believe there are.

ID Theory inferes that a intelligence must be involved for the creation of  irreducible and interdependent complex biological systems,  organelles and body parts, as well as coded, specified, complex information stored in  DNA. It does not however point out who that agent might be, if natural , or supernatural.

ID predicts  irreducible complexity and interdependence  in molecular machines and whole biological systems. The prediction can be falsified , showing that a stepwise, gradual change and increase of complexity can be achieved through natural biochemical interactions, darwinian evolution, and eventually other natural mechanisms, where no intelligence is involved, and furthermore that given biochemical structure can still keep the same function, when reduced of  any component and part, andany gene that encodes given part.

Irreducible complexity is not based  on a negative, namely that there is no evidence for a naturalistic pathway. Rather than that, it makes a positive claim, which can be falsified, upon :  (a) gene knockout, (b) reverse engineering, (c) examining homologous systems, and (d) sequencing the genome of the biochemical structure. ( Dennis Jones ) Gene knockout has been done several times, providing evidence that the organism was unable to replace given gene or protein by natural means. 1 The absence of evidence that evolution is not capable to replace given part is empirical evidence, that falsifies the claim of the ToE. Its therefore not justified to claim the inference is a argument of ignorance. Quit the contrary is the case. As for example, if i ask you : can you change a us$100 bill ? and you answer: sorry, i have no smaller bills. You open your wallet, and and its confirmed, no change in your wallet, then you have proven that you have indeed no smaller bills. You have proven a negative, which is not a argument of ignorance, since you checked and got a empirical proof.

Ifs a fact that i have presented inumerous examples of irreducible and interdependent system  during several years, beside the ones well known and widely propagated by Behe, the Discovery Institute et al, as of the biosynthesis pathway of chlorophyll, Heme, the signal transduction pathway in the eye, DNA, the Cell, human body parts, as the circulatory system, nitrogenase, the ribosome, chaperones etc., and they have shown to be IC until now. These systems do have no precursor. Many enzymes involved in the process have no know different function, and could not have been co-opted at other places. Thats a well founded scientific conclusion. And the hypothesis and theory can be falsified. And some examples are so patently obvious, that there is no need to make scientific experiments to understand that ic is granted. Take photosynthesis for example. Take off chlorophyll, and no light is captures anymore, and the whole process ceases to exist. Take away the blood, and the circulatory system ceases. Take away any one of the 17 enzymes required in the biosynthesis pathway of chlorophyll, and the end product is not synthesized anymore. Neither could the proteins,  organelles and enzymes have any function by their own. So why in the first place would the arise at all ?

Stephen Meyer puts it that way :

Let's take a closer look.

In an explanatory context, arguments from ignorance have the form:

Premise One: Cause X cannot produce or explain evidence E. Conclusion: Therefore, cause Y produced or explains E.

Critics of intelligent design claim that the argument for intelligent design takes this form as well. As one of my frequent debating partners, Michael Shermer, likes to argue, "Intelligent design argues that life is too specifically complex (complex structures like DNA) to have evolved by natural forces. Therefore, life must have been created by an
intelligent designer."  In short, critics claim that ID proponents argue as follows:

Premise One: Material causes cannot produce or explain specified information.
Conclusion: Therefore, an intelligent cause produced specified biological information.

If proponents of intelligent design were arguing in the preceding manner, they would be guilty of arguing from ignorance. But the argument  takes the following form:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example.  

Or to put it more formally, the case for intelligent design made here has the form:

Premise One: Causes A through X do not produce evidence E. Premise Two: Cause Y can and does produce E.
Conclusion: Y explains E better than A through X.


In addition to a premise about how material causes lack demonstrated causal adequacy, the argument for intelligent design as the best explanation also affirms the demonstrated causal adequacy of an alternative cause, namely, intelligence. This argument does not omit a premise providing positive evidence or reasons for preferring an alternative cause or proposition. Instead, it specifically includes such a premise. Therefore, it does not commit the informal fallacy of arguing from ignorance. It's really as simple as that.

1) http://reasonandscience.heavenforum.org/t1995-biologic-institute-s-groundbreaking-peer-reviewed-science-has-now-demonstrated-the-implausibility-of-evolving-new-proteins



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http://www.evolutionnews.org/2006/01/wolfsons_argument_from_ignoran001847.html

Of course, many scientists have argued that to infer design gives up on science. They say that inferring design constitutes an argument from scientific ignorance--a "God of the Gaps" fallacy. Since science doesn't yet know how biological information could have arisen, design theorists invoke a mysterious notion--intelligent design--to fill a gap in scientific knowledge. Many philosophers, for their part, resist reconsidering design, because they assume that Hume's objections to analogical reasoning in classical design arguments still have force. Yet developments in philosophy of science and the information sciences provide the grounds for a decisive refutation of both these objections. First, contemporary design theory does not constitute an argument from ignorance. Design theorists infer design not just because natural processes cannot explain the origin of biological systems, but because these systems manifest the distinctive hallmarks of intelligently designed systems--that is, they possess features that in any other realm of experience would trigger the recognition of an intelligent cause. For example, in his book Darwin's Black Box (1996), Michael Behe has inferred design not only because the gradualistic mechanism of natural selection cannot produce "irreducibly complex" systems, but also because in our experience "irreducible complexity" is a feature of systems known to have been intelligently designed. That is, whenever we see systems that have the feature of irreducible complexity and we know the causal story about how such systems originated, invariably "intelligent design" played a role in the origin of such systems. Thus, Behe infers intelligent design as the best explanation for the origin of irreducible complexity in cellular molecular motors, for example, based upon what we know, not what we don't know, about the causal powers of nature and intelligent agents, respectively.

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When we read the typical newspaper article about intelligent design, we get the impression that the design theorist is an unimaginative fellow thinking,

Gee, I can’t see how an eye or a bat or a butterfly could have randomly evolved. They’re just too darned complicated. Heck, that right there proves evolution is kooky and somebody designed ’em.

Critics of ID are good at showing just how stupid such an argument is. But if we look closer, we’ll notice the straw sticking out of the spot just below the argument’s neck where the clip-on tie has come loose. This is what logicians call a straw man. It’s not the real ID argument. Instead, the critics go after a straw man of the real argument, presumably because it’s easier to knock down. The danger, of course, is that the audience may look
too closely and discover the charade and realize that the actual theory of intelligent design is something else entirely.

To remain open to the possibility of design is the call of the intelligent design movement. It’s a call to apply consistently the methods used in two types of science: science concerned with information, and science that looks for the past causes of present clues. Many special sciences already employ the concept of design and would be inconceivable without it. These include artificial intelligence, the science of code making and code breaking (cryptography), and the science of random number generation (used for video games and many other things). Or take criminal investigation. Detectives employ sophisticated technology, careful observation and logical analysis to discover the best explanation for something that happened in the past. They find a body and ask, Did this person die from an illness, from an accident or from foul play? That is, was the person killed by some unintended event or by design? Was the person murdered? Unless they have been paid off by someone, detectives in such cases don’t rule out death by design before they’ve studied the scene. They keep an open mind and follow the clues in search of the best explanation. Design theorists do the same thing. We look at the finely tuned constants of nature, the sophisticated machinery inside living cells or the genetic information needed to build those machines, and we ask,

Did these things arise by accident or by design? Then we follow the evidence.

ID offers abundant positive evidence that some patterns in nature are the product of a creative intelligence.

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The Irrationality of the God-of-the-Gaps Atheist Assertion
------------------------------------------------------------------

P1. The God-of-the-Gaps Atheist assertion is the assertion that ANY inference to God, or ANY explanation of ANY data that reasonably points to the existence of God is a mere God-of-the-Gaps and is therefore somehow invalid or irrational as a result.

P2. The Epistemology of such a God-of-the-Gaps Atheist-Assertion is Intellectually Dishonest and a FRAUD. See below.

P3. ALL arguments are arguments of the gaps. They try to explain (or fill) a gap in our understanding.

P4. ALL postulated entities are entites of the gaps. The postulation tries to explain (or fill) a gap in our understanding.

P5. ALL Explanations are explanations of the gaps. The explanation tries to explain (or fill) a gap in our understanding.

............................................
C1. So, by the very nature of Epistemology, ALL arguments, ALL postulated entities, ALL explanations are by necessity Fillers-of-the-gaps.

C2. So it is completely IRRATIONAL and Epistemologically Irresponsible to NOT permit a given explanation as an Explanation of the gaps (or to NOT permit God as an explanation of a given set of data).
............................................

P6. So the assertion that we can postulate ANY argument or ANY entity as long is it is NOT God is a completely IRRATIONAL assertion.

P7. Such an assertion (P6) is a mere irrational dogmatic assertion of Atheist Faith. The insistence upon an Atheistic Metaphysical Interpretive Paradigm if you will. Such an insistence is dogmatic and IRRATIONAL.

P8. Such an assertion (P6) is simply Intellectually Dishonest anti-God bigotry and chauvinism.

P9. IF such a ground-rule were allowed in other fields of knowledge (i.e., between hypothesis A and B, hypothesis B is ruled out by definition based on the alelged rule that any appeal to hypothesis B is a B-of-the-gaps and therefore ONLY appeals to hypothesis-A are permitted), there would be NO possibility of coming to truth.

P10. Similarly, if the existence of God is ruled out apriori (with such insane and irrational assertions as B-of-the-gaps are not permitted, or God-of-the-gaps are not permitted, which means that God is NOT permitted as an explanation for ANY data, no matter how reasonable), then there is NO possibility of coming to truth about the existence of God.

In addition.

P11. ALL of our knowledge about reality is Abductive in Nature (apart from the Descartes Minimal Set).

P12. The existence of (a) the Physical Universe, (b) other minds, (c) yesterday --- NONE of these can be absolutely proved. ALL of them are Abductive Inferences based on Abductive evidence (data about reality that is consistent with a given model).

P13. The existence of God is a similar Abductive inference based on the evidence (a) Epistemological, (b) Philosophical, (c) Scientific, (d) Testimonial, (e) personal experience with answered prayers, and (f) personal mystical direct experience of God.
.........................................................
C3. So the atheist assertion that all evidence (or explanations) that point to God are INVALID as being God-of-the-gaps appeals is IRRATIONAL, and Epistemologically Irresponsible.
.........................................................

P14. In addition, the argument from Complex Independently-Specified Functional Information to Intelligent design is NOT a negative God-of-the-gaps argument.

P15. Complex Independently-Specified Functional Information is actually POSITIVE Evidence for Intelligent design. See appendix below.

-------------------------------------------------------------------------------
APPENDIX
-------------------------------------------------------------------------------

Complex Independently-Specified Functional Information as an Abductive Pointer to Intelligent Design of the Biosphere
-----------------------------------------------------------------

Argument:

P1. What is in question is whether Darwinian Non-Purposive (DNP) Evolution (Random-Chance + Natural Selection) can create Complex Independently-Specified Functional Information.

P2. The assertion that DNP evolution can create Complex Independently-Specified Functional Information is merely that -- a Mere Assertion with NO experimental proof that it is true.

P3. There is no independently (independent of DNP-evolution) known non-ID mechanism that can create Complex Independently-Specified Functional Information.

P4. The ONLY source that we know of (independent of what is in question, DNP evolution) that can create Complex Independently-Specified Functional Information is Intelligent Design.

............................................................................
Conclusion
............................................................................

C. Therefore, it is a Reasonable and Rational Abductive Inference that it took Intelligent Design to create the Complex Independently-Specified Functional Information that we see throughout the Biosphere.

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