Yet more on reality's antidarwinian bias

Missing the Goal: Realistic Mutation Rates Stop Evolutionary Algorithms
Ann Gauger November 17, 2015 7:29 AM

Winston Ewert of Biologic Institute has just published a new article in the peer-reviewed journal BIO-Complexity ("Overabundant mutations help potentiate evolution: The effect of biologically realistic mutation rates on computer models of evolution").

He and his colleagues have been engaged in a series of critiques of evolutionary algorithms for the last several years. In case you don't know what an evolutionary algorithm is, it's a computer model that seeks to represent evolution in some way, so that mutation and natural selection can be tested for their ability to produce meaningful change.

The advantage of these computer simulations is that they can be run many, many times and thus approximate the long time necessary for biological evolution. The disadvantage is that they do not replicate true biological evolutionary processes, but use "analogous" algorithms. Typically these models, such as Ev and Avida, are purported to solve complex problems.

Yet Ewert and his colleagues have shown that in every case the necessary information for the models to find their targets was smuggled in, whether intentionally or not, by the respective programmers. You can read some of Ewert and coauthors' critiques here, here, and here.

Here is the abstract of the new paper:

Various existing computer models of evolution attempt to demonstrate the efficacy of Darwinian evolution by solving simple problems. These typically use per-nucleotide (or nearest analogue) mutation rates orders of magnitude higher than biological rates. This paper compares models using typical rates for genetic algorithms with the same models using a realistic mutation rate. It finds that the models with the realistic mutation rates lose the ability to solve the simple problems. This is shown to be the result of the difficulty of evolving mutations that only provide a benefit in combination with other mutations.

Ewert shows that even taking the models as they are, when they are tested using realistic scenarios they fail to accomplish their goals. In fact, they accomplish little beyond their starting positions. He determines the reason for this failure -- the models can only go as far as one step will take them. They can't evolve anything that requires two or more mutations, unless mutation rates are unrealistically high.


This is a showstopper, since making just about anything new requires more than one mutation. Take a look..

Darwinism Vs. the real world XX

How Clotting Factors Form a Fibrin Clot, Completing Hemostasis
Howard Glicksman November 17, 2015 3:04 AM

Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News & Views is delighted to present this series, "The Designed Body."  Dr. Glicksman practices palliative medicine for a hospice organization.


To follow the laws of nature the cardiovascular system must pump enough blood with enough pressure throughout the body to provide its trillions of cells with what they need to live, grow, and work properly. But life is a dynamic process, for us as for our earliest ancestors. When we do things like run, jump, or climb, the effects of these same laws can result in injury to our blood vessels followed by bleeding when we trip and fall or bump and hurt ourselves. Clinical experience shows that, depending on location and severity, if the body can't stop the bleeding fast enough it runs the risk of serious debility and even death. Thus, the body had to develop a mechanism to prevent disabling and life-threatening blood loss from blood vessel injury. This process is called hemostasis.

As I showed in a previous article, hemostasis involves mainly three almost simultaneous actions that take place upon blood vessel injury to stop the bleeding and allow healing to take place. These are; vasoconstriction, platelet aggregation, and activation of the clotting factors. But when it comes to preventing significant blood loss from blood vessel injury, the body faces another dilemma. A well-placed clot in a major blood vessel like an artery supplying blood to the brain, or the heart, or the lungs, can result in permanent debility and even instant death. In other words, hemostasis and the clots it forms must turn on only when it's actually needed and must turn off and stay off when it's not.

My last article looked at the role the injured blood vessel and the platelets play in helping to stop bleeding. I noted that normally the tissue that lines the inside of the blood vessel (endothelium) provides a chemical environment to maintain blood flow by keeping the muscle surrounding the blood vessel relatively relaxed and preventing the platelets from sticking to it and each other. Blood vessel injury and endothelial damage disrupt this chemical milieu, which triggers vasoconstriction and platelet aggregation to form a soft plug to fill the defect. This may be enough to stop the bleeding for some minor injuries, but many others require a stronger substance to fill the gap permanently. Let's consider how activation of the clotting factors to form a fibrin clot completes the process of hemostasis.

The final products from activation of the clotting factors are long protein strands called fibrin. These fibrin strands consist of small identical fibrin molecules that are able to chemically bond with each other to form very large molecular chains. Like thousands of sticky threads, these long strands of fibrin attach to the platelet plug and wrap around it to form a molecular meshwork that entraps red blood cells and plasma to form a fibrin clot. Once the fibrin clot is large and strong enough to fill the defect in the blood vessel wall, the bleeding stops.

But where do the fibrin strands come from? After all, the muscle around the blood vessel is already in place, ready to contract and close it down to prevent further blood loss and help clot formation when the time is right. And the platelets are already in the blood that flows past the injured site, ready to stick to the vessel wall and to each other to form a plug when called for. So what about fibrin? Think about it! If long sticky fibrin strands were always present throughout the bloodstream, they would tend to attach to the walls of small blood vessels and block the flow of blood, which would result in multi-system organ failure and death. So, fibrin must somehow be in the blood and remain inactive until the right time.

In fact, the liver produces a protein called fibrinogen, also known as (clotting) Factor I. Fibrinogen remains in solution being prevented from becoming fibrin and joining together to form large insoluble strands by specific chemical groups at each end of the molecule. Platelets have receptors for fibrinogen and when activated, thousands of fibrinogen molecules attach to them. What causes the conversion of fibrinogen to fibrin and the formation of clot forming strands of fibrin is the presence of an enzyme called thrombin.

Thrombin removes the chemical groups at the ends of the fibrinogen molecule, thereby exposing bonding sites that allow the fibrin molecules to join together end to end to form the long insoluble strands needed for clotting. Thrombin also activates Factor XIII, which allows the fibrin strands to link up across each other as well, which significantly strengthens the clot.

But where does thrombin come from? Again, think about it! If thrombin quickly converts soluble fibrinogen into long insoluble strands of fibrin, resulting in clot formation, then if it were always present throughout the bloodstream, that would result in generalized clotting, multi-system organ failure, and death. In fact, the liver produces another protein called prothrombin, also known as (clotting) Factor II. Under the right set of circumstances an enzyme called prothrombinase forms and breaks two chemical bonds in prothrombin to convert it to thrombin which then goes on to convert fibrinogen to fibrin to form a fibrin clot.

But where does prothrombinase come from? Think about that too! If prothrombinase quickly converts prothrombin to thrombin which then quickly converts fibrinogen to fibrin, then if it were always present throughout the bloodstream that would result in generalized clotting, multi-system organ failure, and death. In fact, just as vasoconstriction and platelet aggregation take place due to changes in the chemical environment brought on by injury to the blood vessel, so too does activation of the clotting factors. Medical science has determined that there are two different pathways involved in the activation of the clotting factors to form prothrombinase.

One, called the Tissue Factor (extrinsic) pathway, works very quickly. With vessel damage, the blood, containing inactive Factor VII, comes in contact with Tissue Factor, a protein on the surface of the tissue that supports the blood vessel, and activates it into a protease, an enzyme that can break the chemical bonds within proteins. Activated Factor VII then breaks chemical bonds in Factor X to activate it, and when it joins to activated Factor V it forms prothrombinase.

The slower pathway, called the contact activation (intrinsic) pathway, takes place due to the direct contact of blood with the damaged tissue and involves other clotting factors. The contact first activates Factor XII, which becomes a protease that breaks chemical bonds to activate Factor XI. Activated Factor XI is also a protease that then activates Factor IX. Activated Factor IX, with the help of Factor VIII, then activates Factor X, which as noted above, joins with activated Factor V to form prothrombinase.

So, after blood vessel injury, whether prothrombinase comes about from either pathway, it then activates prothrombin into thrombin which then activates fibrinogen into fibrinand clot formation takes place. All of this together is known as the coagulation cascade.

It is the liver that produces most of the clotting factors. In fact, the total absence of fibrinogen, or prothrombin, or Tissue Factor, or Factor V, or Factor VII, or Factor VIII, or Factor IX, or Factor X, or Factor XI, or Factor XIII would have made it impossible for our earliest ancestors to have lived long enough to reproduce. Evolutionary biologists seem to think that just showing how each of these factors could have come about from some other protein by a natural process (such as gene duplication) is enough to prove that the coagulation cascade itself came about solely by chance and the laws of nature.

But one can see that since each of these ten factors must be present so the two different pathways can work properly, this is preposterous notion. When comparing invertebrates to vertebrates, they speculate how intermediate organisms must have had intermediate systems with fewer clotting factors without accounting for the extremely high improbability of each new protein fitting perfectly into the right pathway. Since invertebrate circulations are low pressure systems they can seal their injuries by using a softer gel-like material, much like the platelet plugs, whereas for the high pressure systems of the vertebrates, it must have been serendipity that the final product (fibrin) had the exact physical properties to do the job.

Nowhere does evolutionary biology even mention how the high-pressure circulatory system of the vertebrate, which required this more sophisticated clotting mechanism in the first place, could have gradually developed within intermediate forms while the coagulation cascade was evolving as well.


But we're not finished yet. Remember, to keep the blood flowing throughout the circulatory system, the body has to make sure that hemostasis only turns on when it's actually needed and turns off and stays off when it's not. Failure in this respect can lead to widespread clotting, multi-system organ failure, and death. My last article showed that it is the endothelium that provides a chemical environment to prevent the activation of vasoconstriction and platelet aggregation, the first two components of hemostasis. Next time we'll look at what it takes to prevent activation of the clotting factors so the body can control the intricate process of hemostasis.

Disagreeably agreeing?

REC Becomes a Design Proponent
November 16, 2015 Posted by Barry Arrington under Intelligent Design

In the comment thread to a recent post we were discussing the following biological design inference Dr. Moran had made:

Moran:

Craig Venter and his colleagues constructed a synthetic genome and inserted it into a cell. The DNA determined the structure and properties of the organism that grew and after many subsequent generations we have a new species that behaves exactly like it was supposed to based on the genes that the scientists built.

Barry:

Now Dr. Moran, suppose that new species escaped the lab and was captured by a researcher who had no idea about Venter’s work.  Suppose further that researcher concluded that the genome of the creature had been intelligently designed.  Would that researcher’s design inference be the true and best explanation of the creature’s genome’s provenance?

Moran:

The answer is “yes,” the researcher correctly observed that the genome of the synthetic organism is nothing like the genomes of real species. It lacks pseudogenes, transposons, and any trace of junk DNA and the sequence of its genes and regulatory regions is far too perfect to have evolved naturally.

Long time ID critic REC joined the discussion.  REC agreed that Dr. Moran’s design inference was valid.  I decided to take this opportunity to ask REC how he would respond to many of the typical objections to biological design inferences, and I asked him this series of questions:

Suppose someone pushed back at you and said, “REC, your design inference is a scientific show stopper. You have committed the designer-of-the-gaps fallacy. All scientific claims must employ methodological naturalism, and you violate the principle of methodological naturalism when you make a design inference in biology. Besides all that, it all just a cop out unless you can tell me who designed the designer.”  What would you say?

REC responded that the objections could be valid against certain design inferences, but for reasons he did not explain they were “obviously invalid” against his design inference (which he had made based on the scenario provided by Dr. Moran).

I thought this was more than a little hypocritical and thought that he would back off this line if I pointed the hypocrisy out to him, so I provided a summary of his argument that I thought would have made the hypocrisy obvious:

Barry:

Translation: I accept the indicia of design that I accept and I reject those I reject, for my own idiosyncratic reasons. Therefore, the objections are invalid with respect to my design inference, because my design inference is a good one, and yours is not.  Does that pretty much capture it REC?

I was wrong when I assumed REC would walk back his hypocrisy when it was pointed out to him.  Instead, he doubled down:

REC:

“Therefore, the objections are invalid with respect to my design inference, because my design inference is a good one, and yours is not.”

Correct, except that you haven’t even stated your design inference in this thread. I do feel my statements regarding the human-designed synthetic genome are valid and well evidenced. I don’t think any ID inference comes even close.

Shouldn’t we evaluate design inferences based on their validity and the evidence supporting them? Isn’t it illogical and absurd to say ALL design inferences are valid because ONE design inference is?

Let’s explore what is going on here.  First, we have made significant progress.  Notice what Dr. Moran did:

He identified certain indicia of design in the genome of an organism.

He stated that when these indicia of design are present, “design” is the best explanation of the provenance of the features of the genome under consideration.

He went one step further and excluded natural causes as a likely cause.

This is the general approach to biological design detection advocated by ID proponents for the last two decades.  In other words, Dr. Moran admitted that the general approach and methodology of biological design detection advocated by proponents of ID theory is valid.

THIS IS HUGE!

Professor of biochemistry Dr. Laurence A. Moran is an arch-atheist, materialist, super-advocate of modern evolutionary theory and one of the most prominent critics of design theory on the planet.  If even he agrees that the general methodology advocated by ID proponents can lead to a valid design inference, the matter seems to be settled.

We have come to the point where even our most vociferous critics agree that ID proponents’ general methodology is valid.  The dispute is no longer whether ID theory generally is valid; the only dispute is whether particular design inferences are valid.

Which brings us to REC.  The point of the “typical objections” I brought to REC’s attention is that if they are valid with respect to any design inference, they are just as valid against his particular design inference.

For example, consider this typical objection:  “All scientific claims must employ methodological naturalism, and you violate the principle of methodological naturalism when you make a design inference in biology.”

If that objection is valid (it is not, but set that aside for now), it is just as valid against REC’s and Dr. Moran’s design inferences as it is against any other design inference.

The point sailed right over REC’s head.  He responded that the objections were not valid as to his design inference, because his design inference (opposed to ID’s design inferences) was “valid and well evidenced.”

But that is exactly what ID proponents have been saying for decades REC!  We have been saying all along that the various “typical objections” are invalid if the evidence leads to a design inference.

REC, the only difference between you and us is that you are persuaded by the evidence in a particular case and not in our case.  But you are missing the point.  If what is important is the EVIDENCE, then th “typical objections” lose all force all the time.

In other words, the objection “all scientific claims must employ methodological naturalism” is invalid in principle, not in application, if it is even possible to make a valid design inference based on the EVIDENCE.

You agree with us that it is the EVIDENCE that is important, and objections thrown up for the purpose of ruling that evidence out of court before it is even considered are invalid.

REC, welcome to the design movement.

Teliophobia?

Fear of Intelligent Design Prevents Some Biologists from Accepting ENCODE's Results
Casey Luskin November 16, 2015 3:11 AM

Evolutionists who accept ENCODE's results have tried to comprehend why other biologists steadfastly challenge the project's experimentally demonstrated conclusions. Many have suggested that a major force driving anti-ENCODE attitudes is fear of lending credence to intelligent design.

In his retrospective on ENCODE in Nature, Philip Ball acknowledges that there is an "anxiety that admitting any uncertainty about the mechanisms of evolution will be exploited by those who seek to undermine it."1 Likewise, pro-ENCODE biochemists John Mattick and Marcel Dinger observe that "resistance to [ENCODE's] findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design."2 Writing in a slightly different context, eight biologists published a Nature article in 2014 recognizing that scientists self-censor criticisms of neo-Darwinism because, "haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front."3

It's disturbing that scientists oppose empirically based research results or suppress their own doubts about the neo-Darwinian paradigm simply because they don't like the perceived alternative -- ID. These admissions show that evolutionary biology is in an incredibly unhealthy state, where devotion to the paradigm trumps the evidence. A 2003 paper in Science observed that "the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA,"4 but even now that junk DNA has finally been overturned, evolutionary dogmatism still hinders scientific advancement.

In fact, ENCODE proponents aren't the only ones to have acknowledged how ID phobia plays a role in scientists' responses. Even ENCODE-critics have admitted it. The journal Science explained how University of Houston biologist Dan Graur opposes ENCODE because he doesn't like its ID-friendly implications:

Graur's atheism inflamed his anger at ENCODE. He perceives an echo of intelligent design in the consortium's "80% [of the genome is functional] claim," which he takes to imply that most of the genome exists because it serves a purpose.5
But the bluntest summary of why scientists oppose ENCODE came when Graur declared: "If ENCODE is right, then Evolution is wrong."6 With ENCODE's empirical data now showing that the vast bulk of the genome has an important purpose, we can safely say that the fears of ENCODE critics are entirely justified.
Future Forecast

Since 2012, research has continued to uncover specific functions for non-coding DNA, and the case for ENCODE grows stronger and stronger with each passing month.7 Eventually, even the evolutionary holdouts will be unable to deny that virtually our entire genome is functional. Or so you'd like to think.

Evolutionists who believe their paradigm stands only if ENCODE falls have careers, reputations, and deeply held worldviews invested in the view that humans were created by purposeless processes that filled our genomes with useless DNA. Thus, after famously saying, "If ENCODE is right, then Evolution is wrong," Dan Graur's action plan was, in his own words: "Kill ENCODE."8 Human nature may never allow such critics to concede defeat. For them, too much is on the line. Win or lose, they're going down fighting.

The good news is that most scientists aren't evolutionary ideologues. Rank-and-file biologists know compelling empirically based experimental data when they see it. Because they see it in ENCODE, they will build (and may have already built) a new consensus that rejects "junk DNA" and views ENCODE-critics as a footnote -- perhaps one that cautions against putting the paradigm before the evidence.

Some of these biologists are now exploring what they call "post-Darwinian"9 models of evolution, often adopting the same critiques of Darwinism that ID proponents offer. They still seek unguided material evolutionary explanations of life and are resistant to design. But that resistance is weakening. Indeed, widespread fears about aiding intelligent design show that many biologists understand how ENCODE's results represent a major breakthrough for ID. As William Dembski eloquently put it some 14 years pre-ENCODE:

[D]esign is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. ... Design encourages scientists to look for function where evolution discourages it.10
Imagine if scientists had embraced an ID paradigm when Dembski wrote those words in 1998, how much more advanced would molecular biology -- unhindered by evolutionary assumptions -- be today? This much is clear: ID boldly predicted ENCODE's results, and evolutionary biology didn't. This puts ID in a strong position to lead science forward into a post-Darwinian world.
References:

[1.] Philip Ball, "Celebrate the Unknowns," Nature, 496:419-420 (April 25, 2013).

[2.] John Mattick and Marcel Dinger, "The extent of functionality in the human genome," The HUGO Journal, 7:2 (2013).

[3.] Laland et al., "Does evolutionary theory need a rethink? Yes, urgently," Nature, 514:161-164 (October 9, 2014).

[4.] Wojciech Makalowski, "Not Junk After All," Science, 300:1246-1247 (May 23, 2003).

[5.] Yudhit Bhattercharjee, "The Vigilante," Science, 343:1306-1309 (March 21, 2014).

[6.] Dan Graur, "How To Assemble a Human Genome?" (2013).

[7.] The website www.lncrnablog.com documents scientific papers showing function for non-coding DNA.

[8.] Dan Graur, "How To Assemble a Human Genome?" (2013).

[9.] For example, see Simon Conway Morris, "Walcott, the Burgess Shale and rumours of a post-Darwinian world," Current Biology, 19:R927-R931 (2009).


[10.] William Dembski, "Intelligent Science and Design," First Things, 86: 21-27 (October, 1998).

Our creator is a God of order :The Watchtower Society's commentary.

We Need Jehovah’s Organization:
HAVE you ever heard someone say, “I believe in God but not in organized religion”? Similar viewpoints are often expressed by individuals who were once enthusiastic churchgoers but who became disillusioned by the failure of their religion to meet their spiritual needs. Although disappointed by religious organizations in general, many insist that they still want to worship God. They believe, however, that it is better to worship him in their own way than to do so in association with a church or other organization.


What does the Bible say? Does God want Christians to be associated with an organization?

Early Christians Benefited by Being Organized:
At Pentecost 33 C.E., Jehovah poured out his holy spirit, not upon a few isolated believers, but upon a group of men and women who came together “at the same place,” namely, in an upper room in the city of Jerusalem. (Acts 2:1) At that time, the Christian congregation, which became an international organization, was formed. This proved to be a real blessing for those early disciples. Why? For one thing, they had been given an important assignment—that of preaching the good news of God’s Kingdom eventually “in all the inhabited earth.” (Matthew 24:14) In the congregation new converts could learn from experienced fellow believers how to carry on the preaching work.

Soon the Kingdom message spread far beyond the walls of Jerusalem. Between 62 and 64 C.E., the apostle Peter wrote his first letter to Christians who were “scattered about in Pontus, Galatia, Cappadocia, Asia, and Bithynia,” all in modern-day Turkey. (1 Peter 1:1) There were also believers in Palestine, Lebanon, Syria, Cyprus, Greece, Crete, and Italy. As Paul wrote to the Colossians in 60-61 C.E., the good news had been “preached in all creation that is under heaven.”—Colossians 1:23.

A second benefit of associating with an organization was the encouragement Christians could give to one another. In association with the congregation, Christians could hear inspiring discourses, study the Sacred Scriptures together, share faith-strengthening experiences, and join fellow believers in prayer. (1 Corinthians, chapter 14) And mature men could “shepherd the flock of God.”—1 Peter 5:2.

As members of the congregation, Christians also got to know one another and came to love one another. Far from feeling burdened by their association with the congregation, the early Christians were built up and strengthened by it.—Acts 2:42; 14:27; 1 Corinthians 14:26; Colossians 4:15, 16.

Another reason that the united worldwide congregation, or organization, was needed was to promote unity. Christians learned to “speak in agreement.” (1 Corinthians 1:10) This was vital. Members of the congregation came from a variety of educational and social backgrounds. They spoke different languages, and they had obvious differences in personality. (Acts 2:1-11) At times, there were honest differences of opinion. However, Christians were helped to resolve such differences within the congregation.—Acts 15:1, 2; Philippians 4:2, 3.

Serious questions that could not be handled by local elders were referred to mature traveling overseers, such as Paul. Vital doctrinal matters were referred to a central governing body located in Jerusalem. The governing body was initially made up of the apostles of Jesus Christ but was later extended to include older men of the congregation in Jerusalem. Each congregation recognized the God-given authority of the governing body and its representatives to organize the ministry, appoint men to positions of service, and make decisions on doctrinal matters. When an issue was settled by the governing body, the congregations accepted the decision and “rejoiced over the encouragement.”—Acts 15:1, 2, 28, 30, 31.


Yes, Jehovah used an organization in the first century. But what about today?

We Need an Organization Today:
Like their first-century counterparts, Jehovah’s Witnesses today take seriously the commission to preach the good news of the Kingdom. One way they carry out this work is by distributing Bibles and Bible study aids, which calls for organization.

Christian publications must be carefully prepared, checked for accuracy, printed, and then shipped to the congregations. In turn, individual Christians must volunteer to bring the literature to those who want to read it. The Kingdom message has reached millions in this way. Publishers of the good news endeavor to carry out their preaching activity in an orderly fashion, ensuring that no part of the territory is overworked while other parts are neglected. All of this calls for organization.

Since “God is not partial,” Bibles and Bible literature must be translated. (Acts 10:34) Currently, this magazine is available in 132 languages, and its companion, Awake!, is published in 83 languages. That requires well-organized teams of translators around the world.

Members of the congregation receive encouragement when they attend Christian meetings and assemblies. There they hear stimulating Bible discourses, study the Scriptures together, share upbuilding experiences, and join with fellow worshipers in prayer. And as their brothers in the first century, they enjoy faith-strengthening visits from loving traveling overseers. Thus, Christians today form “one flock, one shepherd.”—John 10:16.


Of course, Jehovah’s Witnesses are not perfect, any more than were their early counterparts. Still, they work together in unity. As a result, the Kingdom-preaching work is being accomplished throughout the earth.—Acts 15:36-40; Ephesians 4:13.

On iconoclasm in a one party state.

Training Non-Skeptics One Course at a Time
Joshua Youngkin June 27, 2012 10:51 AM

At Why Evolution Is True, biologist Jerry Coyne complains:

Sometimes I wonder why [Darwin skeptics] thin[k] that so many scientists -- certainly at least 95% of biologists -- are so deluded as to believe in Darwinism? Are we all simply victims of a 150-year hoax, a hoax involving fields as diverse as embryology, geology, morphology, genetics, biochemistry, and biogeography -- all of which erroneously point to the same conclusions? Or do they think it's a vast conspiracy in which scientists in their smoke-filled labs meet to push a theory that's knowingly wrong --perhaps as a way to attain our real goal: universal atheism?
Or maybe none of the above. How about this instead?
To get specialized training in, say, embryology, you've first got to learn to argue from Darwin to Darwin, which is what high school and university biology textbooks and teachers teach students to do. By the time you're an embryologist teaching embryology, you've gotten really good at arguing from within the Darwinian paradigm for Darwinian conclusions. Tying embryology back to Darwin's tree of life is not an act of independent thinking, however. It is what you've been trained to do and what you train others to do.

Coyne notes that he, P.Z. Myers, and Larry Moran are all known for publicly fighting Darwin skeptics on behalf of the orthodoxy. All three are biology teachers. In class or out, they now do what comes naturally, even reflexively.


Biology teachers like Coyne, Myers and Moran train non-skeptics one course at a time, and the biology academy thus replicates itself ad infinitum.

The Quest for the ultimate free lunch rolls on.

Designless" Logic: Is a Neural Net a Budding Brain?
Evolution News & Views September 30, 2015 3:16 AM 


Whenever you harness a random phenomenon for a function, you are doing intelligent design. For instance, raindrops falling on the ground are unpredictable, but the moment you dig a ditch to channel them to run a waterwheel, you have used your goal-directed intelligence for a pre-determined purpose, even if the inputs were random. Evolutionists routinely miss this distinction. Maybe it's because they just hope their bottom-up theory is true.
Designless Logic
The authors of a new paper in Nature Nanotechnology commit the fallacy right in the title: "Evolution of a designless nanoparticle network into reconfigurable Boolean logic." If it's reconfigurable, it's not designless. If they "evolved" it to do logic, it's illogical to call it Darwinian, which they say inspired their approach. If they applied their minds to exploit the physical properties of particles for a purpose, then they circumvented the purposelessness of natural selection.
Natural computers exploit the emergent properties and massive parallelism of interconnected networks of locally active components. Evolution has resulted in systems that compute quickly and that use energy efficiently, utilizingwhatever physical properties are exploitable. Man-made computers, on the other hand, are based on circuits of functional units that follow given design rules. Hence, potentially exploitable physical processes, such as capacitive crosstalk, to solve a problem are left out. Until now,designless nanoscale networks of inanimate matter that exhibit robust computational functionality had not been realized. Here we artificially evolve the electrical properties of a disordered nanomaterials system (by optimizing the values of control voltages using a genetic algorithm) to perform computational tasks reconfigurably. We exploit the rich behaviour that emerges from interconnected metal nanoparticles, which act as strongly nonlinear single-electron transistors, and find that this nanoscale architecture can be configured in situ into any Boolean logic gate. This universal, reconfigurable gate would require about ten transistors in a conventional circuit. Our system meets the criteria for the physical realization of (cellular) neural networks: universality (arbitrary Boolean functions), compactness, robustness and evolvability, which implies scalability to perform more advanced tasks. Our evolutionary approach works around device-to-device variations and the accompanying uncertainties in performance. Moreover, it bears a great potential for more energy-efficient computation, and for solving problems that are very hard to tackle in conventional architectures. [Emphasis added.]
To their credit, the authors do identify their work as "artificial" selection, but they see it on a continuum with natural selection, never making the distinction between unguided natural processes and intelligent processes. They merely assume that intelligence was, at some point in natural selection, an emergent property that allowed their physical brains (which presumably emerged millions of years ago) to "optimize" the properties of "disordered" elements (like the raindrops) into Boolean logic computers (like the waterwheel).
Design is written all over their materials and methods:
The technique employed to fabricate the NP network is dielectrophoresis, whereby a non-uniform electric fieldapplied across the electrodes drives the suspended NPs to the area in between the electrodes. Before the trapping procedure, the Ti/Au electrodes were cleaned with an oxygen-plasma surface treatment followed by an ethanol rinse and dry. The 11 × 11 mm2 chip that contained several eight- and twelve-pin geometries was placed inside a probe station, and a drop of Au NPs suspended in ethylene glycol wasdispensed on it. The trapping was done sequentially with pairs of diametrically opposed electrodes, by contacting the pads with the probes....
(You get the picture.) Yet they persist in claiming there is no design involved. "That our system is truly designless and reconfigurable makes our approach fundamentally different from the designed circuits" of previous attempts, they say. New Scientist falls headlong into the fallacy, comparing what the programmers did with what Darwinian evolution does:
Traditional computers rely on ordered circuits that followpreprogrammed rules, but this limits their efficiency. "The best microprocessors you can buy in a store now can do 1011operations per second, and use a few hundred watts," says Wilfred van der Wiel of the University of Twente in the Netherlands. "The human brain can do orders of magnitude more and uses only 10 to 20 watts. That's a huge gap."
To close that gap, researchers have tried building "brain-like"computers that can do calculations even though their circuitry was not specifically designed to do so. But no one had made one that could reliably perform calculations.
Van der Wiel and his colleagues have hit the jackpot, using gold particles about 20 nanometres across. They laid a few tens of these grains in a rough heap, with each one about 1 nanometre from its nearest neighbours, and placed eight electrodes around them.
When they applied just the right voltages to the cluster at six specific locations, the gold behaved like a network of transistors -- but without the strict sequence of connectionsin a regular microchip. The system not only performed calculations, but also used less energy than conventional circuitry.
Nothing about the particles told the researchers what voltages to try, however. They started with random valuesand learned which were the most useful using a genetic algorithm, a procedure that borrows ideas from Darwinian evolution to home in on the "fittest" ones.
Neural Nets
It's interesting that the authors compare their disordered electrical circuits to neural networks. These are all the rage now, as intelligent designers seek to improve computers by mimicking the networked architecture of biological brains. Traditional computers are predominantly linear in operation: one calculation's output is input for the next. Neural networks, being nonlinear, give the advantage of simultaneous operations.
Deep neural networks mimic the brain by creating hundreds of millions of connections between "artificial neurons" organized in layers. "These types of networks can be trained to perform hard classification tasks over huge datasets," PhysOrg says, "with the remarkable property of extracting information from examples and generalizing them to unseen items." The article explains the advantages:
The way neural networks learn is by tuning their multitude of connections, or synaptic weights, following the signal provided by a learning algorithm that reacts to the input data. This process is in some aspects similar to what happens throughout the nervous system, in which plastic modifications of synapses are considered to be responsible for the formation and stabilization memories. The problem ofdevising efficient and scalable learning algorithms for realistic synapses is crucial for both technological and biological applications.
But are biological neural networks "emergent" properties of cells that were not designed for learning? A primer in Current Biology examines neural nets from the simplest worm to the human brain and tries to see if Darwinian evolution connected the dots.
With the aim of discussing the evolution of neural nets, we focus here mainly on animals in which nerve nets form a major part of the nervous system and that have positions in the animal tree of life that are informative for considerations of how nervous systems have evolved (Figures 2 and 3).
In the article, we learn about the simplest of animals, like jellyfish and hydra (phylum Cnidaria), which possess "simple" nerve nets connected to muscle sheaths that allow them to respond to stimuli. Figure 2 compares nerve nets in various animals. We find in Figure 3 a phylogenetic diagram showing the distribution of nerve nets in the animal kingdom. The authors show a sequence of increasing complexity, from earthworms that use nerve nets to perform rhythmic movements like peristalsis, to fruit flies and vertebrates, whose nerve nets are organized into more complex structures like nerve cords, onward and upward to central nervous systems.
At a gross scale, it seems reasonable to connect the dots between hydra and Hyracotherium. "We see that nerve nets are good for many things and are quite versatile systems that can be integrated in varied ways into animal bodies," the authors say. "...Assuming the nerve net is theearliest neural tissue in which interwoven neurons connect with epithelial sensory cells and internal muscle cells, we might be able to postulate a pathway leading to derived nerve condensations, such as neurite bundles, medullary cords and brains."
Problems for locating a Darwinian pathway, however, mount as we consider the details:
Convergence. The recently-deciphered genome of a comb jelly (phylum Ctenophora) has led to a "robustly debated" notion that it is the basal metazoan. "Sponges (Porifera) and placozoans lack neurons, so if comb jellies are a sister taxon to all other metazoans, then either those two taxa have lost neurons during evolution or neurons (and nerve nets) evolved twice independently (see Figure 3)." Either way, how did the first neurons appear?
Parallel emergence. "In some animals with prominent subepidermal longitudinal nerve cords -- for example, vertebrates, the fruit fly Drosophila melanogaster and the annelidPlatynereis dumerilii -- the molecular and functional organizationof the nerve cord show very striking similarities, which has been argued to reflect an ancient origin of the nerve cord. In contrast, comparative morphology and recent advances in solving animal relationships with molecular tools suggest that internalizations from a basiepidermal to a subepidermal condensationhappened multiple times independently, for example inside the ribbon worms (Nemertea) and segmented worms (Annelida)."
Cell complexity. Neurons are not simple. They have specialized ion channels, genes and enzymes. Moreover, they have to know how to connect to one another and understand each other's signals. "Recent studies indicate that differentially expressed molecular markers -- transcription factors as well asneuropeptides and neurotransmitters -- assign specific neuronsto different identities and functions." How did neurotransmitters emerge to carry the electrical signals across synapses? Additionally, the muscles they connect to have to interpret the signals and respond appropriately.
Development. Nerve nets do not just appear in the adult fully formed. They have to develop in the embryo: meaning, specialized neurons have to diversify from stem cells then migrate into position and make connections. "Thus, theformation of nerve nets presents specific challenges at several levels and it appears that different organisms employ different developmental mechanisms to overcome these challenges andeventually end up with a nerve net-like nervous system." The authors imply that a simple progression is lacking.
Unknowns. "It will also be important to acquire a better understanding of the functional properties of different nerve nets. What types of behaviour do they allow, and what advantages might this confer for life in a particular environment? Only by such a multiplicity of studies on a broad range of species will it be possible to understand how nerve nets can be transformed during evolution into more complex architectures, and whether there might be a common mechanism that can explain how similar-looking central nerve cords evolved independently several times." Clearly this is not understood today, despite a century or study since G.H. Parker proposed in 1919, "The nerve-net of the lower animals contains the germ out of which has grown the central nervous systems of the higher forms."
Promissory notes: "The biology of nerve nets remains a fascinating and poorly understood topic and it is clear that comparative studies of neural development and physiology of non-model systems embedded in an ecological context are paramount to finally understand nervous system evolution."
In other words, someday evolutionists might connect the dots. Right now, even simple nerve nets in jellyfish and hydra are remarkably well designed for what they do.
This paper could not find an evolutionary pathway in biological neural networks. The other had to impose intelligent design on an artificial neural network to claim it was like biological evolution. Perceptive readers detect intelligent design through it all.

Stumbling over nothing?

What Part of "Nothing" Does Lawrence Krauss Not Understand?
James Barham February 27, 2012 6:00 AM

The latest in a series of book trumpeting a supposed solution to the mystery of existence, Lawrence Krauss's A Universe from Nothing (Free Press, 2012) is basically a superior and accessible rehashing of the concept of the "landscape." Also known as the "multiverse," that is the idea that our universe is embedded within an ensemble of other universes.

Though according to this hypothesis our universe is a "part" of the landscape in some sense, it has no spacetime connection with any of the other universes. This means that they can have no causal influence on us, or we on them.

That makes it tough to gather evidence that these other universes actually exist -- but let that pass.

I won't go into the details of the arguments for and against the landscape hypothesis here. There is no lack of popular books covering this material.1

The point of greatest interest is the extent to which the proposal is ad hoc speculation -- as opposed to a genuine inference from hard facts -- and on this point, expert opinion is divided.

In any event, it's irrelevant to Krauss's extravagant principal claim in the book -- that the problem of the mystery of existence has been solved (more on that in a moment). With respect to this claim, it is pretty obvious that the landscape (if it exists) is no closer to being nothing than the visible universe we observe around us. Rather the contrary, I'd have thought.

But more to the point, the landscape idea as such is not even directed at the mystery-of-existence question. Rather, it is directed at the fine-tuning problem.

This is the problem of explaining why there seems to be no good reason why a large number of physical constants take the exact values that they do. What makes this problem more interesting is the fact that if the values in question had been only slightly different, then various conditions necessary for the presence of life would not have been fulfilled.

This leads, naturally enough, to the idea that the universe is a "put-up job," in the memorable words of the late Fred Hoyle, a distinguished astrophysicist who valued plain speaking.

The reason why the landscape idea seems to solve the fine-tuning problem is that it makes room for the thought that the values of the physical constants of all the different universes are set as they are at random.

In that case, it is hardly surprising that we find ourselves living in the universe with the values that make our existence possible. So, the theory does seem to address the fine-tuning problem -- assuming, that is, the landscape exists and the random-constant concept makes sense (and those are big assumptions).

But none of this has anything to do with Krauss's principal claim about science's now having explained the mystery of existence. So, let's take a look at that.

If you haven't encountered it before, the idea can be a little elusive. Indeed, it seems to have eluded Krauss.

The basic idea is traceable to Antiquity. More specifically, it is one of those respects in which Athens had to go to school to Jerusalem, for it was only in the highest reaches of the monotheistic tradition of thought -- Augustine, al-Farabi, Ibn Sina, Anselm of Canterbury, Maimonides -- that the problem of the mystery of existence finally became clearly articulated.

In a nutshell, it's this: There is no contradiction involved in supposing that the universe never existed.

In other words, while I cannot consistently imagine a square circle, I can consistently imagine that nothing at all ever existed.

This means the universe is what philosophers call "contingent" (meaning not logically necessary).

This means that, since the universe apparently did not have to exist, we are entitled to ask why it does in fact exist.

Note that it does not help to say that the universe had to exist according to the laws of nature -- by physical necessity as opposed to logical necessity -- because the concept of natural law already assumes the existence of nature. Or, if one prefers to take a Platonist view of natural law, then one can simply move the question to that plane and inquire into the reason for the existence of Plato's heaven. Therefore, invoking the laws of nature in this context is question-begging.

As an aside, one might well wonder: How is God an improvement over the laws of nature, in this respect?

Theologians speak of God's mode of being as "necessary," unlike the world's, which is contingent, as we have seen. So, it is a crude mistake simply to ask, as atheists are wont to do: "Who made God?"

However, it is not clear (to me, at any rate) that the concept of necessary being is fully intelligible. The question is: What sort of necessity are we really talking about? It certainly seems like we can imagine that God doesn't exist without contradicting ourselves. But if that is so, then all really existing things -- not just the universe, but God as well -- turn out to be contingent.

There are several ways to go here, for the theist. One is to distinguish a third type of necessity, stronger than physical necessity, but weaker than logical necessity. Another is to distinguish among different modes of being. For instance, one might argue that God -- as the source of Being (upper case) itself -- must be distinguished from all individual beings (lower case), including the universe as a whole. And if that is right, then it is easier to see how the former can be necessary, whereas the latter are contingent.

This is a vast subject. Luckily, though, it need not detain us further here. For, I am not defending the claim that God is a sufficient solution to the mystery of existence.

What I am doing is attacking Krauss's claim that science provides such a solution.

To return, then, to the main thread of my argument: It seems a perfectly coherent question to ask why the universe exists, and if that is so, then we evidently have every right to seek an answer to the question.

The late-antique and medieval Christian and Islamic thinkers who first clearly saw all this liked to express the point slightly differently: Creator and creation are two radically distinct things.

As Robert Sokolowski, a distinguished philosopher at the Catholic University of America, has put it:

[T]he Christian understanding introduces a new horizon or context for the modes of possibility, actuality, and necessity . . . [it] distinguishes the divine and the world in such a way that God could be, in undiminished goodness and greatness, even if everything were not.2
The idea received its classical modern statement in a little essay by Leibniz called "On the Radical Origination of Things" (1697). Here is how he put the problem:
For a sufficient reason for existence cannot be found merely in any one individual thing or even in the whole aggregate and series of things. Let us imagine the book on the Elements of Geometry to have been eternal, one copy always being made from another; then it is clear that though we can give a reason for the present book based on the preceding book from which it was copied, we can never arrive at a complete reason, no matter how many books we may assume in the past, for one can always wonder why such books should have existed at all times; why there should be books at all, and why they should be written in this way. What is true of books is true also of the different states of the world; every subsequent state is somehow copied from the preceding one (although according to certain laws of change). No matter how far we may have gone back to earlier states, therefore, we will never discover in them a full reason why there should be a world at all, and why it should be such as it is.3
In modern parlance -- following Leibniz's lead -- the problem of the mystery of existence is most often expressed by means of the formula: "Why is there something rather than nothing?" This phrase also forms the subtitle to Krauss's book.
Put like that, the idea does not seem so difficult to grasp. In fact, it can be reduced to three little words:

Why not nothing?

Nevertheless, Krauss doesn't get it. He titles one of his chapters "Nothing is something." What does he mean by this?

Just the familiar idea that according to quantum field theory, the vacuum state has complex properties such that matter can be created through quantum fluctuation events. As Krauss puts it in the title of another chapter: "Nothing is unstable."

But the properties of the quantum vacuum are simply irrelevant to the question under discussion -- the reason for the existence of anything at all -- which Krauss has brazenly claimed to have solved in the title of his book. For, in spite of his protestations to the contrary, the quantum field is obviously not nothing in the relevant sense.

What, then, is the final verdict on Dr. Krauss's latest book?

Yet another example of a perfectly good scientist out of his philosophical depth.4


References cited:

(1) Stephen Hawking and Leonard Mlodinow, The Grand Design (Bantam, 2010); Lee Smolin, The Life of the Cosmos (Oxford, 1997); Leonard Susskind, The Cosmic Landscape (Little, Brown, 2005); Alex Vilenkin, Many Worlds in One (Hill and Wang, 2006).

(2) Robert Sokolowski, The God of Faith and Reason (University of Notre Dame, 1982); p. 41. See, also, Lloyd P. Gerson, God and Greek Philosophy (Routledge, 1990).


(3) Gottfried Wilhelm Leibniz, Philosophical Papers and Letters, ed. by Leroy E. Loemker (Kluwer Academic, 1989); p. 486.



(4) For further discussion, see John Leslie, Universes (Routledge, 1990); Milton K. Munitz, The Mystery of Existence (Appleton-Century-Crofts, 1965); and Robert Nozick, Philosophical Explanations (Harvard, 1981).

On the mech and tech of the designer

More on the "Mechanism" of Intelligent Design
Ann Gauger November 14, 2015 3:56 AM

Following on my post yesterday ("What's the Mechanism of Intelligent Design?"), here as promised is a helpful passage from Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, pp. 393-398. Biochemist Larry Moran kindly asked how Stephen Meyer thinks design in biology was instantiated. Meyer writes there:

According to [University of Cambridge paleontologist Robert] Asher, the inference to intelligent design is actually "anti-uniformitarian" because it doesn't provide a "mechanism." As he puts it, "by attempting to replace a causal mechanism (natural selection) with an attribution of agency (design), ID advocates such as Meyer are decidedly anti-uniformitarian. What process of today could possibly lead to his understanding of the past?"

The answer to Asher's question seems pretty obvious. The answer is: intelligence. Conscious activity. The deliberate choice of a rational agent. Indeed, we have abundant experience in the present of intelligent agents generating specified information. Our experience of the causal powers of intelligent agents -- of "conscious activity" as "a cause now in operation"-- provides a basis for making inferences about the best explanation of the origin of biological information in the past. In other words, our experience of the cause-and-effect structure of the world -- specifically the cause known to produce large amounts of specified information in the present -- provides a basis for understanding what likely caused large increases in specified information in living systems in the past. It is precisely my reliance on such experience that makes possible an understanding of the type of causes at work in the history of life. It also makes my argument decidedly uniformitarian -- not "anti-uniformitarian" -- in character.

Asher confuses the uniformitarian imperative in historical scientific explanations (the need to cite a presently known or adequate cause) with a demand for citing a material cause, or mechanism. The theory of intelligent design does cite a cause, and indeed one known to produce the effects in question, but it does not necessarily cite a mechanistic or materialistic cause. Proponents of intelligent design may conceive of intelligence as a strictly materialistic phenomenon, something reducible to the neurochemistry of a brain, but they may also conceive of it as part of a mental reality that is irreducible to brain chemistry or any other physical process. They may also understand and define intelligence by reference to their own introspective experience of rational consciousness and take no particular position on the mind-brain question.

Asher assumes that intelligent design denies a materialistic or "physicalist" account of the mind (as I personally do, in fact) and rejects it as unscientific on that basis. But he offers no noncircular reason for making that judgment. He cannot say that the principle of methodological naturalism requires that all genuinely scientific theories invoke only mechanistic causes, because the principle of methodological naturalism itself needs justification. And asserting that "all genuinely scientific theories must provide mechanisms" is just to restate the principle of methodological naturalism in different words. Indeed, to say that all scientific explanations must provide a mechanism is equivalent to saying that they must cite materialistic causes -- precisely what the principle of methodological naturalism asserts. Asher seems to be assuming without justification that all scientifically acceptable causes are mechanistic or materialistic. His argument thus assumes a key point at issue, which is whether there are independent -- that is, metaphysically neutral -- reasons for requiring historical scientific theories to cite materialistic causes in their explanations as opposed to explanations that invoke possibly immaterial entities such as creative intelligence, mind, mental action, agency, or intelligent design.

In any case, he confuses the logical requirement of citing a vera causa, a true or known cause, with an arbitrary requirement to cite only materialistic causes. He confuses uniformitarianism with methodological naturalism. 38 He then critiques my design argument for rejecting the former, though it only rejects the latter. In so doing, he imposes an additional requirement on explanations of past events that leads him to mistake my argument as anti- uniformitarian and to miss the evidence for intelligent design. His implicit commitment to methodological naturalism makes the evidence for intelligent design -- "the postman," as it were -- mentally invisible to him.

Nevertheless, the concern that he raises about the theory of intelligent design not citing a mechanism still troubles people. In fact, I frequently get questions about this issue. People will ask something like this: "I can see your point about digital code providing evidence for intelligent design, but how exactly did the designing intelligence generate that information or arrange matter to form cells or animals?" Or: "How did the intelligent designer that you infer impress its ideas on matter to form animals?" As Asher puts it, "How could a biological phenomenon, even if designed, be simply willed into existence without an actual mechanism?"

To help clear things up, several points need to be considered. First, the theory of intelligent design does not provide a mechanistic account of the origin of biological information or form, nor does it attempt to. Instead, it offers an alternative causal explanation involving a mental, rather than a necessarily or exclusively material, cause for the origin of that reality. It attributes the origin of information in living organisms to thought, to the rational activity of a mind, not a strictly material process or mechanism. That does not make it deficient as a materialistic or mechanistic explanation. It makes it an alternative to that kind of explanation. Advocates of intelligent design do not propose intelligent causes because they cannot think of a possible mechanistic explanation for the origin of form or information. They propose intelligent design because they think it provides a better, more causally adequate explanation for these realities. Given what we know from experience about the origin of information, materialistic explanations are the deficient ones.

There is a different context in which someone might want to ask about a mechanism. He or she may wish to know by what means the information, once originated, is transmitted to the world of matter. In our experience, intelligent agents, after generating information, often use material means to transmit that information. A teacher may write on a chalkboard with a piece of chalk or an ancient scribe may have chiseled an inscription in a piece of rock with a metal implement. Often, those who want to know about the mechanism of intelligent design are not necessarily challenging the idea that information ultimately originates in thought. They want to know how, or by what material means, the intelligent agent responsible for the information in living systems transmitted that information to a material entity such as a strand of DNA. To use a term from philosophy, they want to know about "the efficient cause" at work.

The answer is: We simply don't know. We don't have enough evidence or information about what happened, in the Cambrian explosion or other events in the history of life, to answer questions about what exactly happened, even though we can establish from the clues left behind that an intelligent designer played a causal role in the origin of living forms.

An illustration from archaeology helps explain how this can be so. Years ago explorers of a remote island in the southwestern Pacific Ocean discovered a group of enormous stone figures. The figures displayed the distinctive shape of human faces. These figures left no doubt as to their ultimate origin in thought. Nevertheless, archeologists still don't know the exact means by which they were carved or erected. The ancient head carvers might have used metallic hammers, rock chisels, or lasers for that matter. Though archaeologists lack the evidence to decide between various hypotheses about how the figures were constructed, they can still definitely infer that intelligent agents made them. In the same way, we can infer that an intelligence played a causal role in the origin of the Cambrian animals, even if we cannot decide what material means, if any, the designing intelligence used to transmit the information, or shape matter, or impart its design ideas to living form. Although the theory of intelligent design infers that an intelligent cause played a role in shaping life's history, it does not say how the intelligent cause affected matter. Nor does it have to do so.

There is a logical reason we cannot without further information determine the mechanism or means by which the intelligent agent responsible for life transmitted its design to matter. We can infer an intelligent cause from certain features of the physical world, because intelligence is known to be a necessary cause, the only known cause, of those features. That allows us to infer intelligence retrospectively as a cause by observing its distinctive effects. Nevertheless, we cannot establish a unique scenario describing how the intelligent agent responsible for life arranged or impressed its ideas on matter, because there are many different possible means by which an idea in the mind of an intelligent agent could be transmitted or instantiated in the physical world.

There is another even more profound reason that intelligent design -- indeed, science itself -- may not be able to offer a completely mechanistic account of the instantiation of thought into matter. Robert Asher worries about how "a biological phenomenon, even if designed," could be "simply willed into existence without an actual mechanism." In Asher's understanding, the uniformitarian principle asks for a precedent, a known cause that not only generates information, but translates immaterial thought into material reality, impressing itself on and shaping the physical world. Asher complains that the argument for intelligent design cannot cite such a precedent and is thus "anti- uniformitarian."

Yet a precedent comes very readily to mind, an intimately familiar one for us all. At present no one has any idea how our thoughts -- the decisions and choices that occur in our conscious minds -- affect our material brains, nerves, and muscles, going on to instantiate our will in the material world of objects. However, we know that is exactly what our thoughts do. We have no mechanistic explanation for the mystery of consciousness, nor what is called the "mind- body problem" -- the enigma of how thought affects the material state of our brains, bodies, and the world that we affect with them. Yet there is no doubt that we can -- as the result of events in our conscious minds called decisions or choices -- "will into existence" information-rich arrangements of matter or otherwise affect material states in the world. Professor Asher did this when he wrote the chapter in his book -- representing his ideas impressed as words onto a material object, a printed page -- attempting to refute intelligent design. I am doing this right now. This example, representative of countless daily experiences in life, surely satisfies the demands of uniformitarianism.


Though neuroscience can give no mechanistic explanation for consciousness or the mind-body problem, we also know that we can recognize the product of thought, the effect of intelligent design, in its distinctive information-rich manifestations. Professor Asher recognized evidence of thought when he read the text in my book; I did so when I read his; you are doing so right now. Thus, even though it remains entirely possible that we may never know how minds affect matter and, therefore, that there may always be a gap in our attempt to account for how a designing mind affected the material out of which living systems were formed, it does not follow that we cannot recognize evidence of the activity of mind in living systems.