The design inference is science's security officer?

 Mendel’s Peas and More: Inferring Data Falsification in Science

William Dembski and winston Ewert

Editor’s note: We are delighted to welcome the new and greatly expanded second edition of the design inference, by William Dembski and Winston Ewert. The following is excerpted from Chapter 2, “A Sampler of Design Inferences.”

Drawing design inferences is not an obscure or rare occurrence — it happens daily. We distinguish between a neatly folded pile of clothes and a random heap, between accidental physical contact and a deliberate nudge, between doodling and a work of art. Furthermore, we make important decisions based on this distinction. This chapter examines a variety of areas where we apply the design inference. In each case, what triggers a design inference is a specified event of small probability. 

The eminent statistician Ronald Aylmer Fisher uncovered a classic case of data falsification when he analyzed Gregor Mendel’s data on peas. Fisher inferred that “Mendel’s data were fudged,” as one statistics text puts it, because the data matched Mendel’s theory too closely. Interestingly, the coincidence that elicited this charge of data falsification was a specified event whose probability was roughly 4 in 100,000, or 1 in 25,000. By everyday standards, this probability will seem small enough, but it is huge compared to many of the probabilities we will be encountering. In any case, Fisher saw this probability as small enough to draw a design inference, concluding that Mendel’s experiment was compromised and charging Mendel’s gardening assistant with deception. 

Slutsky — Fast and Furious

For a more recent example of data falsification in science, consider the case of UCSD heart researcher Robert A. Slutsky. Slutsky was publishing fast and furiously. At his peak, he was publishing one new paper every ten days. Intent on increasing the number of publications in his curriculum vitae, he decided to lift a two-by-two table of summary statistics from one of his articles and insert it — unchanged — into another article. Data falsification was clearly implicated because of the vast improbability that data from two separate experiments should produce the same summary table of statistics. When forced to face a review board, Slutsky resigned his academic position rather than try to explain how this coincidence could have occurred without any fault on his part. The incriminating two-by-two table that appeared in both articles consisted of four blocks each containing a three-digit number. Given therefore a total of twelve digits in these blocks, the odds would have been roughly 1 in a trillion (= 1012) that this same table might have appeared by chance twice in his research. 

Why did Slutsky resign rather than defend a 1 in 1012 improbability? Why not simply attribute the coincidence to chance? There were three reasons. First, at the review board Slutsky would have had to produce the experimental protocols for the two experiments that supposedly gave rise to the identical two-by-two tables. If he was guilty of data falsification, these protocols would have incriminated him. Second, even if the protocols were lost, the sheer improbability of producing so unlikely a match between the two papers would have been enough to impugn the researcher’s honesty. Once a specification is in place (the two-by-two table in one paper here specifying the table in the other) and the probabilities become too small, the burden of proof, at least within the scientific community, shifts to the experimenter suspected of data falsification. In lay terms, Slutsky was self-plagiarizing. And third, Slutsky knew that this case of fraud was merely the tip of the iceberg. He had been committing other acts of research fraud right along, and these were now destined all to come into the open. 

Moving from Medicine to Physics

Now consider the case of Jan Hendrik Schön, which parallels the Slutsky case almost point for point. On May 23, 2002, the New York Times reported on the work of “J. Hendrik Schön, 31, a Bell Labs physicist in Murray Hill, NJ, who has produced an extraordinary body of work in the last two and a half years, including seven articles each in Science and Nature, two of the most prestigious journals.” Despite this track record, his career was on the line. The New York Times reported further that Schön published “graphs that were nearly identical even though they appeared in different scientific papers and represented data from different devices. In some graphs, even the tiny squiggles that should arise from purely random fluctuations matched exactly.” (The identical graphs that did in Schön parallel the identical two-by-two tables that did in Slutsky.) Bell Labs therefore appointed an independent panel to determine whether Schön was guilty of “improperly manipulating data in research papers published in prestigious scientific journals.” The hammer fell in September 2002 when the panel concluded that Schön had indeed falsified his data, whereupon Bell Labs fired him.17 

Exactly how a design inference was drawn in the Schön case is illuminating. In determining whether Schön’s numbers were made up fraudulently, the panel noted, if only tacitly, that the first published graph provided a pattern independently identified of the second and thus constituted the type of pattern that, in the presence of improbability, could negate chance to underwrite design (i.e., the pattern was a specification). And indeed, the match between the two graphs in Schön’s articles was highly improbable assuming the graphs arose from random processes (which is how they would have had to arise if, as Schön claimed, they resulted from independent experiments). As with the matching two-by-two tables in the Slutsky example, the match between the two graphs of supposedly random fluctuations would have been too improbable to occur by chance. With specification and improbability both evident, a design inference followed. 

But, as noted earlier, a design inference, by itself, does not implicate any particular intelligence. So how do we know that Schön was guilty? A design inference shows that Schön’s data were cooked. It cannot, without further evidence, show that Schön was the chef. To do that required a more detailed causal analysis — an analysis performed by Bell Labs’ independent panel. From that analysis, the panel concluded that Schön was indeed guilty of data falsification. Not only was he the first author on the problematic articles, but he alone among his co-authors had access to the experimental devices that produced the disturbingly coincident outcomes. Moreover, it was Schön’s responsibility to keep the experimental protocols for these research papers. Yet the protocols mysteriously vanished when the panel requested them for review. The circumstantial evidence connected with this case not only underwrote a design inference but established Schön as the designer responsible.

And from Physics to Parapsychology

As a final example of where data falsification becomes an issue facing science, consider efforts to debunk parapsychology. Parapsychological experiments attempt to show that parapsychological phenomena are real by producing a specified event of small probability. Persuaded that they’ve produced such an event, parapsychological researchers then explain it in terms of a quasi-design-like theoretical construct called psi (i.e., a non-chance factor or faculty supposedly responsible for such events). 

For instance, shuffle some cards and then have a human subject guess their order. Subjects rarely, if ever, guess the correct order with 100 percent accuracy. But to the degree that a subject guesses correctly, the improbability of this coincidence (which will then constitute a specified event of small probability) is regarded as evidence for psi. In attributing such coincidences to psi, the parapsychologist will draw a design inference. The debunker’s task, conversely, will then be to block the parapsychologist’s design inference. In practice, this will mean one of two things: either showing that sloppy experimental method was used that somehow signaled to the subject the order of the cards and thereby enabled the subject, perhaps inadvertently, to overcome chance; or else showing that the experimenter acted fraudulently, whether by making up the data or by otherwise massaging the data to provide evidence for psi. Note that the debunker is as much engaged in drawing a design inference as the parapsychologist — it’s just that one implicates the parapsychologist in fraud, the other implicates psi.

Keeping Science Honest

The takeaway is that science needs the design inference to keep itself honest. In the years since the first edition of this book was published, reports of fraud in science have continued to accumulate. The publish-or-perish mentality that incentivizes inflating the number of one’s publications regardless of quality has only gotten worse. That mentality moves easily from a haste-makes-waste sloppiness to self-serving fudginess to full-orbed fraudulence. Data falsification and other forms of scientific fraud, such as plagiarism, are far too common in science. What keeps scientific fraud in check is our ability to detect it, and it’s the design inference that does the detecting. 

We’ve now seen that the design inference makes design readily detectable in everyday life. Moreover, we’ve just seen that its ability to make design detectable in the data of science is central to keeping scientists honest. The grand ambition of this book is to show that the design inference makes design part of the very fabric of science. 

There are no good guys VI: Black September.

 

First Corinthians Chapter 6 New international version

 6.If any of you has a dispute with another, do you dare to take it before the ungodly for judgment instead of before the Lord’s people? 2Or do you not know that the Lord’s people will judge the world? And if you are to judge the world, are you not competent to judge trivial cases? 3Do you not know that we will judge angels? How much more the things of this life! 4Therefore, if you have disputes about such matters, do you ask for a ruling from those whose way of life is scorned in the church? 5I say this to shame you. Is it possible that there is nobody among you wise enough to judge a dispute between believers? 6But instead, one brother takes another to court—and this in front of unbelievers!

7The very fact that you have lawsuits among you means you have been completely defeated already. Why not rather be wronged? Why not rather be cheated? 8Instead, you yourselves cheat and do wrong, and you do this to your brothers and sisters. 9Or do you not know that wrongdoers will not inherit the kingdom of God? Do not be deceived: Neither the sexually immoral nor idolaters nor adulterers nor men who have sex with men a 10nor thieves nor the greedy nor drunkards nor slanderers nor swindlers will inherit the kingdom of God. 11And that is what some of you were. But you were washed, you were sanctified, you were justified in the name of the Lord Jesus Christ and by the Spirit of our God.

Sexual Immorality

12“I have the right to do anything,” you say—but not everything is beneficial. “I have the right to do anything”—but I will not be mastered by anything. 13You say, “Food for the stomach and the stomach for food, and God will destroy them both.” The body, however, is not meant for sexual immorality but for the Lord, and the Lord for the body. 14By his power God raised the Lord from the dead, and he will raise us also. 15Do you not know that your bodies are members of Christ himself? Shall I then take the members of Christ and unite them with a prostitute? Never! 16Do you not know that he who unites himself with a prostitute is one with her in body? For it is said, “The two will become one flesh.” b 17But whoever is united with the Lord is one with him in spirit. c

18Flee from sexual immorality. All other sins a person commits are outside the body, but whoever sins sexually, sins against their own body. 19Do you not know that your bodies are temples of the Holy Spirit, who is in you, whom you have received from God? You are not your own; 20you were bought at a price. Therefore honor God with your bodies.

Getting the "juice" for a journey to the Jovian satellites

 

The cell is a city under seige?

 

On the universe as God

 A Philosopher Rejects the Multiverse but Embraces Mythology

Eric Hedin

The fine-tuning of our universe is, of course, widely seen as providing evidence for intelligent design. And rightly so, as Stephen Meyer shows in Return of the God Hypothesis. This, however, leaves many a scholar in a quandary. Thus, in a recent article at The Conversation, Durham University philosopher Phillip Goff presents his views on the fine-tuning of the physical parameters, the multiverse postulate, and cosmic purpose. 

Goff acknowledges the significance of the physical constants of the universe and their fine-tuning for life.

One of the most startling scientific discoveries of recent decades is that physics appears to be fine-tuned for life.

Physicist Paul Davies, an agnostic, also acknowledges the reality of fine-tuning and its significance for our lives.

If almost any of the basic features of the universe, from the properties of atoms to the distribution of the galaxies, were different, life would very probably have been impossible… On the face of it, the universe does look as if it had been designed by an intelligent creator.1

Goff’s example of fine-tuning echoes the Goldilocks analogy that Davies uses:

To allow for the possibility of life, the strength of dark energy had to be, like Goldilocks’s porridge, “just right.”

A God-Substitute 

As Goff seeks to interpret the evidence, he reveals the philosophical discomfort that fine-tuning evokes in those who prefer a naturalistic explanation for the universe. In principle, science usually proceeds along these lines: naturalistic explanations for the phenomena of our universe are indeed appropriately sought first. The multiverse scenario, however, has ballooned up to serve as a God-substitute for those with a worldview excluding the possibility of metaphysical causes.

Some physicists aren’t too bothered by the seemingly fine-tuned cosmos. Others have found comfort in the multiverse theory. If our universe is just one of many, some would, statistically speaking, end up looking just like ours.

Goff takes issue with the current default understanding of the multiverse. The attempted rebuttal to the fine-tuning evidence typically proceeds from the following assumption:

If there are enough universes, with different numbers in their physics, it becomes likely that some universe is going to have the right numbers for life.

Multiverse scenarios assume that a putative universe-generating mechanism endows its offspring with physical laws and parameters spanning a wide spectrum of possibilities. However, this notion flies in the face of what we observe as a general feature of the physical realm.

In nature, chance interactions do not necessarily lead to an unlimited variety of outcomes but tend to produce limited variation. For example, throughout the 13.8-billion-year history of the universe, only a finite number of elements (about 94) have ever formed by natural processes. This limitation is a result of constraints on nature due to the laws of physics. The limitations imposed by those laws will prevent the natural formation of elements with, say, 200 protons, or an isotope of carbon with 53 neutrons — no matter how long we might wait.

A God-Substitute 

As Goff seeks to interpret the evidence, he reveals the philosophical discomfort that fine-tuning evokes in those who prefer a naturalistic explanation for the universe. In principle, science usually proceeds along these lines: naturalistic explanations for the phenomena of our universe are indeed appropriately sought first. The multiverse scenario, however, has ballooned up to serve as a God-substitute for those with a worldview excluding the possibility of metaphysical causes.

Some physicists aren’t too bothered by the seemingly fine-tuned cosmos. Others have found comfort in the multiverse theory. If our universe is just one of many, some would, statistically speaking, end up looking just like ours.

Goff takes issue with the current default understanding of the multiverse. The attempted rebuttal to the fine-tuning evidence typically proceeds from the following assumption:

If there are enough universes, with different numbers in their physics, it becomes likely that some universe is going to have the right numbers for life.

Multiverse scenarios assume that a putative universe-generating mechanism endows its offspring with physical laws and parameters spanning a wide spectrum of possibilities. However, this notion flies in the face of what we observe as a general feature of the physical realm.

In nature, chance interactions do not necessarily lead to an unlimited variety of outcomes but tend to produce limited variation. For example, throughout the 13.8-billion-year history of the universe, only a finite number of elements (about 94) have ever formed by natural processes. This limitation is a result of constraints on nature due to the laws of physics. The limitations imposed by those laws will prevent the natural formation of elements with, say, 200 protons, or an isotope of carbon with 53 neutrons — no matter how long we might wait.

Unlimited Physical Outcomes?

In light of all we know of this universe, even if a multiverse of other universes exists, it’s unreasonable to suppose that a near-infinite variety of physical outcomes will result within those universes. 

Goff acknowledges that the idea of the multiverse is consistent with the physics of cosmic inflation, but he denies its utility as a valid explanation for the specific fine-tuning in our universe. 

The scientific theory of inflation — the idea that the early universe blew up hugely in size — supports the multiverse. If inflation can happen once, it is likely to be happening in different areas of space — creating universes in their own right. While this may give us tentative evidence for some kind of multiverse, there is no evidence that the different universes have different numbers in their local physics.

When this particular universe was created, as in a die throw, it still had a specific, low chance of getting the right numbers.

Limited variation in physical parameters is to be expected. Why, then, would this particular universe, the only observable one, have so many parameters fine-tuned to a razor’s edge in support of life?

Goff identifies an additional philosophical error committed by those who appeal to the multiverse.

Experts in the mathematics of probability have identified the inference from fine-tuning to a multiverse as an instance of fallacious reasoning…. Specifically, the charge is that multiverse theorists commit what’s called the inverse gambler’s fallacy.

They think: “Wow, how improbable that our universe has the right numbers for life; there must be many other universes out there with the wrong numbers!”

A low-probability event is not explained by postulating a fictitious multitude of other players in the game. The only game in town is our observable universe, and its highly specific suite of parameters, if naturally occurring, must be explained by what we know exists in nature, not by appealing to what cannot be observed in nature.

The Anthropic Principle

Goff also addresses another common argument made by multiverse proponents:

At this point, multiverse theorists bring in the “anthropic principle” — that because we exist, we could not have observed a universe incompatible with life.

Logically, who can argue with this? If the universe’s parameters didn’t allow life, nobody would be here to discuss the issue, or read articles about it, either. However, this dismissal glosses over a fine point — the universe must be tuned to allow life, or else we wouldn’t be here, but no stretch of logic demands that it be exquisitely fine-tuned for life. Since the tuning for life is balanced on such a sharp knife-edge, intellectual curiosity leads us to legitimately suspect far more at work than an uninteresting axiomatic requirement for our existence. 

If we hold that the constants of our universe were shaped by probabilistic processes — as multiverse explanations suggest — then it is incredibly unlikely that this specific universe, as opposed to some other among millions, would be fine-tuned.

And Now, the God Hypothesis?

Granting that fine-tuning is real, but philosophically rejecting the multiverse as a cure-all for naturalism and its woes, is Goff led to accept “the God hypothesis”? No. He instead idolizes the universe itself, imagined as a sort of fertile incubator for life, pregnant with fine-tuning and the potential for vivification.

The conventional scientific wisdom is that these numbers have remained fixed from the Big Bang onwards. If this is correct, then we face a choice. Either it’s an incredible fluke that our universe happened to have the right numbers. Or the numbers are as they are because nature is somehow driven or directed to develop complexity and life by some invisible, inbuilt principle.

An important point from information theory, however, is that no degree of fine-tuning of physical parameters, so that life is allowed to exist, would by its nature drive life to develop. The material of the physical universe is influenced by just four fundamental forces of nature, and aside from the weak force (involved in radioactive decay), these forces do nothing more than exert an indiscriminate push or pull. 

Ascribing sentience or cosmic purpose to forces or the particles on which they act is to step out of the realm of science into the realm of myth-making. The purpose we observe in the universe is incompatible with inanimate particles but it is totally consistent with an ultimate cause whose attributes transcend the highest categories of human characteristics. However, there is a long history of humans who, faced with the idea of a creator, would prefer to say to a rock, “You gave me birth.”2

The main event: James Tour vs. Lee Cronin

 

It's complicated VIII

 

Mapping the limits of chance and necessity.

 

Due process has fallen?

 

Christendom's house just keeps getting ever more divided.

 

Spaceship earth's nearest star demystified.

 

Yet more on our undeniably designed bodies

 

Chance as blind tinkerer.

 Natural Selection as the Great Designer Substitute

William Dembski and Winston Ewert

Editor’s note: We are delighted to welcome the new and greatly expanded second edition of The design inference, by William Dembski and Winston Ewert. The following is excerpted from the Introduction.

Darwinian critics, however much they were willing to permit design inferences in other contexts, reflexively ruled them out as soon as they impacted biology or cosmology or anyplace where a non-natural designer might be implicated. They thereby gutted the design inference of any larger worldview significance, ensuring that it could never be applied to humanity’s really big and important questions.

Early in The Blind Watchmaker, Richard Dawkins stated that life is special because it exhibits a “quality” that is “specifiable in advance” and “highly unlikely to have been acquired by random chance alone.” All the elements of specified complexity are there in Dawkins’s characterization of life. Yet Dawkins, along with fellow Darwinians, did not see in specified complexity a marker of actual design but rather the outworking of natural selection, naturalism’s great designer substitute. For Dawkins, natural selection removes the small probabilities needed to make the design inference work. As he remarks, the “belief, that Darwinian evolution is ‘random,’ is not merely false. It is the exact opposite of the truth. Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative [i.e., natural] selection, which is quint- essentially nonrandom.” Nonrandom here means, in particular, not all that improbable.

Two Conditions for a Design Inference

For a design inference to properly infer design, two conditions must be met:

an observed outcome matches an independently identifiable pattern, or what we call a specification (what Dawkins means by “specifiable in advance”); and

the event corresponding to that pattern has small probability (think of the pattern as a target and an arrow landing anywhere in it as the corresponding event).

With these conditions satisfied, the design inference ascribes such an observed outcome to design. Dawkins finds no fault with this form of reasoning provided the probabilities are indeed small. He even admits that scientific theories are only “allowed to get away with” so much “sheer unadulterated miraculous luck” but no more. Dawkins is here expressing the widespread intuition that certain events are within the reach of chance but that others are not. He’s right that people widely embrace this intuition, and he’s right that this intuition applies to science.

Given his view that scientific theorizing can only permit a limited amount of luck (a view ID proponents share), Dawkins would be forced to concede that if randomness were operating in the evolution of life, the resulting probabilities would be small, and a design inference would be warranted. As evidence that Dawkins does indeed make this concession, consider the way he commends William Paley’s design argument. In a remarkable moment of candor, Dawkins writes, “I could not imagine being an atheist at any time before 1859, when Darwin’s Origin of Species was published… [A]lthough atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.” According to Dawkins, but for Darwin, we would be stuck with Paley and compelled to be theists.

Breaking Intelligent Design

Darwin, in positing natural selection as the driving force behind evolution, was thus seen as breaking the power of classical design arguments. Natural selection, with its ability to heap up small incremental improvements, would allow evolution to proceed gradually, baby step by baby step, overcoming all evolutionary obstacles. In proceeding by baby steps, Darwinian evolution is supposed to mitigate the vast improbabilities that might otherwise constitute insuperable obstacles to life’s evolution, substituting at each step probabilities that are eminently manageable (not too small).

Darwinian processes, by overcoming probabilistic hurdles in this way, are thus said to banish design inferences from biology. The actual small probabilities needed for a valid design inference, according to Dawkins and fellow Darwinian biologists, thus never arise. Indeed, that was Dawkins’s whole point in following up The Blind Watchmaker with Climbing Mount Improbable. Mount Improbable only seems improbable if you have to scale it in one giant leap, but if you can find a gradual winding path to the top (baby step by baby step), getting there is quite probable.

Dawkins never gets beyond such a broad-brush description of how vast improbabilities that might otherwise dog evolution can be mitigated. As it is, there are plenty of probabilistic situations in which each step is reasonably probable but the coordination of all these reasonably probable events contributes to an outcome that is highly improbable. Flip a coin a hundred times, and at each flip the coin is reasonably likely to land on heads. But getting a hundred heads in a row is highly improbable, and we should not expect it to happen by chance. Dawkins doesn’t just need reasonably sized probabilities at each step, but a kind of coordination or ratcheting that locks in prior benefits and keeps striving for and accumulating future benefits. Showing that natural selection possesses this power universally goes well beyond what he, or any other Darwinian biologist, ever established probabilistically.

Confusing Apparent with Actual

In short, Darwinian critics of the design inference conflate apparent specified complexity with actual specified complexity. Darwinists like Dawkins grant that actual specified complexity warrants a design inference. But they view the Darwinian mechanism of natural selection as a probability amplifier, making otherwise improbable events probable and thus rendering them no longer complex. As a consequence, it does not matter that specified complexity, as a matter of statistical logic, warrants a design inference because, according to Darwinists, life does not actually exhibit specified complexity. Darwinists will, to be sure, claim that the Darwinian mechanism creates specified complexity. But what they really mean is that the Darwinian mechanism causes life to exhibit the illusion of specified complexity. Living systems only seem to be highly improbable, but they’re not once you understand how Darwinian evolution brings them about. In this way, the majority of evolutionary biologists, insofar as they understand the design inference at all, rationalize it away.

Since the publication of the first edition of this book, the debate over the design inference and its applicability to evolution has centered on whether such gradual winding paths exist and how their existence or non-existence would affect the probabilities by which Darwinian processes could originate living forms. Design theorists have identified a variety of biological systems that resist Darwinian explanations and argued that the probability of such systems evolving by Darwinian means is vanishingly small. They thus conclude that these systems are effectively unevolvable by Darwinian means and that their existence warrants a design inference. In this book, we recap that debate and contend that intelligent design has the stronger argument.

The amazing Randi vs. The paranormal

 

We reject the militant stupidity of the trinity

  Psalms ch.83:18KJV"That men may know that thou, whose name alone is JEHOVAH, art the most high over all the earth."

Thus no person or thing not numerically identical to JEHOVAH Can be the most high God ,in as much as JEHOVAH ALONE is the most high God and no person or thing not numerically identical to the most high God can be JEHOVAH in as much as the most High God is JEHOVAH. 

Superlative as defined by Webster's: surpassing all( not most) others : SUPREME

Thus by definition no one can be coequal to the most high God.

Thus in as much as The Jesus of Christendom is by common consent not superlative he simply cannot be the JEHOVAH of scripture.

The equivalence principle demystified

 

How about we just stick to the plain reading of the text II

 John Ch.14:28NKJV"You have heard Me say to you, ‘I am going away and coming back to you.’ If you loved Me, you would rejoice because [h]I said, ‘I am going to the Father,’ for My Father is GREATER than I."

Hebrews Ch.6:13NKJV"For when God made a promise to Abraham, because He could swear by NO ONE greater, He swore by Himself,"

John Ch.17:3 Ch.17:3KJV"And this is life eternal, that they might know THEE (second person singular)the ONLY true God, AND Jesus Christ, whom thou hast sent. "

John Ch.8:50KJV"And I seek NOT mine own glory: there is one that seeketh and judgeth."

John Ch.12:28NIV"FATHER, glorify YOUR(Not our) name!” Then a voice came from heaven, “I have glorified it, and will glorify it again.”"

Matthew Ch.20:23NIV"Jesus said to them, “You will indeed drink from my cup, but to sit at my right or left is not for me to grant. These places belong to those for whom they have been prepared by my FATHER.”"

Luke Ch.18:19NIV"“Why do you call me good?” Jesus answered. “No one is good—except God alone."

It's complicated VII

 

Officially Junk no more?

 Newly Published Paper in BioEssays Recognizes Kuhnian “Paradigm Shift” Against Junk DNA

Casey Luskin

In September, I wrote about prolific functions discovered for short tandem repeats (STRs), formerly considered a type of “junk DNA.” Now a newly published paper in BioEssays has strongly rebuffed the idea of junk DNA — using the language of Kuhnian paradigm shifts. Before we go any further, let’s review just what a Kuhnian paradigm shift is.

The phrase comes from the work of a famous Harvard University historian and philosopher of science, Thomas Kuhn. In his influential book The Structure of Scientific Revolutions, he documented how new ideas in science typically take hold through what are called “paradigm shifts,” where the leading framework within a field (the “paradigm”) starts to accrue evidential problems (goes into “crisis”) until it finally gives way to a new idea that challenges the status quo. Kuhn further showed that most scientists spend most of their time doing “normal science” — basically solving scientific puzzles within the framework of the dominant paradigm. He observed that the scientists of the old guard paradigm are “often intolerant” of “new theories” that are being proposed by new scientists proposing ideas that challenge the reigning paradigm. A new theory “emerges first in the mind of one or a few individuals” but then it spreads because the field faces “crisis-provoking problems,” especially among scientists who are “so young or so new to the crisis-ridden field that practice has committed them less deeply than most of their contemporaries to the world view and rules determined by the old paradigm.”

A Junk DNA Paradigm Shift

This brings us to the article recently published in BioEssays, written by John Mattick, an Australian molecular biologist and Professor of RNA Biology at the University of New South Wales, Sydney. I have no evidence that Mattick has any affinities with intelligent design — but he’s a prime example of a bold scientist who has embraced new theories that challenge the reigning paradigm. Mattick has been indefatigable in following the evidence where it leads regarding evidence of function for “junk DNA.” In part because of his work, biology today has experienced a paradigm shift away from the concept of junk DNA. In fact, Mattick’s new BioEssays article, “A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs,” frames the revolution in thinking over junk DNA precisely in “Kuhnian paradigm shift” terms. The paper has a nice video abstract, but here’s what it says in written form: 

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information.

Mattick describes the previously reigning “junk DNA” paradigm in biology as having come from “prevailing assumptions.” The assumptions hold that “‘genes’ encode proteins, that genetic information is transacted and regulated by proteins, and that there is no heritable communication between somatic and germ cells.” This view that genes encode proteins is a key part of the “central dogma” of biology. Of course, no one denies that genes encode proteins — Mattick’s point is that they can do much more than this. They can also encode RNAs and the evidence shows that many non-protein-coding sequences of DNA actually encode RNAs that perform many types of vital functions in the cell. 

Junk DNA and Evolution

So the central dogma of molecular biology is part of what is perpetuating the idea that if a stretch of DNA doesn’t encode a protein then it isn’t doing anything and is “junk.” But there’s another major driver of the failing junk DNA paradigm in biology — and it stems directly from evolutionary thinking. Mattick explains:  

          [T]heoretical biologists were integrating Mendelian genetics with Darwinian evolution, leading in 1942 to the so-called Modern Synthesis, which made two primary claims: mutations are random and somatic mutations are not inherited. … In 1968 Kimura proposed the neutral theory of molecular evolution, which posited that “an appreciable fraction” of the genome was evolving independently of natural selection. In 1969, Nei concluded that, given the “high probability of accumulating … lethal mutations in duplicated genomes … it is to be expected that higher organisms carry a considerable number of nonfunctional genes (nonsense DNA) in their genome”, leading Ohno to promote the concept of “junk DNA”, also arguing that “in order not to be burdened with an unbearable mutation load, the necessary increase in the number of regulatory systems had to be compensated by simplification of each regulatory system”. 

Against this backdrop — permeated with evolutionary thinking about the origin of the genome — the idea of junk DNA flourished and spread throughout the biology community. 

Jeremiah Chapter 14 American Standard Version.

 14.The word of JEHOVAH that came to Jeremiah concerning the drought.

2Judah mourneth, and the gates thereof languish, they sit in black upon the ground; and the cry of Jerusalem is gone up.

3And their nobles send their little ones to the waters: they come to the cisterns, and find no water; they return with their vessels empty; they are put to shame and confounded, and cover their heads.

4Because of the ground which is cracked, for that no rain hath been in the land, the plowmen are put to shame, they cover their heads.

5Yea, the hind also in the field calveth, and forsaketh her young , because there is no grass.

6And the wild asses stand on the bare heights, they pant for air like jackals; their eyes fail, because there is no herbage.

7Though our iniquities testify against us, work thou for thy name's sake, O JEHOVAH; for our backslidings are many; we have sinned against thee.

8O thou hope of Israel, the Saviour thereof in the time of trouble, why shouldest thou be as a sojourner in the land, and as a wayfaring man that turneth aside to tarry for a night?

9Why shouldest thou be as a man affrighted, as a mighty man that cannot save? yet thou, O JEHOVAH, art in the midst of us, and we are called by thy name; leave us not.

10Thus saith JEHOVAH unto this people, Even so have they loved to wander; they have not refrained their feet: therefore JEHOVAH doth not accept them; now will he remember their iniquity, and visit their sins. 11And JEHOVAH said unto me, Pray not for this people for their good. 12When they fast, I will not hear their cry; and when they offer burnt-offering and meal-offering, I will not accept them; but I will consume them by the sword, and by the famine, and by the pestilence.

13Then said I, Ah, Lord JEHOVAH! behold, the prophets say unto them, Ye shall not see the sword, neither shall ye have famine; but I will give you assured peace in this place. 14Then JEHOVAH said unto me, The prophets prophesy lies in my name; I sent them not, neither have I commanded them, neither spake I unto them: they prophesy unto you a lying vision, and divination, and a thing of nought, and the deceit of their own heart. 15Therefore thus saith JEHOVAH concerning the prophets that prophesy in my name, and I sent them not, yet they say, Sword and famine shall not be in this land: By sword and famine shall those prophets be consumed. 16And the people to whom they prophesy shall be cast out in the streets of Jerusalem because of the famine and the sword; and they shall have none to bury them-them, their wives, nor their sons, nor their daughters: for I will pour their wickedness upon them.

17And thou shalt say this word unto them, Let mine eyes run down with tears night and day, and let them not cease; for the virgin daughter of my people is broken with a great breach, with a very grievous wound.

18If I go forth into the field, then, behold, the slain with the sword! and if I enter into the city, then, behold, they that are sick with famine! for both the prophet and the priest go about in the land, and have no knowledge.

19Hast thou utterly rejected Judah? hath thy soul loathed Zion? why hast thou smitten us, and there is no healing for us? We looked for peace, but no good came; and for a time of healing, and, behold, dismay!

20We acknowledge, O JEHOVAH, our wickedness, and the iniquity of our fathers; for we have sinned against thee.

21Do not abhor us , for thy name's sake; do not disgrace the throne of thy glory: remember, break not thy covenant with us.

22Are there any among the vanities of the nations that can cause rain? or can the heavens give showers? art not thou he, O JEHOVAH our God? therefore we will wait for thee; for thou hast made all these things.

Finally a theory of everything?

 

Consciousness does not compute?

 

The red queen?

 

Romans Chapter 1 Legacy Standard Bible

 1.Paul, a slave of Christ Jesus, called as an apostle, having been set apart for the gospel of God,

2 .which He promised beforehand through His prophets in the holy Scriptures,

3 .concerning His Son, who was born of the seed of David according to the flesh,

4 .who was designated as the Son of God in power, according to the Spirit of holiness, by the resurrection from the dead, Jesus Christ our Lord,

5 .through whom we received grace and apostleship for the obedience of faith among all the Gentiles for the sake of His name,

6 .among whom you also are the called of Jesus Christ;

7 .to all who are beloved of God in Rome, called as saints: Grace to you and peace from God our Father and the Lord Jesus Christ.

8 .First, I thank my God through Jesus Christ for you all, because your faith is being proclaimed throughout the whole world.

9 .For God, whom I serve in my spirit in the gospel of His Son, is my witness as to how without ceasing I make mention of you,

10 .always in my prayers earnestly asking, if perhaps now at last by the will of God I may succeed in coming to you.

11 .For I long to see you so that I may impart some spiritual gift to you, that you may be strengthened;

12 .that is, to be mutually encouraged, while among you, by each other’s faith, both yours and mine.

13 .I do not want you to be unaware, brothers, that often I have planned to come to you (and have been prevented so far) so that I may have some fruit among you also, even as among the rest of the Gentiles.

14 .I am under obligation both to Greeks and to barbarians, both to the wise and to the foolish.

15 .In this way, for my part, I am eager to proclaim the gospel to you also who are in Rome.

16 .For I am not ashamed of the gospel, for it is the power of God for salvation to everyone who believes, to the Jew first and also to the Greek.

17 .For in it the righteousness of God is revealed from faith to faith; as it is written, “But the righteous will live by faith.”

18 .For the wrath of God is revealed from heaven against all ungodliness and unrighteousness of men who suppress the truth in unrighteousness,

19 .because that which is known about God is evident within them; for God made it evident to them.

20 .For since the creation of the world His invisible attributes, both His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse.

21 .For even though they knew God, they did not glorify Him as God or give thanks, but they became futile in their thoughts, and their foolish heart was darkened.

22 .Professing to be wise, they became fools,

23 .and exchanged the glory of the incorruptible God for an image in the likeness of corruptible man and of birds and four-footed animals and crawling creatures.

24 .Therefore God gave them over in the lusts of their hearts to impurity, so that their bodies would be dishonored among them.

25 .For they exchanged the truth of God for a lie, and worshiped and served the creature rather than the Creator, who is blessed forever. Amen.

26 .For this reason God gave them over to dishonorable passions; for their females exchanged the natural function for that which is unnatural,

27 .and in the same way also the males abandoned the natural function of the female and burned in their desire toward one another, males with males committing indecent acts and receiving in their own persons the due penalty of their error.

28 .And just as they did not see fit to acknowledge God, God gave them over to an unfit mind, to do those things which are not proper,

29 .having been filled with all unrighteousness, wickedness, greed, evil; full of envy, murder, strife, deceit, malice; they are gossips,

30 .slanderers, haters of God, violent, arrogant, boastful, inventors of evil, disobedient to parents,

31 .without understanding, untrustworthy, unloving, unmerciful;

32 .and although they know the righteous requirement of God, that those who practice such things are worthy of death, they not only do the same, but also give hearty approval to those who practice them.

Romans Chapter 10 The Bible in Living English.

 10.Brothers, my heart’s goodwill and entreaty to God is in their favor for their salvation. 2 For I testify that they have zeal for God, but not with insight; 3* for, not knowing about God’s righteousness and trying to make good their own, they did not let themselves depend on God’s righteousness. 4 For Christ is the end of the law for righteousness to every believer. 5 For Moses writes of righteousness on the basis of law “the man who does the things will have life” by it; 6 but righteousness on the basis of faith says thus: “Do not say to yourself ‘Who will go up to the sky?’” (that is, to bring Christ down;) 7 “or ‘Who will go down into the abyss?’” (that is, to bring Christ up from the dead). 8 But what does it say? “The word is near you, in your mouth and in your heart”; that is, the word of faith which we are proclaiming; 9 because if by your mouth you acknowledge Jesus to be Lord, and in your heart you believe that God raised him from the dead, you will be saved. 10 For it is with a heart believing is done leading to righteousness, and it is with a mouth acknowledgment is made leading to salvation. 11 For the text says “Anyone who believes in him will not be put to shame”; 12* for there is no distinction between Jew and Greek, for the same one is Lord of all, rich toward all who call on him; 13 for “everyone who shall call on the name of the Lord shall be saved.”

14 How are they then to call on him in whom they have not believed? And how are they to believe in him of whom they have not heard? And how are they to hear without a proclaimer? 15 And how are they to proclaim unless they are sent? as it is written “How beautiful are the feet of those who bring the news of good!”

16 But they did not all listen to the good news; for Isaiah says “Lord, who believed what they heard from us?” 17* Then believing comes out of hearing; and hearing, through Christ’s word. 18 But I say, did they not hear? why, “the noise of them went out into all the earth and their words to the ends of the world.” 19 But I say, did Israel not know? First Moses says “I will challenge your jealousy with what is not a people, provoke you with an insensate nation.” 20 And Isaiah comes out boldly and says “I was found by those who were not looking for me, I showed myself to those who were not inquiring of me.” 21 But as to Israel he says “all day I have spread out my hands to a disobedient and dissident people.”

ID is still in the fight II

 

File under"well said" CV

"Men of genius are admired, men of wealth are envied, men of power are feared; but only men of character are trusted. "

Alfred Adler 

Yet more on why ID is already mainstream.

 Design: A Scientific Proxy for Intelligence

Eric Hedin

Paul Nelson speaks to the pervasive use of design detection in how we infer intelligent agency in various fields of investigation, from archaeology to arson:

What turned my head around about ID — in a good way — in 1991, well before I met Bill Dembski, was a single paragraph in one of his early papers. He pointed out that design detection, far from being an esoteric and inscrutable inference, lay in fact at the center of many normal human inquiries and activities.1

Fine-tuning, in which a low-probability event also matches an independently derived pattern or condition, can serve as a proxy for intelligent design.2 The inference of intelligent agency stems from our experience with generating designed systems, and this applies across multiple fields of inquiry.

Michael Egnor writes,

How could we discern design from non-design? It’s an issue central to archaeology, and obviously would be central to space archaeology. It would be great science to sort out criteria for detecting intelligent agency in an object in nature, especially in a situation in which we have no idea about the nature of the designer.

Yet we find design everywhere in living things, on an immense scale. There’s a breathtaking lack of self-awareness in the scientific community about intelligent design.3

Researchers use proxies to help trace out the existence and progression of a target parameter in cases where the historic values of the parameter are no longer accessible.

A Common Procedure in Science

Using proxies to infer information about the past is a common procedure in science. How it works: For determining the trend of a certain parameter during the geological history of Earth, scientists identify a measurable artifact that has a strong positive correlation with the parameter. If the appropriate artifact is recorded chronologically and can currently be accessed (such as by taking a core sample), then the historical trend in the desired parameter (for example, the atmospheric temperature) can be determined. 

The correlation between the proxy and the target parameter needs to be properly calibrated to avoid systematic errors. Furthermore, researchers need to establish a strong negative correlation between the proxy and other possible effects that might confuse its association with the target parameter. For example

Paleomagnetic records from several sources (volcanics, archeological artifacts, stalagmites, and sedimentary materials) that serve as proxy magnetometers provide access to geomagnetic field evolution before the age of systematic ground and satellite measurements or historical observations of Earth’s magnetic field.4

Triple oxygen isotope measurements of shales have been used as a proxy for the abundance of continental landmasses.5

Paleoclimatology is the study of past climates. Since it is not possible to go back in time to see what climates were like, scientists use imprints created during past climate, known as proxies, to interpret paleoclimate. Organisms, such as diatoms, forams, and coral serve as useful climate proxies. Other proxies include ice cores, tree rings, and sediment cores.

Ice core records- deep ice cores, such as those from Lake Vostok, Antarctica, the Greenland Ice Sheet Project, and North Greenland Ice Sheet Project can be analyzed for trapped gas, stable isotope ratios, and pollen trapped within the layers to infer past climate.6

Intelligent design as a causative explanation can be inferred from proxies that consist of artifacts that contain a level of specified complexity or complex functionality and are known to be associated with intelligence. The negative correlation stems from the complete lack of any examples of such artifacts arising from non-intelligent sources. A negative correlation between design artifacts and natural processes also arises from our knowledge that natural processes systematically destroy information-rich systems with the passage of time.7

From the Caves of Qumran

The Dead Sea Scrolls are an example of a design artifact for which intelligence is inferred as the source.8 These scroll fragments, found in caves near Qumran in 1947-1956, are artifacts of a type known to be produced by intelligent humans, providing a strong positive correlation between the artifacts and intelligent human agency. Further, our comprehensive experience gives a negative correlation between scrolls of this type and any other source besides intelligence. Consequently, the scroll artifacts serve as an example of a robust proxy for human intelligence operating in the historical era to which the scrolls are dated.

When biological systems are examined, the level of specified complexity and complex functionality found in the molecular biochemistry of the cell, and in the irreducibly complex systems of living organisms, far exceeds anything ever designed and constructed by human intelligence. As a result, the mainstream scientific consensus is that this pervasive and profound complexity arose over time by non-intelligent forces of nature acting on fundamental particles. 

One reason that the origin of the specified complexity and complex functionality found in the molecular biochemistry of the cell is attributed to the fundamental forces of nature acting on elementary particles is that a strong positive correlation exists between random mixtures of particles and the subsequent formation of functional biochemistry. (Sarcasm alert!)

Elementary particles, primarily fermions interacting according to the strong force and the electric force, are known to form atoms which can combine into simple molecules such as water (H20) and carbon dioxide (CO2). Slightly more complex molecules, including sugars and amino acids, have also been found to occur naturally. The natural formation of complex bio-polymers becomes problematic, however.

Attempting to get those amino acids to join into any sort of complex molecules has been one long study in failure.9

Suitable Agents for Producing Living Systems?

Is there any warrant to draw a positive correlation between random, natural processes and the artifacts of living systems manifesting profound, functional complexity? Can it be legitimately claimed that living systems serve as a valid proxy for the action of unguided forces of nature? Have unguided forces of nature shown themselves as suitable agents for producing living systems? Only if the forces of nature are acting within a living system to begin with. 

One of biology’s “universal laws” (accredited to Rudolph Virchow) states, “Every cell comes from a preexistent cell.” 

CANCELED SCIENCE, P. 212

Apart from biological reproduction, natural processes have never been known to produce life. So, living organisms and their fossilized remains lack any positive correlation with the forces of nature. Therefore, the existence of life in the history of Earth does not serve as a valid proxy for the actions of natural forces as the agency for producing such life. With the complete absence of a positive correlation between living systems and natural processes, there is no need to establish a negative correlation between the proxy of life and the purported agency of nature.

Despite these arguments, the mainstream scientific community may nonetheless dismiss artifacts of living systems as proxies pointing to intelligent agency. Perhaps a different proxy for intelligent agency would be more convincing. For this, I suggest that the ultimate proxy for intelligent agency is intelligence. “Artifacts” of intelligent minds are available for investigation on Earth today. If researchers are unconvinced that artifacts of biochemistry belonging to living organisms are sufficient proxies for intelligence, perhaps careful scrutiny of their own minds would suggest otherwise. Or, perhaps not.10

Just another revolution devouring its children?

 

The maths of ID

 Bayesian Probability and Intelligent Design: A Beginner’s Guide

Andrew McDiarmid

If the phrase “Bayesian calculus” makes you want to run for the hills, you’re not alone! Bayesian logic can sound intimidating at first, but if you give it a little time, you’ll understand how useful it can be for evaluating the evidence for design in the natural world. On a new episode of ID the Future, biologist Jonathan McLatchie gives us a beginner’s guide to Bayesian thinking and teaches us how it can be used to build a strong cumulative case for intelligent design, as well as how we can use it in our everyday lives.

It is one of the most important formulas in all of probability, and it has been central to scientific discovery for the last two centuries. At its heart, Bayes’s theorem, first developed by 18th century English statistician, philosopher, and minister Thomas Bayes, is a method to quantify the confidence one should have in a particular belief or hypothesis. The process results in a likelihood ratio of a hypothesis being true or false, given the evidence. Here, Dr. McLatchie explains what the theorem is, the components that comprise it, when it would typically be used, and some useful examples of Bayesian reasoning in action. 

Dr. McLatchie shows how Bayesian probability can be applied to the evidence for design in nature. First, he argues that the initial prior probability — the intrinsic plausibility of the hypothesis being true given the background information alone — for the design hypothesis is not low:

In the case of intelligent design and our inferences to design in biology, we have independent reasons, I would contend, to already think that a mind is involved in the origin of our cosmos, including the fine-tuning of the laws and constants of our universe…and the prior environmental fitness of nature.

Secondly, when you add in the evidence we’ve discovered of the complexity of living cells, the infusions of new biological information into the biosphere over time, the evidence for the Big Bang, and more, the cumulative case for intelligent design grows stronger. “If we suppose that a mind is involved,” says McLatchie,

then it’s not hugely improbable that we’d find information content in the cell, and that we’d have information processing systems and that we’d have irreducibly complex machines. But, on the other hand, it is overwhelmingly improbable, I would argue, that such information-rich systems and irreducibly complex machinery would exist on the falsity of the design hypothesis. And so you have this overwhelmingly top-heavy likelihood ratio.

Download the podcast or listen to it here.

The iron fist of the emperor

 

On formalising design recognition

 

Yet more on the future of energy.

 

Chemistry did not beget biology?

Proteins Are Rare and Isolated — And Thus, Cannot Evolve

Brian Miller

Were the laws of physics and chemistry fine-tuned to allow proteins to evolve easily? This claim is a key element in a conception of design advocated by theologian Rope Kojonen. He believes, in effect, that God designed the laws of nature so that proteins and other biological phenomena can evolve. In a previous post, I discussed an article, “On the Relationship between Design and Evolution,” that I wrote with Stephen Dilley, Casey Luskin, and Emily Reeves. Both in the article and in a series at Evolution News, we have been critiquing Kojonen’s book The Compatibility of Evolution and Design, which argues that evolutionary theory can be reconciled with the belief that life demonstrates evidence of design. Here, I will expand my previous argument about proteins, showing functional proteins are rare and isolated — and thus, cannot evolve. If my account is correct, then Kojonen’s view of design is fatally flawed.

The Relationship Between Rarity and Isolation

Kojonen acknowledges that many proteins correspond to such rare sequences that they could not have emerged through a random search. Yet he argues that rarity does not necessarily entail isolation. We summarize the argument as follows: 

Like Kojonen, other thinkers (e.g., Hunt 2007; Venema 2010; Matheson 2010) have argued that rarity in sequence space does not necessarily imply isolation in sequence space to a degree that would pose a barrier to evolution. This line of thinking accepts (or allows) a continuous path of functional sequences from a simple protein to a more complex protein. Under this view, even if proteins are rare, they are (or could be) clustered together. As such, the mutation-selection mechanism would not need to search a large region of sequence space; it would only need to find the continuous pathways close at hand.

A Spacecraft Seeks a Clear Path

We respond to this argument as follows:

Yet a simple analogy shows why this objection is wrong. Imagine a spacecraft lands on the north pole of a planet, and the astronauts wish to drive to the south pole. Their ability to do so depends on the percentage, p, of the planet’s surface that is navigable. If p is 70.0%, a continuous path likely exists between the poles. If p is 0.1%, a path most likely would not exist. The lower the percentage, the less likely a path.

Let us now consider how this analogy would apply to the evolution of new proteins. The rarity of the beta-lactamase domain studied by Axe (2004) would correspond to a planet the size of our entire galaxy, and the total amount of navigable land would correspond to the surface area of an atom. If we extend our analogy to a protein whose rarity is 1 in 1023, this would still be akin to a planet the size of Jupiter with a total area of traversable land the size of a postage stamp. A navigable path from one pole to the other would almost certainly not exist. In other words, even for the protein that Kojonen claims has a sequence probability that is “more common”, the possibility of a continuous functional path leading from it to a typical protein is exceedingly remote. 

Complex proteins appear to be overwhelmingly isolated, including from simple amino acid sequences that can perform basic functions. Collectively, the data show that proteins of typical complexity are beyond the reach of natural selection, random mutation, and other standard evolutionary mechanisms.

Could the laws of physics have been fine-tuned to enable such narrow paths? It seems not:

Kojonen tries to overcome this problem by arguing that the physical properties of proteins are “finely-tuned” to bias the clustering of functional sequences such that a very narrow path could extend to complex proteins with rare functional sequences. The biasing would result in the prevalence of functional sequences along a path to a new protein being much higher than in other regions of sequence space. But such biasing could not possibly assist the evolution of most proteins. Biasing in the distribution of functional sequences in sequence space due to physical laws is arguably subject to the same constraints as the biasing in play in the algorithms employed by evolutionary search programs. Consequently, protein evolution falls under “No Free Lunch” theorems that state that no algorithm will in general find targets (e.g., novel proteins) any faster than a random search. An algorithm might assist in finding one target (e.g., specific protein), but it would just as likely hinder finding another. Thus, although Kojonen acknowledges that proteins are sometimes too rare to have directly emerged from a random search, he fails to appreciate the extent to which rarity necessitates isolation and why this must often pose a barrier to further protein evolution. Different proteins have completely different compositions of amino acids, physical properties, conformational dynamics, and functions. Any biasing that might assist in the evolution of one protein would almost certainly oppose the evolution of another. In other words, the probability of a continuous path leading to some proteins would be even less likely than if the distribution of functional sequences were random

Rare Functional Sequences Entail Isolation

We summarize our general argument as follows:

In the end, evolving new proteins is quite difficult to envision under known laws of nature. This is because a continuous path of functional sequences in sequence space is not plausible — primarily due to both the rarity of functional sequences and the isolation of proteins with entirely different structures and functions. A key point here is that extremely rare functional sequences entail isolation in sequence-space. This hurdle poses a fundamental challenge to Kojonen’s thesis that nature was designed to evolve life. Proteins, like stars, are separated by vast distances. 

Recall that Kojonen’s model holds, in effect, that God designed the laws of nature so that proteins can evolve. This is a key element of Kojonen’s design hypothesis. This hypothesis is testable: is there empirical evidence that known laws of nature allow for proteins to evolve? Or do the data indicate impassable hurdles between functional proteins? The data clearly favor the latter. Functional proteins sequences are rare and isolated, with vast chasms of non-functionality between them.

The unavoidable connection between protein rarity and isolation not only overturns Kojonen’s thesis about design, but also overturns mainstream evolutionary theory in its entirety. Although our primary target is Kojonen’s account of design, the scientific data clearly raise additional troubling problems for evolution.

When and where the party of Ali finally triumphed?