Darwin has his bluff called?

Darwin’s Bluff Is a Number 1 New Release on Amazon!

David Klinghoffer 

Congratulations to our colleague Professor Robert Shedinger on the release of his new book, Darwin’s Bluff: The Mystery of the Book Darwin Never Finished! At this writing it’s the #1 New Release in Scientist Biographies on Amazon, and the #1 New Release in Evolution on Kindle.

Great work, Dr. Shedinger and Discovery Institute Press! It is a remarkable thing that Charles Darwin seems never to have been honest with himself, perhaps to the end of his life, about the implications of the fact that his planned big book about the actual evidence for his theory could not be written, because the evidence wasn’t there. It still isn’t. The famous Origin of Species, he said, was a “mere abstract.” If he could have written the Big One, you can be sure he would have done so. He found time to write other books subsequent to the Origin. Just not the really crucial one.

Back to the future?

 

The state can't handle the truth?

 

Irreconcilable differences?

 

Not an argument from silence.

 Atheist Philosopher Explains Why Intelligent Design Is Not a “God of the Gaps” Argument

Jonathan McLatchie

Jeffrey Jay Lowder is an atheist philosopher and author, whom I would rate as among the top tier of intellectual critics of theistic belief (you can watch him debate Frank Turek here). Not only is he an extremely balanced and nuanced thinker, but he is also quite amicable. I consider him a friend, and we have met for dinner or drinks a couple of times. On Twitter (I refrain from calling it by its hideous new name, “X”), he goes by the handle “Secular Outpost.” Recently Lowder posted the following remark:

Unpopular opinion (among nontheists): the arguments for intelligent design defended by the likes of Moreland, Craig, and Meyer are NOT god of the gaps arguments.

My colleague David Klinghoffer asked Lowder to clarify his thinking on this. In response, Lowder linked to two blog posts he had written addressing the subject. The first, published in 2016, responds to Victor Reppert, who had asked whether there is “any theistic argument [from/in natural theology] that can’t be accused of being a god-of-the-gaps argument,” and if this rejoinder may serve as “an all-purpose reply to all natural theology.” Lowder answers the first of those questions in the affirmative and the second in the negative. 

Why Intelligent Design Is Not a “God of the Gaps’ Argument

(1) There is some puzzling phenomenon P which science cannot at present explain. 

(2) Theism does explain P. 

Therefore, 

(3) P is more likely on the assumption that God exists than on the assumption God does not exist.

I have no issues with Lowder’s reconstruction of a god-of-the-gaps argument. As he explains, “The key feature of this argument — and what makes it a ‘God-of-the-gaps’ argument — is premise (1). The focus is on science’s present inability to explain P.” How might one construct an argument that is not vulnerable to the god-of-the-gaps critique? Suppose you want to advance an argument for theism based on the existence of consciousness. Lowder proposes that the following formulation of the argument (where E is the existence of human consciousness, T is theism, and N is naturalism) evades this charge:

(1) E is known to be true, i.e. Pr(E) is close to 1.

(2) N is not intrinsically much more probable than T, i.e., Pr(|N|) is not much greater than Pr(|T|).

(3) Pr(E | T & B) > Pr(E | N & B).

(4) Other evidence held equal, N is probably false, i.e., Pr(N | B & E) < 1/2.

Put into straightforward English, the argument is as follows:

(1) The existence of human consciousness is known to be true.

(2) Naturalism is not intrinsically much more probable than theism.

(3) The probability of the existence of human consciousness given theism and the background information is greater than the probability of the existence of human consciousness given naturalism and the background information.

(4) Other evidence held equal, naturalism is probably false (i.e., the probability of naturalism given the background and the evidence is less than 50 percent).

Lowder concludes that “Whatever problems may exist within that argument, being a God-of-the-gaps argument clearly isn’t one of them.” I completely agree with Lowder’s assessment. Intelligent design makes the argument that various specific features of life and the universe — in particular, the informational properties of DNA, and the irreducibly complex nature of molecular systems — are rendered vastly more probable than they would otherwise be by the supposition that a conscious mind was involved in their origins. Thus, they are positively confirmatory of design. Since confirmations of design in the universe are significantly less surprising (or, more probable) given the hypothesis of theism than on its falsehood, the evidence of design also translates into positive evidence of the existence of God. Perhaps there are vulnerabilities in this argument structure — but, whatever may be wrong with it, it is certainly not wrong by virtue of being a god-of-the-gaps argument. I would like to commend Lowder for his intellectual integrity in pointing this out, despite our disagreements on the larger question of whether intelligent design is in fact true.

Jeff Lowder Reviews Signature in the Cell

The second article linked by Lowder is a critical review of Stephen Meyer’s book, Signature in the Cell: DNA and the Evidence for Intelligent Design. I had more disagreements with this article than with the first. Lowder remarks that “We are fortunate that Meyer explicitly provides the logical form of his argument,” which he quotes as follows:

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information. 

Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information. 

Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.

Lowder, again to his credit, notes, “I agree with Meyer that it would be a mistake to dismiss his argument as an argument from ignorance.” Furthermore, “We should consider the possibility that the origin of life is a source of potential evidence for intelligent design (and for theism).” What, then, is Lowder’s principle objection to Meyer’s argument? He writes,

The objection I have in mind is this: the design hypothesis is not an explanation because, well, it doesn’t explain. Regarding the origin of biological information, it still isn’t clear to me what Meyers [sic] believes the design explanation is. I don’t find in the book a description of how an intelligent designer created / designed / programmed — not sure what the right verb is — the first biological information. In order to explain biological information, it’s not enough to posit the existence of an intelligent designer as a potential cause of biological information. In addition, it seems to me that a design explanation must also include a description of the mechanism used by the designer to design and build the thing. In other words, in order for design to explain something, we have to know how the designer designed it. If we don’t know or even have a clue about how the designer did it, then we don’t have a design explanation.

However, this seems to me to be mistaken. For example, suppose that future scientists are able to capture high resolution images of Alpha Centauri, the closest star to our sun, and were to discover that a vehicle resembling a Volkswagen Beetle were orbiting a planet there. Presumably, we could justifiably infer design if we had no idea what equipment or processes were used to assemble the vehicle, and even if we could not identity the agent responsible. Those are interesting downstream questions, to be sure. But our inability to answer them does not negate our ability to infer design as an explanation of how the Beetle came to be there. 

Moreover, we all believe that our conscious minds interact with the material world, even though we lack an understanding of how consciousness works. Thus, to postulate that a conscious mind is responsible for complex and functionally specific information content, or an engineered system, is a legitimate explanation, even though we currently cannot give an adequate account of how our minds animate our bodies to accomplish engineering tasks.

Theism and Explanation

Lowder quotes Gregory Dawes’s Theism and Explanation, in which he asserts, objecting to Richard Swinburne’s argument for theism,

It is only when you have specified the divine intention in question that we can test your explanation, by asking what else would follow if God did indeed have this intention. And as we have seen, it will not do merely to substitute the explanandum for the posited goal… As we have already seen, this would be a spurious kind of explanation, seriously lacking in empirical content. 

P. 119

However, to make a compelling argument for theism, it is not necessary to posit that there is a high probability of God having a particular motivation or intention for creating, for example, complex life. It is enough to posit that it is not immensely implausible that God would have such a purpose for creating. Suppose, for example, that God’s purpose in creating a world containing complex embodied creatures is that they might participate in an arena of moral choice, providing them opportunities to mold and shape their character, developing in morally significant ways. In such a scenario, for actions to have predictable consequences, the universe would have to be governed by fixed natural laws. And it is being physically embodied — in a world of pushes and pulls — that accentuates our ability to engage in moral decision-making. I think most readers can see that such a scenario is not at all wildly implausible on the supposition of classical theism. However, the existence of such a world is rendered absurdly improbable if we assume the falsehood of theism. Therefore, the world we observe constitutes strong (I would say, overwhelming) evidence in favor of theism.

Despite our many disagreements, I sincerely appreciate Lowder’s spirit and intellectual honesty. I hope the next generation of secular thinkers follow his lead.

Darwin corrects JEHOVAH?

Darwin’s “God Wouldn’t Do It This Way” Argument 

Robert Schedinger

Editor’s note: We are delighted to present an excerpt from the new book by Dr. Shedinger, Darwin’s Bluff: The Mystery of the Book Darwin Never Finished. This article is adapted from Chapter 3.

Aside from proposing a naturalistic explanation for the mechanism driving evolution, it is clear that one of Charles Darwin’s main goals in his species work was to put the final nail in the coffin of creationist approaches to the diversity of life. Natural selection was actually subordinated to this latter goal. Darwin wrote to Asa Gray on May 11, 1863, “Personally, of course, I care much about Natural Selection; but that seems to me utterly unimportant compared to [the] question of Creation or Modification.” As a result, a book widely hailed as proposing a true mechanism for evolution actually reads more like an anti-creationist polemic.

In contrast to the view that species represent ideal types in the mind of God that were created in the form we see them today and placed in the locations where we encounter them today, Darwin argued that the geographical distribution of species in the world represented evidence for a long history of evolutionary development from common ancestors. There are many places in the Origin of Species where Darwin makes explicit that the evidence he is describing makes little sense on the assumption that species were each specially created.

On Oceanic Islands

For example, when discussing the lack of certain species of animals and plants on oceanic islands, Darwin writes, “He who admits the doctrine of the creation of each separate species, will have to admit that a sufficient number of the best adapted plants and animals were not created for oceanic islands.”1 Here Darwin seems to assume that a creator would have no reason to leave oceanic islands devoid of these “best adapted plants and animals,” so their absence stands as evidence against creationism. A few pages later Darwin argues:

As the amount of modification which animals of all kinds undergo partly depends on the lapse of time, and as islands which are separated from each other or from the mainland by shallow channels, are more likely to have been continuously united within a recent period than the islands separated by deeper channels, we can understand how it is that a relation exists between the depth of the sea separating two mammalian faunas, and the degree of their affinity, — a relation which is quite inexplicable on the theory of independent acts of creation.2

That is, because the mammalian fauna on islands close to continents is more like the continental fauna than that found on oceanic islands much farther away from continents, it is reasonable to believe there is a relationship between continental and island fauna rather than to believe that a creator decided to make the fauna of oceanic islands more different from continental fauna.

Doubling Down

Darwin doubles down on this line of argument when discussing the way in which closely allied species can often be found in separate but nearby locations, suggesting a common ancestor that inhabited both places that then diverged into two new species. To illustrate, he again invokes the island/continent relationship. “We see this in the striking relation of nearly all plants and animals of the Galápagos archipelago, of Juan Fernandez, and of the other American islands, to the plants and animals of the neighboring American mainland; and of those of the Cape de Verde archipelago, and of the other African islands to the African mainland,” he writes. “It must be admitted that these facts receive no explanation on the theory of creation.”3

Time after time Darwin discusses some specific observation about the distribution of living organisms and then insists that a theory of independent creation of each species is powerless to explain it. Yet surely it is hazardous to assume one knows what a creator of the natural world would or would not do.

There is also the fact that many of Darwin’s best examples of geographical distribution pointing to evolutionary change involve rather less than dramatic modifications. In light of this, perhaps natural selection can diversify a species into a family of species and no further. The Darwin skeptic could thus contend, why not the special creation of types that then diverged into families of species via natural processes? Or perhaps the diversification fueled by natural selection reaches another rung or two up the taxonomic ladder, to orders or classes. Or perhaps universal common descent is the case, but it proceeded from intelligent input rather than by a purely blind mechanism.

A Classic Fallacy

One searches the Origin in vain for a thoughtful engagement with these other options. Darwin’s theory of descent with modification may indeed be a better explanation than independent creation of each species, but Darwin does not merely declare his explanation better than this one alternative; he implies it is the only possible explanation. Thus one could be forgiven for seeing in Darwin’s argumentation the classic either/or fallacy, wherein the person knocks down one option and declares a second option the clear winner, never mind that there are other live options available.

In Darwin’s defense, he does invoke a more sweeping defeater for any theory of biological origins invoking a creator. We find this in a passage where he is discussing the phenomenon of typology — the structural similarity between many organisms such as the four-limbed pattern found in mammals, birds, and reptiles: “On the ordinary view of the independent creation of each being, we can only say that it is so; — that it has pleased the Creator to construct all the animals and plants in each great class on a uniform plan; but this is not a scientific explanation.”4

Darwin’s Wider Goal

Darwin’s problem with creationist explanations is not that they are demonstrably false or impossible; it is that they are not, in his view, scientific. Here we find one of Darwin’s wider goals for the Origin: to stamp out creationist explanations and put natural history on a firmly naturalistic (by his lights, scientific) foundation. But it never seems to have occurred to him that his “God wouldn’t do it this way” argument was itself theologically driven, and therefore, on his own accounting, itself not a particularly scientific mode of argument.4

Of course, Darwin knew he would be on firmer ground if he could produce empirical evidence to support his view and overcome various difficulties confronting it. One such difficulty: If all organisms had descended from one or a few common ancestors, how had life spread all over the planet? Certain animals like birds and fish can move over long distances, but what about stationary organisms like plants? How could plants travel over long oceanic distances to colonize islands? Trying to answer this question sent Darwin into a series of experiments related to seed dispersal.

Antimatter is rebellious?

 

On reductionism: Pros and Cons.

 

The thorium dream lives?

 

Prisoner of conscience or public enemy?

 

Conditionalism is not a kook position? Pros and Cons

 

The other prisoner of conscience? II

 

The other prisoner of conscience?

 

The decanonizing of Darwin continues apace?

 In Darwin’s Bluff, Robert Shedinger Rightly Forgoes the Hagiographic Tradition

Neil Thomas

The new book by Robert Shedinger, Darwin’s Bluff: The Mystery of the Book Darwin Never Finished, is a deeply researched and fascinating volume which, like the author’s previous work (The Mystery of Evolutionary Mechanisms, 2019), digs up facts and figures about Darwin’s work which you won’t find elsewhere. The fact that Shedinger avoids the hagiographic tradition of treating Darwin as an inviolable icon is all to the good, chiming as it does with a tendency post-1985 to look honestly at the disabling empirical deficits which reveal Darwin in retrospect to have been engaged more in some rather idiosyncratic Nature mysticism than in evidence-based science.

The fact that the author is a professor of religion (at Luther College) does not in any way define him as what American linguist S. I. Hayakawa once termed the “snarl word” of creationist. The present reader, in company with a host of agnostic biologists and cosmologists, simply finds in Darwin a complete dearth of convincing scientific evidence. For myself and other scholars, the issue of religion is quite irrelevant, a misleading canard which should never be referenced in a properly scientific debate.

Getting fraud down to a science?

 

The Thorium dream dies hard?

 

The book he didn't write said more about him than the ones he did?

 

The fall of the empire of the gene?

 

What could go wrong? II

 

The appeal to engineerless engineering continues to fail..

 Sophisticated Precision in Fruit Fly Sensory Systems

David Coppedge

Last week, we considered the signal “wave” that controls development of the compound eyes in fruit flies and the motor neurons that control their rapid zigzag turns in the air. Pilots have to learn the forces of lift, drag, and thrust, and know how to prevent stalls. They know that rapid banking turns vastly increase G-forces and come with a high risk of stalling. Aerobatic know-how comes built-in for fruit flies. The same is true for all unrelated animals that perform powered flight, whether mammal (bat), reptile (pterosaur), or bird.

Smell Sense

The miniature insect flyers around us also have good olfactory organs that help them smell where to go. They smell good (or well, for you grammarians).

A news item from Ruhr University Bochum in Germany tells, “How Fruit Flies Smell CO2.” This commands our attention. Could fruit flies offer solutions for climate change monitoring? The scientists are inspired by the fly’s sensing ability.

The new findings are to be incorporated into the development of a CO2 biosensor, which the Bochum team is researching in cooperation with the Institute of Aircraft Systems in Stuttgart. “This should enable us to detect CO2in liquid media, which is something that as yet can’t be done,” says Störtkuhl. CO2 sensors are used on the International Space Station, for example, where they must consume as little energy as possible. Given that physical measurement methods are not very energy-efficient, a biosensor could be a great alternative.[

Notice the higher rank bestowed on biological sensors. A biosensor might be able to detect other volatile molecules. And so, curiosity rises about how fruit flies smell carbon dioxide, and why they need to. Some readers may be aware that mosquitoes follow the CO2 in human breath to find their victims. Fruit flies smell CO2 emissions from fermenting fruit for their needs. 

Since CO2 is ubiquitous in the atmosphere, flying insects must be able to detect elevated concentrations along a gradient. The tiny insects’ expertise at finding and following carbon dioxide plumes in the air leads to suspicions of sophisticated systems for detecting the “odorless” gas that we humans exhale with each breath. (Thank goodness it is odorless to us.) So, how do they do it? We look at the paper in PLOS One for answers.

Answer: They’re not sure. The team found two receptors on the third segment of the fly’s antennae that respond strongly to bicarbonate CO2 emissions when those receptors are encoded in frog eggs. The response, however, depends on the mix of receptors.

We found that application of sodium bicarbonate evokes large inward currents in oocytes co-expressing Gr21a and Gr63a. The receptors most likely form hetromultimeric [sic] complexes. Homomultimeric receptors of Gr21a or Gr63a are sufficient for receptor functionality, although oocytes gave significantly lower current responses compared to the probable heteromultimeric receptor.

They also found that citronellol blocks the receptors — good to know for manufacturers of insect repellants.

Taste Sense

In fruit flies, the gustatory and olfactory senses overlap. Dr. Roman Arguello at Queen Mary University of London has been “delving into the genes and cells behind their delicate noses and tongues,” finding that the insects are able to adapt their senses to their environments. He likens it to one fly responding to a ripe peach as if it “tastes and smells like tangy vinegar to one fly, but like a burst of summer to another.” It’s quite common in fruit flies, he says, which inhabit a variety of habitats. But is this evolution?

“It’s like finding hidden islands of diversity within a vast ocean of uniformity,” says Dr Arguello. “These changes in gene expression tell us about the evolution of new smells, new sensitivities, and even new ways of using scent to navigate the world.”

Again,

“These findings open up exciting new avenues for understanding how sex differences evolve and how they impact animal behavior,” says Dr Arguello.

But does this research published in Nature Communications really provide “valuable insights into the general principles of how sensory systems evolve,” as they claim? 

All they found were changes in gene expression — not mutated genes that were naturally selected as Darwinian theory requires. The paper only mentions mutations four times (pleiotropic mutations, at that), but “evolution” 144 times. As for “selection,” most of the 14 mentions involved stabilizing selection (i.e., keeping things the same), not the positive selection required for novelty and innovation. The only mentions of “positive selection” were from another study that contradicted this team’s finding of predominantly “evolutionary constraint.” They had no word on how taste receptors originated in the first place.

Directional Sense

Returning to the fundamental aspect of flight (flies do fly), another paper, this one in Nature, discusses the directional sense in these tiny aerobatic insects. Mathematicians will enjoy the abstract from this paper:

To navigate, we must continuously estimate the direction we are headed in, and we must correct deviations from our goal. Direction estimation is accomplished by ring attractor networks in the head direction system.However, we do not fully understand how the sense of direction is used to guide action. Drosophila connectome analyses reveal three cell populations (PFL3R, PFL3L and PFL2) that connect the head direction system to the locomotor system. Here we use imaging, electrophysiology and chemogenetic stimulation during navigation to show how these populations function. Each population receives a shifted copy of the head direction vector, such that their three reference frames are shifted approximately 120° relative to each other. Each cell type then compares its own head direction vector with a common goal vector; specifically, it evaluates the congruence of these vectors via a nonlinear transformation. The output of all three cell populations is then combined to generate locomotor commands.

For non-mathematicians, we can just recall the coach’s advice in many sports to turn your head in the direction you need to go. Fruit flies automatically know this, because specific cells are doing vector calculus and nonlinear transformations, then giving commands to the legs and wings. If building a robot, this would require some engineering know-how:

Accurate navigation requires us to fix a goal direction and then maintain our orientation towards that goal in the face of perturbations. This is also a basic problem in mechanical engineering: how can we keep the angleof some device directed at a target? One solution to this problem is to use a resolver servomechanism to measure the discrepancy or error between the current angle and the goal angle.

The eight researchers describe how fruit flies keep focused on the goal. They create a model and compare it to live data from fruit fly behavior. Why is a transformation needed? Because, they say, motor commands must convert their coordinates from allocentric space (other-directed) to egocentric space (self-directed). 

This poses a coordinate transformation problem. Here we describe a network that solves this problem. This network creates two opponent copies of the allocentric head direction representation, with equal and opposite shifts (θ ± shift). Each copy is then separately compared with an allocentric goal representation, to measure congruence with the goal. The difference between the two opponent congruence values becomes an egocentric motor command.

The PFL3R and PFL3L cell populations take care of this. But there was a surprise finding:

At the same time, our results highlight the unexpected role of PFL2 cells. These cells provide a solution to a classic problem — namely, the fundamental tradeoff between speed and accuracy. High feedback gain allows a system to converge quickly towards its goal, and so it makes sense that gain should be high when error is large, that is, when there is a large discrepancy between the system’s current state and its goal. However, high gain can cause overshooting of the goal, especially when error is already small. We show that PFL2 cells effectively adjust the system’s gain, depending on the magnitude of the system’s current error.

Wow. That should be enough to make us all pause before swatting. CO2 sensors on the antenna, taste sensor gene regulators that adapt to the environment, and vector calculus in the head and legs — how does all this sensory engineering fit into such a tiny fly? The authors had almost nothing to say about evolution, leapfrogging over it with this statement, “the idea that a neuron’s inputs are adjusted (over development and/or evolution) to fit into some standard dynamic range dictated by the biophysical properties of a typical neuron….”

While admiring the humble fruit fly, let us take a moment to marvel at the human mind that can figure these things out. The next time you see a tiny fly or gnat, imagine inventing tools to study those itty-bitty eyes, wings, and antennae — to say nothing of the genes and proteins regulating them — and figure out how they work, using models and mathematical functions. Our sensory capabilities are well-designed, too.

Hydrogen vs. Lithium?

 

The immortal?

 

Making the elegant the enemy of the obvious?

 Vilenkin: A Physicist in Flight from Intelligent Design

Evolution News

In his discussion with Robert Lawrence Kuhn at Closer to Truth, Tufts physicist and cosmologist Alexander Vilenkin addresses the question, “Is the Universe Fine-Tuned for Life and Mind?” Kuhn asks:

If the deep laws of the universe had been ever so slightly different human beings wouldn’t, and couldn’t, exist. All explanations of this exquisite fine-tuning, obvious and not-so-obvious, have problems or complexities. Natural or supernatural, that is the question.

Vilenkin — who is also a professor of evolutionary science — concedes the main point:

Alexander Vilenkin: [0:40] “Well yeah that’s right. It appears that the Universe is fine-tuned in the sense that there are about 30 constants of nature which take some specific value: if you look at these numbers, they look like totally random numbers. However, if you change these numbers even slightly, the properties of our universe would change quite dramatically so…”

Robert Lawrence Kuhn: “Generally for the bad.”

Alexander Vilenkin: “Yes, generally for the bad and the question is, what do we make of that?”

Vilenkin then introduces the idea that there might be a multiverse in which our universe, one of many, just happens to have these constants. But he admits that efforts to derive the 30 constants from a fundamental theory have failed [7:11]: “There is no question that despite tremendous effort to explain the constants of nature from fundamental theory, there is very little to show for that effort.” 

But what about the more basic cosmological constant?

Should the Cosmological Constant be Close to Zero?

Vilenkin rejects the idea that the universe is designed, in part because the cosmological constant — a repulsive force that acts against gravity — does not have a “special value” like zero or nearly zero:

Alexander Vilenkin: [9:36] “It is hard to disprove that the value was selected by design but it does look like it is a product of entropic selection. The reason is that there is a range of values of the cosmological constant that is consistent with the formation of galaxies and evolution of life This is a narrow range which includes zero actually. And if it is a random selection (and) you have many regions with different values of this cosmological constant, we expect to find ourselves somewhere in the middle of that range. And this is actually what we observe. So what we observe is perfectly consistent with this such random entropic selection. On the other hand, if you think of design, I would think that design would choose some more special value, for example zero, and in fact if the value of the cosmological constant were fine-tuned, more for example much closer to zero than it is, it would be very hard to explain it through the multiverse hypothesis and that would be evidence against this hypothesis.”

What Is the Cosmological Constant?

It’s really hard to know. The constant is generally represented as an equation. But much about it is unclear. From science writer Adam Mann:

The cosmological constant is presumably an enigmatic form of matter or energy that acts in opposition to gravity and is considered by many physicists to be equivalent to dark energy. Nobody really knows what the cosmological constant is exactly, but it is required in cosmological equations in order to reconcile theory with our observations of the universe.

ADAM MANN, WHAT IS THE COSMOLOGICAL CONSTANT?, LIVE SCIENCE, FEBRUARY 16, 2021

Cosmologists use it, Mann says, because they “may not know what it is, but they know that they need it to make the universe make sense.” At Scientific American, it was described in 2021 as “physics’ most embarrassing problem.”

If We Don’t Know What It Is, How Do We Know It Should Equal Zero?

Experimental physicist Rob Sheldon writes to offers some thoughts:

The cosmological constant, also known as dark energy, arises from Big Bang models that have acceleration, where the expansion of the universe is speeding up with time. This is just one of many models of the universe. The observational data supporting this model was so lacking, a Nobel Prize was offered to anyone who could find evidence for it. Perlmutter, Reiss and Schmidt used 75 type Ia supernovae to argue that acceleration was there, and received the Nobel Prizein 2011. But Subhir Sarkhar used >2000 SNIa in a paper in 2021 to show that the acceleration was consistent with zero…

Not only is this “Dark Energy constant” not well supported theoretically (the simplest derivations are 120 orders of magnitude too big), it isn’t even well supported experimentally.

Rather than admit there is something wrong with the model (which shows the power of consensus thinking), Alexander Vilenkin argues for a multiverse to avoid a Designer. But in a multiverse, everything is possible, including Designers. So I really don’t see this as a logical atheistic solution. It reeks of terrified desperation.

So the arguments against the idea that our universe was designed amount to 1) a speculation that there might also be countless flopped universes out there; and 2) a claim that there is a cosmological constant that should equal zero but doesn’t. But the claims for a cosmological constant are not well supported theoretically.

If you are not an ideological materialist atheist, it would make more sense just to assume that our universe is designed because of the clear evidence for fine-tuning. All the rest is up for debate.

Continuing to announce JEHOVAH'S Kingdom.

 

The mind contemplates itself?

 Consciousness, a Hall of Mirrors, Baffles Scientists

Denyse O Leary

To contemplate consciousness is, as professor of religion Greg Peterson put it, like looking into and out of a window at the same time. No surprise then that philosophers of science call it the Hard Problem of Consciousness. The inexorable progress of brain imaging was supposed to dissolve the conundrum but we spoil no surprise by saying that new information and insights only deepened it.

Among the many quests, one has been to discover the seat of consciousness. An image rises unprompted. Seat? Does consciousness have a seat at the table? Wait a minute. Isn’t consciousness the table? You see the difficulty, of course. At any rate, the search is for the specific bit of the brain that spews out the unthinking electrical charges that create consciousness.

It’s been a long and winding road. Brain imaging has not turned out to be a road map of the mind. For example, functional MRI imaging only tells researchers where blood is traveling in the brain. The problem is, as a Duke University research group pointed out, “the level of activity for any given person probably won’t be the same twice, and a measure that changes every time it is collected cannot be applied to predict anyone’s future mental health or behavior.”

Rise and Fall of the Lizard Brain

The most widely popularized theory of mind — the triune brain theory — depends on organization rather than imaging. Originally developed by Yale University physiologist and psychiatrist Paul D. MacLean (1913–2007) decades ago and promoted by celebrity skeptic Carl Sagan (1934–1996), it divides the brain into three parts. The reptilian brain controls things like movement and breathing, the mammalian brain controls emotion, and the human cerebral cortex controls language and reasoning.

This approach resulted in immensely reassuring ideas; for example, a widely disliked boss or politician morphed into a “dinosaur brain.” In 2021, Jeff Hawkins, inventor of the PalmPilot (a smartphone predecessor) even claimed to have figured out how human intelligence works, relying on his model of the mammalian brain.

The human brain was bound to disappoint pop culture in this matter because key functions are distributed throughout. Also triune brain theory doesn’t square with the high animal intelligence recently found in (non-vertebrate) octopuses. Claims for the mammalian brain in particular don’t square with the high intelligence found in some birds. Let alone with the fact that human consciousness remains an absolute outlier.

But MacLean’s idea has proven much too culturally satisfying to be spoiled by mere neuroscience. As one research team notes, “despite the mismatch with current understandings of vertebrate neurobiology, MacLean’s ideas remain popular in psychology. (A citation analysis shows that neuroscientists cite MacLean’s empirical articles, whereas non-neuropsychologists cite MacLean’s triune-brain articles.)”

It’s All in the Connections

Never mind, the exciting new world of -omes (genomes, epigenomes, biomes…) beckons. The connectome — essentially, a complete “wiring diagram” of the brain, might possibly identify human consciousness. In 2010, computational neuroscientist Sebastian Seung told humanity, “I am my connectome,” a thought on which he expanded in his 2012 book, Connectome: How the Brain’s Wiring Makes Us Who We Are. In 2012, National Institutes of Health director Francis Collins was thinking along the same lines: “Ever wonder what is it that makes you, you? Depending on whom you ask, there are a lot of different answers, but these days some of the world’s top neuroscientists might say: ‘You are your connectome.’”

That moment has passed. Harvard neuroscientist Jeff Lichtman, who is trying to map the brain, surveys the awful complexity nearly a decade later and sums up,

…if I asked, “Do you understand New York City?” you would probably respond, “What do you mean?” There’s all this complexity. If you can’t understand New York City, it’s not because you can’t get access to the data. It’s just there’s so much going on at the same time. That’s what a human brain is. It’s millions of things happening simultaneously among different types of cells, neuromodulators, genetic components, things from the outside. There’s no point when you can suddenly say, “I now understand the brain,” just as you wouldn’t say, “I now get New York City.”

GRIGORI GUITCHOUNTS, “AN EXISTENTIAL CRISIS IN NEUROSCIENCE,” NAUTILUS, JANUARY 22, 2020

In short, once we are into abstractions, we are no longer dealing with the concrete substance of the brain.

It’s All in the Electricity

But what about the bioelectric fields that swarm throughout the brain? Bioelectric currents, unlike electric currents, rely on ions rather than electrons but they are still electricity. Evolutionary biologist and lawyer Tam Hunt tells us, “Nature seems to have figured out that electric fields, similar to the role they play in human-created machines, can power a wide array of processes essential to life. Perhaps even consciousness itself.” That’s a remarkable idea because it includes the notion that our individual cells exhibit consciousness: “Something like thinking, they argue, isn’t just something we do in our heads that requires brains. It’s a process even individual cells themselves, and not requiring any kind of brain, also take part in.”

This sounds cool but gets us nowhere. We have no reason to believe that our individual brain cells are conscious; what we know is that we are conscious as whole human beings. We could say the same about claims that everything is conscious (panpsychism) or that nothing is (eliminativism). Whatever else the claims do, they shed no light on the conundrum at hand.

Consciousness as an Undetected State of Matter

Max Tegmark, MIT physicist and author of Our Mathematical Universe: My Quest for the Ultimate Nature of Reality (Knopf, 2014), goes still further. He suggests that consciousness is a so far undetected state of matter, perceptronium, “defined as the most general substance that feels subjectively self-aware.” Which, again, gets us precisely nowhere.

Prominent neuroscientist Christof Koch notes more mundanely that physical distance in the brain matters: “A new study documents an ordering principle to these effects: the farther removed from sensory input or motor output structures, the less likely it is that a region contributes to consciousness.” And that’s about as far as neuroscience has got.

Koch has also written a book, The Feeling of Life Itself (MIT Press, 2019), where he tells us, among many other things, of dogs, Der Ring des Nibelungen, sentient machines, the loss of his belief in a personal God, and sadness, all seen as “signposts in the pursuit of his life’s work — to uncover the roots of consciousness.” And that is where we must leave the subject for now. We are back where we started — but we do have interesting books.

The atom :a brief history.

 

The civil war rages on?

 

The ultimate Rube Goldberg?

 Intelligently Designed Evolution? Sorry, Wrong Universe

Casey Luskin

Many in the intelligent design camp have considered the possibility that the evolutionary process was designed. Leading ID theorists such as Michael Behe, Stephen Meyer, and Jonathan Wells readily acknowledge that while natural mechanisms can’t produce all the complexity of life, they can produce some degree of complexity in organisms. One might even say that evolution is designed to effect small-scale changes within species. 

But theologian Rope Kojonen, at the University of Helsinki, wants to go much further. In his book The Compatibility of Evolution and Design, he offers a model in which evolution succeeds because it is intelligently designed. It’s a thoughtful book, and I regard Rope as a friendly critic of ID. According to Kojonen, mainstream evolutionary theory is true — and it’s not just “compatible” with design, as he says in the title of his book, but biological phenomena even exhibit evidence for design. Let’s take a closer look at this idea.

Serendipity Required

Kojonen argues that evolutionary mechanisms produced the complexity of life. But there’s an intriguing assumption implicit in this: on its own, blind evolution is very unlikely to produce the complex features we see in living organisms. Thus, Kojonen envisions that the evolutionary process receives help from above in the form of the fine-tuning of the initial conditions and natural laws that allow evolution to get the job done. 

Kojonen proposes that our universe might be finely tuned to allow for otherwise unlikely evolutionary events, such as life suddenly co-opting proteins to evolve new functions and evolve into irreducibly complex systems:

Suppose for the sake of the argument that Behe is partially correct: complex machinery exists in nature and is difficult to evolve. Nevertheless, suppose that his critics are also correct, and the evolution of such complexity through Darwinian mechanisms actually happened. Given these premises, a theistic evolutionist could well argue that the irreducible complexity argument merely shows how demanding the conditions for evolvability are, and how much fine-tuning evolution actually requires. In a universe designed to allow for evolution, such serendipity could be expected, rather than being unlikely. Hence, Behe’s argument could simply reveal the extent to which fine-tuning is required by evolution. 

PP. 118-119

Kojonen states that the conditions for evolvability are “demanding,” and unless there is “fine-tuning” which causes “serendipity” to be “expected,” then evolution is “unlikely.” In short, he concedes that evolution only works “in a universe designed to allow for evolution.” 

He says the same about that the evolution of molecular machines like the flagellum. That will only happen if there is “fine-tuning of the landscape of forms” which makes it possible to move from one functional state to another during a blind, trial-and-error evolutionary process: 

According to this view, then, the possibility of evolution depends on the features of the space of possible forms, where all the forms must be arranged in a way that makes an evolutionary search through it possible. This argument shows how the preconditions for the working of the “blind watchmaker” of natural selection can indeed be satisfied by nature in the case of protein evolution, despite an extreme rarity of functional forms. According to this view, then, the possibility of evolution depends on the features of the space of possible forms, where all the forms must be arranged in a way that makes an evolutionary search through it possible. This argument shows how the preconditions for the working of the “blind watchmaker” of natural selection can indeed be satisfied by nature in the case of protein evolution, despite an extreme rarity of functional forms. Behe (2019, 112) argues that Wagner does not yet solve the puzzle of evolving irreducible complexity, arguing that “it doesn’t even try to account for the cellular machinery that is catalysing the chemical reactions to make the needed components. ” However, suppose that, in the case of the bacterial flagellum, though the vast majority of possible arrangements of biological proteins are non-functional, there nevertheless exists a series of possible functional forms, little “machines” that happen to contain increasing numbers of the flagellum’s vital parts while still serving some other function. This then would allow for the seamless transition from no flagellum to a flagellum over time, through small successive steps. In this manner, by moving through such a suitable library of forms, the blind process of evolution would have the ability to produce even the most complex structures without the intervention of a designer. This is the kind of fine-tuning of the landscape of forms that seems to be required to evolve the kind of biological order described by Behe.

It seems, then, that defending the power of the evolutionary mechanism requires assuming that the landscape of possible biological forms has some fairly serendipitous properties. [Emphasis added.]

P. 122

Which Universe Are We In?

There’s a great irony here in the structure of Kojonen’s argument: He implicitly concedes that evolution is very unlikely to work in your average universe that isn’t finely tuned. He says if evolution is going to work, that’s only because natural laws and initial conditions are specially “fine-tuned.” 

Thus, the universe has some pretty lucky properties. The question then becomes: Are we in Kojonen’s universe? His argument for the feasibility of evolution requires a great degree of “fine-tuning” of nature where functional forms are “arranged in a way” such that it is easy to move from one functional state to another functional state via blind evolutionary mechanisms. Are we in a “universe designed to allow for evolution” in this manner? Or are we in a universe where evolutionary mechanisms don’t seem capable of producing the complexity of life — meaning that they didn’t? 

As my colleagues and I have shown both in a review of Kojonen’s book and in an occasional series of posts here, from protein evolution (here, here, and here) to the origin of irreducibly complex molecular machines like the flagellum (here and here), the universe we live in does not seem to allow evolutionary mechanisms to produce the complexity of life. We live in the wrong universe for Kojonen’s proposal. 

But there’s a problem with the structure of Kojonen’s argument that goes even deeper. 

How Do We Detect Design in Kojonen’s Universe?

One of the potential strengths of Kojonen’s thesis is that he wants to join evolution with design. And it’s very important to his argument that he preserves our intuition of design in nature because he wants to attract what he calls the “theist on the street” to his position. See Stephen Dilley’s article yesterday on that. Kojonen says that the “theist on the street” rightly looks at life and sees that it was designed. I would say that life contains a form of complexity that this average theist knows, from experience with the world, does not arise by on its own and requires the input of intelligence. 

Kojonen differs with me. He seeks to preserve and defend the theist on the street’s intuition that life was designed. But in his mind this is not because natural processes are incapable of producing life. In fact, he thinks they are capable of that. That is, while evolutionary processes are inadequate on their own, natural processes in general are capable of producing life. Kojonen thinks this reflects the fact that the laws of nature and the initial conditions of the universe themselves are fine-tuned and designed to make the origin and evolution of life possible — by natural processes. 

But if natural processes are capable of producing the complexity of life, then isn’t the “theist on the street” wrong to conclude that life was designed in the first place? On what basis can this theist know that the natural laws are “fine-tuned” to allow life to evolve? The theist must have some background knowledge that natural laws can’t produce living systems. But if Kojonen’s thesis is correct, then in our universe the theist ought not to have such background knowledge. After all, natural laws are capable of producing such complex systems! 

A Gambling Analogy

In our paper “On the Relationship Between Design and Evolution,” responding to Kojonen’s thesis, we present an analogy from gambling that helps explain the self-defeating nature of this method of fusing evolution and design:

Imagine a jury being asked to try a court case about an allegedly fraudulent casino that was accused of rigging slot machines to yield winning jackpot combinations far less than they should, statistically speaking. On these particular slot machines, there are four reels with 10 symbols on each reel. The machines will pay out a jackpot when the symbols on all four reels line up with an identical symbol — a cherry — something that should happen, on average, 1 in every 104 spins, or 1 in every 10,000 spins.

The prosecution presents evidence that the casino’s machines are producing jackpots far less than they ought to. In fact, the prosecution’s team of experts tested the slot machines and found they only pay out a jackpot 1 in every 100,000 spins — an order of magnitude less frequently than they should.

The defense then takes its turn and makes a counterargument: “Actually, we live in a very special universe where the physical laws that govern slot machines (and their statistical odds) are fine-tuned such that things always happen about an order of magnitude less frequently than you’d expect. In fact, the ‘weird’ behavior of these slot machines proves our theory is true!”.

But how did the defense know that in our “special” universe, “things always happen about an order of magnitude less frequently than you’d expect”? They could only know this based upon background knowledge of how often things ought to happen (in this case, that there ought to be a win 1 in every 10,000 spins) and then, on this basis, compare the behavior of the slot machines to show that winning was occurring actually far “less frequently than you’d expect”.

The problem for the defense’s argument is that if we if we really lived in their universe, then all our knowledge of physical laws and statistics and slot machines would be based upon our experience in that universe. And if the defense’s argument was true then, based upon our experience in that universe, we should “expect” a win 1 in every 100,000 spins — not 1 in every 10,000 spins — and thus the slot machines at stake in the case should appear to be behaving perfectly normal. Thus, in the defense’s universe, we could never know that things were happening “an order of magnitude less frequently than you’d expect”.

The defense must answer this question: If we lived in their universe, how could they possibly “know” that the slots were producing wins less likely than they should? In their universe, the slot machines should behave exactly as experience would suggest — so they could never argue that things were behaving in a weird way. But the fact that the slots are behaving weirdly suggests that the defense’s “fine-tuned universe” argument cannot be true.

Damaging Design Detection

Kojonen wants to preserve the ability of the “theist on the street” to detect design — but we explain in our paper that this doesn’t seem possible even if we did live in his universe: 

This analogy invites us to consider the epistemological effects of living in a universe described by Kojonen’s model (in which evolution is true, design is confined to the advent of the laws of nature, and biological data are in view). In this universe, it is not clear that humans (including theists on the street) would have the basic epistemological dispositions or beliefs that Kojonen believes undergird our ability to detect design in biology. For example, people who grew up in this universe would not likely believe that nature (i.e., non-agent processes) have only limited ability to build biological complexity. After all, in this universe, the continuity of non-agent processes across the advent of everything from bacteria to blue whales seems to suggest that non-agent causes are quite creative. Similarly, people who grew up in this universe would not likely believe that our own experience of creating complex things is at all relevant to the claim that ‘minds have greater creative power than nature does’. Instead, they would likely believe that our minds are simply a manifestation of nature’s creativity (or the creativity of non-agent causes). A similar line of thinking applies to the other elements of design detection discussed above. The bottom line is that human cognition would likely be significantly different in Kojonen’s universe than we actually experience it to be. Conversely, the fact that we have the particular cognitive dispositions and beliefs that we currently possess — instead of the ones we’d have in Kojonen’s universe — suggests that we live in a world notably different than captured in Kojonen’s model. Thus, in a particular sense, Kojonen’s model is inconsistent with the lived experience of some humans, including some theists on the street. This seriously harms the plausibility of his proposal, including its defense of everyday theists.

Thus, even if Kojonen’s argument were correct and the laws of nature were capable of producing living systems, then his “theist on the street” should not be able to detect design in living systems in the manner he suggests. If the laws of our universe are rigged to produce life, then such an event would be fully natural and should not trigger a design inference. We would see no reason to invoke anything other than normal natural processes to explain life’s complexity. The very fact that life does trigger a design inference for Kojonen’s theist suggests that our experience teaches us such events don’t happen due to natural laws. That means Kojonen’s thesis is self-defeating and cannot be true.

On restoring the name of the most high God to its proper place.

 

In Norway the future is now re: net zero?

 

Time crystals?

 

Yet more on one of our planet's other civilization.

 Ants “Think” Differently from Humans

Evolution News

There are some 20 quadrillion ants living in the world today. John Whitfield offers an essay at Aeon on the factors underlying the successful spread of vast colonies from, say, South American to Europe — by piggybacking on human journeys.

Whitfield, author of Lost Animals: The Story of Extinct, Endangered and Rediscovered Species (Welbeck 2020), resists the temptation to compare ant dominance to human dominance of the globe, in part because, well, ants think differently. Here are a couple of the questions he answers in his sparkling and informative essay:

Why Do Ants Work So Well Together?

Recognition looks very different for humans and insects. Human society relies on networks of reciprocity and reputation, underpinned by language and culture. Social insects — ants, wasps, bees and termites — rely on chemical badges of identity. In ants, this badge is a blend of waxy compounds that coat the body, keeping the exoskeleton watertight and clean. The chemicals in this waxy blend, and their relative strengths, are genetically determined and variable. This means that a newborn ant can quickly learn to distinguish between nest mates and outsiders as it becomes sensitive to its colony’s unique scent. Insects carrying the right scent are fed, groomed and defended; those with the wrong one are rejected or fought.

JOHN WHITFIELD, “ANT GEOPOLITICS,” AEON, FEBRUARY 16, 2024

As Eric Cassell notes in Animal Algorithms: Evolution and the Mysterious Origin of Ingenious Instincts (2021) , all species of ants are social; there are no known solitary ants.

How Different Is Ants’ Way of Thinking?

The more I learn, the more I am struck by the ants’ strangeness rather than their similarities with human society. There is another way to be a globalised society — one that is utterly unlike our own. I am not even sure we have the language to convey, for example, a colony’s ability to take bits of information from thousands of tiny brains and turn it into a distributed, constantly updated picture of their world. Even ‘smell’ seems a feeble word to describe the ability of ants’ antennae to read chemicals on the air and on each other. How can we imagine a life where sight goes almost unused and scent forms the primary channel of information, where chemical signals show the way to food, or mobilise a response to threats, or distinguish queens from workers and the living from the dead? 

WHITFIELD, “ANT GEOPOLITICS”

Cassell suggests that colony communication is somewhat like a computer algorithm: The ant processes pheromones (scent signals) as if they were AND gates and STOP in a computer system (p. 91). Thus, the ant is not judging the situation and deciding whether to go along with the group or not — as a human might — but rather, processing a signal. Stanford entomologist Deborah M. Gordon calls the resulting communication without personal understanding the “anternet.”

Whitfield tells the story of Biosphere 2, a giant terrarium in Arizona, designed in the 1980s as a self-sustaining living system with no connection to the outside world. Developed to test the design of biospheres for space exploration, it fell victim in 1996 to the southeast Asian black crazy ant, which turned it into a honeydew factory.

So sometimes, sheer numbers and a viable social algorithm win out over high individual intelligence. But, in fairness, the eight humans who lived inside Biosphere 2 for two years did not seem to enjoy it much:

In pursuit of a third way? II

 Denis Noble in Nature: “Time to Admit Genes Are Not the Blueprint For Life”

Casey Luskin

Last November I reviewed an article in BioEssays which declared a Kuhnian “paradigm shift” away from the concept of junk DNA. That article compellingly argued that we need to abandon the notion that genes only make proteins because our genome is full of “RNA genes” that produce RNAs which perform vital functions. Now another groundbreaking article in Nature by Oxford emeritus biologist Denis Noble is calling for a major “rethink” of biology by charging that “It’s time to admit that genes are not the blueprint for life” because this “view of biology often presented to the public is oversimplified and out of date.” Noble is reviewing a new book, How Life Works, by Philip Ball. 

This is not to say that genes aren’t important for life — of course they are. It’s that they aren’t the fundamental blueprint that controls an organism. In fact, in a surprising twist, Noble argues that it’s the organism that controls the genome! Before we get there, we must review some of Noble’s striking discussions of the complexity of life. 

Life is Complicated

Those who travel in the intelligent design (ID) community know that we have often compared biological systems to machines. Now we have never intended to say that living organisms literally are machines — but rather that machine-like structures exist within living organisms, alongside many other features which may or may not be comparable to machines. The idea that life contains machine-like structure was explained eloquently by former U.S. National Academy of Sciences president Bruce Alberts, who famously wrote in the journal Cell:

[T]he entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.… Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.

Noble’s current Nature paper seemingly disagrees with Alberts’s use of machine-metaphors for biology. I think the metaphor still works in many cases, but before we explore Noble’s view, it must be understood that the reason for Noble’s disagreement with machine-metaphors isn’t because life is less complex than machines, but rather because it is MORE complex and the machine comparison fails to capture the true nature of life’s incredible complexity. Here’s what Noble writes:

For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, says science writer Philip Ball in How Life Works. Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science. “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike.

I don’t think that Noble is saying that the comparison between life and computers or machines is entirely inappropriate or completely irrelevant to anything we find in biology. Rather, I take him to be saying that life is “far more interesting and wonderful” than the idea that life is merely a computer or machine. If that’s what he’s saying, then I agree completely. 

Proteins More Complex than Initially Thought

Another area where Noble argues that biological systems are more complex than often appreciated is “intrinsically disordered proteins” (IDPs) — proteins that don’t have a stable three-dimensional shape. Brian Miller and I wrote about IDPs in a response to critics of Douglas Axe posted last year:

Venema (2018) cites intrinsically disordered proteins (IDPs), noting they “do not need to be stably folded in order to function” and therefore represent a type of protein with sequences that are less tightly constrained and are presumably therefore easier to evolve. Yet IDPs fulfill fundamentally different types of roles (e.g., binding to multiple protein surfaces) compared to the proteins with well-defined structures that Axe (2004) studied (e.g., crucial enzymes involved in catalyzing specific reactions). Axe (2018) also responds by noting that Venema (2018) understates the complexity of IDPs. Axe (2018) points out that IDPs are not entirely unfolded, and “a better term” would be to call them “conditionally folded proteins”. Axe (2018) further notes that a major review paper on IDPs cited by Venema (2018) shows that IDPs are capable of folding — they can undergo “coupled folding and binding”; there is a “mechanism by which disordered interaction motifs associate with and fold upon binding to their targets” (Wright and Dyson 2015). That paper further notes that IDPs often do not perform their functions properly after experiencing mutations, suggesting they have sequences that are specifically tailored to their functions: “mutations in [IDPs] or changes in their cellular abundance are associated with disease” (Wright and Dyson 2015). In light of the complexity of IDPs, Axe (2018) concludes:

“If Venema (2018) pictures these conditional folders as being easy evolutionary onramps for mutation and selection to make unconditionally folded proteins, he’s badly mistaken. Both kinds of proteins are at work in cells in a highly orchestrated way, both requiring just the right amino-acid sequences to perform their component functions, each of which serves the high-level function of the whole organism. (Axe 2018)”

Noble’s essay provides a direct vindication of our view of IDPs as dynamic, multi-functional systems. Yes, IDPs can adopt different three-dimensional structures, but that isn’t because their shape doesn’t matter but rather because they can switch from one shape to another — like miniature transformers — to perform different functions. And the shape is undoubtedly vital to their proper function in each case. Noble’s description of IDPs is striking:

Another metaphor that Ball criticizes is that of a protein with a fixed shape binding to its target being similar to how a key fits into a lock. Many proteins, he points out, have disordered domains — sections whose shape is not fixed, but changes constantly.

This “fuzziness and imprecision” is not sloppy design, but an essential feature of protein interactions. Being disordered makes proteins “versatile communicators”, able to respond rapidly to changes in the cell, binding to different partners and transmitting different signals depending on the circumstance. For example, the protein aconitase can switch from metabolizing sugar to promoting iron intake to red blood cells when iron is scarce. Almost 70% of protein domains might be disordered.

In other words, IDPs can switch from one shape to another in response to environmental cues or signals they encounter, and this allows them to perform multiple vital functions. Once again, the complexity of life appears to be greater than we expected. 

But what are the implications of all this for evolution? 

Questioning Classic Views of Evolution

In his review, Noble comes right out and says that “Classic views of evolution should also be questioned.” Now Noble is an evolutionist and not an ID proponent to be sure. But he seems open to more rapid forms of evolution that, from our vantage in the ID community, seem preprogrammed to yield favorable results that benefit the organism. Here’s what he writes:

Evolution is often regarded as “a slow affair of letting random mutations change one amino acid for another and seeing what effect it produces”. But in fact, proteins are typically made up of several sections called modules — reshuffling, duplicating and tinkering with these modules is a common way to produce a useful new protein.

Noble also thinks there’s a place for “agency and purpose” in biology. He’s not talking about the intelligent design of life by an external agent, but he is acknowledging that much in biology is purposeful, noting that multiple experts now argue that “argue that agency and purpose are definitive characteristics of life that have been overlooked in conventional, gene-centric views of biology.” Again, this isn’t the modern theory of intelligent design, but once we begin to allow agency and purpose into our understanding of how life works, we’re taking important steps towards being able to recognize design in biology. 

So, Where’s the Blueprint?

Noble offers various lines of evidence that the “blueprint” of life cannot be found in the DNA. He notes examples where hundreds of genes are involved in the development of certain diseases, suggesting that “It’s therefore a huge oversimplification … to say that genes cause this trait or that disease.” Moreover, rather than genomes controlling the organism, Noble notes that organisms themselves can “control their genomes” — suggesting genomes aren’t the foundation of life:

Ball is not alone in calling for a drastic rethink of how scientists discuss biology. There has been a flurry of publications in this vein in the past year, written by me and others. All outline reasons to redefine what genes do. All highlight the physiological processes by which organisms control their genomes. 

If “organisms control their genomes” rather than the classical reductionist view that genomes determine organisms, then perhaps it is time for a radical “rethink” of how biology works. Here’s Noble’s vision of the future:

Ultimately, Ball concludes that “we are at the beginning of a profound rethinking of how life works”. In my view, beginning is the key word here. Scientists must take care not to substitute an old set of dogmas with a new one. It’s time to stop pretending that, give or take a few bits and pieces, we know how life works. Instead, we must let our ideas evolve as more discoveries are made in the coming decades. Sitting in uncertainty, while working to make those discoveries, will be biology’s great task for the twenty-first century.

Noble’s vision of biology is one where dogma is discarded, new ideas are considered, agency and purpose are acknowledged, cells are more complex than computers and machines, proteins are like miniature transformers, and organisms control their genomes, is highly compatible with intelligent design — certainly far more compatible than the biological thinking of the past hundred years. This means biology is moving in the right direction.