Search This Blog

Showing posts with label Intelligent design. Show all posts
Showing posts with label Intelligent design. Show all posts

Sunday 24 March 2024

Michael Behe holds court.

 Michael Behe: A Mousetrap for Darwin


On a classic episode of ID the Future, host Eric Anderson interviews biochemist Michael Behe about his book A Mousetrap for Darwin. In this episode, Behe explains that he was spurred to build this collection of essays by a review in the journal Science claiming he had never answered his critics on key points. That annoyed Behe, because he had, multiple times. A Mousetrap for Darwin compiles more than a hundred of his responses, some of them from difficult-to-access places. The book also contains fresh material from Dr. Behe, including some lively behind-the-scenes details about his interactions with colleagues and critics. 

In this episode, the Lehigh University biochemist answers misconceptions about irreducible complexity, responds to the claim that “molecular machines” is a misnomer, relates the surprising confessions some of his fellow biologists have made outside the spotlight about evolutionary theory, and offers his appraisal of why scientists in general don’t know what’s going on with studies in evolution or intelligent design. Behe remains optimistic, though. “You can’t deny the data forever,” he says. Download the podcast or listen to it here

Wednesday 20 March 2024

Yet another Darwinian argument from poor design ages like milk

 

The cell membrane vs. Darwinism's Simple Beginning.

 Secrets of Active Transport Become Visible


Active transport — the ability to move molecules against a concentration gradient — is one of the key distinguishing features between life and non-life. Passive transport, as with osmosis, we know by experience: a fluid will naturally spread through a semipermeable membrane from a region of high concentration to one of low concentration until the concentration is equalized. That’s why bromine tablets in a spa will spread from the filter out into the water. It’s why wildfire smoke will leak into a room through any cracks in the wall, but not out. It would take Maxwell’s Demon to combat this natural tendency which follows from the Second Law of Thermodynamics.

Life cannot operate on the principle of osmosis. A cell with a passive osmotic membrane will die. Cells need to actively bring in or expel substances, often forcing them against a strong concentration gradient. They need to maintain pH homeostasis regardless of conditions outside, often pumping in cations like Na+, K+, Ca2+and Mg2+ or anions like chloride Cl– even when the interior already has a much higher concentration than the exterior. By osmosis, these concentrations would quickly equalize and life would stop. In a real sense, life involves a constant battle against thermodynamic entropy, using energy to combat what natural forces would do.

Unnatural Selection

Biochemists have long known about the existence of specialized membrane channels where active transport takes place, and knew they were highly efficient, but how they operated was long a mystery. Roderick MacKinnon was one scientist who began to figure out the mechanisms of active transport in the 1990s. He won the Nobel Prize in 2003 for his discoveries about “selectivity filters” within ion channels that permit some molecules to pass but not others. Since then, advances in super-resolution microscopy have been revealing details at near-atomic scales about what might be dubbed “unnatural selection” inside these channels.

Membrane channels are often named according to the molecules they transport: anion or cation channels, sodium channels, potassium channels, chloride channels, aquaporins (water channels), and others. Let’s examine the inner workings of one chloride channel, about which scientists’ knowledge has been updated recently. We can share the excitement of discovery about how its “selectivity filter” determines which ions are allowed to pass. As a teaser, consider that the selectivity filter of a potassium channel is much smaller than the width of a potassium ion, yet it can transport 100 million ions per second!

The CFTR Chloride Channel

Last month in PNAS, Levring and Chen announced the “Structural identification of a selectivity filter in CFTR,” a chloride channel responsible for fluid homeostasis in epithelial tissues. It’s called CFTR (Cystic Fibrosis Transmembrane conductance Regulator) because of the fatal disease that occurs when genetic defects hinder passage of chloride ions. At the other extreme, cholera makes the channel too indiscriminate, leading to the diarrhea that causes dehydration and death. Kidney disease can also result from defective CFTR channels. This is not a part to mess with!

The shape of CFTR looks like a curved cornucopia with a narrow constriction inside. Notice how the authors identify precise amino acid residues (indicated by a letter and a position number) along the channel path that interact with the chloride ions passing through:

In this study, we identify a chloride-binding site at the extracellular ends of transmembrane helices 1, 6, and 8, where a dehydrated chloride is coordinated by residues G103, R334, F337, T338, and Y914. Alterations to this site, consistent with its function as a selectivity filter, affect ion selectivity, conductance, and open channel block. This selectivity filter is accessible from the cytosol through a large inner vestibule and opens to the extracellular solvent through a narrow portal. The identification of a chloride-binding site at the intra- and extracellular bridging point leads us to propose a complete conductance path that permits dehydrated chloride ions to traverse the lipid bilayer.

Diagrams of the interior show a chloride ion making electrostatic contacts with amino acid residues on its traverse, as if running the gauntlet through armed guards that each ensure it has a valid permit to pass. The structure “encloses a continuous conduit across the membrane for chloride to permeate down its electrochemical gradient.” Each chloride ion is hydrated with a water jacket but must remove its jacket on the way through:

Hydrated chloride enters the inner vestibule from the cytosol through a lateral portal between TMs [transmembrane domains] 4 and 6…. Chloride remains hydrated in the inner vestibule and is stabilized by a positive electrostatic surface potential. The width of the vestibule tapers down and converges at a selectivity filter, where only dehydrated chloride can enter. Dehydrated chloride moves into this selectivity filter, stabilized by interactions with G103, R334, F337, T338, and Y914 and rehydrates upon exit into the epithelial lumen through a narrow lateral exit between TMs 1 and 6.

Precision Authentication

How does the channel filter out other anions? Fluorine (atomic number 9) is smaller than chlorine (atomic number 17), so why doesn’t it slip through? The authors tested the authentication ability of CFTR by means of amino acid substitutions. They confirmed that four residues in the channel perform a qualification test on incoming anions as they dehydrate:

As was previously reported, and consistent with permeating anions having to dehydrate, wild-type CFTR exhibits a lyotropic permeability sequence, with relative permeabilities inversely related to the enthalpy of dehydration … Upon R334A, F337A, T338A, or Y914F substitution, the relative anion permeabilities were all altered, albeit to different degrees, consistent with previous work.

Figure 5 in the paper shows a chloride ion being inspected by four amino acid residue “cops” on four sides. A rogue molecule is not going to pass! The precision of this filter is astonishing. How much mutation could the system tolerate without breakdown? And how many accidents built this filter by chance in the first place? Details in the following quote will not be on the quiz, but to get a feel for the complexity involved, look at how many residues participate in authenticating chloride ions as they run the gauntlet:

Previous mutational work has identified a plethora of residues, many are arginine and lysine, that influence CFTR ion selectivity and/or conductance. Mapping these residues onto the CFTR structure indicates that basic residues, including K95, R104, R117, K190, R248, R303, K335, R352, K370, K1041, and R1048… are positioned along the cytosolic and extracellular vestibules, with their side chains exposed to solvent. Different from the residues that directly coordinate chloride [the selectivity filter], the function of these arginine and lysine residues is to stabilize the partially hydrated anions through electrostatic interactions and to discriminate against cations.The side chains of Q98 and S341 also face the cytosolic vestibule to form anion–dipole interactions with chloride and contribute to ion selectivity. R334, positioned at the extracellular mouth of the pore, plays a dual role in forming the selectivity filter and attracting anions into the pore through electrostatic interactions. Many other functionally important residues, including P99, L102, I106, Y109, I336, S1118, and T1134…, do not directly interact with chloride. Instead, they form a second coordination sphere of [the selectivity filter] that likely contributes to structuring [selectivity filter] residues with the appropriate geometry to coordinate chloride.

Airport Analogy

Think of these other “important residues” as part of the “coordination sphere” at an airport. The entire structure serves the purpose of narrowing down the flow of passengers to the “selectivity filter” of X-ray machines that inspect passengers and their baggage. The entire superstructure is necessary and must have been planned with the appropriate geometry and personnel to guide the passengers to the inspection site, even though the X-ray machine is as narrow as a human.

TSA workers at airports could never boast of this much quality control in their authentication protocols. And human workers have eyes and minds to think about what they are doing! The CFTR channel operates automatically in the dark, by the delicate “touch” of electrostatic interactions within a precisely structured narrow passageway within the coordination sphere. One source says that CFTR conducts millions of chloride ions per second! The TSA could learn something about efficiency here, as many of us airline passengers could attest.

Speaking of touch, my next article will discuss some other channels that respond when contacted — the so-called mechanosensitive channels.

Useless Darwinese

Did CFTR evolve? Because the CFTR channel has some similarities to other chloride channels like CLC, the authors glibly surmise that it “uniquely evolved from a family of active transporters,” assuming that “unrelated ion channels have evolved to select and conduct chloride using common chemical strategies.” Such a narrative gloss is not only useless, it makes no sense. A strategy implies foresight: seeing a need and designing a solution. While some frequent flyers might be tempted to smirk that TSA strategies seem mindless and unguided, elaborate structures like CFTR channels that operate extremely efficiently and accurately with low tolerance for alteration look engineered. They had to work from the start. Without those precisely placed amino acid residues already present at the right spot within a larger coordination sphere, there would be no authentication, and active transport would stop. The alternative is disease and death. Our uniform experience confirms that elaborate, efficient strategies that work — employing irreducibly complex structures with multiple coordinating parts supporting the function — are always products of intelligent design.

Monday 18 March 2024

Hummingbirds vs. Darwin.

 

 Ingenious Artistry in the Origin of Hummingbirds


Please see below the Abstract of my recent article which asks, “Can Neo-Darwinism Explain the Origin and Variation of the Hummingbirds?”

Abstract

Richard Dawkins is one of the leading spokesmen for the evolutionary theory’s modern synthesis (neo-Darwinism). He is in full agreement with virtually all his colleagues when he asserts that “evolution not only is a gradual process as a matter of fact; it has to be gradual if it is to do any explanatory work.” So, the entire array of the fascinatingly different 366 hummingbird species of the family Trochilidae, being “distinctly different than all other avians,” must have evolved by natural selection through — in Darwin’s words — “infinitesimally small changes,” “infinitesimally slight variations,” “insensibly fine steps,” and “insensibly fine gradations.” Many of those gradations are thought to have been due to mutations with only “invisible effects on the phenotype,” according to Ernst Mayr. However, 

“Even a new mutation that is slightly favorable will usually be lost in the first few generations after it appears in the population, a victim of genetic drift. If a new mutation has a selective advantage of S in the heterozygote in which it appears, then the chance is only 2S that the mutation will ever succeed in taking over the population. So, a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.” (Emphasis added.)

Let us apply this method to individual hummingbird species, including their sexual dimorphism, and the corresponding flower formations of their nectar-producing host plants. Together these imply coordinated inter-kingdom mutations and interactions. Five examples will be discussed in the following article: (1) the strongly curved beaks of the two species of Eutoxeres, (2) Lophornis gouldii (the dot-eared coquette), (3) Docimastes ensifer (Gould) = Ensifera ensifera (the sword-billed hummingbird), (4) Sappho sparganurus (the red-tailed comet), and finally (5) Loddigesia mirabilis (the marvelous spatuletail). 

All five examples display sexual dimorphism. Now, sexual selection stands in clear opposition to natural selection. Here that is the case not only because of the fact that “conspicuously colored males preferentially fall victim to their enemies,” but also because their often astoundingly acrobatic behavior to impress the females necessitates a tremendous expenditure of energy for the show. Ontogenetically, it requires development of a strikingly showy and flamboyant plumage. In the present cases, displays by the males in color, size, and shape almost completely dwarf those of the females. (Compare with this the prime example of the phenomenon among the class Aves: the well-known peacock.)
      Moreover, to evolve a special preference for brightly colored males with specially formed short and/or long decorative feathers, sexual selection presupposes the occurrence of a series of highly unusual mutations in the females. For these mutations, however, there is not the slightest evidence. 

Now, let us look briefly at the species mentioned above, in reverse order. We begin with (5) Loddigesia, whose males possess two stunningly long tail feathers ending in large flat violet-blue discs (see the photo at the top of this article). To evolve in a process of continuous evolution, this would mean thousands of unknown mutations — mutations, again, with “slight or even invisible effects on the phenotype,” each new step implying the substitution of the entire population of birds. All this would have happened regularly in opposition to natural selection. The females, however, have been described as “not easily impressed” by the show of the males. So, one may ask: are there really decisive selective advantages for the survival of spatuletail populations due to changes of about 1 millionth of 1 meter or 1 thousandth of 1 mm of the male’s two tail feathers?

For each species, this immensely improbable process of continuous evolution implies thousands of mutations, with visible or invisible effects on the phenotype, each time selected with certainty by the respective females. This observation applies to (4) the “deeply forked, spectacular, long, iridescent, golden-reddish tail, longer than the length of the body,” of Sappho sparganurus (the red-tailed comet); (3) the enormously long bill distinctive of Docimastes ensifer (the sword-billed hummingbird); (2) the “long dark rufous feathers [that] on its crown form a crest” plus the “long white feathers with shiny green dots [that] make tufts that fan out and back on the cheeks” of Lophornis gouldii (the dot-eared coquette); and (1) the strongly curved beaks of the two species of Eutoxeres (the sicklebills), seemingly in coordination with the flower forms of Centropogon and Heliconia.

If neo-Darwinian theory cannot explain even differences between the hummingbirds themselves (including their sexual dimorphism), what then can we expect when it comes to the origin of the entire family of this anatomically and physiologically well-defined group of birds? From an evolutionary standpoint, we must agree with many hummingbird researchers, including the clear statement of Jillian Mock, that “the origins of hummingbirds are still a major mystery.”

With this in mind, we turn to the theory of intelligent design (ID). According to Stephen Meyer, “The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” ID, writes Michael Behe, is usually recognized by “a purposeful arrangement of parts.” In what follows I argue that the origin of hummingbirds reflects brilliant, ingenious artistry, not the work of an endless number of infinitesimally small coincidences, haphazardly chained together by the “truly hideous process” of natural selection, “rife with happenstance, contingency, incredible waste, death, pain and horror,” etc. 

In contrast with neo-Darwinism, I conclude that an absolutely ingenious artist was at work here, transcending all human abilities, ideas, and powers.

For all details and references, please see,

On ID and reductionism.

 Understanding “Reductionism” and Intelligent Design


The burgeoning field of “systems biology,” as defined by the National Institutes of Health (NIH),

is an approach in biomedical research to understanding the larger picture — be it at the level of the organism, tissue, or cell — by putting its pieces together. It’s in stark contrast to decades of reductionist biology, which involves taking the pieces apart.

I’m sure that statement is designed to make systems biology sound radical and exciting, and it succeeds. It’s especially exciting for proponents of intelligent design, because ID theorists have been arguing against reductionism in biology for a long time. 

But we need to be careful. We don’t want to make an argument based on an equivocation. The word “reductionism” is thrown around a lot, but it can mean several different things. It’s not as simple as saying, “Biologists are learning that reductionism is bad!” 

As it turns out, the move away from reductionism in systems biology is significant for the ID debate, but not simply by word-association. So I want to take some time to suss out the different meanings of the word “reductionism” and what they have to do with intelligent design.  

There are two kinds of reductionism that are relevant to this discussion: methodological reductionism and ontological reductionism. (For a third kind, epistemological reductionism, see this Cartoon.) The opposing philosophies are, respectively, methodological antireductionism and ontological antireductionism. The terms are a bit eye-splitting, but they aren’t difficult to understand. 

Methodological Reductionism

Methodological reductionism is the idea that a thing can best be understood by breaking it down into its parts. The contrary philosophy, methodological antireductionism, says that a thing can be best understood by looking at it as a whole. 

The opposing views are summed up nicely in a conversation between the wizards Saruman and Gandalf in The Lord of the Rings. Saruman shows Gandalf his new rainbow-colored outfit and tells him that he has decided to stop going by “Saruman the White” and go by “Saruman of Many Colours” instead.  

“I liked white better,” says Gandalf. 

“White!” Saruman sneers. “It serves as a beginning. White cloth may be dyed. The white page can be overwritten; and the white light can be broken.” 

“In which case it is no longer white,” says Gandalf. “And he that breaks a thing to find out what it is has left the path of wisdom.” 

Saruman is a methodological reductionist and Gandalf is a methodological antireductionist. 

Methodological reductionism: “The white light can be broken.” 

Methodological antireductionism: “He that breaks a thing to find out what it is has left the path of wisdom.”

Ontological Reductionism

Ontological reductionism, on the other hand, is not about the best way to study something, but rather about what that thing “really is” at the deepest level. Ontological reductionism says that a thing can be reduced to its most basic parts, and that’s what it is — nothing more. According to this theory, a tree is a collection of cells, which in turn are collections of molecules, which are collections of atoms, which are collections of subatomic particles. So in the final analysis, a “tree” is a collection of subatomic particles. 

This view, and its antithesis, is expressed in C. S. Lewis’s Voyage of the Dawn Treader. On an island near the edge of the world, the characters meet a being named Ramandu who claims to be a star.

“In our world,” Eustace Scrubb objects, “a star is a huge ball of flaming gas.”

“Even in your world, my son,” replies Ramandu, “that is not what a star is but only what it is made of.”

Eustace is an ontological reductionist and Ramandu is an ontological antireductionist. (And if Ramandu’s statement seems mind-bending or baffling, that’s because most of us were educated into ontological reductionism.)

Ontological reductionism: “A star is a huge ball of flaming gas.”

Ontological antireductionism: “That is not what a star is but only what it is made of.”  

Gandalf Points to Ramandu

The field of systems biology is methodologically antireductionist. It does not have to be ontologically antireductionist. So, systems biologists do not necessarily reject materialism or physicalism. They do not have to believe in minds, or be willing to posit neo-Platonic souls of cabbages, or think the true meaning of a mushroom can only be found in its wholeness. 

They have simply found it to be the case that looking at living organisms as complete systems yields better results than only taking them apart to focus on their bare components. Researchers are coming to realize that it is more productive to think about the plan of an organism than simply about its physical structure or components. 

But this is important, because whether systems biologists always admit it or not, methodological antireductionism implies ontological antireductionism. Gandalf agrees with Ramandu, not Eustace.  

That’s not to say that ontological antireductionism logically follows from methodological antireductionism, or vice versa. In theory, you could have one without the other. But the success of methodological antireductionism fulfills a prediction of the hypothesis of ontological antireductionism.

That is: if there really is a plan, then you would naturally suppose that looking for a plan would turn out to be a great strategy, and that proceeding as if there were no plan would not be a great strategy. And that is the reality. It turns out that when you take a creature apart to see what it’s parts are, you see a bunch of parts; but when you take a step back and look for a plan, you find a plan

This Is What Intelligent Design Predicts

Intelligent design is a sub-type of ontological antireductionism. To be exact, it is one way of answering the question “if a thing isn’t just the sum of its parts, then what is it?” ID proposes that (at least some) natural entities are more than the sum of their parts because they are ultimately an expression of an idea in a conscious mind. If this is true, then you would predict those entities to be best understood by grasping the idea behind them; you would try to see the scheme, the purpose, the outline, the plan. 

The neo-Darwinian model, in contrast, does not inherently lead to this prediction, because the mechanism of natural selection and random variation is, by definition, an uncoordinated piling-up of useful features, whereas a “plan” is the coordination of useful features. (Michael Behe’s three books and Marcos Eberlin’s Foresight explore this idea in depth.)

This is not proof of the design hypothesis, but it is evidence for it. In fact, this sort of evidence is one of the pillars of the scientific method: the strength of a scientific hypothesis depends on its ability to make predictions that are borne out by investigation. Based on that criterion, the hypothesis of intelligent design is doing very well. The hypothesis of mindless evolution is not doing so well, because although mindless processes might generate great complexity, they do not make plans.

Some systems biologists may want to reject Saruman but stay with Eustace; to reap the practical benefits of methodological antireductionism while avoiding the philosophical costs. But they may find that stance difficult to maintain. An unwary systems biologist could easily drift over to Ramandu’s Island, where the ID theorists are waiting. 

Saturday 16 March 2024

The case for design is muscular?

The Incredible Design of Muscles


To understand the limitations of evolutionary mechanisms, we have to “bite the bullet of complexity,” as biochemist Michael Behe writes. And to appreciate complexity, we have to experience it. On a new episode of ID the Future, Dr. Jonathan McLatchie takes host Andrew McDiarmid on a deep dive into the structure and biochemistry of muscles to gain a better understanding of their incredible design properties.

McLatchie provides an overview of the key parts of muscles, including muscle fibers, connective tissue, and tendons. He describes the two different types of muscles — antagonists and synergists — and provides examples of each. Then he explains the integration of muscle function: how muscle contraction involves the nervous, respiratory, circulatory, and skeletal systems all working together in tandem. 

Did you know our brain predicts and corrects discrepancies between our intended and actual muscle movements? McLatchie explains this remarkable feature and also describes muscle sense and muscle memory. He gives us a taste of the complexity of muscle function at the biochemical level. And while we’re reeling from all that, he explains why all this engineering prowess is fiendishly difficult to explain through evolutionary mechanisms but hardly surprising within an intelligent design framework. Download the podcast or listen to it here.

Hippos vs. Darwin

 Notes on the Mysterious Origin of Hippos

Wolf-Ekkehard Lönnig

Please consider the Abstract of my recently published paper, “Hippo Origin: Accidental DNA Mutations or Ingenious Design?”

Abstract

“To call hippos ‘charming’ may seem a bit of a stretch,”  comments,national Geographic “but they are most certainly among the classic charismatic megafauna of the African continent.” Although the hippos (Hippopotamus amphibius L.) are not a major focus of attention in evolutionary biology, it may nevertheless be quite revealing to appreciate some points about the history of these powerful animals:

The family Hippopotamidae appears abruptly in the fossil record — like all the other groups that I have so far investigated in detail. See here for many more examples.
As compared to the variation possible within living species such as humans and others (see below), the two subfamilies and most of the hippo genera and species, which have been determined solely on the basis of anatomical and morphological criteria, may simply have been special populations of Mendelian recombinants from a genetical point of view (i.e., according to the genetical species concept). These recombinants (putative new subfamilies, species, and genera) also appear abruptly in the fossil record.
The evolutionary derivation currently favored by most paleontologists, of the Hippopotamidae from Anthracotheriidae, has been disproved by the detailed investigations of researcher Martin Pickford (for instance 2009, 2011, 2022). However, his alternative, the Doliochoeridae as ancestors of the hippos, is equally doubtful. 
All three families mentioned above appear abruptly in the fossil record and subsequently display constancy or stasis over long periods of time.[1] In no case is there any documentation of a continuous evolution of one family from another by “infinitesimally small changes” (Darwin) or by mutations with “slight or even invisible effects on the phenotype” (Mayr). Otherwise, there would be no contradictory evolutionary derivations.The popular rejoinder asserts the incompleteness of the fossil record as the reason for these phenomena. But this rejoinder has in principlebeen refuted by (among many others) paleontologist Oskar Kuhn. As Kuhn states, “in many animal groups such a rich, even overwhelming amount of fossil material exists (foraminifers, corals, brachiopods, bryozoans, cephalopods, ostracods, trilobites, etc.), thatthe gaps between the types and subtypes must be viewed as real.” There is no reason that it would be different in the hippos if we had more fossils. The evolutionary “ghost lineage” will forever continue to consist mostly of “ghosts.”
Evolutionary hypotheses and derivations reflect circular reasoning, and cladistics has not refuted this objection. Note that, “Decisions as to whether particular character states are homologous, a precondition of their being synapomorphies, have been challenged as involving circular reasoning and subjective judgements.” And now according to transformed cladistics “it is a mistake to believe even that one fossil species or fossil ‘group’ can be demonstrated to have been ancestral to another” (Nelson).
The truth about hippo origins — apart from the abrupt appearance of this (and virtually all other) families in the fossil record, and drawn from their ingenious blueprints involving structures of irreducible complexity in probably all groups and generally enormous amounts of specified complexity on all biological levels (morphology, anatomy, physiology and genetics) — points to intelligent, ingenious design. Indeed, Georges Cuvier, as the “founding father of paleontology,” as well as renowned researchers such as Louis Agassiz, have argued for “One Supreme Intelligence as the Author of all things.”

You will find a discussion of these and many other  at  “Hippo Origin: Accidental DNA Mutations or Ingenious Design?

Friday 15 March 2024

The technology of JEHOVAH?

 

Design deniers remain gatekeepers of the agrora?

 Healthy Debate? No Thanks, Says National Association of Biology Teachers


A recent article here by Wesley J. Smith highlighted how mainstream science seeks to stifle opposition instead of encouraging open and honest debate. The article reminded me of a recent experience I had involving the Board of Directors of the National Association of Biology Teachers (NABT).

Nothing Unscientific About Design

When I attended the annual conference of the NABT in November 2023, I met Amanda Townley, the president-elect of the NABT. During our conversation I mentioned I had a proposal for amending the NABT Position Statement on Teaching Evolution and I asked her what was the procedure for proposing an amendment to a Position Statement. She asked what it concerned and I said it was a clarification that there is nothing unscientific about a theory of design, including in the field of biology. She said only members of the Board of Directors could propose Position Statements or amendments thereto, but she said she would be willing to present my proposal at an upcoming meeting of the Board. She asked me to send her an explanation of the proposal. The explanation I sent to her is set forth below.

Proposal by Herman B. Bouma for Amending NABT Position Statement on Teaching Evolution

I highly recommend that the NABT Position Statement on Teaching Evolution be amended to make clear that there is nothing inherently unscientific about a theory of design, including in the field of biology.

Suppose an American geologist went to England to study its rock formations and happened to come upon Stonehenge. As a scientist, is he precluded from theorizing that Stonehenge is the result of design? If he cannot refer to design, then he might come up with a theory that Stonehenge is the result of a volcanic eruption or the result of deposition by an ancient river. Those are certainly theories, but not very good ones. 

As a scientist, the geologist might have a predilection to explain Stonehenge in terms of natural processes. However, given what he knows about natural processes and given the layout of the stones in Stonehenge, and realizing science should not rule out any logical possibility, he would rightly conclude that design is the best explanation.

Many well-known scientists have had no problem theorizing about design in biology:

Darwin himself theorized that the first forms of life (at most, 8-10 forms) were the result of design;
Alfred Russel Wallace, who came up with a theory of natural selection at the same time as Darwin, later abandoned that theory and instead subscribed to a theory of design;
Louis Agassiz, a leading naturalist at Harvard University and “the father of the American scientific tradition,” opposed Darwin’s theory of natural selection and subscribed to a theory of design;
Even Richard Dawkins, the evolutionary atheist, has theorized that DNA might be the result of design (by space aliens);
Dr. Sudip Parikh, the CEO of the American Association for the Advancement of Science, addressed the concept of design when he spoke at the National Press Club on April 5, 2021. A questioner noted that Darwin himself theorized that the very first forms of life were the result of design and asked Dr. Parikh if theorizing about design in nature is unscientific. Instead of stating that it is unscientific, he said we should be teaching our students to follow the evidence, “wherever that evidence takes them.”
Of course, if a theory of design is presented in a science classroom of a public school in the United States, then, given the separation of church and state required by the First Amendment to the U.S. Constitution, the theory cannot identify the designer with any particular religion.

Acknowledging that there is nothing unscientific about a theory of design in biology would go a long way toward restoring trust in science, which is now seen by many as ignoring the obvious (design).

In an email to me on February 8, 2024, Ms. Townley (now the president of the NABT) informed me that she presented my proposal for amending the NABT Position Statement on Teaching Evolution at the January 2024 meeting of the Board of Directors. She said, “The board heard the proposal and voted to decline the amendment.”

I replied, “Could the Board give me its reasons for declining the amendment? In particular, could it respond to the arguments set forth in my statement supporting the proposal? That would be much appreciated.”

She replied, “The board declined discussion of the amendment and unanimously declined to amend the statement, therefore there are no counter arguments available to share.”

No Debate, Please; We’re Biology Teachers

In an email on February 9, 2024, I replied that I was “very disappointed the Board wasn’t interested in engaging in a healthy debate on the issue of design, especially since Louis Agassiz and Charles Darwin thought there was nothing unscientific about it.” I stated that scientists and science teachers should be interested in promoting debate, not stifling it. I also noted, “If the NABT is sincerely interested in promoting diversity, equity, and inclusion, it should promote the inclusion of those who share the perspective of Louis Agassiz and Charles Darwin, i.e., that design is a legitimate scientific concept.”

In an email to Ms. Townley on February 22, 2024, I again expressed my disappointment that the Board did not give any reasons for its rejection of my proposal and stated that “I would find it very helpful if you, or someone else at the NCSE [National Center for Science Education], could prepare for me a brief response to the arguments I presented in my proposal.” (I should note that, in addition to being the new president of the NABT, Ms. Townley is now also the new executive director of the NCSE.)

In a response the same day, Ms. Townley thanked me for my email but stated, “As noted previously, the Board deemed that the matter did not warrant discussion or debate and unanimously declined discussion. Your disappointment at that outcome is noted, however, no further discussion or argumentation will be provided.” Like the Board, neither she nor the NCSE had any interest in discussing or debating the question of whether design is a legitimate scientific concept in the field of biology.

It is clear that one way mainstream science seeks to stifle opposition is by simply refusing to discuss or debate opposing views. 

The body's war machine vs. Darwin.

 Newly Discovered War Machines in the Immune System


An armored terrorist lurks in the city. Suddenly, thousands of pieces of sticky rope fly at him from all directions. They bind together, immobilizing him in a net. The net dissolves the intruder’s armor, and simultaneously signals for miniature robotic snipers who land on the net, using it as a scaffold. They fire armor-penetrating bullets through the net and into the terrorist’s compromised armor. Reinforcements install kill switches inside his body, forcing the terrorist to commit involuntary suicide.

Something like that describes a newly discovered molecular machine that helps fight infectious pathogens in our body cells. The news from Yale University says:

Yale scientists have discovered a family of immune proteins, which they describe as a “massive molecular machine,” that could affect the way our bodies fight infection. 

The immune proteins forming the net around the pathogen are called guanylate binding proteins, or GBPs. They have been known for a decade, but their mode of operation was only recently uncovered by Yale researchers. A short video shows these GBP1 proteins (the sticky ropes) as yellow pillar-shaped dimers rushing in, unfolding and linking up, surrounding the outer membrane of a bacterium (its armor). In short order the bacterium is surrounded with an inescapable straitjacket. There can be up to 30,000 of these proteins enclosing the pathogen in a type of body bag.

“What we found is among the most impressive examples of a biological machine in action that I’ve ever seen,” said John MacMicking, a professor of microbial pathogenesis and of immunobiology at Yale, and an Investigator of the Howard Hughes Medical Institute. MacMicking is senior author of the study.

The bacterial cell wall armor is no match for the immune system’s armor-piercing bullets. Even bacteria able to modify the lipopolysaccharides (LPS) that comprise the outer membrane (OM) have no chance. GBP1 knows all the configurations.

Human GBP1 still targeted cytosolic Stm [Salmonella enterica serovar Typhimurium] irrespective of bacterial size, shape, motility, or OM composition; the latter spanned LPS chains of different length, charge, and chemical structure. Such broad ligand promiscuity may help GBP1 combat gram-negative pathogens that modify their LPS moiety in an attempt to evade innate immune recognition and antimicrobial killing.

With the pathogen’s armor covered, the GBP proteins work to disentangle the lipopolysaccharide threads of the outer membrane. Having detected the help signal, reinforcements come in, firing caspase-4 grenades and interferon-γ kill switches into the bacterium, forcing it to commit pyroptosis, a form of programmed cell death.

“We are literally observing Mother Nature at work, looking at how these proteins operate in 3-dimensional space and at a particular location,” said MacMicking. “In just a few minutes they unfold and insert into the bacterial membrane to form a truly remarkable nanomachine and innate immune signaling platform.”

The bacteria coated with GBP straitjackets can be as small as 750 billionths of a meter (nanometers). The scientists found that this body-bag method works on bacteria regardless of shape. It works on viruses, too.

Imaging Design in Detail

This discovery was only made possible by recent advances in imaging technology. With cryo-electron microscopy, the researchers were able to “slice” whole live cells that had been quick-frozen. The resulting slices were assembled into tomograms, giving glimpses of heretofore unseen realities at work inside our body cells.

Our immune system mobilizes numerous proteins to detect viruses and bacteria — and to bring them under control. But until recently, limits to research technology have thwarted scientists’ understanding of how to prevent different pathogens from occupying and replicating within specific parts of our cells in the first place.

Harnessing the latest cryo‐electron microscopy techniques to look inside human cells, researchers at the Yale Systems Biology Institute have identified a family of large immune proteins that assemble into a massive signaling platform directly on the surface of microbial pathogens.

The researchers say they found thousands of GBPs building what amounted to a coat of armor (GBP1 coat complex) around the bacteria, allowing other defense proteins to recognize and kill encapsulated bacteria as well as mobilize immune cells for protection.

This reinforces an ID expectation that the more detail revealed, the more the design evidence becomes apparent. Evolution may look plausible from afar, but the angel is in the details. 

How Reinforcements Are Called

After the bacterium is immobilized, the GBP1 straitjacket becomes a scaffold for snipers to dismantle the intruder’s armor. The GBP family of proteins serve not only as the sticky ropes coating the intruder and disrupting its armor; they are also equipped with radios to call in the snipers and bomb squad. These proteins install the kill switches.

Thus, insertion of human GBP1 seems to disrupt lateral LPS-LPS interactions to compromise OM integrity. This not only activates the caspase-4 inflammasome pathway but allows the passage of small antimicrobial proteins such as APOL3 to directly kill pathogenic bacteria.

Human GBP1 was found to be “obligate for initiating the entire signaling cascade,” the scientists found via knockout experiments. It’s the captain in command.

Irreducible Complexity in Peace and War

ID advocates enjoy the examples of irreducible complexity (IC) in peacetime: the ATP synthase motor, kinesin, and the DNA translation mechanism. But when intruders threaten the life of a cell or its host organism, IC can fight with lethal intensity in an “all hands on deck!” war campaign. Its armed forces are always at the ready.

An emerging paradigm for innate immune signaling cascades is the higher-order assembly of repetitive protein units that generate large polymers capable of amplifying signal transduction. Our results identify human GBP1 as the principal repetitive unit, numbering thousands of proteins per bacillus, that undergoes dramatic conformational opening to establish a host defense platform directly on the surface of gram-negative bacteria. This platform enabled the recruitment of other immune partners, including GBP family members and components of the inflammasome pathway, that initiate protective responses downstream of activating cytokines such as interferon-γ. Elucidating this giant molecular structure not only expands our understanding of how human cells recognize and combat infection but may also have implication for antibacterial approaches within the human population.

Isn’t it nice to know that “eukaryotes have evolved compartment-specific immune surveillance mechanisms that alert the host to infection and recruit antimicrobial proteins that help bring microbial replication under control”? Actually, Charles Darwin never proved that his proposed mechanism of natural selection was capable of creating anything beyond simple variation within a species. His use of rhetoric and the analogy of domestic breeding was recognized even by his contemporaries as a mere suggestive hypothesis lacking scientific demonstration. 

Robert Shedinger shows this in Darwin’s own words in the new book Darwin’s Bluff. Aware that the Origin of Species was a “mere abstract” falling short scientific standards, Darwin promised a “big book” with the evidence. But he never published one. Why? Shedinger suggests he knew the evidence was lacking, and he was afraid of criticism. Instead, he relied on friends to promote his views. Darwin’s friends ran with “natural selection” as an all-purpose can opener to explain nature without an intelligent designer, using imagination and storytelling instead of hard evidence. In my experience reading the best of neo-Darwinian explanations, that’s still all they have to offer. Demonstration of selection’s alleged creative power is lacking, especially for irreducibly complex “massive molecular machines” like this one.

The discovery of a multi-component system able to mount a coordinated response to a threat speaks instead of Foresight: preparedness for a future eventuality. Darwin’s mechanism has no foresight or goal. At best, it can only preserve what it already has. Our uniform experience with foresight is that it is a capability of designing intelligence. That is Undeniable.

Tuesday 12 March 2024

The language of engineering proves superior to Darwinese in describing molecular biology.

 Is It Becoming Acceptable to Speak of Biological Systems and Processes in Terms of Design?


To the question posed in the headline, the answer is: It seems that way sometimes. And can speaking about design in such a context be done without getting hammered by the press, censored, or ridiculed? Perhaps. We’ll see. In the following example, think of the Darwinese as packing peanuts that can be removed to get to the important items inside.

A remarkable paper was published in BioEssays in January, with three authors from the University of Washington, Steven S. Andrews, H. Steven Wiley, and Herbert M. Sauro. None has any known sympathies for intelligent design. And yet much of their paper, “Design patterns of biological cells,” could have been written by any one of the PhDs presenting ideas at the Conference on Engineering in Living Systems (CELS).

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells’ underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

Taken for Granted

The authors do not question Darwinian evolution, taking it for granted some 14 times in the paper. They speak of “the evolution of complex life” and convergent evolution, even speculating on whether life on other planets would evolve the same way as it has on Earth. Such talk is common in biomimetics literature as well: e.g., one writer spoke of an ingenious solution that was “refined over more than 420 million years of evolution,” as if natural selection gave an organism a head start. We can safely dismiss such statements as either poetic license or a misunderstanding of evolution in its usual unguided sense.

The important items are these: a catalog of 21 design patterns presented as solutions to engineering problems that cells have solved. Here’s one example:

Pores and pumps

Problem
Cellular components, from ions to proteins, typically need to be localized to the correct sides of membranes, including the plasma membrane, nuclear membrane, and other organelle membranes.

Solution.
Trans-membrane pores and pumps that use either active or passive transport. These pores and pumps are typically quite selective about what molecules they transmit and are often gated by external signals.

Cell membranes are quite permeable to oxygen, carbon dioxide, and other small nonpolar molecules but are effectively impermeable to larger and more charged species, a property that is essential to establishing and maintaining cell organization. Transport of these latter species occurs via transporters and channels, including ion channels, passive and active transporters for ions or other small molecules, proton pumps, ABC transporters, photosynthetic reaction centers for electron transport, and ATP synthase proteins for mitochondrial proton transport. The nuclear pore complex is a particularly large pore, which enables passive transport of small molecules and performs active transport on proteins that carry nuclear localization or nuclear export signals.

Readers can enjoy all 21 of these design patterns at their leisure in the open-access paper. The key takeaway is that the authors are looking at cells not as poorly designed conglomerations of haphazard parts that some blind tinkerer cobbled together from whatever pieces of stuff were available, but as collections of elegant solutions to real problems familiar to engineers. It represents a noteworthy step toward design thinking in biology from an unexpected source.

Motivation for the Paper

In a video within the paper, Dr. Sauro from the Bioengineering Department explains what motivated the paper. He begins his answer by holding up a copy of Bruce Alberts’s textbook Molecular Biology of the Cell, a thick tome with 1,500 pages. 

We started thinking: Is there any way we could abstract this information at a higher level, to help us comprehend what’s going on in a cell? And we were struck by this other book, which is totally different, Design Patterns. It’s a famous book in computer science by a so-called Gang of Four. It’s an interesting book because it describes how to solve complex problems in a sort of simplified way. And we thought: Is there was any way to marry this book with the Alberts book? That’s basically what motivated us to write this paper.

Following the order of the Design Patterns book, the authors divided systems in molecular biology into the same three basic categories: creational (such as the synthesis of a protein), structural (such as a phosphorylation cascade with inputs and outputs), and behavioral (such as a relaxation oscillator). 

From this outline, the authors correlated the computer scientists’ design patterns with their actual implementations in cells. The implementations look like logic diagrams in circuit design. Mechanisms can be quite different, Sauro explains, and yet the underlying design pattern can be the same when examined at a higher level. 

Importance of the Paper

Dr. Sauro feels the paper is important for a number of reasons. It provides a new way of communicating ideas in molecular biology, so that computational theorists and experimentalists can understand each other. Another benefit of the approach is to motivate other biochemists to build on their scaffolding of design patterns. This assumes many more engineering solutions can be identified; indeed, Sauro hopes others will help construct a searchable database of design patterns. Machine learning, then, could recognize patterns in newly identified networks in living organisms, expanding our understanding cellular networks. This would be very helpful for complex signaling networks, for instance, when it is hard to determine what is going on. Machine learning could compare known design patterns with the input/output behavior of the components, leading to an “Aha!” moment that untangles the complexity into a recognizable logic diagram.

Sauro credits primary author Steven Andrews for the clear and readable form in which the paper was presented. He hopes many scientists will read it, because it covers a wide range of biology and should interest all biologists — and, we would add, engineers. It is a springboard for ideas that also might interest those preparing for the next CELS conference.

Design patterns are recurrent solutions to commonly encountered problems. All biological cells encounter the same problems of how to construct the biochemical components that they are built from, how to connect those components together into useful reaction networks, and how to use those reaction networks to animate life.

The authors are quick to acknowledge certain predecessors in biological design thinking. 

The idea of understanding cellular systems in terms of functional parts is of course not new. For example, Hartwell et al. argued for a modular view of cell biology, Del Vecchio et al. emphasized the central roles of control mechanisms, and Khammash’s group has focused on mechanisms that provide integral feedback control. In contrast to these and other works, our focus is larger, covering a wider swath of cell biology mechanisms. Also, our perspective is subtly different. Rather than focusing on a particular biological topic, our emphasis is on the development of a catalog of the solutions that cells have evolved to solve specific problems. This design pattern concept is useful for abstracting a broad range of cell functions into a manageable set of distinct patterns, enabling one to better see parallels and

Future of the Design Pattern Approach

Clearly, design thinking is a fruitful heuristic for discovery. But what about the “interlinked and hierarchical design patterns” mentioned next? Could those evolve? In the Illustra film Darwin’s Dilemma, such hierarchical patterns (exemplified in the body plans of the Cambrian fauna), are shown to resist Darwinian approaches because they require top-down design, as with a blueprint or logic diagram before assembly begins. Is this not the case with all “design patterns”?

The authors grant too much creativity to the neo-Darwinian mechanism. They assume that problems motivate their own solutions in biology:

Going even farther afield, one can speculate about life on other planets, where again the same problems would likely arise, and again would necessarily be addressed with many of the same solutions. This suggests that the design patterns listed here, along with others not addressed, could be reasonably considered universal principles of life.

Most likely this kind of speculation will wither on its own as the successors of Bruce Alberts add more pages to molecular biology textbooks. If, as the authors conclude, those involved in simulating cells will refer to a database of design patterns in their multiscale modeling, it should become increasingly clear that cells resemble engineered masterpieces. Darwinese would then decline as superfluous words in future research projects focused on design patterns.

Monday 11 March 2024

The tech of muscles vs. Darwin

 

OOL researchers may have tossed the answer in the trash?

 Aliens in the Garbage


Garry Nolan is the Rachford and Carlota A. Harris Professor of Pathology at Stanford University. He is a productive and respected immunologist who has published more than 330 research articles, and is a pioneering inventor of laboratory tools for his field.  

He also believes in extraterrestrials — that is, intelligent non-human visitors to Earth. Though Nolan admits that the publicly available evidence has not yet reached the standard of scientific proof, he says that he has been personally convinced by the evidence he has examined. More importantly, he is adamant that whether extraterrestrial visits have actually happened or not, scientists should be exploring the possibility rather than ignoring it.

Not Everyone Agrees

Some people — whether they would put it in so many words or not — believe that certain types of answers are simply off-limits in a scientific inquiry. Nolan has no patience for this notion. He says: 

That’s not how a scientist operates. If you take a potential solution off the table and you throw it in the garbage, you could spend the rest of eternity searching around on the table for the answer, and you threw it in the garbage. 

That’s very well-put. There’s no harm in keeping a potential answer on the table, and there could be harm in tossing it in the trash. Without saying anything about the evidence itself, the philosophical principle underlying Nolan’s investigation is sound. And it’s a principle with much wider applications. 

By investigating the possibility of intelligent, non-human causes for certain phenomena, Nolan is, in fact, working as an intelligent design researcher — whether he would embrace that label or not (and I see no reason to think he would). The underlying logic of an argument for alien design in mysterious artifacts or conditions is the same logic underlying the arguments for design in the origin of life or the laws of the universe. 

Nolan seems to be aware of this. Asked in a recent interview what he considered the most fascinating aspect of biology at the cellular level, he had this to say:  

The micromachines and the nanomachines that proteins make and become. That to me is the most interesting: the fact that you have this, basically, dynamic computer within every cell that’s constantly processing its environment, and at the heart of it is DNA, which is a dynamic machine, a dynamic computation process. People think of the DNA as a linear code. It’s codes within codes within codes, and it is the, actually, the epigenetic state that’s doing this amazing processing. I mean, if you ever wanted to believe in God, just look inside the cell.

He goes on to say that the appearance of design goes all the way down to the laws of physics and the fabric of the universe itself. 

Yet as far as “wanting to believe in God” goes, Nolan isn’t sure that he does. He prefers to posit alien intelligences and remain agnostic, for the time being, about their natures. Within the bounds of pure science (not getting into philosophy), that’s a perfectly valid stance to take, since examining an artifact can’t tell you everything about its designer. Whether you personally think that God or a non-God extraterrestrial is the more credible explanation, the design inference is the same. 

Since he is making that inference in his research, it is not surprising that Nolan is running up against the same objection that other ID researchers do: the objection that certain types of explanation should be rejected a priori because they are (by definition) unscientific.

This Is All Well and Fine 

That is, as long as scientists happen to be investigating something with a true explanation that belongs to the set of approved options. But suppose it doesn’t? Suppose the real explanation lies in the “off the table” category of answers? (If you don’t think that’s possible, suppose.) Should any scientist spend his or her whole life looking for a type of answer that doesn’t exist? At what point do we start considering the off-limit options? That’s Nolan’s point about throwing a potential solution in the garbage — once you do that, you could be doomed to an eternity of futile searching.  

The pressure to dig around in the garbage for discarded explanations is growing in many scientific disciplines. It is probably strongest, at the moment, in the field of origin of life (OOL) research. The difficulty (read: impossibility) of crafting a coherent explanation for how self-replicating structures could arise through deterministic processes has led some scientists, such as Richard Dawkins and Francis Crick, to admit that alien intelligence is a possible cause. (So Dawkins and Crick join the ranks of intelligent design theorists, albeit unwillingly.) 

Honest OOL researchers admit that they reject ID arguments not because those arguments lack all merit, but simply because they are off the table, out-of-bounds. For example, take some interview comments by OOL researcher Joana Xavier (also discussed by David Klinghoffer in a recent post). She said:  

I read Signature in the Cell by Stephen Meyer… and I must tell you, I found it one of the best books I’ve read in terms of really pointing, putting the finger on the questions. What I didn’t like was the final answer, of course. But I actually tell everyone I can, “Listen, read that book. Let’s not put Intelligent Design in a spike and burn it. Let’s understand what they’re saying and engage.” And it’s a really good book that really exposes a lot of the questions that people try to sweep under the carpet. It’s just … I think we must have a more naturalistic answer to these processes. There must be! Otherwise I’ll be out of a job. [laughs]… I like to see myself as a very open-minded person in terms of metaphysics, but that’s not to say that the molecular study of the cell should just end. I don’t even think that the ID people want it to end — it’s just the pressure to accept that there’s no answer through naturalistic means that I’m a bit against.  

To her credit, Xavier is upfront about her reasoning. Not everyone is; some scientists would prefer to pretend that the case for ID is pure rubbish, rather than admit that they are simply working in a framework that cannot accept a conclusion of intelligent design. 

Xavier, by contrast, makes it quite clear that she does not believe in accepting a non-naturalistic answer to a scientific question. (I’m not sure whether she would apply this to the idea that a “natural” intelligent being, such as an extraterrestrial, created the first life.) It’s great she acknowledges that her community’s philosophical commitments don’t justify sweeping the arguments of ID proponents under the rug. But is it really practical to engage with an argument while giving yourself the rule that you cannot accept it? 

“This Appears Designed”

Xavier’s fear is that to say, “This appears designed,” would be to give up on the quest to find a natural cause: there might be one, but scientists would never find it because they ended their quest by shrugging their shoulders and saying, “I guess God did it.” 

Her fear is justified. It’s a real danger. Sometimes, things that at first glance appear designed turn out to have purely natural causes. We shouldn’t close our minds to naturalistic explanations just because an intelligent designer could have done it. 

But OOL researchers such as Xavier should realize that the opposite danger also exists. If you begin by saying, “Unguided natural causes did it,” then if unguided natural causes didn’t do it, you will miss the true explanation. You might, as Dr. Nolan said, “spend the rest of eternity searching around on the table for the answer, and you threw it in the garbage.”

Intelligent design theory is not opposed to naturalistic explanations. It is merely open to non-naturalistic explanations. You don’t have to throw any explanation in the garbage: not natural processes, not intelligent mind, not God, not aliens. The deeper purpose of science is not to find a naturalistic explanation, but to find the true explanation. Every possibility must remain on the table in the search for truth. 

Out of a Job?

Will that lead to OOL researchers being put “out of a job,” as Xavier fears? Well, it’s certainly true that once you find a definite answer to a problem, you may have little work left to do on that problem. So maybe one day (probably pretty far off) origin-of-life researchers will settle the question once and for all, and have nothing left to do. 

But is that the worst thing that could happen? Scientists work themselves out of a job all the time. Normally, when they do, they just move on to another question. Isn’t that better than throwing the answer in the garbage, just to ensure you can keep searching for it forever? 


Thursday 7 March 2024

Time to end the quest for engineerless engineering?

Time to end the quedt Engineering Innovation from Cuttlefish 



Editor’s note: We are delighted to welcome Daniel Witt as a new contributor. In case you are curious about the background in his author photo, it was taken in a pyramid in Sudan, at Meroë.

Last month, Cambridge University’s science magazine, Bluesci, announced that researchers have developed a new camera based on cuttlefish eyes. Cuttlefish have unusual W-shaped pupils that allow them to see well in both dim and bright conditions as they navigate in deeper or shallower waters. The researchers successfully reverse-engineered the cuttlefish’s eye structure to create a camera that works better in conditions of highly variable luminosity.   

Cuttlefish are extraordinary creatures, and this is not the first time engineers have learned from them. In 2013, the Washington Post reported that the Office of Naval Research was funding a project to mimic the cuttlefish’s color-changing skin, with potential application in submarine camouflage technology. In 2009, NBC reported that MIT scientists had studied cuttlefish skin to design a TV screen that used less than 1 percent of the power that other screens at the time used. The reverse-engineering opportunities just keep coming. 

Usually, “reverse-engineering” implies that … well, engineering took place beforehand; design, in other words. And, as it happens, the news from Cambridge explicitly refers to cuttlefish eyes as “finely-designed.” 

It was probably a slip-up. No doubt the writer would defend this as a mere convention of speech — I doubt that he was trying to imply that actual design took place in the creation of cuttlefish eyes. But isn’t it interesting that it’s so difficult to talk about these things without invoking the language of design? 

Caught in the Weeds

Maybe it doesn’t seem so interesting. But that’s only because we’re so used to this reality. It can be easy to get caught in the weeds in the debate over whether Darwinian mechanisms are sufficient to explain life, and forget the reason the debate is going on in the first place. The debate only exists because these implausibly intricate engineering marvels exist. It did not have to be so. The universe could have been otherwise. It was never a given that when scientists looked deeper into life, they would find such exquisite designs; but they did.   

As we gain the ability to look deeper and deeper into the inner workings of life, we seem to be entering a new renaissance of collaboration between biologists and engineers. Physicist Brian Miller recently noted this trend in the developing field of systems biology:  

[W]hen you look at the design conversation, who controls it? It’s people who don’t have the expertise to really address it. They’re not engineers. They’ve been trained to see the world through this materialist grid, so they assume on faith that there’s no evidence of design, and then they find various reasons to justify that belief. In contrast, what you’re seeing in biology is really a revolution that’s at its early stages, because engineers are working more and more with biologists, and what you’re seeing is, when they do that they use design language, they use design assumptions.

An Engineering Marvel 

As we all know, the prevailing theory insists that this appearance of design is mere illusion. But when engineers team up with biologists to learn how to copy the mechanisms of life, they aren’t thinking about that. Whether a cuttlefish eye is designed, or merely in every way appears to be designed, is irrelevant. The point is that it is an engineering marvel, and engineers can learn from it. 

This fact is important, not because it is in-and-of-itself proof of design, but because it tells us something practical about the competing theories and their respective productivity. 

Proponents of the neo-Darwinian model are fond of asserting that the naysaying arguments of ID-supporters (regarding irreducible complexity, non-traversable fitness landscapes, the probabilistic inability of Darwinian mechanisms to make meaningful changes to life within the lifespan of earth, lack of any confirmed observation of constructive mutations, etc.) make little difference to the actual research underway in biology. That is to say: Life only makes sense “in the light of evolution,” and the critics of that framework are just flies buzzing in the background. 

A Verbal Gloss

The truth is something close to the opposite. Assumptions of macroevolution almost never have any practical bearing on research in biology. Darwinian evolution is invoked as a verbal gloss, not as a vital presupposition. Chemist and National Academy of Sciences member Philip S. Skell famously asked 70 distinguished researchers whether they would have done their work differently if they had believed Darwin’s theory was false. They all answered no.

Dr. Skell isn’t the only one to point this out; it’s the reality of the field. An assumption of design, by contrast, is quite often an essential foundation to successful research projects in biology — whether the design language is expurgated from the final presentation or not. 

Biologists will continue to debate whether this design is real or only apparent. But in the meanwhile, intelligent design-based research will keep moving forward, untroubled by those debates — as it always has.