Exaptation cannot reduce irreducible complexity

 Co-Option and Protein Homology Don’t Explain the Evolution of the Flagellum

Casey Luskin

Critics of intelligent design have not taken arguments for irreducible complexity (IC) sitting down. In a recent post I described how our new peer-reviewed paper, “On the Relationship between Design and Evolution,” in the open-access journal Religions, details the elegant design of the bacterial flagellum. My co-authors (Brian Miller, Stephen Dilley, and Emily Reeves) and I explain why its irreducible complexity poses a challenge to Darwinian evolution. Critics have replied that IC systems can evolve via indirect evolutionary pathways (often called exaptation). That’s where a system might start with one function but then evolve to acquire a new function along the course of its history. Vital to indirect evolutionary pathways is the concept of co-option, which holds that proteins can be borrowed from other systems in the cell, and then modified and retooled to perform entirely new functions in some new system. 

Our article is a response to Rope Kojonen’s book The Compatibility of Evolution and Design. We start by reviewing just what needs to be explained — and ask what is needed to show that such models are plausible.

More generally, a plausible evolutionary explanation of the bacterial flagellum must explain not just the flagellum-chemotaxis propulsion/navigation system but its array of other characteristics, including its delivery system of individual parts, maintenance cycle, feedback loops, and performance efficiencies. In particular, indirect evolutionary accounts (such as co-option or exaptation) must explain how the 35–40 protein parts of the flagellum evolved from parts that originally served different functions in the cell. It must also account for their assembly instructions. The insurmountable barrier to any scenario is the numerous tight constraints identified by Schulz (2021a, 2021b, 2021c) that must be met before the system could function at all. Recall H. Allen Orr’s assessment of co-option (cited by Kojonen above):

“We might think that some of the parts of an irreducibly complex system evolved step by step for some other purpose and were then recruited wholesale to a new function. But this is also unlikely. You may as well hope that half your car’s transmission will suddenly help out in the airbag department. Such things might happen very, very rarely, but they surely do not offer a general solution to irreducible complexity.” (Orr 1996)

So, just how does co-option plausibly explain the origin of the most efficient machine in the universe?

We then note that Kojonen — a very thoughtful critic of ID, who takes ID arguments seriously — endorses such indirect / exaptation / co-option models of flagellar evolution. We explain why this is a question that must be addressed via the scientific evidence:

Kojonen takes the challenge of irreducible complexity head-on. He frames the problem as follows:

“Draper (2002) homes in on the crucial question: Are the requirements for each individual part really as strict as Behe claims? If biological parts are more malleable than Behe assumes, so that less specificity is required for fulfilling their roles, then Behe’s argument against co-option fails. Debunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form. Then, a continuous series of functional forms, leading from no flagellum to a flagellum, must exist so that no change is too large for natural selection to cross, and all modifications can be made. As with Dembski’s argument, it does seem plausible that evolving such complex systems is difficult, and the existence of such an evolutionary pathway has stringent conditions. But difficult or not, it is possible that nature does allow it. Behe thinks that the existence of such pathways is unlikely, but the existence of such pathways is fundamentally an empirical question.24” (Kojonen 2021, p. 118)

Notice two key elements of this passage. First, Kojonen states that the matter is “an empirical question”. Indeed, it is. Once again, the scientific details are paramount. Is there evidence of smooth evolutionary pathways between viable forms or not? This is a fundamentally scientific question. Kojonen’s model hinges in part on empirical evidence.

Protein Rarity Challenges Co-Option

Second, Kojonen also states that “[d]ebunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form”. So, Kojonen believes that successfully countering Behe’s argument depends on how proteins work and the prospects for a protein-to-protein transformation. This makes sense. The flagellum, for example, is made of protein parts. The function of each part, as well as the likelihood of a given part evolving into its present form from an ancestral form, is highly relevant. In short, Kojonen believes that his counter to Behe — an attempt to show that the flagellum’s ‘design’ is compatible with mainstream ‘evolution’ — rests upon the plausibility (or implausibility) of protein evolution.

This is significant. We have already examined strong evidence against fine-tuned preconditions and fitness landscapes that are ‘designed’ to enable proteins to evolve. This means that the calculations above (Section 4) directly impact the viability of Kojonen’s response to Behe. If these calculations are correct, then it is safe to say — by Kojonen’s own lights — that he has not met the challenge of irreducible complexity. The flagellum, thus, appears to display a type of design that conflicts with evolution. Thus, to the extent that Kojonen accepts the bacterial flagellum as evidence of ‘design’, he faces an internal coherence problem for his conjunction of ‘design and evolution’.

What Co-Option Must Explain

So what exactly is needed to yield a viable model of indirect evolution / co-option? Some excellent work has been done on this question by folks within the ID community, as we recount: 

Having raised this crucial challenge to Kojonen’s reply to Behe, we will now take co-option on its own terms for the sake of argument. Yet even on these terms, it still fails to be plausible. Kojonen cites authorities that invoke exaptation (also called “co-option” or “indirect evolution”) to explain the evolutionary origin of the bacterial flagellum. Under this model, evolution proceeds by borrowing parts from different systems, retooling them to change their functions, and then combining them into a new system to perform a new function. Philosopher Angus Menuge lists five elements that any co-option account must provide to explain an irreducibly complex system:

Availability of parts.

Synchronization, in which parts are available at the same time.

Localization, in which parts are available at the same location.

Coordination, in which part production is coordinated for assembly.

Interface compatibility, in which parts are “mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’”. (Menuge 2004, pp. 104–5)

Typically, exaptation or co-option accounts do not explain anything beyond part of element (1). In this vein, Kojonen claims that 90% of flagellar parts have homologues that perform functional roles outside the flagellum. As we will see, this is an inaccurate claim — and co-option/exaptation accounts of the evolution of the flagellum face this and additional obstacles.

Kojonen thus follows in the footsteps of many co-option advocates in only assessing the first element of any successful co-option-based model of evolution, and we thus focus our critique there asking the question of whether sequence similarity between flagellar proteins and other proteins helps us solve the problem of its origin. We recount three main problems with such co-option-based evolutionary model of the flagellum.

Problem 1: Mere Sequence Similarity Is Not Evidence of an Evolutionary Pathway

The first main point we make is that merely establishing that two proteins have similar sequences is not sufficient to show that there is an evolutionary pathway to go from one sequence to the other:

In the context of biochemical evolution, the primary evidence for homology between two proteins is typically said to be similarity between amino acid sequences. An initial mistake made by proponents of co-option is therefore to confuse sequence similarity between two proteins with evidence for an evolutionary pathway. Even if other systems have proteins similar to each component of an irreducibly complex system, at most, this suggests homology, which might reflect common ancestry. Mere sequence similarity does not constitute a stepwise evolutionary explanation. Kojonen seems to miss this important nuance. He states that “parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution” (Kojonen 2021, p. 117). He also writes, “The existence of similar parts in other systems, for example, does provide supporting evidence for evolvability” (Kojonen 2021, p. 118). But similarity does not itself indicate a viable evolutionary pathway. As Behe explains:

“Although useful for determining lines of descent… comparing sequences cannot show how a complex biochemical system achieved its function — the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter… Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?25” (Behe 1996, pp. 175–76)

Behe points out that a single author (or mental agent) could be the cause of two different manuals. Accordingly, mere similarity is not evidence that mindless processes can bring about the system in question.

Problem 2: Useful Flagellar Protein Homology Is Not as Widespread as You’d Think

What we often find when evaluating protein similarity is that not all proteins are similar to other proteins — especially in a manner that is useful for constructing evolutionary explanations. We go through the literature and find what it really shows about flagellar protein homology to non-flagellar systems:

But the problem runs deeper than incorrect reasoning about sequence similarity: many parts of the bacterial flagellum are dissimilar to parts of other biological systems. Thus, a second problem facing the co-option model of evolution is that biological parts are often unique and unavailable to be borrowed from other systems (Khalturin et al. 2009; Beiko 2011). But Kojonen claims this is not a problem for the flagellum:

“Though a complete evolutionary explanation for the bacterial flagellum is still missing, critics of Behe have argued that approximately 90% of the parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution. The type III secretion system, for example, has been argued to represent a viable precursor system to the flagellum. (Musgrave 2004; Pallen and Matzke 2006).” (Kojonen 2021, p. 117)

Kojonen cites two sources for his claim that 90% of flagellar parts are homologous to “parts that have other uses”. (Presumably, he is referring to parts that exist elsewhere besides the flagellum itself.) But this claim is highly problematic. One of his sources, Musgrave (2004, p. 81), provides no comprehensive analysis of flagellar homologues but simply asserts, via citations to other sources, that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems, including the sigma factors and the flagellins” — but those sources (discussed below) do not substantiate this claim. Kojonen’s other source, Pallen and Matzke (2006), does provide a comprehensive study of flagellar proteins that are homologous to other proteins, but they too do not substantiate a claim that “90%” of flagellar proteins are homologous to proteins outside of the flagellum.

According to Table 1 of Pallen and Matzke (2006), 15 of the 42 flagellar proteins they studied did not have known homologues.26 So, at best, they only identified homologues for only about 64% of the flagellar proteins they studied (27 out of 42) — significantly less than 90%. Moreover, the vast majority of the remaining 27 proteins for which they reported homology are highly suspect and/or do not support an evolutionary pathway leading to a flagellum:

Two of the claimed flagellar proteins with detected similarities to other proteins are regulatory proteins with unsurprising similarity to other regulators, yet they are not structural components of the flagellum that contribute to its motility function.27

Three of the allegedly homologous proteins had only slight sequence similarity; they were claimed to be homologous based on “structural or functional considerations”.28 Yet because evolution proceeds by modifying sequences of DNA and proteins, a lack of sequence similarity suggests these other proteins are not a viable source that could have been utilized via an evolutionary pathway.Seven of claimed homologous proteins are strictly homologous to other flagellar proteins,29 what might be called “intraflagellar homology”. One cannot explain the initial evolution of the flagellum by claiming it evolved from itself, so these examples are entirely unhelpful towards explaining the how the flagellum first arose from “parts that have other uses” (Kojonen 2021, p. 117) or from “similar parts in other systems” (Kojonen 2021, p. 118), as Kojonen puts it. This tenuous argument may have been derived from Musgrave (2004, p. 81), who argues that flagellar proteins find homologues in “other systems” including “flagellins”—but flagellin is a strictly flagellar protein that only forms a subunit of the flagellum’s propellor.

Eleven of the claimed homologous proteins were similar to proteins in the Type Three Secretory System (T3SS),30 three of which were also claimed to show intraflagellar homology.31 As quoted above, Kojonen cites the T3SS as a potential “viable precursor system to the flagellum”, but this argument has been long-criticized by intelligent design proponents (Illustra Media 2003) as well as by other scientists. More on this below.

Kojonen’s other source for his 90 percent statistic, Musgrave (2004), provides two citations for his claim that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems” — Aizawa (2001) and Ussery (2004). Ussery (2004) does not discuss homology for flagellar proteins outside of the flagellum; he merely compares sequence diversity across other flagellar proteins that fulfill the same flagellar function in different species of bacteria. Aizawa (2001) does identify some non-flagellar homologues for flagellar proteins, but only finds homologues for four flagellar proteins that were not also identified by Pallen and Matzke (2006).32 All four of these homologues are proteins used in the T3SS. Although there is clear homology between various flagellar proteins and the T3SS, we will explain below that such data are of limited value to account for the evolution of the flagellum.

Adding the four additional flagellar homologues identified by Aizawa (2001) to those identified by Pallen and Matzke (2006) brings the total to 31 out of 42 flagellar proteins that show sequence similarity to other proteins — 74% — which is again moderately less than 90%. But as noted above, the vast majority of these homologues are unhelpful in constructing some kind of an evolutionary pathway. In the end, Kojonen’s citations (and the sources of his citations) reveal at best only 4 out of 42 flagellar proteins (9.5%) are homologous to “similar parts in other systems” which could have potentially served as “precursors” to the flagellum, as Kojonen says. Nine-and-a-half percent is strikingly less than his claimed statistic of 90%.

More on the Type 3 Secretory System (T3SS)

Because the T3SS is so often cited as a potential “precursor” to the flagellum, it’s worth devoting some time to that topic specifically. In our paper we elaborate on various reasons why the T3SS could not have been an evolutionary precursor to the flagellum:

Because quite a few (perhaps up to 15) flagellar proteins appear homologous to proteins in the T3SS, the latter is often cited as a possible evolutionary precursor (or close relative) to the flagellum (Musgrave 2004; Miller 2008, p. 59). It is therefore worth exploring further why the T3SS could not serve as “a viable precursor system to the flagellum”, as Kojonen believes it to be. The T3SS is part of the flagellum itself and is used to pump proteins from inside the cell to outside the cell where they self-assemble into the flagellum. For this function, the T3SS is simply a molecular pump involved in flagellar assembly. Even granting that it could have been co-opted for some function, it is nonetheless unrelated to the flagellum’s motility function and so is unlikely to have been ‘co-opted’ to produce motility, the core function of the flagellum.

Once the flagellum is assembled, the T3SS provides an additional function: a structural component that anchors the flagellum in the cell membrane. Yet even here, it is not part of the motor portion of the assembled flagellum, but could be viewed as something akin to the bracket on an outboard motor. Again, the T3SS is a poor candidate for co-option (and modification) into the proteins that comprise the flagellum’s propulsion function.

Notably, a different molecular machine (called an “injectisome”) uses the T3SS as well (Diepold and Armitage 2015). In the injectisome, the T3SS is involved in both assembling the injectisome and in the injectisome’s function. (The injectisome is used by certain predatory bacteria to inject toxic proteins into eukaryotic cells, which then kill the eukaryotic cells so they can be ingested by the bacterium.) But it is doubtful that the injectisome and its T3SS are useful in explaining the origin of the flagellum. First, there are ecological and phylogenetic considerations that strongly imply the flagellum predates the T3SS and the injectisome and, thus, could not have evolved from these systems (Abby and Rocha 2012a, 2012b; Deng et al. 2017; Coleman et al. 2021).33 As New Scientist reported:”

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later”, says biochemist Howard Ochman at the University of Arizona in Tucson.” (Jones 2008)

Second, even if the T3SS could have served as a precursor to the flagellum, it is not clear that this would provide anything close to a viable evolutionary pathway — a “continuous series of functional forms, leading from no flagellum to a flagellum”, as Kojonen puts it. William Dembski nicely captures the essence of the evolutionary leap required to explain how a flagellum evolved from the T3SS:“[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the T[3]SS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands.” (Dembski 2005, p. 52)

Thus, even if the T3SS were a precursor to the flagellum, it would not necessarily help its evolution. But we further observe that “research indicates that the T3SS and flagellum are so distinct that they may in fact have independent origins (Tan et al. 2021) — a generally unexpected result on an evolutionary view.”

Problem 3: Not Addressing Flagellar Assembly

We further point out in the paper that “even if all the necessary parts were available and co-opted so that they could be constructed in the form of a flagellar motor, co-option does not explain the assembly instructions needed to construct complex systems.” Explaining the assembly of IC systems is something that Behe has called “Irreducible Complexity Squared” — and it is a vital aspect of molecular machines that almost always goes unaddressed by evolutionary models:

It is not just a matter of getting the parts; it’s also putting them together in the right sequence, at the right time, and in the right orientation. Simply having all the ingredients for chocolate cake is not in itself sufficient to produce a cake. Something similar is true for a Corvette engine. So much the more for the most efficient machine in the universe. Microbiologist Scott Minnich and philosopher Stephen Meyer explain this challenge:

“[E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in a factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex.” (Minnich and Meyer 2004)

From beginning to end, the flagellar assembly process is “tightly controlled and regulated in a sequential genetic hierarchy mirroring organelle assembly from the inner membrane to the outer cell surface” (Minnich and Meyer 2004). Indeed, Behe has deemed the origin of flagellar assembly equivalent to “Irreducible Complexity Squared” (Behe 2007, p. 93), because, as he puts it, “not only is the flagellum itself irreducible, but so is its assembly system. The assembly process and the flagellum together constitute irreducible complexity piled on irreducible complexity” (Behe 2019, p. 286).

Yet in his most recent book, Darwin Devolves, Michael Behe observes that when it comes to explaining the evolutionary origin of the flagellum’s assembly, one continues to hear very little from the evolutionary biology community:

“In 1996 [in Darwin’s Black Box] I showed that, despite thousands of papers in journals investigating how that fascinating and medically important molecular machine worked, there were no papers at all that tested how the bacterial flagellum might have arisen by a Darwinian process. The scientific literature was absolutely barren on the topic…. Twenty years on, there has been a grand total of zero serious attempts to show how the elegant molecular motor might have been produced by random processes and natural selection.” (Behe 2019, p. 287; see also Behe 2007, pp. 267–68)

We close this section of our paper by observing that “Like many of his evolutionary colleagues, Kojonen simply elides this problem.” Now this is not necessarily Kojonen’s fault — it’s really just the fact that there is virtually nothing in the mainstream scientific literature trying to explain the evolution of flagellar assembly. 

In the end, we find that the bacterial flagellum contains a form of complexity that challenges not just Darwinian evolution but also co-option-based indirect models of evolution. Rope Kojonen wants us to appreciate the design of the flagellum but also to believe that this form of design can evolve. His project is to harmonize evolution and design (as he envisions them). He wants to count the flagellum as designed, but also wants to ignore the fact that the type of design it displays — irreducible complexity — poses a major problem for evolution. Thus, he wants to join “design and evolution,” but only by setting aside some of the main features of the flagellum. This harms his attempt to reconcile evolution and design in a coherent fashion. As we put it in our article, “Kojonen’s marriage of ‘evolution and design’ has a major problem: the very system that provides strong evidence of design also undercuts evolution. One part of the model saws off the branch upon which the other side sits. Kojonen’s model is internally conflicted.” 

Please read our open-access paper, here, for more details including endnotes and citation information. 

Civil war: Catholic edition.

 

Not merely intelligent but ingenious design. II

 Thanks to Optimal Design, Eyes and Brain Give a Glimpse of the Future

Andrew McDiarmid

Does the vertebrate eye make more sense as the product of engineering or unguided evolutionary processes? On a new episode of ID the Future, I conclude a two-part conversation with physicist Brian Miller about the intelligent design of the vertebrate eye.

Did you know your brain gives you a glimpse of the future before you get to it? Although the brain can process images at breakneck speed, there are physical limits to how fast neural impulses can travel from the eye to the brain. “This is what’s truly amazing,” says Miller. “What happens in the retina is there’s a neural network that anticipates the time it takes for the image to go from the retina to the brain…it actually will send an image a little bit in the future.”

Dr. Miller also explains how engineering principles help us gain a fuller understanding of the vertebrate eye, and he highlights several avenues of research that engineers and biologists could pursue together to enhance our knowledge of this most sophisticated system. 

Oh, and what about claims that the human eye is badly designed? Dr. Miller calls it the “imperfection of the gaps” argument: “Time and time again, what people initially thought was poorly designed was later shown to be optimally designed,” from our appendix to longer pathway nerves to countless organs in our body suspected of being nonfunctional. It turns out the eye is no different, and Miller explains why.

Download the podcast or listen to it here.

The ministry of truth is at it again?

 

Not merely intelligent but ingenious design.

 Paper Digest: Ten Biomechanical Animal Joints Enable Extreme Performance

Emily Reeves

In 2021, engineer and ID proponent, Stuart Burgess analyzed ten linkage mechanisms in animal joints and published his Review of their mechanical functions in Bioinspiration & Biomimetics. He chose animal joints such as fish jaws, knee joints, and bird wings due to their extraordinary performance and the extensive knowledge base regarding how they function. As a veteran mechanical engineer, Burgess is well positioned to assess the mechanics of animal joints. Notice how in the excerpt below, he praises the optimality of animal joint design and notes the potential for bio-inspiration from studying animal joints:

Ten different linkage mechanisms are presented. They are chosen because they cover a wide range of functionality and because they have potential for bioinspired design. Linkage mechanisms enable animal joints to perform highly sophisticated and optimised motions. A key function of animal linkage mechanisms is the optimisation of actuator location and mechanical advantage. This is crucially important for animals where space is highly constrained. Many of the design features used by engineers in linkage mechanisms are seen in nature, such as short coupler links, extended bars, elastic energy storage and latch mechanisms. However, animal joints contain some features rarely seen in engineering such as integrated cam and linkage mechanisms, nonplanar four-bar mechanisms, resonant hinges and highly redundant actuators. The extreme performance of animal joints together with the unusual design features makes them an important area of investigation for bioinspired designs.

As Seen at Home Depot

You may have noticed a four-bar mechanical linkage mechanism if you watched a scissor lift while shopping at Home Depot. That four-bar linkage mechanism allows the lift to extend in order to reach products on high shelves. Collapsing the scissor lift reduces the amount of space the lift takes up. Four bar linkage mechanisms have four bars and four pivot points. The length of the bars may vary as well as how the bars move in relation to each other. By using unique four-bar linkage arrangements, an engineer can optimize mechanical movements. Key points about why engineers use such mechanisms include: 

Four-bar linkage mechanisms can increase force by utilizing bars of different lengths.

They can improve rotation or optimize the direction of compaction.

They move actuators away from the joint providing a mechanical advantage and lowering the energy needed for motion.

In Burgess’s paper, the first four-bar linkage mechanism discussed is the mammalian knee — a joint that has been criticized as poorly designed. As an engineer Burgess is familiar with constraints and design trade-offs. So he first discusses what the mammalian knee requirements are. To summarize, he says the knee must provide a 120o range of motion, be load bearing, and prevent overextension. He explains how through a clever design — an inverted four-bar mechanism — all of these requirements can be accomplished. The four-bar mechanism enables a large extension range, but also has an end stop which locks the knee. This lock decreases the amount of work required by the muscles to stand erect effectively making standing up easier. Because there is a broad area of contact between the femur and tibia, loads can be transferred through the joint and bore. In the knee’s four-bar mechanism, the center of rotation moves, which also provides advantages. When you squat, the center of rotation of the knee joint shifts, which reduces your muscular effort by 35 percent when you rise from the squat position. If you thought squatting was difficult, imagine how difficult it would be without this brilliant design! Burgess points out that one noteworthy constraint for joints of biological systems is that they are restricted from using a shaft inside a hole due to the necessity of a growth and development process. This relevant constraint applies to engineers working to develop self-replicating machines.

The Bird Wing Joint

The second four-bar linkage mechanism discussed is the bird wing joint. Have you ever wondered how birds can fly so long without tiring? Burgess points out that this is due in part to the brilliant engineering in the avian elbow joint, which enables wing tucking and extension. Burgess notes that, according to research done with seagulls, the elbow wing joint decreases 12.3 percent of a bird’s need for force during flapping.

Grasshoppers, dragonflies, and other insects generate lift by flapping and rotating their wings at steep angles. Flapping occurs at a frequency of 20 to 1,000 flapping cycles per second. It’s no surprise that these organisms make such a whirring sound! To accomplish such rapid movement, some incredible hinges are obviously required. Burgess points out that many insect wings have a small bar as part of their four-bar wing mechanism which ends up magnifying the wing rotation. This means that even minor movements on the insect’s body can cause a considerable angle of movement in the wing. Of course, the insect’s body must be correctly built to allow such mobility. Burgess also points out that flapping happens at a resonant frequency, which significantly reduces the inertial energy required to flap. This is only feasible because of the insect’s body architecture.

Another category of four-bar linkage mechanisms Burgess discusses is that of fish jaws. The first example he provides is a sling-jaw wrasse. As it happens, my husband and I owned a wrasse. Why? For the purpose of eliminating flatworms, vermetid snails, and bristle worms from our 75-gallon salt water aquarium. One can’t help but appreciate how incredibly well designed the wrasse’s mouth is. The term “sling-jaw” refers to the fact that these fish can hurl their jaws. Burgess notes that one function of the design is to capture prey with a quick suction approach. The second is that the sling-jaw design minimizes the amount of swimming the fish has to do. Pushing the jaw forward requires significantly less energy than swimming forward when food is nearby. As I was able to observe, the mouth of our wrasse extended so quickly and far that it made the fish an exceptionally agile hunter. Within a month or so of adding the wrasse to our tank, no pests remained — all thanks to the excellent design of the sling-jaw wrasse.

Burgess also describes the four-bar linkage mechanism of the mantis shrimp — a marine creature that punches to eat. The force is produced by a four-bar linkage mechanism connected to a biological battery. When the shrimp is ready to punch, it relaxes a muscle, the latch is released, and the accumulated elastic energy delivers 1000 N of force. That is several orders of magnitude larger than the weight of the organism.

A Gift for Engineers

To conclude, the amazing design structures in organisms provide engineers with inspiring templates for creating better products. Burgess provides three specific examples where direct study could pay impressive dividends:

Improved 3D modeling of avian wing joints has important implications for aircraft wing design.

Jaw mechanisms may result in new and improved designs for robotic clamping.

The punching mechanism of the mantis shrimp could inspire new technology in the field of industrial design.

Burgess’s review has been downloaded over 8,000 times and cited 19 times. The high number of downloads and citations suggests that there is a growing interest among researchers in using nature’s design templates to solve technological challenges. This indicates that biomimetics is becoming an increasingly important field for innovation and advancement in various industries. By studying the intricacies of natural mechanisms like four-bar linkages, scientists can gain valuable knowledge that to enhance human engineering practices. This interdisciplinary approach encourages critical thinking and innovation, ultimately benefiting various industries by inspiring more efficient and sustainable designs.

The not so constant universal constant.

 

A look around the neighborhood.

 

Yet more on why we ought to be grateful for our eyes flawless design.

 Brian Miller on the Gift of Vision

Andrew McDiarmid

Our eyes are easy to take for granted! Yet, the more we dig into this amazingly intricate system, the more thankful we become for them. On a new episode ID the Future, I begin a two-part conversation with physicist Brian Miller about the intelligent design of the vertebrate eye.

First, Dr. Miller reviews the evolutionary scenario for the origins of human vision. Charles Darwin himself acknowledged how absurd an idea it was to assume unguided processes could produce the human eye. But that hasn’t stopped generations of evolutionary biologists from proposing an evolutionary path to get from light-sensitive spots to crisp images produced by spherical eyes. Dr. Miller explains where the evolutionary view collapses for lack of empirical evidence to support it. 

Miller explains why it’s helpful to approach biological systems from an engineering standpoint. He highlights the work of the Engineering Research Group at Discovery Institute, a group of engineers and biologists working together to develop a new approach to researching and understanding living things. 

Part 1 rounds out with Dr. Miller walking listeners through the main subsystems and processes involved in human vision, explaining step by step how we go from gathering light from the outside world to producing high-definition images of it that we can comprehend. He also emphasizes the convergence of design in the visual system and the fine-tuning of the laws of nature for high-resolution vision. 

Download the podcast or listen to it here.

The ministry of truth is a thing. II

 

Some see Frankenstein as an exemplary rather than a cautionary model.

 

Yet more fence straddling?

 

Yet even more on why the skilled trades remain the smart choice.

 

The electric God?/Nick Lane in his own words.

 

An interlude XIII

 Listen for it: It's a long hard road that leads to a brighter day, but don't let your heart grow cold just reach out and call his NAME.

On the quest for a more plausible explaining away of finetuning.

 More on Roger Penrose and Fine-Tuning

Granville Sewell

Earlier this month I discussed a video containing a segment on fine-tuning from an amicable debate between 2020 physics Nobel Prize winner Roger Penrose and Christian philosopher William Lane Craig. The video was interesting to me because Penrose does not like the multiverse/anthropic principle explanation which is nearly always proposed as the only alternative to design.

I suggested that perhaps one reason Penrose does not like the multiverse explanation for fine tuning is that it would require an awful lot of universes to explain the fine-tuning he has himself discovered. I have since found another video interview, this one with Robert Lawrence Kuhn, in which Penrose makes clear that this is indeed one of his main objections to the multiverse/anthropic principle explanation for-fine tuning, at least for his own spectacular “initial entropy” fine-tuning. 

He calls the other examples of fine-tuning “chicken feed” compared to the fine-tuning required for the “special” initial conditions at the Big Bang and says there must be another explanation for this fine-tuning, though he has only “hypotheses.” But even if a better explanation than chance or design were found for these spectacularly special initial conditions, that would still leave the “chicken feed” fine-tunings unexplained, for example, why the gravitational constant had to be exactly what it is out to 30 or 60 digits of precision! 

“We Ought to Be Observing”

I also noted that in the Penrose-Craig debate, Craig summarized one of Penrose’s objections to the multiverse argument as “We ought to be observing a much different universe than we do” if the anthropic principle could explain fine-tuning. And I said that it appears that Penrose sees the same problem with a multiverse explanation that Michael Behe did in The Edge of Evolution: 

On the finite random multiverse view, we should very likely live in a bare-bones world, with little or nothing in life beyond what’s absolutely required to produce intelligent observers. So, if we find ourselves in a world lavished with extras — with much more than the minimum — we should bet heavily against our world being the result of a finite multiverse scenario.

Other “Extras” from Our Universe

It is clear from the Robert Kuhn interview that Penrose’s objection is indeed that the order in our universe extends far beyond what should be required for observers to exist (4:10+), though he is talking about a specific kind of order that relates to the initial entropy of the universe. Other “extras” that our universe (and our planet) seem to provide us, which are far beyond what should be required for observers to exist, include, apparently, fine-tuning for scientific discovery and technological progress, as the clips from the Fire-Maker (Michael Denton) and Privileged Planet (Guillermo Gonzalez and Jay Richards) videos included here suggest.

In the interview with Robert Kuhn, Roger Penrose still offers as an alternative to design only that maybe some very different kind of life might still have been possible without the fine-tunings we see in our universe (1:15+). And the problems with that alternative are still as expressed in the last paragraphs of my earlier post.

Of course, all of these discussions assume that once you get the constants of physics and initial conditions of a universe right, life could arise and conscious observers could evolve without design, an assumption that is, to put it very mildly, questionable.

James Ch.1:13,14 and eternal conscious torment in an afteflife.

 James Ch.1:13,14NLT"Temptation comes from our own desires, which entice us and drag us away. 15These desires give birth to sinful actions. And when sin is allowed to grow, it gives birth to death."

Death(the expression of divine wrath) brings an end to wrong desire and wrong doing. Wrong desire and wrong doing cannot endure the expression of JEHOVAH'S Wrath.

So death is not merely the penalty for wrong desire and wrong doing death totally expunges wrong desire and wrong doing from the creation.

Roman's Ch.6:7NIV"because anyone who has died has been set free from sin."

The dead are non existent and thus incapable of wrong or right doing.

1John Ch.2:17NIV"The world and its desires pass away, but whoever does the will of God lives forever."

The expression of JEHOVAH'S righteous wrath will bring an end to rebellious humans and angels and their selfish longings.

In contrast his loyalists will delight in eternal service to our majestic God.

James Chapter 1 New king James Version.

 1.James, a bondservant of God and of the Lord Jesus Christ,

To the twelve tribes which are scattered abroad:

Greetings.

2My brethren, count it all joy when you fall into various trials, 3knowing that the testing of your faith produces [a]patience. 4But let patience have its perfect work, that you may be [b]perfect and complete, lacking nothing. 5If any of you lacks wisdom, let him ask of God, who gives to all liberally and without reproach, and it will be given to him. 6But let him ask in faith, with no doubting, for he who doubts is like a wave of the sea driven and tossed by the wind. 7For let not that man suppose that he will receive anything from the Lord; 8he is a double-minded man, unstable in all his ways.

9Let the lowly brother glory in his exaltation, 10but the rich in his humiliation, because as a flower of the field he will pass away. 11For no sooner has the sun risen with a burning heat than it withers the grass; its flower falls, and its beautiful appearance perishes. So the rich man also will fade away in his pursuits.

12Blessed is the man who endures temptation; for when he has been approved, he will receive the crown of life which the Lord has promised to those who love Him. 13Let no one say when he is tempted, “I am tempted by God”; for God cannot be tempted by evil, nor does He Himself tempt anyone. 14But each one is tempted when he is drawn away by his own desires and enticed. 15Then, when desire has conceived, it gives birth to sin; and sin, when it is full-grown, brings forth death.

16Do not be deceived, my beloved brethren. 17Every good gift and every perfect gift is from above, and comes down from the Father of lights, with whom there is no variation or shadow of turning. 18Of His own will He brought us forth by the word of truth, that we might be a kind of firstfruits of His creatures.

19[c]So then, my beloved brethren, let every man be swift to hear, slow to speak, slow to wrath; 20for the wrath of man does not produce the righteousness of God.

21Therefore lay aside all filthiness and [d]overflow of wickedness, and receive with meekness the implanted word, which is able to save your souls.

22But be doers of the word, and not hearers only, deceiving yourselves. 23For if anyone is a hearer of the word and not a doer, he is like a man observing his natural face in a mirror; 24for he observes himself, goes away, and immediately forgets what kind of man he was. 25But he who looks into the perfect law of liberty and continues in it, and is not a forgetful hearer but a doer of the work, this one will be blessed in what he does.

26If anyone [e]among you thinks he is religious, and does not bridle his tongue but deceives his own heart, this one’s religion is useless. 27Pure and undefiled religion before God and the Father is this: to visit orphans and widows in their trouble, and to keep oneself unspotted from the world.

Some see Dr. Moreau as an exemplary rather than a cautionary model?

 Return (Yet Again) of the Humanzee

Denyse O Leary

A few days ago, the Templeton Foundation’s mailer for its online magazine Nautilus pointed to a five-year-old article by University of Washington psychology prof (emeritus) David P. Barash, advocating the creation of a humanzee: “Doing so would be a terrific idea.”

But Why Now?

It’s not clear why Nautilus is publicizing the article now. The Soviet Union failed to produce a humanzee. Nothing much has happened since 2018 that suggests that it is imminent. We do learn something of why Barash wants one, though:

Haven’t we learned that Promethean hubris leads only to disaster, as did the efforts of the fictional Dr. Frankenstein? But there are also other disasters, currently ongoing, such as the grotesque abuse of nonhuman animals, facilitated by what might well be the most hurtful theologically-driven myth of all times: that human beings are discontinuous from the rest of the natural world, since we were specially created and endowed with souls, whereas “they” — all other creatures — were not.

DAVID P. BARASH, “IT’S TIME TO MAKE HUMAN-CHIMP HYBRIDS,” NAUTILUS, MARCH 5, 2018

So it comes down to a war on the human soul. Now, here’s the interesting part: Humans are self-evidently unique; otherwise, Barash’s interaction with his readers could not occur. The human minds that enable that interaction are clearly not material things. And no one has any idea how they came to exist. Evolutionary theory provides no significant information here. In the end, however much many thinkers don’t like that fact, everyone eventually admits it.

Yet, on cue, readers — including many with PhDs — will agree with Barash that human exceptionalism is wrongthink. They will not ask why either he or they can maintain such an absurd view — when the very act of maintaining it refutes it. Perhaps all those years of education enable them to be oblivious to contradictions that should be apparent to an alert high schooler.

Barash, although he professes concern for animal rights, is not deterred by concern for the humanzees that a successful experiment would produce:

Neither fish nor fowl, wouldn’t they find themselves intolerably unspecified and inchoate, doomed to a living hell of biological and social indeterminacy? This is possible, but it is at least arguable that the ultimate benefit of teaching human beings their true nature would be worth the sacrifice paid by a few unfortunates. It is also arguable, moreover, that such individuals might not be so unfortunate at all. For every chimphuman or humanzee frustrated by her inability to write a poem or program a computer, there could equally be one delighted by her ability to do so while swinging from a tree branch.

BARASH, “HUMAN-CHIMP HYBRIDS”

The risk of “a living hell of biological and social indeterminacy” … And this is the same David Barash who worries about whether worms feel pain?

What Makes the Suffering Worthwhile?

When claims are made about the “right to life,” invariably the referent is human life, a rigid distinction only possible because of the presumption that human life is somehow uniquely distinct from other forms of life, even though everything we know of biology demonstrates that this is simply untrue. What better, clearer, and more unambiguous way to demonstrate this than by creating viable organisms that are neither human nor animal but certifiably intermediate?

BARASH, “HUMAN-CHIMP HYBRIDS”

So the humanzee’s suffering is rendered worthwhile precisely because it enables the denigration of other human beings. Good to know.

At the time, bioethics commentator Wesley J. Smith, clearly shocked by the moral nullity on display, responded,

We are the only truly moral species in the known universe. Only we can be held morally accountable for our actions. Only we have the capacity to rationally determine issues of right and wrong, ought and ought not, etc. Indeed, if being human — in and of itself — isn’t what gives us the moral obligation to treat animals humanely, what in the world does?

And if that duty arises solely and directly from our humanity — which it indisputably does — that means, by definition, that we are exceptional. All other species are amoral and, as such, they don’t owe a duty to each other, us, or anything. Duties, and moral accountability, are simply beyond their ken.

WESLEY J. SMITH, “DARWINIST WANTS US TO CREATE ‘HUMANZEE,’” NATIONAL REVIEW, MARCH 8, 2018

Of course, that’s both true and obvious, and one needs a lot of education to be rendered unable to see it. So then why does this obviously ridiculous and clearly inhumane idea keep coming back?

An Underlying Cultural Trend

Experimental physicist Rob Sheldon writes to suggest that there may be an underlying cultural trend here: When ridiculous inhumane ideas are routinely aired without pushback, we become more willing to accept inhumane ideas that are in fact quite viable:

It’s like an artillery barrage before the infantry go over the wire. The intent isn’t to be taken seriously, the intent is to make the next move seem innocuous.

The basic idea is the constant exposure to “shocking” material until it stops being shocking. And this response is entirely normal. We couldn’t function as humans without a brain circuit that filters out repetitive stimuli. Anything that happens repetitively gets ignored eventually.

He offers some examples:

The hybridization of animal-human embryos allowed to develop past the 14 day “ethical threshold”. The introduction of animal genes to “improve” the human genetic stock. And of course, the Holy Grail — extending the life of humans.

Once we remove the ethical barriers between humans and animals, we can then experiment on humans with all the tools we’ve perfected for animals.

One can agree or disagree with his thesis. But we will probably find out in the next decade or so whether he is right. If he is, what to do about the relentless march of dehumanization is a huge challenge.

The resurrection is a historical fact.

 

The plagiarizing of the original technologist continues apace.

 

Convergent serendipity?

 Fossil Friday: Scansoriopterygidae, Bizarre Bird-Like Dinosaurs, Illustrate Darwinist Trickery

Gunter Bechly

This Fossil Friday is dedicated to Scansoriopterygidae, which “truly are one of the most bizarre clades of non-avian theropods” (Wang et al. 2019). These fossil animals are known only from the Middle to Late Jurassic of China with the genera Ambopteryx, Epidexipteryx, Scansoriopteryx (= Epidendrosaurus?) and the featured Yi. Scansoriopterygidae were very small (sparrow to crow sized) feathered dinosaurs, characterized by an enlarged third finger and ribbon-like tail feathers (Zhang et al. 2008).

Their phylogenetic position among dinosaurs and early birds is unclear (Turner et al. 2012, Cau 2018) and highly disputed, so that no consensus has emerged in spite of several well-preserved fossils. Czerkas & Yuan (2002) placed scanoriopterygids as close relatives to Archaeopteryx and birds, but outside of theropod dinosaurs, while most other studies consider them as theropod dinosaurs. Some studies placed them in a closer relationship with birds in Avialae (Senter 2007, Zhang et al. 2008), while other studies rejected a position in Avialae and placed them more distantly related to birds among basal paravian dinosaurs (Agnolin & Novas 2011, Godefroit et al. 2013, Brusatte et al. 2014, Lefèvre et al. 2014, Sorkin 2020). Several studies even recovered them among oviraptorid dinosaurs outside of Paraves (Agnolin & Novas 2013, O’Connor & Sullivan 2014; also see Headden 2013, Pittman & Xu 2020).

Against Darwinian Predictions

This scientific disagreement is mainly caused by the fact that the pattern of similarities does not unequivocally fall into a nested hierarchy, as would be predicted by Darwinism, but is highly incongruent. But the large degree of convergences is not restricted to similarities with different groups of dinosaurs but also includes characters of other vertebrate groups. “One of the most surprising of these is that of the scansoriopterygid (Theropoda, Maniraptora) Yi qi, which has membranous wings — a flight apparatus that was previously unknown among theropods but that is used by both the pterosaur and bat lineage” (Wang et al. 2019). The discovery by Xu et al. (2015) was so surprising that it was doubted by some experts (e.g., Padian 2015), but the discovery of a new taxon Ambopteryx longibrachium (Wang et al. 2019) strongly confirmed the findings.

The describers of Yi qi (Xu et al. 2015) concluded that “in having wings with a well-developed membranous component, Yi would differ from other volant paravians but resemble distantly related groups including pterosaurs, bats and many gliding mammals, representing a striking case of convergent evolution of the aerodynamic apparatus among tetrapods.” After the confirmation of membraneous wings in the new scansoriopterygid Ambopteryx, Milligan (2019) commented that “unlike other flying dinosaurs, namely birds, these two species have membranous wings supported by a rod-like wrist bone that is not found in any other dinosaur (but is present in pterosaurs and flying squirrels).” Consequently, “birds, it’s clear, weren’t the only flying dinosaurs — and these fossils reveal that flight itself, whether gliding or powered, evolved multiple times among them” (Gramling 2020). A new aerodynamic study by Dececchi et al. (2020) concluded that scansoriopterygids were a failed experiment in pre-bird theropod flight.

Evo-Babble and Convergence

Don’t let the evo-babble of convergent evolution fool you. Convergence is not evidence for evolution but conflicting evidence against evolution. It is incongruent data that do not fit with the Darwinian prediction of a nested hierarchy. Therefore, such incongruences have to be explained away with ad hoc hypotheses like homoplasy (convergence and/or secondary reduction), incomplete lineage sorting, hydridization, or horizontal gene transfer. Instead of admitting incongruent similarities as conflicting evidence, Darwinists hide this dirty secret with deceptive doublespeak like “convergent evolution.” Even though there are some similarities that are revealed as non-homologous by irreconcilable structural and/or genetic differences, most assumed convergences are just interpretations or rather rationalisations after the fact. It is not like the structure has a label that says “I am a convergence” but rather it is a corollary of the assumed correct tree of life and the optimization of characters on this tree. The latter procedure means that the principle of parsimony is used to minimize the number of gains and losses of a character that have to be assumed to plot its distribution on a given tree. If the distribution of the similarities is not congruent with the nested hierarchy of the tree, then multiple gains (convergence) or multiple losses (reduction) of the character have to be postulated. This is crucial and cannot be emphasized enough: Convergences are not observed, they are postulated (compare Kluge 1999 who defined homoplasy nominally as an operational error)!

Here is a thought experiment to expose the trickery: you’ve probably heard about the example of bat wings and bird wings as a paradigmatic showcase of convergent evolution. This is because both groups have transformed the tetrapod foreleg into wings, but are not closely related. Each is nested deeply within different non-volant tetrapod groups with normally developed legs, so that the wings cannot be interpreted as homologous and inherited from an assumed winged common ancestor. Now imagine the counterfactual case that the majority of evidence (e.g., from comparative morphology and phylogenomics) would rather suggest that birds and bats were closest relatives (so-called sister groups). Suddenly the assumed convergence would of course be interpreted as a shared derived character that was inherited from a winged bat+bird ancestor as a homology (synapomorphy). The differences between both wing constructions would be explained away as autapomorphic specializations from a common ground plan, and biologists would emphasize that birds don’t just have feathered wings, but that beneath the feathers you can find small wing membranes (so-called patagia) that would be considered as homologous to the wing membrane of bats. With the discovery of the membraneous scanosoriopterygid wings, evolutionists would have celebrated the discovery of a predicted transitional form that proves the reconstructed ground plan and provides an indisputable confirmation of the evolutionary scenario linking bats and birds. Only science deniers would doubt such an obvious established fact of evolution, right?

How Darwinists Reason (or don't)

However, since birds and bats are not considered as closely related in the actual world, because birds cluster with dinosaurs and bats within mammals, their wings are interpreted as convergent. Likewise, the membraneous wings of scansoriopterygids are interpreted as another convergence, which would make vertebrate wings originate four times independently in pterosaurs, scansoriopterygids, birds, and bats. Darwinists do not really reason from the evidence to a hypothesis, as all good science should do, but only (re)interpret the evidence on the basis of their hypothesis, which therefore is immune to any challenge by conflicting data. When critics of intelligent design claim that it is not falsifiable, they are not only wrong (ID does make very specific testable predictions), but miss the inconvenient truth that it is Darwinism that is not falsifiable and thus of questionable scientific status.

The eminent philosopher of science Karl Popper explicitly recognized this until he was silenced and pushed to recant (Popper 1978: 345) by the Darwinist thought police. Here is what Popper (1976: 151 and 168) had said: “… because I intend to argue that the theory of natural selection is not a testable scientific theory, but a metaphysical research programme; … I have come to the conclusion that Darwinism is not a testable scientific theory, but a metaphysical research programme …” But even more interesting is what Popper (1957: 106) had said: “What we call the evolutionary hypothesis is an explanation of a host of biological and paleontological observations — for instance, of certain similarities between various species and genera — by the assumption of common ancestry of related forms.” (Emphasis added.) Read that carefully again. Did the penny drop? Common descent is assumed and the evidence interpreted accordingly, rather than common descent being deduced from the evidence. Common descent is the only conceivable materialistic option and thus considered as an unquestionable axiom. It may well be true, but it is hardly proven by this kind of dubious science.

References

Agnolín FL & Novas FE 2011. Unenlagiid theropods: are they members of the Dromaeosauridae (Theropoda, Maniraptora)? Anais da Academia Brasileira de Ciências 83(1), 117–162. DOI: https://doi.org/10.1590/S0001-37652011000100008

Agnolín FL & Novas FE 2013. Chapter 3 Systematic Paleontology. pp. 9–36 in: Avian Ancestors: A Review of the Phylogenetic Relationships of the Theropods Unenlagiidae, Microraptoria, Anchiornis and Scansoriopterygidae. SpringerBriefs in Earth System Sciences. Springer: Dordrecht (NL), ix+96 pp. DOI: https://doi.org/10.1007/978-94-007-5637-3

Brusatte SL, Lloyd GT, Wang SC & Norell MA 2014. Gradual assembly of avian body plan culminated in rapid rates of evolution across the dinosaur-bird transition. Current Biology 24(20), 2386–2392. DOI: https://doi.org/10.1016/j.cub.2014.08.034

Cau A 2018. The assembly of the avian body plan : a 160-million-year long process. Bollettino della Societa Paleontologica Italiana 57(1), 1–25. DOI: https://doi.org/10.4435/BSPI.2018.01 (https://www.researchgate.net/publication/324941372)

Czerkas SA & Yuan C 2002. An arboreal maniraptoran from northeast China. pp. 63–95 in: Czerkas SJ (ed.). Feathered Dinosaurs and the Origin of Flight. The Dinosaur Museum Journal 1. The Dinosaur Museum: Blanding (UT). http://dinosaur-museum.org/featheredinosaurs/arboreal_maniraptoran.pdf

Dececchi TA, Roy A, Pittman M, Kaye TG, Xu X, Habib MB, Larsson HCE, Wang X & Zheng X 2020. Aerodynamics Show Membrane-Winged Theropods Were a Poor Gliding Dead-end. iScience 23(12), 101574, 1–17. DOI: https://doi.org/10.1016/j.isci.2020.101574

Godefroit P, Demuynck H, Dyke G, Hu D, Escuillié F & Claeys P 2013. Reduced plumage and flight ability of a new Jurassic paravian theropod from China. Nature Communications 4: 1394, 1–6. DOI: https://doi.org/10.1038/ncomms2389

Gramling C 2020. Bat-winged dinosaurs were clumsy fliers. ScienceNews October 22, 2020. https://www.sciencenews.org/article/dinosaurs-bat-wings-clumsy-evolution-flying-gliding

Headden JA 2013. Are Scansoriopterygids Oviraptorosaurs? TheBiteStuff March 4, 2013. https://qilong.wordpress.com/2013/03/04/are-scansoriopterygids-oviraptorosaurs/

Kluge AG 1999. The Science of Phylogenetic Systematics: Explanation, Prediction, and Test. Cladistics 15(4), 429–436. DOI: https://doi.org/10.1006/clad.1999.0123

Lefèvre U, Hu D, Escuillié FO, Dyke G & Godefroit P 2014. A new long-tailed basal bird from the Lower Cretaceous of north-eastern China. Biological Journal of the Linnean Society 113(3), 790–804. DOI: https://doi.org/10.1111/bij.12343

Milligan M 2019. New Jurassic non-avian theropod dinosaur sheds light on origin of flight in Dinosauria. Heritage Daily May 8, 2019. https://www.heritagedaily.com/2019/05/new-jurassic-non-avian-theropod-dinosaur-sheds-light-on-origin-of-flight-in-dinosauria/123670

     O’Connor JK & Sullivan C 2014. Reinterpretation of the Early Cretaceous maniraptoran (Dinosauria: Theropoda) Zhongornis haoae as a scansoriopterygid-like non-avian, and morphological resemblances between scansoriopterygids and basal oviraptorosaurs. Vertebrata Palasiatica 52, 3–30. http://www.ivpp.cas.cn/cbw/gjzdwxb/xbwzxz/201401/P020140121386966325113.pdf

Padian K 2015. Dinosaur up in the air. Nature 521, 40–41. DOI: https://doi.org/10.1038/nature14392

Pittman M & Xu X 2020. Pennaraptoran Theropod Dinosaurs Past Progress and New Frontiers. Bulletin of the American Museum of Natural History 440(1), 1–355. DOI: https://doi.org/10.1206/0003-0090.440.1.1

Popper K 1957. The Poverty of Historicism. Routledge. London (UK), 166 pp.

Popper K 1976. Unended Quest: An Intellectual Autobiography. Fontana/Collins: Glasgow (UK), iii+316 pp.

Popper K 1978. Natural selection and the emergence of mind. Dialectica 32(3/4), 339–355. https://www.jstor.org/stable/42970324

Senter P 2007. A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda). Journal of Systematic Palaeontology 5(4), 429–463. DOI: https://doi.org/10.1017/S1477201907002143

Sorkin B 2021. Scansorial and aerial ability in Scansoriopterygidae and basal Oviraptorosauria. Historical Biology 33(12), 3202–3214. DOI: https://doi.org/10.1080/08912963.2020.1855158

Turner AH, Makovicky PJ & Norell M 2012. A Review of Dromaeosaurid Systematics and Paravian Phylogeny. Bulletin of the American Museum of Natural History 371, 1–206. DOI: https://doi.org/10.1206/748.1

Wang M, O’Connor J, Xu X & Zhou Z 2019. A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs. Nature 569, 256–259. DOI: https://doi.org/10.1038/s41586-019-1137-z

Xu X, Zheng X, Sullivan C, Wang X, Xing L, Wang Y, Zhang X, O’Connor JK, Zhang F & Pan Y 2015. A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings. Nature 521, 70–73. DOI: https://doi.org/10.1038/nature14423

Zhang F, Zhou Z, Xu X, Wang X & Sullivan C 2008. A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers. Nature 455(7216), 1105–1108. DOI: https://doi.org/10.1038/npre.2008.2326.1

On explaining (away?) Complexity.

 

ID is the science driver?

 It’s Intelligent Design, Not Darwinism, that Drives Scientific Progress

Casey Luskin

There’s a common objection to intelligent design that the positive case for ID helps us to answer. In his Kitzmiller v. Dover testimony, biologist Kenneth Miller referred to intelligent design as a “science stopper.”1 Similarly, in his book Only a Theory, Miller stated, “The hypothesis of design is compatible with any conceivable data, makes no testable predictions, and suggests no new avenues for research. As such, it’s a literal dead end…”2

Yet in fact, ID makes a variety of testable and successful predictions. This allows ID to serve as a paradigm guiding scientific research to make new discoveries. The list below shows various fields where ID is helping science to generate knowledge. For each field, multiple ID-friendly scientific publications are cited as examples.

How ID Inspires the Progress of Science

Protein science: ID encourages scientists to do research to test for high levels of complex and specified information in biology in the form of the fine-tuning of protein sequences.3 This has practical implications not just for explaining biological origins, but also for engineering enzymes and anticipating and fighting the future evolution of diseases.

Physics and cosmology: ID has inspired scientists to seek and find instances of fine-tuning of the laws and constants of physics to allow for life, leading to new fine-tuning arguments such as the Galactic Habitable Zone. This has implications for proper cosmological models of the universe, hinting at avenues for successful “theories of everything” that must accommodate fine-tuning, and other implications for theoretical physics.4

Information theory: ID leads scientists to understand intelligence as a cause of biological complexity, capable of being scientifically studied, and to understand the types of information it generates.5

Pharmacology: ID directs both experimental and theoretical research to investigate the limitations of Darwinian evolution to produce traits that require multiple mutations in order to function. This has practical implications for fighting problems like antibiotic resistance or engineering bacteria.6

Evolutionary computation: ID produces theoretical research into the information-generative powers of Darwinian searches, leading to the discovery that the search abilities of Darwinian processes are limited, which has practical implications for the viability of using genetic algorithms to solve problems.7

Anatomy and physiology: ID predicts function for allegedly “vestigial” organs, structures, or systems whereas evolution has made many faulty predictions of nonfunction.8

Bioinformatics: ID has helped scientists develop proper measures of biological information, leading to concepts like complex and specified information or functional sequence complexity. This allows us to better quantify complexity and understand what features are, or are not, within the reach of Darwinian evolution.9

Molecular machines: ID encourages scientists to reverse-engineer molecular machines — like the bacterial flagellum — to understand their function like machines, and to understand how the machine-like properties of life allow biological systems to function.10

Cell biology: ID causes scientists to view cellular components as “designed structures rather than accidental by-products of neo-Darwinian evolution,” allowing scientists to propose testable hypotheses about cellular function and causes of cancer.11

Systematics: ID helps scientists explain the cause of the widespread features of conflicting phylogenetic trees and “convergent evolution” by producing models where parts can be reused in non-treelike patterns.12 ID has spawned ideas about life being front-loaded with information such that it is designed to evolve, and has led scientists to expect (and now find!) previously unanticipated “out-of-place” genes in various taxa.13

Paleontology: ID allows scientists to understand and predict patterns in the fossil record, showing explosions of biodiversity (as well as mass extinction) in the history of life.14Genetics: ID has inspired scientists to investigate the computer-like properties of DNA and the genome in the hopes of better understanding genetics and the origin of biological systems.15 ID has also inspired scientists to seek function for noncoding junk-DNA, allowing us to understand development and cellular biology.16

Avenues of Discovery

Critics wrongly charge that ID is just a negative argument against evolution, that ID makes no predictions, that it is a “god of the gaps” argument from ignorance, or that appealing to an intelligent cause means “giving up” or “stopping science.” These charges are misguided. 

Ironically, when critics claim that research is not permitted to detect design because that would stop science, it is they who hold science back by preventing scientists from investigating the scientific theory of intelligent design. When researchers are allowed to infer intelligent agency as the best explanation for information-rich structures in nature, this opens up many avenues of discovery that are bearing good fruit in the scientific community.

Notes

Kenneth R. Miller, Kitzmiller v. Dover, Day 2 AM Testimony (September 27, 2005).

Kenneth R. Miller, Only a Theory: Evolution and the Battle for America’s Soul (New York: Viking Penguin, 2008), 87.

Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors”; Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds”; Behe and Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues”; Axe, “The Case Against a Darwinian Origin of Protein Folds”; Gauger and Axe, “The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway”; Reeves et al., “Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family”; Thorvaldsen and Hössjer, “Using statistical methods to model the fine-tuning of molecular machines and systems.”

Guillermo Gonzalez and Donald Brownlee, “The Galactic Habitable Zone: Galactic Chemical Evolution,” Icarus 152 (2001), 185-200; Guillermo Gonzalez, Donald Brownlee, and Peter D. Ward, “Refuges for Life in a Hostile Universe,” Scientific American (2001), 62-67; Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery (Washington, DC, Regnery, 2004); Guillermo Gonzalez, “Setting the Stage for Habitable Planets,” Life 4 (2014), 34-65; D. Halsmer, J. Asper, N. Roman, and T. Todd, “The Coherence of an Engineered World,” International Journal of Design & Nature and Ecodynamics 4 (2009), 47-65.

William A. Dembski, The Design Inference; William A. Dembski and Robert J. Marks II, “Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search,” Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics(October 2009), 2647-2652; William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search,” Journal of Advanced Computational Intelligence and Intelligent Informatics 14 (2010), 475-486; Øyvind Albert Voie, “Biological function and the genetic code are interdependent,” Chaos, Solitons and Fractals 28 (2006), 1000-1004; McIntosh, “Information and Entropy —Top-Down or Bottom-Up Development in Living Systems?”

Behe and Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues”; Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” BIO-Complexity 2010 (2).

William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success,” IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans 39 (September 2009), 1051-1061; Winston Ewert, William A. Dembski, and Robert J. Marks II, “Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism,” Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics (October 2009); Dembski and Marks, “Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search”; Winston Ewert, George Montanez, William Dembski and Robert J. Marks II, “Efficient Per Query Information Extraction from a Hamming Oracle,” 42nd South Eastern Symposium on System Theory (March 2010), 290-297; Douglas D. Axe, Brendan W. Dixon, and Philip Lu, “Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints,” Plos One 3 (June 2008), e2246.

       Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research”; William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems (Dallas, TX: Foundation for Thought and Ethics, 2008).

Meyer, “The origin of biological information and the higher taxonomic categories”; Kirk K. Durston, David K.Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling 4 (2007), 47; David K.Y. Chiu and Thomas W.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems4 (September 2002), 766-775.

Minnich and Meyer. “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria”; McIntosh, “Information and Entropy—Top-Down or Bottom-Up Development in Living Systems?” 

Jonathan Wells, “Do Centrioles Generate a Polar Ejection Force?,” Rivista di Biologia / Biology Forum, 98 (2005), 71-96; Scott A. Minnich and Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” Proceedings of the Second International Conference on Design & Nature Rhodes Greece (2004); Behe, Darwin’s Black Box; Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity.”

Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity”; Nelson and Jonathan Wells, “Homology in Biology”; Ewert, “The Dependency Graph of Life”; John A. Davison, “A Prescribed Evolutionary Hypothesis,” Rivista di Biologia/Biology Forum 98 (2005), 155-166; Ewert, “The Dependency Graph of Life.”

Sherman, “Universal Genome in the Origin of Metazoa: Thoughts About Evolution”; Albert D.G. de Roos, “Origins of introns based on the definition of exon modules and their conserved interfaces,” Bioinformatics 21 (2005), 2-9; Albert D.G. de Roos, “Conserved intron positions in ancient protein modules,” Biology Direct 2 (2007), 7; Albert D.G. de Roos, “The Origin of the Eukaryotic Cell Based on Conservation of Existing Interfaces,” Artificial Life 12 (2006), 513-523.

Meyer et al., “The Cambrian Explosion: Biology’s Big Bang”; Meyer, “The Cambrian Information Explosion”; Meyer, “The origin of biological information and the higher taxonomic categories”; Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity.”

Richard v. Sternberg, “DNA Codes and Information: Formal Structures and Relational Causes,” Acta Biotheoretica 56 (September 2008), 205-232; Voie, “Biological function and the genetic code are interdependent”; David L. Abel and Jack T. Trevors, “Self-organization vs. self-ordering events in life-origin models,” Physics of Life Reviews 3 (2006), 211-228.

Richard v. Sternberg, “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System”; Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research”; Josiah D. Seaman and John C. Sanford, “Skittle: A 2-Dimensional Genome Visualization Tool,” BMC Informatics 10 (2009), 451.

This article is a modified excerpt from the recent book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. 

The world's most important corporation?

 

Another body blow to the "simple" lifeform trope?

 Quorum Sensing: A Clever Trick by Microbes

David Coppedge

You’re exploring in the dark on a secret mission. You need a dozen compatriots to initiate operations. How do you know when the minimum number is assembled, when you cannot see them or talk to them? The answer is quorum sensing: using techniques to silently count the friends near you. When you have a quorum, you start the mission.

These days, radio communication makes the imaginary secret mission a cinch. Without sight or sound, members of a team can know where their compatriots are on hand-held devices using encrypted messaging. In ordinary life, many people use apps like Apple’s “Find My Friends” to see where family members are before starting a birthday party. We take quorum sensing for granted, but we are purposeful, intelligent agents. Distributed robot systems designed by MIT use biomimetic algorithms pre-programmed into them by engineers.

Quorum sensing is used all the time by… (wait for it…) bacteria. Microbes can wait to commence an activity until a threshold density of neighboring conspecifics is detected. This skill has been observed in other microbes, like slime molds, and in higher organisms that exhibit collective behaviors, like insects, fish, and birds. Robot designers are learning tricks from the simplest of life forms: how to communicate with and respond to other unseen members of a population. Quorum sensing (QS) extends the concept of the interactome from intracellular to intercellular, converting a population of individuals into a super-organism. In this sense, a population of bacteria is a multicellular life form. This puts increased pressure on Darwinian notions of a “simple” cell. Could a lucky protocell, all alone, survive without a population of protocells able to communicate and coordinate their behaviors?

Requirements for Quorum Sensing

Consider the requirements for quorum sensing. The most rudimentary specifications include a sensor, a receptor, and a response plan. Bacteria employ QS by sending out specific molecules into the environment. On their surfaces, they post receptors for molecules from other members of their species. The incoming count is measured. When a threshold is reached, the signal triggers changes in gene expression, leading to pre-programmed actions coordinated with the other members of the swarm. These could include forming a biofilm, altering migration behavior, or switching on defensive maneuvers. Some bioluminescent microbes will only “turn on the lights” when a threshold density is detected.

Already we can see that a QS algorithm is irreducibly complex, but in real life examples, additional requirements become apparent. For instance, there is the need for “quorum quenching” — turning off the response when conditions change. The bacterium must also discern the degree of similarity of incoming signal molecules. In news about QS echoed on Phys.org, researchers from Aalto University in Finland likened the skill to understanding dialects and foreign languages:

“We did a ‘bacterial language check’ and found that bacteria using very similar languages can understand each other, just like a Dutch person might understand some German. We also tested communication between bacteria using very different languages and found that they couldn’t understand each other at all — just like a conversation between people speaking Finnish, Dutch and Arabic wouldn’t get far,” says Christopher Jonkergouw, the doctoral student who led the study. 

In the military, soldiers with different English dialects can generally understand one another to get by and continue their mission. They might even understand natives in other cultures who speak Pidgin, assisted by some gestures and facial expressions. There comes a point of “no comprendo” when the languages are too different, as anyone knows who has traveled abroad. The point is that beyond the threshold of comprehension, more is required for communication: language training, a smartphone translation app, or a human interpreter. Recall the consternation of Japanese soldiers in World War II listening in to the Navajo “code talkers” communicating American military strategies over the radio.

Bacteria Have a Similar Problem

The Aalto researchers identified over 160 bacterial “languages” spoken in molecular “words.” Molecules that are structurally similar can trigger a response up to a point, after which the bacteria do not respond. This knowledge is a first step for scientists wishing to intervene in bacterial responses like antibacterial resistance.

With these tools, the researchers have shown that we can accurately estimate the connections between bacterial languages and predict whether they can be understood. These findings will be valuable in further refining the team’s new treatment approach, and they also have implications for biotechnology — bacterial languages can be used to coordinate tasks between groups in bacterial communities, or even in bacterial microprocessors.

The team’s paper in Angewandte Chemie doesn’t use the language metaphor, but it elaborates on the methods for determining the limits of bacterial responses to similar molecules. Prior work on QS has focused on a few of these molecules, most prominently the homoserine lactones (HSLs). Like dialects, HSLs as a class include structurally similar forms, considered “cognate” — i.e., members of a family.

Here, we move beyond the commonly utilized HSL QS signalling systems and explore how chemical diversity in ligands can serve as a guiding principle to understand and circumvent non-cognate binding interactions. We explore the chemical diversity in a comprehensive set of known QS ligands and, based on the hypothesis that diversity in ligand chemical structures minimizes non-cognate interactions, experimentally assess a set of structurally similar as well as a diverging set of QS signalling systems (Figure 1). Using this approach, we significantly expand upon the known and available synthetic orthogonal QS signalling systems and provide a clear strategy towards future expansion efforts of additional synthetic orthogonal signalling systems.

Beyond the threshold of recognition, the signal molecule no longer triggers a response. The researchers “repaired” one such mutant molecule to see if the response could be regained:

Extensive screening from multiple ligation and transformation attempts generated a limited number of colonies that all contained non-synonymous mutations, resulting in amino acid substitutions. In the case of PauR, four sequenced colonies (from different ligations and transformations) all contained a point mutation in S129 a serine involved in AHL binding, within the autoinducer binding domain (Figure S2). Four clones of PluR contained non-synonymous mutations, all resulting also in amino acid substitutions. We hypothesized that constitutive expression severely affects viability in E. coli, so to overcome this, we controlled the expression of the receptor proteins with L-rhamnose (Figure 4b). This resulted in functional (and sequencing verified) constructs that we were able to experimentally assess.

It was a bit like intervening in a conversation to help a listener understand a word the speaker was mispronouncing. The mutations did not help the bacterium understand the signal. Less likely would a mutation help the listening bacterium come up with an improved response.

QS as a Life Trait

Rocks do not do quorum sensing. Could one boulder care how many others are around, using the information to initiate a programmed response? A critic might point to collective behaviors of particles in clouds, tornados, hurricanes, or other emergent phenomena. Such cases, however, do not send signals, receive signals, and respond by triggering embedded instructions. They simply respond to laws of physics. Life is different. From the smallest cell to the greatest whale or redwood tree, algorithmic processes like QS distinguish the biotic from the abiotic.

QS signalling systems are ubiquitous in prokaryotes, and novel [i.e., previously unknown] QS ligands are continually being identified. Furthermore, increasing evidence alludes to interspecies and even interkingdom signalling systems, expanding the range, scope, and complexity of intercellular signal recognition.

Within our own bodies there are examples of QS, for example in the immune system, hormone signaling, and blood clotting. Additionally, microbes in the gut use quorum sensing to respond to changes in food intake and wellness.

The authors know that QS is a characteristic of living things. They have nothing to say about Darwinian evolution, probably because we humans intuitively know intelligent design when we see it. Else why would scientists try to imitate it with engineering projects?

Cellular cooperation forms one of the defining features of higher organisms. The differentiation into various cell types allows cells to divide tasks and specialize. Prokaryotes have also developed methods to organizemore complex architectures. Bacteria utilize small molecules in quorum sensing (QS) as a form of intercellular signalling, which enables them to synchronize and organize behaviour on a population-wide or even community-wide level to facilitate bacterial biofilm architectures, promote plant colonization, or commence the production of a range of virulence factors. Consequently, these intercellular signalling systems have attracted widespread interest in biotechnology, where the potential to control community-wide responses has sparked innovations in microbiome therapeutics, microbial factories, and cellular computing.

Jonathan McLatchie wrote about quorum sensing here in 2010. His article embedded a TED talk by Bonnie Bassler that is worth watching again. Denyse O’Leary mentioned QS briefly in 2021 as an indicator of cognition, but there has been little mention of it otherwise in these pages. I hope this review of the latest news on QS will raise more awareness about this fascinating phenomenon. Perhaps it will prompt some ID scientists to take the lead in de-Darwinizing it for human health. In the meantime, all of us can use it as one more illustration of specified complexity and low probability that justifies the design inference

On the forgotten holocaust.

 

"Not so fast" re: saltation in Darwinism

 Hitting the Brakes on “Rapid Evolution”

Andrew McDiarmid

Evolutionary biologist Richard Lenski hopes to demonstrate Darwinian evolution in action. But one humble scientist from Northern Idaho says not so fast! On this episode of ID the Future, host Eric Anderson concludes his “Why It Matters” interview with microbiologist Dr. Scott Minnich. 

In Part 2, Dr. Minnich critiques Lenski’s famous Long Term Evolutionary Experiment. Through experiments of his own, Minnich has shown how the practical results of Lenski’s project on E. coli are easily repeatable under different conditions, and how some key changes to E. coli are even reversible, both of which speak more to an organism’s pre-existing capabilities than to a Darwinian explanation. “Overall, [Lenski’s] E. coli haven’t generated anything new,” observes Minnich. “They’re getting rid of stuff they don’t need…they have hyper mutational rates…but in the long run, that’s not an advantage, because you’re just going to acquire too many mutations, and that’s the road to extinction.”

Dr. Minnich also cautions that the authority of science can be abused, sharing his personal experience of being tasked by the Defense Intelligence Agency to look for biochemical weapons in Iraq. In the end, one of the things that most fascinates him about design in nature is DNA, with E. coli’s code-like logic that reminds us of the logical system operations programmed by human engineers.

Download the podcast or listen to it here. This is the second of a two-part conversation. Listen to part 1,