Darwinists: did we say a tree? What we meant was..

 Evolutionists Walk it Back Again: Human Evolution is More a Muddy Delta Than a Branching Tree

Cornelius G Hunter

First it was a tree, then it was a bush, then it was a network, and now it is a muddy delta. The evolutionary model of how the species are supposed to be related has failed over and over. And John Hawks’ latest version of this moving target reveals yet again that the theory of evolution is not explanatory, and that the evidence contradicts the theory. Hawks explains that the latest thinking on how the primates evolved “is no evolutionary tree. Our evolutionary history is like a braided stream.”

Evolution is a blind guide—it is always wrong. It is always pointing in the wrong direction, and evolutionists are always having to walk it back and do their damage control.

When will they learn?

The case for conditionalism

 

On design and "evolution"

 Peer-Reviewed Paper by Discovery Institute Staff Evaluates Synthesis of “Design and Evolution” 

Casey Luskin

We are pleased to announce the publication of a peer-reviewed open-access article by CSC staff members Stephen Dilley, Brian Miller, Emily Reeves, and myself. Published in the journal Religions, our article is titled “On the Relationship Between Design and Evolution,” and it examines and reviews a scholarly book, The Compatibility of Evolution and Design (Palgrave Macmillan / 2021), which is arguably the best current treatment of the relationship between evolution and intelligent design from an evolutionary point of view. The book is written by E. V. Rope Kojonen, a theologian at the University of Helsinki, who offers a potent argument that mainstream evolutionary biology is fully compatible with a robust biological design argument. On his view, the wings of the hummingbird, for example, display evidence of design while also being the product of natural selection, random mutation, and other processes — all without the need for direct guidance, divine intervention, or intelligent supervision per se.  

We regard Kojonen’s model as nuanced, erudite, and fair-minded. It is a model of fine scholarship and deserves serious attention. Even so, we argue that Kojonen’s conception of design is flawed, as is his attempt to harmonize design with evolution. We support our contentions with both scientific and philosophical arguments. Scientifically, we provide perhaps the most comprehensive defense of Douglas Axe’s research written to date as well as an updated analysis of the bacterial flagellum. Philosophically, we argue that Kojonen’s model undercuts itself. It gives an account of “design detection” that actually conflicts with Kojonen’s own design argument.

A Question about Compatibility

The abstract of the article is as follows:

 A longstanding question in science and religion is whether standard evolutionary models are compatible with the claim that the world was designed. In The Compatibility of Evolution and Design, theologian E. V. Rope Kojonen constructs a powerful argument that not only are evolution and design compatible, but that evolutionary processes (and biological data) strongly point to design. Yet Kojonen’s model faces several difficulties, each of which raise hurdles for his understanding of how evolution and design can be harmonized. First, his argument for design (and its compatibility with evolution) relies upon a particular view of nature in which fitness landscapes are “fine-tuned” to allow proteins to evolve from one form to another by mutation and selection. But biological data run contrary to this claim, which poses a problem for Kojonen’s design argument (and, as such, his attempt to harmonize design with evolution). Second, Kojonen appeals to the bacterial flagellum to strengthen his case for design, yet the type of design in the flagellum is incompatible with mainstream evolutionary theory, which (again) damages his reconciliation of design with evolution. Third, Kojonen regards convergent evolution as notable positive evidence in favor of his model (including his version of design), yet convergent evolution actually harms the justification of common ancestry, which Kojonen also accepts. This, too, mars his reconciliation of design and evolution. Finally, Kojonen’s model damages the epistemology that undergirds his own design argument as well as the design intuitions of everyday “theists on the street”, whom he seeks to defend. Thus, despite the remarkable depth, nuance, and erudition of Kojonen’s account, it does not offer a convincing reconciliation of “design” and “evolution”.

A Flawed Account of Design

We’ll have more to say here about this model in the coming weeks, but for now, it’s worth taking a look at some of the main points from our paper’s conclusion:

In this article, we argued that Kojonen’s account of design is flawed. It requires fine-tuned preconditions (and smooth fitness landscapes) so that evolution can successfully search and build viable biological forms. Yet empirical evidence shows that no such preconditions or fitness landscapes exist. At precisely the place we would expect to find evidence of Kojonen’s type of “design”, we find no such thing. Accordingly, his view of design is at odds with the evidence itself. As such, it is poorly situated to add explanatory value to evolution.

We also contended that Kojonen’s conjunction of “design” and “evolution” is internally fragmented. Recall that Kojonen believes that the complexity of the bacterial flagellum adds to his case for joining “design” to “evolution”. Yet Behe’s irreducible complexity argument shows that the type of design manifest in the bacterial flagellum runs contrary to mainstream evolution. Thus, the very system that provides strong evidence of design also undercuts evolution. In effect, this drives a wedge between the two. Kojonen’s conjunction of “design and evolution” is at war with itself.

We also highlighted the internal tension in Kojonen’s attempt to join “design” and “evolution” with respect to convergent evolution. Kojonen draws on convergence as a key argument for the “laws of form”, which are an important element of fine-tuned preconditions and, thus, his case for design. Yet convergent evolution conflicts with Kojonen’s use of co-option and approach to protein evolution. It also conflicts with the general justification of common ancestry. Thus, this element of Kojonen’s case for design chafes against his own reasoning as well as mainstream evolutionary thought. Internal discord surfaces once again.

In each of these criticisms, we have not targeted evolutionary theory itself. Although we believe that the scientific evidence we have covered counters mainstream evolution, we have set this concern aside in this article. Instead, our criticisms are aimed at Kojonen’s conception of design. We have contended that he does not offer sufficient empirical support for it — and so it adds little explanatory merit to “evolution” — and that some of the evidence he does offer actually conflicts with his commitment to evolution, producing incoherence within his model. (We should note, however, that because of the way Kojonen frames the matter, our criticisms of his view of design do have negative implications for the feasibility of evolutionary theory as he understands it. But this is an implication of our argument based on his own framing. It is not the focus of our argument per se. We will return to this point momentarily.)

Finally, we raised epistemological concerns aimed at the fundamental basis of Kojonen’s understanding of design detection. If our concerns are correct, then they cut deeply against Kojonen’s design argument as well as his defense of the theist on the street. In a nutshell, our worry is that a person who takes Kojonen’s model seriously — or who lived in such a universe — would either have defeaters for her biology-based design beliefs or might not have the cognitive dispositions and beliefs that (in our experience) are foundational to the formation of such beliefs in the first place. Kojonen’s reliance on evolution (and non-agent causes) undermines his basis for design detection, in short.

Stepping back, it is important to reiterate, once again, the many strengths of Kojonen’s treatment. The extensive review we have given here is a credit to a book of remarkable sophistication, precision, and erudition. Only a venerable fortress is worthy of a long siege. The Compatibility of Evolution and Design is the best of its class.

Devastating Implications for Evolution

But there’s one more point worth highlighting about Kojonen’s model. He effectively concedes that evolution won’t work to produce biological complexity unless there is some special “fine-tuning” of the “preconditions” for evolution (which themselves arise from designed laws of nature). We might agree with this framing but we have shown that this fine-tuning does not seem to exist. Therefore not only is his case for marrying design and evolution flawed but — if there are no such preconditions — then evolution itself is impotent. Here’s how we frame this in the final paragraph:

Even so, we bring this article to a close on a poignant note: Kojonen’s model may have devastating implications for mainstream evolutionary theory. Recall that the heart of his proposal is that evolution needs design (in the form of fine-tuned preconditions). Evolution on its own is insufficient to produce flora and fauna. But if we are correct that Kojonen’s conception and justification of design are flawed, then it follows — by his own lights — that evolution is impotent to explain biological complexity. Kojonen’s own account of the efficacy of evolution depends upon the success of his case for design. But if the latter stumbles, then so does the former. In a startling way, Kojonen has set the table for the rejection of evolution. If he has failed to make his case for design, then he has left readers with strong reasons to abandon mainstream evolutionary theory. The full implications of this striking result warrant further exploration.

Despite our critique of Kojonen’s model, we find it stimulating and thoughtful. We invite interested readers of Evolution News to read our article and also to read The Compatibility of Evolution and Design.

Yet more primeval tech vs. Darwinism.

 

On the edge of Darwinism

 

Natural selection as conserved.

 

Photosynthesis vs.Darwinism

 

Paved with good intentions? II

 

It's official: Less is more

 

To brash for Mikhail tal?

 

Darwinism does not compute?

 On Evolutionary Computation

 

 Roman V. Yampolskiy

 

 Editor’s note: Dr. Yampolskiy is Associate Professor in the department of Computer Engineering and Computer Science at the Speed School of Engineering, University of Louisville. In this series, he asks: “What Can and Can’t Darwin’s Algorithm Compute?” See also yesterday’s post, the first in the series, “What Can and Can’t Darwin’s Algorithm Compute?“

Inspired by Darwin’s theory1 of biological evolution, evolutionary computation attempts to automate the process of optimization and problem solving by simulating differential survival and reproduction of individual solutions. From the early 1950s, multiple well-documented attempts to make Darwin’s algorithm work on a computer have been published under such names as Evolutionary Programming12, Evolutionary Strategies13, Genetic Algorithms14, Genetic Programming15, Genetic Improvement16, Gene Expression Programming17, Differential Evolution18, Neuroevolution19, and Artificial Embryogeny20. While numerous variants different in their problem representation and metaheuristics exist21-24, all can be reduced to just two main approaches — Genetic Algorithm (GA) and Genetic Programming (GP).

GAs are used to evolve optimized solutions to a particular instance of a problem such as Shortest Total Path25, Maximum Clique26, Battleship27, Sudoku28, Mastermind23, Light Up29, Graph Coloring30, integer factorization31, 32, or efficient halftone patterns for printers33, and so are not the primary focus of this paper. GPs’ purpose, from their inception, was to automate programming by evolving an algorithm or a program for solving a particular class of problems, for example an efficient34 search algorithm. Software design is the type of application most frequently associated with GPs35, but work in automated programming is also sometimes referred to as “real programing,” “object-oriented GP,” “algorithmic programming,” “program synthesis,” “traditional programming,” “Turing Equivalent (TE) programming” or “Turing-complete GP”36-38. 

Tremendous Growth

The sub-field of computation, inspired by evolution in general, and the Genetic Programing paradigm, established by John Koza in 1990s, in particular are thriving and growing exponentially. This is evidenced both by the number of practitioners and of scientific publications. Petke et al. observe “…enormous expansion of number of publications with the Genetic Programming Bibliography passing 10,000 entries … By 2016 there were nineteen GP books including several intended for students …”16. Such tremendous growth has been fueled, since the early days, by belief in the capabilities of evolutionary algorithms, and our ability to overcome obstacles of limited computational power or data as illustrated by the following comments: 

“We will (before long) be able to run genetic algorithms on computers that are sufficiently fast to recreate on a human timescale the same amount of cumulative optimization power that the relevant processes of natural selection instantiated throughout our evolutionary past … ”39

“As computational devices improve in speed, larger problem spaces can be searched.”40 

“Evolution is a slow learner, but the steady increase in computing power, and the fact that the algorithm is inherently suited to parallelization, mean that more and more generations can be executed within practically acceptable timescales.”41

“We believe that in about fifty years’ time it will be possible to program computers by means of evolution. Not merely possible but indeed prevalent.”42 

“The relentless iteration of Moore’s law promises increased availability of computational resources in future years. If available computer capacity continues to double approximately every 18 months over the next decade or so, a computation requiring 80 h will require only about 1% as much computer time (i.e., about 48 min) a decade from now. That same computation will require only about 0.01% as much computer time (i.e., about 48 seconds) in two decades. Thus, looking forward, we believe that genetic programming can be expected to be increasingly used to automatically generate ever-more complex human-competitive results.”43 

“The production of human-competitive results as well as the increased intricacy of the results are broadly correlated to increased availability of computing power tracked by Moore’s law. The production of human-competitive results using genetic programming has been greatly facilitated by the fact that genetic algorithms and other methods of evolutionary computation can be readily and efficiently parallelized. … Additionally, the production of human-competitive results using genetic programming has facilitated to an even greater degree by the increased availability of computing power, over a period of time, as tracked by Moore’s law. Indeed, over the past two decades, the number and level of intricacy of the human-competitive results has progressively grown. … [T]here is, nonetheless, data indicating that the production of human-competitive results using genetic programming is broadly correlated with the increased availability of computer power, from year to year, as tracked by Moore’s Law.”43

“[P]owerful test data generation techniques, an abundance of source code publicly available, and importance of nonfunctional properties have combined to create a technical and scientific environment ripe for the exploitation of genetic improvement.”40

Tomorrow, “State-of-the-Art in Evolutionary Computation.”

References:

Back, T., Evolutionary algorithms in theory and practice: evolution strategies, evolutionary programming, genetic algorithms. 1996: Oxford university press.

Mayr, E., Behavior Programs and Evolutionary Strategies: Natural selection sometimes favors a genetically” closed” behavior program, sometimes an” open” one. American scientist, 1974. 62(6): p. 650-659.

Davis, L., Handbook of genetic algorithms. 1991: Van Nostrand Reinhold.

Koza, J.R., Genetic programming as a means for programming computers by natural selection. Statistics and computing, 1994. 4(2): p. 87-112.

Petke, J., et al., Genetic improvement of software: a comprehensive survey. IEEE Transactions on Evolutionary Computation, 2017.

Ferreira, C., Gene expression programming: mathematical modeling by an artificial intelligence. Vol. 21. 2006: Springer.

Storn, R. and K. Price, Differential evolution–a simple and efficient heuristic for global optimization over continuous spaces. Journal of global optimization, 1997. 11(4): p. 341-359.

Such, F.P., et al., Deep Neuroevolution: Genetic Algorithms Are a Competitive Alternative for Training Deep Neural Networks for Reinforcement Learning. arXiv preprint arXiv:1712.06567, 2017.

Stanley, K.O. and R. Miikkulainen, A taxonomy for artificial embryogeny. Artificial Life, 2003. 9(2): p. 93-130.

Yampolskiy, R.V., L. Ashby, and L. Hassan, Wisdom of Artificial Crowds—A Metaheuristic Algorithm for Optimization. Journal of Intelligent Learning Systems and Applications, 2012. 4(2): p. 98-107.

Yampolskiy, R.V. and A. El-Barkouky, Wisdom of artificial crowds algorithm for solving NP-hard problems. International Journal of Bio-inspired computation, 2011. 3(6): p. 358-369.

Khalifa, A.B. and R.V. Yampolskiy, GA with Wisdom of Artificial Crowds for Solving Mastermind Satisfiability Problem. Int. J. Intell. Games & Simulation, 2011. 6(2): p. 12-17.

Lowrance, C.J., O. Abdelwahab, and R.V. Yampolskiy. Evolution of a Metaheuristic for Aggregating Wisdom from Artificial Crowds. in Portuguese Conference on Artificial Intelligence. 2015. Springer.

Hundley, M.V. and R.V. Yampolskiy, Shortest Total Path Length Spanning Tree via Wisdom of Artificial Crowds Algorithm, in The 28th Modern Artificial Intelligence and Cognitive Science Conference (MAICS2017). April 28-29, 2017: Fort Wayne, IN, USA.

Ouch, R., K. Reese, and R.V. Yampolskiy. Hybrid Genetic Algorithm for the Maximum Clique Problem Combining Sharing and Migration. in MAICS. 2013.

Port, A.C. and R.V. Yampolskiy. Using a GA and Wisdom of Artificial Crowds to solve solitaire battleship puzzles. in Computer Games (CGAMES), 2012 17th International Conference on. 2012. IEEE.

Hughes, R. and R.V. Yampolskiy, Solving Sudoku Puzzles with Wisdom of Artificial Crowds. Int. J. Intell. Games & Simulation, 2012. 7(1): p. 24-29.

Ashby, L.H. and R.V. Yampolskiy. Genetic algorithm and Wisdom of Artificial Crowds algorithm applied to Light up. in Computer Games (CGAMES), 2011 16th International Conference on. 2011. IEEE.

Hindi, M. and R.V. Yampolskiy. Genetic Algorithm Applied to the Graph Coloring Problem. in MAICS. 2012.

Yampolskiy, R.V., Application of bio-inspired algorithm to the problem of integer factorisation. International Journal of Bio-Inspired Computation, 2010. 2(2): p. 115-123.

Mishra, M., S. Pal, and R. Yampolskiy, Nature-Inspired Computing Techniques for Integer Factorization. Evolutionary Computation: Techniques and Applications, 2016: p. 401.

Yampolskiy, R., et al. Printer model integrating genetic algorithm for improvement of halftone patterns. in Western New York Image Processing Workshop (WNYIPW). 2004. Citeseer.

Yampolskiy, R.V., Efficiency Theory: a Unifying Theory for Information, Computation and Intelligence. Journal of Discrete Mathematical Sciences and Cryptography, 2013. 16(4-5): p. 259-277.

Rylander, B., T. Soule, and J. Foster. Computational complexity, genetic programming, and implications. in European Conference on Genetic Programming. 2001. Springer.

White, D.R., et al., Better GP benchmarks: community survey results and proposals. Genetic Programming and Evolvable Machines, 2013. 14(1): p. 3-29.

Woodward, J.R. and R. Bai. Why evolution is not a good paradigm for program induction: a critique of genetic programming. in Proceedings of the first ACM/SIGEVO Summit on Genetic and Evolutionary Computation. 2009. ACM.

Helmuth, T. and L. Spector. General program synthesis benchmark suite. in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. 2015. ACM.

Shulman, C. and N. Bostrom, How hard is artificial intelligence? Evolutionary arguments and selection effects. Journal of Consciousness Studies, 2012. 19(7-8): p. 103-130.

Becker, K. and J. Gottschlich, AI Programmer: Autonomously Creating Software Programs Using Genetic Algorithms. arXiv preprint arXiv:1709.05703, 2017.

Eiben, A.E. and J. Smith, From evolutionary computation to the evolution of things. Nature, 2015. 521(7553): p. 476.

Orlov, M. and M. Sipper, FINCH: A system for evolving Java (bytecode), in Genetic Programming Theory and Practice VIII. 2011, Springer. p. 1-16.

Koza, J.R., Human-competitive results produced by genetic programming. Genetic Programming and Evolvable Machines, 2010. 11(3-4): p. 251-284.

 

 

The decay of western civilisation continues apace?

 

Darwinian evolutions love affair with crabs and the crablike?

 

Past time to engineer a climate solution?

 

The house of Abraham is a house divided?

 

The drone wars?

 

Thomas Jefferson on the book of creation.

 Thomas Jefferson’s Embrace of Intelligent Design

Steven C Meyer

Editor’s note: Dr. Meyer’s most recent book is Return of the God Hypothesis: Three Scientific Discoveries That Reveal the Mind Behind the Universe.

On Independence Day, it is appropriate to review the sources of our rights as citizens. There is one source that is more basic than any other, yet that receives less than the attention it deserves. I refer to the idea that there is an intelligent creator who can be known by reason from nature, a key tenet underlying the Declaration of Independence — as well as, curiously, the modern theory of intelligent design.

The birth of our republic was announced in the Declaration through the pen of Thomas Jefferson. He and the other Founders based their vision on a belief in an intrinsic human dignity, bestowed by virtue of our having been made according to the design and in the image of a purposeful creator.

“We Hold These Truths”

As Jefferson wrote in the Declaration, “We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights.” If we had received our rights only from the government, then the government could justifiably take them away.

Jefferson himself thought that there was scientific evidence for design in nature. In 1823, he insisted so in a letter to John Adams:

I hold (without appeal to revelation) that when we take a view of the Universe, in its parts general or particular, it is impossible for the human mind not to perceive and feel a conviction of design, consummate skill, and indefinite power in every atom of its composition.

Contemplating everything from the heavenly bodies down to the creaturely bodies of men and animals, he argued:

It is impossible, I say, for the human mind not to believe that there is, in all this, design, cause and effect, up to an ultimate cause, a fabricator of all things from matter and motion.

With such thoughts in mind, he wrote the Declaration, asserting the inalienable rights of human beings derived from “the Laws of Nature and of Nature’s God.”

Still Scientifically Credible?

Is Jefferson’s belief still credible in light of current science? The decades following Darwin’s publication of Origin of Species saw the rise of “social” Darwinism and eugenics, which suggested that the Jeffersonian principle of intrinsic dignity had been overturned.

Taken to heart, Darwin’s view of man does undermine the vision of the Founders. As evolutionary biologist George Gaylord Simpson explained, Darwinism denies evidence of design and shows instead that man is the product of a “purposeless process that did not have him mind.” Fortunately, discoveries in modern biology have challenged this perspective and vindicated Jefferson’s thinking.

Since 1953, when Watson and Crick elucidated the structure of the DNA molecule, biologists have increasingly come to recognize the importance of information to living cells. The structure of DNA allows it to store information in the form of a four-character digital code, similar to a computer code. As Bill Gates has noted, “DNA is like a computer program, but far, far more advanced than any software we’ve ever created.”

No theory of undirected chemical evolution has explained the origin of the digital information in DNA needed to build the first living cell on earth. Yet we know from repeated experience — the basis of all scientific reasoning — that information invariably arises from minds rather than from material processes.

Software programs come from programmers. Information — whether inscribed in hieroglyphics, written in a book, or encoded in radio signals — always comes from a designing intelligence. So the discovery of digital code in DNA points decisively back to an intelligent cause as the ultimate source of the information in living cells.

The growing evidence of design in life has stunning and gratifying implications for our understanding of America’s political history — and for our country’s future. On the anniversary of the Declaration of Independence, the evidence for “Nature’s God,” and thus for the reality of our rights, is stronger than ever.

Jonathan Wells vs. Darwinism's undead.

 

Iconclasm?

 

Past time to rethink hell? Pros and Cons II

 

Past time to rethink hell? Pros and Cons.

 

David Berlinski drives a stake through the heart of NeoDarwinism?

 

The God and Father of Jesus is the most high God? Pros and Cons. III

 

Winter is coming?

 

Yet more on reality's anti-Darwinian bias

 

An E.C.T shaped hole?

 

The walls have ears?

 

Paved with good intentions?

 

Phillip Johnson vs. Charles Darwin.

 

The God and Father of Jesus is the most high God? Pros and Cons II.

 

The God and Father of Jesus Christ is the most high God? Pros and Cons

 

Pre:Darwinian design.

 The Design of the Seminal Fluid and Sperm Capacitation

Jonathan McLatchie

In a previous article, I discussed the ways in which sperm cells exhibit irreducible complexity. Here, I will discuss the importance of the seminal fluid and how it contributes to the irreducibly complex core of components needed for successful reproduction. I will then consider the process of sperm capacitation, the mechanism that prepares the sperm cells for successful fusion with the egg.

The Seminal Fluid 

As I mentioned in my previous article, between two hundred and five hundred million sperm, surrounded by seminal fluid, are released with each ejaculation. Such huge numbers are necessary in order to have a significant chance of fertilizing the egg, since many hazards confront the sperm cells as they swim through the uterus and uterine tubes. Following ejaculation, millions of the released sperm cells will either flow out of the vagina, or else die in its acidic environment. Sperm cells also need to pass through the cervix and opening into the uterus, which requires passage through the cervical mucus. Though the mucus is thinned to a waterier consistency during the fertile window, making it more hospitable to sperm, millions of sperm cells will nonetheless die attempting to make it through the mucus. Furthermore, the female reproductive tract has immune defenses that protect against pathogens. These defenses can also target and destroy foreign cells like sperm. Antibodies may recognize sperm as foreign invaders and lead to their inactivation or elimination. There are also tiny cilia in the fallopian tube that propel the egg towards the uterus. Some of the remaining sperm will become trapped in the cilia and die. Only a small handful of the original sperm cells will make it as far as the egg. Thus, it is necessary that hundreds of millions of sperm cells are released in order to have a reasonable chance of the egg cell being fertilized.

           Seminal fluid also provides essential nutrients to support the survival and motility of the sperm. These include fructose — which serves as a source of energy for the sperm, fueling the mitochondrial production of ATP — as well as other sugars, amino acids, and enzymes. If the seminal fluid did not contain fructose, to power the mitochondria, this would have drastic implications for sperm cell motility and viability.

The seminal fluid is also alkaline. This is important because the vagina has an acidic pH, produced by the normal flora (bacterial populations) of the vagina. This environment would be unfavorable to sperm cells. But the alkalinity of the seminal fluid helps to neutralize the vagina’s acidic pH, assisting the survival of the sperm.

Following ejaculation, the seminal fluid initially coagulates to form a gel-like consistency. This coagulation helps to keep the semen in the vagina and cervix, preventing it from immediately leaking out and thereby greatly increasing the odds of a successful fertilization. This occurs upon exposure to the air or the alkaline environment of the female reproductive tract, activating clotting factors present in the seminal fluid, including tissue transglutaminase. The transglutaminase converts semenogelin (a major protein in seminal fluid secreted by the seminal vesicles) into a sticky protein called fibrin. Fibrin forms a network-like structure that entraps sperm and other components of the semen. 

If the semen remained in this state, the sperm would be permanently immobile and unable to fertilize the egg. Over time, however, the coagulated semen liquefies due to enzymes present in the fluid that slowly break down the fibrin network, allowing the sperm to move more freely. Anamthathmakula and Winuthayanon note that “The liquefaction process is crucial for the sperm to gain their motility and successful transport to the fertilization site in Fallopian tubes (or oviducts in animals). Hyperviscous semen or failure in liquefaction is one of the causes of male infertility.”1 In fact, targeting these serine proteases has been suggested as a target for novel non-hormonal contraceptives.2From an evolutionary perspective, it is difficult to envision a scenario where semen coagulation evolved, without simultaneously having a mechanism for liquefaction. This is a prime example of a non-adaptive intermediate that is prohibitive to evolution by natural selection.

Sperm Capacitation

In order for a sperm cell to fertilize an egg, it has to undergo capacitation. This takes place in the female reproductive tract. The process of capacitation involves a series of biochemical and physiological changes that prepare the sperm for successful interaction with the egg and is crucial in order for the sperm cell to acquire the ability to fertilize.

When sperm are initially ejaculated, they possess certain molecules and proteins on their surface that inhibit their ability to fertilize an egg. During capacitation, these surface molecules, such as cholesterol and glycoproteins, are removed or modified, allowing the sperm to become more receptive to the egg. As capacitation progresses, the motility pattern of sperm also changes. They undergo hyperactivation, which is characterized by increased amplitude and asymmetrical beating of the tail. Hyperactivated sperm exhibit vigorous movements, which help them to navigate through the female reproductive tract and reach the egg. Capacitation also involves changes in the composition and fluidity of the sperm cell membrane. These changes allow the sperm to better interact with the egg’s zona pellucida. The acrosome becomes primed for the acrosome reaction, which releases these enzymes to allow penetration of the egg membrane. 

Capacitation is associated with an increase in calcium ion influx into the sperm. Calcium plays a crucial role in various intracellular signaling processes that are necessary for sperm function and fertilization. For a much more detailed treatment of what is known about the mechanisms of sperm capacitation, there are good reviews of this subject, to which I direct readers.3,4

Conclusion

In summary, various features of the head, middle piece, and flagellum, together with the properties of the seminal fluid, are critical to the sperm cell’s function of reaching and fertilizing an egg. If any one of these parts is not present or fails to function properly, the sperm cell is rendered completely impotent, and reproduction cannot occur. The phenomenon of human reproduction points to a cause with foresight — one that can visualize a foreordained outcome and bring together everything needed to realize that end goal. There is no cause in the universe that is known to have such a capacity of foresight other than intelligent design.

Notes

Anamthathmakula P, Winuthayanon W. Mechanism of semen liquefaction and its potential for a novel non-hormonal contraception†. Biol Reprod. 2020 Aug 4;103(2):411-426.

Ibid.

Puga Molina LC, Luque GM, Balestrini PA, Marín-Briggiler CI, Romarowski A, Buffone MG. Molecular Basis of Human Sperm Capacitation. Front Cell Dev Biol. 2018 Jul 27;6:72.

Stival C, Puga Molina Ldel C, Paudel B, Buffone MG, Visconti PE, Krapf D. Sperm Capacitation and Acrosome Reaction in Mammalian Sperm. Adv Anat Embryol Cell Biol. 2016;220:93-106.

Probing the dark

 

The real post fossil future?

 

The future postponed?

 

The future of EVs?

 

On the Caiaphas ossuary.

 

Caiaphas : the Watchtower Society's Commentary.

 Caiaphas:

Joseph Caiaphas was the high priest during Jesus’ earthly ministry. (Lu 3:2) He was the son-in-law of High Priest Annas (Joh 18:13; see ANNAS) and was appointed to office by the predecessor of Pontius Pilate, Valerius Gratus, about the year 18 C.E., although some say as late as the year 26 C.E. He held the office until about the year 36 C.E., longer than any of his immediate predecessors, this being due to his skillful diplomacy and cooperation with Roman rule. He and Pilate were reportedly good friends. Caiaphas was a Sadducee.—Ac 5:17.

A ringleader in the plot to do away with Jesus, Caiaphas prophesied, though not of his own originality, that Jesus would shortly die for the nation, and to that end he gave his wholehearted support. (Joh 11:49-53; 18:12-14) At Jesus’ trial before the Sanhedrin, Caiaphas ripped his garments and said: “He has blasphemed!” (Mt 26:65) When Jesus was before Pilate, Caiaphas was undoubtedly there crying: “Impale him! Impale him!” (Joh 19:6, 11); he was there asking for the release of Barabbas instead of Jesus (Mt 27:20, 21; Mr 15:11); he was there shouting: “We have no king but Caesar” (Joh 19:15); he was also there protesting the sign over Jesus’ head: “The King of the Jews” (Joh 19:21).

The death of Jesus did not mark the end of Caiaphas’ role as a chief persecutor of infant Christianity. The apostles were next haled before this religious ruler; they were sternly commanded to stop their preaching, were threatened, and were even flogged, but to no avail. “Every day in the temple and from house to house they continued without letup,” Caiaphas notwithstanding. (Ac 4:5-7; 5:17, 18, 21, 27, 28, 40, 42) The blood of righteous Stephen was soon added to Jesus’ bloodstains on the skirts of Caiaphas, who also armed Saul of Tarsus with letters of introduction so the murderous campaign could be extended to Damascus. (Ac 7:1, 54-60; 9:1, 2) However, not long thereafter Vitellius, a Roman official, removed Caiaphas from office.

File under "Well said" XCV

 "What gets us into trouble is not what we don't know. It's what we know for sure that just ain't so."

Mark Twain

Rome's Praetorian Guard :a brief history.

 

The Ottoman's struggle for the "empire of God"

 

Tom Sowell utters uncommon sense.

 

On empiricism and Darwinism

 The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence

Cornelius G Hunter

Dennis Venema, professor of biology at Trinity Western University, has written a series of articles that have been noted by evolutionists for their clarity and persuasiveness. So as a collector of evidences and reasons why evolution is a fact, I was interested to see Venema’s articles. What does the professor have to say to help confirm what Samuel Wilberforce rhetorically called “a somewhat startling conclusion”?

One of Venema’s basic points is that the genomes of different species are what we would expect if they evolved. Allied species have similar genomes, and genetic features fall into evolution’s common descent pattern:

If indeed speciation events produced Species A – D from a common ancestral population, we would expect their genomes to exhibit certain features when compared to each other. First and foremost, their overall genome sequence and structure should be highly similar to each other – they should be versions of the same book, with chapters and paragraphs of shared text in the same order. Secondly, the differences between them would be expected to fall into a pattern.

Does the evidence confirm these evolutionary expectations? Venema answers with an emphatic “yes.”

Here Venema is appealing to the empirical evidence. He is comparing the evidence to the theory of evolution, and finding that the evidence confirms evolution’s predictions. This means the theory can be empirically evaluated. And if evolution can be genuinely evaluated empirically, then it is, at least theoretically, possible for evolution to fail. If the evidence can confirm evolution, then it also can disconfirm evolution.

This is important because focusing the attention on the evidence means the non scientific arguments go away and science is allowed to speak. What does it say? Here I will take the opposing view, for it seems that what the science shows is that Venema’s claim, that the genetic evidence confirms evolutionary predictions, is inaccurate.

This is not to say that evolutionary explanations cannot be offered. As philosophers well understand, another sub hypothesis is always possible. Such hypotheses raise more profound questions of parsimony, likelihood and so forth. But it seems that such philosophical questions ought to be addressed after there is a consensus on what the empirical evidence has to say. The goal here is to move toward that consensus. Venema, and evolutionists in general, make a straightforward claim about the evidence. We ought to be able to dispassionately evaluate that claim.

Of course I realize that reaching consensus is not as simple as reading an article. There will be differing interpretations by fair-minded critics. And the topic of origins is certainly not always dispassionate. If you argue against evolution you will be disparaged. My response to such attacks has and always will be to forgive.

One final preliminary is simply to point out that it is a challenge just to do justice to this story. A thorough treatment could easily require an entire volume. But a few, typical, examples will have to suffice. They can provide readers with an approximate understanding how the evidence bears on Venema’s claim.

What does the evidence say?

For starters, phylogenetic incongruence is rampant in evolutionary studies. Genetic sequence data do not fall into the expected evolutionary pattern. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many.

MicroRNAs are short RNA molecules that regulate gene expression, for example, by binding to messenger RNA molecules which otherwise would code for a protein at a ribosome. Increasingly MicroRNAs are understood to be lineage-specific, appearing in a few species, or even in just a single species, and are nowhere else to be found. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional [evolutionary] tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Trichodesmium or “sea sawdust,” a genus of oceanic bacteria described by Captain Cook in the eighteenth century and so prolific it can be seen from space, has a unique, lineage-specific genome. Less than two-thirds of the genome of this crucial ammonium-producing bacteria codes for proteins. No other such bacteria has such a low value, and conversely such a large percentage of the genome that is non coding. This lineage-specific genome, as one report explains, “defies common evolutionary dogma.”

It is not unusual for similar species to have significant differences in their genome. These results have surprised evolutionists and there does not seem to be any let up as new genomes are deciphered.

The mouse and rat genomes are far more different than expected. Before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naive belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

One phylogenetic Study attempted to compute the evolutionary tree relating a couple dozen yeast species using 1,070 genes. The tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”

What is interesting is how this false prediction was accommodated. The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.

These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.”

And how do we know that these genes have strong phylogenetic signal. Because they gave the right answer. This raises the general problem of prefiltering of data. Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.

But even prefiltering cannot always help the theory. For even cleansed data routinely lead to evolutionary trees that are incongruent (the opposite of consilience). As one Study explained, the problem is so confusing that results “can lead to high confidence in incorrect hypotheses.” As one paper Explained, data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence. And although evolutionists thought that more data would solve their problems, the opposite has occurred. With the ever increasing volumes of data (particularly molecular data), incongruence between trees “has become pervasive.”

What is needed now is less data. Specifically, less contradictory data. As one evolutionist Explained, “if you take just the strongly supported genes, then you recover the correct tree.” And what are “strongly supported” genes? Those would be genes that cooperate with the theory. So now in addition to prefiltering we have postfiltering.

Another issue are the striking similarities in otherwise distant species. This so-called convergence is rampant in biology and it takes on several forms.

Consider a Paper from the Royal Society on “The mystery of extreme non-coding conservation” that has been found across many genomes. As the paper explains, there is currently “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Here is how the paper summarizes these findings of extreme sequence conservation:

despite 10 years of research, there has been virtually no progress towards answering the question of the origin of these patterns of extreme conservation. A number of hypotheses have been proposed, but most rely on modes of DNA : protein interactions that have never been observed and seem dubious at best. As a consequence, not only do we still lack a plausible mechanism for the conservation of CNEs—we lack even plausible speculations.

And these repeated designs, in otherwise different species, are rampant in biology. It is not merely a rare occurrence which perhaps evolution could explain as an outlier. That the species do not fall into an evolutionary tree pattern is well established by science.

Furthermore, these repeated designs do not merely occur twice, in two distant species. They often occur repeatedly in a variety of otherwise distant species. So now the evolutionist must not only believe that there are many of these repeating design events, but that in most cases, they repeat multiple times, in disparate species.

Evolutionists have labeled this evidence as recurrent evolution. As a recent paper Explains:

The recent explosion of genome sequences from all major phylogenetic groups has unveiled an unexpected wealth of cases of recurrent evolution of strikingly similar genomic features in different lineages.

In addition, many instances of a third more puzzling phylogenetic pattern have been observed: traits whose distribution is “scattered” across the evolutionary tree, indicating repeated independent evolution of similar genomic features in different lineages.

If the pattern fits the evolutionary tree, then it is explained as common evolutionary history. If not, then it is explained as common evolutionary forces.

With all of this contradictory evidence, even evolutionists have realized in recent years that the traditional evolutionary tree model is failing. As one evolutionist Explained , “The tree of life is being politely buried.”

There are many more fascinating examples of biological patterns that are not consistent with the expected evolutionary pattern. These are not anomalies or rare exceptions. Here we have focused on the genetic level since that was the theme of Venema’s article. It seems that the species and their genomes do not fall into a consistent evolutionary pattern as evolutionists such as Venema claim. This does not mean evolutionists cannot explain any of this. They have a wide spectrum of mechanisms to draw upon, of varying levels of speculation and likelihood. These explanatory mechanisms greatly increase the theory’s complexity. They raise questions of realism, and whether the theory is following the data, or the data is following the theory. But such questions are for another day.

The point here is that evolutionist’s claims that the genomic data broadly and consistently fall into the evolutionary pattern and expectations do not seem to reflect the empirical data. This is the first step in moving the discourse forward. We need to reach consensus on what the evidence reveals.

Next time I will continue with an examination of the next evidences Venema presents.

The amazing Randi vs. Uri Geller

 

The amazing Randi vs. the paranormal

 

PBS interviews one of modern IDs founding fathers

 PBS, Darwin, and Dover: An Interview with Phillip Johnson

Evolution news

On a classic episode of ID the Future, host Casey Luskin interviews Phillip Johnson, former UC Berkeley law professor and one of the founders of the modern intelligent design movement. Back in 2007, Johnson was one of the only intelligent design proponents interviewed for and included in PBS’s long-running science series NOVA in an episode about the Dover case called “Judgment Day: Intelligent Design on Trial.” Johnson weighs in with his thoughts about the ruling issued by Judge Jones, about the scientific status of intelligent design, his views on PBS’s teaching guide about intelligent design, and the popular claim at the time that intelligent design would inject religion into the classroom. Download the podcast or listen to it here.

Johnson was the author of the 1993 bestseller Darwin on Trial, an inspiration to many scientists and scholars in the intelligent design research community. He was an advisor to Discovery Institute’s Center for Science and Culture for many years. He died in 2019.

Miracle working atheist?

 

Tales about tails?

 ScienceAlert Vindicates My Findings About Human “Tails” — They Are NOT an Evolutionary Atavism

Casey Luskin

Back in 2014 I wrote a series of articles at Evolution News (posted as a single piece here) about whether the human “tail” was an atavism — an evolutionary throwback — that provides evidence for evolution. The debate started after scientist and theistic evolutionist Karl Giberson used an image of a human baby with a photoshopped tail that looked completely real — as if it were evidence for evolution. This then led to a deep dive into the literature wherein I learned a lot about the human tail. It’s all documented at the link above, but at the end of the series, I offered the following findings based upon my literature review:

No babies are born with perfectly formed, fully functional tails.

Babies that do have tails typically have serious associated neurological defects.

The exact causes of tails are debated, but because of their persistent association with neurological defects, the most plausible view is that they result from abnormalities and deviations in development.

What the Medical Evidence Shows

Now a very nice new article at ScienceAlert has completely vindicated my arguments about human tails. Titled “Some Babies Are Born With ‘Tails’, But Not For The Reason You Might Think,” the article by Carly Cassella basically comes to the same conclusions I did. She starts by noting that many people still believe that human “tails” are evolutionary throwbacks — but this is not what the medical evidence shows:

[T]he rare case studies tend to generate “an unusual amount of interest, excitement and anxiety”, according to researchers. Often, this is because the ‘tails’ are considered to be benign, evolutionary remnants of a long lost ancestor. 

As it turns out, that’s based on an outdated theory that has been contentious for decades now. The reality for these children may be much darker, and they deserve medical attention, not our morbid fascination.

The appendages some babies are born with have historically been deemed ‘true’ or ‘vestigial’ tails. But that’s a bit of a misnomer, as they aren’t really like any other tail known in nature. They typically don’t contain bones, cartilage, or a spinal cord. They just kind of hang there without a clear function.

Still, that doesn’t mean these appendages are as harmless as scientists used to think.

This is precisely what I found in my literature review, as I Explained:

Human tails are extremely rare, with perhaps only a few hundred cases documented worldwide over the past half-century. Medical researchers who have had the lucky opportunity to study a human tail have divided them into two general categories: “true tails,” which extend from the coccyx (tailbone) where one might expect a so-called “vestigial tail,” and “pseudotails” which are often found in other locations on the lower back, and seem to be obvious aberrations since they are often associated with anomalies.

This distinction is based upon evolutionary assumptions, and in recent years it has become quite controversial as researchers have learned more about the phenomenon. I’ll say more later about why even the “true tails” in humans don’t deserve that name. For now, here’s a crucial fact: even such so-called “tails” aren’t anything like those found in tailed mammals. That is for the simple reason that “true tails” in humans entirely lack vertebrae — or any kind of bone, cartilage, notochord, or spinal cord. As the aforementioned paper in the Journal of Neurosurgery explains:

“In all reported cases, the vestigial human tail lacks bone, cartilage, notochord, and spinal cord. It is unique in this feature.” (Roberto Spiegelmann, Edgardo Schinder, Mordejai Mintz, and Alexander Blakstein, “The human tail: a benign stigma,” Journal of Neurosurgery, 63: 461-462 (1985).)

It All Started with Darwin

Now it turns out that the 1985 paper cited above was actually largely responsible for spreading the myth that human tails are an evolutionary throwback, as the ScienceAlert article explains:

The misunderstanding over the tail’s origin starts with Charles Darwin himself. Over a century ago, Darwin proposed that human vestigial tails are evolutionary accidents, or rudimentary leftovers from a primate ancestor that was once tailed itself.

In the 1980s, scientists took this theory and ran with it. They argued that a genetic mutation, evolved by humans to erase our tails, could sometimes revert back to its ancestral state.

In 1985, a seminal paper defined two different types of ‘tails’ that human babies can be born with. The first, as mentioned before, is a vestigial or true tail, originally thought to be inherited from our ancestors.

But, the article reports that even these supposedly “true tails” are often associated with birth defects, showing that they are not a benign evolutionary atavism that can be ignored but rather a birth defect that ought to be taken very seriously:

As it turns out, both rare appendages probably represent an incomplete fusion of the spinal column, or what’s known as a spinal dysraphism. This suggests their formation is not a harmless ‘regression’ in the evolutionary process but a concerning disturbance in an embryo’s growth most likely resulting from a mix of genetic and environmental factors.

[…]

Roughly half of the cases reviewed were associated with either meningocele or spina bifida occulta.

This suggests babies born with tails need greater medical attention than a simple surgery. And it strongly disagrees with the 1985 paper that argued “the true human tail is a benign condition not associated with any underlying [spinal] cord malformation.”

Not a Harmless Vestigial Trait”

The article goes on to draw a very similar conclusion to the one I did:

Regardless of where a baby’s tail came from, however, evidence strongly suggests it is the result of a congenital issue and is not a harmless vestigial trait.

For the life and health of these children, that’s an important message that needs to be cleared up once and for all.

I agree, and wrote the following in my article:

Thankfully, most doctors today take their view on this not from Darwinian evolution, but from the evidence, the accumulated experience of clinical researchers as represented in the medical literature. Researchers warn that seeing tails as benign structures can lead doctors to miss serious developmental problems.

It’s a good thing, not least for patients, that the Darwinian doctrine, little more than an urban legend, is fast on its way to being abandoned.

The ScienceAlert article cites new literature that has appeared since I published my own review nine years ago. It’s encouraging to see that my findings about the human tail have stood the test of time.

Physics in the doldrums?

 

Question begging much re: the trinity?

 

No solutions only trade offs?

 

The U.S constitution 101

 

Yet more founding myths?

 

Founding myths?

 

Leon Trotsky: a brief history

 

Mission creep?

 

The natives are restless?

 

Is Jesus the most high God?

 

On shadow war and shadow

 

On the status of the dream.

 

Edward Fudge on rethinking hell

 

Questioning the unquestionable.

 

Still no simple beginning

 On the Irreducible Complexity of Sperm Cells

Jonathan McLatchie

Human reproduction is perhaps the quintessential example of teleology in biology. The process by which a fertilized egg develops into an infant over the space of nine months reveals exquisite engineering and ingenious design. Before this intricate process can even begin, there is a need for a sperm cell to fuse with an ovum — each carrying, in the case of humans, 23 chromosomes. This incredible feat bears the unmistakable hallmarks of conscious intent and foresight

Here , I will focus on the design characteristics of sperm cells. In a subsequent post, I will discuss the design features of the seminal fluid, and sperm capacitation. Sperm cells are comprised of three components — the head, the middle piece, and the flagellum — and hundreds of millions of them are carried in the seminal fluid that is released into the cervix through ejaculation during sexual intercourse. With each ejaculation, the male releases between two hundred and five hundred million sperm cells (approximately 100 million per milliliter of semen). Each of these three components, and the seminal fluid, is crucial to the sperm cell’s mission of fusing with an ovum to form a zygote (a fertilized egg). Let us consider each one in turn.

The Head

The head carries densely coiled chromatin fibers, containing the haploid genome — totaling half of the genetic material that will be inherited by the next generation (the other half will come from the mother’s egg cell). The tight packaging of the DNA serves to minimize its volume for transport.

On the tip of the sperm head is a membranous organelle, called the acrosome, that contains various hydrolytic enzymes. When these are secreted, they digest the egg cell membrane, thereby facilitating penetration of the ovum. Without the acrosome, the sperm cell will be unable to penetrate the egg cell membrane to fertilize the ovum. According to a review paper published in Frontiers in Cell and Developmental Biology:

Any structural or functional acrosomal abnormality could impair sperm fusion, and ultimately result in infertility. Moreover, studies have shown that intra-cytoplasmic insemination with sperm containing acrosomal abnormalities did not lead to successful fertilization, even in the absence of fertilization barriers, because the oocyte was unable to be efficiently activated…Thus, the acrosome is indispensable for fertilization.1

When a sperm reaches the vicinity of the egg, it undergoes a series of molecular interactions with the zona pellucida, which is a specialized extracellular matrix surrounding the egg. Specific receptors on the sperm’s plasma membrane, such as spermadhesins or integrins, recognize and bind to corresponding ligands on the zona pellucida. This binding triggers the activation of signaling pathways in the sperm. Binding of the sperm receptors to the zona pellucida ligands leads to an influx of calcium ions (Ca2+) into the sperm cell. This calcium influx is typically mediated by ion channels or receptors on the sperm’s plasma membrane, which are activated upon ligand-receptor binding. The increase in intracellular calcium levels initiates a signaling cascade within the sperm cell. Calcium ions act as second messengers and trigger the activation of various downstream signaling molecules and enzymes, including protein kinases. As a result of the calcium-mediated signaling cascade, the acrosome undergoes exocytosis. The membrane surrounding the acrosome fuses with the sperm’s plasma membrane, causing the release of the acrosomal contents, including enzymes such as hyaluronidase and acrosin. The enzymes released from the acrosome help degrade the glycoprotein matrix of the zona pellucida, allowing the sperm to penetrate and reach the egg’s plasma membrane. The acrosomal contents aid in the breakdown of the protective layers surrounding the egg, facilitating the fusion of the sperm and egg membranes. 

The formation of the acrosome itself is divided into four stages. The first stage, the “Golgi phase,” is dependent upon the Golgi apparatus, which produces and packages the proteins and enzymes needed for acrosome formation. These proteins are then transported into the developing acrosome vesicle. In the second phase, the “cap phase,” the Golgi-derived vesicle (known as the proacrosomal vesicle) fuses with the anterior portion of the nucleus, forming a cap-like structure over the nucleus. The fusion of the vesicle with the nucleus is mediated by membrane trafficking processes. The proacrosomal vesicle contains enzymes, glycoproteins, and other components that are essential for acrosome maturation. In the third phase, the “acrosome phase,” the cap-like structure undergoes a series of structural changes, leading to the formation of the acrosome. The proacrosomal vesicle flattens and elongates, spreading over the anterior region of the nucleus. The Golgi-derived enzymes modify the proteins present in the proacrosomal vesicle, converting them into their active forms. The acrosomal membrane also undergoes changes, becoming specialized for the acrosome’s functions. In the final phase, the “maturation phase,” the acrosome undergoes further modifications and maturation. Enzymes within the acrosome become fully activated and the acrosomal matrix undergoes changes, becoming more condensed. The acrosomal granule, which is the central region of the acrosome, becomes highly electron-dense due to the accumulation of enzymes and proteins. The mature acrosome is now ready for its role in fertilization. For a more detailed description of this incredible process, I refer readers to a review paper on the “Mechanism of Acrosome Biogenesis in Mammals.”2

The Middle Piece

The middle piece consists of a central filamentous core, around which are many strategically placed mitochondria that synthesize the energy molecule adenosine triphosphate (ATP). The complexity and design of energy generation within the mitochondria — including the processes of glycolysis, the citric acid (or, Krebs) cycle, the electron transport chain, and oxidative phosphorylation — could be its own series of articles, but this is a topic for another day. For a good introduction to the phenomenal processes within the mitochondria, here are three animations from Harvard University that bring this fascinating organelle to life:

“Mitochondria: The Cell’s Powerhouse”

“Electron Transport Chain”

“ATP Synthase in action”

The ATP generated by the mitochondria energizes the power strokes of the flagellum, driving its journey through the female cervix, uterus, and uterine tubes. As such, the middle piece of the sperm cell is absolutely essential to its function of swimming through the female uterus and fallopian tube to fertilize her egg. Without the middle piece and its mitochondria, the sperm cells are completely immobile.

The Flagellum

Unlike a bacterial flagellum (which rotates like a motor), a sperm flagellum beats with a whip-like motion to produce motility. How does the flagellum work? In 2018, Jianfeng Lin and Daniela Nicastro elucidated the mechanism of flagellar motility.3 Their data indicated that “bending was generated by the asymmetric distribution of dynein activity on opposite sides of the flagellum”4 (dyneins are ATP-powered molecular motors that “walk” along microtubules towards their minus end). Their results also revealed that alternating flagellar bending occurs due to “a ‘switch-inhibition’ mechanism in which force imbalance is generated by inhibiting…dyneins on alternating sides of the flagellum.”5 In other words, regulatory signals lead to the inhibition of dynein motors on one side of the flagellum. Meanwhile, on the other side, the dyneins walk along the microtubules. The flagellum bends in one direction due to molecular linkers that resist this sliding. The flagellar bending alternates by repeatedly switching the side of dynein inhibition. Look here for an animation showing how this is thought to work.

It goes without saying that, without the flagellum, the sperm cell is completely immotile and has no chance of fertilizing the egg.

Thus far, we have considered the irreducible complexity of the components of a sperm cell. In a subsequent article, we shall consider the design features of the seminal fluid and the process of sperm capacitation that takes place within the female reproductive tract.

Notes

Khawar MB, Gao H, Li W. Mechanism of Acrosome Biogenesis in Mammals. Front Cell Dev Biol. 2019 Sep 18;7:195.

Ibid.

Lin J, Nicastro D. Asymmetric distribution and spatial switching of dynein activity generates ciliary motility. Science. 2018 Apr 27;360(6387):eaar1968.

Ibid.

Ibid.