Tuesday, 4 July 2023
Thomas Jefferson on the book of creation.
Thomas Jefferson’s Embrace of Intelligent Design
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.
Monday, 3 July 2023
Pre:Darwinian design.
The Design of the Seminal Fluid and Sperm Capacitation
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, MarÃn-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.
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
On empiricism and Darwinism
The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence
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.
Sunday, 2 July 2023
PBS interviews one of modern IDs founding fathers
PBS, Darwin, and Dover: An Interview with Phillip Johnson
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.
Tales about tails?
ScienceAlert Vindicates My Findings About Human “Tails” — They Are NOT an Evolutionary Atavism
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.
Saturday, 1 July 2023
Friday, 30 June 2023
Still no simple beginning
On the Irreducible Complexity of Sperm Cells
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.
Continuing to massage the record?
Fossil Friday: Homo rudolfensis, Another Contentious Homo
Last week for Fossil Friday I posted some musings about Homo habilis and its controversial attribution to our genus. This week we will have a look at another disputed relative, Homo rudolfensis. Alexeev (1986) described the new species Homo (Pithecanthropus) rudolfensis from a single skull (KNM-ER 1470) discovered in 1972 by Richard Leakey at the 1.9 million year old Koobi Fora locality of the Turkana Lake (formerly known as Lake Rudolf) basin in East Africa (also see Wood 1999). The material was previously considered to be conspecific with Homo habilis, which is a hypothesis still entertained by some modern experts. However, the skull differs from Homo habilis in its flat face and larger brain volume as well as the more robust-australopithecine-like cheek teeth. Unfortunately, no associated postcranial remains are known yet (Berger et al. 2015), so that the most distinctive characters of the genus Homo and those for bipedal gait are unknown (Tuttle 2006: 253).
A New Digital Reconstruction
As for Homo habilis, Wood & Collard (1999a, 1999b, 2001) and Collard & Wood (2007, 2015) indeed advocated for transferring H. rudolfensis to the genus Australopithecus, which had already been suggested by other researchers (i.e., Walker 1976 and Lieberman et al. 1996). Walker & Shipman (1996) pointed out that “1470 might have a big braincase, but morphologically it was just an australopithecine.” A new digital reconstruction of the skull by Bromage et al. (2008) showed that it was somewhat less flat and the brain volume somewhat smaller, which made it even more similar to australopithecine skulls. Nevertheless, the latter study retained this species in the genus Homo. A co-author of this study was German paleoanthropologist Friedemann Schrenk, who at my university, Tübingen, was known by the sneering nickname the “Möllemann of German paleontology.” That was because he shared a notorious proclivity for PR stunts and media hype with the late German politician Jürgen Möllemann. He discovered a hominin mandible (UR 501) in Malawi, which he attributed to Homo rudolfensis and with an estimated age of 2.4 million years this would be much older than the holotype. Of course, publications on an early Homo make for much more sensational press releases than just another ape-man.
Anyway, Leakey et al. (2001) and Lieberman (2001) noted several striking similarities in the facial architecture of the newly described hominin Kenyanthropus platyops and the 1.6 million year younger H. rudolfensis, who could be a late survivor of the australopithecine-like Kenyanthropus lineage rather than an early Homo. The phylogenetic analysis by Cameron & Groves (2004) strongly confirmed the reclassification as Kenyanthropus rudolfensis by Cameron (2003). Cela-Conde & Ayala (2003) agreed that Homo rudolfensis (and H. habilis) should be grouped with Kenyanthropus platyops, but instead proposed to include all three within the genus Homo. That would place the origin of our genus 3.5 million years ago, in stark contradiction to all other experts and the unequivocal empirical evidence from the fossil record.
Four Hypotheses
Prat (2007) compared the four suggested alternative hypotheses: H. rudolfensis is conspecific with Homo habilis; H. rudolfensis and H. habilis are both distinct species of Homo; both species belong to the genus Australopithecus; or H. rudolfensis belongs to the genus Kenyanthropus. Prat came to the conclusion that Homo rudolfensis is distinct but her cladistic analysis suffers from several flaws. This is evident from the fact that the inclusion of the holotype of Kenyanthropus platyops did not just influence the polarity of some characters but produced a totally different tree topology with hardly any similarity to the tree recovered by excluding this taxon. The confidence level in any such highly unstable analyses should be very low for reasonable and unbiased scientists. However, having two early species of Homo is of course a highly desirable result for evolutionist paleoanthropologists, and so it is hardly surprising that almost all subsequent publications maintained the attribution of these two species to the genus Homo.
Awaiting Better Evidence
More recently, a more ancient origin of our genus has indeed been claimed by the discovery of a 2.8 million year old human mandible at Ledi-Geraru in the Afar region of Ethiopia, which was attributed to an early Homo (Villmoare et al. 2015). But this fossil combines primitive australopithecine traits with more derived features of later Homo, and it also suffers from the absence of any other cranial and postcranial characters that could support this claim. Considering the checkered history of grandiose claims and controversies in paleoanthropology, some caution may be wise until more and better evidence is found.
References
Alexeev VP 1986. The Origin of the Human Race. Progress Publishers, Moscow, 360 pp. https://archive.org/details/originhumanrace/page/1/mode/2up
Berger LR, Hawks J, de Ruiter DJ et al. 2015. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife 4:e09560, 1–35. DOI: https://doi.org/10.7554/eLife.09560
Bromage TG, McMahon JM, Thackeray JF, Kullmer O, Hogg R, Rosenberger AL, Schrenk F & Enlow DH 2008. Craniofacial architectural constraints and their importance for reconstructing the early Homo skull KNM-ER 1470. Journal of Clinical Pediatric Dentistry 33, 43–54. DOI: https://doi.org/10.17796/jcpd.33.1.8168115j12103nut
Cameron DW 2003. Early hominin speciation at the Plio/Pleistocene transition. HOMO 54(1), 1–28. DOI: https://doi.org/10.1078/0018-442X-00057
Cameron DW & Groves CP 2004. Bones, Stones, and Molecules: “Out of Africa” and Human Origins. Academic Press, Burlington (MA), xi+402 pp.
Cela-Conde CJ & Ayala FJ 2003. Genera of the human lineage. PNAS 100(13), 7684–7689.
DOI: https://doi.org/10.1073/pnas.0832372100
Collard M & Wood B 2007. Defining the Genus Homo. pp. 1575–1610 in: Henke W & Tattersall I (eds). Handbook of Paleoanthropology. 3 vols. Springer, Berlin, 2069 pp.
Collard M & Wood B 2015. Defining the Genus Homo. pp. 2107–2144 in: Henke W & Tattersall I (eds). Handbook of Paleoanthropology. 3 vols. Springer, Berlin, xliii+2624 pp. DOI: https://doi.org/10.1007/978-3-642-39979-4_51
Tuttle RH 2006. Are Human Beings Apes, or are Apes People too? pp. 249–258 in: Ishida H, Tuttle R, Pickford M, Ogihara N & Nakatsukasa M (eds). Human Origins and Environmental Backgrounds. Springer Science, Boston (MA), x+282 pp. DOI: https://doi.org/10.1007/0-387-29798-7_19
Leakey MG, Spoor F, Brown FH, Gathogo PN, Kiarie C, Leakey LN & McDougall I 2001. New hominin genus from eastern Africa shows diverse middle Pliocene lineages. Nature 410(6827), 433–440. DOI: https://doi.org/10.1038/35068500
Lieberman DE 2001. Another face in our family tree. Nature 410(6827), 419–420. DOI: https://doi.org/10.1038/35068648
Lieberman DE, Wood BA & Pilbeam DR 1996. Homoplasy and early Homo: An analysis of the evolutionary relationships of H. habilis sensu stricto and H. rudolfensis. Journal of Human Evolution 30, 97–120. DOI: https://doi.org/10.1006/jhev.1996.0008
Prat S 2007. The Quaternary boundary: 1.8 or 2.6 millions years old? Contributions of early Homo. Quaternaire 18(1), 99–107.
DOI: https://doi.org/10.4000/quaternaire.1313
Villmoare B, Kimbel WH, Seyoum C et al. 2015. Early Homo at 2.8 Ma from Ledi-Geraru, Afar, Ethiopia. Science 347(6228), 1352–1355. DOI: https://doi.org/10.1126/science.aaa1343
Walker A 1976. Remains attributable to Australopithecus in the East Rudolf succession. pp 484–489 in: Coppens Y, Howell FC, Isaac GL & Leakey REF (eds). Earliest Man and Environments in the Lake Rudolf Basin. University of Chicago Press, Chicago (IL), 640 pp.
Walker A & Shipman P 1996. The Wisdom of the Bones: In Search of Human Origins. Knopf, New York (NY), 368 pp.
Wood B 1999. Homo rudolfensis Alexeev, 1986: Fact or phantom?. Journal of Human Evolution 36(1), 115–118. DOI: https://doi.org/10.1006/jhev.1998.0246
Wood B & Collard M 1999a. The Human Genus. Science 284(5411), 65–71. DOI: https://doi.org/10.1126/science.284.5411.65
Wood B & Collard M 1999b. The changing face of genus Homo. Evolutionary Anthropology 8(6), 195–207. DOI: https://doi.org/10.1002/(SICI)1520-6505(1999)8:6<195::AID-EVAN1>3.0.CO;2-2
Wood B & Collard M 2001. The meaning of Homo. Ludus Vitalis 9(15), 63–74. http://profmarkcollard.com/wp-content/uploads/2014/09/Wood-and-Collard-2001.pdf
On the anti-Darwinian bias of the natural law.
Intelligence Is Unnatural, and Why That Matters
One of the advantages we have in our study of nature is our ability to observe an entire “unpolluted” universe. By “unpolluted” I mean that as we look out from Earth, we observe an almost unlimited theater of the natural. And what do we observe? Mostly empty space, visibly interspersed with galaxies composed of stars and nebulae. The regularities of the laws of nature also reveal unseen actors such as dark matter and energy, planets, and even black holes.
Speaking of the laws of nature, the heavenly stage extends so far away that light’s finite speed shows us scenes that happened in the past — from about one and one fourth seconds in the past, when we look at the moon, to more than 13 billion years ago in recent images of distant galaxies revealed by the James Webb Space Telescope. The physical universe provides astronomers with a time machine for viewing nature throughout the history of the cosmos. And what we see confirms the unchanging nature of the laws of physics.
What Spectroscopy Reveals
Using spectroscopy, astronomers not only observe the large-scale features of the universe, but through analysis of the specific wavelengths of electromagnetic radiation received, details of the atomic components of stars and gas clouds also are revealed. In the past as well as in the present, both near to home in our solar system and out to the most distant reaches of the visible universe, the same atomic characters fill the arena of the universe. Throughout the entire long history of the universe and in every direction we look, nature has only managed to produce a very limited playlist of elements — 92 different elements, from hydrogen with one proton as its nucleus to uranium with 92 protons.1
The reason I emphasize the limited number of types of elements in the entire universe is to suggest that one of the characteristics of nature is its “sameness” or redundancy. Now, there’s a reason for this: natural outcomes are governed by natural law. Only four fundamental forces of nature exist. Gravity pulls masses together; the electromagnetic force has twice the fun and can both push and pull masses that possess electric charge. The strong nuclear force also pulls,2 but with restrictions. It only acts on nucleons (protons and neutrons, but not electrons), and it has an extremely short range of about one fermi (10-15 m). The weak force neither pushes nor pulls, but is responsible for certain decay processes of elementary particles.
An example of the sameness of the cosmos is seen in the limited range of star masses. From at least a billion trillion stars in the universe, we find that their masses vary only over a range of about 1800, from 8 percent of the sun’s mass up to about 150 times the sun’s mass. These mass limits are not accidental; they are fixed by the laws of physics.
Seemingly Endless Variations
But what about the seemingly endless variations in the palette of sunset colors and patterns in the western sky? Doesn’t that run counter to the concept of limited diversity of natural phenomena? Certainly, we all appreciate the beauty of the rosy colorations of clouds illuminated by the rays of the setting sun. However, if we spent a thousand evenings watching the sun set, the sky would simply depict variations on a theme, with amorphous shapes of clouds shaded with gradations of color. Air, clouds, and light all respond according to the laws of nature, limiting their arrangements to forms devoid of specific complexity. Sameness prevails.
Turning our gaze away from sky and stars to the biosphere of Earth, we are struck by diversity unlimited. First, consider the unbelievable range of sizes and forms and behaviors of the millions of species of creatures that have lived on Earth. From tiny diatoms to enormous dinosaurs, from worms to eagles, and ants to people, the variety of living forms on Earth is astonishing compared to the overall sameness of the entire non-living universe.
The stark contrast between our life-filled planet and the rest of the cosmos sharpens further when we take into account all of the things produced by humans throughout our relatively short history on the stage of existence. Clocks, cars, computers, castles, clothing, and can openers. Besides physical creations, humans have produced a fantastic variety of musical and literary forms and coding for computer programs. Our prolific creativity seems limitless, and the scope of what we make spans an enormously broad spectrum with a variety that’s anything but “more of the same.”
The contrast between variety in living forms on just one planet, compared to the vast sameness of the non-living universe suggests a clear-cut distinction between even the simplest living organisms and non-living arrangements of matter. An objective consideration of the flourishing creativity of human endeavors compared to the routine instinctual behaviors of other creatures further suggests a categorical difference between human beings and other creatures.
A Physics Point of View
The exceptionalism manifested by humans, when compared to the predictably limited outcomes of non-living matter, is evidence that the choices and actions of intelligent beings are not governed by the laws of physics. My body is affected by gravity, but the force of gravity doesn’t determine what I eat for lunch. My cellular biochemistry is affected by the electromagnetic force, but my decision about what topic to address in my next article is not. The strong force holds the nuclei of my carbon atoms together, but it in no way determines what color my wife will choose to paint the living room.
How did we become so unnaturally creative? The Judeo-Christian tradition offers one possible answer. The belief that human beings are made in the image of God resonates with the unique creativity expressed by humanity throughout history. The more closely related the created is to the Creator, the more attributes of the one are to be expected in the other.
With our intelligent and creative minds, we can bring together the raw materials of the natural universe into an unlimited variety of forms that are both functional and purposive. Human expression manifests the unnatural attributes of creating art, literature, and technology — outcomes that would never arise by the influence of natural processes alone. Freedom and creativity complement one another; neither will flourish under controlling forces. If the forces of nature governed our thoughts and actions, would we see the vast panoply of creative human expression displayed throughout the history of civilization? It seems not.
Notes
A few more (or fewer) natural elements could be considered, depending on whether one includes those that are extremely rare or have a very short half-life.
The strong force becomes repulsive for inter-nucleon distances less than about 0.5 fermi.
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