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.

A miracle of biblical proportions

 

Degrowth?

 

Continuing to massage the record?

 Fossil Friday: Homo rudolfensis, Another Contentious Homo

Gunter Bechly

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

There is no meritocracy?:pros and cons.

 

More on how we can all be intellectuals.

 

DNA: a brief history

 

Capitalism vs. democracy?

 

On psychology's replication issue.

 

Following the science is not as straightforward as you think

 

On the science's replication issue.

 

How anyone can become an intellectual

 

The dragon: time to dance or duel?: pros and cons.

The narrative re: race ; Pros and cons.

 

Origin of life science a worthy foe? Pros and Cons.

 

The God the Son is a thing?:Pros and Cons.

 

Climate Apocalypse Now?: Pros And Cons.

 

There is more than enough guilt to go around

 

Let's welcome our AI overlords? Pros and Cons.

 

Wind energy pros and cons.

 

Time for a divided states of America?: Pros and cons.

 

Eliminating poverty by eliminating the poor?

 

A Pax Americana? Pros and cons.

 

On the anti-Darwinian bias of the natural law.

Intelligence Is Unnatural, and Why That Matters

Eric Hadin 

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.

Bacteria: evolving/devolving/revolving?

 

Still the next big thing?

 

A smaller economy is our only hope?

 

Missing links aplenty?

 Long Necks in Sauropod Dinosaurs — By Neo-Darwinism or Intelligent Design?

Wolf-Ekkeard Lonnig

Editor’s note: We are delighted to direct readers to a new paper by geneticist Wolf-Ekkehard Lönnig, “A Brief Note on the Multiple Independent Origins of the Long Necks in Sauropod Dinosaurs: Neo-Darwinism or Intelligent Design?” What follows is the paper’s abstract:

Convergence is a deeply intriguing mystery, given how complex some of the structures are. Some scientists are skeptical that an undirected process like natural selection and mutation would have stumbled upon the same complex structure many different times.

MEYER, MINNICH, MONEYMAKER, NELSON, SEELKE1

Now it is precisely the phenomenon of convergence that poses further major problems for neo-Darwinism. For if the one-time emergence of completely “adapted” organs or characteristics through selection of random mutations can hardly be explained, the multiple formation of similar organs elutes the neo-Darwinian interpretation even further.

HENNING KAHLE2

Abstract

The phenomenon of complex convergences by selection of random mutations is “a deeply intriguing mystery” and “poses further major problems for neo-Darwinism,” because “if it is highly improbable for a complex solution to evolve once, ‘convergent evolution’ only exacerbates the improbability.” In contrast, “what we do know […] is that intelligence can take a solution to a problem and apply it in different circumstances over and over again” (see references in the text). I have chosen 20 examples (of at least 36 according to D’Emic 2023) of such long-necked sauropod dinosaurs and shown and discussed them in the article below.

Chronological occurrence of the 20 genera distributed in 9 families of the sauropod dinosaurs mentioned and shown in the present article. Note please that 5 and 4 of the genera arose almost simultaneously. And “nearly all did arise independently” (D’Emic, mail 26 June 2023 to W.-E. L.). Figure by Roland Slowik (Dietzenbach, Germany) for the present article (20 June 2023).

Now, the origin of the ingeniously intricate long necks (and their correspondingly fine-tuned body anatomy) in sauropod dinosaurs has been postulated to have arisen more than 35 times independently of each other by selection of random mutations. The improbability that such transformations having happened by natural selection of random or accidental or haphazard DNA mutations is again being multiplied almost unimaginably. The improbability of neo-Darwinian evolution thus becomes virtually immeasurable. How do our Darwinian friends react to such objections?

Well, they presuppose their evolutionary worldview as sacrosanct, unassailable, and irrefutable. They then argue that the origin of such sophisticated features must be so very easy, so utterly simple, that they can evolve even many dozens of times independently of each other almost everywhere in the realm of living beings.3 I met that “explanation” first in an article by Mayr and Salvini-Plawen. My comment: Hats off for such naïvety.

Comparing ID with Neo-Darwinism

Applying Dembski’s Explanatory Filter to this question, we get the following answers:

Law: There is no law that produces long necks inevitably under any defined ecological conditions.

Vast improbability: Fulfilled — chance to be excluded.

Specification: Fulfilled.

In comparing neo-Darwinism with the theory of intelligent design, we find the latter to be definitely the superior explanation.

Read the rest at, “A Brief Note on the Multiple Independent Origins of the Long Necks in Sauropod Dinosaurs: Neo-Darwinism or Intelligent Design?”

The worst political system,(except for all the others)?

 

Why alternatives to college should get equal time.

 

Indoctrination is trumping education?

 

Correcting professor Dave on "Darwin devolves"

 Answering Farina on Behe’s Work: Darwin Devolves

Jonathan McLatchie

In three previous articles (here, here, andhere ), I began a series of four responses to You-Tuber “Professor Dave” Farina’s video review of Michael Behe’s three books. In this final post, I will turn my attention to Farina’s comments regarding Darwin Devolves.

Hemoglobin and C-Harlem

In Darwin Devolves, Behe contends that the majority of helpful mutations are deleterious rather than constructive, since there are far more ways to gain an advantage by breaking than by building something. Says the Farina video: 

If Behe had bothered to look at some of the most well-documented examples of evolutionary change, he’d know that this isn’t the case. In fact, he should know this is nonsense based on examples he himself described in his other works. For example, in Edge of Evolution, Behe describes a hemoglobin allele called HbC-Harlem, which, similar to the allele that causes sickle-cell disease, confers resistance to malaria, with, as Behe describes, “the advantages but not the drawbacks of sickle.”

But this “example of evolutionary change” shows precisely the opposite of what Farina wants. As Behe explains in The Edge of Evolution, “Hereditary persistence of fetal hemoglobin (HPFH) is already widespread in Africa, ameliorating the problems of the sickle gene.”1 Surprisingly, however, “the C-Harlem gene, which builds directly on the foundation of the sickle gene and would entirely eliminate the drawbacks of the sickle mutation, has not yet turned up in Africa, where it would do the most good.”2 The reason for this is that the move from regular hemoglobin to C-Harlem would require two co-dependent mutations, whereas the sickle-cell trait requires only one. The probability of getting the sickle-celled trait in any individual is about one in a hundred million. Assuming a population size of a million people, it should thus be expected to arise spontaneously approximately every hundred generations, which is within the reach of evolutionary processes. For the two necessary mutations needed for hemoglobin C-Harlem to occur at the same time, the probability is a hundred million multiplied by a hundred million, which is 1016. As Behe summarizes, “With a generation time of ten years and an average population size of a million people, on average it should take about a hundred billion years for that particular mutation to arise — more than the age of the universe.”3Nonetheless, hemoglobin C-Harlem has arisen, and was first documented relatively recently in New York City.4 But this is because the initial sickle-cell trait was already adaptive, since it conferred resistance to the malarial parasite. Thus, natural selection can preserve the sickle-celled trait (requiring only a single mutation) first and then acquire the second mutation (building on the first), thereby giving rise to the C-Harlem trait, which confers an even greater advantage. It looks like Mr. Farina did not review this example very carefully.

Cit+ in E. coli

As Farina’s second example, he notes,

[Dr. Behe] also describes the aforementioned Cit+ trait in the E. coli of the LTEE [Richard Lenski’s long-term evolution experiment], which has a new metabolic option, without compromising any existing pathways, literally debunking himself yet refusing to acknowledge it.

I have already addressed this example (see here), so I will not belabor the point further. Suffice it to say that Behe discusses Lenski’s work at length in Chapter 7 of Darwin Devolves, and Farina fails to engage with anything Behe writes concerning the long-term evolution experiment.

De Novo Gene Birth

Another complaint in the Farina video is that,

As you are likely beginning to see, creationists [sic] have a sadistic obsession with painting evolution as some kind of destructive force, but to do so they have to ignore a long and expanding list of completely new genes rapidly evolving everywhere we look. There are many papers like this one examining the concept of de novo genes. These are new genes that originate when previously non-expressed DNA becomes protein-coding and preserved via natural selection due to promoters arising near previously non-coding sections of DNA. So, we have a section of DNA that was not a gene, which is now a gene. New genes. We used to think this was rare, but once we figured out how to look for them, by identifying protein-coding sequences that aren’t protein coding in all the most closely related species, we started finding them all over the place.

The review paper Farina cites, by Stephen Branden Van Oss and Anne-Ruxandra Carvunis, notes (as is common in review papers dealing with this subject) that, for a long time, “the consensus view was that virtually all genes were derived from ancestral genes, with Francois Jacob famously remarking in a 1977 essay that ‘the probability that a functional protein would appear de novo by random association of amino acids is practically zero’.”5 But “though de novo gene birth was once viewed as a highly unlikely occurrence, there are now several unequivocal examples of the phenomenon that have been described.”6 In other words, though it was once thought that the origins of fundamentally new genes from non-coding sequences was essentially impossible, the fact that we observe a plethora of taxonomically-restricted genes, rather than being taken as a disconfirmed prediction of evolution, is taken to show that de novo genes can be birthed by evolution quite readily after all. Evolutionary theory, remarkably, is taken to be completely insensitive to disconfirming evidence. 

Moreover, though some examples of taxonomically restricted genes bear some resemblance to non-coding stretches of DNA in related species, this is not so with the majority of cases. Furthermore, there is no convincing mechanistic scenario by which non-coding DNA may be transformed into genes coding for proteins that are ready to fulfil a functional role.

Polar Bears

According to Farina, 

Perhaps the best evidence that Darwin Devolves is nonsense is that Behe had to flat out lie to defend it. In a discussion of Behe’s treatment of documented adaptations in polar bears, Dr. Nathan Lents pointed out that Behe did not accurately represent the findings of a paper he cited, when he claimed that virtually all adaptations that polar bears have to their arctic climate are actually damaging in some way. In response, Behe provided a table from that paper, showing that all the documented mutations are either “possibly damaging” or “probably damaging.” But he must have thought nobody would check up on him, since Dr. Lents showed that Behe sneakily omitted two columns and many rows, and the omitted data, unsurprisingly, tell a very different story… Apart from the two restored columns, look at all those rows that say “benign,” meaning not harmful in effect. You know, the exact opposite of what Behe is claiming?

This claim has been rebutted thoroughly elsewhere (such as here). In brief, Behe nowhere denies that non-adaptive neutral mutations are common in evolution. Rather, his thesis is that the vast majority of positively selectedmutations are damaging, since there are far more ways for an organism to acquire an advantage by breaking something than there are ways to gain an advantage by building something new. In Darwin Devolves, Behe contended that “65 to 83 percent of helpful, positively selected genes are estimated to have suffered at least one damaging mutation.”7 Given that the entire chart from the Liu et al. paper, cited by Behe, is some 47 rows long and 8 columns wide, it made more sense to reproduce only the portion of the chart that was relevant to supporting his point. There is nothing duplicitous here. Behe omitted from the chart the data from the HVar algorithm (instead showing only the results of the HDiv algorithm) and also left out instances where the HDiv algorithm predicted that a mutation was benign. This served Behe’s purpose of confirming for his readers that up to 14 of the 17 genes examined (i.e., 83 percent) were probably or possibly damaging. The instances where a mutation was not predicted to be damaging (i.e., those listed as benign) do not contradict Behe’s thesis, since Behe never denied that many mutations are benign. Indeed, a significant majority of mutations are benign (e.g., the third codon position may be substituted without altering the amino acid sequence). But Behe’s thesis is that the vast majority of adaptive mutations (which make up a minority of mutations overall) are destructive rather than constructive. There is nothing in the chart that invalidates or undermines this thesis.

Conclusion

Farina’s video rebuttal directed at Behe’s work misrepresents Behe at multiple points. Moreover, Farina misreads several papers that he cites in his video, failing to understand how they intersect with Behe’s critiques of evolutionary theory. There is also little that is new to see in his video. Many of his criticisms of Behe have been made before by others and addressed in detail elsewhere. In short, despite Mr. Farina’s smug condescension and patronizing demeanor, he fails to mount a credible critique of Dr. Behe’s thesis.

Notes

Behe MJ, The Edge of Evolution: The Search for the Limits of Darwinism (Free Press, 2007), 29.

Ibid.

Ibid., 110.

Bookchin RM, Nagel RL, and Ranney HM. Structure and properties of hemoglobin C-Harlem, a human hemoglobin variant with amino acid substitutions in 2 residues of the beta-polypeptide chain. Journal of Biological Chemistry 1967; 242:248-255.

Van Oss SB, Carvunis AR. De novo gene birth. PLoS Genet. 2019 May 23;15(5):e1008160.

Ibid.

Behe MJ, Darwin Devolves: The New Science About DNA That Challenges Evolution (HarperOne, 2020), 17.

An interlude