Monday, 23 September 2024
In search of Darwinism in the real world.
Decade-Long Study of Water Fleas Found No Evidence of Darwinian Evolution
Science programs tell us that natural selection explains the development of all life forms from the origin of life to the present, from amoebas to humans:
Natural selection is the adaptation strategy of living organisms on Earth. It occurs when they acquire and evolve a trait with time that provides them a distinct advantage for their survival and reproduction over other organisms in the population. Darwin called them “survival of the fittest.”’ (ScienceFacts.net)
It seems so simple. Philosopher Daniel Dennett (1942–2024) called it the single greatest idea anyone ever had. It was perfect for the stark materialism he espoused.
Times Change
Questions accumulate. Research results don’t add up. And dissatisfaction has grown.
Recently, Arizona State University geneticist Michael Lynch headed up a study published in the venerable journal PNAS that comes as close as any to saying the unsayable: Darwinian evolution, as espoused by, say, Dennett and Richard Dawkins, is not on such firm ground. In a world where huge battles have been fought to entrench it in the school systems, findings like that, published in a key journal, may signal a cultural shift.
The study concerns the common water flea (Daphnia pulex):
Daphnia is a good choice for this kind of study because it is very sensitive to changes in its environment. For that reason, it is used to test water purity. It also reproduces quickly, asexually. So if changes in the environment do change Daphnia’s genome, those changes should be detected.
“Little Consistent Selection Pressure”
The researchers analyzed DNA from 1,000 Daphnia over a decade and did not find evidence of Darwin’s natural selection happening as described. Their findings are phrased in careful science news media prose:
The multi-year, genome-wide analysis of nearly 1,000 genetic samples from a Daphnia pulex population shows that most genetic sites experience varying selection, with an average effect close to zero, indicating little consistent selection pressure over different times and selection spread across many genomic regions.
These findings challenge the usual understanding of genetic diversity and divergence as indicators of random genetic drift and selection intensity.
The study’s Abstract is unusually blunt:
Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multigenerational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a 10-y population-genomic survey of the microcrustacean Daphnia pulex … These results suggest that interannual fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the further development of theoretical expressions for the interpretation of population-genomic data.
The science media release says something else that is quite interesting:
These findings challenge the traditional belief that measuring genetic diversity (the range of different traits in a population) and genetic divergence (the differences between populations) can easily show how natural selection is consistently operating. Instead, natural selection seems to operate with greater subtlety and complexity than previously thought.
“Greater Subtlety and Complexity”?
The whole point of claims for Darwinian evolution is to eliminate subtlety and complexity. To show that merely random mutations in response to environmental changes can create everything from the organized complexity of the beehive to the nearly unfathomable human mind. And the researchers did not find these random but creative mutations.
Since we are here anyway, what is the origin of complexity and subtlety? Do they not suggest a mind in or behind the universe?
To say that “natural selection seems to operate with greater subtlety and complexity than previously thought” is a polite way of saying that Darwinian evolution is not a correct interpretation of the history of life. Culturally, that is very interesting. It means that the only theory permissible in U.S. school systems may not be a correct interpretation of nature.
Sunday, 22 September 2024
The fuse of the cambrian explosion?
Fossil Friday: Update on the Dubious Nature of the Precambrian Gabonionta
In a Fossil Friday article last year (Bechly 2023) I discussed the dubious status of an assemblage of alleged Precambrian macrofossils from West Africa that have been informally called Gabonionta. Meanwhile, two new articles on the subject have been published, so that I here present an updated and expanded version of my article.
“According to conventional thinking, unequivocal evidence for eukaryotic fossils first appeared in the geological record some 1700–1600 million years ago” (Chi Fru et al. 2024). However, in 2008 the Moroccan-French geologist Prof. Abderrazak El Albani from the University Poitiers discovered strange three-dimensionally preserved radial structures in Proterozoic rocks of the Francevillian Formation in the West African country Gabon, which are believed to be about 2.1 billion years old. The ear-shaped structures of up to 6.7 inch size were interpreted as earliest fossil evidence for oxygen-respiring, multicellular eukaryotic life forms and were published two years later in the prestigious journal Nature (El Albani et al. 2010, Maxmen 2010).
Somewhat More Cautious
This original description was somewhat more cautious than the later public presentation of the discovery. The authors said:
We consider it most likely that these structures represent fossilized colonial organisms … it is also possible that they represent colonial eukaryotes. … Although we cannot determine the precise nature and affinities of the 2.1-Gyr macroorganisms from the Francevillian B Formation of Gabon, we interpret these fossils as ancient representatives of multicellular life, which expanded so rapidly 1.5 Gyr later.
In 2014, these findings were first presented to the general public with a special exhibition titled “Experiment Life: The Gabonionta” opened in March 2014 at the Natural History Museum in Vienna (), which also featured a 40-minute documentary film by the University of Poitiers about the discovery. This exhibition was accompanied by a sensationalist media campaign, which included fancy headlines such as: “Gabonionta: sensational discovery in Vienna” (ORF 2014), “Gabonionta, the little revolutionaries of evolution” (Vosatka 2014), or “Gabonionta: How multicellular organism tried to conquer the Earth” (Anonymous 2014).
Remarkable and Highly Unusual
It is remarkable and highly unusual in bioscience that the new taxon Gabonionta was never formally described as scientific name, but only used informally in public presentations and press releases. While El Albani refrained from formally naming the fossils, the new name Gabonionta was first introduced by the head of the paleontology department, Dr. Matthias Harzhauser, on occasion of the mentioned special exhibition at the Natural History Museum of Vienna. Therefore, it is commonly thought that this name Gabonionta, which designates a supposed independent and extinct branch of multicellular life, is not taxonomically valid because it was not properly described according to the international rules of nomenclature. However, this is not true, because these rules do not apply to higher taxa above the family group level. Even if this name was only used in popular science publications, it is as scientifically valid and available just as other higher taxonomic names such as Eukaryota or Metazoa.
Anyway, there are more important issues with this discovery: other experts such as the late great German paleontologist Prof. Adolf Seilacher remained highly sceptical about the interpretation and suggested that the structures rather represent only pseudo-fossils formed by abiotic pyrite crystals during the diagenesis of the rocks. El Albani et al. (2014) responded to this critique and objected that not all of the fossils are pyritized and that the fossils formed at the same time as the sediment and therefore could not have been produced later by metamorphic processes. However, the initial critique was later strongly corroborated by the discovery of very similar structures from 1.1 billion year old sediments of Lake Michigan that were described by the authors as inorganic concretions (Anderson et al. 2016). Therefore, Javaux & Lepot (2018) remarked that “the identity of these macrostructures remains unknown and their biogenicity is questionable”.
Just a year later, El Albani et al. (2019) defended the organic origin and syngenicity of some other alleged fossils from the Francevillian Formation, and boldly suggested that they were analog to “the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds.” This cannot be so easily dismissed, as this publication includes among its co-authors some world renowned experts such as Drs. Stefan Bengtson, Luis Buatois, and Gabriela Mangano. Nevertheless, other experts remained very much unconvinced. More recently, Fakhraee et al. (2023) again came to the devastating finding that these structures could rather represent abiotic concretions and synaeresis cracks. They concluded that “in light of their stratigraphic age, unusual morphology, and the relative rarity of these features, a eukaryote affinity for these features—or affinity with analogously complex multicellular organisms — remains uncertain.” It looks like the dubious name Gabonionta may not even refer to any organism that ever existed. The scientists simply made up a new domain of life, based on nothing but inorganic patterns in ancient rocks.
Nothing But Hype?
Is there any other evidence that this sensational discovery was nothing but hype? Sure there is: after the 2014 media circus nobody ever published any primary research again about these “fossils” and the mysterious Gabonionta, at least until last year (see below). Even in their newer papers about the Francevillian Biota, El Albani and his colleagues only described lenticular structures produced by agglutinated protists (Lekele Baghekema et al. 2017, Reynaud et al. 2017, El Albani et al. 2019, 2023), but no longer promoted the presence of truly multicellular organisms. The silence was deafening!
Even, the mentioned two most recent works on the assumed Francevillian fossils, which appeared after my first article on this subject, again only defended their biogenic origin and eukaryotic nature. Ossa Ossa et al. (2023) did not base their conclusions on a study of the fossil structures but on geochemical evidence from Zinc enrichment, which could be consistent with eukaryotic metabolism. However, they openly admitted that “geochemical evidence presented here also cannot resolve the exact type of eukaryotic organisms that inhabited the Francevillian basin, i.e., colonies of multiple cells or individual, large complex multicellular organisms.” Moreover, there is no independent confirmation yet that the enrichment of Zinc isotopes could not be alternatively better explained with inorganic processes or prokaryotic microbial activity. After all, these structures are pyritized, which is quite typical for bacterial metabolic activity during fossilization (Janssen et al. 2022). Ossa Ossa et al. devote a whole lengthy chapter of their discussion to the question if the Zinc enrichment is based on prokaryotic or eukaryotic metabolic processes, but in the last paragraph they have to admit that:
However, it is important to emphasize here that studies of Zn isotope fractionation by eukaryotes have been focused exclusively on modern photosynthetic eukaryotes. This leaves the uncertainty whether strong enrichment in light Zn isotopes represents a distinct trait of the whole eukaryotic domain and whether the Francevillian Group fossilized structures represent photosynthetic or non-photosynthetic eukaryotes.
Indeed, Ossa Ossa et al. are careful to conclude that their data only “may [my emphasis] point to their eukaryotic rather than prokaryotic affinity” and “once confirmed [my emphasis], this would provide a critical calibration point for eukaryogenesis.”
The Usual Evolutionist Word Salad
The newest study by Chi Fru et al. (2024), which has Dr. El Albani as senior author, did not look at the alleged fossils either, but instead found a correlation of the Francevillian Formation with a “previously unrecognized local pulse in dissolved seawater P concentration, of comparable magnitude to Ediacaran seawater levels”, which seems to have been caused by “an episode of intense submarine hydrothermal alteration of a nutrient-rich seafloor reservoir”. The authors interpret this slim data point as evidence that “hydrothermal seawater eutrophication triggered local macrobiological experimentation in the 2100 Ma Paleoproterozoic Francevillian sub-basin” and “nutrient enrichment initiated localized emergence of large colonial macrofossils in the Franceville sub-basin.” In spite of these weak speculations based on highly circumstantial evidence, the new study was sold to the public in a press release titled “complex life on Earth began around 1.5 billion years earlier than previously thought” (Cardiff University 2024). If you read the original study you will find the usual evolutionist word salad of “may have”, “could have”, “likely have”, “possibly reflects”, and “might explain”. Not exactly the usual vocabulary of hard science.
Here is what I tentatively suggest is more likely what really happened: a surplus of nutrients (such as phosphates) triggered a lot of microbial activity that resulted in different concentrations of elements and the formation of pseudo-fossils. Maybe some of the protists already were eukaryotic and maybe some of them formed colonial aggregations, or maybe not, we have no clue. What we definitely do not find here is any credible evidence for an evolutionary transition to genuine multicellular eukaryotes, as was initially claimed with the overhyped discovery of the Gabonionta.
References
Anderson RP, Tarhan LG, Cummings KE, Planavsky NJ, Bjørnerud M 2016. Macroscopic structures in the 1.1 Ga continental Copper Harbor Formation: Concretions of fossils? Palaios 31(7), 327–338. DOI: https://doi.org/10.2110/palo.2016.013
Anonymous 2014. Gabonionta: Wie Mehrzeller versuchten, die Erde zu erobern. OÖNachrichten March 8, 2014. https://www.nachrichten.at/panorama/weltspiegel/Gabonionta-Wie-Mehrzeller-versuchten-die-Erde-zu-erobern;art17,1323424
Bechly G 2023. Fossil Friday: How an Austrian Scientist Concocted a New Domain of Life called Gabonionta. Evolution News June 2, 2023. https://evolutionnews.org/2023/06/fossil-friday-how-an-austrian-scientist-concocted-a-new-domain-of-life-called-gabonionta/
Cardiff University 2024. Complex life on Earth began around 1.5 billion years earlier than previously thought, new study claims. Phys.org July 29, 2024. https://phys.org/news/2024-07-complex-life-earth-began-billion.html
Chi Fru E, Aubineau J, Bankole O, Ghnahalla M, Soh Tamehe L & El Albani A 2024. Hydrothermal seawater eutrophication triggered local macrobiological experimentation in the 2100 Ma Paleoproterozoic Francevillian sub-basin. Precambrian Research 409: 107453, 1–17. DOI: https://doi.org/10.1016/j.precamres.2024.107453
El Albani A, Bengtson S, Canfield DE et al. 2010. Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago. Nature 466(7302), 100–104. DOI: https://doi.org/10.1038/nature09166El Albani A, Bengtson S, Canfield DE et al. 2014. The 2.1 Ga Old Francevillian Biota: Biogenicity, Taphonomy and Biodiversity. PLoS ONE 9(6):e99438, 1–18. DOI: https://doi.org/10.1371/journal.pone.0099438
El Albani A, Mangano MG, Buatois LA, Bengtson S, Riboulleau A, Bekker A, Konhauser K, Lyons T, Rollion-Bard C, Bankole O, Lekele Baghekema SG, Meunier A, Trentesaux A, Mazurier A, Aubineau J, Laforest C, Fontaine C, Recourt P, Chi Fru E, Macchiarelli R, Reynaud JY, Gauthier-Lafaye F & Canfield DE 2019. Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago. PNAS 116(9), 3431–3436. DOI: https://doi.org/10.1073/pnas.181572111
El Albani A, Konhauser KO, Somogyi A et al. 2023. A search for life in Palaeoproterozoic marine sediments using Zn isotopes and geochemistry. Earth and Planetary Science Letters 612:118169, 1–13. DOI: https://doi.org/10.1016/j.epsl.2023.118169
Fakhraee M, Tarhan LG, Reinhard CT, Crowe SA, Lyons TW & Planavsky NJ 2023. Earth’s surface oxygenation and the rise of eukaryotic life: Relationships to the Lomagundi positive carbon isotope excursion revisited. Earth-Science Reviews 240: 104398. DOI: https://doi.org/10.1016/j.earscirev.2023.104398
Janssen K, Mähler B, Rust J, Bierbaum G & McCoy VE 2022. The complex role of microbial metabolic activity in fossilization. Biological Reviews 97(2), 449–465. DOI: https://doi.org/10.1111/brv.12806
Javaux EJ & Lepot K 2018. The Paleoproterozoic fossil record: Implications for the evolution of the biosphere during Earth’s middle-age. Earth-Science Reviews 176, 68–86. DOI: https://doi.org/10.1016/j.earscirev.2017.10.001
Lekele Baghekema SG, Lepot K, Riboulleau A, Fadel A, Trentesaux A & El Albani A 2017. Nanoscale analysis of preservation of ca. 2.1 Ga old Francevillian microfossils, Gabon. Precambrian Research 301, 1–18. DOI: https://doi.org/10.1016/j.precamres.2017.0
Maxmen A 2010. Ancient macrofossils unearthed in West Africa. Nature News June 30, 2010. DOI: https://doi.org/10.1038/news.2010.323
NHM 2014. Experiment Life – the Gabonionta. Press release March 7, 2014. ORF 2014. „Gabonionta“: Sensationsfund in Wien. ORF.at March 11, 2014. https://wien.orf.at/v2/news/stories/2635417/
Ossa Ossa F, Pons M-L, Bekker A, Hofmann A, Poulton SW, Andersen MB, Agangi A, Gregory D, Reinke C, Steinhilber B, Marin-Carbonne J & Schoenberg R 2023. Zinc enrichment and isotopic fractionation in a marine habitat of the c. 2.1 Ga Francevillian Group: A signature of zinc utilization by eukaryotes? Earth and Planetary Science Letters 611: 118147, 1–13. DOI: https://doi.org/10.1016/j.epsl.2023.118147
Reynaud J-Y, Trentesaux A, El Albani A et al. 2017. Depositional setting of the 2·1 Ga Francevillian macrobiota (Gabon): Rapid mud settling in a shallow basin swept by high-density sand flows. Sedimentology 65(3), 670–701. DOI: https://doi.org/10.1111/sed.12398
Vosatka M 2014. Gabonionta, die kleinen Revolutionäre der Evolution. DerStandard March 11, 2014. https://www.derstandard.at/story/1392687847479/gabonionta-die-kleinen-revolutionaere-der-evolution
JEHOVAH's technology vs. Darwinism
Challenges to the Evolutionary Origins of the Glycolytic Pathway
The purpose of cellular respiration is to convert the energy stored in glucose into adenosine triphosphate (ATP), the primary energy currency of the cell. Cellular respiration occurs in three main stages. Glycolysis involves the breakdown of glucose into pyruvate, producing a small amount of ATP. The citric acid cycle further breaks down pyruvate into carbon dioxide, generating NADH and FADH2. The final step of cellular respiration is the electron transport chain and oxidative phosphorylation, which produce a large amount of ATP, as well as water as a byproduct. In a series of articles, I will discuss features of cellular respiration that provide evidence of intelligent design. In this first installment, I will consider the problem of causal circularity as it pertains to the utilization of ATP in glycolysis.
The first step in cellular representation (glycolysis) is represented by the figure at the top. Glycolysis is ubiquitous across all living organisms. As shown in the figure, glycolysis involves the conversion of glucose, through a series of intermediates, to pyruvate. This pyruvate is then transported into the mitochondria where it is converted into acetyl-CoA by the enzyme pyruvate dehydrogenase. This process also produces NADH and releases one molecule of carbon dioxide (CO2). The acetyl-CoA then feeds into the citric acid cycle, where it is further oxidized, generating more NADH, FADH2, and ATP (or GTP).
Incremental Evolution?
Glycolysis has been proposed to be the first biochemical pathway to arise in evolution. Among the reasons for this are the fact that glycolysis is found ubiquitously across the tree of life (so may be inferred to have been present in the last universal common ancestor). Moreover, glycolysis is an anaerobic reaction sequence, and thus is consistent with the absence of oxygen in the primitive Earth environment.
There are, however, significant challenges to a proposed evolutionary origin of the glycolysis pathway. For example, the conversion of glucose to pyruvate involves as many as ten independent enzymes, typically 300 to 500 amino acids in length. It is extremely implausible that ten enzymes with complementary activities could have arisen at essentially the same time. But could the pathway have evolved incrementally, either forwards or backwards? It is generally rejected that glycolysis arose backwards (i.e., with pyruvate being initially available, then its precursor, etc.) since it was not the oxidized pyruvate, but rather sugar, that would have been present in the early Earth environment. Moreover, every intermediate between glycose and pyruvate is phosphorylated (i.e., has one or two of its hydroxyl groups replaced by phosphate). This involves a condensation reaction (where a water molecule is eliminated). Given the difficulties of this type of reaction, it is questionable whether the various intermediates could have emerged abiotically in high enough quantities to facilitate the origin of glycolysis.
The more popular view is that glycolysis evolved incrementally in the forwards direction. This hypothesis, of course, relies on the presumption that the intermediates could have served their own independent utility. However, since glycolysis is generally thought to have arisen extremely early — before additional utility of the intermediates could have arisen — it seems unlikely that the intermediates could have had independent usages.
Causal Circularity
Notice that the process of glycolysis consumes two ATP molecules — one at the glucose to glucose 6-phosphate step (catalyzed by hexokinase) and one at the fructose 6-phosphate to fructose 1,6-bisphosphate step (catalyzed by phosphofructokinase). The overall ATP yield of glycolysis is four (although many more ATPs will be produced later on), while two are consumed — making the net yield two ATPs. In order for ATP to be produced, ATP must first be consumed. This presents a causal circularity challenge to an evolutionary account of the origins of glycolysis. Strikingly, this causal circularity of ATP being required to manufacture more ATP appears to be ubiquitous across life.1 How could the process of glycolysis be established without an initial supply of ATP? Moreover, after the consumption of the first ATP, there are at least five additional steps (each involving its own enzyme) before any further ATP is produced), and nine before there is a net yield of ATP. Given that natural selection lacks foresight, this renders it extremely implausible that the enzymes early on in the glycolytic pathway could have served any benefit in the absence of the enzymes later in the pathway.
Excluding Water
Of the ten enzymes involved in glycolysis, six catalyze reactions that involve a phosphate group transfer. For a phosphate to react with a hydroxyl group of water to form phosphoric acid is just as energetically favorable as for it to react with the hydroxyl or a sugar or ADP. But this would be of no evolutionary advantage. Thus, water must be excluded from the enzymes’ active sites to prevent hydrolytic reactions from occurring. This is achieved through a mechanism involving conformational changes that resemble a “hinge motion.” Initially, the enzyme’s active site assumes an open conformation, allowing the substrate to enter. When the substrate binds to the active site, it induces a conformational change, causing the enzyme to undergo a “closing” motion, with the domains of the enzyme coming together, effectively shielding the active site. This motion not only secures the substrate but also excludes water from entering the active site.
This phenomenon underscores the engineering sophistication — and the degree of amino acid specificity — of these enzymes. Since the exclusion of water is absolutely critical to the occurrence of the appropriate reactions, there would be no use in having a partly formed enzyme (i.e., one that could catalyze the phosphorylation reaction but failed to exclude water). This casts further doubt on the ability of incremental adaptations to account for the glycolytic pathway.
Relationship Between Enzymes?
A further issue is that, if indeed glycolysis were one of the earliest metabolic pathways to evolve, one might expect that at the time of its origin there existed only a small repertoire of enzymes. Moreover, the compounds on which these enzymes act have similar structures. This might lead us to predict that the enzymes involved in glycolysis are evolutionarily related to one another. However, as Keith Webster notes:
Sequence and crystallographic data favor the divergent evolution of for example monophosphoglycerate mutase and diphosphoglycerate mutase, and possibly glyceraldehyde-3-P dehydrogenase and phosphoglycerate kinase from respective common ancestors, but convergence appears to have played a greater role in the development of all of the other 11 enzymes(Fothergill-Gilmore, 1986; Fothergill-Gilmore and Watson,1989). For example, there is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides, with the exception of those mentioned above. Rather, it seems likely that the pathway resulted from the chance assembly of independently evolving enzymes and genes, probably in association with the co-evolution of other functions and linked pathways.
This seems contrary to what might be predicted on an evolutionary account of the origins of glycolysis.
Intelligent Design
Multiple challenges confront an explanation of the glycolytic pathway in terms of unguided evolutionary mechanisms. The complexity and engineering sophistication comport much better with the hypothesis of design. In particular, the causal circularity of ATP being required to make more ATP is difficult to account for by a stepwise evolutionary process. On the other hand, this sort of phenomenon is totally unsurprising on the supposition of the involvement of an intelligent mind.
Notes
Kun A, Papp B, Szathmáry E. Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks.
Genome Biol. 2008;9(3): R51.
Webster KA. Evolution of the coordinate regulation of glycolytic enzyme genes by hypoxia. J Exp Biol. 2003 Sep; 206(Pt 17):2911-22.
The Origin of Life : the simplified version?
Is Assembling Life Like Assembling LEGOs?
I recently read Sara Walker’s new book, Life as No One Knows It: The Physics of Life’s Emergence. The book is addressed to a popular audience, and although the term is barely used, it is really about assembly theory in origin of life research. Walker asks questions like, What is Life? (with no definitive answer), and calls the origin of matter and the origin of life two hard problems in science. Walker mostly tackles the latter through her explication of assembly theory, but with questionable success.
Illustrating with LEGO Blocks
Because the book is aimed at a popular audience, Walker has the difficult task of explaining technical concepts in ways accessible to general readers. Thus, she resorts to the analogy of LEGO blocks to illustrate how complex structures can be assembled by combining simpler structures through a process called selection. Two LEGO blocks can be combined in only a small number of ways. But as a LEGO figure grows larger, the number of ways to attach new blocks quickly inflates. Randomly attaching new blocks to a complex figure will likely not produce a useful or meaningful figure. But a process of selection at each step can cut a path through this inflating combinatorial space toward the creation of a complex and meaningful figure.
According to Walker, this is how life originated. She writes:
The origin-of-life transition occurs when the combinatorial explosion of possible low assembly molecules gets constrained and funneled to select only a subset of possible molecules. Those are scaffolded to build more assembled objects, where those objects in turn build even more assembled ones. It captures the idea that it is objects building slightly more complex objects all the way down. As Lee [Cronin] sometimes says, to solve the origin of life all we need is to generate a simple machine that can build a slightly more complex machine, and so on. (163)
Unfortunately, Walker provides no clue as to what process does all the “constraining,” “funneling,” and “scaffolding.” And what characteristic marks the non-life-to-life transition if we don’t have a good working definition of life in the first place? Moreover, if Lee Cronin is successful in generating a machine capable of generating more complex machines, it will be Cronin’s intelligence standing at the head of this process. What undirected process would be capable of generating the original machine-generating machine? I came away from Walker’s book with far more questions than answers.
Refreshingly Transparent
To Walker’s credit, however, she is refreshingly transparent on one crucial point. In a discussion of homochirality in organic molecules, she freely admits, “We do not know the mechanism by which this property first arose for the life we observe on Earth.” (173) She does go on to state her hope that assembly theoretic principles might eventually “shed new light on what has been a stubborn mystery.” (173) I wouldn’t bet the house on it. And without a naturalistic explanation for homochirality, one can never have a naturalistic explanation for the origin of life.
One other stylistic feature of Walker’s book is worth mentioning. Against all literary convention, she insists on referring to other scientists by their first names after the first reference where she provides the full name. So, we are regularly treated throughout the book to references to conversations Walker has had with people like Paul, or Lee, or Andy, leaving the reader to scramble to remember that these are references to Paul Davies, Lee Cronin, and Andrew Ellington. I don’t know if she is trying to impress the reader by showing that she is on a first-name basis with all these scientists. But this stylistic decision can be confusing and undercuts the professionalism of the book (I’m surprised the publisher allowed it).
In all honesty, I wouldn’t recommend spending time reading Life as No One Knows It. Sara is well-versed in physics and chemistry, yet she is just as clueless on the origin of life as every other scientist trying to explain it in purely naturalistic terms.
Friday, 20 September 2024
Thursday, 19 September 2024
Tuesday, 17 September 2024
Monday, 16 September 2024
Saturday, 14 September 2024
The fossil record vs. The dinosaur to bird narrative.
Fossil Friday: More Evidence That “Feathered Dinosaurs” Were Secondarily Flightless Birds
in one of my recent Fossil Friday articles (Bechly 2024) I elaborated on the neoflightless hypothesis by paleo-ornithologist Alan Feduccia, who convincingly argues that all those feathered bipedal “dinosaurs” are in fact not related to theropod dinosaurs at all but rather represent secondarily flightless birds. I also discussed new evidence that strongly supports this view. Indeed, Agnolin et al. (2019) already commented in their study on the dinosaur-bird transition:
In a ground-breaking proposal, Xu et al. (2011) hypothesized that Archaeopteryx was more nearly related to deinonychosaurians than to birds and that deinonychosaurs become secondarily flightless, a hypothesis previously envisaged by Paul (2002). This hypothesis was supported by a variety of more recent analyses (Godefroit et al., 2013a; Xu et al., 2015; Hu et al., 2018).
Yet Another Discovery
After my article was published (Bechly 2024), I stumbled upon yet another discovery that may lend additional support to Feduccia’s hypothesis:
Just about a decade ago, Godefroit et al. (2013b) described a new supposed theropod dinosaur from the Middle-Late Jurassic Tiaojishan Formation of Liaoning in China. With an estimated age of 160 million years it is 10 million years older than the famous Archaeopteryx. They named the new species Eosinopteryx brevipenna, because of its reduced plumage. The single known specimen (an artist’s depiction of the living animal is above, or see here for the fossil) represents a very well-preserved fossil and almost complete skeleton, which allowed scientists to identify the new taxon as a close relative of the feathered dinosaur Anchiornis.
But this generated a problem: the new dinosaur appeared to be nested deeply in the tree of feathered dinosaurs, so that its reduced plumage cannot be a primitive state but has to be a secondary reduction from a more complete set of feathers. Furthermore, the bone structures of the shoulder articulation showed that the animal was not capable of flapping its arms or wings. This is even more perplexing, as this case of reduced flight adaptations predates the famous missing link Archaeopteryx. Consequently, the press release to the new study (University of Southampton 2013) announced that this fossil “challenges bird evolution theory” and suggested “that the origin of flight was much more complex than previously thought.” The lead author, Dr. Gareth Dyke from the University of Southampton, is quoted with this remarkable admission: “This discovery sheds further doubt on the theory that the famous fossil Archaeopteryx — or “first bird” as it is sometimes referred to — was pivotal in the evolution of modern birds.”
Challenged by Other Evolutionists
Don’t hold your breath, though, waiting for textbooks to be updated accordingly, because this confounding result was quickly challenged by other evolutionist scientists. They claimed that the distinct features of Eosinopteryx could rather be based on variability of the plumage and incomplete preservation of the tail, so that it could even represent the very same species as Anchiornis huxleyi (Pei et al. 2017, Hu et al. 2018, Agnolin et al. 2019). But these studies partly disagreed on certain crucial issues, such as the question of whether the shorter tail in Eosinopteryx is complete and diagnostic (Pei et al. 2017) or not (Hu et al. 2018, Agnolin et al. 2019). Moreover, other experts had recorded further diagnostic differences between the skeletons of two taxa, such as anteriorly convex pubic shafts that are present in Anchiornis but absent in Eosinopteryx (Foth & Rauhut 2017), or the length and shape of the prefrontal and maxillary processes (Guo et al. 2018). Also the cladistic studies by Lefèvre et al. (2014), Guo et al. (2018), Hu et al. (2018), and Pei et al. (2020) did not recover Eosinopteryx as closest relative of Anchiornis, or even rejected the monophyly of Anchiornithidae. One could almost get the impression that the desire to explain away inconvenient results may have guided the interpretations of those scientists, who denied the distinctness of Eosinopteryx.
There are clearly open questions and it definitely looks like the common dino-to-bird narrative has been massively oversold to the public and represents a theory with numerous holes and problems.
References
Agnolin FL, Motta MJ, Brissón Egli F, Lo Coco G & Novas FE 2019. Paravian Phylogeny and the Dinosaur-Bird Transition: An Overview. Frontiers in Earth Science 6: 252, 1–28. DOI: https://doi.org/10.3389/feart.2018.00252
Bechly G 2024. Fossil Friday: New Study Confirms “Feathered Dinosaurs” Were Secondarily Flightless Birds. Evolution News April 5, 2024. https://evolutionnews.org/2024/04/fossil-friday-new-study-confirms-feathered-dinosaurs-were-secondarily-flightless-birds/
Foth C & Rauhut OWM 2017. Re-evaluation of the Haarlem Archaeopteryx and the radiation of maniraptoran theropod dinosaurs. BMC Evolutionary Biology 17: 236, 1–16. DOI: https://doi.org/10.1186/s12862-017-1076-y
Godefroit P, Cau A, Dong-Yu H, Escuillié F, Wenhao W & Dyke G 2013a. A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds. Nature 498(7454), 359–362. DOI: https://doi.org/10.1038/nature12168
Godefroit P, Demuynck H, Dyke G, Hu D, Escuillié F & Claeys P 2013b. Reduced plumage and flight ability of a new Jurassic paravian theropod from China. Nature Communications 4(1): 1394, 1–5. DOI: https://doi.org/10.1038/ncomms2389
Guo X, Xu L & Jia S 2018. Morphological and Phylogenetic Study Based on New Materials of Anchiornis huxleyi (Dinosauria, Theropoda) from Jianchang, Western Liaoning, China. Acta Geologica Sinica – English Edition 92(1), 1–15. DOI: https://doi.org/10.1111/1755-6724.13491
Hu D, Clarke JA, Eliason CM, Qiu R, Li Q, Shawkey MD, Zhao C, D’Alba L, Jiang J & Xu X 2018. A bony-crested Jurassic dinosaur with evidence of iridescent plumage highlights complexity in early paravian evolution. Nature Communications 9(1): 217, 1–12. DOI: https://doi.org/10.1038/s41467-017-02515-y
Lefèvre U, Hu D, Escuillié FO, Dyke G & Godefroit P 2014. A new long-tailed basal bird from the Lower Cretaceous of north-eastern China. Biological Journal of the Linnean Society 113(3), 790–804. DOI: https://doi.org/10.1111/bij.12343
Paul GS 2002. Dinosaurs of the Air: The Evolution and Loss of Flight in Dinosaurs and Birds. The John Hopkins University Press, Baltimore (MD), 472 pp.
Pei R, Li Q, Meng Q, Norell MA & Gao K-Q 2017. New Specimens of Anchiornis huxleyi (Theropoda: Paraves) from the Late Jurassic of Northeastern China. Bulletin of the American Museum of Natural History 411, 1–67. DOI: https://doi.org/10.1206/0003-0090-411.1.1
Pei R, Pittman M, Goloboff PA, Dececchi TA, Habib MB, Kaye TG, Larsson HCE, Norell MA, Brusatte SL & Xu X 2020. Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds. Current Biology 30(20), 4033–4046.e8. DOI: https://doi.org/10.1016/j.cub.2020.06.105
University of Southampton 2013. Discovery of ‘Bird-Dinosaur’ Eosinopteryx Challenges Bird Evolution Theory. SciTechDaily January 24, 2013. https://scitechdaily.com/discovery-of-bird-dinosaur-eosinopteryx-challenges-bird-evolution-theory/
Xu X, You H, Du K & Han F 2011. An Archaeopteryx-like theropod from China and the origin of Avialae. Nature 475(7357), 465–470. DOI: https://doi.org/10.1038/nature10288
Xu X, Zheng X, Sullivan C, Wang X, Xing L, Wang Y, Zhang X, O’Connor JK, Zhang F & Pan Y 2015. A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings. Nature 521(7550), 70–73. DOI: https://doi.org/10.1038/nature14423
Our fingers point to design?
The Formation of Our Digits Points to a Process with Foresight
Have you ever wondered how our fingers and toes form during embryonic development? Our digits are, in fact, sculpted from a paddle-like structure in the embryo through the process of apoptosis — that is, programmed cell death. During early development, the hands and feet begin as solid, webbed structures. Through carefully controlled apoptosis, the tissue between them is eliminated, facilitating the separation of the digits. As one paper put it, “the role of apoptosis can be compared with the work of a stone sculptor who shapes stone by progressively chipping off small fragments of material from a crude block, eventually creating a form.”1 Apoptosis, of course, serves other important biological functions as well — such as eliminating old, damaged, or infected cells.
When cells die as a consequence of acute injury, they tend to swell and burst, releasing their contents into the surrounding tissue. This is known as necrosis, and it can result in an inflammatory response that can be damaging to the cells around them. Death by apoptosis, by contrast, is much cleaner. During apoptosis, the cytoskeleton breaks down and the nuclear envelope disassembles, and the genetic material is broken down into smaller fragments. The surface of the cell is modified such that it attracts macrophages that phagocytose (engulf) the cell before its contents can spill out into the environment and cause damage.
The process of apoptosis is tightly regulated by genetic and biochemical signals, ensuring that the correct number of cells die in the right areas. But how could such a developmental process involving programmed cell death evolve in a gradual, incremental fashion without any awareness of where the target is? This presents a significant obstacle to unguided evolutionary mechanisms. Here, I will give a brief overview of how this remarkable process is regulated and controlled.
Initiation of Apoptosis
The zones of undifferentiated cells between what will become the digits are called interdigital mesenchyme. It is here that apoptosis is initiated by signaling molecules. For example, bone morphogenetic proteins (BMPs) are secreted signaling molecules that are critical for inducing apoptosis in the cells of the interdigital spaces.2 Indeed, knocking out BMP molecules has been shown to result in webbed feet in chickens.3 BMPs are upregulated in the regions between the forming digits, resulting in cellular death and tissue regression.
These BMPs bind to receptors on the surface of target cells in the developing limb bud.4 This, in turn, activates intracellular SMAD proteins, which translocate to the nucleus and regulate the expression of pro-apoptotic and anti-apoptotic genes.5 For instance, pro-apoptotic genes such as Bax and Bak (discussed later) are upregulated. Anti-apoptotic genes, such as Bcl-2, are also downregulated. This facilitates cell death in areas where tissue needs to be removed.
The activity of BMPs is regulated by antagonists, such as Noggin, which binds directly to BMPs, forming a complex that inhibits them from interacting with their receptors. This ensures that apoptosis only occurs in the interdigital spaces, while preserving the cells that will form the digits.6
Executioner Caspases
A family of proteases called caspases comprise the molecular machinery responsible for apoptosis.7,8 These proteases are initially produced as inactive precursors known as procaspases. In response to apoptosis-inducing signals, they are activated. Executioner caspases are responsible for dismantling essential cellular proteins — these are themselves cleaved (and thereby activated) by initiator caspases. One executioner caspase targets for destruction the lamin proteins that comprise the nuclear lamina, resulting in its disintegration.9 This facilitates the entry of the nucleases into the nucleus where they degrade the cell’s DNA. Other targets of executioner caspases include the cytoskeleton10 and other critical cellular proteins.
Execution of the Death Program: The Intrinsic Pathway
There are two ways in which the cell’s death program can be initiated — the extrinsic and intrinsic pathways. The extrinsic pathway is initiated by external signals through the binding of ligands to death receptors on the cell surface. The intrinsic pathway is triggered by signals from within the cell itself. Since the intrinsic pathway is associated with digit formation, it will be my focus here.
In nucleated animal cells, inactive procaspases roam, waiting for a signal to activate the death program and kill the cell. Unsurprisingly, then, the activity of caspases must be very carefully controlled. This presents another conundrum for their origins — how could they arise without a mechanism in hand for holding them in check until required?
The Bcl2 family of proteins is responsible for regulating caspase activation.11 Some of these proteins promote activation of caspases and apoptosis, while others negatively regulate these processes. Two essential proteins for promoting cell death are Bax and Bak.12 These proteins trigger the release of cytochrome c from the mitochondria. Other Bcl2-family proteins sequester apoptosis by inhibiting Bax and Bak from releasing cytochrome c.13 Critical to a cell’s survival is the balance between the activities of the pro-apoptosis and anti-apoptosis Bcl2-family members.
Image credit: David Goodsell, CC BY 3.0 https://creativecommons.org/licenses/by/3.0, via Wikimedia Commons
Upon release of cytochrome c from the mitochondria, the cytochrome c molecules bind to Apaf-1 (apoptotic protease activating factor 1).14 Apaf-1 has a specific region called the WD40 repeat domain that interacts with cytochrome c.15,16This binding induces a conformational change in Apaf-1, which allows it to oligomerize. The Apaf-1 monomers thus assemble into a large heptameric complex called the apoptosome (shown in the figure above). This wheel-like structure serves as a scaffold for further recruitment of procaspase-9 molecules.17 Within the apoptosome, the proximity of multiple procaspase-9 molecules results in their autocleavage and activation.18 This induces a caspase cascade (involving the activation of downstream effector caspases, such as caspase-3 and caspased-7), ultimately resulting in programmed cell death.19
The Need for Foresight
We began by comparing the role of apoptosis in digit formation to a stone sculptor, chipping off tiny fragments from a block with a view towards ultimately creating a form. Of course, an actual stone sculptor has a vision of the final form — the ability to visualize a distant outcome. Conversely, a feature of natural selection is that it lacks foresight, or any awareness of complex end goals. How can a mindless evolutionary process select for a process of carefully regulated programmed cell death during development, without knowledge of the target? It would seem that any process capable of producing this mechanism would have to possess intelligence and foresight — characteristics uniquely associated with a conscious mind.
Notes
Suzanne M, Steller H. Shaping organisms with apoptosis. Cell Death Differ. 2013 May;20(5):669-75.
Storm EE, Kingsley DM. GDF5 coordinates bone and joint formation during digit development. Dev Biol. 1999 May 1;209(1):11-27.
Zou H, Niswander L. Requirement for BMP signaling in interdigital apoptosis and scale formation. Science. 1996 May 3;272(5262):738-41. doi: 10.1126/science.272.5262.738. PMID: 8614838.
Ovchinnikov DA, Selever J, Wang Y, Chen YT, Mishina Y, Martin JF, Behringer RR. BMP receptor type IA in limb bud mesenchyme regulates distal outgrowth and patterning. Dev Biol. 2006 Jul 1;295(1):103-15.
Gomez-Puerto MC, Iyengar PV, García de Vinuesa A, Ten Dijke P, Sanchez-Duffhues G. Bone morphogenetic protein receptor signal transduction in human disease. J Pathol. 2019 Jan;247(1):9-20.
Guha U, Gomes WA, Kobayashi T, Pestell RG, Kessler JA. In vivo evidence that BMP signaling is necessary for apoptosis in the mouse limb. Dev Biol. 2002 Sep 1;249(1):108-20.
McIlwain DR, Berger T, Mak TW. Caspase functions in cell death and disease. Cold Spring Harb Perspect Biol. 2013 Apr 1;5(4):a008656. Erratum in: Cold Spring Harb Perspect Biol. 2015 Apr 01;7(4):a026716..
Cohen GM. Caspases: the executioners of apoptosis. Biochem J. 1997 Aug 15;326 ( Pt 1)(Pt 1):1-16.
Gheyas R, Menko AS. The involvement of caspases in the process of nuclear removal during lens fiber cell differentiation. Cell Death Discov. 2023 Oct 21;9(1):386.
Vakifahmetoglu-Norberg H, Norberg E, Perdomo AB, Olsson M, Ciccosanti F, Orrenius S, Fimia GM, Piacentini M, Zhivotovsky B. Caspase-2 promotes cytoskeleton protein degradation during apoptotic cell death. Cell Death Dis. 2013 Dec 5;4(12):e940.Kale J, Osterlund EJ, Andrews DW. BCL-2 family proteins: changing partners in the dance towards death. Cell Death Differ.2018 Jan;25(1):65-80.
Westphal D, Kluck RM, Dewson G. Building blocks of the apoptotic pore: how Bax and Bak are activated and oligomerize during apoptosis. Cell Death Differ. 2014 Feb;21(2):196-205.
Dlugosz PJ, Billen LP, Annis MG, Zhu W, Zhang Z, Lin J, Leber B, Andrews DW. Bcl-2 changes conformation to inhibit Bax oligomerization. EMBO J. 2006 Jun 7;25(11):2287-96.
Kim HE, Du F, Fang M, Wang X. Formation of apoptosome is initiated by cytochrome c-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17545-50.
Hu Y, Ding L, Spencer DM, Núñez G. WD-40 repeat region regulates Apaf-1 self-association and procaspase-9 activation. J Biol Chem. 1998 Dec 11;273(50):33489-94.
Shalaeva DN, Dibrova DV, Galperin MY, Mulkidjanian AY. Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol Direct. 2015 May 27;10:29.
Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. Structure of an apoptosome-procaspase-9 CARD complex. Structure. 2010 May 12;18(5):571-83.
Li Y, Zhou M, Hu Q, Bai XC, Huang W, Scheres SH, Shi Y. Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1542-1547.
Li P, Nijhawan D, Budihardjo I, Srinivasula SM, Ahmad M, Alnemri ES, Wang X. Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell. 1997 Nov 14;91(4):479-89.
Wednesday, 11 September 2024
Tuesday, 10 September 2024
Small volume /Big tech?
Intelligent Design — In Miniature
A recent research award from the European Research Council supports the study of some of the world’s tiniest vertebrates, hoping to unravel what is considered the mystery of animal miniaturization. Small vertebrates may be a thousand times larger than single-cell organisms, but they occupy a region of parameter space that presents uniquely fascinating properties.
Within a single cell, the multitude of interacting organelles are basically large, complex molecules with specific structures allowing them to carry out particular functions. Interactions proceed along the lines of biochemistry. At the size scale of insects, spiders, and small vertebrates, multicellular components form the functioning structure of the living organism. At such miniature size scales formidable engineering challenges are encountered, appreciated within the field of micro-robotics.
Among the contenders for the smallest vertebrates are flea toads.
Just seven millimetres long, flea toads are among the smallest vertebrates on Earth. Despite their diminutive size, their organs and functions hardly differ from animals a thousand times larger. While examples of extreme miniaturisation abound in nature, just how these creatures get so small remains a scientific mystery.
Serious Engineering Challenges
Is it easier to construct a micro-robot or a macro-scale robot? From an engineering point of view, the smaller size scale introduces serious challenges.
Over the past years, the field of miniaturized robotics has rapidly expanded with many research groups contributing to the numerous challenges inherent to this field….However, despite all efforts and many available soft materials and innovative technologies, a fully autonomous system-engineered miniaturized robot (SEMR) of any practical relevance has not been developed yet….A careful examination of current SEMRs that are physically, mechanically, and electrically engineered shows that they fall short in many ways concerning miniaturization, full-scale integration, and self-sufficiency.
Physics principles concerning the mechanical properties of a system change appreciably with increasing miniaturization. Designing a functioning miniaturized system involves more difficulties than simply scaling down the physical size of every component.
As the systems become smaller, the relative forces that act on the system change dramatically, and the robots experience an increase in friction and adhesion. At the same time, weight and inertia gradually become irrelevant. Changes in fluid mechanics and stochastic motion challenge fundamental engineering notions of how mechanical elements move and interact. These physical effects form a crucial factor in designing and operating robots on a small scale.
Ingenious Solutions to Miniaturization
Tiny living creatures abound, demonstrating ingenious solutions to miniaturization that surpass human technological skills. A short list of the challenges that engineers face in trying to make robots the size small-scale life is given below, and includes adequate power, “intelligence,” and sensor-feedback-control mechanisms.3
“One of the challenges in designing capable SEMRs [system-engineered miniaturized robots] is the limited power budget, as existing propulsion methods require significant power, and the energy-storage systems (ESSs) are extremely difficult to downscale into the submillimeter range.”
“However, with miniaturization of the robot’s size, it is also clear that robots lose the ability of on-board intelligence and become limited in functionalities.”
“Current SEMRs have no energy on-board and lack any continuous feedback-controlled sensing, actuation, data processing, and communication.”
Observing a tiny spider that built its web in the corner of a window in my house was what set me to thinking about the amazing design in miniature creatures. Although this little critter had taken up its residence on the inside of the window, I let it alone out of fascination. I had to look closely to even see the spider, barely a millimeter or two in size. And yet it had woven this little web stretching several centimeters across the corner of the windowsill. For comparison, this would be like me using rope to construct a web the size of a football field.
This little arachnid warrior had managed to capture prey in its web (several of their remains could be seen) and presumably nourished itself thereby. Think about the capabilities packed into this tiny creature. It’s mobile and autonomous. It can see its surroundings and make decisions based on that sensory input regarding where to make its web. It manufactures and dispenses the finest web strands — not randomly, but with a specific type of design that can trap other small bugs. It can immobilize its prey and appropriately consume it. It metabolizes its food to generate sufficient energy for mobility, web production, and sensory processing. And it can presumably reproduce itself multifold (although my forbearance with its existence in my house may not extend to cover this circumstance!)
An Advancing Discipline
Even though micro-robotics is an advancing discipline, all the efforts of specialists in this field have not come close to manufacturing anything with the capabilities of this one little spider. The smallest spiders discovered on Earth measure only about 0.4 mm across, perhaps five times smaller than my little window dweller. Packing the many sophisticated capabilities of a spider into such a miniscule package speaks of the highest level of engineering design.
Notes
Vineeth Kumar Bandari and Oliver G. Schmidt, “System-Engineered Miniaturized Robots: From Structure to Intelligence,” Adv. Intell. Syst. 2021, 3, 2000284.
Vineeth Kumar Bandari and Oliver G. Schmidt, “System-Engineered Miniaturized Robots: From Structure to Intelligence,” Adv. Intell. Syst. 2021, 3, 2000284.
Vineeth Kumar Bandari and Oliver G. Schmidt, “System-Engineered Miniaturized Robots: From Structure to Intelligence,” Adv. Intell. Syst. 2021, 3, 2000284.
Monday, 9 September 2024
Sunday, 8 September 2024
Second Samuel chapter one New World translation study bible.
After Saul’s death, when David had returned from defeating* the A·malʹek·ites, David stayed at Zikʹlag+ for two days. 2 On the third day, a man came from the camp of Saul with his garments ripped apart and dirt on his head. When he approached David, he fell down to the ground and prostrated himself.
3 David asked him: “Where are you coming from?” He replied: “I have escaped from the camp of Israel.” 4 David asked him: “How did things turn out? Please tell me.” To this he said: “The people have fled from the battle and many have fallen and died. Even Saul and his son Jonʹa·than have died.”+ 5 Then David asked the young man who brought him the news: “How do you know that Saul and his son Jonʹa·than are dead?” 6 The young man replied: “By chance I was on Mount Gil·boʹa,+ and there was Saul supporting himself on his spear, and the chariots and horsemen had caught up with him.+ 7 When he turned around and saw me, he called me, and I said, ‘Here I am!’ 8 He asked me, ‘Who are you?’ I replied, ‘I am an A·malʹek·ite.’+ 9 Then he said, ‘Please stand over me and put me to death, for I am in great agony, but I am still alive.’* 10 So I stood over him and put him to death,+ for I knew that he could not survive after he had fallen down wounded. Then I took the crown* that was on his head and the bracelet that was on his arm, and I brought them here to my lord.”
11 At this David took hold of his garments and ripped them apart, and so did all the men who were with him. 12 And they wailed and wept and fasted+ until evening for Saul, for his son Jonʹa·than, for the people of Jehovah, and for the house of Israel,+ because they had fallen by the sword.
13 David asked the young man who brought him the news: “Where are you from?” He said: “I am the son of a foreign resident, an A·malʹek·ite.” 14 Then David said to him: “Why did you not fear to lift your hand to do away with the anointed of Jehovah?”+ 15 With that David called one of the young men and said: “Step forward and strike him.” So he struck him down, and he died.+ 16 David said to him: “Your blood is on your own head, because your own mouth testified against you by saying, ‘I myself put the anointed of Jehovah to death.’”+
17 Then David chanted this dirge* over Saul and his son Jonʹa·than+ 18 and said that the people of Judah should be taught the dirge called “The Bow,” which is written in the book of Jaʹshar:+
19 “The beauty, O Israel, lies slain upon your high places.+
How the mighty have fallen!
20 Do not tell it in Gath;+
Do not announce it in the streets of Ashʹke·lon,
Or the daughters of the Phi·lisʹtines will rejoice,
Or the daughters of the uncircumcised men will exult.
21 You mountains of Gil·boʹa,+
May there be no dew or rain upon you,
Nor fields producing holy contributions,+
Because there the shield of mighty ones was defiled,
The shield of Saul is no longer anointed with oil.
22 From the blood of the slain, from the fat of mighty ones,
The bow of Jonʹa·than did not turn back,+
And the sword of Saul would not return without success.+
23 Saul and Jonʹa·than,+ beloved and cherished* during their life,
And in death they were not separated.+
Swifter than the eagles they were,+
Mightier than the lions.+
24 O daughters of Israel, weep over Saul,
Who clothed you in scarlet and finery,
Who put gold ornaments upon your clothing.
25 How the mighty have fallen in battle!
Jonʹa·than lies slain upon your high places!+
26 I am distressed over you, my brother Jonʹa·than;
You were very dear to me.+
More wonderful was your love to me than the love of women.+
27 How the mighty have fallen
And the weapons of war have perished!”
Saturday, 7 September 2024
The case for uncommon descent?
Fitness Landscapes Demonstrate Perfection in Vertebrate Limbs Resulted from Intelligent Design
In two previous articles (here, here), I summarized Stuart Burgess’s new paper (“Universal optimal design in the vertebrate limb pattern and lessons for bioinspired design”) that demonstrates common features of vertebrate limbs are better explained by design than by common ancestry, and I explained how embryological studies further support the design hypothesis. Here, I will detail how the conclusion of design is also bolstered by studies of evolutionary fitness landscapes.
Tutorial on Fitness Landscapes
A common metaphor for visualizing evolution is a fitness landscape (here, here, here), which is a three-dimensional plot of the fitness of an organism as a function of variables associated with different traits such as hair color, the shape and length of bones, and the efficiency of digesting toxins. The number of variables can be very large, so the values of all the variables are projected onto the x and y axes of the graph. These axes could also represent individuals’ genetic sequences. The z-axis corresponds to an individual’s fitness, which is commonly understood as the probability that it will produce offspring (Figure 1).
Figure 1. Evolutionary Fitness Landscape. The x and y axes represent the values of all trait variables for individuals in a population. The z-axis represents the fitness of an individual as measured by the probability of producing offspring. Populations tend to move uphill as represented by the white arrow-tipped line leading from point (1) to point (2). The path from (1) to (2) could represent an animal’s hair changing from dark grey to white or a fish transforming into an amphibian. © Thomas Shafee, CC BY 4.0, via Wikimedia Commons.
An individual represents a single point on the landscape, a population represents a cluster of points on the landscape, and the genetic variation in the population corresponds to the area or spread of the cluster. The variation can increase through individuals accumulating mutations. The population tends to move uphill since larger z corresponds to individuals producing more offspring (Figure 2).
Figure 2. Population trajectory on a static fitness landscape. Each dot represents an individual in the population. Within the population, the variation in traits represents the area the dots cover. If the fitness landscape does not change, the population typically moves to the top of the nearest fitness peak and then stops. Refresh this webpage to see the animation. © Randy Olson and Bjørn Østman, CC BY-SA 3.0, via Wikimedia Commons
A dynamic landscape will reshape if environmental conditions change, or individual organisms interact with each other in such a way as to alter their reproductive success (Figure 3). In practice, many peaks will remain relatively fixed since they correspond to the operation of traits in any environment an organism might encounter. If a population reaches the top of a static peak, it could remain trapped there for a period or indefinitely
Figure 3. Population trajectory on a dynamic fitness landscape. The fitness landscape changes with time, so the trajectory of the population also changes. For instance, in rainy seasons finches’ beaks could become thinner and longer, while in dry seasons they could become thicker and shorter. Refresh this webpage to see the animation. © Randy Olson and Bjørn Østman, CC BY-SA 3.0, via Wikimedia Commons
The extent to which a population can traverse a landscape depends on whether the landscape is smooth or rugged. A smooth landscape contains relatively few peaks with gently rising paths connecting the base of one peak to the summit of another (Figures 1 and 4d). An organism could potentially traverse significant distances along such a landscape, resulting in large evolutionary change. In contrast, a rugged landscape contains a multitude of sharp peaks (Figure 4f). Populations will tend to spend most of their time trapped on a local peak, so evolutionary change will be largely confined to minor modifications to existing traits.
The extent to which a landscape is smooth or rugged depends significantly on whether mutations interact additively (Figure 4a) or epistatically (Figure 4c). If they interact additively, the fitness change of two mutations roughly corresponds to the fitness changes of each individual mutation added together. If they interact epistatically, the fitness change from two mutations might be negative (i.e., detrimental) even if the fitness change from each individual mutation is positive (i.e., beneficial). Additive interactions lead to smooth landscapes supporting evolutionary change while epistatic interactions lead to rugged landscapes greatly limiting evolutionary change.
Figure 4. Relationship between mutation interactions and fitness landscapes. The top figures represent the fitness for different combinations of two versions of two genes. Genes a and b are the original genes. Gene A is a mutated version of gene a, and gene B is a mutated version of gene b. a) Mutation interactions are additive, so the fitness change from both mutations is approximately the sum of the fitness change from each individual mutation added together. b) Mutation interactions are partially additive and partially epistatic since the fitness of aB is greater ab, and AB is greater than aB, but Ab is not greater than ab. c) Mutation interactions are epistatic since AB’s fitness is less than aB’s and Ba’s fitness. d) Fitness landscape for additive interactions is a smooth peak. e) Fitness landscape for partially additive and partially epistatic interactions is partially rugged. f) Fitness landscape for epistatic interactions is highly rugged. © Thomas Shafee, CC BY 4.0, via Wikimedia Commons
Assessing the Evidence
Empirical studies and theoretical analyses consistently demonstrate that the fitness landscapes associated with complex traits are highly rugged. For instance, paleobiologist Graham J. Slater (2022) in his article “Topographically distinct adaptive landscapes for teeth, skeletons, and size explain the adaptive radiation of Carnivora (Mammalia)” analyzed the landscape for carnivores based on 16 trait variables. He concluded that the fitness landscape is rugged with multiple fitness peaks:
I found evidence of an early partitioning of mandibulo-dental morphological variation in Carnivora (Mammalia) that occurs on an adaptive landscape with multiple peaks, consistent with classic ideas about adaptive radiation.…The dietary adaptive landscape estimated from the first two mandibulodental PC axes by the PhylogeneticEM algorithm contains 21 peaks that are distinct from the ancestral regime.
The ruggedness of landscapes associating with the mechanical design of anatomical structures is further supported by studies on the use of evolutionary algorithms to assist improving robotic designs. Doncieux et al. (2011) observe in their article “Evolutionary Robotics: Exploring New Horizons”:
The difficulty of a problem often arises with the complexity of the fitness landscape: while a smooth, convex fitness landscape with no noise will be quite easy to deal with, most of the problems from the real world often comes with multimodal, noisy fitness landscapes that feature neutrality regions. The direct consequence is that search may often get stalled, would it be at the very beginning of the algorithm execution (i.e. a boostrap problem) or during the course of evolution (i.e. premature convergence), with no hint on how to escape a local optimum or on how to direct the search within a region where all neighboring candidate solutions are equally rewarded.
The ruggedness appears even more extreme for landscapes based on genetic sequences. Visser and Krug (2014) summarize in their paper “Empirical fitness landscapes and the predictability of evolution” how mutational studies demonstrate that fitness landscapes are rugged even for genetic changes confined to small sections of DNA:
At the small genomic scales considered so far, it is observed that sign epistasis is common, which reduces the number of accessible mutational pathways and leads to rugged landscapes with multiple fitness peaks.
Only a limited number of paths are accessible, and those paths require series of mutations that either do not increase the fitness (aka neutral mutations) or reduce it.
The Implications
The technical literature from paleobiology, robotics, and genetics uniformly concludes that fitness landscapes are generally highly rugged even when only a small portion of relevant variables are studied. The ruggedness and constraints on viable paths is only believed by evolutionary theorists to increase with the number of contributing variables and interactions, and the landscape in sequence space for vertebrate limbs represents a set of variables and interactions of enormous size.
These observations present two dire challenges to undirected evolutionary models considering Burgess’s study. First, the vast number of suboptimal local peaks in the fitness landscape precludes any possibility of an evolutionary search ever discovering the perfection of design consistently seen in vertebrates and in other taxa. Second, the constraints on viable paths require a portion of any trajectory along the landscape to include multiple specific neutral and harmful mutations. Yet the timescales required for obtaining coordinated neutral and deleterious mutations is prohibitively long (here, here).
Compounding the challenge, the fitness landscape is only rugged in regions near existing limb designs. The landscape between these regions represent vast seas of nonviable intermediates (here, here, here, here). The only plausible explanation for the perfection of design observed in vertebrate limbs is that a mind engineered them, for only a mind can choose highly optimized solutions out of a sea of possibilities.
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