Saturday, 3 June 2023
On confirmation bias re: genetic evidence for Darwinism
BioLogos and Vitellogenin Genes
Recently I have been responding to several articles by evolutionist Dennis Venema. Venema has made various arguments about how genetic evidences strongly support evolution and I have provided rebuttals to those claims. For instance, I explained Here that while Venema discusses evidences that are consistent with evolutionary expectations, he does not list or mention the substantial body of scientific findings that are inconsistent with evolution. This is a problem with the evolution literature: the scientific evidence is too often selectively presented. In fact, I have often seen evolutionists claim that there are no contrary evidences, and that the science fully backs evolution. This sort of confirmation bias presents a roadblock to meaningful discourse on the topic of origins.
Next Venema focused his claim on the specific case of human evolution, and the similarity between the human and chimpanzee genomes. Again, Venema made high claims about the evidence. He concluded: “These observations strongly support the hypothesis that our species arose through an evolutionary process.”
But, in fact, as I explainqed Here, there are several significant problems with this claim. For example, the chimpanzee and human genomes have differing patterns that do not fit evolutionary expectations. There is also a big difference between viruses in the genomes of humans and the other primates. Again, these differences do not fit the expected evolutionary pattern. Furthermore, the chimp-human genome beneficial differences are few and appeals to alternate splicing differences (another big difference between the genomes of humans and the other primates) to evolve humans lead to astronomically improbable pathways.
As always, I explained that the point is not that evolutionary explanations are not possible. Speculative explanations are always possible. Perhaps evolution did this, perhaps it did that. But that does not change the fact that the primate genomes do not “strongly support the hypothesis that our species arose through an evolutionary process,” as Venema and the evolutionists claim.
Next Venema focused even more narrowly on a particular genetic detail: human chromosome two, which he presented as a powerful example of an evolutionary confirmation. And yet as I explained here, not only did Venema not mention several scientific problems with his claim but the claim, even if true, would not demonstrate evolution as evolutionists claim. There is no evolutionary relationship revealed. Even if evolution were true, these data would give us no evidence for it. What was disturbing about this example was Venema’s recounting of a deceptive lecturing strategy he uses in presenting this topic in his class.
Next Venema presented pseudogenes which Venema argued are powerful and compelling evidences for common descent. It is, explained Venema, “one of the strongest pieces of evidence in favor of common ancestry between humans and chimpanzees (and other organisms).” And again, I explained, here and here, that there are several, fundamental, problems with this evolutionary claim.
In this case, however, Venema discussed his underlying religious belief that this evidence is a problem for creationism type theories. Venema was highlighting one of the important beliefs at the foundation of evolutionary thought. This belief, if true, does indeed require evolution to be true. But of course it is not falsifiable.
Vitellogenin genes
Now we move on to Venema’s next Topic , the vitellogenins. Vitellogenin genes are found in a wide range of species and, like most genes, perform multiple functions including helping to provide the nutrients in egg yolks. Also like most genes, the pattern they form amongst the species does not always correspond very well to the expected evolutionary pattern. Of course there are always explanations, and evolutionists draw upon a variety of mechanisms, including lineage-specific events, to explain the vitellogenin genes.
For example, this paper focuses on mosquito vitellogenin genes. It concludes that the genes arose by a series of duplication events, and that the pattern of duplication was different in each mosquito genus. The Paper also uses purifying selection, gene conversion, unequal crossover, and concerted evolution to explain the observed pattern of the mosquito vitellogenin genes, and concludes that these mechanisms must have also worked, independently, in other invertebrate species, and vertebrate organisms as well.
Similarly, this Paper examines the evolution of vertebrate vitellogenins and also draws upon a variety of events and lineage-specific mechanisms. As I have discussed many times, while the basic idea of evolution is that the species share common designs as a consequence of common ancestry, in fact biology is loaded with unique, one-off designs for which evolutionists need to appeal to “lineage-specific” evolution. Consequently evolution can explain a wide variety of observations and patterns, and this applies equally well to the vitellogenins.
Clearly evolutionary theory is fine with a range of patterns when it comes to the vitellogenins. Of course this is true for molecular, and morphological, designs in general, as we have seen many times. Designs can fall into an evolutionary common descent pattern, or not.
The advantage of this flexibility is that evolutionary theory can explain a wide range of observables. The disadvantages, however, are many. The theory becomes less parsimonious. It becomes more resistant to falsification. And it loses its evidential arguments. If a theory can explain A, and B, and C, … and so forth, then the finding of A is hardly compelling evidence for the theory.
Yet this is what Venema argues. The vitellogenin genes in chickens share a weak similarity with corresponding genetic segments in humans. Evolutionists view the human segments as pseudogenes—broken versions of vitellogenin genes inherited from their egg-laying ancestors. Given this vitellogenin similarity between humans and chickens, for example, evolutionists such as Venema incredibly conclude that, therefore, humans and chickens evolved by random mutations from a common ancestor. Not only does that not follow, but it takes Venema to the unlikely solution of random mutations creating humans and chickens, and of course all the other species.
Venema also argues that the similarity of the vitellogenin genes between humans and chickens extends to, and is all the more confirmed by, their positioning within their respective genomes. But this argument from synteny is no different from what we saw above. When there is a loss of synteny evolution is not harmed, and the theory has another set of explanatory mechanisms available for just about any outcome. If the vitellogenin genes had been in a different order, evolution could have explained it just fine.
Affirming the consequent
In spite of these problems with his argument, Venema is enthusiastic about this evidence. In fact his enthusiasm leads to the fallacy of affirming the consequent, as he equates shared synteny (genes with similar positioning in the genomes of different species) with common descent
This evidence increases our confidence that we are indeed looking at regions with shared synteny: in other words, a region in two present-day species that was once a region in the genome of their common ancestral population.
That is a fallacy. Ignoring the problems discussed above for the moment, even if evolution did make a hard prediction of shared synteny, and even if it was universally observed, that would not prove evolution. In that case, you would have a confirmed prediction. That is good, but it is not equivalent to a finding of evolution. Venema violates this scientific fundamental when he defines shared synteny as “a region in two present-day species that was once a region in the genome of their common ancestral population.” Unfortunately, affirming the consequent is not uncommon in the evolution literature.
Primeval tech continues to troll Darwinism.
Engineering and Evolution in the Microbial World
This year’s Conference on Engineering in Living Systems (CELS) is going on right now, exploring design principles at work in living things. In case you couldn’t be there, we pulled this classic ID the Future episode from the archive. Host Jonathan Witt gives us a behind-the-scenes interview with Dustin Van Hofwegen, a biology professor at Azusa Pacific University in California. The occasion was a previous Conference on Engineering in Living Systems. The two discuss the event, which brought together biologists and engineers to study how engineering principles and a design perspective can and are being applied to biology — to plants and animals but also to Van Hofwegen’s area of focus, the realm of microbial biology. The two move into a conversation about Van Hofwegen’s article in the Journal of Bacteriology, co-authored with Carolyn Hovde and Scott Minnich, based on research they did at the University of Idaho.
As Van Hofwegen explains, the research focused on one of the most ballyhooed evolutionary changes to come out of Richard Lenski’s long-term evolution experiment, a decades-long study of many thousands of generations of E. coli bacteria. Perhaps the biggest evolutionary development in the course of the experiment involved some bacteria beginning to feed on citric acid. Interesting, to be sure, but as Van Hofwegen explains, E. coli already has this capacity; it’s just a matter of switching it on. Van Hofwegen, Hovde, and Minnich demonstrated this through do-or-die experiments with E. coli, which led to the bacteria developing the capacity not in years or decades, as in the Lenski experiment, but in 14 days, that is, in as little as 100 generations. Van Hofwegen explains why this is an embarrassing result for neo-Darwinism. The pair conclude with a discussion of another study on antibiotic resistance with a similar result, that the resistance observed came not by evolving anything new but by tweaking something already present. Download the podcast or listen to it Here
Friday, 2 June 2023
The ecosystem vs. Darwin.
The Phosphorus Cycle: Cause or Effects
Life would be impossible without phosphorus,” begins an editorial in Nature.
Present in molecules from DNA to membrane lipids to the compounds that shuttle energy in cells, it acts as an essential nutrient alongside nitrogen. Phosphorus moves through the environment in vigorous biogeochemical cycles, reflecting its chemical reactivity and intense competition by hungry organisms.
How did this bio-geo-chemical cycle begin? Scientists at the University of Cambridge are perplexed about “How life and geology worked together to forge Earth’s nutrient rich crust.” In their analysis, they see that the element phosphorus appears to have increased in the crust around the same time as the Cambrian explosion. Was one the cause or the effect of the other? It didn’t seem coincidental.
Around 500 million years ago life in the oceans rapidly diversified. In the blink of an eye — at least in geological terms — life transformed from simple, soft-bodied creatures to complex multicellular organisms with shells and skeletons.
Now, research led by the University of Cambridge has shown that the diversification of life at this time also led to a drastic change in the chemistry of Earth’s crust — the uppermost layer we walk on and, crucially, the layer which provides many of the nutrients essential to life.
They reiterate, as we’ve discussed before, that phosphorus (P) is a limiting factor on biological productivity. Unlike the other most abundant vital elements (C, H, O, N, S), P must be extracted from rocks by chemical weathering — not in its pure form, which is explosive, but as PO43- (phosphate). Microbes and plants can utilize inorganic phosphate (Pi). Then other organisms can use the phosphate-containing molecules made by them (organic phosphate, or Po).
A Biogeochemical Cycle Triggered
Craig Walton of Cambridge points out that once life became abundant in the oceans, a phosphorus recycling program could begin.
When these organisms die, most of the phosphorus is returned back into the oceans. This efficient recycling process is a key control on the amount of total phosphorus in the ocean, which in turn supports life, “It enables us to have all the life we see around us today, so understanding when this process started is really key,” said Walton.
The Oxygen Theory for the Cambrian Explosion plays into his model, although he does not explicitly say he believes oxygen caused the sudden increase in animal life. He only points out the interesting correlation.
But, all of this biological reprocessing power relies on oxygen. This is what fuels the bacteria responsible for the breakdown of dead organic material that returns phosphorus back into the oceans.
The researchers think that a surge in oxygen at around the time of the Cambrian explosion might explain why phosphorus increased in rocks. “If oxygen did increase at that time, then more oxygen may have been available to break down deep sea biomass and recycle phosphorus to shallow coastal regions,” said Walton. Moving this phosphorus back towards the land meant it was better preserved in rocks that make up the continents.“That series of changes were ultimately responsible for fuelling the activity of complex life as we know it,” said Walton.
Oxygen, therefore, is a third essential component in the phosphorus cycle.
“It’s tricky to unravel the sequence of events — whether complex life evolved in part because of increased supplies of oxygen and phosphorus to start with, or if they were in fact fully responsible for increasing availability of both, is still a controversial topic.” Walton and the team now looking to investigate the trigger for and timing of this phosphorus enrichment in the crust in more detail.
Summing up, there is a remarkable interplay of biology with two abiotic elements (oxygen and phosphorus) that sustains life on our planet. The Cambridge scientists were unable to decide which came first, how the cycle was triggered, and how things stayed in balance once the cycle was initiated.
Phosphate Balance and Management
Organisms have remarkable mechanisms for dealing with phosphate limitation, as noted here. The Nature editorial blames man for messing up the cycle by mining phosphorus for fertilizer, which often drains into the oceans, causing toxic algal blooms.
The modern phosphorus cycle has been profoundly meddled with by humans to overcome phosphorus limitation. Half of the phosphorus available to crops in agricultural soils may come from fertilizer application. Fertilizer is a limited resource — often derived from ancient rocks composed of detritus deposited beneath marine upwelling zones — and its depletion will eventually lead to problems for agriculture and other organisms that rely upon it.
In March, Science Magazine featured Dan Egan’s book about phosphorus, The Devil’s Element and a World Out of Balance, “an enjoyable, lively, and thought-provoking read” according to reviewer Robert W. Haworth, an expert on phosphorus and the environment. Wise management of this critical element will be essential, as phosphate runoff can pollute waterways and deplete soils if handled carelessly. Yet its automatic recycling through the crust and biosphere is not mentioned in the review. If the world is “out of balance” now due to human activities, how did it get into balance in the first place?
A commentary by Senjie Lin in Nature Communications explores the complexities of biological responses to phosphorus limitation, including interactions with ocean acidification, climate, and nitrogen fixation. Lin leaves more questions than answers, but notes that phytoplankton differ in their responses to pH, so much more research is needed.
Just-in-Time Delivery
One particularly interesting finding about phosphorus comes from research on fruit flies. A new organelle was found in the intestinal cells of the flies that buffers phosphate to maintain homeostasis. Described by Gemma Conroy in Nature, this “previously unknown” organelle “acts like a reservoir of phosphate, helping to regulate levels of the nutrient inside cells and triggering processes that maintain tissues when it is in short supply.”
Conroy tells how Charles Xu of Rockefeller University noticed some oval-shaped structures surrounded by multiple membranes that were being traversed by a phosphate-sensing transporter protein named PXo:
“These were quite visible, and we wondered what they were,” says Xu. When the scientists took a closer look at the mysterious structures, they saw they had several membrane layers, and the PXo protein was transporting phosphate across them. Once inside the unfamiliar organelles, the phosphate was converted to phospholipids, the main building blocks of cellular membranes.
When the fly cells were deprived of phosphate, the organelles broke apart and released the stored phospholipids into each cell, indicating that they function like reservoirs, says Xu.
His team’s paper in Nature shows microphotographs of these “PXo bodies” and describes how they store and release inorganic phosphate (Pi).
In unicellular organisms, Pi is indicative of environmental nutrient abundance and generally supports cell growth and division1. In metazoans, however, Pi availability is affected by nutrient uptake, systemic metabolism and local Pi usage, thus implicating more complex Pi signalling. In this study, we demonstrated that Pi starvation or PXo deficiency induces hyperproliferation and enterocyte differentiation in the epithelium of the Drosophila midgut, which might be a compensatory mechanism to produce more enterocytes capable of Pi absorption. Given the scarcity of knowledge about cytosolic Pi regulation in animal cells, our findings might have broad implications and open new avenues for studying Pi metabolism and signalling.
The system for just-in-time delivery of phosphates from a reservoir equipped with a sensor is reminiscent of our story about the way cells buffer and deliver heme.
Coincidences vs. Intentions
The Cambridge article says that “life and geology worked together to forge Earth’s nutrient rich crust.” From a materialist perspective, that’s a fallacy of personification. Mindless entities do not work together to forge something like a Cambrian animal body plan or a cell organelle with a sensor able to buffer phosphate for just-in-time delivery.
Scientists are generally wary of explanations that depend on lucky coincidences. In the phosphorus cycle, biology and geology are seen cooperating as to timing, triggers, balance, and homeostasis of essential parts for a functioning biosphere. These are concepts rich with purpose. If a functioning biosphere was intended, then these observational realities would make sense.
It's finally happened
Utah district bans Bible in elementary and middle schools
SALT LAKE CITY (AP) — The Good Book is being treated like a bad book in Utah after a parent frustrated by efforts to ban materials from schools convinced a suburban district that some Bible verses were too vulgar or violent for younger children.
And the Book of Mormon could be next.
The 72,000-student Davis School District north of Salt Lake City removed the Bible from its elementary and middle schools while keeping it in high schools after a committee reviewed the scripture in response to a parental complaint. The district has removed other titles, including Sherman Alexie’s “The Absolutely True Diary of a Part-Time Indian” and John Green’s “Looking for Alaska,” following a 2022 state law requiring districts to include parents in decisions over what constitutes “sensitive material.”
On Friday, a complaint was submitted about the signature scripture of the predominant faith in Utah, The Church of Jesus Christ of Latter-day Saints, also known as the Mormon Church. District spokesperson Chris Williams confirmed that someone filed a review request for the Book of Mormon but would not say what reasons were listed. He also would not say whether it was from the same person who complained about the Bible, citing a school board privacy policy.
Representatives for the church declined to comment on the challenge. Members of the faith also read the Bible.
Williams said the district doesn’t differentiate between requests to review books and doesn’t consider whether complaints may be submitted as satire. The reviews are handled by a committee of made up of teachers, parents and administrators in the largely conservative community. The committee published its decision in an online database of review requests and did not elaborate on its reasoning or which passages of the Bible it found overly violent or vulgar.
The decision comes as conservative parent activists, including state-based chapters of the group Parents United, descend on school boards and statehouses throughout the United States, sowing alarm about how sex and violence are talked about in schools.
It’s unknown, however, who made the request for the Bible to be banned from Davis schools or if they are affiliated with any larger group because of the district’s privacy policy.
A copy of the complaint obtained by The Salt Lake Tribune through a public records request shows that the parent noted the Bible contains instances of incest, prostitution and rape. The complaint derided a “bad faith process” and said the district was “ceding our children’s education, First Amendment Rights, and library access” to Parents United.
“Utah Parents United left off one of the most sex-ridden books around: The Bible,” the parent’s complaint, dated Dec. 11, said. It later went on to add, “You’ll no doubt find that the Bible (under state law) has ‘no serious values for minors’ because it’s pornographic by our new definition.”
The review committee determined the Bible didn’t qualify under Utah’s definition of what’s pornographic or indecent, which is why it remains in high schools, Williams said. The committee can make its own decisions under the new 2022 state law and has applied different standards based on students’ ages in response to multiple challenges, he said.
An unnamed party filed an appeal on Wednesday.
The Bible has long found itself on the American Library Association’s list of most challenged books and was temporarily pulled off shelves last year in school districts in Texas and Missouri.
Concerns about new policies potentially ensnaring the Bible have routinely arisen in statehouses during debates over efforts to expand book banning procedures. That includes Arkansas — one of the states that enacted a law this year that would subject librarians to criminal penalties for providing “harmful” materials to minors, and creates a new process for the public to request materials be relocated in libraries.
“I don’t want people to be able to say, ‘I don’t want the Bible in the library,” Arkansas Democratic state Sen. Linda Chesterfield said during a hearing.
Parents who have pushed for more say in their children’s education and the curriculum and materials available in schools have argued that they should control how their children are taught about matters like gender, sexuality and race.
EveryLibrary, a national political action committee, told The Associated Press last month it was tracking at least 121 different proposals introduced in legislatures this year targeting libraries, librarians, educators and access to materials. The number of attempts to ban or restrict books across the U.S. last year was the highest in the 20 years, according to the American Library Association.
“If folks are outraged about the Bible being banned, they should be outraged about all the books that are being censored in our public schools,” said Kasey Meehan, who directs the Freedom to Read program at the writers’ organization PEN America.
Why the trinity renders a definite answer to the question of JEHOVAH's identity impossible.
Matthew ch.4:11PHB"Then Yeshua said to him, “Depart Satan, for it is written: 'You shall worship THE LORD JEHOVAH your God and him(note the singular personal pronoun) ALONE shall you serve.'"
If the the object of our devotion is a mystical union of co-equals obviously their would be no single person anywhere who is entitled to exclusive devotion even if ,as some have, we make the entire union a single person,thus adding a forth person to our supposed triad. Trinitarians insists that each member of the trinity is entitled to the highest worship effectively meaning that no member of their mystifying concept including the trinity(quadrinity?) Himself is entitled to exclusive devotion
John ch.1:18ASV"No one has seen God at any time. The only begotten [h]Son, who is in the bosom of the Father, He has declared Him."
The coming to earth of our Heavenly Father's nearest and dearest Child was meant to make JEHOVAH plain to his people this is most certainly not the case with the logos of Christendom.
The fossil record trolls Darwinism some more?
Fossil Friday: How an Austrian Scientist Concocted a New Domain of Life called Gabonionta
In 2008 the Moroccan-French geologist Prof. Abderrazak El Albani from the University of 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 the earliest fossil evidence for multicellular eukaryotic life and were published two years later in the prestigious journal Nature (El Albani et al. 2010, Maxmen 2010).
In 2014, these findings were first presented to the general public with a special exhibition titled “Experiment Life – The Gabonionta” which opened in March 2014 at the Natural History Museum in Vienna (NHM 2014), and also featured a 40-minute documentary film by the University of Poitiers about the discovery. This exhibition was accompanied by a sensationalist media campaign in Austria, which included fancy headlines such as: “Gabonionta: sensational discovery in Vienna“ (ORF 2014), “Gabonionta, the little revolutionaries of evolution“ (Vosatka 2014), and “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 an 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 as other higher taxonomic names such as Eukaryota or Metazoa.
More Important Issues
Anyway, there are more important issues with this discovery: other experts such as the famous 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.” Even more recently, Fakhraee et al. (2023) came to a similar devastating conclusion. It looks like the dubious name Gabonionta does 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.
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. Even in their newest paper 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. 2023), but no longer promoted the presence of multicellular organisms. The silence is deafening!
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
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
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, 100–104. DOI: https://doi.org/10.1038/nature09166
El 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, 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
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
Maxmen A 2010. Ancient macrofossils unearthed in West Africa. Nature News June 30, 2010. DOI: https://doi.org/10.1038/news
NHM 2014. Experiment Life – the Gabonionta. Press release March 7, 2014. https://www.nhm-wien.ac.at/presse/experiment_leben_-_die_gabonionta
ORF 2014. “Gabonionta“: Sensationsfund in Wien. ORF.at March 11, 2014. https://wien.orf.at/v2/news/stories/2635417/
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
Plenty of rights to go around?
Should We Give Nature “Rights”? A Premier Science Journal Says Yes
The major science journals are growing increasingly woke. The prestigious journal Science, in particular, has swallowed this ideology — including supporting the “nature rights” movement.
The rights of nature — which include geological features — are generally defined as the right to “exist, persist, maintain and regenerate its vital cycles, structure, functions and its processes in evolution.” Nature is, of course, not sentient. So, this campaign is really about granting environmental extremists legal standing to enforce their policy desires through litigation as legal guardians serving nature’s best interests.
But the movement has a problem. It is clearly ideological rather than rational. So now, three law professors and a biologist writing in Science urge scientists to promote the agenda by giving courts a scientific pretext to enforce nature rights laws, or even, impose the agenda from the bench (as has already been attempted several times). From, “Science and the Legal Rights of Nature”:
By contributing to interdisciplinary analyses of rights-of-nature laws before disputes arise, scientists can help contribute to the effectiveness of these laws. The availability of credible scholarly analysis of legal scientific terms used in law would make these rights more tangible and accessible to the judges whose role it is to apply them. Although scientific uncertainty often cannot be eliminated, it’s reduction in turn reduces legal uncertainty and thus helps meet the objection that rights-of-nature laws are too vague to be applied.
And Here It Really Gets Irrational
More:
Another type of interdisciplinary scholarship that would assist the functioning of rights-of-nature laws would be the examination of the duties of nature. Although some rights-of-nature laws grant rights for nature without corresponding duties, others equate nature to a legal person with both rights and duties. Uncertainty over liabilities and duties of nature has been an impediment to implementing some rights-of-nature laws. Scientists can help legal systems comprehend nature’s potential legal obligations (e.g., “ecosystem services”), and what environmental protection measures may also be legally required to ensure natural entities can continue to fulfill these obligations.
Good grief. Such nonsense in a science journal. “Nature” is not a moral entity. It is not conscious. It is not a discrete thing. It includes everything from rock outcroppings, to algae, swamps, oceans, lion prides, earthquake faults, glaciers, and the moon. It — and its constituent aspects — cannot owe anything or anyone duties. No matter how destructive, a river that floods has done nothing “wrong.” The very notion is nonsensical.
In a second article, the authors identify how scientists can promote the agenda — which often incorporates indigenous people’s spiritual beliefs into legislation, which whatever their merit, are not scientific concepts. (This is one reason I consider the movement a neo-earth religion.)
The “Right to Evolve”
The text is too long to present here, so I will give one example: the “right to evolve.” The authors note that “evolution” has many meanings:
Any or all these definitions can contribute to understanding what a “right to evolve” may entail, whether for a troop of monkeys, a population of wild rice, Lake Erie, or Pachamama [the Incan earth goddess–see what I mean?]. For example, a biological understanding of evolution may be applied to species or subspecies, whereas a more general “slow change over time” may pertain to rivers, lakes, and watersheds.
In other words, scientists should offer courts a scientific patina hook upon which to hang their legal hats to enforce radical environmental policies:
There are many ways that scientists and scientific knowledge can help different legal systems understand nature’s rights. One important way scientists can contribute is by being involved in litigation. Most rights-of-nature laws contain provisions allowing scientists or other members of the public to bring lawsuits. A successful lawsuit necessitates demonstration that the entity in question is protected and that its rights were violated — e.g., how its rights to ecological functions or evolutionary processes were impeded. These are clearly questions requiring scientific input and applications of ecological and evolutionary concepts. Scientists also can provide evidence in lawsuits to which they are not a party in many legal systems [referencing “amicus curiae briefs” and “testimony”].
Why Should You Care?
This is precisely how the most radical public policies are imposed upon our society. The “experts” — really ideologues — lend their gravitas to what is essentially a social rather than scientific agenda. And that “expertise” will only be deemed “legitimate” by the media when it comes from the radical side of the street — as we see in the “gender-affirming care” controversies.
I am continually frustrated that so few people seem to take the threat of nature rights seriously. People need to wake up and legislatures need to pass laws prohibiting rights and legal standing for anything other than human beings and our institutions. Because the most powerful institutions in our society are beginning to swing behind the agenda, Soon, it could be too late.
And yet even more primeval tech vs. Darwin
Natural Engineering in the Lifestyle of Honey Bees
A week ago, my wife came in and announced, “There’s a scary-looking bees’ nest in the lilac bush!” Wasps routinely try to build nests around our house, so I was prepared for the worst when I went out to investigate. What I found was a basketball-sized cluster of honey bees — a “swarm.” There was no nest, only a living ball of thousands of bees hanging from a branch.
I’ve never done any beekeeping, but fortunately, we have some friends who do. We had no idea, but apparently a swarm of bees in May on an easily accessible branch is something to get excited about! Soon, our beekeeper friends rolled up in their pickup truck. One pulled on jacket and bee-proof bonnet, set a large container (a portable hive box) on top of a stepladder underneath the swarm, took hold of the branch, and shook it. The swarm of bees, all festooned together, fell in a clump into the box. Or, rather, most of them did. Hundreds of them draped over the sides, which our undaunted friend scooped into the box (with gloved hands), while hundreds more buzzed around. The couple who came kept reassuring us, “They’re not going to sting because they’re focused on staying with the queen.” I learned that the queen bee’s presence is of utmost importance for the thousands of others.
Thanks for the Bees
Our friends extended thanks for the bees, then went home, while we went inside for a belated supper. The next day, I saw a smaller swarm around a branch in the same lilac bush. Here’s the interesting thing. Our friends said that they didn’t think they had captured the queen since the bees were acting agitated, so they came right back over to recover the remaining small swarm. When they added it to the hive with the bulk of the bees, all of them settled down right away. The queen had come home.
Here was a fascinating example of a finely tuned aspect of living organisms that was surely worth further investigation. A trip to the university library and online research quickly yielded multiple sources of information about honey bees from specialists of all types. As I’ve read up on bee behavior and their life cycles, a striking picture appears of ingenious design in living systems.
Natural Engineering
A recent research article reported on the use of x-ray microscopy to provide three-dimensional, time-resolved details on how bees manufacture their iconic honeycomb structure. Several observations from the authors are worth mentioning:1
Honeycomb is one of nature’s best engineered structures.
Engineers recognize design, and never has good human-level engineering come about by anything other than intelligent design.
Honeycomb is a structure that has both fascinated and inspired humans for millennia, including serving as inspiration for many engineering structures. It is a multifunctional structure that acts as a store for food, a nursery for developing honey bee brood, and a physical structure upon which honey bees live. It is constructed of wax produced by bees in specialized glands in their abdomen. Wax is an expensive commodity and so comb construction can be quite costly for a honey bee colony. Honeycomb is constructed in such a way to minimize wax consumption.
Honeycomb construction is optimized to serve multiple purposes for the bee colony, subject to the constraint of material and labor costs. Sounds like the bees are a responsible engineering firm.
The ability of bees to “know” how to manufacture the structurally optimal hexagonal-packed honeycomb is even more amazing when one considers that the worker bees constructing it hatched less than three weeks earlier.
While not a perfect analogy, a colony of bees may be compared to a multicellular living organism. Each member of the colony seems to know what to do at each stage of its life for the good of the whole “organism.” An isolated bee will soon die, even if supplied with nutrients, suggesting that it is designed to function as part of the whole.
Arranged by a Designer
We could say that the whole honey bee colony is greater than just the sum of its individual members. This state of affairs usually arises when the individual components of a complex system are specifically arranged by a designer to accomplish a predetermined purpose. Consider any complex electrical or mechanical device. All of the components of my laptop would make a fascinating pile if laid out on a table; but they’re even more fascinating when assembled and functioning together as a whole, according to their designed purpose.
A professor of entomology at Iowa State University, studying the behavior of honey bee colonies, writes:
Each bee appears to specialize, for a time at least, on a particular job. Thinking about this, you may decide that a single bee is somewhat like a single cell of your own body. The work force in charge of a particular job, such as feeding larvae, would then correspond to one of your tissues. And if you follow this analogy further, you may conclude that a colony of honey bees is like an organism — a superorganism.2
Aspects of an organism that manifest in a honey bee colony include caring for developing larvae, securing and processing nutrients (similar to metabolism), tending the queen (whose presence coordinates the behavior of the entire colony), guarding the hive and patrolling for intruders (similar to an immune system), temperature regulation (fanning their wings to cool the hive, clustering and vibrating their wings to heat the cluster of bees), growth of the whole colony in terms of the number of individual bees, reproduction of the “organism” (resulting in the phenomenon of the honey bee swarm), coordination of activities mediated by a variety of communication channels, and a sense of purpose.
Observers of complex, functional systems, whether nonliving or alive, rationally conclude that, “If something works, it’s not happening by accident.”3
Beyond Mere Survival
The honey bee colony “works” and accomplishes a purpose beyond mere survival. It diligently stockpiles nectar which its workers convert to honey in amounts exceeding its needs.4 Honey’s unique ingredients give it value as a food source for humans that has been recognized for millennia.
The high total sugar concentration [primarily fructose and glucose, with a smaller amount of sucrose] in honey is beneficial in that most yeasts cannot ferment in it. Also, together with one other constituent (glucose oxidase), it gives the honey antimicrobial properties, and it can be stored safe from spoilage…5
Beyond the direct production of honey for our use, the role of honeybees as pollinators is of critical importance in agriculture:
Bees and other pollinators play a critical role in our food production system. More than 100 U.S. grown crops rely on pollinators. The added revenue to crop production from pollinators is valued at $18 billion.6
Continuing to ponder bee behavior, comments made by Professor Richard Trump of Iowa State University are instructive:
If a honey bee, with her microbrain, knows what she is doing, this is cause for wonder. If she does not know — if she is fully programmed by those sub-microchips of DNA that come to her as a legacy from her ancestors — this is even greater cause for wonder. It is incredible.7
Here are a couple of examples that may cause us to wonder how bees know how to do what they do. Researchers have found that bees possess an internal organic timer, which in conjunction with an awareness of the rotation of the Earth, allows them to efficiently time their foraging activities to arrive at flowers when pollen sources are at their peak.
The famous “waggle dance” that a scout bee performs back at the hive after discovering a food source communicates to other bees (by touching, since the inside of the hive is dark) both the distance and the direction of the food in relation to the current position of the sun. Bee keepers have found that if they reorient the honeycomb on which the bee is dancing, the undaunted bee will adapt its dance so that it still correctly communicates the proper direction to the food source.8 Sometimes the dancing scout bee will continue its dance for more than an hour, and over this time, the position of the sun has changed. In response, the bee will compensate for the sun’s movement across the sky by gradually adjusting the angle of its dance.
How Many Lines of Code?
If humans tried to duplicate the capabilities of honey bees by building and programming mini-robots that could fly, how many lines of code would have to be written and executed to make an artificial bee? We can also ask what the likelihood is of all this coded information arising from unguided natural processes. Someone committed to the evolutionary paradigm might answer that any genomic changes that offered a survival advantage would’ve been locked in by the ratchet-like mechanism of natural selection until primitive bee ancestors evolved into the complex, coordinated colonies of honey bees seen today.
Systems engineer Steve Laufmann, co-author of the recent book Your Designed Body, addresses the engineering hurdles facing any proposed evolutionary explanation:
…when evolutionary biologists hypothesize about small and apparently straightforward changes to a species during its evolutionary history, the biologists tend to skip both the thorny engineering details of what’s necessary to make the system work, and the bigger picture of how any system change has to be integrated with all the other systems it interacts with. The result is that biologists tend to massively underestimate the complexities involved.
And here’s the rub: if they’ve massively underestimated those complexities, then they’ve massively underestimated the challenge for any gradual, materialistic evolutionary process to build up these systems a little bit at a time while maintaining coherence and function.
PP. 324-325
The difficulties outlined by Laufmann are in the context of the human body, but they apply equally well to the complexities of a colony of honey bees. Bee keepers are all too aware of the precarious balance between life and death throughout a single year for a colony of bees. Engineers know that making changes to a delicately balanced complex functional system, even small ones, have a way of upsetting the balance — not towards better function but towards failure and collapse.
Honey bees offer us a glimpse of a remarkable living system involving interdependent, communally cooperative behavior. In some ways, they outshine the best in conscious human attempts to build a thriving society. Perhaps we can learn a thing or two from the humble bee.
Notes
Rahul Franklin, Sridhar Niverty, Brock A. Harpur, Nikhilesh Chawla, “Unraveling the Mechanisms of the Apis mellifera Honeycomb Construction by 4D X-ray Microscopy,” Advanced Materials, Vol. 34, Issue 42, Oct. 20, 2022.
Richard F. Trump, Bees and Their Keepers, (Iowa State University Press, Ames, IA, 1987).
https://evolutionnews.org/2021/12/caltech-finds-amazing-role-for-noncoding-dna/
How do bees make honey? From the hive to the pot | Live Science (accessed 5/28/2023).
Diana Sammataro and Alphonse Avitabile, Beekeeper’s Handbook, (New York: Cornell University Press, 1998).
pollinator_week_factsheet_06.25.2020 (usda.gov).
Trump, Bees and Their Keepers, p. 78.
Trump, Bees and Their Keepers, pp. 80-1.
Thursday, 1 June 2023
Primeval chronometers vs. Darwinism
Epigenetic Biotimer Revealed in Flowers
Biology should never be considered ordinary. Take almost any biological process, and the details are likely to overwhelm the reader. That is certainly the case with a new paper about flowering in plants. Even in the well-studied lab plant Arabidopsis thaliana, researchers described dozens of genes, proteins, and accessory molecules working together to ensure the proper moment for flowering.
The paper in Plant Cell is difficult to read for laymen, because geneticists have given very odd names to genes and proteins. Then, according to custom, some genes for A. thaliana are written in italics, but other genes and their protein products are italicized in ALL CAPS. One must wade through a jungle of names like KNUCKLES, GIANT KILLER, SPOROCYTLESS, DEFECTIVE ANTHER DEHISCIENCE1, and AT HOOK MOTIF NUCLEAR LOCALIZED PROTEIN18. After first mention in a paper, fortunately, these are usually abbreviated to KNU, GKI, SPL, and so forth, but then it is hard to remember what they do, especially when they all interact in complex ways.
Complexifying the situation further, the nomenclature rules have changed over time and are not consistent between publications. Some letters are not capitalized, and some have a suffix consisting of letters and numbers to identify a particular allele. There are also rules for mutant forms and wild type forms. The rules may seem like a mess to non-specialists (read about them at Arabidopsis.org), but I suppose the strange mnemonic names are more helpful than hard-to-memorize strings like g2934ab0x or worse (although rules for epigenetic marks are less mnemonic, like H3K27me3 (“histone 3, lysine 27, methyl group 3”). For this reason, I will try to refrain from referring to the labels and focus instead on processes and functions that go on, which are truly amazing.
The Basics
In a nutshell, scientists at the Nara Institute of Science and Technology (NAIST) in Japan identified key genes, proteins, and epigenetic factors that switch on flowering with precision timing. So accurate was the “biotimer” they found, they could predict when flowering would occur, even if they altered some of the components. They created mutants of some components, and with a mathematical model they designed, they could calculate to the day when an apical meristem (i.e., the tip of a growing stem) would switch its stem cells from proliferation mode to differentiation mode and start to grow the parts of the flower. The precision astonished them. Phys.org says,
The intricate process of flower development has long fascinated scientists seeking to unravel the mysteries behind nature’s precision timing. In a study published in the journal The Plant Cell, a research team led by Nara Institute of Science and Technology (NAIST), Japan has shed light on the inner workings of floral meristem termination and stamen development, uncovering a unique mechanism driven by the interplay of genetic and epigenetic factors.
In Southern California where I live, everyone is thrilled when the poppies bloom. Vast acres of the plants bloom together in late March or early April, as if on cue, painting whole valleys and hillsides in golden orange. The flowers can also close up if the temperature drops or the wind blows and then reopen when the sun shines warmly again. How do they do it? In every part of the world, plants show remarkable timing in their flowering: cherry blossoms in Washington DC, tulips in Holland, daylilies in Taiwan. Their secrets remain mysterious. In California, everyone thought the heavy winter rains would yield a poppy superbloom, but it was only modest compared to those of past years during the drought. Somehow, plants sense just the right combination of external cues to put on their best show.
To unlock the secrets of this remarkable system, the researchers devised a mathematical model capable of predicting gene expression timing with astonishing accuracy. By modifying the length of H3K27me3-marked regions within the genes, they successfully demonstrated that gene activation could be delayed or reduced, confirming the influence of this epigenetic timer. The team’s findings offer a novel perspective on how nature controls the gene expression during flower development.
The Histone Code
The story revolves around epigenetic markers on the genes of the A. thaliana stem cells. Over twenty years ago, David Allis (1951-2023) introduced a bold concept: there was another code at work in the genome: a combinatorial regulatory system. In its obituary, Nature Genetics says,
Perhaps Allis’s most famous conceptual contribution to the field of chromatin research was the elaboration of the ‘histone code’ hypothesis more than 20 years ago. This framework suggested that histone post-translational modifications (PTMs), in different combinations, along with the proteins that can ‘write’, ‘read’ or ‘erase’ them, constitute the basis for a gene regulatory code. In other words, certain histone PTMs could label particular chromatin regions and potentially influence their transcriptional activity. Many of these histone PTMs have been used extensively to characterize or infer a cell state, identity and behavior. For example, methylation marks at H3K27 and H3K9 are mostly associated with gene repression, whereas others, such as H3K4 methylation and H3K27 acetylation, are associated with active regulatory regions.
And so it is in A. thaliana, the authors of the current paper show. The genetic code has the blueprint to make the parts; the epigenetic “histone code” has the switch and the timer.
How It Works
The biotimer described in the paper works by a process of “passive dilution” that is cell cycle dependent. The normal condition for the AGAMOUS transcription factor is to repress flowering. This factor, abbreviated AG, is studded with histone markers (H3K27me3) which repress multiple genes required for “floral meristem termination,” the term for the switch to flowering. Stem cells will proliferate (divide) endlessly by mitosis until the switch is thrown to stop making clones of themselves and start differentiating into stamens, pistils, and petals. It reminds me of Paul Nelson’s comment about chicken egg development in the documentary Flight, where he describes how certain cells in the embryo “are committing themselves, in most cases irreversibly, to particular functional roles.”
For flowers to form, the floral meristem (floral stem cells) must irreversibly commit to becoming cells making up the various floral organs (sepals, petals, stamens, and carpels), a process known as floral meristem termination. Proper timing of floral meristem termination involves temporal activation of the transcription factor gene KNUCKLES (KNU) by its upstream regulator AGAMOUS (AG) via cell cycle-dependent dilution of the repressive histone modification at lysine 27 of histone H3 (H3K27me3) along the KNU coding sequence. This intrinsic ‘biotimer’ will activate KNU at precisely the right time to ensure proper flower development.
Passive dilution involves the washing out of the histone markers at each cell division. AG evicts PRC2, a histone methylator, and prevents histone H3 marks on nucleosomes. If a cell has six of these repressive markers at the beginning, the daughter cells will have three after the next cell division. At some point, there will not be enough markers to repress differentiation, and the cell will commit irreversibly to floral meristem termination. By inserting values into their mathematical model of this passive dilution mechanism, they were able to accurately predict when a plant in the lab would commence flowering. They validated the model with mutant forms of the genes, either speeding up or slowing down this mechanistic “countdown timer” operated by the epigenetic code. When one protein was activated too early, it produced short stamens that were sterile. This shows that attention to timing between parts of the system is crucial to successful flower development.
Interestingly, the biotimer was also temperature dependent. The team grew some of the plants at 18°C (64° F) instead of the usual 22° C (72° F) and observed that flowering was delayed. The explanation is that lower temperature slows down mitosis, which slows down the passive dilution mechanism.
We also observed a delay in KNU activation by growing plants at 18°C, likely due to slower growth kinetics. This observation emphasizes the dynamic regulation of H3K27me3 in response to extracellular and intracellular cues and suggests a role for the cell cycle–dependent biotimer in coordinating the balance between cell proliferation and differentiation.
It’s a wise strategy to ensure that flowers will have good weather conditions for blooming. Temperature is only one external cue that probably affects the timer. “Additional experiments will be necessary,” they say, to clarify the effect of lower temperatures and other external cues. These may include water and nutrient availability, day length, risk of herbivores, presence of fungal partners, or other factors.
Appropriately the paper avoids Darwin. How flowering plants exploded into appearance was an abominable mystery to him. The evolution-free paper and news release used a term alien to unguided natural processes but familiar to engineers and designers of complex systems with multiple cooperating parts:
Through meticulous investigations in the model plant Arabidopsis thaliana, the team discovered that AG serves as a master conductor, orchestrating gene expression through a process known as cell cycle-coupled H3K27me3 dilution. This remarkable phenomenon involves the dilution of a histone modification called H3K27me3 along specific gene sequences, effectively kickstarting gene activation. The scientists identified several key genes directly regulated by AG at various time points of this cycle.
The study revealed a genetic network tightly controlled by AG, with genes such as KNUCKLES (KNU), AT HOOK MOTIF NUCLEAR LOCALIZED PROTEIN18 (AHL18), and PLATZ10 emerging as critical players. “By unraveling the inner workings of this regulatory circuit, we gained unprecedented insight into the intricate timing mechanisms that drive proper floral meristem termination and stamen development,” says first author Margaret Anne Pelayo.
Orchestration: aside from its well-known meaning in music — getting all the skilled instrumentalists to play their own designed parts at the right time in harmony — it also means “the plans or planning necessary to arrange something or cause something to happen.” To see an automatic mechanism in a humble herb working to achieve orchestration of multiple parts within a stem cell in a meristem as it switches to flower preparation is quite remarkable. Yet even that is just the start of an entire concert of orchestrated masterpieces as the organs develop, the petals take on their shapes and colors, and the completed flower opens for business. Below, watch as a musical orchestra celebrates this biological orchestration. Bravo!
<iframe width="460" height="259" src="https://www.youtube.com/embed/LjCzPp-MK48" title="Time-Lapse: Watch Flowers Bloom Before Your Eyes | Short Film Showcase" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
JEHOVAH'S Magnum opus.
Proverbs ch.8:22REB"YAHWEH had constituted me the beginning of his way, Before his works At the commencement of that time;"
Proverbs ch.8:30REB"Then I was beside him as a master worker.+
I was the one he was especially fond of+ day by day;
I rejoiced before him all the time;+ "
Micah Ch.5:2REB"Thou therefore Bethlehem Ephrathah, Though little to be among the thousands of Judah Out of thee shall Mine come forth, to be ruler in Israel,—Whose comings forth have been from of old, from the days of age-past time."
John ch.1:30NLT"He is the one I was talking about when I said, ‘A man is coming after me who is far greater than I am, for he existed long before me.’"
John ch.6:62NIV"Then what if you see the Son of Man ascend to where he was before!"
John ch.8:58NASB"Jesus said unto them, Verily, verily, I say unto you, Before Abraham was, I am(Contrast how the NASB's translators render "eimi"in harmony with the surrounding context at John ch.14:9)."
John ch.17:5NASBAnd now You, Father, glorify Me together with Yourself, with the glory which I HAD(Past tense) with(greek.para=alongside) You before the world existed."
Colossians ch.1:15-17REB"Who is an image of the unseen God, Firstborn(Prototokos) of all creation,—
16 Because in him were created all things(See proverbs 8:30) in the heavens and upon the earth, The things seen and the things unseen, Whether thrones or lordships or principalities or authorities,—They all through him and for him have been created,17 And he is before all And they all in him hold together;"
Hebrews ch.1:2NASB"[a]in these last days has spoken to us [b]in His Son, whom He appointed heir of all things, through whom(see
1John ch.1:1NASB"What was from the beginning(Grk.apo arkhe), what we have heard, what we have seen with our eyes, what we have looked at and touched with our hands, concerning the Word(Grk.logos)+ of Life"
John ch.1:1NASB"In the beginning was the Word(logos), and the Word(logos) was with (The)God(Grk.Ho Theos), and the Word(logos) was God."
John ch.1:3NASB"All things came into being through Him(See proverbs ch.8:30), and apart from Him [b]not even one thing came into being that has come into being. "
Revelation ch.3:14ASV"And to the angel of the church in Laodicea write: These things saith the Amen, the faithful and true witness, the beginning(See proverbs ch.8:22,30) of the creation of God:"
Wednesday, 31 May 2023
Yet even more primeval tech vs. Darwin
Cellulose Doesn’t Just Happen
“Wood” you believe that the most abundant biopolymer on Earth requires a host of machines, genes, proteins, and accessories? Cellulose is only made by life. It doesn’t emerge fully formed from volcanoes or abiotic chemistry. To paraphrase Aristotle, if the art of cellulose manufacture were within atoms, we would have cellulose by the nature of atomic physics.
(Aristotle was reasoning that something else than raw nature was needed for shipbuilding: namely, art, which presupposes intelligence and purpose. “If the art of ship-building were in the wood,” he quipped, “we would have ships by nature.”)
Cellulose is most commonly understood as the chief component of the cell walls of plants. It is also manufactured, however, by some microbes like bacteria and algae, fungi and slime molds, and urochordates (tunicates). Each organism makes cellulose according to its needs; bacteria, for example, do not need the extra machinery to make long fibrils that plants need.
In a Primer in Current Biology, Lise C. Noack and Staffan Persson (hence N&P) described “Cellulose synthesis across kingdoms.” As evolutionists, they attribute the art of cellulose manufacture to evolution: “Other proteins evolved before the emergence of the hexameric rosette structure,” they say in one place.
Cellulose synthesis is present in all kingdoms of life and is characterized by an evolutionarily conserved BcsA/CesA synthase.
Evolutionary conservation is not evolutionary at all, it goes without saying; it means stasis. But having asserted that cellulose synthesis emerged and evolved (or not), the hard work of explaining its origin is put off the table. Most of the article deals with how cellulose is made.
Building Blocks on Other Building Blocks
The basic building block of cellulose is the sugar glucose, a six-carbon ring structure with the formula C6H12O6. Notably, glucose is not found in abiotic nature either. It is only a product of living cells. Although NASA has claimed some sugars have been detected in meteorites, I could find no reference to glucose being formed outside of living organisms.
One NIH paper from 2022 starts, “Gluconeogenesis is the pathway by which glucose is formed from non-hexose precursors such as glycerol, lactate, pyruvate, and glucogenic amino acids.” Already we see, even before cellulose synthesis begins, its monomer glucose must be “formed” by a “pathway” in a living cell. Those words suggest an organized process that assembles prior building blocks. N&P bypass that point, assuming the prior existence of glucose in the cell:
Cellulose consists of glucose molecules connected through beta-1,4-acetal linkages, which are generated by cellulose synthases and result in the formation of unbranched glucan chains.
Bacterial Cellulose Synthase
Surprisingly, N&P’s Figure 1 shows more components in the bacterial synthase machinery than in the plant machinery.
The protein complex that synthesizes cellulose was first discovered in bacteria, where it consists of a core complex composed of two subunits — BcsA and BcsB — and many accessory proteins, the presence of which varies depending on bacterial species (Figure 1A). BcsA is strictly speaking the cellulose synthase because it carries the cytosolic glycosyltransferase domain, as well as a transmembrane domain that allows for cellulose translocation and a regulatory carboxy-terminal PilZ domain that senses cyclic di-GMP (Figure 2A).
We’re just getting started, and already a supply of previously manufactured glucose molecules are needed in the right place at the right time, where the machinery is embedded in the bacterial inner membrane. Then we need the protein complex BcsA with its two subunits, and “many accessory proteins.” But getting the parts list right is only a beginning. The parts have to work together in functional harmony.
The machinery needs to link the glucose molecules together and then translocate them to the outer membrane. This is done by two more protein complexes, BcsB and BcsC. They won’t work correctly without another component: a regulator that senses cyclic di-GMP, abbreviated c-di-GMP. N&P gloss over that detail, so now we must look that up. Nature Reviews says,
c-di-GMP controls cellular processes at the transcriptional, translational and post-translational level, and through an increasing number of c-di-GMP-binding proteins and riboswitches.
We have lost count of the number of components to make cellulose and get it moved to where it is needed, and this is in a bacterium! Consider just one of the other machines:
BcsB is the cocatalytic subunit or co-polymerase because its presence is required for cellulose polymerization. It contains a periplasmic carbohydrate-binding domain that might guide the glycan chain towards the outer membrane secretory components.
The term cocatalytic implies cooperation between machines. This component, furthermore, must guide the chain to where it is needed. Another machine, BcsZ, regulates the arrangement of the polymers.
Plant Cellulose Synthase
The cellulose machinery in plants has fewer components but more functional requirements. It doesn’t need the two translocators BcsB and BcsC, because the polymers go directly from the inner membrane to the cell wall. Instead of the polymerase BcsA, plants and some algae combine the glucose molecules into polymers with a machine called CesA.
The authors speculate about a possible ancestral relationship between CesA and the bacterial BcsA synthase, but admit that “the phylogenetic relevance of terminal complex organization is still somewhat unclear.” Whatever; CesA in plants is arranged in geometrically-perfect “rosettes” of six sets of 3 CesA domains held together with three other proteins, PCR, CSR, and NTD. The rosette structure gives plant cellulose its cable-like formation, woven like strands of a rope. These cables confer the strength needed to support tall trees.
At the risk of getting too deep in the weeds, this quote gives a taste of the complexity of making cellulose. Conserved, remember, means not evolved.
At the level of the amino-acid sequence, the glycosyltransferase domain has four conserved regions: the first three each contain a D residue, whereas the fourth contains a Q(Q/R)xRW motif. The resulting D–D–D–Q(Q/R)xRW motif is conserved in all BcsA and CesA proteins and is essential for glycosyltransferase function. This highlights a remarkable conservation from sequence to tertiary protein folding, indicative of a conserved enzymatic mechanism. Apart from the D–D–D–Q(Q/R)xRW motif, plant and some algae CesA proteins have three additional domains that are likely involved in protein oligomerization: an amino-terminal RING-like zinc-finger domain (NTD), a plant-conserved region (PCR) and a class-specific region (CSR) (Figure 2B). Although the role of the NTD in CesA oligomerization is still unclear, the PCR and CSR domains are thought to be responsible for the rosette architecture of the cellulose synthase complex in plants (Figure 2C).
N&P discuss some of the similarities and differences in these machines within different species. Some parts are interchangeable, they note. Those details do not affect the overall impression that many parts are needed to make cellulose. Bacterial cellulose polymers can be less organized, because they contribute to biofilm formation. In plants, though, the polymers are shaped into microfibrils, sheets, or ribbons.
There is a strong correlation between terminal complex organization and microfibril dimensions. Rosette CesA complexes from plants and algae form small-diameter microfibrils ranging from 2 to 3.5 nm. However, single or multiple row arrangements of terminal complexes can give rise to much wider and thicker microfibrils, up to 25 nm in diameter, or flat ribbons of cellulose up to 100 nm in width. Depending on the structure, cellulose microfibrils engage with a variety of other polysaccharides and glycoproteins to form complex networks.
Just when our heads are spinning trying to remember all the parts, N&P discuss “Additional subunits of the cellulose synthase complexes.” I count at least 17 more proteins “involved in different regulatory aspects of cellulose synthesis.”
Let’s recap the importance of cellulose with this quote from a chemistry lesson from Imperial College London:
Cellulose is another glucose polymer (molecular weight 150,000-1 million) found in the cell walls of plants. Over 50% of the total organic matter in the world is cellulose. For example, wood is about 50% cellulose, and cotton is almost 100% cellulose. It is a strong, rigid linear molecule, and these features allow it to be used as the main structural support for plants. The glucose units are again held together by linkages, but this time every second glucose unit is flipped over. These links are called b,1:4 linkages, and human bodies do not possess the enzymes necessary to break this bond. Therefore any cellulose we eat passes through the digestive tract undigested, and acts as roughage. Grass feeding animals, such as cows, however, can digest cellulose, since they have extra stomachs to contain the grass for long periods while it is broken down by special bacteria.
Because of the enormous number of parts, machines and regulators involved in cellulose manufacture, we have wood, lumber, and shipbuilding. The art of shipbuilding may not be in the wood, but what would Aristotle have thought about the art of cellulose manufacture therein?
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