Saturday, 11 May 2024
Friday, 10 May 2024
Thursday, 9 May 2024
ID is a science driver
Peer-Reviewed Paper Applies Systems Engineering to Bacterial Chemotaxis
Ihave never encountered a hostile critic of intelligent design who honestly attempted to understand the design arguments and the underlying science. In most cases, naysayers simply repeat the misinformation they were fed. One of the most common false claims is that the design framework does not lead to productive research. This assertion can be thoroughly discredited simply by reading the recently updated “Bibliography of Peer-Reviewed and Peer-Edited Scientific Publications Supporting the Theory of Intelligent Design” and the new homepage for the “ID 3.0 Research Program” that David Klinghoffer summarized in a recent article.
Here, I will highlight the first article listed in the bibliography titled “Bacterial chemotaxis control process analysis with SysML,” which was authored by James Johansen and published in the journal Systems Engineering. Johannsen is a design-friendly professor of engineering at Biola University specializing in applying engineering principles and tools to biological research. His article demonstrates how applying the systems engineering modeling tool SysML to bacterial chemotaxis (i.e., navigation) yields valuable insights into its global design logic. The article further demonstrates how only a design-based framework yields significant insight into the higher-level organization of biological systems.
Application of SysML
SysML consists of nine diagrams that map a system’s structure, behavior, requirements, and parameters. Each diagram highlights a different facet of a complex system. Together they generate insights into a system’s design logic and operations.
Johansen incorporated SysML into a methodology he developed to reverse engineer biological systems, which he called Reverse-Engineering Object-Oriented Systems Engineering Method (RE-OOSEM). The methodology includes six elements
(1) Survey academic articles and textbook sources … (2) Capture the descriptive information … (3) Convert the descriptive information summary into prescriptive engineering information for architecture capture. … (4) Generate a high-level functional architecture that maps the prescriptive information to function. … (5) Capture the system architectural details into as many SysML diagrams as necessary … (6) Evaluate the system architecture and fuse information from various SysML diagrams.
Johansen’s application of RE-OOSEM to chemotaxis yielded several insights:
The results show the following engineering perspective observations. (1) Several control components are not dedicated but are available and utilized when needed. (2) Individual chemoreceptors act together as a sensor array. (3) Phosphate groups act as a signaling mechanism. (4) Methylation via CH 3 groups of the chemoreceptor results in sensitivity adaptation. (5) Closed-loop control collaboratively utilizes ligand bonding, phosphorylation, and methylation. (6) Timing relationships of the control subprocesses give insight into the system’s architecture.
Future Research
Johansen describes how future research could compare RE-OOSEM analyses of chemotaxis in diverse species to extract the engineering principles behind the differences between them. It could also incorporate additional mathematical modeling and simulations to “bring further realism to how the chemotaxis process operates and why.” Johansen’s methodology will prove a valuable tool for future research into other systems. It also illustrates the superiority of a design framework over evolution since systems engineering modeling tools only apply to those systems based on a high-level, coherent organizational pattern generated by a mind
Wednesday, 8 May 2024
Tuesday, 7 May 2024
Darwinists continue to major in micros?
Are Guppies Examples of Darwinian Macroevolution?
In 1961, in the steep mountain streams of Trinidad where cascading waterfalls create barriers which predatory fish can’t overcome, a biologist named Caryl Haskins noticed and documented the variety and population structure of communities of the small freshwater fish we call guppies. (Haskins et al. 1961)
This launched a series of beautiful experiments led by professor David N. Reznick, who captured guppies from the downstream pools (where predators are prevalent) and moved them upstream (where predators are rare). The experiments were designed to answer the following question: “How, why, and how fast does adaptive evolution happen in the real world?” (Reznick and Travis 2019) What Reznick’s team observed is that the guppies from the downstream pools underwent rapid transformations when placed into the new upstream environment. The transplants took longer to reach sexual maturity and got larger. But the rate at which this happened was surprisingly fast. When the team calculated the rate of evolution for these genetic changes, using a unit called the Darwin, they reported the guppies changed at a rate of 3,700 to 45,000 Darwins while most of the rates found in fossils are only 0.1 to 1.0 Darwins.
The Darwin is a unit of evolutionary change set by J. B. S. Haldane in 1949. It is mostly used in paleontology to compare macroevolutionary changes in fossils. Since the obvious major difference between the upstream and downstream environments was a lack of predators upstream, the phenotypic observation — that the transplanted guppies had delayed time to sexual maturity and got larger — was interpreted to be the direct effect of no predation by the larger fish. This was initially interpreted as evidence that “evolution in nature could be far more rapid, by several orders of magnitude, than had been inferred from the fossil record.” (Science News Staff 1997) Indeed, Science News reported in 1997:
Because the guppies evolved at rates so much faster than those estimated from the fossil record, Reznick suggests that selection on such short time scales is powerful enough to be behind major evolutionary changes. He argues that the study demonstrates it’s “possible to reconcile large-scale evolutionary phenomena … with what we can see in our lifetimes.” (Science News Staff 1997)
The Humble Guppy
Since this announcement, the humble guppy has been touted not only as an example of evolution happening before our eyes, but also as an example demonstrating that rapid macroevolutionary change is possible. But there were lots of assumptions in these early analyses. For example, everyone (myself included) assumed that predation was directly responsible for the guppy phenotypic differences. This is exemplified in Kenneth Miller’s summary of the experiments in his book Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution. Miller, who is a critic of intelligent design and a biologist at Brown University, explains that natural selection (specifically predator-based selection) would give a big reward to the upstream transplants for a longer period of growth since larger females mean more eggs.
Once the guppies were transplanted upstream to a predator-free environment, natural selection would give any tendency towards a longer period of growth before sexual maturity a big reward — the chance to produce more offspring, as the number of eggs a female can produce goes up with an increase in body size. (Miller 2007)
But Reznick and his group are careful scientists and they realized that a variety of hypotheses could be responsible for the changes they had observed when high-predation downstream guppies were transplanted to the upstream low-predation environment. Luckily, Reznick and his group were up to the challenge of designing and carrying out experiments to test these hypotheses.
The Risk of Being Eaten
According to the predation-driven selection hypothesis, the guppies grew larger when predation was relaxed. This suggests that in the downstream pools where predation is higher, the larger adults must be more at risk of being eaten than the smaller guppies. They came up with a way to mark individual guppies that would allow them to be recaptured, which facilitated Reznick’s team being able to calculate the death rates for adult and juvenile guppies. However, after collecting this data, they found that death rates were similar for these different sizes of guppies. This discovery showed that the cause of change could not be direct predation. So, what was causing the changes?
Let’s fast forward to when Reznick et al. completed many more experiments and published a review of their results. (Reznick and Travis 2019) They reported:
Instead of direct predation affecting the guppies’ life history, the guppies exhibited density dependent selection which means the population density was affecting life history traits. In the upstream pools where there was lower predation, the populations grew larger which meant population density increased. This might also have a selection effect. To directly quote from their abstract: “We have shown that the agent of selection on the life history, behavior, and physiology in low-predation communities is high population density and the cascade of ecological effects that stems from it.” (Reznick and Travis 2019) In other words the purported mechanism is that when the population of guppies is dense, certain individuals harboring specific alleles have a reproductive advantage, leading to allele frequency changes in the population.
Independent populations of guppies from different streams and pools exhibited parallel allele frequency changes after they were moved from downstream to upstream. From the abstract: “This gradient is repeated in many rivers; in each one, we see the same divergence between guppy populations in life history, behavior, morphology, and physiology.” (Reznick and Travis 2019) This means the same allele frequency changes from one group of guppies from stream A were observed in a different group of guppies from stream B. This is not expected if such changes are due to random mutation (RM). (van der Zee et al. 2022) After all, what are the chances that RM would make the exact same changes over and over again?
No new mutations were observed. Instead, the pre-existing allele frequency in the population shifted and this is hypothesized to be due to natural selection (NS) based on standing genetic variation. They say, “the rapid and repeatable evolution of life histories in six introduced populations means that this evolution was fueled by standing genetic variation rather than by new mutations.” This means the adaptive capacity was built into the population of the organism itself. There was no RM that did something new and helpful, that was then picked by the “agent” of NS.
What Kind of “Evolution” Is This Then?
Typically, these repeatable, parallel changes are considered an incredible display of natural selection, with many scientists thinking that the standing genetic variation ultimately arose from random mutation as well as the mechanism that is now maintaining it. Thus, RM/NS are identified as the ultimate cause under both the direct and indirect hypotheses for how predators shape guppy evolution. Is this fair? Reznick’s work shows that standing genetic variation was already baked in within the guppy population, leaving no role for random mutation. Because the variation was baked in, this places novelty-generation farther back in history, into a setting where there is less direct access to the environmental pressures that the variation is responding to. But wait, aren’t RM/NS both required for something to be considered evolution and an example of macroevolution?
The Source of Adaptive Information Is Unknown
Identifying the origin of novelty-generation as random mutation is pivotal to providing an authentic instance of Darwinian macroevolution. Instead, what we have here is an example of how populations rapidly adapt using preexisting genetic variation. Thus, these results do not provide favorable evidence for Darwinian macroevolution. Instead, they demonstrate that a previously touted example of “evolution happening before our eyes” is merely an example of population dynamics. This is where preservation of genetic diversity amongst the population means that individuals within the population represent different optimizations for unique environments. The essential question that many people are curious about remains: What is the source of the standing variation or genetic diversity that enables adaptation?
This leaves us at a place where some questions have been resolved, but the most important persist. Random mutation (RM) has been eliminated as the cause for the rapid parallel changes in the guppies. Predatory-driven selection, a form of natural selection, has also been eliminated as a possibility. However, the outstanding question of where the standing genetic variation ultimately came from remains. In my next post I will explore this question further.
Monday, 6 May 2024
Sunday, 5 May 2024
In the beginning?
Big Bang: While the West Reeled
While the West reeled from America’s stock market crash of 1929, another crisis was brewing in the field of cosmology. One of the most ambitious scientific theories in history — that the universe had a beginning — was beginning to take shape, ushering in a new cosmological paradigm. But the real heroes of the Big Bang revolution have been largely forgotten. A new book from Discovery Institute Press amends the record and tells the remarkable story. On a new episode of ID the Future, I read an excerpt from The Big Bang Revolutionaries, by distinguished astrophysicist Jean-Pierre Luminet.
A scientific revolution occurs when a widely held picture of the universe undergoes a fundamental transformation. The Einsteinian cosmological revolution was the discovery of the expansion of the universe and the recognition that the cosmos emerged from a possible singular origin. But despite its name, Albert Einstein was not the key player in the development of these ideas. Philosopher of science Dr. Stephen Meyer writes that scientific revolutions are “messy, full of unexpected twists and turns, and not without its casualties.” So it is with the Big Bang revolution.
In this brief excerpt from Chapter 1 of the book, Luminet sets the stage by describing the conditions in the early 20th century that inspired three gutsy pioneers to challenge conventional scientific wisdom to offer a compelling view of a singular creation of the universe. Download the podcast or listen to it here.
The cambrian explosion may be the biggest bang of all?
Fossil Friday: Kinorhyncha, Yet Another Animal Body Plan from the Cambrian Explosion
This Fossil Friday we will look at an obscure group of animals from a clade of molting invertebrate animals called Ecdysozoa that include the roundworm phyla (Nematoda, Nematomorpha, Priapulida, Loricifera, and Kinorhyncha) as well as tardigrades, velvet worms (Onychophora), extinct lobopods, and arthropods (Telford et al. 2009). Almost all of these ecdysozoan phyla have been recorded from the Lower Cambrian and thus clearly originated with the burst of biological creativity in the Cambrian Explosion, which brought forth all the different animal body plans. As usual the molecular clock estimates would suggest an ancient origin of ecdysozoans deep within the Ediacaran period (Howard 2021, Howard et al. 2020, 2022), which is “highlighting major discrepancy with the known fossil record of the group” (Wang et al. 2024).
Indeed, apart from some dubious trace fossils and microfossils from the terminal Ediacaran (Vannier et al. 2010, Buatois et al. 2014, Moczydłowska et al. 2015, Parry et al. 2017, Chen et al. 2018, 2019, Kesidis et al. 2019, Turk et al. 2021), unequivocal body fossils of the ecdysozoan phyla (i.e., Priapulida and Loricifera) are first appearing in the Early to Middle Cambrian. The extinct Palaeoscolecida (Early Cambrian – Silurian) are considered to be either stem nematomorphs (Hou & Bergström 1994) or rather stem priapulids (Whitaker et al. 2020). Maas et al. (2010) described a possible stem Nematoida (Nematoda+Nematomorpha) from the Middle Cambrian of Australia, but its closer affinities remain unknown. A notable gap in our knowledge of ecdysozoan history was the phylum Kinorhyncha, which until recently had no known fossil record at all. These animals are small marine invertebrates that are also called mud dragons because of their spiny body.
Hardly a decade ago, Chinese scientists described “three dimensionally phosphatized worm-like fossils from the early Cambrian rocks, approximately 535 million years old, in northern Sichuan and southern Shaanxi provinces” of South China (Zhang et al. 2015; also see Fang 2015 and NGIP 2016). They were interpreted as early kinorhynchs and therefore named Eokinorhynchus rarus (featured above). The 2 mm long animals only differed from their living relatives in having more body segments and more distinct spines. In other words: the earliest kinorhynchs were more complex than modern ones. So much for the evolutionary narrative from simple to complex.
Defying Darwinian Explanations
Five years later, Shao et al. (2020) described Zhongpingscolex qinensis from the Early Cambrian (Fortunian Stage) of South China. Their phylogenetic analysis resolved this new taxon as closest relative (sister group) of Eokinorhynchus in the stem group of Kinorhyncha.The authors did not mention three undescribed taxa of fossil kinorynchs with up to 40 mm length from the Middle Cambrian Qingjiang biota in China (Fu et al. 2019; also see Daley 2019).
Based on these findings we can safely count Kinorhyncha among the large number of animal phyla that originated abruptly in the Cambrian Explosion. The more we learn about the fossil record the more the Cambrian Explosion is confirmed as a key event in the history of life, which defies Darwinian explanations
References
Buatois LA, Narbonne GM, Mangano MG, Carmona NB & Myrow P 2014. Ediacaran matground ecology persisted into the earliest Cambrian. Nature Communications 5: 3544, 1–5. DOI: https://doi.org/10.1038/ncomms4544
Chen Z, Chen X, Zhou C, Yuan X & Xiao S 2018. Late Ediacaran trackways produced by bilaterian animals with paired appendages. Science Advances 4(6): eaao6691, 1–8. DOI: https://doi.org/10.1126/sciadv.aao6691
Chen Z, Zhou C, Yuan XL & Xiao SH 2019. Death march of a segmented and trilobate bilaterian elucidates early animal evolution. Nature 573, 412–415. DOI: https://doi.org/10.1038/s41586-019-1522-7
Daley AC 2019. A treasure trove of Cambrian fossils. Science 363(6433), 1284–1285. DOI: https://doi.org/10.1126/science.aaw8644
Fang J 2015. Spiky, Armored Worm Lived Half A Billion Years Ago. IFL Science November 26, 2015. https://www.iflscience.com/spiky-armored-worm-lived-half-billion-years-ago-32315
Fu D, Tong G, Dai T, Liu W, Yang Y, Zhang Y, Cui L, Li L, Yun H, Wu Y, Sun A, Liu C, Pei W, Gaines RR & Zhang X 2019. The Qingjiang biota—A Burgess Shale–type fossil Lagerstätte from the early Cambrian of South China. Science 363(6433), 1338–1342. DOI: https://doi.org/10.1126/science.aau8800
Howard R 2021. The Deep Evolution of Ecdysozoa. Ph.D. thesis, University of Exeter, 459 pp. https://www.proquest.com/openview/257f91384a25d9c55ea9980ed27b561f/&diss=y
Howard RJ, Edgecombe GD, Shi X, Hou X & Ma X 2020. Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan. BMC Evolutionary Biology 20(1): 156, 1–18. DOI: https://doi.org/10.1186/s12862-020-01720-6
Howard RJ, Giacomelli M, Lozano-Fernandez J, Edgecombe GD, Fleming JF, Kristensen RM, Ma X, Olesen J, Sørensen MV, Thomsen PF, Wills MA, Donoghue PCJ & Pisani D 2022. The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. Journal of the Geological Society 179, 1–14. DOI: https://doi.org/10.1144/jgs2021-107
Hou X & Bergström J 1994. Palaeoscolecid worms may be nematomorphs rather than annelids. Lethaia 27(1), 11–17. DOI: https://doi.org/10.1111/j.1502-3931.1994.tb01548.x
Kesidis G, Slater BJ, Jensen S & Budd GE 2019. Caught in the act: priapulid burrowers in early Cambrian substrates. Proceedings of the Royal Society B 286(1894), 20182505, 1–8. DOI: https://doi.org/10.1098/rspb.2018.2505
Maas A, Waloszek D, Haug J & Müller K 2007. A possible larval roundworm from the Cambrian ‘Orsten’ and its bearing on the phylogeny of Cycloneuralia. Memoirs of the Association of Australasian Palaeontologists 34, 499–519. https://www.researchgate.net/publication/238695144
Moczydłowska M, Budd GE & Agić H 2015. Ecdysozoan-like sclerites among Ediacaran microfossils. Geological Magazine 152(06), 1145–1148. DOI: https://doi.org/10.1017/S001675681500045X
NIGP 2016. Scientists Found the First Fossil Record of Kinorhyncha (Scientific Reports, 2015). Nanjing Institute of Geology and Palaeontology Palaeonews No. 2 2015. http://english.nigpas.cas.cn/ns/palaeonews/no2/201602/t20160205_159614.html
Parry LA, Boggiani PC, Condon DJ, Garwood RJ, Leme JDM, McIlroy D, Brasier MD, Trindade R, Campanha GAC, Pacheco MLAF, Diniz CQC & Liu AG 2017. Ichnological evidence for meiofaunal bilaterians from the terminal Ediacaran and earliest Cambrian of Brazil. Nature Ecology & Evolution 1, 1455–1464. DOI: https://doi.org/10.1038/s41559-017-0301-9
Shao TQ, Wang Q, Liu YH, Qin JC, Zhang YN, Liu MJ, Shao Y, Zhao JY & Zhang HQ 2020. A new scalidophoran animal from the Cambrian Fortunian Stage of South China and its implications for the origin and early evolution of Kinorhyncha. Precambrian Research 349: 105616, 1–9. DOI: https://doi.org/10.1016/j.precamres.2020.105616
Telford MJ, Bourlat SJ, Economou A, Papillon D & Rota-Stabelli O 2009. The origins and evolution of the Ecdysozoa. Chapter 8, pp. 71–79 in: Telford MJ & Littlewood DTJ (eds). Animal Evolution: Genomes, Fossils, and Trees. Oxford University Press, Oxford (UK), xvi+245 pp. DOI: https://doi.org/10.1093/acprof:oso/9780199549429.003.0008
Turk KA, Maloney KM, Laflamme M & Darroch SAF 2021. Priapulid Trace Fossils from the Late Ediacaran of Namibia. Conference GSA Connects 2021, Portland (OR). https://gsa.confex.com/gsa/2021AM/webprogram/Paper369978.html
Vannier J, Calandra I, Gaillard C & Żylińska A 2010. Priapulid worms: Pioneer horizontal burrowers at the Precambrian-Cambrian boundary. Geology 38(8), 711–714. DOI: https://doi.org/10.1130/G30829.1
Wang D, Qiang Y, Guo J, Vannier J, Song Z, Peng J, Zhang B, Sun J, Yu Y, Zhang Y, Zhang T, Yang X & Han J 2024. Early evolution of the ecdysozoan body plan. eLife Preprint, 1–22. DOI: https://doi.org/10.7554/eLife.94709.1
Whitaker AF, Jamison PG, Schiffbauer JD & Kimmig J 2020. Re-description of the Spence Shale palaeoscolecids in light of new morphological features with comments on palaeoscolecid taxonomy and taphonomy. PalZ 94(4), 661–674. DOI: https://doi.org/10.1007/s12542-020-00516-9
Zhang H, Xiao S, Liu Y, Yuan X, Wan B, Muscente AD, Shao T, Gong H & Cao, G. 2015. Armored kinorhynch-like scalidophoran animals from the early Cambrian. Scientific Reports 5(1): 16521, 1–10. DOI: https://doi.org/10.1038/srep16521
Saturday, 4 May 2024
Thursday, 2 May 2024
Wednesday, 1 May 2024
A look at the search for a third way.
Another Call for a “New Synthesis”
recently wrote a post critical of biologist Peter Corning’s “synergism hypothesis.” Afterwards Dr. Corning got in touch and advised me to consider his new paper, “Cooperative Genes in Smart Systems: Toward an Inclusive New Synthesis in Evolution,” in Progress in Biophysics and Molecular Biology.
Of course I was happy to read it. And I’m glad he pointed me to it, because although the paper doesn’t address any of the criticisms from the intelligent design perspective (honestly, I would have been pleasantly surprised if it did) it is quite relevant to the ID/Darwinism debate.
In the new paper, Corning argues that it’s time to throw out the neo-Darwinian synthesis. He goes farther than the call for an “extended synthesis” that was made by some biologists a few years ago. It’s not that the synthesis needs to be extended, he writes — it needs to be replaced.
This paper follows closely behind an article in Nature by Oxford’s Denis Noble arguing for much the same thing, which Casey Luskin reviewed here. Luskin wrote:
Noble’s vision of biology… where dogma is discarded, new ideas are considered, agency and purpose are acknowledged, cells are more complex than computers and machines, proteins are like miniature transformers, and organisms control their genomes, is highly compatible with intelligent design — certainly far more compatible than the biological thinking of the past hundred years. This means biology is moving in the right direction.
In his paper, Corning adds his voice to Noble’s. He cites Noble to argue that genes “play only a minor role” in evolution. Instead, many factors guide the evolution of life. Evolution is complex and unpredictable, he writes, and “biological evolution is not reducible to physics.”
“The time has come,” Corning declares, “to abandon the gene-centered Modern Synthesis and The Selfish Gene model of evolution.” The new synthesis should be a “more inclusive, open-ended synthesis, in recognition of the fact that there may still be more influences yet to be discovered.”
Corning identifies several factors in evolution that are neglected by the Modern Synthesis, including:
Epigenetic guidance of genetic change
Lamarckian evolution (heritable traits introduced by the habits of the parent)
Horizontal gene transfer
Symbiosis (or “cooperative effects,” or “synergy”)
Teleonomy (internal “purposiveness”)
He even cites the panspermia hypothesis, albeit in one of its more modest forms: the idea that the compounds that eventually formed the first life were seeded on Earth by meteors.
If Lamarck Can Do It…
All this points to a truth that is important for the ID position: namely, that “the assured results of modern science” may not be assured forever.
The gene-centered model is a clear example. We were supposed to believe that the “selfish gene” was unassailable and was only doubted by religious fundamentalists and cranks. If ID theorists rejected it, that was because they were at best biased, and at worst, secretly anti-science.
But now, poof! it’s just another discarded model.
Or take Lamarckian evolution. According to Corning, old Lamarck is making something of a comeback. Yet when I was first studying biology, Lamarck’s theory was presented to students as nothing but the debunked historical alternative to Darwinian evolution, faintly ridiculous in hindsight. (And to give you an idea of how quickly that means things can change: I don’t remember 9/11.)
If one theory can return from the dusty, forgotten shelves of the History of Science and spring back to pages of biology journals, then so can another. No theory should be dismissed out of hand simply because the scientific “consensus” is against it. Likewise, no theory is so well-established that it might not someday be discarded.
There Was No Problem, and Also, We Solved the Problem
Granted, the fact that biologists such as Corning are calling for a new synthesis does not, in itself, necessarily indicate a flaw in Darwin’s theory. Yes, you could interpret it as a sign that the contemporary formulation of Darwinism is failing and that its devotees are scrambling to repair or replace it. But you could also put a different spin on it — that Darwin’s mechanism works just fine, but so do many other means of evolution. The call for a new synthesis could simply show that life actually has many ways to evolve.
Corning’s statement in his book Synergistic Selection that “Darwin’s theory does not provide an explanation for the rise of biological complexity” would seem to favor the former view. Yet in this paper, despite the fact that Corning is calling for a new synthesis, he does not seem to want to state that there was ever really any big mystery or explanatory gap in unguided evolution. I suppose to do so would be to admit that ID theorists and critics of Darwin’s theory had a point. That sort of admission would be hard to publish in a peer-reviewed scientific journal (and Corning himself might not like to make it).
This is the sad irony: people will often only admit that an argument against their position has any merit after they think they have come up with a sufficient rebuttal. First, there’s no problem, and you’re ignorant to think that there is — then next thing you know, with no steps in between, you hear that the problem has been solved.
[Editor’s note: Casey Luskin has wryly called this dance move the “retroactive admission of ignorance.” “Years ago,” writes Dr. Luskin, “I began to recognize a repeating phenomenon in the rhetoric of evolutionary literature: Scientists, echoed by science journalists, would only admit a problem with their models or a challenge to their ideas once they thought they had found a solution.” See, for example, here.]
Winning by Not Playing?
Of course, if you’re going to pull the trigger and move on to Phase 2, “The problem has been solved,” you’d better be darn sure that the problem really has been solved. I suspect a major reason the “new synthesis” has yet to become truly mainstream is that its various hypotheses don’t actually resolve any of the problems posed by ID arguments.
Actually, it’s worse than that. They don’t even seem to address the arguments at all.
It’s hard to effectively refute an argument without referencing it. The paper, and the hypotheses it promotes, are presented as being in some sense a rebuttal to the ID position. Yet there are no (even indirect) references to ID arguments in this paper. The mathematical difficulties of getting information for free are not addressed. The fact that only foresight, not natural selection, increases the probability of a system of interworking parts uniting to create a given adaptive feature, is not addressed. The demonstrated improbability of getting even a single truly constructive mutation by chance in the course of Earth’s 4.6-billion-year history is not addressed. The tendency of selective pressures to break things much faster than they build them is not addressed.
If the architects of the new synthesis show no evidence of knowing more about intelligent design arguments than you can learn from Wikipedia, it’s no wonder defenders of Darwinism might be reluctant to embrace this synthesis as the new authoritative explanation for biological complexity. Although it’s rarely said out loud, the point has never been merely to explain complexity; it’s to explain complexity without design. And to do that, sadly, you sometimes have to actually engage with the design arguments (not all of which, by the way, are obvious enough to think of on your own).
As tempting as it may be, simply ignoring the dissidents didn’t work for the old synthesis, and it won’t work for the new synthesis either. Eventually — if the new synthesis survives long enough — its proponents will have to come up with their own answers to the challenges facing unguided evolution.
Tuesday, 30 April 2024
Making ID advocates of us all by lowering the bar?
Do Fungi Have Free-Will?
Nicholas P. Money has a bold hypothesis. Money, a professor of mycology at Miami University in Ohio, has argued in a peer-reviewed paper that fungi have minds.
Whenever a new hypothesis like this is published and calmly debated in scientific journals without arousing any furor, your first instinct may be to scoff: “Why is this absurd thesis acceptable, but intelligent design absolutely anathema?”
Given how often ID theorists have been dismissed without a fair hearing, that reaction is quite understandable. However, given that scientific inquiry is in fact in this sad state, I also think that any case of an out-of-the-box theory being debated civilly is a phenomenon that should be encouraged, not discouraged — especially so when the theory runs against the grain of the old scientific-materialist paradigm. We should consider this kind of thing with an open mind, and expect to receive the same courtesy.
So, with that in mind, let’s take a look at Money’s argument. Why does he think that fungi think?
Actual Mind, or a Facsimile?
Before looking at his evidence, we need to clarify something: what does Money mean by mind? Whenever the idea of “mind” come up in a scientific context, I am resigned to expect that mind will be equated with mere computing power — which isn’t really mind at all. The idea of mind is typically thrown around in a very sloppy manner, and its two key elements — experience and will/agency — are vaguely assumed to be emergent properties of physical systems.
Experience is assumed to arise automatically out of computer-like complexity. No coherent explanation for why is given, and what’s forgotten is that we only know that we possess first-person experience because we get the “inside scoop,” so to speak, from our own experience. A computer that gives certain outputs for certain inputs is only imitating the actions that we have learned (due to that inside scoop) to associate with conscious experience. That carefully crafted imitation is the only reason computers seem conscious, and it doesn’t imply that they actually are conscious (see: philosophical zombies).
Likewise, discussions of will or agency in science tend to omit the most important part: that free will cannot arise in a strictly deterministic system, or by definition it would not be free will. That means that if any system is alleged to manifest free will, we should in theory be able to find some element (however small) behaving in a way that is not predictable by fixed and inflexible laws.
Now, to be sure, “fungal mind” would be interesting from an evolutionary perspective either way. If, on one hand, it is a mere computer, with no true mind attached (no experience or will), this would indicate a very high level of complexity and mechanical sophistication; and if, on the other hand, there is a conscious mind involved, then that would strike at the very heart of the pervading scientific-materialist worldview.
Apparently, Actual Mind!
Given how often scientists (and science writers) ignore these key points, I was expecting Money to present some evidence of extreme complexity and computer like behavior, and equate that with “mind.”
I was pleasantly surprised. Money doesn’t address the metaphysics of experience. But, tentatively — without coming out and saying it in so many words — he seems to want to suggest that fungi might have free will, in the robust sense. He writes:
There is a natural tendency to consider an organism conscious if it appears to engage in decision-making that results in a unique behavioral outcome. Whether or not humans have free will, we take actions that seem willful: she finished her coffee, whereas her friend left her cup half full. On a simpler level, fungi express the same kind of individualistic behavior all the time… Although there is a high degree of predictability in the overall time-dependent form of the emerging fungus, it seems likely that its detailed shape is irreproducible.
Do you see what he’s suggesting? He seems to imply that the growth of the fungus might be non-predictable even in theory. This, in turn, would imply that it is non-deterministic — irreducible to the fixed laws of physics, chemistry, genetics, and so forth — which leaves room for the possibility of either (1) true randomness, or (2) true will or agency in the strict philosophical sense.
This is fascinating, and I do believe it has philosophical merit. (Whether it has experimental merit is a question for other mycology labs to answer.) Money is quite right that the standard way humans intuit free will is by detecting action that cannot be fully explained deterministically by outside causes.
For example: Imagine you are a great inventor in the 1890s. You’ve created a marvelous automaton that can mimic human behavior. To a casual observer it seems lifelike — but not to you. You as its creator know that it has no true freedom; certain inputs inviolably result in certain outputs. You know that chain reactions in its internal gears and switches produce each action, so you aren’t fooled by the illusion of mind.
But suppose, one day, the automaton begins to do and say things that you are quite sure you didn’t design it to do (not even by the one-step-removed process of deterministic “machine learning”). How would you react? Most likely, you would be shocked. You would declare (in your 1890s accent), “My creation has come to life!” — and you would be quite justified in your conclusion.
Likewise, a fungus with behavior that cannot be pinned-down and predicted shows every sign of being alive — in the powerful everyday sense of the word, not merely in the sense we learned in biology class. It’s very hard to prove a negative, and I doubt any mycologist has done so yet (you would probably need to involve a physicist) — but if a fungus’s actions genuinely cannot be reduced to any deterministic process, that suggests free will.
Building Blocks of a Mind
Like a human brain, a fungal brain with true free will would need to be founded on some basic unit of action that is not strictly deterministic. Money believes the origin of non-deterministic action is found in the hyphae, root-like structures that collectively form a subterranean web called a mycelium. Working together, the simple decisions of the hyphae could result in more complex decision-making for the fungal brain as a whole.
“If individual hyphae are conscious, what happens when an interconnected colony, or mycelium, of thousands of these cells forms in the soil?” Money asks. “Is a mycelium more than a sum of its parts? Can it be regarded as an integrated conscious entity?”
As support for this hypothesis, he brings in apparent evidence of complex decision-making capabilities in fungi, including an experiment that seemed to show that when fungi are burned with fire they can remember the experience for up to a day after it occurred and behave differently as a result.
Money argues that it does injustice to the fungal brain to compare it to even a sophisticated mechanical system such as the Internet. He writes in his conclusion
In this brief essay I have considered fungal expressions of consciousness, including sensitivity, decision making, learning, and memory. This rich behavioral repertoire allows fungi to adapt in real time to changes in environmental circumstances. Our internet shows none of this inherent flexibility. It is a network of pathways that generates nothing on its own. Life outshines the limitations of this drab technology in every cell.
More Philosophical Work Needed
Money is a biologist, not a philosopher, and he is prone to semantic imprecision. For example, he writes: “There is nothing artificial about this intelligence. The continuous flow of information in the live cell would overwhelm the most complex robot.”
You have to wish he would clarify what he means by “artificial.” Most dictionaries define the word as meaning human-made, but since no one to my knowledge believes that fungi were made by humans, this would be an odd thing to assert. I suspect he means something more like “merely mechanical.” It would be helpful for the interpretation of the experimental evidence if qualified philosophers of science get involved in the discussion.
That said, Money seems to understand the qualitative difference between real mind and mere artifice, and I hope his paper will be the starting point of a deeper inquiry into which kind of “mind” fungi might have.
As things stand, I don’t claim know whether there truly is any sort of immaterial “fungal mind” — and I doubt that anyone else really knows. But outside the constraining box of methodological materialism, there’s no reason to call it implausible prima facie.
Granted, it might offend an old-school Cartesian who holds to a particular interpretation of the Judeo-Christian imago Dei concept. But for my money, it’s probable. After all, we know from direct experience that we have minds. And we can infer that we and fungi share the same designer.
Monday, 29 April 2024
Sunday, 28 April 2024
The supremacy of the God and Father of Jesus is common sense itself.
Luke Ch.1:32NIV"He will be great and will be called the Son of the MOST HIGH. The LORD God will give him the throne of his father David,"
John Ch.10:29NIV"My Father, who has given them to me, is greater than ALL c ; no one can snatch them out of my Father’s hand. "
The God and Father of Jesus christ is the MOST HIGH God and thus is co equal to no one.
John Ch.8:54NIV"Jesus replied, “If I glorify myself, my glory means nothing. My Father, whom you claim as your God, is the one who glorifies me. "
According to Jesus his God and Father is the one and only God of Israel . By common consent the God and Father of Jesus is not triune. Therefore the one and only God of Israel is not triune.
John ch.20:17NIV"Jesus said, “Do not hold on to me, for I have not yet ascended to the Father. Go instead to my brothers and tell them, ‘I am ascending to my Father and your Father, to my God and your God.’ ”"
The God and Father of Jesus is not triune by common consent . The God and Father of Jesus is also the God and Father of Jesus' disciples . Therefore the God and Father of Jesus' disciples is not triune.
Matthew Ch.24:36NIV"“But about that day or hour no one knows, not even the angels in heaven, nor the Son, f but ONLY the Father. "
ONLY the God and Father of Jesus Christ is omniscient thus only the God and Father of Jesus Christ is the MOST HIGH God.
Roman's Ch.1:9EHV"To be sure, (the)God, whom I serve with my spirit by proclaiming the gospel of his Son, is my witness to how constantly I make mention of you. In all my prayers, "
Roman's Ch.3:30NIV"since there is only ONE(Grk.eis) God, who will justify the circumcised by faith and the uncircumcised through that same faith. "
Paul was an actual monotheist and thus rendered exclusive sacred service to one most high God. Whom he clearly identifies as the God and Father of Jesus Christ.
Matthew Ch.16:16NKJV"Simon Peter answered and said, “You are the Christ, the Son of the living God.”" not merely the living Father but the living God to whom all believers owe EXCLUSIVE Devotion/Sacred Service.
Malachi Ch.2:10NIV"Do we not all have one Father b ? Did not one God create us? Why do we profane the covenant of our ancestors by being unfaithful to one another?"
The God and Father of Jesus Christ is the only true God.
Saturday, 27 April 2024
Friday, 26 April 2024
Necessary but not sufficient.
A Closer Look at Natural Law
In my last post on the science of purpose, I pointed out that modern science took its inspiration from a belief that the universe was governed by immutable laws of nature emanating from the mind of God. This idea originated with the ancient Greeks, including Pythagoras, Plato, and Aristotle. Based on these concepts, in the 13th century, St. Thomas Aquinas defined within a Christian framework the specific ways and means of natural causation.
But the history of Western science took a major detour in the 17th century when René Descartes up-ended Thomistic Aristotelianism. The new Cartesian metaphysics provided fertile ground for reductionist science.
“Life Itself”
In his 1991 book Life Itself, theoretical biologist Robert Rosen attempted to reconcile materialist natural law with “life itself.” He explains that science is the endeavor of observing regularities in nature that allow scientists to create a “model” of natural behavior that is in congruence with natural events. For noncomplex natural events such as diffusion, gravitation, refraction, electricity, magnetism etc., it has been possible for scientists to derive mathematical formalisms that quite remarkably comport very well with these phenomena, such that they have great predictive power. And it has been that astonishing success which has led to the mistaken belief that these models of reality are one with nature itself. But Rosen pointed out that one huge shortcoming remains. There are no such formalisms that apply to life. Does that mean that life is at fault? Or does science need to be reimagined?
Resolving the Impasse
The solution, of course, is that scientists have mistakenly reified their formalisms, which is an obvious error. The laws of science are simply models that reflect regularities seen in nature. But they are not nature itself. They are as separate from the objects and events they describe as words on a page are separate from that which the literature attempts to depict.
Recognizing this problem, a number of innovative philosophers have been developing what seems to be an entirely new description of our world, such that it can include not just noncomplex inorganic material events, but truly all of life itself. This new metaphysics is variously termed dispositionalism, or powers ontology. But actually, it is not new. It is a revival of the insights of Aristotle and Aquinas, in a way quite intelligible to present-day philosophy and biology.
The concepts of Aristotle remain with us after almost 2,400 years because he focused directly on the concrete facts of life on display in the world around him. No computers. No calculators. No telescopes, microscopes, or laboratories. Just real life.
His description of reality was accordingly simple. Every thing has a form, i.e., a shape. And for designed objects it is the form which generates or allows the function. Forks are for gripping and spoons are for sipping. Chairs are made for sitting and ladders are made for climbing. And of course, the function of a thing defines its purpose, what Aristotle named telos
Aristotle offered a broad description of reality including inanimate objects. The form and function of stones and water and wood may seem less obvious to modern man than that of a coffee cup or a coat hanger. But the usefulness, i.e., power inherent in the properties of even these primal material objects was quite evident to earlier men.
The idea is simple because it is so fundamental. Every object has an intrinsic power because it has a corresponding inherent property. Stones have the property of solidity which gives them the power of weight and stability. Water has the property of fluidity which gives it the power of free movement. These simple substances can be further designed to acquire additional properties leading, of course, to complexity. Stones can be chiseled to give them the power to cut or penetrate. Water can be channeled to harness kinetic energy. Wood has the property of buoyancy and can be designed to build objects that float, and it also has the property to be shaped or formed into all the innumerable wooden objects one can imagine.
Now Consider Living Creatures
The property of sharp vision gives birds the power to hunt objects at great distances or pluck tiny insects out of the air. The property of echolocation gives bats the power to snatch insects on the wing even in the dark. The property of a keen sense of smell allows a polar bear to smell a seal miles away under the ice. The property of nectar production gives flowers the power to attract pollinating insects. The property of prehensile digits allows many animals the power to clutch objects needed for survival.
All of what I have said so far is immediately obvious. Now here is the payoff. The carbon atom has the property to form covalent bonds in three dimensions, giving it the power to create the scaffolding for complex molecules. Oxygen has the property of a strong electron valence, giving it the power to create an electronic asymmetry with atoms of lesser power. This is why water is a semipolar compound. Nitrogen has properties of chemical bonding intermediate between carbon, hydrogen, and oxygen, giving it the power to combine with these other three elements to create extremely complex organic compounds. And of course, CHNO (carbon, hydrogen, nitrogen, and oxygen) make up 99 percent of the atomic composition of life itself.
One with Reality Itself
As one’s thinking proceeds in this manner, we suddenly find ourselves talking about all of natural reality, from atoms to stones to vibrant living organisms, in the simple terms of properties which confer powers on matter, by virtue of form and function or telos. Nowhere in all of this is there a mathematical formula or need for materialist natural law.
Finally, and most importantly, describing natural kinds in terms of the properties that give them their power of cause and effect is one with reality itself. There is nothing derivative here. This ontology is at the ground of all we can know
This is in fact the divine natural law defined by Thomas Aquinas. His greatest metaphysical insight was to distinguish being from essence. Materialist natural law is an abstract derivative of natural essence, devoid of being. But real properties that bestow real power instantiate being in essence. For that which is in being also is in act. And according to Aquinas, that which is in act does so only as the result of divine intention.
The Jupiter of atheism?
Compelled by Multiverse Logic
Any “person who is fully knowledgeable about the subjects is compelled by logic to accept the reality of multiverses.”
That emphasis on “compelled” is in the original. From, “The sounds of science — a symphony for many instruments and voices: part II.”
Warning: if one doesn’t accept at least some variant of the multiverse, says co-author and Texas A&M physicist Roland Allen, that refusal “may be potentially harmful to the progress of science, in the same way that not accepting evolutionary biology would be potentially harmful to biology…” He describes six different flavors of the multiverse (1-, 1, 1+, 2, 3 and 4) so if you are still skeptical after stepping away from that cosmological ice cream cart, you’ll have only yourself to blame for being so stubborn and hard to please.
Well, all right then. You’re a Bad Egg if you doubt the multiverse, whatever the flavor, in the same Basket of Bad Eggs as evolution deniers. And like them, standing in the way of scientific progress.
See here for more (see pages 23-28) — a comprehensive guide to current controversies and open problems in physics.
By the way, adjectives such as “fully knowledgeable” function as circularity-guaranteeing loops in a decision tree. Do you doubt the existence of a multiverse? Then you’re not fully knowledgeable (and have no right to an opinion).
Thursday, 25 April 2024
Wednesday, 24 April 2024
Tuesday, 23 April 2024
Monday, 22 April 2024
The lowly butterfly vs. Darwinism
Battle Butterflies
You can probably think of a lot of creatures that a military might decide to copy for its submarine designs. Sharks or giant squids. Whales, perhaps. Or what about… butterflies?
MIT reports that one of their engineers, Dr. Philip Daniel, is collaborating with the U.S. Department of Defense to a create a magnetic navigation system inspired by monarch butterflies. Daniel explains:
They’re able to migrate long distances and find the exact forest that their ancestors were born into. How? One theory is that they’re able to sense the Earth’s magnetic field. They have a compass in their head, and they can use it to get where they want to go. The question is: Can humanity take advantage of the Earth’s magnetic field to accurately navigate without GPS?
Every year, around a billion monarchs travel from across North America to gather overwinter in a few specific locations in Mexico. Because adult monarchs live less than a year, none of these butterflies have made the journey before, yet they all somehow know how to travel hundreds upon hundreds of miles to arrive in the same place. (The sheer awesomeness of this journey is well-presented in the excellent Illustra Media documentary Metamorphosis: The Beauty and Design of Butterflies (2011). If you haven’t seen it, I highly recommend it.)
Magnetic Fingerprints
Daniel calls the navigational mechanism a compass, but this is just a shorthand. The word “compass” doesn’t do justice to the equipment monarchs have, as Daniel himself would no doubt be the first to acknowledge — after all, the U.S. miliary already has compasses. But monarchs have much more. What they need to navigate from different locations across the U.S. and Canada to a specific destination in Mexico is more like a complete GPS system.
So how do they do it? Daniel explains that deposits of metal in the earth’s crust can create ripples in the magnetic field, giving certain sites specific “fingerprints” to a highly sensitive detector. It has been hypothesized that monarchs use such a system, and that’s what he is hoping to create for the U.S. military.
Monarch navigation is still poorly understood, although we have figured out some pieces of it. The hypothesis of a magnetic map is necessary because what they are already known to use wouldn’t be enough to do what they do. So far, it’s known that they have an internal solar compass calibrated with an internal clock, and an internal magnetic compass as a backup for night and cloudy weather, but both of those systems would only tell them latitudinal direction, not longitude.
A reason to suspect that a magnetic map might be the solution is that it has been shown to exist in other animals. Experiments have demonstrated that turtle hatchlings can use magnetic fields to determine both latitude and longitude, implying they possess a sort of internal geographic coordinate system based on the earth’s magnetic field.
Nobody knows how this magnetic mapping system actually works. Whether it’s turtles, monarchs, or one of the other animals with seemingly magical navigational capabilities, we can still only wonder at what they can do. But if Dr. Daniel and his lab can crack the problem and engineer even a large and clumsy human equivalent of a magnetic mapping system, it might yield clues towards the design of the natural systems. A manmade functioning version would show how the system theoretically can work, and those details might enable scientists to make hypotheses that can be experimentally tested on butterflies and other migratory animals.
As always, biologists and engineers working together yields both better manmade designs and better understanding of the designs of living creatures.
Next on the Agenda…Self-Assembling Helicopters?
Incidentally, this navigation system is not even the most impressive thing about butterfly design. Another engineering marvel, also discussed in Metamorphosis, is the metamorphosis itself. It turns out, during the transformation the caterpillar completely dissolves within the chrysalis into a gooey soup, before self-assembling into a butterfly. Needless to say, this requires an incomprehensible level of coordination and planning to succeed.
Who knows? Eventually, the U.S. miliary might invent a tank than can dissolve and reassemble itself as a helicopter.
But I guess we’d better just start where we are. For the time being, the sophistication of butterfly design is far, far beyond us.
Sunday, 21 April 2024
Suboptimal design or suboptimal science?
The Panda’s Thumb: An Extraordinary Instance of Design?
Does the panda’s thumb refute intelligent design? Or is it one of the most extraordinary manipulation systems in the mammalian world, as one respected study has found? On this episode of ID the Future, host Casey Luskin speaks with philosopher Dr. Stephen Dilley about his recent paper evaluating the strengths and weaknesses of the iconic panda’s thumb argument for evolution.
Harvard scientist and historian of science Stephen Jay Gould is well-known for his theory that science and religion are non-overlapping magisteria and best kept separate from one another. Yet one of his favorite arguments for evolutionary processes was the panda’s thumb, which is underpinned by a theology-laden premise: namely, God wouldn’t design the panda’s thumb like this, therefore a clumsy step-wise natural process is responsible. But does this argument hold up to philosophical and scientific scrutiny?
In this conversation, Dr. Dilley challenges the assumptions implicit in the panda’s thumb argument. He also explains that what might be deemed by some as sub-optimal design may actually be an engineering trade-off. Optimizing a structure can sometimes come at the cost of certain design constraints. Ultimately, Dilley holds that the panda’s thumb may be more of a problem for an evolutionary view than a design perspective: “If in fact the very best studies commend the thumb for its efficiency, its dexterity, its precision…then by Gould’s own framing the panda’s thumb would pose a problem” for evolutionists. Download the podcast or listen to it here
On the founding of "the eternal metropolis"
According to legend, Ancient Rome was founded by the two brothers, and demigods, Romulus and Remus, on 21 April 753 BCE. The legend claims that in an argument over who would rule the city (or, in another version, where the city would be located) Romulus killed Remus and named the city after himself. This story of the founding of Rome is the best known but it is not the only one.
Other legends claim the city was named after a woman, Roma, who traveled with Aeneas and the other survivors from Troy after that city fell. Upon landing on the banks of the Tiber River, Roma and the other women objected when the men wanted to move on. She led the women in the burning of the Trojan ships and so effectively stranded the Trojan survivors at the site which would eventually become Rome. Aeneas of Troy is featured in this legend and also, famously, in Virgil's Aeneid, as a founder of Rome and the ancestor of Romulus and Remus, thus linking Rome with the grandeur and might which was once Troy.Still other theories concerning the name of the famous city suggest it came from Rumon, the ancient name for the Tiber River, and was simply a place name given to the small trading center established on its banks or that the name derived from an Etruscan word which could have designated one of their settlements.
Saturday, 20 April 2024
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