Last universal common ancestor

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Last_universal_common_ancestor

Phylogenetic tree linking all major groups of living organisms, namely the bacteria, archaea, and eukarya, as proposed by Woese et al 1990, with the last universal common ancestor (LUCA) shown at the root

The last universal common ancestor (LUCA) is the hypothesized common ancestral cell population from which all subsequent life forms descend, including Bacteria, Archaea, and Eukarya. The cell had a lipid bilayer; it possessed the genetic code and ribosomes which translated from DNA or RNA to proteins. Although the timing of the LUCA cannot be definitively constrained, most studies suggest that the LUCA existed by 3.5 billion years ago, and possibly as early as 4.3 billion years ago or earlier. The nature of this point or stage of divergence remains a topic of research.

All earlier forms of life preceding this divergence and all extant organisms are generally thought to share common ancestry. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported in preference to competing multiple-ancestry hypotheses. The first universal common ancestor (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.

Whether the genesis of viruses falls before or after the LUCA–as well as the diversity of extant viruses and their hosts–remains a subject of investigation.

While no fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes its existence widely accepted by biochemists. Its characteristics can be inferred from shared features of modern genomes. These genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to mRNA to proteins.

Historical background

Further information: Tree of life (biology)

A tree of life, like this one from Charles Darwin's notebooks c. July 1837, implies a single common ancestor at its root (labelled "1").

A phylogenetic tree directly portrays the idea of evolution by descent from a single ancestor. An early tree of life was sketched by Jean-Baptiste Lamarck in his Philosophie zoologique in 1809. Charles Darwin more famously proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859: "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." The last sentence of the book begins with a restatement of the hypothesis:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one ...

By 1871, in another letter to Hooker, Darwin speculated on the natural origin of life itself, writing that life might have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present," an early expression of abiogenesis.

The term "last universal common ancestor" or "LUCA" was first used in the 1990s for such a primordial organism.

Inferring LUCA's features

Biochemical mechanisms

While the anatomy of the LUCA cannot be reconstructed with certainty, its biochemical mechanisms can be deduced and described in some detail, based on properties shared by currently living organisms as well as genetic analysis.

The LUCA certainly had genes and a genetic code. Its genetic material was most likely DNA, so that it lived after the RNA world. The DNA was kept double-stranded by an enzyme, DNA polymerase, which recognises the structure and directionality of DNA. The integrity of the DNA was maintained by a group of repair enzymes including DNA topoisomerase. If the genetic code was based on dual-stranded DNA, it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA. It had multiple DNA-binding proteins, such as histone-fold proteins. The genetic code was expressed into proteins. These were assembled from 20 free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins.

Although LUCA was likely not capable of sexual interaction, gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate genetic recombination. Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the RecA protein in bacteria, the RadA protein in archaea, and the Rad51 and Dmc1 proteins in eukaryota.

The functionality of LUCA as well as evidence for the early evolution of membrane-dependent biological systems together suggest that LUCA had cellularity and cell membranes. As for the cell's structure, it contained a water-based cytoplasm effectively enclosed by a lipid bilayer membrane; it was capable of reproducing by cell division. It tended to exclude sodium and concentrate potassium by means of specific ion transporters (or ion pumps). The cell multiplied by duplicating all its contents followed by cellular division. The cell used chemiosmosis to produce energy. It also reduced CO₂ and oxidized H₂ (methanogenesis or acetogenesis) via acetyl-thioesters.

By phylogenetic bracketing, analysis of the presumed LUCA's offspring groups, LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of the three-domain system, Carl Woese, stated that in its genetic machinery, the LUCA would have been a "simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".

Because both bacteria and archaea have differences in the structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na⁺/H⁺ antiporters likely led to the evolution of impermeable membranes present in eukaryotes, archaea, and bacteria. It is stated that "The late and independent evolution of glycolysis but not gluconeogenesis is entirely consistent with LUCA being powered by natural proton gradients across leaky membranes. Several discordant traits are likely to be linked to the late evolution of cell membranes, notably the cell wall, whose synthesis depends on the membrane and DNA replication". Although LUCA likely had DNA, it is unknown if it could replicate DNA and is suggested that it "might just have been a chemically stable repository for RNA-based replication". It is likely that the permeable membrane of LUCA was composed of archaeal lipids (isoprenoids) and bacterial lipids (fatty acids). Isoprenoids would have enhanced stabilization of LUCA's membrane in the surrounding extreme habitat. Nick Lane and coauthors state that "The advantages and disadvantages of incorporating isoprenoids into cell membranes in different microenvironments may have driven membrane divergence, with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".

A 2024 study suggests that LUCA's genome was similar in size to that of modern prokaryotes, coding for some 2,600 proteins; that it respired anaerobically, and was an acetogen; and that it had an early CAS-based anti-viral immune system.

An anaerobic thermophile

Further information: Phylogenetic bracketing

 

A direct way to infer LUCA's genome would be to find genes common to all surviving descendants, but little can be learnt by this approach, as there are only about 30 such genes. They are mostly for ribosome proteins, proving that LUCA had the genetic code. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.

Three ways to infer genes present in LUCA: universal presence, presence in both the Bacterial and Archaean domains, and presence in two phyla in both domains. The first yields as stated only about 30 genes; the second, some 11,000 with lateral gene transfer (LGT) very likely; the third, 355 genes probably in LUCA, since they were found in at least two phyla in both domains, making LGT an unlikely explanation.

An alternative to the search for "universal" traits is to use genome analysis to identify phylogenetically ancient genes. This gives a picture of a LUCA that could live in a geochemically harsh environment and is like modern prokaryotes. Analysis of biochemical pathways implies the same sort of chemistry as does phylogenetic analysis.

LUCA systems and environment, including the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, and most likely DNA complete with the genetic code and enzymes to replicate it, transcribe it to RNA, and translate it to proteins.

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes representing many phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms." The cofactors also reveal "dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." They show that methanogens and clostridia were basal, near the root of the phylogenetic tree, in the 355 protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂, and iron, where ocean water interacted with hot magma beneath the ocean floor. It is even inferred that LUCA also grew from H₂ and CO₂ via the reverse incomplete Krebs cycle. Other metabolic pathways inferred in LUCA are the pentose phosphate pathway, glycolysis, and gluconeogenesis. Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the origin of life took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.

The LUCA used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, if it was an autotroph, or to respire anaerobically, if it was a heterotroph.

Weiss and colleagues write that "Experiments ... demonstrate that ... acetyl-CoA pathway [chemicals used in anaerobic respiration] formate, methanol, acetyl moieties, and even pyruvate arise spontaneously ... from CO₂, native metals, and water", a combination present in hydrothermal vents.

An experiment shows that Zn²⁺, Cr³⁺, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the reverse Krebs cycle in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.

Undersampled protein families

Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing convergence or horizontal gene transfer events to vertical descent; on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events. A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K⁺-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K⁺/Na⁺ ratio, NH⁺
₄, Fe²⁺, CO²⁺, Ni²⁺, Mg²⁺, Mn²⁺, Zn²⁺, pyrophosphate, and PO³⁻
₄ which would imply a terrestrial hot spring habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to autotrophy (the ability of an organism to create its own organic matter), suggesting that the LUCA had a Heterotrophic lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.

The presence of the energy-handling enzymes CODH/acetyl-coenzyme A synthase in LUCA could be compatible not only with being an autotroph but also with life as a mixotroph or heterotroph. Weiss et al. in 2018 replied that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.

A 2024 study directly estimated the order in which amino acids were added into the genetic code from early protein domain sequences. A total of 969 protein domains were classified as present in LUCA, including 101 domain sequences that dated back to the even-older pre-LUCA communities. 88% of the protein domains annotated as LUCA or pre-LUCA were confirmed by Moody et al. 2024, by being associated with proteins that are more than 50% likely to be present in LUCA. It found that amino acids that bind metals, and those that contain sulphur, came early in the genetic code. The study suggests that sulphur metabolism and catalysis involving metals were important elements of life at the time of LUCA.

Possibly a mesophile

Several lines of evidence suggest that LUCA was non-thermophilic. The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result, they occur more frequently in the rRNA of thermophiles; however, this is not seen in LUCA's reconstructed rRNA.

The identification of thermophilic genes in the LUCA has been challenged, as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via horizontal gene transfer, as in Woese's 1998 hypothesis. For instance, the thermophile-specific topoisomerase, reverse gyrase, was initially attributed to LUCA before an exhaustive phylogenetic study revealed a more recent origin of this enzyme followed by extensive horizontal gene transfer. LUCA could have been a mesophile that fixed CO₂ and relied on H₂, and lived close to hydrothermal vents.

Further evidence that LUCA was mesophilic comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature. According to phylogenetic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.

Evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations, and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.

Age

Further information: Abiogenesis

Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.8 to 3.5 bya (billion years ago) in the Paleoarchean, a few hundred million years before the earliest fossil evidence of life, for which candidates range in age from 4.28 to 3.48 bya. This placed the origin of the first forms of life shortly after the Late Heavy Bombardment which was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied a molecular clock model to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment (making the LUCA over 3.9 bya). A 2022 study suggested an age of around 4.2–3.6 bya for the LUCA. A 2024 study suggested that the LUCA lived around 4.2 bya (with a confidence interval of 4.33–4.09 bya).

Root of the tree of life

2005 tree of life showing horizontal gene transfers between branches including (coloured lines) the symbiogenesis of plastids and mitochondria. "Horizontal gene transfer and how it has impacted the evolution of life is presented through a web connecting bifurcating branches that complicate, yet do not erase, the tree of life".

For branching of bacteria phyla, see Bacterial phyla.

In 1990, a novel concept of the tree of life was presented, dividing the living world into three stems, classified as the domains Bacteria, Archaea, Eukarya. It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form". This tree and its rooting became the subject of debate.

In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g.). Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed. Presumably horizontal gene transfer has decreased with growing cell stability.

A modified version of the tree, based on several molecular studies, has its root between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota. A small minority of studies place the root in the domain bacteria, in the phylum Bacillota, or state that the phylum Chloroflexota (formerly Chloroflexi) is basal to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by Thomas Cavalier-Smith). Metagenomic analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea. With the later gene pool of LUCA's descendants, sharing a common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.

The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (as discussed by Wächtershäuser), Otto Kandler proposed a successive divergence of the three domains of life from a multiphenotypical population of pre-cells, reached by gradual evolutionary improvements (cellularization). The phenotypically diverse pre-cells of this population were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time, the partition into three lines (the three domains) of life. Kandler's pre-cell theory is supported by Wächtershäuser. In 1998, Carl Woese, based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms. Other authors concur that there was a "complex collective genome" at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups; Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."

The theory of a universal common ancestry of life is widely accepted. In 2010, based on "the vast array of molecular sequences now available from all domains of life," D. L. Theobald published a "formal test" of universal common ancestry (UCA). This deals with the common descent of all extant terrestrial organisms, each being a genealogical descendant of a single species from the distant past. His formal test favoured the existence of a universal common ancestry over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles imply that all organisms do have a common ancestry.

A proposed non-cellular ancestor to LUCA is the First universal common ancestor (FUCA). FUCA would therefore be the ancestor to every modern cell as well as to ancient, now-extinct cellular lineages not descending from LUCA. FUCA is assumed to have had descendants other than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have been horizontally transferred into the genome of early descendants of LUCA.

LUCA and viruses

The origin of viruses remains disputed. Since viruses need host cells for their replication, it is likely that they emerged after the formation of cells. Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life. There are different hypotheses for the origins of viruses, for instance an early viral origin from the RNA world or a later viral origin from selfish DNA.

Based on how viruses are currently distributed across the bacteria and archaea, the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts. Furthermore, extensive virus evolution seems to have preceded the LUCA, since the jelly-roll structure of capsid proteins is shared by RNA and DNA viruses across all three domains of life. LUCA's viruses were probably mainly dsDNA viruses in the groups called Duplodnaviria and Varidnaviria. Two other single-stranded DNA virus groups within the Monodnaviria, the Microviridae and the Tubulavirales, likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with RNA viruses directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.

LUCA might have been the ancestor to some viruses, as it might have had at least two descendants: LUCELLA, the Last Universal Cellular Ancestor, the ancestor to all cells, and the archaic virocell ancestor, the ancestor to large-to-medium-sized DNA viruses. Viruses might have evolved before LUCA but after the first universal common ancestor (FUCA), according to the reduction hypothesis, where giant viruses evolved from primordial cells that became parasitic.

Criticism of science

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Criticism_of_science 

Personification of "Science" in front of the Boston Public Library

Criticism of science addresses problems within science in order to improve science as a whole and its role in society. Criticisms come from philosophy, from social movements like feminism, and from within science itself.

The emerging field of metascience seeks to increase the quality of and efficiency of scientific research by improving the scientific process.

Philosophical critiques

"All methodologies, even the most obvious ones, have their limits." ―Paul Feyerabend in Against Method

Philosopher of science Paul Feyerabend advanced the idea of epistemological anarchism, which holds that there are no useful and exception-free methodological rules governing the progress of science or the growth of knowledge, and that the idea that science can or should operate according to universal and fixed rules is unrealistic, pernicious and detrimental to science itself. Feyerabend advocates a democratic society where science is treated as equal to other ideologies or social institutions such as religion, and education, or magic and mythology, and considers the dominance of science in society authoritarian and unjustified. He also contended (along with Imre Lakatos) that the demarcation problem of distinguishing science from pseudoscience on objective grounds is not possible and thus fatal to the notion of science running according to fixed, universal rules.

Feyerabend also criticized science for not having evidence for its own philosophical precepts. Particularly the notion of Uniformity of Law and the Uniformity of Process across time and space, or Uniformitarianism in short, as noted by Stephen Jay Gould. "We have to realize that a unified theory of the physical world simply does not exist" says Feyerabend, "We have theories that work in restricted regions, we have purely formal attempts to condense them into a single formula, we have lots of unfounded claims (such as the claim that all of chemistry can be reduced to physics), phenomena that do not fit into the accepted framework are suppressed; in physics, which many scientists regard as the one really basic science, we have now at least three different points of view...without a promise of conceptual (and not only formal) unification". In other words, science is begging the question when it presupposes that there is a universal truth with no proof thereof.

Historian Jacques Barzun termed science "a faith as fanatical as any in history" and warned against the use of scientific thought to suppress considerations of meaning as integral to human existence.

Sociologist Stanley Aronowitz scrutinized science for operating with the presumption that the only acceptable criticisms of science are those conducted within the methodological framework that science has set up for itself. That science insists that only those who have been inducted into its community, through means of training and credentials, are qualified to make these criticisms. Aronowitz also alleged that while scientists consider it absurd that Fundamentalist Christianity uses biblical references to bolster their claim that the Bible is true, scientists pull the same tactic by using the tools of science to settle disputes concerning its own validity.

New-age writer Alan Watts criticized science for operating under a materialist model of the world that he posited is simply a modified version of the Abrahamic worldview, that "the universe is constructed and maintained by a Lawmaker" (commonly identified as God or the Logos). Watts asserts that during the rise of secularism through the 18th to 20th century when scientific philosophers got rid of the notion of a lawmaker they kept the notion of law, and that the idea that the world is a material machine run by law is a presumption just as unscientific as religious doctrines that affirm it is a material machine made and run by a lawmaker.

Epistemology

David Parkin compared the epistemological stance of science to that of divination. He suggested that, to the degree that divination is an epistemologically specific means of gaining insight into a given question, science itself can be considered a form of divination that is framed from a Western view of the nature (and thus possible applications) of knowledge.

Author and Episkopos of Discordianism Robert Anton Wilson stresses that the instruments used in scientific investigation produce meaningful answers relevant only to the instrument, and that there is no objective vantage point from which science could verify its findings since all findings are relative to begin with.

Ethics

Joseph Wright of Derby (1768): An Experiment on a Bird in an Air Pump, National Gallery, London

Several academics have offered critiques concerning ethics in science. In Science and Ethics, for example, the professor of philosophy Bernard Rollin examines the relevance of ethics to science, and argues in favor of making education in ethics part and parcel of scientific training.

Social science scholars, like social anthropologist Tim Ingold, and scholars from philosophy and the humanities, like critical theorist Adorno, have criticized modern science for subservience to economic and technological interests. A related criticism is the debate on positivism. While before the 19th century science was perceived to be in opposition to religion, in contemporary society science is often defined as the antithesis of the humanities and the arts.

Many thinkers, such as Carolyn Merchant, Theodor Adorno and E. F. Schumacher considered that the 17th century Scientific Revolution shifted science from a focus on understanding nature, or wisdom, to a focus on manipulating nature, i.e. power, and that science's emphasis on manipulating nature leads it inevitably to manipulate people, as well. Science's focus on quantitative measures has led to critiques that it is unable to recognize important qualitative aspects of the world.

Critiques from within science

Metascience is the use of scientific methodology to study science itself, with the goal of increasing the quality of research while reducing waste. Meta-research has identified methodological weaknesses in many areas of science. Critics argue that reforms are needed to address these weaknesses.

Reproducibility

The social sciences, such as social psychology, have long suffered from the problem of their studies being largely not reproducible. Now, medicine has come under similar pressures. In a phenomenon known as the replication crisis, journals are less likely to publish straight replication studies so it may be difficult to disprove results. Another result of publication bias is the Proteus phenomenon: early attempts to replicate results tend to contradict them. However, there are claims that this bias may be beneficial, allowing accurate meta-analysis with fewer publications.

Cognitive biases

Critics argue that the biggest bias within science is motivated reasoning, whereby scientists are more likely to accept evidence that supports their hypothesis and more likely to scrutinize findings that do not. Scientists do not practice pure induction but instead often come into science with preconceived ideas and often will, unconsciously or consciously, interpret observations to support their own hypotheses through confirmation bias. For example, scientists may re-run trials when they do not support a hypothesis but use results from the first trial when they do support their hypothesis. It is often argued that while each individual has cognitive biases, these biases are corrected for when scientific evidence converges. However, systematic issues in the publication system of academic journals can often compound these biases. Issues like publication bias, where studies with non-significant results are less likely to be published, and selective outcome reporting bias, where only the significant outcomes out of a variety of outcomes are likely to be published, are common within academic literature. These biases have widespread implications, such as the distortion of meta-analyses where only studies that include positive results are likely to be included. Statistical outcomes can be manipulated as well, for example large numbers of participants can be used and trials overpowered so that small difference cause significant effects or inclusion criteria can be changed to include those are most likely to respond to a treatment. Whether produced on purpose or not, all of these issues need to be taken into consideration within scientific research, and peer-reviewed published evidence should not be assumed to be outside of the realm of bias and error; some critics are now claiming that many results in scientific journals are false or exaggerated.

Science has been criticized for being too conformist, and for becoming on average less disruptive.

Feminist critiques

See also: Feminist philosophy of science

Feminist scholars and women scientists such as Emily Martin, Evelyn Fox Keller, Ruth Hubbard, Londa Schiebinger and Bonnie Spanier have critiqued science because they believe it presents itself as objective and neutral while ignoring its inherent gender bias. They assert that gender bias exists in the language and practice of science, as well as in the expected appearance and social acceptance of who can be scientists within society.

Sandra Harding says that the "moral and political insights of the women's movement have inspired social scientists and biologists to raise critical questions about the ways traditional researchers have explained gender, sex, and relations within and between the social and natural worlds." Anne Fausto-Sterling is a prominent example of this kind of feminist work within biological science. Some feminists, such as Ruth Hubbard and Evelyn Fox Keller, criticize traditional scientific discourse as being historically biased towards a male perspective. A part of the feminist research agenda is the examination of the ways in which power inequities are created and/or reinforced in scientific and academic institutions.

Other feminist scholars, such as Ann Hibner Koblitz, Lenore Blum, Mary Gray, Mary Beth Ruskai, and Pnina Abir-Am and Dorinda Outram, have criticized some gender and science theories for ignoring the diverse nature of scientific research and the tremendous variation in women's experiences in different cultures and historical periods. For example, the first generation of women to receive advanced university degrees in Europe were almost entirely in the natural sciences and medicine—in part because those fields at the time were much more welcoming of women than were the humanities. Koblitz and others who are interested in increasing the number of women in science have expressed concern that some of the statements by feminist critics of science could undermine those efforts, notably the following assertion by Keller:

Just as surely as inauthenticity is the cost a woman suffers by joining men in misogynist jokes, so it is, equally, the cost suffered by a woman who identifies with an image of the scientist modeled on the patriarchal husband. Only if she undergoes a radical disidentification from self can she share masculine pleasure in mastering a nature cast in the image of woman as passive, inert, and blind.

Language in science

Emily Martin examines the metaphors used in science to support her claim that science reinforces socially constructed ideas about gender rather than objective views of nature. In her study about the fertilization process, Martin describes several cases when gender-biased perception skewed the descriptions of biological processes during fertilization and even possibly hampered the research. She asserts that classic metaphors of the strong dominant sperm racing to an idle egg are products of gendered stereotyping rather than a faithful portrayal of human fertilization. The notion that women are passive and men are active are socially constructed attributes of gender which, according to Martin, scientists have projected onto the events of fertilization and so obscuring the fact that eggs do play an active role. For example, she wrote that "even after having revealed...the egg to be a chemically active sperm catcher, even after discussing the egg's role in tethering the sperm, the research team continued for another three years to describe the sperm's role as actively penetrating the egg." Scott Gilbert, a developmental biologist at Swarthmore College supports her position: "if you don't have an interpretation of fertilization that allows you to look at the egg as active, you won't look for the molecules that can prove it. You simply won't find activities that you don't visualize."

Media and politics

Main article: Politicization of science

The mass media face a number of pressures that can prevent them from accurately depicting competing scientific claims in terms of their credibility within the scientific community as a whole. Determining how much weight to give different sides in a scientific debate requires considerable expertise regarding the matter. Few journalists have real scientific knowledge, and even beat reporters who know a great deal about certain scientific issues may know little about other ones they are suddenly asked to cover.

Many issues damage the relationship of science to the media and the use of science and scientific arguments by politicians. As a very broad generalisation, many politicians seek certainties and facts whilst scientists typically offer probabilities and caveats.^{[citation needed]} However, politicians' ability to be heard in the mass media frequently distorts the scientific understanding by the public. Examples in Britain include the controversy over the MMR inoculation, and the 1988 forced resignation of a government minister, Edwina Currie, for revealing the high probability that battery eggs were contaminated with Salmonella.

Some scientists and philosophers suggest that scientific theories are more or less shaped by the dominant political, economic, or cultural models of the time, even though the scientific community may claim to be exempt from social influences and historical conditions. For example, the Russian philosopher, socialist, and zoologist Peter Kropotkin thought that the Darwinian theory of evolution overstressed a painful "we must struggle to survive" way of life, which he said was influenced by capitalism and the struggling lifestyles people lived within it. Karl Marx also thought that science was largely driven by and used as capital.

Robert Anton Wilson, Stanley Aronowitz, and Paul Feyerabend all thought that the military-industrial complex, large corporations, and the grants that came from them had an immense influence over the research and even results of scientific experiments. Aronowitz even went as far as to say "It does not matter that the scientific community ritualistically denies its alliance with economic/industrial and military power. The evidence is overwhelming that such is the case. Thus, every major power has a national science policy; the United States Military appropriates billions each year for 'basic' as well as 'applied' research".

Anima mundi

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Anima_mundi 

Illustration of the correspondences between all parts of the created cosmos, with its soul depicted as a woman, from Robert Fludd's Utriusque Cosmi Maioris Scilicet et Minoris Metaphysica, Physica atque Technica Historia

The concept of the anima mundi (Latin), world soul (Ancient Greek: ψυχὴ κόσμου, psychḕ kósmou), or soul of the world (ψυχὴ τοῦ κόσμου, psychḕ toû kósmou) posits an intrinsic connection between all living beings, suggesting that the world is animated by a soul much like the human body. Rooted in ancient Greek and Roman philosophy, the idea holds that the world soul infuses the cosmos with life and intelligence. This notion has been influential across various systems of thought, including Stoicism, Gnosticism, Neoplatonism, and Hermeticism, shaping metaphysical and cosmological frameworks throughout history.

In ancient philosophy, Plato's dialogue Timaeus introduces the universe as a living creature endowed with a soul and reason, constructed by the demiurge according to a rational pattern expressed through mathematical principles. Plato describes the world soul as a mixture of sameness and difference, forming a unified, harmonious entity that permeates the cosmos. This soul animates the universe, ensuring its rational structure and function according to a divine plan, with the motions of the seven classical planets reflecting the deep connection between mathematics and reality in Platonic thought.

Stoicism and Gnosticism are two significant philosophical systems that elaborated on this concept. Stoicism, founded by Zeno of Citium in the early 3rd century BCE, posited that the universe is a single, living entity permeated by the divine rational principle known as the logos, which organizes and animates the cosmos, functioning as its soul. Gnosticism, emerging in the early centuries of the Common Era, often associates the world soul with Sophia, who embodies divine wisdom and the descent into the material world. Gnostics believed that esoteric knowledge could transcend the material world and reunite with the divine.

Neoplatonism and Hermeticism also incorporated the concept of the world soul into their cosmologies. Neoplatonism, flourishing in the 3rd century CE through philosophers like Plotinus and Proclus, proposed a hierarchical structure of existence with the World Soul acting as an intermediary between the intelligible realm and the material world, animating and organizing the cosmos. Hermeticism, based on writings attributed to Hermes Trismegistus, views the world soul as a vital force uniting the cosmos. Hermetic texts describe the cosmos as a living being imbued with a divine spirit, emphasizing the unity and interconnection of all things. Aligning oneself with the world soul is seen as a path to spiritual enlightenment and union with the divine, a belief that experienced a resurgence during the Renaissance when Hermeticism was revived and integrated into Renaissance thought, influencing various intellectual and spiritual movements of the time.

Ancient philosophy

Plato described the universe as a living being in his dialogue Timaeus (30b–d):

Thus, then, in accordance with the likely account, we must declare that this Cosmos has verily come into existence as a Living Creature endowed with soul and reason [...] a Living Creature, one and visible, containing within itself all the living creatures which are by nature akin to itself.

Plato's Timaeus describes this living cosmos as being built by the demiurge, constructed to be self-identical and intelligible to reason, according to a rational pattern expressed in mathematical principles and Pythagorean ratios describing the structure of the cosmos, and particularly the motions of the seven classical planets. The living universe is also a god titled Ouranos and Kosmos, which shows, as scholars have argued, that Plato mediates between the poetic and presocratic traditions.

In Timaeus, Plato presents the cosmos as a single, living organism that possesses a soul and intelligence. The demiurge, a divine craftsman, creates the universe by imposing order on pre-existing chaotic matter. This creation is not ex nihilo but rather a process of organizing the cosmos according to the eternal Forms, which are perfect, immutable archetypes of all things.

Plato explains that the world soul is a mixture of the same and the different, woven together to form a unified, harmonious entity. This soul permeates the entire cosmos, animating it and endowing it with life and intelligence. The world soul is responsible for the rational structure of the universe, ensuring that everything functions according to a divine plan.

The rational pattern of the cosmos is expressed through mathematical principles and Pythagorean ratios, reflecting the deep connection between mathematics and the structure of reality in Platonic thought. The motions of the seven classical planets (the Moon, Mercury, Venus, the Sun, Mars, Jupiter, and Saturn) are particularly significant, as they embody the harmony and order of the universe.

Plato's identification of the cosmos as a god, titled Ouranos and Kosmos, reveals his synthesis of different philosophical traditions. The name Ouranos connects the world soul to the ancient Greek personification of the sky, while Kosmos signifies order and beauty. By mediating between poetic and presocratic traditions, Plato integrates mythological and philosophical elements into a coherent cosmological vision.

Stoicism

Further information: Stoic physics § Soul, and Pneuma (Stoic)

The Stoic school of philosophy, founded by Zeno of Citium in the early 3rd century BCE, significantly contributed to the development of the concept of the world soul. Stoicism posits that the universe is a single, living entity permeated by a divine rational principle known as the logos. This principle organizes and animates the cosmos, functioning as its soul.

Central to Stoic cosmology is the belief that the logos operates as the rational structure underlying all existence. This rational principle is equated with God, nature, and the soul of the universe, making the cosmos a living, rational organism. The Stoics identified the world soul with the concept of pneuma, a life-giving force that pervades and sustains all things. Pneuma is a mixture of air and fire, elements considered active and capable of bestowing life and motion.

The Stoic philosopher Cleanthes described the world soul in his "Hymn to Zeus", where he praises Zeus (a personification of the logos) for harmonizing the cosmos and ensuring its rational order. Chrysippus, another prominent Stoic, further developed the idea of the world soul, arguing that it is the animating principle that ensures the coherence and unity of the cosmos.

The Stoic view of the world soul differs from Plato's in that it emphasizes the materiality of the pneuma. For the Stoics, the soul of the universe is not an abstract, separate entity but a physical presence that interpenetrates the cosmos, providing it with structure and purpose. This physicalist interpretation reflects the Stoic commitment to the idea that only bodies can act and be acted upon.

The Stoic concept of the world soul also has ethical implications. Since the logos governs the cosmos rationally, living in accordance with nature means aligning one's life with this rational order. The Stoics believed that by understanding and accepting the world's rational structure, individuals could achieve a state of tranquility and virtue.

Gnosticism and Neoplatonism

Gnosticism

Further information: Sophia (Gnosticism) § As world-soul

Gnosticism, a diverse and syncretic religious movement that emerged in the early centuries of the Common Era, also incorporated the concept of the world soul into its cosmological and theological framework. Gnostic systems generally posited a dualistic worldview, contrasting the material world with a higher, spiritual reality. In this context, the world soul often played a crucial role in bridging the divine and material realms.

In Gnostic thought, the world soul is often associated with the figure of Sophia (Wisdom), who embodies both the divine wisdom and the tragic descent into the material world. Sophia's fall and subsequent redemption are central themes in many Gnostic texts. According to the Apocryphon of John, a key Gnostic scripture, Sophia's emanation resulted in the creation of the material world, which is seen as flawed and distant from the divine pleroma (fullness).

In Gnostic systems, the concept of the world soul often carries significant ethical and soteriological implications. Gnostics believed that by acquiring esoteric knowledge and understanding their divine origin, individuals could transcend the material world and reunite with the divine. This process of gnosis involved recognizing the world soul's entrapment in the material realm and working towards its liberation.

Manichaeism

In Manichaeism, a major Gnostic religion founded by the prophet Mani in the 3rd century CE, the world soul was also called the Light Soul and the Living Soul (Middle Persian: grīw zīndag), contrasting it with matter, which was associated with lifelessness and death and within which the world soul was imprisoned. The world soul was personified as the Suffering Jesus (Jesus patibilis) who, like the historical Jesus, was depicted as being crucified in the world. This mystica cruxificio was present in all parts of the world, including the skies, soil, and trees, as expressed in the Coptic Manichaean psalms.

Mandaeism

Mandaeism, another Gnostic tradition that has survived to the present day, also incorporates a concept akin to the world soul. In Mandaean cosmology, the soul's journey through the material world and its eventual return to the World of Light is a central narrative. The soul's purification and ascent are facilitated by esoteric knowledge and ritual practices.

Neoplatonism

The concept of the world soul continued to influence later philosophical thought, particularly in the development of Neoplatonism. Neoplatonists such as Plotinus and Proclus expanded on Plato's ideas, emphasizing the unity and divinity of the cosmos and its connection to the One, the ultimate source of all existence.

Neoplatonism, which flourished in the 3rd century CE, is a philosophical system that builds upon the teachings of Plato and incorporates metaphysical elements. Plotinus, the founder of Neoplatonism, articulated a vision of reality that centers on a hierarchical structure of existence. At the pinnacle of this hierarchy is the One, an ineffable and transcendent principle from which all reality emanates. The One generates the Nous (Divine Mind), which in turn produces the World Soul.

The World Soul in Neoplatonism functions as an intermediary between the intelligible realm (the realm of the Forms) and the sensible world (the material universe). Plotinus describes the World Soul as the vital force that animates and organizes the cosmos, imbuing it with life and intelligence. It is both one and many, maintaining unity while simultaneously generating individual souls and entities within the cosmos.

Proclus, a prominent later Neoplatonist, further developed these ideas. He posited a more elaborate structure, with the World Soul divided into a higher, more divine aspect and a lower, more material aspect. This dual nature allows the World Soul to mediate between the purely intellectual and the physical realms, ensuring the coherence and order of the universe.

The Neoplatonists viewed the World Soul not only as a metaphysical principle but also as a means to achieve personal and cosmic harmony. By aligning one's soul with the World Soul, individuals could attain a higher state of being and participate in the divine order of the cosmos. This process involves philosophical contemplation, ethical living, and the cultivation of virtues that reflect the harmonious nature of the World Soul.

The influence of Neoplatonism extended beyond the classical period, significantly impacting early Christian, Islamic, and Renaissance thought. The integration of Platonic and Neoplatonic ideas into Christian theology, particularly through the works of Augustine and Pseudo-Dionysius, demonstrates the enduring legacy of the concept of the World Soul.

Medieval and Renaissance thought

Scholasticism

During the 12th-Century Renaissance of the High Middle Ages, the analysis of Plato's Timaeus by members of the School of Chartres like William of Conches and Bernardus Silvestris led them to interpret the world soul as possibly or certainly the same as the Christian Holy Spirit under the covering (integumentum) of another name. As or immediately after Peter Abelard was condemned by Bernard of Clairvaux and the 1141 Council of Sens for doctrines similarly close to pantheism, William condemned his own writings on the subject and revised his De Philosophia Mundi to avoid its discussion.

Hermeticism

Hermeticism, a spiritual, philosophical, and esoteric tradition based primarily on writings attributed to Hermes Trismegistus, integrates the concept of the world soul into its cosmological framework. The Hermetic tradition, which flourished in the Hellenistic period and saw a revival during the Renaissance, views the world soul as a vital, animating force that permeates and unites the cosmos.

Hermetic writings, particularly the Corpus Hermeticum and the Asclepius, emphasize the unity and interconnection of all things in the universe. These texts describe the cosmos as a living being imbued with a divine spirit or soul. The world soul is seen as the intermediary between the divine intellect (Nous) and the material world, ensuring the harmonious functioning of the cosmos.

In the Corpus Hermeticum, the world soul is often depicted as an emanation of the divine that sustains all creation. This soul is responsible for the life, order, and movement within the universe, acting in accordance with the divine will. The Hermetic worldview is deeply rooted in the idea that understanding and aligning oneself with the world soul can lead to spiritual enlightenment and union with the divine.

Paracelsus

The Renaissance alchemist and physician Paracelsus significantly contributed to the Hermetic tradition by integrating the concept of the world soul into his medical and alchemical theories. Paracelsus believed that the world soul, which he referred to as the Archeus, was the vital force that governed the processes of nature and the human body. He posited that health and disease were influenced by the balance and interaction of this vital force within individuals.

Paracelsus' view of the world soul extended to his understanding of the macrocosm and microcosm, where the human body (microcosm) is a reflection of the larger universe (macrocosm). By studying the world soul's manifestations in nature, Paracelsus believed that alchemists and physicians could uncover the secrets of health and transformation.

Giordano Bruno

Giordano Bruno, a 16th-century Italian philosopher, theologian, and occultist, significantly contributed to the Renaissance revival of the Hermetic tradition. His work is known for its bold integration of Hermeticism, Copernican heliocentrism, and an infinite universe theory, which brought the concept of the world soul into a new, expansive context.

Bruno's cosmology was groundbreaking in that it proposed an infinite universe populated by innumerable worlds. Central to this vision was the idea of the world soul, or anima mundi, which Bruno described as an immanent and animating force pervading the entire cosmos. He argued that the world soul is the source of all motion, life, and intelligence in the universe, linking all parts of the cosmos into a single, living entity.

In his work De la causa, principio et uno (On Cause, Principle, and Unity), Bruno articulated his belief in the unity of the universe and the presence of a single, universal spirit. This spirit, akin to the world soul, ensures the cohesion and harmony of the cosmos, reflecting the Hermetic principle of the interconnectedness of all things.

Bruno was deeply influenced by the Hermetic texts, particularly the Corpus Hermeticum, which he saw as containing profound truths about the nature of the universe and the divine. His philosophy integrated the Hermetic concept of the world soul with the revolutionary scientific ideas of his time, leading to a vision of the cosmos that was both mystical and rational.

Bruno's emphasis on the world soul can also be seen in his metaphysical poetry and dialogues, where he often depicted the universe as a divine, living organism animated by an internal spirit. This perspective was revolutionary, challenging the Aristotelian view of a finite, hierarchical cosmos and aligning more closely with the Hermetic and Neoplatonic traditions.

Bruno's radical ideas, including his support for the Copernican model and his concept of an infinite universe with a pervasive world soul, led to his persecution by the Roman Catholic Church. He was tried for heresy and ultimately burned at the stake in 1600. Despite his tragic end, Bruno's ideas significantly influenced later thinkers and contributed to the development of modern cosmology and metaphysics.

Robert Fludd

Another key figure in Hermeticism, Robert Fludd, elaborated on the concept of the world soul in his extensive writings on cosmology and metaphysics. Fludd's works depict the world soul as the divine anima mundi that connects all levels of existence, from the highest spiritual realms to the material world. He emphasized the idea of cosmic harmony, where the world soul orchestrates the symphony of creation, maintaining balance and order.

Fludd's illustrations and writings highlight the Hermetic belief in the interconnection of all things, with the world soul as the binding principle that ensures the unity of the cosmos. His work reflects the Hermetic conviction that by attuning oneself to the world soul, one can achieve deeper knowledge and spiritual enlightenment.

Later European philosophers

Although the concept of a world soul originated in classical antiquity, similar ideas can be found in the thoughts of later European philosophers such as those of Baruch Spinoza, Gottfried Leibniz, Immanuel Kant, Friedrich Schelling, and Georg W.F. Hegel (particularly in his concept of Weltgeist).

Modern relevance

The concept of Anima Mundi, or the World Soul, continues to resonate in contemporary philosophical, ecological, and spiritual discourse. Modern interpretations often explore the interconnectedness of life and the universe, reflecting ancient notions through new lenses.

Ecological perspectives

In contemporary environmental philosophy, the idea of Anima Mundi is often invoked to emphasize the intrinsic value of nature and the interconnectedness of all living things. Ecologists and environmentalists draw parallels between the ancient concept and modern holistic approaches to ecology. James Lovelock's Gaia hypothesis posits that the Earth functions as a self-regulating system, echoing the idea of the World Soul animating and organizing the cosmos. This holistic view suggests that recognizing the Earth as a living entity can foster a deeper environmental ethic and a sense of stewardship for the planet.

Philosophical and scientific discourse

Philosophers like David Abram have explored the phenomenological aspects of Anima Mundi in the context of sensory experience and perception. Abram's work emphasizes the animate qualities of the natural world, suggesting that recognizing the Earth's sentience can foster a deeper ecological awareness and a sense of kinship with all forms of life. Additionally, systems thinking and complexity theory in science reflect a renewed interest in holistic and integrative approaches that resonate with the concept of the World Soul, highlighting the interconnection and interdependence of various components within ecological and social systems.

Spiritual and New Age movements

The Anima Mundi also finds relevance in modern spiritual and New Age movements, where it is often associated with the idea of a living, conscious Earth. Practices such as Earth-centered spirituality, animism, and certain strands of neopaganism embrace the notion of the World Soul as a guiding principle for living in harmony with nature. These movements emphasize rituals, meditations, and practices aimed at connecting with the spirit of the Earth and recognizing the sacredness of all life.

Literature and the arts

The influence of the Anima Mundi extends into contemporary literature and the arts, serving as a metaphor for exploring themes of unity, interconnection, and the mystery of existence. Authors and artists draw on the symbolism of the World Soul to convey a sense of wonder and reverence for the natural world. This is evident in the works of poets like Mary Oliver, who often evoke the living essence of nature in their writings, and in the visual arts, where the interplay of life and the cosmos is a recurring theme.