Integrated information theory does not make plant consciousness more convincing.

It has been proposed by some plant scientists that plants are cognitive and conscious organisms, although this is a minority view. Here we present a brief summary of some of the arguments against this view, followed by a critique of an article in this same issue of Biochemical and Biophysical Research Communications by Calvo, Baluska, and Trewavas (2020) that cites Integrated Information Theory (IIT) as providing additional support for plant consciousness. The authors base their argument on the assumptions that all cells are conscious and that consciousness is confined to life. However, IIT allows for consciousness in various nonliving systems, and thus does not restrict consciousness to living organisms. Therefore, IIT cannot be used to prove plant consciousness, for which there is neither empirical evidence nor support from other, neuron-based, theories of consciousness.

A Traditional Scientific Perspective on the Integrated Information Theory of Consciousness.

This paper assesses two different theories for explaining consciousness, a phenomenon that is widely considered amenable to scientific investigation despite its puzzling subjective aspects. I focus on Integrated Information Theory (IIT), which says that consciousness is integrated information (as ϕMax) and says even simple systems with interacting parts possess some consciousness. First, I evaluate IIT on its own merits. Second, I compare it to a more traditionally derived theory called Neurobiological Naturalism (NN), which says consciousness is an evolved, emergent feature of complex brains. Comparing these theories is informative because it reveals strengths and weaknesses of each, thereby suggesting better ways to study consciousness in the future. IIT's strengths are the reasonable axioms at its core; its strong logic and mathematical formalism; its creative "experience-first" approach to studying consciousness; the way it avoids the mind-body ("hard") problem; its consistency with evolutionary theory; and its many scientifically testable predictions. The potential weakness of IIT is that it contains stretches of logic-based reasoning that were not checked against hard evidence when the theory was being constructed, whereas scientific arguments require such supporting evidence to keep the reasoning on course. This is less of a concern for the other theory, NN, because it incorporated evidence much earlier in its construction process. NN is a less mature theory than IIT, less formalized and quantitative, and less well tested. However, it has identified its own neural correlates of consciousness (NCC) and offers a roadmap through which these NNCs may answer the questions of consciousness using the hypothesize-test-hypothesize-test steps of the scientific method.

A Palaeozoic shark with osteichthyan-like branchial arches.

The evolution of serially arranged, jointed endoskeletal supports internal to the gills--the visceral branchial arches--represents one of the key events in early jawed vertebrate (gnathostome) history, because it provided the morphological basis for the subsequent evolution of jaws. However, until now little was known about visceral arches in early gnathostomes, and theories about gill arch evolution were driven by information gleaned mostly from both modern cartilaginous (chondrichthyan) and bony (osteichthyan) fishes. New fossil discoveries can profoundly affect our understanding of evolutionary history, by revealing hitherto unseen combinations of primitive and derived characters. Here we describe a 325 million year (Myr)-old Palaeozoic shark-like fossil that represents, to our knowledge, the earliest identified chondrichthyan in which the complete gill skeleton is three-dimensionally preserved in its natural position. Its visceral arch arrangement is remarkably osteichthyan-like, suggesting that this may represent the common ancestral condition for crown gnathostomes. Our findings thus reinterpret the polarity of some arch features of the crown jawed vertebrates and invert the classic hypothesis, in which modern sharks retain the ancestral condition. This study underscores the importance of early chondrichthyans in resolving the evolutionary history of jawed vertebrates.

The nature of primary consciousness. A new synthesis.

While the philosophical puzzles about "life" that once confounded biology have all been solved by science, much of the "mystery of consciousness" remains unsolved due to multiple "explanatory gaps" between the brain and conscious experience. One reason for this impasse is that diverse brain architectures both within and across species can create consciousness, thus making any single neurobiological feature insufficient to explain it. We propose instead that an array of general biological features that are found in all living things, combined with a suite of special neurobiological features unique to animals with consciousness, evolved to create subjective experience. Combining philosophical, neurobiological and evolutionary approaches to consciousness, we review our theory of neurobiological naturalism that we argue closes the "explanatory gaps" between the brain and subjective experience and naturalizes the "experiential gaps" between subjectivity and third-person observation of the brain.

The GC content of LSU rRNA evolves across topological and functional regions of the ribosome in all three domains of life.

Large-subunit rRNA is the ribozyme that catalyzes protein synthesis by translation, and many of its features vary along a deep-to-superficial gradient. By measuring the G+C proportions in this rRNA in all three domains of life (60 bacteria, 379 eukaryote, and 23 archaean sequences), we tested whether the proportion of GC nucleotides varies along this in-out gradient. The rRNA regions used were several zones identified by Bokov and Steinberg (2009) as being arranged from deep to superficial within the LSU. To the Bokov-Steinberg zones, we added the most superficial zone of all, the divergent domains (expansion segments), which are greatly enlarged in eukaryotes. Regression lines constructed from the hundreds of species of organisms revealed the expected in-out gradient, showing that species with high %GC (or high %AT) in their rRNA distribute more of these abundant nucleotides into the peripheral zones. This could be explained by the evolutionary rates of replacement of all nucleotides (A, C, G, T), because these latter rates are fastest at the periphery and slowest near the conserved core. As an overall explanation, we propose that when extrinsic factors (whole-genome nucleotide composition, or environmental temperature) demand the percentage of GC in the rRNA of a species be high or low, then the deep-lying zones are buffered against GC variation because they are the slowest to evolve. The deep, conserved zones are also the most involved in translation, hinting that stabilizing selection there prevents a high GC variability that would diminish LSU rRNA's core functions. We found only a few domain-specific trends in rRNA-GC distribution, which relate to many Archaea living at high temperatures or to the highly complex genes and adaptations of Eukaryota. Use of rRNA sequences in molecular phylogenetic studies, for reconstructing the relationships of organisms across the tree of life, requires accurate models of how rRNA evolves. The demonstration that GC distributes in regular patterns across rRNA regions can improve these tree-reconstruction models in the future and should yield phylogenies of greater accuracy.

Pikaia gracilens Walcott: stem chordate, or already specialized in the Cambrian?

For the past 35 years, the Cambrian fossil Pikaia gracilens was widely interpreted as a typical basal chordate based on short descriptions by Conway Morris. Recently, Conway Morris and Caron (CMC) (2012, Biol Rev 87:480-512) described Pikaia extensively, as a basis for new ideas about deuterostome evolution. This new Pikaia has characters with no clear homologues in other animals, so they could be phylogenetically uninformative autapomorphies. These characters include a dorsal organ, posterior ventral area, posterior fusiform structure, and anterior dorsal unit. Yet CMC interpret most of the unusual characters as primitive for chordates, thereby interpreting Pikaia as an even more convincing stem chordate than before. Moreover, they claim that segment (myomere) shape is a reliable guide for defining a chordate and even for assigning animals to their correct place in deuterostome phylogeny. By defining sigmoidal segments as a basal chordate character, they situate Pikaia at the base of the chordates and banish fossil yunnanozoans (which have straight segments) to a position deep within the deuterostomes. In addition, they consider amphioxus, with its conspicuously chevron-shaped segments, to be so highly derived that it is of little use for reconstructing the first chordates. We question their overemphasis on the phylogenetic value of segment shape and their marginalizing of amphioxus. We deduce that Pikaia, not amphioxus, is specialized. We performed a cladistic analysis that showed the character interpretations of CMC are consistent with their wide-ranging evolutionary scenario, but that these interpretations leave unresolved the position of Pikaia within chordates.

Y chromosome phylogeny for cutthroat trout (Oncorhynchus clarkii) subspecies is generally concordant with those of other markers.

Sequence divergence was evaluated in the non-recombining, male-specific OmyY1 region of the Y chromosome among the subspecies of cutthroat trout (Oncorhynchus clarkii) in the western United States. This evaluation identified subspecies-discriminating OmyY1-haplotypes within a ∼1200bp region of the OmyY1 locus and localized the region to the end of the Y chromosome by FISH analysis. OmyY1 sequences were aligned and used to reconstruct a phylogeny of the cutthroat trout subspecies and related species via maximum-parsimony and Bayesian analyses. In the Y-haplotype phylogeny, clade distributions generally corresponded to the geographic distributions of the recognized subspecies. This phylogeny generally corresponded to a mitochondrial tree obtained for these subspecies in a previous study. Both support a clade of trout vs. Pacific salmon, of rainbow trout, and of a Yellowstone cutthroat group within the cutthroat trout. In our OmyY1 tree, however, the cutthroat "clade", although present topologically, was not statistically significant. Some key differences were found between trees obtained from the paternally-inherited OmyY1 vs. maternally-inherited mitochondrial haplotypes in cutthroat trout compared to rainbow trout. Other findings are: The trout OmyY1 region evolves between 3 and 13 times slower than the trout mitochondrial regions that have been studied. The Lahontan cutthroat trout had a fixed OmyY1 sequence throughout ten separate populations, suggesting this subspecies underwent a severe population bottleneck prior to its current dispersal throughout the Great Basin during the pluvial phase of the last ice age. The Yellowstone group is the most derived among the cutthroat trout and consists of the Yellowstone, Bonneville, Colorado, Rio Grande and greenback subspecies. Identification of subspecies and sex with this Y-chromosome marker may prove useful in conservation efforts.

Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis.

This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ~33 of the ~36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/~jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A-F, or 6A-C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin+llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata+Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods+branchiurans+pentastomids+mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.

Multiple Routes to Animal Consciousness: Constrained Multiple Realizability Rather Than Modest Identity Theory.

The multiple realizability thesis (MRT) is an important philosophical and psychological concept. It says any mental state can be constructed by multiple realizability (MR), meaning in many distinct ways from different physical parts. The goal of our study is to find if the MRT applies to the mental state of consciousness among animals. Many things have been written about MRT but the ones most applicable to animal consciousness are by Shapiro in a 2004 book called The Mind Incarnate and by Polger and Shapiro in their 2016 work, The Multiple Realization Book. Standard, classical MRT has been around since 1967 and it says that a mental state can have very many different physical realizations, in a nearly unlimited manner. To the contrary, Shapiro's book reasoned that physical, physiological, and historical constraints force mental traits to evolve in just a few, limited directions, which is seen as convergent evolution of the associated neural traits in different animal lineages. This is his mental constraint thesis (MCT). We examined the evolution of consciousness in animals and found that it arose independently in just three animal clades-vertebrates, arthropods, and cephalopod mollusks-all of which share many consciousness-associated traits: elaborate sensory organs and brains, high capacity for memory, directed mobility, etc. These three constrained, convergently evolved routes to consciousness fit Shapiro's original MCT. More recently, Polger and Shapiro's book presented much the same thesis but changed its name from MCT to a "modest identity thesis." Furthermore, they argued against almost all the classically offered instances of MR in animal evolution, especially against the evidence of neural plasticity and the differently expanded cerebrums of mammals and birds. In contrast, we argue that some of these classical examples of MR are indeed valid and that Shapiro's original MCT correction of MRT is the better account of the evolution of consciousness in animal clades. And we still agree that constraints and convergence refute the standard, nearly unconstrained, MRT.

Anesthetics and plants: no pain, no brain, and therefore no consciousness.

Plants have a rich variety of interactions with their environment, including adaptive responses mediated by electrical signaling. This has prompted claims that information processing in plants is similar to that in animals and, hence, that plants are conscious, intelligent organisms. In several recent reports, the facts that general anesthetics cause plants to lose their sensory responses and behaviors have been taken as support for such beliefs. These lipophilic substances, however, alter multiple molecular, cellular, and systemic functions in almost every organism. In humans and other animals with complex brains, they eliminate the experience of pain and disrupt consciousness. The question therefore arises: do plants feel pain and have consciousness? In this review, we discuss what can be learned from the effects of anesthetics in plants. For this, we describe the mechanisms and structural prerequisites for pain sensations in animals and show that plants lack the neural anatomy and all behaviors that would indicate pain. By explaining the ubiquitous and diverse effects of anesthetics, we discuss whether these substances provide any empirical or logical evidence for "plant consciousness" and whether it makes sense to study the effects of anesthetics on plants for this purpose. In both cases, the answer is a resounding no.

Debunking a myth: plant consciousness.

Claims that plants have conscious experiences have increased in recent years and have received wide coverage, from the popular media to scientific journals. Such claims are misleading and have the potential to misdirect funding and governmental policy decisions. After defining basic, primary consciousness, we provide new arguments against 12 core claims made by the proponents of plant consciousness. Three important new conclusions of our study are (1) plants have not been shown to perform the proactive, anticipatory behaviors associated with consciousness, but only to sense and follow stimulus trails reactively; (2) electrophysiological signaling in plants serves immediate physiological functions rather than integrative-information processing as in nervous systems of animals, giving no indication of plant consciousness; (3) the controversial claim of classical Pavlovian learning in plants, even if correct, is irrelevant because this type of learning does not require consciousness. Finally, we present our own hypothesis, based on two logical assumptions, concerning which organisms possess consciousness. Our first assumption is that affective (emotional) consciousness is marked by an advanced capacity for operant learning about rewards and punishments. Our second assumption is that image-based conscious experience is marked by demonstrably mapped representations of the external environment within the body. Certain animals fit both of these criteria, but plants fit neither. We conclude that claims for plant consciousness are highly speculative and lack sound scientific support.

Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction.

This study (1) uses nearly complete rRNA-gene sequences from across Metazoa (197 taxa) to reconstruct animal phylogeny; (2) presents a highly annotated, manual alignment of these sequences with special reference to rRNA features including paired sites (http://purl.oclc.org/NET/rRNA/Metazoan_alignment) and (3) tests, after eliminating as few disruptive, rogue sequences as possible, if a likelihood framework can recover the main metazoan clades. We found that systematic elimination of approximately 6% of the sequences, including the divergent or unstably placed sequences of cephalopods, arrowworm, symphylan and pauropod myriapods, and of myzostomid and nemertodermatid worms, led to a tree that supported Ecdysozoa, Lophotrochozoa, Protostomia, and Bilateria. Deuterostomia, however, was never recovered, because the rRNA of urochordates goes (nonsignificantly) near the base of the Bilateria. Counterintuitively, when we modeled the evolution of the paired sites, phylogenetic resolution was not increased over traditional tree-building models that assume all sites in rRNA evolve independently. The rRNA genes of non-bilaterians contain a higher % AT than do those of most bilaterians. The rRNA genes of Acoela and Myzostomida were found to be secondarily shortened, AT-enriched, and highly modified, throwing some doubt on the location of these worms at the base of Bilateria in the rRNA tree--especially myzostomids, which other evidence suggests are annelids instead. Other findings are marsupial-with-placental mammals, arrowworms in Ecdysozoa (well supported here but contradicted by morphology), and Placozoa as sister to Cnidaria. Finally, despite the difficulties, the rRNA-gene trees are in strong concordance with trees derived from multiple protein-coding genes in supporting the new animal phylogeny.

Phenomenal Consciousness and Emergence: Eliminating the Explanatory Gap.

The role of emergence in the creation of consciousness has been debated for over a century, but it remains unresolved. In particular there is controversy over the claim that a "strong" or radical form of emergence is required to explain phenomenal consciousness. In this paper we use some ideas of complex system theory to trace the emergent features of life and then of complex brains through three progressive stages or levels: Level 1 (life), Level 2 (nervous systems), and Level 3 (special neurobiological features), each representing increasing biological and neurobiological complexity and ultimately leading to the emergence of phenomenal consciousness, all in physical systems. Along the way we show that consciousness fits the criteria of an emergent property-albeit one with extreme complexity. The formulation Life + Special neurobiological features → Phenomenal consciousness expresses these relationships. Then we consider the implications of our findings for some of the philosophical conundrums entailed by the apparent "explanatory gap" between the brain and phenomenal consciousness. We conclude that consciousness stems from the personal life of an organism with the addition of a complex nervous system that is ideally suited to maximize emergent neurobiological features and that it is an example of standard ("weak") emergence without a scientific explanatory gap. An "experiential" or epistemic gap remains, although this is ontologically untroubling.

Subjectivity "Demystified": Neurobiology, Evolution, and the Explanatory Gap.

While life in general can be explained by the mechanisms of physics, chemistry, and biology, to many scientists and philosophers, it appears that when it comes to explaining consciousness, there is what the philosopher Joseph Levine called an "explanatory gap" between the physical brain and subjective experiences. Here, we deduce the living and neural features behind primary consciousness within a naturalistic biological framework, identify which animal taxa have these features (the vertebrates, arthropods, and cephalopod molluscs), then reconstruct when consciousness first evolved and consider its adaptive value. We theorize that consciousness is based on all the complex system features of life, plus even more complex features of elaborate brains. We argue that the main reason why the explanatory gap between the brain and experience has been so refractory to scientific explanation is that it arises from both life and from varied and diverse brains and brain regions, so bridging the gap requires a complex, multifactorial account that includes the great diversity of consciousness, its personal nature that stems from embodied life, and the special neural features that make consciousness unique in nature.

The origin of the vertebrate jaw: neoclassical ideas versus newer, development-based ideas.

Here I consider ways to test two hypotheses of the origin of jawed vertebrates: my neoclassical hypothesis, which derived from comparative morphology; and the heterotopic hypothesis, which derives from modern developmental findings. The heterotopic hypothesis, unlike the neoclassical hypothesis, says that major developmental changes had to occur before the upper jaws could evolve: a caudal shift in the expression domains of genes that pattern oral structures; and the loss of ancestral, lamprey-like upper lips. To test whether these did occur, I propose studies on the development of chondrichthyans (sharks and chimaeroid ratfishes), an understudied group that is likely to retain primitive features of the jaw region. The heterotopic hypothesis says no gnathostome retains the upper lip that is so prominent in larval lampreys, yet the neoclassical hypothesis identified such lips in sharks and ratfishes, and it predicts that their lip-skeleton likewise develops from premandibular neural crest. The development and innervation of upper-lip muscles in lampreys and chimaeroids can also be compared. The proposed studies can determine if the upper lips of chondrichthyans and lampreys are homologous (which would support the neoclassical hypothesis), or homoplasious (which would support the heterotopic hypothesis). Also, I argue that the evolution of the upper jaws (as lateral structures) was not linked to a nasohypophyseal complex (which is a median structure), although such a link is claimed by the heterotopic hypothesis. Finally, I update the neoclassical hypothesis to address recent evidence that the trabeculae of the lamprey skull are not homologous to the trabeculae cranii of gnathostomes.

Fossil sister group of craniates: predicted and found.

This study investigates whether the recently described Cambrian fossil Haikouella (and the very similar Yunnanozoon) throws light on the longstanding problem of the origin of craniates. In the first rigorous cladistic analysis of the relations of this animal, we took 40 anatomical characters from Haikouella and other taxa (hemichordates, tunicates, cephalochordates, conodont craniates and other craniates, plus protostomes as the outgroup) and subjected these characters to parsimony analysis. The characters included several previously unrecognized traits of Haikouella, such as upper lips resembling those of larval lampreys, the thick nature of the branchial bars, a mandibular branchial artery but no mandibular branchial bar, muscle fibers defining the myomeres, a dark fibrous sheath that defines the notochord, conclusive evidence for paired eyes, and a large hindbrain and diencephalon in the same positions as in the craniate brain. The cladistic analysis produced this tree: (protostomes, hemichordates (tunicates, (cephalochordates, (Haikouella, (conodonts + other craniates))))), with the "Haikouella + craniate" clade supported by bootstrap values that ranged from 81-96%, depending on how the analysis was structured. Thus, Haikouella is concluded to be the sister group of the craniates. Alternate hypotheses that unite Haikouella with hemichordates or cephalochordates, or consider it a basal deuterostome, received little or no support. Although it is the sister group of craniates, Haikouella is skull-less and lacks an ear, but it does have neural-crest derivatives in its branchial bars. Its craniate characters occur mostly in the head and pharynx; its widely spaced, robust branchial bars indicate it ventilated with branchiomeric muscles, not cilia. Despite its craniate mode of ventilation, Haikouella was not a predator but a suspension feeder, as shown by its cephalochordate-like endostyle, and tentacles forming a screen across the mouth. Haikouella was compared to pre-craniates predicted by recent models of craniate evolution and was found to fit these predictions closely. Specifically, it fits Northcutt and Gans' prediction that the change from ciliary to muscular ventilation preceded the change from suspension feeding to predatory feeding; it fits Butler's claim that vision was the first craniate sense to start elaborating; it is consistent with the ideas of Donoghue and others about the ancestor of conodont craniates; and, most strikingly, it resembles Mallatt's prediction of the external appearance of the ancestral craniate head. By contrast, Haikouella does not fit the widespread belief that ancestral craniates resembled hagfishes, because it has no special hagfish characters. Overall, Haikouella agrees so closely with recent predictions about pre-craniates that we conclude that the difficult problem of craniate origins is nearly solved.