A third way of evolution?

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June 2, 2014

Evolution, News

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Evolution
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That’s the new buzz here:

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.

Supporters include Shapiro, Noble, Koonin, Neuman, Jablonka—non-Darwin lobby researchers into evolution. Interested in understanding nature, not getting a judge to agree to enshrine their beliefs in a tax-funded, union-infested school system.

Sounds interesting. Stuff to get started.

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.Dionisio_{July 16, 2017
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.Dionisio_{July 16, 2017
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The correct identification and classification of AS and GD is fundamental to improve the understanding of the evolution of both processes. A single evolutionary model of AS after GD may not be solely responsible for AS events, instead a combination of multiple models is more likely. Identifying the mechanisms governing which models are utilized in specific genes will improve our understanding of the evolutionary relationship between GD and AS.
The Evolutionary Relationship between Alternative Splicing and Gene Duplication Luis P. Iñiguez* and Georgina Hernández Front Genet. 2017; 8: 14. doi: 10.3389/fgene.2017.00014

Where's the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 10, 2017
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The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study.
The Evolutionary Relationship between Alternative Splicing and Gene Duplication Luis P. Iñiguez* and Georgina Hernández Front Genet. 2017; 8: 14. doi: 10.3389/fgene.2017.00014

Dionisio_{July 10, 2017
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Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Hox genes are transcription factors that bind to regulatory regions via a helix-turn-helix domain to enhance or suppress gene transcription [...] [...] other factors, such as unequal rates of genome rearrangements in different lineages and shared enhancers between genes, also might contribute to the genomic evolution of Hox genes.
Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties Sabrina M. Schiemann, José M. Martín-Durán, Aina Børve, Bruno C. Vellutini,a Yale J. Passamaneck,b and Andreas Hejnol Proc Natl Acad Sci U S A. 114(10): E1913–E1922. doi: 10.1073/pnas.1614501114

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Hox genes pattern the anteroposterior axis of all animals that have left and right body sides. In many animals, Hox genes are clustered along the chromosomes and expressed in spatial and temporal order. This coordinated regulation is thought to have preserved the cluster through a developmental constraint. [...] the hard tissues (chaetae and shells) of segmented worms, mollusks, and brachiopods share a common origin that dates back to the Early Cambrian.
Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties Sabrina M. Schiemann, José M. Martín-Durán, Aina Børve, Bruno C. Vellutini,a Yale J. Passamaneck,b and Andreas Hejnol Proc Natl Acad Sci U S A. 114(10): E1913–E1922. doi: 10.1073/pnas.1614501114

expressed in spatial and temporal order? How does it do that? Did somebody say "coordinated regulation"? What does the coordination? Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Future studies will be needed to unravel the biological significance of phyla specific sequences and whether they fine tune telomerase processivity to life history strategy. A future endeavour will be to unravel mechanistic linkages that connect unique sequence evolution and the dynamic regulation of TERT to actual biological roles.
The protein subunit of telomerase displays patterns of dynamic evolution and conservation across different metazoan taxa Alvina G. Lai, Natalia Pouchkina-Stantcheva, Alessia Di Donfrancesco, Gerda Kildisiute, Sounak Sahu, and A. Aziz Aboobaker BMC Evol Biol. 2017; 17: 107. doi: 10.1186/s12862-017-0949-4

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Most animals employ telomerase, which consists of a catalytic subunit known as the telomerase reverse transcriptase (TERT) and an RNA template, to maintain telomere ends. Our work establishes that the evolutionary history and structural evolution of TERT involves previously unappreciated levels of change and the emergence of lineage specific motifs. The sequence conservation we describe within phyla suggests that these new motifs likely serve essential biological functions of TERT, which along with changes in splicing, underpin diverse functions of TERT important for animal life histories.
The protein subunit of telomerase displays patterns of dynamic evolution and conservation across different metazoan taxa Alvina G. Lai, Natalia Pouchkina-Stantcheva, Alessia Di Donfrancesco, Gerda Kildisiute, Sounak Sahu, and A. Aziz Aboobaker BMC Evol Biol. 2017; 17: 107. doi: 10.1186/s12862-017-0949-4

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Our analyses across the broader Malacostraca have allowed us to not only draw analogies with other arthropods but also to identify evolutionary novelties in immune modulation components and form strong hypotheses as to when key pathways have evolved or diverged.
Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species Alvina G. Lai and A. Aziz Aboobaker BMC Genomics. 2017; 18: 389. doi: 10.1186/s12864-017-3769-4

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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[...] the precursor of insect E-cadherin originated through stepwise reductive changes after the earliest divergence of extant arthropod groups. Future studies should investigate the structural mechanisms underlying the multistep transition from the arthropod ancestral type III cadherin to the more recent insect E-cadherin.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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[...] the relationships between the hexapods and other pancrustacean subgroups remain a controversial topic [...] One of the major conflicts regarding the pancrustacean phylogeny concerns the relationships between hexapods, branchiopods, and malacostracans. [...] our phylogenetic proposals remain highly hypothetical.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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[...] questions of how the two N-terminal-most ECs of type IVb cadherin contribute to the functioning of the type IVb cadherin and how the large number of EC domains in type III cadherin are utilized to mediate homophilic cell-cell adhesion are key to a better understanding of the stepwise reductive changes involved in the evolution of insect E-cadherin.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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[...] it is likely that reductive changes also preceded the establishment of the type III cadherin [...] Investigating the mechanism by which the classical cadherins were able to evolve via simplification is a typical challenge in experimentation-based evolutionary biology. [...] type IVa cadherin might have inherited part of an as-yet-uncharacterized mechanism of homophilic binding from the type III cadherin.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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The key issue is what form the last common precursor of type IVa and type IVb cadherins had. To fill the possible gaps in reconstruction of the transition processes between type III and type IVa/IVb cadherins, more data from the myriapod group, as well as from the crustacean group, will be required. [...] the transition from the ancestral type III cadherin to the derived insect type IVa cadherin was a multistep process that involved several progressive reductive changes.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Here are some figures for the referenced paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473995/figure/Fig8/
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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An unexpected and important finding of this work was the identification of a novel form of classical cadherin in isopod and amphipod crustaceans that was similar to, but distinct from, the known hexapod and branchiopod type IV cadherins. This finding led us to propose a revision of the type IV cadherin category and to define two subclasses, type IVa and type IVb.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Did somebody say "unexpected"? Why? Were they expecting something else or nothing at all? Did somebody say "revision"? Another one? :) Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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Classical cadherins are a metazoan-specific family of homophilic cell-cell adhesion molecules that regulate morphogenesis. Although both type III and type IV cadherins have been identified in hexapods and branchiopods, the process by which the type IV cadherin evolved is still largely unclear. [...] following the divergence of early arthropods, the precursor of the insect type IV cadherin evolved through stepwise reductive changes from the ancestral type III state. [...] the complementary distributions of polarized genomic characters related to type IVa/IVb cadherins may have implications for our interpretations of pancrustacean phylogeny.
Evolutionary origin of type IV classical cadherins in arthropods Mizuki Sasaki,1,4 Yasuko Akiyama-Oda,1,2 and Hiroki Oda BMC Evol Biol. 2017; 17: 142. doi: 10.1186/s12862-017-0991-2

Where’s the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 4, 2017
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[...] little is known about the evolutionary processes by which allorecognition novelty is produced. The existence of these commonalities between unrelated metazoan allorecognition systems suggests there are similar selective pressures driving the evolution and function of these divergent systems, regardless of the fact that allorecognition molecules vary markedly between taxa. The AFs appear to have evolved rapidly by mechanisms including exon shuffling and nucleotide mutation, and continue to generate within-species variation required for self–nonself recognition by the means listed above. [...] understanding of the sponge AF gene family sheds light on one of the central features of being an animal, self–nonself recognition.
Origin and Evolution of the Sponge Aggregation Factor Gene Family Laura F. Grice,1 Marie E.A. Gauthier,1 Kathrein E. Roper,1 Xavier Fernàndez-Busquets,2,3,4 Sandie M. Degnan,1 and Bernard M. Degnan Mol Biol Evol. 34(5): 1083–1099. doi: 10.1093/molbev/msx058

Where's the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 3, 2017
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Although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. The evolution of AFs suggests that their diversification occurs via high allelism, and the continual and rapid gain, loss and shuffling of domains over evolutionary time. Given the marked differences in metazoan allorecognition genes, we propose the rapid evolution of AFs in sponges provides a model for understanding the extensive diversification of self–nonself recognition systems in the animal kingdom.
Origin and Evolution of the Sponge Aggregation Factor Gene Family Laura F. Grice,1 Marie E.A. Gauthier,1 Kathrein E. Roper,1 Xavier Fernàndez-Busquets,2,3,4 Sandie M. Degnan,1 and Bernard M. Degnan Mol Biol Evol. 34(5): 1083–1099. doi: 10.1093/molbev/msx058

Where's the beef? Are they talking about the built-in variability framework seen in the biological systems? Can they show valid macroevolution cases using the formulation posted @1090?Dionisio_{July 3, 2017
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@1263 error: It should read "hope" instead of "home". My fault.Dionisio_{July 3, 2017
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We hope that these findings can bring a new viewpoint to understand the mechanisms of brain information transmission and information processing [...]
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

We home so too... :) complex complexity. Where's the beef?Dionisio_{June 27, 2017
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[...] the change of quantum state would likely lead to information transfer if such a state is in quantum entanglement [...]
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

huh? :) complex complexity. Where's the beef?Dionisio_{June 27, 2017
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[...] it is still not clear how the brain carry out neural information transfer, coding and storage via biophotons.
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

complex complexity. Where's the beef?Dionisio_{June 27, 2017
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The work of the brain involves neural information processing that is mainly transmitted along axons and dendrites, which are analogous to optic fibers.
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

Did somebody say “information processing”? :) complex complexity. Where's the beef?Dionisio_{June 27, 2017
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The neocortex in the brain is organized into columnar modules, which seem to be units of information processing (24), analogous to chips in a computer.
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

Did somebody say "information processing"? :) complex complexity. Where's the beef?Dionisio_{June 27, 2017
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There is no universally accepted definition of animal intelligence and no procedure to measure and compare the differences in different species [...]
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

complex complexity. Where's the beef?Dionisio_{June 27, 2017
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Despite remarkable advances in our understanding of brain functions, it is still unclear why human beings hold higher intelligence than other animals on Earth and which brain properties might explain the differences [...]
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

complex complexity. Where's the beef?Dionisio_{June 27, 2017
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Human beings hold higher intelligence than other animals on Earth; however, it is still unclear which brain properties might explain the underlying mechanisms.
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

complex complexity. Where's the beef?Dionisio_{June 27, 2017
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It is still unclear why human beings hold higher intelligence than other animals on Earth and which brain properties might explain the differences. [...] biophotons may play a key role in neural information processing and encoding [...] [...] biophotons may be involved in quantum brain mechanism [...]
Human high intelligence is involved in spectral redshift of biophotonic activities in the brain Zhuo Wang,a,b Niting Wang,a,b Zehua Li,a,b Fangyan Xiao,a,c and Jiapei Dai Proc Natl Acad Sci U S A. 113(31): 8753–8758. doi: 10.1073/pnas.1604855113

complex complexity. Where's the beef?Dionisio_{June 27, 2017
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It turns out that humans have a brain that is roughly eight times larger than expected from average mammalian BBR [...] There is no clear correlation between absolute or relative brain size and intelligence. Thus, other factors have to be considered. However, this alone cannot explain the superiority of primate—including human—intelligence. [...] it is the combination of very many cortical neurons and a relatively high IPC that appears to make our brains very smart. Despite intense search, no anatomical or physiological properties have been identified so far that would distinguish qualitatively the human brain from other mammalian or in general animal brains, except perhaps Broca's speech area. The question remains why corvids and parrots, with absolutely small brains compared with those of most mammals including primates, reveal such a high intelligence. [...] high intelligence can be realized by very different neuronal architectures.
Neuronal factors determining high intelligence Ursula Dicke and Gerhard Roth Philos Trans R Soc Lond B Biol Sci. 371(1685): 20150180. doi: 10.1098/rstb.2015.0180

complex complexity. Where's the beef? So much archaic pseudoscientific hogwash in one paper.Dionisio_{June 26, 2017
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