Phyloepigenetics IV: Lagartija y nemátodo

Herrel et al 2008. Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource. Proc Natl Acad Sci U S A. Mar 25;105(12):4792-5.

Excerpts!

"In 1971 five adult pairs of this species were moved from the small islet of Pod Kopiste (0.09 km2) to the nearby Pod Mrcaru (0.03 km2) by Nevo and coworkers (...). Although the islet of Pod Mrcaru was originally inhabited by another lacertid lizard species (Podarcis melisellensis), repeated visits (twice yearly over the past three years, beginning in 2004) show that this species has become extinct on Pod Mrcaru. Genetic mitochondrial DNA analyses indicate that the lizards currently on Pod Mrcaru are indeed P. sicula and are genetically indistinguishable from lizards from the source population"


"Differences in head size and shape also translate into significant dif ferences in bite force bet ween populations. Our data show that P. sicula lizards consume more plant material on Pod Mrcaru compared with the ancestral population on Pod Kopiste"


"This shift to a predominantly plant-based diet has resulted in the dramatic evolution of intestinal morpholog y. Morphological analysis of preserved specimens shows the presence of cecal valves (Fig. 4) in all individuals, including a hatchling (26.4-mm snout-vent length, umbilical scar present) and a very young juvenile (33.11-mm snout-vent length) examined from Pod Mrcaru."


"The fact that 1% of all currently known species of squamates have cecal valves (13, 14) illustrates the unusual nature of these structures in this population"

"Cecal valves slow down food passage and provide for fermenting chambers, allowing commensal microorganisms to convert cellulose to volatile fatt y acids (15, 16). Indeed, in the lizards f rom Pod Mrcaru, nematodes were common in the hindgut but absent from individuals f rom PodKopiste"

"Because of the larger food base available and the increase in the predict abilit y of the food source, lizard densities on Pod Mrcaru are much greater (..) lizards on Pod Mrcaru do no longer appear to defend territories. Moreover, changes in foraging style (browsing versus active pursuit of mobile prey) and social structure may also have resulted in the dramatic changes in limb proportions and maximal sprint speed previously documented for this population"

"Although the presence of cecal valves and large heads in hatchlings and juveniles suggests a genetic basis for these differences, further studies investigating the potential role of phenotypic plasticity and/or maternal effects in the divergence bet ween populations are needed"

Herrell no discute mucho qué tan relevante puede ser la simbiosis con un nemátodo. Veamos un ejemplo de anfibios


Effects of the nematode Gyrinicola batrachiensis on development, gut morphology, and fermentation in bullfrog tadpoles (Rana catesbeiana): a novel mutualism


Gregory S. Pryor *, Karen A. Bjorndal J. Exp. Zool. 303A:704-712, 2005.


Abstract

We describe a novel mutualism between bullfrog tadpoles (Rana catesbeiana) and a tadpole-specific gastrointestinal nematode (Gyrinicola batrachiensis). Groups of tadpoles were inoculated with viable or nonviable nematode eggs, and development, morphology, and gut fermentation activity were compared between nematode-infected and uninfected tadpoles. Nematode infection accelerated tadpole development; the mean time to metamorphosis was 16 d shorter and the range of times to metamorphosis was narrower in nematode-infected tadpoles than in uninfected tadpoles. At metamorphosis, infected and uninfected bullfrogs did not differ in body size or condition. Colon width, wet mass of colon contents, and concentrations of most fermentation byproducts (short-chain fatty acids: SCFAs) in the hindgut were greater in infected tadpoles. Furthermore, in vitro fermentation yields for all SCFAs combined were over twice as high in infected tadpoles than in uninfected tadpoles. One explanation for accelerated development in infected tadpoles is the altered hindgut fermentation associated with the nematodes. Energetic contributions of fermentation were estimated to be 20% and 9% of the total daily energy requirement for infected and uninfected tadpoles, respectively. Infection by G. batrachiensis nematodes potentially confers major ecological and evolutionary advantages to R. catesbeiana tadpoles. The mutualism between these species broadens our understanding of the taxonomic diversity and physiological contributions of fermentative gut symbionts and suggests that nematodes inhabiting the gut regions of other ectothermic herbivores might have beneficial effects in those hosts.


Si bien algunos nemátodos son parásitos en reptiles, otros no lo son:


Oecologia. 2006 Dec;150(3):355-61. Epub 2006

O'Grady SP, Dearing MD. Isotopic insight into host-endosymbiont relationships in Liolaemid lizards

Nitrogen isotopes have been widely used to investigate trophic levels in ecological systems. Isotopic enrichment of 2-5 per thousand occurs with trophic level increases in food webs. Host-parasite relationships deviate from traditional food webs in that parasites are minimally enriched relative to their hosts. Although this host-parasite enrichment pattern has been shown in multiple systems, few studies have used isotopic relationships to examine other potential symbioses. We examined the relationship between two gut-nematodes and their lizard hosts. One species, Physaloptera retusa, is a documented parasite in the stomach, whereas the relationship of the other species, Parapharyngodon riojensis (pinworms), to the host is putatively commensalistic or mutualistic. Based on the established trophic enrichments, we predicted that, relative to host tissue, parasitic nematodes would be minimally enriched (0-1 per thousand), whereas pinworms, either as commensals or mutualists, would be significantly enriched by 2-5 per thousand. We measured the (15)N values of food, digesta, gut tissue, and nematodes of eight lizard species in the family Liolaemidae. Parasitic worms were enriched 1+/-0.2 per thousand relative to host tissue, while the average enrichment value for pinworms relative to gut tissue was 6.7+/-0.2 per thousand. The results support previous findings that isotopic fractionation in a host-parasite system is lower than traditional food webs. Additionally, the larger enrichment of pinworms relative to known parasites suggests that they are not parasitic and may be several trophic levels beyond the host.



Correlating diet and digestive tract specialization: Examples from the lizard family Liolaemidae

Shannon P. O’Gradya, Mariana Morandob, Luciano Avilab and M. Denise Dearinga
Zoology 2005, 108 : 201-210

Abstract

A range of digestive tract specializations were compared among dietary categories in the family Liolaemidae to test the hypothesis that herbivores require greater gut complexity to process plant matter. Additionally, the hypothesis that herbivory favors the evolution of larger body size was tested. Lastly, the association between diet and hindgut nematodes was explored. Herbivorous liolaemids were larger relative to omnivorous and insectivorous congeners and consequently had larger guts. In addition, small intestine length of herbivorous liolaemids was disproportionately longer than that of congeners. Significant interaction effects between diet and body size among organ dimensions indicate that increases in organ size occur to a greater extent in herbivores than other diet categories. For species with plant matter in their guts, there was a significant positive correlation between the percentage of plant matter consumed and small intestine length. Herbivorous liolaemids examined in this study lacked the gross morphological specializations (cecum and colonic valves) found in herbivores in the families Iguanidae and Agamidae. A significantly greater percentage of herbivorous species had nematodes in their gut. Of the species with nematodes, over 95% of herbivores had nematodes only in the hindgut. Prevalence of nematodes in the hindgut of herbivores was 2× that of omnivores and 4× that of insectivores.


Los dichosos nemátodos se encuentran en todas las especies de reptil que tienen válvulas cecales


Preguntas:


Todo este cambio, en sólo 34 años.... es acaso una acumulación por selección direccional de varios genes? Grano fino, o grano grueso?

Cuánto de este cambios fenotípico drástico se debe más bien al efecto inmediato de diferentes condiciones epigenéticas, como la mentada asociación con el nemátodo?

Natural drifting is not a crime

En dos publicaciones académicas, Nespolo (2003) y Medel (2008) han citado el trabajo de Maturana y Mpodozis (1992, 2000 "El origen de las especies por medio de la deriva natural" ) como una fuente de daño a la biología evolutiva en Chile. Es una discusión de ideas, pero el tema moral-acusatorio nos lleva a la vez a una discusión sobre personas (Sorpresa! esos señores Maturana y Mpodozis). La propuesta de Nespolo y Medel es simple: sencillamente no hay lugar para la deriva natural en la ciencia (y por esto, es dañina, sobre todo si la enseñan en pregrado).

Sin embargo, la idea de esta "mala influencia" está refutada por los hechos. Somos varios los que hemos pasado por el lab de biología del conocer y que desarrollamos investigación en journals de evolución. ¿Cómo es que se llega a ese tipo de acusaciones, entonces?

Algunos se dejan confundir por las apariencias. Para catalogarlo de "no-ciencia", les basta considerar que lo de M&M es medio filosófico, que está publicado en una humilde revistilla local, y que ha sido escrita por investigadores cuyos trabajos de investigación más técnicos son predominantemente en la neurobiología de las aves (y no así en ecología evolutiva, por ejemplo). Pero nada de esto tendría que ver con el contenido de la propuesta de la "deriva natural". No requiere haberla siquiera leído. Cuidado con las brumas del chauvinismo.

La deriva no es un trabajo altamente técnico como el que pueda publicar Nespolo en Evolution. Todos tenemos un "esquema" complejo que inspira nuestra investigación, compuesto de varias ideas conectadas y el cual conviene mucho discutir y reinventar. Esto por lo general no es posible por medio de un sólo trabajo o review técnico, y muchas veces se hace en libros, publicaciones ocasionales y revistillas humildes. Es lo que se llama "inspirational writing" y hacerlo no constituye una abominable práctica anticientífica. Más bien, es una de las tradiciones más queridas de la biología evolutiva (sea del color que sea!).

Tampoco es que necesitemos de la venia académica especial de Medel o Nespolo. Las nociones evolutivas de la deriva natural (Maturana y Varela 1973, 1984, Maturana y Mpodozis 1992) no son ajenas a la discusión teórica de la biología evolutiva (Balon 2003, Roth 1982). También se cita el aporte de Maturana y Varela en temáticas tan importantes para la comprensión de la evolución como lo es la discusión sobre el rol de los genes (Neuman-Held 2000) y la auto-organización en los seres vivos (Kauffman 1996). Los escritos de Maturana y coautores han sido traducidos a distintos idiomas (incluyendo la deriva natural) y han producido discusión en varias ramas de la biología, una de las cuales es la biología evolutiva. Otra es el campo de la abiogénesis (origen de la vida; Luigi Luisi 2006, Margulis 2000).

Medel y Nespolo se concentran en la acusación central de que M&M es un repudiable trabajo no-científico. Como es un trabajo que supuestamente no vale la pena, la discusión del contenido es notablemente rudimentaria y selectiva. Sólo dan a entender dos cosas 1) lo encuentran confuso y mal escrito, que no se entiende y/o 2) no perdonan el destronamiento de la selección natural como principal mecanismo evolutivo o "fuerza" detrás de la adaptación.

Ni una palabra sobre autopoiesis, genotipo total, el campo epigénico, la noción sistémica de herencia, el nicho ontogénico...todos temas recurrentes en M&M y en este blog. No dan la menor luz de comprender el "core" de la propuesta de M&M.

Como el epicentro de la acción es la facultad de ciencias de la universidad de chile, resulta que tenemos muchos amigos en común algunos de los cuales sufren cuando corren estas discrepancias y que desean, correctamente, que seamos todos amigos. Pero tengan en cuenta que nadie les ha hecho a ellos jamás acusaciones públicas (y menos en medios académicos) de tener ideas no científicas y de dañar a la ciencia en Chile. Al acusar de estas cosas, no es como que ellos se dejen a sí mismos mucha opción que no sea el rechazo absoluto

Onde Está o organismo?

A discussão do post anterior tratava dessa metáfora informacionista da Biologia oficial, e coincidentemente agora recebi do professor Nelson Vaz esse artigo publicado hoje na revista Nature. Essa é a figura que, segunda eles, representa um organismo. Está tão preciosa que julguei merecer um post.

É muito interessante essa figura porque além de um emaranhado de fios transportando a informação e de um painel de controle central desta informação, o organismo aí é uma Caixa (não preta, mas cinza, neste desenho).

Está posto claramente ali: NÃO SABEMOS E NÃO NOS IMPORTA SABER O QUE SE PASSA LÁ DENTRO DESSA CAIXA.

hahahahah

Não somos nós que estamos dizendo que esta abordagem da Biologia exclui o organismo, são eles mesmos.

abraços Gustavo

Ref: Nurse, P. Life, logic and information. Nature 454: 424-426

What is so informative about information?

What is so informative about information?
Carlos M. Hamame, Diego Cosmelli, and Francisco Aboitiz (2007) . Comentario sobre: "Précis of Evolution in Four Dimensions" Eva Jablonka and Marion J lamb
Behavioral and Brain Sciences 30: 371 – 372

Abstract: Understanding evolution beyond a gene-centered vision is a fertile ground for new questions and approaches. However, in this systemic perspective, we take issue with the necessity of the concept of information. Through the example of brain and language evolution, we propose the autonomous systems theory as a more biologically relevant framework for the evolutionary perspective offered by Jablonka & Lamb

Hablando del tremendo daño a Chile con que según Medel (2008) carga el legado de Maturana, ya mencionaba anteriormente que por aquel fatídico templo de endoctrinamiento que era el lab "el rayo" había pasado Francisco Aboitiz. Ahora, entiéndase bien: Aboitiz tiene "ADN" darwinista. Al menos donde quedamos la última vez, la cuestión era la selección natural, y le molestaba el manejo de M&M de ese tema.

En realidad, pasar por el lab de Maturana no es un lavado de cerebro. Cada cual termina recogiendo lo que le guste, aunque no esté de acuerdo con otra cosa. Por lo general, se quedan con algo. Es por eso que fue grato leer el artículo arriba citado, donde estos autores producen una elegante crítica de Jablonka y Lamb muy en sintonía con nuestra forma de pensar:

"However, while the authors dispute the gene-centered notion and consider evolution as a systemic multilayered phenomenon, we believe they fall short in one critical aspect: J&L rely heavily on the notion of “information transmission” in a rather loose manner. Their approach is liable to the argument that in order to have any such thing, one needs a transmitter, a message, and a receiver – something that is not easily found when dealing with biological phenomena"

"One influential hypothesis states that living systems are those that maintain organizational closure: they are constituted by networks of self-sustaining processes, regardless of the materials used to instantiate such loops; that is, they are autonomous systems (Maturana & Varela 1973; Varela 1979). When one understands organisms this way, the notion of information transmission becomes less appealing: a closed system cannot “have” information in itself"

El artículo de Hamame et al 2007 está en el grupoyahoo bajo el nombre "Précis of Evolution in Four Dimensions" Muy recomendado

Sobre las Malas Influencias de la Deriva Natural

“Although this doctrine stimulated an interesting debate among

Chilean naturalists it had a strong detrimental impact on several

cohorts of students, ultimately retarding the advance of

evolutionary biology research in Chile”….

(Medel, 2008)

Queridos Amigos,

Después de muchas batallas editoriales, por fin ha salido en papel el quinto artículo y final de mi tesis acerca del aprendizaje olfativo en la búsqueda de pareja en avispas parasitoides (en la base de datos).
Estos trabajos exploran el valor del aprendizaje en diferentes estados de la ontogenia del insecto y como estas instancias están relacionadas con la preferencia de hábitat reproductivo y la fidelidad al hospedero.
En el caso de insectos que viven con fuerte dependencia a otro organismo, como por ejemplo una planta huésped, este tipo de aprendizaje podria estar relacionado con del origen de razas especializadas a hospederos y especiación simpátrica. Esto ha comenzado a reconocerse por varios autores contemporaneos trabajando en interacción insecto-planta (ver referencias en post ¿Búfalo o Buey? por ejemplo).

Estos experimentitos fueron enriquecido por las interesantes conversaciones sobre evolución y comportamiento con Jompoma y Marín en la Chile, las discusiones sobre especiación simpatrica en insectos con el querido Profesor Frías en la UMCE, y esas agradables tardes de viernes del Decenio en el Rayo.

Tal como ha sido el caso de muchos otros investigadores jovenes de Chile y Brasil (estudiantes de esas "cohortes mal influenciadas") este trabajo fué inspirado por el marco teórico de la biología sistémico-histórica.

¡Viva la Revolution!

Cristian Villagra, PhD
Postdoctoral Associate
Dept. Neurobiology and Behavior
Cornell University, Ithaca, NY

Fisiologia (Cardíaca) Desenvolvimental

Um dos maiores problemas da biologia pré-formacionista e adultocêntrica é o desprezo óbvio pela história. Foca-se nos genes do ovo e então se pula direto para se mirar dois adultos competindo por sexo e comida. Bom, esse hiato que nos esconde a história do organismo, um ponto cego na biologia neo-Darwinista, é justamente um dos pontos de interesse de Teorias realmente epigenéticas, como a Deriva Natural.

Curiosamente, ao ser pré-formacionista e adultocêntrica, esta biologia é também finalista. Por esta razão, mesmo no momento em que o desenvolvimento retorna a ser uma disciplina relevante para a Biologia, vemos também surgir o Bad e o Ugly (termos colocados pelo Vargas em outro post), enquanto a história continua ausente do foco no mainstream. E nesta developmental fashion week, continua-se a mirar um embrião como um adulto incompleto, como um simples trânsito para o estágio final – finalismo velado!

Lembro-me que quando o Mpodozis esteve aqui em Florianópolis ele comentou que deveríamos entender um fígado embrionário no contexto da dinâmica do embrião, e não pensando no que ele deverá estar fazendo enquanto um fígado no animal adulto. Por este motivo, me agradou muito encontrar esse artigo que fala de uma “Fisiologia cardíaca desenvolvimental” – termo criado pelo autor, que explicita sua preocupação em compreender o que faz o coração no embrião, no contexto do desenvolvimento, não como um órgão se preparando para bombear sangue no futuro! Isso é muito relevante, pois quase todas as descrições do desenvolvimento cardíaco têm esse viés de explicar a formação de um órgão para bombear sangue. É explicação baseada nas expectativas do observador, que remete ao futuro, e que desreipeita uma lógica de construção histórica.

Agora falando de fato sobre o assunto, vejam vocês, que curioso: nos períodos mais iniciais do desenvolvimento embrionário, o embrião realiza suas trocas gasosas através de uma simples difusão; até que a partir de um certo tamanho isso não é mais possível e então se observa que há ali agora uma circulação sanguínea e um coração batendo! Então isso basta para se dizer que o coração surgiu para manter a oxigenação. Mas vejam neste gráfico. Ao contrário do que se esperava desde uma perspectiva funcionalista (painel superior da figura), o coração começa a bater ANTES do embrião atingir esse tamanho que impossibilita a difusão (figura do painel inferior).

Quer dizer, nos períodos iniciais está lá o animalzinho fazendo difusão e batendo seu coração... Tira-se fora o coração aí e o que se passa? O embrião continua vivendo e oxigenando seus tecidos. O coração surge num contexto independente desta função de nutrição de oxigênio. Não surge para realizar esta função, que atribuímos ao coração no adulto. O que faz o coração aí? Para entender isso, precisamos entender seu contexto de relações e sua história, não sua finalidade (sua função), por isso a explicação funcionalista não nos serve.

Então encontrei este elegante manuscrito de Waddington (1937): “THE DEPENDENCE OF HEAD CURVATURE ON THE DEVELOPMENT OF THE HEART IN THE CHICK EMBRYO”, em que ele remove o coração do embrião para observar as conseqüências disso no resto desenvolvimento. Os principais achados dele eu reproduzo aqui:

"1. The heart was removed from chick embryos of seven to twelve somites, and the embryos cultivated in vitro. The operation abolished the normal twisting of the anterior part of the embryo on to its left side and the general bending of the brain region into an arc. These two processes therefore seem to be dependent on the normal development of the heart.

2. The embryos showed a bending of the forebrain relative to the midbrain, which is therefore independent of the development of the heart.

3. The embryonic blood system, including the aortic arches, developed normally in many cases, but the blood vessels became enormously dilated.

4. The lateral evaginations of the foregut and the visceral arch mesenchyme underwent the first stages of differentiation in atypical positions, seemingly independently of each other or of any other structures

."


Enfim, compartilho com vocês este raro momento em que se mira a construção de um órgão sem se preocupar com a sua finalidade, sem vê-lo como um trânsito para sua futura função.

Abraços,
Gustavo


Referencias

Burggren, W., Crossley, D. A. Comparative cardiovascular development: improving the conceptual framework. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. Volume 132, Issue 4, August 2002, Pages 661-674.

Waddington C_1937.The dependence of head curvature on the development of the heart in the chick embryo. J Exp Biol
14:229]231

¿Búfalo o Buey?

Plasticity in the use of novel environments: Direct Internalization and Secondary isolation mechanisms.

Bufallo bull at Jackson Hole, WY, 2008

A premise of Natural Selection (NS) is that an organism can not avoid environmental pressures and, utterly succumb or succeed under nature’s phenotypic filter. As a consequence, those exaptative phenotypes that survive the filter will be conserved in evolutionary time, meanwhile others are eliminated. 

This selective operation has worked very well for centuries in the history of the relationship of humans and domesticated animals. The breeder can select the phenotypes that she/he wants, and eliminate the others. However, this operation may not apply as an historic explanation for life’s properties and diversity. 

Among several factors that may complicate the selective scenario, lets take a look at the use of novel habitats as a way for an organism to escape its elimination under selective pressures. 

Here I will review the role of phenotypic plasticity and learning, inner properties of organism, in accommodating organism ontogenetic niche for the use of novel habitats. The role of learning as a source of novelty had been largely discussed starting with Balwin’s seminal paper in 1886. Examples of plastic changes in the use of novel habitat or under habitat changes can be found in almost all the living groups. Interestingly, in some of these cases, the plastic changes not only help the organism to withstand NS, but also help to expand their niches and diversify. 

This natural drift can be originated, among other factors, by the direct internalization of novel habitat pressures on the inheritance system of the organism. For example by epigenetic processes, like DNA methylation induced by diet or stress. Other sources of internalization may include mutation induced under stress, like transposable elements activity or DNA polymerase activity among others. Under other category of internalization we can consider all kinds of symbiogenesis, described by DeBary in 1873, as the generation of “individuality by incorporation”. The use of a new host by a parasitic organism, cohabitation, or other kind of long-term living association, results in symbiogenesis: the appearance of new bodies, new organs, and new species. 

Alternatively the diversification in novel habitats can be a consequence of phenotypic canalization of the ontogenetic niche. Under this alternative, plastic changes related with the use of the novel habitat contribute to the sympatric or parapatric isolation of the organism experiencing it, and secondarily, these isolation mechanisms would affect inheritance processes. Evidences of this kid of processes can be found in many orders, many cases of these have been discussed in Nucleo Decenio.

Thus, under the pressures of a phenotypic filter like natural selection, the organism had at least some alternatives beside to be just eliminated, thanks to plasticity and the use of novel environment, leading a change in its ontogenetic niche.

The selective reductionism framework of the “Modern Synthesis” has been proven to be an incomplete picture for understanding evolution. An actualized view of evolutionary biology has to include in first place a theory of the organism, considering its properties as protagonist of its own ontogenetic and phylogenetic change. 

“..Although Charles Darwin’s theory of evolution laid the foundations of modern biology, it did not tell the whole story. Most remarkably, The Origin of Species said very little about, of all things, the origins of species. Darwin and his modern successors have shown very convincingly how inherited variations are naturally selected, but they leave unanswered how variant organisms come to be in the first place..”

Lynn Margulis, 1998.

     Cristian Villagra

References:

Agrawal AA. (2001) Phenotypic Plasticity in the Interaction and Evolution of Species. Science, 294.

Beltman JB., P Haccou & CT Cate (2004) Learning and Colonization of New Niches, A first step towards speciation. Evolution, 58, pp. 35–46.

Donohue K. (2004) Niche construction through phenological plasticity: life history dynamics and ecological consequences. New Phytologist. Vol 166: 83-92.

Dre`s M & Mallet J (2002) Host races in plant-feeding insects and their importance in sympatric speciation. Phil. Trans. R. Soc. Lond. B. 357, 471–492.

Hegrenes S. (2001) Diet-induced phenotypic plasticity of feeding morphology in the orangespotted sunfish, Lepomis humilis. Ecology of Freshwater Fish.10: 35–42.

Jablonka E. & Lamb’ M. J. (1998) Epigenetic inheritance in evolution. J. evol. biol. 11 159-183.

Lozada-Chávez I, Janga S.Ch. & Collado-Vides J. (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Research 2006 34(12):3434-3445.

Margulis L. (1998) Symbiotic Planet: A New Look at Evolution. Basic Books, 147pp.

Maturana-Romesin H & Mpodozis J (2000) The origin of species by means of natural drift. Rev. chil. hist. nat. v.73 n.2.

Stamps J. (2003) Behavioural processes affecting development: Tinbergen’s fourth
question comes of age. Behaviour. 66:1-13.

Trussell GC (2000) Phenotypic Clines, Plasticity, and Morphological Trade-offs in an intertidial Snail. Evolution, 54: 151–166.

NOTHING IN EVOLUTION MAKES SENSE BUT IN THE LIGHT OF BIOLOGY

Inverted Dobzhansky (in Chilean Andes)

This phrase was recently uttered at an evo-devo symposium by MQ Martindale. By turning Dobzhansky's dictum on its head, Martindale was referring to how the study of the development of marine invertebrates is crucial to reconstruct the evolutionary history of metazoa (1). However, this phrase can find unsuspected depths in its resonance, quite beyond the reconstruction of natural history. It reminds us of the big crime that was the elimination of developmental biology from the neodarwinian synthesis (buried in the name of population genetics).
In fact, the actual priority that should be given to organismal biology, including development, continues to evade much mainstream evolutionary biology, which continues to show too much adaptationist-reduccionist nonsense as a result of a doctrinary enthronization of population genetics.
Take the case of Richard Lewontin. He gets close to the truth on many counts but does not acknowledge the centrality of having a theory of organism. Without this, placing the focus on population genetics (his field) will always be misleading: the organism is collapsed between the gene level and the population level. In other words, to get a correct view of evolution Lewontin would have to renounce to population genetics as the basic framework and thus be willing to erase the blackboard for a new starting point. Notice that by erasing the blackboard I do not mean to destroy the achievements of population genetics, denying any of its utility for answering specific questions. It is merely not to consider it as starting point of all evolutionary understanding.
In fact, biology is a larger topic than population genetics, even larger than evolution itself. Yet the absence of a generally accepted theory of organism has led to confuse the branch with the root: thus the vaccum at the roots is not properly acknowledged.
This, however, did not happen to Humberto Maturana upon being asked by a medicine student "what happened at the origin of life, such that we can say that life began?". Suddenly realizing he did not have a theory of organism, Maturana blushed and was only capable of promising the student he would think it over and answer his question next year.
The result, as many chilean and brazilian biologists already know, was the theory of autopoiesis, a theory of the basic organization of the living. A systems perpective providing minimal theoretical terms for understanding exactly what is goig on in organisms, such that they exhibit the properties we observe. This is not a definiton made for evolutionary biology; it is a definition for life, and as such, universal to all biology. This is why the notion of auotopoiesis has proven fruitful in the theoretical discussion of fields of biology that would appear completely dispar, for instance, the study of abiogenesis; inmunology; and neurobiology (not to mention a somewhat distorted use of the term that has become very popular in the social sciences).
And it so happens that the systems perspective of autopoiesis, focused on the organism, has implications for the understanding of evolution, too...

(1): Like myself, Martindale proposes a ctenophore-like ancestor of bilateria: See Vargas and Aboitiz 2005.

¿Qué es una adaptación?

Desde la perspectiva seleccionista, una adaptación es un rasgo que confiere una ventaja selectiva, es decir, algo que tiende a imponerse en la población. Un problema evidente de esta definición es que existen muchas adaptaciones que evidentemente no confieren ninguna ventaja competitiva, ya que estan presentes en todos los miembros de una población, por ejemplo, los ojos.

Desde una perspectiva sistémica, podría argumentarse que un rasgo adpatativo es un rasgo cuya modificación tiene el efecto de que el sistema pierde su organizacion y las propiedades que resultan de esta (generalmente, la desintegración de un ser vivo). Sacamos una parte de la máquina; si sigue funcionando, no era una adaptación, sino un rasgo neutro. Un rasgo estructural concreto, pero de ninguna relevancia sistémica inmediata.

El darwinista reclamará que esta perspectiva no incluye la reproducción: por ejemplo, si le corto un cuerno a un ciervo, puede argumentarse que éste tendrá menor "éxito reproductivo", pero no se morirá. Ya que el ciervo aún conserva su autopoiesis tras perder sus cuernos, ¿podemos afirmar que los cuernos no son una adaptación?

En este punto es interesante priorizar a la autopoiesis sobre la reproducción como condición de lo viviente. La noción sistémica de adaptación no contempla la reproducción. Hay buenos argumentos teóricos y empíricos para justificar esta exclusión. De partida, pese a tener cuernos muchos ciervos no se reproducen, y en muchos agregados sociales de organismos (partiendo por la comunidad celular que consitituyen nuestros cuerpos) se diferencian linajes que no son capaces de reproducirse: en tanto se reúnan las condiciones para que se repita un fenotipo que no se reproduce, este fenotipo se continuará repitiendo y podrá constituir un linaje.

El hacer estas distinciones no implica desconocer el hecho de que los organismos generalmente se generan por algún tipo de reproducción en vez de abiogénesis (nótese que la autoreproducción no es un requisito: puede ser aloreproducción, también). Lo que sucede es que la adaptación se constata a un nivel organísmico más básico. La constitución de un linaje es un fenómeno diferente, que requiere de la previa conservación de la adaptación. Quizás es legítimo decir que para la constitución de un linaje, la reproduccion es una condición adicional. Pero no lo es para constatar la adaptación. ¿Es esta la distinción apropiada? ¿Es necesario agregar algo más?

Nótese que según la noción sistémica, en la constitución de un nuevo linaje, la adaptación se conserva, pero no puede decirse de ninguna manera significativa que la adaptación aumenta. La noción de Fisher, de que un aumento de la adaptación es un requisito para que ocurra evolucion, no reviste ninguna utilidad científica.

Filogenia Rara de las Aves

Phylogenomic Study of Birds Reveals Their Evolutionary History
Shannon J. Hackett, Rebecca T. Kimball, Sushma Reddy, Rauri C. K. Bowie, Edward L. Braun, Michael J. Braun, Jena L. Chojnowski, W. Andrew Cox, Kin-Lan Han, John Harshman, Christopher J. Huddleston, Ben D. Marks, Kathleen J. Miglia, William S. Moore, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, and Tamaki Yuri
Science Jun 27 2008: 1763-1768.

La historia de la biología evolutiva en Chile... según Medel

(ATENCIÓN: NO OLVIDAR LEER ADEMÁS ACLARACIÓN AL PIE DE ESTA NOTA)

Hace poco me llegó un PDF de un trabajo "en prensa" de Rodrigo Medel (Facultad de ciencias de la universidad de chile). Aunque no sé donde se publicará, entiendo que Medel mismo autorizó la distribución de este material y que no existen contraindicaciones para discutirlo acá; el PDF lo encontrarán donde siempre.

El trabajo es lo más reciente en lo que han sido una serie de opininones publicadas sobre el estudio de la biología evolutiva en Chile. Medel encaja claramente en el perfil de lo que el historiador de la biología Ron Amundson (2005) describe como "synthesis historiographer", es decir, alguien cuya narrativa de la historia se entrelaza con una defensa del neodarwinismo. Presenta ciertas distorsiones típicas, especialmente la tendencia a ver la genética de poblaciones como la iniciativa más valiosa: Debido a esto, los logros de personajes de esta área (como Danko Brncic) son enfatizados, mientras que falla en documentar o evaluar apropiadamente el desarrollo e importancia logrado desde otras áreas de la evolución en Chile. Adicionalmente, Medel confronta la crítica al énfasis en la selección natural en Chile como una especie de aberrante enfermedad local, sin reconocer que se trata de un fenómeno internacional que desde los 60's viene desestabilizando la hegemonía alguna vez gozada por el neodarwinismo ( su "edad dorada" fue la postguerra de los 40's-50's)

Una notable omisión histórica hecha por Medel es la corta pero influyente estadía del prestigioso paleontólogo y biólogo argentino Osvaldo Reig, quien trabajó en la facultad de medicina de la U. de Chile, y que fue nada menos que el fundador del instituto de ecología y evolución de la Universidad Austral (según al menos dos obituarios, en J Mammalogy y Genetica). La estadía de Reig fue corta, debiendo escapar para el golpe militar, pero dejó huella , especialmente en el acercamiento citogenético al estudio de la evolución en Chile. Reig también trabajó en el museum of comparative zoology en Harvard, y es un inolvidable de la paleontología de vertebrados tras estudiar el "clásico" dinosaurio temprano Herrerasaurus.

Es notable, además, que Medel no hiciera investigación alguna del interesante conflicto que se dió en la U. de Chile entre los naturalistas-profesores y médicos-experimentalistas, y las fracturas que ante el desprecio mutuo han sido la única solución: la separación del pedagógico de la U. de Chile, y la separación del departamento de ecología y biología al interior de la facultad de ciencias. La patente existencia de los naturalistas-profesores como tradición aparte no es rescatada por Medel. Pero el instituto de entomología de la UMCE sigue ahí. El profesor Daniel Frías, que trabaja en la genética de insectos, ha publicado un interesante libro sobre sus estudios de evolución de insectos, un libro muy serio, de escasa afinidad con la ortodoxia darwinista, y que Medel por supuesto, no incluyó en su censurada "foto" de la diversidad intelectual chilena en materias de evolución.

El siguiente "cuento" muestra los prejuicios torpemente disimulados de Medel:

"When democracy was re-established in 1990, after 17 years of military dictatorship, teaching and research in genetics and evolutionary biology had not changed substantially neither in scope nor depth, in part due to the political isolation of Chile, which restricted the chance of academic and student exchange with foreign countries. The development of evolutionary biology in Chile during that period was kept constant at best. With only a couple of exceptions, the few courses of evolution available emphasized non-scientific topics that provided fertile ground for epistemological discussions but not for scientific research"

De qué se hablaba en la mayoría de las clases de evolución en los 80's? De astrología? Creacionismo?

La calificación de "no-ciencia" nos dice más sobre la visión "positivista simple" de Medel, que separa del todo epistemología de ciencia.
Aunque culpando a los alcances negativos (innegables) de la dictadura imperante, Medel reconoce que en los 70's y 80's hubo un estancamiento dentro de la genética de poblaciones. Sin embargo, en otras áreas (específicamente en el área de la neurobiología) en Chile se desarrollaba un nuevo marco teórico para la biología, basado en la teoría de sistemas, del cual se desprenderían importantes implicaciones evolutivas.
Este nuevo esquema no se construye pensando en la genética de poblaciones, sino para la biología en general. Desde un punto de partida completamente distinto, se recuperan conclusiones sobre la evolución, esbozadas algunas en los libros clásicos Maturana y Varela ("De máquinas y seres vivos" 1973, "El árbol del conocimiento" 1982). Se trata de los únicos libros de biología teórica escritos por chilenos que han disfrutado de verdadero éxito académico y editorial, nacional e internacional. Pero medel decidió no mencionarlos en su historia. Medel se nos hace el loco con el éxito de la noción de autopoiesis introducida por Maturana y Varela para caracterizar a los sistemas vivientes. Desconoce la innegable influencia teórica y experimental que ha tenido la noción de autopoiesis en el campo del origen de la vida. Desconoce los vínculos de Maturana con Heinz Von Foerster, y su categoría como uno de los pioneros de la teoría de sistemas en su aplicación a la biología.

Y por supuesto desconoce todo valor al trabajo de Maturana y Mpodozis 1992, publicación especial del Museo Nacional de Historia Natural de Chile, el cual es un trabajo que Medel aún no es capaz de entender. Si leyera con cuidadito, sabría que este es un trabajo realmente adelantado a su tiempo, que diagnosticó con anticipación la actualmente revindicada importancia de la plasticidad fenotípica, además de introducir nociones sistémicas de herencia y desarrollo, todo esto muy en línea con lo más recientemente expresado por destacados autores como Piggliuccci, West-Eberhardt, Oyama, Weiss y otros.

Medel continúa contando cuentos:

"More specifically, by questioning not only the prevalence but the entire existence of natural selection as a force driving evolutionary change, a peculiar all-inclusive perspective elaborated in the 70s gained adherents in young and uninformed undergraduate students (see Maturana-Romesín & Mpodozis 2000). Although this doctrine stimulated an interesting debate among Chilean naturalists (e.g., Gallardo 1997, Camus 2000, Nespolo 2003), it had a strong detrimental impact on several cohorts of students, ultimately retarding the advance of evolutionary biology research in Chile. Fortunately, the situation has changed in the last few years as an increasing number of students are involved in scientific research on a diverse array of evolutionary questions. For example, although still in their infancy, the areas more developed in Chile are evolutionary ecology, population and quantitative genetics, systematic biology, and biogeography. Areas less represented include genomics-bioinformatics, and paleobiology. The areas still absent include experimental evolution and evodevo (Roberto Nespolo, pers. comm.)"

Este tipo de tonterías son transparentes en su mera motivación denostadora, porque son completamente falsas. Medel intenta tapar el sol con un dedo. La verdad es que, dentro de esas cohortes de pobres alumnos que se "perdieron" en el maligno lavado de cerebro Maturánico, han surgido los únicos exponentes del Evo-Devo en Chile (Que sí, Medel, que el evo-devo en Chile existe, diga lo que te diga nespolito). El más antiguo Evo-Devo de Chile es Francisco Aboitiz, quien estuvo en el lab de Maturana. Aboitiz fue mi tutor de tesis. Estoy yo, colaborador cercano del lab (donde ya pronto estaré instalado!) y también , otro colaborador del lab, Carlos Guerrero (Catelo). En pocas palabras: los pocos chilenos que han encabezado publicaciones en revistas como Evolution & Development y JEZ part B, son todos vinculados al rayo. La solución de Medel? Sencillamente, no existimos. Flor de historiador!

Vale la pena destacar además que en el ex- departamento de morfología (hoy anatomía y desarrollo) de la fac. de medicina de la universidad de Chile ha trabajado por muchos años David Lemus, quien es legítimamente un precursor del evo-devo en el país, estudiando la embriología de reptiles chilenos. Especialmente, a partir de los 80's desarrolló investigación en dientes quiméricos en combinaciones heteroespecíficas de tejidos embrionarios del pollo y lagartijas chilenas, que continúa siendo muy citada en el área Evo-Devo. Ha sido por largo tiempo uno de los pocos preocupados de la enseñanza de la embriología comparada en Chile, manteniendo para esto un notable pequeño museo zoológico- didáctico. Otro de "los olvidados" en el esquema neodarwinista de Medel.

En la incompleta y cuentera historia de Medel, el Chile de las últimas décadas queda parado como un país más patético, más chato, menos diverso, y más dependiente de la influencia del "primer mundo", de lo que realmente es.

Referencias:

Amundson, R. 2005 The changing role of the embryo in evolutionary thought. Cambridge University

ACLARACIÓN: He recibido un email de Roberto Nespolo reclamando por la mención de su nombre en este blog. Asumiendo que este blog sólo lo leían los regulares, me referí a él en tono humorístico como "Nespolito"(supongo que los rumores vuelan!). Usar ese tono humorístico y cómplice (pensando que no necesariamente llegaría a oídos del afectado) fue un error licencioso de mi parte y pido diculpas por ello; por otra parte el incidente produjo en e-mail de Nespolo que sirve para aclarar su propia opinión , ya que él reconoce que la aproximación al Evo-Devo en Chile existe, encontrándose al tanto del trabajo de gente como Francisco Aboitiz y Miguel Concha. Que se entienda entonces claramente que lo que aparece citado por Medel como "Nespolo, pers comm" no refleja la opinión de Nespolo sobre las diferentes áreas de la biología evolutiva representadas en Chile. Aclaración agregada 21/07/08.

Is everything OK with Olfactores? A call to properly assess morphological implications

When molecular phylogenies do not coincide with the morphological phylogenies, this is a serious problem. Experience tells us that its not a matter of assuming the morphological data is equivocal; specially if it is completely uncontroversial within (morphological) phylogenetic systematics. Many times the conflict thereafter disappears, specially upon better taxon sampling of molecular data (Note: increasing the number of adequate taxa seems to be of much greater consequence than increasing the number of genes). We all remember that "sharks are teleosts" thing. This is why it is good to know the exact "morphological cost", or extra morphological transformations, that are implied by molecular hypotheses that openly conflict with morphological phylogenies. If the conflict shows no resolution by further studies, it is not a matter of assuming the molecular data must be "the correct one"; or at least, if you are going to make that assumption, KNOW the implications for the evolution of morphology!

Is something smelling fishy about the phylogeny of the chordates? Or is everything OK? At record speed, the evo-devo community has accepted the results of the latest molecular phylogenies, that vertebrates are closer to urochordates than to cephalochordates. Olfactores = Urochordates + Vertebrates. This term was born in the context of a marginal theory of Jefferies (1981) within his interpretation that the fossil Homalozoa ("calcichordates") are the ancestors of chordates (other paleontologists consider Homalozoa to be basal echinoderms).

The recent publication of the entire genome of Amphioxus has further repeated this result for the comparison of an astounding 1090 genes in a phylogenetic analysis (Putnam et al 2008) that included important groups that are frequently left out, such as an acorn-worm, and a larvacean urochordate.
Given that the Olfactores are becoming accepted as some "new truth", it is interesting to review why never before had this notion attained popularity, the most common assumption being that cephalochordates and vertebrates were closest, conforming a clade Euchordata (also called "Myomerozoa" for the presence of somites). Actually, just a glance at amphioxus, a very fish-looking creature, should make us immediately suspect that the olfactores is probably not consistent with the most parsimonious morphological history; that is, that we may have the proverbial case of a clash of molecular vs morphological phylogenies.

Everybody agrees that urochordates have secondarily lost traits. This is obvious when the traits absent in urochordates are present even in hemichordates , such as coelomic cavities, and several (not just one) pairs of branchial openings. However, the list of things lost in urochordates increases substantially if we consider Olfactores to be real: for instance, the loss of somites, and several vertebrate-like gene expression patterns in the developing neural tube.

In this sense, it is important to point out that the exact morphological cost of the olfactores, in terms of assuming extra steps beyond parsimony, has not being adequately discussed or investigated yet. An important conflict with morphology and gene expression is looming, but people are failing to see it.

For instance, a recent comment (Swalla and Smith 2006) says "an extensive cladistic reanalysis of morphological data found strong support for Olfactores ( Ruppert 2005)". However, the cited work of Ruppert is not a cladistic analysis at all, but a "homology analysis", the mere mapping of proposed events assuming that Olfactores is real, for a limited set of traits. Further, the morphological cost of the olfactores is hardly rescued by Ruppert 2005, which cites only a few of the most notorious losses we must assume occurred in the urochordates (for instance, Ruppert fails to mention any of the similarities of gene expression between the neural tube of cephalochordates and vertebrates)

In good faith, we must assume that Swalla and Smith were thinking about another morphological analysis that is cited as support for the olfactores, namely the cladistic analysis of all metazoa made by Zrzávy et al (1998). While indeed Zrzávy et al. is an extensive analysis (238 traits), it does not specifically address the question of the phylogeny of chordates , but of metazoa in general. So actually only a minority of these traits are bound to be relevant to the question of chordate phylogeny. Further, despite the non-traditional placement of the urochordates retrieved by this analysis, Zrzávy et al did not make any mention of this result in their discussion, concentrating on other aspects of animal phylogeny. No list of "Olfactorian" synapomorphies was discussed. The analysis by Zrzávy has been criticized at length by Jenner 2001 on various grounds, such as the assumptions made in the definition and polarization of traits.

With no explicit cladistic analysis of chordates for an alternative phylogeny , the review by Rowe (2004) of chordate phylogeny does not even mention the work by Zrzávy or the possibility of the olfactores. Indeed, the best references for a cladistic analysis specifically focused on the chordates are earlier works (Maisey 1986, and Schaeffer 1987), which support the euchordata, and are largely accepted within the community of phylogenetic systematics. However, these studies will fail to collect numerous newly described traits shared by cephalochordates and vertebrates, from gene expression patterns to fine structure of the nervous system. So, in fact, a new updated cladistic phylogenetic analysis of the cephalochordates is needed to establish the precise consequences of the Olfactoria for the morphological history of the chordates.

It is certainly possible that this new analysis may show the history implied by olfactores to be too absurd, implying too many reversals or convergences. If this is the case, it is not just a matter of going with the molecular phylogeny over the morphological; rather, the possibility of an artifact in the molecular studies must be taken into account (yes, even with 1090 genes! )


This is the tree of the 1090 genes (Putnam et al 2008). Some observations:

1) As usual, the longest branches of the chordates are the Urochordates. Also, notice that this effect is not mitigated by the large amount of genes; that is, abnormally high substitution rates is a genome-wide phenomenon. Is it possible that high substitution rates may distort the phylogenetic signal of entire genomes? Also, notice the low 76.4 % bootstrap value support for the monophyly of chordates. Traditionally, molecular evidence has had some problems retrieving this node, which is, from a morphological perspective, a very straight-forward conclusion

2) Hagfish, morphologically the most basal vertebrates , were not included in this analysis. In fact, the position of hagfishes haunts this entire issue, since it is a case in which a clear conflict of molecules vs morphology still lives on

3) Despite the general trend of nuclear genes to support the olfactoria, the comparison of entire mitochondrial genomes supports the classic hypothesis of euchordata (Bourlat et al. 2006). Further, this is also the case when discussing the relationships of Hagfishes, supporting them as basalmost vertebrates (Yu et al. 2008). Why this diference ? Is it possible that the mitochondrial genomes have been spared from some source of artifact affecting the phylogenetic signal of nuclear genes?

References.

Bourlat et al 2006 Nature 444:85-8

Jefferies 1981 Zool. J. of Linnean Soc. 73, 351-396

Jenner 2001 Syst. Biol. 50(5):730-742

Putnam et al 2008 Nature 453: 1064-1070 doi:10.1038/nature06967

Rowe 2004 In: Cracraft & Donoghue, Ed. Assembling the tree of life. Oxford. pp 384-409

Ruppert 2005 Can. J. Zool. 83: 8–23

Swalla & Smith 2006 Phil. Trans. R. Soc. B doi:10.1098/rstb.2007.2246

Yu et al. 2008 J. Genet. Genomics 35: 285-290

Zrzávy et al. 1998 Cladistics 14, 249 -285

Evo-Devo: The Good, the Bad, and the Ugly.

THE GOOD: Homology assesment evo-devo, and epigenetic evo-devo. Evo-Devo that works on the pretty empirical task of assessing problematic homologies, with tree-based inferences on the evolution of development, continues to greatly help the reconstruction of the evolutionary history of life on earth. Epigenetic evo-devo's, in turn, understand that developmental biology is not genetics. They have realistically confronted the role of higher level and environmental epigenetic interactions in development, and thus also in the origin of evolutionary novelties. Both of these tend to emphasize how standing developmental mechanisms, and not natural selection alone, are essential to the pathway taken by evolution.

THE BAD: Reductionist "regulatory" evo-devo. Dangerous, because it is is upheld by important figures of evo-devo, presenting itself as a triumph and empirical conclusion. Yes, mutations in cis-regulatory regions are commonplace in evolution, but these people seem to have reductionist difficulties in understanding there is anything more beyond finding such a mutation. The notion that only non-coding "regulatory" sequence changes can produce localized expression (in time or space) simply makes no good developmental sense. As Lillie pointed out, all cells have the same DNA content, including the "regulatory" elements; whether a gene is expressed or not still varies from cell type to cell type depending on something else as well. In other words, Lillie's "paradox" forces the question: "who regulates the regulators"? This question reveals that "regulation" is nothing but a sloppy, semi-nonsensical wastepaper-basket term. Both coding and non-coding sequences can be "regulatory". Even environment can "regulate" gene expression. Genes are expressed differentially in cells, NEVER because of their "regulatory" sequences alone, but ALWAYS including the higher-level and environmental interactions at the cell and tissue level, which explain "Lillies paradox". (again: This is why developmental biology is different from genetics!). Focusing only on one type of mutations (cis-regulatory) is just a re-strengthened version of the old reductionist fallacy that genotype=phenotype. This false equivalence ultimately downplays the role of understanding development, the actual mechanisms that relate genotype to phenotype. Without really introducing developmental mechanisms, no serious challenge is made to the hegemony of population genetics as a way of understanding evolution. Yes: The bad is a traitor of development, for love of genetics. Evo-Devo can now become a mere footnote: The largely uninteresting filling-in of superfluous data on "what the specific mutations were".

THE UGLY. Just plain wrong or artifactual topics, mostly born from the lack of proper integration of different fields of research. Specially silly is the "conflict" between microevolution and macroevolution. Doubtless, the study of microevolution offers many advantages. But this does not mean at all that a macroevolutionary study will not be able to derive sound conclusions: when the evidence is there, there is nothing to say about the micro or macro level in which a question is satisfactorily answered. That comparable experiments can only be tested between closely related species is a myth: gene expression experiments can produce the same phenotypic alteration despite hundreds of millions of years of separation.
This follows in an old lab-bench tradition of being purely "experimental" negating any need to know much about natural history and macroevolution. It also relates to "blind" faith in molecular phylogenies, that is, with little capacity for critically evaluating these studies (such as by morphologica implications). As a result, plain artifacts of the tree become the basis for many weird hypotheses (I have argued before this is happening right now, with new supposed clades such as "urochordates+vertebrates"). Studies continue to emerge where well-established facts of natural history are swept aside in favor of some "groundbreaking hypothesis".

Many Evo-Devos have thought that macroevolution is some kind of truly radical "body plan" change with mechanisms quite different from those observed at a microevolutionary level, appealing to some mysterious happenstance of the past for the origin of phyla or higher "grades". However, Evo-devo's are slowly wisening up to the fact that macro and micro evolutionary change proceeds pretty much in the same way, with the simple fact being that lineages diverging earlier can accumulate greater differences (as pointed out before)

Answering Cuvier: Notes on the systemic/historical nature of living beings

Más literatura subversiva y underground; por fin tenemos el trabajito de Cecchi, Vargas, Villagra y Mpodozis 2004 en pdf (donde siempre!). Releyendo esta joyita (a la cual sólo contribuí afinando el inglés y con modestas pizcas de aliño) surge una bonita reflexión: ¿Qué tan diferente es el desafío de entender el desarrollo al de entender la evolución? Hay muchas cosas en común: La constante coherencia interna y con el medio, a través de un proceso radical de transformación biológica que incluye aumentos de complejidad. Incluso, el desarrollo puede librarse de algunas presunciones que son adhosadas incorrectamnete a la evolución; por ejemplo no es muy defendible que el desarrollo sea un proceso de cada vez mejor ajuste al medio; más bien, contemplando un ciclo de vida, es evidente que cada etapa del desarrollo está ajustada a su medio. En efecto, ambos evolución y desarrollo son procesos de deriva sistémica-histórica, con continua participación del medio y en conservación de la adaptación.



Mientras la visión estructuralista de Cecchi et al. lleva a reconocer a desarrollo y evolución como procesos del mismo tipo, la visión ortodoxa, en vez de preocuparse por entender el desarrollo (la VERDADERA relación genotipo-fenotipo), se contentan con una metáfora de que el fenotipo está programado en el genotipo tal que genotipo = fenotipo. Con este ardid reduccionista, el adaptacionista darwiniano se ha convencido a sí mismo de que no es necesario entender de desarrollo para entender de evolución.

Tsk,tsk.

Cecchi C, Vargas A, Villagra C, Mpodozis J. 2004 Answering Cuvier: Notes on the systemic/historical nature of living beings. Cybernetics and human knowing 11(4): 1-19

contingencia histórica waaaa

Historical contingency and the evolution of a key
innovation in an experimental population of
Escherichia coli

Zachary D. Blount, Christina Z. Borland, and Richard E. Lenski*
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 25, 2006.
Contributed by Richard E. Lenski, April 9, 2008 (sent for review March 26, 2008)

The role of historical contingency in evolution has been much
debated, but rarely tested. Twelve initially identical populations of
Escherichia coli were founded in 1988 to investigate this issue. They
have since evolved in a glucose-limited medium that also contains
citrate, which E. coli cannot use as a carbon source under oxic
conditions. No population evolved the capacity to exploit citrate
for >30,000 generations, although each population tested billions
of mutations. A citrate-using (Cit
) variant finally evolved in one
population by 31,500 generations, causing an increase in population
size and diversity. The long-delayed and unique evolution of
this function might indicate the involvement of some extremely
rare mutation. Alternately, it may involve an ordinary mutation,
but one whose physical occurrence or phenotypic expression is
contingent on prior mutations in that population. We tested these
hypotheses in experiments that ‘‘replayed’’ evolution from different
points in that population’s history. We observed no Cit

mutants among 8.4 1012 ancestral cells, nor among 9 1012 cells
from 60 clones sampled in the first 15,000 generations. However,
we observed a significantly greater tendency for later clones to
evolve Cit
, indicating that some potentiating mutation arose by
20,000 generations. This potentiating change increased the mutation
rate to Cit
but did not cause generalized hypermutability.
Thus, the evolution of this phenotype was contingent on the
particular history of that population. More generally, we suggest
that historical contingency is especially important when it facilitates
the evolution of key innovations that are not easily evolved
by gradual, cumulative selection.


PNAS
June 10, 2008
vol. 105
no. 23
7899–7906


www.pnas.org/cgi/doi/10.1073/pnas.0803151105

Sorry el desorden

Looking for Darwin in all the wrong places

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

AL Hughes

Heredity (2007) 99, 364–373

Recent years have seen an explosion of interest in evidence for positive Darwinian selection at the molecular level. This quest has been hampered by the use of statistical methods that fail adequately to rule out alternative hypotheses, particularly the relaxation of purifying selection and the effects of population bottlenecks, during which the effectiveness of purifying selection is reduced. A further problem has been the assumption that positive selection will generally involve repeated amino-acid changes to a single protein. This model was derived from the case of the vertebrate major histocompatibility complex (MHC), but the MHC proteins are unusual in being involved in protein–protein recognition and in a co-evolutionary process of pathogens. There is no reason to suppose that repeated amino-acid changes to a single protein are involved in selectively advantageous phenotypes in general. Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression.

Heredity (2007) 99, 364–373; doi:10.1038/sj.hdy.6801031;
published online 11 July 2007

Podrán encontrar el pdf en el grupo yahoo...

Epigenetically Acquired Brain Disorders

Cachense este trabajito (hacer click en titulo)...

Epigenetic Mechanisms in Autism Spectrum Disorders

Onde fica a competição?

Fico pensando como é absurda essa noção de um mundo competitivo com organismos carregando consigo suas preciosas mutações nucleotídicas, parecendo um jogador de futebol americano correndo com sua bola escondida debaixo do braço e batendo cabeça com seus oponentes.

Que isso não é assim em bactérias, que há uma imensa transferencia horizontal de genes, já é bem documentado na literatura. Não se pode aceitar a idéia de que "eu guardo minhas mutações pra mim e venço você".

Agora há mais um exemplo muito interessante e curioso mostrando como essa situação se passa no viver de organismos metacelulares - rotíferos bdeóides, invertebrados aquáticos que podem sobreviver a períodos de dissecação.

Vejam só que curioso o que passa!

Science 320, 1210–1213 (2008)
Many single-celled organisms collect genes from other organisms — a process known as horizontal gene transfer — but multicellular organisms tend not to. Now tiny invertebrates called bdelloid rotifers have been found to take on genetic material from a range of other species, including bacteria, fungi and plants.
Multicellular creatures rarely do this because their germ line is sequestered in the gonads, explain Eugene Gladyshev, Matthew Meselson and Irina Arkhipova at Harvard University in Massachusetts. Bdelloid rotifers are different. They often experience desiccation, potentially opening up their cell membranes to chunks of outsider DNA. This unusual way of injecting diversity into their genomes may help to explain why these rotifers have gone 40 million years without sex.


abraços,
Gustavo

Parental Care Usurpation as a model for thinking about Developmental Systems

Parental Care usurpators exploit the social behavior of their hosts, this “modo de vida,” it is present in numerous taxa and involve the partial sequestration of the ontogenetic niche of the host species. In this commentary I will mention two cases of parental care usurpation: the avian brood parasites (e.g. cuckoos) and the ant nest usurpations (often called slave-maker ants or pirate ants).

Due to the very emergent properties involved in the evolution of these life styles; these cases are interesting models for thinking about the value of Developmental System Theory or Evolution by Means of Natural Drift as explanatory backgrounds.

Previously in this blog, we have seen comments about the relevance of the “incomplete isolation” of the multicellulars systems processes as a way to understand certain kinds of dynamic changes in the ontogenetic niche. This “epigenetic permeability”, could be suggested as a property that may help to understand why it is not always necessarily an “Internalization” (i.e incorporation of adaptative traits in the genome of the evolving species) for the development of new life styles or lineage changes in order to get an idea of the points when this “epigenetic permeability” may help to explain the establishment and conservation of these life styles, lets compare the steps of the parasite-host interactions.

In avian brood parasites, the female lays the egg in the host nest, which has been recognized by some authors as the only interaction between the parasite and host species. I would suggest to add a second step that is performed by the parasite chick: the expulsion from the nest of the host offspring (this does not always happen though). For the realization of step one of the interaction, the parasite mother had to find the appropriate host nest and the host parents have to be fooled to keep believing that the extra egg belongs to them. Some parasites species present similar egg pigmentation with their main host, but it is not clear, as far as I´ve read, that this is genetically determined and that this trait can vary inter and intraspecies. The second step is very similar to other kind of parasitic interaction where the allocation of resources is diverted to feed the growing parasite (See Sacculina barnacles post in this blog as an example).

In ant nest usurpation species, the first step involves the usurpation of the queen host throne by the parasite ant. The female searching for nest, sneaking in the nest without being detected as alien by the colony, and (as similar as the avian parasite chick) the diversion towards the reproducing parasite.

In the second step, the parasite queen offspring will search for new host colonies, raid them and kidnap host worker’s larvae. Experiments have demonstrated that when two alternative host are available for the queen and she picks one of them in the first step, the parasite sons will also choose that one for collecting more workers.

This two examples suggest to me that the Developmental System is more than the niche variables and the inheritable organism material, and cannot be reduced to the somatic and germinal part as a satisfactory explanatory background but also the construction of these parasitic life styles due to epigenetic permeability are possible thanks to crucial behavioral operations (“conducta” in Maturana’s approach) that allow the emergence of these very externalized and dependent systems.

Cristian Villagra

Más condenas mortales en cladística

Dénme una mezquita y un altoparlante: Su ayatola de la cladística les tiene listas un par de ricas nuevas condenas a muerte, que se cumplirán sin piedad.
¿Los desdichados en esta ocasión?

1)Pegasoferae: Este clado agrupa murciélagos con perisodáctilos. Se ha justificado por medio de inserciones de trasposones en lugares específicos del genoma (Nishihara et al. 2006) y ha aparecido en algunos otros arbolitos desde entonces (Murphy et al. 2008) pero lo cierto es que hasta el momento ningún estudio formal de secuencias típicas ni de la morfología ha confirmado la existencia de Pegasoferae. Más bien, por el lado de la morfología, esto implicaría asumir que los ungulados no existen, ya que perisodáctilos serían más cercanos a quirópteros que a artiodáctilos; si miramos los datos paleontológicos, no quedaría otra, según Pegasoferae, que concluir que los murciélagos evolucionaron a partir de algo como este lindo Condylarto (ungulado basal)


Qué les parece?

La otra condena de muerte es para este arbolito muy publicado en Nature:



La historia de la evolución del veneno que vende ese paper se ve muy linda, pero nótese: la iguana les salió entremedio de un montón de escleroglossae...es una infracción flagrante de todo lo que sabemos de evolución de lagartos... de hecho la distinción más básica de los lagartos, es entre iguania y scleroglossae. Este modelo implica la reversión de varios ragsos escleroglosos (como la misma lengua queratinizada y mayor desarrollo del órgano de Jacobson).


Referencias:


Nishihara, H., Hasegawa, M., and Okada, N. 2006. Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc. Natl. Acad. Sci. 103: 9929–9934

William J. Murphy, Thomas H. Pringle, Tess A. Crider, Mark S. Springer and Webb Miller 2007 Using genomic data to unravel the root of the placental mammal phylogeny Genome Res.17: 413-421

Fry BG, Vidal N, Norman JA, Vonk FJ, Scheib H, Ramjan SF, Kuruppu S, Fung K, Hedges SB, Richardson MK, Hodgson WC, Ignjatovic V, Summerhayes R, Kochva E. 2006. Early evolution of the venom system in lizards and snakes. Nature.439(7076):584-8.