tRNA nucleares e mitocondriais "parecidos" no genoma humano

quinta-feira, outubro 09, 2014

ORIGINAL RESEARCH ARTICLE Front. Genet., 08 October 2014 | doi: 10.3389/fgene.2014.00344

Nuclear and mitochondrial tRNA-lookalikes in the human genome

Aristeidis G. Telonis, Phillipe Loher, Yohei Kirino and Isidore Rigoutsos*

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA

We are interested in identifying and characterizing loci of the human genome that harbor sequences resembling known mitochondrial and nuclear tRNAs. To this end, we used the known nuclear and mitochondrial tRNA genes (the “tRNA-Reference” set) to search for “tRNA-lookalikes” and found many such loci at different levels of sequence conservation. We find that the large majority of these tRNA-lookalikes resemble mitochondrial tRNAs and exhibit a skewed over-representation in favor of some mitochondrial anticodons. Our analysis shows that the tRNA-lookalikes have infiltrated specific chromosomes and are preferentially located in close proximity to known nuclear tRNAs (z-score ≤ −2.54, P-value ≤ 0.00394). Examination of the transcriptional potential of these tRNA-lookalike loci using public transcript annotations revealed that more than 20% of the lookalikes are transcribed as part of either known protein-coding pre-mRNAs, known lncRNAs, or known non-protein-coding RNAs, while public RNA-seq data perfectly agreed with the endpoints of tRNA-lookalikes. Interestingly, we found that tRNA-lookalikes are significantly depleted in known genetic variations associated with human health and disease whereas the known tRNAs are enriched in such variations. Lastly, a manual comparative analysis of the cloverleaf structure of several of the transcribed tRNA-lookalikes revealed no disruptive mutations suggesting the possibility that these loci give rise to functioning tRNA molecules.

FREE PDF GRATIS: Frontiers in Genetics

A teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários precisa de um upgrade???

Does evolutionary theory need a rethink?

Kevin Laland, Tobias Uller, Marc Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka, John Odling-Smee, Gregory A. Wray, Hopi E. Hoekstra, Douglas J. Futuyma, Richard E. Lenski, Trudy F. C. Mackay, Dolph Schluter& Joan E. Strassmann

08 October 2014

Researchers are divided over what processes should be considered fundamental.

Subject terms: Evolution Developmental biology Philosophy




YES, URGENTLY — Kevin Laland and colleagues

NO, ALL IS WELL — Gregory A. Wray, Hopi E. Hoekstra and colleagues

Does evolutionary theory need a rethink? Yes, urgently

Without an extended evolutionary framework, the theory neglects key processes, say Kevin Laland and colleagues.

Charles Darwin conceived of evolution by natural selection without knowing that genes exist. Now mainstream evolutionary theory has come to focus almost exclusively on genetic inheritance and processes that change gene frequencies.

Yet new data pouring out of adjacent fields are starting to undermine this narrow stance. An alternative vision of evolution is beginning to crystallize, in which the processes by which organisms grow and develop are recognized as causes of evolution.

Some of us first met to discuss these advances six years ago. In the time since, as members of an interdisciplinary team, we have worked intensively to develop a broader framework, termed the extended evolutionary synthesis1 (EES), and to flesh out its structure, assumptions and predictions. In essence, this synthesis maintains that important drivers of evolution, ones that cannot be reduced to genes, must be woven into the very fabric of evolutionary theory.

We believe that the EES will shed new light on how evolution works. We hold that organisms are constructed in development, not simply ‘programmed’ to develop by genes. Living things do not evolve to fit into pre-existing environments, but co-construct and coevolve with their environments, in the process changing the structure of ecosystems.

The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science1, 2. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.

Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders — such as physiologists or developmental biologists — flood into their field.

However, another factor is more important: many conventional evolutionary biologists study the processes that we claim are neglected, but they comprehend them very differently (see ‘No, all is well’). This is no storm in an academic tearoom, it is a struggle for the very soul of the discipline.

Here we articulate the logic of the EES in the hope of taking some heat out of this debate and encouraging open discussion of the fundamental causes of evolutionary change (see Supplementary Information).

Core values

The core of current evolutionary theory was forged in the 1930s and 1940s. It combined natural selection, genetics and other fields into a consensus about how evolution occurs. This ‘modern synthesis’ allowed the evolutionary process to be described mathematically as frequencies of genetic variants in a population change over time — as, for instance, in the spread of genetic resistance to the myxoma virus in rabbits.

In the decades since, evolutionary biology has incorporated developments consistent with the tenets of the modern synthesis. One such is ‘neutral theory’, which emphasizes random events in evolution. However, standard evolutionary theory (SET) largely retains the same assumptions as the original modern synthesis, which continues to channel how people think about evolution.

The story that SET tells is simple: new variation arises through random genetic mutation; inheritance occurs through DNA; and natural selection is the sole cause of adaptation, the process by which organisms become well-suited to their environments. In this view, the complexity of biological development — the changes that occur as an organism grows and ages — are of secondary, even minor, importance.

In our view, this ‘gene-centric’ focus fails to capture the full gamut of processes that direct evolution. Missing pieces include how physical development influences the generation of variation (developmental bias); how the environment directly shapes organisms’ traits (plasticity); how organisms modify environments (niche construction); and how organisms transmit more than genes across generations (extra-genetic inheritance). For SET, these phenomena are just outcomes of evolution. For the EES, they are also causes.

Valuable insight into the causes of adaptation and the appearance of new traits comes from the field of evolutionary developmental biology (‘evo-devo’). Some of its experimental findings are proving tricky to assimilate into SET. Particularly thorny is the observation that much variation is not random because developmental processes generate certain forms more readily than others3. For example, among one group of centipedes, each of the more than 1,000 species has an odd number of leg-bearing segments, because of the mechanisms of segment development3.

In our view, this concept — developmental bias — helps to explain how organisms adapt to their environments and diversify into many different species. For example, cichlid fishes in Lake Malawi are more closely related to other cichlids in Lake Malawi than to those in Lake Tanganyika, but species in both lakes have strikingly similar body shapes4. In each case, some fish have large fleshy lips, others protruding foreheads, and still others short, robust lower jaws.

SET explains such parallels as convergent evolution: similar environmental conditions select for random genetic variation with equivalent results. This account requires extraordinary coincidence to explain the multiple parallel forms that evolved independently in each lake. A more succinct hypothesis is that developmental bias and natural selection work together4, 5. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development5, 6.
...

FREE PDF GRATIS: Nature

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RAZÕES PARA SUPRIMIR AS CRÍTICAS FEITAS POR CIENTISTAS E BIÓLOGOS EVOLUCIONISTAS:

The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.


Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders -- such as physiologists or developmental biologists -- flood into their field.

(Kevin Laland, Tobias Uller, Marc Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka, and John Odling-Smee, "Does evolutionary theory need a rethink? Yes, urgently," Nature, Vol. 514:161-164 (October 9, 2014) (Ênfase deste blogger)

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NOTA DESTE BLOGGER:

Stephen Jay Gould, um evolucionista honesto, afirmou em 1980, em artigo com revisão por pares, junto com Niles Eldredge, que a atual teoria geral da evolução, a Síntese Evolutiva Moderna, era "uma teoria científica morta que teimava posar de ortodoxa somente nos livros didáticos" e que uma nova teoria da evolução se fazia necessária.

A História da Ciência já registrou a postura científica correta de Gould - o neodarwinismo era um referencial morto que não podia ser ressuscitado no contexto de justificação teórica. Este blogger bate nessa tecla desde 1998, e levou ao conhecimento de muitos editores e jornalista científicos de que uma iminente e eminente mudança paradigmática estava para ocorrer em biologia evolucionária. Somente foi levado a sério por Maurício Tuffani, quando trabalhou na editoria de ciência do jornal Folha de São Paulo e na revista Galileu.

Só agora a Nature abre o debate, tarde, mas ainda em tempo de reivindicar este blogger que foi chamado pela Nomenklatura científica e pela Galera dos meninos e meninas de Darwin de não saber o que é ciência e de nem fazer ciência, de medieval, obscurantista y otras cositas mais.

Fui, nem sei por que, rindo da cara de muitos biólogos evolucionistas, professores em universidades públicas de renome que, na ocasião de minhas denúncias disseram que eu estava numa canoa furada ao embarcar na canoa da teoria do Design Inteligente. Respondi: aposto todas as minhas fichas na TDI, pois o pangaré de Darwin não pode ganhar mais a corrida de explicar a origem e evolução das espécies.

Este blogger aprendeu na universidade que a ciência abomina o vazio teórico-epistemológico. Pergunta causticante: Sob qual referencial teórico está sendo feita a biologia evolutiva? Abracadabra? Búzios? Cartas de Tarô? Entranhas de galinha? Leitura das nuvens?

Darwin morreu!!! Viva Darwin!!!

Kauffman: além do impasse mente-corpo consciente e a mecânica quântica

Além do impasse: Mente-Corpo consciente - Mecânica Quântica - Livre arbítrio - Possível pan-psiquismo - Possível interpretação do enigma quântico

Beyond the Stalemate: Conscious Mind-Body - Quantum Mechanics - Free Will - Possible Panpsychism - Possible Interpretation of Quantum Enigma

I wish to discuss a large, interwoven set of topics pointed at in the title above. Much of what I say is highly speculative, some is testable, some is, at present, surely not. It is, I hope, useful, to set these ideas forth for our consideration. What I shall say assumes quantum measurement is real, and that Bohm's interpretation of Quantum Mechanics is not true. The Stalemate: In our contemporary neurobiology and much of the philosophy of mind post Descartes we are classical physics machines and either mindless, or mind is at best epiphenomenal and can have no consequences for the physical world. The first main point of this paper is that we are not forced to this conclusion, but must give up total reliance on classical physics.
Comments:20 pages
Subjects:History and Philosophy of Physics (physics.hist-ph); Quantum Physics (quant-ph)
Cite as:arXiv:1410.2127 [physics.hist-ph]
 (or arXiv:1410.2127v1 [physics.hist-ph] for this version)

Submission history

From: Stuart Kauffman [view email] 
[v1] Tue, 7 Oct 2014 07:49:36 GMT (238kb)
FREE PDF GRATIS: ArXiv

Hélio Schwartsman 'falou e disse': ciência e liberdade andam de mãos dadas!!!

quarta-feira, outubro 08, 2014

“Como qualquer outro empreendimento coletivo, a ciência só se materializa se houver comunicação entre as pessoas que dela se ocupam. Mas, mais do que a maioria dos empreendimentos coletivos, a ciência depende da crítica para avançar. O momento chave da descoberta científica, como apontava Popper, é o erro. Um experimento que refuta uma teoria é muito mais informativo e, assim, decisivo do que um que a corrobora.

Nesse contexto, é importante não só que cientistas possam criticar colegas e superiores como também que tenham liberdade para desafiar os cânones estabelecidos. Até podemos conceber que a ciência seja produzida num cenário de censura a ideias, mas ela provavelmente caminharia de modo hesitante, preocupada em não desagradar aos poderosos.”



Hélio Schwartsman in Ciência e liberdade, Folha de São Paulo, 8 de outubro de 2014.



Leia o texto completo aqui: Folha de São Paulo 

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NOTA DESTE BLOGGER:

Neddy trocou e-mails com Hélio Schwartsman há algum tempo. Convidei-o para almoçar em São Paulo junto com outro jornalista amigo, Maurício Tuffani, mas nunca deu certo. O Tuffani é cético no sentido pirrônico (mantém sistematicamente a dúvida e não fecha a questão sobre a verdade) e o Schwartsman é judeu ateu. 

Pelos e-mails que trocamos, ele não simpatiza com a teoria do Design Inteligente, mas o que escreveu sobre ciência e liberdade na Folha de São Paulo, reflete o que fazemos aqui - desafiar a Nomenklatura científica apontando seus erros e apresentando uma teoria que pode explicar a origem da informação genética: a teoria do Design Inteligente.


Fundamentos de Física confirmados: experimentos testando a dilatação do tempo de Einstein e eletrodinâmica quântica.

Test of Time Dilation Using Stored Li+ Ions as Clocks at Relativistic Speed

We present the concluding result from an Ives-Stilwell-type time dilation experiment using 7Li+ ions confined at a velocity of beta = v/c = 0.338 in the storage ring ESR at Darmstadt. A Lambda-type three-level system within the hyperfine structure of the 7Li+ triplet S1-P2 line is driven by two laser beams aligned parallel and antiparallel relative to the ion beam. The lasers' Doppler shifted frequencies required for resonance are measured with an accuracy of < 4 ppb using optical-optical double resonance spectroscopy. This allows us to verify the Special Relativity relation between the time dilation factor gamma and the velocity beta to within 2.3 ppb at this velocity. The result, which is singled out by a high boost velocity beta, is also interpreted within Lorentz Invariance violating test theories.
Subjects:Atomic Physics (physics.atom-ph)
Journal reference:Phys. Rev. Lett. 113, 120405 - Published 16 September 2014
DOI:10.1103/PhysRevLett.113.120405
Cite as:arXiv:1409.7951 [physics.atom-ph]
(or arXiv:1409.7951v1 [physics.atom-ph] for this version)

Submission history

From: Guido Saathoff [view email] 
[v1] Sun, 28 Sep 2014 19:58:06 GMT (158kb,D)

FREE PDF GRATIS: ArXiv

O teletransporte quântico de múltiplas propriedades de uma partícula quântica

Quantum teleportation of multiple properties of a single quantum particle




Quantum teleportation provides a "disembodied" way to transfer quantum states of an object over arbitrarily long distance, without physical travelling of the object itself. A single quantum particle can possess various degrees of freedom-internal and external-and with coherent coupling among them. Yet, all the previous experiments were limited to teleportation of a single degree of freedom only. A fundamental open challenge is to simultaneously teleport multiple degrees of freedom which is necessary to fully describe an object, thereby truly teleporting it intactly. Here, we demonstrate the first quantum teleportation of both spin and orbital angular momentum of a single photon, in the form of spin-orbit hybrid entangled states. We use spin-orbit hyper-entangled photon pairs as quantum channel, and develop a new technique to discriminate hyper-entangled Bell state exploiting quantum non-demolition measurement. This work demonstrates an enhanced capability for quantum communications, and moves a step toward complete teleportation of complex quantum systems.
Comments:26 pages, 5 figures. Comments are welcome
Subjects:Quantum Physics (quant-ph); Strongly Correlated Electrons (cond-mat.str-el); Popular Physics (physics.pop-ph)
Cite as:arXiv:1409.7769 [quant-ph]
 (or arXiv:1409.7769v1 [quant-ph] for this version)

Submission history

From: Chao-Yang Lu [view email] 
[v1] Sat, 27 Sep 2014 06:09:53 GMT (570kb)

FREE PDF GRATIS: ArXiv

Privileged species (Espécie privilegiada): como o cosmos é planejado intencionalmente para a vida

sábado, outubro 04, 2014

Privileged Species (Espécie privilegiada)

Como o cosmos é planejado intencionalmente para a vida

Sobre o filme

Os humanos são produtos acidentais de um universo cego e indiferente? Ou eles são os beneficiários de uma ordem cósmica que foi antecipadamente planejada para ajuda-los a se desenvolver? Privileged Species (Espécie privilegiada) é um documentário de 33’ do Discovery Institute que explora a crescente evidência da Física, Química, Biologia, e áreas afins de que o nosso universo foi intencionalmente planejado para que grandes seres multicelulares como nós. Apresentando o geneticista e autor Michael Denton, o documentário investiga as propriedades especiais do carbono, água, e oxigênio que tornam a vida humana e a vida de outros organismos, e explora algumas das características exclusivas dos humanos que nos fazem uma espécie verdadeiramente privilegiada.


A arma secreta do Design Inteligente: o mundo!

sexta-feira, outubro 03, 2014

Intelligent Design's Secret Weapon: The World

David Klinghoffer October 3, 2014 11:53 AM | Permalink



Along with the absurd stereotype that support for ID is limited to right-wing fundamentalist Christians -- tell that to Stephen King, as I noted the other day -- there's also the Darwinist agitprop point that advocates of the theory are rare outside the United States. Hardly! An unacknowledged strength of the ID movement is its international character.
Stephen Meyer was asked recently in an interview with World magazine:
[I]s intelligent design gaining any acceptance at the university level?
There is a lot of behind-the-scenes movement, especially in Europe, oddly. I had an email several years ago from a European scientist who said, "Please don't email me back -- call me, but not at the office. Can we talk at my home?" I get a lot of phone calls like that. His problem was he'd come to accept intelligent design, but he was quite prominent in the European evolutionary establishment.
Asia is an up-and-coming ID hot spot, as ENV has reported. See here for Signature in the Cell andExplore Evolution in their recent and handsome Korean editions.
Europe and Asia aside, how about Brazil? From South America's most populous nation, accounting for half the continent's total population, comes news of the First Brazilian Intelligent Design Congress, scheduled for November 14-16 this year at the Royal Palm Plaza in Campinas, in the state of São Paulo.
The hub of ID activity in the country is Universidade Estadual de Campinas (UNICAMP), one of South America's top three universities. (The equivalent of Yale, perhaps, if you go by the U.S. Newsrankings.) The group's Scientific Committee is impressive, most members representing public universities; see here for a rough translation courtesy of Google. Our correspondent on the spot explains:
The Brazilian Intelligent Design Group was founded in August 1998 at UNIMEP (Methodist University) in Piracicaba, São Paulo, Brazil, by some graduate students after reading and discussing Behe's ideas in his book Darwin's Black Box. We were all excited by this knowledge, and in our innocence but true zeal for spreading ID in our country, we almost put everything in jeopardy. The wise words of Philip Johnson still rings in our ears: Be patient and wise, time will come when the truth will prevail! He was right!
Later on in the 2000s, after promoting ID throughout Brazil, giving talks and lectures in some public and private schools and universities, our group perceived that it was better to fly under the radar range so as to avoid being expelled by the scientific establishment as some were in the United States.
After ten years of underground activities, Dr. Augustus Nicodemus Lopes, then Mackenzie Presbyterian University Chancellor, heard about our ID group, and helped some of us to come out of hiding and gave us a friendly platform to promote ID. From 2006-2012, the International Symposium on Darwinism Today was held at Mackenzie Presbyterian University, where [prominent ID advocates] Paul Nelson, Steve Meyer, Scott Minnich, Michael Behe, and Marcos Nogueira Eberlin (UNICAMP professor, member of the Brazilian Academy of Sciences, a signer of the Scientific Dissent from Darwinism list) lectured and debated with Darwinist scientists.
In 2014 we decided that it was time for ID to fly over the radar in Brazil, and we are going to have our first conference and launch of the Brazilian ID Society.
About the upcoming launch event, which sounds like a blast:
We will have lectures by scientists and experts in many scientific areas.
This will be a historic event for it will consolidate the grounds for Intelligent Design Theory as a scientific theory in Brazil, and for the first time it will gather many Intelligent Design proponents and advocates from all parts of our country.
The First Brazilian Intelligent Design Congress will begin on Friday, November 14 with the opening ceremony at 6:30 pm, opening lectures, and a gala dinner with live music.
On Saturday, November 15, we will have lectures and discussions, lunch at The Royal, and an afternoon break (close to 2.5 hours) for socializing in the hotel pool. At 4:30 pm the lectures will resume, and debates till 9:00 pm, and then another gala dinner (Pizza Night).
On Sunday, November 16, we will have more lectures in the morning, followed by a roundtable discussion, and a historic assembly with the launch of the Brazilian Intelligent Design Society, the elaboration of the first public Intelligent Design Theory-Brazil manifesto on teaching evolution and ID in our public schools and universities. We are against [teaching ID in schools], even though the law is on our side.
More details about the First Brazilian Intelligent Design Congress:
01. The First Brazilian Intelligent Design Congress aims to gather all the Brazilian ID scientific community, to get to know better the theory and its fundamentals, and to be organized for better promoting and defending IDT.
02. The Congress's focus is the scientific community formed by undergraduate, graduate students, and post-doc professors and researchers from schools, colleges, universities, and research centers, as well as experts from all scientific areas.
03. The Congress's main goal is the formation of a community of scientists and professionals to defend and spread the IDT in Brazil, through talks, lectures, articles, and mainstream media, so as to defend the IDT with the correct theoretic fundamentals, with true knowledge and full support from the Brazilian Intelligent Design Society (SBDI).
This is all excellent news. Rather than answer us on the merits of the scientific case that ID theorists make, Darwin defenders up to now have largely contented themselves with brandishing clichés derived from H.L. Mencken's twisted reporting on the Scopes Trial and from watching Inherit the Wind. But the stereotypes are hard to maintain in countries where most people lack this cultural baggage and the social and class anxieties that go with it.
Hard, but of course not impossible.
Also in the News, the Brazilian Presidential Election
Further scrambling the usual stereotypes is Brazil's presidential election this Sunday, where leading candidate Marina Silva, a leftist and environmentalist, has been faced with criticisms accusing her of ambivalent support for Darwinian evolution. The New York Times reported on this:
Others have assailed Ms. Silva as a creationist, revealing the tensions over the influence of evangelical politicians and prompting rebukes by Ms. Silva.
"I am not a creationist," Ms. Silva has told a panel of Brazilian journalists. "But I don't need to scientifically justify my faith. I believe that God created all things, including the great contribution given by Darwin."
A Brazilian friend, who regards Silva as a bit of a mystery, comments:
Politically she is left wing, and the party [under whose banner] she is running for the presidency has a very, very strong Communist background. Last election she declared to a gathering of Seventh Day Adventists that she was a creationist, and later she had to recant because mainstream media came after her -- how can you become president holding such weird beliefs? She said that her answer had been distorted and that she believed in God, but believed in Darwin, too. Since then she's been denying she is a creationist.
Gee, that sounds kind of familiar. So Brazil has its Darwin enforcers as well, is all I'm able to clearly discern from it. Well, our friends on the other side of the equator will have their work cut out for them, I suppose. We wish them much success.

Chegando a hora do Primeiro Congresso e da fundação da Sociedade Brasileira de Design Inteligente

quinta-feira, outubro 02, 2014



Por ocasião de abertura do Congresso, o NBDI - Núcleo Brasileiro de Design Inteligente, criado em agosto 1998, em dependências de um Programa de Pós-Graduação da UNIMEP, Piracicaba, SP, deixará de existir para se tornar a SBDI - Sociedade Brasileira de Design Inteligente. Uma longa caminhada de um pequeno grupo de professores, pesquisadores e defensores, cheia de entraves, mal-entendidos, de achaques e vilificações, de proibições de palestras em universidades públicas. Valeu a pena. Faríamos tudo de novo. 


Sem a Nomeklatura científica e sem a Galera dos meninos e meninas de Darwin, não chegaríamos onde chegamos. Somos gratos pela estamina que eles nos forneceram - era a certeza de que estávamos trilhando caminhos epistemológicos que ousou, pela primeira vez no Brasil, a desafiar o consenso científico, os acordos de revisão por pares, de não sermos mais como soldadinhos de chumbo - todo mundo pensando igual e ninguém pensando nada diferente! Ousamos pensar diferente!

Visite o site do Congresso e a página no Facebook

A revolução da poliploidia então... e agora: Stebbins revisitado - um fator importante na evolução das espécies?

quarta-feira, outubro 01, 2014

The polyploidy revolution then…and now: Stebbins revisited1

Douglas E. Soltis2–4⇑, Clayton J. Visger2,3 and Pamela S. Soltis3
- Author Affiliations

2Department of Biology, University of Florida, Gainesville, Florida 32611 USA
3Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA

Received for publication 15 April 2014.
Accepted for publication 30 June 2014.

Next Section

G. Ledyard Stebbins, Jr.


ABSTRACT

Polyploidy has long been considered a major force in plant evolution. G. Ledyard Stebbins, Jr., an architect of the Modern Synthesis, elegantly addressed a broad range of topics, from genes to chromosomes to deep phylogeny, but some of his most lasting insights came in the study of polyploidy. Here, we review the immense impact of his work on polyploidy over more than 60 years, from his entrance into this fledgling field in the 1920s until the end of his career. Stebbins and his contemporaries developed a model of polyploid evolution that persisted for nearly half a century. As new perspectives emerged in the 1980s and new genetic tools for addressing key aspects of polyploidy have become available, a new paradigm of polyploidy has replaced much of the Stebbinsian framework. We review that paradigm shift and emphasize those areas in which the ideas of Stebbins continue to propel the field forward, as well as those areas in which the field was held back; we also note new directions that plant geneticists and evolutionists are now exploring in polyploidy research. Perhaps the most important conclusion from recent and ongoing studies of polyploidy is that, following Levin and others, polyploidy may propel a population into a new adaptive sphere given the myriad changes that accompany genome doubling.

Key words:

autopolyploidy diversification epigenetics evolution genome doubling genomics
G. Ledyard Stebbins, Jr

↵1 The authors thank Betty Smocovitis for helpful comments on the manuscript. This project was supported in part by U. S. National Science Foundation Grant DEB-1146065 and DGE-1315138.

↵4 Author for correspondence (e-mail: dsoltis@ufl.edu)

FREE PDF GRATIS: American Journal of Botany

Manifesto por uma ciência pós-materialista

s

We are a group of internationally known scientists, from a variety of scientific fields (biology, neuroscience, psychology, medicine, psychiatry), who participated in an international summit on post-materialist science, spirituality and society. The summit was co-organized by Gary E. Schwartz, PhD and Mario Beauregard, PhD, the University of Arizona, and Lisa Miller, PhD, Columbia University. This summit was held at Canyon Ranch in Tucson, Arizona, on February 7-9, 2014. Our purpose was to discuss the impact of the materialist ideology on science and the emergence of a post-materialist paradigm for science, spirituality, and society. We have come to the following conclusions:

1. The modern scientific worldview is predominantly predicated on assumptions that are closely associated with classical physics. Materialism—the idea that matter is the only reality—is one of these assumptions. A related assumption is reductionism, the notion that complex things can be understood by reducing them to the interactions of their parts, or to simpler or more fundamental things such as tiny material particles.

2. During the 19th century, these assumptions narrowed, turned into dogmas, and coalesced into an ideological belief system that came to be known as "scientific materialism." This belief system implies that the mind is nothing but the physical activity of the brain, and that our thoughts cannot have any effect upon our brains and bodies, our actions, and the physical world.

3. The ideology of scientific materialism became dominant in academia during the 20th century. So dominant that a majority of scientists started to believe that it was based on established empirical evidence, and represented the only rational view of the world.

4. Scientific methods based upon materialistic philosophy have been highly successful in not only increasing our understanding of nature but also in bringing greater control and freedom through advances in technology.

5. However, the nearly absolute dominance of materialism in the academic world has seriously constricted the sciences and hampered the development of the scientific study of mind and spirituality. Faith in this ideology, as an exclusive explanatory framework for reality, has compelled scientists to neglect the subjective dimension of human experience. This has led to a severely distorted and impoverished understanding of ourselves and our place in nature.

6. Science is first and foremost a non-dogmatic, open-minded method of acquiring knowledge about nature through the observation, experimental investigation, and theoretical explanation of phenomena. Its methodology is not synonymous with materialism and should not be committed to any particular beliefs, dogmas, or ideologies.

7. At the end of the nineteenth century, physicists discovered empirical phenomena that could not be explained by classical physics. This led to the development, during the 1920s and early 1930s, of a revolutionary new branch of physics called quantum mechanics (QM). QM has questioned the material foundations of the world by showing that atoms and subatomic particles are not really solid objects—they do not exist with certainty at definite spatial locations and definite times. Most importantly, QM explicitly introduced the mind into its basic conceptual structure since it was found that particles being observed and the observer—the physicist and the method used for observation—are linked. According to one interpretation of QM, this phenomenon implies that the consciousness of the observer is vital to the existence of the physical events being observed, and that mental events can affect the physical world. The results of recent experiments support this interpretation. These results suggest that the physical world is no longer the primary or sole component of reality, and that it cannot be fully understood without making reference to the mind.

8. Psychological studies have shown that conscious mental activity can causally influence behavior, and that the explanatory and predictive value of agentic factors (e.g. beliefs, goals, desires and expectations) is very high. Moreover, research in psychoneuroimmunology indicates that our thoughts and emotions can markedly affect the activity of the physiological systems (e.g., immune, endocrine, cardiovascular) connected to the brain. In other respects, neuroimaging studies of emotional self-regulation, psychotherapy, and the placebo effect demonstrate that mental events significantly influence the activity of the brain.

9. Studies of the so-called "psi phenomena" indicate that we can sometimes receive meaningful information without the use of ordinary senses, and in ways that transcend the habitual space and time constraints. Furthermore, psi research demonstrates that we can mentally influence—at a distance—physical devices and living organisms (including other human beings). Psi research also shows that distant minds may behave in ways that are nonlocally correlated, i.e. the correlations between distant minds are hypothesized to be unmediated (they are not linked to any known energetic signal), unmitigated (they do not degrade with increasing distance), and immediate (they appear to be simultaneous). These events are so common that they cannot be viewed as anomolous nor as exceptions to natural laws, but as indications of the need for a broader explanatory framework that cannot be predicated exclusively on materialism.

10. Conscious mental activity can be experienced in clinical death during a cardiac arrest (this is what has been called a "near-death experience" [NDE]). Some near-death experiencers (NDErs) have reported veridical out-of-body perceptions (i.e. perceptions that can be proven to coincide with reality) that occurred during cardiac arrest. NDErs also report profound spiritual experiences during NDEs triggered by cardiac arrest. It is noteworthy that the electrical activity of the brain ceases within a few seconds following a cardiac arrest.

11. Controlled laboratory experiments have documented that skilled research mediums (people who claim that they can communicate with the minds of people who have physically died) can sometimes obtain highly accurate information about deceased individuals. This further supports the conclusion that mind can exist separate from the brain.

12. Some materialistically inclined scientists and philosophers refuse to acknowledge these phenomena because they are not consistent with their exclusive conception of the world. Rejection of post-materialist investigation of nature or refusal to publish strong science findings supporting a post-materialist framework are antithetical to the true spirit of scientific inquiry, which is that empirical data must always be adequately dealt with. Data which do not fit favored theories and beliefs cannot be dismissed a priori. Such dismissal is the realm of ideology, not science.

13. It is important to realize that psi phenomena, NDEs in cardiac arrest, and replicable evidence from credible research mediums, appear anomalous only when seen through the lens of materialism.

14. Moreover, materialist theories fail to elucidate how brain could generate the mind, and they are unable to account for the empirical evidence alluded to in this manifesto. This failure tells us that it is now time to free ourselves from the shackles and blinders of the old materialist ideology, to enlarge our concept of the natural world, and to embrace a post-materialist paradigm.

15. According to the post-materialist paradigm:

a) Mind represents an aspect of reality as primordial as the physical world. Mind is fundamental in the universe, i.e. it cannot be derived from matter and reduced to anything more basic.

b) There is a deep interconnectedness between mind and the physical world.

c) Mind (will/intention) can influence the state of the physical world, and operate in a nonlocal (or extended) fashion, i.e. it is not confined to specific points in space, such as brains and bodies, nor to specific points in time, such as the present. Since the mind may nonlocally influence the physical world, the intentions, emotions, and desires of an experimenter may not be completely isolated from experimental outcomes, even in controlled and blinded experimental designs.

d) Minds are apparently unbounded, and may unite in ways suggesting a unitary, One Mind that includes all individual, single minds.

e) NDEs in cardiac arrest suggest that the brain acts as a transceiver of mental activity, i.e. the mind can work through the brain, but is not produced by it. NDEs occurring in cardiac arrest, coupled with evidence from research mediums, further suggest the survival of consciousness, following bodily death, and the existence of other levels of reality that are non-physical.

f) Scientists should not be afraid to investigate spirituality and spiritual experiences since they represent a central aspect of human existence.

16. Post-materialist science does not reject the empirical observations and great value of scientific achievements realized up until now. It seeks to expand the human capacity to better understand the wonders of nature, and in the process rediscover the importance of mind and spirit as being part of the core fabric of the universe. Post-materialism is inclusive of matter, which is seen as a basic constituent of the universe.

17. The post-materialist paradigm has far-reaching implications. It fundamentally alters the vision we have of ourselves, giving us back our dignity and power, as humans and as scientists. This paradigm fosters positive values such as compassion, respect, and peace. By emphasizing a deep connection between ourselves and nature at large, the post-materialist paradigm also promotes environmental awareness and the preservation of our biosphere. In addition, it is not new, but only forgotten for four hundred years, that a lived transmaterial understanding may be the cornerstone of health and wellness, as it has been held and preserved in ancient mind-body-spirit practices, religious traditions, and contemplative approaches.

18. The shift from materialist science to post-materialist science may be of vital importance to the evolution of the human civilization. It may be even more pivotal than the transition from geocentrism to heliocentrism.

We invite you, scientists of the world, to read the Manifesto for a Post-Materialist Science and sign it, if you wish to show your support (see http://opensciences.org/).

* The Manifesto for a Post-Materialist Science was prepared by Mario Beauregard, PhD (University of Arizona), Gary E. Schwartz, PhD (University of Arizona), and Lisa Miller, PhD (Columbia University), in collaboration with Larry Dossey, MD, Alexander Moreira-Almeida, MD, PhD, Marilyn Schlitz, PhD, Rupert Sheldrake, PhD, and Charles Tart, PhD.

**Contact

For further information, please contact Dr Mario Beauregard, Laboratory for Advances in Consciousness and Health, Department of Psychology, University of Arizona, Tucson, USA. Email: mariobeauregard@email.arizona.edu

*** We considered two ways of referring to the emerging paradigm presented in this Manifesto: the hyphenated version (post-materialism) and the non-hyphenated version (postmaterialism). The hyphenated form was selected for the sake of clarity for both scientists and lay people.

**** The Summary Report of the International Summit on Post-Materialist Science, Spirituality and Society can be downloaded here: International Summit on Post-Materialist Science: Summary Report (PDF).

To become a signatory to this manifesto, please email Dr Mario Beauregard with your name, academic degree, fields of study, title and institution.

800.000 visitantes neste blog, Darwin!!!



Darwin, mano! São 800.000 visitantes no mundo inteiro! Razão? 11 entre 10 darwinistas leem este blog! Desde a Nomenklatura científica (rsrsrsrs) até a Galera dos meninos e meninas de Darwin. Os editores e jornalistas científicos da Grande Mídia também leem, mas não ousam abordar o que aqui é livremente publicado. Quando a questão é Darwin, é preciso cojones para isso, e os jornalistas científicos não têm cojones para tal.

Muito obrigado seus 800.000 visitantes. Façam um grande favor a este blogger: recomendem aos seus amigos e parentes! Darwin, muito obrigado! Sem você, mano, o Neddy passaria desapercebido neste mundo! Sou grato a você por ter me lançado ao mundo da blogoesfera, e fazer de mim Persona non grata em alguns espaços acadêmicos e cibernéticos. E Persona grata em outros, Na verdade, eles me admiram e, se me odeiam, dou razão a eles - Darwin é um ídolo, e os ídolos foram feitos para a destruição. 

Darwin Kaput!