Nueva téoria de la evolución
Response to Discover Interview, Tullis Onstott
martes, junio 26, 2012, 03:48 AM
i53b Response to Discover Interview, Tullis Onstott, 06.26.2012

Following you will find a transcription (and my commentaries in parenthesis) of the article Discover Interview: Tullis Onstott by Valerie Ross and published in the 06.26.2012’s edition of Discover magazine.

Tullis Onstott Went 2 Miles Down & Found Microbes That Live on Radiation

Bacteria found in gold mines and frozen caves show the extreme flexibility of life, and hint at where else we might find it in the solar system.

The first time Tullis Onstott ventured underground, he squeezed into an elevator with dozens of South African gold miners and descended a mile into a pit called Mponeng. His goal: Finding the bizarre, hardy microbes that survive in sweltering, inhospitable rock. A geologist by training, Onstott spent his early career studying the Earth’s crust—until he heard a talk in 1993 about colonies of bacteria living thousands of feet below the surface. Ever since, he has made dozens of deep expeditions, sometimes paying his own way, and discovered bacteria living more than two miles beneath the surface in 140-degree-Fahrenheit heat. By investigating microbes in these harsh environments, Onstott is gleaning clues about how life could have begun in Earth’s hot, chaotic early days—and about what it might look like on other worlds. Even his office is underground, in the basement of Princeton University’s geology building, where Onstott met with DISCOVER reporter Valerie Ross.

The first time you went underground to look for life, in 1996, you had no idea what to expect. What was that trip like?

The miners took me into the stopes, the tunnels where they mine gold, to sample the rocks. We were looking at an organic rock layer just millimeters thick that had lots of carbon, because we figured somewhere with a lot of carbon was a good place to look for life. The stopes are a meter high and they tilt downward at a steep angle, so you go down them almost like a slide, passing from one tunnel to the next. I basically slipped into a rabbit hole and got this big chunk of rock. I put it in an autoclave bag [normally used for sterilizing equipment], stuffed it in my knapsack, and then I went down the stope further until I came out the bottom into another, deeper tunnel.

What did you do with the sample you collected?

We measured the rock’s radioactivity. The Geiger counter showed it was hot as a pistol, so we sealed it up in a steel canister and filled the canister with argon gas, which pushed out all the oxygen. Organisms that live deep down are not normally exposed to oxygen, and in fact it could be toxic to them. So we sealed the rock away until we could get it back into the lab. I checked this radioactive rock inside a steel thing as baggage on a plane. This was 1996. Airport security was not like it is today.

When you analyzed the sample back at your lab, did you find any life?

We found one bacterium species similar to one previously identified from a hot spring in New Mexico. But the surprise was that this particular species could do something the other hot spring organisms could not: reduce [i.e., transfer electrons to] iron, which is present in minerals that are abundant in the mine’s rocks, and uranium, part of soluble compounds found in water in the mine. That helped us understand how they got their energy.

Then you found still more perplexing discoveries in other South
African mines—for instance, microbes similar to those previously seen only at the bottom of the ocean.

That’s right. We went back to South Africa in 1998, this time to Driefontein Mine, located about 40 miles southwest of Johannesburg, and took water samples, which are easier to work with than rock and less likely to be contaminated. We started finding the same organisms that people were reporting from deep-sea hydrothermal vents [where hot, mineral-laden fluid flows through volcanic rock into the ocean from deep within the Earth]. We don’t know how the same organisms got to be in both places, because South African crust has not seen ocean water in two-and-a-half billion years. It’s very much a mystery. We published the data, and the National Science Foundation gave us more money to go back again in 2000.

(The concept of the origin of life or of any species in only one place in order to have its distribution throughout the world will keep inhibiting the capacity to create mental images. Please see articles “Not Out of Africa But Regional Continuity” and “Empire of Uniformity” in this same blog. Life is generated wherever there are the elements to be generated from independently of places or times, here and in the rest of the universe. If it were not so, we would be dependant to life coming from older planets of the universe, after life had been generated in those places).

What happened on your third deep excursion in South Africa?

The next time, we purchased a house in one of the villages near the gold mines and set up a semipermanent lab there. Over two years, a rotating team from my lab and six other institutions collected most of the samples that we’re still working on today. One thing we did was expand on our first find and look at more radioactive samples. We began developing an idea that radiation in the rock provides energy for microorganisms. Wherever we had radiation, we tended to see hydrogen gas forming. It made me realize that radiation should produce hydrogen by breaking water bonds. Hydrogen is the key component the bacteria need to make ATP, the molecule they use for energy.

“One bacterium we found is entirely self-sufficient, a one-species ecosystem. Such things aren’t supposed to exist.”

(The concept of the survival of the fittest limits life [given that it has to be the fittest to survive]. Nature makes incredible efforts to insure a lot of diversity. And many creatures survive even when they are not the fittest or fit for one thing and not for another. To begin with a male produces millions and millions of spermatozoids to have a female use one of them and it is not a waste, it is the price paid for the insurance of diversity).

That’s amazing, since we usually think of radioactivity as deadly—but these organisms were actually living on radiation?

Well, not just radiation, but radiation, water, and rock were all that was needed to support life at depth. You don’t need light, food, or anything else from the surface. Plus, it’s a renewable energy source. It turns water into hydrogen and hydrogen peroxide, which helps make the metals that the organisms consume. It is like recharging an electric battery. The radiation keeps on recharging the battery for the bacteria that then do their thing. Those bacteria could then sustain other deep organisms. That finding was really important to NASA because you can imagine anybody in the solar system that has liquid water beneath the surface—like Jupiter’s moon Europa, probably—will have energy for organisms as well.

(Wonderful. With this information they will not be auto limiting themselves in the possibility to find life in different environments. After the closing of an open pit mine in the United States for pumping toxic water to neighboring creeks, a super toxic water lake was formed. Several years later scientists returned to make water analysis and they found abundant life in the toxic water. See article “Three articles of National Geographic and my commentaries” in this same blog).

Can we observe these organisms at work in the lab?

The rule of thumb is that when you get back to the lab, you can grow less than 0.1 percent of what actually exists down there. We tried all sorts of ways to grow them, gave them all sorts of nutrients we thought they might want, and we failed miserably.

Since you couldn’t grow the bacteria that you found deep down, how did you learn just how they functioned?

We looked at their DNA instead, which we filtered out of the water, to determine where these things fit in with other sorts of microbial life.

(Perry Marshall has several years insisting that if you mix the DNA information with computational science it will take us far in this learning. Please see the article “Response to 7 Biology Myths an Electrical Engineer Would Never Tolerate”).

Organisms so far underground, reliant on so few resources, must live a pretty limited existence, right?

Since the population of cells down there is small, most people thought they would just barely be able to eke out a living, that they were organisms with very few capabilities. But it turns out that was totally wrong. We did a full analysis of Candidatus Desulforudis audaxviator, an organism we found again and again in different mines in South Africa at the greatest depths—never above 2 kilometers (1.2 miles)—that made up 99.9 percent of the DNA in some of our samples. This thing had everything. It could take nitrogen directly from its environment, something we did not expect subsurface organisms to do because it takes so much energy. But the real surprise was that it had genes for flagella, tails bacteria use to propel themselves, which basically means it could be swimming around in the environment. It had genes for gas vesicles, which means it can adjust its buoyancy in the environment. And it had genes for chemoreception, which tells us it’s sensing something. The genome is saying it’s a very adaptable organism, and it has the capability of moving around. The idea that organisms down there might be moving around and interacting with the environment—that was really surprising. The only tip-off from the genome that this is a subsurface organism is that it has no protection against oxygen. As soon as it hits air, it’s dead.

(In the article in this same blog “Discover Interview: Lynn Margulis” we have ample information about the flagella and how life is an association of beings with different qualifications in order to share different capacities).

And does that microbe interact with other species down deep?

Candidatus Desulforudis audaxviator is entirely self-sufficient. It has its energy source, radiation. It contains everything it needs to exist, and it requires nothing from another organism. The fact that we’ve found it almost by itself tells us that it’s a one-species ecosystem. Such things aren’t supposed to exist. We thought all organisms depended on others, but this one doesn’t. We’ve found a whole new way to live.

(Diversity to infinitum. Of course that there is life in other planets!).

In addition to bacteria you also discovered more complex, multicellular organisms living 1.5 kilometers down—almost a mile underground. What are they, and how did you find them?

In 2006 I was contacted by Gaetan Borgonie, a Belgian scientist who had found microscopic roundworms, or nematodes, in caves in Central America. After he contacted me, I remembered seeing worms in biofilm, a goop made up of bacteria, in a mine in South Africa, too. So we went down together into the mines in South Africa to collect samples of biofilms. It turned out that the biofilms in the mines were just loaded with them. This nematode has about 1,000 cells, so it’s not exactly a big guy, but still—I never would have expected to find it so deep.

The deepest organisms you have found so far are from 3.8 kilometers (2.4 miles) underground—the farthest that it’s been possible to explore until now. How much deeper might life go?

At Mponeng mine, a company is now drilling a tunnel to explore for gold five-and-a-half kilometers down. Gold prices are so high that for them, it’s economically feasible. For us, we think, “Yay!” The deeper, the hotter, the better. Down that far, it’ll be 90 degrees centigrade, about 195°F. That’s almost boiling. It’s a significant increase in depth, and we’re excited to see what the next several years will turn up.

(Good luck).

What will going that deep into the planet tell us about life and evolution up here on the surface?

We’re trying to see what the base of the biosphere, of all life on Earth, looks like. If DNA organisms exist down that far and at such high temperatures, we want to find them, and if they don’t, we want to understand why. And if there are no DNA organisms, are there other types of organisms that might occur there in very small concentrations? There may exist a shadow biology—very, very primitive organisms that may have come into existence very early on our planet but were completely replaced by DNA organisms everywhere else.

So far you’ve talked only about hot environments, but what about the other extreme? Many of the places elsewhere in the solar system where we’re looking for life, like Mars, are intensely cold. Have you explored any analogous low-temperature environments on Earth?

Mars has this very thick cryosphere, or permanently frozen rock layer, on its surface. So we went to a gold mine deep beneath the permafrost in the high Arctic, in the Nunavut territory in Canada. The mine has a helical tunnel that goes a kilometer and a half down. All this warm air comes up from below, and as soon as it hits the permafrost layer, where the ground is permanently frozen, all the moisture in the air crystallizes and you get huge snowflakes, a couple of feet wide. You get ice stalactites and ice stalagmites all over. It looks like Superman’s sanctuary. It’s easy to imagine there might be something like this on Mars as well. I had an epiphany within these ice caves: This is the kind of environment you’d want to explore if you ever went to Mars; send your rover inside the caves and have a look around. There’s moisture there. There’s plenty of room for life in these environments. Unfortunately, we never really had a chance to explore and look for life in those caves before that mine shut down.

Could we pick out signs of microbial life on Mars even before we go digging around in caves there?

On parts of Mars, there’s methane gas that may be seasonal. It seems to appear and then go away. That means something unusual is happening: There has to be something that makes the methane and something that consumes it. The question is, are life-forms making and consuming the methane? If life is generating and consuming that methane, its chemical signature will change because of those biological processes. So as a project with NASA, we’re developing an instrument that we hope will fly to Mars and measure the composition of the methane gas. If we find that it is going through a seasonal cycle and its composition is changing, that’s a very good indication that there’s something alive on Mars. But whatever that something is, it’s going to be something quite different from anything we’ve seen on Earth because the surface conditions on Mars are pretty inhospitable to life as we know it.

You’ve looked at other extremely cold environments to learn more about life here on Earth, too. What was that like?

We’ve gone up to Axel Heiberg Island, a Canadian island high in the Arctic Ocean, to do some work there at the McGill Arctic Research Station, a.k.a. Mars. It’s one of the largest uninhabited islands in the world, and very beautiful. It has enormous mountain glaciers, almost like a little Swiss Alps, so it’s a nice change from the mines. We went up there to study microbes living in the permafrost that have been frozen for millennia.

The Arctic regions where those microbes live are warming rapidly. What impact might that have on the Earth?

There’s a concern that those microorganisms will all of a sudden kick on and start chewing up organic matter, making carbon dioxide and methane. That could cause a runaway greenhouse effect in the later part of the century. Our mission is to try and understand whether that will happen. We collected 40 ice cores from the island. We’re gradually thawing them to study which microorganisms are doing what, and which gases are being released and how quickly. Then we’re comparing this to field measurements that we can make in the Arctic, to see if the environment seems to be doing the same things as the permafrost in the lab. A lot of groups are doing similar studies across the Arctic. We don’t know the answer yet, but what we all find should further our understanding of what to expect over the next 100 years.

Has studying these various kinds of extreme, deep-dwelling microbes changed your thinking about what’s necessary for life?

The more I learn, the more it seems that the requirements for life are pretty minimal. The niches that life can occupy never cease to amaze me. A place may look terrible to us, but to something else, that’s their Eden.

(I share the concept).


While Onstott searches for microbes in gold mines and permafrost, other researchers are seeking out life in other deep locations. Their results are filling the picture of Earth’s buried ecosystem.

1 Around Hydrothermal Vents.The scalding hot, sulfur-laden waters of hydrothermal vents, where ocean water heated by magma reemerges through cracks in the seafloor, are teeming with microscopic life. These bacteria support complex ecosystems in dark, otherwise sparsely populated ocean depths. Oxford zoologist Alex Rogers and his team explored the life around a 720°F vent off the East Scotia Ridge near Antarctica (shown here). In January they reported a host of unusual animals living near the vent, including a seven-armed sea star, a “ghostly white” octopus, and a new species of yeti crab, its underside covered in hairs.

2 Under the Ocean Floor. Several teams are currently hunting for life beneath the seabed. Earlier this year, geomicrobiologist Katrina Edwards of the University of Southern California and her colleagues drilled into the crust of the Atlantic Ocean and installed small subsurface observatories to monitor microbial life. In 2010 scientists from Oregon State and other institutions drilled into the gabbroic layer—the deepest layer of the oceanic crust, close to the hot, mineral-rich mantle—to find a host of bacterial species capable of gobbling up hydrocarbons from an unknown source.

3 In the Deepest Caves. The world’s deepest known cave, Krubera-Voronja in the Republic of Georgia, extends down a mile and a quarter. Biologist Ana
Sofia Reboleira of the University of Aveiro in Portugal, who has been exploring caves since she was a teenager, recently searched Krubera-Voronja for the rare, small organisms that populate it—a cold business, since temperatures in the pitch-black depths hover just above freezing. This year, she and her team reported four new species of eyeless, wingless insects at various depths, ranging from 60 meters to almost 2,000 meters (more than a mile), near the cave’s bottom.


Onstott calls his trips into the gold mines “underground safaris,” but finding new species in the depths of the Earth is a far cry from spotting them on the savannah. The only species Onstott has observed in action are nematode worms; he could see them squirming under a microscope, and took detailed electron microscopy images of their hundredth-of-an-inch-long bodies. He also found cells of D. audaxviator, a bacterium that made up 99.9% of the organisms he recovered from one of the filters used to extract water from rock fractures deep in the mines. Onstott imaged what he could of those cells with a transmission electron microscope. But he has never been able to see any bacteria moving around, or grow them in the lab. Instead, the vast majority of what he studies is DNA traces. D. audaxviator provided enough genetic material to yield that species’ whole genome, allowing Onstott to ascertain that the organism belonged to a self-sustaining ecosystem and could sense its environment. In other cases he has found bits of free-floating genetic material from other species—just enough, he says, to show that each one exists deep in the mines and is largely specific to the fracture in which it was found. “As you move from one fracture to the next,” Onstott notes, “the microbial species change.”

(It is impossible to have more diversity. This is unequivocal proof that the common trunk does not exist and that life can be generated practically in any place, whether it travels or not. Where is the common trunk enunciated by Charles Darwin and his followers?).

Felix Rocha-Martinez
Saltillo, Coahuila, Mexico
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La entrevista Discover, Tullis Onstott
martes, junio 26, 2012, 03:44 AM
e53b La entrevista Discover, Tullis Onstott, 06.26.2012

A continuación encontrarán mi traducción (y mis comentarios entre paréntesis) al artículo Discover Interview: Tullis Onstott de la revista Discover de la edición de 26 de junio de 2012 escrito por Valerie Ross

Tullis Onstott bajó 3 kilómetros y encontró microbios que viven de la radiación

Las bacterias que se encuentran en las minas de oro y cuevas heladas muestran la flexibilidad extrema de la vida, y un indicio de en dónde más podemos encontrar vida en el sistema solar.

La primera vez que Tullis Onstott se aventuró bajo tierra, fue apretujado en un ascensor con decenas de mineros de oro de Sudáfrica y descendió un kilómetro y medio en una mina llamada Mponeng. Su objetivo: encontrar a los microbios extraños y resistentes que sobreviven en el calor sofocante, en rocas inhóspitas. Geólogo de profesión, Onstott pasó su carrera estudiando la corteza terrestre, hasta que escuchó una conversación en 1993 sobre las colonias de bacterias que viven miles de metros bajo la superficie. Desde entonces, ha realizado decenas de expediciones profundas, a veces pagando los gastos con dinero propio, y descubrió bacterias que viven a más de tres kilómetros bajo la superficie con un calor de 60 grados centígrados. A base de investigar a los microbios en estos ambientes hostiles, Onstott está generando pistas sobre cómo la vida pudo haber comenzado en los días caóticos y calientes de la Tierra y los principios acerca de lo que pudiera haber en otros mundos. Incluso su oficina se encuentra bajo tierra, en el sótano del edificio de geología de la Universidad de Princeton, en donde se reunió con la reportera de Discover, Valerie Ross.

La primera vez que viajó a las profundidades de la tierra a buscar vida, en 1996, no tenía idea de qué esperar. ¿Cómo fue ese viaje?

Los mineros me llevaron a las galeras, los túneles donde se mina el oro, para tomar muestras de las rocas. Estábamos buscando una capa de roca orgánica de sólo milímetros de espesor que tuviera mucho carbono, dado que consideré que en algún lugar con una gran cantidad de carbono era un buen lugar para buscar vida. Los rebajes eran de un metro de altura y la inclinación hacia abajo de un ángulo empinado, por lo que ir a por ellos era casi como una resbaladero, pasando de un túnel a otro. Básicamente, me metí en una madriguera de conejo y conseguí una gran roca. La puse en una bolsa [normalmente se utilizaría para equipo para esterilizado], la metí en mi mochila, y luego me fui por los rebajes aún más hasta que salí de un túnel a otro, más profundo.

¿Qué hizo con la muestra que recogió?

Medimos la radiactividad de la roca. El contador Geiger mostró que era muy alta, por lo que guardé la roca en un contenedor de acero y llené el recipiente con gas argón, que eliminó todo el oxígeno. Los organismos que viven en el fondo de una mina profunda normalmente no están expuestos al oxígeno, y de hecho puede ser tóxico para ellos. Así que sellé la roca hasta que pude transportarla al laboratorio. Introduje la roca que estaba radiactiva dentro de un recipiente de acero como equipaje en un avión. Esto fue en 1996. La seguridad del aeropuerto no era como es hoy.

¿Cuando analizó la muestra en su laboratorio, se encontró algo de vida?

Encontramos una especie de bacteria similar a una ya identificada proveniente de una fuente termal en Nuevo México. Pero la sorpresa fue que ésta especie podía hacer algo que los otros organismos de aguas termales no podían: transferir electrones al hierro que están presentes en los minerales que son abundantes en las rocas de la minas, y del uranio, parte de los compuestos solubles que se encuentran en el agua de la mina. Eso nos ayudó a entender cómo se allegaron de energía.

Entonces encontró descubrimientos todavía más desconcertantes en otras minas del sur de África, por ejemplo, los microbios similares a los anteriormente vistos sólo en el fondo del océano.

Eso es correcto. Fuimos de nuevo a Sudáfrica en 1998, esta vez a la mina de Driefontein, ubicada a unos 64 kilómetros al suroeste de Johannesburgo, y tomé muestras de agua, que son más fáciles de trabajar que las rocas y tienen menos probabilidades de estar contaminadas. Empezamos a encontrar los mismos organismos que personas informan haber encontrado en lo más profundo de las chimeneas hidrotermales [de donde brotan aguas muy calientes, cargadas de minerales y flujos de fluidos a través de roca volcánica en las profundidades del océano]. No sabemos cómo los mismos organismos están en ambos lugares, dado que la corteza de Sudáfrica no ha visto el agua de mar en dos y medio miles de millones de años. Es en gran medida un misterio. Hemos publicado los datos, y la Fundación Nacional de Ciencia nos otorgó más dinero para regresar de nuevo en el año 2000.

(El concepto del origen de la vida o cualquier especie en un solo lugar para luego tener su distribución por el mundo seguirá inhibiendo la capacidad de crear imágenes mentales. Ver los artículos “No ‘fuera de África’ sino ‘continuidad regional’” y “El imperio de la uniformidad” en este mismo blog. La vida se da en donde hay elementos para que se dé independientemente de lugares y tiempos, aquí y en el resto del universo. Si no fuera así, fuéramos dependientes de que la vida llegara de los planetas más antiguos del universo, después de que la vida se diera en esos lugares).

¿Qué ocurrió en su tercera excursión a las profundidades de la Tierra en el sur de África?

Para la siguiente ocasión, compramos una casa en una de las aldeas cercanas a las minas de oro y establecimos un laboratorio semipermanente allí. Por más de dos años, un equipo rotatorio de mi laboratorio y de seis otras instituciones recogieron la mayor parte de las muestras con las que todavía estamos trabajando en la actualidad. Una de las cosas que hicimos fue ampliar esfuerzos en nuestro primer hallazgo y buscar más muestras radiactivas. Comenzamos a desarrollar el concepto de que la radiación en la roca provee de energía a los microorganismos. Siempre que hemos tenido radiación, tendemos a ver la formación de gas hidrógeno. Me hizo darme cuenta de que la radiación debe producir hidrógeno mediante la ruptura de los compuestos del agua. El hidrógeno es el componente clave que las bacterias necesitan para producir adenosina trifosfática (ATP), la molécula que utilizan las bacterias para obtener energía.

Una bacteria que encontramos es totalmente auto suficiente, es un ecosistema de una sola especie. Estas cosas se supone que no existen".

(El concepto de la supervivencia del más apto es limitante de vida [dado que se tiene que ser el más apto para sobrevivir] La naturaleza hace esfuerzos inauditos para que haya mucha diversidad. Y muchos sobreviven aunque no sean tan aptos o aptos para una cosa y no aptos para otra. Para comenzar un varón produce millones y millones de espermatozoides para cuando la mujer utiliza uno de ellos y no es desperdicio, es el precio que se paga con tal de tener diversidad).

Eso es increíble, ya que por lo general pensamos que la radiactividad es mortal, pero ¿estos organismos estaban viviendo realmente de la radiación?

Bueno, no sólo de la radiación, sino que de la radiación, del agua y de la roca, que era todo lo que se necesitaba para mantener la vida en la profundidad. Ahí no se necesita a la luz, la comida, o cualquier otra cosa de la superficie. Además, es una fuente de energía renovable. Se convierte el agua en hidrógeno y peróxido de hidrógeno, lo que ayuda a fabricar los metales que los organismos consumen. Es como recargar una batería eléctrica. La radiación sigue en la recarga de la batería para que las bacterias luego hagan lo suyo. Esas bacterias pudieran sostener otros organismos de la profundidad. Ese hallazgo fue muy importante para la NASA, ya que se puede imaginar cualquier cuerpo del sistema solar que tenga agua líquida bajo la superficie-como la luna Europa de Júpiter, probablemente, tendría la energía para los organismos también.

(Magnífico. Con esta información no se estarán auto limitando en las posibilidades de encontrar vida en otros medios ambientes. Después de la clausura de una mina a cielo abierto en Estados Unidos por bombear agua tóxica a los arroyos vecinos, se formó un lago de agua súper tóxica. Cuando los científicos regresaron años después para hacer análisis encontraron abundante vida en esa agua tóxica. Ver artículo “Traducción y comentarios a 3 artículos de National Geographic” en este mismo blog).

¿Podemos observar estos organismos funcionando en el laboratorio?

La regla general es que cuando llegamos de nuevo al laboratorio, podemos hacer crecer menos del 0.1 por ciento de lo que realmente existe bajo tierra. Tratamos todo tipo de maneras de hacer crecer a esos organismos, se les dio todo tipo de nutrientes que pensamos que pudieran desear, y fracasamos miserablemente.

Puesto que no pudieron hacer crecer a las bacterias que se encuentran en las profundidades, ¿cómo aprendiste cómo funcionaban?

A cambio, nos fijamos en su ADN, que filtramos del agua, para determinar dónde estas cosas encajan con otros tipos de vida microbiana.

(Perry Marshall tiene muchos años de estar insistiendo que la información del ADN mezclado con la ciencia de la computación nos llevará muy lejos en este aprendizaje. Ver el artículo “7 mitos de biología que el Ingeniero Electricista Perry Marshall jamás toleraría”).

Los organismos subterráneos a tanta profundidad, dependientes de tan pocos recursos, tienen que vivir una existencia bastante limitada, ¿verdad?

Dado que la población de las células allí es pequeña, la mayoría de la gente pensaba que apenas podían sobrevivir, que eran organismos con capacidades muy parcas. Pero resulta que esos pensamientos estaban totalmente equivocados. Hicimos un análisis completo de Candidatus Desulforudis audaxviator, un organismo que encontramos una y otra vez en diferentes minas en Sudáfrica en la mayor profundidad, nunca por encima de 2 kilómetros de profundidad que conformaban el 99,9 por ciento del ADN en algunas de nuestras muestras. Este organismo lo tenía todo. Podía tomar el nitrógeno directamente de su entorno, algo que no esperaba que los organismos del subsuelo pudieran hacer dado que se necesita mucha energía. Pero la verdadera sorpresa fue que tenían genes para flagelos, las bacterias utilizaban las colas para impulsarse, lo cual básicamente significa que podrían estar nadando en el medio ambiente. Tenían genes para vesículas de gas, lo que significa que pueden ajustar su flotabilidad en el medio ambiente. Y tenían genes para quimiorrecepción, que nos dice que están sintiendo algo. El genoma está diciendo que es un organismo muy adaptable, y tiene la capacidad de moverse. El concepto de que los organismos de allá abajo podían moverse e interactuar con el medio ambiente era realmente sorprendente. Lo único desconcertante a partir del genoma es que se trata de un organismo del subsuelo que no tiene ninguna protección contra el oxígeno. Tan pronto como llega el aire, está muerto.

(En el artículo en este mismo blog: “La entrevista Discover: Lynn Margulis” nos informa ampliamente sobre estos flagelos y como es que la vida es la asociación de seres de diferentes cualidades para compartir facultades).

Y ¿acaso los microbios interactúan con otras especies en las profundidades?

Candidatus Desulforudis audaxviator es totalmente autosuficiente. Tiene su fuente de energía, la radiación. Contiene todo lo necesario para existir, y no requiere nada de otro organismo. El hecho de que lo hemos encontrado casi por sí solo nos dice que es un ecosistema de una sola especie. Estas cosas se supone que no existen. Pensamos que todos los organismos dependen de otros, pero éste no lo hace. Hemos encontrado una nueva manera de vivir.

(Diversidad hasta el infinito. ¡Por supuesto que hay vida en otros planetas!).

Además de las bacterias también descubrieron organismos multicelulares más complejos, que viven 1.5 kilómetros de profundidad. ¿Qué son y cómo los encontraron?

En el año 2006 fui contactado por Cayetano Borgonie, un científico belga que había encontrado gusanos microscópicos o nemátodos, en cuevas de América Central. Después de que él se puso en contacto conmigo, recordaba haber visto también los gusanos en biopelícula, un pegote formado por bacterias, en una mina en Sudáfrica. Así que nos fuimos juntos a las minas de Sudáfrica para recoger muestras de las biopelículas. Resultó que las biopelículas en las minas simplemente estaban cargadas de gusanos. Estos nemátodos tienen alrededor de 1,000 células, por lo que no es exactamente un tipo grande, pero aún así, nunca me hubiera esperado encontrarlos a esa profundidad.

Los organismos a mayor profundidad que han encontrado hasta ahora son a 3.8 kilómetros bajo tierra -lo más profundo que ha sido posible explorar hasta ahora. ¿A que mayor profundidad cree usted que se pudiera encontrar vida?

En la mina de Mponeng, una empresa está perforando un túnel de exploración de oro a cinco kilómetros y medio de profundidad. Los precios del oro son tan altos que para ellos se hace económicamente viable. Para nosotros, pensamos, "¡Sí!" Cuanto más profunda es, estará más caliente, y será mejor. Tan abajo está, que va a estar a 90 grados centígrados, Eso es casi hirviendo. Se trata de un aumento significativo de la profundidad, y estamos emocionados de ver lo que los próximos años nos traerán.


¿Qué es lo que ir tan profundo en el planeta nos dirá acerca de la vida y de la evolución aquí en la superficie?

Estamos tratando de ver la semblanza de la base de la biósfera, de toda la vida en la Tierra. Si existen organismos con ADN a esas profundidades y a esas altas temperaturas, queremos encontrarlos, y si no existen, queremos saber por qué. Y si no hay organismos con ADN, ¿habrá otros tipos de organismos que pudieran ocurrir allí en concentraciones muy pequeñas? Pudiera existir una biología de las sombras, en donde organismos muy primitivos pudieran haber existido desde muy temprano en nuestro planeta, pero fueron reemplazados por los organismos de ADN en todos los demás lugares.

Hasta ahora hemos hablado sólo de los ambientes calientes, pero ¿qué hay del otro extremo? En muchos de los lugares de otras partes del sistema solar donde estamos buscando vida, como Marte, hace un frío intenso. ¿Ha explorado los ambientes análogos de bajas temperaturas en la Tierra?

Marte tiene una criósfera muy gruesa, o capa de roca permanentemente congelada por debajo de la superficie. Así que fuimos a una mina de oro en las profundidades de la superficie congelada en el Ártico, en el territorio de Nunavut en Canadá. La mina tiene un túnel helicoidal que va hasta un kilómetro y medio hacia abajo. Todo este aire caliente viaja desde abajo, y tan pronto como llega a la superficie permanentemente congelada, toda la humedad en el aire se cristaliza y se obtienen enormes copos de nieve, de 60 centímetros de ancho. Usted puede observar estalactitas y estalagmitas de hielo por todas partes. Parece el santuario de Súperman. Es fácil imaginar que podría haber algo como esto en Marte también. Tuve una epifanía dentro de estas cuevas de hielo: Este es el tipo de ambiente que te gustaría explorar si alguna vez fueras a Marte, envía tu explorador móvil dentro de las cuevas y echa un vistazo por todos lados. Hay humedad allí. Hay un montón de espacio para la vida en estos ambientes. Por desgracia, nunca tuvimos la oportunidad de explorar y buscar la vida en las cuevas antes de que esa mina cerrara.

¿Podríamos seleccionar señales de vida microbiana en Marte, incluso antes de ir hurgando en las cuevas ahí?

En algunas partes de Marte, hay gas metano que pudiera ser estacional. Parece que se observa para luego desaparecer. Eso significa que algo inusual está ocurriendo: Tiene que haber algo que hace al metano y algo que lo consume. La pregunta es, ¿hay formas de vida que producen y consumen el metano? Si la vida es la generación y consumo del metano, su firma química va a cambiar a causa de esos procesos biológicos. Así, como con un proyecto con la NASA, estamos desarrollando un instrumento que esperamos llevar a Marte y medir la composición del gas metano. Si nos encontramos con qué está pasando por un ciclo estacional y su composición está cambiando, eso es una muy buena indicación de que hay algo vivo en Marte. Pero lo que es ese algo, que va a ser algo muy diferente de lo que hemos visto en la Tierra debido a que las condiciones de la superficie de Marte son bastante inhóspitas para la vida tal como la conocemos.

Ha observado también en otros lugares extremadamente fríos para aprender más sobre la vida aquí en la Tierra. ¿Cómo fue eso?

Hemos ido a la isla Axel Heiberg, una isla canadiense muy al norte en el Océano Ártico, para hacer algún trabajo allí en la estación McGill de Investigación del Ártico, también conocida como Marte. Es una de las mayores islas deshabitadas en el mundo, y muy hermosa. Tiene enormes glaciares de montaña, casi como un poco de los Alpes suizos, por lo que es un buen cambio de las minas. Fuimos allí a estudiar a los microbios que viven en la superficie permanentemente congelada desde hace milenios.

Las regiones del Ártico, donde los microbios viven se están calentando rápidamente. ¿Qué impacto podría tener eso en la Tierra?

Hay una preocupación de que los microorganismos se activen de súbito y empiecen a masticar la materia orgánica, generando dióxido de carbono y metano. Eso podría causar un efecto invernadero desbocado en la última parte del siglo. Nuestra misión es tratar de entender si eso va a suceder. Se recogieron 40 muestras de hielo de la isla. Estamos poco a poco descongelando para estudiar cuáles microorganismos están haciendo que, y cuáles gases se están liberando y qué tan rápido. Luego comparamos esto con las mediciones de campo que podemos lograr en el Ártico, para ver si el medio ambiente parece estar haciendo las mismas cosas que la capa de tierra permanentemente congelada en el laboratorio. Una gran cantidad de grupos están haciendo estudios similares en todo el Ártico. No sabemos la respuesta, pero lo que todos deben buscar es mejorar nuestra comprensión de lo que cabe esperar en los próximos 100 años.

¿El haber estudiado estos diversos tipos de microbios extremos que viven en profundidades habrá cambiado su forma de pensar acerca de lo que es necesario para la vida?

Cuanto más aprendo, más me parece que los requisitos para la vida son bastante mínimos. Los nichos que la vida puede ocupar nunca dejan de sorprenderme. Un lugar puede parecer terrible para nosotros, pero para alguien más, es su Edén.

(Comparto el concepto).

Otros hábitats subterráneos

Mientras Onstott busca microbios en las minas de oro y la capa de suelo permanentemente congelado, otros investigadores están buscando vida en otros lugares profundos. Sus resultados están llenando la imagen de un ecosistema enterrado.

1.- Alrededor de los géiseres hidrotermales. Las aguas hirviendo cargadas de azufre de los respiraderos hidrotermales, donde el agua de mar calentada por el magma vuelve a surgir a través de grietas en el fondo del mar, están llenos de vida microscópica. Estas bacterias apoyan a los ecosistemas complejos en oscuras profundidades del océano, a pesar de estar poco pobladas. El zoólogo de Oxford, Alex Rogers, y su equipo exploraron la vida alrededor de un géiser con temperatura de 382 grados centígrados en el desfiladero de Escocia del Este cerca de la Antártida. En enero se informó de una serie de inusuales animales que viven cerca del géiser, incluyendo una estrella de mar de siete brazos, un pulpo "fantasma blanco", y una nueva especie de cangrejo, el Yeti, con su parte inferior cubierta de pelo.

2.- Bajo el suelo marino. Varios equipos están a la caza de la vida bajo el lecho marino. A principios de este año, la geomicrobióloga Katrina Edwards, de la Universidad del Sur de California y sus colegas perforaron en la corteza del océano Atlántico e instalaron en la superficie pequeños observatorios para monitorear la vida microbiana. En el 2010, científicos de la Universidad Estatal de Oregon y otras instituciones perforaron en la capa del gabroica, la capa más profunda de la corteza oceánica, cerca del manto caliente, rico en minerales y encontraron una gran cantidad de especies de bacterias capaces de engullir los hidrocarburos de origen desconocido.

3.- En las cuevas más profundas. La cueva más profunda del mundo conocida como Krubera-Voronja en la República de Georgia, se extiende por unos 2,000 metros. La bióloga Ana Sofia Reboleira de la Universidad de Aveiro en Portugal, ha estado explorando cuevas desde que ella era una adolescente, recientemente buscó en Krubera-Voronja organismos raros, los pequeños que lo pueblan, una tarea fría, ya que las temperaturas en las profundidades negras rondan justo por encima de cero grados. Este año, ella y su equipo reportaron cuatro nuevas especies de insectos sin alas, sin ojos, a distintas profundidades, que van desde los 60 metros a casi 2,000 metros, cerca del fondo de la cueva.


Onstott llama a sus viajes a las minas de oro, "safaris subterráneos", pero la búsqueda de nuevas especies en las profundidades de la Tierra está muy lejos de ser avistadas en la sabana. La única especie que Onstott ha observado en acción son los gusanos nematodos, podía verlos retorcerse bajo un microscopio, y tomó detalladas imágenes de microscopía electrónica de sus cuerpos de una cuarta parte de milímetro. También descubrió las células de D. audaxviator, una bacteria que significa el 99.9% de los organismos que se recuperaron de uno de los filtros utilizados para extraer agua de las fracturas de roca de profundidad en las minas. Onstott reflejó lo que pudo de las células con un microscopio de transmisión electrónica. Pero nunca ha sido capaz de ver moverse a cualquier tipo de bacterias, o verlas crecer en el laboratorio. En vez de eso, la gran mayoría de lo que estudia son trazas de ADN. El D. audaxviator ha proporcionado suficiente material genético para producir el genoma entero de esa especie, lo que permite a Onstott asegurarse de que el organismo pertenece a un ecosistema autosuficiente y podía sentir su entorno. En otros casos se ha encontrado restos de libre flotación de material genético de otra especie, sólo lo suficiente, dice, para demostrar que cada uno de ellos existe en lo profundo de las minas y es en gran parte específica a la fractura de roca en la que se encontró. "A medida que se mueve de una fractura a la siguiente", señala Onstott, “ las especies microbiales cambian".

(Más diversidad imposible. Estas son pruebas inequívocas de que no existe el tronco común y de que la vida se puede generar prácticamente en cualquier lugar, viaje o no viaje. ¿Dónde quedó el tronco común que pregonan Carlos Darwin y sus seguidores?).

Disponible para pláticas sobre mi teoría de la evolución

Félix Rocha Martínez
Saltillo, Coahuila, México
| enlace permanente | ( 3 / 2216 )
Response to Discover Interview, Erik Winfree
lunes, diciembre 5, 2011, 04:21 AM
i52b Response to Discover Interview: Erik Winfree, 05.12. 2011

Following is a transcription of an article published on the edition of the eleventh of August of 2009 of Discover magazine titled Discover Interview: Erick Winfree, written by Stephen Cass. At the end you will find my commentaries.

Discover Interview: Erick Winfree, Thanks, Evolution, For Making the Great Building Material Called DNA

Electronic computers are great at what they do. But to accomplish really complicated physical tasks—like building an insect—Erik Winfree says you have to grow them from DNA.

The humblest amoeba performs feats of molecular manipulation that are the envy of any human engineer. Assembling complex biological structures quickly and with atomic precision, the amoeba is living proof of the power of nanotechnology to transmute inert matter into wondrous forms. Amoebas—and the cells in your body, for that matter—are expert at these skills because they have had billions of years to perfect their molecular tool kit. Erik Winfree, a professor of computer science and bioengineering at Caltech, is determined to harness all that evolution-honed machinery. He is seeking ways to exploit the methods of cellular biology to create a new type of molecular-scale engineering. Although still in its early days, this line of research could lead to revolutionary ways of treating illness or creating complicated machines by growing them rather than assembling them from parts.

Winfree, who in 2000 won a MacArthur “genius grant,” focuses his research particularly on DNA, the molecule that stores genetic information. Our cells use this information to build the proteins that form our bodies’ structure and do nearly all the work involved in being alive. But Winfree is going beyond biology. He wants to exploit DNA’s unique chemical properties to process information like a computer (using novel scientific disciplines known as molecular programming and DNA computing) and even appropriate the DNA molecule as a scaffold on which to build useful structures. Winfree spoke to DISCOVER senior editor Stephen Cass about his work, its implications for understanding the origin of life, and where this kind of research could lead in the far future.

You work in biomolecular computing. What exactly is that?

It is different things to different people. For me, it means understanding that chemical systems can perform information processing and be designed to carry out various tasks. One way I look at it is by analogy: We can design computers to perform all sorts of information tasks, and they are particularly useful when you can hook up those computers to control electromechanical systems. For instance, you can get inputs from a video camera. You can send outputs to a motor. The goal for biomolecular computing is to develop similar controls for chemical and molecular-scale systems. How can you program a set of molecules to carry out instructions?

How did you get involved in this rather exotic field of research?

I got interested in the connection between biology and computation before high school, in the early 1980s. I was just learning how to program an Apple II computer and at the same time was reading books like The Selfish Gene by Richard Dawkins. These things got merged in my mind. I was interested in programming biological systems—playing the games that evolution is playing. And I was interested in biological complications of all forms, particularly neural complications: How do brains work? At the same time I was developing a love for algorithms. I did mathematics and theoretical computer sciences as an undergraduate at the University of Chicago. I went to Caltech as a graduate student, interested in neural networks for robotics. Then I gave a presentation on [University of Southern California computer scientist] Leonard Adleman’s work on DNA computing. It was a whole new way of thinking about the connection between molecular systems and computation. It wasn’t just a theorist’s playground, but an area where you could actually start having ideas for molecular algorithms and testing them in the laboratory.

You’re not the first in your family to win a MacArthur fellowship—your father, Arthur Winfree, got one in 1984 for his work on applying mathematics to biology. How did his thinking influence you?

When I was growing up, he wasn’t a MacArthur fellow; he was just Dad. And eccentric, maybe. He loved showing things to us kids. I developed my habit of never really just believing anything because he would always try to catch us out and make us think for ourselves. A lot of his friends that I met as a kid eventually became fellows themselves, so I grew up thinking that their original way of thinking and being was normal.

Those MacArthur connections have continued to follow you throughout your life, haven’t they?

Some of that has happened by accident, and some of it not. I worked for Stephen Wolfram [an independent mathematician who created the influential Mathematica software package] for a year after meeting him at a MacArthur conference with my dad. So that wasn’t by chance. But later, my Ph.D. adviser, John Hopfield, was a MacArthur fellow I met by chance, I guess because I was seeking out people I really respected. Then other people who I bumped into became fellows. I spent some time at Princeton University and met Michael Elowitz, who taught me about microscopy; he became a fellow in 2007. And there’s Paul Rothemund, who was a postdoc in my lab; he got a fellowship too.

Does that sense of freewheeling community reflect the way you run your lab at Caltech?

I try to encourage a very independent attitude in my lab, partly because I know that my success is largely due to my adviser’s giving me a lot of free rein. Actually, his phrase was that he gave me enough rope to hang myself. I think back to the ancient Greek philosophers and how they would meet and have a discussion where everyone brought their own story and process to the table. So when a student comes into my lab, I like to say, “OK, so come up with a project and tell me next week what you will be doing.” Sometimes it’s an agonizing process for them. They will take not a week but a month or a year or two years before they really figure out what they are interested in. Although that might be painful, I think it’s a better process than telling people to carry out specific things where they get into a mode of not really knowing what they like.

Real biological systems use proteins to handle most jobs, but in your lab you focus on using DNA. Why?

Proteins are much more complicated than DNA. DNA is more predictable, yet it can carry out an enormous range of functions. It’s sort of like a Lego kit for building things at the nanoscale; it’s much easier to fit pieces together than with proteins. In a sense, we’re not doing anything new. Biologists have a hypothesis that there was once an RNA world [RNA is a single-stranded cousin of DNA that acts as a translator between DNA and the protein factories in living cells]. If you look at the history of life on this planet, there was probably a time before proteins evolved. Back then RNA was both an information storage system and an active element, performing a majority of the functions within the cell. That vision tells us we can do an awful lot with nucleic acids, be it RNA or DNA.

OK, so what tasks can you accomplish with engineered DNA?

It’s really exciting. We see different kinds of molecular systems as models of computation. A model of computation, to a computer scientist, is a set of primitive operations and ways of putting those primitives together to get system-level behavior.

For example, digital circuit designers have simple logic gates, such as AND and OR, as primitives. You can wire them together into circuits to do complicated functions. [Your PC operates using those commands, for instance.] But there are many different kinds of models of computation considered in computer science.

I encourage a very independent attitude in my lab, because I know that my success was due to my adviser’s giving me free rein.

One of my main interests is in looking at what models of computation are appropriate for thinking about molecular systems. In the last four years we have gotten interested in chemical reaction networks, where you have a set of reactions: Molecule A plus molecule B reacts to form molecule C, and X plus C forms A. Traditionally, chemical reactions have been used as a descriptive language for explaining things that we see in nature. Instead, we are treating them as elements of a programming language, a way of expressing behaviors that we are trying to obtain. When you can move parts of a molecule from one place to another, it’s like a computer algorithm acting on data. In the molecular world, the data structure is actually a physical structure—for example, in DNA molecules. So growing something out of DNA can be thought of as modifying a data structure. The challenge is taking a program written in that language and implementing it with real molecules—we’ve had some demonstrations of that, and we’re very interested to see how far we can go. We also think about how to take a molecule and control it so it folds up into a very specific structure. Paul Rothemund developed that. [Rothemund made headlines in 2006 for building microscopic smiley faces out of programmed DNA.] And then there are molecular-scale motors. All of these things have been demonstrated in a primitive form with DNA systems.

That sounds fascinating from a theoretical perspective, but what are the practical implications of being able to control molecules that way?

There is a lot of excitement about intelligent therapeutics, where chemistry interfaces with biological systems to cure disease; a view based on computer science could play a role. For that kind of work, we need to distinguish among sensors, actuators, and information-processing units. At the macroscopic scale, we are familiar with the idea that sensors and actuators have to deal with the physical world, but the information-processing unit is isolated from the physical world. It’s completely symbolic: zeros and ones. It doesn’t care what the meaning of the zeros and ones is; it just processes them. With intelligent therapeutics there is going to be a lot of sensor and actuator work required to interface with biological systems in meaningful ways [such as detecting and manipulating molecules in order to cure disease]—that’s really difficult. But the hope is that one day we will be able to build a DNA processing unit that can connect to those sensors and actuators and make decisions about what cells to target or what chemicals to produce. This is fairly speculative. I’m a long way from biomedical research myself.

What about utilizing biomolecular computing to grow devices or machines—how might that work?

Here again, the idea is that there’s a part of the job that can be done by the DNA—the programmable part. And then there’s a part where you need some chemically viable substance that is linked to the DNA; that is the actuator part. There is a whole set of chemistries for attaching things like proteins, carbon nanotubes, or quantum dots [5- to 10-nanometer metal dots with interesting optical properties] to DNA in specific locations. That suggests that if you can build a scaffold out of DNA, you could then chemically process it to get something useful. For example, an arrangement of carbon nanotubes bound to DNA could be turned into an electrically conductive circuit. To build that DNA scaffold, you might have it self-assemble from “tiles” made from short lengths of DNA. The tiles are designed so that they have binding rules for how they stick to each other. That is basically a programmable crystal growth process. You could put in a feed crystal containing your program [placing it into a stew of DNA tiles and other raw materials]. The feed crystal would then grow whatever object you programmed it to create.

On a philosophical level, this work is exciting because it is a purely nonbiological growth process that has many of the features we normally associate with biology. I’m so used to thinking of DNA as the ultimate biological molecule that it’s hard to imagine its being used in a nonbiological way, but there is actually a long tradition of using biological components for nonbiological purposes. Like I’m sitting at a wooden desk, but trees have no intention of making desks or boats or houses or any of the things that we use wood for. So using DNA this way is completely in the human tradition for technology. It seems strange only because all our associations with DNA are biological.

When you regard DNA as a form of technology, does that change the way you look at people or at life in general?

Using DNA in this way certainly makes it possible to have a different perspective on what life is. This is a topic that philosophers often worry about, because you just can’t find a satisfactory definition of life. Biologists often don’t worry about it and just get on with studying it. But when you take the reductionist approach—that the phenomena we see can be explained in terms of components and how those components interact with each other—life is a mechanism, and what you look for are molecules that are capable of doing lots of interesting things. That is exactly what we found with DNA: It’s a kind of information-bearing molecule that is very programmable. We can design DNA molecules to act as gates, act as motors, act as catalysts. These findings make it more plausible to view living things as software in a chemical programming language.

Trees have no intention of making desks or houses. So using DNA this way is completely in the human tradition for technology.

What is the biggest obstacle you face in turning all your amazing concepts into a reality?

I want to be able to make molecules that work the way I ask them to! For someone who is trained in theoretical computer sciences, it is difficult starting a career as an experimental lab researcher. We build and test systems, except the systems that we actually build and test are so much simpler than the systems we can write down on paper. It’s one thing to make a case on paper that we can implement a 5,000-line-long set of chemical reactions with DNA. It’s a different thing to build a system involving three or four reactions—and still not have it work quite the way we want it. There are many interesting things to think about at the conceptual level of how to structure programs, but at the moment we are very concerned about the implementation issue and spending most of our time there. Several issues are limiting us. For example, when we design molecular components there’s all kinds of cross-talk. Our DNA-based components bump into each other. Some of the components that are not supposed to react with each other do, anyway. Certain reactions don’t happen that should.

How do you plan to address those problems?

We need to build in fault tolerance. It’s not clear how that will play out. One proposed reason for why biological systems are constantly making, then destroying, proteins is just so that we always have fresh molecules rather than moldy molecules on hand, which is potentially part of the solution to this cross-talk issue. Another problem is that if you have many components, they all have to be at fairly low concentrations, and at low concentrations you have very slow operations.

Are there ways to make biomolecular computing happen at the brisk pace we associate with conventional computing?

We are not going to compete with electronic computers. We’re doing different things. Think about manufacturing some new kind of instrument or device that’s as incredibly complicated and carefully orchestrated as a fly or an insect. To my mind, to manufacture things like that you need to grow them. Then the comparison is to biological development. If you look at the timescales in biological development, they are often hours or days. You need the right thing to happen and at the right time to grow different parts of a structure.

How long will it be before you can actually design complicated systems and therapeutic treatments with programmed DNA?

I made a plot about a year ago where I looked through influential papers in DNA computing and nanotechnology. In 1980 Ned Seeman at NYU started out the field by making a system with roughly 32 nucleotides [molecules that link together to form DNA]. If you plot the number of nucleotides people have put together since then, the growth is roughly exponential. We have a new paper that describes a system of roughly 14,000 nucleotides. The number of nucleotides in designs is roughly doubling every three years. Six more doublings—roughly 20 years from now—and we are up to a million nucleotides, which is on the order of the size of a bacterial genome. That size is not necessarily a measure of what you can do with the system, but it does tell us that in order to keep increasing at that rate we need to master complexity. We need to play the same games that computer science has been playing to handle systems that complicated. Getting these systems to work is going to be extremely challenging and will probably require real conceptual breakthroughs. Which is why I like the area.

[End of transcription]

My commentaries:

Evolution has not only brought us a great construction material called DNA. It also gave us, in writing (you have to learn to read it), how it is combined to achieve it.

My theory: Evolution is repeated in the development (processes in testicles, ovaries and spawn) and in gestation (processes in the womb) each species according to its own.

In this way, we have the conformation of DNA in testicles and ovaries and the application of the processes once the ovule and the spermatozoid are united in the womb. We Also have de generation of epigenetic changes during the lifetime of beings according to their experiences (See articles Discover Interview: Lynn Margulis and The Sins of the Fathers, Take 2).

Can this information shorten the times of investigation? Yes, if scientists make theirs my theory.

What my theory offers is the pattern of changes and the places in which you can study it and verify it. This pattern “is on writing” and those who study this area already know the necessary elements to read it.

There is a lot more information in this blog including an outline of my theory in my response to Richard Dawkins’s article “The Angry Evolutionist” Please read his article so that you know to what I am giving my response.

I also like extreme challenges that require conceptual breakthroughs that is why I have been studying my theory of evolution on my own since 1965.

Available for talks over my theory.

Felix Rocha-Martinez
Saltillo, Coahuila, Mexico
| enlace permanente | ( 3 / 2369 )
Entrevista Discover, Erik Winfree
lunes, diciembre 5, 2011, 04:01 AM
e52b Entrevista Discover: Erik Winfree, 05.12. 2011

La siguiente es una traducción de un artículo publicado en la edición del 11 de agosto de 2009 de la revista Discover titulado La entrevista: Erick Winfree, escrito por Stephen Cass. Al final se encontrará mis comentarios.

La entrevista Discover: Erick Winfree, gracias, Evolución, por hacer el gran material de construcción llamado ADN

Las computadoras electrónicas son grandes en lo que hacen. Pero para llevar a cabo tareas físicas realmente complicadas como la construcción de un insecto-Erik Winfree dice que tienes que desarrollarlo a partir del ADN.

La ameba más humilde realiza hazañas de manipulación molecular que son la envidia de cualquier ingeniero humano. En el montaje de estructuras biológicas complejas de forma rápida y con precisión atómica, la ameba es prueba viviente del poder de la nanotecnología para transmutar la materia inerte en formas maravillosas que viven. Las amebas y las células de su cuerpo, para el caso, son expertas en estas habilidades, ya que han tenido miles de millones de años para perfeccionar su juego de herramientas moleculares. Erik Winfree, profesor de ciencias de la computación y la bioingeniería en Caltech, está decidido a aprovechar toda la maquinaria pulida por la evolución. Él está buscando formas de explotar los métodos de la biología celular para crear un nuevo tipo de ingeniería a escala molecular. Aunque todavía está en sus primeros días, esta línea de investigación podría conducir a formas revolucionarias de tratamiento de la enfermedad o la creación de máquinas complicadas por su cultivo en lugar de ensamblarlas a partir de piezas.

Winfree, quien en 2000 ganó una "beca para genios", MacArthur centra su investigación particularmente en el ADN, la molécula que almacena la información genética. Nuestras células utilizan esta información para construir las proteínas que forman la estructura de nuestro cuerpo y hacen casi todo el trabajo que supone el estar vivo. Pero Winfree va más allá de la biología. Él quiere explotar las propiedades químicas únicas del ADN para procesar la información como una computadora (usando nuevas disciplinas científicas conocidas como la programación y la informática molecular ADN) e incluso colocar la molécula de ADN como un andamio sobre el cual construir estructuras útiles. Winfree habló con el editor en jefe de Discover, Stephen Cass, sobre su trabajo y sus implicaciones para la comprensión del origen de la vida, y donde este tipo de investigación podría conducir en el futuro lejano.

Usted trabaja en computación biomolecular. ¿Qué es exactamente eso?

Es diferentes cosas para diferentes personas. Para mí, significa entender que los sistemas químicos pueden llevar a cabo el procesamiento de información y estar diseñados para llevar a cabo diversas tareas. Una manera en que yo lo veo es por analogía: Podemos diseñar ordenadores para llevar a cabo todo tipo de tareas de información, y son particularmente útiles cuando se puede conectar esas computadoras para controlar los sistemas electromecánicos. Por ejemplo, usted puede conseguir información desde una cámara de vídeo. Puede enviar los resultados a un motor. La meta para la computación biomolecular es desarrollar controles similares para los sistemas químicos y de escala molecular. ¿Cómo se puede programar un conjunto de moléculas para llevar a cabo las instrucciones?

¿Cómo te involucraste en este campo tan exótico de la investigación?

Me interesé en la conexión entre la biología y la computación antes de la preparatoria, en la década de 1980. Estaba aprendiendo a programar una computadora Apple II y al mismo tiempo estaba leyendo libros como “El gen egoísta” de Richard Dawkins. Estas cosas se fusionaron en mi mente. Yo estaba interesado en la programación de sistemas biológicos, los juegos que la evolución está jugando. Y yo estaba interesado en las complicaciones biológicas de todas las formas, en particular las complicaciones neuronales: ¿Cómo funcionan los cerebros? Al mismo tiempo que estaba desarrollando un amor por algoritmos. Estudié las matemáticas y la teoría de las ciencias de la computación como estudiante en la Universidad de Chicago. Fui a Caltech como estudiante de posgrado, interesado en redes neuronales para la robótica. Entonces di una presentación sobre la obra informática de Leonard Adleman [de la Universidad de California del Sur] en computación del ADN. Era una nueva forma de pensar acerca de la conexión entre los sistemas moleculares y computación. No era sólo el campo de un teórico, sino una área donde usted puede realmente comenzar a tener ideas para los algoritmos moleculares y ponerlas a prueba en el laboratorio.

Usted no es el primero en su familia en ganar una beca MacArthur-su padre, Arthur Winfree, consiguió una en 1984 por su trabajo sobre la aplicación de las matemáticas a la biología. ¿Cómo influyó su pensamiento sobre Usted?

Cuando yo era niño, él no era un ganador de beca MacArthur; era sólo mi papá. Y excéntrico, tal vez. Le encantaba mostrar las cosas a nosotros los niños. He desarrollado mi hábito de nunca acabar de creer cosas porque él siempre trataría de atraparnos y hacernos pensar por nosotros mismos. Una gran cantidad de sus amigos que conocí cuando era niño con el tiempo se convirtieron en becarios por sí mismos, así que crecí pensando que su original forma de pensar y de ser era normal.

Esas conexiones con becarios MacArthur lo han seguido a lo largo de su vida, ¿verdad?

Algo de eso ha ocurrido por accidente, y pero otros no. Trabajé para Stephen Wolfram [un matemático independiente que creó el influyente paquete de software “Mathematica”] durante un año después de conocerlo en una Conferencia MacArthur con mi papá. Así que no fue por casualidad. Pero más tarde, mi asesor de Ph.D., John Hopfield, era un compañero becario MacArthur que conocí por casualidad, supongo que porque yo estaba buscando a la gente que realmente respetara. Luego otras personas que conocí se convirtieron en becarios. Pasé algún tiempo en la Universidad de Princeton y conocí a Michael Elowitz, que me enseñó acerca de la microscopía; se convirtió en un becario en el año 2007. Y luego Paul Rothemund, quien fue un post-doctorado en mi laboratorio; consiguió una beca también.

¿Acaso ese sentido de comunidad libertaria refleja la forma en que funciona su laboratorio en Caltech?

Trato de alentar una actitud muy independiente en mi laboratorio, en parte porque sé que mi éxito se debe en gran parte debido a que mi asesor me dio mucha rienda suelta. En realidad, su frase favorita era que él me daba suficiente cuerda como para ahorcarme. Vuelvo a pensar en los antiguos filósofos griegos y la forma en que se reunían teniendo debates en los que todos llevaban su propia historia y proceso a la mesa de discusiones. Así que, cuando un estudiante entra en mi laboratorio, me gusta decir, "OK, así que trae un proyecto y me dices la semana que viene lo que vas a hacer." A veces es un proceso angustioso para ellos. Ellos no toman una semana, sino un mes o un año o dos años antes de que realmente averigüen lo que les interesa. A pesar de que puede ser doloroso, creo que es un proceso mejor que decirle a la gente que llevan a cabo cosas específicas en las que no encuentren un modo de saber muy bien lo que les gusta.

Los sistemas biológicos reales utilizan proteínas para manejar la mayoría de los trabajos, pero en su práctica de laboratorio se centran en el uso de ADN. ¿Por qué?

Las proteínas son mucho más complicadas que el ADN. El ADN es más predecible, sin embargo, puede llevar a cabo una enorme gama de funciones. Es algo así como un kit de Lego para construir cosas a nanoescala; es mucho más fácil de encajar las piezas juntas que con las proteínas. En un sentido, no estamos haciendo nada nuevo. Los biólogos tienen una hipótesis de que había una vez un mundo de ARN [el ARN es un primo de una sola hebra de ADN que actúa como un traductor entre el ADN y las fábricas de proteínas en las células vivas]. Si nos fijamos en la historia de la vida en este planeta, probablemente hubo un tiempo antes de que las proteínas evolucionaran. En aquel entonces ARN era a la vez un sistema de almacenamiento de información y un elemento activo, llevando a cabo la mayoría de las funciones dentro de la célula. Esa visión nos dice que podemos hacer una gran cantidad de ácidos nucléicos, ya sea ARN o ADN.

Pues bien, ¿qué tipo de tareas se pueden lograr con el ADN de ingeniería?

Es muy emocionante. Vemos diferentes tipos de sistemas moleculares como modelos de computación. Un modelo de cálculo, para un científico de la computación, es un conjunto de operaciones primitivas y formas de poner esas operaciones primitivas en conjunto para obtener el comportamiento a nivel de sistema.

Por ejemplo, los diseñadores de circuitos digitales tienen puertas lógicas simples, tales como ESTO ADICIONAL u OTRO, como operaciones primitivas. Usted puede cablearlas juntas en circuitos para hacer funciones complicadas. [Su PC funciona con los comandos, por ejemplo.] Pero hay muchos tipos diferentes de modelos de computación considerados en ciencias de la computación.

Animo a una actitud muy independiente en mi laboratorio, porque sé que mi éxito se debió a que mi asesor me daba rienda suelta.

Uno de mis principales intereses es en el estudio de cuales modelos de computación son apropiados para pensar en sistemas moleculares. En los últimos cuatro años hemos conseguido interés en las redes de reacción química, donde se tiene un conjunto de reacciones: Molécula A más molécula B reacciona para formar la molécula C y X más C forma A. Tradicionalmente, las reacciones químicas se han utilizado como un descriptivo idioma para explicar las cosas que vemos en la naturaleza. En su lugar, los estamos tratando como elementos de un lenguaje de programación, una forma de expresar comportamientos que estamos tratando de obtener. Cuando se puede mover partes de una molécula de un lugar a otro, es como un algoritmo informático que actúa sobre los datos. En el mundo molecular, la estructura de datos es en realidad un ejemplo de estructura física, en moléculas de ADN. Así, el desarrollar algo de ADN se puede considerar como una modificación de una estructura de datos. El reto es tomar un programa escrito en esa lengua y su aplicación con verdadera moléculas. Hemos tenido algunas manifestaciones de eso, y estamos muy interesados en ver qué tan lejos podemos llegar. También pensamos acerca de cómo tomar una molécula y controlarlo para que se pliegue en una estructura muy específica. Paul Rothemund desarrolló eso. [Rothemund fue noticia en 2006 por la construcción de caras sonrientes microscópicas de ADN programado]. Y luego están los motores de escala molecular. Todas estas cosas se han demostrado en una forma primitiva con sistemas de ADN.

Eso suena fascinante desde una perspectiva teórica, pero ¿cuáles son las implicaciones prácticas de ser capaz de controlar las moléculas de esa manera?

Hay mucho entusiasmo acerca de la terapéutica inteligente, donde las interfaces de química con sistemas biológicos sirven para curar la enfermedad; una visión basada en la informática podría desempeñar un papel. Para ese tipo de trabajo, tenemos que distinguir entre los sensores, actuadores y unidades de procesamiento de información. A escala macroscópica, estamos familiarizados con la idea de que los sensores y actuadores tienen que lidiar con el mundo físico, pero la unidad de procesamiento de información se aísla del mundo físico. Es completamente simbólico: ceros y unos. No le importa lo que el significado de los ceros y unos tengan; sólo los procesa. Con terapias inteligentes en donde habrá mucho trabajo requerido de sensores y actuadores para interactuar con los sistemas biológicos de manera significativa [tales como la detección y manipulación de moléculas con el fin de curar la enfermedad] lo que es realmente difícil. Pero la esperanza es que un día vamos a ser capaces de construir una unidad de procesamiento de ADN que pueda conectarse a los sensores y actuadores y tomar decisiones acerca de a que células dirigirse o que productos químicos producir. Esto es algo especulativo. Estoy muy lejos de ser investigador biomédico personalmente.

¿Qué hay acerca de la utilización de la computación biomolecular desarrollando dispositivos o máquinas, ¿cómo pudiera eso funcionar?

Aquí, de nuevo, la idea es que hay una parte del trabajo que se puede hacer por el ADN como parte programable. Y luego hay una parte donde usted necesita alguna sustancia químicamente viable que esté vinculada al ADN; que es la parte del actuador. Hay toda una serie de químicos para sujetar cosas como las proteínas, los nanotubos de carbono, o puntos cuánticos [puntos metálicos de 5 a 10 nanómetros con propiedades ópticas interesantes] en localizaciones específicas del ADN. Eso sugiere que si se puede construir un andamio de ADN, luego los podría procesar químicamente para conseguir algo útil. Por ejemplo, un arreglo de nanotubos de carbono unido al ADN podría ser convertido en un circuito eléctricamente conductor. Para construir ese andamiaje de ADN, es posible que tenga que auto-ensamblar a partir de "azulejos" hechos de tramos cortos de ADN. Los azulejos estarían diseñados para que tengan normas vinculantes para la forma en que se pegan entre sí. Esto es básicamente un proceso de crecimiento de cristales programable. Se puede poner en un cristal de alimentación que contenga su programa [colocándolo en un compuesto de azulejos de ADN y otras materias primas]. El cristal de la alimentación podría entonces hacer crecer cualquier objeto que haya programado para crear.

En un nivel filosófico, este trabajo es emocionante, porque es un proceso de crecimiento puro no biológico que tiene muchas de las características que normalmente asociamos con la biología. Estoy tan acostumbrado a pensar en el ADN como la molécula biológica final que es difícil imaginar que sea utilizada de manera no biológica, pero en realidad hay una larga tradición de uso de los componentes biológicos con fines no biológicos. Como si estuviera sentado en un escritorio de madera, pero los árboles no tienen intención de hacer escritorios o barcos o casas o cualquiera de las cosas que usamos la madera para construir. El utilizar el ADN de esta forma es completamente en la tradición humana de la tecnología. Parece extraño sólo porque todas nuestras asociaciones con ADN son biológicas.

Cuando considera el ADN como una forma de tecnología, ¿cambia la forma de ver a las personas o la vida en general?

El uso de ADN de esta manera, sin duda hace que sea posible tener una perspectiva diferente de lo que es la vida. Este es un tema que a menudo preocupan a los filósofos, porque usted no puede encontrar una definición satisfactoria de la vida. Los biólogos a menudo no se preocupan por tema y simplemente siguen adelante con sus estudios. Pero cuando toma el enfoque reduccionista de que los fenómenos que vemos pueden ser explicados en términos de componentes y cómo estos componentes interactúan entre sí, la vida es un mecanismo, y lo que usted busca son moléculas que sean capaces de hacer un montón de cosas interesantes. Eso es exactamente lo que nos encontramos con el ADN: Es un tipo de molécula portadora de información que es muy programable. Podemos diseñar moléculas de ADN para actuar como puertas, actuar como motores, actuar como catalizadores. Estos resultados hacen que sea más plausible ver a los seres vivos como software en un lenguaje de programación química.

Los árboles no tienen ninguna intención de hacer escritorios o casas. Así, el utilizar el ADN de esta forma es completamente en la tradición humana de la tecnología.

¿Cuál es el mayor obstáculo que enfrenta en la transformación de todos sus increíbles conceptos en una realidad?

¡Quiero ser capaz de hacer que las moléculas funcionen de la manera que yo les pido que lo hagan! Para alguien que está entrenado en ciencias de la computación teórica, es difícil comenzar una carrera como investigador experimental de laboratorio. Construimos y probamos sistemas, a excepción de que los sistemas que en realidad construimos y probamos son mucho más simples que los sistemas que podemos escribir en un papel. Una cosa es hacer un caso en el papel que podemos poner en práctica con una larga serie de reacciones químicas de 5000 líneas con el ADN y otra cosa diferente es construir un sistema que involucra a tres o cuatro reacciones y todavía no ver que funcione de la manera que queremos. Hay muchas cosas interesantes que pensar en el nivel conceptual de cómo estructurar los programas, pero por el momento estamos muy preocupados por el problema de implementación y pasamos la mayor parte de nuestro tiempo en eso. Varias cuestiones nos están limitando. Por ejemplo, cuando diseñamos los componentes moleculares hay todo tipo de diafonía. Nuestros componentes basados en el ADN chocan entre sí. Algunos de los componentes que se supone que no reaccionen entre sí lo hacen, de todos modos. Ciertas reacciones no suceden aunque deberían hacerlo.

¿Cómo piensa enfrentar a esos problemas?

Tenemos que construir tolerancia a las fallas. No está claro cómo va a salir todo esto. Una razón propuesta al por qué los sistemas biológicos están constantemente haciendo y destruyendo proteínas, es sólo para que siempre tengamos moléculas frescas en lugar de moléculas con moho a la mano, que es potencialmente parte de la solución a este problema de diafonía. El otro problema es que si usted tiene muchos componentes, todos ellos tienen que estar en concentraciones bastante bajas, y en bajas concentraciones tendremos operaciones muy lentas.

¿Hay maneras de hacer que la computación biomolecular ocurra al ritmo acelerado que asociamos con la computación convencional?

No vamos a competir con los ordenadores electrónicos. Estamos haciendo cosas diferentes. Piense en la fabricación de un nuevo tipo de instrumento o dispositivo que es tan increíblemente complicado y cuidadosamente orquestado como una mosca o un insecto. A mi juicio, para la fabricación de ese tipo de cosas se necesita hacerlas crecer. A continuación, la comparación es con el desarrollo biológico. Si nos fijamos en las escalas de tiempo en el desarrollo biológico, a menudo son horas o días. Usted necesita que lo que haya que pasar, que pase en el momento adecuado para hacer crecer diferentes partes de una estructura.

¿Cuánto tiempo pasará antes de que realmente puedan diseñar sistemas complicados y tratamientos terapéuticos con ADN programado?

Hice una gráfica hace aproximadamente un año en el que miré a través de artículos influyentes en computación de ADN y la nanotecnología. En 1980 Ned Seeman de la NYU comenzó el campo de estudio, haciendo un sistema con aproximadamente 32 nucleótidos [moléculas que unen entre sí para formar el ADN]. Si traza el número de nucleótidos que personas han reunido desde entonces, el crecimiento es exponencial. Tenemos un nuevo documento que describe un sistema de aproximadamente 14,000 nucleótidos. El número de nucleótidos en los diseños más o menos se duplica cada tres años. Seis duplicaciones tomarán aproximadamente más de 20 años y llegarán hasta un millón de nucleótidos, que es del orden del tamaño de un genoma bacteriano. El tamaño no es necesariamente una medida de lo que puede hacer con el sistema, pero se nos dice que con el fin de mantener el aumento a ese ritmo necesitamos dominar la complejidad. Tenemos que jugar los mismos juegos que la informática ha estado jugando para manejar sistemas complicados. Conseguir estos sistemas de trabajo va a ser extremadamente difícil y probablemente requerirá avances conceptuales reales. Es por eso que me gusta esta área de estudio.

[Fin de la traducción]

Mis comentarios:

La evolución no sólo nos ha traído un gran material de construcción llamado ADN. También nos dio, por escrito (lo que se tiene que aprender a leer), la forma en que se combina para lograrlo.

Mi teoría: La evolución se repite en el desarrollo (los procesos en los testículos, los ovarios y hueveras) y en la gestación (los procesos en la matriz) cada especie de acuerdo a sí misma.

De esta manera, tenemos la conformación del ADN en los testículos y los ovarios y la aplicación de los procesos una vez que el óvulo y el espermatozoide se unen en el útero. Además de la generación de los cambios epigenéticos durante el tiempo de vida de los seres de acuerdo a sus experiencias (Ver artículos: Entrevista Discover: Lynn Margulis y Los pecados de los padres, segunda enseñanza).

¿Puede esta información acortar los tiempos de la investigación? Sí, si los científicos hacen suya mi teoría.

Lo que mi teoría ofrece es el patrón de cambios y el lugar en donde lo pueden estudiar y verificar. Este patrón “está por escrito” y los que estudian este tema ya conocen los elementos necesarios para leerlo

Hay mucha más información en este blog que incluye un resumen de mi teoría en mi respuesta al artículo de Richard Dawkins "El evolucionista enojado" Lea su artículo para que usted sepa a lo que estoy dando mi respuesta.

También me gustan los retos extremos que requieren avances conceptuales, es por eso que he estado estudiando mi teoría de la evolución por mi cuenta desde 1965.

Disponible para pláticas sobre mi teoría.

Félix Rocha Martínez
Saltillo, Coahuila, México
| enlace permanente | ( 3 / 2304 )
Discover interview: Lynn Margulis, June 17, 2011
sábado, junio 18, 2011, 07:46 PM
Following is a transcription of the Lynn Margulis interview by Discover published in Internet on June 17th, 2011 written by Dick Teresi. In parenthesis you will find my commentaries.

Response to Discover Interview: Lynn Margulis Says She's Not Controversial, She's Right

It's the neo-Darwinists, population geneticists, AIDS researchers, and English-speaking biologists as a whole whom have it all wrong.

A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else.

(In Discover's magazine edition of March 2006 there is an article by the heading of "Unintelligent Design" that speaks intensively about viruses. We should ask Lynn Margulis where does she place viruses in her concepts).

That distinction led to her career-making insight. In a 1967 paper published in the Journal of Theoretical Biology, Margulis suggested that mitochondria and plastids—vital structures within animal and plant cells—evolved from bacteria hundreds of millions of years ago, after bacterial cells started to collect in interactive communities and live symbiotically with one another. The resulting mergers yielded the compound cells known as eukaryotes, which in turn gave rise to all the rest—the protoctists, fungi, plants, and animals, including humans. The notion that we are all the children of bacteria seemed outlandish at the time, but it is now widely supported and accepted. “The evolution of the eukaryotic cells was the single most important event in the history of the organic world,” said Ernst Mayr, the leading evolutionary biologist of last century. “Margulis’s contribution to our understanding the symbiotic factors was of enormous importance.”

Her subsequent ideas remain decidedly more controversial. Margulis came to view symbiosis as the central force behind the evolution of new species, an idea that has been dismissed by modern biologists. The dominant theory of evolution (often called neo-Darwinism) holds that new species arise through the gradual accumulation of random mutations, which are either favored or weeded out by natural selection. To Margulis, random mutation and natural selection are just cogs in the gears of evolution; the big leaps forward result from mergers between different kinds of organisms, what she calls symbiogenesis. Viewing life as one giant network of social connections has set Margulis against the mainstream in other high-profile ways as well. She disputes the current medical understanding of AIDS and considers every kind of life to be “conscious” in a sense.

Margulis herself is a highly social organism. Now 71, she is a well-known sight at the University of Massachusetts at Amherst, where she is on the geosciences faculty, riding her bike in all weather and at all times of day. Interviewer Dick Teresi, a neighbor, almost ran her over when, dressed in a dark coat, she cycled in front of his car late at night. On the three occasions that they met for this interview, Teresi couldn’t help noticing that Margulis shared her home with numerous others: family, students, visiting scholars, friends, friends of friends, and anybody interesting who needed a place to stay.

Most scientists would say there is no controversy over evolution. Why do you disagree?

All scientists agree that evolution has occurred—that all life comes from a common ancestry, that there has been extinction, and that new taxa, new biological groups, have arisen. The question is, is natural selection enough to explain evolution? Is it the driver of evolution?

(I disagree that all life comes from a common ancestry. My theory says that each species has its own evolution, but with general tendencies. "Natural selection" goes against diversity).

And you don’t believe that natural selection is the answer?

This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.

(I consider that random mutations destroy, they do not generate evolution).

That seems like a fairly basic objection. How, then, do you think the neo-Darwinist perspective became so entrenched?

In the first half of the 20th century, neo-Darwinism became the name for the people who reconciled the type of gradual evolutionary change described by Charles Darwin with Gregor Mendel’s rules of heredity [which first gained widespread recognition around 1900], in which fixed traits are passed from one generation to the next. The problem was that the laws of genetics showed stasis, not change. If you have pure breeding red flowers and pure breeding white flowers, like carnations, you cross them and you get pink flowers. You back-cross them to the red parent and you could get three-quarters red, one-quarter white. Mendel showed that the grandparent flowers and the offspring flowers could be identical to each other. There was no change through time.

There’s no doubt that Mendel was correct. But Darwinism says that there has been change through time, since all life comes from a common ancestor—something that appeared to be supported when, early in the 20th century, scientists discovered that X-rays and specific chemicals caused mutations. But did the neo-
Darwinists ever go out of their offices? Did they or their modern followers, the population geneticists, ever go look at what’s happening in nature the way Darwin did? Darwin was a fine naturalist. If you really want to study evolution, you’ve got go outside sometime, because you’ll see symbiosis everywhere!

(Originally, Charles Darwin overwhelmed scientists of his time. He had and has followers that defended and defend furiously his concepts that became everyday thoughts that ended up as a religion and the leaders of these thoughts ended up behaving as if they were a mafia. To corroborate it you just have to read the writings of nonconformist Darwinists: they start their articles with praises to Darwin, they write what they have investigated that does not comply with Darwin, and end up their articles with more praises to Darwin. If they do not do that they do not get to see again any grant money. Some of Darwin's followers become cynical: Scientists like Stephen Jay Gould wrote so much against Darwin's concepts, nevertheless, because in one occasion he wrote that maybe he, Stephen Jay Gould, could be wrong, he was declared a Darwinist).

So did Mendel miss something? Was Darwin wrong?

I’d say both are incomplete. The traits that follow Mendel’s laws are trivial. Do you have a widow’s peak or a straight hairline? Do you have hanging earlobes or attached earlobes? Are you female or male? Mendel found seven traits that followed his laws exactly. But neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change—led to new species. I believed it until I looked for evidence.

(Changes evolve a species, do not create a new one).

What kind of evidence turned you against neo-Darwinism?

What you’d like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record—and preferably in all three. Darwin’s big mystery was why there was no record at all before a specific point [dated to 542 million years ago by modern researchers], and then all of a sudden in the fossil record you get nearly all the major types of animals. The paleontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin’s gradual change from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then—whoop—a whole new species. There is no gradualism in the fossil record.

(Scientists have not been able to visualize that the ediacarans went through a megatransformation, evolution, and "suddenly in the fossil record you get to see almost all the main types of animals". They are not new species, they are the same species evolved by a macromutation, that is why they are so different).

Gould used the term “punctuated equilibrium” to describe what he interpreted as actual leaps in evolutionary change. Most biologists disagreed, suggesting a wealth of missing fossil evidence yet to be found. Where do you stand in the debate?

“Punctuated equilibrium” was invented to describe the discontinuity in the appearance of new species, and symbiogenesis supports the idea that these discontinuities are real. An example: Most clams live in deep, fairly dark waters. Among one group of clams is a species whose ancestors ingested algae—a typical food—but failed to digest them and kept the algae under their shells. The shell, with time, became translucent, allowing sunlight in. The clams fed off their captive algae and their habitat expanded into sunlit waters. So there’s a discontinuity between the dark-dwelling, food-gathering ancestor and the descendants that feed themselves photosynthetically.

(In my theory the evolution evidences are found in corporal vestiges, scars, and in epigenetics. Fossils are also welcomed as evidences, nevertheless, few are those that really are worth looking at given that those who find them end up ignoring them for they are no proof of what they want to prove. In 1913 they found the Boskops, big headed fossils that after 20 years of deliberations were sent to the "dead archives" so that other generations may study them. Recently, it was found a fossilized pelvis with a big birth channel prepared to give birth to big headed babies. Those fossils are more than enough to back up my theory. Following you may find illustration 7b from my book "Scars, New Theory of Evolution". In it you may see that the change in appearance in a species may be abrupt and occasionally almost unbelievable. Every time that there are mutations there is the probability of the apparent creation of new species, opportunity created by great changes in nature. There is an enormous variety of ediacarans, one for each species of "almost all the main types of animals". The species are the same, only evolved [more information in my article "Response to The Angry Evolutionist"]).

What about the famous “beak of the finch” evolutionary studies of the 1970s? Didn’t they vindicate Darwin?

Peter and Rosemary Grant, two married evolutionary biologists, said, ‘To hell with all this theory; we want to get there and look at speciation happening.’ They measured the eggs, beaks, et cetera, of finches on Daphne Island, a small, hilly former volcano top in Ecuador’s Galápagos, year after year. They found that during floods or other times when there are no big seeds, the birds with big beaks can’t eat. The birds die of starvation and go extinct on that island.

(There were not new species).

Did the Grants document the emergence of new species?

They saw this big shift: the large-beaked birds going extinct, the small-beaked ones spreading all over the island and being selected for the kinds of seeds they eat. They saw lots of variation within a species, changes over time. But they never found any new species—ever. They would say that if they waited long enough they’d find a new species.

(A new species could not be seen, it would be microscopic and that was not what they were looking for).

Some of your criticisms of natural selection sound a lot like those of Michael Behe, one of the most famous proponents of “intelligent design,” and yet you have debated Behe. What is the difference between your views?

The critics, including the creationist critics, are right about their criticism. It’s just that they’ve got nothing to offer but intelligent design or “God did it.” They have no alternatives that are scientific.

(Yes, there is a scientific alternative, but creationists do not see it given that they limit themselves. They are not searching for the truth. They want science to say what they want it to say. Given that science is not going to say what they want it to say, then science is wrong. The Bible is clear in saying to search for the truth, for only the truth shall make us free. There is no such a thing as a religious truth and a scientific truth. There is only the truth. I have generated a theory of evolution that is the same for scientists and for Believers. My theory is based on the fact that every time there is a change in the nature of beings there are evidences left "in writing" in the genetic expression of the genome, it leaves behind evidences [that Charles Darwin studied. See the article "The Useless Body Parts"], it leaves behind scars that we all have and that they are the evidences of our evolution [and that the other beings also have, each according to its own evolution]. Does any body need to be a Believer in a Divine Being to believe my theory? Of course not. We have the evidences of our evolution in our bodies, independently of what you believe. To Believers I say: That information got written in the Bible about some 3600 years ago: "God created all the animals each according to its own" [Genesis 1: 21]. Whomever wants to believe it by faith, let it be. Whomever wants to believe by science, let it be. It is the same theory for both of them. Please read an outline of my theory in my "Response to 'The Angry Evolutionist'" by Richard Dawkins, in this same blog).

You claim that the primary mechanism of evolution is not mutation but symbiogenesis, in which new species emerge through the symbiotic relationship between two or more kinds of organisms. How does that work?

All visible organisms are products of symbiogenesis, without exception. The bacteria are the unit. The way I think about the whole world is that it’s like a pointillist painting. You get far away and it looks like Seurat’s famous painting of people in the park (jpg). Look closely: The points are living bodies—different distributions of bacteria. The living world thrived long before the origin of nucleated organisms [the eukaryotic cells, which have genetic material enclosed in well-defined membranes]. There were no animals, no plants, no fungi. It was an all-bacterial world—bacteria that have become very good at finding specialized niches. Symbiogenesis recognizes that every visible life-form is a combination or community of bacteria.

(Following is the illustration 7c of my book "Scars" in which it is shown, looking from bottom up, that 2 independent beings unite to become only one. Those 2 independent beings are the ovule and the spermatozoid. The ovule includes the mitochondria genetics. Each species has its own illustration of evolution. The previous life to the union of the ovule and the spermatozoid is deciphered in the ovaries and in the testicles. The posterior life to the union of the ovule and the spermatozoid you can study it in the womb and both lives, the previous and the posterior lives are correlated, every time there was a genetic change in the testicles and in the ovaries there was a change also in the womb, each species according to its own evolution).

How could communities of bacteria have formed completely new, more complex levels of life?

Symbiogenesis recognizes that the mitochondria [the energy factories] in animal, plant, and fungal cells came from oxygen-respiring bacteria and that chloroplasts in plants and algae—which perform photosynthesis—came from cyanobacteria. These used to be called blue-green algae, and they produce the oxygen that all animals breathe.

Are you saying that a free-living bacterium became part of the cell of another organism? How could that have happened?

At some point an amoeba ate a bacterium but could not digest it. The bacterium produced oxygen or made vitamins, providing a survival advantage to both itself and the amoeba. Eventually the bacteria inside the amoeba became the mitochondria. The green dots you see in the cells of plants originated as cyanobacteria. This has been proved without a doubt.

(In the human being, the ovule eats up the spermatozoid getting rid of the cover and of the tail and generates a union that from there on evolves as only one being. In this way, evolution is repeated with the generation of a new being of that species. In the rest of the beings most of them are very similar, but each one has its own peculiarities).

And that kind of partnership drives major evolutionary change?

The point is that evolution goes in big jumps. That idea has been called macromutation, and I was denigrated in 1967 at Harvard for mentioning it. “You believe in macromutation? You believe in acquired characteristics?” the important professor Keith Porter asked me with a sneer. No, I believe in acquired genomes.

(I do believe in macromutation: we have a caterpillar, a worm, transformed into a moth, a flying insect. Chinese knew about it thousands of years ago. What is the problem of accepting millenary knowledge? That Charles Darwin did not say it? In the illustration in the form of a stair we can see that in one of the stages of our gestation [evolution] we transformed ourselves from an oval wafer with a long protuberance in the middle [similar to the ediacaran Dickensonia] to a being with a big head, belly and tail and without extremities in the following stage [similar to a sea horse]. Is it or is it not a macro mutation? Let laugh whomever wants to laugh!).

Can you give an example of symbiogenesis in action?

Look at this cover of Plant Physiology [a major journal in the field]. The animal is a juvenile slug. It has no photosynthesis ancestry. Then it feeds on algae and takes in chloroplasts. This photo is taken two weeks later. Same animal. The slug is completely green. It took in algae chloroplasts, and it became completely photosynthetic and lies out in the sun. At the end of September, these slugs turn red and yellow and look like dead leaves. When they lay eggs, those eggs contain the gene for photosynthesis inside. Or look at a cow. It is a 40-gallon fermentation tank on four legs. It cannot digest grass and needs a whole mess of symbiotic organisms in its overgrown esophagus to digest it. The difference between cows and related species like bison or musk ox should be traced, in part, to the different symbionts they maintain.

(When they lay eggs they carry the genes of both of them and in the hatching of the eggs evolution is repeated, each species according to its own).

But if these symbiotic partnerships are so stable, how can they also drive evolutionary change?

Symbiosis is an ecological phenomenon where one kind of organism lives in physical contact with another [1]. Long-term symbiosis leads to new intracellular structures, new organs and organ systems, and new species as one being incorporated to another being that is already good at something else [2]. This major mode of evolutionary innovation has been ignored by the so-called evolutionary biologists. They think they own evolution, but they’re basically anthropocentric zoologists [3]. They’re playing the game while missing four out of five of the cards. The five are bacteria, protoctists, fungi, animals, and plants, and they’re playing with just animals—a fifth of the deck [4]. The evolutionary biologists believe the evolutionary pattern is a tree. It’s not. The evolutionary pattern is a web—the branches fuse, like when algae and slugs come together and stay together [5].

(We have seen how the ovule eats up the spermatozoid [1]. All the unions are long term and each union leads to new intercellular structures, new organs and organ systems [2]. If you are not believed being a teacher of an important school, what are the chances that they will believe me? [3]. That is a pandemic in which I am included. I observe life, I make me questions and I study searching for answers wherever I can. I have observed animals and more to the human being. Neither you nor I have observed viruses [4]. The evolutionary pattern is not a tree, nor a web, it is a stair that in its lower part is double and gets united to be only one to evolve together in the same stair as it is shown in the illustration of the ovule and spermatozoid [5]. [I was never good on drawing. Drawings 7b and 7c should have been only one drawing]).

In contrast, the symbiotic view of evolution has a long lineage in Russia, right?

From the very beginning the Russians said natural selection was a process of elimination and could not produce all the diversity we see. They understood that symbiogenesis was a major source of innovation, and they rejected Darwin. If the English-speaking world owns natural selection, the Russians own symbiogenesis. In 1924, this man Boris Mikhaylovich Kozo-Polyansky wrote a book called Symbiogenesis: A New Principle of Evolution, in which he reconciled Darwin’s natural selection as the eliminator and symbiogenesis as the innovator. Kozo-Polyansky looked at cilia—the wavy hairs that some microbes use to move—and said it is not beyond the realm of possibility that cilia, the tails of sperm cells, came from “flagellated cytodes,” by which he clearly meant swimming bacteria.

(Following is illustration 4d of my book "Scars" where it is shown a variety of spermatozoids, each one with different specifications. Life is about diversity).

Has that idea ever been verified?

The sense organs of vertebrates have modified cilia: The rods and cone cells of the eye have cilia, and the balance organ in the inner ear is lined with sensory cilia. You tilt your head to one side and little calcium carbonate stones in your inner ear hit the cilia. This has been known since shortly after electron microscopy came in 1963. Sensory cilia did not come from random mutations. They came by acquiring a whole genome of a symbiotic bacterium that could already sense light or motion. Specifically, I think it was a spirochete [a corkscrew-shaped bacterium] that became the cilium.

Don’t spirochetes cause syphilis?

Yes, and Lyme disease. There are many kinds of spirochetes, and if I’m right, some of them are ancestors to the cilia in our cells. Spirochete bacteria are already optimized for sensitivity to motion, light, and chemicals. All eukaryotic cells have an internal transport system. If I’m right, the whole system—called the cytoskeletal system—came from the incorporation of ancestral spirochetes. Mitosis, or cell division, is a kind of internal motility system that came from these free-living, symbiotic, swimming bacteria. Here [she shows a video] we compare isolated swimming sperm tails to free-swimming spirochetes. Is that clear enough?

And yet these ideas are not generally accepted. Why?

Do you want to believe that your sperm tails come from some spirochetes? Most men, most evolutionary biologists, don’t. When they understand what I’m saying, they don’t like it.

(When I ask: if a man engenders and a woman conceives, gestates, gives birth, breast feeds and rears, who is superior? few men hesitate to say that women are, every one else, men and women without hesitation say that women. Additionally I say: to make a baby a man contributes with a spermatozoid that without a microscope it can not be seen. A woman provides an ovule, a very small sphere, but visible at plain sight. If a woman not only participates with the incubator but also with 99.99% of the material, who is superior? Of course a woman is. Is it that a man is not important whatsoever? Of course he is: a man produces millions and millions of spermatozoids so that a woman may use one, a man does it [unconsciously] with the end goal of achieving diversity. A man is born capable of creating mental images that allows him the potential of creating art, technology and science from birth. I am an example of what I am saying: I obtained a Bachelor of Science in Business Administration from College of the Ozarks in Clarksville, Arkansas, nevertheless, I have generated a theory about evolution. Some men do not like to be told that women are superior. Some women do not like either to be told that women are superior given that I tell them that their superiority does not give them privileges but responsibilities. Scientists put in doubt my concepts because I did not obtain them from an Ivy League School, but from my own studies, also, they resent that someone self taught would tell them that their 30 or 40 years studying Charles Darwin have been a waste of time. People that study religion like to hear that the Bible is not only about religion but also science, history and sociology. Nevertheless, the minute I tell them that the Bible was changed to say that a man was the first human being most of them do not even want to hear what evidences I have to say it. In this way Lynn Margulis and I have in common that many people do not understand or like what we have to say).

We usually think of bacteria as strictly harmful. You disagree?

We couldn’t live without them. They maintain our ecological physiology. There are vitamins in bacteria that you could not live without. The movement of your gas and feces would never take place without bacteria. There are hundreds of ways your body wouldn’t work without bacteria. Between your toes is a jungle; under your arms is a jungle. There are bacteria in your mouth, lots of spirochetes, and other bacteria in your intestines. We take for granted their influence. Bacteria are our ancestors. One of my students years ago cut himself deeply with glass and accidentally inoculated himself with at least 10 million spirochetes. We were all scared but nothing happened. He didn’t even have an allergic reaction. This tells you that unless these microbes have a history with people, they’re harmless.

Are you saying that the only harmful bacteria are the ones that share an evolutionary history with us?

Right. Dangerous spirochetes, like the Treponema of syphilis or the Borrelia of Lyme disease, have long-standing symbiotic relationships with us. Probably they had relationships with the prehuman apes from which humans evolved. Treponema has lost four-fifths of its genes, because you’re doing four-fifths of the work for it. And yet people don’t want to understand that chronic spirochete infection is an example of symbiosis.

(And from where did Lynn Margulis obtained the idea that humans evolved from pre human monkeys? From the same Charles Darwin that she is proving wrong? In the illustration in form of a stair the pre human monkeys from where we supposedly evolved do no exist. Monkeys have their own illustration in the form of a stair of their evolution. Each species according to its own).

You have upset many medical researchers with the suggestion that corkscrew-shaped spirochetes turn into dormant “round bodies.” What’s that debate all about?

Spirochetes turn into round bodies in any unfavorable condition where they survive but cannot grow. The round body is a dormant stage that has all the genes and can start growing again, like a fungal spore. Lyme disease spirochetes become round bodies if you suspend them in distilled water. Then they come out and start to grow as soon as you put them in the proper food medium with serum in it. The common myth is that penicilli_n kills spirochetes and therefore syphilis is not a problem. But syphilis is a major problem because the spirochetes stay hidden as round bodies and become part of the person’s very chemistry, which they commandeer to reproduce themselves. Indeed, the set of symptoms, or syndrome, presented by syphilitics overlaps completely with another syndrome: AIDS.

Wait—you are suggesting that AIDS is really syphilis?

There is a vast body of literature on syphilis spanning from the 1500s until after World War II, when the disease was supposedly cured by penicilli_n. Yet the same symptoms now describe AIDS perfectly. It’s in our paper “Resurgence of the Great Imitator.” Our claim is that there’s no evidence that HIV is an infectious virus, or even an entity at all. There’s no scientific paper that proves the HIV virus causes AIDS. Kary Mullis [winner of the 1993 Nobel Prize for DNA sequencing, and well known for his unconventional scientific views] said in an interview that he went looking for a reference substantiating that HIV causes AIDS and discovered, “There is no such document.”

Syphilis has been called “the great imitator” because patients show a whole range of symptoms in a given order. You have a genital chancre, your symptoms go away, then you have the pox, this skin problem, and then it’s chronic, and you get sicker and sicker. The idea that penicilli_n kills the cause of the disease is nuts. If you treat the painless chancre in the first few days of infection, you may stop the bacterium before the symbiosis develops, but if you really get syphilis, all you can do is live with the spirochete. The spirochete lives permanently as a symbiont in the patient. The infection cannot be killed because it becomes part of the patient’s genome and protein synthesis biochemistry. After syphilis establishes this symbiotic relationship with a person, it becomes dependent on human cells and is undetectable by any testing.

Is there a connection here between syphilis and Lyme disease, which is also caused by a spirochete and which is also said to be difficult to treat when diagnosed late?¨

Both the Treponema that cause syphilis and the Borrelia that cause Lyme disease contain only a fifth of the genes they need to live on their own. Related spirochetes that can live outside by themselves need 5,000 genes, whereas the spirochetes of those two diseases have only 1,000 in their bodies. The 4,000 missing gene products needed for bacterial growth can be supplied by wet, warm human tissue. This is why both the Lyme disease Borrelia and syphilis Treponema are symbionts—they require another body to survive. These Borrelia and Treponema have a long history inside people. Syphilis has been detected in skull abnormalities going back to the ancient Egyptians. But I’m interested in spirochetes only because of our ancestry. I’m not interested in the diseases.

When you talk about the evolutionary intelligence of bacteria, it almost sounds like you think of them as conscious beings.

I do think consciousness is a property of all living cells. All cells are bounded by a membrane of their own making. To sense chemicals—food or poisons—it takes a cell. To have a sense of smell takes a cell. To sense light, it takes a cell. You have to have a bounded entity with photoreceptors inside to sense light. Bacteria are conscious. These bacterial beings have been around since the origin of life and still are running the soil and the air and affecting water quality.

(Viruses are not cells, they are not covered by membranes. Following is a portion of the article "Unintelligent design":

[Few things on Earth are spookier than viruses. The very name virus, from the Latin word for "poisonous slime," speaks to our lowly regard for them. Their anatomy is equally dubious: loose, tiny envelopes of molecules—protein-coated DNA or RNA—that inhabit some netherworld between life and nonlife. Viruses do not have cell membranes, as bacteria do; they are not even cells. They seem most lifelike only when they invade and co-opt the machinery of living cells in order to make more of themselves, often killing their hosts in the process. Their efficiency at doing so ranks them among the most fearsome killers: Ebola virus, HIV, smallpox, flu. Yet they go untouched by antibiotics, having nothing really biotic about them.

The existence of viruses was first surmised just over a century ago by Dutch botanist Martinus Beijerinck. He mashed up disease-riddled tobacco leaves and then passed the juicy pulp through a porcelain filter fine enough to trap everything down to the tiniest bacteria. When even that filtered fluid infected other plants, a world still acclimating to Louis Pasteur's germ theory now had an even tinier class of pathogens to contemplate. Here were entities so wraithlike that they remained unseen until 1935, when scientists armed with the newly invented electron microscope managed to take a picture of the "poison" lurking in Beijerinck's slime, today known as tobacco mosaic virus.

Less an organism than a jumbled collection of biochemical shards, the virus eventually yielded Wendell M. Stanley, the leader of the research team that exposed it, a Nobel Prize in chemistry rather than biology. The discovery also set off an intense scientific and philosophical debate that still rages: What exactly is a virus? Can it properly be described as alive? " 'Life' and 'living' are words that the scientist has borrowed from the plain man," the British virologist Norman Pirie wrote at the time. "Now, however, systems are being discovered and studied which are neither obviously living nor obviously dead, and it is necessary to define these words or else give up using them and coin others"].

The biggest deceptions in my life, and I have had a lot of them, I have experienced them reading articles from purport experts that end them with the recognition that years of study have not taken them to a clear conclusion.

The following is a transcription of an article found in Newsweek Magazine in the issue of August 8th. 2007 by de name of “The Human Family Shrub?” written by Sharon Begley. The Human Family Shrub? [you can see the whole article and my commentaries in this same blog]: A new discovery suggests that Homo erectus may not have evolved from Homo habilis—and that the two may have been contemporaries:

[The phrase "family bush" doesn't trip off the tongue the way "family tree" does, but anyone talking about human evolution had better get used to it. For years, scientists who study human origins have known that the simple model in which one human ancestor evolved into another in a nice, linear fashion is a myth. Instead, starting 4 million years ago, half a dozen species in the genus Australopithecus lived in Africa at the same time. Only one is our direct ancestor; the others were evolutionary dead ends, failed experiments. But experts thought that once the Homo lineage debuted about 2.5 million years ago in East Africa with Homo habilis, things settled down, with habilis evolving into Homo erectus who evolved into Homo sapiens—us—like biblical begats].

The title says more than what a lot of people imagines: The common trunk is a myth!

[Two fossils discovered in Kenya suggest that evolution was a lot messier than that. One of the specimens, found just east of Kenya's Lake Turkana, is the upper jaw bone of a habilis from 1.44 million years ago; habilis was thought to have become extinct about 1.6 million years ago. The other is an erectus, say their discoverers, a well-preserved skull from 1.55 million years ago and the smallest ever found for this species. The more recent date for habilis shows that it and erectus were contemporaries for half a million years, from 1.9 million to 1.44 million years ago. The evidence that Homo habilis and Homo erectus lived at the same time in the Turkana basin makes it "unlikely that Homo erectus evolved from Homo habilis," says Meave Leakey, a lead author of the paper announcing the discovery in tomorrow's issue of the journal Nature –A research associate at the National Museums of Kenya and research professor at Stony Brook University in New York, she is the wife of anthropologist and naturalist Richard Leakey; their daughter Louise, the third generation of her family to go into the fossil-hunting business, is a co-discoverer of the new specimens].

(It is the 3rd. generation of the Leakey family searching for fossils, continuous activity for 100 years, something for which they are recognized worlwide. Now they come to tell us that there is no family tree and maybe not even a family schrub. They are elucubrating, they are imagining, they do not even know how right they are right. Truly, they do not know anything about evolution, nevertheless, they have immediate access to publish every thing that they do not know. More information in the article “The Human Family Shrub?” in this same blog).

Your perspective is rather humbling.

The species of some of the protoctists are 542 million years old. Mammal species have a mean lifetime in the fossil record of about 3 million years. And humans? You know what the index fossil of Homo sapiens in the recent fossil record is going to be? 
The squashed remains of the automobile. There will be a layer in the fossil record where you’re going to know people were here because of the automobiles. It will be a very thin layer.

Do we overrate ourselves as a species?

Yes, but we can’t help it. Look, there are nearly 7,000 million people on earth today and there are 10,000 chimps, and the numbers are getting fewer every day because we’re destroying their habitat. Reg Morrison, who wrote a wonderful book called The Spirit in the Gene, says that although we’re 99 percent genetically in common with chimps, that 1 percent makes a huge difference. Why? Because it makes us believe that we’re the best on earth. But there is lots of evidence that we are “mammalian weeds.” Like many mammals, we overgrow our habitats and that leads to poverty, misery, and wars.

Why do you have a reputation as a heretic?

Anyone who is overtly critical of the foundations of his science is persona non grata. I am critical of evolutionary biology that is based on population genetics. I call it zoocentrism. Zoologists are taught that life starts with animals, and they block out four-fifths of the information in biology [by ignoring the other four major groups of life] and all of the information in geology.

You have attacked population genetics—the foundation of much current evolutionary research—as “numerology.” What do you mean by that term?

When evolutionary biologists use computer modeling to find out how many mutations you need to get from one species to another, it’s not mathematics—it’s numerology. They are limiting the field of study to something that’s manageable and ignoring what’s most important. They tend to know nothing about atmospheric chemistry and the influence it has on the organisms or the influence that the organisms have on the chemistry. They know nothing about biological systems like physiology, ecology, and biochemistry. Darwin was saying that changes accumulate through time, but population geneticists are describing mixtures that are temporary. Whatever is brought together by sex is broken up in the next generation by the same process. Evolutionary biology has been taken over by population geneticists. They are reductionists ad absurdum.

(This is the basis for discarding the theory "Out of Africa". Simple and plainly they do not take in consideration the skin pigmentation of human beings [People came black out of Africa, they transformed to white in Armenia, just to get transformed to yellow in China, to become black again in Australia], the enormous variety of habits, the enormous variety of languages and dialects, [nine families of Indo European languages derived from Sanskrit, 150 families of languages in the American Continent, 4 or 5 in Africa and 16 in Australia).

Population geneticist Richard Lewontin gave a talk here at UMass Amherst, about six years ago, and he mathematized all of it—changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get my grant money.” So he’s an honest man, and that’s an honest answer.

(It satisfies the specification to praise Darwin and that is enough to receive grant money. The inferior layers of Darwinism always insist that an article to have credibility must be published in a recognized science magazine. The superior layers of Darwinism are in charge to see that articles that do not include praises to Darwin do not get published. For what I have said it is obvious that I am condemned to be a blogger for the rest of my life).

Do you ever get tired of being called controversial?

I don’t consider my ideas controversial. I consider them right.

(I also consider mine correct, nevertheless, I am aware that they are controversial, given that I step on somebody's toes anywhere I go. I still cherish the hope that with a lot of persistence I can make a dent in the concepts of a lot of people, including scientists).

Felix Rocha-Martinez
Saltillo, Coahuila, Mexico
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