diumenge, 31 de maig de 2009

CHAPTER 1 OF 13


CHAPTER 1.-THE MODERN EVOLUTIONARY SYNTHESIS


Introduction

For the modern evolutionary synthesis (MES) mutations, genes and DNA[1] are important elements to explain evolution; thus, before we start analyzing specific aspects of the evolutionary process, first, we should know a little bit more about them. DNA is made of two long chains of nucleotides (each nucleotide consists of several molecules and each molecule is formed by atoms) twisted into a double helix and joint by hydrogen bonds between complementary bases (adenine and thymine or cytosine and guanine). Sequences of hundreds of thousands of nucleotides form genes which are hereditary units that determine a particular characteristic in a living organism. Mutations are random changes in the sequence of nucleotides in a cell’s DNA, and are mainly caused by radiation, viruses and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. Due to the damaging effects that mutations can have on cells, organisms have developed mechanisms such as DNA repair to remove them. According to the MES, through mutations, sequences of nucleotides are randomly interchanged, these tiny variations must create a slightly different trait in a living organisms, so tiny that is not perceivable in one or two generations but thousands. This small new trait, if it’s helpful for survival, will make the living organism better adapted, and will have more possibilities of transferring its genome to the next generation.

Thanks to the previous definitions, now we are in a position in which we can establish a common conceptual ground in order to facilitate the understanding of the ideas exposed in this essay. What are the basic requirements that an evolutionary theory must posses?: with a few exceptions, evolution is a dynamic process in which life reaches higher degrees of complexity, hence; a theory with the purpose to relate the evolutionary process should contain at least two basic requirements: what triggers this dynamic process, and once it has started, which mechanism makes living organisms to increase in complexity. By definition, two different theories must necessarily disagree, at least, in one of the basic requirements.

For the MES, these two basic requirements are: mutations, as the events that trigger evolution, and (once the process has started with mutations) natural selection as the mechanism that makes living organisms to increase in complexity; whereas for the Theory of evolution through energetic equilibrium, the two basic requirements are: stimuli, as the trigger of evolution, and (once the process has started with stimuli) energetic equilibrium as the mechanism that makes living organisms to increase in complexity.

It becomes clear, that this essay that you are reading has to explain why the crown jewels of the MES, mutations and natural selection, are not good propositions to explain evolution, and why stimuli and energetic equilibrium are a correct approach. The purpose of this chapter is to show that the theory produced by the MES is inconsistent and has important contradictions regarding its two basic requirements.


1.1 The modern evolutionary synthesis

Before continuing analyzing mutations and natural selection, let’s see the origin of the MES and how explains the evolutionary process with more detail:

In 1859, Charles Darwin detailed the theory of evolution by natural selection with the publication of On the Origin of Species by Means of Natural Selection. Darwin’s work soon led to the acceptance of evolution within the scientific community. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the MES, in which the connection between the units of evolution (genes) and its mechanism (natural selection) was made. This explanatory theory has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth.

The MES establishes:

mutations experimented by genes is the main cause that produces new or altered traits in individuals, resulting in the appearance of heritable differences between organisms; the major mechanism that drives evolution is natural selection, a process causing heritable traits that are helpful for survival and reproduction to become more common in a population, and harmful traits to become more rare. This occurs because individuals with advantageous traits are more likely to reproduce, so that more individuals in the next generation inherit these traits. Over many generations, adaptations occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for the environment. When a species is separated into populations that are prevented from interbreeding, mutations and natural selection cause the accumulation of differences over generations and the emergence of new species.


1.2 The modern evolutionary “entanglement”

Mutations and natural selection are observable events that occur in nature, they exist, they are real; the problem starts when we assume that these events are the two basic requirements to explain evolution. The consequence of this erroneous assumption is what I call, the “modern evolutionary entanglement”. Let’s see the nature of this added enmeshment to the already intricate evolutionary process.

If we falsely assume that mutations are the precursors of evolution the concept new trait becomes affected, let’s see how:

Mutations cause random variations in genes, and these define traits, then, a mutation generates a new trait, after hundreds of thousand of years of consecutive favorable mutations, where before we had a fish, now we have a camel, therefore, mutations “are”evolution.

Once the concept new trait is “contaminated”, this one affects all the observable processes that generate new traits, let’s see how:

Mutations create new traits, and thus evolution, then, all mechanism susceptible to generate new traits[2], must also contribute to evolution.

Mechanisms that create new traits are also known as “mechanism of gene diversity “, therefore:

Mutations and mechanisms that create gene diversity are the precursors of evolution.

In the introduction of this chapter, we have seen how a theory explaining evolution must contain at least two basic requirements; for the MES, mutations is the main mechanism that induces gene diversification, but because of this erroneous conceptual relationship, now we have mutations and other observable phenomena that produce gene variation. If we consider that modern biology observes several sources of mutations AND several mechanisms that can create gene variation, then, evolution looks like an undecipherable gene entanglement of epic proportions that grows in complexity with the passage of time, and that is what I call “the modern evolutionary entanglement “, although evolution is a complex sequence of events, is not that complex.

The parallelism that we established at the introduction of this chapter between mutations and stimuli and natural selection with energetic equilibrium it’s been broken; now the MES has more elements in one of its basic requirements: mutations and mechanisms of gene diversity. We will see in the next section, 1.3 Disentangling the entanglement, that once we elucidate the bad association of ideas provoked by the false assumption that mutations trigger evolution, then, mechanisms of gene diversity and mutations will appear as independent process that neither are related among them nor have further evolutionary implications.

For the MES, as we have seen before, its second basic requirement to explain evolution is natural selection; although this mechanism is also an erroneous assumption, it doesn’t contribute to the conceptual entanglement because happens after mutations (and gene diversity) have occurred.


1.3 Disentangling the entanglement

If we eliminate the false principle that mutations are the precursors of evolution, the evolutionary panorama becomes less entangled and more natural, since we are removing further evolutionary embroilment when we have a mutation. Under this perspective, mechanisms of gene diversity, among them mutations, have simpler implications that are not related with the evolutionary process.

For instance, mutations become natural phenomena consisting in the accidental variation of sequences of nucleotides (It would be surprising if living organisms wouldn’t commit errors during DNA replication or meiosis, since they have to duplicate hundreds of thousands of nucleotides). This new approach makes easier to understand complex molecules such us DNA repair, which corrects transcription errors committed during DNA replication.

In a world without mutations implying evolution, variations in traits coming from mechanisms of gene diversity do not necessarily mean that evolution is taking place; they became just that, spontaneous processes that nature has developed to reshuffle genes among individuals of the same species in order to enrich their genome. For example, in sexual reproduction living organisms exchange genes, their offspring will be a mix of the parents and will have “new traits”, but this doesn’t mean that these new traits are contributing to evolution or the appearance of a more complex[3] species; for instance, if we breed two cats of different colors, the offspring will be a mix of their parents’ tones, they will have new traits, but there is no reason to assume that they are contributing to the creation of a more complex species.

Modern biology, although unwillingly, has already determined that sexual reproduction is not involved with evolution; the Hardy-Weinberg principle states:

Variations in genes in a large population will remain constant if the only forces acting on that population are the random reshuffling of genes during the formation of the sperm or egg and the random combination of the genes in the sex cells during fertilization. Such a population is said to be in Hardy-Weinberg equilibrium: it is not evolving.

From this principle ― since now we are not considering mutations― becomes clear that we must find another catalysts for evolution (we will see how these are stimuli coming from new and forced environments).

Today we know that it is important to enrich the genetic pool of a population with other individuals of the same species living in distant habitats. Organizations that protect endangered species gather semen and eggs from far-flung regions where the compromised animals still exist, and preserve them to have different sources of gene diversity; in contrast, when small and isolated populations only mate between them during long periods of time ― to the point that most members of the group are related by blood― occurs endogamy; in humans, this syndrome generates individuals with mental illnesses. Nature must also have instruments to generate natural gene variability; gene flow is the means that ensures that the exchange of genetic material is performed with success: if animals from remote regions migrate and reproduce with faraway populations of the same species, there will be an enrichment of their genetic material. It is erroneous to presume that the new traits produced through this kind of gene diversity will contribute to the emergence of more complex species.

There is a third mechanism of gene diversity known as genetic drift. It also can be considered as a natural way to ensure gene diversity, like sexual reproduction; we don’t have to presume, that the new traits resulting from the change in the allele frequency from one generation to the next will contribute to the materialization of more sophisticated species.


Horizontal gene transfer

This means of gene variability consists in the conveyance of genetic material from one organism to another that is not its offspring, it occurs among simple organisms like bacteria or viruses. I have excluded it from the previous analysis because it’s an exception: first, the aforementioned mechanisms of gene diversity occur between organisms of the same species, whereas horizontal transfer takes place between organisms of different species; secondly, there is scientific evidence that horizontal transfer spawned more complex forms of life, and therefore, contributed to evolution (we will see this in short); on the other hand, there is not scientific evidence that any mechanism of gene diversity between the same species created a more complex one (this is logical if we don’t consider mutations as generators of evolution).

This instrument of gene variability is important because is one of the proofs that we have that mutations do not trigger evolution [4]; since the MES was formulated in the 1930s, this mechanism has remained “camouflaged” between the other means of gene diversity or in the “modern evolutionary entanglement”; for a long time was a curiosity related with microorganisms; as we have seen, if we take a closer look at the MES, and disentangle the confusion caused by the false assumption that mutations trigger evolution, then, horizontal transfer stands out, it’s an important exception; enough important to make stagger Darwinian evolution.

The importance of this mechanism of gene variation echoes in the Earth’s evolutionary past: around 3,500 millions years ago, horizontal transfer contributed to the differentiation of three basic forms of cell organization: Bacteria, Archaea and Eucarya (cells in eukaryotic organisms like plants and animals). All living organisms descend from one of these primordial branches. We can not tell who is more related to whom because bacteria have characters in common with archaeans; on the other hand, archaeans share attributes with eukaryotes, and there are still other traits that bacteria and eukaryotes share to the exclusion of archaeans. Scientist realized that the three groups of organisms couldn’t be joined to the same root of the tree of life; the startling conclusion is that some genes passed horizontally from one organism to the other, perhaps through a virus or by the uptake of DNA from dead cells.

In the introduction of this chapter, we have already seen which two basic principles are contained in the theory produced by the MES: mutations, as the trigger of evolution, and natural selection as the mechanism that makes living organisms to reach higher degrees of complexity. With horizontal gene transfer, we have an example of evolution without a mutation: when the exchange of genetic material occurred Eons ago, more complex organisms were shaped, and this is what evolution is all about; thus, the MES must be incorrect (at least regarding mutations as the inducers of evolution). It’s not a coincidence, that one of the little scientific evidence that we have where a species becomes more sophisticated ―and hence evolves― is caused by an event different than a mutation. We will see in chapter 7 how horizontal gene transfer is a form of evolution explainable through energetic equilibrium.

This nature’s mechanism of gene variability can be observed today in many microorganisms; however, I consider that it is not relevant to explain evolution in upper branches of the tree of live: it is improbable that viruses and bacteria contributed to the development of complex organs, like eyes or the brain, for the simple reason that this information was not encrypted in their genome. The genes that were horizontally transferred in the earliest annals of life only encoded specific metabolic functions; therefore, horizontal gene transfer contributed to evolution in the first stages of life in our planet Earth.


1.4 Mutations and the MES

At this point, if we don’t consider mutations as the trigger of evolution, it’s apparent that mechanism of gene diversity and mutations are independent events with no evolutionary implications, as noted towards the end of section 1.2 The modern evolutionary “entanglement “, this, will allow us to clear out distracters (mechanisms of gene diversity) and focus in mutations and natural selection in order to unveil the inconsistencies existing in the two requirements left in the MES to explain evolution, i.e. mutations and natural selection.

We can infer the first of the MES’s inconsistencies regarding mutations from the first paragraph in the introduction of this chapter, it’s a well known fact that mutations are extremely harmful for living organisms; it’s contradictory that random mutations will trigger the evolutionary process when living organisms have precisely developed mechanisms to correct them: RNA repair.

The second disparity is revealed by the fossil record: if mutations are the inducers of evolution, since these are random and non-discriminating events, we should be able to observe ― through the fossil record― a constant and lineal apparition of new species during Earth’s life history, and at the same time, the appearance of these should be independent of environmental change; paleontology shows us exactly the opposite: shorts burst of life followed by relative long periods of no evolutionary change, and in synchrony with the planet’s environmental dynamics.[5]


1.5 Natural selection and the MES

The third incongruity is related with both the mechanism of natural selection and mutations. The concept new trait in the MES is vague. What is the nature of an advantageous new trait helpful for survival?, the result of a favorable mutation that occurred hundreds of thousand of years ago in the hips of a pre-hominid, which would have allowed it to stand a fraction of a degree more erect?, or a mutation in a tiny bone in a pre-hominid’s wrist that would have empowered it to slightly oppose its thumb against the rest of the fingers in its hand? Let’s consider that both things happened (I am assuming that the erecting process or the opposable thumb ability in modern humans are the result of an undetermined amount of successful mutations during thousands of generations, it would be irrational to think that this happened only in one generation !) then, the pre-hominid, in order for the advantageous trait to be completed through evolution, would have had to suffer thousands of mutations interspersed by an undefined amount of time; for every mutation, not only the DNA repair would have had to oversee it, (how does the DNA repair recognizes a harmful mutation from a beneficial one that is the first step towards the apparition of a new trait?) but each mutation would have continued the evolutionary process exactly in the right position in the new sequence of nucleotides started a certain amount of time before (may be thousands of years).

The probabilities for this sequence of events to happen are very low: it would be comparable as if different stonecutters would settle a stone, during a span of hundred of thousands of years, and at the end, by chance, the Cathedral of La Sagrada Familia was created; if this would happen, all of us would agree that every single stonecutter had a blueprint and was contributing a little bit to the final result: there was a purpose; and this is the third inconsistency of the MES: it doesn’t give a convincing explanation on how thousands of nucleotides are aligned in perfect sequences during extraordinary spans of time (through mutations) forming genes, and how these variations in new sequences are systematically overseen by a mechanism such as DNA repair. If we consider that most organs are created by several genes (the human eye is defined by four genes) and that genes also determine living organisms’ conduct and metabolic processes, then, the evolutionary theory presented by the MES is definitely unsustainable.


1.5 Conclusion

Mutations and means of gene diversity (with the exception of horizontal gene transfer in the past) are independent phenomena that don’t have further evolutionary implications (related with the creation of more complex life-forms). There is not scientific evidence that a mutation (or a sequence of them) caused a specific beneficial trait helpful for survival in a complex living organism[6]; hence, the theory introduced by the MES has never been confirmed to occur at the higher branches of the tree of life. It is a generally accepted theory because is the only one that was able to establish a relative coherence between a series of interrelated concepts that were available at the time the theory was conceived: natural selection, genes, mutations and some mechanisms that can create gene variability. This theory was an answer to the human need to find a “logical “explanation to the events and processes that we are able to observe.

Natural selection, utilizing MES’ terminology, only works in one direction: if a living organism suffers a mutation, and it’s born with a physical anomaly that hampers its functioning in nature, it will perish because of this disadvantage and will not transfer its genes to the next generation; this organism is “selected against “by natural selection. Natural selection is a practical way for nature to maintain a population with a “healthy “genome; I would describe it with precisely its own words: it’s a natural way for life to select the fittest organisms. Although natural selection and mutations are observable phenomena, and therefore real, they don’t make the theory of evolution by natural selection correct by definition.

So far, we have already seen why mutations and natural selection are two incorrect postulates found in the MES’ logic ―as mentioned in the introduction of this theory―, now we have to take a look at the third flaw and important omission: the MES doesn’t consider the interaction of the genome with the environment. The consequence of this earth-shaking fault, jointly with the wrong presuppositions that mutations and natural selection drive evolution, has resulted in an obsolete and unsatisfactory theory to explicate evolution. The purpose of the next Chapter, Epigenetics, is to fill the gap left by the MES by showing the influence of the environment on genes.





[1] Acronym for deoxyribonucleic acid
[2] See annex 1 for mechanisms that generate gene variation (genetic drift, gene flow and sexual reproduction)

[3] As we have seen in the introduction of this chapter: “evolution is a dynamic process in which living organisms reach higher degrees of complexity “. In Chapter 4 we will refine this statement.
[4] Through this essay, we will see more examples― supported by scientific evidence― of evolution not caused by mutations.
[5] One could dispute that this argument is not solid enough to prove that mutations aren’t possible inducers for evolution, since we can always imagine, that after there is a change in the environment, variations in the genes that before were neutral or harmful now become beneficial, and that new mutations, now will spawn creatures adapted to the novel environment. In this theory we will see how, in fact, the proposed inconsistency has firm fundaments, and I will also present more arguments showing how mutations are not good prospects as inducers of evolution.

[6] Some experiments conducted in laboratories ― in artificial and controlled conditions― with high replicating simple forms of life, like bacteria, viruses or flies, have been able to produce what appears to be favorable mutations. I will go over these experiments later in chapter 8, section 8.6 Adaptation.

INTRODUCCION TEORIA

TEORÍA DE LA EVOLUCIÓN A TRAVÉS DE EQUILIBRIO ENERGÉTICO


Prólogo


Mutaciones y selección natural son dos conceptos importantes relacionados con la evolución. La síntesis evolutiva moderna (SEM) establece que cuando una especie se encuentra separada en poblaciones que no pueden reproducirse entre ellas, mutaciones y selección natural causan la aparición de nuevas especies. Los organismos vivos son susceptibles de sufrir mutaciones beneficiosas o perjudiciales, si experimentan una ventajosa serán "seleccionados a favor " por la selección natural, y continuarán reproduciéndose y transfiriendo sus mejores genes (o deberíamos decir genes afortunados?), por otro lado, si la mutación es desfavorable, los organismos vivos serán "seleccionados en contra" por la selección natural y eventualmente perecerán junto con sus descendientes y genoma menos apto, la acumulación de diferencias causadas por mutaciones beneficiosas durante generaciones crea rasgos útiles para la supervivencia, los organismos vivos se convierten en especies diferentes después de largos períodos de acumular rasgos nuevos.

El siguiente es un caso que ilustra el proceso evolutivo anterior: antes de que Inglaterra hiciera su revolución industrial, en los bosques de las afueras de Londres había una especie de mariposa blanca, Londres se hizo más y más industrializada emitiendo humos negros en la atmósfera y ensuciando los bosques con hollín, que hizo que las mariposas blancas fueran más fáciles de detectar por las aves y otros depredadores, al parecer, uno de los insectos tubo una mutación favorable y nació negro, esta nueva característica lo hizo más difícil de discernir por aves y otros depredadores: la mariposa negra estaba en mejores condiciones de sobrevivir, con el tiempo, la mayoría de ellas eran de color negro. Este ejemplo representa bastante la idea principal de la teoría presentada por la SEM sobre cómo organismos vivos experimentar mutaciones y las implicaciones de supervivencia que conllevan.

El ejemplo anterior es lógico y una historia muy creíble, sin embargo, tengo varias razones para pensar que la teoría producida por la SEM no es muy precisa: ¿cómo es posible que nuestra inteligencia, que es el máximo exponente de la evolución en nuestro planeta, ha surgido gracias a sucesos aleatorios llamados mutaciones? Si usted piensa que la evolución es provocada por mutaciones, debería también de estar de acuerdo que obras maestras de la música clásica, pinturas famosas, todas las expresiones antrópicas de arte y creatividad, junto con las teorías y las leyes descubiertas por una multitud de extraordinarios científicos en todos los campos del conocimiento humano y, en definitiva, todo lo relacionado con el intelecto humano, es también producto de un evento casual y fortuito (o una secuencia de ellos) que dio forma al cerebro de un prehomínido hace unos cuantos millones de años. ¿No sería natural suponer que el proceso evolutivo, que desemboca en la aparición del cerebro y la inteligencia, ha sido causado por un fenómeno diferente de un suceso fortuito y aleatorio?, si precisamente los resultados de nuestra inteligencia son lo contrario de aleatoriedad!


En este ensayo voy a explicar la Teoría de la evolución a través de equilibrio energético, esta es su idea central: los organismos vivos evolucionan hacia nuevas especies— a través de un proceso llamado equilibrio energético—, cuando se ven obligadas a sufrir variaciones permanentes de los estímulos existentes en su entorno. Con el fin de apoyar mi tesis, en primer lugar, vamos a ver cómo la biología moderna contiene importantes incoherencias y contradicciones en relación con la evolución, y cómo no da una explicación convincente de la aparición de especies más complejas. La SEM se basa en dos mecanismos erróneos para explicar la evolución: las mutaciones como los precursores de ella y la selección natural como el mecanismo que la impulsa, y contiene una omisión importante: no tiene en cuenta la interacción de los genes con el entorno.

Una vez expuestos los postulados no viables de la biología moderna, y la necesidad de una teoría evolutiva más coherente que considere el impacto del medio ambiente en los genes, en el capítulo 3, voy a aclarar la Teoría de la relatividad general de los estímulos y el estrés a partir de la cual emana la hipótesis evolutiva en la que la Teoría de la evolución a través del equilibrio energético está construida, y voy a explicar como llegue con su axioma central y todos sus principios.














INTORDUCTION THEORY

THEORY OF EVOLUTION THROUGH ENERGETIC EQUILIBRIUM



Prologue


Mutations and natural selection are two important concepts bound up with evolution. The modern evolutionary synthesis (MES) establishes that when a species is separated into populations that are prevented from interbreeding mutations and natural selection cause the emergence of new species. Living organisms are susceptible to suffer beneficial or harmful mutations; if they experiment an advantageous one they will be “selected for “by natural selection, and will continue reproducing and transferring their better shaped genes (or should we say lucky genes?), on the other hand; if the mutation is adverse, living organisms will be “selected against “by natural selection and eventually will perish along with their descendants and less fit genome; the accumulation of differences caused by beneficial mutations over generations creates traits helpful for survival; living organisms become new species after long periods of time accumulating new traits.

The following is a textbook case that depicts the previous evolutionary process: before England made its industrial revolution, in London’s outskirts’ forests there was a species of white butterfly; London became more and more industrialized casting dark fumes into the atmosphere and soiling the forests with black soot which made the white butterflies more easy to spot by birds and other predators; apparently, one of the insects had a favorable mutation and was born black, this new trait made it more difficult to discern by birds and other predators: the black butterfly was better fit to survive; with time, most of them were black. This example fairly represents the main idea of the theory brought forward by the MES on how living organisms experiment change through mutations and the survival implications that they entail.

The previous example it is a logical and very credible story; however, I have several reasons to think that the theory produced by the MES is not quite accurate: how it is possible that our intelligence, which epitomizes evolution in our planet, has emerged thanks to random events called mutations? If you think that evolution is triggered by mutations, you should also agree that master pieces of classic music, famous paintings, all anthropical expressions of art and creativity, along with theories and laws discovered by a myriad of extraordinary scientists in all fields of human knowledge and, in short, everything related with human intellect, is also product of a fortuitous and chanced event (or a sequence of them) that shaped a pre-hominid’s brain a few millions years ago. Wouldn’t it be natural to suppose that the evolutionary process, that leads to the appearance of the brain and intelligence, it’s been caused by a phenomenon different than a random and fortuitous event?, if precisely the outcomes of our intelligence are the contrary of randomness and fortuitousness !

In this essay I will explain the Theory of evolution through energetic equilibrium; this is its central idea: living organisms evolve towards new species— through a process called energetic equilibrium—, when they are forced to suffer permanent variations of stimuli existing in their environment. In order to support my thesis, first, we will see how modern biology contains important inconsistencies and contradictions regarding evolution, and how it fails to give a convincing explanation for the apparition of more complex species. The MES is build upon two erroneous mechanisms to explain evolution: mutations as the precursors of evolution and natural selection as the mechanism that drives it, and contains an important omission: it doesn’t have in consideration the interaction of genes with the environment.

Once exposed the non-viable postulates of modern biology, and the need for a more coherent evolutionary theory that considers the impact of the environment on genes, in chapter 3, I will elucidate the Theory of general relativity of stimuli and stress from which emanates the evolutionary hypothesis onto which the Theory of evolution through energetic equilibrium is build, and I will explicate how I came with its central axiom and all its principles.