Sunday, December 14, 2014

The Trinity of Suicide and Self Preservation

Today I will give an explanation for the contradiction between Suicide and Self Preservation. It's believed that Self Preservation is the ultimate instinct of any Organism, and when suicidal, there is a Special Math that explains it!

But first, it's important to have in the baggage of thinking a Trinitarian view of reality. Trinity is more than Biology, is a Natural Concept like Evolution, so you will see it in other fields, equally applied to Species as it is to Religion and Ideology.
 

It's important to notice, that Religion and Ideology are synthesis of the Species Will, were Species is the crude version of itself. With time, Human need for explanations and control of their environment, Species evolved to Religion, and finally, to its ultimate state of sophistication, Ideology. However, all the virtues and vicious they have come from the same source, Species.

So, there is the believe that the ultimate goal of Organisms is Self Preservation, were Organisms are Selfish entities like their genes.
"They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.
― Richard Dawkins, The Selfish Gene
This book reveals an ingenious trick, because Organisms are very unpredicted for a Selfish model, he diverts attentions to Genes. The problem is that Genes and Organisms are at the same level, and so aren't the direct subject of Evolution (except in the case of Prokaryotes where there is only Natural Selection). So, if organisms are carriers of Genes, they would also have the ultimate Self Preservation objective. However there is a problem, Suicide. About it Dawkins says the following.
"The minimum requirement for a suicidal altruistic gene to be successful is that it should save more than two siblings (or children or parents), or more than four half-siblings (or uncles, aunts, nephews, nieces, grandparents, grandchildren), or more than eight first cousins, etc. Such a gene, on average, tends to live on in the bodies of enough individuals saved by the altruist to compensate for the death of the altruist itself."
It looks like for suicide to happen you need to have relatives and at the same tame be altruistic, because otherwise the math doesn't sum up! However the great majority of suicides have nothing to do with altruism, they are in reality very selfish, and normally are caused by isolation rather than a familiar environment. So, is there any Selfish Suicide that Dawkins wishes to talk about?

Restricting the usefulness of genes or its success to familiar relationships is a restriction that comes hand to hand with the Genes as the Object of Natural Selection. Genes may be favored by Natural Selection, but in Eukaryotes the ultimate object of Selection is the Species not the Gene. And so, no matter the familiar relationships, the gene will be successful as it will be the Species that encapsulates it. As in the Fisher's geometric model Genes are like a knob in the microscope where is the microscope who is adjusted to the environment not the knob! Strange that Dawkins doesn't realize that, despite Dawkins have named Fisher "the greatest biologist since Darwin". So, genes are supported by Natural Selection as its Species is, and by Sexual Selection as their Organisms are! Restricting evolution to Genes, is the same as restrict evolution to tools in a Factory, or an Organization, some tools make organizations more successful, but the success of those tools is measured by the success of its Organization not the contrary! By other words, Genes are encapsulated by Species when concerning Natural Selection.

So, there is no Selfish Gene, there is only Selfish Species, something that goes beyond any familiar relationship, and so, the so called Self Preservation is only applicable to Species. Organisms and their Genes are ultimately committed to other thing, they are committed to Conformity. An organism is prone to commit suicide if that Conformity is no possible and the resultant frustration pushes him to it, or the glory of a better conformity, were the first case is selfish and the second altruist regardless any familiar relationship.

In reality suicide is so Endemic that a news about a study of CDC concludes that:
Looking deeper into the data, though, shows a second astonishing fact that actually is surprising: just how high the gun-suicide rate really is.  The preamble to the CDC’s National Vital Statistics Reports Vol. 60, No. 3 cites firearms as one of the “four major mechanisms of injury in 2009” (the year of the survey), along with poisoning, motor vehicles, and falling.   In that year, 59.8% of all “firearm injury deaths” were suicides, and 36.7% were homicides. - in Who Knew? The Leading Cause Of Gun Death Is Suicide
So much for Self Preservation! Is this Altruism or just a big family? Organisms have no right to Self Preservation, Species and its derivatives do.

If Self Preservation was the ultimate goal of Organisms, there will be no need for Anti Suicide campaigns, or extremely care to remove from the market drugs that are very lethal, like the Barbiturates, that otherwise would be sold like popcorns thanks to a big demand, the same demand you have with those who have no restrictions to them.
Medical practitioners have a relatively high rate of suicide. Death entry data for doctors who died by suicide or undetermined cause between 1979 and 1995 in England and Wales were used to compare methods used for suicide by doctors with those used by the general population. Methods used were analysed according to gender, occupational status and speciality, to assess the extent to which access to dangerous means influences the pattern of suicide. Self‐poisoning with drugs was more common in the doctors than in general population suicides (57% vs. 26.6%; OR=3.65, 95% CI 2.85–4.68), including in retired doctors. Barbiturates were the most frequent drugs used. Half of the anaesthetists who died used anaesthetic agents. Self‐cutting was also more frequently used as a method of suicide. The finding that the greater proportion of suicide deaths in doctors were by self‐poisoning may reflect the fact that doctors have ready access to drugs, and have knowledge of which drugs and doses are likely to cause death. The specific finding that a large proportion of suicides in anaesthetists involved anaesthetic agents supports this explanation. Availability of method may be a factor contributing to the relatively high suicide rate of doctors. This fact might influence clinical management of doctors who are known to be depressed or suicidal. - in Doctors who kill themselves: a study of the methods used for suicide
 So, what is the ultimate Goal for Organisms, Survival or Conformity?

There is a problem, Species don't make Conformity easy, there are all reasons not to conform and almost no reasons to do so, essentially because there is a single Optimum where all the rest is noise. At the same time Organism heritage from Species a cocktail of pseudo benign feelings pushing them to conformity that in case of failure immediately switch to pain.

Suicide when not a Species tool is a lesser evil. The problem of knowing the causes of suicide is the same as knowing the causes of Biologic Diseases, to many causes for a single consequence. So, is not what causes suicide but what avoids it. Like a Conformist Organism, everyone that is different at the eyes of the Species is a potential problem for it, and the causes of that difference may be infinite. In this way Organisms may be stressed to the point of committing suicide, and species being only concern about conformity have no problems with this side effect. Humans in special are very complex and consequently need to be very well tuned Organisms, and so, their lives must also be very well tuned to a kind of Standard Plot.

In great extent, is the divergence of this Plot that causes Suicide, as a Study shows, those who commit suicide already have a suicidal story, proving a divergence start from that Plot to a point of no return.
In a study published in the November issue of the Journal of Adolescent Health, researchers at the University of Washington surveyed 883 young adults ages 18 or 19 about previous suicide attempts and learned that 78 — close to 9% — had tried to commit suicide. - Study: 40% of Kids Who Attempt Suicide First Try in Elementary or Middle School
Also, suicide may be a species tool in the case when it directly serves its interests, and we may have Altruistic situations that surely go behind those that Dawkins talks about. This is true for Species as it is for Religions and Ideologies. Organisms, Believers and Militants are no more than the needed infrastructure for a given standard Protocol. This protocol may demand them to commit suicide, and compliance is what is expected.

From religious martyrs, to feverous fighters its what they believe that sands still, regardless any voluntarism! So, Species, Religions and Ideologies may promote Suicide given the right conditions, with the ultimate goal of their Self Preservation.


Not surprisingly, Shame is an extensively explored feeling when it comes to Suicide. Like in Sex, its sole propose is absolute conformity, and in this respect is much more powerful than fear has ever been.

One goal to have, is making better Ideologies supported by better technologies, to avoid unnecessary cruelty, recognizing that if conformity is the ultimate human purpose it should be achieved in the most agreeable way possible. Making so, we are creating a Plot which divergence is less likely.

Saturday, December 13, 2014

Overdominance: The Good, the Bad and the Untermensch


Overdominance also known as Heterozygote advantage, is a very good evidence of the concepts that I have been described. Those concepts are all together in the next picture.


As I have been writing, Species are the result of Natural Selection something like Diploid vs. Haploid Organisms, a result of millions of years of evolution, and that is why before Eukaryotes Species have never existed, because species are also the result of millions of years of evolution.

In this new scheme, Species are the repository of the organism blueprint, physical and psychological, so we may view the Species' Will like the Species' Organism.

Now the old Story, the Story of two Fathers and three Sons, those Fathers are Natural and Sexual Selection, the Sons are the Good, the Bad and the Untermensch! All but one are much loved by each one of their Fathers. They are treated in this manner:
  • the Good - Loved by Sexual Selection, he is in the Gene Pool from the beginning, he is the oldest one. Now and ever Sexual Selection has been taking care of him, is a relationship of profound love and absolute dedication that nothing can reach up;
  • the Bad - Supported by Natural Selection, he is the newcomer, an Intruder, he isn't flushed away by Sexual Selection because doesn't represent any real Entropy to be pushed away, and mainly, because Sexual Selection is permeable to Induction carry out by Natural Selection;
  • the Untermensch - The resulting waste of the Bad, its Entropy is unprompted by the Natural Selection and hated by Sexual Selection. Living in the cold with nothing to save him, is doomed to a path destined to him, a path that leads to persecution and eternal extinction, for ever and ever.
In a more techinal description, the Good is the Fixed Gene, the Bad the Recessive Gene and the Untermensch the Deleterious Gene.

Overdominance is the result of diploidity, a characteristic dominant in Eukaryotes organisms, so a modern trait in evolution, mainly concerning Sexual Selection. So simply explained, overdominance is the introduction of a new gene that has a better fitness than the existing one when paired with it (heterozygous), but is deleterious when paired with itself (homozygous). A good example is the case of Sickle-cell disease, the result of a gene that gives protection against Malaria when alone, but a disease when together. But this is just one example, there are many more examples of overdominance, of recessive genes that are diseases once paired with each together, and so never becoming fixed. The problem is that those examples are only the tip of the iceberg, as weel putted in the Fisher's geometric model, in the presence of extreme complexity, evolution has to happen in equally extremely small adjustments, this means that those more fitted genes need to start as a recessive genes, giving room to deleterious homozygous combinations. This reality has been proven in a study titled Heterozygote advantage as a natural consequence of adaptation in diploids, where is stated that:
The larger range of adaptive mutations available to diploids comes with a catch, however; many of these adaptive mutations display heterozygote advantage, and thus will not simply go to fixation.
We argue that adaptation-driven balanced polymorphisms can be an important source of consequential genetic variation. In particular, we believe that the balanced polymorphisms predicted by our model can be associated with human disease. Some of the common disease variants could be mutations that are maintained at high population frequencies because of strong heterozygote advantage, although they are very harmful as homozygotes.
This proves that is the health of the Species that matter, not of its Organisms, a dichotomy that many refuses to view! So, the view of the Good, the Bad and the Untermensch is exclusive to the Species Eyes, organisms have no opinion of their own, because there is only the Species' Will.

This Will permeates all human culture, because is important to maintain the health that really matters, and humans act like actors of a preexisting plot, where conformity to this plot is their only purpose, over the lie of Self Preservation that in reality is only applied to Species. As another study guesses very well:
When you see a difference between your own opinion and that of others, the brain experiences an error signal,” - See more at: http://www.dana.org/News/Details.aspx?id=43112#sthash.AoN8PWrn.dpuf
Vasily Klucharev was able to see the physiology of the Species Will, but the real question is always missing, If the Species Health is all it matters, why it would support organisms Free Will? Mainly when this Free Will could be contradictory to the Species Will!

In this will, the only that really exists, the Untermensch needs to be pursued, and you don't need to look further to see this persecution. Albinos, a result of overdominance, are being so, like the next article shows very well.
In the rural areas of Tanzania, men, women, and children with albinism--a lack of pigment that makes them appear glaringly white--are waging an extensive human rights campaign against communities who routinely attack them for their hair or body parts, used in potions to attract wealth and good luck. - http://www.breitbart.com/Big-Peace/2014/12/10/Tanzania-s-Albinos-Killed-Like-Animals-For-Body-Parts-Used-in-Money-Attracting-Potions

This kind of persecution is heavily associated with superstition, the root of any religion, and that is why that despite all efforts of science to end superstition, it prevails, because this superstition is no more than the excuse that species give to organisms act the way they are supposed to. If you think that this is an isolated case you are wrong. Superstition relates to all situations of difference or non conformity with the standard. Witchcraft accusations against children is just one way of persecution, another is traditional Folklore, like Trolls or the Changeling, where the theme of the swapped child is common among medieval literature and reflects concern over infants thought to be afflicted with unexplained diseases, disorders, or developmental disabilities.

This folklore is transported to our days, in movies or pop icons, like one Troll of Rage Comic characters, were the Forever Alone, not surprisingly, is the most popular.


This and the successful Lord of the Rings are cultural examples of the Species Will against the Untermensch, where individuals are right in clamming innocence due to the fact of having no will in this matter (or any other).


Like Shame in Sex, that I talked about in a post before, the Untermensch is also wrongly associated to ideologies in particularly with Nazism, not realizing that Nazism doesn't borrow only its symbols from ancient folklore, like the Swastika or the SS symbol, it also borrow all the feelings already existing then and that continue to exist now, feelings that you may well guess having one single source.

These feelings that exist to be interpreted and followed by humans, are the ones that glorify all individuals with high levels of conformity, being under the Species Wing gives you a special aura.


Unfortunately Species are very picky and ruthless against non conformity, it has successfully been managing its "guardians" against it. So, in the so called civilized world, and despite being very civilized, the species guardians do their work as they do in Africa. And is not difficult to have news of some of them, now named Bullies. Yes in bullying may be some friendly fire, but we shouldn't delude ourselves, bulling has a very well defined purpose that is not just about young fellows as Workplace Bullying also exists, like a study shows, the victims are well profiled:
Over the years, much attention has been devoted to understanding counterproductive work behavior (CWB) and its related concepts. Less is known, however, about whether certain employees find themselves more than others to be the targets of CWB. To examine this issue, we tested a model that positioned CWB receipt as a function of employees' personality (neuroticism, agreeableness), their appearance (physical attractiveness), and the negative emotions felt toward those employees by their coworkers. Two studies using multiple sources of data revealed that disagreeable and physically unattractive employees received more CWB from their coworkers, coworker negative emotion felt toward employees was associated with CWB receipt, and the relationship between employee agreeableness and CWB receipt was due, in part, to coworker negative emotion. - Beauty, Personality, and Affect as Antecedents of Counterproductive Work Behavior Receipt
To be clear and rest no doubts:
In addition to personality, we examined physical attractiveness, positing that attractive employees would be less likely to elicit negative emotion in their coworkers and receive CWB than unattractive employees. Theories of social acceptance stipulate that characteristics valued by society include both communal qualities such as kindness and warmth (i.e., agreeableness) and superficial qualities such as beauty (Anthony, Holmes, & Wood, 20007). Indeed, research on bullying among school-age children has revealed that victims of bullying are more likely to perceived as physically unattractive by their peers (e.g., Sweeting & West, 2001; see also Olweus, 1978). Thus, by including personality (neuroticism and agreeableness) and appearance (physical attractiveness), our model acknowledges that in predicting the receipt of CWB, it likely is “what's on the inside” and “what's on the outside” that counts. - Beauty, Personality, and Affect as Antecedents of Counterproductive Work Behavior Receipt
So, while things continue to be seen as flat, while we ignore the trinity of the Eukaryotic model, we will continue to make the same mistakes, and search for causes in the wrong place.

Saturday, August 23, 2014

Junk DNA or Junk DENIAL...?

DNA Genome is much bigger in Eukaryotes (Sexual) than Prokaryotes (Asexual), but wait, it's because Sexual Reproduction but not Sexual Selection, is due to their difference however they are equal, Species exist but they aren't Real, DNA explains everything but it's Junk... Confuse? It's meant to be!

Friday, August 22, 2014

There is no Nurture but Nature!

Human monozygotic twins and other genetically identical organisms are almost always strikingly similar in appearance, yet they are often discordant for important phenotypes including complex diseases. Such variation among organisms with virtually identical chromosomal DNA sequences has largely been attributed to the effects of environment. Environmental factors can have a strong effect on some phenotypes, but evidence from both animal and human experiments suggests that the impact of environment has been overstated and that our views on the causes of phenotypic differences in genetically identical organisms require revision. New theoretical and experimental opportunities arise if epigenetic factors are considered as part of the molecular control of phenotype. Epigenetic mechanisms may explain paradoxical findings in twin and inbred animal studies when phenotypic differences occur in the absence of observable environmental differences and also when environmental differences do not significantly increase the degree of phenotypic variation. - In Phenotypic differences in genetically identical organisms: the epigenetic perspective.

Entropy Law: Shit Happens!


Saturday, August 16, 2014

Why Shame on Sex!

Shame is a feeling that has an important role in sex. Its restricting effect is many times seeing as a product of humanity, not a natural thing, contrary to Sex. We see Shame being associated to Religion, Social Morals, Ideologies and Conservatism, what we never see, is Shame being associated to Sex! So, we will show that Shame on Sex it's much older than a few centuries, it has many millions years of existence in this world of Species.

As I already shown in many of my posts, Eukaryote form of life (Three Layers), in with we belong, is different from Prokaryote one (Two Layers). Also, the true place of Species are essential to understand the role of Sexuality.

 
So, Sexual Selection (SS) that connects Organisms with Species, only existent in Eukaryotes, has in it two important feelings, Attraction and Shame. Attraction is a positive feeling, and Shame a negative one. In this dichotomy, attraction between organisms behave like planets formation, trough a process called Accretion!

We may use the planets formation analogy in the following way:

 
In this analogy we have Big (B) and Small (s) planets, where by the Newton's law of universal gravitation, the bigger the planets bigger is the attraction between them! So, if instead Big Planets we think in attractive organisms, we understand the logic how Sexual Selection allows the promotion of better organism in the Gene Pool. However, contrary to Planets, for Species size isn't all! For Species quality matters, because it's what defines it... In this way, Small planets shouldn't be attracted, but instead repulsed, in this way a negative feeling must be introduced. However, this feeling should be implemented in a way that doesn't interrupt the Attraction that matters to Species.

So, here we explain how each interaction must work for those two feelings:
  • Attraction:
    • Big to Big (B-B): Strong attraction due to two big Objects (Two Ways);
    • Big to Small (B-S): Medium attraction due to only one big Object (One Way);
    • Small to Small (S-S): Small or none attraction due to very low mass involved (No Way).
  • Shame:
    • Medium repulsion between any Object due to Embarrassment.

Between this two feelings there is an Equilibrium, that equilibrium works on Shame trough Natural Selection (Evolution) in a way that only Organisms with too much Entropy are wasted. One thing that is important to acknowledge is that in essence all organisms are in some degree handicapped, and the level of deficiency is strongly correlated to attractiveness, or beauty in a negative way. This is easily viewed, for instead in optics where little marge exists for error, and in some countries of Asia you have up to 80% of people with Myopia! Susan Boyle, in the Picture, suffers from Asperger syndrome proving that the prettiest is the cleanest in terms of biological Entropy. Entropy is so present, that many persons considered perfect, turn out not to be, like the well known Ricky Martin or Wentworth Miller, showing us that nothing is safe from Entropy, including sexual orientation (Not surprisingly, Species' Shame is particularly acute in this cases)! You can see more in my older posts how Consanguinity and other issues are interconnected to Sex!

However, because Shame is always present, despite Sexual dimorphism, it requires that even in the cases of Strong Attraction things had to be done in the dark to avoid Embarrassment, also with the extra advantage to species that no feeling of injustice becomes too vivid at the point that excluded Organisms don't play as expected... For Species, making Sex its own business trough Shame enforces that Organism are more operational, being worried only with terrain matters, like food and shelter, something that by itself is a good reason for Species to adopt Shame in its reproduction Scheme!

Attraction and Shame are not exclusive to Humans, despite some illuminated people that glorifies the notion that "only Humans feel", Attraction and Shame are felt in any other Animal and they worked exactly the same way with exactly the same purpose, serve its Species.


We Humans have one advantage relatively to other animals, we can solve problems inherited from nature, and instead of  bury our head in the sand, saying everything is natural, everything is cool, we may admit that a more controlled process of human reproduction is needed, acknowledge for instance that biological differences are in essence an unjust form of exclusion and not something everyone has to live with just because is something "natural" or "romantic"... More than marketing and cheap propaganda, we need to address the truth and take in our hands the reproduction mechanism, where In Vitro Fertility is a possible solution, with a increasing more efficient mechanism of diagnostic when it comes to Birth Defects! We must give to the Species what it wants and in this way put it aside from our way!

More can be done, but nothing will be if we let romantics and their ethics dominate our life with their meaningless words that are nothing more than lies serving only the Species. So, no, it's not Islam or Christianity that represses Sex and promotes Shame, is not even Communism or Fascism, is Sex itself in its Protocol implemented by their Species, where words like "Pretty" and "Ugly" are part of it!

 
But for a broader view of Shame in the Species Protocol, we may define it like:
Shame exists to ensure the conformity to the implemented If and Only If Mating Ritual (Species Protocol), while repressing everything else!
Again, Mating Rituals have nothing of romantic, they exist to serve the Species healthy, were those organisms that for some reason aren't able to play the If and Only If game are kept away due to no disrespect allowed... Disrespect to the Species Protocol of course!
 
In some way moralism is an extension of this Protocol, where its purpose is to say this is the right way, everything else is a Shame, its immoral! And the main source of moral is no more than the actions that least shock the population, their feelings, that in reality aren't their feelings, because being ubiquitous they prove to become from only one place, Species! So this is why Shame on Sex is always present in any moral philosophy, no matter if Religious or Political, because Species aren't possible to be corrupted!
 
 

Wednesday, May 23, 2012

EVOLUTION #4 - CONFUCIUS, ONE PICTURE IS WORTH TEN THOUSAND WORDS

And yet some still asking...!

EVOLUTION #3 - GALILEI, AND YET IT MOVES

Galileo Galilei now seen as a revolutionary figure from the scientific point of view, it was in its time, a blasphemous that dare to say the most ridiculous thing, that earth was not in the center, but the sun instead. Nowadays, the Red Queen paradigm is the same as that centuries ago, where clamming diversity as the reason of Sexual Selection, is the same as it was, that earth doesn't move, and yet it moves!

In a not so much recent study, Synchronous Aggregate Growth in an Abundant New Ediacaran Tubular Organism, Mary L. Droser and James G. Gehling, argues to have identified the Tubes of Funisia dorothea as the first evidence of sexual reproduction. As it's put it next:
"A recent discovery made international headlines when published in Science in March 2008, announcing the discovery of the origin of sex. The paper, by Mary Droser and Jim Gehling, described a new kind of organism from the Ediacara site, which they named Funisia. Funisia was a worm-like tubular organism, the fossils of which are found abundantly at the Ediacara sites, so much so that different stages of its growth can be studied and measured in detail.

Droser and Gehling identified that these organisms were budding off ‘sprats’, or juveniles from the adults, which were all at a similar growth stage. Hence instead of shedding or budding asexually (shedding identical clones of itself), as expected for primitive organisms of this period, it is likely that the ‘sprats’ developed all at the same time due to an act that began them all: sex.

Put simply, if they were budding asexually then a wider range of sizes would be expected in the juveniles. The fact that they were always at the same size suggested an act that was timed, a mutual shedding of sperm and eggs into the water, such as occurs for corals.
" - From Cosmos

 In the Abstract of the previously referred article, it's written:
"The most abundant taxon of the Neoproterozoic soft-bodied biota near Ediacara, South Australia, occurs as clusters of similarly sized individuals, which suggests synchronous aggregate growth by spatfall. Tubes of Funisia dorothea gen. et sp. nov. were anchored within the shallow, sandy sea bed and lived in dense, typically monospecific concentrations. Tubes were composed of modular, serially repeating elements. Individuals grew by adding serial elements to the tubular body and by branching of tubes. Their construction and close-packed association imply likely affinity within the Porifera or Cnidaria. These data suggest that several of the most successful marine invertebrate ecological strategies known today were in place in Earth's oldest known metazoan ecosystems before the advent of skeletonization and widespread predation." - From Synchronous Aggregate Growth in an Abundant New Ediacaran Tubular Organism

Well, it's obvious that all this synchronous is argued as the timing, and not as the form, of Sexual Reproduction. As it's said, you simple have groups of organisms that started their growth at the same time (same size individuals). However, all the Similarity, the Clustering, and the Synchronous nature of Sexual Reproduction should ring a simple idea, that this Clustering is the true Origin of Species. And yet it clusters!


BBC - David Attenborough's First Life - See 46:16.

Sunday, January 15, 2012

EVOLUTION #2 - MENDEL, THE WHYS GUY

In this post I will materialize the importance of the Abstraction’s Environmental Process referred in the previous post. One of the ways this process become a reality is trough the chromosomal Crossing Over, as part of the Meiosis event.

In 1866, Mendel published his now famous paper entitled Experiments in Plant Hybridisation. In this time, evolutionists were attached to the blending kind of hereditary. This blending paradigm is one of the main reasons to the continuous view of evolution. Mendel, and his laws, brings a discrete and independent view of hereditary. However, in the same way only in 1900 his work was really appreciated (more than 30 years later), nowadays; the continuous view of evolution hasn’t yet been substituted by the discrete one. There are always people that simple don’t get it, and get stuck in details, in the following writing, details like not fully independent, or exotic disputes about other details, don’t change the point taken.

The Mendel laws are the base of the Hardy–Weinberg equilibrium, and because of that, this equilibrium, are only applicable to Eukaryotes and not to Prokaryotes. Now, what do you call, to the idea that all life is equally evolving, in a continuous and unstopping way like in Prokaryotes, and then, your examples are invariably involving Eukaryotes? You call it a delusion. Now, what it happens, when you ask to a deluded, if; are we still Evolving? If for the deluded, evolution is an unstoppable continuous process; he has the problem in conciliating the evolutionary force with his unstoppable and continuous concept. This difficulty makes the deluded a treasure hunter, where the treasure is the motive of the Natural Selection bias. If evolution has to be, the motive has to be found. As if it were not enough, you have the sticking species, and the respective speciation process undermining the continuous view of evolution. Now the delusion becomes denial, the denial of species’ existence, transformed in nothing more than a classification.

There is a question that until now hasn’t been well answered. What is the inbreeding effect on the genome quality? Charles Darwin was very concern with this issue, because he rightly suspected, that he and his family was victim of it. In a study entitled Was the Darwin/Wedgwood Dynasty Adversely Affected by Consanguinity?, by Tim M Berra, Gonzalo Alvarez, Francisco C Ceballos, it’s concluded that:
“(...) the high childhood mortality experienced by the Darwin progeny (...) might be a result of increased homozygosity of deleterious recessive alleles produced by the consanguineous marriages within the Darwin/Wedgwood dynasty.”

The experienced mortality wasn’t due exclusively to contagious diseases as many try to prove, but also to pure congenital ones, like the case of the last sun of Charles Darwin named Charles Waring. Many still see this as lack of diversity, as a mean to response to fast genetic change in infectious diseases. The name of this view was coined the Red Queen’s hypothesis.

Here I will give other explanation for the importance of Crossing Over, and show you that the so called arms races has nothing to do with it.

First of all, we will consider the two laws of Mendel. Those laws are:
  1. Law of Segregation – every individual possesses a pair of alleles (assuming diploidy) for any particular trait and that each parent passes a randomly selected copy (allele) of only one of these to its offspring;
  2. Law of Independent Assortment – separate genes for separate traits are passed independently of one another from parents to offspring.
Another thing to have in mind in the next simulations is that we will only consider the crossing over process in meiosis, and consequently; we will always consider haploid genomes for the sake of simplicity.

To help us to see what happens, we will construct an analogy with a picture made by pixels. In the next picture we have our Little Joe. We will consider the genes as the colors in each pixel of his picture. In this way, our analogy has the following meanings:


Original Picture of Little Joe

From the previous full picture we may zoom in to visualize each pixel.


Zoom of the original picture

Next we have the generation tree for the simulation:


Stacking tree per generation

For the first simulation, we approach the merging view of the 19th century for heritably (continuous process), staring with the creation of 16 pictures resulted from the insertion of random noise, each one with the same parameters, in the original picture (Genome) for the 1/16 generation. The first obtained picture, similar in noise to the other 15, looks like this (first arrow):


Sample 1 of 16 from the generation 1/16

For the 1/8 generation, and following the generation tree, we will evenly stack each picture of the 1/16 generation by a methodology similar to focus stacking, resulting 8 pictures with reduced noise. The first obtained picture, similar in noise to the other 7, looks like this (first one of the 1/8 generation):


Sample 1 of 8 from the generation 1/8

Repeating the process for the generation 1/4, the obtained picture, similar in noise to the other 3, looks like this (first one of the 1/4 generation):


Sample 1 of 4 from the generation 1/4

Repeating the process for the generation 1/2, the obtained picture, similar in noise to the other one, looks like this (first one of the 1/2 generation):


Sample 1 of 2 from the generation 1/2

Finally, we get a single picture for the 1/1 generation, with extremely reduced noise comparably with the one on the 1/16 generation.


Final sample from the generation 1/1

In conclusion for this first simulation, the merging process clearly has the ability to reduce noise, however, this ability tend to lose strength for each new generation. This has to do with the merging nature itself. While merging we are making averages, and as many averages we make, we never get the real color of the original picture despite the approximation to with. The maximum that the merging process can provide is an Asymptote to the original color.


Animation from generation 1/16 throughout 1/1

Now we will take a different approach. We will take for granted the species. Species in the next simulation will be represented by the original picture of the Little Joe. Species, a product of Sexual Selection, is seen here as a target of systematic bombardment made by noise. In this way, our analogy has the following added meanings:
  • Original picture – Species;
  • Mask – Threshold between positive and negative allele’s feedback;
  • Mask’s white pixel – Fixed allele;
  • Mask’s black pixel – No fixed allele.

In this simulation we drop de continuous view of the noise, and adopt a Yes or No kind one. In this way, we create a Mask for the picture where is marked if there is or isn’t noise (no fixed allele). For this mask, we use the color white for the pixel without noise, and black for the pixel with noise.

Using the first 16 pictures of the previous simulation, we produce for each one of them, the white and black mask. This mask, and the resultant picture, similar to the other 15, looks like this (first arrow):


Mask sample 1 of 16 from the generation 1/16

As you can see, this mask doesn’t represent a uniform distribution of random noise; however, because it still represents a random situation it makes no difference for this simulation.

You immediately note an important difference, now, due to this discrete approach, the noise looks like sand in a surface, it almost seems like something you may literally clean instead of dimming it.

For the staking process, we consider the product of the Mask’s pixels, so, the white pixel represents 0 and the black one 1. For each pixel we have the following stacking results:

Bellow we will review the mixed staking in more detail, for now we just accept things as they are.
Applying the stacking process, the first obtained Mask, and the resultant picture, similar in noise to the other 7, look like this (first one of the 1/8 generation):


Mask sample 1 of 8 from the generation 1/8

Repeating the process for the generation 1/4, the obtained Mask, and the resultant picture, similar in noise to the other 3, look like this (first one of the 1/4 generation):


Mask sample 1 of 4 from the generation 1/4

Repeating the process for the generation 1/2, the obtained Mask, and the resultant picture, similar in noise to the other one, look like this (first one of the 1/2 generation):


Mask sample 1 of 2 from the generation 1/2

Finally, we get a single Mask and the resultant picture for the 1/1 generation, with practically no noise comparably with the one on the 1/16 generation.


Final mask sample from the generation 1/1

Unlike the merging simulation, here there is no continuity restriction, and so, convergence can be total without any kind of Asymptote, and more importantly, there is no losing strength in reducing noise.


Animation from generation 1/16 throughout 1/1

As told before, we considered the result of a mixed stack, Heterozygous, as always White (0). You may think that it is an over simplification, however is not far from reality.

Firstly, while a no fixed allele will frequently encounter a mixed stacking (Heterozygous), a fixed allele, on the contrary, it will frequently encounter an equal allele (Homozygous), so, in terms of chances and accordingly with the first law of Mendel, a no fixed allele sees his probabilities of being carried on reduced by 1/2 per generation (Exponential decay), while the fixed one, only sporadically gets in that situation.

In top of the exponential decreasing probability, we have the Natural and Sexual Selection, each one with the following three kinds of feedback:
  1. Positive Feedback – Increases offspring relatively to the average;
  2. Neutral Feedback – Maintains offspring relatively to the average;
  3. Negative Feedback – Decreases offspring relatively to the average.
Both Negative Feedbacks, for Natural or Sexual Selection, are the last hope killers for the “lucky” noise, which one, albeit the odds managed to remain in the genome, sees its diminished odds become even more reduced next to nothing.

In conclusion, the exponential decay of the probability of fixation for a no fixed allele, associated with the negative feedbacks of Natural and Sexual Selection, is a good base to consider that the result of the crossing over between a fixed and no fixed allele is the fixed one, mainly if the no fixed one has no evolutionary advantages (noise).

However, knowing that we are considering haploid genomes, we should not view these values as exact ones. For instance, for a new allele get fixed in a population without any inbreeding, the positive feedback of Natural Evolution had to be such, to the point of canceling the Exponential decay previously referred. In this way, that positive feedback would need to produce more than 2 times the average offspring per generation, so that 2*1/2 becomes 1 (same as the fixed allele), and to compensate the initial negative feedback from Sexual Selection.

Now you may ask, but it’s not possible the existence of Positive Feedback from Sexual Selection for the newcomer allele? For the right answer, we need to realize that the positive feedback of Sexual Selection is in the direction of the existing genome that defines the species. As you saw in the last simulation, the mask is the result of the difference between the original picture and the one with the noise, and in this way, Sexual Selection is attached to a referential, something that doesn't happen with Natural Selection. So, if positive feedback for Sexual Selection is relative to an existing referential, only Natural Selection has the ability of giving Positive Feedback for newcomers.

Some of you are in this moment thinking about the peacock's tail, and making the question if that is not an excellent example of Positive Feedback of Sexual Selection for newcomers. Thirst of all, you have to have in mind that tails per se are common in birds, so tails have a Positive Feedback from Natural Selection. What we are discussing is the ornament not the tail, and the ornament may well be explained with correlation. So, if a trait, any trait, positively correlates with some other trait or traits, which have Positive Feedbacks, either from Natural or Sexual Selection, with time, and only through Natural Selection, that trait becomes a fixed trait. When it becomes a fixed trait, and only then, it may receive Positive Feedback from Sexual Selection, simply because it becomes part of the new existing referential (species). In this way, you may think in beautiful bird singing, vibrant feathers colors, and stunning flowers as exclusive products of Natural Selection.

Giving a step forward, we will approach in detail the issue of Consanguineous or Inbreeding reproduction. Since Adam and Eve times, inbreeding reproduction becomes an inevitably, however, we will not explore the Adam and Eve reality; but instead, we will try to understand what we mean by the inexistence of inbreeding, and then, its degree.

Without inbreeding, our heritage (past generations) would follow an exponential Power of Two, and after few generations, would become greater than the existent population. To visualize this reality we will use the demography evolution of Portugal expressed in the next picture.


Numeric simulation with Portuguese population

Using a generation length of 30 years, by the year of 1410 any Portuguese born after 2010 would be relative to all the Portuguese population previous to 1410! This young Portuguese would be a direct descendent of figures like the Henry the Navigator, or even his great father, John of Gaunt. In the next graphics is possible to visualize the interception point, where the population needed for a perfect non consanguineous reproduction meets the real one.


Graphical simulation with Interception point (1410)

Now that it’s clear that inbreeding is an inevitable reality, it’s time to understand its impact in the Crossing over process. More, the real question is not, what is the impact of inbreeding, but instead, what is the impact of inbreeding’s degree. For this degree we use the distance in generations. For example, in case of brothers we have 1 generation distance, in case of first cousins 2 generations, and so on. Using our generation tree, we may construct a table with the impact of consanguineous reproduction, and see the impact in terms of genetic sampling.


Generation tree considered in the simulations

In the last simulation a consanguineous reproduction can be seen as a branch removal. From the way the simulation was carry on, based on the product of the Mask’s pixels, is applicable the concept of Absorbing element, where the White (0) pixel is the Absorbing element. One of the properties associated with the Absorbing element, is that the operation order doesn’t maters, the result is the same, the absorbing element White (0). This means that the reduction of branches is equivalent to the reduction of samples. In the simulation there were 16 samples of masks, as you can see in the next picture, depending on the generation where we have inbreeding; there is a reduced new set of samples. For instance, in the case of an inbreeding in the 1/2 generation, half of the samples are removed from the equation, meaning that only 8 samples become stacked, the same effect as stopping the reproduction series in the 1/2 generation instead the 1/1.


Unremoved noise due to consanguinity

It is possible to see in the image above; that inbreeding in the generation 1/2 has an impact in the picture, maintaining some noise that otherwise would have been removed.

Other conclusion is possible to make, as you can see in the next picture, inbreeding loses its influence in an Exponential decay way as far from the 1/1 generation it occurs. For instance, a single consanguineous has an influence of 2/16 in the 1/8 generation, and an influence of 4/16 in the 1/4 generation, or in other words, the inverse of the possible number of no consanguineous mating for a given generation.


Impact of inbreeding’s degree

Consanguinity is not worldwide equally distributed, some countries, like India and Pakistan, have high rates of consanguinity. The “rat-people” is a crude example of a mal functioning cross over, something promoting fixation of alleles that otherwise would never become fixed.


Worldwide distribution of consanguineous marriages

It’s now possible to conclude that there isn’t any kind of arms race, what we have is deleterious mutations that became easily fixed due to redundant crossing over in the respective locus. These deleterious mutations, like many other symptoms, weaken the immune system to the point of being exploited by infectious diseases. They work in somehow like AIDS, making people much more likely to get infections, including opportunistic infections and tumors that do not affect people with full working immune systems.

There is another problem with the arms race of the Red Queen’s paradigm, that problem is called blood type. Blood types varies in worldwide distribution, with A blood more frequent in Europe, Australia and North America, B blood, more frequent in Asia, and O blood bore frequent in Latin America. If this is considered an arms race, you have to consider races also the result of an arms race, because the distribution of blood type isn’t very different from other racial traits, neither in time or space. In that sense, the black skin of an African person would have to be seen as an arms race against the sun. The problem is that, like in races, there aren’t significant variances in time and space to attribute to other reasons than Natural Selection. However, this arms race is still argued as the reason for Sexual Selection, something essentially different from Natural Selection.

If blood type is no more than a polymorphism, like skin color, and if blood types play an important role in the protection from infectious diseases, there is little credit to be given to Arms Race or any other thing but the old and simple Natural Selection. What you really have in constantly change that crossing over works against it, is not any kind of virus, or bacteria, it’s instead, the old and simple noise. This noise, the product of Dissipation, root of all environmental processes, undermines the complexity in life and the possibility of greater genomes. Crossing over, and the consequent Speciation, is the working solution that no Eukaryote was ever able to be truly free of.


Dependence stacking of environmental processes

So, what crossing over really is? Crossing over is the instrument of the Environmental Abstraction process. This abstraction becomes the new entity subject to evolution. With abstraction, organisms were drained of protagonism, given to the new concept of Species and its Sexual Selection mechanism. This way, species become the real subject of Natural Selection and the consequent Evolution, or simple putted, Strains gave place to Species.

If materialization was needed, you just need to remember the heritage’s Power of Two exponential process. This form of heritage, only possible with crossing over, works like a stairs that connects species with individuals; turning them, not into children of parents, but into children of species. So, for the question, what makes us human? We may simple answer, the Species does.


Stairs connecting species with individuals

In conclusion, there are those who ask how, and those who ask why, Mendel, was one of the last kind. I will end this post with a simple sentence to bear in mind.

“The HOW represses, the WHY frees.”


Prokaryotes vs. Eukaryotes, NS - Natural Selection, SS - Sexual Selection

Sunday, January 8, 2012

EVOLUTION #1 - DARWIN, THE PRIEST OF THE PRIESTS

In this post, I will try to give a new look about life, as a mere result of environmental processes, and not, as a cause of those processes that make life a glorious and almost religious thing.
 
There is one thing that many of the Evolution Priests do forget. That thing is that Evolution is just one process like many others. But because there is a need of Evolution Dissemination, processes like Selection, Mutation and Speciation are wrapped inside the Evolution process. It is possible Evolution without Mutation? No, obviously not. However, you don’t see any one spreading the word Mutation like Evolution (click for 10-fold Google results). So, we end up with the ridiculous thoughts, that Selection makes Evolution, that Mutation is part of Evolution, that Speciation is just a classification, and, consequently, that Migration is no more than a mere curiosity, without a real relationship to Speciation.

Darwin suggested as the perfect spot for the source of life, a warm little pond. Until now, many Evolutionary Priests suggested the miraculous spark for life origin. However, in a landmark discovery, chemist John Sutherland has created the conditions in which the building blocks of RNA, one of the key molecules of life and the probable precursor to DNA, assemble themselves naturally. The problem until now relates to the view of a spontaneous life generation from the ideal environment conditions, like a prebiotic soup of chemicals. If you think a little, this has to do with the view of evolution, that evolution is a product of life, and in this way, you are unable to view evolution previous to life, you are unable to see evolution as a natural process predicted by environment and completely independent of life.

The solution became simple if you get rid of the life restriction, and realize that the complex molecules necessary to life became “cooked”, by important and intermediate steps resulting in new increased complex molecules, instead a single step from a group of ingredients. However, the Evolution Priests don’t predict Evolution outside the biological world, at least in a serious way.


Revealing the Origins of Life (Jul 08, 2011)

There is another reason for this kind of Evolutionary culture. The English culture is made of sounding figures, figures that give extreme force to the Anglo Saxon view of the world. There are three particular figures that any one recognizes. Those figures are:

  1. William Shakespeare;
  2. Charles Darwin;
  3. Isaac Newton.

Albeit they being old in history, we still regard them as contemporary. It’s frequently the references to William Shakespeare in movies and other media. Charles Darwin is referred as a “know all” about evolution, and the fader of all answers in biologic world, at least in conceptual terms. And last but not least, Isaac Newton gave origin to the Apple marketing machine, the biggest Pop culture icon of our times. We may compare those with other similar figures, but with much less recognition. Those figures are:
  1. Miguel de Cervantes;
  2. August Weismann or Gregor Mendel;
  3. Gottfried Leibniz, Rudolf Clausius or Ludwig Boltzmann.
The English culture is like a species, which abstraction needs its eternal figures albeit their real significance, because the real important thing in a species is its survival, not the truth.
Now we will try to put some order in the extended expressions that are interpreted as the same, when in reality, aren’t. Using our English culture analogy, we may ask for the differences between the follow expressions:
  • England;
  • Great Britain;
  • United Kingdom;
  • Common Wealth.


The Difference between the United Kingdom, Great Britain and England Explained

For the majority, the previous expressions basically means the same, because is in the best interest of the English culture that, for instance, England means the same as Common Wealth, and so the ambiguity. Why? Because bigger is better.
The Evolution Priests are equally interested that other expressions became misunderstood with Evolution, and the common people interpret the following expressions has basically meaning the same:
  • Mutation;
  • Replication;
  • Selection;
  • Speciation;
  • Migration.
For instance, if Evolution is the product of Mutation, becomes hard to make Evolution the big deal, unless, Mutation is referred as an instrument of Evolution, and not as a distinct process.

Now we may try to interpret those processes in a distinct way, in an isolated way, and give to them a place like Evolution has. Recognizing that Environment Processes are external to life, we may figure out a layout for those Environment Processes. This layout is a rude expression of what may be, however it gives a good idea of how much it’s possible to realize thinking in distinct environmental processes.


Rude layout for Environmental Processes

Thinking in distinct environmental processes, may give you the answer for why life started only once. The Saturation process may have been triggered only shortly after the Replication one. Thinking in terms of processes you are able to make good analogies, like Internet, or Mobile Phones or even human languages. After the adoption of a particular protocol, the following Saturation makes impossible the appearance of a new one. It will be like a country enacting and replacing an official language.

To end this post, I will explain why the use of the expression Evolution Priests. To start with, I quote the Selfish Gene book of Richard Dawkins in the end of the Immortal coils chapter. He states:
It is good to get into the habit, whenever we are trying to explain the evolution of some characteristic, such as altruistic behavior, of asking ourselves simply: ‘what effect will this characteristic have on frequencies of genes in the gene pool?’” – Richard Dawkins.

Now, what is wrong with the previous quote?

In fact, nothing is.

Now, what is wrong with the next one?
It is good to get into the habit, whenever we are trying to explain the selection of some characteristic, such as altruistic behavior, of asking ourselves simply: ‘what effect will this characteristic have on frequencies of genes in the gene pool?’”

Equally nothing wrong!

We may rephrase with the words, mutation, replication, speciation, migration, and so on, that albeit a different meaning, still has nothing wrong with it.

My point is the following, surely Evolution makes part of genes and life, however, there are other processes equally important and distinct that genes depend on. And more important, in the universe of genes, not all of them have all the processes, for instance, not all life have speciation, because not all of them have greater genomes, because the speciation process has the simple effect on genes of increasing its quantity in the genome (complexity). However, for an Evolution Priest, everything becomes reduced to Evolution.

 
Genome effect of Environmental Processes