Saturday, November 6, 2010

The Truth about Species! - Part 4 (Entropic Nature)

This will be the last post of the series of 4. Today I will try to close this subject about species.

In the post about the Cambrian Mystery, there is a very important thing that was not talked about. Today I want to show that life has a real cancer, this cancer has its roots in the entropic physical world. Nowadays, entropy in evolution is a no man's land. Here the Classic Evolutionist has little to say, for him mutations take millions of years where the deleterious ones are minimized by Natural Selection.

What you don't see a Classic Evolutionist doing, is answer the following questions:
  • How can Natural Selection minimize frequent day by day deleterious mutations being a very slow process?
  • If de novo deleterious mutations are so frequent, why aren't called entropic mutations?
To have an idea of the amount of this deleterious mutations, we may refer the numbers from the CDC showing America's leading types of birth defects. Researchers looked at the U.S. rate of birth defects from 1999-2001.

Here's the list of the six major types of birth defects covered in the CDC's report, along with the number of babies per year born with those conditions:
  1. Genetic defects (Down syndrome and other conditions): 6,916 babies per year;
  2. Mouth/facial defects (cleft lip and/or cleft palate): 6,776 babies per year;
  3. Heart defects: 6,527 babies per year;
  4. Musculoskeletal defects (including arm/leg defects): 5,799 babies per year;
  5. Stomach/intestinal defects: 2,883 babies per year;
  6. Eye defects: 834 babies per year.
Birth defects are the leading cause of infant death and contribute substantially to long-term disability, the CDC reports.

As we can see in the following graphic, the incidence of this kind of diseases is more or less the same along time, something that make us suspect of its systematic character, something that strongly indicates limitations intrinsic to the reproduction system.

From CDC

And this isn't all. If doubts remain, we just have to point out the correlation between age and autosomal trisomy. The Relationship between Maternal Age and Chromosome Size in Autosomal Trisomy by N. Risch et al., proves that not only Trisomy 21 is exponential correlated with the maternal age, but also, many others trisomies.

Exponential incidence of Down Syndrome

In this case, not even Chernobyl can compete with age when it comes to cause birth defects.
"In terms of the sheer number of cases, genetic factors are the most important cause of congenital anomalies. It has been estimated that they cause approximately one third of all birth defects (see Fig. 19-1) and nearly 85% of anomalies with known causes. Any mechanism as complex as mitosis or meiosis may occasionally malfunction; thus, chromosomal aberrations are common and are present in 6% to 7% of zygotes. Many of these early embryos never undergo normal cleavage to become blastocysts. The changes may affect the sex chromosomes, the autosomes, or both (chromosomes other than sex chromosomes). In some instances, both kinds of chromosome are affected. Persons with chromosomal abnormalities usually have characteristic phenotypes, such as the physical characteristics of infants with Down syndrome. Numerical and structural changes occur in chromosome complements." - in Before We Are Born, Keith Moore and T. V. N. Persaud

Fig. 19-1: Aneuploidy - a deviation from the human diploid number of 46

Here the Classic Evolutionist supports Natural Selection exclusivity arguing that the severity of the previous anomalies have a serious effect on health, making impossible the achievement to the reproductive age, and so, minimizing this anomalies in the gene pool. However, they don't have nothing to say about the systematic character of this anomalies.

But even with the argument of the reproductive age we have problems, for instance, if we include the children up to 2-year-old, we have an increase of incidence of birth defects from 3% to 6%! And in the case of including the up to 5-year-old children we have 8% of incidence, due to the fact of some birth defects being only detectable at upper age. And more can be said:
"Congenital anomalies may be single or multiple and of major or minor clinical significance. Single minor anomalies are present in approximately 14% of neonates. Anomalies of the external ear, for example, are of no serious medical significance, but they indicate the possible presence of associated major anomalies. For example, the presence of a single umbilical artery alerts the clinician to the possible presence of cardiovascular and renal anomalies." - in Before We Are Born, Keith Moore and T. V. N. Persaud
Those minor anomalies doesn't necessarily diminishes the population at fertile age, making Natural Selection exclusivity a little bit limited.

Now that we start to realize that Entropic Nature aren't a far-fetched idea, we can see it as a barrier to the development of complex organisms as explained in the following graphic:

Per-site mutation rate versus genome size for CChMVd and other biological

"These primitive replicons would also resemble hammerhead viroids in their extremely error-prone replication. Thus, our results support the notion that the emergence of replication fidelity mechanisms was central to the evolution of complexity in the early history of life." - in Extremely High Mutation Rate of a Hammerhead Viroid by Selma Gago et al.
Complexity is an important issue, and so, it's unsurprisingly that human activities, like production, have to solve the same problems as those that from the beginning undermined life's complexity.

In the end of the 20st century, increased complex products, like chips, demanded a new and more strict kind of quality control. The old 3 Sigma became obsolete to this new increased complexity, and for those new extremely complex products, like mobile phones, computers, and other electronic devices, was drafted the new 6 Sigma, resulting in 3.4 defects per million items, something that makes nature blush of shame. Not so much? Yes, you are right!

We should not misunderstand life. Organisms are of an extremely and unimaginable complexity and incomparable with the most complex devices ever made. However, my point isn't about increased conformity, it's more about the need for a new form of reproduction, the Sexual Reproduction in life.

As told in The Truth about Species! - Part 1 (Why Sex) post, Sexual Selection is the mechanism of speciation. So, this mechanism has to guarantee the health of the specie.

Because the Classic Evolutionist lives obsessed with the sexual dimorphism, that in fact is no more than a curiosity, he became a passionate to the point of believing in this sexual dimorphism as a prerequisite for sexual selection. For me, sexual dimorphism is just a variable trait specific to the specie, so, you may have great dimorphism, middle dimorphism, low dimorphism and no dimorphism at all (see New Mexico whiptail in Why Sex), and yet, because they are all species, they are all sexual mating organisms (see Why Sex). Now I will exemplify how Sexual Selection blocks Replication Entropy accordingly to that same dimorphism in the next manner:

Sexual Reproduction same as Gaussian Product

Sexual Reproduction same as Gaussian Product, because attractive organisms are more likely to inbred between them, and consequently, produce more offspring. It's up to species to guarantee that organisms, albeit similar in traits, doesn't became able to reproduce if aren't conform to its will (sexual attractiveness).

For the special case of two Gaussian probability densities:

the product density has mean and variance given by:

Those two Gaussian curves represent the distribution of Sexual Attraction (relative to a protocol's blueprint) for each sex. Note that as told before, this is a kind of fitness at the species level, that has nothing to due with environmental fitness. This fitness is all about Sexual Selection (a priori) and nothing about Natural Selection (a posteriori).

For a Classic Evolutionist, Sex is all about diversity, and more diversity. So, it's hard to convince him of Sex as a mechanism of Speciation, as a mechanism of sameness, where inducted diversity is the only diversity, as explained in The Truth about Species! - Part 3 (Inductive Nature). But as we can see, Sexual Reproduction reduces variance, because the product of two Gaussian probability densities with variance less than 1 (high levels of replication fidelity), results in a new Gaussian probability function with a reduced variance, reinforcing the Species' Kernel.

Lower variance greater conformity (narrow bell shape)

In An Open Letter about Natural and Sexual Selection, there is a simulation of sexual reproduction as the product of two Gaussian probability densities, where it's concluded that the Mating Process is the most value compared to asexual reproduction.

Asexual vs. sexual reproduction in replication fidelity

If the problem is the expression entropy, we can call it noise, distortion, inefficiency, drift or any other name that essentially means the same, divergence of alignment.

Now we realize that induction is the main tool against entropy, and population number is the fuel of that induction. With low populations induction loses its strength, and the fitness of the organism can't be sexual selected accordingly to the now weakened fitness of the respective specie, because this species starts to act more as a singular organism than a group of them.

There is a miss-intuition that says that genetic homogeneity is the cause of genetic diseases (intrinsic to the organism). But if genetic diseases are distortions how can we say that there is a genetic homogeneity? In fact, it's the other way around. What we have is a distortion trough entropic mutations that become accumulated in the gene pool, and finally, because the mechanism of induction is weakened, those mutations start to being fixed trough genetic drift, and it's this fixation that indicates a greater vulnerability to intrinsic diseases that have never before been able to fixate.

For instance, the Cheetah species accumulated intrinsic genetic diseases, due to low population size able to induce otherwise, and so, it become divergent of its own otherwise normal specie, trough genetic drift and resultant genetic diseases.

Random genetic drift of a single given allele (Bigger the Population lesser the diversity)

By other words, we are assisting to a Population bottleneck, something that doesn't only supports the notion of Species' Kernel, but also the irreversibility of a species opposed to what it happens in the case of a polymorphism, just as supported in all the previous posts (see Inductive Nature).

To end this series of posts, I can add to the second post about the Cambrian Mystery, that the explosion may also happened mainly due to this entropic nature conquered by the new speciation skill, with induction as his essence.

An Open Letter about Natural and Sexual Selection by Rui Monteiro - 2010
The Relationship between Maternal Age and Chromosome Size in Autosomal Trisomy by N. Risch et al.
Before We Are Born, Keith Moore and T. V. N. Persaud
The Truth about Species! - Part 1 (Why Sex)
The Truth about Species! - Part 2 (Cambrian Mystery)
The Truth about Species! - Part 3 (Inductive Nature)

Monday, November 1, 2010

The Truth about Species! - Part 3 (Inductive Nature)

Today I will specify the terms I have been used before. One of the terms are Software. When I say that Sexual Selection it's more about Software than Hardware what I'm really saying?

For Software I mean what Faraday expresses about Matter and its Lines of Force, whose theory holds that all reality is made up of force itself. So, I will explore this Lines of Force to explain speciation.

In An Open Letter about Natural and Sexual Selection, we have a new scheme, that gives a new meaning to the word Species.

Scheme for the The Survival of the Fittest

Next we see stated the following about the The Survival of the Fittest:
"By analogy, it means the survival of the most adapted object to the environment. By induction, it means the survival of the most adapted protocol to the environment induced by its objects." - in An Open Letter about Natural and Sexual Selection
Looking to the scheme, we can see that speciation doesn't apply to Prokaryotes. There is a void in the line of species.

In the sentence that follows, we see speciation associated with induction, that supports a take off of a new layer, here called protocol. The organisms aren't considered in an isolated way, the fitness is now made collectively, it's the species the most fitted not the organism, supporting a strict differentiation between organism and specie.

Recognizing this layer of species as a reality, and not just as a mere classification, we are able to frame Sexual and Natural Selection per interfaces. So we have for each interface:
  • Concept/Protocol: Natural Selection;
  • Protocol/Object: Sexual Selection.

This view is fundamental for any step further in the explanation of evolution.

Now we will take the concept induction a little further. We will try to construct a good metaphor for this induction idea.

The Electromagnetic Induction is a good example of Induction, where a systematic variation of a magnetic field results in an inducted electric current.

We know that the most efficient way to induce an electric current it's trough a solenoid, or a coil if you prefer. This solenoid is made of loops or turns, where the Inductance (the induced electric voltage) is proportional to the square of the number of loops, and some how to the coil radius.

Solenoid as a group of loops

Now we will construct our metaphor. I stress the word metaphor, to rest no doubts about this reasoning.

In this metaphor we have:
  1. Magnetic field = Environmental Opportunity;
  2. Solenoid = Species;
  3. Loop = Organism;
  4. Induction = Selection;
  5. Loop Fitting = Sexual Fitting;
  6. Alignment (torque vector) = Environmental Fitting.
In this example we will think in a species of birds and two differing environmental opportunities (small seeds in patch A, large seeds in patch B). This two differing environmental opportunities can result in two polymorphisms or in two species through a speciation process. This environmental opportunities need to be two previously unexplored opportunities, or else, they aren't opportunities at all.

Thinking in the Solenoid metaphor we have the following two scenarios:

1. Polymorphism as a single bended solenoid (specie)

2. Speciation as two straight solenoids (species)

We may argue that there is a Ultimate Limit State beyond which the species breaks up. The line of force comes from the opportunity that resembles a strong magnetic field.

This disruption is well described in the following images:

Simulated speciation with the punctual population split - in On the Origin of Species by Natural and Sexual Selection

Simulated speciation with the punctual mutational process - in An Open Letter about Natural and Sexual Selection
"In this way, a polymorphism is reversible if, for any case, the associated opportunity ceases its effect. On the other hand, a speciation has its own kernel, ending the previous implication, that is, a speciation is not reversible if, for any case, the associated opportunity ceases its effect." - in An Open Letter about Natural and Sexual Selection
In the same article sited before it's stated the following:
"However, there is one thing that I think as a wrong presumption. The presumption that the migration rate leads the speciation, because is another example of bad intuition. In the Fig. 3 of your article, where you correlate migration rate with sigma, there is a clear symmetry. This symmetry reveals a correlation between sigma and migration rate, with the first causing the last! Being so, migration rate is the consequence, and not the cause." - in An Open Letter about Natural and Sexual Selection

Fig. 3. Effect of ecological parameters on the rate of speciation. - in On the Origin of Species by Natural and Sexual Selection

For the question, in which way it's Sexual Selection the mechanism of speciation? We may answer that Sex; Selects the Fitting of the Organism accordingly to the Fitting of the Specie, which in turn, Fits the Species to the Environmental Opportunity, or metaphorically saying, Inducts the Alignment of the Loop accordingly to the Alignment of the Solenoid, which in turn, Aligns the Solenoid to the Magnetic field. In other words, this opportunity is always expressed on Species, because there is always a significant population of Loops that retain its Fitting as Sexual Fitting.

By other words, Sexual Selection forces the integrity of the Species (Solenoid), not allowing any change by nothing else than an opportunity acting in an aggregated way, and it's exactly because of this aggregated way, that species, instead of polymorphisms, are reversible only by extinction.

So Sexual Selection isn't about diversity as many try to prove! Sexual Selection is about aggregated exploitation of existing opportunities. Sexual Selection doesn't support diversity by itself, Sexual Selection "accepts" aggregated diversity at the cost of an opportunistic exploitation.

For this aggregated diversity, we may even think in the premises of another kind of induction, the mathematical induction. Here we basically need two conditions:
  1. The basis: One chosen organism within one given aggregated diversity represents an opportunistic exploitation;
  2. The inductive step: An opportunistic exploitation by one organism within one given aggregated diversity, implies the same opportunistic exploitation by one other subsequent organism within the same aggregated diversity.
The previous conditions are needed to any specific diversity become dominant in an opportunistic niche.
"Mutation is the resource of information for any species, however, it has to be amplified by an Opportunistic Exploitation to be convergent at the Species level." - in An Open Letter about Natural and Sexual Selection
The speciation skill forces the integrity of the species with the respective kernel, so we should expect long periods of stability and short periods of fast change (speciation). In general, we may conclude:
  1. Prokaryotes - Phyletic gradualism;
  2. Eukaryotes - Punctuated equilibrium.
This is probably one of the main reasons why transitional fossils tend to be missing links.

To be continued...

References:An Open Letter about Natural and Sexual Selection by Rui Monteiro - 2010
On the Origin of Species by Natural and Sexual Selection by G. Sander van Doorn, Pim Edelaar, Franz J. Weissing - 2009
The Truth about Species! - Part 1 (Why Sex)
The Truth about Species! - Part 2 (Cambrian Mystery)