Cladistics: A new classification of living beings

Tree of life
https://evogeneao.s3.amazonaws.com/
images/content/es/tree-of-life_2000.png

In 1735, the Swedish naturalist Carl von Linné (Linnaeus) created the binomial system of biological nomenclature still in use today, and a classification system for living things that is becoming obsolete. This system used at first seven successive categories: kingdom, phylum, class, order, family, genus, and species. The last two categories are used to name the species. Thus, according to Linnaeus's classification, the human species belongs to the animal kingdom, the phylum Chordata, the class Mammalia, the order Primates, the family Hominidae, the genus Homo, and the species sapiens. Its scientific name, according to Linnaeus's binomial system, is therefore Homo sapiens.

The origin of eukaryotes

John Maynard Smith

As I have said several times in this blog, the theory of evolution is now well established. However, it is far from explaining everything. Many mysteries still remain. I listed some of them in a previous post. A book by J. Maynard Smith and E. Szathmáry, The Major Transitions in Evolution (Oxford University Press, 1995), describes them in more detail.

One of these problems refers to the changes of level that have taken place in the history of life, which I made the central idea of ​​my book The Fifth Level of Evolution. As its title implies, during evolution, things have not happened in an orderly or stable manner. At various points, there were changes of state (similar to those in physics) where evolution passed a critical point that made it possible to reach higher levels and opened up huge new fields in the configuration space. These points are the following:

Arguments against the theory of evolution

Drosophila melanogaster

Despite what I said in the last paragraph of my previous post, there are still well-intentioned people who oppose the theory of evolution (although this is very rare among biologists), and sometimes offer arguments to defend their way of thinking. I will consider some of those arguments here and offer my answers.

Answer: The claim that evolution has not been successfully reproduced artificially is mistaken. We have been doing this for thousands of years through artificial selection, which gave Darwin the idea of ​​natural selection. We have been doing it for decades in the laboratory in a controlled way, as this Wikipedia article explains: Experimental evolution. And this has been done not just with bacteria, which have a very short life cycle, but also with higher animals.

The theory of evolution, is it science?

In three previous posts (this was the latest), I wrote more or less the following words:

The scientific theory of evolution is strongly supported by data from other sciences, such as embryology, comparative anatomy, paleontology, biogeography, and molecular biology (DNA analysis).

Since, despite everything, there are still those who doubt the scientific nature of this theory, in this post I will expand on the previous paragraph, explaining in a little more detail the scientific data that favor evolution.

What is the theory of evolution?

Tree of Life

The theory of evolution, in its current form, asserts that the transformation of species (the evolution of life) depends on five factors:

1.      Spontaneous variations in the genome (mutations, genetic recombination, and other events that modify the genome).

2.      Spontaneous variations in the environment. This factor is often overlooked, as the environment is usually quite stable, although sudden changes sometimes occur that can have huge consequences.

3.      Inheritance, through which the variations that occur as a result of the first factor are passed on to offspring and are subject to the action of natural selection.

4.      Natural selection, which means that those individuals whose genome is best adapted to the environment will leave more offspring (at least statistically).

5.      The basic laws of the universe, which are currently represented by quantum theory and the theory of relativity.

Evolutionary convergence

Stephen Jay Gould

One of the most spectacular controversies to have arisen in biology at the end of the 20th century was that between two famous biologists: the American Stephen Jay Gould and the British Simon Conway Morris. The controversy began with the former's book, published in 1989, Wonderful Life: The Burgess Shale and the Nature of History, to which Conway Morris responded in 1997 with another book, The Crucible of Creation. As the subtitle of Gould's book indicates, both biologists based their work on the discoveries of the Cambrian fauna of the Burgess Shale (Canada), which I referred to in another post, and which was discovered and studied precisely by Conway Morris.

In his study, Stephen Jay Gould focuses in particular on the surprising and abrupt diversification that took place 550 million years ago and left its mark on the Burgess Shale fauna to argue that evolution is dominated by the effects of chance, so that, if we rewound the history of life and repeated the evolutionary process, the results would not resemble anything we have now. As a corollary, if there is animal life on other worlds, around other stars, it won’t resemble anything on Earth. And if there is intelligent life outside Earth, their physical appearance will not resemble ours.

Was Teilhard de Chardin persecuted for defending evolution?

Pierre Teilhard de Chardin

In a previous post I have mentioned some myths related to the persecution of scientists as a result of their scientific ideas, for religious reasons. I mentioned, for example, Giordano Bruno and Miguel Servet, wrongly presented as martyrs of science, when in reality they were persecuted for their religious ideas, not for their scientific activities, which in the case of Bruno were practically non-existent.

The presentation of a recently published video publicizes one of these myths, also widespread: the claim that Teilhard de Chardin was repressed by his Jesuit order for advocating evolution. That this is false can easily be deduced from the fact that Teilhard was able to publish dozens of articles on the evolution of the ancestors of man in scientific and philosophical journals of impact, without being prevented from doing so by his order. One of these journals was Études, edited by the Jesuits. A curious way of repressing him for advocating evolution.

Mistakes regarding natural selection

Charles Darwin

Since Charles Darwin coined this term, and included it in the title of his famous book, published in 1859, the term natural selection has been poorly understood, especially by non-specialists. Let’s review a few of the most frequent mistakes:

• Natural selection is a force that acts on living beings to cause evolution. This is not true. Natural selection is not a force, nor an object, nor an interaction, nor a phenomenon. It is simply a statistical observation. What is observed is the fact that, in general, individuals better adapted to their environment tend to leave more descendants than those less adapted. Nothing else. It is, therefore, a matter of common sense, not the result of the external action of a mysterious force.

Neuromania and Darwinitis

Raymond Tallis

Chapter 11 of the book The Naturalist Worldview of Moisés Pérez Marcos, which I discussed in the previous post, is dedicated entirely to the philosopher and neuroscientist Raymond Tallis, who despite his atheistic religious stance opposes some of the modern exaggerations of reductionist naturalism. Tallis published a book in 2011 titled, significantly, Aping Mankind: Neuromania, Darwinitis and the misrepresentation of humanity. This book describes two very widespread philosophical pathologies, which emerge from professional journals and educated colloquiums to discussions in the pub or TV screens. (Pérez Marcos, paraphrasing Tallis). They are the following:

Genes arising from nothing?

I have been asked me to clarify a recent piece of news that has hit the popular science press with headlines like the following:

New genes found that can arise from nothing. (Phys.org, 12/8/2023)

The tenacity of the media (and some scientists) to abuse the concept of nothing is unbelievable. They don’t know that nothing does not exist, and that nothing can arise from what does not exist. This is something that pre-Socratic Greek philosophers did know. (The first to assert this was Parmenides). Twenty-five centuries later, modern man, so proud of the advancement of science and technology, makes the same mistake once and again. In these posts I have often criticized the phrase, common today, that the universe arose spontaneously from nothing, which atheists often formulate to deny the creation and, therefore, the existence of God. This phrase does not belong to science (because current theories do not let us go back to the moment of the Big Bang). As philosophy, it’s just a flagrant proof of ignorance.

A new fine-tuning case and the “great design”

Almost every case of fine-tuning discussed so far concerns nuclear reactions and their consequences, in the realm of the very small. This is what could happen if the universal constants and parameters were not fine-tuned:

• Either there would be no hydrogen in the universe, and the stars would last too short a time for life to appear.
• Or the fusion of hydrogen to give helium would not be possible, so there would be no stars.
• Or oxygen or carbon, essential elements for life, would not be generated in stars.

In all these cases, concepts and ideas are drawn from particle physics, astronomy, and cosmology.

An Evolving Universe: PopulScience in Book Form

CEU Ediciones has published in book form, under the title Un universo en evolución (An evolving universe), a compilation of about a hundred posts published in this blog and its Spanish version, Divulciencia, over nine years, thematically arranged. Currently this book is only available in Spanish. These are the titles of the fifteen chapters:

1. Introduction (3 posts)
2. The beginning (5 posts)
3. The standard cosmological model (9 posts)
4. The fine-tuning problem and the theories of the multiverse (7 posts)
5. The problem of time (7 posts)
6. Life on Earth and on other worlds (3 posts)
7. The evolution of life (7 posts)
8. Man (5 posts)
9. Natural and artificial intelligence (7 posts)
10. Synthetic life and artificial life (3 posts)
11. The future of man (8 posts)
12. The end of man and of the universe (4 posts)
13. Science, faith, and atheism (14 posts)
14. About science in general (17 posts)
15. Conclusion (1 article)

Julio A. Gonzalo

The book starts by a presentation by Javier Pérez Castells, and a prologue by Julio A. Gonzalo. This is a paragraph from the presentation, which has been highlighted on the back cover of the book:

Manuel Alfonseca presents us in this book with a selection of posts from his blogs arranged by topic. The guiding thread is the story of creation. Beginning with the start of the universe (where he expands more, given his experience and knowledge on this subject), going through the origin of life and evolution, ending with anthropological conceptions of the human being. After that, he turns towards the supposed conflict between science and faith, grouping together a set of posts where he answers to this false tirade. Along the way, he stops to deal with the issue of artificial intelligence, the author’s favorite subject, and devotes a good number of chapters to an optimistical look at the future, albeit not forgetting that everything, together with the story of creation, will have an end. The book concludes with a few pertinent reflections on the limits of science, today considered by many as the only source of knowledge, in the exacerbation of what we call scientism.

Most of the posts (about one hundred) that have become part of the book have been previously published on the blogs Divulciencia and PopulScience, although a few are completely new, others have been built from several consecutive original posts or from those that dealt with the same topics, and the rest, those who have passed directly from the blogs to the book, have been updated.

The same post in Spanish

Thematic Thread on Anniversaries and Organization: Previous Next

Manuel Alfonseca

Biological evolution and cultural evolution in the history of life and man

The title of this post is the translation into English of a book of mine, published in 2017 by the publisher CEU Ediciones. As its name implies, the book is divided into three main parts, the first of which (the first four chapters) reviews the origin, evolution and history of life (biological evolution), while the second (chapters 5 and 6) focuses on the origin, evolution and history of man (cultural evolution). Finally, the third part (chapters 7 to 9) compares both types of evolution, emphasizing their similarities and differences; reviews the current situation of human evolution; and offers some ideas about the future.

As is often the case, this book did not come out of nowhere, but rather builds on previous works of mine. Especially in the first part, some of the titles of some chapters and subchapters may be familiar to the readers of my blog, because they are similar to some of my posts:

Chance and certainty

In a comment to the Spanish version of a previous post of mine, JL advised me to read the book entitled Chance and Certainty, by Georges Salet, who wrote it to prove that the origin of life and its subsequent evolution are impossible, if we apply the calculus of probabilities. In addition, he challenged me to refute at least one of the arguments proposed by the book, in the following words:

The work contains hundreds of arguments and demonstrations; if you, or anyone else whose help you ask, are able to refute a single argument or demonstration, I will readily admit that life can indeed arise spontaneously.

Salet's book is out of print and very hard to come by. I am grateful to another comment contributor, who provided me with the opportunity to read this book. I can therefore accept JL's challenge.

Intelligent design or random evolution?

Charles Darwin

As all scientific theories, the theory of evolution will always be provisional, but in a century and a half it has been quite well contrasted. It's not likely that a scientific revolution will declare it wrong or obsolete, although perhaps there will be fine tuning, as with Newton's physics and Einstein's theory of general relativity. An attack on the theory of evolution should be based on finding discrepant facts, which up to now have never appeared.

The problem is, some of those who defend the theory of evolution go one step further and offer philosophical speculations and dogmatic statements as though they were testable scientific theories.

As every scientific theory, the theory of evolution is a set of hypotheses that try to explain certain facts. It is based on the verification that species change, and studies the mechanisms that can lead to this change: mutations, DNA, natural selection... Added philosophical connotations are not scientific, whether it is affirmed, with believers, that there is intelligent design; or with atheists, that everything is a consequence of chance.

Atheism, theism and science

Today, the world’s population is divided between two competing, irreconcilable systems: atheism and theism. They are irreconcilable, because they start from opposite fundamental axioms (God does not exist and God exists). The approximate distribution of the population is this:

• About 10% convinced atheists, willing to defend their ideas.
• 10-20% convinced theists, who try to live according to their beliefs.
• 10% agnostics, who in theory don’t accept either of the two axioms, although in practice they tend to approach one of the two opposite poles.
• 60-70% indifferent, either because they don’t care about the debate; or because they live as if God does not exist, without considering whether He exists; or because they have beliefs, but don’t let them affect their way of life.

Ant colonies, real and virtual

Formica fusca

Ants, hymenoptera related to wasps, are social insects. An anthill or ant colony can contain, from a few dozen individuals, to over half a million. The number of castes varies, depending on the species, between three (fertile males and females, sterile female workers) and over twenty. The feeding a larva receives decides the caste to which it will belong.

Strange forms of parasitism have arisen among ants, as in Amazons ants (Polyergus), whose workers specialize in fighting and starve in the presence of food, unless a worker of Formica fusca feeds them. To seize these auxiliaries, the Amazons attack the nests of Formica fusca, kill their queen and enslave the workers. In extreme cases, such as ants of the Anergates genus, the queen invades a nest of Tetramorium, supplants its queen, and fed by the workers of the other species, produces eggs that become queens and males, but no workers, which are not needed.

Evolution in social insects probably reached the highest levels of instinctive complexity that can be achieved with a nervous system as limited as that of arthropods. In the tens of million years since the origin of these societies, evolution has introduced secondary changes, which have led to great diversity: there are more than three thousand species of ants, but there seems to have been no progress in their social structure. They are highly successful animals, very abundant, and spread throughout the world, but stagnant.

The Fifth Level of Evolution

The theory of evolution is well established by scientific evidence, but is far from explaining everything. Some puzzles remain pending whose resolution does not seem to be immediate:

• The origin of life. We do not know how, when and where it happened. There are many theories, but none has been proven and are very difficult to prove, because the origin of life, rather than a scientific fact, is a historical fact. It is not enough if we were able to reproduce it in the laboratory, it’s necessary to find documentary evidence that this is how it happened, not otherwise. It’s very likely that these tests cannot be found, because the paleontological traces of the origin of life have surely been lost.
• The mystery of the change in level. Throughout the history of life on Earth, living things have gone through several successive levels:

Interview with Manuel Alfonseca in a Spanish Newspaper

On February 23, 2018, a Spanish Newspaper (La Opinión, El Correo de Zamora) published this interview with me, performed by Ana Arias, which I am now translating into English. The interview was re-published a few days later (March 10) in the website ReligionEnLibertad (ReligionInFreedom). This is the translation of the interview:

He took an interest in science since he was quite small, as he says. At age 16 he wrote a book of zoology in two volumes that was never published. Anyway, whenever he has to consult information about some little known animal, he consults his book. "And I can find almost everything there," he adds. Now, at 71, he is an honorary professor at the Autonomous University of Madrid.

He believes in science. And also in God. Under the sponsorship of the Caja Rural Foundation and the Science-Religion University Forum held yesterday at the University College, Manuel Alfonseca gave a lecture about The Faith of Contemporary Atheist Scientists.

What is the faith of those scientists?

That God does not exist.

Evolution in the twenty-first century

A little over thirty years ago, during the eighties, some of the fundamental concepts of evolution seemed to be quite clear. Let us look at a few:

• The DNA of every living being is an encrypted message that perfectly describes how to build the corresponding phenotype (the adult individual). All the information is in the genes. (Mechanistic reductionism).
• Most DNA is unnecessary (junk DNA) and has been accumulated due to errors and repetitions in the transcription of the genomes of living beings.
• The best metaphor to represent the organization of a genome is a set of beads on a string.
• Genes are the repositories of inheritance, and each gene specifies a biological function.
• Evolutionary processes take place through random mutations that act on a single gene, which are subject to natural selection, which results in small incremental increases in the adaptation of living beings to the environment.