Missing the forest for the trees?

 

Phylogenetic Conflict Is Common and the “Hierarchy” Is Far from “Perfect”

Casey Luskin

As I discussed earlier, we were recently asked to comment on a video at FORA.tv. In the video, Richard Dawkins argues that the best way to refute “creationists” is to show them that genetic data forms “a perfectly hierarchy — a perfect family tree.” Let’s review again just how strongly he emphasizes this point in the video:

Compare the genes of any pair of animals you like — pair of animals, pair of plants — and then plot out the resemblances and they fall on a perfectly hierarchy — a perfect family tree.

It’s simply false for Dawkins to claim that when you compare genes of different animals, they “fall on a perfectly hierarchy — a perfect family tree.” The scientific literature is replete with conflicts among evolutionary trees, where phylogenetic analysis of different genes in the same group of plants, animals, or other organisms generate conflicting family trees. It also abounds with examples of where analyzing gene similarities in a group of organisms generates a tree that conflicts with the tree generated by analyzing similar anatomical characters in the same group of plants or animals in the fossil record. One paper in the journal Genome Research put it plainly, that “different proteins generate different phylogenetic tree[s].” 

Meyer Reviews the Literature

Stephen Meyer documents these sorts of papers and much more in Chapter 6 of Darwin’s Doubt, where he writes:

Just as the molecular data do not point unequivocally to a single date for the last common ancestor of all the Cambrian animals (the point of deep divergence), they do not point unequivocally to a single coherent tree depicting the evolution of animals in the Precambrian. Numerous papers have noted the prevalence of contradictory trees based on evidence from molecular genetics. A 2009 paper in Trends in Ecology and Evolution notes that “evolutionary trees from different genes often have conflicting branching patterns.” Likewise, a 2012 paper in Biological Reviews acknowledges that “phylogenetic conflict is common, and frequently the norm rather than the exception.” Echoing these views, a January 2009 cover story and review article in New Scientist observed that today the tree-of-life project “lies in tatters, torn to pieces by an onslaught of negative evidence.” As the article explains, “Many biologists now argue that the tree concept is obsolete and needs to be discarded,” because the evidence suggests that “the evolution of animals and plants isn’t exactly tree-like.”

The New Scientist article cited a study by Michael Syvanen, a biologist at the University of California at Davis, who studied the relationships among several phyla that first arose in the Cambrian. Syvanen’s study compared two thousand genes in six animals spanning phyla as diverse as chordates, echinoderms, arthropods, and nematodes. His analysis yielded no consistent tree-like pattern. As the New Scientist reported, “In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories.” Syvanen himself summarized the results in the bluntest of terms: “We’ve just annihilated the tree of life. It’s not a tree anymore, it’s a different topology [pattern of history] entirely. What would Darwin have made of that?” 

Other studies trying to clarify the evolutionary history and phylogenetic relationships of the animal phyla have encountered similar difficulties. Vanderbilt University molecular systematist Antonis Rokas is a leader among biologists using molecular data to study animal phylogenetic relationships. Nevertheless, he concedes that a century and a half after The Origin of Species, “a complete and accurate tree of life remains an elusive goal.” In 2005, during the course of an authoritative study he eventually co-published in Science, Rokas was confronted with this stark reality. The study had sought to determine the evolutionary history of the animal phyla by analyzing fifty genes across seventeen taxa. He hoped that a single dominant phylogenetic tree would emerge. Rokas and his team reported that “a 50- gene data matrix does not resolve relationships among most metazoan phyla” because it generated numerous conflicting phylogenies and historical signals. Their conclusion was candid: “Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.” 

In a paper published the following year, Rokas and University of Wisconsin at Madison biologist Sean B. Carroll went so far as to assert that “certain critical parts of the TOL [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” This problem applies specifically to the relationships of the animal phyla, where “[m]any recent studies have reported support for many alternative conflicting phylogenies.” Investigators studying the animal tree found that “a large fraction of single genes produce phylogenies of poor quality” such that in one case, a study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” Rokas and Carroll tried to explain the many contradictory trees by proposing that the animal phyla might have evolved too quickly for the genes to record some signal of phylogenetic relationships into the respective genomes. In their view, if the evolutionary process responsible for anatomical novelty works quickly enough, there would not be sufficient time for differences to accumulate in key molecular markers, in particular those used to infer evolutionary relationships in different animal phyla. Then, given enough time, whatever signal did exist might become lost. Thus, when groups of organisms branch rapidly and then evolve separately for long periods of time, this “can overwhelm the true historical signal” — leading to the inability to determine evolutionary relationships. 

DARWIN’S DOUBT, PP. 120-121

“Phylogenomic Conflict”

Such conflicts in the grand tree of life have continued to mount. Recently I participated in a journal club discussion of a 2021 paper in Proceedings of the National Academy of Sciences (PNAS) titled “Phylogenomic conflict coincides with rapid morphological innovation.” The paper explores the abrupt appearance of new types of organisms — or as they put it, “episodes of rapid phenotypic innovation that underlie the emergence of major lineages.” The paper observes that rapid appearance of new types of organisms often coincides with “conflicts” among trees based upon different types of genes:

One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. … Regions of high conflict often coincide with the emergence of major clades, such as mammals, angiosperms, and metazoa. … We demonstrate that instances of high gene-tree conflict (discordance in phylogenetic signal across genes) in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation.

Conflicts that Should Not Exist

It is precisely these types of “conflicts” among gene-based trees that Dawkins says aren’t supposed to exist in the “perfect” (Dawkins’s word) tree of life. The PNAS paper goes on to make the intriguing observation that researchers often ignore conflicts between these trees as noise in the data, when in reality these conflicts may be telling us something very important about life’s history:

Most large-scale phylogenetic and phylogenomic studies meant to resolve species relationships have treated gene-tree discordance as an analytical nuisance to be filtered or accommodated. However, since phylogenomic conflict often represents the imprint of past population genetic processes on the genome, studying its correlation with other macroevolutionary patterns may shed light on the microevolutionary processes underlying major transitions across the Tree of Life.

Researchers have long recognized that rates of morphological evolution vary across the Tree of Life, with pronounced bursts in morphological change interspersed with periods of relative stasis. … Phylogenomic conflict often appears to coincide with important episodes of morphological differentiation among major lineages. For example, the major differences in life history and body plan that distinguish mammalian orders emerged rapidly among ancestral taxa following the Cretaceous-Paleogene (K-Pg) mass extinction. … The early avian radiation has proved similarly challenging and is notable for the rapid establishment of phenotypically and ecologically disparate lineages. Several large-scale studies using massive genomic datasets have revealed extensive conflict among phylogenetic branches coinciding with the early radiation of crown Aves. Since the origin of land plants, there have been numerous major phases of morphological and ecological innovation, ranging from the initial appearance of vascular plant body plans in the late Silurian to distinct phases of angiosperm radiation from the Cretaceous to the present. As with the vertebrate lineages, the origins of many major plant clades show elevated levels of phylogenomic conflict… 

Eliminate Unreliable Data?

Similarly a 2016 paper in Molecular Phylogenetics and Evolution warns that many evolutionary systematists ignore phylogenetic conflicts, seeing them as a “nuisance,” rather than a signal that is telling us something important about biological origins:

Biologists should therefore be more aware that “phylogenetic incongruence [is] a signal, rather than a problem” (Nakhleh, 2013) and treat it accordingly. In the case of the tree shrew, and many other lineages in vertebrate phylogenetics, different algorithms may yield different trees because of the mosaic nature of the data (Kumar et al., 2013) and the inability of a bifurcating tree to explain the patterns.

In a presentation, my friend and colleague Paul Nelson recently quoted a chapter from a textbook, Molecular Systematics, which contains a section heading titled “Eliminate Unreliable Data,” justifying the practice because the authors reassure themselves “It is unrealistic to think that subjectivity in a molecular systematic study can be entirely avoided.” That seems like a most unreassuringly way to reassure oneself. The chapter goes on to say that “the benefits of excluding clearly unreliable regions” — i.e., genes which yield trees that don’t fit the standard hierarchy — “however subjectively determined—outweigh the dangers.” To summarize, what you’re seeing here are admissions that conflicts among evolutionary trees are common (admissions that themselves are actually quite common), coupled with rarer admissions that data is sometimes eliminated or ignored simply because it doesn’t fit the standard tree.

My Vantage as a Skeptic

Returning to the 2021 PNAS paper, it finds a correlation between periods of rapid innovation and the degree of conflict in gene-based trees. From my vantage point, as a skeptic of universal common ancestry, conflicts between genes that seem to have appeared during periods of morphological innovation indicate that common ancestry is not what generates new types of organisms. The paper, of course, does not question common ancestry. Instead it invokes various ad hoc explanations for the conflicts, attributing these conflicts to population processes such a “changes in population size, rapid speciation, and incomplete lineage sorting.” 

Regardless of whether universal common ancestry is right or wrong, the point here is that conflict in phylogenetic trees is very common, and the genetic data is far from producing a “perfect hierarchy,” as Dawkins put it. In fact, phylogenetic conflict seems to be greatest precisely in genes associated with the appearance of new types of organisms in the history of life. Dawkins got this point wrong, and he got it wrong precisely because this sort of conflicting phylogenetic data is not what a standard neo-Darwinian model would lead one to expect!

The 'Christian' right.

 The Christian right (known as the religious right in the United States) is the name for right-wing Christian political and social movements. They also exist in other countries, such as Canada. However, the term is most often used in the United States.^[1] These groups have a strong support of conservative social and political ideas. Usually, this comes from a belief that the United States was founded on a strong belief in God. It also come from a belief that American laws and policies should be based on what is in the Bible. Members of the Christian right can be from any branch of Christianity, including Catholicism. However, the religious right is most often used with Evangelical Christians, Fundamentalists (such as Born-agains) and Mormons. About 15% of Americans say they are part of the Christian or religious right.

People who have been conservative due to their religion have been in the United States for hundreds of years. For example, the people who put John Scopes on trial would later be called members of the religious right. However, the term first came into use in the 1970s. Jerry Falwell was one of the first people to use it. He and others felt that the country and its institutions (such as schools and colleges) were run by left-wing intellectuals who did not believe in God. They thought that in reality most people believed in God and did not care for left-wing intellectuals. The fight between left-wing intellectuals and the religious right is often called the "culture wars".

Presidents Ronald Reagan, George H. W. Bush and Donald Trump were elected in part due to support from the religious right.

As well as the Christian right, there is something called the Christian left. However, it is not as well-known or powerful.

The 'Christian' left: a brief history.

The Christian left is a range of center-left and left-wing Christian political and social movements that largely embrace social justice viewpoints and uphold a social gospel.

Given the inherent diversity in international political thought, the term Christian left can have different meanings and applications in different countries. While there is much overlap, the Christian left is distinct from liberal Christianity, meaning not all Christian leftists are liberal Christians and vice versa. Christian anarchism, Christian communism and Christian socialism are subsects of the socialist Christian left, although it also includes more moderate Christian left-liberal and social-democratic viewpoints.

Charles Darwin's magnum opus: a brief history.

 On the Origin of Species (or, more completely, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life), published on 24 November 1859, is a work of scientific literature by Charles Darwin that is considered to be the foundation of evolutionary biology. Darwin's book introduced the scientific theory that populations evolve over the course of generations through a process of natural selection. The book presented a body of evidence that the diversity of life arose by common descent through a branching pattern of evolution. Darwin included evidence that he had collected on the Beagle expedition in the 1830s and his subsequent findings from research, correspondence, and experimentation.

Various evolutionary ideas had already been proposed to explain new findings in biology. There was growing support for such ideas among dissident anatomists and the general public, but during the first half of the 19th century the English scientific establishment was closely tied to the Church of England, while science was part of natural theology. Ideas about the transmutation of species were controversial as they conflicted with the beliefs that species were unchanging parts of a designed hierarchy and that humans were unique, unrelated to other animals. The political and theological implications were intensely debated, but transmutation was not accepted by the scientific mainstream.

The book was written for non-specialist readers and attracted widespread interest upon its publication. As Darwin was an eminent scientist, his findings were taken seriously and the evidence he presented generated scientific, philosophical, and religious discussion. The debate over the book contributed to the campaign by T. H. Huxley and his fellow members of the X Club to secularise science by promoting scientific naturalism. Within two decades there was widespread scientific agreement that evolution, with a branching pattern of common descent, had occurred, but scientists were slow to give natural selection the significance that Darwin thought appropriate. During "the eclipse of Darwinism" from the 1880s to the 1930s, various other mechanisms of evolution were given more credit. With the development of the modern evolutionary synthesis in the 1930s and 1940s, Darwin's concept of evolutionary adaptation through natural selection became central to modern evolutionary theory, and it has now become the unifying concept of the life sciences.

The periodic table: a brief history.

•  The periodic table, also known as the periodic table of elements, is a tabular display of the chemical elements, which are arranged by atomic number, electron configuration, and recurring chemical properties. The structure of the table shows periodic trends. The seven rows of the table, called periods, generally have metals on the left and nonmetals on the right. The columns, called groups, contain elements with similar chemical behaviours. Six groups have accepted names as well as assigned numbers: for example, group 17 elements are the halogens; and group 18 are the noble gases. Also displayed are four simple rectangular areas or blocks associated with the filling of different atomic orbitals.
• 
  
• The elements from atomic numbers 1 (hydrogen) to 118 (oganesson) have all been discovered or synthesized, completing seven full rows of the periodic table. The first 94 elements, hydrogen to plutonium, all occur naturally, though some are found only in trace amounts and a few were discovered in nature only after having first been synthesized. Elements 95 to 118 have only been synthesized in laboratories, nuclear reactors, or nuclear explosions. The synthesis of elements having higher atomic numbers is currently being pursued: these elements would begin an eighth row, and theoretical work has been done to suggest possible candidates for this extension. Numerous synthetic radioisotopes of naturally occurring elements have also been produced in laboratories.
• 
  
• The organization of the periodic table can be used to derive relationships between the various element properties, and also to predict chemical properties and behaviours of undiscovered or newly synthesized elements. Russian chemist Dmitri Mendeleev published the first recognizable periodic table in 1869, developed mainly to illustrate periodic trends of the then-known elements. He also predicted some properties of unidentified elements that were expected to fill gaps within the table. Most of his forecasts soon proved to be correct, culminating with the discovery of gallium and germanium in 1875 and 1886 respectively, which corroborated his predictions. Mendeleev's idea has been slowly expanded and refined with the discovery or synthesis of further new elements and the development of new theoretical models to explain chemical behaviour. The modern periodic table now provides a useful framework for analyzing chemical reactions, and continues to be widely used in chemistry, nuclear physics and other sciences. Some discussion remains ongoing regarding the placement and categorisation of specific elements, the future extension and limits of the table, and whether there is an optimal form of the table.

The Mexican revolution: a brief history.

 The Mexican Revolution (Spanish: Revolución Mexicana, 1910–1920) was a major revolution that included a sequence of armed struggles that transformed Mexican culture and government. Although the regime of President Porfirio Díaz was increasingly unpopular after 31 years, there was no foreboding that a revolution was about to break out in 1910. The regime failed to find a controlled solution to the issue of presidential succession, resulting in a power struggle among competing elites, and elites and the middle classes that sometimes involved the "masses". This provided the opportunity in some places for agrarian insurrection. Although often studied as an event solely of Mexican history, "From the beginning to the end, foreign activities figured crucially in the Revolution's course, not simple antagonism from the U.S. government, but complicated Euro-American imperialist rivalries, extremely intricate during the first world war."

Díaz had initially said he would not run again for election, setting off a flurry of political activity, but he then reneged. Wealthy landowner Francisco I. Madero challenged Díaz in the 1910 presidential election, and gained considerable popular support, causing Díaz to jail him. Following rigged election that Díaz won, Madero called for a revolt 1910 in his October Plan of San Luis Potosí. Armed conflict broke out in earnest in November 1910 starting in northern Mexico, led by Madero, Pascual Orozco and Pancho Villa. These Maderista forces received support from portions of the middle class, the peasantry, and organized labor, enabling them to pursue a military campaign in the north, ending with Orozco's capture of Ciudad Juárez in May 1911. Díaz was forced out of office by the Treaty of Ciudad Juárez in which he resigned and went into exile, new elections were scheduled for the fall, and Francisco León de la Barra became the interim president. Madero's advisers Venustiano Carranza and Luis Cabrera warned against allowing the old regime to linger in power, since the revolutionaries had won the contest against the regime in armed combat. Madero ignored them and the elections took place in October 1911 in a free and fair vote. Madero overwhelmingly won the presidential contest and took office in November. He won a political victory, but did not make revolutionary changes.

Once in power (November 1911-February 1913), Madero's opposition rapidly grew, from old supporters of the Díaz regime, foreign governments and investors; revolutionaries who had brought about Díaz's ouster but whom Madero dismissed in favor of the Federal Army they had defeated; peasants who felt betrayed that Madero did not implement agrarian reform; urban workers who did not see Madero helping their interests. Peasants revolted, urban worker' strikes grew in number, and the press newly freed from Díaz's censorship chronicled Madero's failings. Madero kept his hold on power with the aid of the Federal Army, but in February 1913, the army in a conspiracy with political opponents to Madero and the support of the U.S. Ambassador, staged a successful coup d'etat. The Ten Tragic Days (Spanish: La Decena Trágica), Madero and Vice President Pino Suárez were forced to resign and were assassinated.

The counterrevolutionary regime of General Victoriano Huerta (February 1913-July 1914) came to power moved by his own interests, and other supporters of the old regime. Huerta remained in power until July 1914, when he was forced out by a coalition of different regional revolutionary forces under the leadership of wealthy land owner and civilian Governor of Coahuila, Venustiano Carranza, with the Constitutionalist Army led by two brilliant generals in the north, Álvaro Obregón and Pancho Villa. Peasant forces led by Emiliano Zapata had continuously opposed the regimes of Díaz, Madero, and Huerta, none of whom had been responsive to their demands for land reform. Although Huerta's Federal Army had more men than the revolutionary forces, the revolutionaries in northern Mexico were increasingly successful, particularly as the U.S. policy tilted toward them, allowing arms sales. Huerta resigned and went into exile in July 1914.

The winners met, attempting to reach political agreement about power. The Constitutionalist faction led by Carranza split, with Villa allying with Zapata and Obregón remaining loyal to Carranza. Mexico plunged into a civil war between the factions (1914–15). Carranza, with Obregón's military leadership, the support of the urban working class emerged as the victor in 1915. Obregón's army defeated Villa's in the Battle of Celaya in April, ending Villa as an effective opponent to the Constitutionalist. Zapata's armies were defeated as well, and they resumed guerrilla warfare in Morelos.

The sequence of armed conflicts saw an evolution of military technology from Villa's old style cavalry charges to Obregón's use of machine-gun nests protected by barbed wire. One major result of the revolution was the dissolution in 1914 of Mexico's Federal Army, which Madero had kept intact when elected in 1911 and Huerta had used to oust Madero. Although the conflict was primarily a civil war, foreign powers, which had important economic and strategic interests in Mexico, figured in the outcome of Mexico's power struggles. The United States played an especially significant role. The losses amongst Mexico's population of 15 million were high, but numerical estimates vary a great deal. Perhaps 1.5 million people died, and nearly 200,000 refugees fled abroad, especially to the United States.

The constitutional convention was called in late 1916. One historian calls it "the most important single event in the history of the Revolution." The promulgation of the Mexican Constitution of 1917 (Spanish: Constitución de 1917) set new nationalist, social, and economic goals for Mexico, curtailed the power of some foreign interests, and enhanced the power of the central state. "Economic and social conditions improved in accordance with revolutionary policies, so that the new society took shape within a framework of official revolutionary institutions," with the constitution providing that framework. Capitalism was retained and bourgeois reform enacted, not dissimilar to what happened in Peru, Chile and Argentina without civil war.

The death toll and displacement of population due to the Revolution is difficult to calculate. and the economic damage it caused lasted for years. All the major leaders of the Revolution were later assassinated (Madero in 1913, Zapata in 1919, Carranza in 1920, Villa in 1923, and Obregón in 1928). The nation would not regain the level of development reached in 1910 for another twenty years.

The period 1920–40 is generally considered to be one of revolutionary consolidation, with the leaders seeking to return Mexico to the level of development it had reached in 1910, but under new parameters of state control. Authoritarian tendencies rather than Liberal democratic principles characterized the period, with generals of the revolution holding the presidency and designating their successors. In the late 1920s, anticlerical provisions of the 1917 Constitution were stringently enforced, leading to a major grassroots uprising against the government, the bloody Cristero War.

There is a vast historiography on the Mexican Revolution, with many different interpretations, and over time it has become more fragmented. There is consensus as to when the revolution began, that is in 1910, but there is no consensus when it ended. The Constitutionalists defeated their major rivals and called the constitutional convention that drafted the 1917 Constitution, but did not effectively control all regions. The year 1920 was the last successful military rebellion, bringing the northern revolutionary generals to power. According to Álvaro Matute, "By the time Obregón was sworn in as president on December 1, 1920, the armed stage of the Mexican Revolution was effectively over." The year 1940 saw revolutionary general and President Lázaro Cárdenas choose Manuel Avila Camacho, a moderate, to succeed him. A 1966 anthology by scholars of the revolution was entitled Is the Mexican Revolution Dead?. Historian Alan Knight has identified "orthodox" interpretation of the revolution as a monolithic, popular, nationalist revolution, while revisionism has focused on regional differences, and challenges its credentials revolution. One scholar classifies the conflict as a "great rebellion" rather than a revolution. Although social movements emerged during the revolution, "their defeat or subordination mattered more." At the very least, it was a decade-long civil war, bringing to power a new political elite that ruled Mexico through a single political party until the presidential election of 2000

Kashmir: a brief history.

Kashmir (IPA: [kaʃmiːr]) is the northernmost geographical region of the Indian subcontinent. Until the mid-19th century, the term "Kashmir" denoted only the Kashmir Valley between the Great Himalayas and the Pir Panjal Range. Today, the term encompasses a larger area that includes the Indian-administered territories of Jammu and Kashmir and Ladakh, the Pakistani-administered territories of Azad Kashmir and Gilgit-Baltistan, and the Chinese-administered territories of Aksai Chin and the Trans-Karakoram Tract.

In the first half of the first millennium, the Kashmir region became an important centre of Hinduism and later of Buddhism; later still, in the ninth century, Kashmir Shaivism arose. In 1339, Shah Mir became the first Muslim ruler of Kashmir, inaugurating the Salatin-i-Kashmir or Shah Mir dynasty. The region was part of the Mughal Empire from 1586 to 1751, and thereafter, until 1820, of the Afghan Durrani Empire. That year, the Sikh Empire, under Ranjit Singh, annexed Kashmir. In 1846, after the Sikh defeat in the First Anglo-Sikh War, and upon the purchase of the region from the British under the Treaty of Amritsar, the Raja of Jammu, Gulab Singh, became the new ruler of Kashmir. The rule of his descendants, under the paramountcy (or tutelage) of the British Crown, lasted until the Partition of India in 1947, when the former princely state of the British Indian Empire became a disputed territory, now administered by three countries: India, Pakistan, and China.