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There are numerous misconceptions on evolutionary trees, and they all, of course, go back to this notion of “progressive” evolution and people may believe these trees show that one organism is “more evolved”. However, these false notions from looking at evolutionary trees intuitively show how one may misinterpret these evolutionary trees. I’ve shown PumpkinPerson numerous times that he’s reading the trees wrong and interpreting it to fit Rushton’s 3-way race model. He, however, doesn’t want to listen to the data and continuously attempts to salvage his position that have been continuously broken apart.
These notions that PP is espousing are common misconceptions on evolutionary trees.  He doesn’t realize that he’s not scientifically reading the trees correctly and is using his intuition on what the trees mean (where he’s extremely wrong).

Intuitive Interpretation: Taxa (diferent groups of living thinigs) are organized into a Great Chain of Being, which some taxa (e.g., humans) are higher or more advanced than others. 1, 2, 3, 4

Scientific Interpretation: The relationships among taxa are best represented by a branching tree-like structure (a phylogeny), in white taxa appear at the tips of the phylogeny, visually reinforcing the idea that no taxon has a higher or lower status than  others.

The way that PP reads these trees is, in a way, attempting to interpret it as a “great chain of being”, which evolutionary biologists do not believe anymore. I’ve said numerous times that evolution is a branching tree, not a linear line. A branching tree makes more sense than slow and gradual change; basically the difference between Punctuated Equilibria and phyletic gradualism. And here is Berkeley’s explanation for how to really read it:

Explanation: The idea of “higher” and “lower” organisms is intuitively appealing and has many antedents in the history of science; however, this idea refelcts a human-centered, biased perspective on the biological world in which other organisms are measured by their similarity to humans. Taking an unbiased view, it is clear there is no universal yardstick against which we can measure species. For example, we could focuse on photosynthetic ability (which would make plants the “higher” beings), sheer number of indviduals (which would pick out bacteria and microorganisms as special),or any number of other traits. Each trait would suggest a very different group of “higher” organisms. Diagrams that represent relationships using a central trunk with side branches reinforce the incorrect idea that evolution is directional and progressive. Phylogenetic trees are preffered because they convey information about evolutionary relationships without reinforcing intuitive ideas about evolutionary progress by placing some taxa above or below others. A similar intuitive idea is that some living species are more evolved than others; this idea is explored in the section about time.

Perfectly comprehensible that it doesn’t mean that one organism is “more evolved” than another.

I don’t even know any serious evolutionary biologist who would read a tree like that. It’s ridiculous and it in no way fits the data on how an actual tree will be read.

These differing trees show that it’s easy to see how one may say that there is a sort of “progression” to evolution, however there is no “progress” to evolution so in reading the tree in this way, one would have these misconceptions that PP has.

Another popular intuitive way to reduce a tree is stating that a branch that’s further away from the beginning of the lineage is “more evolved” or has “progressed more” than the common ancestor. However, a taxon’s relationship on phylogeny is a function of its relationship to other taxa and how the branches are rotated. The position of an organism on the tree is not any type of specialization, adaptation or any extreme traits in comparison to other organisms “lower” on the tree.  Thusly, an organism’s placement on the tree is meaningless.

One of the biggest misconceptions PP has is not just on evolutionary trees, but the fact that organism have been “evolving” more than other organisms.

The above graph shows that since all species alive today share a common ancestor, that they all have had the same time evolving.

In most evolutionary trees, branch length doesn’t indicate anything about amount of evolutionary change. All though, when branch length is used to depict evolutionary change, branch length is then used. But this doesn’t mean that the organism at the end of that branch is ‘more evolved’ or has ‘progressed’ more than another; it just shows that more selective pressures had species adapt genotypically, which led to phenotypic changes over time to better survive in that environment. That’s it.

Now, here is the kicker (which goes with the previous picture from Berkely) and this is what directly refutes his rudimentary understanding of phylogenetic trees:

Intuitive Interpretation: Some living (i.e., extant) species have longer evolutionary histories than others (i.e., have been evolving for a longer time), and so some species are more or less “evolved” than other extant species.

Scientific Interpretation: Since all extant species are alive today and share a common ancestor (one that lived more than 3.5 billion years ago!), all extant species have been evolving the same amount of time.

Explanation: Some living organisms such as mosses and sharks represent clades that appear early in the geological record. Others (such as grasses and birds) represent clades that appear more recently. It is tempting to think of living members of a clade that appeared 160 million years ago (such as the mammals) as having a shorter history than members of a clade that appeared 440 million years ago (such as the cartilaginous fishes, sharks and rays). However, this intuition does not apply because of all living clades trace their evolutionary history back to shared ancestors among the earliest forms of life. For example, the fact that the clade that includes sharks appears early in the fossil record does not mean that modern sharks have had a longer evolutionary history than any other modern species.

What is really so hard to grasp about this?

While on this subject, PP has moderated my comments on his blog since “I’m repeating arguements he’s already responded to”, so I’ll post it here:

“You haven’t shown anything. As the above tree shows, among members of the same taxonomical level, there’s a high correlation between the degree of branching and (1) brain size, and (2) intelligence. I’ve demonstrated at least one measure of evolutionary progress that can be empirically tested.”

Haha. And now brain size is decreasing. Even then, as I said last night, there is no accepted definition and there is no accepted of these traits, and even terms like progression through fitness and the like don’t have an accepted definition, because, as I’ve shown again, the environment is ever changing. I’m sorry this is hard for you to grasp. There is no way to quantify more evolved superior and progressive evolution. I don’t know how to make you get it.

PP do me a favor. Go to Razib’s blog and post on his open thread and ask him how to read an evolutionary tree and then tell him how you read it. I would love to see his response.

“Politically correct platitudes are not science. Calling something primitive is not a value judgement, it’s a description. Replacing it with the more politically correct term “ancestral” doesn’t change anything, it’s just playing word games.”

You’re the one playing word games. You don’t have to agree that primitive and advanced mean nothing in evolutionary terms, you’d be extremely wrong though. You’re the one playing word games. I showed that there is no unidirectional line of progress and you’re still going on with this:

Because of the frequency of environmental change, the multiplicity of factors underlying fitness, the possibility of frequency-dependent and epistatic interactions among features, and the consequent possibility of nontransitive fitness relations between phenotypes, selection acting within populations frequently, though not inevitably, fails to produce unidirectional trends. The extent to which unidirectional trends dominate, or fail to dominate, the fossil record is therefore not a measure of the adequacy of neo-Darwinian mechanisms as causes of large-scale patterns in evolution.”

Progress in Organismal Design

Simple enough to grasp. Directly refutes your notion too.

Saying that an organism is more advanced is not quantifiable. Each one is adapted to its environment. You’re the one playing word games to show your crackpot hypothesis, continually quoting pages 292 to 294 of Race, Evolution, and Behavior. But that doesn’t make it true. It’s not true.

“Yawn. I’ve debunked this stupid quote back in 2014. Splits on an evolutionary tree typically reflect periods of evolutionary growth after long periods of stasis. So if you’re a descendent of many splits, you’re typically a descendent of more evolution.”

You’ve debunked nothing. Ask Razib how to read an evolutionary tree then tell him how do and come back and show me his reaction. Please do this. I know what he’ll say. I directly proves your misconception wrong and you’re still going with it. It is true that when people are shown they’re wrong they attempt to gather any information to try to fix their shattered worldview. PP you’re just rehashing the great chain of being garbage and evolutionary theorists have abandoned that archaic notion. Join us in the year 2016, and ask actual experts how to read those trees instead of your misunderstanding. And a blog writing one sentence means…. What exact? It means nothing. I’ve shown my argument is stronger than yours and that you are reading evolutionary trees wrong, provided exact quotations from a respected authority and you still say it’s wrong. Too funny. Rushton isn’t the be all end all of evolution. He was wrong on a lot he was not perfect. And even then, he only implied this. The fact that he cited Aristotle and the great chain of being is laughable as people don’t even believe that anymore.

Please join us in the present PP, and stop living in the past.

Since PP is using Rushton as a reference, I’ll directly quote Race, Evolution, and Behavior (pg. 292-4) for Rushton’s exact words:

Progress in Evolution?

In their reviews, Lynn (1996a) and Peters (1995) both referred to my ranking of species on evolutionary scales. For Peters, this was a highly contentious idea but in Lynn’s positive review, he described me as proposing that the K-strategy was “evolutionarily more advanced” and that the Oriental race was “the most evolved.” In fact, I did not use either of these phrases in the book, although I had alluded to similar ideas in previous writing. Regardless, the topic of evolutionary progress provides an intellectual challenge of the first order and needs to be addressed. Figure 10.2 (p. 202) does imply a move from simple r-type animals producing thousands of eggs but providing no parental care to more complex K-type animals producing very few offspring.

The question of progress in nature has fascinated since Aristotle. Aristotle suggested that organisms could be hierarchically graded along ascala naturae marked by minute continuous steps from the inanimate, through plants, to the animals. He offered overlapping criteria for ranking along this scale including “perfectibility” (closeness to a Platonic God), “soul” (capacity for rational discourse), and method of reproduction. For example, regarding reproduction, he wrote in the History of Animals:

“Now some simply like plants accomplish their own reproduction according to the seasons; others take trouble as well to complete the nourishing of their young, but once accomplished they separate from them and have no further association; but those that have more understanding and possess some memory continue the association, and have a more social relationship with their offspring.”

The Greek philosopher’s biology is remarkably current. Based on detailed observation, Aristotle noted many of the principles that lie at the heart of the r-K analysis undertaken in this book including the inverse relations between seed output, parental care, and intelligence. The historian Arthur Lovejoy, in his 1936 book The Great Chain of Being, concluded that Aristotle’s arrangement of all things in a single order of magnitude was one of the most important ideas in Western thought.

Darwin (1859) referred frequently to evolutionary progress in the Origin of Species. This was necessary not only to refute concepts of a steady-state world but also to counter a newly developed school that denied any difference in perfection between the simplest and the most complex organisms, which would be an implicit denial of improvement through natural selection. In his book Sociobiology (1975), E. O. Wilson also promoted the idea of biological progression, outlining four pinnacles in the history of life on Earth: first, the beginning of life itself in the form of primitive prokaryotes, with no nucleus; then the origin of eukaryotes, with nucleus and mitochondria; next the evolution of large, multicellular organisms, which could evolve complex organs such as eyes and brains; and finally the beginnings of the human mind.

John Bonner (1980), in his book The Evolution of Culture in Animals, showed that the later an animal emerged in earth history the larger was its brain and the greater was its culture. Pursuing the issue in a subsequent book, The Evolution of Complexity (1988), he asked “Why has there been an evolution from the primitive bacteria of billions of years ago to the large and complex organisms of today?” Bonner held that it was quite permissible for paleontologists to refer to strata as upper and lower, for they are literally above and below each other and, because the fossils in the lower strata will, in general, be more primitive in structure as well as belong to a fauna or flora of earlier times, so “lower” and “higher” were acceptable terms. Bonner (1988: 6) noted that it was even acceptable to refer to lower and higher plants, slime molds versus angiosperms for example. It only became a “sin” when a worm was classified as a lower animal and a vertebrate a higher one, even though their fossils too will be found in lower and higher strata.

Paleontologist Dale Russell (1983,1989) quantified increasing neurological complexity through 700 million years of Earth history in invertebrates and vertebrates alike. The trend was increasing encephalization among the dinosaurs that existed for 140 million years and vanished 65 million years ago. Russell (1989) proposed that if they had not gone extinct, dinosaurs would have progressed to a large-brained, bipedal descendent. For living mammals he set the mean encephalization, the ratio of brain size to body size, at 1.00, and calculated that 65 million years ago it was only about 0.30. Encephalization quotients for living molluscs vary between 0.043 and 0.31, and for living insects between 0.008 and 0.045 but in these groups the less encephalized living species resemble forms that appeared relatively early in the geologic record, and the more encephalized species resemble those that appeared later.

The hominid brain has nearly tripled in size over the last 4 million years. Australopithecenes averaged a brain size of about 500 cm3 , the size of a chimpanzee. Homo habilis averaged about 800 cm3 , Homo erectus about 1,000 cm3 , and modern Homo sapiens about 1,350 cm3 . In Figure 10.3 of this book (p. 205) Homo sapiens is to be found at the end of a scala naturae of characteristics. The once traditional view that man is the “most developed” of species, gains novel support from the perspective of an r-K dimension. As E. O. Wilson (1975) put it: “In general, higher forms of social evolution should be favored by K selection” (p. 101)

Darwin had contradictory notions on the concept of ‘progress’ in evolution:

THE SECOND RIDDLE

Gould’s second riddle asks why Darwin never used the word “evolution”. In short, it is because “evolution” means progress and Darwin’s theory was uniquely non-progressive. Darwin was well aware that natural selection as a mechanism describes only adaptation within local environments. He wrote a marginal note to himself “Never say higher or lower in referring to organisms”.

So why do we call the process evolution? Herbert Spencer, an eminent Victorian, was tremendously influential in Darwin’s age. His writings were explicitly progressive, not only with regard to biological change, but economic, artistic, human, ad infinitum.

Gould notes “Since 19th century thinkers wouldn’t accept Darwin’s radicalism anymore than we would today, they were very comfortable with Spencer’s notion that you ought to use a word that means inherent progress…because that’s how they wanted to see it.”

Wow! He wrote a note to himself to “never say higher or lower in referring to organism”. What does that mean….? It seems to mean that he didn’t take to “progressive” evolution and he didn’t think that organisms were “higher” or “lower” than others.

On E.O. Wilson’s prokaryote argument: he’s just describing different lifeforms, not that they’re “more evolved” than any organisms that came previously. This notion, as I’ve documented over the past month here, is baseless in evolutionary biology and these terms don’t let us see evolution for what it really is: ongoing change, not progress. With our notion of “progress” we may think that things are “reversing”, but that’s just our perception and evolution through natural selection just happens, with no end goal in sight.

On what Rushton says about dinosaurs possibly developing an intelligence similar to our own: evolution isn’t linear, as I’ve been saying for months now. Let’s say that one thing was different in a rewind of life on earth, and everything else that led up to us arriving here occurred as is. That ONE difference may possibly have us not be here. That’s not too hard to grasp.

On his citing Bonner: a worm isn’t “lower” than flora or fauna; it’s just adapted to its specific niche. This, once again, is basic evolutionary biology.

Homo erectus and others were adapted to their environment and still persisted after Homo sapiens appeared on the scene.

On John Bonner:

Dr. John Bonner, professor emeritus of ecology and evolutionary biology at Princeton University and author of “The Evolution of Complexity” (Princeton University Press), said the newest findings were perfectly in line with the idea that he has continued to press that increases in complexity need not be explained as the result of any drive or force in any particular direction.

“Bacteria still exist today,” he said. “There hasn’t been a trend just toward more complex things, there’s been that trend but others have gotten simpler and less complex and smaller. But if things keep getting both more and less complex, the upper limit is going to keep rising.”

According to Dr. McShea, the perception of drives toward complexity may be more a reflection of scientists’ desires to see some sort of progress in evolution rather than a reflection of any biological reality. As Dr. Maynard Smith, explained: “If there’s going to be any change, there will have to be increases in complexity. Moreover, there will also be some decreases. It’s inevitable. There’s a poem by a chap that goes: ‘Nowhere to go but out, Nowhere to come but back.’”

I’ve cited Daniel McShea in these series of articles. What he’s saying is correct; we just look for notions of so-called “progress”. We have an implicit bias that we are the so-called “top of the ladder” in this “Great Chain of Being”. However, this term was discontinued by biologists in the 19th century.

PP is living in the past. He should join us in current year, because what he’s saying is old and debunked. Moreover, he really should learn how to read an evolutionary tree properly, because every single misconception that he has on the trees is included in the Berkely link above. This information is freely accessible to anyone; you’d just have to be willingly ignorant to a) not read it or b) read it and still hold these views. Moreover, the Great Chain of Being nonsense hasn’t been taken serious by evolutionary biologists since the 19th century. Yet PP still holds on to these notions. Saying that one is “more complex” than another is still a holdover from the GCoB days.

Evolution is NOT progressive, and PLEASE learn how to read phylogenetic trees correctly! That, or ask Razib how to read them then tell him how you read them. I’d love to see his reaction.