The Family Tree of Life

Great stuff. One concern: The diagram above may give the impression that lemurs and lorises looked the same 18 million years ago.

Ah dint come from no orangutan lemur bat panda meerkat sloth wombat platypus turtle frog sturgeon lamprey starfish beetle mushroom algea !!!!

(See what I did there?)

I don''t know what to do with monkeys. "The last common ancestor of monkeys and apes lived about 25 million years ago." Monkeys as pictured are not a clade, so how do they have a common ancestor with anything?

Maybe it's best to say new branches form by speciation, and then become different by divergence.

Anyway, I note that this tree has the standard left-right order that puts humans rightmost, as if we were the goal of evolution. It's hard to find one that doesn't do this. Once I drew one like this, and just to be contrary put the chimp rightmost with the human just before it. It's the same phylogeny, of course, as left-right is arbitrary at each fork.

But a member of my audience, a nonscientist, told me that I "drew it wrong". The Great Chain of Being strikes again!

I think it's worth pointing out that words like "monkey" and "ape" do not represent scientific categories. Phylogenetics usually uses much more specific words to represent the various branches of the tree.

I often see statements like "It's not a monkey, it's an ape. It doesn't have a tail." Well, in the casual sense that's true, because that's what society has defined the word "ape" to mean. But since the "apes" all rest completely inside the clade casually referred to as "old world monkeys", they are technically monkeys as well.

I'd also note that, in reinforcing the misconception pointed to by fnxtr and Joe, the branches are shorter, the closer one gets to humans.

The orangs, do they have a longer existence as a species than the African apes? Doesn't grouping together chimps and bonobos mask the need to have them have shorter branches than humans? Other than that combination, all of the branches for African apes represent a single species (well, maybe gorillas are more than one species), as if they are more important than each of monkeys?

Yes, I know that I'm suggesting a diagram that has too much information to grasp by a beginner, but maybe it is important to show the "messiness" of biology. Maybe that overall impression is more important than showing H. sapiens's relatives?

Maybe if one took some other Order of familiar animals, where there is no bias that has to be guarded against, say the Carnivora (taking care not to give either cats or dogs the priveleged position!)?

Joe Felsenstein said: Maybe it's best to say new branches form by speciation, and then become different by divergence. Anyway, I note that this tree has the standard left-right order that puts humans rightmost, as if we were the goal of evolution. It's hard to find one that doesn't do this. Once I drew one like this, and just to be contrary put the chimp rightmost with the human just before it. It's the same phylogeny, of course, as left-right is arbitrary at each fork. But a member of my audience, a nonscientist, told me that I "drew it wrong". The Great Chain of Being strikes again!

"The closer two species are to a common ancestor on the phylogenetic tree, the more closely the two are related."
That is the reverse of the proper reasoning. A phylogenetic tree gives (an evolutonairy hypothesis about ) relatedness, and the common ancestor is inferred from that. That reversal between procedure in evolutionary biology and popular statements does not lead to understanding of evolutionary biology, but fosters the charge of evolution as a dogma.

Joe Felsenstein said: I note that this tree has the standard left-right order that puts humans rightmost, as if we were the goal of evolution. It's hard to find one that doesn't do this. Once I drew one like this, and just to be contrary put the chimp rightmost with the human just before it. It's the same phylogeny, of course, as left-right is arbitrary at each fork. But a member of my audience, a nonscientist, told me that I "drew it wrong". The Great Chain of Being strikes again!

There is no right answer to the question of which of two lineages should be on the left and which on the right after a speciation. It is arbitrary. I can flip the lineages left-right at enough forks to place any species on the right of the whole diagram, for example, and all those trees are correct. The problem is that people tend to read the left-right order across the top as a one-dimensional trend from the leftmost to the rightmost species. This is the ancient Great Chain of Being haunting us.

The reason why present-day forms on the left of the tree seem further from the root of the tree is (partly) that we are less interested in those lineages, so we do not show all species. For example, there are about 50 species of lemurs, about 53 species of New World Monkeys, and 123 species of Old World Monkeys, as well as a number of species of gibbons and two species of chimpanzees. These have been collapsed into single lineages each as we are less interested in those parts of the tree. The result is to make it look as if it branches more finely on the right side. But that is mostly an artifact of where our interest lies.

The diagram is very confusing where it is attempting to show relationships between prosimians and monkeys + apes common ancestor. I think that part needs to be redrawn.

Joe Felsenstein said: The problem is that people tend to read the left-right order across the top as a one-dimensional trend from the leftmost to the rightmost species. This is the ancient Great Chain of Being haunting us.

AltairIV said: But since the "apes" all rest completely inside the clade casually referred to as "old world monkeys", they are technically monkeys as well.

gerdien.dejongx said: "The closer two species are to a common ancestor on the phylogenetic tree, the more closely the two are related." That is the reverse of the proper reasoning.

A phylogenetic tree gives (an evolutonairy hypothesis about ) relatedness, and the common ancestor is inferred from that. That reversal between procedure in evolutionary biology and popular statements does not lead to understanding of evolutionary biology, but fosters the charge of evolution as a dogma.

It is missing the hierarchical nature of groups - all of these groups would be Primates
the tarsiers, monkeys and apes in the Haplorrhini, the monkeys and apes in the Simiiformes, the apes in the Catarrhini etc. etc.

Yes why promote paraphyly?

(Sorry, Emily Thompson, but Reed threw you into the shark tank where we normally eat creationists. Not your fault.)

The tree is inadequate in four ways (to summarize what a lot of people in this thread have said):

1. The left-right order of tips is arranged in a way that makes humans appear to be the culmination of evolution.

2. The brackets above the tips, designating groups, show two paraphyletic groups, "prosimians" and "monkeys". In reality we and our fellow apes are monkeys too.

3. The label of the "last common ancestor of monkeys and apes" actually uses a different definition of "monkey" than does the bracket above.

4. Groups of less interest to us are represented by single lineages, some of which actually lead to over 100 species.

5. Some of the splits have one lineage going straight up, while the other one goes sideways at first. This gives the impression that the lineage going straight up is the "main line" of evolution.

It's rather astonishing how many mistaken impressions can be conveyed by one diagram like this -- when the tree topology is basically correct! (Maybe it is better to say that it is remarkable that a tree ever is drawn in a way that avoids giving any mistaken impression.)

Joe Felsenstein said: (Sorry, Emily Thompson, but Reed threw you into the shark tank where we normally eat creationists. Not your fault.)

I've never seen anything written down on this. But there seems to be almost universal practice, in drawing a tree of two clades branching off a hypothetical common ancestor, to place the apomorphic (less like the common ancestor) clade on the right, and the plesiomorphic (more like the common ancestor) on the left. I did ask a colleague about this one time, and that was the impression he gave me.

Jim Thomerson said: I've never seen anything written down on this. But there seems to be almost universal practice, in drawing a tree of two clades branching off a hypothetical common ancestor, to place the apomorphic (less like the common ancestor) clade on the right, and the plesiomorphic (more like the common ancestor) on the left. I did ask a colleague about this one time, and that was the impression he gave me.

Most classification schemes generally group things by similarities, and further by branches off those similarities. Further organization within the classification schemes generally allows one to see relationships to other sets within the classification scheme.

Whether we do this with library classification schemes or with merchandise sold in stores, the organization is supposed to represent interrelatedness and allow one to get logically from one place to another within the classification scheme.

Humans have done this for as long as we have records of classification schemes. The brain recognizes interrelationships and tries to summarize the interconnections.

The periodic table of elements is particularly interesting in that it not only arranges by atomic number, it also arranges in columns by chemical properties. It is interesting that the arrangement of the table was already quite accurate and further justified by the development of quantum mechanics; only a relatively few interrelationships had to be corrected.

The "trees" of interrelationships among species are certainly meant to outline our current understanding of evolution; and we would certainly expect that those trees would be modified as we obtain more details.

I find it interesting that our minds do indeed pick out patterns; but I find it particularly fascinating that we are able to see patterns and interrelationships among living organisms that actually have some foundation in the evolution of those organisms. We were able to do this even before we recognized that the patterns pointed to evolution.

Joe Felsenstein said:

Jim Thomerson said: I've never seen anything written down on this. But there seems to be almost universal practice, in drawing a tree of two clades branching off a hypothetical common ancestor, to place the apomorphic (less like the common ancestor) clade on the right, and the plesiomorphic (more like the common ancestor) on the left. I did ask a colleague about this one time, and that was the impression he gave me.

As you get more and more molecular sequence data, which form is more "apomorphic" gets less and less clear. John Harshman, any comments on this issue? We need a real systematist for that.

John Harshman said: Another common practice is simply "ladderize right", in which at every node the most diverse clade gets the right-hand position, and that's at least an objective principle. Of course, which is most diverse depends on your taxon sampling, which may have been done with a bias toward some group of interest, and so that group finds itself on the right, where God surely intended it to be. And yes, I think it's a pernicious practice. It tends to imply a scala nature and promote talk of "primitive" or "basal" groups, as well as a "main branch" and "side branches".

@John: I think you meant scala naturae.

The fundamental problem is that phylogenies are high-dimensional objects, and we are trying to flatten them down and display them in two dimensions. For example, humans and chimps diverged about 6 million years ago. Both of them are about 9 million years diverged from gorilla. We could represent the three as vertices of an isosceles triangle.

Toss in orangutang, about 18 million years diverged from all three, and you have to place a point above the isosceles triangle, in a third dimension, to form a pyramid with the isosceles triangle as base.

Add a gibbon, equidistant from all four, and you are off into a fourth dimension. And so on, until for the 9 species shown you need 8 dimensions. When we flatten that tree down onto paper it is hard to avoid giving any misleading impression. For example, in the tree in this post, you get the impression that orangutangs are "closer" to gibbons than we are. And no matter how we flip lineages around at forks, we get one or another misleading impression like that one.

Mike Elzinga said: Are there any classification schemes that catalog loss of some function; for example, fish that have lost vision being placed, say, on the left and later in time? Or are there not enough examples of this to make it a standardized feature in a classification scheme? I realize, of course, that any classification scheme in an evolutionary tree depends on what has actually been found. There might not be any record of many things that would belong in the tree, so we just wouldn't know how to diagram the relationships.

Joe Felsenstein said: @John: I think you meant scala naturae.

...phylogenies are high-dimensional objects

John Harshman said: I'm not sure what you mean by "classification scheme" here. A phylogenetic tree isn't a classification scheme, merely an estimate of history, specifically phylogenetic relationships. And the only variable that counts for time is time, specifically time since divergence. The nature of that divergence doesn't enter into it. Also, as Joe and others have noted, the left-right positions of species and branches is arbitrary and meaningless; or, that is, any meaning is erroneously imposed by the viewer.

The irony is I selected the figure because it was purdy.

Mike Elzinga said: Most classification schemes generally group things by similarities, and further by branches off those similarities. Further organization within the classification schemes generally allows one to see relationships to other sets within the classification scheme. Whether we do this with library classification schemes or with merchandise sold in stores, the organization is supposed to represent interrelatedness and allow one to get logically from one place to another within the classification scheme. Humans have done this for as long as we have records of classification schemes. The brain recognizes interrelationships and tries to summarize the interconnections. The periodic table of elements is particularly interesting in that it not only arranges by atomic number, it also arranges in columns by chemical properties. It is interesting that the arrangement of the table was already quite accurate and further justified by the development of quantum mechanics; only a relatively few interrelationships had to be corrected. The "trees" of interrelationships among species are certainly meant to outline our current understanding of evolution; and we would certainly expect that those trees would be modified as we obtain more details. I find it interesting that our minds do indeed pick out patterns; but I find it particularly fascinating that we are able to see patterns and interrelationships among living organisms that actually have some foundation in the evolution of those organisms. We were able to do this even before we recognized that the patterns pointed to evolution.

Cladistic classification does arise from a tree, but as you might imagine every time the tree changes due to new data or new analytical methods the classification changes. Not to mention a group like fish would include amphibians and amniotes too rather than what we would often think of as fish - its the paraphyly issue that makes it not exactly tree based.

Mike Elzinga said:

John Harshman said: I'm not sure what you mean by "classification scheme" here. A phylogenetic tree isn't a classification scheme, merely an estimate of history, specifically phylogenetic relationships. And the only variable that counts for time is time, specifically time since divergence. The nature of that divergence doesn't enter into it. Also, as Joe and others have noted, the left-right positions of species and branches is arbitrary and meaningless; or, that is, any meaning is erroneously imposed by the viewer.

I think I understand the time direction. Apparently I am confused by the groupings then; e.g., "apes," "great apes,"monkeys," etc. I thought that groupings would emerge somewhat naturally out of such a dendritic structure such that taxonomies would become evident. I'm not sure what I am missing here. If I understand the history of this, taxonomy came before phylogenetic histories; in fact, actually hinted at such histories.

1. The left-right order of tips is arranged in a way that makes humans appear to be the culmination of evolution.

Amen. Comparing physical traits and dna is the ONLY justification for these trees.In reality its just lines of reasoning and devoid of scientific investigation.
It presumes like equals like equals like origin.
A creationist, easily, argues common design explains likeness in biology and at basic levels.
Dna is ONLY a mimic of physical trait likeness and not more evidence. Watch the math here.
You can't just say eyeballs being a like proves evolutionary relationships.
A creator also would give created kinds eyeballs because its a good idea and one size fits all.
A common blueprint easily explains ike eyeballs.
Is there any evidence that demonstrates like traits, ONL:Y, can be the result of like origin??
Test your hypothesis here.

Mike Elzinga, your unhappiness with the lack of correspondence between branching structure in phylogenies and groups such as "monkeys" and "prosimians" is not just you, you have noticed a major problem that has taken decades to clean up.

Basically the traditional Linnean classification system has often been described as completely consistent with the tree, but it wasn't. It contained many paraphyletic groups, groups sharing a common ancestor but having some subgroup removed. An example is "reptiles" which is all amniotes except birds and mammals. Similarly "prosimians" are all primates with the monkeys and apes removed.

Nowadays there are not any groups like "prosimians" or "reptiles" in the formal classification system -- there is a requirement that all groups be monophyletic, so each consists of all of the descendants of a common ancestor.

But it has taken even longer to get biology textbooks to stop cheerfully declaring that Darwin's work showed why Linnaeus's classification system was hierarchical, because it corresponded perfectly to the tree.

So don't feel bad if you don't understand why those bracketed groups don't correspond to the tree -- you are right to see that they don't.

Robert Byers said: In reality its just lines of reasoning and devoid of scientific investigation.

A creationist, easily, argues common design explains likeness in biology and at basic levels.

A creator also would give created kinds eyeballs because its a good idea and one size fits all.

A common blueprint easily explains ike eyeballs.

I learned about this interesting problem by watching Aron Ra's video on youtube, wherein I learned what "phylogeny" means and what the odds are between "monophylatic" and "polyphylatic", and why this is important. (I was, for example, aware of the odd position of "reptiles" that Joe describes above, but hadn't managed to comprehend why this was an anomaly that had to be resolved.)

But the perfect-nested hierarchy of living things arises ineluctably when rigorous imposition of monophylogeny is applied. Ignoramuses like Byers, also above, do not understand why this is a lay-down slam for common descent, but it is. I'd explain why to Byers, but he won't read a word of it, and couldn't comprehend it anyway.

Byers comment is just lines of text and devoid of any meaning.

Joe Felsenstein said: Mike Elzinga, your unhappiness with the lack of correspondence between branching structure in phylogenies and groups such as "monkeys" and "prosimians" is not just you, you have noticed a major problem that has taken decades to clean up.

Mike Elzinga said: I think I understand the time direction. Apparently I am confused by the groupings then; e.g., "apes," "great apes,"monkeys," etc. I thought that groupings would emerge somewhat naturally out of such a dendritic structure such that taxonomies would become evident. I'm not sure what I am missing here. If I understand the history of this, taxonomy came before phylogenetic histories; in fact, actually hinted at such histories.

John Harshman said: Yes, taxonomy predated phylogenies and the structure of early taxonomies can be considered a groping after the structure we see in phylogeny. But I still don't understand, apparently, what you're asking.

As it seems to me as a non-scientist outsider scientists are intent on using non-scientific ordinary language terms for their own purposes. They have decided to use the word "ape" to mean the same as a member of the clade Hominoidea, or hominoid. Homo sapiens is a hominoid. But the animal which used to be called a "Barbary ape" has been renamed a "Barbary macaque", because it is not a hominoid. But it happens to be that the noun "ape" is the earliest word in English for an "old world monkey", the only non-human primates known to English-speakers before the explosion of world travel starting in the 15th century. For some unknown reason, and from some unknown source, the word "monkey" was adopted in the English language at roughly the same time as totally new kinds of primate were being discovered. I do not think that there is a similar case of two distinct words in other languages. But there were these new primates: tarsiers, lemurs, lorises, gorillas, chimpanzees, bonobos, orangutans, gibbons, and a whole passel of primates from the New World. And at the same time the science of taxonomy was developing. Is it any surprise that there would be confusion? And then we have the revolution in taxonomy, cladistics, so some of the original decrees of the taxonomists have been revoked. Where it was respectable to speak of a family of great apes, the Pongidae, or pongids, and a family of humans, Hominidae, or hominids - and up until quite recently, paleoanthopologists would speak of the fossils that interested them as hominids, rather than being persuaded to start calling them hominins - Where it was respectable to speak of a family Pongidae there is the clade Hominidae which includes the former pongids as well as the old-time hominids. (And I have just invented a device called non-scientists license which excuses me from mentioning another issue, the disappearance of ranks like "family".)

If only someone had thought of the useful choice to say that the New World monkeys would thereafter be called the only "true monkeys", and the Old World monkeys together with the apes would be called true apes, in recognition of the major distinctions between the New World primates and the Old World's ones (and now the issue of "prosimians" can no longer be ignored - but I will, invoking non-scientist's license). Who was it that decided on the awful choice of the same word for such different animals, while excluding the closer-related relatives? We could be getting on happily, we English-speakers, calling Barbary apes and baboons "apes", calling howlers and titis "monkeys".

Mike Elzinga said: But, as Joe explained, the textbooks haven't caught up with the fact that such a method of inferring trees often gets it wrong; inferring trees doesn't rely just on such things as Linnean classification any longer.

The other thing to say, a theme of mine but not uncontroversial, is that inference of phylogenies does not in any way depend on classification (except for the delimitation of species). We take the biological data, our models of how the characters change, and make our reconstruction of the tree.

After that, if we want, we can also make a classification. We might make all groups monophyletic, as is standard now. But we might make paraphyletic groups according to some other scheme. Whatever we do about classification, it doesn't matter to any conclusions we draw about how particular characters have evolved. Does not matter because we need only the phylogeny to make that inference, and we might even not have bothered to make a classification yet at that point.

This is the position of the fourth great school of classification, the IDMVM school (for It Doesn't Matter Very Much).

I am the founder of this school, at least nominally. I think there are others who are sympathetic to it, but cannot be sure because they do not say so out loud. Everyone who speaks out on the issue considers this view on classification to be "a bizarre thumb in the eye to systematics", to quote a good friend who was nevertheless outraged by this position.

Mike Elzinga said: After the development of quantum mechanics and its contribution to the understanding of the "shell structure" of atoms, the periodic table was fine tuned and became very logically organized.

eric said: Okay, thus ends the digression.

Mike Elzinga said: One of the things I have also noted about the ID/creationist movement is that they often dig up some of these old ideas and try to use them as "arguments" against modern science. Since their sectarian notions haven't changed since the middle ages, it is probably not surprising that they would find some of these old outdated arguments attractive.

Mike Elzinga said: ... When I look at the historical classification schemes that were tried for both chemistry and living organisms, I find it amazing that people were able to eventually slog their way through all the preconceived notions that went into those schemes. But that is how science has progressed; it emerged out of a history of ideas that were taken for granted and thought to be obvious at the time. ...

Joe Felsenstein said:

Mike Elzinga said: ... When I look at the historical classification schemes that were tried for both chemistry and living organisms, I find it amazing that people were able to eventually slog their way through all the preconceived notions that went into those schemes. But that is how science has progressed; it emerged out of a history of ideas that were taken for granted and thought to be obvious at the time. ...

When I teach my upper-undergraduate class on Evolutionary Genetics, I start out with 3-4 lectures on the history of evolutionary biology and evolutionary genetics. Organisms being big (in numbers of molecules), messy, and ill-understood, old ideas frequently have a major influence. So knowing about Lamarck, or about mutationism, or about orthogenesis is helpful in understanding strange things that biologists say, or "obvious" notions that will ultimately turn out to be wrong. By contrast, physics courses do not start with a historical introduction including explanation of Aristotle's theory of flight of projectiles through the air, or an explanation of phlogiston or of the luminiferous ether. Biology students sometimes are puzzled that I bother with the history, unaware what a hold it has on our ideas. Darwin's failure, in discussing the "origin of species", to separate evolution of a lineage from speciation is one example. Reading the discussions in his era, it is hard for us now to understand why they did not see the distinction more clearly. Lack of understanding of the effects of "gene flow" owing to not knowing about genes is probably why.

TomS said: ... When I read through the history of thought, am struck by the amount of work expended by countless people, including those forgotten people who spent their lives on "dead ends", but ideas that had to be explored, and I give them thanks. ...

Joe Felsenstein said: By contrast, physics courses do not start with a historical introduction including explanation of Aristotle's theory of flight of projectiles through the air, or an explanation of phlogiston or of the luminiferous ether. Biology students sometimes are puzzled that I bother with the history, unaware what a hold it has on our ideas.

eric said: And I'm sure most physics classes that introduce relativity are going to talk at least a little bit about Michelson and Morley.

Joe Felsenstein said: By contrast, physics courses do not start with a historical introduction including explanation of Aristotle's theory of flight of projectiles through the air, or an explanation of phlogiston or of the luminiferous ether. Biology students sometimes are puzzled that I bother with the history, unaware what a hold it has on our ideas.

John Harshman said:

Joe Felsenstein said: @John: I think you meant scala naturae.

I did indeed.

...phylogenies are high-dimensional objects

I wouldn't say so. I'd say they're about 1.5-dimensional objects embedded in two dimensions. Extra dimensions are necessary only if you want to represent divergence as euclidean distance between tips. But nobody does that, and it's adequately represented by patristic distances. I will agree that many people appear to be misreading trees as if that euclidean distance were meaningful. But I think education is the solution.

riandouglas said: Sorry if I'm feeding the Byers, but...

Robert Byers said: In reality its just lines of reasoning and devoid of scientific investigation.

Robert, how do you think "lines of reasoning" differs from "scientific investigation". Wouldn't you agree that an scientific investigation worthy of the name would involve reasoning from the evidence (ie. "lines of reasoning")?

A creationist, easily, argues common design explains likeness in biology and at basic levels.

A creationist can easily CLAIM this, but what this claim would lack would be the "lines of reasoning" and "scientific investigation" that you seem fixated upon.

A creator also would give created kinds eyeballs because its a good idea and one size fits all.

But one size does not fit all Robert. There are many and varied eyeballs in nature.

A common blueprint easily explains ike eyeballs.

And what explains unlike eyeballs like mammalian and insectoid eyeballs? What explains similar but different eyeballs like mammalian and cephalopod eyes? What "lines of reasoning" or "scientific investigation" yields the differences and similarities we find in nature?

If only Robert would define "common design" for us. Can you do that Robert? You know what it is, don't you?

A relevant point may be the fact that after God had designed the octopus' eye, he decided to crown his effort with creating humans with a poorer design. And that applies not only the eye, but several other poor designs in the human body that no human designer would have been foolish enough to make.

But I am not in doubt about Robert creating "lines of reasoning" to explain everything to his own satisfaction without regard for facts.

Joe Felsenstein said: The other thing to say, a theme of mine but not uncontroversial, is that inference of phylogenies does not in any way depend on classification (except for the delimitation of species). We take the biological data, our models of how the characters change, and make our reconstruction of the tree. After that, if we want, we can also make a classification. We might make all groups monophyletic, as is standard now. But we might make paraphyletic groups according to some other scheme. Whatever we do about classification, it doesn't matter to any conclusions we draw about how particular characters have evolved. Does not matter because we need only the phylogeny to make that inference, and we might even not have bothered to make a classification yet at that point. This is the position of the fourth great school of classification, the IDMVM school (for It Doesn't Matter Very Much). I am the founder of this school, at least nominally. I think there are others who are sympathetic to it, but cannot be sure because they do not say so out loud. Everyone who speaks out on the issue considers this view on classification to be "a bizarre thumb in the eye to systematics", to quote a good friend who was nevertheless outraged by this position.

I am in charge here, and as I usually do, I'm going to move any further comments by our usual trolls to the Bathroom Wall. In this case it is Robert Byers who is showing up. Byers has shown in hundreds of comments that he is unwilling to actually deal with any questions that arise, except to repeat his conclusions.

This also applies to any replies to Byers -- they will go to the BW too.

Scott F said: ... Funny you should mention that. This tree, highlighted by PZ Myers, does attempt show degrees of divergence by the physical distances between nodes and tips of the branches. It doesn't have the rigid regularity and the pretty pictures of the OP, but it does a much better job of showing the diversity of each lineage after the various branching points. And being an "unrooted" tree (or perhaps in addition to being an "unrooted" tree), it doesn't hold a special place for "humans" at one "end" of the tree.

Scott F said:

Joe Felsenstein said: By contrast, physics courses do not start with a historical introduction including explanation of Aristotle's theory of flight of projectiles through the air, or an explanation of phlogiston or of the luminiferous ether. Biology students sometimes are puzzled that I bother with the history, unaware what a hold it has on our ideas.

Hmm. I find it odd that you say that. The physics courses that I took were divided into roughly three sections: mechanics, electro-optics, and atomic. Each section explicitly started out with a review of the history of those sciences, to help explain how we got to where we are today. I found that it really helped to understand the concepts. By walking us through the history, we could see the mistakes that were made in understanding along the way, helping us to avoid those same misconceptions. The historical "mistakes" were often the "intuitive" understandings that we (the students) had brought to the class. It was certainly a better start than "dry" equations and memorization of facts. By starting with the stories of the scientists, it brought a "human" perspective to the subjects, and a better understanding of the give and take of the scientific process as a whole.

Joe Felsenstein said:

Scott F said: ... Funny you should mention that. This tree, highlighted by PZ Myers, does attempt show degrees of divergence by the physical distances between nodes and tips of the branches. It doesn't have the rigid regularity and the pretty pictures of the OP, but it does a much better job of showing the diversity of each lineage after the various branching points. And being an "unrooted" tree (or perhaps in addition to being an "unrooted" tree), it doesn't hold a special place for "humans" at one "end" of the tree.

It has humans at the upper-right. And it still has the problem that (for example) Central Chimpanzees appear to be much closer hiumans than are Eastern Chimpanzees. One can reverse that by flipping branches at interior nodes in ways that do not change the topology or branch lengths of the tree.

TomS said:

Joe Felsenstein said:

Scott F said: ... Funny you should mention that. This tree, highlighted by PZ Myers, does attempt show degrees of divergence by the physical distances between nodes and tips of the branches. It doesn't have the rigid regularity and the pretty pictures of the OP, but it does a much better job of showing the diversity of each lineage after the various branching points. And being an "unrooted" tree (or perhaps in addition to being an "unrooted" tree), it doesn't hold a special place for "humans" at one "end" of the tree.

It has humans at the upper-right. And it still has the problem that (for example) Central Chimpanzees appear to be much closer hiumans than are Eastern Chimpanzees. One can reverse that by flipping branches at interior nodes in ways that do not change the topology or branch lengths of the tree.

I wonder whether it would be worth the trouble (or even introduce more misconceptions) to make it 3-D. Also, I'm curious about the meaning of color.

Joe Felsenstein said: The reason for my "odd" comment is simple: I was stereotyping. I am happy to hear that I am wrong, and that physics and chemistry courses do cover the history of the concepts that they introduce.

Joe Felsenstein said: I am in charge here, and as I usually do, I'm going to move any further comments by our usual trolls to the Bathroom Wall. In this case it is Robert Byers who is showing up. Byers has shown in hundreds of comments that he is unwilling to actually deal with any questions that arise, except to repeat his conclusions. This also applies to any replies to Byers -- they will go to the BW too.

Scott F said: Funny you should mention that. This tree, highlighted by PZ Myers, does attempt show degrees of divergence by the physical distances between nodes and tips of the branches.

Joe Felsenstein said: (And I disagree with John Harshman that 1.5 dimensions is enough. After all, 2 dimensions isn't enough.)

Apologies for my previous 2 comments Joe - I responded prior to reading subsequent comments (and seeing yours relating to Byers and responses to him) :-(

Joe Felsenstein said: The reason for my "odd" comment is simple: I was stereotyping. I am happy to hear that I am wrong, and that physics and chemistry courses do cover the history of the concepts that they introduce.

Mike Elzinga said: Unfortunately, a lot of the interesting history has been eliminated to make room for other legitimate pedagogical concerns. Personally I think that is a loss because a good case study in the historical development of a concept is itself very good pedagogy. Admittedly, case studies do in fact take up a lot of time relative to other pedagogical approaches; and assigning them as supplementary material probably means that a lot of students won't bother to read them.

Mike Elzinga said:

Joe Felsenstein said: The reason for my "odd" comment is simple: I was stereotyping. I am happy to hear that I am wrong, and that physics and chemistry courses do cover the history of the concepts that they introduce.

My suspicion is that it depends on the particular program one is following toward a degree and/or the particular college or university. Many of the physics textbooks back before the 1950s contained a pretty good overview of historical developments. Authors were writing for students they perceived would be much like themselves in their interests. Many engineering programs don't appear to delve into the history of their subject very much; I think most engineering students just want to get on with the course material and leapfrog off current technology. Some physics programs - particularly the applied physics programs - don't appear to include much history. Back in the 1960s and early 70s there was a big push to reform the science curriculum, not just at the high school level but to modernize the college and university textbooks as well. This push was in response to Sputnik. Among the materials generated in that reform was the Harvard Project Physics which delved into the history of various physics concepts by developing a series of case studies. Those case studies found their way into textbooks at both the high school and college level; and they were very well done. Since the 1960s and early 70s, there have been several waves of "reform" driven by other pedagogical concerns and by politics. I think some of the history may have been subsequently cut out of the science and math curriculum - and, of course, we have those sectarian political activists attempting to rewrite history and get their pseudo-histories into the textbooks at all levels. Many of these reforms, both at the pre-college and college level, have significantly improved the math and science curriculum. It is much better organized and pedagogically more sound overall. Unfortunately, a lot of the interesting history has been eliminated to make room for other legitimate pedagogical concerns. Personally I think that is a loss because a good case study in the historical development of a concept is itself very good pedagogy. Admittedly, case studies do in fact take up a lot of time relative to other pedagogical approaches; and assigning them as supplementary material probably means that a lot of students won't bother to read them.

riandouglas said: Apologies for my previous 2 comments Joe - I responded prior to reading subsequent comments (and seeing yours relating to Byers and responses to him) :-(

In the '90s there was concern that science was not being taught in a way attractive, or effective, to sudents. I recall a general criticisim that physics involved too much problem solving. I had thought that physics is all about problem solving.

A colleague used to say that teaching biology was just telling stories. I tended to agree with him. I fortunately had an excellent history of biology course at the PhD level, which reenforced my interest in the history of science.

I have a copy of Isaac Asimov's, "Biographical History of Science", 2nd ed.,which I have found most interesting and useful. I look up someone, and an hour later I am still reading, following cross references.

TomS said:

Mike Elzinga said: Unfortunately, a lot of the interesting history has been eliminated to make room for other legitimate pedagogical concerns. Personally I think that is a loss because a good case study in the historical development of a concept is itself very good pedagogy. Admittedly, case studies do in fact take up a lot of time relative to other pedagogical approaches; and assigning them as supplementary material probably means that a lot of students won't bother to read them.

One concern that I have is that what is presented as the history of the subject is not up to the current standards of historiography.

harold said: In medical school there was some tendency for some books and professors to talk about the historical development of current concepts. I was good-naturedly but heartily mocked for taking an interest in such things, for example caring who things were named after and so on. And to some degree rightfully so; we had enough on our plates. On the other hand, interest in the history of biomedical science is not rare among physicians either.

To Robert Byers:

I have responded to, and directly challenged, your comments over on the Bathroom Wall. If you are interested in a "free discussion," that's the place. So take a gander and let's have the discussion. -- If you really are interested in a "free discussion," of course.

Regards,

Matt

mattdance18 said: To Robert Byers: I have responded to, and directly challenged, your comments over on the Bathroom Wall. If you are interested in a "free discussion," that's the place. So take a gander and let's have the discussion. -- If you really are interested in a "free discussion," of course. Regards, Matt

Joe Felsenstein said:

mattdance18 said: To Robert Byers: I have responded to, and directly challenged, your comments over on the Bathroom Wall. If you are interested in a "free discussion," that's the place. So take a gander and let's have the discussion. -- If you really are interested in a "free discussion," of course. Regards, Matt

I'm allowing that comment here, but all others on Byers's comment will go there, to the BW. Maybe some day Byers will find the BW and discuss with people there.

Mike Elzinga said:

harold said: In medical school there was some tendency for some books and professors to talk about the historical development of current concepts. I was good-naturedly but heartily mocked for taking an interest in such things, for example caring who things were named after and so on. And to some degree rightfully so; we had enough on our plates. On the other hand, interest in the history of biomedical science is not rare among physicians either.

My general impression about primary care physicians and medical specialists is that the best ones generally try to keep abreast of ongoing research, clinical trials, and technological developments within the various health areas in which they specialize. In that regard, they are analogous to engineers and other technologists in being highly skilled at applying the science. The ability to recognize patterns, diagnose illnesses, and apply up-to-date research and technology would be skills that don't necessarily benefit from a deep knowledge of history. If I am on an operating table or have a serious illness, I think I wouldn't care about what history my physician knows. On the other hand, if one is involved in medical research, I would think that familiarity with the historical developments in one's field would be helpful in addition to having a robust knowledge of the underlying science.

harold said: ... There is an honor code, or was, among the professors who discuss historical stuff before moving on, that they won't test on it. ...

Joe Felsenstein said:

harold said: ... There is an honor code, or was, among the professors who discuss historical stuff before moving on, that they won't test on it. ...

Maybe in medicine. But I bloody well do give test questions on the historical stuff. Not the details of the history, but on how pre-Darwin theories differed from Darwin, and how genetics affected evolutionary biology.

harold said:

Joe Felsenstein said:

harold said: ... There is an honor code, or was, among the professors who discuss historical stuff before moving on, that they won't test on it. ...

Maybe in medicine. But I bloody well do give test questions on the historical stuff. Not the details of the history, but on how pre-Darwin theories differed from Darwin, and how genetics affected evolutionary biology.

Let me clarify - when the historical material is critical to an understanding of the current material, it is covered and tested. For example, Koch and his postulates, and the way that we have evolved our identification of pathogens since then, are fairly extensively covered in microbiology. Some of us have historical interests that go beyond that, including some professors. Stuff like the historical feud between Golgi and Cajal isn't tested. It may be touched on that Golgi didn't think that the CNS was made of cells, even though his own technique in Cajal's hands proved that it is, even by a professor with little historical interest, but even then "what Golgi thought" isn't likely to be tested on.

harold said:

Joe Felsenstein said:

harold said: ... There is an honor code, or was, among the professors who discuss historical stuff before moving on, that they won't test on it. ...

Maybe in medicine. But I bloody well do give test questions on the historical stuff. Not the details of the history, but on how pre-Darwin theories differed from Darwin, and how genetics affected evolutionary biology.

Let me clarify - when the historical material is critical to an understanding of the current material, it is covered and tested. For example, Koch and his postulates, and the way that we have evolved our identification of pathogens since then, are fairly extensively covered in microbiology. Some of us have historical interests that go beyond that, including some professors. Stuff like the historical feud between Golgi and Cajal isn't tested. It may be touched on that Golgi didn't think that the CNS was made of cells, even though his own technique in Cajal's hands proved that it is, even by a professor with little historical interest, but even then "what Golgi thought" isn't likely to be tested on.

TomS said:

harold said:

Joe Felsenstein said:

harold said: ... There is an honor code, or was, among the professors who discuss historical stuff before moving on, that they won't test on it. ...

Maybe in medicine. But I bloody well do give test questions on the historical stuff. Not the details of the history, but on how pre-Darwin theories differed from Darwin, and how genetics affected evolutionary biology.

Let me clarify - when the historical material is critical to an understanding of the current material, it is covered and tested. For example, Koch and his postulates, and the way that we have evolved our identification of pathogens since then, are fairly extensively covered in microbiology. Some of us have historical interests that go beyond that, including some professors. Stuff like the historical feud between Golgi and Cajal isn't tested. It may be touched on that Golgi didn't think that the CNS was made of cells, even though his own technique in Cajal's hands proved that it is, even by a professor with little historical interest, but even then "what Golgi thought" isn't likely to be tested on.

Perhaps I am a Pollyanna, but wouldn't at least some students find something about a subject to be interesting even if they knew that they were not to be tested about it?

Jim Thomerson said: In the '90s there was concern that science was not being taught in a way attractive, or effective, to sudents. I recall a general criticisim that physics involved too much problem solving. I had thought that physics is all about problem solving.

I wonder how many molecular geneticists there are who have not heard of Gregor Mendel.

Jim Thomerson said: I wonder how many molecular geneticists there are who have not heard of Gregor Mendel.

Joe Felsenstein said:

Jim Thomerson said: I wonder how many molecular geneticists there are who have not heard of Gregor Mendel.

Probably few, but quite a lot more have never heard of Thomas Hunt Morgan or of H. J. Muller.

TomS said:

Joe Felsenstein said:

Jim Thomerson said: I wonder how many molecular geneticists there are who have not heard of Gregor Mendel.

Probably few, but quite a lot more have never heard of Thomas Hunt Morgan or of H. J. Muller.

How many have Morgan or Muller (who was a student of Morgan) in their academic pedigree (that is, they are students of students of .... ), and know that?

Joe Felsenstein said:

Jim Thomerson said: I wonder how many molecular geneticists there are who have not heard of Gregor Mendel.

Probably few, but quite a lot more have never heard of Thomas Hunt Morgan or of H. J. Muller.

Hah! It remembered.

DS said:

TomS said: ... How many have Morgan or Muller (who was a student of Morgan) in their academic pedigree (that is, they are students of students of .... ), and know that?

Sounds like a project for another family tree of life.

Joe Felsenstein said:

DS said:

TomS said: ... How many have Morgan or Muller (who was a student of Morgan) in their academic pedigree (that is, they are students of students of .... ), and know that?

Sounds like a project for another family tree of life.

Been done. See here.