Category Archives: Evolution

Birds and dinosaurs, collagen, and Huxley.

Posted on by

I have already blogged about this topic in a short post [Yet another link between dinosaurs and birds], so I will just point out the existence of another paper along these lines using phylogenetic analyses of collagen amino acid sequences recovered from T. rex fossils to demonstrate a close affinity between theropod dinosaurs and birds (Organ et al. 2008), a link first proposed by T.H. Huxley in 1868. This newest analysis was led by Chris Organ, who also did the dinosaur cell/genome size estimation study (Organ et al. 2007; Zimmer 2007). They also looked at mastodons. The data from mastodons and dinosaur aren’t new (Asara et al. 2007; Schweitzer et al. 2007) — the main update is the inclusion extant species and of a phylogenetic component.


There are plenty of news stories about it, including the following.

Molecular Analysis Confirms Tyrannosaurus Rex’s Evolutionary Link To Birds (ScienceDaily)

From T. Rex to Chicken: The Dino-Bird Connection(Discovery News)

T. rex confirmed as great granddaddy of all birds (New Scientist)

Phylogenetic Tree: Dinosaurs, Alligators And … Ostriches? (Scientific Blogging)

Gunk in T. Rex Fossil Confirms Dino-Bird Lineage (LiveScience)

Finally, a reminder about how species names should be listed.
_______

References

Asara, J.M., M.H. Schweitzer, L.M. Freimark, M. Phillips, and L.C. Cantley. 2007. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316: 280-285.

Huxley, T.H. 1868. On the animals which are most nearly intermediate between birds and the reptiles. Annals and Magazine of Natural History, Series 4, 2: 66-75.

Organ, C.L., A.M. Shedlock, A. Meade, M. Pagel, and S.V. Edwards. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184.

Organ, C.L., M.H. Schweitzer, W. Zheng, L.M. Freimark, L.C. Cantley, and J.M. Asara. 2008. Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science 320: 499.

Schweitzer, M.H., Z. Suo, R. Avci, J.M. Asara, M.A. Allen, F.T. Arce, and J.R. Horner. 2007. Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein. Science 316: 277-280.

Zimmer, C. 2007. Jurassic genome. Science 315: 1358-1359.



My growing respect for New Scientist.

Posted on by

I have said some nice things about New Scientist, such as noting that they printed one of the best popular treatments of “junk DNA” I have read [New Scientist gets it right]. On the other hand, I also criticized one of their headlines as perpetuating misconceptions about how evolution works [Chimps are not more evolved than humans or anyone else]. Today, New Scientist shows that they are far more worthy of endorsement than nitpicking in their publication of a special issue on evolution. Not only this, but the online version of one of the articles links to my aforementioned criticism, which I consider very decent.

My local bookstore does not have the April 19 issue yet, so I have not seen the print version, but their collection of 24 myths and misconceptions can be accessed freely online:

Shared misconceptions:

Everything is an adaptation produced by natural selection

Natural selection is the only means of evolution

Natural selection leads to ever-greater complexity

Evolution produces creatures perfectly adapted to their environment

Evolution always promotes the survival of species

It doesn’t matter if people do not understand evolution

“Survival of the fittest” justifies “everyone for themselves”

Evolution is limitlessly creative

Evolution cannot explain traits such as homosexuality

Creationism provides a coherent alternative to evolution

Creationist myths:

Evolution must be wrong because the Bible is inerrant

Accepting evolution undermines morality

Evolutionary theory leads to racism and genocide

Religion and evolution are incompatible

Half a wing is no use to anyone

Evolutionary science is not predictive

Evolution cannot be disproved so is not science

Evolution is just so unlikely to produce complex life forms

Evolution is an entirely random process

Mutations can only destroy information, not create it

Darwin is the ultimate authority on evolution

The bacterial flagellum is irreducibly complex

Yet more creationist misconceptions

Evolution violates the second law of thermodynamics

[Tipped hats to Panda’s Thumb and Sandwalk]



Primitive versus [blank].

Posted on by

Wilhelm Johannsen, who coined such terms as “gene”, “genotype”, and “phenotype”, noted in 1911 that,

It is a well-established fact that language is not only our servant, when we wish to express – or even to conceal – our thoughts, but that it may also be our master, overpowering us by means of the notions attached to the current words.

Even widely used and (apparently) simple terms can cause substantial confusion when the notions attached to them are unwarranted, a problem that is particularly common in evolutionary biology. Think “theory“, a term that is not only poorly understood to begin with in its scientific context but is actively misrepresented by anti-evolutionists.

The misinterpretation of other terms may cause, or be caused by, particular assumptions about the nature of the evolutionary process. Take the term “primitive” for example. The use of the term can be either deeply misleading or entirely appropriate depending on what one considers to be the opposite of the term. Here are the two most common uses, the first problematic and the second legitimate.

1) Primitive versus advanced.
In this comparison, the term “primitive” has pejorative connotations of inferiority relative to “more evolved” species. Evolution is implied to be a progressive process characterized by improvement rather than simply of change. This is the usage one finds in popular media, for example in the all-too-well-known “evolutionary line-up” showing progressive improvement in anything from primate species to any manner of product being advertised as new and improved. However, biological evolution is not a progressive process, and this use of the term is inappropriate.

2) Primitive versus derived.
In technical parlance, “primitive” can be used to mean that one form of a trait is “more like a common ancestor” relative to another form of the trait (i.e., as synonymous with “ancestral”). It is an expression of the differential quantity of change that has occurred since two or more lineages diverged. The opposite of primitive in this usage is not “advanced” but “derived”. There is no automatic implication that change has been progressive in this sense.

So, one should not draw a comparison between “primitive versus advanced”, but “primitive versus derived” is not problematic. It bears noting, though, that the terms primitive (or ancestral) and derived are actually applicable to particular characters, not to entire organisms. As Crisp and Cook (2005) noted,

Once two lineages have separated, each evolves new characters independently of the other and, with time, each will show a mixture of plesiomorphic [inherited largely unchanged from the ancestor] and apomorphic [newly evolved and thus not possessed by the ancestor] character states. Therefore, extant species in both lineages resemble, to varying degrees, their common ancestor. Consequently, whereas character states can be relatively ancestral (plesiomorphic) or derived (apomorphic), these concepts are nonsensical when applied to whole organisms.

_______

Crisp, M.D. and L.G. Cook. 2005. Do early branching lineages signify ancestral traits? Trends in Ecology and Evolution 20: 122-128.

Johannsen, W. 1911. The genotype conception of heredity. American Naturalist 45: 129-159.


Phylogenetic fallacies: "branching from a main line".

Posted on by

In my previous post, written in response to a more egregious fallacy about evolutionary trees presented in a science news story, I focused on the misconception that an “early branching” lineage was necessarily “primitive” (i.e., very similar to a distant ancestor). This time, I want to discuss something slightly more subtle, but nonetheless important, with regard to interpreting phylogenies. Specifically, I want to note a problem with the very concept of one lineage “branching off from” another lineage.

There can be a tendency to consider evolutionary trees as reflecting a main line with a series of “side branches”. This is especially true when the tree is “unbalanced” (lineages are depicted with uneven amounts of diversity) and “ladderized” (the more diverse branches are placed on the same side of each node). The following is a general unbalanced, right-ladderized tree.


This sort of diagram is often interpreted as implying that there is a “main line” leading from a distant ancestor up through time to species A, and that the lineages now represented by species H, G, F, E, D, C, and B “branched off” from this main line earlier or later, in that order. However, one can just as accurately represent this phylogeny with several of the branch points (nodes) rotated with no effect on the order of branching (topology), as shown in the next figure. A is still closest to B, then C, then D, and so on, just as with the previous representation.

Looking at the most recent split, between A and B, in this version of the phylogeny, it would not make much sense to argue that one branched off from the lineage of the other — they are both derived from a common ancestor from whom their respective lineages diverged at the same time. Likewise, the lineage leading to H did not branch first off a main lineage leading to A, rather it and the lineage that ended up leading to G and all the other species split into two.

Looking at a real example, one can see how the main line fallacy creeps in when interpreting evolutionary trees. Here is a phylogeny showing the relationships among several lineages of vertebrates, namely cartilaginous fishes, some bony fishes, and some tetrapods. It might be tempting to see this as indicating that sharks branched first, then bony fishes, then amphibians, then birds.
This, like the abstract trees presented previously, is unbalanced and ladderized. Humans are placed at one end, as they usually are (even though this is an arbitrary decision — birds could just as accurately assume the rightmost position by rotating their shared node). However, notice what happens when we rotate some nodes and change the sampling of species presented in the phylogeny. In this case, sharks, humans, frogs, and bony fishes are included, but the diversity of bony fishes, which make up about half of all vertebrates, is slightly better reflected.
If one were to interpret the revised phylogeny in the same way as the first one, then one would conclude that sharks branched first from the main line leading to perch, then the lineage leading to humans and frogs, then the lineage represented by trout, then the one represented by goldfish.

The point here is that one can only talk about which lineages “branched first” when one has a main line in mind from which other lineages can be considered side tracks. In the case of the “earliest branching animals” discussed in the last post, the lineage now represented by ctenophores and the one that ended up including all the other living animal lineages would simply have split from a common ancestor, and at the time it would not have been possible to identify either line as a branch off the other.

________

Images from Gregory TR. 2008. Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137.


Phylogenetic fallacies: "early branching equals primitive".

Posted on by

Evolutionary trees, or “phylogenies”, are a major part of modern evolutionary science. They depict hypotheses regarding the relationships among taxa, and are therefore important in reconstructions of the historical path of evolution (Gregory 2008a,b). Various approaches can be taken to formulating phylogenetic hypotheses, including analyses based on morphological, fossil, and/or molecular data. These methods often agree well, but sometimes one or another can throw up some surprises and challenge previous hypotheses about the relationships among groups of organisms. Reconstructing the tree of life is a difficult and complicated process, and one should expect there to be significant refinements and revisions along the way. This is especially true of the deepest branches of the tree, which are often the most difficult to resolve.

Case in point, the Tree of Life Web Project gives the following summary of deep branches among major animal lineages:
Two things are apparent from this phylogeny. First, most of the branchings (“nodes”) are unresolved at the deepest point. This is known as a “soft polytomy”, meaning that these lineages probably did not emerge all at the same time from a distant ancestor, but rather that the data simply are not sufficient at present to determine the order of their branching. Second, sponges (Phylum Porifera) are typically considered to represent descendants of the earliest branching lineage.

Sponges are simple, sessile, filter-feeding animals comprised of only a handful of cell types. It has commonly been suggested that they retain characteristics similar to those of some of the earliest animals to appear. In other words, even though they are modern species, it is thought that their simplified morphology reflects the ancestral condition, having undergone little change over hundreds of millions of years of evolution.

Recently, a study by Dunn et al. (2008) using a comparatively large genetic dataset suggested something of a shake-up of the evolutionary tree at the deepest branches. Specifically, their data suggested that comb jellies (Phylum Ctenophora), rather than sponges, are modern representatives of the earliest branching lineage.

From Dunn et al. (2008). Click for larger view.

Ctenophores are superficially similar to jellyfish, and are much more complex than sponges. On the face of it, finding that ctenophores are descended from the earliest-branching animals is surprising. However, this should not be taken too far, as it has in some of the press surrounding the article. For example, LiveScience presented a report entitled “Shock: First animal on Earth was surprisingly complex“. As they describe the situation,

Earth’s first animal was the ocean-drifting comb jelly, not the simple sponge, according to a new find that has shocked scientists who didn’t imagine the earliest critter could be so complex.

This interpretation illustrates a common misconception about evolutionary trees, one that I addressed in a recent paper on the topic (Gregory 2008b). Specifically, it draws the false conclusion that a modern member of an early branching lineage is very similar to the distant ancestor that it shares with other lineages. In actuality, the species under consideration are all modern species whose lineages have been evolving for exactly the same amount of time since their divergence from a common ancestor. The comb jelly lineage may have branched first, but the common ancestor from which it and the other animals lineages diverged probably looked nothing like a comb jelly. It is entirely possible that comb jellies are highly derived (i.e., very different from their early ancestor), just as other animal lineages are.

Consider the phylogeny below, which presents relationships among the living groups of echinoderms:

From Gregory (2008b).

In this case, humans are presented as the outgroup of the tree. Even though humans are shown as having branched earliest in this phylogeny, one cannot conclude that they look anything like the common ancestor shared by vertebrates and echinoderms. Unfortunately, this sort of misinterpretation is not uncommon for less obvious comparisons, even in the primary literature (Crisp and Cook 2005).

Dunn et al. (2008) provide a very reasonable interpretation of the data that does not mesh with that presented in the opening of the LiveScience report:

The placement of ctenophores (comb jellies) as the sister group to all other sampled metazoans is strongly supported in all our analyses. This result, which has not been postulated before, should be viewed as provisional until more data are considered from placozoans and additional sponges. If corroborated by further analyses, it would have major implications for early animal evolution, indicating either that sponges have been greatly simplified or that the complex morphology of ctenophores has arisen independently from that of other metazoans.

This is to say, one cannot take the finding as well established without further data, and even if it is corroborated it simply means that either ctenophores evolved their level of complexity independently of other animal lineages (i.e., the common ancestor was simple), or sponges are secondarily simplified (i.e., the common ancestor was fairly complex). Neither scenario is especially shocking, given that the sponges and comb jellies being studied are modern groups.

Strangely enough, the LiveScience story includes this information, but the implications of it apparently were not grasped:

Dunn says that two evolutionary scenarios can explain why the comb jellies would actually have been first among animals. The first is that the comb jelly evolved its complexity independent of other animals after branching off to forge its own path.

The second is that the sponge evolved its simpler form from the more complex form. This second possibility underscores the fact that “evolution is not necessarily just a march towards increased complexity,” Dunn said.

The first animals probably were not very similar to comb jellies as we now know them, namely as representatives of a lineage that has been evolving for hundreds of millions of years since diverging from those of other major animal groups. Sponges, too, have been evolving for hundreds of millions of years, and there is no reason to assume that they have not undergone any significant morphological changes in that time. Molecular data provide insights into the order of branching, but fossils are required in order to reach conclusions about morphological change or lack thereof over evolutionary timescales.

In short, one cannot assume that a modern representative of an early branching lineage is the same as the ancestor from which it is descended.

_______

Crisp, M.D. and L.G. Cook. 2005. Do early branching lineages signify ancestral traits? Trends in Ecology and Evolution 20: 122-128.

Dunn, C.W., A. Hejnol, D.Q. Matus, K. Pang, W.E. Brown, S.A. Smith, E. Seaver, G.W. Rouse, M. Obst, G.D. Edgecombe, M.V. Sorensen, S.H.D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R.M. Kristensen, W.C. Wheeler, M.Q. Martindale, and G. Giribet. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452: 745-749.

Gregory, T.R. 2008a. Evolution as fact, theory, and path. Evolution: Education and Outreach 1: 46-52.

Gregory, T.R. 2008b. Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137.

______

Update:

See also Stranger Fruit and Nimravid. I should also have noted that this comparison only includes representatives of lineages that survived to the present. Ctenophores may be members of the earliest branching living lineage (I remain skeptical, mind you), but many lineages may have diverged earlier but subsequently vanished — again, this would mean that modern ctenophores were not the first animals (and, besides, it’s quite possible that the Ediacarans were the first animals but neither sponge nor ctenophore). And the whole notion of “diverged first” is somewhat misleading — there was a split and two lineages diverged from each other; one is not a side branch of a main line.


What is a just-so story?

Posted on by

As I and others have noted many times, facts, theories, and hypotheses are independent elements in the scientific process. Contrary to their vernacular meanings, they are not ranks indicating differential degrees of certainty in some claim.

Evolution is scientific fact, meaning that the numerous types of evidence point so overwhelmingly to shared ancestry that scientists have accepted it as true about the world, in the same provisional-but-extremely-likely sense that they accept other facts like gravity or the existence of atoms.

Evolution is also a theory, meaning that there is a cohesive body of mechanistic explanations that seeks to explain the historical fact of common descent. This includes, but is not limited to, random processes like genetic drift, quasi-random ones such as mutation, and absolutely non-random ones like natural selection.

In addition to being a fact (that species are related through common ancestry) and a theory (well supported mechanisms that explain how evolutionary change happens), evolution represents the unique historical path that living lineages have followed. Whereas there is no longer any real disagreement in biology (or indeed, in science in general) over the historical factuality of common relatedness, evolutionary biology is rife with heated debate regarding the mechanisms and their relative importance, the specific historical relationships linking related groups, and the intermediate steps that occurred in the origin of particular features. As such, hypotheses are also important in evolutionary biology, because they represent testable statements that are used to support or refute specific details of theory or path.

One of the more stinging criticisms that evolutionary biologists level at each other when they argue about evolution as path is to call a proposed account a “just-so story”. The phrase itself comes from Rudyard Kipling’s Just So Stories from the early 1900s, many of which included fantastical accounts of the origins of particular features, like the elephant’s trunk, the leopard’s spots, and the giraffe’s neck. According to Wikipedia,

A just-so story, also called the ad hoc fallacy, is a term used in academic anthropology, biological sciences, and social sciences. It describes an unverifiable and unfalsifiable narrative explanation for a cultural practice or a biological trait or behavior of humans or other animals. The use of the term is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. Such tales are common in folklore and mythology.

The important criterion in whether something represents a just-so story rather than a hypothesis is a lack of testability and hence unfalsifiability. A lack of complete supporting data in itself is not an indicator that something is a just-so story, because many hypotheses also lack these prior to being subjected to testing. In other words, what matters is whether it can be tested, not whether it has already been tested, though obviously some supporting data must be provided eventually if the hypothesis is to be considered seriously.

Creationists, who seem unequipped with irony detectors, tend to dismiss all hypotheses about evolutionary path, even ones for which there is substantial supporting evidence, as just-so stories. In fact, they often demand an absurd amount of evidence and detail, such as an observable, repeatable, mutation-by-mutation demonstration of some feature evolving. When this obviously cannot be delivered (nor could its counterpart in any science), they believe this supports their unobservable, unrepeatable, vague explanation for the feature’s origins. Theirs is the ultimate just-so story, but that does not prevent them from projecting onto scientists.

As a case in point, consider the infamous bombardier beetles, which I mentioned briefly in a recent post. Along with eyes, blood clotting, the immune system, and bacterial flagella, the defence mechanism of these intriguing beetles supposedly represents an un-evolvable feature due to its irreducible complexity.

The claims made by creationists about these beetles relate to both fact and path. In terms of fact, they often suggest that the reagents used in its defensive system will explode when mixed together, and thus that their mechanism of storing them separately must have arisen fully formed. This is demonstrably false. A catalyst is required, as Dawkins showed by mixing the liquids.

With regard to path, they argue that a series of functional intermediates in the gradual evolution of the defensive apparatus is impossible in principle. This claim is also easily refuted by the presentation of plausible, testable hypotheses showing how functional intermediates could have occurred. One example is given in this video.

Now, is this the answer to how the spectacular defence system of bombardier beetles arose? I do not know, but I suspect probably not. A similar point of view is presented by Mark Isaak, who authored the Talk.Origins article Bombardier beetles and the argument of design:

The scenario above is hypothetical; the actual evolution of bombardier beetles probably did not happen exactly like that … Determining the actual sequence of development would require a great deal more research into the genetics, comparative anatomy, and paleontology of beetles. The scenario does show, however, that the evolution of a complex structure is far from impossible. The existence of alternative scenarios only strengthens that conclusion.

Are such scenarios just-so stories? No, they are hypotheses, and they are testable. For example, are the hypothetical intermediate stages found to be functional in any other species? Are the chemicals used in combination in the defence system also functional on their own elsewhere in the beetle’s body? Are there genetic differences between bombardier beetles and other Carabidae related to this system?

Without clear answers to these and other questions, the path of bombardier beetle evolution will remain an open and interesting question. However, biologists do not assume that these beetles did not evolve simply because the specific path has yet to be elucidated. And they certainly would not assume that an untestable, supernatural just-so story of cosmic proportions is the null hypothesis.

That, of course, is the difference between science and pseudoscience.


Bombardier beetles.

Posted on by

Last night, after Larry Moran‘s interesting and informative talk, a student (not one who had taken my evolution course, I should say) brought up irreducible complexity. Not flagella, as I was expecting, but the bombardier beetle. How could this evolve when you need all the chemicals and they explode when you combine them? You know the story. Larry responded graciously (note: that is not a typo) and explained about shifts in function and used an example from his own area of study, biochemistry.

For those who think that the bombardier beetle is a problem to explain, here are some resources you may find helpful.

Bombardier beetles and the argument from design (Talk.Origins)


The great headline mismatch.

Posted on by

So, on ScienceDaily there is a story (adapted from a press release by the University of Bath) about an interesting study in PNAS regarding patterns of macroevolution in crustaceans. In particular, it seems that there is often an increase in morphological complexity over time in different lineages within this group, which makes sense because complexity in this case relates to specialization of limbs and so on. (Lineages necessarily begin simple, with repeated segments that are the same, then some limbs evolve to become specialized for feeding, walking, swimming, and so on — it’s probably a driven trend in that it is adaptive to have specialized features, but one also can really only increase in complexity when the beginning is around some minimum level of simplicity, as one of the authors notes in the story).

Here is the abstract:

The prospect of finding macroevolutionary trends and rules in the history of life is tremendously appealing, but very few pervasive trends have been found. Here, we demonstrate a parallel increase in the morphological complexity of most of the deep lineages within a major clade. We focus on the Crustacea, measuring the morphological differentiation of limbs. First, we show a clear trend of increasing complexity among 66 free-living, ordinal-level taxa from the Phanerozoic fossil record. We next demonstrate that this trend is pervasive, occurring in 10 or 11 of 12 matched-pair comparisons (across five morphological diversity indices) between extinct Paleozoic and related Recent taxa. This clearly differentiates the pattern from the effects of lineage sorting. Furthermore, newly appearing taxa tend to have had more types of limbs and a higher degree of limb differentiation than the contemporaneous average, whereas those going extinct showed higher-than-average limb redundancy. Patterns of contemporary species diversity partially reflect the paleontological trend. These results provide a rare demonstration of a large-scale and probably driven trend occurring across multiple independent lineages and influencing both the form and number of species through deep time and in the present day.

The news release itself is interesting, and includes an excellent quote from the study’s lead author Sarah Adamowicz:

Our results apply to a group of animals with bodies made of repeated units. We must not forget that bacteria – very simple organisms – are among the most successful living things. Therefore, the trend towards complexity is compelling but does not describe the history of all life.

And yet, the headline of the piece is…

First ‘Rule’ Of Evolution Suggests That Life Is Destined To Become More Complex

Do the people who determine headlines not even read the stories?


Evolutionary trees for Darwin Day.

Posted on by

In time for Darwin Day, my article on “Understanding evolutionary trees” in the forthcoming issue of Evolution: Education and Outreach is now freely available as a preprint online.

Here is the article abstract:

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Gregory, TR. 2008. Understanding evolutionary trees. Evolution: Education and Outreach 1: in press.

I have also started a series on the topic at DNA and Diversity.

My earlier piece “Evolution as fact, theory, and path” is also free to access.


Darwin Day.

Posted on by

Today is the 199th anniversary of Charles Darwin’s (and Abraham Lincoln’s) birth, and is being celebrated around the globe as Darwin Day. Here are some things to check out.

The evidence and the quality of the theory, not the man, is the source of authority.
Source