Google Earth for The Tree of Life

Head over to The Loom and see Carl Zimmer’s New York Times article on Crunching the data for the tree of life. I quite like the “Google Earth” analogy, and I certainly look forward to the day that we can zoom in and out of phylogenetic trees. (There is one major difference, however: the form of the planet shown in Google Earth is based on direct photos, whereas every phylogeny is a hypothesis that must be tested).

CBC Sunday Edition on Darwin.

Today’s Sunday Edition on CBC was about Darwin. Guests included Brian Alters, Ken Miller, and Ruth Padel. (Padel is Darwin’s great-great-granddaughter and has a book entitled Darwin: A Life in Poems).

A schedule of the program is available here. The podcast is not up yet, but when it is, it will be here.

Evolution: Education and Outreach, vol. 2 issue 1.

This year, Evolution: Education and Outreach will have a special (but not exclusive) focus on Darwin in celebration of the 200th anniversary of his birth and the 150th anniversary of the Origin of Species.

The first issue in volume 2 is now available, once again free online.

Evolution: Education and Outreach
Volume 2, Issue 1

Editorial: Darwin’s Year
Niles Eldredge and Gregory Eldredge
1

Why Darwin?
Niles Eldredge
2-4

Artificial Selection and Domestication: Modern Lessons from Darwin’s Enduring Analogy
T. Ryan Gregory
5-27

Charles Darwin and Human Evolution
Ian Tattersall
28-34

Experimenting with Transmutation: Darwin, the Beagle, and Evolution
Niles Eldredge
35-54

Studying Cultural Evolution at the Tips: Human Cross-cultural Ecology
Lauren W. McCall
55-62

Industrial Melanism in the Peppered Moth, Biston betularia: An Excellent Teaching Example of Darwinian Evolution in Action
Michael E. N. Majerus
63-74

Assessment of Biology Majors’ Versus Nonmajors’ Views on Evolution, Creationism, and Intelligent Design
Guillermo Paz-y-Miño C. and Avelina Espinosa
75-83

Darwin’s “Extreme” Imperfection?
Anastasia Thanukos
84-89

Don’t Call it “Darwinism”
Eugenie C. Scott and Glenn Branch
90-94

Educational Malpractice: The Impact of Including Creationism in High School Biology Courses
Randy Moore and Sehoya Cotner
95-100

Scholar’s Dilemma: “Green Darwin” vs. “Paper Darwin,” An Interview with David Kohn
Mick Wycoff
101-106

The “Popular Press” Responds to Charles Darwin, The Origin of Species and His Other Works
Sidney Horenstein
107-116

Paleontology and Evolution in the News
Sidney Horenstein
117-121

Charles Darwin’s Manuscripts and Publications on the World Wide Web
Adam M. Goldstein
122-135

Teaching Evolution in Primary Schools: An Example in French Classrooms

Bruno Chanet and François Lusignan
136-140

Why Why Darwin Matters Matters
Why Darwin Matters: The Case Against Intelligent Design, by Michael Shermer. New York: Henry Holt, 2006.
Tania Lombrozo
141-143

DeSalle’s and Tattersall’s Human Origins: A Companion to The Museum of Natural History’s Hall of Human Origins and More
Human Origins: What Bones and Genomes Tell Us about Ourselves, by Rob DeSalle and Ian Tattersall. College Station: Texas A & M University Press, 2008. Pp. 216. H/b $ 29.95
Robert Wald Sussman
144-147

I am not certain whether the dedication we wrote to the late Dr. Majerus will appear online, but I am hoping it will be included in the print issue. Here it is, just in case.

This issue of Evolution: Education and Outreach includes a paper by Prof. Michael Majerus of Cambridge University, a world expert on industrial melanism and a champion of the peppered moth as an excellent example of natural selection in the wild. In it, Prof. Majerus describes the controversy surrounding the peppered moth, much of it based on misrepresentations and misunderstandings. He also describes, with extraordinary modesty, his own widely respected research which has refuted the misplaced criticism of the peppered moth example.

We consider the paper a testament to Prof. Majerus’s patience and dedication to settling debates in science as they should be settled – with evidence rather than rhetoric. In this regard, Prof. Majerus’s paper not only highlights an exquisite example of evolution in action, but also serves to illustrate how careful scientific study generates outstanding results.

It is with deep regret that we note that Prof. Majerus passed away peacefully during the night of January 26/27 from a brief but severe illness. As Prof. David Summers, Head of the Department of Genetics at Cambridge, wrote

“Mike Majerus was a traditional Cambridge scientist; a charismatic individual for whom the boundaries between life and work, and teaching and research, were very hard to discern. He was a world authority in his field, a tireless advocate of evolution and an enthusiastic educator of graduate and undergraduate students.”

We are proud to present Prof. Majerus’s article on the peppered moth and are grateful for his contribution to the journal, for his important and diligent research, and for his dedication to defending and enhancing science education. We extend our deepest condolences to his family, friends, and colleagues. He will be missed.

T. Ryan Gregory
Associate Editor

Niles Eldredge
Editor-in-Chief

Facebook groups.

I tend to use Facebook only occasionally, but the existence of more and more evolution-related groups there has me thinking about logging in more frequently. Here are just a few. If you use Facebook, maybe stop in and see if any are of interest to you.

Bird strikes and DNA barcodes.

I don’t know if the same people are giving the same arguments against DNA barcoding anymore as I have pretty much stopped following those old discussions out of exhaustion. We can argue about how much influence DNA methods should have on alpha taxonomy (ranging from “none” to “who needs names, just use DNA sequences” — the latter being DNA taxonomy rather than DNA barcoding, and not a position that I endorse). What is silly to argue is that DNA barcoding would not have any practical roles that can’t already be covered just as easily, cheaply, and accurately by morphology-based identification.

Here’s a story in the New York Times about the importance of identifying which species are involved in airplane bird strikes.

Identifying the Bird, When Not Much Bird Is Left

It talks about the use of feathers and feet (i.e., morphology) and also describes the use of DNA (new word: “snarge“). It does not mention DNA barcoding per se, but it bears noting that the FAA and USAF support DNA barcoding efforts at the Smithsonian. In general, it would be best to have as many tools as possible, including sequencing DNA and comparing this against the bird DNA barcode dataset, which already encompasses more than 2600 species (out of about 10,000) and means to include every bird on the planet within the next several years.

Arguments creationists should not use.

Creation Ministries International (formerly Answers in Genesis) has an interesting list of “Arguments we think creationists should not use“. Of course, anti-evolutionists regularly engage in less than honest tactics, including quote-mining, propaganda, and outright distortions, but in this case I applaud their candor. Here are some of the notable arguments listed, many of which you have undoubtedly heard many times — next time, just point out that even one of the leading creationist groups recognizes that these are not valid. (Obviously, the spin provided on these differs from what scientists think — see the original list for their explanations).

Which arguments should definitely not be used?

  • Darwin recanted on his deathbed.
  • Moon-dust thickness proves a young moon.
  • NASA computers, in calculating the positions of planets, found a missing day and 40 minutes, proving Joshua’s “long day” and Hezekiah’s sundial movement of Joshua 10 and 2 Kings 20.
  • The Japanese trawler Zuiyo Maru caught a dead plesiosaur near New Zealand.
  • If we evolved from apes, why are there still apes today?
  • Women have one more rib than men.
  • Archaeopteryx is a fraud.
  • There are no beneficial mutations.
  • No new species have been produced.
  • Paluxy tracks prove that humans and dinosaurs co-existed.
  • Darwin’s quote about the absurdity of eye evolution from Origin of Species.
  • Light was created in transit.

What arguments are doubtful, hence inadvisable to use?

  • Natural selection as tautology.
  • Evolution is just a theory.
  • There is amazing modern scientific insight in the Bible.
  • The speed of light has decreased over time.
  • There are no transitional forms.
  • Creationists believe in microevolution but not macroevolution.

American stimulus package gutted of science.

Of the many things cut from the revised American stimulus package…

• $75 million from Smithsonian (original bill $150 million)

• $200 million from Environmental Protection Agency Superfund (original bill $800 million)

• $100 million from National Oceanic and Atmospheric Administration (original bill $427 million)

• $65 million for watershed rehabilitation

• $50 million for aquaculture

• $2 billion for broadband

• $50 million for NASA

• $50 million for aeronautics

• $200 million for National Science Foundation

• $100 million for science

• $25 million for Fish and Wildlife

• $3.5 billion for higher education construction

Well, it was a nice dream while it lasted.

On the Origin of Species – Chapter 3.

Chapter 3 – Struggle for Existence

This is the chapter in which Darwin really picks things up. Whereas the first two may have been more like, in Darwin’s own words, “a dry list of facts”, this one is written in a very passionate tone. Having established that individuals vary both in domesticated breeds and in nature, he now moves into the second major ingredient of natural selection: overproduction.

Some important things in this chapter:

1) Darwin strongly emphasizes adaptation. This is not very surprising, given that he considered natural selection as the main (but not only) mechanism of evolution.

“But the mere existence of individual variability and of some few well-marked varieties, though necessary as the foundation for the work, helps us but little in understanding how species arise in nature. How have all those exquisite adaptations of one part of the organisation to another part, and to the conditions of life, and of one distinct organic being to another being, been perfected? We see these beautiful co-adaptations most plainly in the woodpecker and missletoe; and only a little less plainly in the humblest parasite which clings to the hairs of a quadruped or feathers of a bird; in the structure of the beetle which dives through the water; in the plumed seed which is wafted by the gentlest breeze; in short, we see beautiful adaptations everywhere and in every part of the organic world.”

2) We may think life is well balanced and peaceful, but there is carnage going on all around, if not right this moment then at the very least during difficult seasons.

“We behold the face of nature bright with gladness, we often see superabundance of food; we do not see, or we forget, that the birds which are idly singing round us mostly live on insects or seeds, and are thus constantly destroying life; or we forget how largely these songsters, or their eggs, or their nestlings, are destroyed by birds and beasts of prey; we do not always bear in mind, that though food may be now superabundant, it is not so at all seasons of each recurring year.”

“Although some species may be now increasing, more or less rapidly, in numbers, all cannot do so, for the world would not hold them.”

3) The struggle for life can be against the environment (e.g., surviving in cold or dry habitats), but the major factor is the biotic environment. He also points out that what matters more than survival is reproduction.

“I should premise that I use the term Struggle for Existence in a large and metaphorical sense, including dependence of one being on another, and including (which is more important) not only the life of the individual, but success in leaving progeny. Two canine animals in a time of dearth, may be truly said to struggle with each other which shall get food and live. But a plant on the edge of a desert is said to struggle for life against the drought, though more properly it should be said to be dependent on the moisture. A plant which annually produces a thousand seeds, of which on an average only one comes to maturity, may be more truly said to struggle with the plants of the same and other kinds which already clothe the ground. The missletoe is dependent on the apple and a few other trees, but can only in a far-fetched sense be said to struggle with these trees, for if too many of these parasites grow on the same tree, it will languish and die. But several seedling missletoes, growing close together on the same branch, may more truly be said to struggle with each other. As the missletoe is disseminated by birds, its existence depends on birds; and it may metaphorically be said to struggle with other fruit-bearing plants, in order to tempt birds to devour and thus disseminate its seeds rather than those of other plants. In these several senses, which pass into each other, I use for convenience sake the general term of struggle for existence.”

4) Darwin considers extinction to be gradual, not catastrophic (he acknowledges what we now call background extinction but not mass extinctions).

“Battle within battle must ever be recurring with varying success; and yet in the long-run the forces are so nicely balanced, that the face of nature remains uniform for long periods of time, though assuredly the merest trifle would often give the victory to one organic being over another. Nevertheless so profound is our ignorance, and so high our presumption, that we marvel when we hear of the extinction of an organic being; and as we do not see the cause, we invoke cataclysms to desolate the world, or invent laws on the duration of the forms of life!”

5) Darwin recognizes different strategies of reproduction (what we now call r-selection and K-selection).

“A large number of eggs is of some importance to those species, which depend on a rapidly fluctuating amount of food, for it allows them rapidly to increase in number. But the real importance of a large number of eggs or seeds is to make up for much destruction at some period of life; and this period in the great majority of cases is an early one. If an animal can in any way protect its own eggs or young, a small number may be produced, and yet the average stock be fully kept up; but if many eggs or young are destroyed, many must be produced, or the species will become extinct.”

6) Competition is most intense between members of the same species because their requirements are so similar.

“But the struggle almost invariably will be most severe between the individuals of the same species, for they frequent the same districts, require the same food, and are exposed to the same dangers.”

7) At higher levels, closely related species experience more intense competition than distantly related species, again because their requirements are similar.

“As species of the same genus have usually, though by no means invariably, some similarity in habits and constitution, and always in structure, the struggle will generally be more severe between species of the same genus, when they come into competition with each other, than between species of distinct genera.

Some famous quotes:

“Again, it may be asked, how is it that varieties, which I have called incipient species, become ultimately converted into good and distinct species, which in most cases obviously differ from each other far more than do the varieties of the same species? How do those groups of species, which constitute what are called distinct genera, and which differ from each other more than do the species of the same genus, arise? All these results, as we shall more fully see in the next chapter, follow inevitably from the struggle for life. Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man’s power of selection. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.”

“We can dimly see why the competition should be most severe between allied forms, which fill nearly the same place in the economy of nature; but probably in no one case could we precisely say why one species has been victorious over another in the great battle of life.”