Brief response to comments on E:EO.

Various bloggers on my must-read list have weighed in on the latest issue of Evolution: Education and Outreach, which focuses on transitional fossils (guest editor, Don Prothero). It is great to see the articles being discussed and recommended. A couple of minor responses to the apt comments (not criticisms per se, or at least mostly constructive ones).

@ Sandwalk: Larry is absolutely right that I did not get into the role of drift alongside natural selection in any significant way. This is a more advanced subject that will be covered in a follow-up article “What natural selection does and does not do”.

@ Laelaps: Why no humans? Special issue unto itself coming.

@ Pharyngula: Articles are not really useful for talking with creationists. I agree, but the target audience is teachers, students, postsecondary educators, researchers, and interested laypeople. That said, an article on effective strategies for entering into reasoned discussions with creationist proponents would be appropriate and welcome.

A new transposable element blog.

One of my graduate students has launched a new blog called The Mobilome. As he describes it in his inaugural post,

The goal of this blog is to spread the word about how cool TEs and other parasitic nucleic acids are by talking about interesting elements, papers both old and new and perhaps some educational posts about what TEs in general and why they are important to understand.

He is a voracious reader of the TE literature — heck, his initials are T.E. — so you know this is going to be very interesting…

Head on over to get his hit count up and don’t forget to subscribe here.

Evolution: Education and Outreach, Special issue on transitional fossils.

The latest issue of Evolution: Education and Outreach is now online. This is a special issue on transitional forms edited by Don Prothero, author of Evolution: What the Fossils Say and Why It Matters. The papers are available without charge. Remember to also check out the special issue on the evolution of eyes edited by yours truly from last year.

Evolution: Education and Outreach
Vol 2, Iss 2

Editorials

Editorial
Niles Eldredge and Gregory Eldredge

A Question of Individuality: Charles Darwin, George Gaylord Simpson and Transitional Fossils

Niles Eldredge

Evolutionary Concepts

Understanding Natural Selection: Essential Concepts and Common Misconceptions
T. Ryan Gregory

Special Issue on Transitional Fossils

Introduction
Donald R. Prothero

Palaeontological and Molecular Evidence Linking Arthropods, Onychophorans, and other Ecdysozoa
Gregory D. Edgecombe

Monoplacophorans and the Origin and Relationships of Mollusks
David R. Lindberg

The Evolutionary Emergence of Vertebrates From Among Their Spineless Relatives
Philip C. J. Donoghue and Mark A. Purnell

The Fish-Tetrapod Transition: New Fossils and Interpretations
Jennifer A. Clack

The Evolution of Marine Reptiles
Ryosuke Motani

Evolutionary Transitions Among Dinosaurs: Examples from the Jurassic of China
James M. Clark and Xing Xu

Downsized Dinosaurs: The Evolutionary Transition to Modern Birds
Luis M. Chiappe

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution
Kenneth D. Angielczyk

From Land to Water: the Origin of Whales, Dolphins, and Porpoises
J. G. M. Thewissen, Lisa Noelle Cooper, John C. George and Sunil Bajpai

Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals

Donald R. Prothero

Educational Papers

A Name by Any Other Tree
Anastasia Thanukos

Transforming Our Thinking about Transitional Forms
Louise S. Mead

Access to Evolution
Lara Eldredge

News

Paleontology and Evolution in the News
Sidney Horenstein

Book Reviews

The Charms of Nature: Darwin on Meaning and Value
Darwin Loves You: Natural Selection and the Re-enchantment of the World, by George Levine. Princeton: Princeton University Press, 2006. pp. xxiii + 304, s/b $18.95
Adam M. Goldstein

Illuminating Charles Darwin’s Morality: Slavery, Humanity’s Origin and Unity, and Darwin’s Evolutionary Theory
Adrian Desmond and James Moore, Darwin’s Sacred Cause: How a Hatred of Slavery Shaped Darwin’s Views on Human Evolution. Boston & New York: Houghton Mifflin Harcourt, 2009. Pp. xxi + 485. H/b $30.00
Joel Schwartz

Your Inner Fish
Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the Human Body, by Neil Shubin. Pantheon Books, 2008, 229 pages
Michael Gaspar

WARNING: May bring a tear to your eye and a smile to your face.

Those of you who have been reading this blog for a while will know that my father and stepmother have relocated to Livingstone, Zambia where they are creating a musical theatre program to employ local performers and generate revenue for the community [Webpage / Blog / RSS]. I am very pleased to note that they are now at the point of performing the show.

As a side project, they have also been raising money to help support the Linda West Basic School. This includes installing toilets, painting, drilling a new well, and opening a library. In addition, they have been raising donations to cover uniform and school fees for orphaned kids. What I like most about this is that they are actually there and they know these kids, plus the fact that 100% of the money goes directly to the intended recipient. Along those lines, I thought I’d share an email that my Dad sent to me a couple of days ago.

Warning: may bring a tear to your eye and a smile to your face.

I’m so pleased to finally introduce you to the young students who are now enrolled in Linda West Basic School in Livingstone, thanks to your sponsorship. I’m meeting next week to select some older kids and will let you know about the other two you are helping as soon as I meet up with them.

In any event, yesterday, I met all the kids being sponsored at Linda West and we handed out new school uniforms and books, pens, etc. to each child. The girls each received two dresses and the boys each got two shirts, one pair of shorts, and one pair of pants. Next week we will outfit them with shoes.

[JS] is a real sweetheart and she was thrilled to get her new dress. Notice how she is holding it out in the picture. She was eager to ask how this was all possible and couldn’t believe that she would be returning to school. I think “friends in Canada” is something she did figure out but maybe didn’t even know she had any friends in Canada until now.


[JS] is 12 years old and in Grade 5. She is what is termed a “double orphan” because both her parents have died. She currently lives with her grandfather who has been unable to pay the school fees and uniform costs. She just kept coming to school anyway and eventually the teachers just let her sit in class. Still, it isn’t the same when you don’t dress the same as the others and know you might not be able to continue. She said she likes to sing and play games. When she grows up, she wants to be a teacher or a “business lady”.

[MK] never stopped smiling after he put on his new shorts and shirt. What a beautiful face he has. How can this 11 year old be so spirited after losing both his parents at such a young age? He lives with his grandmother in Linda Compound which is close to where we live so I will see if I can find out more about his living arrangement. Most of the buildings in Linda Compound are one room cement structure often housing several children and adults. That’s the Compound where I donated soccer balls and uniforms and now see about 100 kids playing on the field every weekend.

[MK]’s teachers said he was a “keener’ and loved to read when he was in school before. I’m sure he’ll like the new library we’re opening at the end this month at Linda West. He told me he likes gymnastics and wants to be a soldier or policeman when he grows up. I’ll have to see if his dad was a cop or something.

If you write to either of these kids Marilyn and I will deliver your correspondence. If you have any specific questions about either child just let us know and we’ll find out the answers.

Thanks again for your wonderful gift.

Love you. Miss you.
DAD & Marilyn

Love you and miss you too.

Lamarck on Genome Research (2004).

I came across this cover of the journal Genome Research from 2004.

Genomic imprinting is an epigenetic phenomenon where expression of a gene in this generation depends on whether it resided in a male or female the previous generation, a Lamarckian-like inheritance (portrait: Jean Baptiste Lamarck). Comparative phylogenetic footprint analysis of mammalian species from the nonimprinted monotremes (purple region) and the imprinted marsupials (magenta region) and eutherian mammals (pink region) was used to identify putative cis-acting elements (sequence shown) involved in the origins and evolutionary maintenance of genomic imprinting. Members of the oviparous monotremes (echidna and platypus) and viviparous marsupials (opossum) and eutherians (mouse, lemur, and human) are pictured.

It does not bother me that people want to rescue Lamarck’s reputation — he deserves vastly more respect than he currently gets for his major contributions to taxonomy and evolutionary biology. What bothers me is the effort to present anything remotely resembling the inheritance of acquired characters as Lamarckian. This is just bad history for several reasons, given that Lamarck rejected any direct input from the environment and that the inheritance of acquired traits was not original to Lamarck. It’s disappointing to see a journal fall for this in the same way that others have.

Darwinius masillae.


Participating in Darwin conference this week, so not much time to comment on this announcement. The discovery of Darwinius masillae is pretty intriguing, and I am eager to read the published study. But check out this hype…

Update:
This is a big mess. See these posts by others for the scoop.

Again with the Lamarckism…

Press release from the Quarterly Review of Biology.

100 Reasons to Change How We Think About Genetics

Article Reviews Evidence for Epigenetic Inheritance in Wide Range of Species
For years, genes have been considered the one and only way biological traits could be passed down through generations of organisms.

Not anymore.

Increasingly, biologists are finding that non-genetic variation acquired during the life of an organism can sometimes be passed on to offspring—a phenomenon known as epigenetic inheritance. An article to be published this week in The Quarterly Review of Biology lists over 100 well-documented cases of epigenetic inheritance between generations of organisms, and suggests that non-DNA inheritance happens much more often than scientists previously thought.

Biologists have suspected for years that some kind of epigenetic inheritance occurs at the cellular level. The different kinds of cells in our bodies provide an example. Skin cells and brain cells have different forms and functions, despite having exactly the same DNA. There must be mechanisms—other than DNA—that make sure skin cells stay skin cells when they divide.

Only recently, however, have researchers begun to find molecular evidence of non-DNA inheritance between organisms as well as between cells. The main question now is: How often does it happen?

“The analysis of these data shows that epigenetic inheritance is ubiquitous …,” write Eva Jablonka and Gal Raz, both of Tel-Aviv University in Israel. Their article outlines inherited epigenetic variation in bacteria, protists, fungi, plants, and animals.

These findings “represent the tip of a very large iceberg,” the authors say.

For example, Jablonka and Raz cite a study finding that when fruit flies are exposed to certain chemicals, at least 13 generations of their descendants are born with bristly outgrowths on their eyes. Another study found that exposing a pregnant rat to a chemical that alters reproductive hormones leads to generations of sick offspring. Yet another study shows higher rates of heart disease and diabetes in the children and grandchildren of people who were malnourished in adolescence.

In these cases, as well as the rest of the cases Jablonka and Raz cite, the source of the variation in subsequent generations was not DNA. Rather, the new traits were carried on through epigenetic means.

There are four known mechanisms for epigenetic inheritance. According to Jablonka and Raz, the best understood of these is “DNA methylation.” Methyls, small chemical groups within cells, latch on to certain areas along the DNA strand. The methyls serve as a kind of switch that renders genes active or inactive.

By turning genes on and off, methyls can have a profound impact on the form and function of cells and organisms, without changing the underlying DNA. If the normal pattern of methyls is altered—by a chemical agent, for example—that new pattern can be passed to future generations.

The result, as in the case of the pregnant rats, can be dramatic and stick around for generations, despite the fact that underlying DNA remains unchanged.

LAMARCK REVISITED

New evidence for epigenetic inheritance has profound implications for the study of evolution, Jablonka and Raz say.

“Incorporating epigenetic inheritance into evolutionary theory extends the scope of evolutionary thinking and leads to notions of heredity and evolution that incorporate development,” they write.

This is a vindication of sorts for 18th century naturalist Jean Baptiste Lamarck. Lamarck, whose writings on evolution predated Charles Darwin’s, believed that evolution was driven in part by the inheritance of acquired traits. His classic example was the giraffe. Giraffe ancestors, Lamarck surmised, reached with their necks to munch leaves high in trees. The reaching caused their necks to become slightly longer—a trait that was passed on to descendants. Generation after generation inherited slightly longer necks, and the result is what we see in giraffes today.

With the advent of Mendelian genetics and the later discovery of DNA, Lamarck’s ideas fell out of favor entirely. Research on epigenetics, while yet to uncover anything as dramatic as Lamarck’s giraffes, does suggest that acquired traits can be heritable, and that Lamarck was not so wrong after all.


Eva Jablonka and Gal Raz, “Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution,” The Quarterly Review of Biology, June 2009.

Tell me, how does short-term heritability of methylation, presumably within genetically determined boundaries, bear any resemblance to giraffes stretching their necks?

Why is the “Lamarck was kinda correct” angle so irresistible?

Anyway, I look forward to seeing the argument for how this has major evolutionary impacts, and not just relevance for phenotypic plasticity.