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Wednesday, October 06, 2004

How often do biologists talk about this evolution stuff, anyway?

Echoed on the Panda's Thumb

Creationists like to say that evolution's influence is dying and that it is of little importance to doing biology. They take advantage of the layperson's lack of familiarity with the scientific literature to argue that evolution has little relevance, or that Dobzhansky's aphorism that "nothing makes sense in biology except in the light of evolution" is false. Anyone who actually reads the biological literature, though, will come away with exactly the opposite impression: the journals are full of references to evolution, even in disciplines and journals that don't have "evolution" in their title. The concept is central; it's as ubiquitous as references to "genes".

To demonstrate, I've carried out a quick exercise, similar to one I've done before. The latest copy of one of the major journals in my field, Developmental Biology, just arrived in my mailbox. It's a top-notch journal, affiliated with our biggest organization, the Society for Developmental Biology. It's not evolutionary biology directly, but there has been an increasing awareness of the significance of evolution to our field, so it's a good representative of an expanding, hot field which is experiencing some synergy with other disciplines.

What I did was to quickly skim through each of the 21 articles in Volume 274, Issue 2, of Developmental Biology, and ask myself how much each article depended upon or discussed the topic of evolution. I categorized and color-coded each one by the following criteria:

Blue articles are explicit in their discussion of evolution, proposing evolutionary connections or even testing evolutionary hypotheses. The evolutionary aspect may not be the major point of the paper, but it is discussed.
Green articles treat evolution as implicit; they may work with molecules homologous between different species, but they don't specifically address evolutionary ideas. This is not to say that they have a lesser commitment to evolution, but more that they take it for granted.
Gray articles don't say anything one way or the other about evolutionary relationships. Most often these are papers that are tightly focused on analysis of data from a single species. It's entirely possible to imagine a creationist writing these, but of course there is no implication that the authors deny evolution.
Black articles would be ones that directly discuss Intelligent Design or other anti-evolutionary ideas about science. This is a hypothetical category; none were found.

Here is my classification of each of those articles, with a brief justification for why I put each in its particular category.

PaperJustification
Cellular recruitment and the development of the myocardium
(Review article)
Leonard M. Eisenberg and Roger R. Markwald
"the key to understanding the distinct neural crest contributions to heart development between zebrafish and higher vertebrates relates to the mechanisms that determine their migration patterns among species", but also says that detailed discussion of the issue is beyond the scope of this particular paper
Early neural cell death: dying to become neurons
(Review article)
Weeteck Yeo and Jean Gautier
discusses signalling cascade for apoptosis in C. elegans, and draws analogies with vertebrate cascade that has yet to be demonstrated (a prediction based on evolution);extensive phylogenetic comparisons
The zebrafish onecut gene hnf-6 functions in an evolutionarily conserved genetic pathway that regulates vertebrate biliary development
Randolph P. Matthews, Kristin Lorent, Pierre Russo and Michael Pack
discusses bile duct formation as part of an evolutionarily conserved pathway
WAVE/SCAR, a multifunctional complex coordinating different aspects of neuronal connectivity
Annette Schenck, Abrar Qurashi, Pilar Carrera, Barbara Bardoni, Céline Diebold, Eyal Schejter, Jean-Louis Mandel and Angela Giangrande
focused on the role of the WAVE/SCAR complex in Drosophila; briefly mentions that these same genes also play a role in human mental retardation
SOX9 is up-regulated by the transient expression of SRY specifically in Sertoli cell precursors
Ryohei Sekido, Isabelle Bar, Véronica Narváez, Graeme Penny and Robin Lovell-Badge
only discusses SRY/SOX9 activity in mouse cells
Embryonic development of the Drosophila corpus cardiacum, a neuroendocrine gland with similarity to the vertebrate pituitary, is controlled by sine oculis and glass
Begona De Velasco, Jennifer Shen, Sheryllene Go and Volker Hartenstein
discusses conserved pathways between flies and vertebrates in neuroendocrine development
Requirement for Mab21l2 during development of murine retina and ventral body wall
Ryuichi Yamada, Yoko Mizutani-Koseki, Haruhiko Koseki and Naoki Takahashi
this is a mouse homolog to a C. elegans gene
Multi-state, 4-aminopyridine-sensitive ion channels in human spermatozoa
Y. Gu, J.C. Kirkman-Brown, Y. Korchev, C.L.R Barratt and S.J. Publicover
channel physiology in human sperm only
Differences in expression pattern and function between zebrafish hoxc13 orthologs: recruitment of Hoxc13b into an early embryonic role
Ryan Thummel, Li Li, Carmen Tanase, Michael P. Sarras, Jr. and Alan R. Godwin
testing predictions of theories of gene duplication and evolution in vertebrates
Coordinate regulation of neural tube patterning and proliferation by TGFβ and WNT activity
Catherine Chesnutt, Laura W. Burrus, Anthony M.C. Brown and Lee Niswander
TGFβ and WNT are found to have similar roles in diverse organisms, but the paper only discusses the specifics of its role in chick
The epaxial–hypaxial subdivision of the avian somite
Louise Cheng, Lúcia E. Alvares, Mohi U. Ahmed, Amira S. El-Hanfy and Susanne Dietrich
Many details focused exclusively on chick, but introduced as part of an effort to resolve differences in somite organization within the gnathostomes
Mammalian phospholipase Cζ induces oocyte activation from the sperm perinuclear matrix
Satoko Fujimoto, Naoko Yoshida, Tomoyuki Fukui, Manami Amanai, Toshiaki Isobe, Chiharu Itagaki, Tomonori Izumi and Anthony C.F. Perry
details of a molecule in mouse oocyte activation
Specific PKC isoforms regulate blastocoel formation during mouse preimplantation development
Judith J. Eckert, Amanda McCallum, Andrew Mears, Martin G. Rumsby, Iain T. Cameron and Tom P. Fleming
details of a molecule in mouse blastocyst cavitation
RNT-1, the C. elegans homologue of mammalian RUNX transcription factors, regulates body size and male tail development
Yon-Ju Ji, Seunghee Nam, Yun-Hye Jin, Eun-Jung Cha, Kyeong-Sook Lee, Kyu-Yeong Choi, Hyun-Ok Song, Junho Lee, Suk-Chul Bae and Joohong Ahnn
mostly focused on only C. elegans, only a brief mention of mammalian homology (and would have been more interesting with more discussion of the mammalian connection!)
Formin3 is required for assembly of the F-actin structure that mediates tracheal fusion in Drosophila
Hiromasa Tanaka, Etsuko Takasu, Toshiro Aigaki, Kagayaki Kato, Shigeo Hayashi and Akinao Nose
highly conserved gene family found in yeast and vertebrates, too
Enkurin is a novel calmodulin and TRPC channel binding protein in sperm
Keith A. Sutton, Melissa K. Jungnickel, Yanli Wang, Kay Cullen, Stephen Lambert and Harvey M. Florman
introduction is all about PLC and TRPC activation and Ca++ entry as a universal property in a wide range of animal sperm
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres
Roger Revilla-i-Domingo, Takuya Minokawa and Eric H. Davidson
very detailed, mechanistic analysis of regulation of a specific gene, with a comparison of two urchin species that diverged 50 million years ago
Tissue-specific expression of FoxD reporter constructs in amphioxus embryos
Jr-Kai Yu, Nicholas D. Holland and Linda Z. Holland
this is all about molecules central to the evolution of vertebrate innovations, such as neural crest
Discovery of genes implicated in placode formation
Kathryn L. McCabe, Andrea Manzo, Laura S. Gammill and Marianne Bronner-Fraser
commonalities of gene expression support the hypothesis that neural crest and placodal cells evolved from a common cell type
Identification of downstream genes of the ascidian muscle determinant gene Ci-macho1
Kasumi Yagi, Nori Satoh and Yutaka Satou
evolution of Ciona Zic zinc-finger genes; relationship to patterning genes in flies and vertebrates
Differential requirement for ptf1a in endocrine and exocrine lineages of developing zebrafish pancreas
John W. Lin, Andrew V. Biankin, Marko E. Horb, Bidyut Ghosh, Nijaguna B. Prasad, Nelson S. Yee, Michael A. Pack and Steven D. Leach
phylogenetic comparison of genes involved in formation of the pancreas

Twelve articles explicitly address issues in evolution. Four simply assume evolution, using molecules found in different lineages without bothering to discuss the phylogenetic significance (although the Schenck article was borderline, in that it did mention it, but didn't deal with it much). Five were single species or even single molecule studies that didn't try to relate their results to a comparative picture (which is not a criticism of the work; they are good, detail-oriented papers). The distribution, that a clear majority of the papers contain a significant amount of consideration of evolutionary concepts, is typical of the journals I read.

I would also add that lacking a discussion of evolution in one paper on a subject doesn't mean that the subject as a whole is lacking the concept. The Gu paper on sperm channel physiology is only talking about channel properties in one species, but people interested in that topic would also read the Sutton paper, which spends a fair amount of spacing discussing the phylogenetic significance of channel activation molecules.

None of the papers had or could say anything about Intelligent Design. Creationism simply isn't a legitimate or useful component of our analysis of the data.

I don't expect high school students to be able to open up an issue of Developmental Biology and be able to read any article; I think everyone can tell from the titles that there is some rather esoteric stuff in there. But they will be grossly disadvantaged in learning this material later if they completely lack one of the basic conceptual foundations of the work, evolution. It really would be like trying to read the literature while disbelieving in those godless "genes", or that "catalysts" can't possibly work because they violate the laws of thermodynamics.

Dobzhansky was right.

There are some high school teachers and school board members who can't figure this out…unfortunately, the ones who argue against evolution in the classroom don't seem to be the ones who understand how biology is actually done.


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Comments:
#6813: — 10/06  at  05:50 PM
What a nice exercise and unsurprisingly as well as wonderfully the codes (unlike the homeland security colors or ID) come with evidence that one may examine. I like that you point out there are times, e.g., in single species/molecular studies there is often no need to discuss them in terms of Dobzhansky's dictum but that they are understood in these terms by reading other related papers, a must. And is evolution alive and well, indeed getting better: you bet! Evolutionary concepts? You can't get along with out them if you are to understand the life sciences or the world. Thanks for taking time to do this so colorfully, too.



#6814: Reed A. Cartwright — 10/06  at  06:03 PM
Maybe I should start doing this for Genetics.



's avatar #6815: PZ Myers — 10/06  at  06:15 PM
Yeah, I thought about hitting up a couple of different journals, but it was a bit of work to skim through every article in one issue.

I suspect that if I did J. Neuroscience, the number of evo. related articles would be a bit lower, but still significant. Genetics would probably have a similar proportion. J. Ecology, maybe a bit higher (but I don't usually read that one, so I'm guessing). Something like BioEssays is just crammed full of the stuff.

It's hard to think of a biology discipline that isn't riddled with evolutionary concepts.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#6818: — 10/07  at  02:55 AM
Ah, you see, this just goes to show; you're getting biased, lib-rull journals.

Real red-meat journals with actual content would be very different.

(Look, an avian porcine!)



#6820: Reed A. Cartwright — 10/07  at  03:25 AM
What I'd like to see is how common evolution is mentioned in Biochemistry since there are a handful of anti-evolution biochemists who have remarked that evolution is not critical to their field.



#6821: — 10/07  at  06:11 AM
I think the numbers drop off as you get into the hard-core molecular biology and biochemistry literature... in Oct 8th issue of JBC, out of 119 articles only 11 mention the word evolution, and only 4 explicitly deal with evolutionary concepts, while the rest have only a passing mention of evolution.



#6823: — 10/07  at  07:25 AM
Sniff sniff.

This smells like a job for text mining to me. We could look at all of MEDLINE and tag terms in the abstracts, like "conserved," "ortholog," "paralog," "evolution," etc, then do some basic clustering on the journal name, authors, etc...

Well, it'd be useful for arguing with people who won't be convinced anyway, but I don't know who would publish it.

Bah.



#6841: Loren Petrich — 10/07  at  10:00 PM
It's also worth noting that evolution can happen by "intelligent design"; the IDers are making a false dichotomy.

And the ID'ers also have very closed mind about the multiple-designer hypothesis; that hypothesis seems to me like a self-evident consequence of Archdeacon Paley's watch-needs-a-watchmaker reasoning.



#6843: — 10/08  at  06:25 AM
Sometimes, pz has something valid and interesting to say about biology. Unfortunately, he doesn't seem to realize that railing against ID is neither valid nor even interesting, especially given his tirelessness in loudly and arrhythmically banging on this particular bongo.

For example, consider the following pair of sentences: "None of the papers (in Developmental Biology) had or could say anything about Intelligent Design. Creationism simply isn’t a legitimate or useful component of our analysis of the data."

In this single non sequitur, pz reveals that

(1) ID equals creationism, despite the fact that the ID hypothesis is explicitly more general than creationism (as witness the fact that only a fraction of those who embrace ID also embrace creationism in the conventional sense);

(2) the scientific irrelevance of "Intelligent Design creationism" is somehow implied by its non-mention in a particular science journal, as though no other conceivable reason exists for its exclusion;

(3) in addition to being useless, ID is illegitimate because a single issue of a single journal fails to mention it.

1 is simply a miscarriage of semantics; if pz or anyone else can show that the ID hypothesis implies what has been traditionally understood as "creationism", it's a well- kept secret. 2 and 3 are arguments from authority, which as we all know, carry no actual scientific weight. Moreover, these arguments from authority are tenuous as best. Merely failing to mention a hypothesis is not the same as pronouncing it invalid; although evolution and the ID hypothesis are not in conflict, they address biological phenomena on different levels, and most of the papers in this journal are written on a level that does not require mention of the ID hypothesis.

That is, the purpose of most papers in developmental biology is not to confirm evolution to the exclusion of ID - in all likelihood, that can't be done - but merely to elucidate particular facts or relationships using a certain generic subset of evolutionary principles perfectly compatible with the ID hypothesis, and to that extent confirming ID.

Perhaps pz can show how specific evolutionary principles cited in these papers are inconsistent with ID. But he hasn't done so here (or anywhere else), and it's not merely because he's too busy. It's because he lacks a model of evolutionary causation which excludes ID.



's avatar #6844: PZ Myers — 10/08  at  06:39 AM
1. Intelligent Design is creationism. People do not accept it because there is a convincing body of evidence for it; there is no evidence. They accept it because they want it to be true.

2. My main point was that evolution is a useful, productive framework for doing science, and that as such it is heavily used in my discipline. ID creationists claim that their dogma is also a useful framework...so why isn't it used?

3. This single issue was an exemplar, nothing more. However, we could look through a thousand issues, if we had time, and we'd find the same thing: no intelligent design crap. This is not an argument from authority: it specifically refutes the ID creationist claim that evolution is in decline and that ID creationism is making inroads into scientific thought.

If I lack a model which excludes ID, don't blame me, blame the creationist ideologues behind ID. They've come up with a useless, vague 'theory' that explains nothing.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#6903: Abiola Lapite — 10/10  at  12:07 AM
ID equals creationism, despite the fact that the ID hypothesis is explicitly more general than creationism


Isn't the entire point of ID that there is some sort of intelligent being at work <ahem> creating new lifeforms? What does it mean to say that there is "intelligent" design if one refuses to admit a designer? And if such a designer exists, what is he up to then, if not creating? Sure looks like creationism to me ...



#6904: Tom Morris — 10/10  at  03:10 AM
Neurode...

1. You talk of "the ID hypothesis". Which hypothesis is this? That IC is a valid philosophical argument? Or that one can actually locate IC within organisms and these can not be explained by the theory of evolution? Is it that if we remove regularity and chance, we are only left with design (ie. Dembski's CSI arguments)? Those have yet to make a valid statement about what we will find if these arguments are true. But I'm open to persuasion - precisely what is the ID hypothesis of which you speak, and how can we verify/falsify it?

2. The point that Dr. Myers was making was quite simple - ID advocates (and creationists) claim that evolution does not play an important part in biology - in fact that it is receding. Yet, this small sample goes reasonably far to show how one issue of a biology journal - the SDB's Developmental Biology - utilises evolution as the kernel behind a large chunk of the work that it publishes. The large scale support that the theory of evolution has is not political/religious (like the support that the ID movement has from it's faithful) but is because it has significant explanatory power for the fields which are studied.

3. I am trying to find where Dr Myers suggested that the applicability of ID to the DevBio journal is the only attack that he can make on ID. But here, there is a conflation of what Myers is attacking: the claim that evolution is "of little importance" to the study of biology. Myers demonstrates this through this small scale literature study, and does so pretty well. Of course, there are many other fields than just dev-bio and many more journals to read. But this small sample is a good criticism of that claim. But it is not the only criticism of intelligent design claims. Far from their being a non-sequiter in Myers post, there is a straw man in Neurodes: criticising Myers because, and here's the leap of faith, he has attempted to criticise ID in full. But Myers was only fighting one claim - that of the "little importance" with evolution plays. This, quite rightly, says nothing about any of the other claims. For that, there are still many, many places to look. Talk.Origins archive for one. EvoWiki for another. And any number of other websites, books, journals and other sources of information.

Unlike with ID, we actually have a testable hypothesis here - is evolution useful? My gut says yes. This post says yes. I am predicting that evolution is useful. By useful, I mean that it serves as an explanatory framework accepted by many parts of the academic study of biology and related fields. This sample of DevBio indicates this. I confidently predict that whether you go for journals in genetics, zoology, neuroscience, biochemistry, ecology, taxonomy, anatomy, botany, immunology, or just about any other relevant field, you will find a highly significant amount of papers which utilise the knowledge brought to the field by evolutionary theory.

(Unfortunately, I'm not in a position to confirm whether or not this is true. Philosophy libraries don't hold many journals about biology. Unfortunately.)



#6905: ~DS~ — 10/10  at  06:02 AM
Neurode I could envision that someday we might find evidence that aliens intervened in the course of evolution, or that abiogenesis stated when the Gort Mother Ship purged it's sewage tanks on the Hadaean Earth, or even that the universe is a manufactured item. And who knows, maybe even the discoverer of the first such evidence will have been inspired serendipitously by reading IDC tracts as a youngster.
But what the DI is turning out now is the same shit we've seen from Young Earth Creationists and Hugh Ross for years; there are no transitionals, evo can't increase genetic 'information', evo can't explain the Cambrian Explosion, science cannot address the supernatural becuase it's philosophically bankrupt ... yada yada yada. IDC is not science. Unless by science we're talking about an exclusively anti-evolution ideology which employs the same steaming piles of duplicitous shit used by Creationists, and almost all the adherents to IDC as well as the purveyors of it have a prior commitment to a fundamentalist religious view.



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