HAP DAP.

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(Re-posted from Genomicron 2.0)

In one of my snarkier moments, I coined the term “Dog’s Ass Plot” (DAP) in reference to

A graphical representation of data in any field that, through a lack of clear axis labels, selective inclusion/exclusion of data, visual presentation style, and/or other questionable characteristics, generates a misleading interpretation of the data in the viewer, especially by implying an illusory pattern that is not supported by the available data.

This was based on a figure that purported to demonstrate a relationship between non-coding DNA and complexity.

As I noted,

The sloping of the bars within taxa suggests that this is meant to imply a relationship between genome size and complexity within groups as well, with the largest genomes (i.e., the most non-coding DNA) found in the most complex organisms. This would negate the goal of placing humans at the extreme, as our genome is average for a mammal and at the lower end of the vertebrate spectrum (some salamanders have 20x more DNA than humans). Indeed, the human datum would accurately be placed roughly below the dog’s ass in this figure if it included a proper sampling of diversity.

Now, GraphJam has posted a figure that is not only a superb DAP (i.e., the presentation implies a pattern that extends beyond the data themselves), but a Human’s Ass Plot, or a HAP DAP:

New Educational Model For A New Century

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Over at the home of Genomicron 2.0 (ScientificBlogging.com), physicist, education expert, and Nobel laureate Carl Wieman has an important post about 21st century post-secondary science education.

Optimizing The University – Why We Need a New Educational Model For A New Century

There are currently great needs and great opportunities for improvement in post-secondary science education. As world education improves, we need to provide more students with complex understanding and problem solving skills in technical subjects to allow them to be responsible and successful citizens in modern society.

Emerging research indicates that our colleges and universities are not achieving this. However, there are great opportunities to improve this situation using advances in the understanding of how people learn science and advances in educational technology.

The Woodstock of Evolutionary Biology and eye rolling

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In a recent issue of Science there was a piece by Elizabeth Pennisi on the "Altenberg 16" who will be attending what overhyping journalist Suzan Mazur calls the "Woodstock of Evolutionary Biology", only it "promises to be far more transforming for the world".

Puh-lease. People have been saying that the Modern Synthesis is neither modern nor a synthesis and needs to be expanded for some time. And there are a lot more than 16 people saying it.

Thankfully, Pennisi uses the nonsensical hype to discuss some relevant issues, and even points out that the people involved themselves do not see it as a revolution.

Massimo Pigliucci is no Jimi Hendrix. This soft-spoken evolutionary biologist from Stony Brook University in New York state looks nothing like that radical hard-rock musician whose dramatic guitar solos helped revolutionize rock 'n'roll. But to Suzan Mazur, a veteran journalist who occasionally covers science, Pigliucci is the headliner this week at a small meeting she believes will be the equivalent of Woodstock for evolutionary biology. The invitation-only conference, being held in Altenberg, Austria, "promises to be far more transforming for the world" than the 1969 music festival, Mazur wrote online in March for Scoop.co.nz, an independent news publication in New Zealand.

That hyperbole has reverberated throughout the evolutionary biology community, putting Pigliucci and the 15 other participants at the forefront of a debate over whether ideas about evolution need updating. The mere mention of the "Altenberg 16," as Mazur dubbed the group, causes some evolutionary biologists to roll their eyes. It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing." Mazur's attention, Pigliucci admits, "frankly caused me embarrassment."

My eyes have rolled — and did so again at the sight of this latest report, until I saw that it was much more reasonable.

…no one truly expects a scientific Woodstock. "Woodstock was an immensely popular event celebrating a new musical mainstream," says Newman. "I imagine this will be more like a jam session circa 1962."

I look forward to reading the papers that emerge from the meeting, but I don't expect anything revolutionary — more like some cool ideas to continue discussing.

 

Did Darwin delay?

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In my evolution course, I note that "Darwin spent 20 years working out his ideas and gathering evidence" before releasing On the Origin of Species in 1859. I don't say he "delayed" publication purposely, though in many cases this long period from idea to outcome has been attributed to fear of the reaction from the clergy, colleagues, society at large, his wife, etc. On this issue, a few bloggers have pointed to a recent essay by John van Wyhe (2007), in which it is argued that there was no delay based on fear, only a protracted writing period. Other historians do not necessarily agree, though the blogs I saw did not mention this. As Odling-Smee (2007) says,

…several Darwin scholars are not convinced. Kohn and others agree that the way in which cultural and social pressures influenced Darwin's decisions may have been overplayed, particularly in the public arena, with less attention being paid to the involved process of scientific discovery. But the consensus in the field is likely to remain that a multitude of factors underpinned Darwin's delay.

Kohn points out that searching for explicit references to a "delay" is a simplistic approach to the problem, and that other factors should be considered. For example, Darwin often criticized religion in his notebooks, which suggests that he would have been aware of the probable implications of his theory for religion. It is hard to see how the absence of specific references to a delay rules out any influence of cultural and societal factors on Darwin's decisions, agrees David Quammen, author of The Reluctant Mr Darwin.

Kohn also points out that in Darwin's later publication The Descent of Man, which applied the theory of evolution to humans, Darwin specifically states in the opening lines that he delayed publishing this tome until he was convinced that the climate was right. It seems likely, therefore, that he would have been aware of the controversy his theories would cause from the outset, and probably avoided discussing humans in Origin of Species for this reason.

I think "yes or no" to the question of whether Darwin delayed publication out of fear is very simplistic. Anyone who has written anything of substance knows that sometimes the effect of fear of reaction is procrastination and/or excessive desire to include every piece of information available. Both can cause writing to take longer than it otherwise would. Was Darwin thorough? Yes. Is that one reason it took so long? Undoubtedly. Was he so thorough because of a fear of reaction? Probably at least in part.

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Odling-Smee, L. 2007. Darwin and the 20-year publication gap. Nature 446: 478-479.

Van Wyhe, J. 2007. Mind the gap: did Darwin avoid publishing his theory for many years? Notes and Records of the Royal Society 61: 177-205.

 

 

A few more quotes about non-coding DNA.

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Just for fun, here are some quotes I came across while reading a few sources for a paper I am writing.

Remember, a significant number of creationists, science writers, and molecular biologists want us to believe that non-coding DNA was totally ignored after the term “junk DNA” was published in 1972, that the authors of the “junk DNA” and “selfish DNA” papers denied any possible functions for non-coding elements, and, in the case of creationists, that “Darwinism” is to blame for this oversight. The latter of these is nonsensical as the very ideas of “junk DNA” and “selfish DNA” were postulated as antidotes to excessive adaptationist expectations based on too strong a focus on Darwinian natural selection at the organism level.

For those of you who didn’t read the earlier series, see if you can guess when these statements were made.

(A)

There is a strong and widely held belief that all organisms are perfect and that everything within them is there for a function. Believers ascribe to the Darwinian natural selection process a fastidious prescience that it cannot possibly have and some go so far as to think that patently useless features of existing organisms are there as investments for the future.

I have especially encountered this belief in the context of the much larger quantity of DNA in the genomes of humans and other mammals than in the genomes of other species.

Even today, long after the discovery of repetitive sequences and introns, pointing out that 25% of our genome consists of millions of copies of one boring sequence, fails to move audiences. They are all convinced by the argument that if this DNA were totally useless, natural selection would already have removed it. Consequently, it must have a function that still remains to be discovered. Some think that it could even be there for evolution in the future — that is, to allow the creation of new genes. As this was done in the past, they argue, why not in the future?

(B)

A survey of previous literature reveals two emerging traditions of argument, both based on the selectionist assumption that repetitive DNA must be good for something if so much of it exists. One tradition … holds that repeated copies are conventional adaptations, selected for an immediate role in regulation (by bringing previously isolated parts of the genome into new and favorable combinations, for example, when repeated copies disperse among several chromosomes). We do not doubt that conventional adaptation explains the preservation of much repeated DNA in this manner.

But many molecular evolutionists now strongly suspect that direct adaptation cannot explain the existence of all repetitive DNA: there is simply too much of it. The second tradition therefore holds that repetitive DNA must exist because evolution needs it so badly for a flexible future–as in the favored argument that “unemployed,” redundant copies are free to alter because their necessary product is still being generated by the original copy.

(C)

These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.

(D)

There is a hierarchy of types of explanations we use in efforts to rationalize, in neo-darwinian terms, DNA sequences which do not code for protein. Untranslated messenger RNA sequences which precede, follow or interrupt protein-coding sequences are often assigned a phenotypic role in regulating messenger RNA maturation, transport or translation. Portions of transcripts discarded in processing are considered to be required for processing. Non-transcribed DNA, and in particular repetitive sequences, are thought of as regulatory or somehow essential to chromosome structure or pairing. When all attempts to assign a given sequence or class of DNA functions of immediate phenotypic benefit to the organism fail, we resort to evolutionary explanations. The DNA is there because it facilitates genetic rearrangements which increase evolutionary versatility (and hence long-term phenotypic benefit), or because it is a repository from which new functional sequences can be recruited or, at worst, because it is the yet-to-be eliminated by-product of past chromosomal rearrangements of evolutionary significance.

(E)

This is what I emphasized earlier, that this DNA must have a functional value since nothing is known so widespread and universal in nature that has proven useless.

(F)

I’ve stopped using the term [‘junk’] …Think about it the way you think about stuff you keep in your basement. Stuff you might need some time. Go down, rummage around, pull it out if you might need it.

Answers to be provided in the comments.

No such thing as natural selection?

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In reading an interesting article in the New York Times (in part because it quotes my colleague Andrew MacDougall), I came upon this statement that caused a bit of a cough.

“There’s no such thing as natural selection,” Ziska confides. He is not, he hastens to explain, a creationist. He is merely pointing out that the original 19th-century view of evolution, the one presented by Charles Darwin and Alfred Wallace, is obsolete. Their model presented evolution as a process taking place in a nature independent of human interference. That is almost never the situation today — even at sea, where less than 4 percent of the oceans remain unaffected by human activity, according to a recent article in the journal Science. This interference with nature has set the stage for the success of a growing category of weeds, one exemplified by cheatgrass: invasive plant species.

Yes, humans have some impact on a great portion of the globe, but this is nonsense for at least three reasons. One, just because humans are involved does not make something "artificial selection" and therefore disqualify it as natural selection, even within the formulation of Darwin and Wallace which drew a distinction . Artificial selection is the intentional breeding of organisms on the basis of some characteristic (e.g., sleek body shape in dogs or high yield in crops). If we dump waste in the ocean and this creates new selective pressures on marine animals, this hardly counts as artificial selection. From the point of view of the organisms involved, it is simply a change in the environment, and natural selection will then operate as usual. (As a matter of fact, I don't consider "artificial" and "natural" selection to be fundamentally distinct processes anyhow — feel free to discuss in the comment section). Two, we may influence environments generally, but there are, as we speak, gazillions of organisms out there struggling for survival and hunting, parasitising, avoiding, mating with, and otherwise interacting with one another independent of human action. Three, natural selection is still occurring both in human populations and indeed within human bodies (among pathogenic agents, for example).

(Hat tip: John Hawks blog)

 

E:EO 1(3).

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I have previously been pleased to announce on Genomicron the release of the first two issues of Volume 1 of Evolution: Education and Outreach. I am equally pleased to point out that Issue 3 is now available free online.

As a special treat, I note that editors-in-chief Greg and Niles Eldredge mention Genomicron in their editorial.

Here are the contents of Vol 1, Issue 3

Editorial – Gregory Eldredge and Niles Eldredge

Some Thoughts on “Adaptive Peaks,” “Dobzhansky’s Dilemma”—and How to Think About Evolution – Niles Eldredge

The Concept of Co-option: Why Evolution Often Looks Miraculous – Deborah A. McLennan

Evolutionary Trends – Some Guy

Speciation and Bursts of Evolution – Chris Venditti and Mark Pagel

A Look at Linguistic Evolution – Anastasia Thanukos

“Theory” in Theory and Practice – Glenn Branch and Louise S. Mead

The Importance of Understanding the Nature of Science for Accepting Evolution –

Tania Lombrozo, Anastasia Thanukos, and Michael Weisberg

Do Students See the “Selection” in Organic Evolution? A Critical Review of the Causal Structure of Student Explanations – Abhijeet Bardapurkar

Celebrate Darwin Day, An Event for Education and Outreach in Evolutionary Biology – Rachel M. Goodman

What Conceptions do Greek School Students Form about Biological Evolution? –

Lucia Prinou, Lia Halkia, and Constantine Skordoulis

The Evolution of Evolutionary Thinking in Chile – Rodrigo Medel

Ben Sangari: “It’s About the Science, Stupid!” – Mick Wycoff

Evolution from Darwin to DNA on Show in Brazil – Mick Wycoff

Evolution, Just Say Yes: Prothero on Fossils – Bruce Lieberman

Through a Glass Darkly: Dava Sobel’s Galileo’s Daughter: A Historical Memoir of Science, Faith and Love – Kristin P. Jenkins

“Just So Stories:” Richardson Against Evolutionary Psychology – Ryan D. Tweney

T-Rex in Wonderland: Kentucky’s 27-million-dollar Creation Museum Turns One – Gordy Slack

In The News – Sidney Horenstein

Gecko genome size and cell size.

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One of the many aggravations I encounter when reviewing manuscripts is that some authors greatly overstate the applicability of statistically significant patterns they report. For example, a statistically significant pattern in a small comparison of a few animals may be extrapolated in the discussion to the kingdom at large.

Today I was disappointed to see a paper that is soon to come out in Zoology that does the opposite — i.e. takes a non-significant relationship in a handful of species and pretends that it challenges the importance of broad relationships that have been considered important for decades.

The paper in question is:

Starostova, Z., L. Kratochvil, and M. Flajshans. 2008. Cell size does not always correspond to genome size: phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution. Zoology, in press.

They compared genome size and cell size across 15 geckos and found no correlation. From this, they went on to argue that genome size does not causally influence cell size and that genome size is not under selection due to cell size impacts.

First, let me point out that strong, positive correlations between genome size and cell size have been reported within and across all vertebrate classes including reptiles. So, on a broad scale, the relationship is clear.

Genome size and cell size in reptiles. From Gregory (2001), based on data from Olmo and Odierna (1982).

Second, let me say that I have issues with their methods. For example, they used DAPI as the fluorochrome, which is base-pair specific and can give biased determinations (they recognize this but assume the species are all the same in AT content). Second, they produced fairly substantial error ranges in their measurements given that these were all raised in the lab or obtained from pet shops and not taken from different wild populations (i.e., the variability between conspecifics is probably artifact). Third, they counted “forms” of the same species from different places as being independent in their analyses — so it wasn’t 15 species, rather it was 12 species with several represented by multiple points.

These are not the main problems, though. The first is that they clearly had outliers in the dataset. In particular, Coleomyx brevis (CB) and Coleomyx variegatus (CV) have “large” (~2pg) genomes but comparatively small cells. I don’t think I even need to draw the line through the remaining points, but in case eyeball statistics don’t do it, the correlation is highly significant without them (r = 0.74, p < 0.006) (they recognize this, too, but note the title they chose for the paper nonetheless).

From Starostova et al. (2008).

So, how can this be explained? Well, you have to know something about nucleotypic theory, which these authors actually did mention. It’s not genome size all alone that is the determining factor — nucleus size is critical. The “nucleotype” is defined as “that condition of the nucleus that affects the phenotype independently of the informational content of the DNA” (Bennett 1971). As has been pointed out repeatedly (e.g., by me, Cavalier-Smith, Bennett, and others), the compaction level of DNA in the nucleus adds a second dimension to the relationship. More DNA is one thing, but if it is compressed into a tightly packed, reduced nucleus, then cell size may still be small.

That leads to the second major problem. Looking at the data reported in a previous study (Starostova et al 2005), there is no correlation between genome size and nucleus size. There is, however, a positive correlation between nucleus size and cell size across these reptiles.

Based on databy Starostova et al. (2005).

The two outliers in the genome size vs cell size comparison have more compact nuclei and this allows smaller cell sizes with larger genome size. Cell size is correlated with body size in these geckos, and these two species are “dwarfs” (~4.5g) relative to other species (as big as ~90g). So, there could very easily be selection for reduced cell size which, in this narrow range in DNA amount, was met by a compaction of the nucleus rather than a loss of DNA.

This actually reinforces the strength of nucleotypic theory.

______

Bennett, M.D. 1971. The duration of meiosis. Proceedings of the Royal Society of London B 178: 277-299.

Gregory, T.R. 2001. The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cells, Molecules, and Diseases 27: 830-843.

Olmo, E. and G. Odierna. 1982. Relationships between DNA content and cell morphometric parameters in reptiles. Basic and Applied Histochemistry 26: 27-34.

Starostova, Z., L. Kratchovil, and D. Frynta. 2005. Dwarf and giant geckos from the cellular perspective: the bigger the animal, the bigger its erythrocytes? Functional Ecology 19: 744-749.