Monthly Archives: September 2009

CSI: Common Scientific Illiteracy.

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I don’t watch CSI. Ok, that’s not totally true or this post wouldn’t exist. I almost never watch it. I did catch a re-run while I was eating lunch on the weekend, an episode called “Overload” (some guy was electrocuted and fell off a building — I can’t exactly remember why).

In one scene, the lead character says, in what I assume is his typical “know it all” tone, “Terminal velocity is 9.81 metres per second per second”.

No, it ain’t — the acceleration due to gravity (on Earth) is 9.81 m/s2. The second time unit gives it away — this isn’t a velocity, it is a rate of change of a velocity.

So what?

Well, any kid in high school physics could have picked out that error. But here we have a screenwriter (probably a team of them), a director, producers, all the actors, sound techs, cameramen, editors, and post-production people involved in the scene, and evidently not one of them knows even the most basic physics concepts. More seriously, the producers of the show must assume that it doesn’t matter whether basic facts are checked because the audience is likely similarly uninformed. This really isn’t artistic license, and it adds nothing to the drama. It’s just a goofy mistake that could have been prevented — as Carl Sagan recommended in The Demon-Haunted World — by hiring a grad student to check the script.

Nitpicking? Maybe. But I think it’s a sad situation when no one involved in a science-themed show is even qualified to nitpick.

Omnigenomics.

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Sometimes it is helpful to have a catchy word to describe one’s type of research. I think that’s why “omics” words are so popular — they encapsulate a complex combination of approaches (usually something + genomics, or something-more-than-genomics) in a memorable way that immediately conveys the gist of the field. “Metagenomics” is a good example — it’s the study of a larger assemblage of genomes than just one, usually from an environmental sample of microbes. “Proteiomics” is another, or “transcriptomics”. Of course, this can get out of hand (see here). However, I think the study of genome size (which predates molecular genetics, let alone genomics) deserves a catchy moniker. The problem is, I haven’t really come up with one in the past, so I just end up saying “I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and…” — well, you get the idea.

People like me study entire genomes — every component included, be it gene or pseudogene or repeat or transposable element. We also are interested, not in a few model organisms, but in everything (people usually stare blankly when, to the question “which animals do you work on?”, I reply “all of them”). But what to call such a discipline?

Proposed neologism: “Omnigenomics”

Etymology: Latin “omnis” (all or everything) + genomics (study of genomes)

Sample usage: “What do you do?” / “Omnigenomics” / “What’s that?” / “I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and…”

(The alternative Greek version, “pangenomics”, is already being used and sounds way less cool).

(Yes, I note the irony of getting a “worst new omics word award” from a blog called phylogenomics.blogspot.com!)

Blackberry apps that rock.

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I have been a CrackBerry user for several years, and am rarely seen without it in my hand or on my belt. Last week I traded my 8700 for the Bold (9000) — wow, what a good move! The Bold is faster, sleeker, and has 3G capabilities for functions that I would not have tried on the older EDGE network. Anyhow, I have been having fun looking for additional apps for it, and have come up with a good list. Here they are…

Poynt
An absolutely outstanding free app with local searches for people, businesses, restaurants, and movies, including the ability to watch trailers.

LaunchPad
An easy program that allows you to create icons for specific websites, SMS contacts, or phone contacts.

Vlingo
A voice recognition program that lets you speak commands, dial contacts by voice, and compose messages by talking rather than typing. The recognition is pretty good. Available in a free and a pro version.

Google Mobile
A tool for accessing various Google programs (which can also be installed separately), including Google Maps, Gmail, Youtube, Search, and so on.

WeatherEye
Local weather with current and 5-day forecast from the Weather Network.

THE Flashlight
Simple little app that activates the camera LED, letting you use the BlackBerry as a flashlight (nice to set one of the side buttons for this for use in the dark). There are also free apps that turn on the message LED and produce a white screen (such as BerryTorch), but these are far less bright.

BlackBerry App World
RIM’s app store, with both free and purchase apps.

Viigo
Combination RSS reader, news, weather, and other functions.

Does evolutionary biology make predictions?

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A commenter on my other blog at ScientificBlogging (basically a subset of posts from this one) seems to have objected to the claim that evolutionary science makes predictions.

gimme 5 examples of predictions, i mean real predictions: not fit the model hogwash

Marilyn

Here’s a list that I put together in around 10 minutes.

1) That a transitional fossil linking fishes and tetrapods would be found in rocks of a specific age (from the Devonian) and formed in freshwater environments. CONFIRMED.

2) That human chromosome 2 would show clear signs of fusion of two chromosomes that are separate in other apes when examined at the level of DNA sequence. CONFIRMED.

3) That genes for producing features thought to have existed in ancestors but absent in descendants will still be found when genomes are examined in detail or even through atavism. CONFIRMED (see also the paper mentioned in the original post).

4) That proteins in the bacterial flagellum will turn out to be similar to proteins with other functions. CONFIRMED.

And a classic…

5) Darwin predicted that the evidence would show that humans evolved in Africa based on similarities to other apes. CONFIRMED.

Others have put together some decent videos about this as well.

Want to share your own favourite examples?

Are we descended from monkeys?

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Today I gave my lecture on mammal diversity and evolution in the 4th year vertebrate course. We have been talking a fair bit about paraphyletic groups, common vs. scientific names, and so on. Within this context, we explored the issue of whether we’re “descended from monkeys”, by taking a look at a phylogeny of relevant primates:

The issues that we noted were:

  1. “Apes”, as defined as orangutans, gorillas, and chimps, but not humans, is paraphyletic. In other words, either “apes” is not a scientifically defensible term or else it must include humans.
  2. “Monkeys” is paraphyletic, and in particular Old World monkeys are more closely related to “apes” than they are to New World monkeys. (Also, humans and Old World monkeys are equally closely related to New World monkeys).
  3. We are not descended from any modern “monkeys” or “apes”, rather we share common ancestors with them. (In that sense, the answer is NO to whether we’re descended from monkeys).
  4. The last ancestor shared by all apes (including humans) would itself probably have qualified as an ape. (In that sense, the answer is YES we are descended from an ape, but not any of the modern species).
  5. For “monkeys” not to be problematic, it would have to include apes. In that sense, we would be apes AND monkeys. (And, for that matter, we’re also lobe-finned fishes). As above, it may very well be that the ancestor of all monkeys and apes (the very bottom node on the phylogeny) would have been considered a monkey, and therefore YES we are descended from a monkey (but again, not any modern species).

After class, one of my students emailed me a link to this video, which explores the issues nicely. The author takes a cladistic approach and concludes that we are descended from monkeys for the reasons listed above.

What do you think?

Evolution of the nervous system.

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To the list of special issues dealing with the evolution of eyes (E:EO, Phil Trans R Soc B), you can now add one on nervous systems in Nature Reviews Neuroscience.

Nature Reviews Neuroscience

Vol. 10, Oct. 2009

Charles Darwin’s theory of descent with modification by means of natural selection has stood the test of time, with new discoveries in genetics and the mathematical basis of natural selection providing ever growing evidence for the theory. This focus issue of Nature Reviews Neuroscience — sponsored by the Wellcome Trust — celebrates the contribution of Darwin’s ideas to our current understanding of the evolution of the nervous system. The articles in this special issue discuss the molecular, cellular and structural changes that have contributed to CNS evolution and their functional consequences.

The origin and evolution of synapses

Tomás J. Ryan & Seth G. N. Grant

Nature Reviews Neuroscience 10, 701-712 (2009)

Tracing the phylogeny of the molecular components of synapses, Ryan and Grant speculate on the core components of the last common ancestor of all synapses and posit that the diversification of upstream signalling components contributed to increased signalling complexity later in evolution.

Considering the evolution of regeneration in the central nervous system

Elly M. Tanaka & Patrizia Ferretti

Nature Reviews Neuroscience 10, 713-723 (2009)

What allows some species, but not others, to regenerate their nervous system? In this Review, the authors compare CNS regeneration among vertebrates looking for clues that might explain how this ability might have emerged or been restricted through evolution.

Evolution of the neocortex: a perspective from developmental biology

Pasko Rakic

Nature Reviews Neuroscience 10, 724-735 (2009)

Focusing on mammalian species, Pasko Rakic uses evo–devo studies to model how gene mutations may have affected neuron number and neuronal migration, which in turn may have contributed to the species-specific expansion and elaboration of the cerebral cortex.

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

Linda Z. Holland

Nature Reviews Neuroscience 10, 736-746 (2009)

By comparing developmental gene expression and neuroanatomy of vertebrates and the basal chordate amphioxus, Linda Holland sheds light on the molecular changes that may have facilitated the evolution of the vertebrate brain.

HT: Evolving Thoughts

Kill or Cure?

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This is too funny. A website called Kill or Cure? has been compiling links to science stories in The Daily Mail (UK) and their apparent “ongoing effort to classify every inanimate object into those that cause cancer and those that prevent it”.

A snippet of the entries under “M”…

The Junk DNA myth strikes again (next up: media hype).

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Here’s the abstract of a paper set to be published in Molecular Biology and Evolution. Now, I think this kind of study is interesting and important. But it’s predictable that they start out with the standard (and historically false) claim that “non-coding DNA was long dismissed as junk” (seriously, do reviewers require authors to insert this line or something?). It’s also predictable that the amount of non-coding DNA that they report as showing signs of constraints (about 5% of the genome) will be reported in science news as “junk DNA functional after all!”.

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.
Eory L, Halligan DL, Keightley PD

Protein-coding sequences make up only about 1% of the mammalian genome. Much of the remaining 99% has been long assumed to be junk DNA, with little or no functional significance. Here we show that in hominids, a group with historically low effective population sizes, all classes of non-coding DNA evolve more slowly than ancestral transposable elements, and so appear to be subject to significant evolutionary constraints. Under the nearly neutral theory, we expected to see lower levels of selective constraints on most sequence types in hominids than murids, a group that is thought to have a higher effective population size. We found that this is the case for many sequence types examined, the most extreme example being 5′ UTRs, for which constraint in hominids is only about one-third that of murids. Surprisingly, however, we observed higher constraints for some sequence types in hominids, notably four-fold sites, where constraint is more than twice as high as in murids. This implies that more than about one-fifth of mutations at four-fold sites are effectively selected against in hominids. The higher constraint at four-fold sites in hominids suggests a more complex protein-coding gene structure than murids, and indicates that methods for detecting selection on protein coding sequences (e.g., using the d(N) /d(S) ratio), with four-fold sites as a neutral standard, may lead to biased estimates, particularly in hominids. Our constraint estimates imply that 5.4% of nucleotide sites in the human genome are subject to effective negative selection, and that there are three times as many constrained sites within non-coding sequences as within protein-coding sequences. Including coding and non-coding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids.

Update: See BIOpinionated for a silly critique and Sandwalk for a fine reply.

Mark Siddall on leeches, cooking, and cooking leeches.

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Dr. Mark Siddall is a friend of mine who is a curator at the American Museum of Natural History and a world expert on leech evolution. He also likes to cook. Leeches, not so tasty it turns out.

He is the first researcher to be featured on PBS’s new web series, The Secret Life of Scientists. Check it out.

Interview on ABC News Now:

The Secret Life of Scientists:

And don’t forget this NOVA clip: