Tuesday, February 28, 2006

Neandertals for dummies

There's a (possibly subscription) brief description of recent research into Neandertals, in the form of a "quick guide," over at Current Biology.

An argument against Supplementary Data in publications

Genome Biology is carrying an editorial by Gregory Petsko arguing that Supplementary Data is a losing game. Web versions of scientific papers often contain links to additional tables, methods, and results for which there is not enough space in the print version. In my experience this is often where the goodies are hiding, like the information that the experiment must be done only with certain reagents, or that a whole other line of experiments gave negative results and have to be interpreted cautiously.

Petsko has, uh, a different opinion:
I hate supplementary material. It's one of the worst ideas in the history of bad ideas. It's the scientific publishing equivalent of fighting a land war in Asia.

He and I actually on the same page (pun intended) about what these massive data supplements do: by eliminating the word limit, it means reviewers can demand quite a lot more out of submitting researchers; then this mass is organized such that the tidy results and diagrams go "up front" and the wet science drifts into the back pages. And I think the "land war in Asia" analogy is correct: looking through the February 10th Cell, I see papers with 1,8,4,1 and 3 supplemental figures. What that means is a huge amount of extra work has become "published" (which affects its money and communication status for the corresponding author). There is no longer an upper limit to the amount of data which could be sucked in. And finally, especially with Cell, those files are inconveniently organized in nests of links and slow to download-- so they are at a qualitatively lower accessibility than the main data, which comes in a single pdf.

However, it used to be that these details didn't go into the paper at all, especially in Nature and Science. I agree with his objection that critical methods are frequently absent from the main text. But wasn't that always the case?

Monday, February 27, 2006

Life outside of kids II: Great grandma

This is the second one of about four posts dealing with the grandmother effect. Menopause, and the relatively extended life in human women after the cessation of reproduction, distinguishes humans from their primate relatives and possibly earlier hominins. The "grandmother effect" proposes that postreproductive women can nevertheless contribute to the propagation of their genes, specifically by helping their juvenile grandchildren reach adulthood. The first post talked about searching for the grandmother effect in other species. This post will talk about the evidence for the grandmother effect in humans and some speculation about the evolutionary mechanics.

It should be pointed out right away that the grandmother effect really does refer only to post-menopausal women. Men survive for similar lengths of time, but retain their fertility. This concept is only invoked to explain how the survival of the human species might have been enhanced by the presence of vigorous, non-reproductive women.

Strong evidence for grandmothers' contributions to survival of their grandkids came in a 2004 demographic study of 19th century Finnish and Canadian villages. In new families with a surviving mother-in-law, the newlyweds had their first child sooner, had more closely spaced kids, and those kids made it to adulthood with greater frequency. The Finnish records were detailed enough to show that the grandma's impact was greatest during the early post-weaning years, and might correspond to feeding and helping with young kids. So it's pretty clear that, in modern human societies, a grandma is a big help.

Comparative biology and the fossil record both suggest that "senior citizens" are a bigger proportion of human than non-human primate demographics. Among modern-day primates, the ratio of lifespan to age at maturity is relatively constant.Humans are at the far end of this relation, being very long-lived (thus with lots of surviving seniors) and very slow to grow up (both physically and cognitively). This special place on the curve is also true of hunter-gatherer societies.
A similar picture comes from the fossil record. By looking how worn-out the teeth are, especially the late-erupting 3rd molars (wisdom teeth), you can classify fossil jaws as belonging to a young adult or a "senior." Scientists who scored many fossils with this approach found the percentage of seniors keeps increasing in the hominin line, reaching a peak in upper paleolithic modern humans. It's important to keep in mind, though, that this analysis does not give the gender of the senior.

Putting it all together, the grandmother effect concept suggests that as human ancestors started taking longer to develop, it became advantageous for somone else with free hands to help. The increased number of humans surviving into old age would be a combination of better success of the human lifestyle and, perhaps, active selection for a vigorous grandma.

Another, gender neutral, factor which might have contributed to human longevity would be the complexity of the human lifestyle and the value of accumulated wisdom. This whole issue gets very interesting in the case of the Neanderthals, who probably grew up very fast but who had reasonable numbers of elders, And who might have cared for their elderly into their dotage. Neanderthal grandmas might have had a much less direct impact on the survival of the fast-growing grandkids, but the wisdom of the ages would still have been valuable.

UPDATEs: The Oscars and human evolution?

Also, I had this bookmarked but didn't get to it: the idea (from fossilized teeth)that Neanderthals grew up faster than H. Sapiens is disputed.

William Shakespeare's bust

The Beeb says that a portrait bust sitting in a gentleman's club in England matches the death mask of wordsmith will. There's a bit more in the Scotsman (gotta love Google) which says that the forensic scientist making the match also sees evidence of tumors near his eye orbits in several of the authenticated Shakespeare portraits. Alas, poor Yorick.



From the Scotsman, a dose of skepticism:
Prof McLuskie said comparing images ran the risk of circular logic - one fake image might be confirmed by another that was based on it. "A lot of these portraits tend to be of a generic bald guy with a beard," she said.

Of course, I'm partial to his portrait with the earring.

Friday, February 24, 2006

In the zone

National Geographic (and some other sites) are listing the five extrasolar planets estimated to be most habitable to life. Searching through our neighborhood they basically looked for stars of about our sun's age, with fair amounts of metals, which did not flare too often. Seems amazing that you could come up with a list of only five...

Thursday, February 23, 2006

Life outside of kids Part I: The Fish Bowl

Birth, copulation, and death. That's all the facts
when you come to brass tacks.

- T. S. Eliot, Sweeney Agonistes

Monty python fish2 honour-roll

As the fish from Monty Python's Meaning of Life could tell you, it's hard to understand the forces shaping lifespan-- not least because many get yanked from the tank prematurely. Natural selection, of course, puts a premium on living long enough to reproduce, and should even pay dividends for seeing the offspring make it to adulthood. But in many species, including humans, the natural lifespan extends far past the reproductive age. It's very interesting in this regard that extended lifespan seems to be relatively recent in human evolutionary history (more on this later).In humans, this added lifetime has been hypothesized to contribute to Darwinian fitness via the "grandmother effect," in which post-menopausal women help out with their grandchildren, and thereby promote the survival of their own genes over more than one generation. This effect should be greatest in cases where parents (or groups) take extended care of their offspring. But this idea has been difficult to test, and in fact baboons and lions, both of which do take care of their young socially, do not display "grandmotherly" lifespans.

An article in the December PLoS Biology takes an negative test of the grandmother effect by looking at lifespan in guppies. Guppies do not take care of their young, so the grandmother effect should not affect their lifespan. Reznick et al. took advantage of closely related guppies which have made major adaptations to high- or low- predation environments. Reznick et al. measured three features of reproduction in these fish- time at first brood; brooding interval; and life after brooding (which turns out to be non-zero). Guppies from high predation environments give birth early and often, and continued reproducing longer than those from low predation environments.
What is cool, though, is that this seems to operate independently of the lifespan after the last brood; so that in fact the guppies adapted to high predation lived longer. It's as if the extra reproductive rounds, necessary for life on the edge, were just plopped into the middle of the guppy lifespan (you can see this in Figure 4 of the paper). More to the point for the grandmother effect, lifespan of individuals after the the last brood was essentially stochastic, and the same in both groups(long-lived or shorter-lived). It follows a random decay, to risk a pun.
So guppies show no grandmother effect, which is predicted, since they don't care for their young. The authors of the paper point out, though, that this kind of actuarial analysis remains very hard to do for longer lived animals; and the positive presence of the grandmother effect in a place where it's expected might require some other approach.

This article was also referenced at the anti-ageing and science blog.

Tuesday, February 21, 2006

Advancing science: Science education is crucial

Via Pharyngula, Matthew Nesbit has a list of recommendations for engaging the public on scientific controversies . Advancing science in America requires both short term, politically informed tactics and longer term efforts at science education.

Very interesting reading.

Monday, February 20, 2006

The "coastal route" for populating the Americas

Some talks at the AAAS meeting in St. Louis revive the discussion about the route taken by the first humans entering the Americas. These first peoples could have been big-game hunters following mammoth across the interior of the land bridge connecting Asia and North America, or they could have been fishers who followed the coasts. The coastal migration theory relies on the immense productivity of coastal kelp beds, and suggests that fishers could have made a very good living by just following the kelp highway.

The biggest difficulty with the coastal hypothesis has been the lack of archaeological evidence, presumably because the camps would be submerged as the ocean levels rose after thelast ice age. I have been able to see a few abstracts ( here and here ) suggesting that these data are slowly coming in.

It's not clear to me that these two routes are mutually exclusive. With that said, mtDNA from a tooth found in a coastal cave Alaska shows kinship with contemporary native americans throughout the New World, suggesting that at least the coastal people prospered.

Sunday, February 19, 2006

Transitions- evolution blog aimed at high school students

I only just became aware of Afarensis' effort called Transitions ,a blog aimed at high school to early college students who are fairly serious about evolutionary biology, with an emphasis on the fossil record. The posts I looked through are very well written. Take a look!

UPDATE: The BBC has a whole series called In our time dedicated to human evolution.
And, via Slashdot, science fair entries from hell . Pot muffins in Santa Cruz-- who woulda thought?

Saturday, February 18, 2006

Electronic forms for U.S. government grants- Windows only?

The Washington Post reported earlier this week that the new umbrella site for applying for U.S. government funding, grants.gov, uses electonic forms that won't work on Mac. A client program which reads and edits the forms only runs on windows. The government is scrambling to get this fixed, and the NIH will delay the requirement that the big R01 grants are submitted electronically (this affects me personally!). However the smaller NIH grants apparently must be sent via this program.

I was using the handy technorati feature that the Washington Post includes with its articles, and I found that Suresh has already written about this, including referring to an open-access workaround for Mac from the University of Wisconsin. If you're in grant-writing mode, this may be a solution.

This isn't a simple issue. Have a look at Behind the Curtain for electronic document issues, creating an acceptable umbrella standard, and some other history.

Mimiviruses-- a different kind of life

[I got started on this post via Digg , a social version of Slashdot. Lots of science stuff pops up over there.]

Discover magazine's March issue has a great account of the discoverers of Mimiviruses, an extraordinarily large virus ( and maybe one of many ) which may have relevance to understanding the origins of life. Most viruses are very stripped-down infection machines, and their DNA or RNA contents are so spare that studying their deep evolutionary history via sequence comparisions is very difficult. The genome of Mimivirus, in contrast, is larger than that of some parasitic bacteria (in fact Mimivirus might be independently alive, and at a minimum blurs the boundaries. See Wikipedia ), and the full genome has been a gold-mine of evolutionary remnants.

Mimi's genome contains elements with similarity to many of the major DNA viruses known as NCLDV (including poxviruses), plus a whole lot more. This observation by itself strongly suggests that NCLDV viruses are descendants of an ancestor at least as complex as Mimi-- thus, possibly independently alive-- with their excess genetic material lost during reductive evolution in the transition to their current parasitic niche. In addition, several mimi genes and gene control elements seem to be equally related to eukaryotic and archaeal sequences, suggesting that the Mimi-like ancestor, and its NCLDV descendants, deserve their own branch in the tree of life next to eukaryotes, archaea, and bacteria. (This is controversial. See this technical comment and a well-written summary here. In my opinion the evidence for independent ancestry looks pretty good.)

I guess what's coolest to me as an outsider is how intimately locked in parasites are with evolutionary history. (Of course, we humans are parasites on plants.) Many evolutionary innovations have come as an attempt either by hosts to evade parasites, or for parasites to evade host defenses. Secondly, oddball organisms often have a lot to tell. Lastly, the nature of mimiviruses as probably barely alive means that the next few years could bring some pretty detailed ideas about what it means to be alive, here on Earth and elsewhere.

UPDATE: Some evidence based on conserved structure for an early origin of viruses

Friday, February 17, 2006

Paleoproteomics- getting protein out of fossils

There's going to be a really cool symposium at the AAAS meeting in St. Louis about analysis of protein recovered from fossils. Some proteins and DNA can survive the fossilization process and be preserved for amazing periods. Meanwhile, methods for recovering and analyzing tiny amounts of these substances continue to get better and better.

One speaker at the symposium, Peggy Ostrom, is using mass spectrometry to sequence proteins (probably osteocalcin ) from bone powder half a million years old.

For an excellent article about the challenges still facing ancient DNA analysis, go here . The caveats and opportunities listed there are probably going to apply to paleoproteomics as well. For example, protein analysis of osteocalcin should be pretty hard to troubleshoot, because the human protein is going to be almost identical to what you'd expect from any mammalian fossil.

UPDATE: Some more details on the symposium at afarensis

Having trouble deciding? Don't think about it

People have a lot of strategies for deciding among complex options. There are the list-makers, the snap-deciders, and the procrastinators. A study coming out in Science this week suggests that a good strategy for complex decisions is essentially to sleep on it. It seems that you can only hold so much information in your conscious mind at once-- good enough for fairly simple situations-- but that your unconscious mind might be better at dealing with all those variables. Here is a block quote from the Science blurb:

To test the idea, Dijksterhuis and colleagues asked volunteers to read brief descriptions of four hypothetical cars and pick the one they'd like to buy after mulling it over for 4 minutes. The researchers made the decision far simpler than it is in real life by limiting the descriptions to just four attributes such as good gas mileage or poor legroom. One of the cars had more plusses than the others, and most participants chose this car. But when the researchers made the decision more complex by listing 12 attributes for each car, people identified the best car only about 25% of the time--no better than chance. The real surprise came when the researchers distracted the participants with anagram puzzles for 4 minutes before asking for their choices. More than half picked the best car. The counterintuitive conclusion, Dijksterhuis says, is that complex decisions are best made without conscious attention to the problem at hand.

The BBC writeup is here .
An older story, that in emotionally charged situations we tend to go with our gut, is here . Finally, Zack Lynch at Brainwaves ran a story about how the pleasure centers of the brain can override the decision-making process, and speculates about drugs which could improve snap decisions by traders by affecting this balance.

Wednesday, February 08, 2006

Biology Direct- a completely different way to publish

The open access journal collection BioMed Central is launching a very different biology journal called Biology Direct. Not only will the publication be open access, but the reviews of the paper will also appear, unedited (even if they're harsh), alongside the data.

The traditional way of publishing is that an editor referees the interaction between the submitting scientist and the reviewers, and makes the final call about whether something will be published. The costs (editor's salary and endless secretarial support) are generally recovered in part by subscriptions to the magazine in question, but there have been increasing complaints that this shuts out the public from work which is after all tax funded. Open access journals let you download all the publications for free, but still have the editor infrastructure, which is paid for in part by a fee charged to the researcher. I guess Biology Direct (which again charges the researcher) would fall one step closer to self-editing communities like Wikipedia, in that there is a in house stable of reviewers (the Editorial Board) who have to be approached by the scientists in order to get a review. If you get a review and you pay your dime, apparently, your work goes up on the web page.

This seems to put a lot on the Editorial Board, and also I wonder if reviewers won't pull punches since they know the full text of their critique is going up. I took a look at the most recent accepted paper, Glazko et al. (link is to abstract; the article, reviews, and responses to reviews are in one large pdf) and the reviewers did seem to have gone over the paper pretty thoroughly. It looks like revisions are put into the main body of the paper without special designation (this is the practice in more conventional publications).

A good statement of Biology Direct's working philosophy and rationale is here (keep scrolling down), and there's a very good and link-filled writeup of the rationale for the new proposal by Jamais Cascio over at worldchanging. Very interesting, and a bit of a risk.

Wallace and Grommit live!

I laughed when I saw this on Digg : It's a sleeping back that also serves as your day clothes . Handy.

Tuesday, February 07, 2006

Bird-to-dinosaur transitional fossils

Hedwig at Living the Scientific Life has a great summary of some recent fossil finds showing intermediate morphology between birds and dinosaurs. The expedition that identified these finds was documented by the Discovery channel and will appear on TV. It looks like the work is not yet published but should come out sometime this year.

Monday, February 06, 2006

Caffeinated soap

Erik Bangemann at Ars Technica tries out Shower Shock, a soap laced with caffeine and peppermint oil. Erik's a coffee drinker and didn't get much except the peppermint pick-me-up, but his wife possibly got something. The article runs toward my first guess, which is that caffeine shouldn't penetrate skin very well. If you want to absorb the caffeine quickly you should wash your mouth out with the soap, or just make a bunch of small cuts. However, caffeine soap might help with psoriasis .

I googled around and see that Shower shock has been offered by thinkgeek for a while now. Dave Barry has weighed in with a serving suggestion.

...but you knew that already

Gina Kolata at the NYTimes has an interesting article about discovering the already discovered. People working on new mathematical algorithms might publish and name an improvement, only to find out later that the math had been done under a different name years earlier. Worse, small scale drug trials, showing benefits of a drug after surgery, could be needlessly repeated (including placebo controls) because the work was not published.

Final word goes to Larry Shepp: "Yes, but when I discovered it, it stayed discovered."

Saturday, February 04, 2006

Big....hoof

Pharyngula describes an identification of Sasquatch, based on a tuft of fur found just after the beast was sighted. 9 Canadians saw this particular Sasquatch through the kitchen window. (They build big windows up there.)

I'll give you a hint-- it's not a biped.


Meanwhile, Scottish police are on the trail of the dread Beast of Balbirnie and even have pawprints. Or, possibly not.

UPDATE: Malaysians are seeking their local snaggle-toothed ghost . Look at the bones!

Was Oetzi the iceman infertile?

The BBC is saying that initial DNA analysis of Oetzi, the Copper Age man found frozen in 1991 in the Italian Alps, has been completed. DNA samples were retrieved from inside his intestines and stretches of mitochondrial DNA were sequenced. They were able to get more sequence than a 1994 DNA analysis.

The main result is that his DNA falls into a known haplotype cluster called K1, which is still found in that region of the Alps, but his exact variant is difficult to place within subclusters of K1.

The Beeb also says that Oetzi had more than one mtDNA stretch associated with male infertility. The medical side of this is that the sperm rely on mitochondrial output to do their swimming, so faulty mitochondria can affect sperm motility . I can't find out just yet what mutations Oetzi might have had. Of course, he may not have been interested in having kids anyway.

Dienekes had this story about a week ago.