Tag: human evolution

The bitterness goes way back

August 17, 2009 • 8:54 am

by Greg Mayer

In a soon to be published paper in the Royal Society’s Biology Letters (abstract only), Carles Lalueza-Fox of Universitat Pompeu Fabra ( website in Catalan!) in Barcelona and colleagues report that they have sequenced the gene TAS2R38 from a Neanderthal man (press coverage by the BBC and NY Times). The ability to sequence genes from fossil material is remarkable enough in itself, but this study has particular interest, and not just because it was done on one of our fossil relatives.  Variation in the gene they sequenced is responsible for the polymorphism in modern man for the ability to perceive bitter tastes (some people can tast bitter, some can’t). Determining the frequency of the two forms (or alleles) of the gene is a classic high school biology exercise, carried out by seeing who can taste the bitter chemical PTC.  People who have either one or two copies (humans are diploid, so most genes are present in each individual’s genome in two copies) of the taster allele can taste bitter; those with two copies of the non-taster allele cannot. Today, the two alleles are about equally frequent, so that about 25% of people have two taster alleles (i.e. they are homozygous for the taster allele), about 50% have one taster and one non-taster (they are heterozygotes), and 25% are homozygous for the non-taster allele.

The Neanderthal they sequenced was a heterozygote, and thus could taste bitter (and also [with sample of only 1, mind you] had the same allele frequencies as we do). The polymorphism thus goes back somewhere on the order of 40,000 years. But Neanderthals split from the lineage leading to modern humans on the order of 300,000 years ago, with little or no subsequent interbreeding. So the polymorphism probably goes back even further, predating the modern Homo sapiens/Neanderthal split. Although an exciting find, this is not a record for the antiquity of a modern polymorphism: some are known to predate the human/chimp split (abstract only), and that’s millions of years ago.

The evolution of laughter

June 5, 2009 • 8:55 am

Laughter appears to be a “human universal”: one of those many traits that Donald Brown, in his book Human Universals, found in every society.  Well, does that mean it is a trait that evolved in our ancestors, or did it merely appear as a cultural phenomenon early in human society, and spread to all other societies?  One bit of evidence is that children who are deaf and blind, and thus can’t see or hear other people laughing, still laugh.  This suggests (but of course does not prove) that it is an innate, genetically coded trait, though it says nothing about whether it might have been an adaptive trait.

New research just reported in Current Biology by Davila Ross et al. (see here for a short BBC summary of the work; be sure to click on the video to see a gorilla “laughing”!) suggests that laughter is at least an evolved phenomenon, for our relatives appear to show similar vocalizations when tickled, and our closer relatives show more similar vocalizations.

Davila Ross et al. tickled 3 human infants, 7 orangutas, 5 gorillas, 4 chimpanzees, 5 bonobos (pygmy chimps) and 1 siamang, recording their vocalizations. (What a great job!)  Acoustic analysis of the vocalizations produced a phylogeny, or “family tree” of their similarities.  Strikingly, the family tree based on “tickle-vocalization” analysis is congruent with the known phylogeny based on DNA analysis:

laffs

Importantly,  the authors note that several features of human laughter, like its rapid “ha ha ha” type of vocalization, and its expression only during “egressive airflow” (science-ese for “breathing out”) are found in our relatives as well.

So laughter, at least when being tickled, appears to be an evolved, innate phenomenon.  As I emphasized above, this says nothing about whether it was selected for directly, whether it was a byproduct of something else that was selected, or is simply a nonadaptive epiphenomenon.  But as I write, evolutionary psychologists are working on why evolution may have promoted laughter.  Stay tuned.

Did cooking make us human?

May 30, 2009 • 2:06 pm

Well, everybody’s looking for what propelled us from our common ancestor with chimps to the wonderful species we are today. If it’s not genes, it’s culture.  Today’s NYT discusses Richard Wrangham’s new theory (previously mentioned on this website) about how the taming of fire and its use to cook food were crucial events in making our species what it is today.  I am skeptical (I’ve seen many of these theories come and go), but still looking forward to reading Wrangham’s. new book, Catching Fire: How Cooking Made us Human.

A gene for human speech?

May 30, 2009 • 8:16 am

In yesterday’s New York Times, Nicholas Wade reports new research on the FOXP2 gene (see original Cell paper by Enard et al. here).   If you’ve read WEIT, you’ll remember that I discuss FOXP2 as one of those potential genes that “makes us human.”  In other words, evolutionary change at this gene was supposed to have been involved in one of the key traits — speech –that distinguish us from other primates.   This supposition is based on some genetic and developmental observations:

1.  When mutated, FOXP2 causes both speech and speech comprehension difficulties in humans,

2.  The gene has evolved very quickly on the “human” side of our lineage since we split from the chimp lineage (and very slowly among mammals in general), leading researchers to suppose that natural selection for its effect on speech caused the rapid evolution, and

3.  When FOXP2 is mutated in mice, the young mouse pups have trouble making ultrasonic squeaks (a way of communicating with their mother). These squeaks were taken to be homologous with human speech.

However, I’ve been pretty cautious about considering FOXP2 a “human-ness” gene, for there is a lot of wishful thinking in this are.  We (and especially journalists!) are just so eager to find those genes that differentiate us from our “lower” relatives.  The new paper describes research designed to address this question.

What Enard et al. did was to change the sequence of the FOXP2 gene in mice so that it produced a protein having the same two amino acids that differentiate chimps from humans (there is also one amino acid difference between mice and chimps, so the “human” gene in mice actually was not exactly identical to the real human gene).  They then looked at the behavior, brains, and bodies of mice who had two copies of the “human” allele compared to mice having their own “mouse” allele.   The major effects of this genetic engineering were the following:

1.  The human gene reduced the “exploratory behavior” of mice,

2. The human gene increased the length of brain dendrites (inter-nerve-cell connections) in mice compared to those in carriers of the “mouse” allele, and

3.  Mice “pups” with the human gene produced ultrasonic “squeak calls” that had a significantly lower frequency (i.e., vibrations per second) than those produced by mice with the normal mouse allele.

From this the authors conclude that this transgenic experiment sheds light on the evolution of speech and language in humans.  It’s this conclusion (and the transgenic manipulation itself, which is the first time that an evolutionary hypothesis has been studied by changing a mouse protein to a human protein) that gave the authors such publicity, and got their work promoted in the Times.   But, as in the case of the darwinius primate fossil, I think the results are overblown.

All the authors have shown is that putting the human copy of a gene into a mouse changes the structure of the mouse brain and changes the squeaks of babies (what about the adult squeaks, by the way? Why weren’t they studied?).  While this is consistent with a role of FOXP2 in the evolution of human speech, it’s not very impressive.  FOXP2 is active in many tissues, and these effects could be merely pathologies.

Of course the definitive experiment, swapping a human or chimp gene with the copy from the other species, and observing the result, is unethical.

At any rate, I don’t think we’re much closer to finding “humanness” genes than we were before.  Indeed, there may be many, many genes that differentiate us from chimps (see WEIT for an estimate); and if the effet of each gene is very small, we won’t readily find those elusive “humanness”” genes.

The lesson is caveat emptor, at least when it comes to reading about science in the newspapers.

__________________________

Enard et al. (2009).  A humanized version of FOXP2 affects cortico-basal ganglia circuits in mice.  Cell 137:961-971.

Darwinius: what’s at issue?

May 21, 2009 • 3:10 pm

by Greg Mayer

I’m leaving in a few days for Costa Rica, and Jerry is back, so this will be my last post on Darwinius, at least for awhile. At least three different issues have been debated in the blogosphere concerning “Ida“: 1) What are her phylogenetic relationships; 2) Was the media campaign excessive; and 3) Has the name been published?

Darwinius on toast1) What are her phylogenetic relationships? This is the most important one, because it is, as John Maynard Smith once put it, about the world, and not about names. Is Darwinius close to the common ancestor of monkeys, apes, and men, or is it a member of the group that includes lemurs and lorises? The question has been raised and discussed most forcefully by Brian Switek at Laelaps, who thinks the evidence presented for relationship to monkeys and apes is weak. To my mind (and I’m not a specialist in primates or even mammals), he’s got a strong point, and we can look forward to a publication by Brian (or some other critic) on this issue.

2) Was the media campaign excessive? The short answer is yes. I expressed some uneasiness over the media campaign here at WEIT, and many others have documented the extravagant claims and consequent media misunderstandings further. See especially what Carl Zimmer had at the Loom, Brian at Laelaps, and PZ Myers at Pharyngula. But by far the best (or at least funniest) take on this was Ed Yong’s satirical evisceration of the inflated media campaign at Not Exactly Rocket Science, from which I have been kindly permitted to reproduce the by now iconic “Darwinius on Toast” above. There are many unresolved questions concerning how to present science to the public, and differing views concerning how aggressive a media campaign should be, but this one was at least one step beyond.

3) Has the name been published? This is the most technical issue, and is about names (rather than the world), but it’s attracted the most attention. See the posts here at WEIT, the Loom (and here), the Lancelet, and Laelaps, including the ensuing commentary by, among others, Henry Gee, Martin Brazeau, and Larry Witmer. There are several issues, and I’ll treat them very briefly (since this is a blog post, and not a paper in the Bulletin of Zoological Nomenclature!).  For reference, The International Code is online here.

3a) Has the name Darwinius masillae been published (in the sense of the Code) in Plosone? No. Many people have noted that Art. 8.6 requires non-paper works to be deposited in 5 major libraries, and that a statement to this effect must be included in the paper. No such statement is in the paper. More importantly, although it has been noted in only one comment I’ve seen, Art. 9 goes on to specify that nothing distributed by the web counts as being published. The non-paper works envisioned in Art. 8 are things like CDs, not web postings. So, the various remedies proposed, such as reposting on Plosone with the requisite statement, would not work. To be published, a non-Web work must be made: paper, CD, DVD (the latter two requiring the fulfillment of the 5 major libraries rule), or something else which satisfies Arts. 8 and 9.

3ai) Can the name be made available by publishing a short paper (on paper) with a bibliographic reference to the Plosone posting? No, because availability by bibliographic reference must be by reference to a published work (Art. 13.1.2), and anything on the Web is not published (Art. 9.8).

3b) Has the name been published elsewhere? I hope not, but fear it may have been. I pointed out that the various newspaper articles may count as publication, because they meet the various criteria for publication (obtainability, simultaneity, etc.; Art. 8), and also contain 1) the name, and 2) are “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Art. 13.11), and even follow Recommendation 13A: “a summary of the characters that differentiate the new nominal taxon from related or similar taxa.” Many newspaper articles, in addition to a general description, included explicit differentia– incisors, grooming toes– from related taxa, thus providing a diagnosis.

3bi) Can newspapers provide a public and permanent scientific record? In my post, I considered that the newspaper articles might be discounted, because perhaps they had not been issued “for the purpose of providing a public and permanent scientific record” (Art. 8.1.1). Some commenters have taken the position that this is self-evidently the case, but it’s not crystal clear to me.  The Code has always been loath to mandate specific formats of publication, specifying rather general properties (availability, simultaneity, identity, etc.) that a variety of formats might fulfill.  Historically, a huge variety of things have counted as publications (although no newspaper examples come to mind). Some newspapers have science sections, some are “papers of record”; I think the spirit of the Code is to approach each case on its individual merits. That is why the Code urges authors and editors to avoid anything that might make the situation murky, but it does so through recommendations (see my previous post for the specific recommendations).

3bii) Doesn’t the Code try to avoid “accidental” publication? Yes it does, as several commentators have pointed out. It has added meeting and symposium abstracts to the list of formats that are not permissible (Art. 9.9) to help avoid what the Code calls “unintentional publication”; but newspapers, as such, are not mentioned. The Code also now requires that the intention to establish a new name be explicit (Art. 16.1). This article is intended to prevent new names, especially a replacement name (nomen novum) to be introduced without mention, en passant if you will. Unfortunately, the newspaper articles make it absolutely clear that a new nominal taxon has been discovered and is being given a new name, and that this is the intention of the authors (on which, see next paragraph).  The Daily Mail article even uses the word “christened”. The Code urges authors to use “sp. nov.” or some other appropriate indication (Rec. 16A), but, again, does not require it. The Code recommends that any appearance of a new name in a work prior to its intended publication be accompanied by a disclaimer, making the new name unavailable (Art. 8.2 and Rec. 8D). The Daily Mail article contains the phrase “a scientific study to be published”: this might be taken to be such a disclaimer, and while it’s not as clear as one might want, it’s perhaps the most straightforward way of discounting the Daily Mail article. Such phrases may (or may not) appear in the other newspaper articles.

3biii) If it has been published elsewhere, who is the author of the name? The Code provides that when it is clear from the contents of a publication that the name and the conditions that make it available other than publication (i.e. the description or diagnosis) are the work of a person(s) other than the author of the publication, then the author of the name is the other person (Art. 50.1.1). In this case, the newspaper articles make clear that the name and its description were provided by someone else, many mentioning Jorn Hurum and Phil Gingerich. They (or whoever is mentioned in the earliest article published) are thus the authors.  This is a good thing, because it gives credit to at least some of the people actually involved in the work. The newspaper reporter would not be the author of the name.

To summarize the question of publication, the name has not been published in Plosone, but it may have been published in a newspaper. I hope the latter is not the case, and perhaps the Commission could issue a clarifying opinion (following an appropriate application) on the status of names published in newspapers (the problem may be distinguishing newspapers from newsletters from cheaply printed bulletins, and so on).

There are some other issues that have been discussed– the merits of paper vs. the web, the nature of peer review– but these go well beyond the particulars of Darwinius, although it might provide a case study for some of these issues. But one of the take home lessons here is that the recommendations of the Code should be taken to heart, and authors and editors should ensure that works affecting nomenclature are “self-evidently published within the meaning of the Code“(Rec. 8B), and that new names should not appear in works prior to their intended publication, or, if they do, they should “contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work” (Rec. 8D).

Update. While I was writing this, Carl Zimmer got a reply from the Executive Secretary of the ICZN. She confirms that posting on Plosone does not make a name nomenclaturally available. The issue of the newspaper publication was not addressed; I’m not sure if Carl asked about this. I’m leaning myself toward the idea that inclusion of the statement that the study is going to appear somewhere else could be construed as a disclaimer, thus avoiding newspaper publication of the name (I’m still not sure that all newspaper articles included such a statement).

Update 2. Carl Zimmer at the Loom has a nice account of the PR run-up to the press conference, which he titles “Science Held Hostage“. And, also from Carl, Plosone has today printed a 50 copy paper edition. If we can dismiss the newspaper versions (which, as I indicate in my first update, I think we can because they can be plausibly interpreted to have a disclaimer), then the name is now published with the intended authorship; the date of publication is 21 May 2009 (not 19 May, which is when it was posted to the web). Carl also succinctly explains why the nomenclatural rules are necessary:

To those not steeped in species, genera, suborders and suprafamilies, all of these bylaws and codes may trigger vertigo. But keeping the world’s biodiversity in order is not for the faint of heart. With 1.8 million species on the books, and tens of thousands of new ones being added every year, taxonomists need an intricate set of rules to keep it all straight. The fact that taxonomists share a set of rules, no matter how intricate, was one of the great advances in the history of biology.

Has the name Darwinius masillae been published? And if so, by who?

May 20, 2009 • 1:27 pm

by Greg Mayer

In a previous post on the hype surrounding the online posting of a paper on ‘Ida’, the Eocene primate from the Messel Lagerstatte, I noted that the

from Hurun et al. 2009. Plosone. www.plosone.org
from Franzen et al. 2009. Plosone. http://www.plosone.org

authors had made a nomenclatural faux pas in allowing the name and a description to be published before their paper appeared, thus making the authorship and date of publication of the name murky. At Laelaps, cromercrox (comment 35 here and comment 16 here), and at the Loom, Martin Brazeau and Larry Witmer (comments 27 & 29) have also noted nomenclatural problems, since online posting does not constitute publication under the International Code of Zoological Nomenclature, unless copies “have been deposited in 5 major publicly accessible libraries which are identified by name in the work itself”, (ICZN 8.6), which didn’t happen. As posted by Plosone, the paper is not published for nomenclatural purposes.

My concern was not that the name was unpublished, but that it had already been published, in one or more of the newspapers or perhaps even magazines that covered the pre-press conference hoopla. In the Code, Article 8 defines publication, Articles 10 and 11 cover general conditions of availability of a name, and Article 13 gives the particulars for names published after 1930 (the rules are stricter after 1930). The requirements may be summarized by saying that a proper new name must be published (sensu Article 8), and must “be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (ICZN 13.1.1). I fear these requirements have been met by some of the pre-press conference articles.

The earliest one I have found is the one in the Daily Mail from May 10 (there may be earlier ones– I haven’t looked very hard). (I also don’t have a paper copy, and am assuming the web article appeared in the paper.  If it didn’t, I could illustrate the exact same points for the New York Times, for which I do have paper copies.) In the article, by Sharon Churcher, the name appears:

Christened Darwinius masillae, it belonged to an extinct group of primates which lived in rainforests.

It also includes characters that are purported to differentiate the taxon:

The study’s authors insist that the fossil can’t be a lemur because it lacks two features: the ‘toothcomb’, a set of lower front teeth used to groom fur; and ‘toilet claws’, toes on the hind feet used for scratching.

The Mail is also mass produced in identical copies obtainable for free or by purchase, publicly available, and permanently archived in many libraries. So it looks like the name has been published.  The one possible out is that you could argue that the Mail isn’t issued for the purpose of providing a scientific record, but purposes are slippery things. Does a newspaper with a science section (which is of course quite purposeful) meet the requirement, but perhaps one without doesn’t? I don’t know. That’s why it’s murky. It is to avoid murkiness that the Code makes Recommendation 8B:

Authors and publishers are strongly urged to ensure that a new scientific name or nomenclatural act is first published in a work printed on paper.

also Recommendation 8D:

Authors, editors and publishers have a responsibility to ensure that works containing new names, nomenclatural acts, or information likely to affect nomenclature are self-evidently published within the meaning of the Code. Editors and publishers should ensure that works contain the date of publication, and information about where they may be obtained. (emphasis added)

and Recommendation 8E:

Editors and publishers should avoid including new names and the information that might appear to make the names available, or new nomenclatural acts, in works that are not issued for public and permanent scientific record (such as pre-symposium abstracts, or notices of papers to be delivered at a meeting). They should ensure that such documents contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work. (emphasis added)

But it looks to me like the Mail (or the Times, or whoever published it first) is the first valid publication of the name. The Code provides that the author of a name need not be the author of the work:

However, if it is clear from the contents that some person other than an author of the work is alone responsible both for the name or act and for satisfying the criteria of availability other than actual publication, then that other person is the author of the name or act. If the identity of that other person is not explicit in the work itself, then the author is deemed to be the person who publishes the work. (ICZN 50.1.1; emphasis added)

Jorn Hurum and Phil Gingerich are mentioned in the article as people who did the work, with Hurum given precedence.  So what’s the proper citation of this new taxon? It’s

Darwinius masillae Hurum and Gingerich in Churcher 2009.

Paleontology and the media

May 19, 2009 • 12:15 am

by Greg Mayer

The New York Times is reporting some major media event at the American Museum of Natural History on Tuesday concerning a 47 million year old primate fossil from Germany.  There’re reports of secrecy, exclusivity, and high priced documentaries. It seems a tad curious, since by available reports, the American Museum has nothing to do with the research or the fossil, which is in the collection of the Natural History Museum in Oslo, and the fossil was already reported on by the Times a few days ago and by the Daily Mail over a week ago. The fossil is from the Messel shale an important lagerstatte. Keep an eye out for the reports later today.

(PS The American Museum has what seems to be a really neat new mammal exhibit, reviewed here.  If you’re in New York, go see it.)

Update. The press conference has been held. The BBC has a few videos here. The specimen is a very well preserved, nearly complete, articulated skeleton, with remnants of fur and stomach contents (as is often the case in specimens from the Messel Lagerstatte), of a basal higher primate (i.e. near the ancestry of monkeys, apes, and man). The authors of the paper made a taxonomic faux pas in allowing the name of the new creature, along with a description, to be published prior to the appearance of their paper. The authorship of the name, and its date of publication, are now murky.

Update 2. As I feared, a big media roll out is not always conducive to getting the story right.  Just now on the Rachel Maddow Show, the features reporter said that the new primate might be the missing link between man and ape. It is of course nothing of the sort, and the authors never said it was, but using the term “missing link” as the key descriptor of the find (see the Daily Mail link above for an example) was bound to lead to some such misunderstanding. He also stressed that it could be “upright”, which many may take to mean bipedal, but, of course, it wasn’t. Laelaps and PZ concur about the doleful effects of the media hype. More from Laelaps here. The hype is even more overheated than I realized: from the promoters: “WORLD RENOWNED SCIENTISTS REVEAL A REVOLUTIONARY SCIENTIFIC FIND THAT WILL CHANGE EVERYTHING | Ground-Breaking Global Announcement”. Money quote from Laelaps:

I have the feeling that this fossil, while spectacular, is being oversold. This raises an important question about the way scientific discoveries, particularly fossil finds, are being popularized. Darwinius is just the latest is a string of significant fossils to be hyped in the media before being scientifically described (or at least before that information is released to the public). Other recent examples include “Dakota” the Edmontosaurus, the pliosaur “Predator X“, and “Lyuba” the baby mammoth. I am glad that these finds are stirring excitement, but I am a bit put off by the way they are presented.

Update 3 (May 20). Carl Zimmer and Ed Yong add to the critical pile on. A sample of Ed Yong’s wonderful satirical evisceration:

Around the world, signs that everything has changed have already begun to appear. Jeanette Gould from Stoke-on-Trent was shocked to discover the outline of Darwinius emblazoned on her morning toast. “Well, it ruined breakfast,” said Ms Gould, failing to appreciate the detail of the creature’s stomach contents outlined in bread crumbs. “I couldn’t very well spread raspberry jam over the direct ancestor of my children, could I?”

There is a wonderful accompanying illustration of the piece of toast.