SciBlogs

Archive May 2010

When is a gene really an allele? Hilary Miller May 18

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The way some sections of the media use the word “gene” has become a bit of a pet peeve of mine.  Here’s an example from ScienceDaily:

Tibetans Developed Genes to Help Them Adapt to Life at High Elevations

Researchers have long wondered why the people of the Tibetan Highlands can live at elevations that cause some humans to become life-threateningly ill — and a new study answers that mystery, in part, by showing that through thousands of years of natural selection, those hardy inhabitants of south-central Asia evolved 10 unique oxygen-processing genes that help them live in higher climes.

Closer inspection of this research, which was published in Science last week, reveals that Tibetans don’t actually have 10 genes that are missing in the rest of humanity, what they have are different variants of the same genes.  These variants are called alleles, or haplotypes (there is a subtle difference between these two terms which I won’t go into here – but they both basically refer to different forms of the same gene or chromosomal region).  When geneticists refer to genetic variation in a species or population they are referring to the changes in the DNA sequence that results in multiple variant forms (alleles) of any given gene, the stuff that natural selection works on.

This study found that the Tibetan population have DNA changes in 10 genes that appear to be the result of natural selection.  Two of these genes, EGLN1 and PPARA have haplotypes that are significantly associated with the “decreased hemoglobin phenotype”, which is thought to be an adaptation to high altitude living.  These haplotypes appear to be selected for in the Tibetan population.  We all have EGLN1 and PPARA, but the Tibetan populations have unique haplotypes of these genes that help them live in higher climes.

This sort of incorrect usage of the word gene is pervasive in the popular media.  The phrase ’the gene for’ seems to be everywhere — the gene for breast cancer, the gene for schizophrenia, the gene for diabetes etc etc.  This gives the wrong impression of what these studies actually show, and is just plain incorrect.  What is actually being referred to in these studies is an allele or haplotype of a gene that we all have, and usually it is an allele that is correlated with a slightly higher incidence of the disease, not necessarily one that causes the disease.  Perhaps its time for for biologists to be more clear about what they mean by the word “gene”, and for journalists to incorporate the word “allele” or even just “genetic variant” into their vernacular.

If you want to read more about the Tibetans, the original paper is here, and an excellent summary of it by Razib Khan at Discover Magazine is here.

What are the limits of non-stop flight? Hilary Miller May 14

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In 2007, an Alaskan bar-tailed godwit (Limosa lapponica baueri) flew 11,000 kms over 8 days from Siberia to New Zealand.  Nonstop.  Thats without feeding, sitting down on the ocean to rest, or calling in for a break at a tropical island on the way.  In Plos Biology this week, Anders Hedenström looks at the physiological and aerodynamic requirements for such feats of endurance, and finds that current models can explain such feats.

Hedenstrom compared the rate of fuel consumption in godwits with that of other birds, and found that godwit’s fuel consumption is very efficient, but lies within a normal range.  The godwits body shape and flight speed also mean it is close to the “optimal design” for long-distance flight from an aerodynamic standpoint.  However, many shorebirds share these features and once again the godwit doesn’t stand out as being exceptional.  Hedenstrom suggests that the godwit may stand out from other birds in its ability to navigate, but exactly how the birds maintain their orientation during their non-stop flight across the ocean remains a mystery.

Satellite tracks of the Bar-tailed Godwit Limosa lapponica. Image created by USGS Alaskan Science Center.

Reference: Hedenström A (2010) Extreme Endurance Migration: What Is the Limit to Non-Stop Flight? PLoS Biol 8(5): e1000362. doi:10.1371/journal.pbio.1000362

Cloning extinct species #2: Should we bother? Hilary Miller May 10

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Two weeks ago I posted about how, theoretically at least, one could go about bringing an extinct species back to life by cloning.  Its clear that for long-extinct species like the mammoth, where only degraded remains are available, cloning is still a very long way off and in fact may not ever be possible.  But for species that have only recently gone extinct, or are on the verge of extinction, correct preservation of tissues could see clones created (in fact this has already happened in the case of the pyrenean ibex).  But should we bother going down this path?

Some people would say that we have a moral imperative to bring back extinct species, once we have the technology to do so, in situations where humans caused the extinction.  However in many cases the original extinction was caused by hunting, habitat loss and/or the introduction of predators, and these underlying issues are still present.  For instance, mammoth habitat of cold tundra grasslands, which during the ice ages ranged across northern Europe and the Americas, is now restricted to the Arctic, and is increasingly at risk from climate change.  Loss of this habitat at the end of the last ice age is thought to be one of the main reasons mammoths went extinct in the first place, and the situation hasn’t improved.  Should we really be contemplating bringing back populations of extinct species when we have trouble even saving the species we still have, and we are destroying habitat at an ever-increasing rate?  Introductions of long-extinct species could also significantly alter already fragile ecosystems and have disastrous consequences for the organisms already present.

Aside from suitable habitat, for a species to be viable and self-sustaining there needs to be sufficient genetic diversity in the population to guard against the detrimental effects of inbreeding depression, and for the species to be able to adapt to new environmental challenges.  Simply producing several clones from one specimen would not create a viable breeding population – for one thing you would at least need one male and one female.  Clones of several genetically different individuals would be required to ensure the population’s survival.  This may not be too difficult for critically endangered or recently extinct species where several well-preserved tissue specimens are available.  However, for the majority of extinct species the genome would have to be artificially “rebuilt” before cloning could take place, so you would need to have genome sequences of several different individuals in order to produce genetically different clones.  For many extinct species we simply don’t have enough different well-preserved specimens to achieve this.

There is a danger that cloning will be persued for the sake of it, because wouldn’t it be cool to see a live mammoth/tasmanian tiger/huia once again?  However, with this attitude the cloned animal is likely to end up being little more than a curiosity in an amusement park.  There may be some merit in bring back an extinct species for what it could tell us about evolution and physiology, but I don’t think this is enough to justify the enormous cost.  The millions of dollars it would take to bring back a few specimens of an extinct species would be better spent on preserving large chunks of habitat, eradicting introduced predators, and educating the public about for our critically endangered species, to ensure that in future we don’t have to rely on cloning to save the species we still have.

Footnote: The Neanderthal genome was published in Science last week, and along with it is an interesting news focus article about cloning Neanderthals. Its an interesting read (unfortunately its behind a pay-wall, so for those without full-text access to Science, the brief synopsis is that the ethical and technical issues around cloning Neanderthals are so great is unlikely they’ll ever be overcome).

Mammoth hemoglobin back from the dead Hilary Miller May 05

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While we’re on the subject of extinct species, Prof Kevin Campbell and colleagues in Canada and Australia have reported resurrecting mammoth hemoglobin in a paper out this week in Nature Genetics.  This won’t help at all with cloning a mammoth, but provides a fascinating insight into mammoth physiology and evolution.

Hemoglobin is the protein which transports oxygen in the blood.  It is made up of two subunits, alpha and beta globin, which are coded for by two different genes.  Campbell and colleagues used fairly basic molecular biology techniques to isolate these genes from mammoth remains and express the protein in bacterial cells.  Firstly, they amplified both elephant and mammoth hemoglobin genes using PCR and compared their sequences, finding that mammoth beta-globin protein differs from the elephant protein at three amino acid sites.

They then inserted the elephant hemoglobin genes into a bacterial carrier molecule called a plasmid, which had previously been designed to express human hemoglobin.  This carrier molecule basically contains the elephant hemoglobin genes and a bacterial promoter – a little sequence of DNA which is recognized by bacterial proteins that switch on the genes to produce the hemoglobin protein.  Producing mammoth hemoglobin was slightly more complicated because the mammoth DNA was degraded so the hemoglobin genes had to be isolated in pieces.  This meant they couldn’t insert the genes directly into the plasmid, so instead they recreated the mammoth sequence by modifying the elephant construct at the sites where it differs from mammoths.

Once they had the expressed hemoglobin, they then compared the oxygen-binding properties of the elephant and mammoth proteins using standard physiological tests and chemical modelling.  The changes in the amino acid sequence of the mammoth hemoglobin protein, when compared with elephants, appear to be important for cold tolerance, as they allow the mammoth blood to deliver oxygen to cells even at very low temperatures.

“This is true paleobiology, as we can study and measure how these animals functioned as if they were alive today” says Professor Alan Cooper, Director of the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide, where the mammoth hemoglobin sequences were determined.  You can hear more about this research from Alan Cooper on Radio New Zealand here.

Reference:  Campbell KL, Roberts JEE, Watson LN, et al. Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics doi:10.1038/ng.574

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The statistics of the ultimate TED talk Hilary Miller May 04

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TED.com is one of my favourite websites – every week they have fantastic new talks from “the worlds most fascinating thinkers and doers”.  This weeks highlight is this talk from Sebastian Wernicke, where he does the stats on what makes the “most favorited” TED talks, and comes up with how to construct the ultimate TED talk.  I wonder if these stats hold true for other talks outside of TED? Maybe something to think about next time you’re asked to give a presentation…

In a brilliantly tongue-in-cheek analysis, Sebastian Wernicke turns the tools of statistical analysis on TEDTalks, to come up with a metric for creating “the optimum TEDTalk” based on user ratings. How do you rate it? “Jaw-dropping”? “Unconvincing”? Or just plain “Funny”?

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