When is a gene really an allele?

May 18, 2010

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?

May 14, 2010

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?

May 10, 2010

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? Read the rest of this entry »

Mammoth hemoglobin back from the dead

May 5, 2010

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.

Read the rest of this entry »

The statistics of the ultimate TED talk

May 4, 2010

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”?