I had my wallet stolen by a Madrid pickpocket on my recent honeymoon.
A recent post at Genomicron prompted me to go Googling for an excellent email I received while I was doing my postdoc. Unusually for chain emails, it comes with an explanation by the author of how it came about. Here’s the link, and here’s the geeky lab humour:
“Lord of the Rings: an allegory of the PhD?
The story starts with Frodo: a young hobbit, quite bright, a bit dissatisfied with what he’s learnt so far and with his mates back home who just seem to want to get jobs and settle down and drink beer. He’s also very much in awe of his tutor and mentor, the very senior professor Gandalf, so when Gandalf suggests he take on a short project for him (carrying the Ring to Rivendell), he agrees.
Frodo very quickly encounters the shadowy forces of fear and despair which will haunt the rest of his journey and leave permanent scars on his psyche, but he also makes some useful friends. In particular, he spends an evening down the pub with Aragorn, who has been wandering the world for many years as Gandalf’s postdoc and becomes his adviser when Gandalf isn’t around.
After Frodo has completed his first project, Gandalf (along with head of department Elrond) proposes that the work should be extended. He assembles a large research group, including visiting students Gimli and Legolas, the foreign postdoc Boromir, and several of Frodo’s own friends from his undergraduate days. Frodo agrees to tackle this larger project, though he has mixed feelings about it. (“‘I will take the Ring’, he said, ‘although I do not know the way.'”)
Very rapidly, things go wrong. First, Gandalf disappears and has no more interaction with Frodo until everything is over. (Frodo assumes his supervisor is dead: in fact, he’s simply found a more interesting topic and is working on that instead.) At his first international conference in Lorien, Frodo is cross-questioned terrifyingly by Galadriel, and betrayed by Boromir, who is anxious to get the credit for the work himself. Frodo cuts himself off from the rest of his team: from now on, he will only discuss his work with Sam, an old friend who doesn’t really understand what it’s all about, but in any case is prepared to give Frodo credit for being rather cleverer than he is. Then he sets out towards Mordor.
The last and darkest period of Frodo’s journey clearly represents the writing-up stage, as he struggles towards Mount Doom (submission), finding his burden growing heavier and heavier yet more and more a part of himself; more and more terrified of failure; plagued by the figure of Gollum, the student who carried the Ring before him but never wrote up and still hangs around as a burnt-out, jealous shadow; talking less and less even to Sam. When he submits the Ring to the fire, it is in desperate confusion rather than with confidence, and for a while the world seems empty.
Eventually it is over: the Ring is gone, everyone congratulates him, and for a few days he can convince himself that his troubles are over. But there is one more obstacle to overcome: months later, back in the Shire, he must confront the external examiner Saruman, an old enemy of Gandalf, who seeks to humiliate and destroy his rival’s protege. With the help of his friends and colleagues, Frodo passes through this ordeal, but discovers at the end that victory has no value left for him. While his friends return to settling down and finding jobs and starting families, Frodo remains in limbo; finally, along with Gandalf, Elrond and many others, he joins the brain drain across the Western ocean to the new land
beyond”.
I don’t want to scare those who are just beginning the journey, but it seems quite accurate to me…
I’m back! Did I miss anything?
Taking a month off work is excellent, I can highly recommend it. However, as my science brain is stubbornly still on holiday, it may be a few days before I get around to any science-related posts.
In the mean time, I wanted to share some direct quotes from the most hilarious phrase book ever, which was clearly written with a couple of distinct types of British tourists in mind. Take the section on “Getting to Know People”. It starts innocently enough, with “Do you have any hobbies?” and “I like painting / playing the guitar / piano”. The next items are, in order, “I think I’m falling in love with you”, “Will you stay with me tonight?”, “I’ll only go as far as you want to”, “I always use a condom” and “Are you worried about AIDS?”.
Of course, it’s no use being able to read a question directly from a phrase book if you can’t understand the answer. The book therefore contains a helpful list of potential responses to the phrases in each chapter. In this case, the complete list is as follows:
“I’ve already got a boyfriend / girlfriend”
“I need more time”
“We mustn’t take any risks”
“I’m not prepared to do that”
“I’d rather talk more about this tomorrow”
“We don’t know each other well enough yet”.
Good stuff, and definitely more useful than any other phrase book I’ve seen.
The “In a Restaurant or Cafe” section seems to be written for a different group of people, perhaps the parents of the young ‘uns trying to discuss their hobbies with local members of the opposite sex. Definitely the “I don’t eat any of this foreign muck, bring me the full English breakfast” crowd.
“Can I have a plain omelette”, “I’d like a plain salad / a salad without salt / without olive oil”, “We’ve been waiting for 20 minutes”, “Is there garlic in this dish?”, “This isn’t what I ordered”, “I’d like to see the manager”, “This wine is not good”, “The food is very salty”, “Can I have the complaints book?” “We won’t come back here”.
Disappointingly, the list of potential answers concerns itself with offers of extra drinks and does not provide the more likely responses to some of the phrases above. It’s probably a good thing for international relations.
Of course, everyone we met spoke perfect English. In fact, most people we met were English. Beautiful country, great beaches, good food and wine, world cup rugby on the telly, decent English breakfasts (and fantastic curries), great holiday.
Oh well, back to work. I might try to dig out some interesting papers from my email inbox later, although it’s a daunting task when it contains 600 new messages…
This article rang a few bells, and yes, I’m going to have to put my blogging Out of Office message up for a few weeks.
But it’s for an excellent reason! I’m getting married in a few days, and then my new hubby and I will be gallivanting around Europe on our honeymoon.
I’ll be back with more science and monkeys at the end of September. Until then, why not delurk, talk amongst yourselves, or leave me some marriage advice?
The latest edition of Tangled Bank is up at Fish Feet.
Today’s paper revisits a topic that seems to have become a recurring theme for this blog – the evolution of gene regulation. (It also involves primates, which is always a bonus). Ryuichi Sakate, from the Japanese Biological Informatics Consortium, and colleagues from across Japan recently published what they call an “initial analysis” of potential differences in gene expression between humans and chimpanzees. “Initial” and “potential” are important words here – this paper really is just one small step towards cataloguing all regulatory differences that evolved since humans and chimps went their separate ways around 5 million years ago.
But small steps still take us forwards.
The researchers took brain tissue from a chimpanzee who had died of natural causes, and a skin sample from a healthy chimpanzee. They then worked backwards from the RNA gene transcripts present in each tissue to determine exactly which pieces of chimp genomic DNA were actively expressed in brain and skin. These copy DNA sequences (cDNAs) were then compared to the human genome, and to databases of human cDNAs, to look for any inter-species differences in the transcription of the 87 genes under study.
The bulk of the paper is made up of statistics detailing the occurrence, location and type of differences between human and chimpanzee gene transcripts. The differences include single nucleotide changes, small insertions or deletions, and splicing of different pieces of genomic DNA (exons) into the transcript. In general, the protein-coding segments of the transcripts contained the fewest changes. This finding is in line with many other studies; most changes to the protein sequence will be harmful, and therefore subject to negative selective pressure, while relatively more mutations are tolerated in the non-coding regions of the transcript. Human and chimpanzee transcripts were more likely to differ in their site of initiation, rather than termination, and may therefore be regulated by different initiating signals.
One possible explanation for this finding is that many different sequences can act as transcription initiation sites, whereas the transcript termination signal is more precisely defined, i.e. it is “easier” to evolve a new initiation signal. However, it is also true that many, if not most, genes use a range of different transcription initiation sites, and the researchers seem to realise that they may not be comparing the full spectrum of chimpanzee transcripts to their human equivalents. This was, to me, the major weakness in the study, and one that the authors acknowledge. As they say in relation to one particular difference they found, “…it is difficult to distinguish the difference between inter-species and intra-species types of [variation]; further data collection is needed”.
Primate researchers are definitely at a disadvantage here. The human cDNAs in the public databases have been accumulated over many years, usually involving multiple independent studies. They therefore represent a reasonably accurate picture of the many different ways in which the same gene can be regulated in different individuals, different tissues, and in response to different environmental cues. The human databases contain examples of single nucleotide polymorphisms (SNPs, single base changes that are present in some, but not all, humans), alternative exon splicing events, alternative gene promoters, and alternative transcription start sites within the same promoter. The full picture is still far from complete, but we’ve made an excellent start.
The chimpanzee cDNA databases are much less comprehensive. Chimpanzees are rightly protected, and I know from experience that obtaining tissue samples is no easy task. Therefore when a new study finds differences between a chimp cDNA and the equivalent human transcript, it is often impossible to say that this is a genuine species-specific difference rather than a rare chimpanzee SNP or alternative splicing event. We’re going to need to sequence many more chimpanzee cDNAs before we can start to make truly meaningful comparisons to human gene transcription.
The paper by Sakate et al did not quite live up to the promise of its title. Don’t get me wrong, this is an important piece of work, and I’m glad that someone did it. But I think that the addition of more chimpanzee cDNAs to the public databases is a more valuable contribution than the paper’s somewhat premature comparative analysis.
The latest Gene Genie carnival is up at The Genetic Genealogist. The highlights for me are the two posts on how to stay up to date in Genetics / Genomics – advice I definitely need at the moment!
I’ll try to post something more substantial soon…
This week’s
cheeky chappy was a stowaway on a flight from Florida to New York. He escaped notice on his flight from Peru to Florida and during a subsequent stopover, but finally crawled out from under his owner’s hat on the way to New York. Reminds me of a line from Friends – “hey, that monkey has a Ross on its ass”.As far as monkeys go, there are worse species to sit next to on a plane1. Hell, I’d rather sit next to this cute little fella than some of the people I’ve endured on long flights.
1. Howler monkeys and any species that throws faeces2 spring to mind
2. Hey, that rhymed! I’m a poet and I didn’t realise it. Anyone wanna start a limerick? Or maybe a monkey rap?
