Digital smiles

17 October 2009

I have a nightmare vision of a near-future world of inane smiles.

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Monkey business, or is my uncle also my Dad?

17 October 2009

For a short while I had a temporary gravatar as a infant pygmy marmoset, clutching a human finger. I’ve revised it to a posterised image of me. It’s not as if I was convincing anyone I was as cute as the baby marmoset… While reading about these cute little guys (and gals), I learnt that family relations for them really is monkey business.

Here’s an adult pygmy marmoset:

pygmy-marmoset

(From: http://worldmysteries9.blogspot.com/2009/06/beautiful-complexity-of-animal-hands.html)

Pygmy marmosets are the world’s smallest living primates. As a primate, he (she?) is one of us!

To give yourself a better idea of the size of a pygmy marmoset’s body, give your computer screen that universally understood single finger gesture. You know the one I mean. The smaller species of pygmy marmosets have bodies a little bigger than that extended finger, about 13cm. Given that they’re tiny, furry and cute, it hardly surprising that there is plenty of photographs of them on-line. (I’ve listed a few below.) Sharp readers will spot that they lack opposable thumbs and have claws rather than fingernails.

One fact struck me while learning a little about pygmy marmosets: according to one research paperpygmy marmosets the only primate known to have germline chimerism! This has the startling effect that occasionally a male marmoset can—in a sense—have a mixture of their own and their brother’s sperm, and pass the genes of it’s brother to it’s children. Or put another way, a kid’s uncle could also be it’s father, in a manner of speaking. Women don’t need to worry that they’ve been left out just yet. The same may be true of females, but wasn’t observed in the research study.

In humans, all the cells in our body come from a single fertilised egg; they all from the same genetic stock. In a chimera, the cells in the body are a mixture coming from more than one embryo.

Twins are relatively rare in humans. Part of the reason chimeras are common in marmosets is that marmoset mothers usually give birth to fraternal twins, non-identical twins from two different egg cells fertilised by two different sperm cells.

Chimeras are rare in mammals and when they occur it is usually only the blood cells that are a mixture from the two embryos. One example of what can happen is for early embryos from twins to share or partially share their placenta, so that the developing blood systems of the two zygotes are able to swop blood cells, so that when the zygotes go on to form separate infants, they have a mixture of blood cells. Only the blood cells get mixed, all the other kinds of cells are all from their particular egg.

(Pickier readers will realise that the cells that are mixed are the stem cells that are the “mother cells” of the different types of blood cells, that is, hematopoietic stem cells.)

So, if you looked at the different cells of a chimeric monkey, you would expect to find the blood cells to be a mixture of cells from each twin, but all the other kinds of cells to be from the same genetic stock. Orti’s research group in the University of Nebraska had clues that this might not be the case for pygmy marmosets and checked. They found that in marmosets lots of other kinds of cells from twins were a mixture, including germ cells, the cells that give rise to sperm (or eggs). Zygotes with a mixture of germ cells will grow to have sperm (or eggs) that are a mixture of those derived from germ cells from their embryo and from germ cells from their twin. When these chimeric children, in turn, have children, they could pass on their genes, or the genes of their twin, depending on if the germ cells the formed the sperm (or egg) that the made the child’s zygote originally came from their embyro, or their twin’s embryo.

This study saw examples of males passing on their brother’s genes, but it may be that females can do the equivalent, as I’m sure the equal rights movement might demand! The researchers observed one female who picked up genes from her brother, and had mixed sex (XY) germ cells that were able to make fertile egg cells. It wasn’t known if this female could pass her brother’s genes on to her offspring, but the possibility is there. Maybe some feminists need to get together and fund this research group to check this loose end out…

Postscript

I’d explain the use of microsatellites in this study, but this would make for a very long article. Microsatellites are small, highly variable regions of DNA that can be used to “fingerprint” cells or organisms, like they do in those CSI-type TV programs to match the criminal to the crime scene. Here they’ve been used to check if particular cell types have the same genetics, or are a mixture.

Towards the completion of this article I realised that this story was well-covered by some parts of the media and in blogs at the time the paper was published (2007). It was too much fun to stop, so here it is!

References

1. Ross C. N. et al Proc. Natl. Acad. Sci. USA 104(15)6278-6282 (2007). Germ-line chimerism and paternal care in marmosets (Callithrix kuhlii) (This PDF copy of this short paper available free for those that want to read it.)

2. Infant pygmy marmosets are incredibly cute, their photographs are all over the WWW. I’d include one of the cuter ones in this article, but I’m unsure of it’s copyright status (I’ve tracked it down to the Everland Zoo in Korea, via the Zooborns blog, but the trail runs cold at that point). Other particularly cute photos include two infant marmosets for sale and in Jeffrey Gordon’s articleCuter Sapsuckers.

3. Nierhardt, Mareen Pygmy Marmosets. (Link to PDF file of article at the Rare Species Conservatory Foundation website.) This article contains many interesting details about these animals, especially about hand-raising orphans.

© Grant Jacobs, all rights reserved.

Sales-fest or science?

15 October 2009

Like many biologists and medical professionals, I’m disturbed by the plainly wrong and misleading nature of anti-vaccine and natural remedy claims I’ve seen.

An advertised “Natural Health Expo” to be held this weekend in New Zealand has caused me to revisit how an earlier blog article on Crank “scientific” conferences suggested one simple test for credibility of scientific claims at these events.

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Book review: Victorian Popularizers of Science

15 October 2009

Victorian Popularizers of Science: Designing Nature for new audiences by Bernard Lightman

Victorian Popularizers of Science

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TV psychics: not in the real world, please

15 October 2009

Before getting back to science pieces, I’d like to join fellow sciblings Petter Griffith and Mike Kilpatrick in expressing disappointment over TVNZ’s encouragement of the services of their “TV psychic” for the family of missing toddler Aisling Symes.

Entertainment often plays on fantasies, asking viewers to temporarily accept some clearly fictional plot devices. There’s a place for “psychic abilities” as “super” powers to make a central character be more than a mere mortal for harmless fun.

But encouraging the use of a “psychic” to assist in a serious, real-world, matter?

Not in the real world, please.

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Small world pictures

15 October 2009

Time-waster alert: stunning photographs, free screen-savers and wallpapers.

Kwon-10401-312306_3_van_Egmond

The Small world competition website has some stunning micrographs, photographs taken through a microscope.

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The 2009 Nobel Peace Prize

15 October 2009

Internationally there has been much fuss about Barack Obama being awarded the 2009 Nobel Peace Prize.

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Peter Lawrence’s Kafka tale of research grant funding

15 October 2009

Recently a very readable perspective article Real Lives and White Lies in the Funding of Scientific Research was published in the scientific journal, PLoS Biology (PLoS = Public Library of Science), by senior scientist Peter Lawrence FRS. (I mean senior in the sense of achievements, notwithstanding that his first publication was in 1965.) Peter’s concern at the state of the grant funding system no doubt stems from his move to Cambridge University’s Department of Zoology in 2006, after roughly 37 years working at the MRC LMB, based on the outskirts of Cambridge. (Disclosure: I was post-graduate student at the LMB.) As his article notes, he wrote his first grant application after 40 years as a scientist, which will startle many scientists on this forum!

Woven through this article is the story of a new principle investigator ‘K.’ who, like K. from Kafka’s The Castle, is eaten up by bureaucracy. For some (many?) scientists here, I am sure this story may have an all too familiar ring to it.

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Scientists can’t write?

15 October 2009

Currently I’m reading sections of Investigating science communication in the information age: implications for public engagement and popular media. In chapter 4.1, Making science newsworthy: exploring the conventions of science journalism, Stuart Allan cites journalist W. T. Stead who wrote in 1906 (see page  152):

In editing a newspaper, never employ an expert to write a popular article on his own subject, better employ someone who knows nothing about it to tap the expert’s brains, and write the article, sending the proof to the expert to correct. If the expert writes he will always forget that he is not writing for experts [b]ut for the public, and will assume that they need not be told things which, although familiar to him as ABC, are nevertheless totally unknown to the general reader.

While Allan, perhaps wisely, does not make direct comment on this—in his words—“telling bit of advice”, my impression is that he agrees with it. I’ve heard very similar lines elsewhere, including at a presentation for science writing in New Zealand.

I think it’s wrong and that it misses the real point.

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Introducing Code for Life

29 September 2009

Welcome to Code for Life. I hope you get something out of my modest efforts to educate and entertain.

This blog is a mirror of sorts of my blog Code for Life the New Zealand Sciblogs website. At some point I’ll decide if I should syndicate this site to the other blog. The main difference to users are the commenting policy and the style of the blog. Commenting here doesn’t require registration and will remain open indefinitely.

The material below can also be found in the “About” page. I’m popping it in here by way of introduction.

What’s with the name of the blog?

Code4Life was a name I considered for my consultancy, BioinfoTools. It plays on a number of things related to my work. It plays on a whole lot of things relevant to my work and what I write about:

  • My work involves programming (coding) for life sciences (molecular biology and genetics).
  • The data I examine and write algorithms for are the sequences of bases in DNA (genes, genomes), the amino acid sequences of proteins (enzymes, hormone receptors, etc.) and the three-dimensional atomic structures of proteins. These are the codes in life, the “information base” of biology and life. (If readers are interested in an introduction to this, let me know.)
  • It can mean moral codes and other “rules” people guide their lives with. I won’t be writing about this much about this in the sense of rules for life, but I may look at role of honest skepticism, logic and testing in science.
  • You can stretch it to be about writing about life sciences, writing being a code of sorts.
  • It has nothing to do with The Code for Life, an album by the heavy metal band Warrior. I am not a fan of heavy metal.

The banner photograph

My current banner may later be replaced with something reflecting the title of the blog… In the meantime it shows where I used to do my science. I work from a home office most of the time and until very recently I was based in a village in the Otago peninsula, near the Otago harbour. The village is near the right of the image. Science from a semi-rural, near maritime location! (The image is open source, obtained from wikimedia and edited using GraphicConverterv6.5.1.)

Topics

Most articles will target a general audience. I’ll try remember to let you know if I think an article is a bit geeky for general readers; once in a while I may write assuming a little basic background for those with deeper interests.

Likely topic areas include:

  • Genetics, genomics and evolution. Stunning new findings pour out each week…
  • Human biology, esp. cognitive neuroscience and rare diseases or disabilities. The workings of our minds is fascinating stuff and it’s intriguing to explore others’ lives.
  • “What science is”, what the basic terms mean, how to read a report on science, sorting out the good stuff from the bad.
  • Science and the media.
  • “Natural remedies” vs. science-based medicine. The naïve presentation of some of the “woo” out there by various people (including, sadly, a considerable number of media reports) is appalling.
  • Vaccinations. (No “flame wars”, please. Seriously.)
  • Issues within science, especially within New Zealand. Science is a great enterprise, but there’s always room for improvement.
  • Developments in computational biology (my profession).
  • Computing & computers (the tools of my trade).
  • Plain old ruminations. We all have our navel-gazing days…

Please feel free to ask questions and suggest topics you’d like covered. If possible, I’d like to try base a few posts every month on a subject that a reader has brought up.

I don’t claim to be some gifted philosopher or expert on matters far and wide, in fact I’m frequently embarrassed by my sheer stupidity… (Aren’t we all?) Some of my articles will be off my specialist expertise, in fact probably most will and I’ll let you know. Readers are most welcome to correct any errors but please substantiate your claims.

My background

By training I’m a computational biologist, a biologist who uses computers (algorithms, statistics, etc.) to explore biological problems, and who develops computer tools for biologists to explore data from genes, genomes and proteins. I work as an independent scientist through my consultancy, BioinfoTools, contracting to research groups and biotech companies.

A more commonly-known name for the field is ‘bioinformatics’ but “strictly-speaking” this originally referred to a subset of the field. Some of us who started before the “genome era” prefer the computational biology label, for reasons I’ll explain sometime… ‘BioinfoTools’ is a contraction of ‘bioinformatics tools’.

I have strong interests in science communication and am open to writing contracts or other work (e.g. editing) in this area.

Copyright

The material on my blog is copyright. Journalists, editors & publishers are welcome to contact me if you wish to use this material.