Archive for genetics

In Dog We Trust – The Case For Man’s Best Friend

Posted in biology, personal views with tags , , , on April 20, 2010 by cpolsonb

According to a recent survey about 36% of households in the USA have at least one dog. According to the Pet Food Institute this totals to around 57.6 million dogs, meaning there are nearly 3 times the amount of dogs in America as there are humans in Australia. Americans spend around $5.6 billion on food for their dogs and the American Veterinary Medical Association estimates around $7 billion dollars are spent annually on keeping dogs healthy. Why and how are humans so connected to an entirely separate and distantly related species like Canis familiaris? What makes dogs stand out from other domesticated animals and what can the study of human-canine co-habitation tell us about our own evolutionary history?

Let’s start with a very brief look at the ancestry of both dogs and humans. The canine group has its origins in North America and were originally small forest dwelling carnivores around the size of a fox. When open herd grazing ungulates like horse and antelope began to dominate the vast plains of North America the ancient canines radiated out from the forest onto the open ground. This created a canine ancestor that began evolving into a swift pack hunter in order to tackle the ungulate herds. It is thought that some of these ancestors migrated over the Bering straight into Asia, Europe and Africa around 10 million years ago. Over the next few million years these canids formed into the wolves, jackals, coyotes and painted dogs (not actually ‘dogs’) that we are familiar with today. The grey wolf (Canis lupus), the species from which domestic dogs arose evolved at the end of the Late Pleistocene around 300,000 years ago.

Meanwhile in Africa the ancestors of humans had been evolving steadily. The earliest member of the homo genus is currently identified as Homo habilis who lived from around 2.4-1.4 million years ago. Homo habilis was already using stone tools though it’s leg structure was more suited to tree dwelling than plains walking. After (and alongside) habilis arose Homo ergaster, who later gave rise to Homo erectus and Homo antecessor. Erectus and Antecessor were the first human ancestors to move far out of Africa and into Asia and Europe, both around 1.2 million years ago. Then from Antecessor came Rhodesiensis which finally evolved into Homo sapiens and Homo neanderthalensis. Homo sapiens have lived from around 250,000 years ago till present while poor old neanderthalensis disappeared around 30,000 years ago. So while canid ancestors beat us into Europe and Asia by a good margin the grey wolf from which dogs evolved arose at around the same time as modern humans.

The exact circumstances surrounding the first co-habitations of wolf and man are not known but evidence suggests the earliest interactions took place more than 100,000 years ago. Even before this time it is thought that humans may have been observing and learning from the wolves about how to hunt large ungulates on the tundra. What is known is that by 30,000 years ago dogs had split from wolves and were living alongside humans. The earliest clearly identified dog skeleton was found in Belgium and dates to 31,000 years ago. The March 2010 edition of the Journal Nature published a study that looked at tracing the geographic origins of the domestic dog using genetic markers. The genetic evidence shows that the domestic dog originated in the Middle-East, rather than East Asia as previously thought. It is logical to assume therefore that if the oldest dog remains we have are from Western Europe but dogs evolved in the Mid-East then the split must have taken placed many thousands of years before our oldest skeleton.

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“Science is the Poetry of Reality”

Posted in biology with tags , on March 26, 2010 by cpolsonb

In “enemies of reason” Richard Dawkins states that he thinks of Science as “the poetry of reality”. That idea may soon be more fully realized than perhaps Dawkins ever imagined, thanks to Canadian poet Christian Bok. Bok is a world renown experimental poet most famous for his poetry book Eunoia in which he only uses a single vowel per chapter (of which there are five). His latest attempt at experimental poetry is to literally insert a poem of his into the DNA of a living organism.

The organism in question is the bacteria Deinococcus radiodurans, the choice of which was no arbitrary decision. Deinococcus radiodurans is nicknamed “Conan the Bacterium” because it holds the world title for most resistant organism to radiation. The amazing resistance to radiation that this bacterium shows is thanks to a unique ring structure into which it’s DNA is formed. What the ring structure means is that pressure is applied all the way along the chain in such a degree that the normal severing of DNA by radiation does not occur. Radiation is still able to split the polypeptide chain in the DNA molecule but instead of the pieces floating away like in a normal DNA strand the pressure caused by the circular structure holds the pieces in place until they are able to “glue” themselves back together. This unique structure is therefore important if Bok wants his poetry to be preserved in future generations. If the poetic sequence were encoded into a different species of bacterium then over time radiation would sever and re-arrange the words into nonsense.

So the questions remains of how this will be achieved and what the poem will be. While I haven’t found much information on the specific mechanism that will be used to encode the sequence the most likely candidate is via plasmid integration. Without going into too much detail plasmids are small rings of DNA that occur separately in the cell to the chromosomal DNA in the nucleus. Plasmids are not considered life as they do not encode any genes for replicating or reproducing. Instead they are physically passed from one bacteria to the next through a process called conjugation. To cut to the chase, scientists are easily able to insert new plasmids into a bacterium that will integrate permanently into the chromosomal DNA. This is process is so easy that undergraduates like me are even able to do it!

As for the particular poem that Bok is going to insert, that remains to be seen. Unfortunately for Bok the genetic alphabet consists of only four letters; A,G,C,T which correspond to the nucleotides Aadenine, guanine, cytosine, and thymine. In order to construct an intelligible piece Bok is in the process of developing a cipher in which particular each triplet of nucleotides (i.e. AGT, TCA, AAG) will correspond to a particular letter of the English alphabet. All Bok has said so far about the content of the poem is that it will likely have an incantatory quality similar to a spell or ritual.