Tuesday, March 17, 2015

Happy St. Patricks



Ruins of Ross Errilly Friary
Connemara, County Galway, Ireland

Untamed and largely uninhabited, Connemara is Ireland's windswept wild west, a landscape of hills, heath, and peat bogs characterized by what Oscar Wilde described as "savage beauty." Picturesque ruins enhance the rugged, romantic scene, including those of Clifden Castle and the medieval Ross Errilly Friary (commonly, though incorrectly, known as Ross Abbey), abandoned since 1832.

Tuesday, March 10, 2015

Searching for an Incubator

IN an 1877 book called The Poultry Yard and Market by Prof. Corbett, he cites that the Egyptians used "ovens" of wheat for incubator in temples dedicated to Isis. He goes on to say that the invention is attributed to the priests of Isis for the generation of more ducks than the typical broody hen could sit; pretty identical to our purposes today. Alas there is no record of how the ovens were constructed.


Corbett continues this thread, of "there is nothing new under the Sun" and finds that Emperor Constantine of the Byzantine Empire had "read" of these ovens and sent people to Egypt to find some and figure out their construction, realizing that a full stomach would make a happier populace; something Bonaparte epitomized i his epithet, An army travels on is stomach. Alas so does a populace as the Emperor was soon to find out.


Constantine's men found no record, other than holes in the earth leading some to believe that the Egyptians copied the Ostrich and let the sun's heat do its bidding. That unfortunately would not work in the more northern Istanbul except in the very warm days of summer and even then would need some protection from predators, errant pedestrians & inclement weather. Housing is the key, but then so is controlling the temperature.


Corbett himself tried housing the eggs with glass domes. No good as the glass was a great conductor of weather and when it was hot the inside shot up to 120F. When it was dark at night, the glass contracted and the heat left and the temperatures plummeted. Glass was out. Besides would have the Egyptians used such a pricey material? doubtful at best.


During the heydays of the Renaissance, when a whole rekindling of Classical times began in earnest, the Republics of Florence and Naples, built a series of these ovens. These, Professor Corbett, tells us are more like kilns, and built heavily into the ground, actually over a ditch beneath. The eggs were kept warm by the earth, and water was thrown upon it every so often, so that the dome did not overheat. Besides cooling down the kilns and the surrounding earth, the water would also serve of adding some humidity to the incubating eggs. Nice idea but on a large scale earth movers are required as Florence did not have readily the slaves of Egypt nor the space of the Nile Delta. Still it worked and both places hatched by the dozen and this allowed a lot more research into the duck and chicken to occur.


It wasn't until after the thermometer was invented by Galileo Galilei in 1592 that actually knowikng the correct temperature could be determined; before it was a practised eye like most of the natural sciences. But alas there was no correct scale of measurement that could be used reliably.


That changed when the Dutch physicist, Daniel Gabriel Fahrenheit in 1700–30 produced accurate mercury thermometers calibrated to a standard scale that ranged from 32°, the melting point of ice, to 96° for body temperature. The unit of temperature (degree) on the Fahrenheit temperature scale is 1/180 of the difference between the boiling (212°) and freezing points of water.


Celsius a scale made up of 100 degrees is attributed to the Swedish astronomer Anders Celsius, who developed it several years after Fahrenheit in 1742. Celsius used 0° for the boiling point of water and 100° for the melting point of snow, being in Sweden this made sense but this was later inverted to put 0° on the cold end and 100° on the hot end, and it was i that form it gained widespread use. Le Napoleon, him again, endorsed it as the French method and it was known simply as the centigrade scale until in 1948 the name was changed to the Celsius temperature scale.

Then in 1848 the British physicist William Thomson (later Lord Kelvin) proposed a system that used the degree Celsius keyed to absolute zero (−273.15 °C); the unit of this scale is now known as the kelvin while the Rankine scale employs the Fahrenheit degree keyed to absolute zero (−459.67 °F). (I'm a stalwart Fahrenheit fan btw).

So it was not until 1777 that a French physician, Bonnemain,  amred with both a thermometer and the Celsius scale, was able to actually establish hatching ovens en masse,  by heating them by circulating tubes of hot water.  He was so good at controlling the temperature that he moved his business to Paris and was able to hatch out one thousand little chicks a day.  While this sounds incredible, and it maybe, there are historical records it seems that show that Bonnemain was able to sell a good "abundance" of chickens every day of the year.

We do not know what chickens he used but in 1814 a major fire destroyed his establishment and so to recoup his losses, Dr Bonnemain, sold subscriptions to buy and build new ovens.  Being ever the industrious Frenchman, he also sold a  pamphlet describing his operation, but not mentioning the actual setup i.e. the temperatures for the water.  Obviously Bonnemain was no fool, but nevertheless 30 years later, Monsieur Bir, brought his hatching box to the Jardin des Plantes in Paris for exhibition where he hatched, on site, 100 eggs.

No mention of his chickens either.

By 1853 Mr Cantallo, of England, was making incubators in London, all heated with lamps.  Here we suppose that he was using his native Ligurian Chickens, i.e. the Leghorn, a known stalwart producer.

Twenty years later, a French American dentist, Dr Preterre, made an incubator in New York City and he showed it off at the Farmer's Club at the Cooper Institute (now part of the Smithsonian), March 1874.  His method of heating would raise most people's eyebrows, he used horse manure and steam.
The key, and Prof Corbett did investigate this, is that the manure must be from horses fed with grain (not grass or hay)and it must be fresh, old rotting manure is good for the garden but not for the incubator.

Monday, February 9, 2015

Moose Antlers the fastest cells on earth



Totally off-topic but I like them...


Moose antlers are formed by the fastest-growing cells in nature. The main purpose of moose antlers is as a weapon for fighting for a mate, a period that generally only lasts from September to October. Therefore, antlers are unneeded after that point. The growth is prompted by the release of hormones that occurs around April or May, and each new set of antlers is generally increasingly larger than the last as a moose reaches its prime at around six years. After that, the cells in the antlers decrease in growth speed until the antlers eventually recede.


from Wise-Geek.

Alleles and Hardy Weinberg


Enter into the evolution debate, the Hardy-Weinberg law,  which is an algebraic equation that describes the genetic equilibrium within a population. It was discovered independently in 1908 by Wilhelm Weinberg, a German physician, and Godfrey Harold Hardy, a British mathematician and codified into a set of algebraic laws used primarily in population genetics.
 
The idea is, that in a large, random-mating population, the proportion of dominant and recessive genes tend to remain constant from generation to generation unless outside forces act to change it. This means that even the rarest forms of genes, from long ago in the ancestry of the species are preserved.

So if we know the number of individuals in any given population,looking back at the SvartHona example we know that they took 12  samples from their whole population.  Then the Hardy-Weinberg equation is applied to calculate the allele frequency over a period of time.

It is that last bit, that is always problematic, as you need the same starting point, which is why they often grow their specimens and start their calculations from that point.  With eggs like seeds, that is easy enough to do as they have relatively short incubation periods.



What's an Allele, understanding lethal poultry genetics.

Evolution is a change in the frequencies of alleles in the gene pool of a population.

A gene is a stretch of DNA or RNA  chemicals that determine a certain trait. DNA, or deoxyribonucleic acid, is like a blueprint of biological guidelines that a living organism must follow to exist and remain functional i.e. why a cow is  a cow and cat a cat.   DNA is also self-replicating.

RNA, or ribonucleic acid, helps carry out the DNA's instruction and while more  versatile than DNA, and capable of performing numerous, DNA is stabler and holds more complex information for longer periods of time.


In animal breeding, there is a controlled propagation of domestic animals in order to improve desirable qualities and typically the DNA traits (genotype) are unknown, so farmers have traditionally relied on phenotypes (appearance and characteristics) to modify domesticated animals to better suit human needs for centuries.

This is done via Selective breeding i.e. breeding a larger rooster against a medium size hen or vice or verse to get a large chicken.  Genetically this happens as genes mutate and can take two or more alternative forms based on the allele it receives from the parents.  For example, the gene for eye color has several variations (alleles) such as an allele for blue eye color or an allele for brown eyes etc.


An allele is found at a fixed spot on a chromosome and now thanks to genetic research scientists know where on the chromosome each point controls.  When you see Locus 32, that means that at Spot #32 was discovered to control X.  Locus being Latin for Spot or location.

As chromosomes occur in pairs, organisms always have two alleles for each gene — one allele for each chromosome in the pairing. Since each chromosome in the pair comes from a different parent, organisms inherit one allele from each parent for each gene and the two alleles inherited can either be the same (homozygous) or different (heterozygous).


The Swedish Black + the Silkie

Jamie Watter's Svart Hona Rooster
The Swedish Black chicken, shown, is for its dermal hyperpigmentation phenotype (it is all black).  While most have dark skin, like the Silkie and the Ayami Cemani, there are some that have lighter skin.

The paper by Anna M. Johannson in the Dept of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, in  Uppsala, Sweden, discusses this in depth.

I've taken some of the highlights of Ms Johannsson's paper and put them here.

If you want the whole paper, contact me and I will gladly send the PDF with her contact details as well if you would like to follow up with further questions about her findings.

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There are 11 Swedish local chicken breeds of which two, the SvartHona and the Hedemorahona are discussed, because these as the breeds that are notably all-black.  Ms Johannsson's study was really about the their comb colour, that can be categorized into three categories: red, semi-dark and dark.

It was noted by the owners of these birds over several generation.  The males in particular
Jean Cavanagh's BIS Black Bearded Silkie Blessing
have all three comb colours while females tend to have only red or dark combs.  (I could find no examples of these combs, sorry).

The appearance of a red comb points to the involvement of the Z chromosome in the trait. Additional observations from a bird owner, who is interested in genetics, showed that the inheritance of comb colour can mostly be explained as a Z-linked inheritance, but that there are exceptions that do not fit with a single Z-linked locus (Johansson cites, Swedish breeder Thomas Englund, in  personal communications).

The Fm and id loci are known to be involved in the dark pigmentation phenotype in the Japanese Silkie (Bateson and Punnett, 1911; Dorshorst et al., 2010) as well (see an example of the Silkie from my friend Jean).

The now living birds in both of these breeds originate from small relics of earlier larger populations.

What we want to do is map the  loci associated with the comb colour trait segregated within the two breeds. To do this we genotyped 12 Bohuslän-Dals svarthöna and Hedemorahöna with the 60k SNP chip produced by Illumina for the GWMAS Consortium (Groenen et al., 2011). An association study was performed on the genotypes given the recorded comb colour phenotype.  The huslän-Dals svarthöna originates from the northern part of Bohuslän in western Sweden (close to the Norwegian border -- see map below for the location of Bohuslan, taken from Yahoo Maps.)

What was discovered was that around 1899, a woman got the ancestors of the current population of this breed as a wedding gift. Her two sons inherited the flock,  and in 1958 a man got the birds from the two brothers (Olsson, 2004).  These black birds are said to have be common in this area in old times and there is a legend stating that they are the descendants of birds that sailors brought back from long tours overseas to a foreign country.

 More than that is not explored in the paper but the diversity and inbreeding of the two breeds was,  with the mean inbreeding coefficient (F)  considerably larger in the samples from  Hedemorahöna than in the samples from Bohuslän-Dals svarthöna, and so it was concluded by genetic testing  that the Bohuslän-Dals svarthöna (black Swedish)  individuals were not inbred despite expectations.  That conclusion was derived as their  F coefficient was  less than or close to  zero, which under the Hardy-Weinberg equilibrium means that the these birds  are more heterozygous (different and less inbred) than higher numbers.

 However  half the Hedemorahöna individuals had a F coefficient that was great 0.1 and most of these had F>0.2  (see the supplementary Table 3 in the Johansson paper), with the most inbred  Hedemorahönas had F=0.45. 

Wednesday, February 4, 2015

Bigger is Better

In the latest WATT Poultry newsletter they have a set of panellists talking about industry trends.  one that they all agreed on was the trend towards more and larger broilers will continue.  Large here is 8 pounds liveweight.
 
Ttypically that as a standard bred is a Jersey Giant, Orpington or Brahma.  But they are slow growers so the Barred Rocks are typically preferred.) broilers being produced will continue.  We had Brahmas and it did take 6 months to get to 11 pounds and we had him for Thanksgiving.  He was delicious.  We have never had Giants or Orps though a friend, Bob R.,  from Aberdeen, South Dakota,  wants to change that.  He sells a lot of Jersey Giants to the home market for just that purpose, keeping the "lookers" for his show pen.  If you are interested, go to their site, read about the Giant and see if one is in your future.  Bob btw is the Veep.
 
The reason is the cost advantage towards processing larger birds especially 9 pounders.  And there is one processing plant is getting 10 pounds birds. How does compute?  Well everything is larger and easier to clean i.e. process.  Most home birders like small single serving birds or if they have small kids, they go for the colourful and very pettable Silkies.  
 
The article continues that the "chase" towards bigger birds will until either the genetics or economics dictate otherwise.  In the meantime, increased chicken production over the next  2 two 3 years will come from more birds and heavier birds.