Tuesday 31 December 2019

New Year

Happy New Year, and happy birthday to lovely Adhara and her littermates, 6 years old today!

Sunday 15 December 2019

'Embark' dog DNA analysis

People have been asking me for a while about a DNA testing lab that offers a test called 'Embark' that seems to have started up a couple of years ago. A few months ago I tried this test on one of my dogs and had an email exchange with some of the people involved about the test and the results. The staff were generally helpful, but I found my queries got passed around a lot and a lot of them ended up not being answered. I was asked to write a review of it, which I did, and someone contacted me to ask if I could explain the points I made in the review a bit more, which I did as best as I could by email. I have been meaning to write a more detailed response on my blog about the thoughts I had on it, so this is me getting round to it.

'Embark' seems to be set up as a direct competitor to Genoscoper's product 'mydogdna' which I have been using for some years, and is a DNA analysis that provides health tests relevant to a dog's breed as well as other genetic information, such as coat colour, and some information the lab has collected for the breed as a whole, to give an insight on things like heterosis and how your dog compares to its breed. Unfortunately my main conclusion was that Genoscoper's website and tools at their current stage of development are far better designed than Embark's, perhaps as the inevitable result of the headstart it's had.

One of the things that complicates this as a resource for breeders so much is that 'Embark' tries to be something for everyone, and one of the things it tries to be is a toy so that people who have a mixed-breed dog from a shelter can find out what ancestry their dog might have. No doubt this is a really enjoyable feature for the audience it's intended for, and I am absolutely not averse to science as cool toys, particularly if funding from it is (hopefully) being used to bankroll research into more useful things. But unfortunately the software for breeders, which ought to be serious and not a toy, seems to be built on the same architecture as the fun test, which means a lot of it is irrelevant, uninteresting, or just outright bizarre:

I know this dog is a poodle because that's what I wrote on the form when I sent it in. I want hard data on what this analysis has found about the breed and I'm not interested in all this fluff. Furthermore, the 'software' itself is a website that is difficult to navigate and seems to be intended for use on mobile phones. The information that is relevant is sparse and spread over many different pages and difficult to access.

This is something that potentially is interesting -- it's identification of the dog's mitochondria and y-chromosome. This relates to the matriline and patriline of the pedigree, something I've written about before. And the image above is actually all the worthwhile information on two pages, with the rest being similar fluff of no relevance to breeders. It's good that they at least identify the markers, but there is no breed-specific information given -- how many different ones have been found in this breed, and at what occurrence? Which are common, and which are unusual in this breed?

This is completely useless. It concerns the dog leukocyte antigen which has been the subject of various studies in the past. There is no explanation given of what 'low diversity' means (possibly that the dog is homozygous?) There is nothing to identify the DLA haplotypes so they can't be compared with other dogs if you were involved with the other studies. The pie chart manages to convey no information about anything.

These are the colour test results for the dog. This is one thing it does do well (and for once has managed to fit all the data onto one page) so no complaints with that.

This is the health test component. In order to see all the results on one page I had to download a PDF. The two bottom tests I am not really sure why are included as being relevant to standard poodles, as I don't recall seeing any research or hearing of them occurring in the breed. The blue icon on the right I believe is OFA (a registry in the USA that records test results on American dogs) so presumably the OFA doesn't recognise them. The first condition so far as I can find out isn't a disease, but a probably harmless trait found in a spaniel breed that can confuse diagnosis of other issues that occur specifically in this breed. The other tests are widely accepted to be relevant to standard poodles, and this is one of the main benefits for using this test. I have written before about caution in interpreting the results of tests that may not be relevant to a dog's breed.

This is very similar to something Genoscoper's test includes. Unfortunately there is not a lot of information given. 'Genetic COI' is a bizarre term (COI or F is generally considered to be a probability-based estimate of homozygosity calculated from a pedigree). The research papers I've seen by the lab that runs 'Embark' use a term FROH where ROH are runs of homozygosity used to estimate the same thing. I can only assume that FROH is what's on the x-axis in this graph, and that it's calibrated to be directly comparable to F, the inbreeding coefficient calculated from a pedigree. Genoscoper allows people to set their dogs to public view so you can actually compare different dogs, and on their test the heterozygosity tended to come out in the same sort of magnitude to what an accurate 15-generation COI predicted, with slight variation as to be expected (siblings from a line-bred pedigree tested as 33.8 and 34.4 homozygous). The dog this analysis was of has a 15-generation COI of around 4%. It's not possible to compare that with other dogs as there don't seem to be any public data accessible on the site, or if there are, I wasn't able to find them.

This is the most interesting part, and unfortunately it's buried right at the bottom of the results and difficult to find. It's actually a map of the dog's chromosomes showing which regions are homozygous as ascertained by the markers sampled in the analysis (really it should be called homozygosity by chromosome, not 'inbreeding'). This sort of map has huge potential and it's not really being used yet. In the mixed-breed dogs that are on the website, although they are rather difficult to find, there were maps of paired chromosomes that showed six-way-plus mutts and chromosomes recombining in real time, which is absolutely fascinating.

A unique 5-way proper salt-of-the-Earth mutt! It's possible to tell from the proportions and distributions that one of this dog's parents was descended from Shih Tzus and Chihuahuas and the other from the other heritage.

How do they do this? I use analogies a lot and people seem to find it helps. So I am going to say, chromosomes are like books. Books tend to fall apart in particular ways, as do chromosomes when they undergo meiosis to produce sperm and ova. When gametes are formed, each pair of chromosomes in the parent, contributed from each grandparent, break into segments and recombine randomly to make a new single chromosome that will be packed into a sperm or egg ready to make a new organism. A roughly-handled or well-used old book might crack at the spine and the pages might come out in four or five chunks, and this is what happens in the first generation. But if you continue to use the book, you will damage it further, separating individual pages, and you can even rip up pages. But even on a ripped page, certain phrases can be identified as coming from a particular book, for example: It was the best of times, it was the worst of times is is instantly identifiable. By using large 'runs' of genetic data (according to the literature on the test, they are 50 kb, i.e. fifty thousand base pairs) the test presumably identifies genetic 'phrases' found in each breed.

A funny book, in the early stages of meiosis, possibly a victim of its own success.

If a dog's pair of chromosomes both have a long paragraph that is completely identical, this indicates those areas are identical by descent, and probably came about from recent inbreeding. If the areas are fundamentally the same with some small differences, such as American instead of British spelling, this suggests there was a more distant relationship between the parents. If the areas are different, this suggests relative unrelatedness.

The soul becomes dyed with the colour of its thoughts”:"The soul becomes dyed with the colour of its thoughts
The soul becomes dyed with the colour of its thoughts”:"The soul becomes dyed with the color of its thoughts
(one mutation, possibly indicating more distant inbreeding)
The soul becomes dyed with the colour of its thoughts”:"The soul is dyed with the color of its thought
(similar with obvious changes, implies very distant ancestral relationship)
The soul becomes dyed with the colour of its thoughts”:"The pigment of thought stains the soul
(same meaning, same language, but different -- heterozygous and relatively unrelated origins)

From this kind of data, it should be possible to find out more about a gene pool by looking at homozygosity and comparing dogs to each other. Two dogs of separate breed of very different origin, such as poodles and Pharaoh hounds, would be likely when compared to each other to be almost entirely the fourth example with perhaps some of the third. A breed or species that has already entered the extinction vortex due to depletion of its gene pool, when individuals were compared to each other, would be mainly the first example with some of the second. A breed or species with a viable and properly maintained gene pool is likely to be evenly distributed with perhaps a slight skew to the second and third examples, and it should be possible to find individuals unrelated to each other within the population relatively easily. Unfortunately 'Embark' doesn't provide information on any of this in its present state.

The accuracy of identifying the chromosome fragmentation depends on how close together the ROHs are and what 'blind spots' there are, which I don't know, but from the mixed-breed examples, it seems to be quite high resolution. Unfortunately it's not surprising considering the rest of the results that more effort has been spent developing this into a toy for owners of mixed-breed dogs than a tool for breed conservationists. This has huge potential and the chromosomes could be coloured to show if areas are over- or under-represented in the breed, or you could analyse a dog's parents and grandparents or farther and the test could show you which areas likely came from which ancestor.

The grey vertical lines on the chromosomes are the 'STR tracks' toggle on the bottom of the image If you click 'learn more' it does have some information on this in that these are markers that have been used in some studies of breed populations in the past, and if you mouse over the lines it give some identifying information, but infuriatingly again it doesn't give you any actual results so that you can compare your dog with any dogs that might have been in any of the studies it mentions.

One thing 'Embark' does allow that Genoscoper's version doesn't, is for you to download your dog's raw data. In theory this could be used to compare dogs using third-party software, but I'm not aware of any software available at present. The data itself is a spreadsheet containing a huge list of base pairs, so if someone does write software for it, it's likely to require hard work and someone with serious programming skills.

At the moment, this product shows promise, but it's unfortunately let down by seriously poor tools that fail to allow people to get meaningful information for their results. I understand from the people responsible for it that this is in part because of wanting to thoroughly test any tools they do offer before making them available, which is a valid point. But at the current juncture, it only allows you to look at very limited information on the heterosis of your dog and doesn't allow any comparisons with other dogs in the breed. Genoscoper's test, perhaps showing evidence of being around longer and having had more time to develop, is currently cheaper and lets you compare dogs of the same breed and different breeds, using interactive 3-D plots, and is probably the better option, at least for now.

I should add that while genetic analysis tools like these are fascinating new areas that provide worthwhile information on the gene pool of breeds as a whole, and can be really useful if pedigree information is not available or suspected of being incorrect, I do not think they are a substitute for accurate deep pedigree information for breeding decisions concerning individual dogs, i.e. COI, at their current level of development. That may change as more evidence becomes available, but at the current level of understanding I feel results like this should be used as supplemental information.

Monday 25 November 2019

Camilla the Camelid

I was on the road yesterday, specifically the Fosse Way, and I went to Stow and so I came back with what I suppose is a Stow-away:

As it turned I decided not to remate Poppy this year because of some problems we had, which would not have mattered so much as we had the other four. But then after we tragically lost Bess, having only three of them pregnant, which experience has shown can end up with only one or two viable cria, I decided this was going nowhere fast. Unfortunately I have had problems with all three female alpacas I originally bought, and on top of this two of them turned out to be terrible quality and this is impacting the genetic base I have to work with. I wanted to find a new female alpaca who would bring genetics that will improve what I have now, so I hope this is what Camilla will be able to do.

Camilla has a good strong frame (in fact, to be honest, she's huge!) Below you can see her with Patience who is the smallest alpaca I have, with her cria Zaphod.

Patience is small and gracile, which are traits I don't particularly want, and her fleece is not very dense and is a sort of rusty black. Camilla's fleece is raven black apart from a couple of grey spots. Her fleece analysis results are similar to Poppy's, who is a similar age to her and has the best fleece of the alpacas I previously had.

I separated Patience and Zaphod when he was a bit over 5 months, as he was nearly as big as Patience, and in good condition and eating concentrate, and also as he was friends with Bess's orphaned cria and I thought he might get along better with a companion. Hopefully Patience's milk has dried up by now and they can go back together until the remaining cria need to be weaned. Zaphod is a strong and good-looking boy who in terms of his fleece is an improvement over his father, but as I have his father and his mother, and as Bess was his grandmother, it seemed when he was born he would have to be sold. But as things have now changed and there are now more females unrelated to him, I have decided I will keep Zaphod. As I only have a small herd of alpacas, I don't keep more than three males as studs as that's the minimum ideal number to live together long-term. Therefore I will be selling Zaphod's sire Costa, as well as the other three young males born last year, in the spring.

Saturday 9 November 2019

Indi's Retirement

Indi's last litter in July was always intended to be her final one. Indi loves everyone, loves puppies, but she's a very unassertive dog and some of my other dogs tend to pick on her a bit. Indi is the kind of dog who gets pushed to the bottom of the pile living in a house with multiple dogs, and would do better in a quieter environment as either an only dog or with one other calm and quiet dog. An opportunity became available for Indi to go to a new home that had everything she needs to thrive, and so Indi has now gone to live with a new family comprising two self-employed adults and an elderly toy poodle, and is doing well there.

We will miss Indi, but she has done her bit for the breed and deserves a peaceful retirement. We have her two daughters Saffi and Cally II, and two of her sons are co-owned and may be used for breeding in future.

Sunday 20 October 2019

Stand with Sainsbury's

The supermarket chain Sainsbury's has made the decision to stop selling fireworks. I don't usually use this blog to write about this sort of thing, but I hope others will join me in supporting this, and to buy from their shops in October and November.

Every year petitions go out asking the government to ban the sale of fireworks to the public. So far, despite gathering large numbers of signatures, the government have declined to agree to the demand. Year by year I reluctantly sign these petitions. Reluctantly, because although I agree with the idea, I don't agree that banning or legislating against things is always a good idea.

Banning something or using legislation to make it unviable has several drawbacks. Frequently all that happens is the industry decamps abroad. In the UK, the production of a kind of goose liver paté called foie gras is not allowed because it involves keeping geese in conditions horrific for their welfare and force feeding them. However, this does nothing to stop the same product being imported from countries with laxer standards.

Forcing compliance with standards across the board can make it harder for the public to tell the difference between providers with truly high standards and cowboys who only do the bare minimum that is required. For example, if all breeders were forced to do certain health tests on their animals, the breeders who researched and chose of their own initiative to do such tests become harder to see. These people have generally researched many other aspects of what they do and are more knowledgeable, whereas someone who only does something because the law says they have to probably isn't and is likely not thorough in any other aspect they feel they can get away with. It can limit opportunities for the truly exceptional to distinguish themselves from the mediocre. In 2006, docking (amputating puppies' tails or applying a tourniquet so that part of the tail would die) was banned in the UK. Before this, breeders who put the welfare of the dogs at the forefront of their programme and would never cut parts off their puppies were easily distinguishable from others.

There is unfortunately a 'slippery slope' phenomenon, whereby banning and legislating tends to lead to extreme mindsets and more restrictive and illiberal pursuits. For example, animal welfare, which is scientific and concerns making sure animals are able to express their natural behaviour and are treated properly, is overtaken by animal rights, which is a pseudoreligious philosophy that preaches that people should exist in an artificial environment and never be allowed to interact with other animals, and promotes the extinction of domestic breeds.

So what is the alternative?

Interestingly, since the 2006 ban on docking, the amputation of puppies' dew claws seems to have gone into steep decline, even though this practice was not affected by the legislation. This seems to have come about because breeders are more open minded and better educated, and the people who buy puppies hopefully are as well. Tail-cutting seems to be declining in countries where it isn't banned, with many breeders in the USA and Canada promoting the fact that their puppies are entire and natural. It is a hopeful and positive thing that people can make good decisions and things like this can die a natural death by enlightenment.

It is ridiculous that shops sell small explosives and incendiary devices to the general public. Every year the NHS is inundated with injuries caused by fireworks, many of them to children. People are left scarred, blinded, mutilated, or even dead, because of something that is completely unnecessary. Animals and many people are frightened by the noise -- my dogs have never had a problem with this, but one November morning, a relative's pet pony was found dead in the hedge. The atmosphere and general environment are polluted, with spent shells littering the landscape where they can harm wildlife and livestock. This is before taking into account the kinds of damage they can do when they fall into the hands of the malicious or mentally ill: repurposed into bombs or used by lunatics to deliberately harm people or animals.

I hope the stand taken by Sainsbury's will prove the beginning of the end for this outdated practice.

Thursday 17 October 2019

Bess 26/6/2008-17/10/2019

Tragically Bess had to be shot this morning, leaving her orphaned 4-month-old cria and her daughter Patience from two years ago. Bess was found collapsed suddenly after being in perfectly good health and the vet was called. While waiting for the vet to arrive, Bess became distended and started to have trouble breathing and it was clear she was in a lot of pain and I suspected some sort of gastric torsion or blockage. The vet arrived and agreed that this was the most likely explanation, and tried to pass a stomach tube, which was not possible, and made an incision. Unfortunately there was immediate evidence of necrosis and the only thing we could offer her was a clean death and an end to the pain she was in.

Bess was not by any objective standard a quality alpaca. She had a horrible fleece approaching 40 micron AFD that was full of white hairs. She did have the nicest temperament of any of the alpacas I have, and although she'd previously been difficult to get pregnant, she was a good mother to the cria she did have. Her current cria is enormous and despite this, she was still in good body condition at the time of her death. After he was born she was remated and took immediately, so we also lost the unborn we might otherwise have had next year. Bess also tended to be used by other alpaca mothers to dump their cria on. She was often to be seen with her grandson from Patience along with her own cria, while Patience was off hanging around with her friend Fleur. She will be missed for the personality she was and her future cria she didn't live to have and enjoy.

Thursday 26 September 2019

What Research Science Is and Isn't

It seems to be common today for some people to make some claims about science, particularly about medicine and food for animals. These claims are usually not correct and show a fundamental distrust and failure to understand the scientific process.

There are many problems in science today, but what the lay public thinks are not among them. The worst experience I had in research was caused by an incompetent lab manager. This person was highly intelligent and a good scientist. He was also a terrible person and should never have been put in a management position. He would get in people's personal space and threaten them and shout in their faces. He would regularly tell people their work was bad privately and in group meetings in front of others. I later realised that he watched a television programme called The Apprentice where people pretend to be employed by a nasty boss who insults and humiliates them as entertainment, and used that as a model for his management style (I AM NOT JOKING). He also blamed a serious incident for which he was responsible on a junior person.

This boss brought out the absolute worst of everyone under him. Not only was I bullied by the boss, I was also bullied by another employee who took to behaving like a clown and doing dangerous things whenever the boss was not around, despite actually being a very intelligent young man. One of my coworkers became slovenly and apathetic, arriving in a dishevelled state with his flies undone, and when the boss was away, would not turn up until the afternoon, if at all. I remember struggling to help the student he was supposed to be supervising, who was trying very hard to do a project I didn't really know enough about to help her effectively with, and later how the boss sneered at the student for not caring about her work and not trying hard enough, ignorant of the behaviour of her supervisor. Disgusted with this colleague's apparent laziness and treatment of the student, I started ridiculing him and I'm sorry to say I behaved in a way that was unprofessional and probably constituted bullying in turn, when I should have considered that his behaviour might have been a symptom of stress or even depression.

Most of the ex-scientists I know who jacked in their training for a scientific career to do something else can cite a bad manager as the cause or a strongly influencing factor. Unfortunately I suspect it's also a factor in many science sector employees who commit suicide. Unsuitable people getting into management positions from my experience is the biggest problem in science. Someone doing good research or being able to bring in grants and funding does not mean they are suitable for a HR position, and until something is done about this, careers being ruined and problems like this are going to continue.

The issues in science I have experience of have nothing to do with any claims I've seen made on the Internet about scientific research being 'biased'. In an effort to try to help people understand what research science is about, I'm going to explain why these are not correct.

Firstly, the whole scientific process is designed to make things as objective as possible. Research papers are 'peer reviewed' before being published. What does peer review mean? It means the paper is sent to several other scientists who work in the same or closely related areas, what you'd consider 'rivals' really, who have to pick out any inaccuracies or unclear areas. Papers to be published have to include detailed results and a description of how the results were obtained, so if any question arises, any other qualified person would be able to repeat the experiment and see if the same results were obtained or not. While this isn't infallible, it's the best system we have for assessing evidence. Scientists who submit fraudulent papers and get caught are sacked and become unemployable in the field, as was the case of Andrew Wakefield.

Funding for research comes from various sources. Most funding comes from professional bodies and companies, and it stands to reason that larger companies can afford to fund more research in areas that are relevant to them. But it does not follow that research is biased because of the source of its funding. Research is often carried out by independent laboratories, and the laboratory and the employees have no personal involvement in the research. When companies have their own R&D departments, the researchers are still not personally invested in any products the company might produce, but strive to get the most accurate result as clearly it is beneficial for the company as a whole to change their products if research finds that an alternative would be more effective. When larger businesses carry out research, it invariably benefits smaller companies who don't have the resources to bankroll experimenting on their products when it's published. A friend of mine used to work for a large company that manufactured crisps and was involved in research to study harmful substances caused by cooking the crisps at high temperature, and investigated ideas such as cooking the crisps at low pressure to reduce the substances. No doubt smaller crisp manufacturers were able to implement new techniques based on the results of this sort of work without having to repeat it themselves.

It is not correct that research from universities and smaller businesses is 'better' than research from larger or more profit-motivated businesses. If anything, there may be a little incentive for quite the opposite. Universities are very dependent on receiving funding from outside sources and their reputation and that of their employees depends on having published research. Some results are more publishable than others -- for example, if a study sets out to find if x performs better than y, and finds that neither is really better than the other, this result isn't particularly publishable and studies that are likely to result in this sort of outcome is less attractive for universities. However, for a big business that has its own R&D department for its own products, this kind of result is just as valuable in helping with its development. Therefore, researchers in universities and small institutes may feel more pressure to get publishable results and only take on projects that are likely to work out well. Some important and interesting areas of science are not being studied enough for this sort of reason. However, it's still unlikely that researchers would fudge their results as the consequences of being caught doing this are severe, and the likelihood of being caught during the peer-review process is high.

Remember that in science, there's no such thing as 'the truth'. There is just evidence and science is about assessing the evidence on balance and deciding if the evidence in favour or against something is sufficient to demonstrate it is so beyond reasonable doubt. That balance can and frequently does change as more evidence becomes available over time, and we have to constantly re-evaluate evidence. Often, the more we know about a subject, the more nuanced it becomes, and the more it is apparent that we do not know.

Friday 20 September 2019

Responsible Rehoming

There is increasing publicity warning about bad animal breeders and how to identify good animal breeders. Frequently sources recommend rehoming unwanted animals instead of buying from a breeder, but many providers of these animals can also be unethical, and little seems to be known of this and even less warning given. Rehoming an animal can be a wonderful experience and there are many deserving animals needing new owners, but, just as when buying from a breeder, it's important to only support good rehoming organisations.

How to Identify Responsible Sanctuaries and Rehomes:

The facilities. Are they reasonably clean and well-kept? Just as importantly, are they suitable for the animals’ species, breed, or type? Using dogs as an example, hound breeds are fine in a kennel environment with other hounds as long as they get adequate exercise, but when companion breeds such as poodles end up in rehoming situations, responsible organisations will have volunteers who will temporarily take the dogs into their home. For dogs, most breed-specific rescues are good sources as they understand the specific needs of the breed.

Where the animals came from. Were these animals voluntarily surrendered by their previous owner? Did the previous owner give them away because they didn’t want them? Or were they sold, or did the owner not consent to them being taken? If you bought a ‘rescue’ pet and it turned out that the pet had been confiscated from someone who was struggling to care for it because they had terminal cancer, and the pet had been a huge source of comfort in their last days, how would that make you feel? There are charities around such as The Cinnamon Trust that help people who are struggling to care for their animals (and I’ve never heard anything bad about them) and these charities deserve to be supported more than charities that confiscate animals to sell. How about if you bought the same animal, and then found out the person you got it from had in fact bought it from a breeder and sold it on to you for more than they paid for it? You might feel one way about giving your money to a ‘sanctuary’ that ‘rescues’ animals from horrible situations, but you might feel differently if the ‘sanctuary’ was just a private menagerie and your money enabled the owner to fund their own lifestyle and buy and keep animals on the cheap. Beware of horror stories which may be exaggerated or fabricated. There is nothing wrong with an honest petting zoo and such places can be run with a high welfare standard, but what is dishonest is someone using their private menagerie as a front for begging.

Are the animals suitable for you, or indeed any other potential owner? Animals that are unpredictable or potentially dangerous should not be rehomed. There are worse things that can happen than euthanasia or humane slaughter in cases where it’s not reasonable or fair on the animal to rehome it. I’m aware of situations where elderly or semi-feral animals were chased around and transported in stressful situations for the sake of publicity stunts, where onsite euthanasia might well have been the kinder option. Responsible rehomers just like responsible breeders will accept back an animal if its new home doesn’t work out. They will assess animals and try to match them to suitable new owners, and won’t blame or guilt trip the owner if things don’t work out.

Do they specialise, or do they just collect anything? For example, a sanctuary specialising in unwanted horses and donkeys is much more likely to be a serious organisation able to meet the animals' needs than a 'sanctuary' that wants as many different animals as possible, probably to make it more attractive to tourists.

If you don’t take heed of what to look out for when rehoming an animal, be aware you could be contributing to the following (real) examples:

Irresponsible ‘charity’ and ‘rescue’ examples in order of increasing severity:

  • Posts on social media of the general gist: “We have 1,000 chickens in horrible condition rescued from a battery farm that will be sent for slaughter if people don’t take them and rehabilitate them and keep them as pets.” There is nothing wrong with buying knackered battery chickens because they’re cheap or you enjoy them. However, doing so does nothing to address the problem that people want to buy cheap eggs, nor does it improve the welfare of laying chickens. Chickens will continue to be produced and used in battery farms and the vast majority of them will be slaughtered. Slaughtered battery chickens are used to make chicken soup, which feeds people, and pet food, which feeds pets. They are not wasted. If you care about chicken welfare, you would bring more benefit by buying either eggs or laying hens from a farmer who uses a higher-welfare system.

  • We once bought two cats from a feral cat rescue. On the phone, the person said they were a male and a female, both spayed and neutered. The person who later delivered them, said they were two females, both spayed. One of the cats was orange and a friend who is a cat lover told me that the majority of orange cats are male. The next summer, I and several other people observed the other cat loitering about the place accompanied by a kitten that looked very similar to the orange cat.

  • A person who has a webpage describing themselves as a ‘rescued animal shelter’ buys some healthy and well-cared-for animals from a breeder or other reputable source. The person then posts a picture of the animals on their website with a fictitious horror story about how they ‘rescued’ the animals and begging for ‘donations’ to pay for veterinary care the animals supposedly need and people to volunteer to do unpaid work helping them care for their animals.

  • Some rehoming centres with dogs for sale advertise ‘puppies rescued from a puppy farm’ for a similar price as puppies from a decent breeder. Frequently the puppies have been bought from a puppy farm and puppies bought in this way are just dogs bred irresponsibly and sold via a dealer, exactly the sort of source people should be discouraged from using.

  • Some operations calling themselves dog rescues specialise in taking feral dogs from the streets in foreign countries and importing them and selling them as pets. Not only are these feral dogs likely to make unsuitable pets and struggle to adjust to this sort of life, this practice has a large carbon footprint, risks bringing disease into the country, and does nothing to solve the problem of feral dogs in the country of origin. Shockingly, some of these street dogs might also be breeds or landraces genetically unique to the region, and this amounts to Westerners pillaging cultural currency. Working with local people to help them value and care for their street dogs and utilising trap, neuter, release programmes to ensure the dog populations are managed would be a far more ethical (but less profitable and less marketable) approach.

  • Some high-profile animal charities no longer accept voluntary surrenders of animals whose owners can no longer care for them, and instead are focused on generating money and publicity by confiscating animals from people who are often vulnerable or may have mental or physical issues, and selling the animals and suing the owners for mistreating them and extortionate expenses in keeping them during the meantime. There is a serious conflict of interest in these cases. While some people unfortunately do wilfully neglect or deliberately harm animals, these people should be dealt with by the police, not charities. Vulnerable people who are struggling to meet the needs of themselves and their animals need to be treated with compassion, not dragged through the legal system. People who find they can no longer care adequately for an animal they own need places that will take and rehome their animals, whether it’s the animal’s breeder, a breed rescue, or another provider.

  • Some zoos claim to be involved in conservation breeding of wild species – when in fact they keep animals in poor conditions that do not meet their welfare needs and squander genetic resources by breeding animals in a way that does not support conservation. For example, the Sea World aquaria keep orcas in unsuitable habitats to use in circus performances, as animals with difficult to achieve welfare requirements, and previously bred them by mating together first-degree relatives and animals of different species. A man in the USA who claimed to be rescuing big cats and breeding them for conservation was in fact using them to breed novelties such as ligers that are no use to conservation and could not be released into the wild.

Monday 2 September 2019

How Do You Choose?

L-R White collar pup, Blondi, Quintus, Purple collar pup

"How do you choose?" is a question people often ask me as a dog breeder. While most people have some general idea that breeders are there to preserve a breed and breed so that they can keep a puppy to further their breeding programme, how the choice of puppy is arrived at seems to be considered arcane knowledge. Several people who otherwise know me quite well have been known to ask if I know which puppy I am keeping when they are 2 weeks old and I can't possibly tell, and recently my own mother asked me if I let the people who were having pups from the litter come and pick any pup and I just keep whatever was left. So I've decided to write something about the process that goes into choosing a puppy and deciding which puppies are best suited for the other people waiting for them.

I do not let people on the waiting list pick pups on a whim. The people come and visit and handle the pups and I explain to them what I know about the pups' personalities as they develop. The people visiting do not have the experience of observing the pups for long periods, and playing with the pup for half an hour does not give them the insight into it that I have. When the puppies are old enough, I do some exercises with them to assess them and use that in addition to the picture I've developed of them to recommend which pups would be suitable for them. Depending on their position on the waiting list, they may have a choice out of a few pups best suited for them. This is a temperament assessment and not a test, as there is not 'one ideal' for every person and a puppy ideal for a companion to a quiet older person is very different to one ideal for a noisy family, or a person wanting to do a competitive sport. The person who always occupies first place on the waiting list is myself.

Puppies are assessed for temperament and conformation, and this cannot be accurately done before the puppies are 7 weeks old. However, some narrowing down does often take place as some traits are obvious earlier, so in some cases I can give people an indication of which pups might be available to them earlier than this. No puppy is perfect and the breeder chooses the puppy who is closest to their goals and can contribute the most to their breeding programme, and just because the other puppies are not chosen, does not mean they are somehow defective or unsuitable for their new owners. Conformation does not mean choosing which puppy is 'prettiest'; it means assessing how closely each one conforms to the breed standard; that is, which one is most recognisable as a poodle.

Pandora on the right with a sibling. Pandora's head was the best in the litter and one of the reasons she was hands-down the best puppy for me to keep. The other puppy still has a nice face and there is nothing wrong with his head, but Pandora has the more poodle-like face.

The Brown Bros: Trilby on the right with his brother Porthos, showing different head strengths. Trilby's eye shape and colour are strong and his head planes are not bad, whereas Porthos had strong head planes and muzzle shape but his eyes were not as lovely. In this case the decision of which to keep was not clear-cut and much harder.

There are a great many traits to consider when assessing pups that all have to be weighed up, which is why it can sometimes be difficult to decide. The previous litter, the Brown Bros, the final choice was hard because the two puppies I narrowed it down to were very different, but strong in different ways. The current litter are actually quite similar to each other with slight strengths over each other.

Quintus is not in the running for the simple reason that he's a boy and I don't have room for any more boys. He will be going to a great family who already have an older poodle I bred. Quintus is friendly and likes people, and often seems to be a bit 'independent' from the rest of the litter. He did not test as being very toy motivated, although he is more interested in noisy toys than soft ones. Quintus is built like a bricklayer but carries himself like a prince.

White collar pup is a lovely cuddly pup who tested as not as toy motivated nor as confident in herself as the other two girls. She's also not quite as balanced in her structure and movement and I can recognise some of the same traits I see in Indi and Saffi's conformation that I want to work away from, so she will be a nice pet.

This leaves Purple collar pup and Blondi to choose between. The first thing people notice about them is the difference in colour, but really they are quite similar to each other. Purple pup at the moment seems to be slightly better in how she's put together, whereas Blondi is slightly bolder and more enthusiastic, however, there's not a big gap on either count. Blondi is obviously not the ideal colour for my breeding programme... but colour is superficial and the structure and temperament of the puppy are far more important. I will spend some more time with these two pups individually and probably wash them also to help decide, as seeing them wet can sometimes make things a bit clearer.

Sunday 1 September 2019


This is Poppy's cria Trillian. Trillian's neck you may observe has turned orange. Poppy and Trillian were doing well until Poppy was remated a little over two weeks after giving birth, which is the normal time to mate alpacas as pregnancies take about a year. Poppy has always been ridiculously friendly to people when not pregnant, but quite difficult to handle when she is, and this has got worse over time and I suspect may have resulted from overhandling when she was young as I didn't breed her. She became very unpleasant soon after being mated, which suggested she had ovulated, but unfortunately she also started to reject poor Trillian and began to attack her whenever she tried to nurse. This became extremely difficult to manage, as at the worst point I suspect Trillian was getting nothing and was going around trying to nurse off other alpacas and my crotch, and Poppy's udder looked like she had an inflated medical exam glove stuck between her legs. Whenever I tried to feed the alpacas, Poppy would charge into the pen and unprovokedly and deliberately spit in my face, and Trillian of course would run after her and try to feed while Poppy was eating, and Poppy would go berserk and kick Trillian and the feed buckets about the pen and spit all over everything.

This was a dreadful thing to have to watch, as Trillian was only three weeks old and clearly suffering psychologically from her mother's rejection. One of the other alpacas, Olivia, although she has improved a little over time, never has enough milk for her cria, and they never grow as quickly as the others and I always need to try to supplement feed them for at least the first few weeks, which is a nuisance as they never really want to drink the supplemental milk. But at least these cria still receive the love and emotional care they need from their mother despite her shortcomings. Poppy had to be haltered and tied up, and her leg held to stop her from kicking Trillian so Trillian could feed. I considered separating them and trying to feed Trillian myself, but this was not straightforward as it could lead to Trillian becoming dependent on me and imprinting on people and potentially developing the same behavioural problems that Poppy seems to have.

About two weeks after mating, Poppy's horrible behaviour subsided and she started taking care of Trillian properly again, and it turned out she hadn't become pregnant. Trillian's fleece on her neck seems to have been permanently discoloured from Poppy biting and spitting on her. Unfortunately I have decided it is not worth the risk for Poppy to be mated again now as Trillian's interests have to come first. She will have to remain open for the winter and be mated in spring when Trillian no longer needs a mother, which will mean no cria from her next year.

The other alpacas and cria are doing well, and hopefully we will finish up mating soon for the chance of cria from the other four in 2020.

Monday 29 July 2019

Poppy's Cria & Genetics

Alpaca birthing season for the year finished yesterday with the arrival of Poppy's cria, a spotted girl, who is sired by outside stud Classical Mile End Rococo. The cria weighed 19 and a half pounds when born, which makes her the heaviest birthweight we've had yet, and weighs the same this morning.

This spotted pattern seems to be caused by a dominant gene, and Poppy either produces a solid-coloured cria or a white cria with spots of the solid colour. Technically it's a cria with white spots rather than a white cria with coloured spots, as the cria is genetically the colour of its spots and the gene causes there to be large depigmented areas in the fleece. I'd quite like to get rid of this gene and have solid-coloured crias, as Poppy's bloodline has the best quality fleeces of my alpacas and solid coloured ones are better for spinning. Interestingly, Poppy's offspring seem to be more heavily spotted than she is, which suggests the causative gene is a long repeating string of DNA which has been developed by breeders in the alpacas' native countries selecting for mostly white animals. Because of how chromosomes recombine when animals reproduce, often if selection pressure is applied for a particular trait, the genetics for the trait are duplicated. For example, if the DNA sequence GAATC in a particular position causes the animal to have depigmented areas of coat, it becomes GAATCGAATCGAATC and so on over several generations, causing the depigmentation to be more extensive. That chromosomes are able to do this is an adaptation that causes animals to be able to change and adapt rapidly instead of having to rely on random mutation, and it's one of those genetic things that don't follow the most commonly understood concepts of dominance and recessiveness. While breeding together animals that are predominantly white over time will increase the white-spottedness, selecting away from it and breeding to solid coloured animals should have the opposite effect and cause the string of DNA to shorten over generations, so even where the gene is passed on the phenotype should slowly change to look more like a dark animal with white spots.

Meanwhile, here are the other crias.


James Bond and Zaphod Beeblebrox


Sunday 21 July 2019

The Life of an Animal Breeder

What is the life of an animal breeder like?
Being an animal breeder is going to the emergency vet out of hours because your animal has run into problems giving birth, and emptying out your bank account to pay for surgery she needs. After the surgery, the vet tells you one of the offspring didn't make it and there is a charge to incinerate it, so you say you will take it home and give it a decent burial and save money. The vet brings it out to give you in a towel and doesn't ask for the towel back, and you are grateful for small things because the towel is nicer than any of the towels you already own, and that includes the ones you use for yourself and not just the ones that are for the animals.
(I have never made a profit from any of the animals I breed, and I don't expect to. Please be aware when you buy an animal from a caring breeder, the cost of purchasing the animal is to subsidise the breeding programme so the breeder can conserve the breed, not so the breeder can buy luxuries like new towels)
Indi's puppies are now 1 week old and all doing well. Today's smell is anise.

Wednesday 17 July 2019

Fleur's Cria

Fleur had another boy cria at 10:30 this morning, a suri with spots and fawn/brown feet and weighing 13 pounds. This happened just before I was taking Indi to the vet because I suspect she may be developing mastitis, so Fleur and the cria were shoved in a pen out of the way of the other alpacas once it was established the cria was breathing and appeared normal, and left to work things out for themselves. It seems to have worked as when I came back the cria was already feeding, so they have been let out to rejoin the others, at which point the battery on the camera went flat. Indi is having antibiotics as a precaution.

Monday 15 July 2019

Olivia's Cria

This is why I usually try to avoid having pups in the summer because I'm too busy! Olivia has just had another male cria weighing 12 pounds.

Indi's Puppies

Indi went into labour yesterday morning and delivered three girl puppies without any difficulty. Unfortunately we ran into problems after the third, as Indi started having intermittent bouts of unproductive straining, and there was nothing in her birth canal when I examined her despite there clearly being a few pups left inside her, When a bitch has difficulty with delivery, it's necessary to weigh up the risks to the bitch herself and any puppies already born against the risk to the unborn, as if it's suspected a puppy has suffered a placental abruption it's often better all around to give her the chance to pass it naturally whether dead or alive, as it will certainly be dead by the time the bitch has arrived at the vet and you've signed the consent form and the vet has anaesthetised her and opened her up. However, this wasn't one of those cases. Indi was already trying hard to pass the pup and it clearly wasn't working, and waiting was not in her interests as she'd likely become exhausted and unwell and this wasn't in the interests of the pups she had, and any pups alive inside her would be lost.

Unfortunately Indi had picked a day the normal vet was shut, so we had to go to the expensive out of hours franchise vet. Fortunately the staff were lovely and the only thing harmed was my bank account, as the obstruction turned out to be a dead puppy with severe oedema that would never have been viable whatever happened. Oedema is a buildup of fluid in tissue. A normal poodle whelp on the larger side can weigh about a pound, but this puppy weighed more than twice that and it was obvious it would never have fitted through Indi's pelvis and it wasn't even recognisable as a puppy. The puppy would have been black and had a jagged unpigmented line running down the underside of his body from his throat to his groin, which suggested a midline defect that probably had affected internal parts. Midline defects can occur in all vertebrates when something doesn't work as intended very early in embryonic development, as the embryo develops a structure called a neural crest from which all the body parts form. Cells migrate from the neural crest, which later turns into the spinal cord and brain, and meet up on the ventral side of the body. The most vital bodily part that forms from this meeting of cells is the heart, so I can only speculate that as heart problems can cause oedema, this would explain this unfortunate puppy that was not to be.

More happily, behind the obstruction the 5th and final puppy, a boy, was recovered safe and well during the surgery, and Indi has now been spayed. The pups so far are feeding normally and seem healthy, and I put them in a basket for a couple of hours at a time overnight so I could get some sleep in between watching Indi with them. Indi has recovered from the drugs and is licking the pups again and seems bright and well. I will be keeping one of these pups and the others at this point I believe all to have people waiting for them. I'm sorry yet again for the people who were waiting for a pup from this litter that there aren't going to be enough to go round. I think I've contacted everyone who was waiting.

The boy is the lighter of the two cream puppies

Tuesday 9 July 2019

Indi's Pregnancy

Indi is 8 weeks pregnant. The waiting list for this litter is now closed for the time being until the pups arrive, as the first 6 places are reserved and I have additional people who have expressed an interest and not yet visited.

Monday 1 July 2019

Alpaca Fleece

I have a few alpaca fleeces for sale, due to not having enough time to spin them all myself. Most of these are from slightly older animals and are not superfine, but a lot are great for beginners and can still be used to make nice things. I taught myself to spin using Costa's and Olivia's fleeces last year and made a nice blanket and ruana from them. Fleeces are £10-£20 each or can be broken up into smaller amounts for the equivalent cost.

Costa, rose grey, about 30 micron AFD and 3 1/2 inch staple length. Really easy to spin and can be broken up by hand with very little preparation. Also good for carding and blending. I have sold half this fleece already so I have half left available.

Poppy, 5" staple length, mostly white, decent crimp, around 25 micron AFD. Great for combing and dyeing and still has a soft feel nicer than any native sheep breed.

Marius, brown suri alpaca, 8" staple. Older animal so a fairly coarse fleece, but a lot easier for someone who has never spun suri before and wants to try it than starting with really fine suri. It also makes a really strong thread. Suri ideally has to be combed and spun worsted to get the best out of it. This is 2 years' growth and quite a lot of fleece. I am going to use some of it myself but have too much.

Olivia, fawn, about 32 micron AFD with decent crimp and fairly short staple at 3". Great for carding and blending and can also just be broken up by hand and spun with very little prep.

Saturday 22 June 2019


I'm not going to pretend I wouldn't have preferred them to be female, but these two boys are strong and bonny and I'm probably going to do the same matings that produced them again next week. Everyone who breeds animals for any length of time will experience having to deal with births and pregnancies that don't go right and sickly runts where it's often hard to tell when you need to stop and let nature take its course for the sake of the animal as well as your own sanity. It is nice once in a while to have things go so smoothly and be able to sit back and enjoy.

Suri cria is starting to develop his lock structure -- his fleece looked tufty when he was first born.

Fleur is pregnant and looks it, and will likely be the next to give birth, but likely not until the 6th of July or after.

Wednesday 12 June 2019

Indi's Dutch Tryst

I usually try to avoid having pups in summer as there's so much other stuff going on. I had been intending to mate Indi, who previously had a litter in 2017, on her next season, and I wanted to use an overseas sire, but her next season is likely to be in November and because politicians won't stop fighting with each other and sort something out, I wanted to avoid a potentially complicated scenario where it might not be possible for Indi to go. So, as something of a last minute decision (Indi's passport was only ready a week or so before she came in heat) Indi and I travelled to the Netherlands. Indi enjoyed herself there and recently I've found out she brought some souvenirs back with her.

Indi's souvenirs will be much more tasteful than these ones

So we are hoping to have some Indi pups in July. Because of the late change in plans and having told previous enquirers I wasn't having any more pups until early 2020, there are probably a few places available on the waiting list for Indi's pups depending on how many there are, so if you think an Indi pup would be right for you and you can give it the loving home it deserves, please get in touch.

It seems to be trendy at the moment for people to make what looks like tacky movie posters about forthcoming litters, so I made the tackiest most tongue-in-cheek one I could come up with! There are proper pictures of the dogs and information on the litter page on the website.