He writes this essay in response to someone who writes about their "gut level emotional response when [they] thought about dogs being likely killed by an as yet unproven and dangerous medical procedure." 

I recommend the whole thing. If you are going to read it all, note that some text is duplicated near the end, though there is one paragraph at the very end which is not. 

First, he describes how animals share empathy and emotions with humans:

It is a maxim of the Animal Rights ideologues that "a rat is a dog is a boy." [PETA] This is patently not true, and might just be denounced as absurd on its face. But, it is true that rats, dogs and boys share important properties, or more generally, that rats, dogs and people share important properties. I have a huge reservoir of experience with rats, dogs and people. All three have a well developed sense of self, the ability to read my face and determine my mental state, and, obviously, the ability to experience most, if not all of the basic emotions and mental states that humans experience: anxiety, fear, emotional attachment to others (or their own and other species), sexual arousal and release, anticipation, enjoyment, curiosity, and so on. Most importantly, they have the ability to experience empathy - to extend their internal feelings to others. Well socialized rats and dogs know that the people they interact with can be hurt, provoked, pleased, and otherwise be emotionally and physically affected by their actions and they, in turn, act accordingly within the limits of their abilities to do so. Neither "pet" dogs nor rats bite their owners with abandon nor destroy their homes. This isn't just "conditioned behavior," but rather is the result of a more global understanding that humans, like them, can feel; and thus can be rewarded or made to suffer.

This is a very important and valuable property to people. it is so valuable that, when members of our own species fail to demonstrate it, we imprison them or even kill them! Jails and prisons are full of people who either lack empathy, or lack the ability to act upon it. What then does it say of us if we treat animals in ways that demonstrate a lack of understanding or respect for their feelings - for their ability to suffer or experience pleasure?

The answer is that it would, at first glance, say that we were either sociopaths, profoundly ignorant of the nature of animals, or taken over by some ideology which induced a state of perceptual blindness to their plight. Thus, what I am saying here is that I agree that it is neither reasonable nor moral (within our value structure as empathetic beings) to regard animals as unfeeling automatons, let alone treat them as such.

However, there is a problem with this approach to dealing both with our fellow humans and with other animals as the sole guide to our actions. The problem is, put simply, this: The native state of man and beast is one of unfathomable suffering.

Next, he explains ethics in a way that seems to correspond with a lot of Eliezer's writing: 

The central moral kernel of almost every religion is that we are born into a world of injustice and suffering. There can be little quibbling with that observation, since everywhere we turn we see living systems whose very structure brings them into "conflict" with their environment and causes enormous suffering. This is how it has always been. It is the reality of our existence in this universe. Evolution, the beautiful star studded sky at night, the cool lapping ocean - they don't give a damn about anything, least of all a mouse in a cage with cancer or a woman with her breast rotting off. And as far we can tell, they never will.

The best the universe has done so far is to produce us - creatures who both can and do care about injustice and suffering. If you believe in a Grand Design, or some other teleological explanation that results in universal justice, then, go to the mirror right now and take a long hard look, because buddy, you are it - you are as good as it has gotten, so far.

Then, unless you are cretin or a fool, or both, realize that suffering and injustice are both inescapable contemporary and future realities which you have to deal with rationally (or not) as you choose. You do not get to choose Door Number 3, which is "no suffering and injustice." In fact, even you kill yourself straightaway to avoid inconveniencing a mouse with a plow, the suffering and injustice will continue to march on, even for billions and billions of years.

There are no easy choices.

The best you can do is to choose carefully and rationally what kinds of misery you will inflict and to work, relentlessly, to minimize it and to make the universe a more just place. Those decisions will be informed by your values - by what you hold most worthy and in highest esteem. You are, of course, free to choose mice over men, a hunter-gatherer life over that of an agrarian, the world of the primitive or technological civilization.

Next, he tackles questions about whether animal research is, on net, beneficial: 

However, what you are not free to do, at least not around me, is to spew out lies and moral falsehoods about the supposed real nature of the universe and the real consequences of the choices you (and others like you) make. If you think that animal's have rights in the classical and real sense that has historically been applied to humans, then I will call you a liar and a moral blackguard who would, and has, condemned not only countless humans to unnecessary suffering and death, but countless animals whom humans value highly (our companion animals and livestock) as well - because much of veterinary medicine is a direct result of animal research.

If you argue that humans should be used in research, there I would agree with you. Most of the pharmacological research done with rodents is junk science which has led to few real medical advances. But be advised that such research will be ugly and terrifying and very likely costly in some meaningful proportion to the benefit it yields.

I am sorry to be so harsh, but technological civilization has robbed most of the Western world of any sense of reality - of how the universe works and of just how much suffering accrues from every frozen ready meal and every lipstick or plastic bottle of beverage consumed.

That dreamy, soft-bellied state of unreality is intolerable and it is also incompatible with our continued existence as a technological species, and probably as a species at all.

And it is most certainly incompatible with any hope we can currently see of the universe becoming a more just, decent and humane place.

Thus, I see your feelings and attitudes as profoundly incompatible both with your long term personal survival, and that of our species. As such, they evoke in me a feeling of revulsion and strong feeling of anger for the damage they have already caused to biomedical research - and will likely continue to cause.

Next, he goes into details of what animal lifespan research entails: 

I would also like to note that "the worst" of animal research in terms of inflicting suffering is not the acute experimental work conducted by cryonicists and most other mainstream medical research, but rather is to be found in the work of gerontologists conducting life span studies on rodents and primates. Research which virtually all on this list serve avidly lap up and never criticize - even though much, if not most of it, is junk science.

I can say, without reservation, that of all the pain, horror and cruelty that I have inflicted, either inadvertently, or as an anticipated consequence of research, by far the most cruel work I've ever (done or) observed is that of the gerontologist doing lifespan studies. ... 

The fact is, that aging animals get a dreadful array of truly horrible and disgusting pathologies and, because they are not humans receiving human medical care, they die in fantastically gruesome ways more often than not. ...

Rodents often develop not only mammary neoplasms [breast cancers], but tumors of the food pouches and buccal mucosa [inside lining of the cheeks]. Since there is no surgical intervention, these masses often grow to colossal size, ulcerate, break down and fungate. A common cause of death is starvation, which is truly terrible to watch. Sometimes, the animals lose the ability to drink, in which case death is mercifully faster and less painful as a result of dehydration.

The visceral and bone pain that results from tumor invasion of vital organs, the skeleton and joints must be unimaginable. And cancers kills the majority of animals in gerontological lifespan studies. I've seen animals languish in their cages for weeks or months being slowly consumed by lesions so revolting I could barely force myself to handle them in order to document their decline.

And of what the lucky ones who don't die of cancer? Are they in rodent care homes in tiny beds with tiny egg crate mattresses with a staff of rodents careers to lick their bums and turn them? Hardly. As animals age and develop spondylosis [spine osteoarthritis] and sarcopenia [age-related loss of muscle mass], they become unable to reach their anuses and urogential areas with their mouths. As a result, they cannot clean themselves, and they develop an ammonia-generating, bacteria infested crusting of urea and feces in these delicate areas, which, not infrequently results in ulceration. They are often blind from cataracts, and are, of necessity, usually housed one to a cage (they have a propensity to cannibalism, especially if calorie restricted), so they die alone, slowly, most often of starvation and dehydration.

Of course, the first question that likely comes to most peoples' minds upon hearing this a tale of horror is, "For the love of god man, why don't you euthanize such poor creatures, or at least medicate them for pain?" The answer is that you can't, not without developing a whole new, complex and costly model which has highly specific (and uniform) and almost completely NONSUBJECTIVE algorithms for when euthanasia should take place. And, you can forget about knowing what the "maximum lifespan" is, because it is flat out impossible to tell how long a moribund and likely suffering animal will live. I've seen animals I thought were certain to die within days survive for MONTHS! And so has every other experienced gerontological researcher.

That is the reality gerontological lifespan research.

So, you want to trespass on the territory of the gods and life forever, or even just another 50 or 500 years longer and you want to do it whilst being a nice guy? Give me a break!

The ending is poignant, and I think an excusable violation of Godwin's law: 

Cryonics has largely been taken over by this moral world-view and with an understandable, if inexcusable accompanying moral cowardice which dictates that we hide our animal research and cower in fear because the "Animal Rights" people will attack us (and by implication our poorly protected patients stored in vulnerable, unhardened facilities). This is the direct path to the Dark Ages or to the Soviet, or to the Third Reich, which was ironically, the only nation-state to completely ban animal research because of its cruelty and inhumanity. Instead, they built concentration camps and turned loose the likes of Holzhoner, Rascher, Mengle, Whichtman, Caluberg and countless others like them on humans, who, unlike animals, have the rich perceptual ability to comprehend their own mortality and to contemplate, at length, the certain inevitability of their fate.

Darwin does not mention it in this essay, but he is a vegetarian, and his dog is cryopreserved at Alcor. 

About a month ago kalla724 posted a number of comments on this post, many of which were highly upvoted.

Synopsis: I) I think that kalla724 is too pessimistic about the practice of cryopreservation to preserve personal identity, because we don't know what level of synapse/active zone/protein structure is preserved in human brains, and we also don't know what level is required for personal identity. II) I think kalla724 is wrong about the required detail necessary to simulate a C. elegans. This is testable in the relatively near-term, and the results of that test might yield insight into whose argument in point I is stronger. 

I

kalla724's main argument: it is not possible (p = 10^-22) that cryonics will preserve personal identity, because replacing water with cryoprotectant will cause too much damage to proteins and lipids in the brain.

My view is that kalla724 is too pessimistic. To find a specific example to expand upon this intuition, I searched for "c elegans memory". I chose one of the first reviews in the results: http://learnmem.cshlp.org/content/17/4/191.full, published in 2010 by Ardiel and Rankin. Here's their first example: 

Rankin et al. (1990) were the first to characterize learning and memory in C. elegans. They studied plasticity of the “tap-withdrawal response” (TWR), a behavior whereby worms swim backward in response to a nonlocalized mechanical stimulus generated by tapping the Petri plate containing the worm. The magnitude of this reversal response is around 1 mm (roughly the length of the worm), but this can change with experience. Repeated administration of the tap results in a decrement of both the amplitude and the frequency of the response

The specific neurons mediating this are known: 

Using the circuits described by Chalfie et al. (1985) in conjunction with the neural wiring diagram (White et al. 1986), Wicks and Rankin (1995) identified the mechanosensory cells (ALM, AVM, PLM, and PVD) and interneurons (AVD, AVA, AVB, PVC, and DVA) mediating the TWR.

Through more science, they found that: 

the locus of mechanosensory habituation is in a part of the circuit unique to the TWR, i.e., the touch cells and/or the synapses between the touch cells and the interneurons. Now the hunt for the underlying molecular mechanism could begin.

There is some evidence for how the short-term component of the tap-withdrawal response plasticity. This is it: 

repeated activation of the touch cells results in autophosphorylation of the SHW-3–MPS-1 complex, thus diminishing K+ flux and prolonging the duration of mechanoreceptor potentials. This would slow the recovery from inactivation of EGL-19 (the L-type calcium channel mediating touch-evoked calcium currents) (Suzuki et al. 2003) and dampen cell excitability

This means that the complexes of proteins, working together, add phosphate groups to themselves as a post-translational modification. Each individual complex functions as a potassium ion channel, so changing its structure can alter the excitability of the cell.

Whether vitrification will preserve this specific post-translational modification is, as far as I know, an open question. The current cryoprotectant solution, M22, is pretty physiologic, which means that it functions similarly to water. But, we don't have this data. 

It's likely that when the protein complex undergoes autophosphorylation, other changes occur in the cell as well. If this led to changes in the cell's epigenome, which is very common, and the structure of the epigenome is retained by the cryopreservation, then the cell's epigenome could allow reverse inference of the state of its ion channels. We also don't have this data. 

The authors also discuss evidence for the long-term component of the tap-withdrawal response plasticity: 

the AMPA-type glutamate receptor subunit, GLR-1, was required for long-term habituation—glr-1 loss-of-function mutants habituated but did not retain decremented responses ... long-term habituation was associated with a significant reduction in the size, but not the number, of the GLR-1::GFP clusters in the posterior ventral nerve cord

This means that the number and distribution of a well characterized protein at the synapses of cells is highly correlated with the strength of the memory. This is consistent with current paradigms of long-term memory. 

Under ideal cryopreservation conditions, synaptic vesicles and receptor distributions are likely retained, even if some of the proteins may be a bit denatured. The data is far from perfect here, either. 

It's also important to stress that this only occurs under ideal conditions. Given the current practice of cryonics, cryoprotectant will not reach many or most areas of the brain. In these cases, there is a large amount of ice damage and the information is much more likely to be irretrievable. 

II

kalla724 says:

Uploading a particular C. elegans, so that the simulation reflects learning and experiences of that particular animal? Orders of magnitude more difficult. Might be possible, if we have really good technology and are looking at the living animal.

kalla724's requirement is that we look at live C. elegans to simulate them. But, the evidence above indicates a good correlation between AMPA receptor distribution and tap-withdrawal reflex. And there is good reason to believe that these features are retained by vitrification under ideal conditions. 

So, it seems to me that if you were to emulate a particular C elegans, you could add more receptors (or just up the strength parameter) at those synapses, and thus mimic the plasticity of the tap-withdrawal reflex. Looking at live animals would not be required. 

One more note:

Extrapolating results on personal identity from C. elegans to humans is not ideal. If the results are biased in one direction, we should expect more redundancy in mammalian neural systems than there are in nematode ones, because mammals have so many more brain cells. 

Edit 6/15: fixed format of quotes. 

Edit 6/16: added synopsis to clarify main points.