Don Bennet, DAS, in his video "Protein Explained" on his channel health101DOTorg, trying to explain / claim "how protein can cause autoimmune disease," mentioned that there is "unusable protein" and connected it to cooking. 

I asked: 

Don, could you please link to the studies that would support your statements about unusability of cooked proteins?

Don answered: 

Lena, these statements are not derived from studies; the affects of high temps on foods have been known for a while and are borne of science, but they are not common knowledge because people appear to be doing just fine eating a diet that contains a high percentage of cooked food, even though "fine" is a relative term. And since the cooked food industry, although not an official industry, is the largest industry in the world when you consider what it encompasses, they are not going to be disseminating this information. And just like the global warming deniers who base their contentions on spurious "facts", so do the anti-raw food practitioners who state that we need cooked food for reasons such as cooking makes lycopene more bioavailable, while not discussing the many nutrients that are made less bioavailable (and not bothering to mention that 100% raw foodists get sufficient lycopene), and that certain foods, like legumes, can't be eaten unless cooked. And the anti-vegan crowd makes the case for cooking by saying that we can't consume meat and dairy unless they are cooked. But I say that helps make the case against cooking.

But to the point of protein, here's an experiment you can do at home. Take the "white" of an egg and examine it. Note its texture, color, taste, smell, and appearance, and keep in mind that the albumin of the egg is pure protein. Now drop it into a hot frying pan and watch all those attributes change, and change very significantly. The affect that the heat has on this protein can only fall into one of three categories: improves it, neutral, damages it. I've not found many things that remain neutral after being exposed to such temps, so let's leave that one out. Of the two that are left, absent any scientific knowledge on the subject, and just going by intuition, what do you think is the affect of cooking that albumin?

An experiment that you should not do at home, one that demonstrates the damage to organic matter by cooking, is to substitute your hand for the albumin in the above experiment. And to be fair, there are some educators who contend that cooking does not change the characteristics of minerals in food. But they will admit that it does change the bioavailability of vitamins, lipids, and proteins. But they mention the "minerals hold up just fine" in the promotion of a "high-raw" diet (one that includes cooked food in the last meal of the day). 

So at the end of the day, it is up to each of us to decide where we sit on the "cooking damages the bioavailability of nutrients" issue. There is likely goodly amounts of hard-science on the affects of cooking on lipids, carbohydrates, and proteins on the Internet (my 40+ years of research contains boatloads of hardcopy evidence that sits in storage). Just be aware of any junk-science that talks about the benefits of cooking. :)

I responded: 

Don, you are using scientific terms and suggest scientific-like conclusions - it would be nice if you had stated that those are just your opinions.

I am not going to make your egg experiment (which would demonstrate not much relevant to this discussion) because I am vegan.

Materials in your 40-year-old books or magazines are unlikely to serve as evidence, especially after you admitted that your statements are not based on scientific research.

• What "junk-science that talks about the benefits of cooking" are you referring to - any examples?
• Why do you assume that I am unaware of pseudo-science?
• How would you describe digestion of proteins? Do you think amino-acids become unusable after exposing to any duration of any cooking temperature?

Don: 

Lena, I was not recommending that the egg experiment actually be done, I was just mentioning it to make a point (I've been vegan for 40+ years, so I don't do that demonstration at my talks). And the evidence in books much older than 40 years about the nature of our solar system is still valid, and will be centuries from now. So the age of evidence does not necessarily discredit information. And my statements are based on scientific fact and not on anyone's opinion, including my own. If people don't want to believe that cooking food damages various components of the food, that's fine... everyone is entitled to their own opinions, but everyone is not entitled to their own facts (myself included). And I don't assume you are unaware of pseudo-science, I mention it because my comments here are in a public forum and others will be reading them. And it's not a question of my belief as to whether or not proteins are denatured by the temps of cooking, this is fact. And even though the heat of cooking doesn't deaminize amino acids, the denaturing of proteins is harmful to us because of making those proteins that are damaged unusable AND causing autoimmune reactions.

My response was: 

I need to break bad news to you then: 1) nutritional science is very different from physics, 2) the age of research might matter a lot, especially in nutrition, especially for complex systems. If your "evidence" would be in the books (even though you said yourself that your opinion is not based on studies), why couldn't you point out to the publication online, the author, the book listing or anything like that?

How can you even maintain that your statements are based on scientific facts after you started with "these statements are not derived from studies?"

Yes, let's talk about denatured proteins: that's why I asked what do you think happens during digestion (you did not answer). Hint: denaturation is the first step in protein digestion. Maybe this can help you understand what called denaturation: http://fruitarians.net/definitions/144-protein-structure-cooked-and-denatured-proteins

Actually, you did not answer three of my questions.