Okay most of my 35 corn snake eggs have "hatched"... and I just wonder if it could be the male to blame!
The biggest problem is that I understand experimental design, I understand variables and cause and effect. I know it's going to be impossible to know right off what the real cause of this year's failures stem from... however...
Variables that could be at fault:
I used tap water to moisten the vermiculite
I used Vermiculite
They all have the same papa
They all experienced the same temperature spike
The defects of spine/head/jaw only happened to corn eggs all fathered by the same snake. The kingsnake eggs incubated in the same way did NOT experience those defects, though I did lose a whole clutch, and two of the second clutch.
Next year I plan on changing all variables but one (and even changing that for all clutches but one)....
I'm going to try a no-substrate method and/or different methods to see if this helps. I will not use the same male except for one control clutch. I will use purified water only... both for drinking for the snakes during brumation/breeding/gestation and the eggs during incubation. I will hopefully not have an Air Conditioner Failure.
My results from this year breeding my normal stripe male to my females:
Normal Het Motley (but perhaps Not?) het Amel
10 eggs: 10% good babies
9 normals, 1 amel. 8 died with kinked spines and/or huge bulging foreheads and/or deformed/missing jaws. kinked spines were the MOST prevalent in this clutch with some very severe kinks. This clutch is the only one that had too much moisture to begin with.
Anery Stripe
5 eggs 40% good babies
(1 bad egg, 6 slugs). 2 perfect broken stripes hatched out... the remainder didn't... inside were two kinked spine babies with deformed heads/spines and one perfect but dead in egg baby. The kinks and deformities were less on this clutch than the previous clutch which was laid 2 days before this one, and started hatching two days before this one.
Reverse Okeetee
21 eggs approximately 10% definately good babies, could be up to 25% good babies.
(1 went bad early in incubation, 1 went bad late)
two normals pipped two days after the previous clutch... both with perfect normals. Then I got impatient (48 hours with no pipping) and pipped the rest. Of those 9 were dead or so deformed they should have been dead. (missing lower jaws and bulging foreheads but no, or only mild spinal kinks)... I still have three more that appear to be dead in the egg, and 2 that are deformed but not horribly so, at least not obviously, and still hatching, and two normals and an amel that have noses poked out and appear fine so I'm not disturbing them. (I only investigated further on the ones with obvious difficulties or deformities.)
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SO.... is it the papa snake that is to blame? Could he carry some hideous dominant "deformation" gene but not express it himself? And if so do I consider all the babies that have hatched out as culls? (whether in the traditional "kill" sense, or the less traditional and secure "give as pets" sense.)
My thoughts on this issue is that I give away the babies that are not so deformed they can't live and flourish (dinosuar-heads but insignificantly kinked and with functional lower jaws) and keep all the perfect looking babies at least for a year until the papa snake is bred again and his babies examined for defects. If he has a "perfect" clutch next year without any sort of defects or problems, then I would consider this to be something environmental in nature, and the ones who live and flourish with no signs of defects could be sold without too many qualms.
My plans for next year include:
Striped but possibly genetically bad Papa x Anery female (not bred this year)
Snow Motley Male x Anery Stripe Female and x normal het motley female
Creamsicle male by normalsicle female and poss. creamsicle female.
We'll see what happens.
It's been a bad year... almost enough to make a person give it all up! 
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~Sasheena