I am not aware of concern about papaya seed consumption because of carpaine. Carpaine is an alkaloid that may be found in papaya seeds but is more concentrated in papaya leaves. The only published study on this papaya alkaloid that I've seen was conducted in laboratory animals in 1978, and it did not involve papaya seeds. The leaves of the papaya plant were used for that study.
Yet, I have seen published controversy about papaya seeds in two basic areas.
The first of these areas involves genetic engineering of the seeds. Problems with ringspot virus, particularly in Hawaii, initially prompted growers to gravitate toward genetically modified papaya seeds that could produce plants better able to withstand damage from this virus. Because evidence of the genetic modification began to show up in organically grown papaya fruit (organically grown foods are not allowed to undergo any type of genetic modification), Hawaiian growers protested that their food quality and livelihood were being jeopardized. I have not seen any published data on health risks associated with consumption of genetically modified papaya, but I always favor purchase of organically-grown foods (including papaya) to avoid any unknown but potential risks in this area.
The second issue I've seen with papaya seeds is toxicity related to chloroform or other synthetic extracts derived from the seeds. Animal studies have shown increased problems with infertility resulting from consumption of these very high-dose synthetic extracts. These problems have included reduced sperm count and reduced sperm motility. I don't believe these studies on animals (involving high-dose synthetic-seed extracts) apply in any direct way to human consumption of papaya seeds. I would also note that some of these animal studies involved intramuscular injection of the seed extracts—making the studies even less applicable to the situation of a human eating fresh papaya with seeds included.
I have seen one study that showed potential immune benefits associated with consumption of papaya seeds.
Based on all of the above evidence, I continue to believe that papaya seeds are safe to eat in an amount proportional to the natural amount of fresh papaya fruit being enjoyed.
For more information on this topic, please see:
Adebiyi A, Ganesan Adaikan P, Prasad RN. Tocolytic and toxic activity of papaya seed extract on isolated rat uterus. Life Sci. 2003;74(5):581-92.
Hornick CA, Sanders LI, Lin YC. Effect of carpaine, a papaya alkaloid, on the circulatory function in the rat. Res Commun Chem Pathol Pharmacol. 1978;22(2):277-89.
Kermanshai R, McCarry BE, Rosenfeld J, et al. Benzyl isothiocyanate is the chief or sole anthelmintic in papaya seed extracts. Phytochemistry. 2001;57(3):427-35.
Mojica-Henshaw MP, Francisco AD, De Guzman F, et al. Possible immunomodulatory actions of Carica papaya seed extract. Clin Hemorheol Microcirc. 2003;29(3-4):219-29.
Verma RJ, Nambiar D, Chinoy NJ. Toxicological effects of Carica papaya seed extract on spermatozoa of mice. J Appl Toxicol. 2006;26(6):533-5.