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That a male's preconception behaviors and exposure to all sorts of environmental contaminants (alcohol, drugs, medicines, chemicals at work, pesticides, etc) has effects on sperm and is linked to birth defects has been known for decades. What is new is the focus on epigenetics, or as some researchers call it: inherited paternal epigenetics. Three different paternal influences that affect the fetus and child (thus paternal experiences influence what the child inherits) are discussed in a review article: paternal age, environmental factors, and alcohol consumption.The researchers also found that environmental effects during the lifetime of a father can affect not only his immediate offspring, but also future generations.

What is epigenetics? Researchers in the study summarized it as: "Epigenetics are heritable alterations in gene expression that do not involve changes in the germline DNA sequence. It works primarily through three mechanisms: DNA methylation, histone modification, and microRNA (miRNA) expression."

Huh? This means that in epigenetics, the DNA doesn't change, but external or environmental factors switch genes on and off and affect how cells read genes. In other words, it's how the environment can alter gene expression without changing the genetic code. Epigenetic change is a regular and natural occurrence, but can also be influenced by several factors: age, the environment/lifestyle (such as diet, alcohol consumption, and chemical exposure), and disease state.  For example, what you eat and how much you drink (alcohol), where you live, what chemicals you're exposed to, how you exercise, even aging – all of these can eventually cause chemical modifications around the genes that will turn those genes on or off over time. Additionally, in certain diseases such as cancer or Alzheimer’s, various genes will be switched into the opposite state, away from the normal/healthy state. From Science Daily:

Fathers' age, lifestyle associated with birth defects

A growing body of research is revealing associations between birth defects and a father's age, alcohol use and environmental factors, say researchers at Georgetown University Medical Center. They say these defects result from epigenetic alterations that can potentially affect multiple generations. The study, published in the American Journal of Stem Cells, suggest both parents contribute to the health status of their offspring -- a common sense conclusion which science is only now beginning to demonstrate, says the study's senior investigator, Joanna Kitlinska, PhD, an associate professor in biochemistry, and molecular and cellular biology.

"We know the nutritional, hormonal and psychological environment provided by the mother permanently alters organ structure, cellular response and gene expression in her offspring," she says. "But our study shows the same thing to be true with fathers -- his lifestyle, and how old he is, can be reflected in molecules that control gene function," she says. "In this way, a father can affect not only his immediate offspring, but future generations as well."

For example, a newborn can be diagnosed with fetal alcohol spectrum disorder (FASD), even though the mother has never consumed alcohol, Kitlinska says. "Up to 75 percent of children with FASD have biological fathers who are alcoholics, suggesting that preconceptual paternal alcohol consumption negatively impacts their offspring."

The report is a review of evidence, human and animal, published to date on the link between fathers and heritable epigenetic programming. Among the studies reviewed are ones that find: - Advanced age of a father is correlated with elevated rates of schizophrenia, autism, and birth defects in his children; - A limited diet during a father's pre-adolescence has been linked to reduced risk of cardiovascular death in his children and grandchildren; - Paternal obesity is linked to enlarged fat cells, changes in metabolic regulation, diabetes, obesity and development of brain cancer; - Psychosocial stress on the father is linked to defective behavioral traits in his offspring; and - Paternal alcohol use leads to decreased newborn birth weight, marked reduction in overall brain size and impaired cognitive function.

Coffee consumption overall seems to be beneficial to health in various ways, such as lowering the risk of colorectal cancer. But there are times one should limit how much one drinks, such as during the  preconception period for both the male and female, and also during pregnancy, to lower the risk of miscarriage.

From Science Daily: Coffee consumption linked to decreased risk of colorectal cancer

Researchers have found that coffee consumption, including decaf, instant and espresso, decreases the risk of colorectal cancer. Moreover, these benefits increase the more coffee you drink. The study examined over 5,100 men and women who had been diagnosed with colorectal cancer within the past six months, along with an additional 4,000 men and women with no history of colorectal cancer to serve as a control group. Participants reported their daily consumption of boiled (espresso), instant, decaffeinated and filtered coffee, as well as their total consumption of other liquids.....

The data showed that even moderate coffee consumption, between one to two servings a day, was associated with a 26 percent reduction in the odds of developing colorectal cancer after adjusting for known risk factors. Moreover, the risk of developing colorectal cancer continued to decrease to up to 50 percent when participants drank more than 2.5 servings of coffee each day. The indication of decreased risk was seen across all types of coffee, both caffeinated and decaffeinated.

Coffee contains many elements that contribute to overall colorectal health and may explain the preventive properties. Caffeine and polyphenol can act as antioxidants, limiting the growth of potential colon cancer cells. Melanoidins generated during the roasting process have been hypothesized to encourage colon mobility. Diterpenes may prevent cancer by enhancing the body's defense against oxidative damage. "The levels of beneficial compounds per serving of coffee vary depending on the bean, roast and brewing method," said first author Stephanie Schmit, PhD, MPH. 

Colorectal cancer is the third most common cancer that is diagnosed in both men and women in the United States, with nearly five percent of men and just over four percent of women developing the disease over their lifetime. The American Cancer Society (ACS) estimates that in the United States, over 95,000 new cases of colon cancer and 39,000 new cases of rectal cancer will be diagnosed in this year alone.

Both males and females should limit coffee consumption in the preconception period to no more than 2 caffeinated drinks daily to lower the female's risk of miscarriage. From Medscape:

Even Men Need to Cut Back on Coffee Before Pregnancy

Women already know they need to cut back on coffee during pregnancy, if not sooner, to lower the risk of miscarriage. But a new study suggests the men in their lives need to limit caffeine too. Pregnant women who had more than two caffeinated drinks a day while trying to conceive had a 74% higher risk of miscarriage than their peers who drank less coffee, tea, soda and energy drinks, the study found.

When their husbands and boyfriends had more than two caffeinated drinks a day during the preconception phase, however, these pregnant women ended up with almost the same increased risk of miscarriage they would get from drinking coffee or soda themselves...."We did not find drinking one to two daily caffeinated beverages to increase the risk of miscarriage." Scientists aren't sure how caffeine contributes to miscarriage, but it's possible it affects egg or sperm production, implantation of the fertilized egg, or the ability of the embryo to grow in the uterus.

To assess how lifestyle choices may influence miscarriage risk, Louis and colleagues followed 344 couples in Texas and Michigan through the first seven weeks of pregnancy....Overall, 98 women, or 28%, experienced a miscarriage during the study, as reported March 24 in the journal Fertility and Sterility. Women 35 or older had nearly double the miscarriage risk of younger women, the study found. When women took daily multivitamins, their miscarriage risk was 55% lower than for their peers who didn't do this.

One surprise in the study is that researchers didn't find an increased miscarriage risk associated with smoking or alcohol, however. This doesn't mesh with previous research, noted Dr. Jeffrey Goldberg, a reproductive health researcher at Cleveland Clinic in Ohio who wasn't involved in the study.