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Broiling Base Pairs: Is It Unnatural to have a CRISPR Genome?

Experiments in China using CRISPR on nonviable human embryos has caused a stir in scientific and ethical circles. CRISPR will allow for targeted gene editing and people have raised concerns about using CRISPR to create designer babies. Additionally, gene edits made using CRISPR would affect the germline; changes made to an embryo’s genome would be passed on to their offspring. Many scientists and ethicists have expressed concern over germline changes.

While I appreciate the concerns people have expressed, I think that sometimes these concerns can arise from misunderstandings about genes and gene expression. An individual’s genome is never static completely. Each time a cell divides, replication errors can occur, even with proofreading enzymes correcting mistakes. Mutations can be replicated as well. I’ve written about these ideas in the context of human cloning before, so for the conversation at hand I will focus on genomic imprinting and epigenetics.

Genes can be affected by the environment, including lifestyle choices that a person makes. This often takes the form of methylation. DNA methylation is when a methyl group is attached to a nucleotide in DNA (cytosine or adenine specifically), silencing the expression of a gene. Methylation is a normal part of the human genome, and plays a role in genomic imprinting as well as X chromosome down regulation in women. But problems can also arise from methylation, and this is relevant for this discussion because it can affect one’s offspring.

Genomic imprinting is important for mammalian genetics and genes that are imprinted do not undergo the demethylation process that other genes go through. Sperm and egg cells are imprinted paternally or maternally but the zygote removes this imprint for most genes, allowing a new imprint to be formed matching the sex of the new individual. Genes that do not undergo this process are known as imprinted because they will retain their previous paternal or maternal imprint in the new individual. Imprinted genes make up less than 1% of the genome and only occur on 9 chromosomes, but they represent a natural form of inherited change. Imprinted genes only have one of the alleles expressed (for a maternally imprinted gene, the maternal allele and vice versa). Problems can arise then if there is a mutation in the functioning allele.

Genomic imprinting is different than CRISPR, however, because it does not affect the germline cells. Those cells strip all parental imprinting away, so the parental gene expression only carries to one’s immediate offspring, and then their offspring are affected by their imprinting. It is not a change to the human genome, but a change in expression that is transmitted a single generation.

I am not suggesting that genomic imprinting makes CRISPR a non-issue ethically speaking. I am merely trying to point out that there are other ways in which gene expression can be changed outside of human directed gene editing. It seems that people are concerned about deliberate changes to the human genome, but if the basis of concern is not wanting to influence human evolution by affecting gene expression, then people should give just as much attention to DNA methylation from lifestyle choices. Perhaps even more attention, because these changes in gene expression are ongoing currently, and not a possibility or eventuality like CRISPR once the technique is deemed safe enough for use in humans.


Absence of Evidence is not Evidence of Absence

The question of the likelihood of life elsewhere in the universe is a hot topic at the moment, and several people have mentioned this particular piece to me.

I will start my reflection by saying that I believe the existence of God is not a question that science can answer, so I am skeptical of any claim that science has proven or disproven the existence of God. Such claims are philosophical or theological arguments that interpret science, but cannot be considered science.
Scholars, at least to my knowledge, are not in agreement over how abundant life in the universe. Some believe that life is very rare, while others believe that there should be plenty of life elsewhere in the universe. There is also a distinction made between microbial life and intelligent life. It seems that more people are willing to accept that microbial life could exist other places. The criticism levied against those who hold that the universe is fertile often takes the form of the Fermi Paradox. In other words, if life is so prevalent in the universe, why have we been unable to find any evidence for it?

Fine tuning
The fine tuning argument presented in this piece is that the natural laws needed for life to exist are so specific, that the universe appears tailor-made for life, and therefore the universe must have been designed for life. It can be considered a statistical argument because proponents say that the odds of all of these things happening purely by chance is astronomically small, that therefore chance alone is not a valid hypothesis.
I do not claim to be an expert in these things, but my proximity to the science and theology dialogue in general has given me glimpses into the conversation. The author of this post quotes Paul Davies as saying that design appears likely. As far as I know, I do not believe that Paul Davies would consider himself a proponent of intelligent design, and while he might agree that SETI is not well served by looking beyond the planet for other life forms, he does advocate continuing the search. He proposes examining extreme conditions on earth to try and identify life that evolved in a way different than we currently know. I believe that he would say life has been able to evolve more than once, which the author of this piece is trying to argue against.

Theology Shaping Science
The author also says that Hoyle’s atheism was shaken by big bang cosmology. What it doesn’t mention, and what physicist and theologian Bob Russell speaks of frequently, is that Hoyle is a prime example of using a theological commitment to influence science. Because he felt that big bang cosmology supported the idea of Christian creation, he used the existing data at the time and constructed the steady state model of the universe, a model in which there was no time of origin. At the time that Bob Russell was working on his Ph.D., graduate students in physics had to choose which model to work with, and both equally fit the data. Bob uses this as an example of theology being a selection criterion between competing theories when competing theories are equally valid, scientifically speaking.

And this, I believe is what proponents of design are attempting to do. They are trying to say that based on the available data, it is just as reasonable, if not more reasonable, to argue that the universe was designed by some kind of intelligence. They are looking at the data and saying there is no evidence of life anywhere else in the universe and our understanding of what it takes to bring about life is much more complicated than when we started looking for life elsewhere.

Time: The universe is over 13 billion years old, life on Earth is at least 3.6 billion years old. Why did life take so long to evolve? Life as we know it requires certain elements, and those elements did not exist in the universe at first. It took at least a billion years for stars to create elements heavier than hydrogen, helium, and lithium. Multicellular life is only 1 billion years old and modern humans are only 200,000 years old. We are an extremely young species, and while life could have began elsewhere earlier, if the conditions are as specific as we believe, the conditions might be met later elsewhere. We’ve been looking for life elsewhere in the universe since roughly 1960 – less than 60 years. Kepler has been trying to identify exoplanets for 5 years and scientists interpreting the data from the close to 1000 verified exoplanets believe that they could number in the billions. The alternative is that time on a cosmic scale doesn’t rule out life elsewhere yet.

Extinct: It is possible that intelligent life did evolve elsewhere but they have gone extinct. The Kardashev scale hypothesizes the kinds of energy that technological civilizations could use. It is possible that in trying to harness energy, or through warfare, natural disasters, etc. other intelligent species have gone extinct. The problem is that there is no evidence of technology in the universe either.

Hiding: Another thought is that there are many intelligent species in the universe, but there are dangers that lead intelligent life to hide their existence from other intelligent life. Stephen Hawking has said that humans should not seeking out intelligent life elsewhere in the universe because they could pose a threat to humans and Earth.

Different kind of life: As the op ed piece makes clear, our understanding of what it takes to have life as we know it exist has expanded and complexified. This is not to say, however, that other kinds of life could exist.

This list is not meant to be exhaustive, but merely to suggest alternatives to the design hypothesis.

Theological Implications
Since it could be its own subject of inquiry I will limit my remarks, but I do think that the prevalence of life in the universe has theological implications. This post is already far longer than I anticipated so I will present only two questions:

If the universe is designed for life, why is life only found on one planet?

I believe that some would see this as emphasizing how important God views humans, and it certainly makes our species appear to be the telos of creation. On the other hand, I believe that some would find it puzzling that a God who desires to be in relationship with creation would create so much that is unable to conceive or relate to God (I’m sidestepping the whole question regarding other species on earth, that’s a whole other issue).

If the universe is designed for life, and Earth is the only place life exists, why will life on Earth cease to exist in five billion years?

The sun will eventually become a red giant star and this expansion would envelop Earth. Now most people believe this will not be an issue whatsoever for a variety of reasons, whether it be the destruction of the planet, space colonization, or the second coming. But it does raise the question often posed to proponents of design. That of optimal design. If the intelligence is God and God is all powerful, why would God choose to create life in this way? Surely God could have devised conditions for life that did not necessitate the destruction of the only planet where life exists.

Concupiscence and Evolution

Augustine takes a great deal of time thinking about Adam and Eve prior to the fall and what their lives would have been like. This includes reproduction. There was a time when Augustine didn’t believe they would have reproduced in the way that humans do after the fall; instead he believed God would have provided a different way. Eventually he decides that sexual reproduction would have been the case, but that the conjugal act would have been completely governed by reason. Adam and Eve would decide that they need to reproduce, come together, and reason will compel their bodies to act properly for procreation.

The reason Augustine takes this approach is due to his views on lust. Augustine certainly had his own struggles with lust and I think this absolutely shaped his views. Using the language of “concupiscence” predominantly, Augustine attributes sexual desire and lust to the fall. He understands it as a punishment for sin. Concupiscence for Augustine did not exist prior to the fall, and even after it exists, there is a dual punishment of not only having concupiscence, but also that it overrides reason.

Part of my dissertation is examining Reinhold Niebuhr’s take on original sin and to put his take into conversation with insights from the sciences. Although he is Augustinian in many ways, he does not read the account of the fall in Genesis as literal, for Niebuhr it is symbolic. If we look at the evolutionary origins of humans, it is clear that sexual reproduction existed long before modern humans were alive. So the question can be asked as to whether concupiscence also predates human existence.

I thought an obvious place to start would be to consider the pleasurable aspects of human reproduction and see if there is something there that could be inherited. Scholars are able to speak about the evolution of the male orgasm in terms of adaption, but there is also disagreement as to whether this is actually the case, or how it came about. This is complicated by the fact that many of the markers used to identify the achievement of orgasm may not be able to be studied in other organisms because it is unobservable or we cannot communicate with them. The male orgasm seems to be adaptive because it provides pleasure when engaging in sexual reproduction, providing motivation to engage in coitus. And even if scientists did have a consensus on the evolution of the male orgasm, it still would not provide enough of a basis to support the claim that concupiscence predates human existence because it would only be in reference to men. That being said, there is even more controversy about the science of the female orgasm so I feel that this is not something I want to pursue for the dissertation, but I did find it interesting enough to raise the question.

Ultimately I do believe that concupiscence does indeed predate the existence of modern humans (I would actually say the same about sin, but to hear more about that you’ll have to read the dissertation) but the evolution of the human orgasm does not provide sufficient evidence to make a scientific claim. I would say that sexual reproduction has existed for a very long time and it is advantageous because it provides addition genetic mixing, so the reasoning for why engaging in coitus is more likely to occur if it is pleasurable makes sense to me. Also contrary to Augustine, I would say that concupiscence predates rationality in animals, and that concupiscence does not necessarily have to always override reason. I do agree with Aristotle that humans have a weak spot when it comes to pleasure and that because of this we are likely to seek out things that will increase our pleasure even when we know it isn’t the right thing to do.

I’m not trying to make this post a sexual ethics post, I will simply say that reproduction and sexual activity are not always combined in many species, including humans. Having a predisposition towards sexual desire does not mean one must act in ways that are unethical, but it does present us with challenges that are partly beyond our control. We are the product of sexual reproduction, we cannot choose otherwise, and part of that legacy is inheriting traits and tendencies, but I am not a reductionist so I do not think that is the sum of human nature. Human nature is paradoxical and there are things from our past that shape the way we see the world and act in it, and is that not at the core of the truth to which original sin attempts to speak?

Self-Assertion as a Virtue

In working on my dissertation, I’ve come to the conclusion that self-assertion is a virtue. And this comes mainly from looking at theological anthropology. Reinhold Niebuhr presents an understanding of human nature that in my opinion, can be thought of in terms of virtue ethics. He divides human nature into two aspects, creatureliness of humanity and the spirit/freedom aspect. The perfection of the latter is the theological virtues (according to Niebuhr, I’m not even putting words in his mouth) and human perfection in general would consist of harmony between God and self, within the self (an ordered soul), and between self and the rest of creation. Sound familiar to people who read Aristotle and Aquinas?

Feminist critiques of Niebuhr, however, argue that his understanding of sin in flawed because he identifies pride as the primary form of sin, and the other form of sin, sensuality, is viewed as a derivative of pride. I agree with this assessment but contend that viewing Niebuhr in a virtue framework allows for sensuality to hold equal importance to pride.

A virtue is a mean between an excess and deficiency. In this case, self-assertion would be the mean between selfishness (pride) and self-abnegation (sensuality). Additionally, people are born with dispositions and tendencies toward the excess or deficiency, so some people struggle with pride, while others struggle with sensuality. This could fall along gender lines, but doesn’t have to (and I think it would be a mistake to do so). Though some feminist scholars such as Judith Plaskow identify sensuality as being more in line with women’s experience, she also admits that women can also have problems with pride. I would also say that men as susceptible to sensuality as well. In terms of my own studies, there have been times where I’ve bailed on my academic responsibilities and focused on what was for dinner that night or making plans to have a happy hour with friends.

The question is what kind of virtue is self-assertion. Since all of the moral virtues are collapsible to the cardinal virtues (temperance, fortitude, justice, and prudence), self-assertion would be a subcategory of one of these virtues. I think the likeliest candidates are temperance and justice. Temperance is a good fit because it is the virtue of self-restraint. One would usually consider moderation of food, drink, sexual activity, etc. to this virtue. Self-assertion is related to self-restraint but it is not identical. Humility is also one of the aspects of temperance, but self-assertion in the context I am discussing is not humility either. It is acknowledging one’s self as a self that has claims and obligations. Justice is a distant second because justice deals with what people are due. Self-assertion in this context would be taking what is appropriate, not more or less. It is easy to see how self-assertion would fit into justice, but modern views on justice have focused on the more material aspects of the virtue (economics for instance) and self-assertion is less about that than it is about identity and responsibility.

So what do you think? I don’t believe that I’m over thinking this by being unsure where to place self-assertion. Of course, maybe I’m overlooking the obvious.

Mitochondrial Replacement: The Issue isn’t Mitochondria

My parents sent me a link today and it really got me thinking. It was about the meeting the FDA is having regarding whether or not to allow human trials for mitochondrial replacement. The U.K. is working on drafting regulations that would be put to a vote in 2015. I’m not sure how fast things would happen in the United States if the FDA ruled favorably this week, but this would be substantial news. I thought some of the wording seemed off in the link they sent, but when I found a link from a local news site, they were using the same AP piece from a health writer who uses “nucleus DNA” and not “nuclear DNA.” I thought perhaps the terminology had changed since my undergraduate degree in genetics, but that doesn’t seem to be the case, at least in general practice. But I digress.

You may be wondering what mitochondrial replacement is and why this is a big deal. I’ll try and fill in some of the information, but to be honest, my head is spinning right now with differing views. Mitochondrial replacement is not new; researchers in Oregon, according to the news article, have been working with monkeys for four years and would like to move to human trials. Mitochondrial replacement is taking the nuclear DNA (what people typically think of as DNA, the chromosomes) from a woman and place it into a donor egg. Why would this be done? There are organelles called mitochondria that produce the chemical energy that our cells use (ATP) and these organelles have some genetic material known as mitochondrial DNA (mtDNA). mtDNA is a small amount roughly 16,500 base pairs and 37 genes versus the 3 billion base pairs and approximately 20,000-25,000 according to this NIH site. Although mitochondria are fascinating and have an important history, I can’t really take the time to go into that here. Needless to say, there can be mutations in these 37 genes and there are genetic diseases that are linked to mitochondrial genes. The problem is that only the egg cell passes mitochondria onto the resulting embryo. The sperm’s mitochondria are in its tail and only the sperm’s nuclear DNA enters the egg. So if a woman has a mitochondrial genetic disease, it will be passed on to her offspring. Mitochondrial replacement would allow affected women to have a child that is genetically related to them, but not inheriting the genetic condition.

Why is this a big deal? It depends who you ask. I think it is a big deal because I wrote about the possibility of using mitochondrial replacement as motivation for utilizing reproductive cloning in an article published in 2011. There are some people who are upset because they argue the child would have three parents. The two parents who provided nuclear DNA and the donor who supplied the egg containing mitochondria. Others are concerned because changing mitochondrial DNA would be the first recorded instance of germ line therapy. In other words, the changes made in this instance would be genetic changes made by humans that would pass on to any offspring the children resulting from these trials would have. I am unsure how many countries currently ban germline changes, But according to this website, Australia, Canada, Germany, Switzerland, and the Netherlands appear to have laws against it. There is also worry from people that allowing these kinds of changes is a slippery slope to designing children.

I will say there is probably very little new about ethical concerns around the ethics of reproductive technologies presented by this case. These kinds of concerns have existed with assisted reproduction, human cloning, and stem cell research. There are a few things, however, that I would like to mention.

The first is that when digging to find multiple sources to back up the FDA’s meeting to discuss this I came across a post in Nature. What I found most disturbing in this post was the following statement: “The FDA, unlike the HFEA, does not consider ethics, and that worries Marcy Darnovsky, executive director of the Center for Genetics and Society, an advocacy group in Berkeley, California.”

If this statement is true, that the FDA does not consider ethics, how did I not know about this? It seems far too big to not know this is the case. I imagine this is editorial and not factual. I find it very hard to believe that the FDA would not take ethics into consideration at all. People may be displeased with specific outcomes, or disagree with decisions they have made, but I have to believe that ethics play a role in their decision making process.

In the original article there is this quote: “We want to replace these mutated genes, which by nature have become pathogenic to humans,” says Dr. Shoukhrat Mitalipov, who will present on Tuesday. “We’re reversing them back to normal, so I don’t understand why you would be opposing that.”

I find it disconcerting that there is no reflection on what normal means in this case. The degree I’m working on is in ethics and social theory, and I’ve read enough medical sociology (though by no means am I an expert) to say that what medicine considers “normal” is not necessarily objective fact. Normal and healthy are things that we often take for granted, but we are already seeing normal used two different ways in this case study. People are arguing that mitochondrial replacement is not normal because it would produce embryos with three biological parents. While on the other side, experts are claiming to restore normal function to these mitochondrial genes. Even as a theological ethicist who believes in a normative understanding of human nature, I will need more convincing from experts as to how they define normal in this case.

Related to the discussion of normal, there is the consideration of people who are differently abled. Transhumanist Evan Reese in disagreeing with the position of the Center for Genetics and Society wonders whether society should do everything possible to help people with help problems and that children born with mitochondrial problems could be upset that they were denied the chance to not have these conditions.

I will also say that mitochondrial replacement also would affect genealogical studies using mitochondrial DNA. This is not an argument against the procedure per se, but this was something that came to mind when I was thinking through the implications.

In principle, I am not opposed to mitochondrial replacement itself. If the numbers cited in these articles are correct, then this would only affect 1000-5000 births per year (I’m assuming that number is in the United States alone). Although you cannot draw a hard line between health and enhancement, I do think there is a difference between this case and choosing particular traits for nonmedical reasons. In regards to affecting the germline, the number of genes affected would be so small and the population that would have the replacement done is so small, that the overall impact on humanity’s gene pool is likely small. There could be unforeseen consequences and there are other ways to have children (or adopt children). I would not mind us taking our time in making a decision about making substantial germline modifications, even though according to a speaker at a transhumanism conference I attended recently, any restraint on life extension research should be criminalized.

Off the cuff thoughts about NCAA and student compensation

August means several things. One of them is that football is right around the corner. When I read in the news that Johnny Manziel was being investigated by the NCAA for being paid to sign autographs, something he is not allowed to do because he is an amateur athlete. Now I do not claim to be an expert on the NCAA, or how college athletic programs are funded, but for the past several years at least, I’ve question the NCAA’s stance on their student athlete compensation. Schools and the NCAA are making billions of dollars and the students receive no compensation above their scholarships. Any additional compensation in any form, including water from a hose, can be met with fines, suspensions, and depending on the extent of the violation, sanctions against the athletic program. However, the NCAA still makes money off of these students and schools, even the ones that are punished.

Now I know, because I’ve heard it before. You will say that they are receiving compensation, a free education. A college education is certainly nothing to sneeze at, but it is a drop in the bucket in terms of the total amount of tax exempt revenue being generated by collegiate sports. I’ve heard the same people make this argument for college football, then side with striking workers asking for additional compensation. These student athletes don’t have the choice that other workers have. They can’t leave their school and find one that will pay them more money; no school is allowed to provide more than the scholarship, but I’m not hearing the anti-trust argument. And let’s look at what it means to be a student athlete. It certainly means practices, games, travel, all on top of school.  I didn’t take the time to gather significant data, but it is clear from articles like this that being a student athlete does not always mean the student side is emphasized.

But even in spite of all of that, I can be persuaded that there is no fair way to compensate all student athletes with an additional stipend. Even if I can concede this point, I can’t concede endorsements. It seems to me that students should be allowed to sign endorsement deals, except that it takes money away from the NCAA and the school, you know, the ones making the rules. I’m sure I’ll get blasted for even suggesting this, but I’d be willing to consider the endorsement goes to a trust that the student athlete can use for school expenses or to help family, at least until they go pro or graduate, we’ll work out the details if necessary. It wouldn’t be my first choice, but it would undoubtedly address some of the concerns people would have about college students signing multimillion dollar deals.

I thoroughly enjoy football, and will likely see at least one game in person this season, and watch countless other games. Sure, some student athletes go pro, but not most and even those that do are not guaranteed large contracts. There is plenty of money to go around. How about cutting the bowls out of the economic loop and giving the ones who day in day out work hard a bigger slice of the pie?

Gene Patents and Justice: Better Late than Never

With the Supreme Court’s recent ruling on gene patents, I was reminded of work I did in the first year of my doctoral program. I examined gene patents using Robert Nozick’s understanding of property.  In full disclosure let me be clear that I have always been opposed to gene patents because I do not believe they qualify for patents because there is no novelty. The processes and technology used to isolate and sequence DNA, sure, but the actual sequence itself, I don’t think so.

But I digress. In terms of using a justice theorist to examine a contemporary issue, I chose to use Nozick and gene patents because I thought there was an interesting connection. The central question of justice in that kind of perspective is the ownership of genes. Assuming that genes were previously unowned, the question shifts to whether society is worse off as a result of this ownership. While it is possible to answer no, because the patent on the BRCA1 and 2 alleles allowed for tests to be develop to determine whether individuals had these particular variants, I would argue that ultimately the answer has to be that society is worse off through the ownership of genes. It may allow a company to pursue research, but it makes it much more difficult for others to pursue similar work. Anyone wanting to do anything in terms of the study of those sequences had to pay for the rights to do so, slowing research and increasing costs to consumers. In fact, a rival company has stated they can now offer BRCA 1 and 2 tests at a third of the cost.

The other argument that can be made is that genes were not previously unowned. It doesn’t really make sense to think of individual ownership of genes, but rather I’d argue that our species as a whole owns our genetic legacy and thus the acquisition of gene patents by biotech companies was never just in the first place.

Now ultimately, this ruling is a mixed bag. The patents specifically involved in the case were set to expire in 2016 anyway and the company’s stock shot up because the Supreme Court is still allowing for patents on cDNA (an issue that would take another post to really explore). It should help lower costs for people who want genetic tests, and make it easier for researchers to share work. The downside is that some believe it could present precedent regarding naturally occurring nonhuman products (derived from bacteria, plants, etc.). The actual ruling seems to speak directly to human genes, but I guess time will tell.

And it would also take a whole post (or more) to get into the added opinion of Justice Scalia at the end of the ruling where he writes “I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied the opinions below and the expert briefs presented here, that the portion of DNA isolated from its natural state sought to be patented is identical to that portion of the DNA in its natural state; and that complementary DNA (cDNA) is a synthetic creation not normally present in nature.”

Let’s just say that even though I am fairly happy with the ruling, that scientific literacy would have enabled an even better ruling.