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

Introduction
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.

Alternatives
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.


Review of Cosmos Episode 1: Giordano Bruno Steals the Show

When I was a kid I loved Carl Sagan’s Cosmos.  My dad recorded the shows on our new VCR and I watched the episodes over and over again, the way children like to do. Cosmos made me want to be a scientist, which eventually I did become, if only for a few years, before turning to ethics. Carl Sagan did a good job.

I re-watched the original Cosmos a few years ago, some of the episodes with my kids.  They are still fun to watch, but I realized something in seeing them again. Sagan made mistakes. Big mistakes, as with Hypatia and the burning of Library of Alexandria (I read a letter in graduate school by one of Hypatia’s friends, the Catholic bishop Synesius whose side protected her in what was effectively a class-based civil war – not quite the simple raving Christian hoards that Sagan described). That discovery was saddening to me, but I knew Sagan was an atheist, and I know that people get blinded by their biases, even otherwise very intelligent people.

I was looking forward to the new Cosmos.  But I saw the trailer and Bruno getting burned, so I knew it was just going to be more of the same. but I didn’t know how much more of the same it would be.

I’m not sure exactly how long it lasted, but is seemed like the segment on Giordano Bruno went on for about 20 minutes. Bruno is interesting, and Tyson made a few attempts to clarify the ridiculous cartoonish depiction of Bruno’s life (e.g., saying he was not really much of a scientist, and his theories were untestable). But the  question remains. Why so much time on Bruno? Why Bruno at all? Galileo is the usual guy for this stuff. Why a cartoon? Why not re-enactments with humans like in the original Cosmos?

Here are my thoughts. I think they chose Bruno because somebody said Galileo was getting a bit old, let’s find another scientist that religious people persecuted. Then they hit a problem. There really are not that many besides Galileo. In fact, there aren’t really any more good examples, at least not in Catholic Europe, where the Church over the ages was stuffed full of scientists and scientists-wannabes, including (quoting Wikipedia):

Nicolaus Copernicus, Gregor Mendel, Georges Lemaître, Albertus Magnus, Roger Bacon, Pierre Gassendi, Roger Joseph Boscovich, Marin Mersenne, Bernard Bolzano, Francesco Maria Grimaldi, Nicole Oresme, Jean Buridan, Robert Grosseteste, Christopher Clavius, Nicolas Steno, Athanasius Kircher, Giovanni Battista Riccioli, William of Ockham

And so on. Thanks, Wikipedia. So, it is hard to make your case with at least 99 of 100 examples against you. But try anyway. Bruno is the #2 go-to for this “war on science” stuff, so him it had to be.

Problem was, Bruno was not much of a scientist, he was a weird mystic hermeticist who liked to insult people. Becky Ferreira at Motherboard gets it right:

[T]he truth is that Bruno’s scientific theories weren’t what got him killed. Sure, his refusal to recant his belief in a plurality of worlds contributed to his sentence. But it’s important to note that the Catholic Church didn’t even have an official position on the heliocentric universe in 1600, and support for it was not considered heresy during Bruno’s trial…

Bruno was a walking, talking shit storm, with a black belt in burning bridges…

For years, he’d set up shop in some city, find new patrons, and promptly make enemies of them with his combative sarcasm and relentless arguments. Even fellow Copernican pioneers Galileo and Kepler had no love for Bruno. In fact, in light of his difficult personality, it’s kind of a mystery that he survived as long as he did.

The many-worlds idea was interesting, but the Church had already talked about God’s infinite creative power 300 years before and decided it was no big deal. What was a big deal was living in an honor-based culture and going around insulting people. After a while he had insulted everyone who could protect him, and that left him pretty much in the hands of the Inquisition.

I make no excuses for the Inquisition.  They shouldn’t have turned Bruno over to be burned. Quite frankly, lighting people on fire is not a good argument. It does not make your case. Resorting to physical strength makes you look rationally weak, and they had fine rational arguments on their side. Stupid idea to kill Bruno, wrong thing to do. But seriously, he wasn’t being killed for his science. Nobody cared about that stuff compared to him insulting the honor of the Virgin Mary, denying the Trinity and transubstantiation, other theological stuff.

Okay, enough.  The other question is: why a cartoon? Obviously, having the creator of “The Family Guy” running the show might have had something to do with it. That’s a reason from the past, a mechanical reason for it. But what was the teleological reasoning? They could have chosen another means had they so desired.

I think they chose a cartoon for several reasons, #1 being in order to appeal to children.

Twitter was full of people mentioning they had let their kids stay up late to watch Cosmos. And some mentioned how great it was that the Catholic Church got so ripped down in front of their kids eyes. That bothers me a lot, because it is lying to children. It is just as bad as followers of 6-day creationism denying science in order to protect their religion – it is followers of scientism denying history in order to protect their ideology.

They say Americans are ignorant of science because of religion, but now we can also be ignorant of history because of “science.” Thanks, Cosmos.

All right, now I’m going to say something nice. I liked Tyson’s tribute to Sagan at the end. That was beautiful.

I will be watching more episodes of Cosmos. Maybe they will mention the Big Bang model was first proposed by the Catholic priest Georges Lemaitre.  Maybe they won’t. I hope Tyson and crew will surprise me, but after this first episode I don’t expect much.


The Transhuman Visions Conference – My Synopsis

On February 1st at Fort Mason Center in San Francisco, the Brighter Brains Institute convened the first Transhuman Visions conference.

I found the event to be really interesting and I will be participating in future conferences, not only as an audience member, but also as a speaker (at their May 10th conference on Transhumanism and Religion). Though I must admit, I do not consider myself to be a “transhumanist” – I am a bit of a skeptic about such things, and too academic to join all-out. But I find the ideas fascinating and excellent fun for stretching ideas of all sorts – technological, scientific, philosophical, religious, etc. – to their breaking points. And, of course, also seeing what ideas do not break; those are the particularly interesting ones (the infinity of God vs. the desired “infinity” of humans is one I have definitely been thinking about – that is an idea that will be hard to break).

If you want to read more about the conference, I did a write-up for the Markkula Center for Applied Ethics website at Santa Clara University.  Here is a taste:

While I see no intrinsic moral problems with extending healthy human life as long as we can (realizing that important related questions of justice, cost, accessibility, side-effects, etc., would also need to be addressed), I do not think material immortality is possible in this world. As material creatures subject to entropy, we must eventually break down and die. The existential denial of our own mortality is an evasion, not a solution. But transhumanism does not stop at evasion; it is a social movement with a lot of highly motivated and intelligent people, and is actively researching solutions of many types. I was very impressed by several of the people I spoke to. Some were there because they were deeply concerned about the health of their loved ones and they saw transhumanism as the chance to save their loved one’s lives.

I am looking forward to future conferences.


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