Sunspots 758

Things I have recently spotted that may be of interest to someone else:

The Arts (and Education): NPR reports that Carroll Spinney, who played Big Bird and Oscar the Grouch from the beginning of Sesame Street until a year or so ago, has died.

Christianity: (and politics) There is an attempt, in Congress, to pass legislation that would protect the rights of homosexuals, and also the rights of Christian organizations and small businesses.

(and science) BioLogos reports that one of this year's Nobel laureates in Chemistry is a believing Christian.
  Humor: (or something) Listverse describes the 10 best board games ever created.


Politics: Another way in which the Department of Education is hindering, not helping, students with disabilities, and Congress is not happy, according to NPR.

Science: Listverse has a compilation of arguments used to prove that evolution is false. None of these arguments do that.

NPR reports on a comet that has apparently come from another solar system.

NPR also reports on a fascinating Dubna, Russia-Oak Ridge, TN scientific collaboration that resulted in the production of six short-live atoms of a new element, Tennessine. There is one mistake in the report: "Element 117 fits in a column of the periodic table filled with compounds called halogens - fluorine, chlorine, bromine." It should have been "elements called halogens."

And NPR reports that fresh-water mussels are dying, and on why this matters.

Gizmodo reports on using wood as the basis of optical fibers.

Gizmodo also reports on a newly discovered widow spider, which lays purple eggs.

The Scientist reports that it is now possible to store instructions for replicating the object in the object itself. A related application might be to store information on how a medical device or implant was made in the device or implant, itself. This sort of study may be coming close to creating a new kind of life.

The graphic used in these posts is from NASA, hence, it is free to use like this.
Thanks for looking!

Germline gene modification: the issues. (Book by Jennifer Doudna)

"And all long-term exercises of power, especially in breeding, must mean the power of early generations over later ones." - C. S. Lewis, The Abolition of Man 

I have recently read a book by Jennifer Doudna, entitled A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution. There is a co-author, but it seems clear that most of what is said came from Doudna. As the Wikipedia puts it, "Doudna has been a leading figure in what is referred to as the 'CRISPR revolution' for her fundamental work and leadership in developing CRISPR-mediated genome editing." I would expect that she will be getting a Nobel Prize in the next year or so. (She is also part owner of a company which has, or is expected to commercialize these techniques.)

CRISPR stands for clustered regularly interspaced short palindromic repeats, [and] is a family of DNA sequences found within the genomes of ... organisms such as bacteria ... These sequences are derived from DNA fragments from viruses that have previously infected the [organisms] and are used to detect and destroy DNA from similar viruses during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes. (From the Wikipedia article on CRISPR.)

The discoveries of Doudna, and many others, have made it possible to use the CRISPR immune system of bacteria to make targeted changes in DNA. It's a little more complicated than this, but, basically, if you know the nucleotide sequence of the DNA you want to change, you can use CRISPR to delete as little as a single base pair, or to change small sections of DNA. The technique does not require lots of expensive equipment. This has made it possible to alter the genomes of laboratory organisms, domestic animals, crop plants, and even human cells. In a recent case, it may have been used to modify human embryos. A Chinese scientist claims to have modified twin girls so that they could not contract AIDS. The claim has been questioned, and the timing, if the report is correct, has been seriously questioned -- preliminary experiments, at least, should have been done. The Chinese government has acted to punish the scientist. Many people fear that we don't know enough about the safety of the CRISPR system. Could it be that other DNA can be altered, rather than the target, with unforseen consequences?

The book is well written, although there is a lot of name-dropping -- scientists Doudna has worked with. Documentation is good, and it is at the end of the book, where it doesn't interfere with the train of thought.

It is clear that Doudna believes that CRISPR should be used on humans, carefully, and after considerable thought and planning. (Lots of which we haven't done yet.) She even believes that, after considerable more study and experimentation, we (speaking for the majority) may come to accept alteration of germ cells in humans.

What's a germ cell? First, what isn't one? Almost all of our cells are somatic cells. That is, they are cells that do not become sperm or eggs. Somatic cells may be altered -- in fact are altered, all the time, by random mistakes in cell copying, or by agents like Ultraviolet light, or others that cause cancers. Or we remove billions of them when we take out an appendix, or some other part of us. But the offspring of people with changed somatic cells do not inherit these changes. I had a skin cancer removed from my face. If I were to get married, and my wife have a child, the child would not be more likely to have skin cancer than another baby born to a couple who had never had skin cancer. I had my tonsils out when I was a child, but my daughters were born with tonsils.

Germ cell alteration, changing the cells that produce sperm, or egg cells, would mean that an organism's offspring, for the forseeable future, would be different, in subtle or major ways, from what that organism was. And, eventually, that change might spread through an entire population, or an entire species, as more and more descendants of that organism appeared.

Why not encourage germ cell alteration? There are some possible objections:

It's unnatural. But so are lots of things that most of us take for granted, such as eyeglasses, Caesarean sections and other surgery, antibiotics made from fungi, artificial limbs, and much more, which are unnatural -- not the way things would be without deliberate action by humans. Unless there's some safety problem, such as if eyeglasses caused cancer, or the procedure or apparatus is prohibitively expensive, there doesn't seem to be a good reason to object to these types of things.

There was a time when the use of anesthetics was considered to be unnatural, and one when vaccination for smallpox (using material from cows) was so considered. Hardly anyone thinks that way now.

C. S. Lewis, for one, would have thought the idea unnatural -- see the opening quotation.

It might lead to ethical problems. Doudna points out that it might be possible for wealthy or powerful people to have germ cell alteration in the early embryos they have as their offspring, and thus to make class differences of power or money even more pronounced, by having more intelligent, talented, athletic, or disease-resistant descendants, because of genetic changes. (Intelligence is not easy to pinpoint, and is not simply inherited, and it's doubtful that we could modify an embryo to make it more intelligent, even if we badly wanted to, at present. Maybe never. But it's an example of something that might lead to class differentiation by inheritance, in addition to the class disparity problems that already exist.)

An ethical problem that Doudna doesn't consider a lot is the likelihood that human embryos will be produced, and discarded, which would be a serious ethical problem for many people. There are some embryos that are produced during in vitro fertilization that are not able to develop much past fertilization, and these might be used in experiments without cutting off the potential life of an embryo. But, of course, this begs the question of whether in vitro fertilization should be allowed.

There's the question of safety. By this, Doudna means that unforeseen consequences, changes in DNA that weren't planned, might be possible. It seems impossible to know about this possibility without engaging in extensive laboratory experiments.

So why should anyone want to do germ line alteration with CRISPR? It might, in fact has, produced crops and animals that are beneficial to us, cows with more muscle and less fat, for example. But the most important possibility is that an inherited disease might be eliminated, in some people, or in humans as a whole. An acquaintance of mine recently passed away because she had Huntington's disease, which is inherited. If the germ cells of people with this terrible condition could be modified, the disease could theoretically be eliminated, except for persons having it because of a new mutation. Doudna has spoken to people who are parents of children with genetic diseases, and they are much in favor of moving toward use of CRISPR to attack such conditions.

The Golden Rule of Matthew 7:12 says "Therefore whatever you desire for men to do to you, you shall also do to them; for this is the law and the prophets." This could be taken as guidance toward developing the technology, and using it to eliminate genetic diseases. However, on the other hand, it may be taken as guidance toward not doing anything that would harm a human embryo. See here for a discussion of abortion, in light of the Bible, a related topic.

The scientific community, with lots of input from others, has already considered the potential risks and benefits of altering genes, in bacteria and other organisms. One part of such consideration was the Asilomar Conference on recombinant DNA, in 1975. This led to a general consensus as to what kinds of work could be done, and what safety precautions should be used, and there have, to date, been no disasters because of recombinant DNA research.

I'm not aware of any conferences on human cloning, but the scientific community, at large, seems to have decided that such procedures simply shouldn't be done, and it is doubtful that they have been done. If they had, they would have led to an adult human with the same genes as some previous one.

Doudna and others, including some participants in the Asilomar Conference, met a couple of years ago, and collaborated on a document, "A prudent path forward for genomic engineering and germline gene modification," in April of 2015. This document has been published elsewhere, including here.

The following recommendations are given at the end of the article:

1. Strongly discourage, even in those countries with lax jurisdictions where it might be permitted, any attempts at germline genome modification for clinical application in humans, while societal, environmental, and ethical implications of such activity are discussed among scientific and governmental organizations. (In countries with a highly developed bioscience capacity, germline genome modification in humans is currently illegal or tightly regulated.) This will enable pathways to responsible uses of this technology, if any, to be identified.
2. Create forums in which experts from the scientific and bioethics communities can provide information and education about this new era of human biology, the issues accompanying the risks and rewards of using such powerful technology for a wide variety of applications including the potential to treat or cure human genetic disease, and the attendant ethical, social, and legal implications of genome modification.
3. Encourage and support transparent research to evaluate the efficacy and specificity of CRISPR-Cas9 genome engineering technology in human and nonhuman model systems relevant to its potential applications for germline gene therapy. Such research is essential to inform deliberations about what clinical applications, if any, might in the future be deemed permissible.
4. Convene a globally representative group of developers and users of genome engineering technology and experts in genetics, law, and bioethics, as well as members of the scientific community, the public, and relevant government agencies and interest groups—to further consider these important issues, and where appropriate, recommend policies.

National Public Radio and other sources report that the World Health Organization has appointed a group to establish "uniform guidelines for editing human DNA in ways that can be passed down to future generations." Doudna is not part of the group. That group seems to fulfill item 4 in the above list. (I checked the WHO web site on February 15, 2019, and was unable to find any reference to this group.)

How CRISPR works:
Vox has published an explanation of how CRISPR works, with graphics, and lists some of the things it might be used for.  Carl Zimmer, noted science writer, wrote another article on CRISPR, which, although a little older than the Vox article, is a fine introduction to how CRISPR was discovered, and how it works. This is the Wikipedia article, which is more technical than the others linked above.

Thanks for reading. We have responsibilities to other people, less fortunate than we are. Perhaps, in the near future, we may decide that those responsibilities are best carried out by somatic or germline DNA modification. May God help us.

Thanks for reading! 

Note: on February 20, 2019, I ran across an article that discusses most or all of the ethical issues involved in germline gene modification. It may be read here.

Sunspots 496

Things I have recently spotted that may be of interest to someone else:

Education: A former University of North Carolina football player has filed suit, claiming that the university did not provide him with the substantial education that he was promised when recruited. (The university apparently let some students "take" classes that they didn't even attend.)
Health: (or not) We're running out of chocolate, according to The Washington Post and other outlets.
Science: Wired reports on how a study of the cat genome sheds some light on how domestic cats are genetically different from their wild relatives.

National Public Radio has a fine series on color. One post is about how our perception plays tricks on us when we are considering color. Another is about how animals get color from what they eat, partly -- flamingos are an example -- and how rare blue coloring in animals is.
Wired also reports on nudibranches, sea slugs, who eat defensive mechanisms from other creatures, and use them to defend themselves. They are also spectacularly colored -- some are blue.

 Image source (public domain)

Sunspots 209

Things I have recently spotted that may be of interest to someone else:

Humor:
10 top reasons why men should not be ordained.

Science:
Finally! The cow genome has been sequenced, according to NPR.

According to The Curious Mister Catesby, a documentary film aired on South Carolina Public TV on April 23rd, Mark Catesby, an early naturalist who wrote about, and painted, the wildlife and flora of South Carolina (and other places, but less so) was probably the first modern writer to write about habitat degradation, and also the first to suggest that birds migrate for long distances.

Computing:
(or something) A stop-action video of a pig and a wolf, a little less than 4 minutes, on YouTube. It's had over a million hits.

There's a possible danger, if you use GMail. Here's the way to, at least partly, fix it.

Literature:
(or something, probably several things) Wired on the Georgia Guidestones, which is, as they say, the strangest monument in the US, perhaps the world. They are near Elberton, Georgia. I have seen them from the nearby road a couple of times, but never close-up.

Christianity:
olsuit has begun posting a series of excellent sermons on the Ten Commandments. Here's the first one.

Image source (public domain)

Francis Crick, atheist

I recently read Francis Crick: Discoverer of the Genetic Code, by Matt Ridley. (New York: HarperCollins, 2006) The title itself should strike a careful reader as curious. In the first place, Francis H. C. Crick is best known for the discovery of the double helix, with Watson, not for the discovery of the genetic code. In the second, genetics textbooks, and other sources, such as the Wikipedia article on the genetic code, do not give Crick much, if any credit for cracking the code whereby sequences of messenger RNA are transformed into sequences of amino acids.

But there is something to the claim that Crick was the discoverer of the genetic code. Francis Crick theorized about protein synthesis. Secondly, Crick (who was not known as an experimentalist) did do critical experiments that led to the realization that the code was a triplet code. Ridley describes how Crick also was the catalyst that cajoled others into doing the work that led to the discovery. In that, he appears to have been something like Neils Bohr, who, collaborating with many scientists, lectured, thought, wrote and discussed, playing a pivotal role in the discovery of quantum physics in the previous century.

Watson, in his best-selling The Double Helix, began by writing that he had "never seen Francis Crick in a modest mood." Ridley is not modest in his biography, as he anoints Crick as "the greatest biologist of the twentieth century" (p. 5). No doubt that claim, however important, could be disputed. (Eugene Odum, Edward O. Wilson, and Niko Tinbergen, and many others might merit consideration.) Nonetheless, Crick was important. It is unfortunate that he was an atheist. (So was Watson, unless he has made a radical change recently.)

Ridley says that what really motivated Crick was a desire to discredit vitalism, the idea that living things cannot be explained and understood completely in terms of physics and chemistry. Crick believed that they could be so explained. So did many other scientists. Depending on what is meant by explanation, so do I. Crick and Watson apparently felt that they had explained life when the DNA helix was proposed. Crick went on to study consciousness, which he was continued to do until the end of his life, as, says Ridley, the last bastion of vitalism. He did not live to see the achievement of his goal of being able to understand consciousness in terms of neuron activity. We are probably a long way from that yet.

What is meant by explanation? If, by explanation, we mean that we can, at least in principle, describe how a cell works, in chemical and physical terms, most biologists of today would agree. This has not yet been done, at least not completely, but, within my lifetime, enormous strides have been made. I would not be surprised to see the construction of a working living cell, capable of metabolism and reproduction, produced from laboratory chemicals, in the first half of this century. There does not seem to be any reason to suppose that any aspect of cell function cannot be explained and understood in terms of the chemistry of the cell. Does this rule out Divine action? Certainly not. In principle, it is possible to understand, say, all the parts, and the functioning, of a Ford Explorer. If I did so understand it, that would not mean that it wasn't a wonderful piece of equipment, nor would it mean that it wasn't designed and planned. In the same way, even if we did understand all of the molecular activity of organisms, it wouldn't make their existence any less wonderful, nor would it rule out supernatural design and planning.

If, by explanation, we consider some other questions, such as "How did life begin?" "Why do Carbon atoms and other chemical entities have the properties that make life possible?" "Why are humans interested in this sort of question?" then we can't explain life. Crick, nor anyone else, has done so, and I don't believe it is possible to do so. (More and more plausible naturalistic answers for the first question may be produced, but they will never amount to a certain description of what actually did happen.) Crick, in fact, according to Ridley, put forward panspermia as an explanation for the origin of life on earth, at least half-seriously. Why would an otherwise intelligent person consider that living things may have been placed here by extraterrestrials, and reject that they were placed here by a supernatural being?

It is unfortunate that Crick, who was noted for discussing serious issues for extended periods with intelligent people, including, or especially, when they didn't agree with him on all points, didn't really come to grips with the issues of the meaning of life, and the origin of living things, and the universe that makes them possible. Perhaps he didn't really want to come to grips with these questions. Perhaps he was turned off by interpretations of the Bible that claim to rule out some of the important findings of science. I don't know. But it is unfortunate.

Thanks for reading. God's best in the New Year!