Gene-Edited Babies: What a Chinese Scientist Told an American Mentor
(originally posted 21 Nov 2019)
Good evening all,
As I indicated during class on Wednesday, we will not meet for lecture tomorrow (Friday 22 Nov), but instead will consider some topical science news:
We finished one of our recent lectures by introducing the concepts of gene therapy and cloning. Both of these stem from the application of modern genetic methods, and both exist already - but not without controversy.
As described in your text, gene therapy is an attempt to correct defective or missing genes, by using viruses to insert them into a person's cells. It remains very controversial and of relatively limited use, because many of the risks and complications of the technique have yet to be overcome. Indeed, some human gene therapy trials have resulted in patient deaths, and few would say that the technique has been proven to the point at which broad use is possible. Still, for some people with very specific types of genetic defects, gene therapy has proven to be a lifesaver (literally). We can expect to continue to hear much about gene therapy in the years to come.
Related to gene therapy is the concept of gene editing. The goal of this technique is not to replace defective genes with normal copies, but rather to use enzymes to edit (correct) the defective genes in place (e.g., within the cells of the organism). Gene editing utilizes techniques more recent than those employed in gene therapy, so it has been tested, and used, relatively less. Thus, it was of great surprise to the scientific community last Fall when a Chinese scientist (He Jiankui) claimed to have performed gene editing on several artificially (in lab) created human embryos, and then to have implanted those embryos into female surrogates to carry the developing embryos until birth.
The technique of gene editing is new enough that, one year ago, the ethical guidelines governing its use had not been fully developed. Nonetheless, there was a general understanding that the technique was not to be used in human embryonic tissue, that would result in *all* cells in the body inheriting the edited gene. This understanding was very broad, but was not universal, and scientists in several countries did use (or attempt to use) the technique on human embryos, in the hopes of creating a gene-edited person - a "designer baby".
The scientific backlash against this first report of human embryonic (germline) gene editing was relatively swift, and relatively severe. The scientist who conducted these first trials has been stripped of his research position, and charged with violating his country's biomedical research laws. The infants (twin girls) were reported to have been born, but little is known about their condition. Some researchers have suggested that they are at risk of a shortened life expectancy because of the gene editing. The gene that was edited in these now-children is thought to promote resistance to HIV infection, but also seems to play other roles in cells.
The article I am forwarding here comes from a few months ago, when the investigations into this researcher and his colleagues was still in process. In particular, there were a number of scientists here in the U.S. who were implicated as having supported this work. The researchers here have generally been cleared of any wrongdoing, but significant questions remain about who knew what, and the motivations (money? fame? patent-able technology?) for their involvement. This article also includes links to a number of related stories, of which there are many.
https://www.nytimes.com/2019/04/14/health/gene-editing-babies.html
It is worth noting that somatic (non-germline gene editing) is gaining ground as a very powerful and promising technique. This variant of gene editing does not change the DNA in every cell in one's body, but only in focal tissues (such as a single organ) that may be malfunctioning due to a defective gene. Indeed, news reports of the promise of this (more-limited) application of gene editing are also prominent in the recent news, including:
https://www.forbes.com/sites/leahrosenbaum/2019/11/19/human-crispr-trials-promising/#340301322daa
I suspect that your generation will be forced to come to terms with the promises and perils of gene editing - it seems both incredibly promising, and incredibly dangerous at the same time. Having a robust set of regulations and ethical guidelines will be very important. If you were faced with the opportunity to correct a gene in yourself, in a loved one, would you? That's a very difficult question to answer a the moment, as we do not yet have enough experience with the pros and cons of these techniques. But, the evidence is beginning to accumulate...
Here's wishing you all the very best Thanksgiving break - please be safe, rest, relax, eat, and enjoy.
Sincerely,
Dr. Nealen
(originally posted 21 Nov 2019)
Good evening all,
As I indicated during class on Wednesday, we will not meet for lecture tomorrow (Friday 22 Nov), but instead will consider some topical science news:
We finished one of our recent lectures by introducing the concepts of gene therapy and cloning. Both of these stem from the application of modern genetic methods, and both exist already - but not without controversy.
As described in your text, gene therapy is an attempt to correct defective or missing genes, by using viruses to insert them into a person's cells. It remains very controversial and of relatively limited use, because many of the risks and complications of the technique have yet to be overcome. Indeed, some human gene therapy trials have resulted in patient deaths, and few would say that the technique has been proven to the point at which broad use is possible. Still, for some people with very specific types of genetic defects, gene therapy has proven to be a lifesaver (literally). We can expect to continue to hear much about gene therapy in the years to come.
Related to gene therapy is the concept of gene editing. The goal of this technique is not to replace defective genes with normal copies, but rather to use enzymes to edit (correct) the defective genes in place (e.g., within the cells of the organism). Gene editing utilizes techniques more recent than those employed in gene therapy, so it has been tested, and used, relatively less. Thus, it was of great surprise to the scientific community last Fall when a Chinese scientist (He Jiankui) claimed to have performed gene editing on several artificially (in lab) created human embryos, and then to have implanted those embryos into female surrogates to carry the developing embryos until birth.
The technique of gene editing is new enough that, one year ago, the ethical guidelines governing its use had not been fully developed. Nonetheless, there was a general understanding that the technique was not to be used in human embryonic tissue, that would result in *all* cells in the body inheriting the edited gene. This understanding was very broad, but was not universal, and scientists in several countries did use (or attempt to use) the technique on human embryos, in the hopes of creating a gene-edited person - a "designer baby".
The scientific backlash against this first report of human embryonic (germline) gene editing was relatively swift, and relatively severe. The scientist who conducted these first trials has been stripped of his research position, and charged with violating his country's biomedical research laws. The infants (twin girls) were reported to have been born, but little is known about their condition. Some researchers have suggested that they are at risk of a shortened life expectancy because of the gene editing. The gene that was edited in these now-children is thought to promote resistance to HIV infection, but also seems to play other roles in cells.
The article I am forwarding here comes from a few months ago, when the investigations into this researcher and his colleagues was still in process. In particular, there were a number of scientists here in the U.S. who were implicated as having supported this work. The researchers here have generally been cleared of any wrongdoing, but significant questions remain about who knew what, and the motivations (money? fame? patent-able technology?) for their involvement. This article also includes links to a number of related stories, of which there are many.
https://www.nytimes.com/2019/04/14/health/gene-editing-babies.html
It is worth noting that somatic (non-germline gene editing) is gaining ground as a very powerful and promising technique. This variant of gene editing does not change the DNA in every cell in one's body, but only in focal tissues (such as a single organ) that may be malfunctioning due to a defective gene. Indeed, news reports of the promise of this (more-limited) application of gene editing are also prominent in the recent news, including:
https://www.forbes.com/sites/leahrosenbaum/2019/11/19/human-crispr-trials-promising/#340301322daa
I suspect that your generation will be forced to come to terms with the promises and perils of gene editing - it seems both incredibly promising, and incredibly dangerous at the same time. Having a robust set of regulations and ethical guidelines will be very important. If you were faced with the opportunity to correct a gene in yourself, in a loved one, would you? That's a very difficult question to answer a the moment, as we do not yet have enough experience with the pros and cons of these techniques. But, the evidence is beginning to accumulate...
Here's wishing you all the very best Thanksgiving break - please be safe, rest, relax, eat, and enjoy.
Sincerely,
Dr. Nealen
New human ancestor fossil find, and designer gene editing
(originally posted 04 May 2019)
Good morning all,
As our term comes to a close, I'll use my last news message to send along the latest news from two ongoing news stories in genetics:
The first bit of news is about a newly reported fossil find, from a branch of ancestral hominins known as the Denisovans. While scientists and anthropologists have been studying our Neanderthal relatives for decades, Denisovans are only recently discovered. They are thought to have represented a 3rd lineage of ancestral hominin, that co-existed with and likely inter-bred with both Neanderthals as well as early humans.
Until very recently, all information on Denisovans came from fossils collected from a single location, the Denisova cave in modern Siberia (Russia). This new report describes a Denisova fossil from much farther south, in modern Tibet, which suggests that Denisovans were more broadly distributed, expanding the ranges of times and locations over which they may have interacted with modern humans. We know so little about Denisovans that this new information has been described as 'game changing'. If you recall the patterns of early human migration we considered, the first humans may well have had opportunity to interact with the last Denisovans. We all likely have some 'Neanderthal DNA' in us; we may come to realize that we all have a little 'Denisovan DNA', too.
https://www.nytimes.com/2019/05/01/science/denisovans-tibet-jawbone-dna.html
The second news story I will send here relates to the promise, and difficulty, of genome editing. We've discussed a number of times the concept of genes and alleles, and we've considered both gene therapy as well as some of the news related to human genome editing. Recently, a group of prominent scientists has argued that, given our current state of knowledge, the use of gene editing to produce 'designer babies' is more fiction than fact. Even apart from the difficulty of successfully edited the human genome, they suggest that the likelihood of finding individual genes with pronounced effects is very, very low. If you remember, genome-wide association studies (GWAS) can be used to identify genes associated with particular aspects of our physiology and health, but the strength of these associations normally is very low (e.g., often <1%). As such, we may not yet have good, individual targets for gene manipulation.
https://www.npr.org/sections/health-shots/2019/05/02/719665841/why-making-a-designer-baby-would-be-easier-said-than-done
That said, it is very likely that both our gene-editing as well as our genome evaluation skills are going to improve over time, so perhaps the current limitations on the likelihood of 'designer genome editing' are just that: current, but not permanent. It seems impossible that this topic, or interest in it, is going away any time soon.
I'm signing off for the term now. I hope that these weekly news messages have been useful to you. This is the first semester that I have used them to this extent, and it has been a learning experience for me. In particular,
In the end, though, I remain very optimistic. Science is "mankind's organized quest for knowledge" (Floyd Bloom), and we already know that "knowledge is power" (Francis Bacon). It is science that offers us the best hope to deeper understanding, new therapies and treatments, new cures, and new adventures. We will encounter many speed-bumps along the way, to be sure. I hope that our course has inspired you to be a part of this quest, and to make the best use of the knowledge that you gain while on it.
Have a great weekend, and best of luck with all of your exams next week.
Dr. Nealen
(originally posted 04 May 2019)
Good morning all,
As our term comes to a close, I'll use my last news message to send along the latest news from two ongoing news stories in genetics:
The first bit of news is about a newly reported fossil find, from a branch of ancestral hominins known as the Denisovans. While scientists and anthropologists have been studying our Neanderthal relatives for decades, Denisovans are only recently discovered. They are thought to have represented a 3rd lineage of ancestral hominin, that co-existed with and likely inter-bred with both Neanderthals as well as early humans.
Until very recently, all information on Denisovans came from fossils collected from a single location, the Denisova cave in modern Siberia (Russia). This new report describes a Denisova fossil from much farther south, in modern Tibet, which suggests that Denisovans were more broadly distributed, expanding the ranges of times and locations over which they may have interacted with modern humans. We know so little about Denisovans that this new information has been described as 'game changing'. If you recall the patterns of early human migration we considered, the first humans may well have had opportunity to interact with the last Denisovans. We all likely have some 'Neanderthal DNA' in us; we may come to realize that we all have a little 'Denisovan DNA', too.
https://www.nytimes.com/2019/05/01/science/denisovans-tibet-jawbone-dna.html
The second news story I will send here relates to the promise, and difficulty, of genome editing. We've discussed a number of times the concept of genes and alleles, and we've considered both gene therapy as well as some of the news related to human genome editing. Recently, a group of prominent scientists has argued that, given our current state of knowledge, the use of gene editing to produce 'designer babies' is more fiction than fact. Even apart from the difficulty of successfully edited the human genome, they suggest that the likelihood of finding individual genes with pronounced effects is very, very low. If you remember, genome-wide association studies (GWAS) can be used to identify genes associated with particular aspects of our physiology and health, but the strength of these associations normally is very low (e.g., often <1%). As such, we may not yet have good, individual targets for gene manipulation.
https://www.npr.org/sections/health-shots/2019/05/02/719665841/why-making-a-designer-baby-would-be-easier-said-than-done
That said, it is very likely that both our gene-editing as well as our genome evaluation skills are going to improve over time, so perhaps the current limitations on the likelihood of 'designer genome editing' are just that: current, but not permanent. It seems impossible that this topic, or interest in it, is going away any time soon.
I'm signing off for the term now. I hope that these weekly news messages have been useful to you. This is the first semester that I have used them to this extent, and it has been a learning experience for me. In particular,
- I'm surprised how difficult it has been to find good outlets of timely science news that is digestible by the general public. I hope that my go-to sources become regular stops on your tours of Internet science and health news:
https://www.nytimes.com/section/science
https://www.nytimes.com/section/health
https://www.bbc.com/news/science_and_environment
https://www.bbc.com/news/health
https://www.sciencedaily.com
https://www.washingtonpost.com/health
https://www.sciencenews.org
https://science.sciencemag.org
https://www.livescience.com
https://www.npr.org/sections/science
- I'm also surprised how a relatively small number of science topics with little direct application to the majority of our population (like space exploration and dinosaurs) occupy such a large portion of the science news. In some weeks, it was relatively difficult to find recent news related to our topics.
- I'm impressed by, and proud of, the courageous women (and men) of science who are speaking out in support of the MeToo movement, in an effort to 'level the playing field' and make science more inclusive, equal, and safe for all. I sat in your seats as an undergraduate more than 30 yrs ago, and saw then how male-dominated science was, and had been. Since then, it hasn't changed as much as it should have - we still have a long ways to go...
- I'm discouraged how 'big money' from insurance companies, tobacco companies, and environmental lobbyists influences science and health policy. Blending money and politics seems inevitably to lead to bad policy, and bad science policy seems inevitably to set us back in our social progress.
In the end, though, I remain very optimistic. Science is "mankind's organized quest for knowledge" (Floyd Bloom), and we already know that "knowledge is power" (Francis Bacon). It is science that offers us the best hope to deeper understanding, new therapies and treatments, new cures, and new adventures. We will encounter many speed-bumps along the way, to be sure. I hope that our course has inspired you to be a part of this quest, and to make the best use of the knowledge that you gain while on it.
Have a great weekend, and best of luck with all of your exams next week.
Dr. Nealen
WHO | UV Index
(originally posted 27 Apr 2019)
Good morning all,
As we head into warmer weather, thoughts inevitably turn to outdoor activities. With them comes, of course, exposure to sunlight and its radiation. Natural light offers us warmth, pleasurable sensations, and stimulates vitamin D production. As we have been discussing in lab, sunlight also contains dangerous levels of UV radiation.
One of the safety concepts we hear reported related to outdoor activities is the "UV index". This is a scale meant to represent the relative degree of exposure risk posed by harmful UV radiation. The World Health Organization, in partnership with other health agencies, promotes the use of this index as a way to keep the public quickly and easily informed of their exposure risk. The index is fairly easy to interpret: low index numbers, relatively low risk; higher numbers, more risk.
https://www.who.int/uv/intersunprogramme/activities/uv_index/en/
Behind the index is a fair amount of science, in which measured amounts of UV exposure were assessed for their ability to cause cell and tissue damage. Many of the initial studies were done without direct knowledge of what was changing in cells, or what was driving tissue damage. Now, health scientists are able to marry environmental exposure studies to genetic studies, leading to genetic profiles for many of our genes. For example, we now know that the gene responsible for directing production of the melanocortin 1 receptor (gene MC1R) is often mutated by UV radiation; its mutation is one of the leading agents of skin cancer. The normal role of the MC1R gene product is to regulate the production of melanin (eumelanin) in our skin cells, the same melanin which gives us a 'tan' after UV exposure. We all have different levels of melanin production; those of us with lighter skin produce relatively less of it and are at higher risk of UV damage.
https://ghr.nlm.nih.gov/gene/MC1R#conditions
Our lab exercise of the past two weeks demonstrated how even short durations of UV exposure can mutate DNA, and also showed how critical DNA monitoring/repair is to continued health. The plate coverings that we used all provided some degree of protection from radiation. While it may be impractical to cover ourselves with tin foil when we venture outside, sunscreen or even thin cloth provided very useful protection. Remember those plates which were empty of yeast the next time you think about spending long hours in the sun - be sure to use sunscreen!
Have a great weekend -
Dr. Nealen
(originally posted 27 Apr 2019)
Good morning all,
As we head into warmer weather, thoughts inevitably turn to outdoor activities. With them comes, of course, exposure to sunlight and its radiation. Natural light offers us warmth, pleasurable sensations, and stimulates vitamin D production. As we have been discussing in lab, sunlight also contains dangerous levels of UV radiation.
One of the safety concepts we hear reported related to outdoor activities is the "UV index". This is a scale meant to represent the relative degree of exposure risk posed by harmful UV radiation. The World Health Organization, in partnership with other health agencies, promotes the use of this index as a way to keep the public quickly and easily informed of their exposure risk. The index is fairly easy to interpret: low index numbers, relatively low risk; higher numbers, more risk.
https://www.who.int/uv/intersunprogramme/activities/uv_index/en/
Behind the index is a fair amount of science, in which measured amounts of UV exposure were assessed for their ability to cause cell and tissue damage. Many of the initial studies were done without direct knowledge of what was changing in cells, or what was driving tissue damage. Now, health scientists are able to marry environmental exposure studies to genetic studies, leading to genetic profiles for many of our genes. For example, we now know that the gene responsible for directing production of the melanocortin 1 receptor (gene MC1R) is often mutated by UV radiation; its mutation is one of the leading agents of skin cancer. The normal role of the MC1R gene product is to regulate the production of melanin (eumelanin) in our skin cells, the same melanin which gives us a 'tan' after UV exposure. We all have different levels of melanin production; those of us with lighter skin produce relatively less of it and are at higher risk of UV damage.
https://ghr.nlm.nih.gov/gene/MC1R#conditions
Our lab exercise of the past two weeks demonstrated how even short durations of UV exposure can mutate DNA, and also showed how critical DNA monitoring/repair is to continued health. The plate coverings that we used all provided some degree of protection from radiation. While it may be impractical to cover ourselves with tin foil when we venture outside, sunscreen or even thin cloth provided very useful protection. Remember those plates which were empty of yeast the next time you think about spending long hours in the sun - be sure to use sunscreen!
Have a great weekend -
Dr. Nealen
Don’t Count on 23andMe to Detect Most Breast Cancer Risks, Study Warns - The New York Times
(originally posted 20 Apr 2019)
Good morning all,
In lab recently, we have been considering some of the aspects of personalized genetics, with particular reference to genetic ancestry and the use of DNA databases in forensic and criminal investigations. During our introduction to this topic of personalized genetics, I noted that there also are significant interests in using personalized genetics as a way to assess health. Indeed, many of the commercial entities that offer to analyze an individual's DNA also offer to provide some estimate of their health risks for a variety of conditions. I also said at the time that, in our discussions, we would largely stay away from the health aspects of these services, as they are much less well-established than are the ancestry ones.
I described to you recently how using DNA in criminal investigations relies upon combining two large databases (of individual genomes, and police records) to look for intersections, in order to highlight potential crime suspects or their relatives. Using DNA to assess health risks works in a very similar way, this time by evaluating databases of individual gene sequences against databases of individual health and lifestyle records. These types of tests are called genome-wide association studies (GWAS). GWAS are useful only when based upon thousands (usually, hundreds of thousands) of individuals. These are not experimental methods, so they cannot provide definitive proof of anything, but they can reveal interesting "associations" - places where genetics and health vary in consistent ways.
There are lots of large databases of public health records and DNA sequences, and many researchers and even some governments are using them to investigate public health. The commercial operatives also offer to do the same for their subscribers. In the news this week is a reminder that simply claiming that such a service is available does not mean that it is a complete or accurate one. Researchers at not-for-profit health institutions are warning that those who use 23andMe health assessments of genetic risks for breast cancer (the leading type of cancer in women) are potentially being misinformed of their genetic risks. This is a big deal - many people make dramatic decisions about their health and life when learning of their genetic risks for breast cancer, such as undergoing mastectomy (breast removal). At the opposite extreme, what if a person has a substantial risk, but is told that they do not?
https://www.nytimes.com/2019/04/16/health/23andme-brca-gene-testing.html
The federal Food and Drug Administration (FDA) has given its approval for 23andMe (and other commercial) genetic health assessments, and this is an important reminder that FDA approval is not meant to imply that the services are the best available, more so that the services are generally safe and perhaps useful. Anyone who is using a commercial service to evaluate their genetic health risk should follow-up with their physician if they have any concerns - the better hospitals can perform some of these tests on their own. "Caveat emptor", or "buyer beware" - commercials services, by design, place emphases on their interests, first. When in doubt, a second opinion from an independent health professional is the best course of action.
Have a great weekend -
Dr. Nealen
(originally posted 20 Apr 2019)
Good morning all,
In lab recently, we have been considering some of the aspects of personalized genetics, with particular reference to genetic ancestry and the use of DNA databases in forensic and criminal investigations. During our introduction to this topic of personalized genetics, I noted that there also are significant interests in using personalized genetics as a way to assess health. Indeed, many of the commercial entities that offer to analyze an individual's DNA also offer to provide some estimate of their health risks for a variety of conditions. I also said at the time that, in our discussions, we would largely stay away from the health aspects of these services, as they are much less well-established than are the ancestry ones.
I described to you recently how using DNA in criminal investigations relies upon combining two large databases (of individual genomes, and police records) to look for intersections, in order to highlight potential crime suspects or their relatives. Using DNA to assess health risks works in a very similar way, this time by evaluating databases of individual gene sequences against databases of individual health and lifestyle records. These types of tests are called genome-wide association studies (GWAS). GWAS are useful only when based upon thousands (usually, hundreds of thousands) of individuals. These are not experimental methods, so they cannot provide definitive proof of anything, but they can reveal interesting "associations" - places where genetics and health vary in consistent ways.
There are lots of large databases of public health records and DNA sequences, and many researchers and even some governments are using them to investigate public health. The commercial operatives also offer to do the same for their subscribers. In the news this week is a reminder that simply claiming that such a service is available does not mean that it is a complete or accurate one. Researchers at not-for-profit health institutions are warning that those who use 23andMe health assessments of genetic risks for breast cancer (the leading type of cancer in women) are potentially being misinformed of their genetic risks. This is a big deal - many people make dramatic decisions about their health and life when learning of their genetic risks for breast cancer, such as undergoing mastectomy (breast removal). At the opposite extreme, what if a person has a substantial risk, but is told that they do not?
https://www.nytimes.com/2019/04/16/health/23andme-brca-gene-testing.html
The federal Food and Drug Administration (FDA) has given its approval for 23andMe (and other commercial) genetic health assessments, and this is an important reminder that FDA approval is not meant to imply that the services are the best available, more so that the services are generally safe and perhaps useful. Anyone who is using a commercial service to evaluate their genetic health risk should follow-up with their physician if they have any concerns - the better hospitals can perform some of these tests on their own. "Caveat emptor", or "buyer beware" - commercials services, by design, place emphases on their interests, first. When in doubt, a second opinion from an independent health professional is the best course of action.
Have a great weekend -
Dr. Nealen
A cold case killing from 1972 was cracked with the help of genetic genealogy - CNN
(originally posted 13 Apr 2019)
Good morning all,
In lab this past week, we considered some of the aspects of personalized genetic testing, including the ability to estimate one's genetic heritage and family history through evaluation of genetic dissimilarities to others. Fresh on the heels of that discussion is another news report of more decades-old crimes being solved by similar kinds of genetic comparisons.
https://www.cnn.com/2019/04/11/us/cold-case-genetic-genealogy-washington/index.html
When a person offers their genetic information to 23andMe, Ancestry.com, or other of the genetic history services, their DNA sequence and its identified markers are entered into massive databases. It is only against these databases that useful comparisons can be made - we can't learn much about our genetic history by comparing our DNA to that of one or two others.
Remember that these DNA sequences can be compared for similarities and dissimilarities, and they also can be clustered into haplotypes - groups that share some common ancestry. Haplotypes are the basis for construction of genetic pedigrees, or genetic 'family trees'.
How can we solve crimes using this information? Imagine that 5 or 10% of the population of a city have their DNA stored in one of these databases. If a crime (new or old) is committed, investigators can
1) collect DNA evidence from a crime scene (easy to do, as we leave hair and cells everywhere we go)
2) compare the DNA from the crime scene to that of the collected database
3) Evaluate whether there is a direct DNA match to someone in the database. If so, that person may be the culprit! Well, if only 10% of a population has been genetically profiled, the odds of that are low. It's also likely that that people who commit crimes are not likely to freely offer their DNA to public databases.
4) But, we all have relatives. Investigators can often find similarities between the DNA collected at a crime scene, and the DNA of some family group within a database. Then, they look at the personal and family backgrounds of just those individuals. Are any of those people in the DNA database related to someone who has committed other crimes, and has a criminal history already in the police records?
This represents a very powerful way to quickly sort through a lot of information. One the one hand is a large database of genetic information. On the other hand is a large database of police records of crimes and criminals. Finding out specifically where they intersect is the key, and such a comparison often produces leads to a small number of individuals as suspects.
5) Suspects can then be watched/followed, and their DNA then sampled (for example, by collecting from the trash a drinking cup they had used). If this new DNA sample matches that collected at the crime scene, the crime may be solved.
It is exactly these methods which are being used in many cases, both new and old. Notice that they rely very heavily on personal genetic data, and, importantly, notice that suspects can be identified even if they don't offer their own DNA, as long as someone related to them already has. This is a challenge for the courts, too - what is an individual's right to privacy and protection from suspicion when your relatives implicate you, just by being related?
It's exciting to think of the possibilities for learning about one's self through DNA. It's equally important to remember that these are discoveries that we cannot make on our own - we are relying upon public and commercial databases, that can be used in ways we may not have intended or not even thought about. Science is about progress - new ideas, information, and abilities. Even as we reap the benefits of these advances, it is important that, as a society, we stay abreast of the social and ethical challenges that come with them.
https://www.gedmatch.com/login1.php
https://www.23andme.com/privacy/
https://www.cnbc.com/2018/06/16/5-biggest-risks-of-sharing-dna-with-consumer-genetic-testing-companies.html
Have a great weekend -
Dr. Nealen
(originally posted 13 Apr 2019)
Good morning all,
In lab this past week, we considered some of the aspects of personalized genetic testing, including the ability to estimate one's genetic heritage and family history through evaluation of genetic dissimilarities to others. Fresh on the heels of that discussion is another news report of more decades-old crimes being solved by similar kinds of genetic comparisons.
https://www.cnn.com/2019/04/11/us/cold-case-genetic-genealogy-washington/index.html
When a person offers their genetic information to 23andMe, Ancestry.com, or other of the genetic history services, their DNA sequence and its identified markers are entered into massive databases. It is only against these databases that useful comparisons can be made - we can't learn much about our genetic history by comparing our DNA to that of one or two others.
Remember that these DNA sequences can be compared for similarities and dissimilarities, and they also can be clustered into haplotypes - groups that share some common ancestry. Haplotypes are the basis for construction of genetic pedigrees, or genetic 'family trees'.
How can we solve crimes using this information? Imagine that 5 or 10% of the population of a city have their DNA stored in one of these databases. If a crime (new or old) is committed, investigators can
1) collect DNA evidence from a crime scene (easy to do, as we leave hair and cells everywhere we go)
2) compare the DNA from the crime scene to that of the collected database
3) Evaluate whether there is a direct DNA match to someone in the database. If so, that person may be the culprit! Well, if only 10% of a population has been genetically profiled, the odds of that are low. It's also likely that that people who commit crimes are not likely to freely offer their DNA to public databases.
4) But, we all have relatives. Investigators can often find similarities between the DNA collected at a crime scene, and the DNA of some family group within a database. Then, they look at the personal and family backgrounds of just those individuals. Are any of those people in the DNA database related to someone who has committed other crimes, and has a criminal history already in the police records?
This represents a very powerful way to quickly sort through a lot of information. One the one hand is a large database of genetic information. On the other hand is a large database of police records of crimes and criminals. Finding out specifically where they intersect is the key, and such a comparison often produces leads to a small number of individuals as suspects.
5) Suspects can then be watched/followed, and their DNA then sampled (for example, by collecting from the trash a drinking cup they had used). If this new DNA sample matches that collected at the crime scene, the crime may be solved.
It is exactly these methods which are being used in many cases, both new and old. Notice that they rely very heavily on personal genetic data, and, importantly, notice that suspects can be identified even if they don't offer their own DNA, as long as someone related to them already has. This is a challenge for the courts, too - what is an individual's right to privacy and protection from suspicion when your relatives implicate you, just by being related?
It's exciting to think of the possibilities for learning about one's self through DNA. It's equally important to remember that these are discoveries that we cannot make on our own - we are relying upon public and commercial databases, that can be used in ways we may not have intended or not even thought about. Science is about progress - new ideas, information, and abilities. Even as we reap the benefits of these advances, it is important that, as a society, we stay abreast of the social and ethical challenges that come with them.
https://www.gedmatch.com/login1.php
https://www.23andme.com/privacy/
https://www.cnbc.com/2018/06/16/5-biggest-risks-of-sharing-dna-with-consumer-genetic-testing-companies.html
Have a great weekend -
Dr. Nealen
‘Game-changing’ gene edit turned this anole lizard into an albino | Science | AAAS
(originally posted 06 Apr 2019)
Good morning all,
We've talked about genes, and modifications of gene structure (gene editing) or use (gene expression) a number of times this term, and I am sure that you understand both the power and peril that these methods embody. Editing DNA is, at its most basic level, very profound: it really is the 'stuff' that defines us.
In the science news this week comes a recent report, that at first glance, seems unimportant: scientists have performed gene editing, and made an albino lizard. But, this simple summary doesn't quite capture the importance of this work.
For most of its history, molecular biology (and its recent growth into genomics) have focused upon a few model organisms, chosen for their practicality of study. These have included bacteria, yeast, roundworms, fruit flies, zebrafish, and mice, to name a few. Much has been learned from these models, and most of what we know about molecular biology and genetics comes from work on them. But, their use excludes several prominent groups of organisms, including birds and reptiles. That may be coming to an end.
One research group recently employed a modern gene-editing technique (CRISPR) to modify gene expression in Anolis lizard eggs to produce albino offspring. This, in and of itself, is not necessarily an earth-shattering result. What is new is the fact these researchers were able to use CRISPR on a new family of vertebrates, suggesting that it really is going to be a general and powerful technique. Even more importantly, however, these researchers were able to edit the genome of immature eggs, which means that the effects they caused were then propagated throughout the entire organism that resulted from those eggs.
Remember when we talked about gene therapy, and introducing new genes into specific tissues (only)? Here now is a more powerful technique: performing targeted gene editing on the whole-organism genome.
http://www.sciencemag.org/news/2019/04/game-changing-gene-edit-turned-anole-lizard-albino
Stay tuned: this gene (and now genome) editing ride is going to be a wild one for a few years, until our understanding of it, our ethical evaluations, and our regulations mature.
Have a great weekend -
Dr. Nealen
(originally posted 06 Apr 2019)
Good morning all,
We've talked about genes, and modifications of gene structure (gene editing) or use (gene expression) a number of times this term, and I am sure that you understand both the power and peril that these methods embody. Editing DNA is, at its most basic level, very profound: it really is the 'stuff' that defines us.
In the science news this week comes a recent report, that at first glance, seems unimportant: scientists have performed gene editing, and made an albino lizard. But, this simple summary doesn't quite capture the importance of this work.
For most of its history, molecular biology (and its recent growth into genomics) have focused upon a few model organisms, chosen for their practicality of study. These have included bacteria, yeast, roundworms, fruit flies, zebrafish, and mice, to name a few. Much has been learned from these models, and most of what we know about molecular biology and genetics comes from work on them. But, their use excludes several prominent groups of organisms, including birds and reptiles. That may be coming to an end.
One research group recently employed a modern gene-editing technique (CRISPR) to modify gene expression in Anolis lizard eggs to produce albino offspring. This, in and of itself, is not necessarily an earth-shattering result. What is new is the fact these researchers were able to use CRISPR on a new family of vertebrates, suggesting that it really is going to be a general and powerful technique. Even more importantly, however, these researchers were able to edit the genome of immature eggs, which means that the effects they caused were then propagated throughout the entire organism that resulted from those eggs.
Remember when we talked about gene therapy, and introducing new genes into specific tissues (only)? Here now is a more powerful technique: performing targeted gene editing on the whole-organism genome.
http://www.sciencemag.org/news/2019/04/game-changing-gene-edit-turned-anole-lizard-albino
Stay tuned: this gene (and now genome) editing ride is going to be a wild one for a few years, until our understanding of it, our ethical evaluations, and our regulations mature.
Have a great weekend -
Dr. Nealen
This Woman Doesn’t Feel Pain. A Tiny Mutation May Be to Thank.
(originally posted 31 Mar 2019)
Good morning everyone,
In our lab this term, we have talked numerous times about the 'central dogma of information flow', the idea that information encoded in DNA is used during the process of transcription to make RNA, which itself is used during translation to make protein. This concept is part of the 'one gene, one protein' idea, that each gene encodes information to make a single type of protein.
During our discussions, we've also used estimates of the number of genes that we possess (perhaps 25,000), and our most recent lab included discussion of how effective any single one of them may be in influencing phenotype. Most individual genes are likely to have little or no obvious effects on phenotype, while some 'master regulator' genes, or other single genes that are responsible for the production of a key molecule in a cell, may exert more-pronounced effects.
In the news this week comes description of one such gene (gene FAAH, so called), which had been identified previously but whose function was unknown. It is now known that it is a crucial player in mammalian pain perception, for a woman has been described who has led a 'pain-free' life, and who has a genetic mutation in this one gene. Interestingly, this mutation also influences mood - she is described as never feeling anxiety as well.
https://www.livescience.com/65100-woman-cant-feel-pain.html
While pain is unpleasant, do not wish for none of it, for it is a useful 'warning system' that alerts us to tissue damage. There have been others described who 'feel no pain', and their existence is pretty awful, for they experience injury after injury (many of them self-inflicted). Much of their story was described in a superb documentary from a few years ago, entitled A Life Without Pain - if you are interested in the topic, it is very worthwhile.
The subject in this most recent report is mostly, but not entirely pain-free, so her life is mostly normal. But, her case illustrates well the potential power of individual genes. They need not always be 'master regulators' to have individually-profound effects. Sometimes, being just a single link in an important chain is crucial.
Have a great weekend -
Dr. Nealen
(originally posted 31 Mar 2019)
Good morning everyone,
In our lab this term, we have talked numerous times about the 'central dogma of information flow', the idea that information encoded in DNA is used during the process of transcription to make RNA, which itself is used during translation to make protein. This concept is part of the 'one gene, one protein' idea, that each gene encodes information to make a single type of protein.
During our discussions, we've also used estimates of the number of genes that we possess (perhaps 25,000), and our most recent lab included discussion of how effective any single one of them may be in influencing phenotype. Most individual genes are likely to have little or no obvious effects on phenotype, while some 'master regulator' genes, or other single genes that are responsible for the production of a key molecule in a cell, may exert more-pronounced effects.
In the news this week comes description of one such gene (gene FAAH, so called), which had been identified previously but whose function was unknown. It is now known that it is a crucial player in mammalian pain perception, for a woman has been described who has led a 'pain-free' life, and who has a genetic mutation in this one gene. Interestingly, this mutation also influences mood - she is described as never feeling anxiety as well.
https://www.livescience.com/65100-woman-cant-feel-pain.html
While pain is unpleasant, do not wish for none of it, for it is a useful 'warning system' that alerts us to tissue damage. There have been others described who 'feel no pain', and their existence is pretty awful, for they experience injury after injury (many of them self-inflicted). Much of their story was described in a superb documentary from a few years ago, entitled A Life Without Pain - if you are interested in the topic, it is very worthwhile.
The subject in this most recent report is mostly, but not entirely pain-free, so her life is mostly normal. But, her case illustrates well the potential power of individual genes. They need not always be 'master regulators' to have individually-profound effects. Sometimes, being just a single link in an important chain is crucial.
Have a great weekend -
Dr. Nealen
Chop Up a Worm. It Will Regenerate. Scientists Figured Out Why. - The New York Times
(originally posted 23 Mar 2019)
Good morning,
As we conclude our regeneration experiment this week, a new study comes along that suggests that part of the regeneration process is regulated by 'master genes', a concept that we explored earlier during our discussion of 'snake genes and human spines'. While our recent evaluation of regeneration focused upon stem cells, remember that it is the genes that these cells express that ultimately determines their cellular fate. This new study suggests that one particular gene EGR ("early growth response") is necessary for regeneration to occur.
This new study showed that EGR activation is necessary for regeneration in the marine three-banded panther worm (very similar to the planaria we used in our lab). While much remains to investigate regarding EGR and its function, the authors do note that humans also possess this same gene, and that it is known to be activated by injury. So, these studies performed in tiny flatworms are very relevant to us. And, once again, the topics we explore in lab remain at the forefront of genetic science. Very cool, I think!
https://www.nytimes.com/2019/03/20/science/worm-regeneration.html
Have a great weekend -
Dr. Nealen
(originally posted 23 Mar 2019)
Good morning,
As we conclude our regeneration experiment this week, a new study comes along that suggests that part of the regeneration process is regulated by 'master genes', a concept that we explored earlier during our discussion of 'snake genes and human spines'. While our recent evaluation of regeneration focused upon stem cells, remember that it is the genes that these cells express that ultimately determines their cellular fate. This new study suggests that one particular gene EGR ("early growth response") is necessary for regeneration to occur.
This new study showed that EGR activation is necessary for regeneration in the marine three-banded panther worm (very similar to the planaria we used in our lab). While much remains to investigate regarding EGR and its function, the authors do note that humans also possess this same gene, and that it is known to be activated by injury. So, these studies performed in tiny flatworms are very relevant to us. And, once again, the topics we explore in lab remain at the forefront of genetic science. Very cool, I think!
https://www.nytimes.com/2019/03/20/science/worm-regeneration.html
Have a great weekend -
Dr. Nealen
New call to ban gene-edited babies divides biologists | Science | AAAS
(originally posted 16 Mar 2019)
Good morning all,
I'm sure that you have heard recent news about gene editing that was performed on two human embryos by a Chinese scientist, in an attempt to introduce resistance to HIV infection. His efforts only came to light after the children were born, and have been roundly criticized as 'crossing the bridge too soon' - there seems to have been little or no oversight of his work, and most geneticists agree that it is too early for us to consider human genome editing, before we better understand the risks, and the opportunities, it poses.
But, calls for a moratorium on this type of work are not universal - some believe that the time is now to proceed, and that the potential risks of waiting are greater than the potential for doing harm. Others say that this is simply scientific progress - messy, risky, but in the end, advancing our knowledge and capabilities. That this debate is prominent in the science literature is a sign that this is truly the cutting-edge of research and its application. I'm sure that we haven't heard the last on this issue, and I also am sure that in your lifetimes there will be increasing opportunity to perform exactly this kind of genome editing.
Think about children you might have in the future - would you edit their genomes to improve their health? Or to make them smarter? Or kinder? What if you could only choose one of these characteristics? What if improving one caused reductions in another? There is still much to learn, and much to discuss...
https://www.sciencemag.org/news/2019/03/new-call-ban-gene-edited-babies-divides-biologists?utm_campaign=news_weekly_2019-03-15&et_rid=17390186&et_cid=2717665
Hope that you all have had a great Break, and are ready for the second half of our semester! I have been taking care of our planaria, and they are almost ready for your evaluation.
Travel safely back to campus - see you on Wednesday.
Dr. Nealen
(originally posted 16 Mar 2019)
Good morning all,
I'm sure that you have heard recent news about gene editing that was performed on two human embryos by a Chinese scientist, in an attempt to introduce resistance to HIV infection. His efforts only came to light after the children were born, and have been roundly criticized as 'crossing the bridge too soon' - there seems to have been little or no oversight of his work, and most geneticists agree that it is too early for us to consider human genome editing, before we better understand the risks, and the opportunities, it poses.
But, calls for a moratorium on this type of work are not universal - some believe that the time is now to proceed, and that the potential risks of waiting are greater than the potential for doing harm. Others say that this is simply scientific progress - messy, risky, but in the end, advancing our knowledge and capabilities. That this debate is prominent in the science literature is a sign that this is truly the cutting-edge of research and its application. I'm sure that we haven't heard the last on this issue, and I also am sure that in your lifetimes there will be increasing opportunity to perform exactly this kind of genome editing.
Think about children you might have in the future - would you edit their genomes to improve their health? Or to make them smarter? Or kinder? What if you could only choose one of these characteristics? What if improving one caused reductions in another? There is still much to learn, and much to discuss...
https://www.sciencemag.org/news/2019/03/new-call-ban-gene-edited-babies-divides-biologists?utm_campaign=news_weekly_2019-03-15&et_rid=17390186&et_cid=2717665
Hope that you all have had a great Break, and are ready for the second half of our semester! I have been taking care of our planaria, and they are almost ready for your evaluation.
Travel safely back to campus - see you on Wednesday.
Dr. Nealen
DNA's Coding Power Doubled | The Scientist Magazine®
(originally posted 10 Mar 2019)
Good morning everyone,
As I scan the science news each day, I often read articles that are interesting, and potentially useful. Less frequently do I encounter news reports that make me say 'wow!". Here is a link to a news report about a recent study that did, for it potentially changes something that has been fixed for perhaps a billion years.
You've heard much about DNA in your lecture and our lab, and you know the basics of its structure: two twisted strands of a sugar-phosphate backbone, with paired nucleotides along their length. You also know that the nucleotides in use are four only (A, C, G, and T) and that they pair in only two possibilities (A-T, C-G).
Recently, scientists have created synthetic DNA molecules that have not four, but eight different nucleotides (by adding synthetic nucleotides Z, P, S, and B).
There are LOTS of potential implications from this - from the spread of artificial DNA, to the possibility of new life forms, and the potential therapeutic uses of new forms of DNA. One of the more intriguing possibilities is the expanded possibility for use of DNA as a storage molecule. Computer scientists and bioengineers have long been testing methods for using DNA as a way to store digital information (after all, evolution has refined DNA structure/function for a long time, to the point at which it is highly efficient and reliable). Having additional base pairs is akin to adding letters to our alphabet - it makes the number of words or combinations of bases much, much greater, and it dramatically raises the density of data which could be stored by a molecule of DNA..
There are lots of details to work out, but this is a scientific breakthrough that will be a top contender for 'science advance of the year', if not the decade - and you can say that you are well-informed about it!
https://www.the-scientist.com/news-opinion/dnas-coding-power-doubled-65499
Hope that your Break is a good one!
Dr. Nealen
(originally posted 10 Mar 2019)
Good morning everyone,
As I scan the science news each day, I often read articles that are interesting, and potentially useful. Less frequently do I encounter news reports that make me say 'wow!". Here is a link to a news report about a recent study that did, for it potentially changes something that has been fixed for perhaps a billion years.
You've heard much about DNA in your lecture and our lab, and you know the basics of its structure: two twisted strands of a sugar-phosphate backbone, with paired nucleotides along their length. You also know that the nucleotides in use are four only (A, C, G, and T) and that they pair in only two possibilities (A-T, C-G).
Recently, scientists have created synthetic DNA molecules that have not four, but eight different nucleotides (by adding synthetic nucleotides Z, P, S, and B).
There are LOTS of potential implications from this - from the spread of artificial DNA, to the possibility of new life forms, and the potential therapeutic uses of new forms of DNA. One of the more intriguing possibilities is the expanded possibility for use of DNA as a storage molecule. Computer scientists and bioengineers have long been testing methods for using DNA as a way to store digital information (after all, evolution has refined DNA structure/function for a long time, to the point at which it is highly efficient and reliable). Having additional base pairs is akin to adding letters to our alphabet - it makes the number of words or combinations of bases much, much greater, and it dramatically raises the density of data which could be stored by a molecule of DNA..
There are lots of details to work out, but this is a scientific breakthrough that will be a top contender for 'science advance of the year', if not the decade - and you can say that you are well-informed about it!
https://www.the-scientist.com/news-opinion/dnas-coding-power-doubled-65499
Hope that your Break is a good one!
Dr. Nealen
Semi-identical twins 'identified for only the second time' - BBC News
(originally posted 02 Mar 2019)
Hello everyone,
In science education, we like to categorize - things are either "this way", or "that way". Simplifying the variety and pointing out the differences is a proven way to aid understanding, and "boiling things down" to their general features is usually also scientifically accurate - except when it isn't.
In our labs this term, we have talked about meiosis and chromosomes, how chromosomes are paired to give us our genotype, how genotype determines what gametes can be passed on, and how our alleles direct our phenotype. Much of those discussions, as is typical, are of a 'this-of-that' format - we either have this genotype or that one, this phenotype or that one. But exceptions to these general rules are interesting, and often enlightening.
Several weeks ago I sent you a news story about a bird that was spotted in Erie, PA that appeared to be a gynandromorph - a genetic mosaic of both male and female tissues. Gynandromorphs are rare, and form when something other than the normal pattern of gamete combinations, chromosome sorting, and cell division occurs during early embryonic formation.
This week, there is news of another, even rarer genetic variant, this time in humans: a semi-identical pair of twins. You are already familiar with identical twins, which form when a fertilized zygote splits into two genetically-equal cells that develop into separate individuals. Identical twins share 100% of their DNA.
You also know about fraternal twins, formed when two (separate) fertilized eggs, rather than one, develop at the same time. Fraternal twins share 50% of their DNA (on average), just like any two siblings born at different times from the same parents.
In this, case we have something different. Semi-identical (sesquizygotic) twins form when a single female egg is fertilized by not one, but two, male sperm. This early embryo divides and begins to develop into not one fetus, but two fetuses. These fetuses develop at the same time and are born as twins. In this case, though, they are predicted to share 75% of their DNA, because they share 100% of their mother's DNA and only 50% (on average) of their fathers DNA, which together average 75%. In the case reported here, the twins share a slightly higher value (89%).
It is likely that this unusual pattern of fertilization actually happens with some frequency, but that the early embryos do not typically survive. This chance occurrence will give geneticists a new data point in their ability to test hypotheses of genes and relatedness - no longer are all twins in their databases either 50% or 100% related, now there is a known 3rd possibility.
https://www.bbc.com/news/health-47371431
Have a great weekend -
Dr. Nealen
(originally posted 02 Mar 2019)
Hello everyone,
In science education, we like to categorize - things are either "this way", or "that way". Simplifying the variety and pointing out the differences is a proven way to aid understanding, and "boiling things down" to their general features is usually also scientifically accurate - except when it isn't.
In our labs this term, we have talked about meiosis and chromosomes, how chromosomes are paired to give us our genotype, how genotype determines what gametes can be passed on, and how our alleles direct our phenotype. Much of those discussions, as is typical, are of a 'this-of-that' format - we either have this genotype or that one, this phenotype or that one. But exceptions to these general rules are interesting, and often enlightening.
Several weeks ago I sent you a news story about a bird that was spotted in Erie, PA that appeared to be a gynandromorph - a genetic mosaic of both male and female tissues. Gynandromorphs are rare, and form when something other than the normal pattern of gamete combinations, chromosome sorting, and cell division occurs during early embryonic formation.
This week, there is news of another, even rarer genetic variant, this time in humans: a semi-identical pair of twins. You are already familiar with identical twins, which form when a fertilized zygote splits into two genetically-equal cells that develop into separate individuals. Identical twins share 100% of their DNA.
You also know about fraternal twins, formed when two (separate) fertilized eggs, rather than one, develop at the same time. Fraternal twins share 50% of their DNA (on average), just like any two siblings born at different times from the same parents.
In this, case we have something different. Semi-identical (sesquizygotic) twins form when a single female egg is fertilized by not one, but two, male sperm. This early embryo divides and begins to develop into not one fetus, but two fetuses. These fetuses develop at the same time and are born as twins. In this case, though, they are predicted to share 75% of their DNA, because they share 100% of their mother's DNA and only 50% (on average) of their fathers DNA, which together average 75%. In the case reported here, the twins share a slightly higher value (89%).
It is likely that this unusual pattern of fertilization actually happens with some frequency, but that the early embryos do not typically survive. This chance occurrence will give geneticists a new data point in their ability to test hypotheses of genes and relatedness - no longer are all twins in their databases either 50% or 100% related, now there is a known 3rd possibility.
https://www.bbc.com/news/health-47371431
Have a great weekend -
Dr. Nealen
Japan Approves iPS Cell Therapy Trial for Spinal Cord Injury | The Scientist Magazine®
(originally posted 23 Feb 2019)
Good morning all,
Our lab topics remain at the forefront of science news: this week, Japanese scientists announced a new stem cell therapy for treatment of spinal cord injuries. In lab this past week, we considered both stem cells as well as genes related to the spinal column - together, these are evidence that very basic studies of individual genes can often lead to useful results! And, we will talk more about this specific kind of stem cells (induced pluripotent stem cells) in an upcoming lab...
https://www.the-scientist.com/news-opinion/japan-approves-ips-cell-therapy-trial-for-spinal-cord-injury-65484
Have a great weekend -
Dr. Nealen
(originally posted 23 Feb 2019)
Good morning all,
Our lab topics remain at the forefront of science news: this week, Japanese scientists announced a new stem cell therapy for treatment of spinal cord injuries. In lab this past week, we considered both stem cells as well as genes related to the spinal column - together, these are evidence that very basic studies of individual genes can often lead to useful results! And, we will talk more about this specific kind of stem cells (induced pluripotent stem cells) in an upcoming lab...
https://www.the-scientist.com/news-opinion/japan-approves-ips-cell-therapy-trial-for-spinal-cord-injury-65484
Have a great weekend -
Dr. Nealen
Rare half-male, half-female cardinal spotted in Pennsylvania
(originally posted 16 Feb 2019)
Good morning all,
In our labs these past two weeks, we have explored the shuffling of chromosomes that occurs during meiosis, and how the alleles of the genes on the chromosomes get sorted into gametes, which then combine to give offspring unique genotypes (sets of chromosomes and alleles) and phenotypes (physical features). Some of our examples this week included our 'sex chromosomes', the X and the Y, which combine to give us female (XX) or male (XY) characteristics.
When we discussed the phenomenon of nondisjunction, we noted that sometimes things don't quite work according to plan, and that unusual chromosome numbers occur. How about when unusual chromosome combinations occur?
You may have seen a news story recently abut an unusual bird (spotted in Erie, PA) that appeared to be male on one side of its body and female on the other. This is likely to be a gynandromorph, an individual that has male chromosomes (genotype) and characteristics (phenotype) on one side, and female genotype and phenotype on the other side.
A few examples of gynandromorphy have been reported in animals over the years. They appear relatively normal (as male and female organs are generally the same), but their ability to mate and breed is likely very low (as male and female mating behaviors and reproductive structures are very different, of course).
This individual was spotted because, in this species (the Northern cardinal), male and female phenotypes are very obviously different in color (dimorphic). In most bird species, you can't tell females and males apart, as they look the same (monomorphic). It makes me wonder: how many gynandromorphs are out there, and we just don't know about them? And, does this occur in humans?
https://www.nationalgeographic.com/animals/2019/01/half-male-half-female-cardinal-pennsylvania/
Have a great weekend -
Dr. Nealen
(originally posted 16 Feb 2019)
Good morning all,
In our labs these past two weeks, we have explored the shuffling of chromosomes that occurs during meiosis, and how the alleles of the genes on the chromosomes get sorted into gametes, which then combine to give offspring unique genotypes (sets of chromosomes and alleles) and phenotypes (physical features). Some of our examples this week included our 'sex chromosomes', the X and the Y, which combine to give us female (XX) or male (XY) characteristics.
When we discussed the phenomenon of nondisjunction, we noted that sometimes things don't quite work according to plan, and that unusual chromosome numbers occur. How about when unusual chromosome combinations occur?
You may have seen a news story recently abut an unusual bird (spotted in Erie, PA) that appeared to be male on one side of its body and female on the other. This is likely to be a gynandromorph, an individual that has male chromosomes (genotype) and characteristics (phenotype) on one side, and female genotype and phenotype on the other side.
A few examples of gynandromorphy have been reported in animals over the years. They appear relatively normal (as male and female organs are generally the same), but their ability to mate and breed is likely very low (as male and female mating behaviors and reproductive structures are very different, of course).
This individual was spotted because, in this species (the Northern cardinal), male and female phenotypes are very obviously different in color (dimorphic). In most bird species, you can't tell females and males apart, as they look the same (monomorphic). It makes me wonder: how many gynandromorphs are out there, and we just don't know about them? And, does this occur in humans?
https://www.nationalgeographic.com/animals/2019/01/half-male-half-female-cardinal-pennsylvania/
Have a great weekend -
Dr. Nealen
What FamilyTreeDNA sharing genetic data with police means for you | Science News
(originally posted 09 Feb 2019)
Good morning,
When we met for our first class, I ave you a survey asking about some of the science topics that you find interesting, and the idea of 'personalized genetics' came up in a number of your responses. We'll tackle aspects of this issue several times this semester.
Today, I am passing along a link to a news article about the use of unexpected sharing of personalized genetic databases with law enforcement agencies. While there is the potential for much good to come from this sort of exchange, it also raises some concerns, especially as it does not align with the reason that most people seek out their genetic background. This problem will be good fodder for our discussions...
https://www.sciencenews.org/article/family-tree-dna-sharing-genetic-data-police-privacy
Have a great weekend -
Dr. Nealen
(originally posted 09 Feb 2019)
Good morning,
When we met for our first class, I ave you a survey asking about some of the science topics that you find interesting, and the idea of 'personalized genetics' came up in a number of your responses. We'll tackle aspects of this issue several times this semester.
Today, I am passing along a link to a news article about the use of unexpected sharing of personalized genetic databases with law enforcement agencies. While there is the potential for much good to come from this sort of exchange, it also raises some concerns, especially as it does not align with the reason that most people seek out their genetic background. This problem will be good fodder for our discussions...
https://www.sciencenews.org/article/family-tree-dna-sharing-genetic-data-police-privacy
Have a great weekend -
Dr. Nealen
Seeking Superpowers in the Axolotl Genome - The New York Times
(originally posted 30 Jan 2019)
Good morning,
As you have heard by now, our lab (like all classes at IUP main campus) is canceled for today. Please stay safe while this cold front passes.
We'll resume our schedule next week, and pick-up our meiosis exercise then. In the meantime, I'll pass along a recent news article about axolotl salamanders, and efforts to decode their DNA. Axolotls are of great interest in medicine because they are the only vertebrate animal that is able to regenerate nearly any of its body parts if they are lost.
Imagine if humans had the ability to re-grow lost fingers or limbs? Perhaps learning about how axolotls achieve this kind of regrowth will someday get us there.
https://www.nytimes.com/2019/01/29/science/axolotl-dna-genome-sequence.html
See you next week -
Dr. Nealen
(originally posted 30 Jan 2019)
Good morning,
As you have heard by now, our lab (like all classes at IUP main campus) is canceled for today. Please stay safe while this cold front passes.
We'll resume our schedule next week, and pick-up our meiosis exercise then. In the meantime, I'll pass along a recent news article about axolotl salamanders, and efforts to decode their DNA. Axolotls are of great interest in medicine because they are the only vertebrate animal that is able to regenerate nearly any of its body parts if they are lost.
Imagine if humans had the ability to re-grow lost fingers or limbs? Perhaps learning about how axolotls achieve this kind of regrowth will someday get us there.
https://www.nytimes.com/2019/01/29/science/axolotl-dna-genome-sequence.html
See you next week -
Dr. Nealen
Coming Soon to a Police Station Near You: The DNA ‘Magic Box’
(originally posted 26 Jan 2019)
Good morning all,
I'm passing along here a link to a recent news article about advanced technology for the analysis of DNA, and its use in fighting crime. This type of instrument is made possible through the application of advanced electronics and engineering to human biology, a trend that is only going to increase over time. While these devices are exciting and interesting, remember also that there is risk associated with their use, in the collection/banking of personal data, and the need to safeguard one's privacy.
I will occasionally pass along articles of this type during the semester. My purpose in doing so is to help you to become more aware of topics at the interface of biology and society, and also to help you assess how you obtain your science and health news.
Those of us working in science obtain our scientific news, quite often, directly from the original sources: the people conducting the studies and reporting the results. They publish their findings in science journals, or present them at conferences.
Most people do not obtain their news directly, but hear news via secondary sources, such as news releases from scientific organizations, or news stories from the major news outlets. These secondary reports often are then carried by tertiary outlets (smaller/other reporting sources).
Along the way from source to audience, science news is normally distilled (a lot) - much of the detail is excluded or simplified, and the reports often are boiled-down to singular take-home messages, which may (or may not) be good representations of the original work.
When you browse the links that I will forward, or when you access science and health news on your own, I'd encourage you to delve a little bit deeper into them, to read more than just the summaries, and to follow links back to original sources when possible. I'd also encourage you to think a little about the translation of news from source to consumer, and the reputability of the news outlets that you use.
You will not be formally tested on any of the material in the news stories that I will send you, but I do hope that the material in them makes its way into our classroom conversations.
This first link is from the New York Times, which provides one of the best (e.g., best funded and most reliable) secondary sources of science and health news. They do limit access to only a handful of free articles each month, so I will use them sparingly.
https://www.nytimes.com/2019/01/21/science/dna-crime-gene-technology.html
Have a great weekend -
Dr. Nealen
(originally posted 26 Jan 2019)
Good morning all,
I'm passing along here a link to a recent news article about advanced technology for the analysis of DNA, and its use in fighting crime. This type of instrument is made possible through the application of advanced electronics and engineering to human biology, a trend that is only going to increase over time. While these devices are exciting and interesting, remember also that there is risk associated with their use, in the collection/banking of personal data, and the need to safeguard one's privacy.
I will occasionally pass along articles of this type during the semester. My purpose in doing so is to help you to become more aware of topics at the interface of biology and society, and also to help you assess how you obtain your science and health news.
Those of us working in science obtain our scientific news, quite often, directly from the original sources: the people conducting the studies and reporting the results. They publish their findings in science journals, or present them at conferences.
Most people do not obtain their news directly, but hear news via secondary sources, such as news releases from scientific organizations, or news stories from the major news outlets. These secondary reports often are then carried by tertiary outlets (smaller/other reporting sources).
Along the way from source to audience, science news is normally distilled (a lot) - much of the detail is excluded or simplified, and the reports often are boiled-down to singular take-home messages, which may (or may not) be good representations of the original work.
When you browse the links that I will forward, or when you access science and health news on your own, I'd encourage you to delve a little bit deeper into them, to read more than just the summaries, and to follow links back to original sources when possible. I'd also encourage you to think a little about the translation of news from source to consumer, and the reputability of the news outlets that you use.
You will not be formally tested on any of the material in the news stories that I will send you, but I do hope that the material in them makes its way into our classroom conversations.
This first link is from the New York Times, which provides one of the best (e.g., best funded and most reliable) secondary sources of science and health news. They do limit access to only a handful of free articles each month, so I will use them sparingly.
https://www.nytimes.com/2019/01/21/science/dna-crime-gene-technology.html
Have a great weekend -
Dr. Nealen
The new frontier of gene doping will modify athlete DNA - CNN
(originally posted 16 Apr 2018)
Good morning all,
Just thought that I would pass along a recent news article about gene doping. One of the interesting items in the article is that the scientist who first developed some of these genetic methods (Lee Sweeney) is now an advisor for the WADA!
https://www.cnn.com/2018/04/13/health/athletes-gene-editing-doping-sport-intl/index.html
Cheers,
Dr. Nealen
(originally posted 16 Apr 2018)
Good morning all,
Just thought that I would pass along a recent news article about gene doping. One of the interesting items in the article is that the scientist who first developed some of these genetic methods (Lee Sweeney) is now an advisor for the WADA!
https://www.cnn.com/2018/04/13/health/athletes-gene-editing-doping-sport-intl/index.html
Cheers,
Dr. Nealen
Gene doping articles
(originally posted 06 Mar 2018)
Good morning all,
Yesterday, I sent you all a link to a news story about 'doping' in sports, and the controversies revolving around it. That article was a useful introduction to the topic of doping in general, and it focused upon chemical doping, which is the traditional form of the problem.
Our lab topic this week, however, is 'gene doping', which is a related, but more difficult problem.
I'm appending below a few more links that might help bring you up-to-speed on gene doping, in particular. In lab, we'll have a reading and some questions (as usual), but I wanted to give you these reading options in advance. If you get a few minutes, scan a couple of these links - they will help put our in-lab discussion into a broader context. You can also use these readings once we gather for lab, to help with the questions we'll consider.
http://www.bbc.com/news/magazine-25687002
https://en.wikipedia.org/wiki/Gene_doping
http://theconversation.com/explainer-what-is-gene-doping-and-will-any-athletes-at-rio-2016-have-tried-it-63230
https://www.researchgate.net/publication/8549500_Gene_Doping_in_Sports
See you tomorrow -
Dr. Nealen
Barbra Streisand Cloned Her Dog. For $50,000, You Can Clone Yours. - The New York Times
(originally posted 28 Feb 2018)
Good evening everyone,
Here's a link to cloning story that I mentioned in lab today:
https://www.nytimes.com/2018/02/28/science/barbra-streisand-clone-dogs.html
Here's a second link about a recent discussion of the ethics associated with cloning which also arrived in my mailbox today:
https://omnia.sas.upenn.edu/story/omnia-qa-china-cloning-and-gene-editing
If one has the money, the technology and services exist! And, clearly these issues are timely.
Dr. Nealen
(originally posted 28 Feb 2018)
Good evening everyone,
Here's a link to cloning story that I mentioned in lab today:
https://www.nytimes.com/2018/02/28/science/barbra-streisand-clone-dogs.html
Here's a second link about a recent discussion of the ethics associated with cloning which also arrived in my mailbox today:
https://omnia.sas.upenn.edu/story/omnia-qa-china-cloning-and-gene-editing
If one has the money, the technology and services exist! And, clearly these issues are timely.
Dr. Nealen