The Planetary News Radio – Episode 10: Ancient North Siberians, Octopuses as Lab Rats, and Microplastics Invade Deep Sea

Hello. Welcome to the Planetary News Radio Episode Number 10 with your host, Bryan White. I’m going to be doing a Science in the News segment today, which is a brief summary of trending science news articles. I haven’t reed or researched most of these articles unless it was something controversial. So I’m just giving background information based on the headline. So depending how good the headlines are kind of influences how much information I can give about the article.

First up, I have here “DNA from 31,000 year old milk teeth leads to the discovery of a new group of ancient Siberians”. Ancient humans. This is a really exciting area of research because we found out that pretty much anything say, around the last 50,000 years, we can get DNA from now if we can find bones and the bones haven’t been completely fossilized. There’s still organic material in the bones. We can extract DNA and do genetic and genomic analysis on these bones and teeth are a great example of that. [There is] lots of organic material inside of teeth. And so we’ve discovered there’s several species of ancient humans in Eastern Europe, across through Russia, and Siberia, and in Asia. And so while there were radiations of humans out of Africa multiple times, some of those radiations included ancient humans that migrated into Siberia and Asia. In Europe, some of those became Neanderthals. [In Russia and Asia,] some of those became Denisovans, and I don’t know if this new species has been named yet [(Ancient North Siberians)]. This is really considered a subspecies of [ancient human, which are still considered Homo sapiens sp.].

Most of these species would have been able to interbreed with each other. So a good rule of thumb for mammals is if the divergence time for two groups is less than 200,000 years, then hybridization was most likely possible. So modern humans and Neanderthals were [able to hybridize, which] we know it’s proven for a fact that they hybridized because we have genomic data. Using [just] the rule of thumb, we know that Neanderthals and modern humans diverged about 300,000 years ago, and when they met again in Europe, they were only separated by about 200,000 years of evolution, and so they were able to hybridize. So the same thing with this [newly discovered group whose] teeth are only 31,000 years, so certainly these would have been able to hybridize and interbreed with modern humans, Homo sapiens sapiens.

So [this is] just more evidence of new, different groups of ancient humans. And why is that important? Well, it helps paint the picture of the migration and really the prolific amount of adaptation that modern humans underwent in terms of evolutionary change over the last 200,000 years. We really had our own adaptive radiation, just like birds and reptiles and dinosaurs. Humans are one of our own great adaptive radiation stories in terms of evolutionary history, so it’s always cool when we find new human species or unique genetic groups.

So let’s see, we [have] another StarLink article. “Astronomers call for urgent action on you on SpaceX’s StarLink satellites”. Apparently, astronomers are still concerned over the magnitude of the number of satellites that Elon Musk is going to be putting out into orbit around. [It will be] 12,000 satellites [in total], and this is now still a trending story every week for the last couple weeks since the initial launch has occurred. Like I said last time, I think it’s a fair criticism, but it also forces us to think about space junk in general, which is good. So Maybe Elon Musk is doing us a favor by forcing the conversation, and hopefully there’s some resolution with these satellites and [policies towards “space junk”].

Here’s another interesting evolution biology topic or medical two. The newest lab rat has eight arms octopuses, big brains and unique behaviour spur basic research. Why would octopuses be a really good animal to use in the lab as a research subject? Well, let’s think about rats. Rats are intelligent. They’re small. They’re relatively easy to cultivate. You could have a colony [colony of rats]. They reproduce in the lab. They have a short lifespan, and that life span is about the time that it takes most experiments to perform. But what are the problems with rats? There’s a lot of problems with rats. One of them is that rats get cancer very easily, [upwards of 80% in some cases]. At least in lab stocks of rats, as opposed to wild rats. We’ve been cultivating rats for so long in the lab in a lab setting that they’re very, very likely to get cancer over the course of a two year life span. And so, if you want to do a cancer study on rats, that’s a problem because most of these rats will inevitably get cancer no matter what, whether they’re being exposed to something that is actually increasing their cancer risk or if they’re just living over the course of a normal life span.

[What are some reasons octopuses might make good lab animals?] Octopuses are less cultivated in the lab, [or at least were used in lab experiments more recently], so we probably don’t have very many generations worth of octopus evolution happening in a lab. It would be easier to collect them from the wild and generate a new stock [to improve and maintain lab-strain genetics]. Since lab rats are so domesticated compared to their wild counterparts, it would be problematic to intermix lab rats with wild rats, especially because you have the problem of aggression. So you don’t want to create really aggressive lab rats. It might improve their genetic stock, but then again, you have a problem of having more wild, aggressive rats.

Octopus can be aggressive, but it’s different. They’re a very different animal in terms of behavior. They’re contained in a marine environment. They’re probably not really being handled by the researchers. In other words, an octopus is less likely to reach around and bite a researcher because the environment that the octopus is being stored in isn’t going to be one where the researchers are routinely handling them with their hands. I imagine you can create these lab complexes for octopus to live in, where the researchers don’t really have to interact with them, and they don’t have to worry about getting bit. Octopuses do have a beak that could hurt a human. It could draw blood. But again, they’re not really aggressive, they’re mostly defensive animals, so octopus is not really threatened. Even a wild octopus shouldn’t be a problem. Now they will try to escape, but that’s part of their intelligence. So you have this animal that has a really fast generation time, it has a genetic stock could be easily replenished from the wild, it’s highly intelligent, it’s probably smarter than rats. It’s not really aggressive [compared to rats]. On the negative side, it’s probably more expensive to cultivate because you need all the marine equipment. But stuff like that is coming down in terms of pricing because of advances in material science. So as material science advances, it becomes easier to cultivate an animal like an octopus and then for sets of experiments that will work on an octopus. In other words, if you’re not trying to test a [mammal-specific] hormone, obviously that won’t work. Or it might if you could genetically engineer octopus to do something like a mammal. So maybe we can even test human medicine on octopuses if it’s easy to genetically modify them.

The great dying nearly erased life on Earth. Scientists see similarities today, the great dying, of course, being the Permian extinction, where 90 percent of marine life went extinct at the end of the Permian period around 300,000,000 years ago. And I think maybe 70% of all land life went extinct. And so we see Similar is of that today because of the rapid extinction rates that were seen on the Earth. And so we know that the Permian extinction was accompanied by rapid changes in climate, and a lot of those changes would have been recorded in the geological history in the fossils in the rocks around that time. So we’re probably seen similar patterns of a very rapid global climate change too rapid for animals to adapt, especially marine animals that tend to be more sensitive.

Apparently, the Mars lander Insight is having a problem with its instruments. So “NASA finally has a plan to free Insight’s extremely stuck probe”. So it sounds like the heat probe on Insight os stuck. Insight is an interesting probe on Mars because it’s not a robotic rover like Opportunity [and Spirit were]. It is a It is a stationary probe whose primary mission is to study the geology and geologic activity of Mars. So it has a seismometer that is actually measuring earthquakes on Mars and some other types of thermal instruments. So the fact that one of its probes are stuck is not good, but maybe this can be resolved.

Here’s another controversial topic. “Microplastics have invaded the deep ocean and the food chain”. That’s not good. So micro plastics real problem, because we’re finding out now that it’s permeated our entire water system, including the ocean and freshwater. These are microscopic bits of plastic that now we know we’re drinking and eating, and not just us [(humans)]. All life on earth now potentially being exposed to this. We don’t know the cumulative effects or long term effects of this because it’s just recently happened [the article says we are] finding out that microplastics have permeated all the way down to the deep sea, which means the entire oceanic ecosystem can be impacted from this all the way from the bottom up. So [some of] the primary producers in the ocean are phytoplankton or very tiny, tiny animals [(zooplankton)]. Phytoplankton are photosynthesizing organisms that float up and down in the water. And so now it sounds like, they’re saying, is that microplastics have permeated the entire oceanic column, which means primary producers will be affected as well as secondary producers and secondary consumers.

So if the oceanic ecosystem has been permeated to this degree with microplastic suggests that there could be a cumulative effect and this could lead to an ecosystem collapse. And so I think that’s kind of what we’re waiting for right now. In terms of conservation biology, we’re waiting to start seeing signs of these major ecosystem crashes. We already see signs of top level consumers [being harmed, such as] whales, sea turtles, things like that that are eating fish all the way up the food chain. We already see that they’re being impacted because they’re getting the worst degree of bio-accumulation because they’re eating fish and crustaceans that even in phytoplankton have been absorbing microplastics. So, you know, at the highest level we already get an impact. We get birds stomachs filled with plastic, things like that. So this microplastic problem is really scary. And hopefully my guess is that there will be some extreme measures taken, probably in the next five years to alleviate this. That’s my hope. But I think that it will happen because I think we’ll start seeing more direct [negative] impacts of it that will drive some of those changes.

All right, and that’s all I had today for this Science in the News segment. That’s Bryan White signing out the Planetary News Radio. Thanks for listening. If you’d like to support this podcast that had a patreon going, the link for that is in the feed. The transcripts for all of these podcasts are also on the website, so there’s a link to the website in the feed, and if you would like to join a discord chat, that link is also there. Hopefully, we get people asking questions and things like that in the discord, so thanks for listening. Have a great day.

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The Planetary News Radio – Episode 7: Preserving Biodiversity – Insects, Fungus, and Plastic

Hello. Welcome to the Planetary News Radio Episode 7 with Bryan White. The date is May 29th. It’s around four o’clock in the afternoon in Corvallis, Oregon. I’m outside again. So I apologize in advance for any strange sounds, although I’m in a quiet area, and that’s a good segue way to what I’m going to talk about today, which are insects. Now, the air temperature is finally warming up and I saw a Mayfly today, a little late in the season, although I haven’t been looking for them. But mayflies typically will emerge in May into adulthood. The order name for mayflies is Ephemeroptera, probably from the root ephemeral meaning temporary, which is strange because they’re actually quite long lived as larva, so Mayfly larva might spend two or three years eating in the stream and then swim up, moult, metamorphose into an adult, reproduce, and then die all in about a week. In fact, they’re so short lived as adults that their mouth parts are fused shut. They don’t eat anymore. So unlike a butterfly, that eats as a caterpillar and continues to eat as an adult, Mayflies are done once they pass through the larval form. And so that’s what’s going on now. Mayflies. They’re out and about, seasonal insects.

[Which brings me to the topic of this podcast,] “Why are insects special”? I mentioned in the previous talk about my idea for why we should preserve all biodiversity. Why should we value all biodiversity? It’s not physically possible to preserve every species, but we can certainly agree that there is a scientific value to preserving biodiversity, and insects are a great example. Insects or one of the most speciose as animal groups go. They might be the most speciose animal group, aside from maybe nematodes. Estimates of the total number of species for insects might range somewhere to 5 million, [up to 30 million including undiscovered species] with the total number of all animal species being [at least] 10 million. So that would mean insects make up maybe [at least] half of all animal species by count, maybe not by biomass, but that’s an incredible amount of diversity.

So what’s going on when that much diversity is happening [within a single taxonomic group]? A couple of things. One is that insects are different from vertebrates [in some key ways]. What allows them to adapt in terms of evolutionary time more quickly than vertebrates? [For one], they’re less constrained by their skeleton and by their body plan. So insects are more tolerant of maybe minor changes in their body structures: mouthparts, feeding structures, reproductive structures, and their flying/walking structures. So all of these things are much more flexible, whereas even a small change and the number of fingers that a human has could be could have a severe impact. Maybe not in modern times missing a finger isn’t too big of a deal. But maybe 1 million years ago, missing a finger was a big deal, and you might not have survived. So you see, chimpanzees have 10 fingers and humans have 10 fingers. We’re separated by 7 million years of evolution. [In the case of insects], within that same amount of time, [you’ll see them] duplicating appendages, losing appendages and things like that much more frequently, so insects are hyper adaptable. They’re out there filling all of these ecological niche spaces.

A good way to think about an ecological niche is that the environment is an N-dimensional hypervolume. There’s all these dimensions that could be occupied, [where each dimension represents a unique ecological environment], and an organism will go and occupy what it’s already adapted to, but then it might shift and adjust and fill various other dimensions in the ecological hyperspace. [After some more time] it might divide into more species, and those species might diverge and fill more of this space, until eventually the entire ecosystem space is filled by something. In a small ecosystem, this might be only one or two species. In a large ecosystem, it could be hundreds or thousands of species all the way up [through the trophic levels], from bacteria up to primary apex predators.

Insects are hyper adaptable, which means they can go into an ecosystem and fill all those little voids in the N-dimensional hypervolume that aren’t currently being occupied by an organism. You have primary producers, secondary producers, you have consumers, all within the insect world, so you have a full ecosystem just based on insects. That’s a lot of biodiversity. Every one of those ecological niches requires a genetic change in the organism, so every time a new species evolves, or diverges from an old species, one species splits for some reason, or even new variability within the species. Anytime a species gains in new adaptation, that’s a new piece in the genome. It’s a new genetic element that’s [translates into a] new physiological element. It’s a new piece of biological information, and my argument is that biological information is extremely important, but not just the genome. The genome isn’t enough. We need the phenotype, so we need to know how the genome builds itself. Builds the proteins in the organism. So we want to be able to see organism’s alive in their natural habitat in order to understand the genomic component to that diversity.

[To recap] what I’m just presenting here, is an argument that insects are very speciose, therefore, they have lots of biodiversity, and therefore they have lots of unique genetic elements. Now here’s a question someone might pose to me. Are any of those genetic elements useful? And the answer is, “I don’t know”. Maybe they might be. Some of them might be useful, and some of them might not. It depends on your definition of useful. For example, a fungus that grows on a tree might not be immediately useful, however, fungus growing on a tree [might be] breaking down wood lignin the molecule, and so this fungus is secreting a chemical that can break down lignin. Wood is a very strong material we know, because wood survive thousands and thousands of years intact. We use it to build houses, things like that. It’s kind of similar to plastic. Lignin is a polymer. Trees are building themselves as a polymer. So if we want to develop a chemical process for breaking down plastic [(a polymer)], we might look at something like a fungus that eats wood, [specifically] the wood rot class of fungus.

[Suppose someone did experiment to see if wood rot fungus could break down plastic, but it didn’t work. Then you might say,] “Well, lignin is too different from plastic. We can’t use this fungus to break down lignin because the molecule is too different from plastic”. And I might respond, “Well, okay, are there any organisms that do produce a molecule that do break down plastic”? [Which it just so happens that] there are. There are bacteria that will happily degrade petroleum based products like oil. However, these bacteria, they may be marine and have to be grown in [sea water], and so we want to do is create a genetically modified organism that has the structural properties of a fungus, [but the chemical properties of the bacteria]. We want to make a wood rot fungus that can degrade plastic, and so we could take the gene from the bacteria and [transfer it into the fungus so that the fungus can] produce the plastic degradation chemical. And now we have a fungus that can break down plastic.

[Using this method we end up with something] a little more useful than the bacteria, because now you could do is you could take a landfill and create an environment that will grow this fungus and plastic mashed in together, and we can erode the plastic. While you could do this directly with the bacteria [that can decay plastic], then you would have to do an active process because you have to keep the bacteria alive. You have to culture the bacteria, and so you need energy. And so my suggestion is to use the fungus because it doesn’t require extra input energy. All you do is you put it outside and you let it go, but it has [to have] that chemical [acquired from bacteria] to break down plastic, otherwise, it’ll just sit there. And maybe we can tweak the fungus a few other ways so it can grow in soil and we might have to modify its habitat a little bit. We want to keep the soil moist so the fungus has water to conduct its chemical reactions when it add some nutrients. But for the most part, [with] fungus, you just put it out and it grows. And if this fungus has a chemical that breaks down bacteria, we could create landfills that can destroy plastic. And that will help solve our plastic problem.

What about with insects? Well, maybe we could do the same thing. We can make a caterpillar that can break down plastic. Maybe there’s a parasite that lives inside of caterpillar that digests compounds similar to plastic, and so maybe there already is a caterpillar out there that can break down plastic. [The point is, if we have the available biodiversity, we can create as many different types of “plastic degrading organisms as feasible]. We could just have the fungus. Or we could have the fungus and the caterpillars, and so we could create an entire ecosystem where the fungus and the caterpillar are growing and living together. The caterpillars eat, deposit, nitrogen and things like that into the soil. The fungus grows, and it’s a whole little life cycle, all based on the degradation of plastic without any added energy input. We don’t need to run an expensive, dirty, fire based bioreactor that burns trash puts out chemicals. It’s all passive.

So how does that link back to my original statement? Well, if we lose that species of caterpillar, then we lose [the ability to create] that entire system. So if a caterpillar that could break down plastic goes extinct before we’ve figured out how to cultivate it in the lab, then we lose this entire opportunity to degrade plastic and this really efficient, really cool way. And we don’t know what’s out there, [there might be other organisms and biochemicals out there that we haven’t even imagined possible yet]. So every time we lose a species, we don’t know what we lost. Maybe we’re losing plastic degraders. And maybe it doesn’t matter most of the time, and probably 90% of the time it didn’t matter, [in terms of biochemical diversity when a species was lost]. Maybe the special biochemical adaptations that the organism had were already duplicated [in another species], and other members of the genus, or the order, [or some other] higher taxonomic level. Maybe that animal wasn’t that unique and so we didn’t really lose that much information. [But again,] we don’t know what’s out there, [so we don’t know what we’re losing in terms of physiological biodiversity]. We don’t [really have] anything cataloged [in a meaningful way to address this problem].

If we really wanted to answer the questions, “What are we losing [in terms of genetic engineering potential]?” and “Are we losing an important species?”, we have to catalog the species [in a meaningful way]. Now, how could we do that? Well, we have to find them and sequence their DNA. Sequencing DNA is really good for cataloging [and understanding diversity]. But if we want to actually create real biological systems, we need to have the animals or the organism’s alive. And so that’s why biodiversity [itself] is so important and why preserving [as much] biodiversity [as possible] is so important. If we think of [living organisms as being filled with] these as tiny molecular machines that are jam packed full of information that we can learn from for how to create our own systems, our own molecular machinery, then biodiversity becomes really important.

And sure, maybe someday in the future of humanity, there will be a time where we don’t need animals anymore. And maybe that’s a question for future humans to answer. [In a future where] biodiversity no longer serves a function in the human economy. [In other words, when even the knowledge we could gain from the genetics of animals is no longer relevant], will we still keep animals? Will our descendants 500 years from now have zoos just for fun, just to look at animals and remember where we originated from? Remember that we are animals. Maybe we’ll have zoos. Maybe we’ll make new animals. Maybe humans will merge and split and divide into 10 new different species. We don’t know what’s going to happen [in 500 years], but when we lose the species, we lose the option.

So that is more insight into my thinking and the reason I think this way is because again, as I mentioned previously, my goal is not to just be a animal rights activist. My goal is to be pragmatic. I’m saying there is a real pragmatic reason to keep animal diversity life, [and all] biodiversity alive. And so this argument should work across the entire political spectrum. I should be able to convince a fiscal conservative or liberal that preserving biodiversity is important because it’s an investment in humanity. It’s not just to feel good, although it might make us feel good. Feeling good about animals is just an added benefit. And trees, we are, after all, apes. We were born in the trees. We left them, but we still need them. It’s okay to like trees. We should enjoy wildlife and the outdoors and nature, and we should be able to have a good reason for keeping it around. So that’s what I’m offering, [a reason to preserve biodiversity that can appeal to all humans].

I’m sure I’ll talk more about this as I formalize the idea more, but I think this was a really good example. Insects and fungus. Interestingly, both organisms that use chitin as there primary structural bio-protein. There’s something special about chitin. It’s an interesting molecule for evolutionary genetics, but I won’t say more in this episode. I’ll let everyone think about this topic. This is Bryan White signing off with The Planetary News Radio. Have a good day.

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The Planetary News Radio – Episode 5: Fear and Censorship in Scientific Communication

Hello. Welcome to the Planetary News Radio Episode. The date is May 30th. It’s a cloudy day in Corvallis, but not raining. Enjoying the temperature. [Let’s talk today about] popular science and censorship. So a great example of censorship in science recently has been climate science. And this is it’s kind of scary how well accepted it is that the censorship is occurring. Strange things like purging the word climate from government documents put out by environmental agencies. So it’s very strange to experience, a blatant, systematic censorship like that by the government, well, specifically by the Trump administration. Attempts to quantify that [censorship] and paint a picture of how widespread that actually is are even more disturbing. I’m looking at an article here that counts the number of times that federal departments and agencies were involved in an act of censorship and sense put out by a group, Columbia Climate Law. So I don’t know if that’s associated with Columbia University or what that is. I haven’t really researched it. I’m just looking at a Scientific American article here, but before I talk about those numbers, let’s talk about my own personal experience with censorship [link to Columbia Climate Law Silencing Science Tracker].

When I was a graduate student, I worked in environmental genetics and the agencies that were interested in environmental genetics were sanitation departments and water districts, at least for the ones that I worked for. More broadly, the U.S. Geological Survey was interested in environmental DNA (eDNA) as a way to track fish or aquatic mammals or other vertebrates. And so I spent a lot of time working on informatics methods to identify species using genetics. And this was really one of those projects in science, which happens quite a bit where we all think we have a really good idea of what is going on. We have a hypothesis. We can test a hypothesis, but maybe it’s something that we’ve already known for years. And so when we went in to test the hypothesis that using genetics to identify species improves are our ability to identify a pollution in a stream, we were reasonably confident that this would be the case, and so it wasn’t really expected it not to be better. It was more of the question, “Could we do it?” And so a lot of what we did were methods studies, and so really, it was developing a method to apply this theory that we already thought would be good.

Some publications had represented data that would suggest using genetics to identify impacted streams. I shouldn’t just say polluted streams, [but streams] that were impacted by either human modification or by pollution or something like that, and it did make sense that genetics would improve our ability to do that because the way that we identify those streams, the way that was historically done was to identify species by looking at them visually. And so we know that some percentages species, especially insects, cannot be identified visually. So we knew there are more species out there. And so the idea was that if we’ve confined more species, then we’ll have a more sensitive tool. So it wasn’t really a question of, well, this will be better. It was more of a question of “How much does it cost? And can we do it? Is it practical?” And so we set out to answer those questions at the group that I was working for, and so I spent about three years working on that project. But every time we found a example where we would find more species or find specific species at different sites, this was always ignored. And so we thought that we had done a good job developing a tool that could improve our ability to detect human impact in the environment, but this was ignored by the supporting agencies of our group.

Not really ignored [outright], but ridiculously high standards were put on us, much higher than other studies. So everything was scrutinized. Money, sensitivity. Any mistake was highlighted. And so it’s overall if you add up everything. This was an act of censorship, and so individually the acts were not censorship. In other words, nobody ever said, “Oh, you can’t publish that result”. All right. Nobody has ever told me you cannot publish that result, however, I have had results that were scrutinized not because not for their scientific validity but for their philosophical impact. So we had many empirically correct results that suggested this would be a better method, and those results were ignored for philosophical questions. So I have experienced censorship and it was government censorship, and that was during the Obama administration. But this is not unusual in biology. Biology is one of the most censored scientific fields in modern times because of the philosophical component, because of the way that it makes people feel uncomfortable about their [world view].

It was not surprising to me that that study did not take off or that those methods were not implemented. And as far as my knowledge, those methods that we were developing are still not implemented by the United States government routinely. Now, there is one thing that has been implemented, and that is the use of eDNA. In that case, the cost of benefit argument worked in favor of the science.The ability to go out and collect a sample of water from a stream and be able to know what species of fish are in that stream based on the DNA and the water is a very powerful analysis because it can be done relatively inexpensively. Now the question is, well, why do you want to know what species are in the stream? And the second question is, Do you need to know how many? Because there’s a very specific limitation of the technology in genomic sequencing. And so the same technology that’s used to sequence a genome is the one that will be used to sequence water to identify DNA in that water sample.

There’s a limitation of that [genomic sequencing] technology that makes it very difficult to determine the abundance, the original abundance of the animals that created the DNA, and so the challenge of the eDNA work was to be able to determine abundance from the sample, and that has been worked on four years for five years now. eDNA is being implemented by the U.S. Geological Service in the United States. And so that’s a federal government agency acknowledging the usefulness of genetics for environmental monitoring. Now, as I read the article that I just read, the conclusion of the article is that developing this on a wide scale would be cost prohibitive. So again, is that an act of censorship? By saying that this technology that allows you two very quickly and rapidly assess the community structure of a stream using genetics is to cost prohibitive? Maybe, Maybe not. I don’t think so. I don’t believe that that is true [that it is more expensive]. The sequencing technology, the cost of DNA sequencing is almost negligible for the amount of sequencing [needed to conduct a routine stream sample]. So really the cost here it would be the labor to conduct the analysis. And so then the question is, what is the labor cost to conduct a genomic analysis versus the labor cost to conduct a visual analysis? And so when someone says that is to cost prohibitive to conduct genetic analysis, you’re saying that it costs more for someone to go out and collect a bottle of water from a stream and put it in their car and drive back to the lab or collect 10 bottles of water and put him in there in a in a cooler and drive those back to the lab later in the day, that it cost more to do that than it does to send a team of 20 people out to count fish visually in a stream. And not only that, but that the extra information gained by doing the genetic analysis is not useful at all has no monetary value.

So that’s what the federal state governments will say, is that genetic testing is to cost prohibitive. And so, let’s see. Let’s look at numbers here that have been published by this group. 51 Instances of Censorship in the Environmental Protection Agency, 35 by The Department of Interior, 25 of the White House, 17 by Health and Human Services, 16 by The Energy Department, 6 at NASA. [The reason] for these [censorship acts] could be science is told they can’t talk publicly, studies discounted in policy making budget cuts for scientific research programs, removing scientists visit from positions limiting the teaching of theories, self censorship, the research hindrance. So the censorship that I experienced would be classified under was self censorship by the scientists that I was working with because they all knew what not to say to avoid budget cuts. [Ultimately, that] research program was defunded.

[Listing types of censorship from the article]

We could not get funding, to research genetics. Some forced personnel changes were experienced that might have been considered censorship. [I didn’t see any] overt interference with education. That’s something you would expect to happen, [for example], at the EPA. [If I wanted to] put out a pamphlet or informational document on environmental DNA and [some authority in the] government said, “Well, you can’t put that out” or if I wanted to put out something on climate change and the government said, “No, you can’t do that”. Well, [we were never specifically told not put out educational materials]. So we tried, and spent a lot of time trying to educate people about [environmental] genetic testing. And so then it became apparent, though it didn’t matter how much people understood they were. Still, there was still a fear of the technology. And so in some cases you didn’t need to censor it because the people who would be making the decisions about money we’re so already inherently biased, and were already afraid of the implications, or just didn’t know just didn’t understand the implications [of adopting the technology], even if we tell them “Look, these are good implications for science, the scientific method will let us improve our current systems”. It didn’t matter. They’re afraid. And so fear is a big driver of censorship, and fear is a human is part of humanity.

We always have a tendency to fear the unknown, and that is part of what being a scientist is: Knowing that the unknown is scary. Particle physics is potentially scary. Genomics is scary. All of these things have impacts that we don’t understand. We don’t know how CRISPr gene modification is going to affect humanity in the next 10 years. We hope that it’s used for good, but it could be used for bad. We don’t know how particle physics is going to affect us in the next 10 years. If we discover a new particle that could modify gravity, that would be amazing. It could be terrifying. We don’t know. We don’t know enough about subatomic physics to conjecture what will happen with the development of new technologies. So does that mean we shouldn’t do it? Should we not investigate neutrinos because we might develop anti-gravity technology? No. I and so that’s why being a scientist is being an adventurer because it’s an adventure. We don’t know where genomics is going to bring us, but we should explore it.

So while fears a big part of, human nature, so is exploration. And so when you have a government entity, the highest levels of the government, continually systematically censoring good science, that’s a problem. And really, this is hindering not just the United States but the entire planet. All of humanity is going to suffer because of the censorship, the anti-science climate in America, because we are the greatest, well, we’re the largest producer of scientific research still, to this day, out of all the countries that produce science. We have a responsibility to conduct the scientific method in a way that is open and fair. And so again, I’ll link back to how I’ve talked about moral consistency. It’s difficult for us to criticize China for its government, censoring its citizens, controlling its science, when we’re now doing the same thing here. So I don’t view the Trump administration as taking a different stance then the ruling administration in China in terms of science censorship. Now, sure, China’s more ingrained. They have the great firewall. They have control over Google in that country. But arguably the United States has a very be strong control of the entire Internet.

While the censorship isn’t [exactly] the same [between the US and China], It’s potentially as effective. So if you have a scientist in the United States who’s the top researcher in climate, and they are barred from speaking at a international scientific conference, then you have effectively stopped the transmission of that idea. And that’s the same thing that China is doing, stopping the transmission of ideas, or at least controlling the transmission. I’m sure that within China ideas are shared freely, and so the scientific research that is being done there is probably very advanced [regarding what’s] known within the country, and what’s published outside of the country is probably much more [limited/controlled]. These are different types of censorship, but, I imagine, that in some ways a scientist working for the government in China almost has more freedom. They’ve given up their ability to transmit ideas internationally, but China is very well aware of the fact that they have a climate problem. And so I imagine that the ruling class in China is very concerned about pollution and, I can imagine that a scientist working on pollution in China is potentially very highly regarded. Their work, if successful, might not be published broadly, at least not initially, because they’re very competitive and they want to use that within the country to promote the ruling class [first].

Whereas in America you see something almost worse, because now you’re telling a scientist you cannot tell anyone about your work. You cannot even tell your friends, and to me, that’s scary. If I can’t tell my friends about genetic testing, that is scary. If I can’t talk about but something that I believe is an empirical fact on climate, that’s scary. And so the regime that is in charge of the greatest scientific producer of scientific work in the history of the Earth is conducting a scary level of censorship. And I’m not trying to scare people by saying that, I’m using an emotive term, and what I mean is that we should be aware that that’s what’s going on. While I have never been barred from a scientific conference, I can imagine what it would feel like to be barred from a conference. I have been questioned for ideas that are well accepted in the scientific community. But again, I’ve never been personally barred from a conference. And so the conclusion here is censorship in the United States. It’s disturbing. I don’t know if I would use the word scary. I suppose I could, it depends on how you you feel about the year 2050. If you plan on being alive in the next 30 or so years, I would say that climate change could be scary. It should be. You should have a healthy, fearful respect for what could happen to the Earth in 30 years.

I think that think the presence of censorship is scary. So I think we should allow ourselves a little bit of fear and use that as motivation. And so maybe that’s the conclusion here is censorship should motivate us, and that’s what motivates me. So this project, aside from all the other things that I’ve talked about, this is a project about censorship as well, and so hopefully I will not be censored. Hopefully, my ideas are relevant, valid, and not censored, but maybe, hopefully my ideas are worth being censored because someone has to take a stance, and a lot of government employed scientists are not in that position. So that’s also kind of where I see is my position is, that since I’m not employed by the government, I can’t really be censored. It would be difficult for the government to censor me. In other words, I’m not going to lose my job over this podcast. This podcast is my job. So that’s my goal. To say what I think scientists can’t say in America. I want to be the voice of people that are being censored. So, if what I’m saying is something that’s worthy of being censored, that would make me proud.

[On that note,] I will sign off for the day. This is Bryan White with The Planetary News Radio, and I hope you enjoy this podcast. Thanks for listening.

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The Planetary News Radio – Episode 2: Linguistics and Genetics

Hello. Welcome to The Planetary News Radio, Episode 2 with Bryan White. So I’m outside today. I don’t know what this is going to sound like. So I apologize if there’s any strange car noises in the background. Hopefully there’s nice bird noises in the background instead. Let’s talk a little bit about projects and let’s talk about news. So the date is Sunday, May 26. I’m in Oregon,Corvallis and so I’m taking an opportunity here to be outside while there is currently no rain. So this year was an ENSO event, which I don’t remember if it was El Nino or La Nina. But either way, the rain patterns in this part of the world, which is the Pacific Northwest, have been altered. And so what we’re getting is a longer, warmer, wetter winter, [with] less snow but much more rainfall, and you’ll see that kind of translated across the United States in different ways.

So California, for the first time, [the drought] has ended officially for the first time in seven years, so they got a lot more water [than usual]. But anyways, the point is, here [in Oregon] we are at May 26 and just barely getting in a week here without rain. So I’m happy to be outside talking about science and projects. So again, I mentioned last time I’m developing software to support this science news project. And so one of the interesting things that I’m looking at is the similarity between genetics and linguistics, or really computational linguistics and computational genetics. So why are these things similar? And so this is just an interesting idea to talk about.

In human language, [sentences have] a grammar. A document is a collection of sentences, and sentences have small ideas in them. Paragraphs have, greater ideas. When you’re constructing a paragraph, you’re weaving together a more complex idea. But you could think of a paragraph as a unit and a sentence as a unit, and a word within a sentence as a unit. And then you have the document as a whole. And so you have this multilayered system of grammar [and language] that humans have developed and evolved and is a very rigid structural part of our brains. Language is not something that is abstract completely. It is bound by our physical constraints to process information. And so we have specific areas in the brain to think about language, and that is reflected in the way in our writing systems. So maybe another time we’ll talk more about the biology of language.

But let’s just take what I just said about human language and compare it to genetics. And so, in genetics, you have DNA, which is a sugar molecule that can bond together and form very strong molecular structures that can last for potentially 1,000,000 years. Actually, the half life of DNA is such that the longest living DNA molecule could not be [more than] 1.5 million years old. So DNA is a very stable molecule, and there’s a lot of molecular properties that go into that. The interesting corollary to that is that it would be impossible for us to find dinosaur DNA because dinosaurs went extinct 65,000,000 years ago, and the oldest DNA, under the best preservation conditions, say a woolly mammoth in Siberia or something like that that died in the ice and has been frozen for 1,000,000 years. It’s DNA would degrade after 1.5 million years. And so we’re stuck without dinosaurs, unfortunately, but we have these very stable molecules, so DNA is a molecule, [a base unit in the language of genetics].

Now there’s four letters in this language. So if we think of DNA as a language, there’s an A [adenine] and T [thymine] and G [guanine] and C [cytosine]. Now, I don’t have a map sitting in front of me of the genetic code. I’m just going from memory. So forgive my memory here of the [lack of] base pairing, but DNA is a double helix. You have these four letters paired with each other in such a way that every DNA molecule has a identical copy of the same information paired to itself. And so that’s why you you have this zipper effect, so if you unzip the DNA molecule on one side, you have version A of the information on the other side, you have version B of the information [on the other] sort of like an inverse [copy]. And so you always have the information duplicated in DNA. So there’s a redundancy. If you lose 1/2 the other, the other half can be repaired. And that’s how we get mutations.

When pieces of DNA are damaged and our cellular machinery goes in and repairs it, sometimes it makes mistakes. When DNA copies itself during gametogenesis, it also makes mistakes. And so you have mutations that can happen, say, in a skin cell due to ultraviolet radiation, or you have mutations that can happen when a [gamete] is developing during gametogenesis. So those mutations [(gametic)] [will be] carried on into the next generation, whereas, somatic mutations will cause things like cancer and or be removed. That’s the brief intro to the molecular side of DNA. Now, what about this hierarchy of information that I talked about with human language? So you have DNA as the base molecule. But how is DNA arranged? In most living organisms that we know of, DNA has evolved to be arranged in genetic units, which we call genes, but we could just also call them the “basic genetic unit”. A gene is really the sentence of genetics and a lot of times we in colloquial terminology will talk about [having a] a gene for red hair, a gene for [hair] color, a gene for height or, running ability, or skin color.

But really, a lot of times, there’s multiple genes involved, [particularly in the cases of height or skin color]. And not only that, even when there’s only one gene, one gene [potentially] has many pieces involved on. So genes themselves can have multiple subunits. There’s really [(at least)] two layers to a gene. There are the base units of genes that can be found next to each other [(introns/exons/open reading frames)]. So called these sequences of DNA that are consecutive and these consecutive sequences are [part of] a chromosome so a chromosome could be thought of as a chapter in a book. So this is a very complex document.

If we think of a chromosome is a chapter in a book and a gene as having both paragraphs and sentences, what’s the intermediate level? What’s the page in a chapter of the book? This is where genetics is slightly different from human language. The the information hierarchy from a gene up to the chromosome is a little fuzzy. [One way to think of it is that] genes have parts of them that are like sentences, they have parts of them that are like paragraphs, and they have parts of them that are like entire pages. And so some genes are very simple. Maybe some genes are only one paragraph, and they have 10 sentences. So in [terms of language, it might be] a complex idea. [In terms of genetics, it might be] a complex protein, but it’s not super complex. Now, some genes are extremely complex, and they could take up many pages, so it might take many paragraphs to describe this protein. And I could talk more about how that process [(transcription and translation)] happens at a molecular level. But that could be later.

[Essentially,] the genome is arranged in this similar hierarchy [(sentences, to paragraphs, to pages, to chapters, to documents)]. [For example], if [a genome were a book] and you were to turn to a [page in] chapter one, chromosome one, page one might start with a simple paragraph that describes eye color. But then it might very quickly go into an extremely a complex set of paragraphs that began to talk about how to build muscle proteins. And so building muscle proteins then becomes an epic poem, [but just for that section of the chapter/chromosome]. And so that’s how the genome goes.

So we have linear chromosomes, so humans have 23 pairs of linear chromosomes. So we have 23 chapters in our book. And so you go on to chapter two and now chapter two might begin to focus more on hair structure. And so you might start with the paragraph on hair structure, and then you might go into a paragraph on fingernails, and teeth and things like that [built from keratin]. And so you could spend 30 pages talking about how to build keratin proteins, what time to activate them, where to put them, and how to make them. And that’s kind of how the human genome can be thought of as a book.

And so you go on through chapters one through 21 on and then you have these other kind of appendices we could say, [which are] the sex chromosomes. So the X chromosome and the Y chromosome in humans are the sex determining chromosomes and so we have the 21 somatic chromosomes and the 2 sex determining chromosomes. And so that’s our book. 23 chapters duplicated, you get one set of chapters from your mom and one set from your dad. And they have a little mini guide on the side – the mitochondria, which is a short little piece of DNA, well, the mitochondria is an organelle, like the nucleus, that has a piece of DNA in it. The mitochondrial genome. And so that’s how I think of the similarity between language. Sorry, I’m just checking my time here.

Language and genetics. So when I am thinking about how to use these [two concepts] in the news, what I’m looking at are algorithms that have been developed to understand genetics and apply them to human [written] language. And so we spent a lot of time since the development of the Human Genome Project creating very sophisticated computer algorithms for comparing DNA sequences. And now what I want to do is go back in and use those same algorithms to compare human written text. So that’s that’s the beginning of the of the idea [for this news project] there.

Let’s talk briefly about the news. We have, sorry, had paused for a moment there. We have one recent interesting development in science news. There’s a debate right now in the United States in Congress and NASA and probably the [scientific/space exploration] community, whether we should go to Mars or the Moon first. And so this has largely been settled by the United States government supporting the moon [first], whereas private industry supporting Mars. Now, that doesn’t mean that private industry isn’t still doing both. It’s just the priority of the federal government of the United States is currently going to be the Moon. This would be to send humans to the moon again. Recently we have the first major step here, which is the award of a contract to a company called Maxar to develop a orbital platform for [creating] an [orbital] stop point for sending astronauts to the Moon and, presumably cosmonauts and any other international collaborators to the Moon as well. So we’re seen headway there.

One of the reasons I’m doing this show is that, [for example], the top news for science news today or this week is this Moon mission. And so my question is: Why is space science always the most popular science news in the Internet? And so when I say that, I mean in terms of Google news or websites that aggregate news and science news, usually space flight announcements are very popular. So you see them capturing the biggest audience. My question to myself to solve is: Why is this [space the most popular science in the news]? Why is space so captivating in terms of Internet popularity? And so I’m going to explore that, and my first intuition is that people like space. I like space. I like the fact that we’re developing a Moon mission. I don’t know how useful going to the Moon is aside for the fact that it forces us to develop technologies that I think we should have. So I like it. I support it. I just don’t know that it’s the most important thing happening right now in on the planet Earth. In terms of scientific development, that’s something to focus on, understanding science popularity. But I’ll leave the listeners there to think about that. Why is the Moon so popular? Why is space so popular? So that’s Bryan White, with The Planetary News Radio signing off. Have a good day and thanks for listening.

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