Category Archives: Transhuman News

Recently, geologist Casey Luskin interviewed Eric Cassell, author of Animal Algorithms: Evolution and the Mysterious Origin of Ingenious Instincts (2021) on one of the central mysteries of biology: How do animals know things that they cant have figured out on their own? Heres the first part, with transcript and notes. Below is the second part, which looks at some how questions.

Eric Cassell is an expert in navigation systems, including GPS whose experience includes more than four decades of experience in systems engineering related to aircraft, navigation and safety. He has long had an interest in animal navigation. His model for animal navigation is the natural algorithm: The animals brain is programmed to enable navigation.

Heres Part II of our three-part series on Animal Algorithms Webinar: One of Natures Biggest Mysteries, (January 20, 2022), where a partial transcript and notes follow:

Casey Luskin: We already talked about this a little bit, the idea of path integration, where animals keep track of their compass heading and distance traveled so they can fly directly home but not necessarily along the path that they took. And you say that they can do this without necessarily following landmarks. You talk about honeybees and their ability to navigate using the suns angle. So they can learn how to navigate using the suns angle at different times of day to find their way home, regardless of what time it is. Or they can use polarized light by studying different regions of the sky to determine the position of the sun. (21:23)

This requires doing trigonometry, spherical geometry, and other complex math. They [insects] have a brain with a million neurons and I have supposedly a hundred billion neurons in my brain. And I dont think I can do those kinds of calculations in my brain. I find this all incredible.

There are cases that seem to require inherited know-how. How does a sea turtle innately know how to swim to its feeding area hundreds of miles through murky water and return to its exact nesting beach 35 years later? How do chicks of the Pacific golden plover find the Hawaiian Islands, mere specks in the trackless ocean, never having been there before? How do monarch butterflies in Canada get to the same trees in Mexico their great-grandparents wintered on? Some of these natural miracles cannot be dismissed easily with other labels like a map sense or other terms of art.

Casey Luskin: So the fact that these kinds of features evolved really just makes me wonder, how could they arise by an unguided, stepwise Darwinian process. Id love to see a stepwise evolutionary explanation for this, if it exists. And Im wondering, are you aware of attempts to explain behaviors like this through a standard typical Darwinian model? (21:58)

Eric Cassell: The short answer is no. I have not come across any name in the literature about those kinds of behaviors and how they could have evolved. I think its such a daunting task to try to explain how something is sophisticated as an algorithm, particularly a mathematical type of algorithm, could have evolved in the first place.

It has to be in the genome somehow. And then that information thats in the genome has to be encoded in a neural network when the brain develops, and then it all has to be run, as the animal is performing the behavior. So theres a lot of unanswered questions about how all that takes place. (22:42)

Casey Luskin: Figure 3.3 [in the book] it talks about the different components necessary for animal navigation and migration behavior to work. Youve got to have navigation sensor physiology, a navigation algorithm. Youve got to have destination location information, migration decision algorithm, and migratory physiology to implement all of this. And if youre missing one of those components, one of those elements, then it doesnt work. Those five separate groups of genes, and as you put it, other genetic information in the genome, all have to be there in order for these navigation and migration algorithms to work. (23:36)

So lets talk about another example you give, the Monarch butterfly, which in North America requires three generations for the migration to complete itself. And so that has to be, genetically programmed because, obviously, the butterflies that are maybe in the middle of that migration pathway how could they have learned where theyre going? They werent even alive when the migration started. So how did they know where to go? Theyve never been to the destination. to me that obviously implies Im- Im sure you- you argue this in the book, very persuasively that the information had to be pre-loaded into those organisms, when theyre born, you call it pre-loaded software. So where do they get the pre-loaded software that tells them where to go and how does this evolve by an unguided Darwinian process? (24:22)

Eric Cassell: Again, thats a really difficult question that nobody has an answer for. Theres, there are some theories out there about how, in some cases, animals might have developed a behavior, or basically learned the behavior, and then somehow that behavior gets transferred into the genome. How that happens, thats a good question. Its a theory that Ive seen, people propose, but I dont understand how it could even work, in reality because you have a behavior that somehow then gets transmitted into the gametes and the genomes. But its a serious proposal that a number of people, believe in. (25:09)

Casey Luskin: It sounds very Lamarckian So maybe there is some influence of, you know, inheritance of acquired characteristics going on here, but as you said, its yet to be demonstrated. So these sound very mysterious at the present time. (26:05)

Note: Jean-Baptiste Lamarck (17441829) was a French evolutionary thinker who held that characteristics could be acquired during the lifetime of a life form and passed on to offspring. Although at one time widely dismissed, this mechanism of evolution is becoming more widely accepted in the form of epigenetics.

Casey Luskin: Maybe 100 years ago or 2000 years ago, humans navigated much differently than they do today. So how has technology changed the way we navigate? (26:28)

Eric Cassell: Fundamentally animals are better navigators than humans. Were able to use that information and landmarks, but other than that, humans are very poor natural navigators, whereas all of these animals are actually expert navigators. Theyre all designed to perform, accurate navigation, to suit their own purposes. (27:09)

Its only been in within the last couple of hundred years that weve even developed any, any useful technology for navigation. Were basically just trying to catch up to what animals have been doing for a long time. (27:51)

Casey Luskin: I did not appreciate how important the sun is for human navigation till I moved to the Southern hemisphere during my PhD. Obviously if youre living in the Northern hemisphere, which is where I grew up, the sun is always in the south. but when I moved to South Africa, the sun is always in the north. I lived just north of the university and there were literally a couple times where I would get in my car to drive home from school and start driving in the opposite direction, south, because in my mind I was orientating myself with the sun. I knew I was supposed to go north, and for me going north meant you drive away from the sun. I didnt even think about it. I did not even appreciate how much, intuitively as a human being, I used the sun to navigate until the sun was in the wrong place and I was going in the wrong direction. (28:28)

You also talk about spider webs in your book and, theyre probably one of the most famous examples of an amazing animal behavior. How do spiders produce silk and what does the theory say about how spiders know instinctively how to produce a web. Are there evolutionary explanations for the origin of spiderwebs? If so, what do, what do you think of them? (29:19)

Eric Cassell: The question about silk, its a very complex material that involves a lot of, proteins and its a very complex process to produce the material. Humans have been trying to duplicate [spider] silk artificially for a long time. Basically weve never been able to do it because its so complex. We have some materials that sort of approximate the composition of silk, but never really duplicate it. So thats one thing there. (30:00)

And the process that the spiders use to generate it is a complex process, also. There has been a lot of research into web designs and, how they possibly could have evolved over time. But there are issues there as well because, for example, there are species of spiders that are completely unrelated, but yet produce the same exact web design. So how do you explain that? (30:42)

The typical Darwinian explanation that its convergent evolution, selection pressure, or some other vague term but really, the origin of the webs and then how spiders are able to manipulate them is really a complex behavior thats pretty sophisticated. (31:16)

Casey Luskin: I note that you provide a really striking quote in your book from Jerry Fodor and Massimo Piattelli-Palmarini from their book What Darwin Got Wrong (2010). Theyre talking about animal behavior and they say that, Such complex sequential, rigidly pre-programmed behavior could have gone wrong in many ways, at any one of its steps And they say spiderwebs, bee foraging, as we saw above and many more, cannot be accounted for by means of optimizing physical, chemical, or geometric factors. (32:26)

They go on to say that, They can hardly be accounted for by gradual adaptation either. Its fair to acknowledge that, although we bet some naturalistic explanation will one day be found, we have no such explanation at present. If we insist that natural selection is the only way to try, we will never have one. (32:59)

These are two authors who describe themselves in their book as outright, card carrying, signed up, dyed in the wool, no-holds-barred atheists. And yet theyre saying that there is no Darwinian natural selection-based explanation and theyre really doubtful there ever will be for the origin of these complex behaviors. You also talk about a textbook that says, We still know little about the rate and type of evolutionary change, experienced by behavioral traits. (33:20)

Eric Cassell: In my research in the literature, for the most part, there is only one, theres one particular type of behavior [for which] at least some theories have been proposed and that concerns insect social behavior. The basic theory is that there are, insects ants, et cetera that exhibit solitary behaviors. Theres, in other words, theres a difference between those that are social and those that are solitary. (34:14)

The theory is that when an animal transitions from a solitary lifestyle to a social lifestyle, its just a matter of adding a few algorithms, if you will, a few steps to integrating that information into a social environment. Well, at first that sounds somewhat plausible, but the evidence really is not there that thats the case, for two reasons. One is that the social behaviors that these animals exhibit far exceed the behaviors that solitary animals do. Thats one thing. (34:47)

The other is that insect social behavior is one area that has seen quite a bit of research into the genomes, And whats been found is that the genomes of the social insects have undergone significant change, when they transition from solitary to social. So theres literally hundreds of thousands of genetic changes that take place in these animals, when theyre social. So how that could have happened through a step by step linear Darwinian fashion is not very plausible. (35:28)

Casey Luskin: So, okay. Well, this will, I think, lead into my final question during our conversational part of the interview. It sounds like a lot of information goes into the origin of these animal behaviors. So how does information important for the origin of these animal behaviors and what is your view on what this implies for intelligent design? (36:18)

Eric Cassell: These behaviors, for the most part, are controlled by algorithms in one form or another. And to have an algorithm, you have to have the information. Where does information come from that even defines the algorithm in the first place? So thats the part thats challenging. A lot of the research thats been done by the ID community tends to indicate that you really cant generate information through a- random process, which is, you know, mutations and natural selection. (36:44)

Its just incapable of doing that. If you look at the work of design theorist William Dembski and some others, regarding these No Free Lunch theorems, thats basically what they say. Its difficult to explain the origin of this kind of information through a purely random process. I think thats one of the biggest hurdles to overcome in trying to explain, the origin of these kinds of behaviors. (37:24)

Next: Challenges from the audience, as well as challenges from nature

Heres the earlier portion of the episode, with transcript and notes.

Neuroscience mystery: How do tiny brains enable complex behavior? Eric Cassell notes that insects with brains of only a million neurons exhibit principles found only in the most advanced manmade navigation systems. How? Cassell argues in his recent book that an algorithm model is best suited to understanding the insect mind and that of many animals.

You may also wish to read: A navigator asks animals: How do you find your way? The results are amazing. Many life forms do math they know nothing about. The question Eric Cassell: asks is, how, exactly, is so much information packed into simple brain with so few neurons?

Go here to read the rest:
Can Animal Behavior Simply Be Transferred Into the Genome? - Walter Bradley Center for Natural and Artificial Intelligence

31 January 2022

The UK government has investigated possible future applications of genomics beyond healthcare and the potential risks involved in its growing use, published in an open report.

The technology to sequence the human genome has developed rapidly in recent years from costing 4 billion twenty years ago to only around 800 today. Genome sequencing is already widely used in the UK to screen for genetic diseases. But in their Genomics Beyond Health report, the Government Office for Science highlights how growing access to genomics could continue its use beyond health, from DNA based predictions of children's behavioural traits and educational achievement to an athlete's inherent capabilities. The report also indicates that while there are many benefits to this information, predictions based on genomics are open to misinterpretation and they raise ethical questions surrounding discrimination based on DNA.

'Now is the time to consider what might be possible, and what actions government and the public could take to ensure the widespread application of genomics can occur in a way that protects and benefits us all', said Sir Patrick Vallance, UK Government Chief Scientific Advisor.

In their 198-page report, the authors outline how genomics can help determine certain disease risks, identify suspects at crime-scenes and develop crops resistant to pests and harsh climates.

But they point to several ethical and practical issues where genomics is heading next. Genome based predictions of how well a child will perform at school could help tailor education to individual needs. But the authors note that other factors such as parental education currently predict academic performance much more accurately, yet there are no regulations in the UK to limit genomic testing marketed at parents.

Another possibility is the use of genomics in hiring to select workers with optimal health and the desired personality traits. The authors argue this would be inherently discriminatory and lack scientific grounding by disregarding environmental influence.

The report suggests that as genomics sequencing technologies become increasingly advances and increase in use more consideration should be given to policy and regulation. A structured framework governing how genomic information is collected and used could protect by law the privacy, anonymity, and security of the genome sequences of UK citizens.

'The use of genomic data outside the healthcare setting needs careful scrutiny, and safeguards are needed to protect the public from any potential misuse of their data' said Sarah Norcross, director of the Progress Educational Trust. 'This report must be acted on expeditiously, as genomics is such a fast-moving area.'

The report was produced together with thirty experts in science, technology and policy to provide a 'basis for discussion within government departments', helping engage with future issues before they arise.

More:
Genomics' role beyond healthcare and medical research - BioNews

Seed companies are promising sweeter strawberries, drought-resistant cabbage and healthier tomatoes in less time and at lower cost thanks to genome editing technology. Theres a catch though: In some cases, rules are so lax that we may never know our food was genome edited.

Jessica covers the good, the bad, and the ugly when it comes to big global companies and their impact in Switzerland and abroad. Shes always looking for a Swiss connection with her native San Francisco and will happily discuss why her hometown has produced some of the greatest innovations but cant seem to solve its housing crisis.

More from this author| English Department

On the northern coast of the Netherlands, around 30 companies are working in fields and greenhouses to develop the next greatest thing in vegetables. The region calls itself Seed Valley. It is the heartland of European vegetable breeding the way Silicon Valley is the center of IT and software innovation. During a Syngenta media field trip last autumn, the rows of vegetables reminded me of a Disneyland park before all the guests arrive pristine, bright and trimmed to perfection almost make-believe.

All the vegetables here are bred using conventional methods, which Syngenta explains, are very scientific and can take years, sometimes decades, to bear fruit (literally). There is no talk of genome editing or CRISPR in these fields because it isnt allowed in Europe. But several thousand kilometres in either direction to the US and China seed companies like Syngenta are starting to show off their latest CRISPR creations.

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Thats the fragmented regulatory world we live in right now, but it is quickly changing. More governments are opening their doors to genome editing with tools like CRISPR. Covid vaccine nationalism left its mark countries are gripped by the F.O.B.L.B the Fear Of Being Left Behind as other countries pourmoney into genome edited seed research. Everyone wants an invention they can call their own.

Governments arent just allowing genome editing in food, they arent regulating it at all in some cases. This means no strict safety checks, no labelling, and no transparency that our food was genome edited. Some seed companies argue genome editing is simply speeding up something that could happen in nature so why should it be treated any differently. Critics argue otherwise.

What do you think? Ive created a debateExternal link to engage with readers on the topic. Curious to hear your thoughts. jessica.davis@swissinfo.ch.

Nestl will pay African cocoa farmers to keep children in schools. Some 10,000 farmers in Ivory Coast stand to gain extra cash if they follow a set of guidelines set down by Nestl including refraining from child labour by enrolling all children in school and increasing the productivity of their cocoa farms with best practice techniques. The company plans to expand the programme to 160,000 cocoa farmersby 2030 and introduce a new range of products under the scheme. This may the greatest hope yet of a child labour-free chocolate bar from a big multinational.

Switzerland is keeping its options open to compensate for losses from the minimum corporate tax deal. After relying for so long on low tax rates as its calling card with big companies, the country is trying to figure out what else it can do to stay attractive in the face of the global minimum tax rate. Should the country loosen immigration restrictions? Should it have less regulation? Or more regulation on dirty industries? Should the government fund company researchExternal link and promising start-ups? All options are on the table. One idea being floated is to lower the tax burden on wealthy executives to keep them, and their companies, in the country. This idea is unlikely to go over well with the public when the cries to raise taxes from billionaires, even from a few billionaires themselvesExternal link, are getting louder.

Big food has a big problem with nutrition. According to an investigation by Swiss public television, RTS, the food industry lobby is pushing back on regulation aimed at curbing skyrocketing obesity ratesExternal link in some countries. RTS uncovered an email exchange from Swiss food giant Nestl calling on the Swiss governments support to reject a new law on nutrition labelling in Mexico. The company told RTS it supported the purpose of the law but believed it had no scientific basis and would restrict consumer choice.

Mergers and acquisitions boomed last year. Rock bottom interest rates and excess cash sloshing around Swiss companies saw a three-fold increaseExternal link in the value of mergers and acquisitions (M&A), rising to CHF170 billion ($186 billion) last year. The pharmaceutical and life science sectors saw M&A deal activity surge from CHF6 billion in 2020 to CHF56 billion last year, comprising four of the ten largest corporate deals. More biotech deals are expected this year with many wondering how Novartis is planning to spend the CHF19 billion from the sale of the Roche stake.In an interview in Finanz & Wirtschaft, Novartis CEO Vas Narasimhan indicated that there may be smaller acquisitionsExternal link on the way.

Switzerland stumbles in the latest corruption ranking. Transparency International ranked Switzerland 7th, down four spots from last year, in its annual Corruption Perceptions Index. A series of scandals last year didnt help. The Swiss public sector is especially vulnerable to nepotism, says the NGO. Its a small country, we know each other, we went to school together often this implies conflicts of interest. But there are bigger problems not captured by the Index, says the NGOs director, Martin Hilti. Specifically, money laundering and the entire enabling industry including lawyers, notaries and real estate agents.

Thanks for reading.

Follow this link:
The seed revolution is coming - SWI swissinfo.ch - swissinfo.ch

Our article (1) describing a widespread loss of uncoupling protein 1 (UCP1) in cetaceans, sirenians (the manatee), and one pinniped (the Antarctic fur seal, Arctocephalus gazella) as a convergent mechanism to minimize heat loss has raised questions from experts in the field of mammalian energy metabolism (2).

Briefly, Gaudry etal. (2) argue, after examining raw high-throughput sequencing data from National Center for Biotechnology Information Sequence Read Archive, that 1) while UCP1 inactivation is likely associated with a higher reliance on insulation in fully aquatic mammals (cetaceans and sirenians), this is likely not the case for pinnipeds; 2) our findings reflect a misassembly of the A. gazella genome (generated by ref. 3); and 3) when UCP1 is lost in pinnipeds, this event is possibly associated with a greater body size (case in point, the northern and southern elephant seals).

Apparent UCP1 loss is observed in A. gazella in a genome assembly derived from PacBio sequencing data (v1.2 and subsequent versions) (3), while an assembly derived from Illumina sequencing (v1.1) (4) indicates that the gene is intact (Fig. 1). We are very grateful to Gaudry etal. (2) for pointing out this error. This reminds us that it is not only important to assess the quality of published genomes prior to data analysis but also necessary to cross-validate using data from multiple sources before conclusions are made.

Differences in exon 1 and exon 6 sequences of UCP1 in Antarctic fur seal PacBio and Illumina genome assemblies. Gray blocks indicate regions unique to the Antarctic fur seal PacBio assembly. For comparison, the sequences of northern fur seal, walrus, and California sea lion are shown.

Gaudry etal. (2) describe pseudogenization of UCP1 in the northern and southern elephant seals and speculate that this is linked with the large body size of the two species. While this extrapolation is fascinating, we argue that this conclusion is not necessarily valid. Firstly, the frameshift in exon 1 is located in the ostensibly 5 untranslated region; another start codon appears about 10 amino acids later (Fig. 2A). Considering that we did not detect a signal of relaxed selection in these species (Fig. 2B), we cannot fully confirm, without transcriptomic data, that this gene has been pseudogenized. Secondly, even if this gene has been lost in elephant seals, a link between loss of UCP1 and body size, in our opinion, is not straightforward. UCP1 loss could reflect an adaptive thermoregulatory mechanism coincidentally associated with a larger body size. However, we agree with Gaudry etal., in general, that the thermoregulatory strategy is likely to be different between fully aquatic and semiaquatic marine mammals.

(A) Alignment of exon 1 and exon 3 of the UCP1 of southern elephant seal and northern elephant seal. The gray blocks and the red arrows show the position of the start codon, and the yellow blocks indicate amino acids missing in the elephant seals. (B) Summary of relaxed selection test of northern and southern elephant seal UCP1. A red star indicates the foreground branch.

The project was partially supported by the National Natural Science Foundation of China (Grants 41422604 and 41306169), One Belt and One Road Science and Technology Cooperation Special Program of the International Partnership Program of the Chinese Academy of Sciences (Grant 183446KYSB20200016), the Key Deployment Project of Center for Ocean Mega-Science of the Chinese Academy of Sciences (Grant COMS2020Q15), and the Research Funds for Interdisciplinary Subject, Northwestern Polytechnical University (Grant 19SH030408).

Author contributions: K.W. and S.L. designed research; Y.Y., P.Z., H.K., G.F., K.W., and S.L. performed research; Y.Y., I.S., K.W., and S.L. contributed new reagents/analytic tools; Y.Y. and Y.Z. analyzed data; and Y.Y., I.S., A.R.H., D.W., K.W., and S.L. wrote the paper.

The authors declare no competing interest.

Link:
Reply to Gaudry et al.: Cross-validation is necessary for the identification of pseudogenes - pnas.org

By Bio-IT World Staff

January 31, 2022 | The American Society of Human Genetics (ASHG) today announced the launch of the ASHG Genetics and Genomics Impact Partnerships program. Illumina, a leader in next-generation genomic sequencing technologies, and Invitae, a leading medical genetics company, have joined as founding partners.

The opportunity to apply human genetics and genomics research to build a more equitable world is urgent and ASHG is grateful for Illuminas and Invitaes support to help drive progress forward. said ASHG President Charles Rotimi, PhD in a press release. The commitment were sharing will help the researchers of today and tomorrow to make new discoveries that serve populations worldwide, apply genetics knowledge in more just and equitable ways, and inspire and support others to join the field. We thank these organizations for their tireless dedication to equity as we work toward a better future together.

As the worlds largest professional organization for human genetics and genomics, ASHG believes itself to be uniquely positioned to advance diversity, equity, and inclusion (DEI) in human genetics and genomics research on a global scale. The Society is working strategically and programmatically to expand participation and strengthen careers of researchers from diverse backgrounds, sustain emphasis on increasing diversity and inclusion in research cohorts, and develop a knowledge network and professional education for researchers.

Knowing that collective effort is required to ensure all people benefit from genetics and genomics research, ASHG Impact Partners include organizations likewise dedicated to advancing DEI in human genetics and genomics. Through their financial contributions, Impact Partners support the ASHG Fund for Equity in Genetics and Genomics Research, which helps the Society to design innovative programs with demonstrable impacts on DEI; enhance capacity to expand DEI efforts in future years; and sustain DEI programs and initiatives.

Joining as founding Impact Partners, Illumina and Invitae recognize the critical importance of advancing DEI in the field of human genetics and genomics.

At Illumina, we recognize that our efforts to improve human health can be magnified if all people and places have access to genomic technology, said Illuminas Global Head of Diversity and Inclusion Lisa Toppin, EdD in the same statement. We know that there are still significant gaps in access to genomic technology, personalized medicine, and even representative data to understand genomes in the context of global diversity. Through this exciting new partnership with ASHG, we will continue to close those gaps to increase access, improve the equity of representation, and expand the transformative benefits of genomics for all.

We are proud to support this initiative which aligns with our mission to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people, added Invitaes Chief Medical Officer Robert Nussbaum, MD. The era of Genome Management is now here, and equity in genomics is paramount in order to transform the way medicine is practiced.

As part of this historic partnership, ASHG and Impact Partners will meet periodically to share knowledge and experiences and learn about effective DEI strategies that institutions and individual researchers can implement to advance more inclusive and equitable workforces and research study populations.

We remain focused on fostering enduring change in the human genetics and genomic field and our newest partnership with Illumina and Invitae will further that effort, Rotimi said. Recruiting, retaining and engaging a robustly diverse and inclusive human genetics community is essential to identifying and addressing the profound questions in human genetics and advancing health equity, and everyone has a role to play in this critical mission.

Link:
Illumina, Invitae Founding Members of ASHG's Genetics and Genomics Impact Partnerships Program - Bio-IT World

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