Category Archives: Transhuman News

Today, sea cows are only found in tropical waters. Credit: Colourbox

Giants of the Ice Age: International research team on molecular trail.

The giant sea cow from the Ice Age was discovered in 1741 by Georg Wilhelm Steller and later named after him. The 18th-century naturalist was interested not only in the enormous size of this animal species but also in its unusual, bark-like skin. He described it as a skin so thick that it is more like the bark of old oaks than the skin of an animal.

Such a bark-like structure of the epidermis is not found in related sirenians, which today live exclusively in tropical waters. In scientific circles, it was previously assumed that the bark-like epidermis was the result of parasite feeding, but also insulated heat and thus protected the sea cow well from the cold during the Ice Age and from injuries in the polar seas.

In the current study, the scientists led by Dr. Diana Le Duc and Professor Torsten Schneberg from Leipzig University, Professor Michael Hofreiter from the University of Potsdam, and Professor Beth Shapiro from the University of California, show that the paleogenomes of Stellers sea cow reveal functional changes. These changes were responsible for the bark-like skin and the adaptation to cold.

To find this out, an international research team from Germany and the US reconstructed the genome of this extinct species from fossil bone remains of a total of twelve different individuals. The most spectacular result of our investigations is that we have clarified why this giant of the sea had bark-like skin, said Diana Le Duc from the Institute of Human Genetics at Leipzig University Hospital. The scientists found inactivations of genes in the sea cow genome that are necessary for the normal structure of the outermost layer of the epidermis. These genes are also used in human skin.

Hereditary defects in these so-called lipoxygenase genes lead to what is known as ichthyosis in humans. This is characterized by a thickening and hardening of the top layer of skin with large scales, and is sometimes also known as fish scale disease, said Schneberg from the Rudolph Schnheimer Institute of Biochemistry. The results of our research thus also sharpen our view of this clinical picture, explained the biochemist, adding: Here may lie the key to new therapeutic approaches.

The scientists pinpointed the genetic defect by comparing the genome with that of the closest relative, the dugong. The researchers received support with their investigations from the Max Planck Institute for Evolutionary Anthropology in Leipzig, which contributed its bioinformatics expertise in the analysis of ancient DNA. As a result, they identified important evidence of genetic changes that may have contributed to adaptation to the cool North Pacific habitat.

This is an impressive example of how gene defects can not only cause disease, but also have advantages depending on the habitat, said Hofreiter from the University of Potsdam. Furthermore, the genome data revealed a dramatic reduction in population size. This began 500,000 years before the species was discovered and may have contributed to its extinction. Hofreiter summed it up as follows: With todays molecular genetic clarification, our study closes the circle of an exact observation by a German naturalist in the early 18th century.

Background

Georg Wilhelm Steller (17091746) studied medicine and the natural sciences in Leipzig, Jena and Halle and took part in the legendary expedition by Danish captain Vitus Bering to Alaska in 1741. Bering, after whom todays Bering Strait was named, and many of the ships crew died during this expedition. Steller survived and was the first and only explorer ever to see and scientifically describe one of these gigantic sea cows alive. The related sea cows (sirenians) that exist today manatees and dugongs are found exclusively in tropical waters. They grow to a maximum length of three meters, less than half the body length of their ice-age ancestors. Of the former population of Stellers sea cow of around 100,000 animals in the 18th century, only bones can be found today on the coasts of Bering Strait islands. Georg Steller first described the sea cow from the Ice Age in 1741. His landmark work was completed by his secretary on the basis of his manuscript and academic tributes. It was published in 1753, a few years after Stellers death. He died on his return journey from eastern Siberia to St Petersburg.

Reference: Genomic basis for skin phenotype and cold adaptation in the extinct Stellers sea cow by Diana Le Duc, Akhil Velluva, Molly Cassatt-Johnstone, Remi-Andre Olsen, Sina Baleka, Chen-Ching Lin, Johannes R. Lemke, John R. Southon, Alexander Burdin, Ming-Shan Wang, Sonja Grunewald, Wilfried Rosendahl, Ulrich Joger, Sereina Rutschmann, Thomas B. Hildebrandt, Guido Fritsch, James A. Estes, Janet Kelso, Love Daln, Michael Hofreiter, Beth Shapiro and Torsten Schneberg, 4 February 2022, Science Advances.DOI: 10.1126/sciadv.abl6496

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Giants of the Ice Age: Genome of Stellers Sea Cow Decoded - SciTechDaily

CAMBRIDGE, Mass., Feb. 14, 2022 /PRNewswire/ --InsideTracker, the leading truly personalized performance and nutrition system, today announced the addition of Dr. Ali Torkamani, who currently serves as director of genome informatics for Scripps Research Translational Institute's Department of Integrative Structural and Computational Biology, to its scientific advisory board.

Torkamani's research career has covered a broad range of areas centered on the use of genomic technologies to uncover the genetic causes and underlying mechanisms of disease and identify precision therapies. His major focus areas include human genome interpretation and genetic dissection of novel rare diseases, predictive genomic signatures of response to therapy and novel sequencing-based assays as biomarkers of disease.

In his role on the InsideTracker scientific advisory board, he will advise the company on new genetic approaches, developing advanced genetics scores and utilizing Mendelian randomization techniques on InsideTracker's growing database of biometric data from well people thought to be the largest in the world.

"Ali brings a wealth of expertise in genomics and bioinformatics to our scientific advisory board, which is vital to the research and development of our personalized health and wellness product," said Dr. Gil Blander, chief scientific officer and co-founder, InsideTracker. "As InsideTracker pursues our mission of creating the ultimate human optimization platform, we look forward to his guidance on further predicting which interventions will have maximum value on an individual level."

"The human body offers an incredibly complex network of genomic, physiological and biological data that can be applied not just to reverse disease, but to improve healthspan," said Torkamani. "InsideTracker unites this information, decodes it and offers everyday people unprecedented insight into their inner health, and I'm excited to apply my expertise in making personalized analysis and effective interventions more broadly available."

As a member of the InsideTracker scientific advisory board, Torkamani joins notable academics and subject-matter experts that include Dr. David Sinclair, Dr. David Katz, Dr. Jeffrey Blumberg, Dr. Lenny Guarante and Dr. Roger Fielding.

About InsideTrackerFounded in 2009 by top scientists from acclaimed universities in the fields of aging, genetics and biology, InsideTracker is a truly personalized nutrition and performance system. InsideTracker's mission is to help people add years to their lives and life to their years by optimizing their bodies from the inside out. By analyzing the body's data from blood, DNA and fitness trackers, InsideTracker gives a crystal clear picture of what's going on inside, along with a science-backed action plan for improving your health and becoming your best self. Read our peer-reviewed papers inScientific Reportsand Current Developments in Nutrition.

Follow InsideTracker on Instagram, Twitterand Facebook.

Media Contact:Heather Hawkins [emailprotected] (415) 598-8662

SOURCE InsideTracker

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InsideTracker Grows Genomics, Bioinformatics Expertise on Scientific Advisory Board with Appointment of Ali Torkamani, PhD - PRNewswire

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With its generally high-quality online content, Khan Academy exercises a remarkable influence on what students and teachers alike learn about science and other subjects. Thats why I have devoted four posts to analyzing the outdated junk science in their video on Evidence for Evolution. After going through supposed lines of evidence fromembryos,homology, andfossil horses, the video ends by looking at biochemical similarities between organisms, presented as a suite of arguments for common ancestry.

Khan claims that How the DNA gets replicated and translated and transcribed is very similar from one life-form to another. Yet a2020 papernoted that the Origin of DNA replication is an enigma because the replicative DNA polymerases (DNAPs) are not homologous among the three domains of life, Bacteria, Archaea, and Eukarya. These differences are so great that one paper asked Did DNA replication evolve twice independently? The paper proposes that the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal / eukaryotic lineages. And while were discussing fundamental biomolecular similarities, anotherpapercompared the genomes of 1,000 different prokaryotic organisms and found that of the 1,000 genomes available, not a single protein is conserved across all genomes.

It is of course true that all life uses DNA and proteins. The video argues that this universal similarity across life hints at a common ancestry. True, universal common ancestry is one possible explanation for such biochemical similarities but are there others that go unmentioned by Khan? As we saw withhomology in vertebrate limbs, its key to appreciate functional requirements. Last year Emily Reevesexplainedthat many properties of the amino acids used in life appear optimal for our biochemical needs. So, there are good functional reasons why all life should use these same molecules.

Moreover, because all life-forms use DNA (which contains nucleotides) and proteins (made of amino acids), we are able to gain nutrients we need amino acids and nucleotide bases from the plants, animals, and other organisms that we eat. The fact that all life uses the same basic building blocks is precisely what makes the food web possible! These universally shared similarities might indicate the design of the ecosystem, not common ancestry.

Once we appreciate that there are good functional reasons for life re-using the same basic molecules (e.g., DNA, proteins), common design becomes an alternative explanation. Intelligent agents frequently re-use the same types of parts in different designs to meet functional requirements. Think of how both cars and airplanes use wheels, or how different versions of Microsoft Windows re-use key computer codes. As Paul Nelson and Jonathan Wells observe in the bookDarwinism, Design, and Public Education:

An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently. If we suppose that an intelligent designer constructed organisms using a common set of polyfunctional genetic modules just as human designers, for instance, may employ the same transistor or capacitor in a car radio or a computer, devices that are not homologous as artifacts then we can explain why we find the same genes expressed in the development of what are very different organisms.

The Khan Academy video never considers this possibility, but again, common design the intentional re-use of a common blueprint or components is a viable explanation for the widespread functional similarities among the biomolecules found in different types of organisms.

The video then compares humans and chimps, saying that the latters behaviors and facial expressions are eerily human. I could say the same thing about the behavior of my family cat, Bonsai who is very intelligent and often seems able to read my mind and anticipate my behaviors. This doesnt necessarily mean were genetically related it means we were built with minds and mental outlooks that have important overlap. And the fact that our minds and behaviors have important overlap means that we can relate to one another quite well. In fact there are numerous examples of animals within species or across species being able to relate to one another. Just Google animal friend videos and make sure youve got an hour to kill! Heres my point: if the designer is a being that is into relationships, then designing species with mental and emotional similarities that foster inter- or intra-species deep emotional connections and friendships should not come as a surprise. No common ancestry needed.

But that overlap has significant limits. Just like chimpanzees, my cat doesnt use complex language, build complex tools, use fire, wear clothing, engage in abstract reasoning, do math, compose music, write poetry, ponder the mysteries of the universe, practice religion, or engage in any number of advanced cognitive or spiritual activities. (I would say that he doesnt engage in moral reasoning. However, I am pretty sure that he knows there are things I dont want him to do and he deliberately does those things, apparently for that very reason, like when he recently woke me up from a badly-needed nap by crying at my bedroom door. In any case, my cat definitely lacks an appreciation for morality as found in humans.) So, while some basic behaviors link all mammals, there are numerous higher behaviors found only in humans. Somehow these points get left out of the Khan Academy video.

The video then claims that humans and chimps are 98 percent genetically similar, saying their genes show just how close to human beings they actually are. That statistic is false: it overstates human-chimp genetic similarity, as I explained here last year; see, Human-Chimp Similarity: What Is It and What Does It Mean? At that post, I further explained that any given percent genetic similarity between two species does not necessarily imply an ancestral relationship since that similarity could be present for functional reasonsreflecting their common design.

The video closes by saying that the fact that we can measure how far things are away allows us to create a very accurate tree of life. This sounds like the claim I responded to from Richard Dawkins last year that genetics data allow us to create a perfect hierarchy a perfect family tree. Except when you dig into the technical literature you find out this isnt true at all. I also reviewed this evidence last year in response to Dawkins at Phylogenetic Conflict Is Common and the Hierarchy Is Far from Perfect. A very nice treatment of problems with the tree of life is given in Jonathan Wellss sequel to his bookIcons of Evolution,titledZombie Science: More Icons of Evolution. He summarizes there the many problems facing the tree-of-life hypothesis, including:

Perhaps Wellss most relevant point in rebuttal to Khan Academy comes when the video claims that we can easily determine percent genetic similarity between organisms. And then out pops a tree. Heres what Wells writes inZombie Science:

Since the rise of molecular biology in the mid-twentieth century, biologists have increasingly used comparisons of sequences in DNA, RNA and protein to construct phylogenetic trees. For example, a particular DNA sequence might be present in different species, though with minor variations. Comparing the sequence differences in species A, B, and C could lead to an inference that species A is more closely related (that is, more similar) to species B than it is to species C. The similarity between two sequences (often called homology) can be expressed as a percentage, representing how many subunits at corresponding positions are identical between them.

Similarity may be assumed to imply genealogy, but this is only an assumption. Any inference to genealogy based on sequence similarity is hypothetical. And since molecular sequences (with rare exceptions) are available only from living organisms, any inference about the evolutionary past of those organisms-including their ancestors-is even more hypothetical.

This is exactly right. As I haveexplained in the past, the basic logic behind building molecular trees is relatively simple. First, investigators choose a gene, or a suite of genes, found across multiple organisms. Next, those genes are analyzed to determine their nucleotide or amino acid sequences, so the gene sequences of various organisms can then be compared. Finally, an evolutionary tree is constructed based upon the principle that the more similar the nucleotide sequence, the more closely related the species.But the whole process is based upon theassumptionthat genetic similarities between different species necessarily result from common ancestry.But theres no need for that assumption. If the similarities being compared are functional similarities which is always the case when you are comparing gene sequences between organisms then those functional similarities could reflect common design rather than common descent.

The Khan Academy video opens by quoting Theodosius Dobzhansky who famously stated, Nothing in biology makes sense except in the light of evolution. Khan further says that the modern theory of evolution is about as strong as theories get. But when, to make the case for the theory, you have to resort to all these old, long-refuted icons of evolution, how strong is the evidence really? Its worth recalling Jonathan Wellss remarks at the end ofIcons of Evolution:

[T]he claim that nothing in biology makes sense except in the light of evolution is demonstrably false. The icons of evolution are a logical consequence of the dogma that nothing in biology makes sense except in the light of evolution. All the misleading claims we have examined in this book follow from the sort of thinking represented by Dobzhanskys profoundly anti-scientific starting-point. [S]cience at its best pursues the truth. Dobzhansky was dead wrong, and so are those who continue to chant his antiscientific mantra. To a true scientist, nothing in biology makes sense except in the light of evidence.

Wells is correct that when you start with Dobzhanskys dogmatic statement, you get bad science. You also get bad science education. Its very unfortunate that Khan Academy which is so good on so many other subjects is misinforming students about the evidence, or lack of it, for evolution.

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Khan Academy Video Misleads on Common Ancestry - Discovery Institute

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It has long been believed that dogs age seven times faster than humans, but a new study has busted the myth and wants to shed light on how our canine friends actually age.

The old adage would mean that a one-year-old dog is seven in human years. However, different breeds age at different rates, with large breeds ageing ten times quicker than humans and some small dogs can be half of that.

A major study called The Dog Ageing Project aims to examine the genomes of 10,000 dogs to see why super centenarian dogs that can live till the age of 20 survive for so long.

The researchers want to identify specific biomarkers of canine ageing and translate to apply their findings to human ageing.

Professor Joshua Akey, at Princeton University, said: This is a very large, ambitious, wildly interdisciplinary project that has the potential to be a powerful resource for the broader scientific community.

Personally, I find this project exciting because I think it will improve dog, and ultimately, human health.

Prof Akey said that that the study , believed to be the first of its kind, will produce one of the largest genetics data sets ever produced for dogs, which will help scientists understand how genetics impact ageing.

The research will also help answer more fundamental questions about the evolutionary history and domestication of dogs, he added.

The super-centenarian part of the study will compare the DNA of dogs that live for an exceptionally long time to those that live to the average age for their breed.

Dogs are one of the most genetically diverse species in the world and have been bred into a huge array of difference sizes, colours, and body types.

According to the RSPCA, the average lifespan of certain popular dog breeds can vary from 5.5 years for a Dogue de Bordeaux (also known as a French Mastiff) to 14.2 years for a miniature poodle.

The researchers from The Dog Ageing Project anticipate their findings will apply to human ageing because dogs experience almost the same functional decline and diseases of ageing that humans do.

Story continues

Veterinary care also has many parallels with human healthcare, and dogs share much of the same lived environment as humans, which is a major determinant of ageing and one that cannot be recreated in any lab setting.

Professor Daniel Promislow, from the University of Washington and the principal investigator of the study, said: Given that dogs share the human environment and have a sophisticated health care system but are much shorter-lived than people, they offer a unique opportunity to identify the genetic, environmental and lifestyle factors associated with healthy lifespan.

The project has been outlined in the journal Nature.

Additional reporting by SWNS

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Researchers bust the seven-year dog myth - Yahoo! Voices

Some people don't get COVID despite being exposed to the virus a mystery researchers are trying to unravel.

Why it matters: Understanding the small cohort of "never COVID" people could lead to new vaccine targets or other protections as the world enters the third year of the pandemic.

Driving the news: Using a highly debated method called a human challenge study, a British trial deliberately exposed people who were unvaccinated and had no evidence of prior infection by placing a droplet of SARS-CoV-2 in their nose. They found 16 out of 34 participants did not get infected, according to the pre-print paper posted recently.

The latest: Researchers are now trying to zero in on that question.

1. Cross-immunity from the four endemic human coronaviruses is one hypothesis. Those other coronaviruses cause many of the colds people catch and could prime B-cell and T-cell response to this new coronavirus in some people.

2. Multiple genetic variations may make someone's immune system more or less susceptible to the virus.

3. Mucosal immunity may play an underrecognized role in mounting a defense.

4. Where the virus settled on the human body, how large the particle was, the amount and length of exposure, how good the ventilation was and other environmental circumstances may also play a role, Openshaw says.

The bottom line: Vaccination and boosters, wearing masks, washing hands and good ventilation remain our most important tools in preventing infection or mitigating symptoms, Brooks says.

Editor's note: This story originally published on Feb. 10.

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Unlocking the mystery of the "never COVID" cohort - Axios