Tag: evolution

Horizontal gene transfer

A mechanism for evolution where big chunks of DNA migrate between different species via bacteria. This results in faster and more sudden evolutionary branching than what you get with the more familiar mechanisms of sexual selection or random single-point

a massive network of recent gene exchange connecting bacteria from around the world: 10K unique genes flowing via HGT among 2235 bacterial genomes.

2008-10-05: The transfer can lead to recursive genomes

Scientists have discovered a copy of the entire genome of a bacterial parasite residing inside the genome of its host species. Lateral gene transfer may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, with dramatic implications for evolution. This may allow species to acquire new genes and functions extremely quickly.

2013-11-12: The transfer can also be time-shifted

You can compare it to a bunch of bacteria which poke around a trash pile looking for fragments they can use. Occasionally they hit some ‘second-hand gold,’ which they can use right away. At other times they run the risk of cutting themselves up. There is potential risk when multi-resistant bacteria exchange small fragments of ‘dangerous’ DNA, e.g., at hospitals, in biological waste and in wastewater.

2021-06-09: It might even happen in animals, perhaps via sperm.

The barriers to horizontal transfer in eukaryotes looked insurmountable until the herring genome was published. The herring genome holds many copies of transposons, mobile chunks of DNA that can copy and paste themselves in a genome, but they are absent from other fish with 1 exception. 3 of them flank the rainbow smelt’s AFP gene, in the same order seen around the herring AFP gene. These sequences are “definitive proof” that a small chunk of a herring chromosome made its way into a smelt’s. 94% of the transfers involved ray-finned fishes; less than 3% involved birds or mammals. The explanation could hinge on herring’s famously exuberant spawning efforts. The vast majority of sperm fail to find eggs, degrade, and release their DNA. The DNA could stick to the gametes from other species spawning in the same area, and then get dragged into an egg cell during fertilization.


2021-10-21: It also happens in the human microbiome, which is less surprising since that’s just bacteria.

when humans started to colonize the island of japan 40 ka ago, they did not have the genes for digesting seaweed. Bacteria in the japanese gut borrowed the necessary genes from marine bacteria via horizontal gene transfer, and since the adaption proved evolutionarily beneficial, it was preserved. of course, anti-GMO nuts fear this horizontal gene transfer the most (if they are scientifically literate enough to understand the concept, and not just spout confused concepts like “natural” vs “artificial”). it should be quite obvious from this awesome example that mammals have had to cope with horizontal gene transfer throughout their history. GMO offers nothing new we haven’t encountered before.

2022-10-28: Transfer via viruses or parasites could explain how HGT happens between Eukaryotes.

The involvement of viruses could also help to solve another puzzle about horizontal transfers in eukaryotes. For the transfers to occur, the traveling genes need to clear an entire series of hurdles. First they must get from the donor species to the new host species. Then they must get into the nucleus and ensconce themselves in the host genome. But getting into the genome of just any cell won’t do: In multicellular creatures like frogs and herrings, a gene won’t be passed down to the animal’s offspring unless it can sneak into a germline cell — a sperm or an egg.

Is there something about the environment of Madagascar that makes it a hot spot for gene transfers? The abundance of parasites on the island might also be a contributing factor. Leeches may bring blood containing the snake’s jumping gene into the frogs, or perhaps the jumping gene is already in the leech’s own genome from previous contacts with snakes. Then maybe an unidentified virus does the rest.

2023-01-19: Tycheposons

The findings describe a new class of genetic agents involved in horizontal gene transfer, in which genetic information is passed directly between organisms — whether of the same or different species — through means other than lineal descent. The researchers have dubbed the agents that carry out this transfer “tycheposons,” which are sequences of DNA that can include several entire genes as well as surrounding sequences, and can spontaneously separate out from the surrounding DNA. Then, they can be transported to other organisms by one or another possible carrier system including tiny bubbles known as vesicles that cells can produce from their own membranes.

2023-08-04: Mavericks, or Polintons, are large DNA transposons that contain genes with homology to viral proteins. They are the largest and most complex DNA transposons known. Mavericks are one of the long-sought vectors of horizontal gene transfer. They are related to giant viruses and virophages.

Mavericks are an ancient and fragmented class of jumping genes prevalent in the genomes of protists, fungi and animals, including humans. These massive mobile elements were initially assumed to be inactive, mutated relics of obsolete genes. But later research revealed that Mavericks can be reactivated, and that they can mediate horizontal gene transfer between some species of protists. Complete, intact Mavericks had never been characterized in a multicellular organism.

Consciousness

A self-published tome on whether humans are robots.

The idea that we are robots – nothing more than machines automatically carrying out pre-programmed instructions – has to be one of the most difficult concepts for the human mind to accept.

After all, if there’s one thing that appears to be perfectly obvious about being human it’s that we’re free to make our own choices, free to do what we like with our lives.

The purpose of Conscious Robots is to encourage us to face up to the reality of being human

to help us accept that we’re robots
to understand how ‘being a robot’ affects our lives
most importantly, to understand how it affects our chances of getting what we want out of life.

2007-03-12: Rat Metacognition

Jonathon Crystal figured out a clever experiment to test rats’ awareness of their thinking. They presented the rats with a “sound classification” test: They trained the rats to associate a long, 8-second burst of static with pushing 1 particular lever, and then trained them to associate a short, 2-second burst of static with a different lever. They’d play 1 of the 2 sounds, and if the rats pushed the correct lever, they’d get 6 food pellets; pushing the wrong lever got them nothing. The rats quickly learned to distinguish the 2 sounds by duration, and ate tons of pellets. Then things got interesting. The scientists made the test harder. They started playing bursts of static that were of intermediate length — 4 seconds, 5 seconds, 6 seconds — and thus harder to classify as “long” or “short”. Suddenly, the rats decided to forgo the test and simply stick their noses in the food trough to get the smaller reward. Apparently, the rats realized that they were now unlikely to pass this much-harder test, so they skipped it

2007-04-04: Animal metacognition. It would be helpful to have a chart with the various components of sentience / intelligence, and give examples for which species have which.

The demonstration of metacognition in nonhuman primates has important implications regarding the emergence of self-reflective mind during humans’ cognitive evolution

2007-08-22: Lack of metacognition in children and rats might be due to experimental deficiencies.

most tests of metacognition asked the participants to use words to describe their internal states — which is why little kids couldn’t do it very well. The barrier was linguistic, not cognitive. So she devised a metacognition test that asked preschoolers instead to point to pictures to illustrate their internal state. Ghetti would pose the kids a question, and ask them to point to a picture of a confident-looking child if they were sure of the answer, or a doubtful-looking child if they weren’t sure.

2007-12-29: Role of the thalamus

Some seemingly unconscious patients have startlingly complex brain activity. What can it tell us about the nature of consciousness? Early evidence indicates a link between consciousness and the ability to integrate information. In a study of 60 patients in the vegetative state, the 7 patients who later awakened recovered brain metabolism in regions that connect the cortex with the thalamus, a relay center in the brain.

2009-06-27: Whale Cognition

They might even deserve to be considered people.

Not human people, but as occupying a similar range on the spectrum as the great apes, for whom the idea of personhood has moved from preposterous to possible. Chimpanzees, gorillas and bonobos possess self-awareness, feelings and high-level cognitive powers. So do whales and dolphins. Their capacities could be even more ancient than our own, dating to an evolutionary explosion in brain size that took place millions of years before the last common ancestor of the great apes existed.

2013-12-12: the network is the computer

What happens to the brain under anesthesia suggests that the synthesis and integration of information among many different parts of the brain is the best measure of consciousness. This communication among regions is consciousness itself.

2015-12-01: Fish consciousness?

Researchers have made the first observations in fish of an increase in body temperature of 2–4 ºC when zebrafish were subjected to a stressful situation. This phenomenon is called “emotional fever” because it’s related to the emotions that animals feel in the face of an external stimulus, which been linked, controversially, with their consciousness. Until now, emotional fever had been observed in mammals, birds and certain reptiles, but never in fish, which is why fish have been regarded as animals without emotions or consciousness. Despite the small size of the fish brain, detailed morphological and behavioral analyses have highlighted similarities between some fish brain structures and those seen in other vertebrates, such as the hippocampus (linked to learning and spatial memory) and the amygdala (linked to emotions) of mammals.

2015-12-14: Bicameralism

Although Julian Jaynes, who died in 1997, never completed another book, The Origins of Consciousness in Breakdown of the Bicameral Mind will carry his name into eternity. John Updike wrote in The New Yorker that when Jaynes “speculates that until 3 ka BP men had no consciousness but were automatically obeying the voices of gods … we are astounded but compelled to follow this remarkable thesis through all the corroborative evidence he finds in ancient literature, modern behaviorism, and aberrant psychological phenomenon such as hypnotism, possession, glossolalia, prophecy, poetry, and schizophrenia

2016-04-27: Insects are conscious

“Brain scans of insects appear to indicate that they have the capacity to be conscious and show egocentrico, apparently indicating that they have such a thing as subjective experience.” Consciousness appeared to be associated with the “midbrain”. That part of the brain is the ancient core of the brain, which supports awareness for us and apparently for insects, too.

2016-06-19: Split brain

So, if your brain is split, who is the ‘you’ in this situation? From the outside, it’s tempting to think of the part of the brain that’s speaking as the person, but something is hearing and answering questions. And, though right brain can’t speak, it does understand faces, which left brain can’t. If this is you, you don’t know who your friends and family are in a crowd. This act of cutting exposes two minds in one head, and the talking mind doesn’t know there’s someone else in the house. The left brain can describe the situation it’s in, but nonetheless will constantly be surprised by right brain’s actions and explain them away. There’s a question to be asked here: Why, after separation, does right brain not totally freak out, but instead plays along helpfully, answering questions, and listening to left-brain’s dumb stories about what’s happening.

2016-11-11: Seats of consciousness?

Neurologists haves identified 3 specific regions of the brain that appear to be critical components of consciousness: 1 in the brainstem, involved in arousal; and 2 cortical regions involved in awareness. “This is most relevant if we can use these networks as a target for brain stimulation for people with disorders of consciousness. If we zero in on the regions and network involved, can we someday wake someone up who is in a persistent vegetative state? That’s the ultimate question.”


2018-01-05: Awake Under Anesthesia

There are no perfect studies of awareness under anesthesia. Studies like Russell’s, which use real patients, tend be poorly designed; those that use volunteers don’t involve real surgery. Investigating anesthetized awareness without surgery “is a bit like testing your windshield wipers without rain.” “A surgical incision has a galvanizing effect even on an anesthetized patient,. As the scalpel enters, her heart beats faster, her blood pressure rises, sometimes she jerks. She might edge closer to consciousness.” Another approach, of course, is simply to ask large numbers of people what they remember after they emerge from surgery. A study published in The Lancet in 2000 surveyed 12K patients who had undergone surgery. The researchers found 18 people whom they could be confident had been awake. The patients were surveyed at different times—just after the operation and at various intervals thereafter. Some remembered their experiences right away; others had no recollections at first but recalled the surgery after 1 week or 2. 1 remembered the surgery in detail only 24 days afterward.

2019-03-18: Consciousness Origin

Kurzgesagt explores how scientists believe consciousness first evolved, from organisms moving more quickly when consuming food to animals who can remember where they hid food to reading the minds of competitors and allies

2019-07-07: Animal consciousness

Despite groans of anthropomorphism, it’s not your imagination. Animals have a far deeper internal life than we’ve known.

and

For many scientists, the resonant mystery is no longer which animals are conscious, but which are not.

2019-09-26: Consciousness without Language

There is ample evidence from split-brain patients that consciousness can be preserved in the nonspeaking cortical hemisphere, usually the right one. These are patients whose corpus callosum has been surgically cut to prevent aberrant electrical activity from spreading from one to the other hemisphere. Almost half a century of research demonstrates that these patients have 2 conscious minds. Each cortical hemisphere has its own mind, each with its own peculiarities. The left cortex supports normal linguistic processing and speech; the right hemisphere is nearly mute but can read whole words and, in some cases at least, can understand syntax and produce simple speech and song.

It could be countered that language is necessary for the proper development of consciousness but that once this has taken place, language is no longer needed to experience. This hypothesis is difficult to address comprehensively, as it would require raising a child under severe social deprivation.

2020-10-31: Electromagnetic Consciousness

It’s far too early to claim that the brain’s electromagnetic fields are the primary seat of consciousness with much confidence. But philosophers and neuroscientists who have proposed electromagnetic field theories of consciousness, of which my own General Resonance Theory is one variety, are building up evidence.

2022-07-18: Bee cognition

Bees can count, recognize images of human faces and learn simple tool use and abstract concepts. He thinks bees have emotions, can plan and imagine things, and can recognize themselves as unique entities distinct from other bees. When Chittka deliberately trained a “demonstrator bee” to carry out a task in a sub-optimal way, the “observer bee” would not simply ape the demonstrator and copy the action she had seen, but would spontaneously improve her technique to solve the task more efficiently “without any kind of trial and error”. He thinks the level of sophisticated cognition bees exhibit means it’s unlikely they do not feel any emotions at all.

2023-07-08: Adversarial collaborations

What helped resolve the wager was the outcome, or rather the lack of a decisive outcome, of an “adversarial collaboration” organized by a consortium called COGITATE. Adversarial collaborations encourage researchers from different theoretical camps to jointly design experiments that can distinguish between their theories. In this case, the theories in question were integrated information theory (IIT), the brainchild of Giulio Tononi, and the neuronal  global workspace theory (GWT), championed by Stanislas Dehaene. The 2 scientists made predictions, based on their respective theories, about what kinds of brain activity would be recorded in an experiment in which participants looked at a series of images—but neither predicted outcome fully played out.

Intelligent Design Sort

The probability of the original input list being in the exact order it’s in is 1/(n!). There is such a small likelihood of this that it’s clearly absurd to say that this happened by chance, so it must have been consciously put in that order by an intelligent Sorter. Therefore it’s safe to assume that it’s already optimally Sorted in some way that transcends our naïve mortal understanding of “ascending order”.

The Seoul of a New Machine

Rity is the ghost in the machine: an autonomous agent that can transfer itself into desktop computers, PDAs, servers and robotic avatars, and adapt and evolve like a genetic organism. As researchers go from place to place, they are captured and recognized by a network of cameras in the building, allowing Rity to follow them from computer to computer.The “sobot” can upload itself into a mobile robot — a simpler cousin of HanSaRam called MyBot — and follow Kuppuswamy from room to room on its servo-controlled wheels, fetching objects for the researcher with its mechanical arms. If it sees Kuppuswamy sit in front of his office PC, Rity can abandon MyBot like a husk and slip into the desktop machine, to better put itself at its human master’s disposal.

when i was in school, ai was all about embodiment. now we have a more fluid, body-snatching approach. an agent following you around, without being limited to one manifestation, is both very scifi and very interesting