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Author Topic:   The Koala, Lamark and Epigenetics
LamarkNewAge
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Posts: 909
Joined: 12-22-2015


Message 31 of 43 (774922)
12-24-2015 9:56 PM
Reply to: Message 30 by Dr Adequate
12-24-2015 9:24 PM


Getting back to something earlier.
quote:

Dr. Adequate
Imagine an alien who thinks that humans are stupid. So when he finds a bicycle, he declares that it's way too sophisticated to have been designed and built by humans unaided. No, he explains, it must have been designed and built by some sort of industrial robot, and all the poor dumb humans did was perform the relatively simple task of pushing the big red ON button on the front of the robot --- and pushing buttons, he smugly explains, is well within their primitive capacities ...

Well, he hasn't made things any easier for himself, has he? Because now he needs to explain how those dumb humans who're too stupid to build a mere bicycle managed to produce the robot.

LamarkNewAge
I think "learning" brings about self-organization at the biological level. Information is added then much of it gets lost in time. But DNA doesn't tell the whole story.


With evidence coming in that learning can be an acquired characteristic, one has to wonder if there was a quasi-brain in early life forms 4 billion years ago. I was amazed when a friend told me that she worked for an organization that actually trained Octopi to disarm bombs. I was shocked that an animal with no "brain" could do such a thing. The conversation started when she was telling me how smart her per lizard was, and I told her how small the reptile brains were and how amazing it was.

Which came first; the brain or the thoughts? Did epigenetic information help the learning to start with? Did the (specific)biological matter come second? Did the DNA follow Lamarckian type of events like epigenesist?

Sociologists (trained in history, anthropology, and psychiatry as part of their degree) have long had theories of a "racial memory" which seemed "acquired" (that ugly word to the hard-nosed scientists).

The scientific evidence needs to be built up and careful controls are needed but preliminary data show us that the scientists themselves are catching up with the common horse-sense many of us possessed long ago. I know for a fact that at age 14, I felt our brain was somewhat like a floppy disk (all were writable when CD's were "ROM"- Read Only Memory- for a while) and that animal offspring were like a floppy being copied.

The dominant view is still that the meat and bones DNA came first then mutated the brain and its thought abilities came later through slow, random mutations. But do DNA changes and the mutations that cause it follow something that already was there to start with. Do biomes (gut bacteria) come first and influence our diet and then the DNA catches up later after the dietary changes? Does RNA and epigenetics come first and then DNA changes come 2nd in many cases?

The possibility must be considered.


This message is a reply to:
 Message 30 by Dr Adequate, posted 12-24-2015 9:24 PM Dr Adequate has responded

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Dr Adequate
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Member Rating: 5.6


(1)
Message 32 of 43 (774924)
12-24-2015 10:44 PM
Reply to: Message 31 by LamarkNewAge
12-24-2015 9:56 PM


Octopods
I was amazed when a friend told me that she worked for an organization that actually trained Octopi to disarm bombs. I was shocked that an animal with no "brain" could do such a thing.

But an octopus does have a brain, and quite a large one for its size. I read here:

The typical adult octopus has a relatively large brain, estimated at 300 million neurons. The ratio of octopus brain to body mass is much higher than that of most fish and amphibians, a ratio more similar to that of birds and mammals.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
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NoNukes
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From: Central NC USA
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Member Rating: 2.2


(1)
Message 33 of 43 (774939)
12-25-2015 10:59 AM
Reply to: Message 31 by LamarkNewAge
12-24-2015 9:56 PM


Re: Getting back to something earlier.
Which came first; the brain or the thoughts?

Oooh. I think I've got this one.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


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Blue Jay
Member (Idle past 256 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(3)
Message 34 of 43 (775067)
12-26-2015 5:47 PM


Clear up some things
Hi, LamarkNewAge.

Welcome to EvC!

I want to clear up a few things.

LNA writes:

The late Farrell Till said that the koala has a very narrow diet; infact some are so specialized that they not only can't eat anything but eucalyptus leaves but they also cannot eat from eucalyptus trees outside their local eucalyptus woods (or something like that).

What the hell would Farrell Till know about koalas?

I'm not a marsupial biologist, but Farrell Till wasn't any kind of biologist, so I'm fairly comfortable suggesting that Farrell Till is most likely wrong about how specialized a koala's diet is.

LNA writes:

A random mutation (or series of mutations) that lead to such a narrow diet that by coincidence only enables digestion of a single type of plant just doesn't seems to fit what must go on in nature (so my thinking goes anyway).

Keep in mind that the word "eucalyptus" refers to a group of several hundred species, most of which are found in Australia. In fact, eucalyptus is one of the most abundant and widespread types of food in Australian forests. So, specializing on it seems like a reasonable way for an herbivore to make a relatively easy living in Australia.

Another thing to remember is that the claim that koalas cannot digest other foods is probably wrong. More likely, they simply have a preference for eucalyptus; or they have only been trained to eat eucalyptus, and since eucalyptus is everywhere, they've never had to look for something else. Over time, the close association selects for specialized adaptations.

LNA writes:

Selection for an animal going blind happens when the animal species will live in a (nearly or)100% dark environment. It takes a lot of molecular energy for eyes to (be able to) see so selection can and does lead to that gene-for-seeing getting turned off in increasingly large numbers of the species over time.

The same sort of process works for digestion. If you're only eating one thing, why would you maintain a diversified digestive system? It would be like a factory choosing to specialize in producing cars, but still performing regular upkeep in the machinery for tooling airplane parts.

LNA writes:

have been thinking of using the example of a human breeding foxes so that by the 26th generation, all in a breed we able to respond to the "sit" command when none could at first. But Darwinian theory supporters will just say the genetic information "was there to start with" or some DNA change (or some "standard theory" change) can be explained.

In every population, there is variation in virtually every trait. In the famous Russian fox-breeding program, they selected the foxes that had the 'tamest' temperament in each generation, and bred them to make the next generation. So, each generation, genes associated with docile and sociable traits became more and more pervasive, while genes associated with wild and aggressive traits became less and leas pervasive. It isn't surprising that, 26 generations later, they had foxes that were highly compliant and responsive to social cues from humans.

LNA writes:

I was amazed when a friend told me that she worked for an organization that actually trained Octopi to disarm bombs.

I'm calling bullshit on this one, too. I have always had a bit of a soft spot for octopus, and I am generally very credulous when it comes to stories about their cognitive abilities. But, nobody has trained octopus to disarm bombs. I have heard some people propose to train them to locate bombs, but I doubt that they have even done that.

LNA writes:

With evidence coming in that learning can be an acquired characteristic...

My PhD and postdoctoral research has involved studies into the learning abilities of arthropods. When you say "learning can be an acquired characteristic," what do you mean? Most animals have the ability to learn, and learning is a way to acquire new behaviors, but I have never seen any evidence that learned behaviors can be passed on without teaching, so I'm not sure what learning has to do with Lamarckian evolution


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


Replies to this message:
 Message 35 by LamarkNewAge, posted 12-26-2015 8:26 PM Blue Jay has responded

  
LamarkNewAge
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Posts: 909
Joined: 12-22-2015


Message 35 of 43 (775072)
12-26-2015 8:26 PM
Reply to: Message 34 by Blue Jay
12-26-2015 5:47 PM


Fear of something (like a serpent) among species
Does is come from:

1 a random mutation that turns on the fear gene if the senses detect a serpent?
(if so then selective breeding, by a geneticist qualified to detect the mutation in the gene code, will pass the trait to offspring OR slow "natural-selection" will kill off those without the mutation - especially/only if serpents are part of the environment, and those with the beneficial mutation will eventually predominate)

or

2 a member of a specie "learning" to fear a serpent then making sure it teaches the successive offspring the same "fear" generation after generation so that this social transmission becomes a characteristic of each specimen in the species except in rare circumstances?

(if so then an extremely careful and controlled experiment can figure out a way to reproduce an offspring while preventing social-contact of any sort with the parent)

NOW

The above biological transmission (#1) and social transmission (#2) both are within the neo-Darwinian theory and would not require a "Lamarckian" interpretation.

BUT pay attention to the #2 sentence in parentheses. Notice that I did not say what the result will show. That remains to be seen. Stay tuned.
.............................................

See my posts 26 and 27.
http://phenomena.nationalgeographic.com/...cause-epigenetics

Edited by LamarkNewAge, : No reason given.


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 Message 34 by Blue Jay, posted 12-26-2015 5:47 PM Blue Jay has responded

Replies to this message:
 Message 36 by Blue Jay, posted 12-26-2015 11:25 PM LamarkNewAge has responded

    
Blue Jay
Member (Idle past 256 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 36 of 43 (775075)
12-26-2015 11:25 PM
Reply to: Message 35 by LamarkNewAge
12-26-2015 8:26 PM


Re: Fear of something (like a serpent) among species
H, LamarkNewAge.

LNA writes:

a random mutation that turns on the fear gene if the senses detect a serpent?
(if so then selective breeding, by a geneticist qualified to detect the mutation in the gene code, will pass the trait to offspring OR slow "natural-selection" will kill off those without the mutation - especially/only if serpents are part of the environment, and those with the beneficial mutation will eventually predominate)

Here is a concept paper about the genetics of fear in domesticated animals.

Here is a good review paper about modern views on behavioral genetics (I should be able to get a PDF once I get back to my work computer). It's considerably more sophisticated than the simplistic idea of a "fear gene."

In a nutshell, behavioral syndromes are general patterns of behavior, such as "aggressive" or "docile," which influence how an organism responds to a wide range of stimuli (e.g., foraging, territoriality, and predator avoidance). They are driven by whole suites of genes. An animal has genes that give it sensory receptors to respond to specific sensory stimuli (e.g., the scent or sight of a snake), and other genes that govern how it decides to respond to those stimuli (e.g., hide, run away, bluff, fight).


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 35 by LamarkNewAge, posted 12-26-2015 8:26 PM LamarkNewAge has responded

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LamarkNewAge
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Posts: 909
Joined: 12-22-2015


Message 37 of 43 (775090)
12-27-2015 6:56 PM
Reply to: Message 36 by Blue Jay
12-26-2015 11:25 PM


Re: Fear of something (like a serpent) among species
I'm glad EVC doesn't delete post material after so many months or years. After15 years, it seems everything stays put). I can always reference this post of yours (if) whenever I have access to JSTOR.

PDFs don't work with my computer though. If the pasting option is available, perhaps you can quote a few paragraphs? No problem if you cant.

Thanks for those links. Some day I will download them.


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Dr Adequate
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Posts: 15960
Joined: 07-20-2006
Member Rating: 5.6


Message 38 of 43 (775141)
12-28-2015 9:21 PM


Epigenetics Does Not A Revolution Make
Article here.

I don't know how much of it you'll find interesting. Here's a good quote:

If quasi-Lamarckian heritable epigenetic patterns within the genome were so powerful and ubiquitous as to overturn a Mendelian understanding of heritability, then the Mendelian model of inheritance would not have been so persuasive and crystal clear in the first place.

  
RAZD
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Posts: 19089
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.5


(1)
Message 39 of 43 (775334)
12-31-2015 10:38 AM
Reply to: Message 25 by Tanypteryx
12-24-2015 5:08 PM


Re: learned behavior aka memes
Birds do a lot of training also, and apparently with some birds like parrots vocalization is also involved.

Any species where the young follow and watch and imitate parents or older members would likely be learning behavior that has been beneficial or neutral to survival or reproduction.

Any behavior that would be lethal or injurious would tend to be self eliminating.

This is the only way I can see how purely behavioral traits can be passed from one generation to the next: there has to be a teaching\learning cycle.

The classic lamarkian example of the giraffe neck elongating from use stretching for food fails to have a path to pass on that elongation (but selection for longer neck genes does have a path).

Another classic lamarkian example of a blacksmith being big, brawny and muscular from use of muscles is not so clear cut, as learning the trade would involve (teaching\learning) muscle building, ... but there would also likely be some selection of apprentices for those with more natural (genetic) disposition to be muscular doing better at the job than those less naturally (genetic) endowed, so observed long term trends would see beefier and beefier blacksmiths.

Stretching the neck out does not significantly change the length of the neck vertibrae, but continual body building can significantly alter the size of the muscles - one is bone and the other is tissue.

I am most fascinated by complex behaviors that are programmed into the genes of insects. They seem to work as cascade effects where a stimulus triggers a series sensory signals and behaviors. Many of these behaviors seem to be similar to complex "if > then" loops in computer programs. When I am in the field with other Odonatists we endlessly discuss dragonfly behavior and how it is programmed.

The way I see this, is that such "programmed" behavior is "learned" by by the species through selection (genetic) of those who successfully (survived, improved reproduction) passed the stimulus reaction test, and over time the accumulation of such programmed behaviors become more complex.

This would be comparable to "teaching" AI behavior to randomly programmed robots by providing a series of stimulation reaction test and selecting the programs that made the desired choice.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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RAZD
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Posts: 19089
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.5


Message 40 of 43 (775561)
01-02-2016 4:55 PM
Reply to: Message 11 by LamarkNewAge
12-24-2015 1:03 PM


neo-lamark, epigenetics and learned behavior
Getting back to you as promised:

Selection for an animal going blind happens when the animal species will live in a (nearly or)100% dark environment. It takes a lot of molecular energy for eyes to (be able to) see so selection can and does lead to that gene-for-seeing getting turned off in increasingly large numbers of the species over time.

Indeed, and there are many many many similar examples (fish, shrimp, cockroaches, spiders, etc etc etc).

But how can 1 million different types of food to possibly eat(represented in an animal by 1 million hypothetical genetic variants) out of 1,000,001 genetic variant possibilities in time get driven out of the gene pool of an animal. ...

Each species occupies selected habitats, in that they become adapted to the ones that are available and choose among those by being better at surviving and reproducing in them. Each habitat has limited available resources rather than millions, and so species make the best of the resources available to them. Koalas cannot fly to North America, for instance, so they are limited to habitats near them, ones dominated by eucalyptus plants.

In addition there is an ecological equilibrium distribution for habitats -- they can only support a relatively fixed number of grass grazers (resource limited) and a (smaller) relatively fixed number grass-grazer predators (also resource limited). It doesn't matter what species the grazers or predators are. This has been demonstrated by experiments on islands where all the existing species were documented and then removed, and new ones allowed to colonize the island: after a few years the same ratios of species in the habitat reached the same basic equilibrium as existed previously. (E.O.Wilson)

So there are only a few available resources in a given habitat, and some will be more competitively guarded\accessed than others.

... know it CAN HAPPEN according to neo-Darwinian theory but how DOES it happen in practice? ...

A slow moving herbivore with little aggressiveness or defensive ability (koala, sloth, etc) would tend to be driven to what would be marginal resources for the other species. This limits their access to types of resources even smaller.

Adaptation over generations would improve their ability to use such resources and become specialists in it compared to other species.

... Eventually, the molecular mutations won't do what they might be capable of. They can but won't keep on eliminating all the various DNA codes except the one that allows just one (!) type of food to eat. ...

What is to prevent it? There is no drive for mutations to occur just so they can benefit a species -- they are random. What causes the adaptation process to move in a direction of benefit to the species is selection of those mutations that offer the best ability to survive and reproduce. That selection process has no stop button.

Evolution is a slow stagger towards adaption to any specific habitat:

Imagine walking across the US, starting in Boston with a "habitat goal" of getting to San Francisco. For each step you throw 3 dice, where the faces are marked with degrees azimuth (0°, 60°, 120°, 180°, 240°, and 300°) and you can select the one closest to your path to the "habitat goal" ... you will get there eventually even though you may have to take an occasional back-step and many side-steps. Your chances of getting there without selection is virtually zero.

... I agree that it might be molecularly efficient and AGAIN I agree that it is genetically possible.

Indeed, it is possible with appropriate mutations to change a mouse into (something similar to) an elephant. Their basic genetics are the same, just different variations in the patterns of the DNA. But again, without selection the chances of this occurring is virtually zero.

(Lamarkian?) Epigenetics is far faster than the lone neo-Darwinian mechanism and might follow a pattern in nature we can picture if we imagine how a chicken learned how to cross the street (it just learned!). ...

Epigenetics is not learned behavior either. Epigenetics is the effects of the environment on the development of the individual. For example the sex of an alligator is determined not by DNA but by the temperature of the nest during incubation (something monitored fairly closely by the mamma gator) where variations within the nest result in some males and some females. By contrast the female displays learned\imprinted\instinctive behavior in choosing the temperatures so that the average ration is 1 male to 5 females, a ratio that apparently provides for long term survival of the species (more males = fewer females = fewer alligators; less males = more females = more not reproducing = fewer alligators).

Other epigenetic effects are more often observed with birth defects, such as the notorious Thalidomide drug effects circa 1957.

Usually the epigenetic effects occur through hormone imbalance (too much or too little) and the (chemicals in the) environment is capable of altering the hormonal balance of the mothers during pregnancy. DDT and bird egg shell thickness\strength.

The "taming" of the Siberian silver foxes that you mention occurred through a generations long experiment where the only actor selected for was relative tameness. The purpose was to develop a fox that was easier to raise to provide fur for the industry. The result was tame foxes, as intended, but with unintended changes to the ears, tail, voice and especially to the fur coloration (which rendered the "product" unusable for the fur industry). This is apparently because the amount of adrenaline was lower in the selected individuals and that affected their growth during development. Similar color\behavior patterns are seen in other domesticated animals.

... How do migratory birds know where to fly (even if their parents weren't around to teach them)? How do we learn anything? Random mutations? We just learn.

We learn by what has been tested over generations to be better for survival.

When we talk about basic instinct\reflex we say it gets imprinted into the species behavioral matrix through a series of random "tests" -- behavior that leads to fatality is eliminated, behavior that permits survival and reproduction continues.

Over time this approach builds up quite complex behavioral patterns (dancing bees, mating cranes, etc) all being tested by multiple trial and error tests selecting what works from what doesn't.

When we talk about learned behavior we say it is learned from another individual by observation and imitation, it is a conscious learning process, but it too is the result of a series of random "tests" -- behavior that leads to fatality is eliminated, behavior that permits survival and reproduction continues.

Or the behavior is survival neutral but preferred:

http://www.blueplanetbiomes.org/japanese_macaque.htm

quote:
Potato washing by a troop in Koshima was first started by a one and a half year old female named Imo. Researchers would put sweet potatoes along the beach to bring the monkeys out in the open. Imo found that she could get the sand off the potato better by dipping it into the river water, rather than brushing it off with her hands, like the other monkeys were doing. Her brothers and sisters imitated her first and then their mother. Over time the entire troop took to washing sand off potatoes with river water. At first they simply washed the sand off, but Imo soon found that the potatoes tasted better if seasoned with salt water from the ocean. They began to bite into the potato then dip it into the sea water to season it and bite again. Imo was a bit of a genius for a monkey because she also discovered wheat washing. She would make a ball of wheat and sand and throw it into the water. The wheat would float up to the top where she could pick it up and eat it without the sand.

New learned behavior requires innovators that add to the behavioral matrix those that are beneficial or neutral. If it works then "add to cart" and if it doesn't then discard it.

Over time this approach also builds up quite complex behavioral patterns, and probably the most complex developed to date is our ability to record and compare results.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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caffeine
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Posts: 1346
From: Prague, Czech Republic
Joined: 10-22-2008
Member Rating: 2.4


Message 41 of 43 (775563)
01-02-2016 5:15 PM
Reply to: Message 39 by RAZD
12-31-2015 10:38 AM


Re: learned behavior aka memes
Stretching the neck out does not significantly change the length of the neck vertibrae, but continual body building can significantly alter the size of the muscles - one is bone and the other is tissue.

Minor nitpick - bone is also tissue and, at least in mammals*, can also be altered significantly by training.

*maybe in all vertebrates? Not sure on this.

Edited by caffeine, : No reason given.


This message is a reply to:
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RAZD
Member
Posts: 19089
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.5


Message 42 of 43 (775564)
01-02-2016 5:20 PM
Reply to: Message 41 by caffeine
01-02-2016 5:15 PM


Re: learned behavior aka memes
Minor nitpick - bone is also tissue and, at least in mammals*, can also be altered significantly by training.

I thought bone mass etc was more diet driven, but okay IB corrected.

But in any case the changes are not passed to the offspring genetically, and can only be transmitted through learned behavior. Lose the trainer(s) and the changes will be lost.

Thanks.


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
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RAZD
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Posts: 19089
From: the other end of the sidewalk
Joined: 03-14-2004
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Message 43 of 43 (776950)
01-23-2016 2:15 PM
Reply to: Message 1 by LamarkNewAge
12-24-2015 8:42 AM


Interesting Article
Curiously, I ran across this article the other day:

quote:
Previously thought impossible: Body cells transfer genetic information directly into sperm cells

A paradigm shifting new study titled, "Soma-to-Germline Transmission of RNA in Mice Xenografted with Human Tumour Cells: Possible Transport by Exosomes," promises to overturn several core tenets of classical genetics, including collapsing the timescale necessary for the transfer of genetic information through the germline of a species (e.g. sperm) from hundreds of thousands of years to what amounts to 'real time' changes in biological systems.

The new study, however, has uncovered a novel mechanism through which somatic-to-germline transmission of genetic information is made possible. Mice grafted with human melanoma tumor cells genetically manipulated to express genes for a fluorescent tracer enzyme (EGFP-encoding plasmid) were found to release information-containing molecules containing the EGFP tracer into the animals' blood; since EGFP is a non-human and non-murine expressed tracer, there was little doubt that the observed phenomenon was real. These EGFP trackable molecules included exosomes (small nanoparticles produced by all eukaryotic cells (including plants and animals), which contain RNA and DNA molecules), which were verified to deliver RNAs to mature sperm cells (spermatozoa) and remain stored there. The authors of the study pointed out that RNA of this kind has been found in mouse models to behave as a "transgenerational determinant of inheritable epigenetic variations and that spermatozoal RNA can carry and deliver information that cause phenotypic variations in the progeny."

The researchers further expanded on the implications of their findings:

"Work from our and other laboratories indicates that spermatozoa act as vectors not only of their own genome, but also of foreign genetic information, based on their spontaneous ability to take up exogenous DNA and RNA molecules that are then delivered to oocytes at fertilization with the ensuing generation of phenotypically modified animals [35] - [37]. In cases in which this has been thoroughly investigated, the sperm-delivered sequences have been seen to remain extrachromosomal and to be sexually transmitted to the next generation in a non-Mendelian fashion [38]. The modes of genetic information delivery in this process are closely reminiscent of those operating in RNA-mediated paramutation inheritance, whereby RNA is the determinant of inheritable epigenetic variations [16], [17]. In conclusion, this work reveals that a flow of information can be transferred from the soma to the germline, escaping the principle of the Weismann barrier[39] which postulates that somatically acquired genetic variations cannot be transferred to the germline."

Not affecting the genes but affecting the development of the phenotype.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
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