Science News Thread (for articles that don't relate to ongoing discussions)

[darthgently]

10 hours ago, JoeSchmuckatelli said:

Evolution May Be Purposeful And It’s Freaking Scientists Out

https://www.forbes.com/sites/andreamorris/2024/06/14/evolution-may-be-purposeful-and-its-freaking-scientists-out/

I'm finding this line of inquiry very interesting.  If you recall the 'Selfish Gene' line of thinking - where everything in biology is determined by DNA (predestined, if you will)... This is *sort of* the opposite. 

The 'standard model' is that DNA is determinative and that the germ ( reproductive cells) is isolated from the rest of the organism, such that over time (millions of generations) variations in the combination of germs from the successful individuals drives the evolution of the species - regardless of events within the individual's experience / lifetime.  It's a very binary theory - successful individuals survive to procreate, failures die, and the successful genome (established before birth) is passed on (in combination with another successful individual) to succeeding generations.   This is the standard view of evolution. 

Iconoclasts are making waves. 

They start with the notion that the germ isn't isolated from entity and that experience within the lifetime of the organism can rewrite portions the germ DNA. This makes sense to me - especially in light of research I read decades ago regarding heritability of stress response: parent generation experiencing great stress can pass on heightened stress response to the next generation. 

Serious consternation is ensuing - as is publication & counterpublication. 

MIT just published some of this for anyone willing to shell out the $75.

Anyway - interesting developments in biology afoot 

This fits my empirical experience anyway.  Seems implicitly related to Assembly Theory in some way

(Edit: below is unrelated.  Probably.  But the  forum merged my reply and post making it unclear.  Anyway... )

Mind expanding ponderations 

 

Edited June 17 by darthgently

[darthgently]

The mystery of the mechanism of anesthesia is a deep one.  Yet we've relied on it immensely for over a century (iirc).  And obviously it is entangled with our ignorance of the nature of consciousness itself.  If Penrose's microtubule hunch pans out it could end up indicating that consciousness is more photon based than electron based.   The ancient term "light of consciousness" comes to mind.  Or even the phrase "beat the daylights" out of someone.  Then there is Musk's stated goal to prevent the light of consciousness from being extinguished by making terrestrial life interplanetary.  What next?  Microtubule based AI?  Anyway, time will tell

 

Edited June 18 by darthgently

[JoeSchmuckatelli]

Timeliness of this article is eerie. 

https://www.theguardian.com/books/article/2024/jun/17/the-big-idea-can-you-inherit-memories-from-your-ancestors

The title is misleading - no heritability of memories, per se, but stress response?  Yes.  

This challenges a very early, cornerstone precept of the neo-Darwinist thought - the Weissman barrier. (See above post re: standard model). 

Spoiler

Since the early twentieth century it has been common in both psychology and behavioral biology to draw a sharp distinction between learned and innate behavior, or elements of behavior. The persistence of this dichotomy may be attributed in part to the fundamental importance of the separation of inherited and acquired characters within neo-Darwinian evolutionary theory, one of the essential foundations for the modern study of behavior. A cornerstone of early neo-Darwinian thought was August Weismann's theory of the germ plasm, which proposed a segregation between germinal and somatic cells during development, thus ruling out the possibility that acquired characters could be inherited. This denial of Lamarckian hereditary mechanisms became one of the hallmarks of neo-Darwinism, as opposed to classical Darwinism. Within the neo-Darwinian framework it thus became important, as Weismann himself pointed out, to distinguish sharply between inherited and acquired characters. Although the dichotomy has frequently been criticized it remains tenacious, surfacing in different guises as older versions of it became terminologically unacceptable. The analysis offered here suggests that this tenacity may partly be explained by the implications of Weismann's germ-plasm theory, and its modern incarnation in the central dogma of molecular genetics, and by the central thematic position of those ideas in the neo-Darwinian foundations of modern behavioral biology

https://pubmed.ncbi.nlm.nih.gov/7602088/#:~:text=A cornerstone of early neo,acquired characters could be inherited.

 

See also, https://en.m.wikipedia.org/wiki/Weismann_barrier

 

What caught my attention {prompting this and the post above} was a line in a video about the misdirection of resources and research in genetics, especially the medical application of our understanding of genetics. 

With the exception of about 5% of our genetic code, merely deactivating a known 'switch' for a disorder does not provide a cure. The body has a way of bypassing the deactivated segment and continues to exhibit the trait.  (Exceptions are for things like cystic fibrosis which have extremely specific genetic causes). 

The new approach if adopted would allow / require looking at the whole individual, including environmental factors when seeking genetic cures. 

The problem for the neo-Darwinist is apparently the idea of 'purpose' - as in it's  not just random chance and mutation in the germ line between generations that drives evolution - but the experience of the cell / organism and its purpose to survive and procreate that can drive genetic changes (evolution) within the lifetime of the cell/ organism and be passed on successfully to the offspring.   In other words, the experience of the individual and gene expression via environmental stress / success can be passed back to the germ line to the following generations - it's not just random.  Evolution could be purposeful and happen in a lifetime. 

That is apparently as dramatic a statement to a biologist as challenging determinism to a physicist. 

Edited June 18 by JoeSchmuckatelli

[DDE]

1 hour ago, JoeSchmuckatelli said:

August Weismann's theory of the germ plasm

Fun fact: Trofim Lysenko argued he was defending Darwinism from Wesimann's heresy.

[JoeSchmuckatelli]

3 hours ago, DDE said:

Fun fact: Trofim Lysenko argued he was defending Darwinism from Wesimann's heresy.

He also discredited belief in DNA, didn't he? 

Edit - among other criminally stupid things.  Just looked him up and reminded myself of this period in history.  Stalin and cronies.  SMH. 

Edited June 19 by JoeSchmuckatelli

[DDE]

Simply mentioning scientific ethics in a scientific article makes readers more suspicious

https://pubmed.ncbi.nlm.nih.gov/27150266/

[JoeSchmuckatelli]

9 hours ago, DDE said:

ethics in a scientific article makes readers more suspicious

Makes sense - we've been prepped by history and media to think that when scientists are doing things on the edge of the ethical - they have probably already crossed the line 

[kerbiloid]

Say, between the nuclear physicists only Sakharov got obsessed by the ethics, and only after brainwashing from his second wife, having her own personal poorly ethical reasons and background (daughter of a political brainwasher), and due to his personal mental problems (grown in the ivory tower of academic family, so being sensitive to mental attacks).

Edited June 23 by kerbiloid

[AckSed]

Eris and Makemake may be geologically active

Pluto has been found to be geologically active and have a thin atmosphere. Going by the hydrogen/deuterium ratio in their methane spectra, the lower deuterium count in the methane on the surfaces of Eris and Makemake indicate it may be produced by abiotic and thermogenic processes, and thus be active too.

Once is happenstance, twice is coincidence, three times is geological action. :-) What this means for other Kuiper Belt Objects isn't clear, but it is interesting.

[darthgently]

26 minutes ago, AckSed said:

Eris and Makemake may be geologically active

Pluto has been found to be geologically active and have a thin atmosphere. Going by the hydrogen/deuterium ratio in their methane spectra, the lower deuterium count in the methane on the surfaces of Eris and Makemake indicate it may be produced by abiotic and thermogenic processes, and thus be active too.

Once is happenstance, twice is coincidence, three times is geological action. :-) What this means for other Kuiper Belt Objects isn't clear, but it is interesting.

I wonder about Neptune's moon Triton now given the latest suspicion that it and Pluto are basically twins and orbited each other until a Neptune encounter broke them apart, keeping Triton

https://spacemath.gsfc.nasa.gov/Pluto/PlutoC.pdf

 

Edited June 27 by darthgently
Replaced pay-walled link with NASA pdf link

[kerbiloid]

_{Happily, Pluto then met Charon!
The Pluto's "heart" is a tattoo for memories.}

_{Eris and Sedna were competing Charon, but failed.}

_{Netflix should film this drama!}

Edited June 28 by kerbiloid

[magnemoe]

On 6/27/2024 at 9:13 PM, darthgently said:

I wonder about Neptune's moon Triton now given the latest suspicion that it and Pluto are basically twins and orbited each other until a Neptune encounter broke them apart, keeping Triton

https://spacemath.gsfc.nasa.gov/Pluto/PlutoC.pdf

 

Unlikely as Pluto has so many moons, Triton was another Kuiper Belt Object who got captured by Neptune, its not like their rare. 

[kerbiloid]

_{These were their kids from previous (gravitational) relations before Triton was kidnapped / cheatingly escaped.}

[AckSed]

ExoMars orbiter finds deposits of iron, magnesium and aluminium on Mars' Mawrth Vallis: https://www.esa.int/ESA_Multimedia/Images/2024/06/Metallic_Mars

[kerbiloid]

They should search better. There should be a lot of silicon and oxygen there. As any rocky planet, Mars literally consists of Fe, Mg, Al, Si, and O.

[AckSed]

Someone named Element 118 in 2015 and no-one told me: https://en.wikipedia.org/wiki/Oganesson

[kerbiloid]

2 hours ago, AckSed said:

Someone named Element 118 in 2015 and no-one told me: https://en.wikipedia.org/wiki/Oganesson

Still writing "ununoctium" in chemical equations?..

[Nuke]

ants observed performing surgery.

https://www.cell.com/current-biology/fulltext/S0960-9822(24)00805-4

[AckSed]

43 minutes ago, Nuke said:

ants observed performing surgery.

https://www.cell.com/current-biology/fulltext/S0960-9822(24)00805-4

When all you have are pincers, everything looks like something to clamp.

But seriously, quite cool.

[AckSed]

Exoplanet may be an icy eyeball: https://news.umich.edu/astronomers-find-surprising-ice-world-in-the-habitable-zone-with-jwst-data/

[K^2]

I've said it elsewhere, but I am going to repeat here that we should insist that pop-sci articles put asterisks next to "habitable," because an eyeball planet is about the worst hellhole imaginable that is technically survivable for some kind of a life form.

[KSK]

On 6/17/2024 at 1:32 AM, JoeSchmuckatelli said:

Evolution May Be Purposeful And It’s Freaking Scientists Out

https://www.forbes.com/sites/andreamorris/2024/06/14/evolution-may-be-purposeful-and-its-freaking-scientists-out/

I'm finding this line of inquiry very interesting.  If you recall the 'Selfish Gene' line of thinking - where everything in biology is determined by DNA (predestined, if you will)... This is *sort of* the opposite. 

The 'standard model' is that DNA is determinative and that the germ ( reproductive cells) is isolated from the rest of the organism, such that over time (millions of generations) variations in the combination of germs from the successful individuals drives the evolution of the species - regardless of events within the individual's experience / lifetime.  It's a very binary theory - successful individuals survive to procreate, failures die, and the successful genome (established before birth) is passed on (in combination with another successful individual) to succeeding generations.   This is the standard view of evolution. 

Iconoclasts are making waves. 

They start with the notion that the germ isn't isolated from entity and that experience within the lifetime of the organism can rewrite portions the germ DNA. This makes sense to me - especially in light of research I read decades ago regarding heritability of stress response: parent generation experiencing great stress can pass on heightened stress response to the next generation. 

Serious consternation is ensuing - as is publication & counterpublication. 

MIT just published some of this for anyone willing to shell out the $75.

Anyway - interesting developments in biology afoot 

Urgh.  Didn't like this article at all.  Sensationalist, muddled, and technically out of date.

The opening part about 'the genetic cures will never happen' is flat out wrong. Not only are they happening, they're available now.  Admittedly, they've taken longer than expected but that's mostly because there's a hell of a difference between looking at a genome and goint 'yeah if we correct that gene, it should cure such-and-such a disease', and developing a reliable way of altering that gene in-vivo that doesn't screw up other parts of the genome in the process.

It's the difference between reading Tsiolkovsky and building Apollo 11.  Hell, it's the difference between reading Tsiolkovsky and building Goddard's rocket.

Not to mention that genetics, especially regulation of gene expression, turned out to be whole lot more complicated than expected. Perhaps unsurprisingly, given that DNA is an elaborate molecular Turing Machine, the outputs of which just happen to be a staggeringly vast array of living organisms. The Human Genome Project was a necessary first step for developing genetic cures - its kind of hard to even know what questions to ask until you have that baseline data available - but it was only the first step.

Pedantic aside, the 2003 human genome was a rough draft. The complete version was only finished in 2022 and it turns out the missing parts were quite important, From Wikipedia: 

"In 2022, the Telomere-to-Telomere (T2T) consortium reported the complete sequence of a human female genome,[4] filling all the gaps in the X chromosome (2020) and the 22 autosomes (May 2021).[4][66] The previously unsequenced parts contain immune response genes that help to adapt to and survive infections, as well as genes that are important for predicting drug response.[67] The completed human genome sequence will also provide better understanding of human formation as an individual organism and how humans vary both between each other and other species.[67]" Emphasis added.

Moving on, what does this even mean?

"This development required a sort of intention or cognition within emergent networks of molecules to create and sustain biological functions."

The whole point of emergent things is that they're, well, emergent. No intention or cognition required by definition.

Also, the notion that the germ is separate from the organism has been out of date since at least 2019.  A 30 second search for 'transmissable epigenetic marks' found this review  paper:

" Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.

OUTCOMES

We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events."

In other words, they found strong evidence that environmental modifications to the genome can be inherited and that those changes endure the processes which erase epigenetic marks across the genome. That's important because erasing epigenetic marks is thought to be important for making totipent cells, e.g. the fundamental stem cells which can develop into any other kind of cells at all.  The starting point for embryogenesis if you like.

From the fine article:  "“Do you, you people working in gene-centric biology, do you realize what has already been published?” asks an incredulous Noble."

Et tu, Brutus.

It's possible that that Forbes article did have something useful to say, but in my opinion, it was buried under a heaping load of sensationalism, factual errors, and underdog-against-the-Establishment guff.

Edited July 21 by KSK

[magnemoe]

7 hours ago, KSK said:

Urgh.  Didn't like this article at all.  Sensationalist, muddled, and technically out of date.

The opening part about 'the genetic cures will never happen' is flat out wrong. Not only are they happening, they're available now.  Admittedly, they've taken longer than expected but that's mostly because there's a hell of a difference between looking at a genome and goint 'yeah if we correct that gene, it should cure such-and-such a disease', and developing a reliable way of altering that gene in-vivo that doesn't screw up other parts of the genome in the process.

It's the difference between reading Tsiolkovsky and building Apollo 11.  Hell, it's the difference between reading Tsiolkovsky and building Goddard's rocket.

Not to mention that genetics, especially regulation of gene expression, turned out to be whole lot more complicated than expected. Perhaps unsurprisingly, given that DNA is an elaborate molecular Turing Machine, the outputs of which just happen to be a staggeringly vast array of living organisms. The Human Genome Project was a necessary first step for developing genetic cures - its kind of hard to even know what questions to ask until you have that baseline data available - but it was only the first step.

Pedantic aside, the 2003 human genome was a rough draft. The complete version was only finished in 2022 and it turns out the missing parts were quite important, From Wikipedia: 

"In 2022, the Telomere-to-Telomere (T2T) consortium reported the complete sequence of a human female genome,[4] filling all the gaps in the X chromosome (2020) and the 22 autosomes (May 2021).[4][66] The previously unsequenced parts contain immune response genes that help to adapt to and survive infections, as well as genes that are important for predicting drug response.[67] The completed human genome sequence will also provide better understanding of human formation as an individual organism and how humans vary both between each other and other species.[67]" Emphasis added.

Moving on, what does this even mean?

"This development required a sort of intention or cognition within emergent networks of molecules to create and sustain biological functions."

The whole point of emergent things is that they're, well, emergent. No intention or cognition required by definition.

Also, the notion that the germ is separate from the organism has been out of date since at least 2019.  A 30 second search for 'transmissable epigenetic marks' found this review  paper:

" Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.

OUTCOMES

We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events."

In other words, they found strong evidence that environmental modifications to the genome can be inherited and that those changes endure the processes which erase epigenetic marks across the genome. That's important because erasing epigenetic marks is thought to be important for making totipent cells, e.g. the fundamental stem cells which can develop into any other kind of cells at all.  The starting point for embryogenesis if you like.

From the fine article:  "“Do you, you people working in gene-centric biology, do you realize what has already been published?” asks an incredulous Noble."

Et tu, Brutus.

It's possible that that Forbes article did have something useful to say, but in my opinion, it was buried under a heaping load of sensationalism, factual errors, and underdog-against-the-Establishment guff.

This, an very interesting example is from thalidomide victims (Remember YouTube documentary from some years ago so might not be true)
Issue was cases of thalidomide victims falling in love and creating families, they shared fates after all. Their kids had an increase chance of limb deformities. 

Why its an drug no longer used (for this) Turned out lots of of the thalidomide victims had an higher chance to limb deformities in the first place and thalidomide pushed them over the threshold often after low usage. 
Well you now have two parents with  this issue and kids might inherit it. 
Did not, mother used lots of thalidomide  and you had no bad genes or your rolled an 2 not 1 gene mixing.  
(does not matter if correct) it sounds plausible on why environmental effects are inherited.

Animals getting scared of loud noises will do better after firearms is used for hunting, this was 200 years ago for common use. 
Add that mammals are smart. Pretty sure deer know they are not hunted in suburbs for good reasons, but they are getting annoying.  

[K^2]

We are learning that methylation has a larger impact on gene expression than was used to be believed, and that environmental factors can impact methylation, which means your lived experience can absolutely impact gene expression in your children, but at the same time, there is a big gap in understanding any of the specifics. While the idea that there can be a beneficial feedback between environment and gene expression in subsequent generations is not entirely implausible, the evidence for it is not there. We both need patterns that cannot be explained by selection, with that later part requiring a lot more evidence than we have now just to have statistical significance, and at least some indication of a mechanism by which a feedback to specific genes can be established.

There's an abyss between a claim that, "Your environment can have impact on gene expression of your children," and "There is a mechanism in place to make it more likely for gene expression of your children to be more suited to the environment based on your own exposure to the environment." Getting to the former and claiming that it proves the latter is just stupid.

That said, research on the topic is warranted. You just have to be clear about the objectives of a study. You aren't trying to prove that future generations are more fit. We know that already. You have to prove that they are more fit in ways that selection alone does not explain, which is a lot harder.

[JoeSchmuckatelli]

On 7/21/2024 at 6:50 AM, KSK said:

Didn't like this article at all

 

On 7/21/2024 at 5:57 PM, K^2 said:

You have to prove that they are more fit in ways that selection alone does not explain, which is a lot harder

The article is interesting to me in that we see an open challenge by qualified individuals to a long standing 'hard line'. 

I'm the first to admit that I am not deeply read into the nuances of this. But my basic understanding was that the 'standard view' is that evolutionary pressure ignored events / experience within the lifetime of the organism and only worked in multi-generational, population-wide process completely dependent on seemingly random variations in the germ line.  One infant would have a variation of a gene that would turn out to be beneficial and its offspring (that inherit) would have advantages that compound over generations. 

That hard-line rule conflicts with articles I started reading decades ago - such as the heritability of stress response in children of holocaust survivors. 

Other reading from the 20 years of war America played in suggesting that combat PTSD may be an indication of gene expression are in line with the above. 

 

I don't think the authors and proponents are suggesting that Finch beaks grew longer in the lifetime of a bird... Just that the line may be not so hard.  One important thing is the bit about clones not developing in the same environment - that is interesting